Differences in soil biological activity by terrain types at the sub-field scale in central Iowa US

DOE PAGES

Kaleita, Amy L.; Schott, Linda R.; Hargreaves, Sarah K.; ...

2017-07-07

Soil microbial communities are structured by biogeochemical processes that occur at many different spatial scales, which makes soil sampling difficult. Because soil microbial communities are important in nutrient cycling and soil fertility, it is important to understand how microbial communities function within the heterogeneous soil landscape. In this study, a self-organizing map was used to determine whether landscape data can be used to characterize the distribution of microbial biomass and activity in order to provide an improved understanding of soil microbial community function. Points within a row crop field in south-central Iowa were clustered via a self-organizing map using sixmore » landscape properties into three separate landscape clusters. Twelve sampling locations per cluster were chosen for a total of 36 locations. After the soil samples were collected, the samples were then analysed for various metabolic indicators, such as nitrogen and carbon mineralization, extractable organic carbon, microbial biomass, etc. It was found that sampling locations located in the potholes and toe slope positions had significantly greater microbial biomass nitrogen and carbon, total carbon, total nitrogen and extractable organic carbon than the other two landscape position clusters, while locations located on the upslope did not differ significantly from the other landscape clusters. However, factors such as nitrate, ammonia, and nitrogen and carbon mineralization did not differ significantly across the landscape. Altogether, this research demonstrates the effectiveness of a terrain-based clustering method for guiding soil sampling of microbial communities.« less

Differences in soil biological activity by terrain types at the sub-field scale in central Iowa US

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaleita, Amy L.; Schott, Linda R.; Hargreaves, Sarah K.

Soil microbial communities are structured by biogeochemical processes that occur at many different spatial scales, which makes soil sampling difficult. Because soil microbial communities are important in nutrient cycling and soil fertility, it is important to understand how microbial communities function within the heterogeneous soil landscape. In this study, a self-organizing map was used to determine whether landscape data can be used to characterize the distribution of microbial biomass and activity in order to provide an improved understanding of soil microbial community function. Points within a row crop field in south-central Iowa were clustered via a self-organizing map using sixmore » landscape properties into three separate landscape clusters. Twelve sampling locations per cluster were chosen for a total of 36 locations. After the soil samples were collected, the samples were then analysed for various metabolic indicators, such as nitrogen and carbon mineralization, extractable organic carbon, microbial biomass, etc. It was found that sampling locations located in the potholes and toe slope positions had significantly greater microbial biomass nitrogen and carbon, total carbon, total nitrogen and extractable organic carbon than the other two landscape position clusters, while locations located on the upslope did not differ significantly from the other landscape clusters. However, factors such as nitrate, ammonia, and nitrogen and carbon mineralization did not differ significantly across the landscape. Altogether, this research demonstrates the effectiveness of a terrain-based clustering method for guiding soil sampling of microbial communities.« less

[Microbial Community Structure on the Root Surface of Patients with Periodontitis.

PubMed

Zhang, Ju-Mei; Zhou, Jian-Ye; Bo, Lei; Hu, Xiao-Pan; Jiao, Kang-Li; Li, Zhi-Jie; Li, Yue-Hong; Li, Zhi-Qiang

2016-11-01

To study the microbial community structure on the root surface of patients with periodontitis. Bacterial plaque and tissues from the root neck (RN group),root middle (RM group) and root tine (RT group) of six teeth with mobility 3 in one patient with periodontitis were sampled.The V3V4 region of 16S rRNA was sequenced on the Illumina MiSeq platform.The microbial community structure was analyzed by Mothur,Qiime and SPSS software. The principal component analysis (PCoA) results indicated that the RM samples had a similar microbial community structure as that of the RT samples,which was significant different from that of the RN samples.Thirteen phyla were detected in the three groups of samples,which included 7 dominant phyla.29 dominant genera were detected in 184 genera.The abundance of Bacteroidetes _[G-6] and Peptostre ptococcaceae _[XI][G-4] had a positive correlation with the depth of the collection site of samples ( P <0.05),while the abundance of Prevotella,Selenomonas,Corynebacterium and Olsenella had a negative correlation with the depth of the collection site of samples ( P <0.05). There is region-specificity of microbial community structure on the root surface of patients with periodontitis.

Microbial Community Profiles in Wastewaters from Onsite Wastewater Treatment Systems Technology

PubMed Central

Jałowiecki, Łukasz; Chojniak, Joanna Małgorzata; Dorgeloh, Elmar; Hegedusova, Berta; Ejhed, Helene; Magnér, Jörgen; Płaza, Grażyna Anna

2016-01-01

The aim of the study was to determine the potential of community-level physiological profiles (CLPPs) methodology as an assay for characterization of the metabolic diversity of wastewater samples and to link the metabolic diversity patterns to efficiency of select onsite biological wastewater facilities. Metabolic fingerprints obtained from the selected samples were used to understand functional diversity implied by the carbon substrate shifts. Three different biological facilities of onsite wastewater treatment were evaluated: fixed bed reactor (technology A), trickling filter/biofilter system (technology B), and aerated filter system (the fluidized bed reactor, technology C). High similarities of the microbial community functional structures were found among the samples from the three onsite wastewater treatment plants (WWTPs), as shown by the diversity indices. Principal components analysis (PCA) showed that the diversity and CLPPs of microbial communities depended on the working efficiency of the wastewater treatment technologies. This study provided an overall picture of microbial community functional structures of investigated samples in WWTPs and discerned the linkages between microbial communities and technologies of onsite WWTPs used. The results obtained confirmed that metabolic profiles could be used to monitor treatment processes as valuable biological indicators of onsite wastewater treatment technologies efficiency. This is the first step toward understanding relations of technology types with microbial community patterns in raw and treated wastewaters. PMID:26807728

Response and resilience of soil microbial communities inhabiting in edible oil stress/contamination from industrial estates.

PubMed

Patel, Vrutika; Sharma, Anukriti; Lal, Rup; Al-Dhabi, Naif Abdullah; Madamwar, Datta

2016-03-22

Gauging the microbial community structures and functions become imperative to understand the ecological processes. To understand the impact of long-term oil contamination on microbial community structure soil samples were taken from oil fields located in different industrial regions across Kadi, near Ahmedabad, India. Soil collected was hence used for metagenomic DNA extraction to study the capabilities of intrinsic microbial community in tolerating the oil perturbation. Taxonomic profiling was carried out by two different complementary approaches i.e. 16S rDNA and lowest common ancestor. The community profiling revealed the enrichment of phylum "Proteobacteria" and genus "Chromobacterium," respectively for polluted soil sample. Our results indicated that soil microbial diversity (Shannon diversity index) decreased significantly with contamination. Further, assignment of obtained metagenome reads to Clusters of Orthologous Groups (COG) of protein and Kyoto Encyclopedia of Genes and Genomes (KEGG) hits revealed metabolic potential of indigenous microbial community. Enzymes were mapped on fatty acid biosynthesis pathway to elucidate their roles in possible catalytic reactions. To the best of our knowledge this is first study for influence of edible oil on soil microbial communities via shotgun sequencing. The results indicated that long-term oil contamination significantly affects soil microbial community structure by acting as an environmental filter to decrease the regional differences distinguishing soil microbial communities.

Buccal Swabbing as a Noninvasive Method To Determine Bacterial, Archaeal, and Eukaryotic Microbial Community Structures in the Rumen

PubMed Central

Kirk, Michelle R.; Jonker, Arjan; McCulloch, Alan

2015-01-01

Analysis of rumen microbial community structure based on small-subunit rRNA marker genes in metagenomic DNA samples provides important insights into the dominant taxa present in the rumen and allows assessment of community differences between individuals or in response to treatments applied to ruminants. However, natural animal-to-animal variation in rumen microbial community composition can limit the power of a study considerably, especially when only subtle differences are expected between treatment groups. Thus, trials with large numbers of animals may be necessary to overcome this variation. Because ruminants pass large amounts of rumen material to their oral cavities when they chew their cud, oral samples may contain good representations of the rumen microbiota and be useful in lieu of rumen samples to study rumen microbial communities. We compared bacterial, archaeal, and eukaryotic community structures in DNAs extracted from buccal swabs to those in DNAs from samples collected directly from the rumen by use of a stomach tube for sheep on four different diets. After bioinformatic depletion of potential oral taxa from libraries of samples collected via buccal swabs, bacterial communities showed significant clustering by diet (R = 0.37; analysis of similarity [ANOSIM]) rather than by sampling method (R = 0.07). Archaeal, ciliate protozoal, and anaerobic fungal communities also showed significant clustering by diet rather than by sampling method, even without adjustment for potentially orally associated microorganisms. These findings indicate that buccal swabs may in future allow quick and noninvasive sampling for analysis of rumen microbial communities in large numbers of ruminants. PMID:26276109

Characterization of bacterial community dynamics in a full-scale drinking water treatment plant.

PubMed

Li, Cuiping; Ling, Fangqiong; Zhang, Minglu; Liu, Wen-Tso; Li, Yuxian; Liu, Wenjun

2017-01-01

Understanding the spatial and temporal dynamics of microbial communities in drinking water systems is vital to securing the microbial safety of drinking water. The objective of this study was to comprehensively characterize the dynamics of microbial biomass and bacterial communities at each step of a full-scale drinking water treatment plant in Beijing, China. Both bulk water and biofilm samples on granular activated carbon (GAC) were collected over 9months. The proportion of cultivable cells decreased during the treatment processes, and this proportion was higher in warm season than cool season, suggesting that treatment processes and water temperature probably had considerable impact on the R2A cultivability of total bacteria. 16s rRNA gene based 454 pyrosequencing analysis of the bacterial community revealed that Proteobacteria predominated in all samples. The GAC biofilm harbored a distinct population with a much higher relative abundance of Acidobacteria than water samples. Principle coordinate analysis and one-way analysis of similarity indicated that the dynamics of the microbial communities in bulk water and biofilm samples were better explained by the treatment processes rather than by sampling time, and distinctive changes of the microbial communities in water occurred after GAC filtration. Furthermore, 20 distinct OTUs contributing most to the dissimilarity among samples of different sampling locations and 6 persistent OTUs present in the entire treatment process flow were identified. Overall, our findings demonstrate the significant effects that treatment processes have on the microbial biomass and community fluctuation and provide implications for further targeted investigation on particular bacteria populations. Copyright © 2016. Published by Elsevier B.V.

The Effect of the 2015 Earthquake on the Bacterial Community Compositions in Water in Nepal

PubMed Central

Uprety, Sital; Hong, Pei-Ying; Sadik, Nora; Dangol, Bipin; Adhikari, Rameswor; Jutla, Antarpreet; Shisler, Joanna L.; Degnan, Patrick; Nguyen, Thanh H.

2017-01-01

We conducted a study to examine the effect of seasonal variations and the disruptive effects of the 2015 Nepal earthquake on microbial communities associated with drinking water sources. We first characterized the microbial communities of water samples in two Nepali regions (Kathmandu and Jhapa) to understand the stability of microbial communities in water samples collected in 2014. We analyzed additional water samples from the same sources collected from May to August 2015, allowing the comparison of samples from dry-to-dry season and from dry-to-monsoon seasons. Emphasis was placed on microbes responsible for maintaining the geobiochemical characteristics of water (e.g., ammonia-oxidizing and nitrite-oxidizing bacteria and archaea and sulfate-reducing bacteria) and opportunistic pathogens often found in water (Acinetobacter). When examining samples from Jhapa, we identified that most geobiochemical microbe populations remained similar. When examining samples from Kathmandu, the abundance of microbial genera responsible for maintaining the geobiochemical characteristics of water increased immediately after the earthquake and decreased 8 months later (December 2015). In addition, microbial source tracking was used to monitor human fecal contamination and revealed deteriorated water quality in some specific sampling sites in Kathmandu post-earthquake. This study highlights a disruption of the environmental microbiome after an earthquake and the restoration of these microbial communities as a function of time and sanitation practices. PMID:29270153

Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input

PubMed Central

Armstrong, Alacia; Valverde, Angel; Ramond, Jean-Baptiste; Makhalanyane, Thulani P.; Jansson, Janet K.; Hopkins, David W.; Aspray, Thomas J.; Seely, Mary; Trindade, Marla I.; Cowan, Don A.

2016-01-01

The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more important than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall. PMID:27680878

Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input.

PubMed

Armstrong, Alacia; Valverde, Angel; Ramond, Jean-Baptiste; Makhalanyane, Thulani P; Jansson, Janet K; Hopkins, David W; Aspray, Thomas J; Seely, Mary; Trindade, Marla I; Cowan, Don A

2016-09-29

The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more important than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO 2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall.

Successive DNA extractions improve characterization of soil microbial communities

PubMed Central

de Hollander, Mattias; Smidt, Hauke; van Veen, Johannes A.

2017-01-01

Currently, characterization of soil microbial communities relies heavily on the use of molecular approaches. Independently of the approach used, soil DNA extraction is a crucial step, and success of downstream procedures will depend on how well DNA extraction was performed. Often, studies describing and comparing soil microbial communities are based on a single DNA extraction, which may not lead to a representative recovery of DNA from all organisms present in the soil. The use of successive DNA extractions might improve soil microbial characterization, but the benefit of this approach has only been limitedly studied. To determine whether successive DNA extractions of the same soil sample would lead to different observations in terms of microbial abundance and community composition, we performed three successive extractions, with two widely used commercial kits, on a range of clay and sandy soils. Successive extractions increased DNA yield considerably (1–374%), as well as total bacterial and fungal abundances in most of the soil samples. Analysis of the 16S and 18S ribosomal RNA genes using 454-pyrosequencing, revealed that microbial community composition (taxonomic groups) observed in the successive DNA extractions were similar. However, successive DNA extractions did reveal several additional microbial groups. For some soil samples, shifts in microbial community composition were observed, mainly due to shifts in relative abundance of a number of microbial groups. Our results highlight that performing successive DNA extractions optimize DNA yield, and can lead to a better picture of overall community composition. PMID:28168105

A role for the endometrial microbiome in dysfunctional menstrual bleeding.

PubMed

Pelzer, Elise S; Willner, Dana; Buttini, Melissa; Huygens, Flavia

2018-06-01

This study aimed to characterise the microbial community within the endometrial cavity and endocervix in women with menorrhagia or dysmenorrhea. Paired endocervical and endometrial biopsy samples were collected from women undergoing operative hysteroscopy and/or laparoscopy. Samples were cohorted based on pathology, indications for surgery, and histological dating of the endometrium. Samples were interrogated for the presence of microbial DNA using a two-step next generation sequencing technology approach to exploit the V5-V8 regions of the 16S rRNA gene. Pyrosequencing revealed that the endocervix and endometrium share a minor microbial community, but that each site harbours a separate and distinct microbial population (p = 0.024). This was also the case for women with menorrhagia and dysmenorrhea (p = 0.017). Lactobacillus spp. were the most abundant microbial taxa present in 50% of the cohorts, and across all endocervical groups. Members of the genera Prevotella, Fusobacterium and Jonquetella were the most abundant taxa identified in samples collected from nulliparous women. It can be concluded that the female upper genital tract is not sterile. Microbial community profiling revealed differences in the endometrial microbial community profiles for: (1) the endocervix compared to the endometrium, and (2), women with menorrhagia versus dysmenorrhea. The distinct microbial community profiles in these women may offer insight into the pathology and clinical management of dysfunctional menstrual bleeding.

Changes in microbial community structure in the wake of Hurricanes Katrina and Rita.

PubMed

Amaral-Zettler, Linda A; Rocca, Jennifer D; Lamontagne, Michael G; Dennett, Mark R; Gast, Rebecca J

2008-12-15

Hurricanes have the potential to alter the structures of coastal ecosystems and generate pathogen-laden floodwaters thatthreaten public health. To examine the impact of hurricanes on urban systems, we compared microbial community structures in samples collected after Hurricane Katrina and before and after Hurricane Rita. We extracted environmental DNA and sequenced small-subunit rRNA (SSU rRNA) gene clone libraries to survey microbial communities in floodwater, water, and sediment samples collected from Lake Charles, Lake Pontchartrain, the 17th Street and Industrial Canals in New Orleans, and raw sewage. Correspondence analysis showed that microbial communities associated with sediments formed one cluster while communities associated with lake and Industrial Canal water formed a second. Communities associated with water from the 17th Street Canal and floodwaters collected in New Orleans showed similarity to communities in raw sewage and contained a number of sequences associated with possible pathogenic microbes. This suggests that a distinct microbial community developed in floodwaters following Hurricane Katrina and that microbial community structures as a whole might be sensitive indicators of ecosystem health and serve as "sentinels" of water quality in the environment.

Microbial communities in methane seep sediments along US Atlantic Margin are structured by organic matter and seepage dynamics

NASA Astrophysics Data System (ADS)

Graw, M. F.; Pohlman, J.; Treude, T.; Ruppel, C. D.; Colwell, F. S.

2016-12-01

Methane seeps are dynamic environments on continental margins where subsurface methane reaches the ocean. Microbial communities play a critical role in carbon cycling within seep sediments via organic carbon degradation, methane production, and anaerobic oxidation of methane (AOM), which consumes 20-80% of methane in seep sediments. However, biogeochemical controls on microbial community structure at seeps on a margin-wide scale remain unclear. The passive US Atlantic Margin (USAM) has been identified as a region of active methane seepage. Passive margin seeps have traditionally been understudied relative to seeps on active margins. Passive margins exhibit large cross-margin variability in organic carbon deposition and are anticipated to have divergent seep dynamics from active margins. Thus, the USAM offers a unique opportunity to investigate controls on microbial communities in seep sediments. We undertook analysis of microbial communities inhabiting seep sediments at 6 biogeochemically distinct sites along the USAM. Microbiological samples were co-located with measurements of sediment geochemistry and AOM and sulfate reduction rates. Illumina sequencing of the 16S rRNA gene, using both universal (83 samples) and archaeal-specific (64 samples) primers, and the mcrA gene (18 samples) identified 44 bacterial phyla and 7 archaeal phyla. Seeps in canyons and on open slope, likely representing high and low organic content sediments, hosted distinct communities; the former was dominated by ammonia-oxidizing Marine Group I Thaumarchaeota and the latter by mixotrophic Hadesarchaeota. Seep stability also impacted microbial community structure, and in particular the establishment of an AOM community rather than a Bathyarchaeota-dominated community. These findings contribute to understanding how microbial communities are structured within methane seep sediments and pave the way for investigating broad differences in carbon cycling between seeps on passive and active margins.

Microbial community functional structures in wastewater treatment plants as characterized by GeoChip.

PubMed

Wang, Xiaohui; Xia, Yu; Wen, Xianghua; Yang, Yunfeng; Zhou, Jizhong

2014-01-01

Biological WWTPs must be functionally stable to continuously and steadily remove contaminants which rely upon the activity of complex microbial communities. However, knowledge is still lacking in regard to microbial community functional structures and their linkages to environmental variables. To investigate microbial community functional structures of activated sludge in wastewater treatment plants (WWTPs) and to understand the effects of environmental factors on their structure. 12 activated sludge samples were collected from four WWTPs in Beijing. A comprehensive functional gene array named GeoChip 4.2 was used to determine the microbial functional genes involved in a variety of biogeochemical processes such as carbon, nitrogen, phosphorous and sulfur cycles, metal resistance, antibiotic resistance and organic contaminant degradation. High similarities of the microbial community functional structures were found among activated sludge samples from the four WWTPs, as shown by both diversity indices and the overlapped genes. For individual gene category, such as egl, amyA, lip, nirS, nirK, nosZ, ureC, ppx, ppk, aprA, dsrA, sox and benAB, there were a number of microorganisms shared by all 12 samples. Canonical correspondence analysis (CCA) showed that the microbial functional patterns were highly correlated with water temperature, dissolved oxygen (DO), ammonia concentrations and loading rate of chemical oxygen demand (COD). Based on the variance partitioning analyses (VPA), a total of 53% of microbial community variation from GeoChip data can be explained by wastewater characteristics (25%) and operational parameters (23%), respectively. This study provided an overall picture of microbial community functional structures of activated sludge in WWTPs and discerned the linkages between microbial communities and environmental variables in WWTPs.

Influences of space, soil, nematodes and plants on microbial community composition of chalk grassland soils.

PubMed

Yergeau, Etienne; Bezemer, T Martijn; Hedlund, Katarina; Mortimer, Simon R; Kowalchuk, George A; Van Der Putten, Wim H

2010-08-01

Microbial communities respond to a variety of environmental factors related to resources (e.g. plant and soil organic matter), habitat (e.g. soil characteristics) and predation (e.g. nematodes, protozoa and viruses). However, the relative contribution of these factors on microbial community composition is poorly understood. Here, we sampled soils from 30 chalk grassland fields located in three different chalk hill ridges of Southern England, using a spatially explicit sampling scheme. We assessed microbial communities via phospholipid fatty acid (PLFA) analyses and PCR-denaturing gradient gel electrophoresis (DGGE) and measured soil characteristics, as well as nematode and plant community composition. The relative influences of space, soil, vegetation and nematodes on soil microorganisms were contrasted using variation partitioning and path analysis. Results indicate that soil characteristics and plant community composition, representing habitat and resources, shape soil microbial community composition, whereas the influence of nematodes, a potential predation factor, appears to be relatively small. Spatial variation in microbial community structure was detected at broad (between fields) and fine (within fields) scales, suggesting that microbial communities exhibit biogeographic patterns at different scales. Although our analysis included several relevant explanatory data sets, a large part of the variation in microbial communities remained unexplained (up to 92% in some analyses). However, in several analyses, significant parts of the variation in microbial community structure could be explained. The results of this study contribute to our understanding of the relative importance of different environmental and spatial factors in driving the composition of soil-borne microbial communities. © 2009 Society for Applied Microbiology and Blackwell Publishing Ltd.

Interactions between Snow Chemistry, Mercury Inputs and Microbial Population Dynamics in an Arctic Snowpack

PubMed Central

Larose, Catherine; Prestat, Emmanuel; Cecillon, Sébastien; Berger, Sibel; Malandain, Cédric; Lyon, Delina; Ferrari, Christophe; Schneider, Dominique; Dommergue, Aurélien; Vogel, Timothy M.

2013-01-01

We investigated the interactions between snowpack chemistry, mercury (Hg) contamination and microbial community structure and function in Arctic snow. Snowpack chemistry (inorganic and organic ions) including mercury (Hg) speciation was studied in samples collected during a two-month field study in a high Arctic site, Svalbard, Norway (79°N). Shifts in microbial community structure were determined by using a 16S rRNA gene phylogenetic microarray. We linked snowpack and meltwater chemistry to changes in microbial community structure by using co-inertia analyses (CIA) and explored changes in community function due to Hg contamination by q-PCR quantification of Hg-resistance genes in metagenomic samples. Based on the CIA, chemical and microbial data were linked (p = 0.006) with bioavailable Hg (BioHg) and methylmercury (MeHg) contributing significantly to the ordination of samples. Mercury was shown to influence community function with increases in merA gene copy numbers at low BioHg levels. Our results show that snowpacks can be considered as dynamic habitats with microbial and chemical components responding rapidly to environmental changes. PMID:24282515

Bacterial Community Associated with the Reef Coral Mussismilia braziliensis's Momentum Boundary Layer over a Diel Cycle.

PubMed

Silveira, Cynthia B; Gregoracci, Gustavo B; Coutinho, Felipe H; Silva, Genivaldo G Z; Haggerty, John M; de Oliveira, Louisi S; Cabral, Anderson S; Rezende, Carlos E; Thompson, Cristiane C; Francini-Filho, Ronaldo B; Edwards, Robert A; Dinsdale, Elizabeth A; Thompson, Fabiano L

2017-01-01

Corals display circadian physiological cycles, changing from autotrophy during the day to heterotrophy during the night. Such physiological transition offers distinct environments to the microbial community associated with corals: an oxygen-rich environment during daylight hours and an oxygen-depleted environment during the night. Most studies of coral reef microbes have been performed on samples taken during the day, representing a bias in the understanding of the composition and function of these communities. We hypothesized that coral circadian physiology alters the composition and function of microbial communities in reef boundary layers. Here, we analyzed microbial communities associated with the momentum boundary layer (MBL) of the Brazilian endemic reef coral Mussismilia braziliensis during a diurnal cycle, and compared them to the water column. We determined microbial abundance and nutrient concentration in samples taken within a few centimeters of the coral's surface every 6 h for 48 h, and sequenced microbial metagenomes from a subset of the samples. We found that dominant taxa and functions in the coral MBL community were stable over the time scale of our sampling, with no significant shifts between night and day samples. Interestingly, the two water column metagenomes sampled 1 m above the corals were also very similar to the MBL metagenomes. When all samples were analyzed together, nutrient concentration significantly explained 40% of the taxonomic dissimilarity among dominant genera in the community. Functional profiles were highly homogenous and not significantly predicted by any environmental variables measured. Our data indicated that water flow may overrule the effects of coral physiology in the MBL bacterial community, at the scale of centimeters, and suggested that sampling resolution at the scale of millimeters may be necessary to address diurnal variation in community composition.

Buccal swabbing as a noninvasive method to determine bacterial, archaeal, and eukaryotic microbial community structures in the rumen.

PubMed

Kittelmann, Sandra; Kirk, Michelle R; Jonker, Arjan; McCulloch, Alan; Janssen, Peter H

2015-11-01

Analysis of rumen microbial community structure based on small-subunit rRNA marker genes in metagenomic DNA samples provides important insights into the dominant taxa present in the rumen and allows assessment of community differences between individuals or in response to treatments applied to ruminants. However, natural animal-to-animal variation in rumen microbial community composition can limit the power of a study considerably, especially when only subtle differences are expected between treatment groups. Thus, trials with large numbers of animals may be necessary to overcome this variation. Because ruminants pass large amounts of rumen material to their oral cavities when they chew their cud, oral samples may contain good representations of the rumen microbiota and be useful in lieu of rumen samples to study rumen microbial communities. We compared bacterial, archaeal, and eukaryotic community structures in DNAs extracted from buccal swabs to those in DNAs from samples collected directly from the rumen by use of a stomach tube for sheep on four different diets. After bioinformatic depletion of potential oral taxa from libraries of samples collected via buccal swabs, bacterial communities showed significant clustering by diet (R = 0.37; analysis of similarity [ANOSIM]) rather than by sampling method (R = 0.07). Archaeal, ciliate protozoal, and anaerobic fungal communities also showed significant clustering by diet rather than by sampling method, even without adjustment for potentially orally associated microorganisms. These findings indicate that buccal swabs may in future allow quick and noninvasive sampling for analysis of rumen microbial communities in large numbers of ruminants. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Differential Impacts of Land-Based Sources of Pollution on the Microbiota of Southeast Florida Coral Reefs

PubMed Central

Staley, Christopher; Kaiser, Thomas; Gidley, Maribeth L.; Enochs, Ian C.; Jones, Paul R.; Goodwin, Kelly D.; Sinigalliano, Christopher D.

2017-01-01

ABSTRACT Coral reefs are dynamic ecosystems known for decades to be endangered due, in large part, to anthropogenic impacts from land-based sources of pollution (LBSP). In this study, we utilized an Illumina-based next-generation sequencing approach to characterize prokaryotic and fungal communities from samples collected off the southeast coast of Florida. Water samples from coastal inlet discharges, oceanic outfalls of municipal wastewater treatment plants, treated wastewater effluent before discharge, open ocean samples, and coral tissue samples (mucus and polyps) were characterized to determine the relationships between microbial communities in these matrices and those in reef water and coral tissues. Significant differences in microbial communities were noted among all sample types but varied between sampling areas. Contamination from outfalls was found to be the greatest potential source of LBSP influencing native microbial community structure among all reef samples, although pollution from inlets was also noted. Notably, reef water and coral tissue communities were found to be more greatly impacted by LBSP at southern reefs, which also experienced the most degradation during the course of the study. The results of this study provide new insights into how microbial communities from LBSP can impact coral reefs in southeast Florida and suggest that wastewater outfalls may have a greater influence on the microbial diversity and structure of these reef communities than do contaminants carried in runoff, although the influences of runoff and coastal inlet discharge on coral reefs are still substantial. IMPORTANCE Coral reefs are known to be endangered due to sewage discharge and to runoff of nutrients, pesticides, and other substances associated with anthropogenic activity. Here, we used next-generation sequencing to characterize the microbial communities of potential contaminant sources in order to determine how environmental discharges of microbiota and their genetic material may influence the microbiomes of coral reef communities and coastal receiving waters. Runoff delivered through inlet discharges impacted coral microbial communities, but impacts from oceanic outfalls carrying treated wastewater were greater. Geographic differences in the degree of impact suggest that coral microbiomes may be influenced by the microbiological quality of treated wastewater. PMID:28341673

Differential Impacts of Land-Based Sources of Pollution on the Microbiota of Southeast Florida Coral Reefs.

PubMed

Staley, Christopher; Kaiser, Thomas; Gidley, Maribeth L; Enochs, Ian C; Jones, Paul R; Goodwin, Kelly D; Sinigalliano, Christopher D; Sadowsky, Michael J; Chun, Chan Lan

2017-05-15

Coral reefs are dynamic ecosystems known for decades to be endangered due, in large part, to anthropogenic impacts from land-based sources of pollution (LBSP). In this study, we utilized an Illumina-based next-generation sequencing approach to characterize prokaryotic and fungal communities from samples collected off the southeast coast of Florida. Water samples from coastal inlet discharges, oceanic outfalls of municipal wastewater treatment plants, treated wastewater effluent before discharge, open ocean samples, and coral tissue samples (mucus and polyps) were characterized to determine the relationships between microbial communities in these matrices and those in reef water and coral tissues. Significant differences in microbial communities were noted among all sample types but varied between sampling areas. Contamination from outfalls was found to be the greatest potential source of LBSP influencing native microbial community structure among all reef samples, although pollution from inlets was also noted. Notably, reef water and coral tissue communities were found to be more greatly impacted by LBSP at southern reefs, which also experienced the most degradation during the course of the study. The results of this study provide new insights into how microbial communities from LBSP can impact coral reefs in southeast Florida and suggest that wastewater outfalls may have a greater influence on the microbial diversity and structure of these reef communities than do contaminants carried in runoff, although the influences of runoff and coastal inlet discharge on coral reefs are still substantial. IMPORTANCE Coral reefs are known to be endangered due to sewage discharge and to runoff of nutrients, pesticides, and other substances associated with anthropogenic activity. Here, we used next-generation sequencing to characterize the microbial communities of potential contaminant sources in order to determine how environmental discharges of microbiota and their genetic material may influence the microbiomes of coral reef communities and coastal receiving waters. Runoff delivered through inlet discharges impacted coral microbial communities, but impacts from oceanic outfalls carrying treated wastewater were greater. Geographic differences in the degree of impact suggest that coral microbiomes may be influenced by the microbiological quality of treated wastewater. Copyright © 2017 Staley et al.

Development of a Novel Method for Temporal Analysis of Airborne Microbial Communities

NASA Astrophysics Data System (ADS)

Spring, A.; Domingue, K. D.; Mooney, M. M.; Kerber, T. V.; Lemmer, K. M.; Docherty, K. M.

2017-12-01

Microorganisms are ubiquitous in the atmosphere, which serves as an important vector for microbial dispersal to all terrestrial habitats. Very little is known about the mechanisms that control microbial dispersal, because sampling of airborne microbial communities beyond 2 m above the ground is limited. The goal of this study was to construct and test an airborne microbial sampling system to collect sufficient DNA for conducting next generation sequencing and microbial community analyses. The system we designed employs helium-filled helikites as a mechanism for launching samplers to various altitudes. The samplers use a passive collection dish system, weigh under 6 lbs and are operated by remote control from the ground. We conducted several troubleshooting experiments to test sampler functionality. We extracted DNA from sterile collection dish surfaces and examined communities using amplicons of the V4 region of 16S rRNA in bacteria using Illumina Mi-Seq. The results of these experiments demonstrate that the samplers we designed 1) remain decontaminated when closed and collect sufficient microbial biomass for DNA-based analyses when open for 6 hours; 2) are optimally decontaminated with 15 minutes of UV exposure; 3) require 8 collection dish surfaces to collect sufficient biomass. We also determined that DNA extraction conducted within 24 hours of collection has less of an impact on community composition than extraction after frozen storage. Using this sampling system, we collected samples from multiple altitudes in December 2016 and May 2017 at 3 sites in Kalamazoo and Pellston, Michigan. In Kalamazoo, areas sampled were primarily developed or agricultural, while in Pellston they were primarily forested. We observed significant differences between airborne bacterial communities collected at each location and time point. Additionally, bacterial communities did not differ with altitude, suggesting that terrestrial land use has an important influence on the upward distribution of bacteria. Proteobacteria were predominant in air samples from Kalamazoo, while Firmicutes were more prevalent in Pellston. Our results demonstrate that the sampling platform we designed is a useful tool for exploring ecological questions related to distribution of airborne microbial communities across a vertical transect.

Statistical differences between relative quantitative molecular fingerprints from microbial communities.

PubMed

Portillo, M C; Gonzalez, J M

2008-08-01

Molecular fingerprints of microbial communities are a common method for the analysis and comparison of environmental samples. The significance of differences between microbial community fingerprints was analyzed considering the presence of different phylotypes and their relative abundance. A method is proposed by simulating coverage of the analyzed communities as a function of sampling size applying a Cramér-von Mises statistic. Comparisons were performed by a Monte Carlo testing procedure. As an example, this procedure was used to compare several sediment samples from freshwater ponds using a relative quantitative PCR-DGGE profiling technique. The method was able to discriminate among different samples based on their molecular fingerprints, and confirmed the lack of differences between aliquots from a single sample.

Comparative Study of Effects of CO 2 Concentration and pH on Microbial Communities from a Saline Aquifer, a Depleted Oil Reservoir, and a Freshwater Aquifer

DOE PAGES

Gulliver, Djuna M.; Lowry, Gregory V.; Gregory, Kelvin B.

2016-08-09

Injected CO 2 from geologic carbon storage is expected to impact the microbial communities of proposed storage sites, such as depleted oil reservoirs and deep saline aquifers, as well as overlying freshwater aquifers at risk of receiving leaking CO 2. Microbial community change in these subsurface sites may affect injectivity of CO 2, permanence of stored CO 2, and shallow subsurface water quality. The effect of CO 2 concentration on the microbial communities in fluid collected from a depleted oil reservoir and a freshwater aquifer was examined at subsurface pressures and temperatures. The community was exposed to 0%, 1%, 10%,more » and 100% pCO 2 for 56 days. Bacterial community structure was analyzed through 16S rRNA gene clone libraries, and total bacterial abundance was estimated through quantitative polymerase chain reaction. Changes in the microbial community observed in the depleted oil reservoir samples and freshwater samples were compared to previous results from CO 2-exposed deep saline aquifer fluids. Overall, results suggest that CO 2 exposure to microbial communities will result in pH-dependent population change, and the CO 2-selected microbial communities will vary among sites. In conclusion, this is the first study to compare the response of multiple subsurface microbial communities at conditions expected during geologic carbon storage, increasing the understanding of environmental drivers for microbial community changes in CO 2-exposed environments.« less

Comparative Study of Effects of CO 2 Concentration and pH on Microbial Communities from a Saline Aquifer, a Depleted Oil Reservoir, and a Freshwater Aquifer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gulliver, Djuna M.; Lowry, Gregory V.; Gregory, Kelvin B.

Injected CO 2 from geologic carbon storage is expected to impact the microbial communities of proposed storage sites, such as depleted oil reservoirs and deep saline aquifers, as well as overlying freshwater aquifers at risk of receiving leaking CO 2. Microbial community change in these subsurface sites may affect injectivity of CO 2, permanence of stored CO 2, and shallow subsurface water quality. The effect of CO 2 concentration on the microbial communities in fluid collected from a depleted oil reservoir and a freshwater aquifer was examined at subsurface pressures and temperatures. The community was exposed to 0%, 1%, 10%,more » and 100% pCO 2 for 56 days. Bacterial community structure was analyzed through 16S rRNA gene clone libraries, and total bacterial abundance was estimated through quantitative polymerase chain reaction. Changes in the microbial community observed in the depleted oil reservoir samples and freshwater samples were compared to previous results from CO 2-exposed deep saline aquifer fluids. Overall, results suggest that CO 2 exposure to microbial communities will result in pH-dependent population change, and the CO 2-selected microbial communities will vary among sites. In conclusion, this is the first study to compare the response of multiple subsurface microbial communities at conditions expected during geologic carbon storage, increasing the understanding of environmental drivers for microbial community changes in CO 2-exposed environments.« less

Sources of Variation in the Gut Microbial Community of Lycaeides melissa Caterpillars.

PubMed

Chaturvedi, Samridhi; Rego, Alexandre; Lucas, Lauren K; Gompert, Zachariah

2017-09-12

Microbes can mediate insect-plant interactions and have been implicated in major evolutionary transitions to herbivory. Whether microbes also play a role in more modest host shifts or expansions in herbivorous insects is less clear. Here we evaluate the potential for gut microbial communities to constrain or facilitate host plant use in the Melissa blue butterfly (Lycaeides melissa). We conducted a larval rearing experiment where caterpillars from two populations were fed plant tissue from two hosts. We used 16S rRNA sequencing to quantify the relative effects of sample type (frass versus whole caterpillar), diet (plant species), butterfly population and development (caterpillar age) on the composition and diversity of the caterpillar gut microbial communities, and secondly, to test for a relationship between microbial community and larval performance. Gut microbial communities varied over time (that is, with caterpillar age) and differed between frass and whole caterpillar samples. Diet (host plant) and butterfly population had much more limited effects on microbial communities. We found no evidence that gut microbe community composition was associated with caterpillar weight, and thus, our results provide no support for the hypothesis that variation in microbial community affects performance in L. melissa.

Patterns in bacterial and archaeal community structure and diversity in western Beaufort Sea sediments and waters

NASA Astrophysics Data System (ADS)

Hamdan, L. J.; Sikaroodi, M.; Coffin, R. B.; Gillevet, P. M.

2010-12-01

A culture-independent phylogenetic study of microbial communities in water samples and sediment cores recovered from the Beaufort Sea slope east of Point Barrow, Alaska was conducted. The goal of the work was to describe community composition in sediment and water samples and determine the influence of local environmental conditions on microbial populations. Archaeal and bacterial community composition was studied using length heterogeneity-polymerase chain reaction (LH-PCR) and multitag pyrosequencing (MTPS). Sediment samples were obtained from three piston cores on the slope (~1000m depth) arrayed along an east-west transect and one core from a depth of approximately 2000m. Discrete water samples were obtained using a CTD-rosette from three locations adjacent to piston core sites. Water sample were selected at three discrete depths within a vertically stratified (density) water column. The microbial community in near surface waters was distinct from the community observed in deeper stratified layers of the water column. Multidimensional scaling analysis (MDS) revealed that water samples from mid and deep stratified layers bore high similarity to communities in cores collected in close proximity. Overall, the highest diversity (bacteria and archaea) was observed in a core which had elevated methane concentration relative to other locations. Geochemical (e.g., bulk organic and inorganic carbon pools, nutrients, metabolites) and physical data (e.g. depth, water content) were used to reveal the abiotic factors structuring microbial communities. The analysis indicates that sediment water content (porosity) and inorganic carbon concentration are the most significant structuring elements on Beaufort shelf sedimentary microbial communities.

Linking geology and microbiology: inactive pockmarks affect sediment microbial community structure.

PubMed

Haverkamp, Thomas H A; Hammer, Øyvind; Jakobsen, Kjetill S

2014-01-01

Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm) sediment communities are affected by local conditions within the sediment.

Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input

DOE Office of Scientific and Technical Information (OSTI.GOV)

Armstrong, Alacia; Valverde, Angel; Ramond, Jean-Baptiste

The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more importantmore » than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall.« less

Reactor performances and microbial communities of biogas reactors: effects of inoculum sources.

PubMed

Han, Sheng; Liu, Yafeng; Zhang, Shicheng; Luo, Gang

2016-01-01

Anaerobic digestion is a very complex process that is mediated by various microorganisms, and the understanding of the microbial community assembly and its corresponding function is critical in order to better control the anaerobic process. The present study investigated the effect of different inocula on the microbial community assembly in biogas reactors treating cellulose with various inocula, and three parallel biogas reactors with the same inoculum were also operated in order to reveal the reproducibility of both microbial communities and functions of the biogas reactors. The results showed that the biogas production, volatile fatty acid (VFA) concentrations, and pH were different for the biogas reactors with different inocula, and different steady-state microbial community patterns were also obtained in different biogas reactors as reflected by Bray-Curtis similarity matrices and taxonomic classification. It indicated that inoculum played an important role in shaping the microbial communities of biogas reactor in the present study, and the microbial community assembly in biogas reactor did not follow the niche-based ecology theory. Furthermore, it was found that the microbial communities and reactor performances of parallel biogas reactors with the same inoculum were different, which could be explained by the neutral-based ecology theory and stochastic factors should played important roles in the microbial community assembly in the biogas reactors. The Bray-Curtis similarity matrices analysis suggested that inoculum affected more on the microbial community assembly compared to stochastic factors, since the samples with different inocula had lower similarity (10-20 %) compared to the samples from the parallel biogas reactors (30 %).

Changes in microbial community structure in the wake of Hurricanes Katrina and Rita

PubMed Central

Amaral-Zettler, Linda A.; Rocca, Jennifer D.; LaMontagne, Michael G.; Dennett, Mark R.; Gast, Rebecca J.

2009-01-01

Hurricanes have the potential to alter the structures of coastal ecosystems and generate pathogen-laden floodwaters that threaten public health. To examine the impact of hurricanes on urban systems, we compared microbial community structures in samples collected after Hurricane Katrina and before and after Hurricane Rita. We extracted environmental DNA and sequenced small-subunit ribosomal RNA (SSU rRNA) gene clone libraries to survey microbial communities in floodwater, water and sediment samples collected from Lake Charles, Lake Pontchartrain, the 17th Street and Industrial Canals in New Orleans and raw sewage. Correspondence Analysis showed that microbial communities associated with sediments formed one cluster while communities associated with lake and Industrial Canal water formed a second. Communities associated with water from the 17th Street Canal and floodwaters collected in New Orleans showed similarity to communities in raw sewage and contained a number of sequences associated with possible pathogenic microbes. This suggests that a distinct microbial community developed in floodwaters following Hurricane Katrina and that microbial community structures as a whole might be sensitive indicators of ecosystem health and serve as “sentinels” of water quality in the environment. PMID:19174873

Effects of Cd and Pb on soil microbial community structure and activities.

PubMed

Khan, Sardar; Hesham, Abd El-Latif; Qiao, Min; Rehman, Shafiqur; He, Ji-Zheng

2010-02-01

Soil contamination with heavy metals occurs as a result of both anthropogenic and natural activities. Heavy metals could have long-term hazardous impacts on the health of soil ecosystems and adverse influences on soil biological processes. Soil enzymatic activities are recognized as sensors towards any natural and anthropogenic disturbance occurring in the soil ecosystem. Similarly, microbial biomass carbon (MBC) is also considered as one of the important soil biological activities frequently influenced by heavy metal contamination. The polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) has recently been used to investigate changes in soil microbial community composition in response to environmental stresses. Soil microbial community structure and activities are difficult to elucidate using single monitoring approach; therefore, for a better insight and complete depiction of the soil microbial situation, different approaches need to be used. This study was conducted in a greenhouse for a period of 12 weeks to evaluate the changes in indigenous microbial community structure and activities in the soil amended with different application rates of Cd, Pb, and Cd/Pb mix. In a field environment, soil is contaminated with single or mixed heavy metals; so that, in this research, we used the selected metals in both single and mixed forms at different application rates and investigated their toxic effects on microbial community structure and activities, using soil enzyme assays, plate counting, and advanced molecular DGGE technique. Soil microbial activities, including acid phosphatase (ACP), urease (URE), and MBC, and microbial community structure were studied. A soil sample (0-20 cm) with an unknown history of heavy metal contamination was collected and amended with Cd, Pb, and Cd/Pb mix using the CdSO(4) and Pb(NO(3))(2) solutions at different application rates. The amended soils were incubated in the greenhouse at 25 +/- 4 degrees C and 60% water-holding capacity for 12 weeks. During the incubation period, samples were collected from each pot at 0, 2, 9, and 12 weeks for enzyme assays, MBC, numeration of microbes, and DNA extraction. Fumigation-extraction method was used to measure the MBC, while plate counting techniques were used to numerate viable heterotrophic bacteria, fungi, and actinomycetes. Soil DNAs were extracted from the samples and used for DGGE analysis. ACP, URE, and MBC activities of microbial community were significantly lower (p < 0.05) in the metal-amended samples than those in the control. The enzyme inhibition extent was obvious between different incubation periods and varied as the incubation proceeded, and the highest rate was detected in the samples after 2 weeks. However, the lowest values of ACP and URE activities (35.6% and 36.6% of the control, respectively) were found in the Cd(3)/Pb(3)-treated sample after 2 weeks. Similarly, MBC was strongly decreased in both Cd/Pb-amended samples and highest reduction (52.4%) was detected for Cd(3)/Pb(3) treatment. The number of bacteria and actinomycetes were significantly decreased in the heavy metal-amended samples compared to the control, while fungal cells were not significantly different (from 2.3% to 23.87%). In this study, the DGGE profile indicated that the high dose of metal amendment caused a greater change in the number of bands. DGGE banding patterns confirmed that the addition of metals had a significant impact on microbial community structure. In soil ecosystem, heavy metals exhibit toxicological effects on soil microbes which may lead to the decrease of their numbers and activities. This study demonstrated that toxicological effects of heavy metals on soil microbial community structure and activities depend largely on the type and concentration of metal and incubation time. The inhibition extent varied widely among different incubation periods for these enzymes. Furthermore, the rapid inhibition in microbial activities such as ACP, URE, and MBC were observed in the 2 weeks, which should be related to the fact that the microbes were suddenly exposed to heavy metals. The increased inhibition of soil microbial activities is likely to be related to tolerance and adaptation of the microbial community, concentration of pollutants, and mechanisms of heavy metals. The DGGE profile has shown that the structure of the bacterial community changed in amended heavy metal samples. In this research, the microbial community structure was highly affected, consistent with the lower microbial activities in different levels of heavy metals. Furthermore, a great community change in this study, particularly at a high level of contamination, was probably a result of metal toxicity and also unavailability of nutrients because no nutrients were supplied during the whole incubation period. The added concentrations of heavy metals have changed the soil microbial community structure and activities. The highest inhibitory effects on soil microbial activities were observed at 2 weeks of incubation. The bacteria were more sensitive than actinomycetes and fungi. The DGGE profile indicated that bacterial community structure was changed in the Cd/Pb-amended samples, particularly at high concentrations. The investigation of soil microbial community structure and activities together could give more reliable and accurate information about the toxic effects of heavy metals on soil health.

Shifts of microbial communities of wheat (Triticum aestivum L.) cultivation in a closed artificial ecosystem.

PubMed

Qin, Youcai; Fu, Yuming; Dong, Chen; Jia, Nannan; Liu, Hong

2016-05-01

The microbial communities of plant ecosystems are in relation to plant growing environment, but the alteration in biodiversity of rhizosphere and phyllosphere microbial communities in closed and controlled environments is unknown. The purpose of this study is to analyze the change regularity of microbial communities with wheat plants dependent-cultivated in a closed artificial ecosystem. The microbial community structures in closed-environment treatment plants were investigated by a culture-dependent approach, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), and Illumina Miseq high-throughput sequencing. The results indicated that the number of microbes decreased along with time, and the magnitude of bacteria, fungi, and actinomycetes were 10(7)-10(8), 10(5), and 10(3)-10(4) CFU/g (dry weight), respectively. The analysis of PCR-DGGE and Illumina Miseq revealed that the wheat leaf surface and near-root substrate had different microbial communities at different periods of wheat ecosystem development and showed that the relative highest diversity of microbial communities appeared at late and middle periods of the plant ecosystem, respectively. The results also indicated that the wheat leaf and substrate had different microbial community compositions, and the wheat substrate had higher richness of microbial community than the leaf. Flavobacterium, Pseudomonas, Paenibacillus, Enterobacter, Penicillium, Rhodotorula, Acremonium, and Alternaria were dominant in the wheat leaf samples, and Pedobacter, Flavobacterium, Halomonas, Marinobacter, Salinimicrobium, Lysobacter, Pseudomonas, Halobacillus, Xanthomonas, Acremonium, Monographella, and Penicillium were dominant populations in the wheat near-root substrate samples.

Salinity shapes microbial diversity and community structure in surface sediments of the Qinghai-Tibetan Lakes.

PubMed

Yang, Jian; Ma, Li'an; Jiang, Hongchen; Wu, Geng; Dong, Hailiang

2016-04-26

Investigating microbial response to environmental variables is of great importance for understanding of microbial acclimatization and evolution in natural environments. However, little is known about how microbial communities responded to environmental factors (e.g. salinity, geographic distance) in lake surface sediments of the Qinghai-Tibetan Plateau (QTP). In this study, microbial diversity and community structure in the surface sediments of nine lakes on the QTP were investigated by using the Illumina Miseq sequencing technique and the resulting microbial data were statistically analyzed in combination with environmental variables. The results showed total microbial community of the studied lakes was significantly correlated (r = 0.631, P < 0.001) with lake salinity instead of geographic distance. This suggests that lake salinity is more important than geographic distance in shaping the microbial diversity and community structure in the studied samples. In addition, the abundant and rare taxa (OTUs with relative abundance higher than 1% and lower than 0.01% within one sample, respectively) were significantly (P < 0.05) correlated (r = 0.427 and 0.783, respectively) with salinity, suggesting rare taxa might be more sensitive to salinity than their abundant counterparts, thus cautions should be taken in future when evaluating microbial response (abundant vs. rare sub-communities) to environmental conditions.

The effect of thermal stratification on microbial community diversity and structure in a temperate reservoir

NASA Astrophysics Data System (ADS)

Qu, Jiangqi; Jia, Chengxia; Zhao, Meng; Li, Wentong; Liu, Pan; Yang, Mu; Zhang, Qingjing

2018-02-01

Miyun reservoir is a typical temperate deep reservoir located in the northeast of Beijing, China. In order to explore the effect of thermal stratification on microbial community diversity, structure and its influencing environmental factors, stratified sampling at three sites was conducted during the summer period. Field observations indicate that the water temperature and dissolved oxygen concentrations dropped to 11.9 °C and 1.57 mg/L, respectively, leading to the development of anoxia in the hypolimnetic layer. The Illumina Miseq sequencing results showed that microbial communities from different thermal stratification showed obvious differences, the highest microbial diversity and richness in the hypolimnion samples. RDA ordination analysis suggested that the microbial communities in the epilimnion and metalimnion were mainly affected by water temperature, pH and dissolved oxygen, while total nitrogen was the key environmental factor which shaped the microbial structure in hypolimnion.

Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity

PubMed Central

Wolfe, Benjamin E.; Button, Julie E.; Santarelli, Marcela; Dutton, Rachel J.

2014-01-01

SUMMARY Tractable microbial communities are needed to bridge the gap between observations of patterns of microbial diversity and mechanisms that can explain these patterns. We developed cheese rinds as model microbial communities by characterizing in situ patterns of diversity and by developing an in vitro system for community reconstruction. Sequencing of 137 different rind communities across 10 countries revealed 24 widely distributed and culturable genera of bacteria and fungi as dominant community members. Reproducible community types formed independent of geographic location of production. Intensive temporal sampling demonstrated that assembly of these communities is highly reproducible. Patterns of community composition and succession observed in situ can be recapitulated in a simple in vitro system. Widespread positive and negative interactions were identified between bacterial and fungal community members. Cheese rind microbial communities represent an experimentally tractable system for defining mechanisms that influence microbial community assembly and function. PMID:25036636

Subsurface Environment Sampler for Improved In Situ Characterization of Subsurface Microbial Communities

NASA Astrophysics Data System (ADS)

Barnhart, E. P.; Ruppert, L. F.; Orem, W. H.; McIntosh, J. C.; Cunningham, A. B.; Fields, M. W.; Hiebert, R.; Hyatt, R.

2016-12-01

There is an increasing threat that deep aquifers, an important drinking water resource, may be contaminated by the extraction and transport of fossil fuels. This threat increases the need for improved groundwater monitoring and the ability to predict the extent to which microbial activity may remediate such contamination. The characterization of subsurface microbial communities could provide an ideal biomonitoring tool for the assessment of subsurface contamination due to prokaryotes environmental ubiquity, rapidity of response to environmental perturbation and the important role they play in hydrocarbon degradation and bioremediation. New DNA sequencing technologies provide the opportunity to cost-effectively identify the vast subsurface microbial ecosystem, but use of this new technology is restricted due to issues with sampling. Prior subsurface microbiology studies have relied on core samples that are expensive to obtain hard to collect aseptically and/or ground water samples that do not reflect in situ microbial densities or activities. The development of down-well incubation of sterile sediment with a Diffusive Microbial Sampler (DMS) has emerged as an alternative method to sample subsurface microbial communities that minimizes cost and contamination issues associated with traditional methods. We have designed a Subsurface Environment Sampler with a DMS module that could enable the anaerobic transport of the in situ microbial community from the field for laboratory bioremediation studies. This sampler could provide an inexpensive and standard method for subsurface microbial sampling which would make this tool useful for Federal, State, private and local agencies interested in monitoring contamination or the effectiveness of bioremediation activities in subsurface aquifers.

Supercritical fluid extraction and ultra performance liquid chromatography of respiratory quinones for microbial community analysis in environmental and biological samples.

PubMed

Hanif, Muhammad; Atsuta, Yoichi; Fujie, Koichi; Daimon, Hiroyuki

2012-03-05

Microbial community structure plays a significant role in environmental assessment and animal health management. The development of a superior analytical strategy for the characterization of microbial community structure is an ongoing challenge. In this study, we developed an effective supercritical fluid extraction (SFE) and ultra performance liquid chromatography (UPLC) method for the analysis of bacterial respiratory quinones (RQ) in environmental and biological samples. RQ profile analysis is one of the most widely used culture-independent tools for characterizing microbial community structure. A UPLC equipped with a photo diode array (PDA) detector was successfully applied to the simultaneous determination of ubiquinones (UQ) and menaquinones (MK) without tedious pretreatment. Supercritical carbon dioxide (scCO(2)) extraction with the solid-phase cartridge trap proved to be a more effective and rapid method for extracting respiratory quinones, compared to a conventional organic solvent extraction method. This methodology leads to a successful analytical procedure that involves a significant reduction in the complexity and sample preparation time. Application of the optimized methodology to characterize microbial communities based on the RQ profile was demonstrated for a variety of environmental samples (activated sludge, digested sludge, and compost) and biological samples (swine and Japanese quail feces).

Biogeography and Biodiversity in Sulfide Structures of Active and Inactive Vents at Deep-Sea Hydrothermal Fields of the Southern Mariana Trough▿ †

PubMed Central

Kato, Shingo; Takano, Yoshinori; Kakegawa, Takeshi; Oba, Hironori; Inoue, Kazuhiko; Kobayashi, Chiyori; Utsumi, Motoo; Marumo, Katsumi; Kobayashi, Kensei; Ito, Yuki; Ishibashi, Jun-ichiro; Yamagishi, Akihiko

2010-01-01

The abundance, diversity, activity, and composition of microbial communities in sulfide structures both of active and inactive vents were investigated by culture-independent methods. These sulfide structures were collected at four hydrothermal fields, both on- and off-axis of the back-arc spreading center of the Southern Mariana Trough. The microbial abundance and activity in the samples were determined by analyzing total organic content, enzymatic activity, and copy number of the 16S rRNA gene. To assess the diversity and composition of the microbial communities, 16S rRNA gene clone libraries including bacterial and archaeal phylotypes were constructed from the sulfide structures. Despite the differences in the geological settings among the sampling points, phylotypes related to the Epsilonproteobacteria and cultured hyperthermophilic archaea were abundant in the libraries from the samples of active vents. In contrast, the relative abundance of these phylotypes was extremely low in the libraries from the samples of inactive vents. These results suggest that the composition of microbial communities within sulfide structures dramatically changes depending on the degree of hydrothermal activity, which was supported by statistical analyses. Comparative analyses suggest that the abundance, activity and diversity of microbial communities within sulfide structures of inactive vents are likely to be comparable to or higher than those in active vent structures, even though the microbial community composition is different between these two types of vents. The microbial community compositions in the sulfide structures of inactive vents were similar to those in seafloor basaltic rocks rather than those in marine sediments or the sulfide structures of active vents, suggesting that the microbial community compositions on the seafloor may be constrained by the available energy sources. Our findings provide helpful information for understanding the biogeography, biodiversity and microbial ecosystems in marine environments. PMID:20228114

Effect of Increasing Nitrogen Deposition on Soil Microbial Communities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xiao, Shengmu; Xue, Kai; He, Zhili

2010-05-17

Increasing nitrogen deposition, increasing atmospheric CO2, and decreasing biodiversity are three main environmental changes occurring on a global scale. The BioCON (Biodiversity, CO2, and Nitrogen) ecological experiment site at the University of Minnesota's Cedar Creek Ecosystem Science Reserve started in 1997, to better understand how these changes would affect soil systems. To understand how increasing nitrogen deposition affects the microbial community diversity, heterogeneity, and functional structure impact soil microbial communities, 12 samples were collected from the BioCON plots in which nitrogenous fertilizer was added to simulate the effect of increasing nitrogen deposition and 12 samples from without added fertilizer. DNAmore » from the 24 samples was extracted using a freeze-grind protocol, amplified, labeled with a fluorescent dye, and then hybridized to GeoChip, a functional gene array containing probes for genes involved in N, S and C cycling, metal resistance and organic contaminant degradation. Detrended correspondence analysis (DCA) of all genes detected was performed to analyze microbial community patterns. The first two axes accounted for 23.5percent of the total variation. The samples fell into two major groups: fertilized and non-fertilized, suggesting that nitrogenous fertilizer had a significant impact on soil microbial community structure and diversity. The functional gene numbers detected in fertilized samples was less that detected in non-fertilizer samples. Functional genes involving in the N cycling were mainly discussed.« less

It's all relative: ranking the diversity of aquatic bacterial communities.

PubMed

Shaw, Allison K; Halpern, Aaron L; Beeson, Karen; Tran, Bao; Venter, J Craig; Martiny, Jennifer B H

2008-09-01

The study of microbial diversity patterns is hampered by the enormous diversity of microbial communities and the lack of resources to sample them exhaustively. For many questions about richness and evenness, however, one only needs to know the relative order of diversity among samples rather than total diversity. We used 16S libraries from the Global Ocean Survey to investigate the ability of 10 diversity statistics (including rarefaction, non-parametric, parametric, curve extrapolation and diversity indices) to assess the relative diversity of six aquatic bacterial communities. Overall, we found that the statistics yielded remarkably similar rankings of the samples for a given sequence similarity cut-off. This correspondence, despite the different underlying assumptions of the statistics, suggests that diversity statistics are a useful tool for ranking samples of microbial diversity. In addition, sequence similarity cut-off influenced the diversity ranking of the samples, demonstrating that diversity statistics can also be used to detect differences in phylogenetic structure among microbial communities. Finally, a subsampling analysis suggests that further sequencing from these particular clone libraries would not have substantially changed the richness rankings of the samples.

A Comparison of Microbial Community Structures by Depth and Season Under Switchgrass

NASA Astrophysics Data System (ADS)

Fansler, S. J.; Smith, J. L.; Bolton, H.; Bailey, V. L.

2008-12-01

As part of a multidisciplinary study of C sequestration in switchgrass production systems, the soil microbial community structure was monitored at 6 different depths (reaching 90 cm) in both spring and autumn. Microbial community structure was assessed using ribosomal intergenic spacer analysis (RISA), and primers were used specific to either bacteria or fungi, generating microbial community fingerprints for each taxonomic group. Diverse microbial communities for both groups were detected throughout the soil profile. It is notable that while community structure clearly changed with depth, there was the deepest soil samples still retained relatively diverse communities. Seasonally, differences are clearly evident within plots at the surface. As the plots were replicated, significant differences in the community fingerprints with depth and season are reported.

Adaption of the microbial community to continuous exposures of multiple residual antibiotics in sediments from a salt-water aquacultural farm.

PubMed

Xi, Xiuping; Wang, Min; Chen, Yongshan; Yu, Shen; Hong, Youwei; Ma, Jun; Wu, Qian; Lin, Qiaoyin; Xu, Xiangrong

2015-06-15

Residual antibiotics from aquacultural farming may alter microbial community structure in aquatic environments in ways that may adversely or positively impact microbially-mediated ecological functions. This study investigated 26 ponds (26 composited samples) used to produce fish, razor clam and shrimp (farming and drying) and 2 channels (10 samples) in a saltwater aquacultural farm in southern China to characterize microbial community structure (represented by phospholipid fatty acids) in surface sediments (0-10 cm) with long-term exposure to residual antibiotics. 11 out of 14 widely-used antibiotics were quantifiable at μg kg(-1) levels in sediments but their concentrations did not statistically differ among ponds and channels, except norfloxacin in drying shrimp ponds and thiamphenicol in razor clam ponds. Concentrations of protozoan PLFAs were significantly increased in sediments from razor clam ponds while other microbial groups were similar among ponds and channels. Both canonical-correlation and stepwise-multiple-regression analyses on microbial community and residual antibiotics suggested that roxithromycin residuals were significantly related to shifts in microbial community structure in sediments. This study provided field evidence that multiple residual antibiotics at low environmental levels from aquacultural farming do not produce fundamental shifts in microbial community structure. Copyright © 2015 Elsevier B.V. All rights reserved.

Soil microbial succession along a chronosequence on a High Arctic glacier foreland, Ny-Ålesund, Svalbard: 10 years' change

NASA Astrophysics Data System (ADS)

Yoshitake, Shinpei; Uchida, Masaki; Iimura, Yasuo; Ohtsuka, Toshiyuki; Nakatsubo, Takayuki

2018-06-01

Rapid glacial retreat in the High Arctic causes the expansion of new habitats, but the successional trajectories of soil microbial communities are not fully understood. We examined microbial succession along a chronosequence twice with a 10-year interval in a High Arctic glacier foreland. Soil samples were collected from five study sites with different ages and phospholipid fatty acids analysis was conducted to investigate the microbial biomass and community structure. Microbial biomass did not differ significantly between the two sampling times but tended to increase with the chronosequence and showed a significant correlation with soil carbon (C) and nitrogen (N) content. Microbial community structure clearly differed along the chronosequence and was correlated with C and N content. The largest shift in community structure over 10 years was observed in the newly exposed sites after deglaciation. The accumulation of soil organic matter was regarded as an important determinant both of microbial biomass and community structure over the successional period. In contrast, the initial microbial community on the newly exposed soil changed rapidly even in the High Arctic, suggesting that some key soil processes such as C and N cycling can also shift within the relatively short period after rapid glacial retreat.

Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions.

PubMed

Yu, Chaowei; Reddy, Amitha P; Simmons, Christopher W; Simmons, Blake A; Singer, Steven W; VanderGheynst, Jean S

2015-01-01

Microbial communities enriched from diverse environments have shown considerable promise for the targeted discovery of microorganisms and enzymes for bioconversion of lignocellulose to liquid fuels. While preservation of microbial communities is important for commercialization and research, few studies have examined storage conditions ideal for preservation. The goal of this study was to evaluate the impact of preservation method on composition of microbial communities enriched on switchgrass before and after storage. The enrichments were completed in a high-solid and aerobic environment at 55 °C. Community composition was examined for each enrichment to determine when a stable community was achieved. Preservation methods included cryopreservation with the cryoprotective agents DMSO and glycerol, and cryopreservation without cryoprotective agents. Revived communities were examined for their ability to decompose switchgrass under high-solid and thermophilic conditions. High-throughput 16S rRNA gene sequencing of DNA extracted from enrichment samples showed that the majority of the shift in composition of the switchgrass-degrading community occurred during the initial three 2-week enrichments. Shifts in community structure upon storage occurred in all cryopreserved samples. Storage in liquid nitrogen in the absence of cryoprotectant resulted in variable preservation of dominant microorganisms in enriched samples. Cryopreservation with either DMSO or glycerol provided consistent and equivalent preservation of dominant organisms. A stable switchgrass-degrading microbial community was achieved after three 2-week enrichments. Dominant microorganisms were preserved equally well with DMSO and glycerol. DMSO-preserved communities required more incubation time upon revival to achieve pre-storage activity levels during high-solid thermophilic cultivation on switchgrass. Despite shifts in the community with storage, the samples were active upon revival under thermophilic and high-solid conditions. The results suggest that the presence of microorganisms may be more important than their relative abundance in retaining an active microbial community.

Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions

DOE PAGES

Yu, Chaowei; Reddy, Amitha P.; Simmons, Christopher W.; ...

2015-12-02

Microbial communities enriched from diverse environments have shown considerable promise for the targeted discovery of microorganisms and enzymes for bioconversion of lignocellulose to liquid fuels. While preservation of microbial communities is important for commercialization and research, few studies have examined storage conditions ideal for preservation. The goal of this study was to evaluate the impact of preservation method on composition of microbial communities enriched on switchgrass before and after storage. The enrichments were completed in a high-solid and aerobic environment at 55 °C. Community composition was examined for each enrichment to determine when a stable community was achieved. Preservation methodsmore » included cryopreservation with the cryoprotective agents DMSO and glycerol, and cryopreservation without cryoprotective agents. Revived communities were examined for their ability to decompose switchgrass under high-solid and thermophilic conditions. High-throughput 16S rRNA gene sequencing of DNA extracted from enrichment samples showed that the majority of the shift in composition of the switchgrass-degrading community occurred during the initial three 2-week enrichments. Shifts in community structure upon storage occurred in all cryopreserved samples. Storage in liquid nitrogen in the absence of cryoprotectant resulted in variable preservation of dominant microorganisms in enriched samples. Cryopreservation with either DMSO or glycerol provided consistent and equivalent preservation of dominant organisms. In conclusion, a stable switchgrass-degrading microbial community was achieved after three 2-week enrichments. Dominant microorganisms were preserved equally well with DMSO and glycerol. DMSO-preserved communities required more incubation time upon revival to achieve pre-storage activity levels during high-solid thermophilic cultivation on switchgrass. Despite shifts in the community with storage, the samples were active upon revival under thermophilic and high-solid conditions. The results suggest that the presence of microorganisms may be more important than their relative abundance in retaining an active microbial community.« less

Metagenomic analyses of drinking water receiving different disinfection treatments.

PubMed

Gomez-Alvarez, Vicente; Revetta, Randy P; Santo Domingo, Jorge W

2012-09-01

A metagenome-based approach was used to assess the taxonomic affiliation and function potential of microbial populations in free-chlorine-treated (CHL) and monochloramine-treated (CHM) drinking water (DW). In all, 362,640 (averaging 544 bp) and 155,593 (averaging 554 bp) pyrosequencing reads were analyzed for the CHL and CHM samples, respectively. Most annotated proteins were found to be of bacterial origin, although eukaryotic, archaeal, and viral proteins were also identified. Differences in community structure and function were noted. Most notably, Legionella-like genes were more abundant in the CHL samples while mycobacterial genes were more abundant in CHM samples. Genes associated with multiple disinfectant mechanisms were identified in both communities. Moreover, sequences linked to virulence factors, such as antibiotic resistance mechanisms, were observed in both microbial communities. This study provides new insights into the genetic network and potential biological processes associated with the molecular microbial ecology of DW microbial communities.

Metagenomic Analyses of Drinking Water Receiving Different Disinfection Treatments

PubMed Central

Gomez-Alvarez, Vicente; Revetta, Randy P.

2012-01-01

A metagenome-based approach was used to assess the taxonomic affiliation and function potential of microbial populations in free-chlorine-treated (CHL) and monochloramine-treated (CHM) drinking water (DW). In all, 362,640 (averaging 544 bp) and 155,593 (averaging 554 bp) pyrosequencing reads were analyzed for the CHL and CHM samples, respectively. Most annotated proteins were found to be of bacterial origin, although eukaryotic, archaeal, and viral proteins were also identified. Differences in community structure and function were noted. Most notably, Legionella-like genes were more abundant in the CHL samples while mycobacterial genes were more abundant in CHM samples. Genes associated with multiple disinfectant mechanisms were identified in both communities. Moreover, sequences linked to virulence factors, such as antibiotic resistance mechanisms, were observed in both microbial communities. This study provides new insights into the genetic network and potential biological processes associated with the molecular microbial ecology of DW microbial communities. PMID:22729545

A survey of alterations in microbial community diversity in marine sediments in response to oil from the Deepwater Horizon spill: Northern Gulf of Mexico shoreline, Texas to Florida

USGS Publications Warehouse

Lisle, John T.

2011-01-01

Microbial community genomic DNA was extracted from sediment samples collected from the northern Gulf of Mexico (NGOM) coast. These samples had a high probability of being impacted by Macondo-1 (M-1) well oil from the Deepwater Horizon (DWH) drilling site. The hypothesis for this project was that presence of M-1 oil in coastal sediments would significantly alter the diversity within the microbial communities associated with the impacted sediments. To determine if community-level changes did or did not occur following exposure to M-1 oil, microbial community-diversity fingerprints were generated and compared. Specific sequences within the community's genomic DNA were first amplified using the polymerase chain reaction (PCR) using a primer set that provides possible resolution to the species level. A second nested PCR that was performed on the primary PCR products using a primer set on which a GC-clamp was attached to one of the primers. These nested PCR products were separated using denaturing-gradient gel electrophoresis (DGGE) that resolves the nested PCR products based on sequence dissimilarities (or similarities), forming a genomic fingerprint of the microbial diversity within the respective samples. Sediment samples with similar fingerprints were grouped and compared to oil-fingerprint data from Rosenbauer and others (2010). The microbial community fingerprints grouped closely when identifying those sites that had been impacted by M-1 oil (N=12) and/or some mixture of M-1 and other oil (N=4), based upon the oil fingerprints. This report represents some of the first information on naturally occurring microbial communities in sediment from shorelines along the NGOM coast. These communities contain microbes capable of degrading oil and related hydrocarbons, making this information relevant to response and recovery of the NGOM from the DWH incident.

Environmental drivers of differences in microbial community structure in crude oil reservoirs across a methanogenic gradient

USGS Publications Warehouse

Shelton, Jenna L.; Akob, Denise M.; McIntosh, Jennifer C.; Fierer, Noah; Spear, John R.; Warwick, Peter D.; McCray, John E.

2016-01-01

Stimulating in situ microbial communities in oil reservoirs to produce natural gas is a potentially viable strategy for recovering additional fossil fuel resources following traditional recovery operations. Little is known about what geochemical parameters drive microbial population dynamics in biodegraded, methanogenic oil reservoirs. We investigated if microbial community structure was significantly impacted by the extent of crude oil biodegradation, extent of biogenic methane production, and formation water chemistry. Twenty-two oil production wells from north central Louisiana, USA, were sampled for analysis of microbial community structure and fluid geochemistry. Archaea were the dominant microbial community in the majority of the wells sampled. Methanogens, including hydrogenotrophic and methylotrophic organisms, were numerically dominant in every well, accounting for, on average, over 98% of the total Archaea present. The dominant Bacteria groups were Pseudomonas, Acinetobacter, Enterobacteriaceae, and Clostridiales, which have also been identified in other microbially-altered oil reservoirs. Comparing microbial community structure to fluid (gas, water, and oil) geochemistry revealed that the relative extent of biodegradation, salinity, and spatial location were the major drivers of microbial diversity. Archaeal relative abundance was independent of the extent of methanogenesis, but closely correlated to the extent of crude oil biodegradation; therefore, microbial community structure is likely not a good sole predictor of methanogenic activity, but may predict the extent of crude oil biodegradation. However, when the shallow, highly biodegraded, low salinity wells were excluded from the statistical analysis, no environmental parameters could explain the differences in microbial community structure. This suggests that the microbial community structure of the 5 shallow, up-dip wells was different than the 17 deeper, down-dip wells. Also, the 17 down-dip wells had statistically similar microbial communities despite significant changes in environmental parameters between oil fields. Together, this implies that no single microbial population is a reliable indicator of a reservoir's ability to degrade crude oil to methane, and that geochemistry may be a more important indicator for selecting a reservoir suitable for microbial enhancement of natural gas generation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Chaowei; Reddy, Amitha P.; Simmons, Christopher W.

Microbial communities enriched from diverse environments have shown considerable promise for the targeted discovery of microorganisms and enzymes for bioconversion of lignocellulose to liquid fuels. While preservation of microbial communities is important for commercialization and research, few studies have examined storage conditions ideal for preservation. The goal of this study was to evaluate the impact of preservation method on composition of microbial communities enriched on switchgrass before and after storage. The enrichments were completed in a high-solid and aerobic environment at 55 °C. Community composition was examined for each enrichment to determine when a stable community was achieved. Preservation methodsmore » included cryopreservation with the cryoprotective agents DMSO and glycerol, and cryopreservation without cryoprotective agents. Revived communities were examined for their ability to decompose switchgrass under high-solid and thermophilic conditions. High-throughput 16S rRNA gene sequencing of DNA extracted from enrichment samples showed that the majority of the shift in composition of the switchgrass-degrading community occurred during the initial three 2-week enrichments. Shifts in community structure upon storage occurred in all cryopreserved samples. Storage in liquid nitrogen in the absence of cryoprotectant resulted in variable preservation of dominant microorganisms in enriched samples. Cryopreservation with either DMSO or glycerol provided consistent and equivalent preservation of dominant organisms. In conclusion, a stable switchgrass-degrading microbial community was achieved after three 2-week enrichments. Dominant microorganisms were preserved equally well with DMSO and glycerol. DMSO-preserved communities required more incubation time upon revival to achieve pre-storage activity levels during high-solid thermophilic cultivation on switchgrass. Despite shifts in the community with storage, the samples were active upon revival under thermophilic and high-solid conditions. The results suggest that the presence of microorganisms may be more important than their relative abundance in retaining an active microbial community.« less

Community-Level Physiological Profiling of Microbial Communities in Constructed Wetlands: Effects of Sample Preparation.

PubMed

Button, Mark; Weber, Kela; Nivala, Jaime; Aubron, Thomas; Müller, Roland Arno

2016-03-01

Community-level physiological profiling (CLPP) using BIOLOG® EcoPlates™ has become a popular method for characterizing and comparing the functional diversity, functional potential, and metabolic activity of heterotrophic microbial communities. The method was originally developed for profiling soil communities; however, its usage has expanded into the fields of ecotoxicology, agronomy, and the monitoring and profiling of microbial communities in various wastewater treatment systems, including constructed wetlands for water pollution control. When performing CLPP on aqueous samples from constructed wetlands, a wide variety of sample characteristics can be encountered and challenges may arise due to excessive solids, color, or turbidity. The aim of this study was to investigate the impacts of different sample preparation methods on CLPP performed on a variety of aqueous samples covering a broad range of physical and chemical characteristics. The results show that using filter paper, centrifugation, or settling helped clarify samples for subsequent CLPP analysis, however did not do so as effectively as dilution for the darkest samples. Dilution was able to provide suitable clarity for the darkest samples; however, 100-fold dilution significantly affected the carbon source utilization patterns (CSUPs), particularly with samples that were already partially or fully clear. Ten-fold dilution also had some effect on the CSUPs of samples which were originally clear; however, the effect was minimal. Based on these findings, for this specific set of samples, a 10-fold dilution provided a good balance between ease of use, sufficient clarity (for dark samples), and limited effect on CSUPs. The process and findings outlined here can hopefully serve future studies looking to utilize CLPP for functional analysis of microbial communities and also assist in comparing data from studies where different sample preparation methods were utilized.

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer.

PubMed

Tully, Benjamin J; Wheat, C Geoff; Glazer, Brain T; Huber, Julie A

2018-01-01

The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized metagenomic libraries of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement to query microbial diversity. Twenty-one samples were collected during a 2-year period to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the 2 years, yet the microbial community present in the crustal fluids underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the data set and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in members of the Proteobacteria, specifically the Alpha-, Gamma- and Zetaproteobacteria, the Epsilonbacteraeota and the Planctomycetes. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes, such as cbb 3 - and bd-type cytochromes, and alternative electron acceptors, like nitrate and sulfate. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles. Collectively, the repeated sampling at multiple sites, together with the successful binning of hundreds of genomes, provides an unprecedented data set for investigation of microbial communities in the cold, oxic crustal aquifer.

Sequencing Insights into Microbial Communities in the Water and Sediments of Fenghe River, China.

PubMed

Lu, Sidan; Sun, Yujiao; Zhao, Xuan; Wang, Lei; Ding, Aizhong; Zhao, Xiaohui

2016-07-01

The connection between microbial community structure and spatial variation and pollution in river waters has been widely investigated. However, water and sediments together have rarely been explored. In this study, Illumina high-throughput sequencing was performed to analyze microbes in 24 water and sediment samples from natural to anthropogenic sources and from headstream to downstream areas. These data were used to assess variability in microbial community structure and diversity along in the Fenghe River, China. The relationship between bacterial diversity and environmental parameters was statistically analyzed. An average of 1682 operational taxonomic units was obtained. Microbial diversity increased from the headstream to downstream and tended to be greater in sediment compared with water. The water samples near the headstream endured relatively low Shannon and Chao1 indices. These diversity indices and the number of observed species in the water and sediment samples increase downstream. The parameters also differ in the two river tributaries. Community structures shift based on the extent of nitrogen pollution variation in the sediment and water samples. The four most dominant genera in the water community were Escherichia, Acinetobacter, Comamonadaceae, and Pseudomonas. In the sediments, the most dominant genera were Stramenopiles, Flavobacterium, Pseudomonas, and Comamonadaceae. The number of ammonia-oxidizing archaea in the headstream water slightly differed from that in the sediment but varied considerably in the downstream sediments. Statistical analysis showed that community variation is correlated with changes in ammonia nitrogen, total nitrogen, and nitrate nitrogen. This study identified different microbial community structures in river water and sediments. Overall this study emphasized the need to elucidate spatial variations in bacterial diversity in water and sediments associated with physicochemical gradients and to show the effects of such variation on waterborne microbial community structures.

Microbial Community in High Arsenic Shallow Groundwater Aquifers in Hetao Basin of Inner Mongolia, China

PubMed Central

Li, Ping; Wang, Yanhong; Dai, Xinyue; Zhang, Rui; Jiang, Zhou; Jiang, Dawei; Wang, Shang; Jiang, Hongchen; Wang, Yanxin; Dong, Hailiang

2015-01-01

A survey was carried out on the microbial community of 20 groundwater samples (4 low and 16 high arsenic groundwater) and 19 sediments from three boreholes (two high arsenic and one low arsenic boreholes) in a high arsenic groundwater system located in Hetao Basin, Inner Mongolia, using the 454 pyrosequencing approach. A total of 233,704 sequence reads were obtained and classified into 12–267 operational taxonomic units (OTUs). Groundwater and sediment samples were divided into low and high arsenic groups based on measured geochemical parameters and microbial communities, by hierarchical clustering and principal coordinates analysis. Richness and diversity of the microbial communities in high arsenic sediments are higher than those in high arsenic groundwater. Microbial community structure was significantly different either between low and high arsenic samples or between groundwater and sediments. Acinetobacter, Pseudomonas, Psychrobacter and Alishewanella were the top four genera in high arsenic groundwater, while Thiobacillus, Pseudomonas, Hydrogenophaga, Enterobacteriaceae, Sulfuricurvum and Arthrobacter dominated high arsenic sediments. Archaeal sequences in high arsenic groundwater were mostly related to methanogens. Biota-environment matching and co-inertia analyses showed that arsenic, total organic carbon, SO4 2-, SO4 2-/total sulfur ratio, and Fe2+ were important environmental factors shaping the observed microbial communities. The results of this study expand our current understanding of microbial ecology in high arsenic groundwater aquifers and emphasize the potential importance of microbes in arsenic transformation in the Hetao Basin, Inner Mongolia. PMID:25970606

Microbial community in high arsenic shallow groundwater aquifers in Hetao Basin of Inner Mongolia, China.

PubMed

Li, Ping; Wang, Yanhong; Dai, Xinyue; Zhang, Rui; Jiang, Zhou; Jiang, Dawei; Wang, Shang; Jiang, Hongchen; Wang, Yanxin; Dong, Hailiang

2015-01-01

A survey was carried out on the microbial community of 20 groundwater samples (4 low and 16 high arsenic groundwater) and 19 sediments from three boreholes (two high arsenic and one low arsenic boreholes) in a high arsenic groundwater system located in Hetao Basin, Inner Mongolia, using the 454 pyrosequencing approach. A total of 233,704 sequence reads were obtained and classified into 12-267 operational taxonomic units (OTUs). Groundwater and sediment samples were divided into low and high arsenic groups based on measured geochemical parameters and microbial communities, by hierarchical clustering and principal coordinates analysis. Richness and diversity of the microbial communities in high arsenic sediments are higher than those in high arsenic groundwater. Microbial community structure was significantly different either between low and high arsenic samples or between groundwater and sediments. Acinetobacter, Pseudomonas, Psychrobacter and Alishewanella were the top four genera in high arsenic groundwater, while Thiobacillus, Pseudomonas, Hydrogenophaga, Enterobacteriaceae, Sulfuricurvum and Arthrobacter dominated high arsenic sediments. Archaeal sequences in high arsenic groundwater were mostly related to methanogens. Biota-environment matching and co-inertia analyses showed that arsenic, total organic carbon, SO4(2-), SO4(2-)/total sulfur ratio, and Fe(2+) were important environmental factors shaping the observed microbial communities. The results of this study expand our current understanding of microbial ecology in high arsenic groundwater aquifers and emphasize the potential importance of microbes in arsenic transformation in the Hetao Basin, Inner Mongolia.

Diversity and Contributions to Nitrogen Cycling and Carbon Fixation of Soil Salinity Shaped Microbial Communities in Tarim Basin

PubMed Central

Ren, Min; Zhang, Zhufeng; Wang, Xuelian; Zhou, Zhiwei; Chen, Dong; Zeng, Hui; Zhao, Shumiao; Chen, Lingling; Hu, Yuanliang; Zhang, Changyi; Liang, Yunxiang; She, Qunxin; Zhang, Yi; Peng, Nan

2018-01-01

Arid and semi-arid regions comprise nearly one-fifth of the earth's terrestrial surface. However, the diversities and functions of their soil microbial communities are not well understood, despite microbial ecological importance in driving biogeochemical cycling. Here, we analyzed the geochemistry and microbial communities of the desert soils from Tarim Basin, northwestern China. Our geochemical data indicated half of these soils are saline. Metagenomic analysis showed that bacterial phylotypes (89.72% on average) dominated the community, with relatively small proportions of Archaea (7.36%) and Eukaryota (2.21%). Proteobacteria, Firmicutes, Actinobacteria, and Euryarchaeota were most abundant based on metagenomic data, whereas genes attributed to Proteobacteria, Actinobacteria, Euryarchaeota, and Thaumarchaeota most actively transcribed. The most abundant phylotypes (Halobacterium, Halomonas, Burkholderia, Lactococcus, Clavibacter, Cellulomonas, Actinomycetospora, Beutenbergia, Pseudomonas, and Marinobacter) in each soil sample, based on metagenomic data, contributed marginally to the population of all microbial communities, whereas the putative halophiles, which contributed the most abundant transcripts, were in the majority of the active microbial population and is consistent with the soil salinity. Sample correlation analyses according to the detected and active genotypes showed significant differences, indicating high diversity of microbial communities among the Tarim soil samples. Regarding ecological functions based on the metatranscriptomic data, transcription of genes involved in various steps of nitrogen cycling, as well as carbon fixation, were observed in the tested soil samples. Metatranscriptomic data also indicated that Thaumarchaeota are crucial for ammonia oxidation and Proteobacteria play the most important role in other steps of nitrogen cycle. The reductive TCA pathway and dicarboxylate-hydroxybutyrate cycle attributed to Proteobacteria and Crenarchaeota, respectively, were highly represented in carbon fixation. Our study reveals that the microbial communities could provide carbon and nitrogen nutrients for higher plants in the sandy saline soils of Tarim Basin. PMID:29593680

Optimization of whole-transcriptome amplification from low cell density deep-sea microbial samples for metatranscriptomic analysis.

PubMed

Wu, Jieying; Gao, Weimin; Zhang, Weiwen; Meldrum, Deirdre R

2011-01-01

Limitation in sample quality and quantity is one of the big obstacles for applying metatranscriptomic technologies to explore gene expression and functionality of microbial communities in natural environments. In this study, several amplification methods were evaluated for whole-transcriptome amplification of deep-sea microbial samples, which are of low cell density and high impurity. The best amplification method was identified and incorporated into a complete protocol to isolate and amplify deep-sea microbial samples. In the protocol, total RNA was first isolated by a modified method combining Trizol (Invitrogen, CA) and RNeasy (QIAGEN, CA) method, amplified with a WT-Ovation™ Pico RNA Amplification System (NuGEN, CA), and then converted to double-strand DNA from single-strand cDNA with a WT-Ovation™ Exon Module (NuGEN, CA). The products from the whole-transcriptome amplification of deep-sea microbial samples were assessed first through random clone library sequencing. The BLAST search results showed that marine-based sequences are dominant in the libraries, consistent with the ecological source of the samples. The products were then used for next-generation Roche GS FLX Titanium sequencing to obtain metatranscriptome data. Preliminary analysis of the metatranscriptomic data showed good sequencing quality. Although the protocol was designed and demonstrated to be effective for deep-sea microbial samples, it should be applicable to similar samples from other extreme environments in exploring community structure and functionality of microbial communities. Copyright © 2010 Elsevier B.V. All rights reserved.

Microbial community succession in alkaline, saline bauxite residue: a cross-refinery study

NASA Astrophysics Data System (ADS)

Santini, T.; Malcolm, L. I.; Tyson, G. W.; Warren, L. A.

2015-12-01

Bauxite residue, a byproduct of the Bayer process for alumina refining, is an alkaline, saline tailings material that is generally considered to be inhospitable to microbial life. In situ remediation strategies promote soil formation in bauxite residue by enhancing leaching of saline, alkaline pore water, and through incorporation of amendments to boost organic matter content, decrease pH, and improve physical structure. The amelioration of chemical and physical conditions in bauxite residue is assumed to support diversification of microbial communities from narrow, poorly functioning microbial communities towards diverse, well-functioning communities. This study aimed to characterise microbial communities in fresh and remediated bauxite residues from refineries worldwide, to identify (a) whether initial microbial communities differed between refineries; (b) major environmental controls on microbial community composition; and (c) whether remediation successfully shifts the composition of microbial communities in bauxite residue towards those found in reference (desired endpoint) soils. Samples were collected from 16 refineries and characterised using 16S amplicon sequencing to examine microbial community composition and structure, in conjunction with physicochemical analyses. Initial microbial community composition was similar across refineries but partitioned into two major groups. Microbial community composition changes slowly over time and indicates that alkalinity and salinity inhibit diversification. Microbially-based strategies for in situ remediation should consider the initial microbial community composition and whether the pre-treatment of chemical properties would optimise subsequent bioremediation outcomes. During in situ remediation, microbial communities become more diverse and develop wider functional capacity, indicating progression towards communities more commonly observed in natural grassland and forest soils.

Robust estimation of microbial diversity in theory and in practice

PubMed Central

Haegeman, Bart; Hamelin, Jérôme; Moriarty, John; Neal, Peter; Dushoff, Jonathan; Weitz, Joshua S

2013-01-01

Quantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of microbial diversity has received renewed attention with the advent of large-scale metagenomic studies. Here, we consider what the diversity observed in a sample tells us about the diversity of the community being sampled. First, we argue that one cannot reliably estimate the absolute and relative number of microbial species present in a community without making unsupported assumptions about species abundance distributions. The reason for this is that sample data do not contain information about the number of rare species in the tail of species abundance distributions. We illustrate the difficulty in comparing species richness estimates by applying Chao's estimator of species richness to a set of in silico communities: they are ranked incorrectly in the presence of large numbers of rare species. Next, we extend our analysis to a general family of diversity metrics (‘Hill diversities'), and construct lower and upper estimates of diversity values consistent with the sample data. The theory generalizes Chao's estimator, which we retrieve as the lower estimate of species richness. We show that Shannon and Simpson diversity can be robustly estimated for the in silico communities. We analyze nine metagenomic data sets from a wide range of environments, and show that our findings are relevant for empirically-sampled communities. Hence, we recommend the use of Shannon and Simpson diversity rather than species richness in efforts to quantify and compare microbial diversity. PMID:23407313

Plant community influence on soil microbial response after a wildfire in Sierra Nevada National Park (Spain).

PubMed

Bárcenas-Moreno, Gema; García-Orenes, Fuensanta; Mataix-Solera, Jorge; Mataix-Beneyto, Jorge

2016-12-15

Plant community influence on microbial response after fire has been studied in a Sierra Nevada National Park area affected by a wildfire in 2005. Two different plant communities adapted to different altitudes were selected to analyse possible differences on soil microbial recolonisation process after fire, in oak forest and high mountain shrub communities. Microbial abundance, activity and community composition were monitored to evaluate medium-term changes. Microbial abundance was studied by mean of microbial biomass carbon and plate count methods; microbial activity was analysed by microbial respiration and bacterial growth while microbial community composition was determined by analysing phospholipid fatty acid pattern. Under unburnt conditions oak forest showed higher nutrient content, pH and microbial abundance and activity values than the high mountain shrubs community. Different parameters studied showed different trends with time, highlighting important changes in microbial community composition in high mountain shrubs from first sampling to the second one. Post-fire recolonisation process was different depending on plant community studied. Highlighting fungal response and microbial activity were stimulated in burnt high mountain shrubs community whilst it was negatively affected in oak forest. Fire induced changes in oak forest were almost neutralized 20months after the fire, while high mountain shrubs community still showed fire-induced changes at the end of the study. Copyright © 2016 Elsevier B.V. All rights reserved.

Dining local: the microbial diet of a snail that grazes microbial communities is geographically structured.

PubMed

O'Rorke, Richard; Cobian, Gerald M; Holland, Brenden S; Price, Melissa R; Costello, Vincent; Amend, Anthony S

2015-05-01

Achatinella mustelina is a critically endangered tree snail that subsists entirely by grazing microbes from leaf surfaces of native trees. Little is known about the fundamental aspects of these microbe assemblages: not taxonomic composition, how this varies with host plant or location, nor whether snails selectively consume microbes. To address these questions, we collected 102 snail faecal samples as a proxy for diet, and 102 matched-leaf samples from four locations. We used Illumina amplicon sequencing to determine bacterial and fungal community composition. Microbial community structure was significantly distinct between snail faeces and leaf samples, but the same microbes occurred in both. We conclude that snails are not 'picky' eaters at the microbial level, but graze the surface of whatever plant they are on. In a second experiment, the gut was dissected from non-endangered native tree snails in the same family as Achatinella to confirm that faecal samples reflect gut contents. Over 60% of fungal reads were shared between faeces, gut and leaf samples. Overall, location, sample type (faeces or leaf) and host plant identity all significantly explained the community composition and variation among samples. Understanding the microbial ecology of microbes grazed by tree snails enables effective management when conservation requires captive breeding or field relocation. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Microbial Life in Ridge Flank Crustal Fluids at Baby Bare Seamount, Juan de Fuca Ridge

NASA Astrophysics Data System (ADS)

Huber, J. A.; Johnson, H. P.; Butterfield, D. A.; Baross, J. A.

2005-12-01

To determine the microbial community diversity within old oceanic crust, a novel sampling strategy was used to collect crustal fluids at Baby Bare Seamount, a 3.5 Ma old outcrop located in the northeast Pacific Ocean on the eastern flank of the Juan de Fuca Ridge. Stainless steel probes were driven directly into the igneous ocean crust to obtain samples of ridge flank crustal fluids. Genetic signatures and enrichment cultures of microorganisms demonstrate that these crustal fluids host a microbial community composed of species indigenous to the subseafloor, including anaerobic thermophiles, and species from other deep-sea habitats, such as seawater and sediments. Evidence using molecular techniques indicates the presence of a relatively small but active microbial population, dominated by bacteria. The microbial community diversity found in the crustal fluids may indicate habitat variability in old oceanic crust, with inputs of nutrients from seawater, sediment pore-water fluids and possibly hydrothermal sources. This report further supports the presence of an indigenous microbial community in ridge flank crustal fluids and advances our understanding of the potential physiological and phylogenetic diversity of this community.

Microbial community structure and diversity in the soil spatial profile of 5-year-old Robinia pseudoacacia 'Idaho,' determined by 454 sequencing of the 16S RNA gene.

PubMed

Chang, Yanping; Bu, Xiangpan; Niu, Weibo; Xiu, Yu; Wang, Huafang

2013-01-01

Relatively little information is available regarding the variability of microbial communities inhabiting deeper soil layers. We investigated the distribution of soil microbial communities down to 1.2 m in 5-year-old Robinia pseudoacacia 'Idaho' soil by 454 sequencing of the 16S RNA gene. The average number of sequences per sample was 12,802. The Shannon and Chao 1 indices revealed various relative microbial abundances and even distribution of microbial diversity for all evaluated sample depths. The predicted diversity in the topsoil exceeded that of the corresponding subsoil. The changes in the relative abundance of the major soil bacterial phyla showed decreasing, increasing, or no consistent trends with respect to sampling depth. Despite their novelty, members of the new candidate phyla OD1 and TM7 were widespread. Environmental variables affecting the bacterial community within the environment appeared to differ from those reported previously, especially the lack of detectable effect from pH. Overall, we found that the overall relative abundance fluctuated with the physical and chemical properties of the soil, root system, and sampling depth. Such information may facilitate forest soil management.

Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities.

PubMed

Campbell, Barbara J; Polson, Shawn W; Zeigler Allen, Lisa; Williamson, Shannon J; Lee, Charles K; Wommack, K Eric; Cary, S Craig

2013-01-01

Hydrothermal vents differ both in surface input and subsurface geochemistry. The effects of these differences on their microbial communities are not clear. Here, we investigated both alpha and beta diversity of diffuse flow-associated microbial communities emanating from vents at a basalt-based hydrothermal system along the East Pacific Rise (EPR) and a sediment-based hydrothermal system, Guaymas Basin. Both Bacteria and Archaea were targeted using high throughput 16S rRNA gene pyrosequencing analyses. A unique aspect of this study was the use of a universal set of 16S rRNA gene primers to characterize total and diffuse flow-specific microbial communities from varied deep-sea hydrothermal environments. Both surrounding seawater and diffuse flow water samples contained large numbers of Marine Group I (MGI) Thaumarchaea and Gammaproteobacteria taxa previously observed in deep-sea systems. However, these taxa were geographically distinct and segregated according to type of spreading center. Diffuse flow microbial community profiles were highly differentiated. In particular, EPR dominant diffuse flow taxa were most closely associated with chemolithoautotrophs, and off axis water was dominated by heterotrophic-related taxa, whereas the opposite was true for Guaymas Basin. The diversity and richness of diffuse flow-specific microbial communities were strongly correlated to the relative abundance of Epsilonproteobacteria, proximity to macrofauna, and hydrothermal system type. Archaeal diversity was higher than or equivalent to bacterial diversity in about one third of the samples. Most diffuse flow-specific communities were dominated by OTUs associated with Epsilonproteobacteria, but many of the Guaymas Basin diffuse flow samples were dominated by either OTUs within the Planctomycetes or hyperthermophilic Archaea. This study emphasizes the unique microbial communities associated with geochemically and geographically distinct hydrothermal diffuse flow environments.

Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities

PubMed Central

Campbell, Barbara J.; Polson, Shawn W.; Zeigler Allen, Lisa; Williamson, Shannon J.; Lee, Charles K.; Wommack, K. Eric; Cary, S. Craig

2013-01-01

Hydrothermal vents differ both in surface input and subsurface geochemistry. The effects of these differences on their microbial communities are not clear. Here, we investigated both alpha and beta diversity of diffuse flow-associated microbial communities emanating from vents at a basalt-based hydrothermal system along the East Pacific Rise (EPR) and a sediment-based hydrothermal system, Guaymas Basin. Both Bacteria and Archaea were targeted using high throughput 16S rRNA gene pyrosequencing analyses. A unique aspect of this study was the use of a universal set of 16S rRNA gene primers to characterize total and diffuse flow-specific microbial communities from varied deep-sea hydrothermal environments. Both surrounding seawater and diffuse flow water samples contained large numbers of Marine Group I (MGI) Thaumarchaea and Gammaproteobacteria taxa previously observed in deep-sea systems. However, these taxa were geographically distinct and segregated according to type of spreading center. Diffuse flow microbial community profiles were highly differentiated. In particular, EPR dominant diffuse flow taxa were most closely associated with chemolithoautotrophs, and off axis water was dominated by heterotrophic-related taxa, whereas the opposite was true for Guaymas Basin. The diversity and richness of diffuse flow-specific microbial communities were strongly correlated to the relative abundance of Epsilonproteobacteria, proximity to macrofauna, and hydrothermal system type. Archaeal diversity was higher than or equivalent to bacterial diversity in about one third of the samples. Most diffuse flow-specific communities were dominated by OTUs associated with Epsilonproteobacteria, but many of the Guaymas Basin diffuse flow samples were dominated by either OTUs within the Planctomycetes or hyperthermophilic Archaea. This study emphasizes the unique microbial communities associated with geochemically and geographically distinct hydrothermal diffuse flow environments. PMID:23898323

Biological Characterization of Microenvironments in a Hypersaline Cold Spring Mars Analog

PubMed Central

Sapers, Haley M.; Ronholm, Jennifer; Raymond-Bouchard, Isabelle; Comrey, Raven; Osinski, Gordon R.; Whyte, Lyle G.

2017-01-01

While many habitable niches on Earth are characterized by permanently cold conditions, little is known about the spatial structure of seasonal communities and the importance of substrate-cell associations in terrestrial cyroenvironments. Here we use the 16S rRNA gene as a marker for genetic diversity to compare two visually distinct but spatially integrated surface microbial mats on Axel Heiberg Island, Canadian high arctic, proximal to a perennial saline spring. This is the first study to describe the bacterial diversity in microbial mats on Axel Heiberg Island. The hypersaline springs on Axel Heiberg represent a unique analog to putative subsurface aquifers on Mars. The Martian subsurface represents the longest-lived potentially habitable environment on Mars and a better understanding of the microbial communities on Earth that thrive in analog conditions will help direct future life detection missions. The microbial mats sampled on Axel Heiberg are only visible during the summer months in seasonal flood plains formed by melt water and run-off from the proximal spring. Targeted-amplicon sequencing revealed that not only does the bacterial composition of the two mat communities differ substantially from the sediment community of the proximal cold spring, but that the mat communities are distinct from any other microbial community in proximity to the Arctic springs studied to date. All samples are dominated by Gammaproteobacteria: Thiotichales is dominant within the spring samples while Alteromonadales comprises a significant component of the mat communities. The two mat samples differ in their Thiotichales:Alteromonadales ratio and contribution of Bacteroidetes to overall diversity. The red mats have a greater proportion of Alteromonadales and Bacteroidetes reads. The distinct bacterial composition of the mat bacterial communities suggests that the spring communities are not sourced from the surface, and that seasonal melt events create ephemerally habitable niches with distinct microbial communities in the Canadian high arctic. The finding that these surficial complex microbial communities exist in close proximity to perennial springs demonstrates the existence of a transiently habitable niche in an important Mars analog site. PMID:29312221

Biological Characterization of Microenvironments in a Hypersaline Cold Spring Mars Analog.

PubMed

Sapers, Haley M; Ronholm, Jennifer; Raymond-Bouchard, Isabelle; Comrey, Raven; Osinski, Gordon R; Whyte, Lyle G

2017-01-01

While many habitable niches on Earth are characterized by permanently cold conditions, little is known about the spatial structure of seasonal communities and the importance of substrate-cell associations in terrestrial cyroenvironments. Here we use the 16S rRNA gene as a marker for genetic diversity to compare two visually distinct but spatially integrated surface microbial mats on Axel Heiberg Island, Canadian high arctic, proximal to a perennial saline spring. This is the first study to describe the bacterial diversity in microbial mats on Axel Heiberg Island. The hypersaline springs on Axel Heiberg represent a unique analog to putative subsurface aquifers on Mars. The Martian subsurface represents the longest-lived potentially habitable environment on Mars and a better understanding of the microbial communities on Earth that thrive in analog conditions will help direct future life detection missions. The microbial mats sampled on Axel Heiberg are only visible during the summer months in seasonal flood plains formed by melt water and run-off from the proximal spring. Targeted-amplicon sequencing revealed that not only does the bacterial composition of the two mat communities differ substantially from the sediment community of the proximal cold spring, but that the mat communities are distinct from any other microbial community in proximity to the Arctic springs studied to date. All samples are dominated by Gammaproteobacteria: Thiotichales is dominant within the spring samples while Alteromonadales comprises a significant component of the mat communities. The two mat samples differ in their Thiotichales:Alteromonadales ratio and contribution of Bacteroidetes to overall diversity. The red mats have a greater proportion of Alteromonadales and Bacteroidetes reads. The distinct bacterial composition of the mat bacterial communities suggests that the spring communities are not sourced from the surface, and that seasonal melt events create ephemerally habitable niches with distinct microbial communities in the Canadian high arctic. The finding that these surficial complex microbial communities exist in close proximity to perennial springs demonstrates the existence of a transiently habitable niche in an important Mars analog site.

Greatest soil microbial diversity found in micro-habitats

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bach, Elizabeth M.; Williams, Ryan J.; Hargreaves, Sarah K.

Microbial interactions occur in habitats much smaller than typically considered in classic ecological studies. This study uses soil aggregates to examine soil microbial community composition and structure of both bacteria and fungi at a microbially relevant scale. Aggregates were isolated from three land management systems in central Iowa, USA to test if aggregate-level microbial responses were sensitive to large-scale shifts in plant community and management practices. Bacteria and fungi exhibited similar patterns of community structure and diversity among soil aggregates, regardless of land management. Microaggregates supported more diverse microbial communities, both taxonomically and functionally. Calculation of a weighted proportional wholemore » soil diversity, which accounted for microbes found in aggregate fractions, resulted in 65% greater bacterial richness and 100% greater fungal richness over independently sampled whole soil. Our results show microaggregates support a previously unrecognized diverse microbial community that likely effects microbial access and metabolism of soil substrates.« less

Functional gene diversity of soil microbial communities from five oil-contaminated fields in China.

PubMed

Liang, Yuting; Van Nostrand, Joy D; Deng, Ye; He, Zhili; Wu, Liyou; Zhang, Xu; Li, Guanghe; Zhou, Jizhong

2011-03-01

To compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of China. GeoChip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. Our results indicated that the overall microbial community structures were distinct in each oil-contaminated field, and samples were clustered by geographic locations. The organic contaminant degradation genes were most abundant in all samples and presented a similar pattern under oil contaminant stress among the five fields. In addition, alkane and aromatic hydrocarbon degradation genes such as monooxygenase and dioxygenase were detected in high abundance in the oil-contaminated fields. Canonical correspondence analysis indicated that the microbial functional patterns were highly correlated to the local environmental variables, such as oil contaminant concentration, nitrogen and phosphorus contents, salt and pH. Finally, a total of 59% of microbial community variation from GeoChip data can be explained by oil contamination, geographic location and soil geochemical parameters. This study provided insights into the in situ microbial functional structures in oil-contaminated fields and discerned the linkages between microbial communities and environmental variables, which is important to the application of bioremediation in oil-contaminated sites.

Functional gene diversity of soil microbial communities from five oil-contaminated fields in China

PubMed Central

Liang, Yuting; Van Nostrand, Joy D; Deng, Ye; He, Zhili; Wu, Liyou; Zhang, Xu; Li, Guanghe; Zhou, Jizhong

2011-01-01

To compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of China. GeoChip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. Our results indicated that the overall microbial community structures were distinct in each oil-contaminated field, and samples were clustered by geographic locations. The organic contaminant degradation genes were most abundant in all samples and presented a similar pattern under oil contaminant stress among the five fields. In addition, alkane and aromatic hydrocarbon degradation genes such as monooxygenase and dioxygenase were detected in high abundance in the oil-contaminated fields. Canonical correspondence analysis indicated that the microbial functional patterns were highly correlated to the local environmental variables, such as oil contaminant concentration, nitrogen and phosphorus contents, salt and pH. Finally, a total of 59% of microbial community variation from GeoChip data can be explained by oil contamination, geographic location and soil geochemical parameters. This study provided insights into the in situ microbial functional structures in oil-contaminated fields and discerned the linkages between microbial communities and environmental variables, which is important to the application of bioremediation in oil-contaminated sites. PMID:20861922

Microbial community composition and endolith colonization at an Arctic thermal spring are driven by calcite precipitation

USGS Publications Warehouse

Starke, Verena; Kirshtein, Julie; Fogel, Marilyn L.; Steele, Andrew

2013-01-01

Environmental conditions shape community composition. Arctic thermal springs provide an opportunity to study how environmental gradients can impose strong selective pressures on microbial communities and provide a continuum of niche opportunities. We use microscopic and molecular methods to conduct a survey of microbial community composition at Troll Springs on Svalbard, Norway, in the high Arctic. Microorganisms there exist under a wide range of environmental conditions: in warm water as periphyton, in moist granular materials, and in cold, dry rock as endoliths. Troll Springs has two distinct ecosystems, aquatic and terrestrial, together in close proximity, with different underlying environmental factors shaping each microbial community. Periphyton are entrapped during precipitation of calcium carbonate from the spring's waters, providing microbial populations that serve as precursors for the development of endolithic communities. This process differs from most endolith colonization, in which the rock predates the communities that colonize it. Community composition is modulated as environmental conditions change within the springs. At Troll, the aquatic environments show a small number of dominant operational taxonomic units (OTUs) that are specific to each sample. The terrestrial environments show a more even distribution of OTUs common to multiple samples.

Spatial and Temporal Variation in Enterococcal Abundance and Its Relationship to the Microbial Community in Hawaii Beach Sand and Water

PubMed Central

Cui, Henglin; Yang, Kun; Pagaling, Eulyn

2013-01-01

Recent studies have reported high levels of fecal indicator enterococci in marine beach sand. This study aimed to determine the spatial and temporal variation of enterococcal abundance and to evaluate its relationships with microbial community parameters in Hawaii beach sand and water. Sampling at 23 beaches on the Island of Oahu detected higher levels of enterococci in beach foreshore sand than in beach water on a mass unit basis. Subsequent 8-week consecutive samplings at two selected beaches (Waialae and Kualoa) consistently detected significantly higher levels of enterococci in backshore sand than in foreshore/nearshore sand and beach water. Comparison between the abundance of enterococci and the microbial communities showed that enterococci correlated significantly with total Vibrio in all beach zones but less significantly with total bacterial density and Escherichia coli. Samples from the different zones of Waialae beach were sequenced by 16S rRNA gene pyrosequencing to determine the microbial community structure and diversity. The backshore sand had a significantly more diverse community and contained different major bacterial populations than the other beach zones, which corresponded to the spatial distribution pattern of enterococcal abundance. Taken together, multiple lines of evidence support the possibility of enterococci as autochthonous members of the microbial community in Hawaii beach sand. PMID:23563940

Microbial diversity and community structure across environmental gradients in an seawater intruded shallow confined aquifer

NASA Astrophysics Data System (ADS)

Zhang, X.; Hu, B.

2017-12-01

Seawater intrusion has been an important topic in coastal hydrogeology and making previously freshwater ecosystems saline. Plant and animal responses to variation in the freshwater-saline interface have been well studied in the coastal zone. However, little is known about the biogeography or stability of microbial community response to seawater intrusion. The objective of this study is to characterize and compare bacterial and archaea community diversity and composition in 15 groundwater samples with varied salinity using high-throughput-sequencing of 16S ribosomal RNA genes. The dominant taxonomic group identified in all samples are proteobacteria for bacteria and crenarchaeota for archaea. The other main bacterial groups are varied in samples with different salinities including bacteroidetes, firmicutes and several unidentified taxonomys. A combination of environmental factors seems to influence the microbial community composition where organic carbon is a primary factor shaping microbial communities. Correlation analysis between the relative abundance of bacterial taxa and geochemical parameters uggested that rare taxa may contribute to biogeochemical processes taking place at the mixing zone of freshewater and saltwater. Our results help to understand how the physical and chemical factors shape the microbial community composition and set a baseline for upcoming studies to evaluate the response of this ecosystem to future changes and the efficacy of new remediation efforts.

Introducing OTUshuff and DwOdum: A new set of tools for estimating beta diversity for under-sampled communities

USDA-ARS?s Scientific Manuscript database

Characterization of complex microbial communities by DNA sequencing has become a standard technique in microbial ecology. Yet, particular features of this approach render traditional methods of community comparison problematic. In particular, a very low proportion of community members are typically ...

Estimating beta diversity for under-sampled communities using the variably weighted Odum dissimilarity index and OTUshuff

USDA-ARS?s Scientific Manuscript database

Characterization of complex microbial communities by DNA sequencing has become a standard technique in microbial ecology. Yet, particular features of this approach render traditional methods of community comparison problematic. In particular, a very low proportion of community members are typically ...

Microbial community diversity patterns are related to physical and chemical differences among temperate lakes near Beaver Island, MI

PubMed Central

Hengy, Miranda H.; Horton, Dean J.; Uzarski, Donald G.

2017-01-01

Lakes are dynamic and complex ecosystems that can be influenced by physical, chemical, and biological processes. Additionally, individual lakes are often chemically and physically distinct, even within the same geographic region. Here we show that differences in physicochemical conditions among freshwater lakes located on (and around) the same island, as well as within the water column of each lake, are significantly related to aquatic microbial community diversity. Water samples were collected over time from the surface and bottom-water within four freshwater lakes located around Beaver Island, MI within the Laurentian Great Lakes region. Three of the sampled lakes experienced seasonal lake mixing events, impacting either O2, pH, temperature, or a combination of the three. Microbial community alpha and beta diversity were assessed and individual microbial taxa were identified via high-throughput sequencing of the 16S rRNA gene. Results demonstrated that physical and chemical variability (temperature, dissolved oxygen, and pH) were significantly related to divergence in the beta diversity of surface and bottom-water microbial communities. Despite its correlation to microbial community structure in unconstrained analyses, constrained analyses demonstrated that dissolved organic carbon (DOC) concentration was not strongly related to microbial community structure among or within lakes. Additionally, several taxa were correlated (either positively or negatively) to environmental variables, which could be related to aerobic and anaerobic metabolisms. This study highlights the measurable relationships between environmental conditions and microbial communities within freshwater temperate lakes around the same island. PMID:29062609

Microbial communities in carbonate rocks-from soil via groundwater to rocks.

PubMed

Meier, Aileen; Singh, Manu K; Kastner, Anne; Merten, Dirk; Büchel, Georg; Kothe, Erika

2017-09-01

Microbial communities in soil, groundwater, and rock of two sites in limestone were investigated to determine community parameters differentiating habitats in two lithostratigraphic untis. Lower Muschelkalk and Middle Muschelkalk associated soils, groundwater, and rock samples showed different, but overlapping microbial communities linked to carbon fluxes. The microbial diversities in soil were highest, groundwater revealed overlapping taxa but lower diversity, and rock samples were predominantly characterized by endospore forming bacteria and few archaea. Physiological profiles could establish a differentiation between habitats (soil, groundwater, rock). From community analyses and physiological profiles, different element cycles in limestone could be identified for the three habitats. While in soil, nitrogen cycling was identified as specific determinant, in rock methanogenesis linked carbonate rock to atmospheric methane cycles. These patterns specifically allowed for delineation of lithostratigraphic connections to physiological parameters. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer

PubMed Central

Tully, Benjamin J; Wheat, C Geoff; Glazer, Brain T; Huber, Julie A

2018-01-01

The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized metagenomic libraries of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement to query microbial diversity. Twenty-one samples were collected during a 2-year period to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the 2 years, yet the microbial community present in the crustal fluids underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the data set and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in members of the Proteobacteria, specifically the Alpha-, Gamma- and Zetaproteobacteria, the Epsilonbacteraeota and the Planctomycetes. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes, such as cbb3- and bd-type cytochromes, and alternative electron acceptors, like nitrate and sulfate. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles. Collectively, the repeated sampling at multiple sites, together with the successful binning of hundreds of genomes, provides an unprecedented data set for investigation of microbial communities in the cold, oxic crustal aquifer. PMID:29099490

A confidence interval analysis of sampling effort, sequencing depth, and taxonomic resolution of fungal community ecology in the era of high-throughput sequencing.

PubMed

Oono, Ryoko

2017-01-01

High-throughput sequencing technology has helped microbial community ecologists explore ecological and evolutionary patterns at unprecedented scales. The benefits of a large sample size still typically outweigh that of greater sequencing depths per sample for accurate estimations of ecological inferences. However, excluding or not sequencing rare taxa may mislead the answers to the questions 'how and why are communities different?' This study evaluates the confidence intervals of ecological inferences from high-throughput sequencing data of foliar fungal endophytes as case studies through a range of sampling efforts, sequencing depths, and taxonomic resolutions to understand how technical and analytical practices may affect our interpretations. Increasing sampling size reliably decreased confidence intervals across multiple community comparisons. However, the effects of sequencing depths on confidence intervals depended on how rare taxa influenced the dissimilarity estimates among communities and did not significantly decrease confidence intervals for all community comparisons. A comparison of simulated communities under random drift suggests that sequencing depths are important in estimating dissimilarities between microbial communities under neutral selective processes. Confidence interval analyses reveal important biases as well as biological trends in microbial community studies that otherwise may be ignored when communities are only compared for statistically significant differences.

A confidence interval analysis of sampling effort, sequencing depth, and taxonomic resolution of fungal community ecology in the era of high-throughput sequencing

PubMed Central

2017-01-01

High-throughput sequencing technology has helped microbial community ecologists explore ecological and evolutionary patterns at unprecedented scales. The benefits of a large sample size still typically outweigh that of greater sequencing depths per sample for accurate estimations of ecological inferences. However, excluding or not sequencing rare taxa may mislead the answers to the questions ‘how and why are communities different?’ This study evaluates the confidence intervals of ecological inferences from high-throughput sequencing data of foliar fungal endophytes as case studies through a range of sampling efforts, sequencing depths, and taxonomic resolutions to understand how technical and analytical practices may affect our interpretations. Increasing sampling size reliably decreased confidence intervals across multiple community comparisons. However, the effects of sequencing depths on confidence intervals depended on how rare taxa influenced the dissimilarity estimates among communities and did not significantly decrease confidence intervals for all community comparisons. A comparison of simulated communities under random drift suggests that sequencing depths are important in estimating dissimilarities between microbial communities under neutral selective processes. Confidence interval analyses reveal important biases as well as biological trends in microbial community studies that otherwise may be ignored when communities are only compared for statistically significant differences. PMID:29253889

Comparison of DNA extraction protocols for microbial communities from soil treated with biochar

PubMed Central

Leite, D.C.A.; Balieiro, F.C.; Pires, C.A.; Madari, B.E.; Rosado, A.S.; Coutinho, H.L.C.; Peixoto, R.S.

2014-01-01

Many studies have evaluated the effects of biochar application on soil structure and plant growth. However, there are very few studies describing the effect of biochar on native soil microbial communities. Microbial analysis of environmental samples requires accurate and reproducible methods for the extraction of DNA from samples. Because of the variety among microbial species and the strong adsorption of the phosphate backbone of the DNA molecule to biochar, extracting and purifying high quality microbial DNA from biochar-amended soil is not a trivial process and can be considerably more difficult than the extraction of DNA from other environmental samples. The aim of this study was to compare the relative efficacies of three commercial DNA extraction kits, the FastDNA® SPIN Kit for Soil (FD kit), the PowerSoil® DNA Isolation Kit (PS kit) and the ZR Soil Microbe DNA Kit Miniprep™ (ZR kit), for extracting microbial genomic DNA from sand treated with different types of biochar. The methods were evaluated by comparing the DNA yields and purity and by analysing the bacterial and fungal community profiles generated by PCR-DGGE. Our results showed that the PCR-DGGE profiles for bacterial and fungal communities were highly affected by the purity and yield of the different DNA extracts. Among the tested kits, the PS kit was the most efficient with respect to the amount and purity of recovered DNA and considering the complexity of the generated DGGE microbial fingerprint from the sand-biochar samples. PMID:24948928

Comparison of DNA extraction protocols for microbial communities from soil treated with biochar.

PubMed

Leite, D C A; Balieiro, F C; Pires, C A; Madari, B E; Rosado, A S; Coutinho, H L C; Peixoto, R S

2014-01-01

Many studies have evaluated the effects of biochar application on soil structure and plant growth. However, there are very few studies describing the effect of biochar on native soil microbial communities. Microbial analysis of environmental samples requires accurate and reproducible methods for the extraction of DNA from samples. Because of the variety among microbial species and the strong adsorption of the phosphate backbone of the DNA molecule to biochar, extracting and purifying high quality microbial DNA from biochar-amended soil is not a trivial process and can be considerably more difficult than the extraction of DNA from other environmental samples. The aim of this study was to compare the relative efficacies of three commercial DNA extraction kits, the FastDNA® SPIN Kit for Soil (FD kit), the PowerSoil® DNA Isolation Kit (PS kit) and the ZR Soil Microbe DNA Kit Miniprep™ (ZR kit), for extracting microbial genomic DNA from sand treated with different types of biochar. The methods were evaluated by comparing the DNA yields and purity and by analysing the bacterial and fungal community profiles generated by PCR-DGGE. Our results showed that the PCR-DGGE profiles for bacterial and fungal communities were highly affected by the purity and yield of the different DNA extracts. Among the tested kits, the PS kit was the most efficient with respect to the amount and purity of recovered DNA and considering the complexity of the generated DGGE microbial fingerprint from the sand-biochar samples.

Genome-reconstruction for eukaryotes from complex natural microbial communities.

PubMed

West, Patrick T; Probst, Alexander J; Grigoriev, Igor V; Thomas, Brian C; Banfield, Jillian F

2018-04-01

Microbial eukaryotes are integral components of natural microbial communities, and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, we propose a method to recover eukaryotic genomes from complex metagenomic samples. A key step for genome recovery is separation of eukaryotic and prokaryotic fragments. We developed a k -mer-based strategy, EukRep, for eukaryotic sequence identification and applied it to environmental samples to show that it enables genome recovery, genome completeness evaluation, and prediction of metabolic potential. We used this approach to test the effect of addition of organic carbon on a geyser-associated microbial community and detected a substantial change of the community metabolism, with selection against almost all candidate phyla bacteria and archaea and for eukaryotes. Near complete genomes were reconstructed for three fungi placed within the Eurotiomycetes and an arthropod. While carbon fixation and sulfur oxidation were important functions in the geyser community prior to carbon addition, the organic carbon-impacted community showed enrichment for secreted proteases, secreted lipases, cellulose targeting CAZymes, and methanol oxidation. We demonstrate the broader utility of EukRep by reconstructing and evaluating relatively high-quality fungal, protist, and rotifer genomes from complex environmental samples. This approach opens the way for cultivation-independent analyses of whole microbial communities. © 2018 West et al.; Published by Cold Spring Harbor Laboratory Press.

A Lipid Extraction and Analysis Method for Characterizing Soil Microbes in Experiments with Many Samples

PubMed Central

Oates, Lawrence G.; Read, Harry W.; Gutknecht, Jessica L. M.; Duncan, David S.; Balser, Teri B.; Jackson, Randall D.

2017-01-01

Microbial communities are important drivers and regulators of ecosystem processes. To understand how management of ecosystems may affect microbial communities, a relatively precise but effort-intensive technique to assay microbial community composition is phospholipid fatty acid (PLFA) analysis. PLFA was developed to analyze phospholipid biomarkers, which can be used as indicators of microbial biomass and the composition of broad functional groups of fungi and bacteria. It has commonly been used to compare soils under alternative plant communities, ecology, and management regimes. The PLFA method has been shown to be sensitive to detecting shifts in microbial community composition. An alternative method, fatty acid methyl ester extraction and analysis (MIDI-FA) was developed for rapid extraction of total lipids, without separation of the phospholipid fraction, from pure cultures as a microbial identification technique. This method is rapid but is less suited for soil samples because it lacks an initial step separating soil particles and begins instead with a saponification reaction that likely produces artifacts from the background organic matter in the soil. This article describes a method that increases throughput while balancing effort and accuracy for extraction of lipids from the cell membranes of microorganisms for use in characterizing both total lipids and the relative abundance of indicator lipids to determine soil microbial community structure in studies with many samples. The method combines the accuracy achieved through PLFA profiling by extracting and concentrating soil lipids as a first step, and a reduction in effort by saponifying the organic material extracted and processing with the MIDI-FA method as a second step. PMID:28745639

Microbial communities from different subsystems in biological heap leaching system play different roles in iron and sulfur metabolisms.

PubMed

Xiao, Yunhua; Liu, Xueduan; Ma, Liyuan; Liang, Yili; Niu, Jiaojiao; Gu, Yabing; Zhang, Xian; Hao, Xiaodong; Dong, Weiling; She, Siyuan; Yin, Huaqun

2016-08-01

The microbial communities are important for minerals decomposition in biological heap leaching system. However, the differentiation and relationship of composition and function of microbial communities between leaching heap (LH) and leaching solution (LS) are still unclear. In this study, 16S rRNA gene sequencing was used to assess the microbial communities from the two subsystems in ZiJinShan copper mine (Fujian province, China). Results of PCoA and dissimilarity test showed that microbial communities in LH samples were significantly different from those in LS samples. The dominant genera of LH was Acidithiobacillus (57.2 ∼ 87.9 %), while Leptospirillum (48.6 ∼ 73.7 %) was predominant in LS. Environmental parameters (especially pH) were the major factors to influence the composition and structure of microbial community by analysis of Mantel tests. Results of functional test showed that microbial communities in LH utilized sodium thiosulfate more quickly and utilized ferrous sulfate more slowly than those in LS, which further indicated that the most sulfur-oxidizing processes of bioleaching took place in LH and the most iron-oxidizing processes were in LS. Further study found that microbial communities in LH had stronger pyrite leaching ability, and iron extraction efficiency was significantly positively correlated with Acidithiobacillus (dominated in LH), which suggested that higher abundance ratio of sulfur-oxidizing microbes might in favor of minerals decomposition. Finally, a conceptual model was designed through the above results to better exhibit the sulfur and iron metabolism in bioleaching systems.

Seasonality and vertical structure of microbial communities in an ocean gyre.

PubMed

Treusch, Alexander H; Vergin, Kevin L; Finlay, Liam A; Donatz, Michael G; Burton, Robert M; Carlson, Craig A; Giovannoni, Stephen J

2009-10-01

Vertical, seasonal and geographical patterns in ocean microbial communities have been observed in many studies, but the resolution of community dynamics has been limited by the scope of data sets, which are seldom up to the task of illuminating the highly structured and rhythmic patterns of change found in ocean ecosystems. We studied vertical and temporal patterns in the microbial community composition in a set of 412 samples collected from the upper 300 m of the water column in the northwestern Sargasso Sea, on cruises between 1991 and 2004. The region sampled spans the extent of deep winter mixing and the transition between the euphotic and the upper mesopelagic zones, where most carbon fixation and reoxidation occurs. A bioinformatic pipeline was developed to de-noise, normalize and align terminal restriction fragment length polymorphism (T-RFLP) data from three restriction enzymes and link T-RFLP peaks to microbial clades. Non-metric multidimensional scaling statistics resolved three microbial communities with distinctive composition during seasonal stratification: a surface community in the region of lowest nutrients, a deep chlorophyll maximum community and an upper mesopelagic community. A fourth microbial community was associated with annual spring blooms of eukaryotic phytoplankton that occur in the northwestern Sargasso Sea as a consequence of winter convective mixing that entrains nutrients to the surface. Many bacterial clades bloomed in seasonal patterns that shifted with the progression of stratification. These richly detailed patterns of community change suggest that highly specialized adaptations and interactions govern the success of microbial populations in the oligotrophic ocean.

Microbial Communities in Produced Water of the Green River Basin in Southeast Wyoming.

NASA Astrophysics Data System (ADS)

Wawrousek, K.; Drogos, D. L.; Urynowicz, M. A.; Nye, C.; Quillinan, S.

2017-12-01

Despite the prevalence of hydraulic fracturing for natural gas production, little is understood about the downhole microbial ecosystems encountered. Illumina MiSeq 16S rRNA sequencing has been performed on waters collected from the water-gas separator of five hydraulically fractured wells in the Green River Basin in southeast Wyoming, and identification of bacteria and archaea reveal the presence of several microbes. Well depths ranged from approximately 9,500ft to 11,500ft. Correlations between inorganic chemistry, such as pH, salinity, and metals naturally present in the groundwater, as well as biocides used during fracturing and production were made when analyzing different microbial communities. Preliminary results identify several microbial families including: Clostridiales, Thermoanaerobacterales, Synergistales, Alteromonadales, and Thermotogales. Of the 5 sampled oil wells in the Greater Green River Basin, 16 microbes were identified in all samples. These included microbes such as Anaerobaculum, Thermovirga, and an unclassified Clostridiaceae. Ongoing work includes matching unclassified 16S sequences present in multiple samples and correlating microbial populations across wells to understand better the microbial communities present in these exotic environmental conditions.

Microbial Community-Level Physiological Profiles (CLPP) and herbicide mineralization potential in groundwater affected by agricultural land use

NASA Astrophysics Data System (ADS)

Janniche, Gry Sander; Spliid, Henrik; Albrechtsen, Hans-Jørgen

2012-10-01

Diffuse groundwater pollution from agricultural land use may impact the microbial groundwater community, which was investigated as Community-Level Physiological Profiles (CLPP) using EcoPlate™. Water was sampled from seven piezometers and a spring in a small agricultural catchment with diffuse herbicide and nitrate pollution. Based on the Shannon-Wiener and Simpson's diversity indices the diversity in the microbial communities was high. The response from the EcoPlates™ showed which substrates support groundwater bacteria, and all 31 carbon sources were utilized by organisms from at least one water sample. However, only nine carbon sources were utilized by all water samples: D-Mannitol, N-acetyl-D-glucosamine, putrescine, D-galacturonic acid, itaconic acid, 4-hydroxy benzoic acid, tween 40, tween 80, and L-asparagine. In all water samples the microorganisms preferred D-mannitol, D-galacturonic acid, tween 40, and 4-hydroxy benzoic acid as substrates, whereas none preferred 2-hydroxy benzoic acid, α-D-lactose, D,L-α-glycerol phosphate, α-ketobutyric acid, L-threonine and glycyl-L-glutamic acid. Principal Component Analysis of the CLPP's clustered the most agriculturally affected groundwater samples, indicating that the agricultural land use affects the groundwater microbial communities. Furthermore, the ability to mineralize atrazine and isoproturon, which have been used in the catchment, was also associated with this cluster.

Microbial community structure in fermentation process of Shaoxing rice wine by Illumina-based metagenomic sequencing.

PubMed

Xie, Guangfa; Wang, Lan; Gao, Qikang; Yu, Wenjing; Hong, Xutao; Zhao, Lingyun; Zou, Huijun

2013-09-01

To understand the role of the community structure of microbes in the environment in the fermentation of Shaoxing rice wine, samples collected from a wine factory were subjected to Illumina-based metagenomic sequencing. De novo assembly of the sequencing reads allowed the characterisation of more than 23 thousand microbial genes derived from 1.7 and 1.88 Gbp of sequences from two samples fermented for 5 and 30 days respectively. The microbial community structure at different fermentation times of Shaoxing rice wine was revealed, showing the different roles of the microbiota in the fermentation process of Shaoxing rice wine. The gene function of both samples was also studied in the COG database, with most genes belonging to category S (function unknown), category E (amino acid transport and metabolism) and unclassified group. The results show that both the microbial community structure and gene function composition change greatly at different time points of Shaoxing rice wine fermentation. © 2013 Society of Chemical Industry.

Understanding Cultivar-Specificity and Soil Determinants of the Cannabis Microbiome

DOE PAGES

Winston, Max E.; Hampton-Marcell, Jarrad; Zarraonaindia, Iratxe; ...

2014-06-16

Understanding microbial partnerships with the medicinally and economically important crop Cannabis has the potential to affect agricultural practice by improving plant fitness and production yield. Furthermore, Cannabis presents an interesting model to explore plant-microbiome interactions as it produces numerous secondary metabolic compounds. Here we present the first description of the endorhiza-, rhizosphere-, and bulk soil-associated microbiome of five distinct Cannabis cultivars. Bacterial communities of the endorhiza showed significant cultivar-specificity. When controlling cultivar and soil type the microbial community structure was significantly different between plant cultivars, soil types, and between the endorhiza, rhizosphere and soil. In conclusion, the influence of soilmore » type, plant cultivar and sample type differentiation on the microbial community structure provides support for a previously published two-tier selection model, whereby community composition across sample types is determined mainly by soil type, while community structure within endorhiza samples is determined mainly by host cultivar.« less

Understanding Cultivar-Specificity and Soil Determinants of the Cannabis Microbiome

DOE Office of Scientific and Technical Information (OSTI.GOV)

Winston, Max E.; Hampton-Marcell, Jarrad; Zarraonaindia, Iratxe

Understanding microbial partnerships with the medicinally and economically important crop Cannabis has the potential to affect agricultural practice by improving plant fitness and production yield. Furthermore, Cannabis presents an interesting model to explore plant-microbiome interactions as it produces numerous secondary metabolic compounds. Here we present the first description of the endorhiza-, rhizosphere-, and bulk soil-associated microbiome of five distinct Cannabis cultivars. Bacterial communities of the endorhiza showed significant cultivar-specificity. When controlling cultivar and soil type the microbial community structure was significantly different between plant cultivars, soil types, and between the endorhiza, rhizosphere and soil. In conclusion, the influence of soilmore » type, plant cultivar and sample type differentiation on the microbial community structure provides support for a previously published two-tier selection model, whereby community composition across sample types is determined mainly by soil type, while community structure within endorhiza samples is determined mainly by host cultivar.« less

'FloraArray' for screening of specific DNA probes representing the characteristics of a certain microbial community.

PubMed

Yokoi, Takahide; Kaku, Yoshiko; Suzuki, Hiroyuki; Ohta, Masayuki; Ikuta, Hajime; Isaka, Kazuichi; Sumino, Tatsuo; Wagatsuma, Masako

2007-08-01

To investigate uncharacterized microbial communities, a custom DNA microarray named 'FloraArray' was developed for screening specific probes that would represent the characteristics of a microbial community. The array was prepared by spotting 2000 plasmid DNAs from a genomic shotgun library of a sludge sample on a DNA microarray. By comparative hybridization of the array with two different samples of genomic DNA, one from the activated sludge and the other from a nonactivated sludge sample of an anaerobic ammonium oxidation (anammox) bacterial community, specific spots were visualized as a definite fluctuating profile in an MA (differential intensity ratio vs. spot intensity) plot. About 300 spots of the array accounted for the candidate probes to represent anammox reaction of the activated sludge. After sequence analysis of the probes and examination of the results of blastn searches against the reported anammox reference sequence, complete matches were found for 161 probes (58.3%) and >90% matches were found for 242 probes (87.1%). These results demonstrate that 'FloraArray' could be a useful tool for screening specific DNA molecules of unknown microbial communities.

Anaerobic microbial communities in Lake Pavin, a unique meromictic lake in France.

PubMed

Lehours, Anne-C; Bardot, Corinne; Thenot, Aurelie; Debroas, Didier; Fonty, Gerard

2005-11-01

The Bacteria and Archaea from the meromictic Lake Pavin were analyzed in samples collected along a vertical profile in the anoxic monimolimnion and were compared to those in samples from the oxic mixolimnion. Nine targeted 16S rRNA oligonucleotide probes were used to assess the distribution of Bacteria and Archaea and to investigate the in situ occurrence of sulfate-reducing bacteria and methane-producing Archaea involved in the terminal steps of the anaerobic degradation of organic material. The diversity of the complex microbial communities was assessed from the 16S rRNA polymorphisms present in terminal restriction fragment (TRF) depth patterns. The densities of the microbial community increased in the anoxic layer, and Archaea detected with probe ARCH915 represented the largest microbial group in the water column, with a mean Archaea/Eubacteria ratio of 1.5. Terminal restriction fragment length polymorphism (TRFLP) analysis revealed an elevated archaeal and bacterial phylotype richness in anoxic bottom-water samples. The structure of the Archaea community remained rather homogeneous, while TRFLP patterns for the eubacterial community revealed a heterogeneous distribution of eubacterial TRFs.

Microbial Community Composition and Putative Biogeochemical Functions in the Sediment and Water of Tropical Granite Quarry Lakes.

PubMed

Kumar, Amit; Ng, Daphne H P; Wu, Yichao; Cao, Bin

2018-05-28

Re-naturalized quarry lakes are important ecosystems, which support complex communities of flora and fauna. Microorganisms associated with sediment and water form the lowest trophic level in these ecosystems and drive biogeochemical cycles. A direct comparison of microbial taxa in water and sediment microbial communities is lacking, which limits our understanding of the dominant functions that are carried out by the water and sediment microbial communities in quarry lakes. In this study, using the 16S rDNA amplicon sequencing approach, we compared microbial communities in the water and sediment in two re-naturalized quarry lakes in Singapore and elucidated putative functions of the sediment and water microbial communities in driving major biogeochemical processes. The richness and diversity of microbial communities in sediments of the quarry lakes were higher than those in the water. The composition of the microbial communities in the sediments from the two quarries was highly similar to one another, while those in the water differed greatly. Although the microbial communities of the sediment and water samples shared some common members, a large number of microbial taxa (at the phylum and genus levels) were prevalent either in sediment or water alone. Our results provide valuable insights into the prevalent biogeochemical processes carried out by water and sediment microbial communities in tropical granite quarry lakes, highlighting distinct microbial processes in water and sediment that contribute to the natural purification of the resident water.

Plant rhizosphere species-specific stoichiometry and regulation of extracellular enzyme and microbial community structure

NASA Astrophysics Data System (ADS)

Bell, C. W.; Calderon, F.; Pendall, E.; Wallenstein, M. D.

2012-12-01

Plant communities affect the activity and composition of soil microbial communities through alteration of the soil environment during root growth; substrate availability through root exudation; nutrient availability through plant uptake; and moisture regimes through transpiration. As a result, positive feedbacks in soil properties can result from alterations in microbial community composition and function in the rhizosphere zone. At the ecosystem-scale, many properties of soil microbial communities can vary between forest stands dominated by different species, including community composition and stoichiometry. However, the influence of smaller individual plants on grassland soils and microbial communities is less well documented. There is evidence to suggest that some plants can modify their soil environment in a manner that favors their persistence. For example, when Bromus tectorum plants invade, soil microbial communities tend to have higher N mineralization rates (in the rhizosphere zone) relative to native plants. If tight linkages between individual plant species and microbial communities inhabiting the rhizosphere exist, we hypothesized that any differences among plant species specific rhizosphere zones could be observed by shifts in: 1) soil -rhizosphere microbial community structure, 2) enzymatic C:N:P acquisition activities, 3) alterations in the soil C chemistry composition in the rhizosphere, and 4) plant - soil - microbial C:N:P elemental stoichiometry. We selected and grew 4 different C3 grasses species including three species native to the Shortgrass Steppe region (Pascopyrum smithii, Koeleria macrantha, and Vulpia octoflora) and one exotic invasive plant species (B. tectorum) in root-boxes that are designed to allow for easy access to the rhizosphere. The field soil was homogenized using a 4mm sieve and mixed 1:1 with sterile sand and seeded as monocultures (24 replicate root - boxes for each species). Plant and soil samples (along with no - plant control soil samples) were collected on day 28, 78, and 148 (N = 4 /sample period/species). Microbial community structure was quantified using the barcoded pyrosequencing protocols. We measured the potential activity of seven hydrolytic soil enzymes to represent the degradation of C, N, and P-rich substrates. Soil microbial C:N biomass responses to specific plant rhizospheres (MBC and MBN) were measured using the chloroform fumigation extraction method followed by DOC & N analysis. Fourier Transform Infrared Spectroscopy was used to assess differences in plant and soil C chemistry. We found that species specific rhizospheres are characteristic of very different soil chemical, edaphic, and microbial properties. These plant species act as gateways that introduce variability into soil C, N, and P ecosystem functional dynamics directly facilitated by rhizosphere - microbe associations. Our results suggest that nutrient stoichiometry within plant species' rhizospheres is a useful tool for identifying intra-ecosystem functional patterns. By identifying what and how specific species rhizospheres differ among the overall plant community, we can better predict how below-ground microbial community function and subsequent ecosystem processes can be influenced by alterations in plant community shifts based on the rhizosphere effects.

The MPLEx Protocol for Multi-omic Analyses of Soil Samples

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nicora, Carrie D.; Burnum-Johnson, Kristin E.; Nakayasu, Ernesto S.

Mass spectrometry (MS)-based integrated metaproteomic, metabolomic and lipidomic (multi-omic) studies are transforming our ability to understand and characterize microbial communities in environmental and biological systems. These measurements are even enabling enhanced analyses of complex soil microbial communities, which are the most complex microbial systems known to date. Multi-omic analyses, however, do have sample preparation challenges since separate extractions are typically needed for each omic study, thereby greatly amplifying the preparation time and amount of sample required. To address this limitation, a 3-in-1 method for simultaneous metabolite, protein, and lipid extraction (MPLEx) from the exact same soil sample was created bymore » adapting a solvent-based approach. This MPLEx protocol has proven to be simple yet robust for many sample types and even when utilized for limited quantities of complex soil samples. The MPLEx method also greatly enabled the rapid multi-omic measurements needed to gain a better understanding of the members of each microbial community, while evaluating the changes taking place upon biological and environmental perturbations.« less

Unique honey bee (Apis mellifera) hive component-based communities as detected by a hybrid of phospholipid fatty-acid and fatty-acid methyl ester analyses.

PubMed

Grubbs, Kirk J; Scott, Jarrod J; Budsberg, Kevin J; Read, Harry; Balser, Teri C; Currie, Cameron R

2015-01-01

Microbial communities (microbiomes) are associated with almost all metazoans, including the honey bee Apis mellifera. Honey bees are social insects, maintaining complex hive systems composed of a variety of integral components including bees, comb, propolis, honey, and stored pollen. Given that the different components within hives can be physically separated and are nutritionally variable, we hypothesize that unique microbial communities may occur within the different microenvironments of honey bee colonies. To explore this hypothesis and to provide further insights into the microbiome of honey bees, we use a hybrid of fatty acid methyl ester (FAME) and phospholipid-derived fatty acid (PLFA) analysis to produce broad, lipid-based microbial community profiles of stored pollen, adults, pupae, honey, empty comb, and propolis for 11 honey bee hives. Averaging component lipid profiles by hive, we show that, in decreasing order, lipid markers representing fungi, Gram-negative bacteria, and Gram-positive bacteria have the highest relative abundances within honey bee colonies. Our lipid profiles reveal the presence of viable microbial communities in each of the six hive components sampled, with overall microbial community richness varying from lowest to highest in honey, comb, pupae, pollen, adults and propolis, respectively. Finally, microbial community lipid profiles were more similar when compared by component than by hive, location, or sampling year. Specifically, we found that individual hive components typically exhibited several dominant lipids and that these dominant lipids differ between components. Principal component and two-way clustering analyses both support significant grouping of lipids by hive component. Our findings indicate that in addition to the microbial communities present in individual workers, honey bee hives have resident microbial communities associated with different colony components.

Unique Honey Bee (Apis mellifera) Hive Component-Based Communities as Detected by a Hybrid of Phospholipid Fatty-Acid and Fatty-Acid Methyl Ester Analyses

PubMed Central

2015-01-01

Microbial communities (microbiomes) are associated with almost all metazoans, including the honey bee Apis mellifera. Honey bees are social insects, maintaining complex hive systems composed of a variety of integral components including bees, comb, propolis, honey, and stored pollen. Given that the different components within hives can be physically separated and are nutritionally variable, we hypothesize that unique microbial communities may occur within the different microenvironments of honey bee colonies. To explore this hypothesis and to provide further insights into the microbiome of honey bees, we use a hybrid of fatty acid methyl ester (FAME) and phospholipid-derived fatty acid (PLFA) analysis to produce broad, lipid-based microbial community profiles of stored pollen, adults, pupae, honey, empty comb, and propolis for 11 honey bee hives. Averaging component lipid profiles by hive, we show that, in decreasing order, lipid markers representing fungi, Gram-negative bacteria, and Gram-positive bacteria have the highest relative abundances within honey bee colonies. Our lipid profiles reveal the presence of viable microbial communities in each of the six hive components sampled, with overall microbial community richness varying from lowest to highest in honey, comb, pupae, pollen, adults and propolis, respectively. Finally, microbial community lipid profiles were more similar when compared by component than by hive, location, or sampling year. Specifically, we found that individual hive components typically exhibited several dominant lipids and that these dominant lipids differ between components. Principal component and two-way clustering analyses both support significant grouping of lipids by hive component. Our findings indicate that in addition to the microbial communities present in individual workers, honey bee hives have resident microbial communities associated with different colony components. PMID:25849080

Quantitative comparison of the in situ microbial communities in different biomes

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, D.C.; Ringelberg, D.B.; Palmer, R.J.

1995-12-31

A system to define microbial communities in different biomes requires the application of non-traditional methodology. Classical microbiological methods have severe limitations for the analysis of environmental samples. Pure-culture isolation, biochemical testing, and/or enumeration by direct microscopic counting are not well suited for the estimation of total biomass or the assessment of community composition within environmental samples. Such methods provide little insight into the in situ phenotypic activity of the extant microbiota since these techniques are dependent on microbial growth and thus select against many environmental microorganisms which are non- culturable under a wide range of conditions. It has been repeatedlymore » documented in the literature that viable counts or direct counts of bacteria attached to sediment grains are difficult to quantitative and may grossly underestimate the extent of the existing community. The traditional tests provide little indication of the in situ nutritional status or for evidence of toxicity within the microbial community. A more recent development (MIDI Microbial Identification System), measure free and ester-linked fatty acids from isolated microorganisms. Bacterial isolates are identified by comparing their fatty acid profiles to the MIKI database which contains over 8000 entries. The application of the MIKI system to the analysis of environmental samples however, has significant drawbacks. The MIDI system was developed to identify clinical microorganisms and requires their isolation and culture on trypticase soy agar at 27{degrees}C. Since many isolates are unable to grow at these restrictive growth conditions, the system does not lend itself to identification of some environmental organisms. A more applicable methodology for environmental microbial analysis is based on the liquid extrication and separation of microbial lipids from environmental samples, followed by quantitative analysis using gas chromatography/« less

Microbial processes and communities in sediment samples along a transect across the Lusi mud volcano, Indonesia

NASA Astrophysics Data System (ADS)

Krueger, Martin; Straaten, Nontje; Mazzini, Adriano

2015-04-01

The Lusi eruption represents one of the largest ongoing sedimentary hosted geothermal systems. This eruption started in 2006 following to a 6.3 M earthquake that stroke Java Island. Since then it has been spewing boiling mud from a central crater with peaks reaching 180.000 m3 per day. Today an area of about 8 km2 is covered by locally dried mud breccia where a network of hundreds of satellite seeping pools is active. Numerous investigations focused on the study of offshore microbial colonies that commonly thrive at offshore methane seeps and mud volcanoes, however very little has been done for onshore seeping structures. Lusi represents a unique opportunity to complete a comprehensive study of onshore microbial communities fed by the seepage of CH4 and CO2 as well as of heavier liquid hydrocarbons originating from several km below the surface. We conducted a sampling campaign at the Lusi site collecting samples of fresh mud close to the erupting crater using a remote controlled drone. In addition we completed a transect towards outer parts of the crater to collect older, weathered samples for comparison. In all samples active microorganisms were present. The highest activities for CO2 and CH4 production as well as for CH4 oxidation and hydrocarbon degradation were observed in medium-age mud samples collected roughly in the middle of the transect. Rates for aerobic methane oxidation were high, as was the potential of the microbial communities to degrade hydrocarbons (oils, alkanes, BTEX tested). The data suggests a transition of microbial populations from an anaerobic, hydrocarbon-driven metabolism in fresher samples from center or from small seeps to more generalistic, aerobic microbial communities in older, more consolidated sediments. Currently, the microbial communities in the different sediment samples are analyzed using quantitative PCR and T-RFLP combined with MiSeq sequencing. This study represents an initial step to better understand onshore seepage systems and provides an ideal analogue for comparison with the better investigated offshore structures.

Analysis of the functional gene structure and metabolic potential of microbial community in high arsenic groundwater.

PubMed

Li, Ping; Jiang, Zhou; Wang, Yanhong; Deng, Ye; Van Nostrand, Joy D; Yuan, Tong; Liu, Han; Wei, Dazhun; Zhou, Jizhong

2017-10-15

Microbial functional potential in high arsenic (As) groundwater ecosystems remains largely unknown. In this study, the microbial community functional composition of nineteen groundwater samples was investigated using a functional gene array (GeoChip 5.0). Samples were divided into low and high As groups based on the clustering analysis of geochemical parameters and microbial functional structures. The results showed that As related genes (arsC, arrA), sulfate related genes (dsrA and dsrB), nitrogen cycling related genes (ureC, amoA, and hzo) and methanogen genes (mcrA, hdrB) in groundwater samples were correlated with As, SO 4 2- , NH 4 + or CH 4 concentrations, respectively. Canonical correspondence analysis (CCA) results indicated that some geochemical parameters including As, total organic content, SO 4 2- , NH 4 + , oxidation-reduction potential (ORP) and pH were important factors shaping the functional microbial community structures. Alkaline and reducing conditions with relatively low SO 4 2- , ORP, and high NH 4 + , as well as SO 4 2- and Fe reduction and ammonification involved in microbially-mediated geochemical processes could be associated with As enrichment in groundwater. This study provides an overall picture of functional microbial communities in high As groundwater aquifers, and also provides insights into the critical role of microorganisms in As biogeochemical cycling. Copyright © 2017 Elsevier Ltd. All rights reserved.

HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes.

PubMed

Forster, Samuel C; Browne, Hilary P; Kumar, Nitin; Hunt, Martin; Denise, Hubert; Mitchell, Alex; Finn, Robert D; Lawley, Trevor D

2016-01-04

The Human Pan-Microbe Communities (HPMC) database (http://www.hpmcd.org/) provides a manually curated, searchable, metagenomic resource to facilitate investigation of human gastrointestinal microbiota. Over the past decade, the application of metagenome sequencing to elucidate the microbial composition and functional capacity present in the human microbiome has revolutionized many concepts in our basic biology. When sufficient high quality reference genomes are available, whole genome metagenomic sequencing can provide direct biological insights and high-resolution classification. The HPMC database provides species level, standardized phylogenetic classification of over 1800 human gastrointestinal metagenomic samples. This is achieved by combining a manually curated list of bacterial genomes from human faecal samples with over 21000 additional reference genomes representing bacteria, viruses, archaea and fungi with manually curated species classification and enhanced sample metadata annotation. A user-friendly, web-based interface provides the ability to search for (i) microbial groups associated with health or disease state, (ii) health or disease states and community structure associated with a microbial group, (iii) the enrichment of a microbial gene or sequence and (iv) enrichment of a functional annotation. The HPMC database enables detailed analysis of human microbial communities and supports research from basic microbiology and immunology to therapeutic development in human health and disease. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Taxonomic and Functional Differences between Microbial Communities in Qinghai Lake and Its Input Streams

PubMed Central

Ren, Ze; Wang, Fang; Qu, Xiaodong; Elser, James J.; Liu, Yang; Chu, Limin

2017-01-01

Understanding microbial communities in terms of taxon and function is essential to decipher the biogeochemical cycling in aquatic ecosystems. Lakes and their input streams are highly linked. However, the differences between microbial assemblages in streams and lakes are still unclear. In this study, we conducted an intensive field sampling of microbial communities from lake water and stream biofilms in the Qinghai Lake watershed, the largest lake in China. We determined bacterial communities using high-throughput 16S rRNA gene sequencing and predicted functional profiles using PICRUSt to determine the taxonomic and functional differences between microbial communities in stream biofilms and lake water. The results showed that stream biofilms and lake water harbored distinct microbial communities. The microbial communities were different taxonomically and functionally between stream and lake. Moreover, streams biofilms had a microbial network with higher connectivity and modularity than lake water. Functional beta diversity was strongly correlated with taxonomic beta diversity in both the stream and lake microbial communities. Lake microbial assemblages displayed greater predicted metabolic potentials of many metabolism pathways while the microbial assemblages in stream biofilms were more abundant in xenobiotic biodegradation and metabolism and lipid metabolism. Furthermore, lake microbial assemblages had stronger predicted metabolic potentials in amino acid metabolism, carbon fixation, and photosynthesis while stream microbial assemblages were higher in carbohydrate metabolism, oxidative phosphorylation, and nitrogen metabolism. This study adds to our knowledge of stream-lake linkages from the functional and taxonomic composition of microbial assemblages. PMID:29213266

An improved method to set significance thresholds for β diversity testing in microbial community comparisons.

PubMed

Gülay, Arda; Smets, Barth F

2015-09-01

Exploring the variation in microbial community diversity between locations (β diversity) is a central topic in microbial ecology. Currently, there is no consensus on how to set the significance threshold for β diversity. Here, we describe and quantify the technical components of β diversity, including those associated with the process of subsampling. These components exist for any proposed β diversity measurement procedure. Further, we introduce a strategy to set significance thresholds for β diversity of any group of microbial samples using rarefaction, invoking the notion of a meta-community. The proposed technique was applied to several in silico generated operational taxonomic unit (OTU) libraries and experimental 16S rRNA pyrosequencing libraries. The latter represented microbial communities from different biological rapid sand filters at a full-scale waterworks. We observe that β diversity, after subsampling, is inflated by intra-sample differences; this inflation is avoided in the proposed method. In addition, microbial community evenness (Gini > 0.08) strongly affects all β diversity estimations due to bias associated with rarefaction. Where published methods to test β significance often fail, the proposed meta-community-based estimator is more successful at rejecting insignificant β diversity values. Applying our approach, we reveal the heterogeneous microbial structure of biological rapid sand filters both within and across filters. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Intestinal Microbial Community Differs between Acute Pancreatitis Patients and Healthy Volunteers.

PubMed

Zhang, Xi Mei; Zhang, Zheng Yu; Zhang, Chen Huan; Wu, Jing; Wang, You Xin; Zhang, Guo Xin

2018-01-01

A case control study including 45 acute pancreatitis and 44 healthy volunteers was performed to investigate the association between intestinal microbial community and acute pancreatitis. High-throughput 16S rRNA gene amplicon sequencing was used to profile the microbiological composition of the samples. In total, 27 microbial phyla were detected and the samples of pancreatitis patients contained fewer phyla. Samples from acute pancreatitis patients contained more Bacteroidetes and Proteobacteria and fewer Firmicutes and Actinobacteria than those from healthy volunteers. PCoA analyses distinguished the fecal microbial communities of acute pancreatitis patients from those of healthy volunteers. The intestinal microbes of acute pancreatitis patients are different from those of healthy volunteers. Modulation of the intestinal microbiome may serve as an alternative strategy for treating acute pancreatitis. Copyright © 2018 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

Exploration of Human Salivary Microbiomes—Insights into the Novel Characteristics of Microbial Community Structure in Caries and Caries-Free Subjects

PubMed Central

Wang, Shaoguo; Hu, Xiaopan; Jiao, Kangli; He, Xiangyi; Li, Zhiqiang; Wang, Jizeng

2016-01-01

Recently, high-throughput sequencing has improved the understanding of the microbiological etiology of caries, but the characteristics of the microbial community structure in the human oral cavity with and without caries are not completely clear. To better understand these characteristics, Illumina MiSeq high-throughput sequencing was utilized to analyze 20 salivary samples (10 caries-free and 10 caries) from subjects from the same town in Dongxiang, Gansu, China. A total of 5,113 OTUs (Operational Taxonomic Units, 97% cutoff) were characterized in all of the salivary samples obtained from the 20 subjects. A comparison of the two groups revealed that (i) the predominant phyla were constant between the two groups; (ii) the relative abundance of the genera Veillonella, Bifidobacterium, Selenomonas, Olsenella, Parascardovia, Scardovia, Chryseobacterium, Terrimonas, Burkholderia and Sporobacter was significantly higher in the group with caries (P < 0.05); and (iii) four genera with low relative abundance (< 0.01% on average), including two characteristic genera in caries (Chryseobacterium and Scardovia), significantly influenced the microbial community structure at the genus and OTU levels. Moreover, via co-occurrence and principal component analyses, the co-prevalence of the pathogenic genera was detected in the caries samples, but in the caries-free samples, the function of clustered genera was more random. This result suggests that a synergistic effect may be influencing the assembly of the caries microbial community, whereas competition may play a more dominant role in governing the microbial community in the caries-free group. Our findings regarding the characteristics of the microbial communities of the groups with and without caries might improve the understanding of the microbiological etiology of caries and might improve the prevention and cure of caries in the future. PMID:26784334

Colonization in the Photic Zone and Subsequent Changes during Sinking Determine Bacterial Community Composition in Marine Snow

PubMed Central

Thiele, Stefan; Fuchs, Bernhard M.; Amann, Rudolf

2014-01-01

Due to sampling difficulties, little is known about microbial communities associated with sinking marine snow in the twilight zone. A drifting sediment trap was equipped with a viscous cryogel and deployed to collect intact marine snow from depths of 100 and 400 m off Cape Blanc (Mauritania). Marine snow aggregates were fixed and washed in situ to prevent changes in microbial community composition and to enable subsequent analysis using catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). The attached microbial communities collected at 100 m were similar to the free-living community at the depth of the fluorescence maximum (20 m) but different from those at other depths (150, 400, 550, and 700 m). Therefore, the attached microbial community seemed to be “inherited” from that at the fluorescence maximum. The attached microbial community structure at 400 m differed from that of the attached community at 100 m and from that of any free-living community at the tested depths, except that collected near the sediment at 700 m. The differences between the particle-associated communities at 400 m and 100 m appeared to be due to internal changes in the attached microbial community rather than de novo colonization, detachment, or grazing during the sinking of marine snow. The new sampling method presented here will facilitate future investigations into the mechanisms that shape the bacterial community within sinking marine snow, leading to better understanding of the mechanisms which regulate biogeochemical cycling of settling organic matter. PMID:25527538

Noninvasive methods for dynamic mapping of microbial populations across the landscape

NASA Astrophysics Data System (ADS)

Meredith, L. K.; Sengupta, A.; Troch, P. A.; Volkmann, T. H. M.

2017-12-01

Soil microorganisms drive key ecosystem processes, and yet characterizing their distribution and activity in soil has been notoriously difficult. This is due, in part, to the heterogeneous nature of their response to changing environmental and nutrient conditions across time and space. These dynamics are challenging to constrain in both natural and experimental systems because of sampling difficulty and constraints. For example, soil microbial sampling at the Landscape Evolution Observatory (LEO) infrastructure in Biosphere 2 is limited in efforts to minimize soil disruption to the long term experiment that aims to characterize the interacting biological, hydrological, and geochemical processes driving soil evolution. In this and other systems, new methods are needed to monitor soil microbial communities and their genetic potential over time. In this study, we take advantage of the well-defined boundary conditions on hydrological flow at LEO to develop a new method to nondestructively characterize in situ microbial populations. In our approach, we sample microbes from the seepage flow at the base of each of three replicate LEO hillslopes and use hydrological models to `map back' in situ microbial populations. Over the course of a 3-month periodic rainfall experiment we collected samples from the LEO outflow for DNA and extraction and microbial community composition analysis. These data will be used to describe changes in microbial community composition over the course of the experiment. In addition, we will use hydrological flow models to identify the changing source region of discharge water over the course of periodic rainfall pulses, thereby mapping back microbial populations onto their geographic origin in the slope. These predictions of in situ microbial populations will be ground-truthed against those derived from destructive soil sampling at the beginning and end of the rainfall experiment. Our results will show the suitability of this method for long-term, non-destructive monitoring of the microbial communities that contribute to soil evolution in this large-scale model system. Furthermore, this method may be useful for other study systems with limitations to destructive sampling including other model infrastructures and natural landscapes.

Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing.

PubMed

Qian, Pei-Yuan; Wang, Yong; Lee, On On; Lau, Stanley C K; Yang, Jiangke; Lafi, Feras F; Al-Suwailem, Abdulaziz; Wong, Tim Y H

2011-03-01

The ecosystems of the Red Sea are among the least-explored microbial habitats in the marine environment. In this study, we investigated the microbial communities in the water column overlying the Atlantis II Deep and Discovery Deep in the Red Sea. Taxonomic classification of pyrosequencing reads of the 16S rRNA gene amplicons showed vertical stratification of microbial diversity from the surface water to 1500 m below the surface. Significant differences in both bacterial and archaeal diversity were observed in the upper (20 [corrected] and 50 m) and deeper layers (200 and 1500 m). There were no obvious differences in community structure at the same depth for the two sampling stations. The bacterial community in the upper layer was dominated by Cyanobacteria whereas the deeper layer harbored a large proportion of Proteobacteria. Among Archaea, Euryarchaeota, especially Halobacteriales, were dominant in the upper layer but diminished drastically in the deeper layer where Desulfurococcales belonging to Crenarchaeota became the dominant group. The results of our study indicate that the microbial communities sampled in this study are different from those identified in water column in other parts of the world. The depth-wise compositional variation in the microbial communities is attributable to their adaptations to the various environments in the Red Sea.

Biogeography and ecology of the rare and abundant microbial lineages in deep-sea hydrothermal vents.

PubMed

Anderson, Rika E; Sogin, Mitchell L; Baross, John A

2015-01-01

Environmental gradients generate countless ecological niches in deep-sea hydrothermal vent systems, which foster diverse microbial communities. The majority of distinct microbial lineages in these communities occur in very low abundance. However, the ecological role and distribution of rare and abundant lineages, particularly in deep, hot subsurface environments, remain unclear. Here, we use 16S rRNA tag sequencing to describe biogeographic patterning and microbial community structure of both rare and abundant archaea and bacteria in hydrothermal vent systems. We show that while rare archaeal lineages and almost all bacterial lineages displayed geographically restricted community structuring patterns, the abundant lineages of archaeal communities displayed a much more cosmopolitan distribution. Finally, analysis of one high-volume, high-temperature fluid sample representative of the deep hot biosphere described a unique microbial community that differed from microbial populations in diffuse flow fluid or sulfide samples, yet the rare thermophilic archaeal groups showed similarities to those that occur in sulfides. These results suggest that while most archaeal and bacterial lineages in vents are rare and display a highly regional distribution, a small percentage of lineages, particularly within the archaeal domain, are successful at widespread dispersal and colonization. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Microbial communities inhabiting oil-contaminated soils from two major oilfields in Northern China: Implications for active petroleum-degrading capacity.

PubMed

Sun, Weimin; Dong, Yiran; Gao, Pin; Fu, Meiyan; Ta, Kaiwen; Li, Jiwei

2015-06-01

Although oilfields harbor a wide diversity of microorganisms with various metabolic potentials, our current knowledge about oil-degrading bacteria is limited because the vast majority of oil-degrading bacteria remain uncultured. In the present study, microbial communities in nine oil-contaminated soils collected from Daqing and Changqing, two of the largest oil fields in China, were characterized through highthroughput sequencing of 16S rRNA genes. Bacteria related to the phyla Proteobacteria and Actinobacteria were dominant in four and three samples, respectively. At the genus level, Alkanindiges, Arthrobacter, Pseudomonas, Mycobacterium, and Rhodococcus were frequently detected in nine soil samples. Many of the dominant genera were phylogenetically related to the known oil-degrading species. The correlation between physiochemical parameters within the microbial communities was also investigated. Canonical correspondence analysis revealed that soil moisture, nitrate, TOC, and pH had an important impact in shaping the microbial communities of the hydrocarbon-contaminated soil. This study provided an in-depth analysis of microbial communities in oilcontaminated soil and useful information for future bioremediation of oil contamination.

Comparison of microbial community shifts in two parallel multi-step drinking water treatment processes.

PubMed

Xu, Jiajiong; Tang, Wei; Ma, Jun; Wang, Hong

2017-07-01

Drinking water treatment processes remove undesirable chemicals and microorganisms from source water, which is vital to public health protection. The purpose of this study was to investigate the effects of treatment processes and configuration on the microbiome by comparing microbial community shifts in two series of different treatment processes operated in parallel within a full-scale drinking water treatment plant (DWTP) in Southeast China. Illumina sequencing of 16S rRNA genes of water samples demonstrated little effect of coagulation/sedimentation and pre-oxidation steps on bacterial communities, in contrast to dramatic and concurrent microbial community shifts during ozonation, granular activated carbon treatment, sand filtration, and disinfection for both series. A large number of unique operational taxonomic units (OTUs) at these four treatment steps further illustrated their strong shaping power towards the drinking water microbial communities. Interestingly, multidimensional scaling analysis revealed tight clustering of biofilm samples collected from different treatment steps, with Nitrospira, the nitrite-oxidizing bacteria, noted at higher relative abundances in biofilm compared to water samples. Overall, this study provides a snapshot of step-to-step microbial evolvement in multi-step drinking water treatment systems, and the results provide insight to control and manipulation of the drinking water microbiome via optimization of DWTP design and operation.

Human and Environmental Impacts on River Sediment Microbial Communities

DOE PAGES

Gibbons, Sean M.; Jones, Edwin; Bearquiver, Angelita; ...

2014-05-19

Sediment microbial communities are responsible for a majority of the metabolic activity in river and stream ecosystems. Understanding the dynamics in community structure and function across freshwater environments will help us to predict how these ecosystems will change in response to human land-use practices. Here we present a spatiotemporal study of sediments in the Tongue River (Montana, USA), comprising six sites along 134 km of river sampled in both spring and fall for two years. Sequencing of 16S rRNA amplicons and shotgun metagenomes revealed that these sediments are the richest (~65,000 microbial ‘species’ identified) and most novel (93% of OTUsmore » do not match known microbial diversity) ecosystems analyzed by the Earth Microbiome Project to date, and display more functional diversity than was detected in a recent review of global soil metagenomes. Community structure and functional potential have been significantly altered by anthropogenic drivers, including increased pathogenicity and antibiotic metabolism markers near towns and metabolic signatures of coal and coalbed methane extraction byproducts. The core (OTUs shared across all samples) and the overall microbial community exhibited highly similar structure, and phylogeny was weakly coupled with functional potential. Together, these results suggest that microbial community structure is shaped by environmental drivers and niche filtering, though stochastic assembly processes likely play a role as well. These results indicate that sediment microbial communities are highly complex and sensitive to changes in land use practices.« less

Spatial and Temporal Variability in Microbial Communities from Pre- and Post-Eruption Microbial Mats Collected from Loihi Seamount, Hawaii: An Update

NASA Astrophysics Data System (ADS)

Moyer, C. L.; Davis, R. E.; Curtis, A. C.; Rassa, A. C.

2007-12-01

Loihi Seamount is an active submarine volcano that marks the southernmost extent of the Hawaiian hotspot. Loihi rises over 3000 meters from the seafloor and summits nearly 1000 meters below sea level. Hydrothermal activity was discovered at Loihi in 1987, yielding diffuse vent effluent (Tmax 37°C) with associated high CO2 and Fe(II) concentrations and luxuriant microbial mats located near the summit of the volcano. Loihi erupted most recently in 1996 forming a new 300 meter deep caldera (Pele's Pit) with hydrothermal venting up to 200°C. Pele's Pit has cooled and now contains multiple hydrothermal vents with hydrothermal fluids ranging from 8-58°C with concentrations of Fe(II) remaining between 50 and 750 μM. Community fingerprints from over 75 microbial mat samples have now been collected from Loihi Seamount from 1993 to 2006, with temperatures ranging from ambient (~4°C) up to nearly ~200°C. These samples were analyzed using Pearson product-moment coupled with UPGMA cluster analysis of terminal- restriction fragment length polymorphisms (T-RFLP) coupled with traditional clone library and sequence analysis to identify the primary populations within each community. These mat samples form two distinct community clusters (Loihi Cluster Group 1 and Group 2) representing a combined 90% of all mat samples collected. Loihi Cluster Group 1 is by far the largest group (n = 45) and contains the most mat samples collected over time. Group 1 is dominated by phylotypes closely related to the recently described zeta- Proteobacteria that includes the type strain Mariprofundus ferrooxydans, an obligately lithotrophic, Fe-oxidizing bacterium. Loihi Cluster Group 2 is comprised of only post-eruption communities (n = 18) that generally contain greater diversity (in terms of richness) than Group 1 communities. Group 2 communities are primarily dominated by a unique array of phylotypes belonging to the Nitrospira division and by the class epsilon- Proteobacteria, including many putative sulphur-oxidizing bacteria. Interestingly, we have recently witnessed a shift away from the Group 2 communities back to the Group 1 communities. Only 2 of 11 microbial mat samples collected in 2004 exhibited the Group 2 community structure. All 10 of the mat samples collected in 2006 from multiple locations exhibited the Group 1 community structure, indicating a reduced overall diversity within Pele's Pit and a return to the microbial mats being dominated by Fe-oxidizing bacteria.

Spatial variation in the bacterial and denitrifying bacterial community in a biofilter treating subsurface agricultural drainage.

PubMed

Andrus, J Malia; Porter, Matthew D; Rodríguez, Luis F; Kuehlhorn, Timothy; Cooke, Richard A C; Zhang, Yuanhui; Kent, Angela D; Zilles, Julie L

2014-02-01

Denitrifying biofilters can remove agricultural nitrates from subsurface drainage, reducing nitrate pollution that contributes to coastal hypoxic zones. The performance and reliability of natural and engineered systems dependent upon microbially mediated processes, such as the denitrifying biofilters, can be affected by the spatial structure of their microbial communities. Furthermore, our understanding of the relationship between microbial community composition and function is influenced by the spatial distribution of samples.In this study we characterized the spatial structure of bacterial communities in a denitrifying biofilter in central Illinois. Bacterial communities were assessed using automated ribosomal intergenic spacer analysis for bacteria and terminal restriction fragment length polymorphism of nosZ for denitrifying bacteria.Non-metric multidimensional scaling and analysis of similarity (ANOSIM) analyses indicated that bacteria showed statistically significant spatial structure by depth and transect,while denitrifying bacteria did not exhibit significant spatial structure. For determination of spatial patterns, we developed a package of automated functions for the R statistical environment that allows directional analysis of microbial community composition data using either ANOSIM or Mantel statistics.Applying this package to the biofilter data, the flow path correlation range for the bacterial community was 6.4 m at the shallower, periodically in undated depth and 10.7 m at the deeper, continually submerged depth. These spatial structures suggest a strong influence of hydrology on the microbial community composition in these denitrifying biofilters. Understanding such spatial structure can also guide optimal sample collection strategies for microbial community analyses.

Interactions between Natural Organic Matter and Native Microbes in the Oak Ridge FRC Groundwater

NASA Astrophysics Data System (ADS)

Wu, X.; Hazen, T.; Fox, P. M.; Nico, P. S.; Li, Q.; Yang, W.; Liu, Y.; Hess, N. J.; Zhang, P.; Qin, Y.; Zhou, J.; Chakraborty, R.

2016-12-01

Natural organic matter (NOM) is central to microbial food webs; however, little is known about the interplay between the physical and chemical characteristics of the carbon in NOM and its turnover by microbial communities. Microbial activity changes NOM's structure and properties, which may further influence the bioavailability of NOM. The change of NOM may reversely affect the microbial community structure as well. To date, our understanding of these interactions is insufficient, and it is critical to identify the role of NOM to carbon turnover, structure of microbial community and to the metabolic potential of that community. In this study, we aimed to study the interactions between NOM and native microbial communities present in groundwater at a background site (FW305 well) at Oak Ridge Field Research Center, TN. The total organic carbon and inorganic carbon in FW305 deep sediment samples were 0.071% and 0.011%, respectively. Water-soluble NOM was extracted from these sediment samples, the extraction efficiencies were 3.2% for organic carbon and 1.6% for inorganic carbon. The extracted NOM was then provided as the sole carbon source to native microbes present in groundwater. Subsamples were harvested several times from these incubations during a 50-day study. 16S rRNA gene amplicon sequencing and Geochip were used to identify the changes of microbial communities and expression of functional genes during transformation of the NOM. Several advanced chemical techniques including FTICR-MS and NEXAFS were used to characterize the C pool (i.e., NOM metabolites and microbial byproducts). Preliminary data clearly showed that microbial community responded to NOM, and shifted as functional groups in NOM transformed. Further detailed metabolite and gene-based analysis to elucidate these changes is currently being conducted.

Functional Diversity of Microbial Communities in Sludge-Amended Soils

NASA Astrophysics Data System (ADS)

Sun, Y. H.; Yang, Z. H.; Zhao, J. J.; Li, Q.

The BIOLOG method was applied to exploration of functional diversity of soil microbial communities in sludge-amended soils sampled from the Yangtze River Delta. Results indicated that metabolic profile, functional diversity indexes and Kinetic parameters of the soil microbial communities changed following soil amendment with sewage sludge, suggesting that the changes occurred in population of the microbes capable of exploiting carbon substrates and in this capability as well. The kinetic study of the functional diversity revealed that the metabolic profile of the soil microbial communities exhibited non-linear correlation with the incubation time, showing a curse of sigmoid that fits the dynamic model of growth of the soil microbial communities. In all the treatments, except for treatments of coastal fluvo-aquic soil amended with fresh sludge and dried sludge from Hangzhou, kinetic parameters K and r of the functional diversity of the soil microbial communities decreased significantly and parameter S increased. Changes in characteristics of the functional diversity well reflected differences in C utilizing capacity and model of the soil microbial communities in the sludge-amended soils, and changes in functional diversity of the soil microbial communities in a particular eco-environment, like soil amended with sewage sludge.

Characterisation of microbial communities in Chinese liquor fermentation starters Daqu using nested PCR-DGGE.

PubMed

Zhang, Liqiang; Wu, Chongde; Ding, Xiaofei; Zheng, Jia; Zhou, Rongqing

2014-12-01

In this study, characterises of the microbial community structures of three typical Chinese liquor Daqu, as well as different kinds of light flavour Daqu were investigated using nested PCR-denaturing gradient gel electrophoresis (DGGE). The results showed that microbial diversity was considerably different, and the microfloral compositions were highly variable among various Daqu. Lactic acid bacteria, which accounted for 30.95 % of all identified bacteria, were dominant in all Daqu samples, whereas Bacillus species were also predominant in the Luzhou (14.8 %) and Langjiu Daqu (18.2 %). Citrobacter and Burkholderia were first identified in light flavour Daqu. Aspergillus was the dominant moulds, and the non-Saccharomyces yeast species, Saccharomycopsis fibuligera, Wallemia sebi, Wallemia muriae, and Pichia subpelliculosa, were the dominant yeasts. Rasamsonia, Galactomyces, Geotrichum and Wallemia were first identified using nested PCR-DGGE. Cluster analysis indicated that the microbial community structures of different Daqu samples exhibited some differences. These may be ascribed to the different peak production temperatures, raw material constituents and microhabitats around the liquor enterprises. The current study provides insights into the microbial community structures of three typical Daqu samples, and may facilitate the development of starter cultures for manufacturing Chinese liquor.

Response of soil organic carbon fractions, microbial community composition and carbon mineralization to high-input fertilizer practices under an intensive agricultural system

PubMed Central

Wu, Xueping; Gebremikael, Mesfin Tsegaye; Wu, Huijun; Cai, Dianxiong; Wang, Bisheng; Li, Baoguo; Zhang, Jiancheng; Li, Yongshan; Xi, Jilong

2018-01-01

Microbial mechanisms associated with soil organic carbon (SOC) decomposition are poorly understood. We aim to determine the effects of inorganic and organic fertilizers on soil labile carbon (C) pools, microbial community structure and C mineralization rate under an intensive wheat-maize double cropping system in Northern China. Soil samples in 0–10 cm layer were collected from a nine-year field trial involved four treatments: no fertilizer, CK; nitrogen (N) and phosphorus (P) fertilizers, NP; maize straw combined with NP fertilizers, NPS; and manure plus straw and NP fertilizers, NPSM. Soil samples were analyzed to determine labile C pools (including dissolved organic C, DOC; light free organic C, LFOC; and microbial biomass C, MBC), microbial community composition (using phospholipid fatty acid (PLFA) profiles) and SOC mineralization rate (from a 124-day incubation experiment). This study demonstrated that the application of chemical fertilizers (NP) alone did not alter labile C fractions, soil microbial communities and SOC mineralization rate from those observed in the CK treatment. Whereas the use of straw in conjunction with chemical fertilizers (NPS) became an additional labile substrate supply that decreased C limitation, stimulated growth of all PLFA-related microbial communities, and resulted in 53% higher cumulative mineralization of C compared to that of CK. The SOC and its labile fractions explained 78.7% of the variance of microbial community structure. Further addition of manure on the top of straw in the NPSM treatment did not significantly increase microbial community abundances, but it did alter microbial community structure by increasing G+/G- ratio compared to that of NPS. The cumulative mineralization of C was 85% higher under NPSM fertilization compared to that of CK. Particularly, the NPSM treatment increased the mineralization rate of the resistant pool. This has to be carefully taken into account when setting realistic and effective goals for long-term soil C stabilization. PMID:29668702

Response of soil organic carbon fractions, microbial community composition and carbon mineralization to high-input fertilizer practices under an intensive agricultural system.

PubMed

Li, Jing; Wu, Xueping; Gebremikael, Mesfin Tsegaye; Wu, Huijun; Cai, Dianxiong; Wang, Bisheng; Li, Baoguo; Zhang, Jiancheng; Li, Yongshan; Xi, Jilong

2018-01-01

Microbial mechanisms associated with soil organic carbon (SOC) decomposition are poorly understood. We aim to determine the effects of inorganic and organic fertilizers on soil labile carbon (C) pools, microbial community structure and C mineralization rate under an intensive wheat-maize double cropping system in Northern China. Soil samples in 0-10 cm layer were collected from a nine-year field trial involved four treatments: no fertilizer, CK; nitrogen (N) and phosphorus (P) fertilizers, NP; maize straw combined with NP fertilizers, NPS; and manure plus straw and NP fertilizers, NPSM. Soil samples were analyzed to determine labile C pools (including dissolved organic C, DOC; light free organic C, LFOC; and microbial biomass C, MBC), microbial community composition (using phospholipid fatty acid (PLFA) profiles) and SOC mineralization rate (from a 124-day incubation experiment). This study demonstrated that the application of chemical fertilizers (NP) alone did not alter labile C fractions, soil microbial communities and SOC mineralization rate from those observed in the CK treatment. Whereas the use of straw in conjunction with chemical fertilizers (NPS) became an additional labile substrate supply that decreased C limitation, stimulated growth of all PLFA-related microbial communities, and resulted in 53% higher cumulative mineralization of C compared to that of CK. The SOC and its labile fractions explained 78.7% of the variance of microbial community structure. Further addition of manure on the top of straw in the NPSM treatment did not significantly increase microbial community abundances, but it did alter microbial community structure by increasing G+/G- ratio compared to that of NPS. The cumulative mineralization of C was 85% higher under NPSM fertilization compared to that of CK. Particularly, the NPSM treatment increased the mineralization rate of the resistant pool. This has to be carefully taken into account when setting realistic and effective goals for long-term soil C stabilization.

Microbial Community of High Arsenic Groundwater in Agricultural Irrigation Area of Hetao Plain, Inner Mongolia

PubMed Central

Wang, Yanhong; Li, Ping; Jiang, Zhou; Sinkkonen, Aki; Wang, Shi; Tu, Jin; Wei, Dazhun; Dong, Hailiang; Wang, Yanxin

2016-01-01

Microbial communities can play important role in arsenic release in groundwater aquifers. To investigate the microbial communities in high arsenic groundwater aquifers in agricultural irrigation area, 17 groundwater samples with different arsenic concentrations were collected along the agricultural drainage channels of Hangjinhouqi County, Inner Mongolia and examined by illumina MiSeq sequencing approach targeting the V4 region of the 16S rRNA genes. Both principal component analysis and hierarchical clustering results indicated that these samples were divided into two groups (high and low arsenic groups) according to the variation of geochemical characteristics. Arsenic concentrations showed strongly positive correlations with NH4+ and total organic carbon (TOC). Sequencing results revealed that a total of 329–2823 operational taxonomic units (OTUs) were observed at the 97% OTU level. Microbial richness and diversity of high arsenic groundwater samples along the drainage channels were lower than those of low arsenic groundwater samples but higher than those of high arsenic groundwaters from strongly reducing areas. The microbial community structure in groundwater along the drainage channels was different from those in strongly reducing arsenic-rich aquifers of Hetao Plain and other high arsenic groundwater aquifers including Bangladesh, West Bengal, and Vietnam. Acinetobacter and Pseudomonas dominated with high percentages in both high and low arsenic groundwaters. Alishewanella, Psychrobacter, Methylotenera, and Crenothrix showed relatively high abundances in high arsenic groundwater, while Rheinheimera and the unidentified OP3 were predominant populations in low arsenic groundwater. Archaeal populations displayed a low occurrence and mainly dominated by methanogens such as Methanocorpusculum and Methanospirillum. Microbial community compositions were different between high and low arsenic groundwater samples based on the results of principal coordinate analysis and co-inertia analysis. Other geochemical variables including TOC, NH4+, oxidation-reduction potential, and Fe might also affect the microbial composition. PMID:27999565

Sediment microbial communities in Great Boiling Spring are controlled by temperature and distinct from water communities

PubMed Central

Cole, Jessica K; Peacock, Joseph P; Dodsworth, Jeremy A; Williams, Amanda J; Thompson, Daniel B; Dong, Hailiang; Wu, Geng; Hedlund, Brian P

2013-01-01

Great Boiling Spring is a large, circumneutral, geothermal spring in the US Great Basin. Twelve samples were collected from water and four different sediment sites on four different dates. Microbial community composition and diversity were assessed by PCR amplification of a portion of the small subunit rRNA gene using a universal primer set followed by pyrosequencing of the V8 region. Analysis of 164 178 quality-filtered pyrotags clearly distinguished sediment and water microbial communities. Water communities were extremely uneven and dominated by the bacterium Thermocrinis. Sediment microbial communities grouped according to temperature and sampling location, with a strong, negative, linear relationship between temperature and richness at all taxonomic levels. Two sediment locations, Site A (87–80 °C) and Site B (79 °C), were predominantly composed of single phylotypes of the bacterial lineage GAL35 (p̂=36.1%), Aeropyrum (p̂=16.6%), the archaeal lineage pSL4 (p̂=15.9%), the archaeal lineage NAG1 (p̂=10.6%) and Thermocrinis (p̂=7.6%). The ammonia-oxidizing archaeon ‘Candidatus Nitrosocaldus' was relatively abundant in all sediment samples <82 °C (p̂=9.51%), delineating the upper temperature limit for chemolithotrophic ammonia oxidation in this spring. This study underscores the distinctness of water and sediment communities in GBS and the importance of temperature in driving microbial diversity, composition and, ultimately, the functioning of biogeochemical cycles. PMID:23235293

Microbial Communities in Pre-Columbian Coprolites

PubMed Central

Santiago-Rodriguez, Tasha M.; Narganes-Storde, Yvonne M.; Chanlatte, Luis; Crespo-Torres, Edwin; Toranzos, Gary A.; Jimenez-Flores, Rafael; Hamrick, Alice; Cano, Raul J.

2013-01-01

The study of coprolites from earlier cultures represents a great opportunity to study an “unaltered” composition of the intestinal microbiota. To test this, pre-Columbian coprolites from two cultures, the Huecoid and Saladoid, were evaluated for the presence of DNA, proteins and lipids by cytochemical staining, human and/or dog-specific Bacteroides spp. by PCR, as well as bacteria, fungi and archaea using Terminal Restriction Fragment analyses. DNA, proteins and lipids, and human-specific Bacteroides DNA were detected in all coprolites. Multidimensional scaling analyses resulted in spatial arrangements of microbial profiles by culture, further supported by cluster analysis and ANOSIM. Differences between the microbial communities were positively correlated with culture, and SIMPER analysis indicated 68.8% dissimilarity between the Huecoid and Saladoid. Proteobacteria, Bacteroidetes and methanogens were found in all coprolite samples. Propionebacteria, Shewanella and lactic acid bacteria dominated in the Huecoid samples, while Acidobacteria, and peptococci were dominant in Saladoid samples. Yeasts, including Candida albicans and Crypotococcus spp. were found in all samples. Basidiomycetes were the most notable fungi in Huecoid samples while Ascomycetes predominated in Saladoid samples, suggesting differences in dietary habits. Our study provides an approach for the study of the microbial communities of coprolite samples from various cultures. PMID:23755194

Microbial life associated with low-temperature alteration of ultramafic rocks in the Leka ophiolite complex.

PubMed

Daae, F L; Økland, I; Dahle, H; Jørgensen, S L; Thorseth, I H; Pedersen, R B

2013-07-01

Water-rock interactions in ultramafic lithosphere generate reduced chemical species such as hydrogen that can fuel subsurface microbial communities. Sampling of this environment is expensive and technically demanding. However, highly accessible, uplifted oceanic lithospheres emplaced onto continental margins (ophiolites) are potential model systems for studies of the subsurface biosphere in ultramafic rocks. Here, we describe a microbiological investigation of partially serpentinized dunite from the Leka ophiolite (Norway). We analysed samples of mineral coatings on subsurface fracture surfaces from different depths (10-160 cm) and groundwater from a 50-m-deep borehole that penetrates several major fracture zones in the rock. The samples are suggested to represent subsurface habitats ranging from highly anaerobic to aerobic conditions. Water from a surface pond was analysed for comparison. To explore the microbial diversity and to make assessments about potential metabolisms, the samples were analysed by microscopy, construction of small subunit ribosomal RNA gene clone libraries, culturing and quantitative-PCR. Different microbial communities were observed in the groundwater, the fracture-coating material and the surface water, indicating that distinct microbial ecosystems exist in the rock. Close relatives of hydrogen-oxidizing Hydrogenophaga dominated (30% of the bacterial clones) in the oxic groundwater, indicating that microbial communities in ultramafic rocks at Leka could partially be driven by H2 produced by low-temperature water-rock reactions. Heterotrophic organisms, including close relatives of hydrocarbon degraders possibly feeding on products from Fischer-Tropsch-type reactions, dominated in the fracture-coating material. Putative hydrogen-, ammonia-, manganese- and iron-oxidizers were also detected in fracture coatings and the groundwater. The microbial communities reflect the existence of different subsurface redox conditions generated by differences in fracture size and distribution, and mixing of fluids. The particularly dense microbial communities in the shallow fracture coatings seem to be fuelled by both photosynthesis and oxidation of reduced chemical species produced by water-rock reactions. © 2013 John Wiley & Sons Ltd.

Gastrointestinal microbial community changes in Atlantic cod (Gadus morhua) exposed to crude oil.

PubMed

Bagi, Andrea; Riiser, Even Sannes; Molland, Hilde Steine; Star, Bastiaan; Haverkamp, Thomas H A; Sydnes, Magne Olav; Pampanin, Daniela Maria

2018-04-02

The expansion of offshore oil exploration increases the risk of marine species being exposed to oil pollution in currently pristine areas. The adverse effects of oil exposure through toxic properties of polycyclic aromatic hydrocarbons (PAHs) have been well studied in Atlantic cod (Gadus morhua). Nevertheless, the fate of conjugated metabolites in the intestinal tract and their effect on the diversity of intestinal microbial community in fish is less understood. Here, we investigated the intestinal microbial community composition of Atlantic cod after 28 days of exposure to crude oil (concentration range 0.0-0.1 mg/L). Analysis of PAH metabolites in bile samples confirmed that uptake and biotransformation of oil compounds occurred as a result of the exposure. Various evidence for altered microbial communities was found in fish exposed to high (0.1 mg/L) and medium (0.05 mg/L) concentrations of oil when compared to fish exposed to low oil concentration (0.01 mg/L) or no oil (control). First, altered banding patterns were observed on denaturing gradient gel electrophoresis for samples pooled from each treatment group. Secondly, based on 16S rRNA sequences, higher levels of oil exposure were associated with a loss of overall diversity of the gut microbial communities. Furthermore, 8 operational taxonomic units (OTUs) were found to have significantly different relative abundances in samples from fishes exposed to high and medium oil concentrations when compared to samples from the control group and low oil concentration. Among these, only one OTU, a Deferribacterales, had increased relative abundance in samples from fish exposed to high oil concentration. The results presented herein contribute to a better understanding of the effects of oil contamination on the gut microbial community changes in fish and highlight the importance of further studies into the area. Our findings suggest that increased relative abundance of bacteria belonging to the order Deferribacterales may be indicative of exposure to oil at concentrations higher than 0.05 mg/L.

Filter forensics: microbiota recovery from residential HVAC filters.

PubMed

Maestre, Juan P; Jennings, Wiley; Wylie, Dennis; Horner, Sharon D; Siegel, Jeffrey; Kinney, Kerry A

2018-01-30

Establishing reliable methods for assessing the microbiome within the built environment is critical for understanding the impact of biological exposures on human health. High-throughput DNA sequencing of dust samples provides valuable insights into the microbiome present in human-occupied spaces. However, the effect that different sampling methods have on the microbial community recovered from dust samples is not well understood across sample types. Heating, ventilation, and air conditioning (HVAC) filters hold promise as long-term, spatially integrated, high volume samplers to characterize the airborne microbiome in homes and other climate-controlled spaces. In this study, the effect that dust recovery method (i.e., cut and elution, swabbing, or vacuuming) has on the microbial community structure, membership, and repeatability inferred by Illumina sequencing was evaluated. The results indicate that vacuum samples captured higher quantities of total, bacterial, and fungal DNA than swab or cut samples. Repeated swab and vacuum samples collected from the same filter were less variable than cut samples with respect to both quantitative DNA recovery and bacterial community structure. Vacuum samples captured substantially greater bacterial diversity than the other methods, whereas fungal diversity was similar across all three methods. Vacuum and swab samples of HVAC filter dust were repeatable and generally superior to cut samples. Nevertheless, the contribution of environmental and human sources to the bacterial and fungal communities recovered via each sampling method was generally consistent across the methods investigated. Dust recovery methodologies have been shown to affect the recovery, repeatability, structure, and membership of microbial communities recovered from dust samples in the built environment. The results of this study are directly applicable to indoor microbiota studies utilizing the filter forensics approach. More broadly, this study provides a better understanding of the microbial community variability attributable to sampling methodology and helps inform interpretation of data collected from other types of dust samples collected from indoor environments.

Field and Lab-Based Microbiological Investigations of the Marcellus Shale

NASA Astrophysics Data System (ADS)

Wishart, J. R.; Neumann, K.; Edenborn, H. M.; Hakala, A.; Yang, J.; Torres, M. E.; Colwell, F. S.

2013-12-01

The recent exploration of shales for natural gas resources has provided the opportunity to study their subsurface geochemistry and microbiology. Evidence indicates that shale environments are marked by extreme conditions such as high temperature and pressure, low porosity, permeability and connectivity, and the presence of heavy metals and radionuclides. It has been postulated that many of these shales are naturally sterile due to the high pressure and temperature conditions under which they were formed. However, it has been shown in the Antrim and New Albany shales that microbial communities do exist in these environments. Here we review geochemical and microbiological evidence for the possible habitation of the Marcellus shale by microorganisms and compare these conditions to other shales in the U.S. Furthermore, we describe the development of sampling and analysis techniques used to evaluate microbial communities present in the Marcellus shale and associated hydraulic fracturing fluid. Sampling techniques thus far have consisted of collecting flowback fluids from wells and water impoundments and collecting core material from previous drilling expeditions. Furthermore, DNA extraction was performed on Marcellus shale sub-core with a MoBio PowerSoil kit to determine its efficiency. Assessment of the Marcellus shale indicates that it has low porosity and permeability that are not conducive to dense microbial populations; however, moderate temperatures and a natural fracture network may support a microbial community especially in zones where the Marcellus intersects more porous geologic formations. Also, hydraulic fracturing extends this fracture network providing more environments where microbial communities can exist. Previous research which collected flowback fluids has revealed a diverse microbial community that may be derived from hydrofrac fluid production or from the subsurface. DNA extraction from 10 g samples of Marcellus shale sub-core were unsuccessful even when samples were spiked with 8x108 cells/g of shale. This indicated that constituents of shale such as high levels of carbonates, humic acids and metals likely inhibited components of the PowerSoil kit. Future research is focused on refining sample collection and analyses to gain a full understanding of the microbiology of the Marcellus shale and associated flowback fluids. This includes the development of an in situ osmosampler, which will collect temporally relevant fluid and colonized substrate samples. The design of the osmosampler for hydraulic fracturing wells is being adapted from those used to sample marine environments. Furthermore, incubation experiments are underway to study interactions between microbial communities associated with hydraulic fracturing fluid and Marcellus shale samples. In conclusion, evidence suggests that the Marcellus shale is a possible component of the subsurface biosphere. Future studies will be valuable in determining the microbial community structure and function in relation to the geochemistry of the Marcellus shale and its future development as a natural gas resource.

[Effects of Perfluoroalkyl Substances on the Microbial Community Structure in Surface Sediments of Typical River, China].

PubMed

Sun, Ya-jun; Wang, Tie-yu; Peng, Xia-wei; Wang, Pei

2015-07-01

In order to reveal the relationship between Perfluoroalkyl substances (PFASs) contamination and the bacterial community composition, surface sediment samples were collected along the Xiaoqing River in Shandong Province in April and July 2014 (XQ1-XQ10), where many PFASs manufacturers were located. PFASs were quantified by HPLC/MS-MS, related environmental factors affecting the microbial community structure were measured, and the microbial community structure in surface sediments was measured by the second-generation sequencing technology Illumina MiSeq. The results not only revealed the degree of PFASs pollution in the sediments of Xiaoqing River, but also illustrated the relationship between PFASs pollution and the microbial community structure. Among the twelve kinds of PFASs detected in this study, PFOA was the predominant compound, and the highest PFOA concentrations were detected in the sample of XQ5 (April: 456. 2 ng. g-1; July: 748.7 ng . g-1) located at the downstream of Xiaoqing River with many fluoropolymer producing facilities. PFOA contamination was the main factor affecting the microbial community structure in April, accordingly community richness and evenness were significantly negatively correlated with PFOA levels. The abundance of Thiobacillus increased with the increasing PFOA concentration in the sediment PFOA. This suggested that Thiobacillus was sensitive to PFOA pollution and might be the potential indicator to reveal the degree of PFOA pollution in sediment. When the concentrations of PFOA were below 100 ng . g-1, no significant effects on the microbial community structure were observed.

Characterisation of culture-independent and -dependent microbial communities in a high-temperature offshore chalk petroleum reservoir.

PubMed

Kaster, Krista M; Bonaunet, Kristin; Berland, Harald; Kjeilen-Eilertsen, Grethe; Brakstad, Odd Gunnar

2009-11-01

Recent studies have indicated that oil reservoirs harbour diverse microbial communities. Culture-dependent and culture-independent methods were used to evaluate the microbial diversity in produced water samples of the Ekofisk oil field, a high temperature, and fractured chalk reservoir in the North Sea. DGGE analyses of 16S rRNA gene fragments were used to assess the microbial diversity of both archaeal and bacterial communities in produced water samples and enrichment cultures from 4 different wells (B-08, X-08, X-18 and X-25). Low diversity communities were found when 16S rDNA libraries of bacterial and archaeal assemblages were generated from total community DNA obtained from produced water samples and enrichment cultures. Sequence analysis of the clones indicated close matches to microbes associated with high-temperature oil reservoirs or other similar environments. Sequences were found to be similar to members of the genera Thermotoga, Caminicella, Thermoanaerobacter, Archaeoglobus, Thermococcus, and Methanobulbus. Enrichment cultures obtained from the produced water samples were dominated by sheathed rods. Sequence analyses of the cultures indicated predominance of the genera Petrotoga, Arcobacter, Archaeoglobus and Thermococcus. The communities of both produced water and enrichment cultures appeared to be dominated by thermophilic fermenters capable of reducing sulphur compounds. These results suggest that the biochemical processes in the Ekofisk chalk reservoir are similar to those observed in high-temperature sandstone reservoirs.

Temporal dynamics of soil microbial communities under different moisture regimes: high-throughput sequencing and bioinformatics analysis

NASA Astrophysics Data System (ADS)

Semenov, Mikhail; Zhuravleva, Anna; Semenov, Vyacheslav; Yevdokimov, Ilya; Larionova, Alla

2017-04-01

Recent climate scenarios predict not only continued global warming but also an increased frequency and intensity of extreme climatic events such as strong changes in temperature and precipitation regimes. Microorganisms are well known to be more sensitive to changes in environmental conditions than to other soil chemical and physical parameters. In this study, we determined the shifts in soil microbial community structure as well as indicative taxa in soils under three moisture regimes using high-throughput Illumina sequencing and range of bioinformatics approaches for the assessment of sequence data. Incubation experiments were performed in soil-filled (Greyic Phaeozems Albic) rhizoboxes with maize and without plants. Three contrasting moisture regimes were being simulated: 1) optimal wetting (OW), a watering 2-3 times per week to maintain soil moisture of 20-25% by weight; 2) periodic wetting (PW), with alternating periods of wetting and drought; and 3) constant insufficient wetting (IW), while soil moisture of 12% by weight was permanently maintained. Sampled fresh soils were homogenized, and the total DNA of three replicates was extracted using the FastDNA® SPIN kit for Soil. DNA replicates were combined in a pooled sample and the DNA was used for PCR with specific primers for the 16S V3 and V4 regions. In order to compare variability between different samples and replicates within a single sample, some DNA replicates treated separately. The products were purified and submitted to Illumina MiSeq sequencing. Sequence data were evaluated by alpha-diversity (Chao1 and Shannon H' diversity indexes), beta-diversity (UniFrac and Bray-Curtis dissimilarity), heatmap, tagcloud, and plot-bar analyses using the MiSeq Reporter Metagenomics Workflow and R packages (phyloseq, vegan, tagcloud). Shannon index varied in a rather narrow range (4.4-4.9) with the lowest values for microbial communities under PW treatment. Chao1 index varied from 385 to 480, being a more flexible indicator than Shannon index. Chao1 had similar values for OW and IW communities, but alpha-diversity of microbial communities has sharply decreased under PW treatment. There was no visible difference in beta-diversity depending on sampling date and wetting regime, however, it could be possible to distinguish microbial communities in soils with maize and without plants. The presence of maize was acting as scattering agent, making microbial communities more distinguished. In all studied samples, the most dominant phyla were Proteobacteria, Firmicutes, Verrucomicrobia, Actinobacteria, and Acidobacteria. Chthoniobacter, Bacillus, Alicyclobacillus, Rhodoplanes, Cohnella, Kaistobacter, and Solibacter were the most abundant genera. Moreover, these genera were found as the most reactive and variable taxa in microbial community. Thus, DNA high-throughput sequencing revealed no dramatic shifts in bacterial community structure in soils under different moisture regimes. However, this technique allowed us to determine the effect of wetting regime and the presence of plants on soil microbial community which were adaptable to insufficient wetting, but lost diversity under periodic wetting. Furthermore, we detected the indicative taxa which dominate in microbial communities and at the same time strongly react to environmental changes.

Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets.

PubMed

Washburne, Alex D; Silverman, Justin D; Leff, Jonathan W; Bennett, Dominic J; Darcy, John L; Mukherjee, Sayan; Fierer, Noah; David, Lawrence A

2017-01-01

Marker gene sequencing of microbial communities has generated big datasets of microbial relative abundances varying across environmental conditions, sample sites and treatments. These data often come with putative phylogenies, providing unique opportunities to investigate how shared evolutionary history affects microbial abundance patterns. Here, we present a method to identify the phylogenetic factors driving patterns in microbial community composition. We use the method, "phylofactorization," to re-analyze datasets from the human body and soil microbial communities, demonstrating how phylofactorization is a dimensionality-reducing tool, an ordination-visualization tool, and an inferential tool for identifying edges in the phylogeny along which putative functional ecological traits may have arisen.

Methodological approaches for studying the microbial ecology of drinking water distribution systems.

PubMed

Douterelo, Isabel; Boxall, Joby B; Deines, Peter; Sekar, Raju; Fish, Katherine E; Biggs, Catherine A

2014-11-15

The study of the microbial ecology of drinking water distribution systems (DWDS) has traditionally been based on culturing organisms from bulk water samples. The development and application of molecular methods has supplied new tools for examining the microbial diversity and activity of environmental samples, yielding new insights into the microbial community and its diversity within these engineered ecosystems. In this review, the currently available methods and emerging approaches for characterising microbial communities, including both planktonic and biofilm ways of life, are critically evaluated. The study of biofilms is considered particularly important as it plays a critical role in the processes and interactions occurring at the pipe wall and bulk water interface. The advantages, limitations and usefulness of methods that can be used to detect and assess microbial abundance, community composition and function are discussed in a DWDS context. This review will assist hydraulic engineers and microbial ecologists in choosing the most appropriate tools to assess drinking water microbiology and related aspects. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Microbial communities associated with wet flue gas desulfurization systems

PubMed Central

Brown, Bryan P.; Brown, Shannon R.; Senko, John M.

2012-01-01

Flue gas desulfurization (FGD) systems are employed to remove SOx gasses that are produced by the combustion of coal for electric power generation, and consequently limit acid rain associated with these activities. Wet FGDs represent a physicochemically extreme environment due to the high operating temperatures and total dissolved solids (TDS) of fluids in the interior of the FGD units. Despite the potential importance of microbial activities in the performance and operation of FGD systems, the microbial communities associated with them have not been evaluated. Microbial communities associated with distinct process points of FGD systems at several coal-fired electricity generation facilities were evaluated using culture-dependent and -independent approaches. Due to the high solute concentrations and temperatures in the FGD absorber units, culturable halothermophilic/tolerant bacteria were more abundant in samples collected from within the absorber units than in samples collected from the makeup waters that are used to replenish fluids inside the absorber units. Evaluation of bacterial 16S rRNA genes recovered from scale deposits on the walls of absorber units revealed that the microbial communities associated with these deposits are primarily composed of thermophilic bacterial lineages. These findings suggest that unique microbial communities develop in FGD systems in response to physicochemical characteristics of the different process points within the systems. The activities of the thermophilic microbial communities that develop within scale deposits could play a role in the corrosion of steel structures in FGD systems. PMID:23226147

Reference independent species level profiling of the largest marine microbial ecosystem.

NASA Astrophysics Data System (ADS)

Mende, D. R.; DeLong, E.; Aylward, F.

2016-02-01

Marine microbes are of immense importance for the flux of matter and energy within the global oceans. Yet, the temporal variability of microbial communities in response to seasonal and environmental changes remains understudied. In addition, there is only a very limited understanding of the effects that changes within microbial communities at a certain depth have on the other microbes within the water column. Further, existing studies have mostly been limited by the lack of good reference databases. Here we present an reference independent analysis of a year long time series at 5 different water depth of the microbial communities at Station ALOHA, a sampling location representative of the largest contiguous ecosystem on earth, the North Pacific Subtropical Gyre (NPSG). Due to the lack the lack of closely related reference genomes most recent meta-genomic studies of marine microbial ecosystems have been limited to a coarse grained view at higher taxonomic levels. In order to gain a fine grained picture of the microbial communities and their dynamics within the NPSG, we extended the mOTU approach that has been successfully applied to the human microbiome to this marine ecosystem using more than 60 deeply sequenced metagenomic samples. This method allows for species level community profiling and diversity estimates, revealing seasonal shifts within the microbial communities. Additionally, we detected a number of microbes that respond to changes of different changing environmental conditions. We further surveyed the depth specificity of microbes at station ALOHA, showing species specific patterns of presence at different depths.

Microbial diversity in degraded and non-degraded petroleum samples and comparison across oil reservoirs at local and global scales.

PubMed

Sierra-Garcia, Isabel Natalia; Dellagnezze, Bruna M; Santos, Viviane P; Chaves B, Michel R; Capilla, Ramsés; Santos Neto, Eugenio V; Gray, Neil; Oliveira, Valeria M

2017-01-01

Microorganisms have shown their ability to colonize extreme environments including deep subsurface petroleum reservoirs. Physicochemical parameters may vary greatly among petroleum reservoirs worldwide and so do the microbial communities inhabiting these different environments. The present work aimed at the characterization of the microbiota in biodegraded and non-degraded petroleum samples from three Brazilian reservoirs and the comparison of microbial community diversity across oil reservoirs at local and global scales using 16S rRNA clone libraries. The analysis of 620 16S rRNA bacterial and archaeal sequences obtained from Brazilian oil samples revealed 42 bacterial OTUs and 21 archaeal OTUs. The bacterial community from the degraded oil was more diverse than the non-degraded samples. Non-degraded oil samples were overwhelmingly dominated by gammaproteobacterial sequences with a predominance of the genera Marinobacter and Marinobacterium. Comparisons of microbial diversity among oil reservoirs worldwide suggested an apparent correlation of prokaryotic communities with reservoir temperature and depth and no influence of geographic distance among reservoirs. The detailed analysis of the phylogenetic diversity across reservoirs allowed us to define a core microbiome encompassing three bacterial classes (Gammaproteobacteria, Clostridia, and Bacteroidia) and one archaeal class (Methanomicrobia) ubiquitous in petroleum reservoirs and presumably owning the abilities to sustain life in these environments.

Profiling microbial community structures across six large oilfields in China and the potential role of dominant microorganisms in bioremediation.

PubMed

Sun, Weimin; Li, Jiwei; Jiang, Lei; Sun, Zhilei; Fu, Meiyan; Peng, Xiaotong

2015-10-01

Successful bioremediation of oil pollution is based on a comprehensive understanding of the in situ physicochemical conditions and indigenous microbial communities as well as the interaction between microorganisms and geochemical variables. Nineteen oil-contaminated soil samples and five uncontaminated controls were taken from six major oilfields across different geoclimatic regions in China to investigate the spatial distribution of the microbial ecosystem. Microbial community analysis revealed remarkable variation in microbial diversity between oil-contaminated soils taken from different oilfields. Canonical correspondence analysis (CCA) further demonstrated that a suite of in situ geochemical parameters, including soil moisture and sulfate concentrations, were among the factors that influenced the overall microbial community structure and composition. Phylogenetic analysis indicated that the vast majority of sequences were related to the genera Arthrobacter, Dietzia, Pseudomonas, Rhodococcus, and Marinobacter, many of which contain known oil-degrading or oil-emulsifying species. Remarkably, a number of archaeal genera including Halalkalicoccus, Natronomonas, Haloterrigena, and Natrinema were found in relatively high abundance in some of the oil-contaminated soil samples, indicating that these Euryarchaeota may play an important ecological role in some oil-contaminated soils. This study offers a direct and reliable reference of the diversity of the microbial community in various oil-contaminated soils and may influence strategies for in situ bioremediation of oil pollution.

Context dependency and saturating effects of loss of rare soil microbes on plant productivity.

PubMed

Hol, W H Gera; de Boer, Wietse; de Hollander, Mattias; Kuramae, Eiko E; Meisner, Annelein; van der Putten, Wim H

2015-01-01

Land use intensification is associated with loss of biodiversity and altered ecosystem functioning. Until now most studies on the relationship between biodiversity and ecosystem functioning focused on random loss of species, while loss of rare species that usually are the first to disappear received less attention. Here we test if the effect of rare microbial species loss on plant productivity depends on the origin of the microbial soil community. Soils were sampled from three land use types at two farms. Microbial communities with increasing loss of rare species were created by inoculating sterilized soils with serially diluted soil suspensions. After 8 months of incubation, the effects of the different soil communities on abiotic soil properties, soil processes, microbial community composition, and plant productivity was measured. Dilution treatments resulted in increasing species loss, which was in relation to abundance of bacteria in the original field soil, without affecting most of the other soil parameters and processes. Microbial species loss affected plant biomass positively, negatively or not at all, depending on soil origin, but not on land use history. Even within fields the effects of dilution on plant biomass varied between replicates, suggesting heterogeneity in microbial community composition. The effects of medium and severe species loss on plant biomass were similar, pointing toward a saturating effect of species loss. We conclude that changes in the composition of the soil microbial community, including rare species loss, can affect plant productivity, depending on the composition of the initial microbial community. Future work on the relation between function and species loss effects should address this variation by including multiple sampling origins.

Analysis of the global ocean sampling (GOS) project for trends in iron uptake by surface ocean microbes.

PubMed

Toulza, Eve; Tagliabue, Alessandro; Blain, Stéphane; Piganeau, Gwenael

2012-01-01

Microbial metagenomes are DNA samples of the most abundant, and therefore most successful organisms at the sampling time and location for a given cell size range. The study of microbial communities via their DNA content has revolutionized our understanding of microbial ecology and evolution. Iron availability is a critical resource that limits microbial communities' growth in many oceanic areas. Here, we built a database of 2319 sequences, corresponding to 140 gene families of iron metabolism with a large phylogenetic spread, to explore the microbial strategies of iron acquisition in the ocean's bacterial community. We estimate iron metabolism strategies from metagenome gene content and investigate whether their prevalence varies with dissolved iron concentrations obtained from a biogeochemical model. We show significant quantitative and qualitative variations in iron metabolism pathways, with a higher proportion of iron metabolism genes in low iron environments. We found a striking difference between coastal and open ocean sites regarding Fe(2+) versus Fe(3+) uptake gene prevalence. We also show that non-specific siderophore uptake increases in low iron open ocean environments, suggesting bacteria may acquire iron from natural siderophore-like organic complexes. Despite the lack of knowledge of iron uptake mechanisms in most marine microorganisms, our approach provides insights into how the iron metabolic pathways of microbial communities may vary with seawater iron concentrations.

Research on florfenicol residue in coastal area of dalian (northern china) and analysis of functional diversity of the microbial community in marine sediment.

PubMed

Zong, Humin; Ma, Deyi; Wang, Juying; Hu, Jiangtao

2010-02-01

An analytical method based on high performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS) has been developed to investigate florfenicol residues. Among 11 stations, florfenicol was detected in six water samples. The concentrations of florfenicol in the six samples were 64.2 microg L(-1), 390.6 microg L(-1), 1.1 x 10(4) microg L(-1), 29.8 microg L(-1), 61.6 microg L(-1), 34.9 microg L(-1), respectively. These results showed that high levels of florfenicol were observed in water samples collected from stations influenced by aquaculture discharges. However, no florfenicol residue was detected in the sediment samples. Furthermore, the functional diversities of microbial community in four marine sediment samples were analyzed by Biolog microplate. For the sediment samples from the stations where antibacterials had been used, the functional diversity of microbial community was much lower than those from the stations where antibacterials were not used.

Differences in Intertidal Microbial Assemblages on Urban Structures and Natural Rocky Reef

PubMed Central

Tan, Elisa L.-Y.; Mayer-Pinto, Mariana; Johnston, Emma L.; Dafforn, Katherine A.

2015-01-01

Global seascapes are increasingly modified to support high levels of human activity in the coastal zone. Modifications include the addition of defense structures and boating infrastructure, such as seawalls and marinas that replace natural habitats. Artificial structures support different macrofaunal communities to those found on natural rocky shores; however, little is known about differences in microbial community structure or function in urban seascapes. Understanding how artificial constructions in marine environments influence microbial communities is important as these assemblages contribute to many basic ecological processes. In this study, the bacterial communities of intertidal biofilms were compared between artificial structures (seawalls) and natural habitats (rocky shores) within Sydney Harbour. Plots were cleared on each type of habitat at eight locations. After 3 weeks the newly formed biofilm was sampled and the 16S rRNA gene sequenced using the Illumina Miseq platform. To account for differences in orientation and substrate material between seawalls and rocky shores that might have influenced our survey, we also deployed recruitment blocks next to the habitats at all locations for 3 weeks and then sampled and sequenced their microbial communities. Intertidal bacterial community structure sampled from plots differed between seawalls and rocky shores, but when substrate material, age and orientation were kept constant (with recruitment blocks) then bacterial communities were similar in composition and structure among habitats. This suggests that changes in bacterial communities on seawalls are not related to environmental differences between locations, but may be related to other intrinsic factors that differ between the habitats such as orientation, complexity, or predation. This is one of the first comparisons of intertidal microbial communities on natural and artificial surfaces and illustrates substantial ecological differences with potential consequences for biofilm function and the recruitment of macrofauna. PMID:26635747

Soil microbial abundance, activity and diversity response in two different altitude-adapted plant communities affected by wildfire in Sierra Nevada National Park (Granada, Spain)

NASA Astrophysics Data System (ADS)

Bárcenas-Moreno, Gema; Zavala, Lorena; Jordan, Antonio; Bååth, Erland; Mataix-Beneyto, Jorge

2013-04-01

Plant communities can play an important role in fire severity and post-fire ecosystem recovery due to their role as combustible and different plant-soil microorganisms interactions. Possible differences induced by plant and microorganisms response after fire could affect the general ecosystem short and long-term response and its sustainability. The main objective of this work was the evaluation of the effect of wildfire on soil microbial abundance, activity and diversity in two different plant communities associated to different altitudes in Sierra Nevada National Park (Granada, Spain). Samples were collected in two areas located on the Sierra Nevada Mountain between 1700 and 2000 m above sea level which were affected by a large wildfire in 2005. Two samplings were carried out 8 and 20 months after fire and samples were collected in both burned and unburned (control) zones in each plant community area. Area A is located at 1700m and it is formed by Quercus rotundifolia forest while area B is located at 2000 m altitude and is composed of alpine vegetation formed by creeping bearing shrubs. Microbial biomass measured by Fumigation-Extraction method followed the same trend in both areas showing slight and no significant differences between burned and unburned area during the study period while viable and cultivable bacteria abundance were markedly higher in fire affected samples than in the control ones in both samplings. Viable and cultivable filamentous fungi had different behavior depending of plant vegetation community studied showing no differences between burned and unburned area in area A while was significantly higher in burned samples than in the control ones in area B. Microbial activity monitoring with soil microbial respiration appears to had been affected immediately after fire since microbial respiration was lower in burned samples from area A than in unburned one only 8 months after fire and no significant differences were observed between burned and unburned samples in area B. Soil microbial community composition studied by Principal Component Analyses (PCA) of the PLFA pattern revealed both fire and seasonal effects. General overview of the results could lead to think in a slight negative or even positive effect of fire on soil microbial parameters studied, mainly in zone B. Nevertheless if we calculate the ratio between C-biomass and organic-C we find lower ratio in fire-affected samples than in the control ones in both areas, showing the most marked effect on area B which remain with this tendency 20 months after fire. Acknowledgements: This research was supported by the CICYT co-financed FEDER project CGL2006-11107-C02-01/BOS. We are grateful for the Sierra Nevada National Park support during the study.

Comparison of Microbial Communities Isolated from Feces of Asymptomatic Salmonella-Shedding and Non-Salmonella Shedding Dairy Cows

PubMed Central

Haley, Bradd J.; Pettengill, James; Gorham, Sasha; Ottesen, Andrea; Karns, Jeffrey S.; Van Kessel, Jo Ann S.

2016-01-01

In the United States Salmonella enterica subsp. enterica serotypes Kentucky and Cerro are frequently isolated from asymptomatic dairy cows. However, factors that contribute to colonization of the bovine gut by these two serotypes have not been identified. To investigate associations between Salmonella status and bacterial diversity, as well as the diversity of the microbial community in the dairy cow hindgut, the bacterial and archaeal communities of fecal samples from cows on a single dairy farm were determined by high-throughput sequencing of 16S rRNA gene amplicons. Fecal grab samples were collected from two Salmonella-positive cows and two Salmonella-negative cows on five sampling dates (n = 20 cows), and 16S rRNA gene amplicons from these samples were sequenced on the Illumina MiSeq platform. A high level of alpha (within) and beta diversity (between) samples demonstrated that microbial profiles of dairy cow hindguts are quite diverse. To determine whether Salmonella presence, sampling year, or sampling date explained a significant amount of the variation in microbial diversity, we performed constrained ordination analyses (distance based RDA) on the unifrac distance matrix produced with QIIME. Results indicated that there was not a significant difference in the microbial diversity associated with Salmonella presence (P > 0.05), but there were significant differences between sampling dates and years (Pseudo-F = 2.157 to 4.385, P < 0.05). Based on these data, it appears that commensal Salmonella infections with serotypes Cerro and Kentucky in dairy cows have little or no association with changes in the abundance of major bacterial groups in the hindgut. Rather, our results indicated that temporal dynamics and other undescribed parameters associated with them were the most influential drivers of the differences in microbial diversity and community structure in the dairy cow hindgut. PMID:27313565

Metaproteomics: Harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities

PubMed Central

Hettich, Robert L.; Pan, Chongle; Chourey, Karuna; Giannone, Richard J.

2013-01-01

Summary The availability of extensive genome information for many different microbes, including unculturable species in mixed communities from environmental samples, has enabled systems-biology interrogation by providing a means to access genomic, transcriptomic, and proteomic information. To this end, metaproteomics exploits the power of high performance mass spectrometry for extensive characterization of the complete suite of proteins expressed by a microbial community in an environmental sample. PMID:23469896

Rapid Shifts in Soil and Forest Floor Microbial Communities with Changes in Vegetation during Secondary Tropical Forest Succession

NASA Astrophysics Data System (ADS)

Smith, A.; Marin-Spiotta, E.; Balser, T. C.

2012-12-01

Soil microorganisms regulate fundamental biochemical processes in plant litter decomposition and soil organic matter (SOM) transformations. In order to predict how disturbance affects belowground carbon storage, it is important to understand how the forest floor and soil microbial community respond to changes in land cover, and the consequences on SOM formation and stabilization. We are measuring microbial functional diversity and activity across a long-term successional chronosequence of secondary forests regrowing on abandoned pastures in the wet subtropical forest life zone of Puerto Rico. Here we report intra- and interannual data on soil and litter microbial community composition (via phospholipid fatty acid analysis, PLFA) and microbial activity (via extracellular enzyme activity) from active pastures, secondary forests aged 20, 30, 40, 70, and 90-years, and primary forests. Microbial community composition and extracellular enzyme activity differed significantly by season in these wet subtropical ecosystems, even though differences in mean monthly precipitation between the middle of the dry season (January) and the wet season (July) is only 30mm. Despite seasonal differences, there was a persistent strong effect of land cover type and forest successional stage, or age, on overall microbial community PLFA structure. Using principal component analysis, we found differences in microbial community structure among active pastures, early, and late successional forests. The separation of soil microbes into early and late successional communities parallels the clustering of tree composition data. While the successional patterns held across seasons, the importance of different microbial groups driving these patterns differed seasonally. Biomarkers for gram-positive and actinobacteria (i15:0 and 16:0 10Me) were associated with early (20, 30 & 40 year old) secondary forests in the dry season. These younger forest communities were identified by the biomarker for anaerobic gram-negative bacteria (c19:0) in the wet season, which suggests the presence of anaerobic microsites in these very clayey Oxisols. Enzymatic activity did not differ with succession but was highest in the dry season. We expect this may be due to decreased turnover of enzymes with low soil moisture. Interannual sampling has revealed a very rapid microbial response to changes in aboveground cover. Within a year following woody biomass encroachment, we detected a shift in the soil microbial community from a pasture-associated community to an early secondary forest community in one of our replicate pasture sites. This very rapid response in the belowground microbial community structure to changes in vegetation has not been strongly documented in the literature. This data supports a direct link between aboveground and belowground biotic community structures and highlights the importance of long-term repeated sampling of microbial communities in dynamic ecosystems. Our findings have implications for predicting rapid ecological responses to land-cover change.

Forensic analysis of the microbiome of phones and shoes

DOE PAGES

Lax, Simon; Hampton-Marcell, Jarrad T.; Gibbons, Sean M.; ...

2015-05-12

Background: Microbial interaction between human-associated objects and the environments we inhabit may have forensic implications, and the extent to which microbes are shared between individuals inhabiting the same space may be relevant to human health and disease transmission. In this study, two participants sampled the front and back of their cell phones, four different locations on the soles of their shoes, and the floor beneath them every waking hour over a 2-day period. A further 89 participants took individual samples of their shoes and phones at three different scientific conferences. Results: Samples taken from different surface types maintained significantly differentmore » microbial community structures. The impact of the floor microbial community on that of the shoe environments was strong and immediate, as evidenced by Procrustes analysis of shoe replicates and significant correlation between shoe and floor samples taken at the same time point. Supervised learning was highly effective at determining which participant had taken a given shoe or phone sample, and a Bayesian method was able to determine which participant had taken each shoe sample based entirely on its similarity to the floor samples. Both shoe and phone samples taken by conference participants clustered into distinct groups based on location, though much more so when an unweighted distance metric was used, suggesting sharing of low-abundance microbial taxa between individuals inhabiting the same space. In conclusion, correlations between microbial community sources and sinks allow for inference of the interactions between humans and their environment.« less

Forensic analysis of the microbiome of phones and shoes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lax, Simon; Hampton-Marcell, Jarrad T.; Gibbons, Sean M.

Background: Microbial interaction between human-associated objects and the environments we inhabit may have forensic implications, and the extent to which microbes are shared between individuals inhabiting the same space may be relevant to human health and disease transmission. In this study, two participants sampled the front and back of their cell phones, four different locations on the soles of their shoes, and the floor beneath them every waking hour over a 2-day period. A further 89 participants took individual samples of their shoes and phones at three different scientific conferences. Results: Samples taken from different surface types maintained significantly differentmore » microbial community structures. The impact of the floor microbial community on that of the shoe environments was strong and immediate, as evidenced by Procrustes analysis of shoe replicates and significant correlation between shoe and floor samples taken at the same time point. Supervised learning was highly effective at determining which participant had taken a given shoe or phone sample, and a Bayesian method was able to determine which participant had taken each shoe sample based entirely on its similarity to the floor samples. Both shoe and phone samples taken by conference participants clustered into distinct groups based on location, though much more so when an unweighted distance metric was used, suggesting sharing of low-abundance microbial taxa between individuals inhabiting the same space. In conclusion, correlations between microbial community sources and sinks allow for inference of the interactions between humans and their environment.« less

Soil microbial structure and function post-volcanic eruption on Kasatochi Island and regional controls on microbial heterogeneity

NASA Astrophysics Data System (ADS)

Zeglin, L. H.; Rainey, F.; Wang, B.; Waythomas, C.; Talbot, S. L.

2013-12-01

Microorganisms are abundant and diverse in soil and their integrated activity drives nutrient cycling on the ecosystem scale. Organic matter (OM) inputs from plant production support microbial heterotrophic life, and soil geochemistry constrains microbial activity and diversity. As vegetation and soil develops over time, these factors change, modifying the controls on microbial heterogeneity. Following a volcanic eruption, ash deposition creates new surfaces where both organismal growth and weathering processes are effectively reset. The trajectory of microbial community development following this disturbance depends on both organic matter accumulation and geochemical constraints. Also, dispersal of microbial cells to the sterile ash surface may determine microbial community succession. The Aleutian Islands (Alaska, USA) are a dynamic volcanic region, with active and dormant volcanoes distributed across the volcanic arc. One of these volcanoes, Kasatochi, erupted violently in August 2008, burying a small lush island in pryoclastic flows and fine ash. Since, plants and birds are beginning to re-establish on developing surfaces, including legacy soils exposed by rapid erosion of pyroclastic deposits, suggesting that recovery of microbial life is also proceeding. However, soil microbial diversity and function has not been examined on Kasatochi Island or across the greater Aleutian region. The project goal is to address these questions: How is soil microbial community structure and function developing following the Kasatochi eruption? What is the relative importance of dispersal, soil OM and geochemistry to microbial community heterogeneity across the Aleutians? Surface mineral soil (20-cm depth) samples were collected from Kasatochi Island in summer 2013, five years after the 2008 eruption, and from eight additional Aleutian islands. On Kasatochi, pryoclastic deposits, exposed legacy soils supporting regrowth of remnant dune wild-rye (Leymus mollis) and mesic meadow plant communities, and soils impacted by recovering seabird rookeries were sampled. On the other islands, soils supporting both Leymus and mesic meadow communities (representative of dominant vegetation types on Kasatochi pre-eruption) were sampled. For each soil category and island combination, three transects of soil cores at 10-cm, 50-cm, 1-m, 5-m and 10-m distance were collected; with distances between sites and islands included (up to >700 km), the range of geographic distance examined covers over 7 orders of magnitude. For all samples, data on fundamental geochemical and OM factors, bacterial and fungal biomass, activity and diversity (via QPCR, extracellular enzyme potential assays and T-RFLP) are being collected. Covariance analysis is being used to evaluate the scale of maximum spatial heterogeneity in microbial structure and function, and ordination and matrix correlation analyses are being used to identify the key environmental covariates with heterogeneity. We hypothesize that heterogeneity at small (cm) scales will reflect predominant geochemical controls, at medium (m) scales will reflect predominant OM (vegetation) controls and at large (km) scales will reflect dispersal-related controls on microbial community structure and function.

Biogeochemical and Microbial Variation across 5500 km of Antarctic Surface Sediment Implicates Organic Matter as a Driver of Benthic Community Structure

PubMed Central

Learman, Deric R.; Henson, Michael W.; Thrash, J. Cameron; Temperton, Ben; Brannock, Pamela M.; Santos, Scott R.; Mahon, Andrew R.; Halanych, Kenneth M.

2016-01-01

Western Antarctica, one of the fastest warming locations on Earth, is a unique environment that is underexplored with regards to biodiversity. Although pelagic microbial communities in the Southern Ocean and coastal Antarctic waters have been well-studied, there are fewer investigations of benthic communities and most have a focused geographic range. We sampled surface sediment from 24 sites across a 5500 km region of Western Antarctica (covering the Ross Sea to the Weddell Sea) to examine relationships between microbial communities and sediment geochemistry. Sequencing of the 16S and 18S rRNA genes showed microbial communities in sediments from the Antarctic Peninsula (AP) and Western Antarctica (WA), including the Ross, Amundsen, and Bellingshausen Seas, could be distinguished by correlations with organic matter concentrations and stable isotope fractionation (total organic carbon; TOC, total nitrogen; TN, and δ13C). Overall, samples from the AP were higher in nutrient content (TOC, TN, and NH4+) and communities in these samples had higher relative abundances of operational taxonomic units (OTUs) classified as the diatom, Chaetoceros, a marine cercozoan, and four OTUs classified as Flammeovirgaceae or Flavobacteria. As these OTUs were strongly correlated with TOC, the data suggests the diatoms could be a source of organic matter and the Bacteroidetes and cercozoan are grazers that consume the organic matter. Additionally, samples from WA have lower nutrients and were dominated by Thaumarchaeota, which could be related to their known ability to thrive as lithotrophs. This study documents the largest analysis of benthic microbial communities to date in the Southern Ocean, representing almost half the continental shoreline of Antarctica, and documents trophic interactions and coupling of pelagic and benthic communities. Our results indicate potential modifications in carbon sequestration processes related to change in community composition, identifying a prospective mechanism that links climate change to carbon availability. PMID:27047451

Microbial community changes as a possible factor controlling carbon sequestration in subsoil

NASA Astrophysics Data System (ADS)

Strücker, Juliane; Jörgensen, Rainer Georg

2015-04-01

In order to gain more knowledge regarding the microbial community and their influence on carbon sequestration in subsoil two depth profiles with different soil organic carbon (SOC) concentrations were sampled. The SOC concentrations developed naturally due to deposition and erosion. This experiment offers the opportunity to investigate to which extend natural SOC availability or other subsoil specific conditions influence the composition and the functional diversity of the microbial community and in return if there is any evidence how the microbial community composition affects carbon sequestration under these conditions. Soil samples were taken at four different depths on two neighbouring arable sites; one Kolluvisol with high SOC concentrations (8-12 g/kg) throughout the profile and one Luvisol with low SOC concentrations (3-4 g/kg) below 30 cm depth. The multi substrate induced respiration (MSIR) method was used to identify shifts in the functional diversity of the microbial community along the depth profiles. Amino sugars Muramic Acid and Glucosamine were measured as indicators for bacterial and fungal residues and ergosterol was determined as marker for saprotrophic fungi. The results of the discriminant analysis of the respiration values obtained from the 17 substrates used in the MSIR show that the substrate use in subsoil is different from the substrate use in topsoil. The amino sugar analysis and the ratio of ergosterol to microbial biomass C indicate that the fungal dominance of the microbial community decreases with depth. The results from this study support previous findings, which also observed decreasing fungal dominance with depth. Furthermore the MSIR approach shows clearly that not only the composition of the microbial community but also their substrate use changes with depth. Thus, a different microbial community with altered substrate requirements could be an important reason for enhanced carbon sequestration in subsoil. The fact that the MSIR was also able to differentiate between the two sites proves the assumption that resources are an important factor controlling the functional diversity of the microbial community, as abiotic factors are very similar for the two profiles, but the sites show a different depth gradient for SOC.

Structure, inter-annual recurrence, and global-scale connectivity of airborne microbial communities.

PubMed

Barberán, Albert; Henley, Jessica; Fierer, Noah; Casamayor, Emilio O

2014-07-15

Dust coming from the large deserts on Earth, such as the Sahara, can travel long distances and be dispersed over thousands of square kilometers. Remote dust deposition rates are increasing as a consequence of global change and may represent a mechanism for intercontinental microbial dispersal. Remote oligotrophic alpine lakes are particularly sensitive to dust inputs and can serve as sentinels of airborne microbial transport and the ecological consequences of accelerated intercontinental microbial migration. In this study, we applied high-throughput sequencing techniques (16S rRNA amplicon pyrosequencing) to characterize the microbial communities of atmospheric deposition collected in the Central Pyrenees (NE Spain) along three years. Additionally, bacteria from soils in Mauritania and from the air-water interface of high altitude Pyrenean lakes were also examined. Communities in aerosol deposition varied in time with a strong seasonal component of interannual similarity. Communities from the same season tended to resemble more each other than those from different seasons. Samples from disparate dates, in turn, slightly tended to have more dissimilar microbial assemblages (i.e., temporal distance decay), overall suggesting that atmospheric deposition may influence sink habitats in a temporally predictable manner. The three habitats examined (soil, deposition, and air-water interface) harbored distinct microbial communities, although airborne samples collected in the Pyrenees during Saharan dust outbreaks were closer to Mauritian soil samples than those collected during no Saharan dust episodes. The three habitats shared c.a. 1.4% of the total number of microbial sequences in the dataset. Such successful immigrants were spread in different bacterial classes. Overall, this study suggests that local and regional features may generate global trends in the dynamics and distribution of airborne microbial assemblages, and that the diversity of viable cells in the high atmosphere is likely higher than previously expected. Copyright © 2014 Elsevier B.V. All rights reserved.

Key factors controlling microbial community response after a fire: importance of severity and recurrence

NASA Astrophysics Data System (ADS)

Lombao, Alba; Barreiro, Ana; Martín, Ángela; Díaz-Raviña, Montserrat

2015-04-01

Microorganisms play an important role in forest ecosystems, especially after fire when vegetation is destroyed and soil is bared. Fire severity and recurrence might be one of main factors controlling the microbial response after a wildfire but information about this topic is scarce. The aim of this study is to evaluate the influence of fire regimen (recurrence and severity) on soil microbial community structure by means of the analysis of phospholipid fatty acid (PLFA). The study was performed with unburned and burned samples collected from the top layer of a soil affected by a high severity fire (Laza, NW Spain) heated under laboratory conditions at different temperatures (50°C, 75°C, 100°C, 125°C, 150°C, 175°C, 200°C, 300°C) to simulate different fire intensities; the process was repeated after further soil recovery (1 month incubation) to simulate fire recurrence. The soil temperature was measured with thermocouples and used to calculate the degree-hours as estimation of the amount of heat supplied to the samples (fire severity). The PLFA analysis was used to estimate total biomass and the biomass of specific groups (bacteria, fungi, gram-positive bacteria and gram-negative bacteria) as well as microbial community structure (PLFA pattern) and PLFA data were analyzed by means of principal component analysis (PCA) in order to identify main factors determining microbial community structure. The results of PCA, performed with the whole PLFA data set, showed that first component explained 35% of variation and clearly allow us to differentiate unburned samples from the corresponding burned samples, while the second component, explaining 16% of variation, separated samples according the heating temperature. A marked impact of fire regimen on soil microorganisms was detected; the microbial community response varied depending on previous history of soil heating and the magnitude of changes in the PLFA pattern was related to the amount of heat supplied to the samples. Thus, wildfire was the main factor determining the microbial community structure followed, in less extent, by fire severity. The total biomass and the biomass of specifics microbial groups decreased notably as consequence of wildfire and minor changes were detected due to soil heating under laboratory conditions. The results clearly showed the usefulness of PLFA pattern combined with PCA to study the relationships between fire regimen (recurrence and severity) and associated direct and indirect changes in soil microorganisms. The data also indicated that degree-hours methodology rather than temperature is adequate for evaluating the impact of soil heating on microbial communities. Keywords: wildfire, heating temperature, degree-hours, PLFA pattern, microbial biomass Acknowledgements. This study was supported by the Ministerio Español de Economía y Competitividad (AGL2012-39688-C02-01). A Lombao is recipient of FPU grant from Ministerio Español de Educación.

Comparison of bacterial communities from lava cave microbial mats to overlying surface soils from Lava Beds National Monument, USA

PubMed Central

Read, Kaitlyn J. H.; Hughes, Evan M.; Spilde, Michael N.

2017-01-01

Subsurface habitats harbor novel diversity that has received little attention until recently. Accessible subsurface habitats include lava caves around the world that often support extensive microbial mats on ceilings and walls in a range of colors. Little is known about lava cave microbial diversity and how these subsurface mats differ from microbial communities in overlying surface soils. To investigate these differences, we analyzed bacterial 16S rDNA from 454 pyrosequencing from three colors of microbial mats (tan, white, and yellow) from seven lava caves in Lava Beds National Monument, CA, USA, and compared them with surface soil overlying each cave. The same phyla were represented in both surface soils and cave microbial mats, but the overlap in shared OTUs (operational taxonomic unit) was only 11.2%. Number of entrances per cave and temperature contributed to observed differences in diversity. In terms of species richness, diversity by mat color differed, but not significantly. Actinobacteria dominated in all cave samples, with 39% from caves and 21% from surface soils. Proteobacteria made up 30% of phyla from caves and 36% from surface soil. Other major phyla in caves were Nitrospirae (7%) followed by minor phyla (7%), compared to surface soils with Bacteroidetes (8%) and minor phyla (8%). Many of the most abundant sequences could not be identified to genus, indicating a high degree of novelty. Surface soil samples had more OTUs and greater diversity indices than cave samples. Although surface soil microbes immigrate into underlying caves, the environment selects for microbes able to live in the cave habitats, resulting in very different cave microbial communities. This study is the first comprehensive comparison of bacterial communities in lava caves with the overlying soil community. PMID:28199330

Recently Deglaciated High-Altitude Soils of the Himalaya: Diverse Environments, Heterogenous Bacterial Communities and Long-Range Dust Inputs from the Upper Troposphere

PubMed Central

Stres, Blaz; Sul, Woo Jun; Murovec, Bostjan; Tiedje, James M.

2013-01-01

Background The Himalaya with its altitude and geographical position forms a barrier to atmospheric transport, which produces much aqueous-particle monsoon precipitation and makes it the largest continuous ice-covered area outside polar regions. There is a paucity of data on high-altitude microbial communities, their native environments and responses to environmental-spatial variables relative to seasonal and deglaciation events. Methodology/Principal Findings Soils were sampled along altitude transects from 5000 m to 6000 m to determine environmental, spatial and seasonal factors structuring bacterial communities characterized by 16 S rRNA gene deep sequencing. Dust traps and fresh-snow samples were used to assess dust abundance and viability, community structure and abundance of dust associated microbial communities. Significantly different habitats among the altitude-transect samples corresponded to both phylogenetically distant and closely-related communities at distances as short as 50 m showing high community spatial divergence. High within-group variability that was related to an order of magnitude higher dust deposition obscured seasonal and temporal rearrangements in microbial communities. Although dust particle and associated cell deposition rates were highly correlated, seasonal dust communities of bacteria were distinct and differed significantly from recipient soil communities. Analysis of closest relatives to dust OTUs, HYSPLIT back-calculation of airmass trajectories and small dust particle size (4–12 µm) suggested that the deposited dust and microbes came from distant continental, lacustrine and marine sources, e.g. Sahara, India, Caspian Sea and Tibetan plateau. Cyanobacteria represented less than 0.5% of microbial communities suggesting that the microbial communities benefitted from (co)deposited carbon which was reflected in the psychrotolerant nature of dust-particle associated bacteria. Conclusions/Significance The spatial, environmental and temporal complexity of the high-altitude soils of the Himalaya generates ongoing disturbance and colonization events that subject heterogeneous microniches to stochastic colonization by far away dust associated microbes and result in the observed spatially divergent bacterial communities. PMID:24086740

Experimental incubations elicit profound changes in community transcription in OMZ bacterioplankton.

PubMed

Stewart, Frank J; Dalsgaard, Tage; Young, Curtis R; Thamdrup, Bo; Revsbech, Niels Peter; Ulloa, Osvaldo; Canfield, Don E; Delong, Edward F

2012-01-01

Sequencing of microbial community RNA (metatranscriptome) is a useful approach for assessing gene expression in microorganisms from the natural environment. This method has revealed transcriptional patterns in situ, but can also be used to detect transcriptional cascades in microcosms following experimental perturbation. Unambiguously identifying differential transcription between control and experimental treatments requires constraining effects that are simply due to sampling and bottle enclosure. These effects remain largely uncharacterized for "challenging" microbial samples, such as those from anoxic regions that require special handling to maintain in situ conditions. Here, we demonstrate substantial changes in microbial transcription induced by sample collection and incubation in experimental bioreactors. Microbial communities were sampled from the water column of a marine oxygen minimum zone by a pump system that introduced minimal oxygen contamination and subsequently incubated in bioreactors under near in situ oxygen and temperature conditions. Relative to the source water, experimental samples became dominated by transcripts suggestive of cell stress, including chaperone, protease, and RNA degradation genes from diverse taxa, with strong representation from SAR11-like alphaproteobacteria. In tandem, transcripts matching facultative anaerobic gammaproteobacteria of the Alteromonadales (e.g., Colwellia) increased 4-13 fold up to 43% of coding transcripts, and encoded a diverse gene set suggestive of protein synthesis and cell growth. We interpret these patterns as taxon-specific responses to combined environmental changes in the bioreactors, including shifts in substrate or oxygen availability, and minor temperature and pressure changes during sampling with the pump system. Whether such changes confound analysis of transcriptional patterns may vary based on the design of the experiment, the taxonomic composition of the source community, and on the metabolic linkages between community members. These data highlight the impressive capacity for transcriptional changes within complex microbial communities, underscoring the need for caution when inferring in situ metabolism based on transcript abundances in experimental incubations.

Experimental Incubations Elicit Profound Changes in Community Transcription in OMZ Bacterioplankton

PubMed Central

Stewart, Frank J.; Dalsgaard, Tage; Young, Curtis R.; Thamdrup, Bo; Revsbech, Niels Peter; Ulloa, Osvaldo; Canfield, Don E.; DeLong, Edward F.

2012-01-01

Sequencing of microbial community RNA (metatranscriptome) is a useful approach for assessing gene expression in microorganisms from the natural environment. This method has revealed transcriptional patterns in situ, but can also be used to detect transcriptional cascades in microcosms following experimental perturbation. Unambiguously identifying differential transcription between control and experimental treatments requires constraining effects that are simply due to sampling and bottle enclosure. These effects remain largely uncharacterized for “challenging” microbial samples, such as those from anoxic regions that require special handling to maintain in situ conditions. Here, we demonstrate substantial changes in microbial transcription induced by sample collection and incubation in experimental bioreactors. Microbial communities were sampled from the water column of a marine oxygen minimum zone by a pump system that introduced minimal oxygen contamination and subsequently incubated in bioreactors under near in situ oxygen and temperature conditions. Relative to the source water, experimental samples became dominated by transcripts suggestive of cell stress, including chaperone, protease, and RNA degradation genes from diverse taxa, with strong representation from SAR11-like alphaproteobacteria. In tandem, transcripts matching facultative anaerobic gammaproteobacteria of the Alteromonadales (e.g., Colwellia) increased 4–13 fold up to 43% of coding transcripts, and encoded a diverse gene set suggestive of protein synthesis and cell growth. We interpret these patterns as taxon-specific responses to combined environmental changes in the bioreactors, including shifts in substrate or oxygen availability, and minor temperature and pressure changes during sampling with the pump system. Whether such changes confound analysis of transcriptional patterns may vary based on the design of the experiment, the taxonomic composition of the source community, and on the metabolic linkages between community members. These data highlight the impressive capacity for transcriptional changes within complex microbial communities, underscoring the need for caution when inferring in situ metabolism based on transcript abundances in experimental incubations. PMID:22615914

Long-term soil transplant simulating climate change with latitude significantly alters microbial temporal turnover.

PubMed

Liang, Yuting; Jiang, Yuji; Wang, Feng; Wen, Chongqing; Deng, Ye; Xue, Kai; Qin, Yujia; Yang, Yunfeng; Wu, Liyou; Zhou, Jizhong; Sun, Bo

2015-12-01

To understand soil microbial community stability and temporal turnover in response to climate change, a long-term soil transplant experiment was conducted in three agricultural experiment stations over large transects from a warm temperate zone (Fengqiu station in central China) to a subtropical zone (Yingtan station in southern China) and a cold temperate zone (Hailun station in northern China). Annual soil samples were collected from these three stations from 2005 to 2011, and microbial communities were analyzed by sequencing microbial 16S ribosomal RNA gene amplicons using Illumina MiSeq technology. Our results revealed a distinctly differential pattern of microbial communities in both northward and southward transplantations, along with an increase in microbial richness with climate cooling and a corresponding decrease with climate warming. The microbial succession rate was estimated by the slope (w value) of linear regression of a log-transformed microbial community similarity with time (time-decay relationship). Compared with the low turnover rate of microbial communities in situ (w=0.046, P<0.001), the succession rate at the community level was significantly higher in the northward transplant (w=0.058, P<0.001) and highest in the southward transplant (w=0.094, P<0.001). Climate warming lead to a faster succession rate of microbial communities as well as lower species richness and compositional changes compared with in situ and climate cooling, which may be related to the high metabolic rates and intense competition under higher temperature. This study provides new insights into the impacts of climate change on the fundamental temporal scaling of soil microbial communities and microbial phylogenetic biodiversity.

Inferring Intra-Community Microbial Interaction Patterns from Metagenomic Datasets Using Associative Rule Mining Techniques

PubMed Central

Mande, Sharmila S.

2016-01-01

The nature of inter-microbial metabolic interactions defines the stability of microbial communities residing in any ecological niche. Deciphering these interaction patterns is crucial for understanding the mode/mechanism(s) through which an individual microbial community transitions from one state to another (e.g. from a healthy to a diseased state). Statistical correlation techniques have been traditionally employed for mining microbial interaction patterns from taxonomic abundance data corresponding to a given microbial community. In spite of their efficiency, these correlation techniques can capture only 'pair-wise interactions'. Moreover, their emphasis on statistical significance can potentially result in missing out on several interactions that are relevant from a biological standpoint. This study explores the applicability of one of the earliest association rule mining algorithm i.e. the 'Apriori algorithm' for deriving 'microbial association rules' from the taxonomic profile of given microbial community. The classical Apriori approach derives association rules by analysing patterns of co-occurrence/co-exclusion between various '(subsets of) features/items' across various samples. Using real-world microbiome data, the efficiency/utility of this rule mining approach in deciphering multiple (biologically meaningful) association patterns between 'subsets/subgroups' of microbes (constituting microbiome samples) is demonstrated. As an example, association rules derived from publicly available gut microbiome datasets indicate an association between a group of microbes (Faecalibacterium, Dorea, and Blautia) that are known to have mutualistic metabolic associations among themselves. Application of the rule mining approach on gut microbiomes (sourced from the Human Microbiome Project) further indicated similar microbial association patterns in gut microbiomes irrespective of the gender of the subjects. A Linux implementation of the Association Rule Mining (ARM) software (customised for deriving 'microbial association rules' from microbiome data) is freely available for download from the following link: http://metagenomics.atc.tcs.com/arm. PMID:27124399

Inferring Intra-Community Microbial Interaction Patterns from Metagenomic Datasets Using Associative Rule Mining Techniques.

PubMed

Tandon, Disha; Haque, Mohammed Monzoorul; Mande, Sharmila S

2016-01-01

The nature of inter-microbial metabolic interactions defines the stability of microbial communities residing in any ecological niche. Deciphering these interaction patterns is crucial for understanding the mode/mechanism(s) through which an individual microbial community transitions from one state to another (e.g. from a healthy to a diseased state). Statistical correlation techniques have been traditionally employed for mining microbial interaction patterns from taxonomic abundance data corresponding to a given microbial community. In spite of their efficiency, these correlation techniques can capture only 'pair-wise interactions'. Moreover, their emphasis on statistical significance can potentially result in missing out on several interactions that are relevant from a biological standpoint. This study explores the applicability of one of the earliest association rule mining algorithm i.e. the 'Apriori algorithm' for deriving 'microbial association rules' from the taxonomic profile of given microbial community. The classical Apriori approach derives association rules by analysing patterns of co-occurrence/co-exclusion between various '(subsets of) features/items' across various samples. Using real-world microbiome data, the efficiency/utility of this rule mining approach in deciphering multiple (biologically meaningful) association patterns between 'subsets/subgroups' of microbes (constituting microbiome samples) is demonstrated. As an example, association rules derived from publicly available gut microbiome datasets indicate an association between a group of microbes (Faecalibacterium, Dorea, and Blautia) that are known to have mutualistic metabolic associations among themselves. Application of the rule mining approach on gut microbiomes (sourced from the Human Microbiome Project) further indicated similar microbial association patterns in gut microbiomes irrespective of the gender of the subjects. A Linux implementation of the Association Rule Mining (ARM) software (customised for deriving 'microbial association rules' from microbiome data) is freely available for download from the following link: http://metagenomics.atc.tcs.com/arm.

Similar soil microbial community structure across different environments after long-term succession: evidence from volcanoes of different ages.

PubMed

Xu, Shangqi; Zhang, Jianfeng; Luo, Shasha; Zhou, Xue; Shi, Shaohua; Tian, Chunjie

2018-06-08

Soil microbes play critical roles in global biogeochemical cycles, but their succession patterns across long temporal scales have rarely been studied. In this study, soil samples were collected from three volcanoes in Wudalianchi, northeastern China: Laoheishan (LH, approximately 240 years old), Dongjiaodebushan (DJ, 0.45-0.6 million years old), and Nangelaqiushan (NG, 0.8-1.3 million years old). For each volcano, both southern (S) and northern (N) slope aspects were sampled. Soil microbial communities were analyzed using phospholipid fatty acid analysis (PLFA). The results showed that soil properties and microbial biomass changed perceptibly among different volcanoes and different slope aspects. Almost all of the detected soil nutrient contents of LH were lowest, and total microbial biomass of LH was 40 and 36% lower than those of NG and DJ, respectively. LH was significantly different from NG and DJ in soil microbial community structure with a higher relative abundance of fungi and a lower relative abundance of actinomycetes and bacteria. However, for the two ancient volcanoes (NG and DJ), soil microbial community structures were highly similar among different ages and different slope aspects. No difference was detected in any of the measured microbial indices, including richness, evenness, Shannon's diversity, Simpson's diversity and the relative abundance of different microbial groups. The results indicated that while soil microbial biomass may change across different soil environments after long-term succession, soil microbial community structure can remain relatively stable. The results further indicated that soil microbes may show different successional patterns in different stages of succession. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spatial and seasonal variation in diversity and structure of microbial biofilms on marine plastics in Northern European waters.

PubMed

Oberbeckmann, Sonja; Loeder, Martin G J; Gerdts, Gunnar; Osborn, A Mark

2014-11-01

Plastic pollution is now recognised as a major threat to marine environments and marine biota. Recent research highlights that diverse microbial species are found to colonise plastic surfaces (the plastisphere) within marine waters. Here, we investigate how the structure and diversity of marine plastisphere microbial community vary with respect to season, location and plastic substrate type. We performed a 6-week exposure experiment with polyethylene terephthalate (PET) bottles in the North Sea (UK) as well as sea surface sampling of plastic polymers in Northern European waters. Scanning electron microscopy revealed diverse plastisphere communities comprising prokaryotic and eukaryotic microorganisms. Denaturing gradient gel electrophoresis (DGGE) and sequencing analysis revealed that plastisphere microbial communities on PET fragments varied both with season and location and comprised of bacteria belonging to Bacteroidetes, Proteobacteria, Cyanobacteria and members of the eukaryotes Bacillariophyceae and Phaeophyceae. Polymers sampled from the sea surface mainly comprised polyethylene, polystyrene and polypropylene particles. Variation within plastisphere communities on different polymer types was observed, but communities were primarily dominated by Cyanobacteria. This research reveals that the composition of plastisphere microbial communities in marine waters varies with season, geographical location and plastic substrate type. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Oral Samples as Non-Invasive Proxies for Assessing the Composition of the Rumen Microbial Community.

PubMed

Tapio, Ilma; Shingfield, Kevin J; McKain, Nest; Bonin, Aurélie; Fischer, Daniel; Bayat, Ali R; Vilkki, Johanna; Taberlet, Pierre; Snelling, Timothy J; Wallace, R John

2016-01-01

Microbial community analysis was carried out on ruminal digesta obtained directly via rumen fistula and buccal fluid, regurgitated digesta (bolus) and faeces of dairy cattle to assess if non-invasive samples could be used as proxies for ruminal digesta. Samples were collected from five cows receiving grass silage based diets containing no additional lipid or four different lipid supplements in a 5 x 5 Latin square design. Extracted DNA was analysed by qPCR and by sequencing 16S and 18S rRNA genes or the fungal ITS1 amplicons. Faeces contained few protozoa, and bacterial, fungal and archaeal communities were substantially different to ruminal digesta. Buccal and bolus samples gave much more similar profiles to ruminal digesta, although fewer archaea were detected in buccal and bolus samples. Bolus samples overall were most similar to ruminal samples. The differences between both buccal and bolus samples and ruminal digesta were consistent across all treatments. It can be concluded that either proxy sample type could be used as a predictor of the rumen microbial community, thereby enabling more convenient large-scale animal sampling for phenotyping and possible use in future animal breeding programs aimed at selecting cattle with a lower environmental footprint.

Oral Samples as Non-Invasive Proxies for Assessing the Composition of the Rumen Microbial Community

PubMed Central

Tapio, Ilma; Shingfield, Kevin J.; McKain, Nest; Bonin, Aurélie; Fischer, Daniel; Bayat, Ali R.; Vilkki, Johanna; Taberlet, Pierre; Snelling, Timothy J.; Wallace, R. John

2016-01-01

Microbial community analysis was carried out on ruminal digesta obtained directly via rumen fistula and buccal fluid, regurgitated digesta (bolus) and faeces of dairy cattle to assess if non-invasive samples could be used as proxies for ruminal digesta. Samples were collected from five cows receiving grass silage based diets containing no additional lipid or four different lipid supplements in a 5 x 5 Latin square design. Extracted DNA was analysed by qPCR and by sequencing 16S and 18S rRNA genes or the fungal ITS1 amplicons. Faeces contained few protozoa, and bacterial, fungal and archaeal communities were substantially different to ruminal digesta. Buccal and bolus samples gave much more similar profiles to ruminal digesta, although fewer archaea were detected in buccal and bolus samples. Bolus samples overall were most similar to ruminal samples. The differences between both buccal and bolus samples and ruminal digesta were consistent across all treatments. It can be concluded that either proxy sample type could be used as a predictor of the rumen microbial community, thereby enabling more convenient large-scale animal sampling for phenotyping and possible use in future animal breeding programs aimed at selecting cattle with a lower environmental footprint. PMID:26986467

Searching for signatures across microbial communities: Metagenomic analysis of soil samples from mangrove and other ecosystems.

PubMed

Imchen, Madangchanok; Kumavath, Ranjith; Barh, Debmalya; Azevedo, Vasco; Ghosh, Preetam; Viana, Marcus; Wattam, Alice R

2017-08-18

In this study, we categorize the microbial community in mangrove sediment samples from four different locations within a vast mangrove system in Kerala, India. We compared this data to other samples taken from the other known mangrove data, a tropical rainforest, and ocean sediment. An examination of the microbial communities from a large mangrove forest that stretches across southwestern India showed strong similarities across the higher taxonomic levels. When ocean sediment and a single isolate from a tropical rain forest were included in the analysis, a strong pattern emerged with Bacteria from the phylum Proteobacteria being the prominent taxon among the forest samples. The ocean samples were predominantly Archaea, with Euryarchaeota as the dominant phylum. Principal component and functional analyses grouped the samples isolated from forests, including those from disparate mangrove forests and the tropical rain forest, from the ocean. Our findings show similar patterns in samples were isolated from forests, and these were distinct from the ocean sediment isolates. The taxonomic structure was maintained to the level of class, and functional analysis of the genes present also displayed these similarities. Our report for the first time shows the richness of microbial diversity in the Kerala coast and its differences with tropical rain forest and ocean microbiome.

Adaptation of Aquatic Microbial Communities to Hg2+ Stress †

PubMed Central

Barkay, Tamar

1987-01-01

The mechanism of adaptation to Hg2+ in four aquatic habitats was studied by correlating microbially mediated Hg2+ volatilization with the adaptive state of the exposed communities. Community diversity, heterotrophic activity, and Hg2+ resistance measurements indicated that adaptation of all four communities was stimulated by preexposure to Hg2+. In saline water communities, adaptation was associated with rapid volatilization after an initial lag period. This mechanism, however, did not promote adaptation in a freshwater sample, in which Hg2+ was volatilized slowly, regardless of the resistance level of the microbial community. Distribution of the mer operon among representative colonies of the communities was not related to adaptation to Hg2+. Thus, although volatilization enabled some microbial communities to sustain their functions in Hg2+-stressed environments, it was not mediated by the genes that serve as a model system in molecular studies of bacterial resistance to mercurials. PMID:16347488

Environmental Filtering Process Has More Important Roles than Dispersal Limitation in Shaping Large-Scale Prokaryotic Beta Diversity Patterns of Grassland Soils.

PubMed

Cao, Peng; Wang, Jun-Tao; Hu, Hang-Wei; Zheng, Yuan-Ming; Ge, Yuan; Shen, Ju-Pei; He, Ji-Zheng

2016-07-01

Despite the utmost importance of microorganisms in maintaining ecosystem functioning and their ubiquitous distribution, our knowledge of the large-scale pattern of microbial diversity is limited, particularly in grassland soils. In this study, the microbial communities of 99 soil samples spanning over 3000 km across grassland ecosystems in northern China were investigated using high-throughput sequencing to analyze the beta diversity pattern and the underlying ecological processes. The microbial communities were dominated by Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, and Planctomycetes across all the soil samples. Spearman's correlation analysis indicated that climatic factors and soil pH were significantly correlated with the dominant microbial taxa, while soil microbial richness was positively linked to annual precipitation. The environmental divergence-dissimilarity relationship was significantly positive, suggesting the importance of environmental filtering processes in shaping soil microbial communities. Structural equation modeling found that the deterministic process played a more important role than the stochastic process on the pattern of soil microbial beta diversity, which supported the predictions of niche theory. Partial mantel test analysis have showed that the contribution of independent environmental variables has a significant effect on beta diversity, while independent spatial distance has no such relationship, confirming that the deterministic process was dominant in structuring soil microbial communities. Overall, environmental filtering process has more important roles than dispersal limitation in shaping microbial beta diversity patterns in the grassland soils.

A Stoichioproteomic Analysis of Samples from the Human Microbiome Project

PubMed Central

Vecchio-Pagan, Briana; Bewick, Sharon; Mainali, Kumar; Karig, David K.; Fagan, William F.

2017-01-01

Ecological stoichiometry (ES) uses organism-specific elemental content to explain differences in species life histories, species interactions, community organization, environmental constraints and even ecosystem function. Although ES has been successfully applied to a range of different organisms, most emphasis on microbial ecological stoichiometry focuses on lake, ocean, and soil communities. With the recent advances in human microbiome research, however, large amounts of data are being generated that describe differences in community composition across body sites and individuals. We suggest that ES may provide a framework for beginning to understand the structure, organization, and function of human microbial communities, including why certain organisms exist at certain locations, and how they interact with both the other microbes in their environment and their human host. As a first step, we undertake a stoichioproteomic analysis of microbial communities from different body sites. Specifically, we compare and contrast the elemental composition of microbial protein samples using annotated sequencing data from 690 gut, vaginal, oral, nares, and skin samples currently available through the Human Microbiome Project. Our results suggest significant differences in both the median and variance of the carbon, oxygen, nitrogen, and sulfur contents of microbial protein samples from different locations. For example, whereas proteins from vaginal sites are high in carbon, proteins from skin and nasal sites are high in nitrogen and oxygen. Meanwhile, proteins from stool (the gut) are particularly high in sulfur content. We interpret these differences in terms of the local environments at different human body sites, including atmospheric exposure and food intake rates. PMID:28769875

Radiochemically-Supported Microbial Communities: A Potential Mechanism for Biocolloid Production of Importance to Actinide Transport

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moser, Duane P.; Hamilton-Brehm, Scott D.; Fisher, Jenny C.

Due to the legacy of Cold War nuclear weapons testing, the Nevada National Security Site (NNSS, formerly known as the Nevada Test Site (NTS)) contains millions of Curies of radioactive contamination. Presented here is a summary of the results of the first comprehensive study of subsurface microbial communities of radioactive and nonradioactive aquifers at this site. To achieve the objectives of this project, cooperative actions between the Desert Research Institute (DRI), the Nevada Field Office of the National Nuclear Security Administration (NNSA), the Underground Test Area Activity (UGTA), and contractors such as Navarro-Interra (NI), were required. Ultimately, fluids from 17more » boreholes and two water-filled tunnels were sampled (sometimes on multiple occasions and from multiple depths) from the NNSS, the adjacent Nevada Test and Training Range (NTTR), and a reference hole in the Amargosa Valley near Death Valley. The sites sampled ranged from highly-radioactive nuclear device test cavities to uncontaminated perched and regional aquifers. Specific areas sampled included recharge, intermediate, and discharge zones of a 100,000-km2 internally-draining province, known as the Death Valley Regional Flow System (DVRFS), which encompasses the entirety of the NNSS/NTTR and surrounding areas. Specific geological features sampled included: West Pahute and Ranier Mesas (recharge zone), Yucca and Frenchman Flats (transitional zone), and the Western edge of the Amargosa Valley near Death Valley (discharge zone). The original overarching question underlying the proposal supporting this work was stated as: Can radiochemically-produced substrates support indigenous microbial communities and subsequently stimulate biocolloid formation that can affect radionuclides in NNSS subsurface nuclear test/detonation sites? Radioactive and non-radioactive groundwater samples were thus characterized for physical parameters, aqueous geochemistry, and microbial communities using both DNA- and cultivation-based tools in an effort to understand the drivers of microbial community structure (including radioactivity) and microbial interactions with select radionuclides and other factors across the range of habitats surveyed.« less

The Biogeography of Endorheic Soda Lakes in the Western United States

NASA Astrophysics Data System (ADS)

Stamps, B. W.; Petryshyn, V.; Johnson, H.; Berelson, W.; Nunn, H. S.; Stevenson, B. S.; Loyd, S. J.; Oremland, R. S.; Miller, L. G.; Rosen, M. R.; Corsetti, F. A.; Spear, J. R.

2016-12-01

Closed-basin (endorheic) soda lakes are of economic, social, and ecological importance. Shifts in global climate, which in turn affects local climate, significantly impact the distribution and diversity of microbial communities and lake ecologies. In California, the Mono Lake Basin (MLB) is especially fragile, as it has undergone a significant decline in lake level beginning in the early twentieth century due to both climatic effects and water diversion. The result is a lake with elevated salinity (60-90 g/L) and pH (9.8). The diversion of MLB water has created a unique lake environment dominated by a single macroeukaryote (Artemia monica) in which primary production is controlled at all depths by the microalgae Picocystis sp. In order to better understand the microbial diversity and functional potential of Mono Lake during an on-going drought and climatic upheaval, a combined geochemical, metagenomic, and metatranscriptomic study was undertaken. Members of The International GeoBiology course sampled the water column at multiple depths in the summer of 2016, during a large bloom of Picocystis. A mud spring from a volcanic island (Paoha) near the center of the lake was also sampled. The spring was recently submerged and interacts intermittently with Mono Lake, which may allow for mixing of microbial communities as lake levels fluctuate. Surface sediment samples were also taken from 7 m water depth. Finally, via SSU rRNA gene sequence analyses, the microbial communities of nearby soda lakes were compared in an attempt to place the Mono Lake community in the context of the overall regional biodiversity of endorheic soda lakes. Overall the microbial communities at Mono Lake were distinct both in the bacterial community composition and the abundance of Picocystis from those found at other sampled soda lakes or the surrounding rivers and springs. Our results reveal diverse microbial ecosystems at multiple lakes potentially at risk to continued climate change.

A fungal mock community control for amplicon sequencing experiments

USDA-ARS?s Scientific Manuscript database

Microbial ecology has been profoundly advanced by the ability to profile complex microbial communities by sequencing of marker genes amplified from environmental samples. However, inclusion of appropriate controls is vital to revealing the limitations and biases of this technique. “Mock community” s...

Microbial community analysis in rice paddy soils irrigated by acid mine drainage contaminated water.

PubMed

Sun, Min; Xiao, Tangfu; Ning, Zengping; Xiao, Enzong; Sun, Weimin

2015-03-01

Five rice paddy soils located in southwest China were selected for geochemical and microbial community analysis. These rice fields were irrigated with river water which was contaminated by Fe-S-rich acid mine drainage. Microbial communities were characterized by high-throughput sequencing, which showed 39 different phyla/groups in these samples. Among these phyla/groups, Proteobacteria was the most abundant phylum in all samples. Chloroflexi, Acidobacteria, Nitrospirae, and Bacteroidetes exhibited higher relative abundances than other phyla. A number of rare and candidate phyla were also detected. Moreover, canonical correspondence analysis suggested that pH, sulfate, and nitrate were significant factors that shaped the microbial community structure. In addition, a wide diversity of Fe- and S-related bacteria, such as GOUTA19, Shewanella, Geobacter, Desulfobacca, Thiobacillus, Desulfobacterium, and Anaeromyxobacter, might be responsible for biogeochemical Fe and S cycles in the tested rice paddy soils. Among the dominant genera, GOUTA19 and Shewanella were seldom detected in rice paddy soils.

Microbial community structures in high rate algae ponds for bioconversion of agricultural wastes from livestock industry for feed production.

PubMed

Mark Ibekwe, A; Murinda, Shelton E; Murry, Marcia A; Schwartz, Gregory; Lundquist, Trygve

2017-02-15

Dynamics of seasonal microbial community compositions in algae cultivation ponds are complex. However, there is very limited knowledge on bacterial communities that may play significant roles with algae in the bioconversion of manure nutrients to animal feed. In this study, water samples were collected during winter, spring, summer, and fall from the dairy lagoon effluent (DLE), high rate algae ponds (HRAP) that were fed with diluted DLE, and municipal waste water treatment plant (WWTP) effluent which was included as a comparison system for the analysis of total bacteria, Cyanobacteria, and microalgae communities using MiSeq Illumina sequencing targeting the 16S V4 rDNA region. The main objective was to examine dynamics in microbial community composition in the HRAP used for the production of algal biomass. DNA was extracted from the different sample types using three commercially available DNA extraction kits; MoBio Power water extraction kit, Zymo fungi/bacterial extraction kit, and MP Biomedicals FastDNA SPIN Kit. Permutational analysis of variance (PERMANOVA) using distance matrices on each variable showed significant differences (P=0.001) in beta-diversity based on sample source. Environmental variables such as hydraulic retention time (HRT; P<0.031), total N (P<0.002), total inorganic N (P<0.002), total P (P<0.002), alkalinity (P<0.002), pH (P<0.022), total suspended solid (TSS; P<0.003), and volatile suspended solids (VSS; P<0.002) significantly affected microbial communities in DLE, HRAP, and WWTP. Of the operational taxonomic units (OTUs) identified to phyla level, the dominant classes of bacteria identified were: Cyanobacteria, Alpha-, Beta-, Gamma-, Epsilon-, and Delta-proteobacteria, Bacteroidetes, Firmicutes, and Planctomycetes. Our data suggest that microbial communities were significantly affected in HRAP by different environmental variables, and care must be taken in extraction procedures when evaluating specific groups of microbial communities for specific functions. Published by Elsevier B.V.

Microbial stratification and microbially catalyzed processes along a hypersaline chemocline

NASA Astrophysics Data System (ADS)

Hyde, A.; Joye, S. B.; Teske, A.

2017-12-01

Orca Basin is the largest deep hypersaline anoxic basin in the world, covering over 400 km2. Located at the bottom of the Gulf of Mexico, this body of water reaches depths of 200 meters and is 8 times denser (and more saline) than the overlying seawater. The sharp pycnocline prevents any significant vertical mixing and serves as a particle trap for sinking organic matter. These rapid changes in salinity, oxygen, organic matter, and other geochemical parameters present unique conditions for the microbial communities present. We collected samples in 10m intervals throughout the chemocline. After filtering the water, we used high-throughput bacterial and archaeal 16S rRNA gene sequencing to characterize the changing microbial community along the Orca Basin chemocline. The results reveal a dominance of microbial taxa whose biogeochemical function is entirely unknown. We then used metagenomic sequencing and reconstructed genomes for select samples, revealing the potential dominant metabolic processes in the Orca Basin chemocline. Understanding how these unique geochemical conditions shape microbial communities and metabolic capabilities will have implications for the ocean's biogeochemical cycles and the consequences of expanding oxygen minimum zones.

Metagenomics Reveals the Influence of Land Use and Rain on the Benthic Microbial Communities in a Tropical Urban Waterway

PubMed Central

2018-01-01

ABSTRACT Growing demands for potable water have led to extensive reliance on waterways in tropical megacities. Attempts to manage these waterways in an environmentally sustainable way generally lack an understanding of microbial processes and how they are influenced by urban factors, such as land use and rain. Here, we describe the composition and functional potential of benthic microbial communities from an urban waterway network and analyze the effects of land use and rain perturbations on these communities. With a sequence depth of 3 billion reads from 48 samples, these metagenomes represent nearly full coverage of microbial communities. The predominant taxa in these waterways were Nitrospira and Coleofasciculus, indicating the presence of nitrogen and carbon fixation in this system. Gene functions from carbohydrate, protein, and nucleic acid metabolism suggest the presence of primary and secondary productivity in such nutrient-deficient systems. Comparison of microbial communities by land use type and rain showed that while there are significant differences in microbial communities in land use, differences due to rain perturbations were rain event specific. The more diverse microbial communities in the residential areas featured a higher abundance of reads assigned to genes related to community competition. However, the less diverse communities from industrial areas showed a higher abundance of reads assigned to specialized functions such as organic remediation. Finally, our study demonstrates that microbially diverse populations in well-managed waterways, where contaminant levels are within defined limits, are comparable to those in other relatively undisturbed freshwater systems. IMPORTANCE Unravelling the microbial metagenomes of urban waterway sediments suggest that well-managed urban waterways have the potential to support diverse sedimentary microbial communities, similar to those of undisturbed natural freshwaters. Despite the fact that these urban waterways are well managed, our study shows that environmental pressures from land use and rain perturbations play a role in shaping the structure and functions of microbial communities in these waterways. We propose that although pulsed disturbances, such as rain perturbations, influence microbial communities, press disturbances, including land usage history, have a long-term and stronger influence on microbial communities. Our study found that the functions of microbial communities were less affected by environmental factors than the structure of microbial communities was, indicating that core microbial functions largely remain conserved in challenging environments. PMID:29896568

Metagenomics Reveals the Influence of Land Use and Rain on the Benthic Microbial Communities in a Tropical Urban Waterway.

PubMed

Saxena, Gourvendu; Mitra, Suparna; Marzinelli, Ezequiel M; Xie, Chao; Wei, Toh Jun; Steinberg, Peter D; Williams, Rohan B H; Kjelleberg, Staffan; Lauro, Federico M; Swarup, Sanjay

2018-01-01

Growing demands for potable water have led to extensive reliance on waterways in tropical megacities. Attempts to manage these waterways in an environmentally sustainable way generally lack an understanding of microbial processes and how they are influenced by urban factors, such as land use and rain. Here, we describe the composition and functional potential of benthic microbial communities from an urban waterway network and analyze the effects of land use and rain perturbations on these communities. With a sequence depth of 3 billion reads from 48 samples, these metagenomes represent nearly full coverage of microbial communities. The predominant taxa in these waterways were Nitrospira and Coleofasciculus , indicating the presence of nitrogen and carbon fixation in this system. Gene functions from carbohydrate, protein, and nucleic acid metabolism suggest the presence of primary and secondary productivity in such nutrient-deficient systems. Comparison of microbial communities by land use type and rain showed that while there are significant differences in microbial communities in land use, differences due to rain perturbations were rain event specific. The more diverse microbial communities in the residential areas featured a higher abundance of reads assigned to genes related to community competition. However, the less diverse communities from industrial areas showed a higher abundance of reads assigned to specialized functions such as organic remediation. Finally, our study demonstrates that microbially diverse populations in well-managed waterways, where contaminant levels are within defined limits, are comparable to those in other relatively undisturbed freshwater systems. IMPORTANCE Unravelling the microbial metagenomes of urban waterway sediments suggest that well-managed urban waterways have the potential to support diverse sedimentary microbial communities, similar to those of undisturbed natural freshwaters. Despite the fact that these urban waterways are well managed, our study shows that environmental pressures from land use and rain perturbations play a role in shaping the structure and functions of microbial communities in these waterways. We propose that although pulsed disturbances, such as rain perturbations, influence microbial communities, press disturbances, including land usage history, have a long-term and stronger influence on microbial communities. Our study found that the functions of microbial communities were less affected by environmental factors than the structure of microbial communities was, indicating that core microbial functions largely remain conserved in challenging environments.

Impacts of Sampling and Handling Procedures on DNA- and RNA-based Microbial Characterization and Quantification of Groundwater and Saturated Soil

DTIC Science & Technology

2012-07-01

use of molecular biological techniques (MBTs) has allowed microbial ecologists and environmental engineers to determine microbial community...metabolic genes). The most common approaches used in bioremediation research are those based on the polymerase chain reaction (PCR) amplification of... bioremediation . Because of its sensitivity compared to direct hybridization/probing, PCR is increasingly used to analyze groundwater samples and soil samples

Microbial Response to High Temperature Hydrothermal Forcing: AISICS Vent (Lucky Strike, 37°N, MAR) and Prokaryote Community as Example.

NASA Astrophysics Data System (ADS)

Henri, P. A.; Rommevaux, C.; Chavagnac, V.; Degboe, J.; Destrigneville, C.; Boulart, C.; Lesongeur, F.; Castillo, A.; Goodfroy, A.

2015-12-01

To study the hydrothermal forcing on microbial colonization, and impacts on the oceanic crust alteration, an integrated study was led at the Tour Eiffel hydrothermal site (Lucky Strike hydrothermal field, 37°N, MAR). We benefited from an annual survey between 2009 and 2011 of temperatures, along with sampling of focused and diffused fluids for chemical analysis, and chimney sampling and samples from microbial colonization experiments analyzed for prokaryotic composition and rock alteration study. The chemical composition of the fluids show an important increase in the CO2 concentration at the Eiffel Tower site between 2009 and 2010 followed by a decrease between 2010 and 2011. In 2011, several fluid samples show an important depletion in Si, suggesting that some Si was removed by interaction with the stockwork before emission. Our observations, regarding the previous studies of chemical fluid affected by a magmatic event lead us to suppose that a magmatic/tectonic event occurred under the Lucky Strike hydrothermal field between 2009 and 2010. The results of the prokaryotic communities' analysis show that a shift occurred in the dominant microbial metabolisms present in the colonizer retrieved in 2010 and the one retrieved in 2011. Archaeal communities shifted from chemolithoautotropic sulfite/thiosulfate reducers-dominated in 2010 to ammonia oxidizers-dominated in 2011. The bacterial communities also undergo a shift, from a community with diversified metabolisms in 2010 to a community strongly dominated by chemolithoautotrophic sulfide or hydrogen oxidation in 2011. Moreover, in terms of ecological preferendum, the Archaeal communities shifted from thermophilic-dominated to mesophilic-dominated. The present study underline the influence of modifications in gases compositions of hydrothermal fluids subsequently to a degassing of the magma chamber and their impact on the microbial communities living in the vicinity of hydrothermal vents at the Eiffel Tower site.

Biotic and Abiotic Properties Mediating Plant Diversity Effects on Soil Microbial Communities in an Experimental Grassland

PubMed Central

Lange, Markus; Habekost, Maike; Eisenhauer, Nico; Roscher, Christiane; Bessler, Holger; Engels, Christof; Oelmann, Yvonne; Scheu, Stefan; Wilcke, Wolfgang; Schulze, Ernst-Detlef; Gleixner, Gerd

2014-01-01

Plant diversity drives changes in the soil microbial community which may result in alterations in ecosystem functions. However, the governing factors between the composition of soil microbial communities and plant diversity are not well understood. We investigated the impact of plant diversity (plant species richness and functional group richness) and plant functional group identity on soil microbial biomass and soil microbial community structure in experimental grassland ecosystems. Total microbial biomass and community structure were determined by phospholipid fatty acid (PLFA) analysis. The diversity gradient covered 1, 2, 4, 8, 16 and 60 plant species and 1, 2, 3 and 4 plant functional groups (grasses, legumes, small herbs and tall herbs). In May 2007, soil samples were taken from experimental plots and from nearby fields and meadows. Beside soil texture, plant species richness was the main driver of soil microbial biomass. Structural equation modeling revealed that the positive plant diversity effect was mainly mediated by higher leaf area index resulting in higher soil moisture in the top soil layer. The fungal-to-bacterial biomass ratio was positively affected by plant functional group richness and negatively by the presence of legumes. Bacteria were more closely related to abiotic differences caused by plant diversity, while fungi were more affected by plant-derived organic matter inputs. We found diverse plant communities promoted faster transition of soil microbial communities typical for arable land towards grassland communities. Although some mechanisms underlying the plant diversity effect on soil microorganisms could be identified, future studies have to determine plant traits shaping soil microbial community structure. We suspect differences in root traits among different plant communities, such as root turnover rates and chemical composition of root exudates, to structure soil microbial communities. PMID:24816860

Impacts of chemical gradients on microbial community structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E.

Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the ‘redox tower’. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobicmore » and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems.« less

Impacts of chemical gradients on microbial community structure

DOE PAGES

Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E.; ...

2017-01-17

Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the ‘redox tower’. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobicmore » and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems.« less

Relating belowground microbial composition to the taxonomic, phylogenetic, and functional trait distributions of trees in a tropical forest.

PubMed

Barberán, Albert; McGuire, Krista L; Wolf, Jeffrey A; Jones, F Andrew; Wright, Stuart Joseph; Turner, Benjamin L; Essene, Adam; Hubbell, Stephen P; Faircloth, Brant C; Fierer, Noah

2015-12-01

The complexities of the relationships between plant and soil microbial communities remain unresolved. We determined the associations between plant aboveground and belowground (root) distributions and the communities of soil fungi and bacteria found across a diverse tropical forest plot. Soil microbial community composition was correlated with the taxonomic and phylogenetic structure of the aboveground plant assemblages even after controlling for differences in soil characteristics, but these relationships were stronger for fungi than for bacteria. In contrast to expectations, the species composition of roots in our soil core samples was a poor predictor of microbial community composition perhaps due to the patchy, ephemeral, and highly overlapping nature of fine root distributions. Our ability to predict soil microbial composition was not improved by incorporating information on plant functional traits suggesting that the most commonly measured plant traits are not particularly useful for predicting the plot-level variability in belowground microbial communities. © 2015 John Wiley & Sons Ltd/CNRS.

Impacts of chemical gradients on microbial community structure

PubMed Central

Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E; Kattelmann, Ines; Sharma, Ritin; Hamann, Emmo; Hargesheimer, Theresa; Kraft, Beate; Lenk, Sabine; Geelhoed, Jeanine S; Hettich, Robert L; Strous, Marc

2017-01-01

Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the ‘redox tower'. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobic and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems. PMID:28094795

Impacts of chemical gradients on microbial community structure.

PubMed

Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E; Kattelmann, Ines; Sharma, Ritin; Hamann, Emmo; Hargesheimer, Theresa; Kraft, Beate; Lenk, Sabine; Geelhoed, Jeanine S; Hettich, Robert L; Strous, Marc

2017-04-01

Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the 'redox tower'. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobic and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems.

Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities

PubMed Central

Kittelmann, Sandra; Seedorf, Henning; Walters, William A.; Clemente, Jose C.; Knight, Rob; Gordon, Jeffrey I.; Janssen, Peter H.

2013-01-01

Ruminants rely on a complex rumen microbial community to convert dietary plant material to energy-yielding products. Here we developed a method to simultaneously analyze the community's bacterial and archaeal 16S rRNA genes, ciliate 18S rRNA genes and anaerobic fungal internal transcribed spacer 1 genes using 12 DNA samples derived from 11 different rumen samples from three host species (Ovis aries, Bos taurus, Cervus elephas) and multiplex 454 Titanium pyrosequencing. We show that the mixing ratio of the group-specific DNA templates before emulsion PCR is crucial to compensate for differences in amplicon length. This method, in contrast to using a non-specific universal primer pair, avoids sequencing non-targeted DNA, such as plant- or endophyte-derived rRNA genes, and allows increased or decreased levels of community structure resolution for each microbial group as needed. Communities analyzed with different primers always grouped by sample origin rather than by the primers used. However, primer choice had a greater impact on apparent archaeal community structure than on bacterial community structure, and biases for certain methanogen groups were detected. Co-occurrence analysis of microbial taxa from all three domains of life suggested strong within- and between-domain correlations between different groups of microorganisms within the rumen. The approach used to simultaneously characterize bacterial, archaeal and eukaryotic components of a microbiota should be applicable to other communities occupying diverse habitats. PMID:23408926

Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities.

PubMed

Kittelmann, Sandra; Seedorf, Henning; Walters, William A; Clemente, Jose C; Knight, Rob; Gordon, Jeffrey I; Janssen, Peter H

2013-01-01

Ruminants rely on a complex rumen microbial community to convert dietary plant material to energy-yielding products. Here we developed a method to simultaneously analyze the community's bacterial and archaeal 16S rRNA genes, ciliate 18S rRNA genes and anaerobic fungal internal transcribed spacer 1 genes using 12 DNA samples derived from 11 different rumen samples from three host species (Ovis aries, Bos taurus, Cervus elephas) and multiplex 454 Titanium pyrosequencing. We show that the mixing ratio of the group-specific DNA templates before emulsion PCR is crucial to compensate for differences in amplicon length. This method, in contrast to using a non-specific universal primer pair, avoids sequencing non-targeted DNA, such as plant- or endophyte-derived rRNA genes, and allows increased or decreased levels of community structure resolution for each microbial group as needed. Communities analyzed with different primers always grouped by sample origin rather than by the primers used. However, primer choice had a greater impact on apparent archaeal community structure than on bacterial community structure, and biases for certain methanogen groups were detected. Co-occurrence analysis of microbial taxa from all three domains of life suggested strong within- and between-domain correlations between different groups of microorganisms within the rumen. The approach used to simultaneously characterize bacterial, archaeal and eukaryotic components of a microbiota should be applicable to other communities occupying diverse habitats.

Successional and seasonal variations in soil and litter microbial community structure and function during tropical postagricultural forest regeneration: a multiyear study.

PubMed

Smith, A Peyton; Marín-Spiotta, Erika; Balser, Teri

2015-09-01

Soil microorganisms regulate fundamental biochemical processes in plant litter decomposition and soil organic matter (SOM) transformations. Understanding how microbial communities respond to changes in vegetation is critical for improving predictions of how land-cover change affects belowground carbon storage and nutrient availability. We measured intra- and interannual variability in soil and forest litter microbial community composition and activity via phospholipid fatty acid analysis (PLFA) and extracellular enzyme activity across a well-replicated, long-term chronosequence of secondary forests growing on abandoned pastures in the wet subtropical forest life zone of Puerto Rico. Microbial community PLFA structure differed between young secondary forests and older secondary and primary forests, following successional shifts in tree species composition. These successional patterns held across seasons, but the microbial groups driving these patterns differed over time. Microbial community composition from the forest litter differed greatly from those in the soil, but did not show the same successional trends. Extracellular enzyme activity did not differ with forest succession, but varied by season with greater rates of potential activity in the dry seasons. We found few robust significant relationships among microbial community parameters and soil pH, moisture, carbon, and nitrogen concentrations. Observed inter- and intrannual variability in microbial community structure and activity reveal the importance of a multiple, temporal sampling strategy when investigating microbial community dynamics with land-use change. Successional control over microbial composition with forest recovery suggests strong links between above and belowground communities. © 2015 John Wiley & Sons Ltd.

Effects of forest management practices in temperate beech forests on bacterial and fungal communities involved in leaf litter degradation.

PubMed

Purahong, Witoon; Kapturska, Danuta; Pecyna, Marek J; Jariyavidyanont, Katalee; Kaunzner, Jennifer; Juncheed, Kantida; Uengwetwanit, Tanaporn; Rudloff, Renate; Schulz, Elke; Hofrichter, Martin; Schloter, Michael; Krüger, Dirk; Buscot, François

2015-05-01

Forest management practices (FMPs) significantly influence important ecological processes and services in Central European forests, such as leaf litter decomposition and nutrient cycling. Changes in leaf litter diversity, and thus, its quality as well as microbial community structure and function induced by different FMPs were hypothesized to be the main drivers causing shifts in decomposition rates and nutrient release in managed forests. In a litterbag experiment lasting 473 days, we aimed to investigate the effects of FMPs (even-aged timber management, selective logging and unmanaged) on bacterial and fungal communities involved in leaf litter degradation over time. Our results showed that microbial communities in leaf litter were strongly influenced by both FMPs and sampling date. The results from nonmetric multidimensional scaling (NMDS) ordination revealed distinct patterns of bacterial and fungal successions over time in leaf litter. We demonstrated that FMPs and sampling dates can influence a range of factors, including leaf litter quality, microbial macronutrients, and pH, which significantly correlate with microbial community successions.

Microplastic-associated bacterial assemblages in the intertidal zone of the Yangtze Estuary.

PubMed

Jiang, Peilin; Zhao, Shiye; Zhu, Lixin; Li, Daoji

2018-05-15

Plastic trash is common in oceans. Terrestrial and marine ecosystem interactions occur in the intertidal zone where accumulation of plastic frequently occurs. However, knowledge of the plastic-associated microbial community (the plastisphere) in the intertidal zone is scanty. We used high-throughput sequencing to profile the bacterial communities attached to microplastic samples from intertidal locations around the Yangtze estuary in China. The structure and composition of plastisphere communities varied significantly among the locations. We found the taxonomic composition on microplastic samples was related to their sedimentary and aquatic origins. Correlation network analysis was used to identify keystone bacterial genera (e.g. Rhodobacterales, Sphingomonadales and Rhizobiales), which represented important microbial associations within the plastisphere community. Other species (i.e. potential pathogens) were considered as hitchhikers in the plastic attached microbial communities. Metabolic pathway analysis suggested adaptations of these bacterial assemblages to the plastic surface-colonization lifestyle. These adaptations included reduced "cell motility" and greater "xenobiotics biodegradation and metabolism." The findings illustrate the diverse microbial assemblages that occur on microplastic and increase our understanding of plastisphere ecology. Copyright © 2017 Elsevier B.V. All rights reserved.

Aerobic microbial taxa dominate deep subsurface cores from the Alberta oil sands.

PubMed

Ridley, Christina M; Voordouw, Gerrit

2018-06-01

Little is known about the microbial ecology of the subsurface oil sands in Northern Alberta, Canada. Biodegradation of low molecular weight hydrocarbons by indigenous microbes has enriched high molecular weight hydrocarbons, resulting in highly viscous bitumen. This extreme subsurface environment is further characterized by low nutrient availability and limited access to water, thus resulting in low microbial biomass. Improved DNA isolation protocols and increasingly sensitive sequencing methods have allowed an in-depth investigation of the microbial ecology of this unique subsurface environmental niche. Community analysis was performed on core samples (n = 62) that were retrieved from two adjacent sites located in the Athabasca Oil Sands at depths from 220 to 320 m below the surface. Microbial communities were dominated by aerobic taxa, including Pseudomonas and Acinetobacter. Only one core sample microbial community was dominated by anaerobic taxa, including the methanogen Methanoculleus, as well as Desulfomicrobium and Thauera. Although the temperature of the bitumen-containing subsurface is low (8°C), two core samples had high fractions of the potentially thermophilic taxon, Thermus. Predominance of aerobic taxa in the subsurface suggests the potential for in situ aerobic hydrocarbon degradation; however, more studies are required to determine the functional role of these taxa within this unique environment.

Influence of heavy metals and PCBs pollution on the enzyme activity and microbial community of paddy soils around an e-waste recycling workshop.

PubMed

Tang, Xianjin; Hashmi, Muhammad Z; Long, Dongyan; Chen, Litao; Khan, Muhammad I; Shen, Chaofeng

2014-03-14

Due to the emerging environmental issues related to e-waste there is concern about the quality of paddy soils near e-waste workshops. The levels of heavy metals and PCBs and their influence on the enzyme activity and microbial community of paddy soils obtained from the immediate vicinity of an e-waste workshop were investigated in the present study. The results indicated that the heavy metal and PCB pollution did not differ significantly with an increase of the sampling point distances (5 to 30 m). The concentration of Cd (2.16 mg·kg-1) and Cu (69.2 mg·kg-1) were higher, and the PCB pollution was also serious, ranging from 4.9 to 21.6 μg·kg-1. The highest enzyme activity was found for urease compared to phosphatase and catalase, and a fluctuating trend in soil enzyme activity was observed in soils from different sampling sites. The microbial analysis revealed that there was no apparent correlation between the microbial community and the pollutants. However, a slight influence for soil microbial communities could be found based on DGGE, the Shannon index and PCA analysis. The present study suggests that the contamination stress of heavy metals and PCBs might have a slight influence on microbial activity in paddy soils. This study provides the baseline data for enzyme activities and microbial communities in paddy soil under the influence of mixed contamination.

Influence of Heavy Metals and PCBs Pollution on the Enzyme Activity and Microbial Community of Paddy Soils around an E-Waste Recycling Workshop

PubMed Central

Tang, Xianjin; Hashmi, Muhammad Z.; Long, Dongyan; Chen, Litao; Khan, Muhammad I.; Shen, Chaofeng

2014-01-01

Due to the emerging environmental issues related to e-waste there is concern about the quality of paddy soils near e-waste workshops. The levels of heavy metals and PCBs and their influence on the enzyme activity and microbial community of paddy soils obtained from the immediate vicinity of an e-waste workshop were investigated in the present study. The results indicated that the heavy metal and PCB pollution did not differ significantly with an increase of the sampling point distances (5 to 30 m). The concentration of Cd (2.16 mg·kg−1) and Cu (69.2 mg·kg−1) were higher, and the PCB pollution was also serious, ranging from 4.9 to 21.6 μg·kg−1. The highest enzyme activity was found for urease compared to phosphatase and catalase, and a fluctuating trend in soil enzyme activity was observed in soils from different sampling sites. The microbial analysis revealed that there was no apparent correlation between the microbial community and the pollutants. However, a slight influence for soil microbial communities could be found based on DGGE, the Shannon index and PCA analysis. The present study suggests that the contamination stress of heavy metals and PCBs might have a slight influence on microbial activity in paddy soils. This study provides the baseline data for enzyme activities and microbial communities in paddy soil under the influence of mixed contamination. PMID:24637907

Microbial community composition and trophic role along a marked salinity gradient in Laguna Puilar, Salar de Atacama, Chile.

PubMed

Dorador, Cristina; Fink, Patrick; Hengst, Martha; Icaza, Gonzalo; Villalobos, Alvaro S; Vejar, Drina; Meneses, Daniela; Zadjelovic, Vinko; Burmann, Lisa; Moelzner, Jana; Harrod, Chris

2018-05-09

The geological, hydrological and microbiological features of the Salar de Atacama, the most extensive evaporitic sedimentary basin in the Atacama Desert of northern Chile, have been extensively studied. In contrast, relatively little attention has been paid to the composition and roles of microbial communities in hypersaline lakes which are a unique feature in the Salar. In the present study biochemical, chemical and molecular biological tools were used to determine the composition and roles of microbial communities in water, microbial mats and sediments along a marked salinity gradient in Laguna Puilar which is located in the "Los Flamencos" National Reserve. The bacterial communities at the sampling sites were dominated by members of the phyla Bacteroidetes, Chloroflexi, Cyanobacteria and Proteobacteria. Stable isotope and fatty acid analyses revealed marked variability in the composition of microbial mats at different sampling sites both horizontally (at different sites) and vertically (in the different layers). The Laguna Puilar was shown to be a microbially dominated ecosystem in which more than 60% of the fatty acids at particular sites are of bacterial origin. Our pioneering studies also suggest that the energy budgets of avian consumers (three flamingo species) and dominant invertebrates (amphipods and gastropods) use minerals as a source of energy and nutrients. Overall, the results of this study support the view that the Salar de Atacama is a heterogeneous and fragile ecosystem where small changes in environmental conditions may alter the balance of microbial communities with possible consequences at different trophic levels.

PhyloChip™ microarray comparison of sampling methods used for coral microbial ecology

USGS Publications Warehouse

Kellogg, Christina A.; Piceno, Yvette M.; Tom, Lauren M.; DeSantis, Todd Z.; Zawada, David G.; Andersen, Gary L.

2012-01-01

Interest in coral microbial ecology has been increasing steadily over the last decade, yet standardized methods of sample collection still have not been defined. Two methods were compared for their ability to sample coral-associated microbial communities: tissue punches and foam swabs, the latter being less invasive and preferred by reef managers. Four colonies of star coral, Montastraea annularis, were sampled in the Dry Tortugas National Park (two healthy and two with white plague disease). The PhyloChip™ G3 microarray was used to assess microbial community structure of amplified 16S rRNA gene sequences. Samples clustered based on methodology rather than coral colony. Punch samples from healthy and diseased corals were distinct. All swab samples clustered closely together with the seawater control and did not group according to the health state of the corals. Although more microbial taxa were detected by the swab method, there is a much larger overlap between the water control and swab samples than punch samples, suggesting some of the additional diversity is due to contamination from water absorbed by the swab. While swabs are useful for noninvasive studies of the coral surface mucus layer, these results show that they are not optimal for studies of coral disease.

PhyloChip™ microarray comparison of sampling methods used for coral microbial ecology.

PubMed

Kellogg, Christina A; Piceno, Yvette M; Tom, Lauren M; DeSantis, Todd Z; Zawada, David G; Andersen, Gary L

2012-01-01

Interest in coral microbial ecology has been increasing steadily over the last decade, yet standardized methods of sample collection still have not been defined. Two methods were compared for their ability to sample coral-associated microbial communities: tissue punches and foam swabs, the latter being less invasive and preferred by reef managers. Four colonies of star coral, Montastraea annularis, were sampled in the Dry Tortugas National Park (two healthy and two with white plague disease). The PhyloChip™ G3 microarray was used to assess microbial community structure of amplified 16S rRNA gene sequences. Samples clustered based on methodology rather than coral colony. Punch samples from healthy and diseased corals were distinct. All swab samples clustered closely together with the seawater control and did not group according to the health state of the corals. Although more microbial taxa were detected by the swab method, there is a much larger overlap between the water control and swab samples than punch samples, suggesting some of the additional diversity is due to contamination from water absorbed by the swab. While swabs are useful for noninvasive studies of the coral surface mucus layer, these results show that they are not optimal for studies of coral disease. Published by Elsevier B.V.

Characterization of microbial communities in heavy crude oil from Saudi Arabia.

PubMed

Albokari, Majed; Mashhour, Ibrahim; Alshehri, Mohammed; Boothman, Chris; Al-Enezi, Mousa

The complete mineralization of crude oil into carbon dioxide, water, inorganic compounds and cellular constituents can be carried out as part of a bioremediation strategy. This involves the transformation of complex organic contaminants into simpler organic compounds by microbial communities, mainly bacteria. A crude oil sample and an oil sludge sample were obtained from Saudi ARAMCO Oil Company and investigated to identify the microbial communities present using PCR-based culture-independent techniques. In total, analysis of 177 clones yielded 30 distinct bacterial sequences. Clone library analysis of the oil sample was found to contain Bacillus , Clostridia and Gammaproteobacteria species while the sludge sample revealed the presence of members of the Alphaproteobacteria , Betaproteobacteria , Gammaproteobacteria , Clostridia , Spingobacteria and Flavobacteria . The dominant bacterial class identified in oil and sludge samples was found to be Bacilli and Flavobacteria , respectively. Phylogenetic analysis showed that the dominant bacterium in the oil sample has the closest sequence identity to Enterococcus aquimarinus and the dominant bacterium in the sludge sample is most closely related to the uncultured Bacteroidetes bacterium designated AH.KK.

Multilevel samplers as microcosms to assess microbial response to biostimulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baldwin, Brett R.; Peacock, Aaron D.; Park, Melora M.

Passive multilevel samplers (MLS) containing a solid matrix for microbial colonization were used in conjunction with a push-pull biostimulation experiment designed to promote biological U(VI) and Tc(VII) reduction. MLS were deployed at 24 elevations in the injection well and two down gradient wells to investigate the spatial variability in microbial community composition and growth prior to and following biostimulation. The microbial community was characterized by real-time PCR (Q-PCR) quantification of Bacteria, NO3- reducing bacteria (nirS and nirK), δ-proteobacteria, Geobacter sp., and methanogens (mcrA). Pretest cell densities were low overall but varied substantially with significantly greater Bacterial populations detected at circumneutralmore » pH (T-test, α=0.05) suggesting carbon substrate and low pH limitations of microbial activity. Although pretest cell densities were low, denitrifying bacteria were dominant members of the microbial community. Biostimulation with an ethanol amended groundwater resulted in concurrent NO3- and Tc(VII) reduction followed by U(VI) reduction. Q-PCR analysis of MLS revealed significant (1-2 orders of magnitude, T-test, α=0.05) increases in cell densities of Bacteria, denitrifiers, δ-proteobacteria, Geobacter sp., and methanogens in response to biostimulation. Traditionally characterization of sediment samples has been used to investigate the microbial community response to biostimulation, however, collection of sediment samples is expensive and not conducive to deep aquifers or temporal studies. The results presented demonstrate that push-pull tests with passive MLS provide an inexpensive approach to determine the effect of biostimulation on contaminant concentrations, geochemical conditions, and the microbial community composition and function.« less

A microbiology-based multi-parametric approach towards assessing biological stability in drinking water distribution networks.

PubMed

Lautenschlager, Karin; Hwang, Chiachi; Liu, Wen-Tso; Boon, Nico; Köster, Oliver; Vrouwenvelder, Hans; Egli, Thomas; Hammes, Frederik

2013-06-01

Biological stability of drinking water implies that the concentration of bacterial cells and composition of the microbial community should not change during distribution. In this study, we used a multi-parametric approach that encompasses different aspects of microbial water quality including microbial growth potential, microbial abundance, and microbial community composition, to monitor biological stability in drinking water of the non-chlorinated distribution system of Zürich. Drinking water was collected directly after treatment from the reservoir and in the network at several locations with varied average hydraulic retention times (6-52 h) over a period of four months, with a single repetition two years later. Total cell concentrations (TCC) measured with flow cytometry remained remarkably stable at 9.5 (± 0.6) × 10(4) cells/ml from water in the reservoir throughout most of the distribution network, and during the whole time period. Conventional microbial methods like heterotrophic plate counts, the concentration of adenosine tri-phosphate, total organic carbon and assimilable organic carbon remained also constant. Samples taken two years apart showed more than 80% similarity for the microbial communities analysed with denaturing gradient gel electrophoresis and 454 pyrosequencing. Only the two sampling locations with the longest water retention times were the exceptions and, so far for unknown reasons, recorded a slight but significantly higher TCC (1.3 (± 0.1) × 10(5) cells/ml) compared to the other locations. This small change in microbial abundance detected by flow cytometry was also clearly observed in a shift in the microbial community profiles to a higher abundance of members from the Comamonadaceae (60% vs. 2% at other locations). Conventional microbial detection methods were not able to detect changes as observed with flow cytometric cell counts and microbial community analysis. Our findings demonstrate that the multi-parametric approach used provides a powerful and sensitive tool to assess and evaluate biological stability and microbial processes in drinking water distribution systems. Copyright © 2013 Elsevier Ltd. All rights reserved.

Spatial variability of isoproturon mineralizing activity within an agricultural field: geostatistical analysis of simple physicochemical and microbiological soil parameters.

PubMed

El Sebai, T; Lagacherie, B; Soulas, G; Martin-Laurent, F

2007-02-01

We assessed the spatial variability of isoproturon mineralization in relation to that of physicochemical and biological parameters in fifty soil samples regularly collected along a sampling grid delimited across a 0.36 ha field plot (40 x 90 m). Only faint relationships were observed between isoproturon mineralization and the soil pH, microbial C biomass, and organic nitrogen. Considerable spatial variability was observed for six of the nine parameters tested (isoproturon mineralization rates, organic nitrogen, genetic structure of the microbial communities, soil pH, microbial biomass and equivalent humidity). The map of isoproturon mineralization rates distribution was similar to that of soil pH, microbial biomass, and organic nitrogen but different from those of structure of the microbial communities and equivalent humidity. Geostatistics revealed that the spatial heterogeneity in the rate of degradation of isoproturon corresponded to that of soil pH and microbial biomass.

Characterization of Early Microbial Communities on Volcanic Deposits along a Vegetation Gradient on the Island of Miyake, Japan

PubMed Central

Guo, Yong; Fujimura, Reiko; Sato, Yoshinori; Suda, Wataru; Kim, Seok-won; Oshima, Kenshiro; Hattori, Masahira; Kamijo, Takashi; Narisawa, Kazuhiko; Ohta, Hiroyuki

2014-01-01

The 2000 eruption of Mount Oyama on the island of Miyake (Miyake-jima) created a unique opportunity to study the early ecosystem development on newly exposed terrestrial substrates. In this study, bacterial and fungal communities on 9- and 11-year-old volcanic deposits at poorly to fully vegetation-recovered sites in Miyake-jima, Japan, were characterized by conventional culture-based methods and pyrosequencing of 16S rRNA and 18S rRNA genes. Despite the differences in the vegetation cover, the upper volcanic deposit layer samples displayed low among-site variation for chemical properties (pH, total organic carbon, and total nitrogen) and microbial population densities (total direct count and culturable count). Statistical analyses of pyrosequencing data revealed that the microbial communities of volcanic deposit samples were phylogenetically diverse, in spite of very low-carbon environmental conditions, and their diversity was comparable to that in the lower soil layer (buried soil) samples. Comparing with the microbial communities in buried soil, the volcanic deposit communities were characterized by the presence of Betaproteobacteria and Gammaproteobacteria as the main bacterial class, Deinococcus- Thermus as the minor bacterial phyla, and Ascomycota as the major fungal phyla. Multivariate analysis revealed that several bacterial families and fungal classes correlated positively or negatively with plant species. PMID:24463576

Gut microbial and short-chain fatty acid profiles in adults with chronic constipation before and after treatment with lubiprostone.

PubMed

Kang, Dae-Wook; DiBaise, John K; Ilhan, Zehra Esra; Crowell, Michael D; Rideout, Jai Ram; Caporaso, J Gregory; Rittmann, Bruce E; Krajmalnik-Brown, Rosa

2015-06-01

Identifying specific gut microorganisms associated with chronic constipation may be useful for diagnostic and therapeutic purposes. The objective of this study was to evaluate whether or not the gut microbial community of constipated subjects had specific microbial signatures and to assess the effects of lubiprostone treatment on the gut microbial community. Stool diaries, breath H2 and CH4 levels, and stool samples were collected from ten healthy subjects and nine patients meeting the Rome III criteria for chronic functional constipation. Constipated subjects received lubiprostone for four weeks, during which stool diaries were maintained. Stool samples were evaluated for gut microbial communities using pyrosequencing and quantitative real-time PCR (qPCR) targeting 16S-rRNA gene, along with concentrations of short-chain fatty acids (SCFAs) using high-performance liquid chromatography. Prior to treatment, gut microbial profiles were similar between constipated subjects and healthy subjects, while iso-butyrate levels were significantly higher in constipated subjects compared with healthy subjects. Despite increases in stool frequency and improvements in consistency after lubiprostone treatment, gut microbial profiles and community diversity after treatment showed no significant change compared to before treatment. While we did not observe a significant difference in either breath methane or archaeal abundance between the stool samples of healthy and constipated subjects, we confirmed a strong correlation between archaeal abundance measured by qPCR and the amount of methane gas exhaled in the fasting breath. Butyrate levels, however, were significantly higher in the stool samples of constipated subjects after lubiprostone treatment, suggesting that lubiprostone treatment had an effect on the net accumulation of SCFAs in the gut. In conclusion, lubiprostone treatment improved constipation symptoms and increased levels of butyrate without substantial modification of the gut microbial structure. Copyright © 2015 Elsevier Ltd. All rights reserved.

Examining the diversity and distribution of microbial communities from newly discovered methane seeps along the Cascadia Margin

NASA Astrophysics Data System (ADS)

Seabrook, S.; Thurber, A. R.; Embley, R. W.; Raineault, N.; Baumberger, T.; Merle, S. G.

2016-12-01

Methane seeps provide biogeochemical and microbial heterogeneity in deep-sea habitats. In June of 2016 the E/V Nautilus, exploring for methane seeps along the Cascadia continental margin, discovered over 450 bubble streams, indicative of active seepage, and collected biological samples at 6 of the resulting newly discovered seeps. These seeps covered a range of depths, latitudes, habitat types and biogeochemical environments and included: Juan de Fuca (150m), Astoria canyon (800m and 500m), Nehalem Bank (185m), Heceta SW (1200m), SW Coquille Bank (600m), and Klamath Knoll seep (700m). Geologic environment types included continental shelf, canyons and slopes, and these sites spanned the zone of hydrate stability and the Oxygen Minimum Zone. A range of seep-specific habitat were found and sampled including: reduced sediments, microbial mats, methane hydrates, clam beds (Calyptogena spp.), Siboglinidae tubeworm assemblages and sparse assemblages of stalked barnacles. Here, we present an initial characterization of the microbial communities collected via push cores by a remotely operated vehicle (ROV) at the six aforementioned sites. With high throughput amplicon sequencing of the V4-V5 region of the 16S rRNA gene, we characterize the diversity and microbial composition of the seep sites sampled. This characterization is furthered with digital drop PCR of the pmoA gene (involved with aerobic methanotrophy) to allow for a comparison of the community composition with functional gene abundance of critical microbial processes. These data will be placed in the greater biogeochemical context of the region, including direct comparison with paired gas-tight sampling at key locations. The results of these analyses will provide the first microbial description of this broad range of seep ecosystems along the Cascadia Margin adding to our overall understanding of microbial diversity, the dominant physiological processes at seep ecosystems, and the connection between community structure, function and biogeochemistry in habitats which we are just starting to appreciate for their ubiquity in marine environments.

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer

NASA Astrophysics Data System (ADS)

Tully, B. J.; Wheat, C. G.; Glazer, B. T.; Huber, J. A.

2017-12-01

The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized genomic reconstruction of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement. Twenty-one samples were collected during a two-year period at three different depths and two locations with the basaltic aquifer to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the two years, yet a dynamic microbial community was present in the crustal fluids that underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the dataset and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in a diverse group of microorganisms. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes and alternative electron acceptors. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles.

Capillary absorption spectrometer and process for isotopic analysis of small samples

DOEpatents

Alexander, M. Lizabeth; Kelly, James F.; Sams, Robert L.; Moran, James J.; Newburn, Matthew K.; Blake, Thomas A.

2016-03-29

A capillary absorption spectrometer and process are described that provide highly sensitive and accurate stable absorption measurements of analytes in a sample gas that may include isotopologues of carbon and oxygen obtained from gas and biological samples. It further provides isotopic images of microbial communities that allow tracking of nutrients at the single cell level. It further targets naturally occurring variations in carbon and oxygen isotopes that avoids need for expensive isotopically labeled mixtures which allows study of samples taken from the field without modification. The method also permits sampling in vivo permitting real-time ambient studies of microbial communities.

Capillary absorption spectrometer and process for isotopic analysis of small samples

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alexander, M. Lizabeth; Kelly, James F.; Sams, Robert L.

A capillary absorption spectrometer and process are described that provide highly sensitive and accurate stable absorption measurements of analytes in a sample gas that may include isotopologues of carbon and oxygen obtained from gas and biological samples. It further provides isotopic images of microbial communities that allow tracking of nutrients at the single cell level. It further targets naturally occurring variations in carbon and oxygen isotopes that avoids need for expensive isotopically labeled mixtures which allows study of samples taken from the field without modification. The process also permits sampling in vivo permitting real-time ambient studies of microbial communities.

Assessing impacts of unconventional natural gas extraction on microbial communities in headwater stream ecosystems in Northwestern Pennsylvania

PubMed Central

Trexler, Ryan; Solomon, Caroline; Brislawn, Colin J.; Wright, Justin R.; Rosenberger, Abigail; McClure, Erin E.; Grube, Alyssa M.; Peterson, Mark P.; Keddache, Mehdi; Mason, Olivia U.; Hazen, Terry C.; Grant, Christopher J.; Lamendella, Regina

2014-01-01

Hydraulic fracturing and horizontal drilling have increased dramatically in Pennsylvania Marcellus shale formations, however the potential for major environmental impacts are still incompletely understood. High-throughput sequencing of the 16S rRNA gene was performed to characterize the microbial community structure of water, sediment, bryophyte, and biofilm samples from 26 headwater stream sites in northwestern Pennsylvania with different histories of fracking activity within Marcellus shale formations. Further, we describe the relationship between microbial community structure and environmental parameters measured. Approximately 3.2 million 16S rRNA gene sequences were retrieved from a total of 58 samples. Microbial community analyses showed significant reductions in species richness as well as evenness in sites with Marcellus shale activity. Beta diversity analyses revealed distinct microbial community structure between sites with and without Marcellus shale activity. For example, operational taxonomic units (OTUs) within the Acetobacteracea, Methylocystaceae, Acidobacteriaceae, and Phenylobacterium were greater than three log-fold more abundant in MSA+ sites as compared to MSA− sites. Further, several of these OTUs were strongly negatively correlated with pH and positively correlated with the number of wellpads in a watershed. It should be noted that many of the OTUs enriched in MSA+ sites are putative acidophilic and/or methanotrophic populations. This study revealed apparent shifts in the autochthonous microbial communities and highlighted potential members that could be responding to changing stream conditions as a result of nascent industrial activity in these aquatic ecosystems. PMID:25408683

Analysis of microbial communities in the oil reservoir subjected to CO2-flooding by using functional genes as molecular biomarkers for microbial CO2 sequestration

PubMed Central

Liu, Jin-Feng; Sun, Xiao-Bo; Yang, Guang-Chao; Mbadinga, Serge M.; Gu, Ji-Dong; Mu, Bo-Zhong

2015-01-01

Sequestration of CO2 in oil reservoirs is considered to be one of the feasible options for mitigating atmospheric CO2 building up and also for the in situ potential bioconversion of stored CO2 to methane. However, the information on these functional microbial communities and the impact of CO2 storage on them is hardly available. In this paper a comprehensive molecular survey was performed on microbial communities in production water samples from oil reservoirs experienced CO2-flooding by analysis of functional genes involved in the process, including cbbM, cbbL, fthfs, [FeFe]-hydrogenase, and mcrA. As a comparison, these functional genes in the production water samples from oil reservoir only experienced water-flooding in areas of the same oil bearing bed were also analyzed. It showed that these functional genes were all of rich diversity in these samples, and the functional microbial communities and their diversity were strongly affected by a long-term exposure to injected CO2. More interestingly, microorganisms affiliated with members of the genera Methanothemobacter, Acetobacterium, and Halothiobacillus as well as hydrogen producers in CO2 injected area either increased or remained unchanged in relative abundance compared to that in water-flooded area, which implied that these microorganisms could adapt to CO2 injection and, if so, demonstrated the potential for microbial fixation and conversion of CO2 into methane in subsurface oil reservoirs. PMID:25873911

Metaproteomics of complex microbial communities in biogas plants

PubMed Central

Heyer, Robert; Kohrs, Fabian; Reichl, Udo; Benndorf, Dirk

2015-01-01

Production of biogas from agricultural biomass or organic wastes is an important source of renewable energy. Although thousands of biogas plants (BGPs) are operating in Germany, there is still a significant potential to improve yields, e.g. from fibrous substrates. In addition, process stability should be optimized. Besides evaluating technical measures, improving our understanding of microbial communities involved into the biogas process is considered as key issue to achieve both goals. Microscopic and genetic approaches to analyse community composition provide valuable experimental data, but fail to detect presence of enzymes and overall metabolic activity of microbial communities. Therefore, metaproteomics can significantly contribute to elucidate critical steps in the conversion of biomass to methane as it delivers combined functional and phylogenetic data. Although metaproteomics analyses are challenged by sample impurities, sample complexity and redundant protein identification, and are still limited by the availability of genome sequences, recent studies have shown promising results. In the following, the workflow and potential pitfalls for metaproteomics of samples from full-scale BGP are discussed. In addition, the value of metaproteomics to contribute to the further advancement of microbial ecology is evaluated. Finally, synergistic effects expected when metaproteomics is combined with advanced imaging techniques, metagenomics, metatranscriptomics and metabolomics are addressed. PMID:25874383

Potential sources of hydrocarbons and their microbial degradation in sediments from the deep geothermal Lusi site, Indonesia

NASA Astrophysics Data System (ADS)

Krueger, Martin; Mazzini, Adriano; Scheeder, Georg; Blumenberg, Martin

2017-04-01

The Lusi eruption represents one of the largest ongoing sedimentary hosted geothermal systems, which started in 2006 following an earthquake on Java Island. Since then it has been continuously producing hot and hydrocarbon rich mud from a central crater with peaks reaching 180.000 m3 per day. Numerous investigations focused on the study of microbial communities which thrive at offshore methane and oil seeps and mud volcanoes, however very little has been done on onshore seeping structures. Lusi represents a unique opportunity to complete a comprehensive study of onshore microbial communities fed by the seepage of CH4 as well as of liquid hydrocarbons originating from one or more km below the surface. While the source of the methane at Lusi is unambiuous, the origin of the seeping oil is still discussed. Both, source and maturity estimates from biomarkers, are in favor of a type II/III organic matter source. Likely the oils were formed from the studied black shales (deeper Ngimbang Fm.) which contained a Type III component in the Type II predominated organic matter. In all samples large numbers of active microorganisms were present. Rates for aerobic methane oxidation were high, as was the potential of the microbial communities to degrade different hydrocarbons. The data suggests a transition of microbial populations from an anaerobic, hydrocarbon-driven metabolism in fresher samples from center or from small seeps to more generalistic, aerobic microbial communities in older, more consolidated sediments. Ongoing microbial activity in crater sediment samples under high temperatures (80-95C) indicate a deep origin of the involved microorganisms. First results of molecular analyses of the microbial community compositions confirm the above findings. This study represents an initial step to better understand onshore seepage systems and provides an ideal analogue for comparison with the better investigated offshore structures.

Characterization of Microbial Community in Lascaux Cave by High Throughput Sequencing

NASA Astrophysics Data System (ADS)

Alonso, Lise; Dubost, Audrey; Luis, Patricia; Pommier, Thomas; Moënne-Loccoz, Yvan

2017-04-01

The Lascaux Cave in South-Est France is an archeological landmark renowned for its Paleolithic paintings dating back c.18.000 years. Extensive touristic frequenting and repeated chemical treatments have resulted in the development of microbial stains on cave walls, which is a major issue in terms of art conservation. Therefore, it is of prime importance to better understand the microbial ecology of Lascaux Cave. Like many other caves, Lascaux is quite heterogeneous in terms of the nature and surface properties of rock walls within cave rooms, as well as the succession of rooms/galleries from the entrance to deeper areas of the cave. Lascaux Cave displays an additional levels of heterogeneity related to the presence of discontinuous stains on certain types of cave walls. We compared the microbial community (i.e. both prokaryotic and eukaryotic microbial populations) colonizing cave walls of different rooms/galleries, in and outside stains and in different cave layers, in successive years. Quantitative PCR analysis of cave wall samples gave in the order of 102 copies of 18S rRNA genes and 105 copies of 16S rRNA genes per ng of DNA, indicating significant colonization of all cave walls by micro-eukaryotes and especially bacteria. Illumina metagenomic analyses of cave wall samples was carried out based on four ribosomal DNA markers targeting bacteria, archaea, fungi, and other micro-eukaryotes. The results showed that the four microbial communities were highly diverse in and outside stains, as several hundred genera of microorganisms were identified in each. Proteobacteria were more prominent within stains whereas Bacteroidetes and Sordariomycetes were more prominent outside stains. High-throughput sequencing also showed that the nature/surface properties of cave walls were the main factor determining the structure and composition of microbial communities, ahead of the other heterogeneity factors studied i.e. location within the cave, presence of stain and sampling season. This work provides a global view of the microbial community of Lascaux Cave, which could be useful to guide conservation efforts.

Long-term soil transplant simulating climate change with latitude significantly alters microbial temporal turnover

PubMed Central

Liang, Yuting; Jiang, Yuji; Wang, Feng; Wen, Chongqing; Deng, Ye; Xue, Kai; Qin, Yujia; Yang, Yunfeng; Wu, Liyou; Zhou, Jizhong; Sun, Bo

2015-01-01

To understand soil microbial community stability and temporal turnover in response to climate change, a long-term soil transplant experiment was conducted in three agricultural experiment stations over large transects from a warm temperate zone (Fengqiu station in central China) to a subtropical zone (Yingtan station in southern China) and a cold temperate zone (Hailun station in northern China). Annual soil samples were collected from these three stations from 2005 to 2011, and microbial communities were analyzed by sequencing microbial 16S ribosomal RNA gene amplicons using Illumina MiSeq technology. Our results revealed a distinctly differential pattern of microbial communities in both northward and southward transplantations, along with an increase in microbial richness with climate cooling and a corresponding decrease with climate warming. The microbial succession rate was estimated by the slope (w value) of linear regression of a log-transformed microbial community similarity with time (time–decay relationship). Compared with the low turnover rate of microbial communities in situ (w=0.046, P<0.001), the succession rate at the community level was significantly higher in the northward transplant (w=0.058, P<0.001) and highest in the southward transplant (w=0.094, P<0.001). Climate warming lead to a faster succession rate of microbial communities as well as lower species richness and compositional changes compared with in situ and climate cooling, which may be related to the high metabolic rates and intense competition under higher temperature. This study provides new insights into the impacts of climate change on the fundamental temporal scaling of soil microbial communities and microbial phylogenetic biodiversity. PMID:25989371

Indoor-Air Microbiome in an Urban Subway Network: Diversity and Dynamics

PubMed Central

Leung, Marcus H. Y.; Wilkins, David; Li, Ellen K. T.; Kong, Fred K. F.

2014-01-01

Subway systems are indispensable for urban societies, but microbiological characteristics of subway aerosols are relatively unknown. Previous studies investigating microbial compositions in subways employed methodologies that underestimated the diversity of microbial exposure for commuters, with little focus on factors governing subway air microbiology, which may have public health implications. Here, a culture-independent approach unraveling the bacterial diversity within the urban subway network in Hong Kong is presented. Aerosol samples from multiple subway lines and outdoor locations were collected. Targeting the 16S rRNA gene V4 region, extensive taxonomic diversity was found, with the most common bacterial genera in the subway environment among those associated with skin. Overall, subway lines harbored different phylogenetic communities based on α- and β-diversity comparisons, and closer inspection suggests that each community within a line is dependent on architectural characteristics, nearby outdoor microbiomes, and connectedness with other lines. Microbial diversities and assemblages also varied depending on the day sampled, as well as the time of day, and changes in microbial communities between peak and nonpeak commuting hours were attributed largely to increases in skin-associated genera in peak samples. Microbial diversities within the subway were influenced by temperature and relative humidity, while carbon dioxide levels showed a positive correlation with abundances of commuter-associated genera. This Hong Kong data set and communities from previous studies conducted in the United States formed distinct community clusters, indicating that additional work is required to unravel the mechanisms that shape subway microbiomes around the globe. PMID:25172855

Greater temporal changes of sediment microbial community than its waterborne counterpart in Tengchong hot springs, Yunnan Province, China

PubMed Central

Wang, Shang; Dong, Hailiang; Hou, Weiguo; Jiang, Hongchen; Huang, Qiuyuan; Briggs, Brandon R.; Huang, Liuqin

2014-01-01

Temporal variation in geochemistry can cause changes in microbial community structure and diversity. Here we studied temporal changes of microbial communities in Tengchong hot springs of Yunnan Province, China in response to geochemical variations by using microbial and geochemical data collected in January, June and August of 2011. Greater temporal variations were observed in individual taxa than at the whole community structure level. Water and sediment communities exhibited different temporal variation patterns. Water communities were largely stable across three sampling times and dominated by similar microbial lineages: Hydrogenobaculum in moderate-temperature acidic springs, Sulfolobus in high-temperature acidic springs, and Hydrogenobacter in high-temperature circumneutral to alkaline springs. Sediment communities were more diverse and responsive to changing physicochemical conditions. Most of the sediment communities in January and June were similar to those in waters. However, the August sediment community was more diverse and contained more anaerobic heterotrophs than the January and June: Desulfurella and Acidicaldus in moderate-temperature acidic springs, Ignisphaera and Desulfurococcus in high-temperature acidic springs, the candidate division OP1 and Fervidobacterium in alkaline springs, and Thermus and GAL35 in neutral springs. Temporal variations in physicochemical parameters including temperature, pH, and dissolved organic carbon may have triggered the observed microbial community shifts. PMID:25524763

Comparison of DNA preservation methods for environmental bacterial community samples

USGS Publications Warehouse

Gray, Michael A.; Pratte, Zoe A.; Kellogg, Christina A.

2013-01-01

Field collections of environmental samples, for example corals, for molecular microbial analyses present distinct challenges. The lack of laboratory facilities in remote locations is common, and preservation of microbial community DNA for later study is critical. A particular challenge is keeping samples frozen in transit. Five nucleic acid preservation methods that do not require cold storage were compared for effectiveness over time and ease of use. Mixed microbial communities of known composition were created and preserved by DNAgard™, RNAlater®, DMSO–EDTA–salt (DESS), FTA® cards, and FTA Elute® cards. Automated ribosomal intergenic spacer analysis and clone libraries were used to detect specific changes in the faux communities over weeks and months of storage. A previously known bias in FTA® cards that results in lower recovery of pure cultures of Gram-positive bacteria was also detected in mixed community samples. There appears to be a uniform bias across all five preservation methods against microorganisms with high G + C DNA. Overall, the liquid-based preservatives (DNAgard™, RNAlater®, and DESS) outperformed the card-based methods. No single liquid method clearly outperformed the others, leaving method choice to be based on experimental design, field facilities, shipping constraints, and allowable cost.

Employment of Near Full-Length Ribosome Gene TA-Cloning and Primer-Blast to Detect Multiple Species in a Natural Complex Microbial Community Using Species-Specific Primers Designed with Their Genome Sequences.

PubMed

Zhang, Huimin; He, Hongkui; Yu, Xiujuan; Xu, Zhaohui; Zhang, Zhizhou

2016-11-01

It remains an unsolved problem to quantify a natural microbial community by rapidly and conveniently measuring multiple species with functional significance. Most widely used high throughput next-generation sequencing methods can only generate information mainly for genus-level taxonomic identification and quantification, and detection of multiple species in a complex microbial community is still heavily dependent on approaches based on near full-length ribosome RNA gene or genome sequence information. In this study, we used near full-length rRNA gene library sequencing plus Primer-Blast to design species-specific primers based on whole microbial genome sequences. The primers were intended to be specific at the species level within relevant microbial communities, i.e., a defined genomics background. The primers were tested with samples collected from the Daqu (also called fermentation starters) and pit mud of a traditional Chinese liquor production plant. Sixteen pairs of primers were found to be suitable for identification of individual species. Among them, seven pairs were chosen to measure the abundance of microbial species through quantitative PCR. The combination of near full-length ribosome RNA gene library sequencing and Primer-Blast may represent a broadly useful protocol to quantify multiple species in complex microbial population samples with species-specific primers.

Gut microbiota of liver transplantation recipients.

PubMed

Sun, Li-Ying; Yang, Yun-Sheng; Qu, Wei; Zhu, Zhi-Jun; Wei, Lin; Ye, Zhi-Sheng; Zhang, Jian-Rui; Sun, Xiao-Ye; Zeng, Zhi-Gui

2017-06-19

The characteristics of intestinal microbial communities may be affected by changes in the pathophysiology of patients with end-stage liver disease. Here, we focused on the characteristics of intestinal fecal microbial communities in post-liver transplantation (LT) patients in comparison with those in the same individuals pre-LT and in healthy individuals. The fecal microbial communities were analyzed via MiSeq-PE250 sequencing of the V4 region of 16S ribosomal RNA and were then compared between groups. We found that the gut microbiota of patients with severe liver disease who were awaiting LT was significantly different from that of healthy controls, as represented by the first principal component (p = 0.0066). Additionally, the second principal component represented a significant difference in the gut microbiota of patients between pre-LT and post-LT surgery (p = 0.03125). After LT, there was a significant decrease in the abundance of certain microbial species, such as Actinobacillus, Escherichia, and Shigella, and a significant increase in the abundance of other microbial species, such as Micromonosporaceae, Desulfobacterales, the Sarcina genus of Eubacteriaceae, and Akkermansia. Based on KEGG profiles, 15 functional modules were enriched and 21 functional modules were less represented in the post-LT samples compared with the pre-LT samples. Our study demonstrates that fecal microbial communities were significantly altered by LT.

What is the extent of prokaryotic diversity?

PubMed Central

Curtis, Thomas P; Head, Ian M; Lunn, Mary; Woodcock, Stephen; Schloss, Patrick D; Sloan, William T

2006-01-01

The extent of microbial diversity is an intrinsically fascinating subject of profound practical importance. The term ‘diversity’ may allude to the number of taxa or species richness as well as their relative abundance. There is uncertainty about both, primarily because sample sizes are too small. Non-parametric diversity estimators make gross underestimates if used with small sample sizes on unevenly distributed communities. One can make richness estimates over many scales using small samples by assuming a species/taxa-abundance distribution. However, no one knows what the underlying taxa-abundance distributions are for bacterial communities. Latterly, diversity has been estimated by fitting data from gene clone libraries and extrapolating from this to taxa-abundance curves to estimate richness. However, since sample sizes are small, we cannot be sure that such samples are representative of the community from which they were drawn. It is however possible to formulate, and calibrate, models that predict the diversity of local communities and of samples drawn from that local community. The calibration of such models suggests that migration rates are small and decrease as the community gets larger. The preliminary predictions of the model are qualitatively consistent with the patterns seen in clone libraries in ‘real life’. The validation of this model is also confounded by small sample sizes. However, if such models were properly validated, they could form invaluable tools for the prediction of microbial diversity and a basis for the systematic exploration of microbial diversity on the planet. PMID:17028084

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ottesen, Elizabeth A.; Marin, Roman; Preston, Christina M.

Planktonic microbial activity and community structure is dynamic, and can change dramatically on time scales of hours to days. Yet for logistical reasons, this temporal scale is typically undersampled in the marine environment. In order to facilitate higher-resolution, long-term observation of microbial diversity and activity, we developed a protocol for automated collection and fixation of marine microbes using the Environmental Sample Processor (ESP) platform. The protocol applies a preservative (RNALater) to cells collected on filters, for long-term storage and preservation of total cellular RNA. Microbial samples preserved using this protocol yielded high-quality RNA after 30 days of storage at roommore » temperature, or onboard the ESP at in situ temperatures. Pyrosequencing of complementary DNA libraries generated from ESP-collected and preserved samples yielded transcript abundance profiles nearly indistinguishable from those derived from conventionally treated replicate samples. To demonstrate the utility of the method, we used a moored ESP to remotely and autonomously collect Monterey Bay seawater for metatranscriptomic analysis. Community RNA was extracted and pyrosequenced from samples collected at four time points over the course of a single day. In all four samples, the oxygenic photoautotrophs were predominantly eukaryotic, while the bacterial community was dominated by Polaribacter-like Flavobacteria and a Rhodobacterales bacterium sharing high similarity with Rhodobacterales sp. HTCC2255. However, each time point was associated with distinct species abundance and gene transcript profiles. These laboratory and field tests confirmed that autonomous collection and preservation is a feasible and useful approach for characterizing the expressed genes and environmental responses of marine microbial communities.« less

Experimental warming reveals positive feedbacks to climate change in the Eurasian Steppe.

PubMed

Zhang, Ximei; Johnston, Eric R; Li, Linghao; Konstantinidis, Konstantinos T; Han, Xingguo

2017-04-01

Identifying soil microbial feedbacks to increasing temperatures and moisture alterations is critical for predicting how terrestrial ecosystems will respond to climate change. We performed a 5-year field experiment manipulating warming, watering and their combination in a semiarid temperate steppe in northern China. Warming stimulated the abundance of genes responsible for degrading recalcitrant soil organic matter (SOM) and reduced SOM content by 13%. Watering, and warming plus watering also increased the abundance of recalcitrant SOM catabolism pathways, but concurrently promoted plant growth and increased labile SOM content, which somewhat offset SOM loss. The treatments also increased microbial biomass, community complexity and metabolic potential for nitrogen and sulfur assimilation. Both microbial and plant community composition shifted with the treatment conditions, and the sample-to-sample compositional variations of the two communities (pairwise β-diversity distances) were significantly correlated. In particular, microbial community composition was substantially correlated with the dominant plant species (~0.54 Spearman correlation coefficient), much more than with measured soil indices, affirming a tight coupling between both biological communities. Collectively, our study revealed the direction and underlying mechanisms of microbial feedbacks to warming and suggested that semiarid regions of northern steppes could act as a net carbon source under increased temperatures, unless precipitation increases concurrently.

Carcass mass has little influence on the structure of gravesoil microbial communities.

PubMed

Weiss, Sophie; Carter, David O; Metcalf, Jessica L; Knight, Rob

2016-01-01

Little is known about how variables, such as carcass mass, affect the succession pattern of microbes in soils during decomposition. To investigate the effects of carcass mass on the soil microbial community, soils associated with swine (Sus scrofa domesticus) carcasses of four different masses were sampled until the 15th day of decomposition during the month of June in a pasture near Lincoln, Nebraska. Soils underneath swine of 1, 20, 40, and 50 kg masses were investigated in triplicate, as well as control sites not associated with a carcass. Soil microbial communities were characterized by sequencing the archaeal, bacterial (16S), and eukaryotic (18S) rRNA genes in soil samples. We conclude that time of decomposition was a significant influence on the microbial community, but carcass mass was not. The gravesoil associated with 1 kg mass carcasses differs most compared to the gravesoil associated with other carcass masses. We also identify the 15 most abundant bacterial and eukaryotic taxa, and discuss changes in their abundance as carcass decomposition progressed. Finally, we show significant decreases in alpha diversity for carcasses of differing mass in pre-carcass rupture (days 0, 1, 2, 4, 5, and 6 postmortem) versus post-carcass rupture (days 9 and 15 postmortem) microbial communities.

Relationships between microbial communities and environmental parameters at sites impacted by mining of volcanogenic massive sulfide deposits, Prince William Sound, Alaska

USGS Publications Warehouse

Foster, A.L.; Munk, L.; Koski, R.A.; Shanks, Wayne C.; Stillings, L.L.

2008-01-01

The relations among geochemical parameters and sediment microbial communities were examined at three shoreline sites in the Prince William Sound, Alaska, which display varying degrees of impact by acid-rock drainage (ARD) associated with historic mining of volcanogenic massive sulfide deposits. Microbial communities were examined using total fatty acid methyl esters (FAMEs), a class of compounds derived from lipids produced by eukaryotes and prokaryotes (bacteria and Archaea); standard extraction techniques detect FAMEs from both living (viable) and dead (non-viable) biomass, but do not detect Archaeal FAMEs. Biomass and diversity (as estimated by FAMEs) varied strongly as a function of position in the tidal zone, not by study site; subtidal muds, Fe oxyhydroxide undergoing biogenic reductive dissolution, and peat-rich intertidal sediment had the highest values. These estimates were lowest in acid-generating, intertidal zone sediment; if valid, the estimates suggest that only one or two bacterial species predominate in these communities, and/or that Archeal species are important members of the microbial community in this sediment. All samples were dominated by bacterial FAMEs (median value >90%). Samples with the highest absolute abundance of eukaryotic FAMEs were biogenic Fe oxyhydroxides from shallow freshwater pools (fungi) and subtidal muds (diatoms). Eukaryotic FAMEs were practically absent from low-pH, sulfide-rich intertidal zone sediments. The relative abundance of general microbial functional groups such as aerobes/anaerobes and gram(+)/gram(-) was not estimated due to severe inconsistency among the results obtained using several metrics reported in the literature. Principal component analyses (PCAs) were performed to investigate the relationship among samples as separate functions of water, sediment, and FAMEs data. PCAs based on water chemistry and FAMEs data resulted in similar relations among samples, whereas the PCA based on sediment chemistry produced a very different sample arrangement. Specifically, the sediment parameter PCA grouped samples with high bulk trace metal concentration regardless of whether the metals were incorporated into secondary precipitates or primary sulfides. The water chemistry PCA and FAMEs PCA appear to be less prone to this type of artifact. Signature lipids in sulfide-rich sediments could indicate the presence of acid-tolerant and/or acidophilic members of the genus Thiobacillus or they could indicate the presence of SO4-reducing bacteria. The microbial community documented in subtidal and offshore sediments is rich in SRB and/or facultative anaerobes of the Cytophaga-Flavobacterium group; both could reasonably be expected in PWS coastal environments. The results of this study provide evidence for substantial feedback between local (meter to centimeter-scale) geochemical variations, and sediment microbial community composition, and show that microbial community signatures in the intertidal zone are significantly altered at sites where ARD drainage is present relative to sites where it is not, even if the sediment geochemistry indicates net accumulation of ARD-generated trace metals in the intertidal zone. ?? 2007 Elsevier Ltd. All rights reserved.

Nutrient and Rainfall Additions Shift Phylogenetically Estimated Traits of Soil Microbial Communities.

PubMed

Gravuer, Kelly; Eskelinen, Anu

2017-01-01

Microbial traits related to ecological responses and functions could provide a common currency facilitating synthesis and prediction; however, such traits are difficult to measure directly for all taxa in environmental samples. Past efforts to estimate trait values based on phylogenetic relationships have not always distinguished between traits with high and low phylogenetic conservatism, limiting reliability, especially in poorly known environments, such as soil. Using updated reference trees and phylogenetic relationships, we estimated two phylogenetically conserved traits hypothesized to be ecologically important from DNA sequences of the 16S rRNA gene from soil bacterial and archaeal communities. We sampled these communities from an environmental change experiment in California grassland applying factorial addition of late-season precipitation and soil nutrients to multiple soil types for 3 years prior to sampling. Estimated traits were rRNA gene copy number, which contributes to how rapidly a microbe can respond to an increase in resources and may be related to its maximum growth rate, and genome size, which suggests the breadth of environmental and substrate conditions in which a microbe can thrive. Nutrient addition increased community-weighted mean estimated rRNA gene copy number and marginally increased estimated genome size, whereas precipitation addition decreased these community means for both estimated traits. The effects of both treatments on both traits were associated with soil properties, such as ammonium, available phosphorus, and pH. Estimated trait responses within several phyla were opposite to the community mean response, indicating that microbial responses, although largely consistent among soil types, were not uniform across the tree of life. Our results show that phylogenetic estimation of microbial traits can provide insight into how microbial ecological strategies interact with environmental changes. The method could easily be applied to any of the thousands of existing 16S rRNA sequence data sets and offers potential to improve our understanding of how microbial communities mediate ecosystem function responses to global changes.

Microbial communities and arsenic biogeochemistry at the outflow of an alkaline sulfide-rich hot spring.

PubMed

Jiang, Zhou; Li, Ping; Van Nostrand, Joy D; Zhang, Ping; Zhou, Jizhong; Wang, Yanhong; Dai, Xinyue; Zhang, Rui; Jiang, Dawei; Wang, Yanxin

2016-04-29

Alkaline sulfide-rich hot springs provide a unique environment for microbial community and arsenic (As) biogeochemistry. In this study, a representative alkaline sulfide-rich hot spring, Zimeiquan in the Tengchong geothermal area, was chosen to study arsenic geochemistry and microbial community using Illumina MiSeq sequencing. Over 0.26 million 16S rRNA sequence reads were obtained from 5-paired parallel water and sediment samples along the hot spring's outflow channel. High ratios of As(V)/AsSum (total combined arsenate and arsenite concentrations) (0.59-0.78), coupled with high sulfide (up to 5.87 mg/L), were present in the hot spring's pools, which suggested As(III) oxidation occurred. Along the outflow channel, AsSum increased from 5.45 to 13.86 μmol/L, and the combined sulfide and sulfate concentrations increased from 292.02 to 364.28 μmol/L. These increases were primarily attributed to thioarsenic transformation. Temperature, sulfide, As and dissolved oxygen significantly shaped the microbial communities between not only the pools and downstream samples, but also water and sediment samples. Results implied that the upstream Thermocrinis was responsible for the transformation of thioarsenic to As(III) and the downstream Thermus contributed to derived As(III) oxidation. This study improves our understanding of microbially-mediated As transformation in alkaline sulfide-rich hot springs.

Microbial communities and arsenic biogeochemistry at the outflow of an alkaline sulfide-rich hot spring

PubMed Central

Jiang, Zhou; Li, Ping; Van Nostrand, Joy D.; Zhang, Ping; Zhou, Jizhong; Wang, Yanhong; Dai, Xinyue; Zhang, Rui; Jiang, Dawei; Wang, Yanxin

2016-01-01

Alkaline sulfide-rich hot springs provide a unique environment for microbial community and arsenic (As) biogeochemistry. In this study, a representative alkaline sulfide-rich hot spring, Zimeiquan in the Tengchong geothermal area, was chosen to study arsenic geochemistry and microbial community using Illumina MiSeq sequencing. Over 0.26 million 16S rRNA sequence reads were obtained from 5-paired parallel water and sediment samples along the hot spring’s outflow channel. High ratios of As(V)/AsSum (total combined arsenate and arsenite concentrations) (0.59–0.78), coupled with high sulfide (up to 5.87 mg/L), were present in the hot spring’s pools, which suggested As(III) oxidation occurred. Along the outflow channel, AsSum increased from 5.45 to 13.86 μmol/L, and the combined sulfide and sulfate concentrations increased from 292.02 to 364.28 μmol/L. These increases were primarily attributed to thioarsenic transformation. Temperature, sulfide, As and dissolved oxygen significantly shaped the microbial communities between not only the pools and downstream samples, but also water and sediment samples. Results implied that the upstream Thermocrinis was responsible for the transformation of thioarsenic to As(III) and the downstream Thermus contributed to derived As(III) oxidation. This study improves our understanding of microbially-mediated As transformation in alkaline sulfide-rich hot springs. PMID:27126380

High-resolution phylogenetic microbial community profiling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singer, Esther; Coleman-Derr, Devin; Bowman, Brett

2014-03-17

The representation of bacterial and archaeal genome sequences is strongly biased towards cultivated organisms, which belong to merely four phylogenetic groups. Functional information and inter-phylum level relationships are still largely underexplored for candidate phyla, which are often referred to as microbial dark matter. Furthermore, a large portion of the 16S rRNA gene records in the GenBank database are labeled as environmental samples and unclassified, which is in part due to low read accuracy, potential chimeric sequences produced during PCR amplifications and the low resolution of short amplicons. In order to improve the phylogenetic classification of novel species and advance ourmore » knowledge of the ecosystem function of uncultivated microorganisms, high-throughput full length 16S rRNA gene sequencing methodologies with reduced biases are needed. We evaluated the performance of PacBio single-molecule real-time (SMRT) sequencing in high-resolution phylogenetic microbial community profiling. For this purpose, we compared PacBio and Illumina metagenomic shotgun and 16S rRNA gene sequencing of a mock community as well as of an environmental sample from Sakinaw Lake, British Columbia. Sakinaw Lake is known to contain a large age of microbial species from candidate phyla. Sequencing results show that community structure based on PacBio shotgun and 16S rRNA gene sequences is highly similar in both the mock and the environmental communities. Resolution power and community representation accuracy from SMRT sequencing data appeared to be independent of GC content of microbial genomes and was higher when compared to Illumina-based metagenome shotgun and 16S rRNA gene (iTag) sequences, e.g. full-length sequencing resolved all 23 OTUs in the mock community, while iTags did not resolve closely related species. SMRT sequencing hence offers various potential benefits when characterizing uncharted microbial communities.« less

Microbial profiling of South African acid mine water samples using next generation sequencing platform.

PubMed

Kamika, I; Azizi, S; Tekere, M

2016-07-01

This study monitored changes in bacterial and fungal structure in a mine water in a monthly basis over 4 months. Over the 4-month study period, mine water samples contained more bacteria (91.06 %) compared to fungi (8.94 %). For bacteria, mine water samples were dominated by Proteobacteria (39.14 to 65.06 %) followed by Firmicutes (26.34 to 28.9 %) in summer, and Cyanobacteria (27.05 %) in winter. In the collected samples, 18 % of bacteria could not be assigned to a phylum and remained unclassified suggesting hitherto vast untapped microbial diversity especially during winter. The fungal domain was the sole eukaryotic microorganism found in the mine water samples with unclassified fungi (68.2 to 91 %) as the predominant group, followed by Basidiomycota (6.9 to 27.8 %). The time of collection, which was linked to the weather, had higher impact on bacterial community than fungal community. The bacterial operational taxonomic units (OTUs) ranged from 865 to 4052 over the 4-month sampling period, while fungal OTUs varied from 73 to 249. The diversity indices suggested that the bacterial community inhabiting the mine water samples were more diverse than the fungal community. The canonical correspondence analysis (CCA) results highlighted that the bacterial community variance had the strongest relationship with water temperature, conductivity, pH, and dissolved oxygen (DO) content, as compared to fungi and water characteristics, had the greatest contribution to both bacterial and fungal community variance. The results provided the relationships between microbial community and environmental variables in the studied mining sites.

Land-use change and soil type are drivers of fungal and archaeal communities in the Pampa biome.

PubMed

Lupatini, Manoeli; Jacques, Rodrigo Josemar Seminoti; Antoniolli, Zaida Inês; Suleiman, Afnan Khalil Ahmad; Fulthorpe, Roberta R; Roesch, Luiz Fernando Würdig

2013-02-01

The current study aimed to test the hypothesis that both land-use change and soil type are responsible for the major changes in the fungal and archaeal community structure and functioning of the soil microbial community in Brazilian Pampa biome. Soil samples were collected at sites with different land-uses (native grassland, native forest, Eucalyptus and Acacia plantation, soybean and watermelon field) and in a typical toposequence in Pampa biome formed by Paleudult, Albaqualf and alluvial soils. The structure of soil microbial community (archaeal and fungal) was evaluated by ribosomal intergenic spacer analysis and soil functional capabilities were measured by microbial biomass carbon and metabolic quotient. We detected different patterns in microbial community driven by land-use change and soil type, showing that both factors are significant drivers of fungal and archaeal community structure and biomass and microbial activity. Fungal community structure was more affected by land-use and archaeal community was more affected by soil type. Irrespective of the land-use or soil type, a large percentage of operational taxonomic unit were shared among the soils. We accepted the hypothesis that both land-use change and soil type are drivers of archaeal and fungal community structure and soil functional capabilities. Moreover, we also suggest the existence of a soil microbial core.

Centralized Drinking Water Treatment Operations Shape Bacterial and Fungal Community Structure.

PubMed

Ma, Xiao; Vikram, Amit; Casson, Leonard; Bibby, Kyle

2017-07-05

Drinking water microbial communities impact opportunistic pathogen colonization and corrosion of water distribution systems, and centralized drinking water treatment represents a potential control for microbial community structure in finished drinking water. In this article, we examine bacterial and fungal abundance and diversity, as well as the microbial community taxonomic structure following each unit operation in a conventional surface water treatment plant. Treatment operations drove the microbial composition more strongly than sampling time. Both bacterial and fungal abundance and diversity decreased following sedimentation and filtration; however, only bacterial abundance and diversity was significantly impacted by free chlorine disinfection. Similarly, each treatment step was found to shift bacterial and fungal community beta-diversity, with the exception of disinfection on the fungal community structure. We observed the enrichment of bacterial and fungal taxa commonly found in drinking water distribution systems through the treatment process, for example, Sphingomonas following filtration and Leptospirillium and Penicillium following disinfection. Study results suggest that centralized drinking water treatment processes shape the final drinking water microbial community via selection of community members and that the bacterial community is primarily driven by disinfection while the eukaryotic community is primarily controlled by physical treatment processes.

Effects of dissolved CO2 on Shallow Freshwater Microbial Communities simulating a CO2 Leakage Scenario

NASA Astrophysics Data System (ADS)

Gulliver, D. M.; Lowry, G. V.; Gregory, K.

2013-12-01

Geological carbon sequestration is likely to be part of a comprehensive strategy to minimize the atmospheric release of greenhouse gasses, establishing a concern of sequestered CO2 leakage into overlying potable aquifers. Leaking CO2 may affect existing biogeochemical processes and therefore water quality. There is a critical need to understand the evolution of CO2 exposed microbial communities that influence the biogeochemistry in these freshwater aquifers. The evolution of microbial ecology for different CO2 exposure concentrations was investigated using fluid-slurry samples obtained from a shallow freshwater aquifer (55 m depth, 0.5 MPa, 22 °C, Escatawpa, MS). The microbial community of well samples upstream and downstream of CO2 injection was characterized. In addition, batch vessel experiments were conducted with the upstream aquifer samples exposed to varying pCO2 from 0% to 100% under reservoir temperature and pressure for up to 56 days. The microbial community of the in situ experiment and the batch reactor experiment were analyzed with 16S rRNA clone libraries and qPCR. In both the in situ experiment and the batch reactor experiment, DNA concentration did not correlate with CO2 exposure. Both the in situ experiment and the batch reactors displayed a changing microbial community with increased CO2 exposure. The well water isolate, Curvibacter, appeared to be the most tolerant genus to high CO2 concentrations in the in situ experiments and to mid-CO2 concentrations in the batch reactors. In batch reactors with pCO2 concentrations higher than experienced in situ (pCO2 = 0.5 MPa), Pseudomonas appeared to be the most tolerant genus. Findings provide insight into a dynamic biogeochemical system that will alter with CO2 exposure. Adapted microbial populations will eventually give rise to the community that will impact the metal mobility and water quality. Knowledge of the surviving microbial populations will enable improved models for predicting the fate of CO2 following leakage and lead to better strategies for ensuring the quality of potable aquifer water.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shade, Ashley

Local diversity (within-sample or alpha diversity) is often implicated as a cause of success or failure of a microbial community. However, the relationships between diversity and emergent properties of a community, such as its stability, productivity or invasibility, are much more nuanced. In this paper, I argue that diversity without context provides limited insights into the mechanisms underpinning community patterns. I provide examples from traditional and microbial ecology to discuss common complications and assumptions about within-sample diversity that may prevent us from digging deeper into the more specific mechanisms underpinning community outcomes. I suggest that measurement of diversity should servemore » as a starting point for further inquiry of ecological mechanisms rather than an 'answer' to community outcomes.« less

Abiotic factors shape microbial diversity in Sonoran Desert soils.

PubMed

Andrew, David R; Fitak, Robert R; Munguia-Vega, Adrian; Racolta, Adriana; Martinson, Vincent G; Dontsova, Katerina

2012-11-01

High-throughput, culture-independent surveys of bacterial and archaeal communities in soil have illuminated the importance of both edaphic and biotic influences on microbial diversity, yet few studies compare the relative importance of these factors. Here, we employ multiplexed pyrosequencing of the 16S rRNA gene to examine soil- and cactus-associated rhizosphere microbial communities of the Sonoran Desert and the artificial desert biome of the Biosphere2 research facility. The results of our replicate sampling approach show that microbial communities are shaped primarily by soil characteristics associated with geographic locations, while rhizosphere associations are secondary factors. We found little difference between rhizosphere communities of the ecologically similar saguaro (Carnegiea gigantea) and cardón (Pachycereus pringlei) cacti. Both rhizosphere and soil communities were dominated by the disproportionately abundant Crenarchaeota class Thermoprotei, which comprised 18.7% of 183,320 total pyrosequencing reads from a comparatively small number (1,337 or 3.7%) of the 36,162 total operational taxonomic units (OTUs). OTUs common to both soil and rhizosphere samples comprised the bulk of raw sequence reads, suggesting that the shared community of soil and rhizosphere microbes constitute common and abundant taxa, particularly in the bacterial phyla Proteobacteria, Actinobacteria, Planctomycetes, Firmicutes, Bacteroidetes, Chloroflexi, and Acidobacteria. The vast majority of OTUs, however, were rare and unique to either soil or rhizosphere communities and differed among locations dozens of kilometers apart. Several soil properties, particularly soil pH and carbon content, were significantly correlated with community diversity measurements. Our results highlight the importance of culture-independent approaches in surveying microbial communities of extreme environments.

Abiotic Factors Shape Microbial Diversity in Sonoran Desert Soils

PubMed Central

Fitak, Robert R.; Munguia-Vega, Adrian; Racolta, Adriana; Martinson, Vincent G.; Dontsova, Katerina

2012-01-01

High-throughput, culture-independent surveys of bacterial and archaeal communities in soil have illuminated the importance of both edaphic and biotic influences on microbial diversity, yet few studies compare the relative importance of these factors. Here, we employ multiplexed pyrosequencing of the 16S rRNA gene to examine soil- and cactus-associated rhizosphere microbial communities of the Sonoran Desert and the artificial desert biome of the Biosphere2 research facility. The results of our replicate sampling approach show that microbial communities are shaped primarily by soil characteristics associated with geographic locations, while rhizosphere associations are secondary factors. We found little difference between rhizosphere communities of the ecologically similar saguaro (Carnegiea gigantea) and cardón (Pachycereus pringlei) cacti. Both rhizosphere and soil communities were dominated by the disproportionately abundant Crenarchaeota class Thermoprotei, which comprised 18.7% of 183,320 total pyrosequencing reads from a comparatively small number (1,337 or 3.7%) of the 36,162 total operational taxonomic units (OTUs). OTUs common to both soil and rhizosphere samples comprised the bulk of raw sequence reads, suggesting that the shared community of soil and rhizosphere microbes constitute common and abundant taxa, particularly in the bacterial phyla Proteobacteria, Actinobacteria, Planctomycetes, Firmicutes, Bacteroidetes, Chloroflexi, and Acidobacteria. The vast majority of OTUs, however, were rare and unique to either soil or rhizosphere communities and differed among locations dozens of kilometers apart. Several soil properties, particularly soil pH and carbon content, were significantly correlated with community diversity measurements. Our results highlight the importance of culture-independent approaches in surveying microbial communities of extreme environments. PMID:22885757

A comparison of microbial communities in deep-sea polymetallic nodules and the surrounding sediments in the Pacific Ocean

NASA Astrophysics Data System (ADS)

Wu, Yue-Hong; Liao, Li; Wang, Chun-Sheng; Ma, Wei-Lin; Meng, Fan-Xu; Wu, Min; Xu, Xue-Wei

2013-09-01

Deep-sea polymetallic nodules, rich in metals such as Fe, Mn, and Ni, are potential resources for future exploitation. Early culturing and microscopy studies suggest that polymetallic nodules are at least partially biogenic. To understand the microbial communities in this environment, we compared microbial community composition and diversity inside nodules and in the surrounding sediments. Three sampling sites in the Pacific Ocean containing polymetallic nodules were used for culture-independent investigations of microbial diversity. A total of 1013 near full-length bacterial 16S rRNA gene sequences and 640 archaeal 16S rRNA gene sequences with ~650 bp from nodules and the surrounding sediments were analyzed. Bacteria showed higher diversity than archaea. Interestingly, sediments contained more diverse bacterial communities than nodules, while the opposite was detected for archaea. Bacterial communities tend to be mostly unique to sediments or nodules, with only 13.3% of sequences shared. The most abundant bacterial groups detected only in nodules were Pseudoalteromonas and Alteromonas, which were predicted to play a role in building matrix outside cells to induce or control mineralization. However, archaeal communities were mostly shared between sediments and nodules, including the most abundant OTU containing 290 sequences from marine group I Thaumarchaeota. PcoA analysis indicated that microhabitat (i.e., nodule or sediment) seemed to be a major factor influencing microbial community composition, rather than sampling locations or distances between locations.

A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments.

PubMed

Olesen, Scott W; Vora, Suhani; Techtmann, Stephen M; Fortney, Julian L; Bastidas-Oyanedel, Juan R; Rodríguez, Jorge; Hazen, Terry C; Alm, Eric J

2016-01-01

Many microbial ecology experiments use sequencing data to measure a community's response to an experimental treatment. In a common experimental design, two units, one control and one experimental, are sampled before and after the treatment is applied to the experimental unit. The four resulting samples contain information about the dynamics of organisms that respond to the treatment, but there are no analytical methods designed to extract exactly this type of information from this configuration of samples. Here we present an analytical method specifically designed to visualize and generate hypotheses about microbial community dynamics in experiments that have paired samples and few or no replicates. The method is based on the Poisson lognormal distribution, long studied in macroecology, which we found accurately models the abundance distribution of taxa counts from 16S rRNA surveys. To demonstrate the method's validity and potential, we analyzed an experiment that measured the effect of crude oil on ocean microbial communities in microcosm. Our method identified known oil degraders as well as two clades, Maricurvus and Rhodobacteraceae, that responded to amendment with oil but do not include known oil degraders. Our approach is sensitive to organisms that increased in abundance only in the experimental unit but less sensitive to organisms that increased in both control and experimental units, thus mitigating the role of "bottle effects".

Replicating the microbial community and water quality performance of full-scale slow sand filters in laboratory-scale filters.

PubMed

Haig, Sarah-Jane; Quince, Christopher; Davies, Robert L; Dorea, Caetano C; Collins, Gavin

2014-09-15

Previous laboratory-scale studies to characterise the functional microbial ecology of slow sand filters have suffered from methodological limitations that could compromise their relevance to full-scale systems. Therefore, to ascertain if laboratory-scale slow sand filters (L-SSFs) can replicate the microbial community and water quality production of industrially operated full-scale slow sand filters (I-SSFs), eight cylindrical L-SSFs were constructed and were used to treat water from the same source as the I-SSFs. Half of the L-SSFs sand beds were composed of sterilized sand (sterile) from the industrial filters and the other half with sand taken directly from the same industrial filter (non-sterile). All filters were operated for 10 weeks, with the microbial community and water quality parameters sampled and analysed weekly. To characterize the microbial community phyla-specific qPCR assays and 454 pyrosequencing of the 16S rRNA gene were used in conjunction with an array of statistical techniques. The results demonstrate that it is possible to mimic both the water quality production and the structure of the microbial community of full-scale filters in the laboratory - at all levels of taxonomic classification except OTU - thus allowing comparison of LSSF experiments with full-scale units. Further, it was found that the sand type composing the filter bed (non-sterile or sterile), the water quality produced, the age of the filters and the depth of sand samples were all significant factors in explaining observed differences in the structure of the microbial consortia. This study is the first to the authors' knowledge that demonstrates that scaled-down slow sand filters can accurately reproduce the water quality and microbial consortia of full-scale slow sand filters. Copyright © 2014 Elsevier Ltd. All rights reserved.

Vertical structure and pH as factors for chitinolytic and pectinolytic microbial community of soils and terrestrial ecosystems of different climatic zones

NASA Astrophysics Data System (ADS)

Lukacheva, Evgeniya; Natalia, Manucharova

2016-04-01

Chitin is a naturally occurring fibre-forming polymer that plays a protective role in many lower animals similar to that of cellulose in plants. Also it's a compound of cell walls of fungi. Chemically it is a long-chain unbranched polysaccharide made of N-acetylglucosamine residues; it is the second most abundant organic compound in nature, after cellulose. Pectin is a structural heteropolysaccharide contained in the primary cell walls of terrestrial plants. Roots of the plants and root crops contain pectin. Chitin and pectin are widely distributed throughout the natural world. Structural and functional features of the complex microbial degradation of biopolymers one of the most important direction in microbial ecology. But there is no a lot of data concerns degradation in vertical structure of terrestrial ecosystems and detailed studies concerning certain abiotic features as pH. Microbial complexes of natural areas were analyzed only as humus horizons (A1) of the soil profile. Only small part of microbial community could be studied with this approach. It is known that ecosystems have their own structure. It is possible to allocate some vertical tiers: phylloplane, litter (soil covering), soil. We investigated chitinolytic and pectinolytic microbial communities dedicated to different layers of the ecosystems. Also it was described depending on pH dominated in certain ecosystem with certain conditions. Quantity of eukaryote and procaryote organisms increased in the test samples with chitin and pectin. Increasing of eukaryote in samples with pectin was more then in samples with chitin. Also should be noted the significant increasing of actinomycet's quantity in the samples with chitin in comparison with samples with pectin. The variety and abundance of bacteria in the litter samples increased an order of magnitude as compared to other probes. Further prokaryote community was investigated by method FISH (fluorescence in situ hybridization). FISH is a cytogenetic technique developed that is used to detect and localize the presence or absence of specific DNA sequences on chromosomes. pH as one of the factors which can have influence on degradation of biopolymers was studied for chitiolytic communities of different zones. And results were compared with direct studyings by method of "sowing" on a Petri dishes. Thus, we compared old classical methods with modern molecular studies. The difference between climatic zones was studied and the mathematical model was created. The mathematic model could be use in different aims, such as prognosis of microbial community composition and their classification.

The patterns of bacterial community and relationships between sulfate-reducing bacteria and hydrochemistry in sulfate-polluted groundwater of Baogang rare earth tailings.

PubMed

An, Xinli; Baker, Paul; Li, Hu; Su, Jianqiang; Yu, Changping; Cai, Chao

2016-11-01

Microorganisms are the primary agents responsible for the modification, degradation, and/or detoxification of pollutants, and thus, they play a major role in their natural attenuation; yet, little is known about the structure and diversity of the subsurface community and relationships between microbial community and groundwater hydrochemistry. In this study, denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) allowed a comparative microbial community analysis of sulfate-contaminated groundwater samples from nine different wells in the region of Baogang rare earth tailings. Using real-time PCR, the abundance of total bacteria and the sulfate-reducing genes of aprA and dsrB were quantified. Statistical analyses showed a clear distinction of the microbial community diversity between the contaminated and uncontaminated samples, with Proteobacteria being the most dominant members of the microbial community. SO 4 2- concentrations exerted a significant effect on the variation of the bacterial community (P < 0.05), with higher concentrations of sulfate reducing the microbial diversity (H' index), indicating that human activity (e.g., mining industries) was a possible factor disturbing the structure of the bacterial community. Quantitative analysis of the functional genes showed that the proportions of dsrB to total bacteria were 0.002-2.85 %, and the sulfate-reducing bacteria (SRB) were predominant within the prokaryotic community in the groundwater. The uncontaminated groundwater with low sulfate concentration harbored higher abundance of SRB than that in the polluted samples, while no significant correlation was observed between sulfate concentrations and SRB abundances in this study, suggesting other environmental factors possibly contributed to different distributions and abundances of SRB in the different sites. The results should facilitate expanded studies to identify robust microbe-environment interactions and provide a strong foundation for qualitative exploration of the bacterial diversity in rare earth tailings groundwater that might ultimately be incorporated into the remediation of environmental contamination.

Comparison of the Microbial Community Structures of Untreated Wastewaters from Different Geographic Locales

PubMed Central

Shanks, Orin C.; Newton, Ryan J.; Kelty, Catherine A.; Huse, Susan M.; Sogin, Mitchell L.

2013-01-01

Microbial sewage communities consist of a combination of human fecal microorganisms and nonfecal microorganisms, which may be residents of urban sewer infrastructure or flowthrough originating from gray water or rainwater inputs. Together, these different microorganism sources form an identifiable community structure that may serve as a signature for sewage discharges and as candidates for alternative indicators specific for human fecal pollution. However, the structure and variability of this community across geographic space remains uncharacterized. We used massively parallel 454 pyrosequencing of the V6 region in 16S rRNA genes to profile microbial communities from 13 untreated sewage influent samples collected from a wide range of geographic locations in the United States. We obtained a total of 380,175 high-quality sequences for sequence-based clustering, taxonomic analyses, and profile comparisons. The sewage profile included a discernible core human fecal signature made up of several abundant taxonomic groups within Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. DNA sequences were also classified into fecal, sewage infrastructure (i.e., nonfecal), and transient groups based on data comparisons with fecal samples. Across all sewage samples, an estimated 12.1% of sequences were fecal in origin, while 81.4% were consistently associated with the sewage infrastructure. The composition of feces-derived operational taxonomic units remained congruent across all sewage samples regardless of geographic locale; however, the sewage infrastructure community composition varied among cities, with city latitude best explaining this variation. Together, these results suggest that untreated sewage microbial communities harbor a core group of fecal bacteria across geographically dispersed wastewater sewage lines and that ambient water quality indicators targeting these select core microorganisms may perform well across the United States. PMID:23435885

Clustering behavior in microbial communities from acute endodontic infections.

PubMed

Montagner, Francisco; Jacinto, Rogério C; Signoretti, Fernanda G C; Sanches, Paula F; Gomes, Brenda P F A

2012-02-01

Acute endodontic infections harbor heterogeneous microbial communities in both the root canal (RC) system and apical tissues. Data comparing the microbial structure and diversity in endodontic infections in related ecosystems, such as RC with necrotic pulp and acute apical abscess (AAA), are scarce in the literature. The aim of this study was to examine the presence of selected endodontic pathogens in paired samples from necrotic RC and AAA using polymerase chain reaction (PCR) followed by the construction of cluster profiles. Paired samples of RC and AAA exudates were collected from 20 subjects and analyzed by PCR for the presence of selected strict and facultative anaerobic strains. The frequency of species was compared between the RC and the AAA samples. A stringent neighboring clustering algorithm was applied to investigate the existence of similar high-order groups of samples. A dendrogram was constructed to show the arrangement of the sample groups produced by the hierarchical clustering. All samples harbored bacterial DNA. Porphyromonas endodontalis, Prevotella nigrescens, Filifactor alocis, and Tannerela forsythia were frequently detected in both RC and AAA samples. The selected anaerobic species were distributed in diverse small bacteria consortia. The samples of RC and AAA that presented at least one of the targeted microorganisms were grouped in small clusters. Anaerobic species were frequently detected in acute endodontic infections and heterogeneous microbial communities with low clustering behavior were observed in paired samples of RC and AAA. Copyright © 2012. Published by Elsevier Inc.

Size really does matter: effects of filter fractionation on microbial community structure in a model oxygen minimum zone.

NASA Astrophysics Data System (ADS)

Torres Beltran, M.

2016-02-01

The Scientific Committee on Oceanographic Research (SCOR) Working Group 144 "Microbial Community Responses to Ocean Deoxygenation" workshop held in Vancouver, British Columbia in July 2014 had the primary objective of kick-starting the establishment of a minimal core of technologies, techniques and standard operating procedures (SOPs) to enable compatible process rate and multi-molecular data (DNA, RNA and protein) collection in marine oxygen minimum zones (OMZs) and other oxygen starved waters. Experimental activities conducted in Saanich Inlet, a seasonally anoxic fjord on Vancouver Island British Columbia, were designed to compare and cross-calibrate in situ sampling devices (McLane PPS system) with conventional bottle sampling and incubation methods. Bottle effects on microbial community composition, and activity were tested using different filter combinations and sample volumes to compare PPS/IPS (0.4 µm) versus Sterivex (0.22 µm) filtration methods with and without prefilters (2.7 µm). Resulting biomass was processed for small subunit ribosomal RNA gene sequencing across all three domains of life on the 454 platform followed by downstream community structure analyses. Significant community shifts occurred within and between filter fractions for in situ versus on-ship processed samples. For instance, the relative abundance of several bacterial phyla including Bacteroidetes, Delta and Gammaproteobacteria decreased five-fold on-ship when compared to in situ filtration. Similarly, experimental mesocosms showed similar community structure and activity to in situ filtered samples indicating the need to cross-calibrate incubations to constrain bottle effects. In addition, alpha and beta diversity significantly changed as function of filter size and volume, as well as the operational taxonomic units identified using indicator species analysis for each filter size. Our results provide statistical support that microbial community structure is systematically biased by filter fraction methods and highlight the need for establishing compatible techniques among researchers that facilitate comparative and reproducible science for the whole community.

Microbial populations in contaminant plumes

USGS Publications Warehouse

Haack, S.K.; Bekins, B.A.

2000-01-01

Efficient biodegradation of subsurface contaminants requires two elements: (1) microbial populations with the necessary degradative capabilities, and (2) favorable subsurface geochemical and hydrological conditions. Practical constraints on experimental design and interpretation in both the hydrogeological and microbiological sciences have resulted in limited knowledge of the interaction between hydrogeological and microbiological features of subsurface environments. These practical constraints include: (1) inconsistencies between the scales of investigation in the hydrogeological and microbiological sciences, and (2) practical limitations on the ability to accurately define microbial populations in environmental samples. However, advances in application of small-scale sampling methods and interdisciplinary approaches to site investigations are beginning to significantly improve understanding of hydrogeological and microbiological interactions. Likewise, culture-based and molecular analyses of microbial populations in subsurface contaminant plumes have revealed significant adaptation of microbial populations to plume environmental conditions. Results of recent studies suggest that variability in subsurface geochemical and hydrological conditions significantly influences subsurface microbial-community structure. Combined investigations of site conditions and microbial-community structure provide the knowledge needed to understand interactions between subsurface microbial populations, plume geochemistry, and contaminant biodegradation.

The Inter-Valley Soil Comparative Survey: the ecology of Dry Valley edaphic microbial communities

PubMed Central

Lee, Charles K; Barbier, Béatrice A; Bottos, Eric M; McDonald, Ian R; Cary, Stephen Craig

2012-01-01

Recent applications of molecular genetics to edaphic microbial communities of the McMurdo Dry Valleys and elsewhere have rejected a long-held belief that Antarctic soils contain extremely limited microbial diversity. The Inter-Valley Soil Comparative Survey aims to elucidate the factors shaping these unique microbial communities and their biogeography by integrating molecular genetic approaches with biogeochemical analyses. Although the microbial communities of Dry Valley soils may be complex, there is little doubt that the ecosystem's food web is relatively simple, and evidence suggests that physicochemical conditions may have the dominant role in shaping microbial communities. To examine this hypothesis, bacterial communities from representative soil samples collected in four geographically disparate Dry Valleys were analyzed using molecular genetic tools, including pyrosequencing of 16S rRNA gene PCR amplicons. Results show that the four communities are structurally and phylogenetically distinct, and possess significantly different levels of diversity. Strikingly, only 2 of 214 phylotypes were found in all four valleys, challenging a widespread assumption that the microbiota of the Dry Valleys is composed of a few cosmopolitan species. Analysis of soil geochemical properties indicated that salt content, alongside altitude and Cu2+, was significantly correlated with differences in microbial communities. Our results indicate that the microbial ecology of Dry Valley soils is highly localized and that physicochemical factors potentially have major roles in shaping the microbiology of ice-free areas of Antarctica. These findings hint at links between Dry Valley glacial geomorphology and microbial ecology, and raise previously unrecognized issues related to environmental management of this unique ecosystem. PMID:22170424

Changes in microbial structure and functional communities at different soil depths during 13C labelled root litter degradation

NASA Astrophysics Data System (ADS)

Sanaullah, Muhammad; Baumann, Karen; Chabbi, Abad; Dignac, Marie-France; Maron, Pierre-Alain; Kuzyakov, Yakov; Rumpel, Cornelia

2014-05-01

Soil organic matter turnover depends on substrate quality and microbial activity in soil but little is known about how addition of freshly added organic material modifies the diversity of soil microbial communities with in a soil profile. We took advantage of a decomposition experiment, which was carried out at different soil depths under field conditions and sampled litterbags with 13C-labelled wheat roots, incubated in subsoil horizons at 30, 60 and 90 cm depth for up to 36 months. The effect of root litter addition on microbial community structure, diversity and activity was studied by determining total microbial biomass, PLFA signatures, molecular tools (DNA genotyping and pyrosequencing of 16S and 18S rDNAs) and extracellular enzyme activities. Automated ribosomal intergenic spacer analysis (ARISA) was also carried out to determine the differences in microbial community structure. We found that with the addition of root litter, total microbial biomass as well as microbial community composition and structure changed at different soil depths and change was significantly higher at top 30cm soil layer. Moreover, in the topsoil, population of both gram-positive and gram-negative bacteria increased with root litter addition over time, while subsoil horizons were relatively dominated by fungal community. Extra-cellular enzyme activities confirmed relatively higher fungal community at subsoil horizons compared with surface soil layer with bacteria dominant microbial population. Bacterial-ARISA profiling illustrated that the addition of root litter enhanced the abundance of Actinobacteria and Proteobacteria, at all three soil depths. These bacteria correspond to copiotrophic attributes, which can preferentially consume of labile soil organic C pools. While disappearance of oligotrophic Acidobacteria confirmed the shifting of microbial communities due to the addition of readily available substrate. We concluded that root litter mixing altered microbial community development which was soil horizon specific and its effects on soil microbial activity may impact on nutrient cycling.

Planktonic microbial community responses to added copper.

PubMed

Le Jeune, Anne-Hélène; Charpin, Marie; Sargos, Denis; Lenain, Jean-François; Deluchat, Véronique; Ngayila, Nadine; Baudu, Michel; Amblard, Christian

2007-07-20

It is generally agreed that autotrophic organisms and especially phytoplanktonic species can be harmed by copper through its effect on photosystem. However, the impact of copper on other components of the pelagic food web, such as the microbial loop (autotrophic and heterotrophic picoplankton, pigmented and non-pigmented flagellates and ciliates) has received little attention. Indoor experiments were conducted to evaluate the direct and indirect effects of copper, supplied in the range of concentrations used to control cyanobacteria growth in ponds, on non-targeted organisms of natural microbial loop communities sampled in spring and summer. Two copper concentrations were tested (80microgL(-1) and 160microgL(-1) final concentrations), set, respectively, below and above the ligand binding capacity of the water samples. Both caused a significant decrease in the biomass and diversity of pigmented organisms (picophytoplankton and pigmented flagellates). Conversely, the heterotrophic bacterioplankton and the heterotrophic flagellates did not seem to be directly affected by either copper treatment in terms of biomass or diversity, according to the descriptor chosen. The ciliate biomass was significantly reduced with increasing copper concentrations, but differences in sensitivity appeared between spring and summer communities. Potential mixotrophic and nanoplanktorivorous ciliates appeared to be more sensitive to copper treatments than bacterivorous ciliates, suggesting a stronger direct and (or) indirect effect of copper on the former. Copper sulphate treatments had a significant restructuring effect on the microbial loop communities, resulting in a dominance of heterotrophic bacterioplankton among microbial microorganisms 27 days after the beginning of the treatment. The spring microbial communities exhibited a greater sensitivity than the summer communities with respect to their initial compositions.

Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism.

PubMed

Graham, Emily B; Crump, Alex R; Resch, Charles T; Fansler, Sarah; Arntzen, Evan; Kennedy, David W; Fredrickson, Jim K; Stegen, James C

2016-01-01

Community assembly processes generate shifts in species abundances that influence ecosystem cycling of carbon and nutrients, yet our understanding of assembly remains largely separate from ecosystem-level functioning. Here, we investigate relationships between assembly and changes in microbial metabolism across space and time in hyporheic microbial communities. We pair sampling of two habitat types (i.e., attached and planktonic) through seasonal and sub-hourly hydrologic fluctuation with null modeling and temporally explicit multivariate statistics. We demonstrate that multiple selective pressures-imposed by sediment and porewater physicochemistry-integrate to generate changes in microbial community composition at distinct timescales among habitat types. These changes in composition are reflective of contrasting associations of Betaproteobacteria and Thaumarchaeota with ecological selection and with seasonal changes in microbial metabolism. We present a conceptual model based on our results in which metabolism increases when oscillating selective pressures oppose temporally stable selective pressures. Our conceptual model is pertinent to both macrobial and microbial systems experiencing multiple selective pressures and presents an avenue for assimilating community assembly processes into predictions of ecosystem-level functioning.

Reactivation of Deep Subsurface Microbial Community in Response to Methane or Methanol Amendment

PubMed Central

Rajala, Pauliina; Bomberg, Malin

2017-01-01

Microbial communities in deep subsurface environments comprise a large portion of Earth’s biomass, but the microbial activity in these habitats is largely unknown. Here, we studied how microorganisms from two isolated groundwater fractures at 180 and 500 m depths of the Outokumpu Deep Drillhole (Finland) responded to methane or methanol amendment, in the presence or absence of sulfate as an additional electron acceptor. Methane is a plausible intermediate in the deep subsurface carbon cycle, and electron acceptors such as sulfate are critical components for oxidation processes. In fact, the majority of the available carbon in the Outokumpu deep biosphere is present as methane. Methanol is an intermediate of methane oxidation, but may also be produced through degradation of organic matter. The fracture fluid samples were incubated in vitro with methane or methanol in the presence or absence of sulfate as electron acceptor. The metabolic response of microbial communities was measured by staining the microbial cells with fluorescent redox sensitive dye combined with flow cytometry, and DNA or cDNA-derived amplicon sequencing. The microbial community of the fracture zone at the 180 m depth was originally considerably more respiratory active and 10-fold more numerous (105 cells ml-1 at 180 m depth and 104 cells ml-1 at 500 m depth) than the community of the fracture zone at the 500 m. However, the dormant microbial community at the 500 m depth rapidly reactivated their transcription and respiration systems in the presence of methane or methanol, whereas in the shallower fracture zone only a small sub-population was able to utilize the newly available carbon source. In addition, the composition of substrate activated microbial communities differed at both depths from original microbial communities. The results demonstrate that OTUs representing minor groups of the total microbial communities play an important role when microbial communities face changes in environmental conditions. PMID:28367144

Microbial communities and natural fermentation of corn silages prepared with farm bunker-silo in Southwest China.

PubMed

Guan, Hao; Yan, Yanhong; Li, Xiaoling; Li, Xiaomei; Shuai, Yang; Feng, Guangyan; Ran, Qifan; Cai, Yimin; Li, Ying; Zhang, Xinquan

2018-06-08

This study analyzed the variation of microbial communities, their achieved fermentation quality, and the association between microbial diversity and environmental factors after ensiling of 96 samples prepared with bunker-silo in Southwest China. Most of natural corn silages achieved good fermentation, e.g., low pH value (<4.2) and high levels of lactic acid (36.26-79.83 mg/g DM). Weissella species were the dominant epiphytic bacteria in raw material, while Lactobacillus and Acetobacter species were prevalent in silages. Natural Lactobacillus and Pediococcus species produced more lactic acid during ensiling, while the production of acetic acid was highly positively correlated with both Acetobacter and Bradyrhizobium species. Rainfall and humidity affected community of epiphytic bacteria on the corn material, and the temperature affected richness of bacterial species during ensiling. The results confirmed that microbial community of silages in hot and humid area is unique and climatic factors ultimately affect the fermentation quality through influencing microbial community. Copyright © 2018 Elsevier Ltd. All rights reserved.

GeoChip-based analysis of microbial functional gene diversity in a landfill leachate-contaminated aquifer

USGS Publications Warehouse

Lu, Zhenmei; He, Zhili; Parisi, Victoria A.; Kang, Sanghoon; Deng, Ye; Van Nostrand, Joy D.; Masoner, Jason R.; Cozzarelli, Isabelle M.; Suflita, Joseph M.; Zhou, Jizhong

2012-01-01

The functional gene diversity and structure of microbial communities in a shallow landfill leachate-contaminated aquifer were assessed using a comprehensive functional gene array (GeoChip 3.0). Water samples were obtained from eight wells at the same aquifer depth immediately below a municipal landfill or along the predominant downgradient groundwater flowpath. Functional gene richness and diversity immediately below the landfill and the closest well were considerably lower than those in downgradient wells. Mantel tests and canonical correspondence analysis (CCA) suggested that various geochemical parameters had a significant impact on the subsurface microbial community structure. That is, leachate from the unlined landfill impacted the diversity, composition, structure, and functional potential of groundwater microbial communities as a function of groundwater pH, and concentrations of sulfate, ammonia, and dissolved organic carbon (DOC). Historical geochemical records indicate that all sampled wells chronically received leachate, and the increase in microbial diversity as a function of distance from the landfill is consistent with mitigation of the impact of leachate on the groundwater system by natural attenuation mechanisms.

A Multi-Omics Approach to Evaluate the Quality of Milk Whey Used in Ricotta Cheese Production

PubMed Central

Sattin, Eleonora; Andreani, Nadia A.; Carraro, Lisa; Lucchini, Rosaria; Fasolato, Luca; Telatin, Andrea; Balzan, Stefania; Novelli, Enrico; Simionati, Barbara; Cardazzo, Barbara

2016-01-01

In the past, milk whey was only a by-product of cheese production, but currently, it has a high commercial value for use in the food industries. However, the regulation of whey management (i.e., storage and hygienic properties) has not been updated, and as a consequence, its microbiological quality is very challenging for food safety. The Next Generation Sequencing (NGS) technique was applied to several whey samples used for Ricotta production to evaluate the microbial community composition in depth using both RNA and DNA as templates for NGS library construction. Whey samples demonstrating a high microbial and aerobic spore load contained mostly Firmicutes; although variable, some samples contained a relevant amount of Gammaproteobacteria. Several lots of whey acquired as raw material for Ricotta production presented defective organoleptic properties. To define the volatile compounds in normal and defective whey samples, a headspace gas chromatography/mass spectrometry (GC/MS) analysis was conducted. The statistical analysis demonstrated that different microbial communities resulted from DNA or cDNA library sequencing, and distinguishable microbiota composed the communities contained in the organoleptic-defective whey samples. PMID:27582735

Microbial diversity and carbon cycling in San Francisco Bay wetlands

DOE Office of Scientific and Technical Information (OSTI.GOV)

Theroux, Susanna; Hartman, Wyatt; He, Shaomei

Wetland restoration efforts in San Francisco Bay aim to rebuild habitat for endangered species and provide an effective carbon storage solution, reversing land subsidence caused by a century of industrial and agricultural development. However, the benefits of carbon sequestration may be negated by increased methane production in newly constructed wetlands, making these wetlands net greenhouse gas (GHG) sources to the atmosphere. We investigated the effects of wetland restoration on below-ground microbial communities responsible for GHG cycling in a suite of historic and restored wetlands in SF Bay. Using DNA and RNA sequencing, coupled with real-time GHG monitoring, we profiled themore » diversity and metabolic potential of wetland soil microbial communities. The wetland soils harbor diverse communities of bacteria and archaea whose membership varies with sampling location, proximity to plant roots and sampling depth. Our results also highlight the dramatic differences in GHG production between historic and restored wetlands and allow us to link microbial community composition and GHG cycling with key environmental variables including salinity, soil carbon and plant species.« less

From lithotroph- to organotroph-dominant: directional shift of microbial community in sulphidic tailings during phytostabilization

PubMed Central

Li, Xiaofang; Bond, Philip L.; Van Nostrand, Joy D.; Zhou, Jizhong; Huang, Longbin

2015-01-01

Engineering microbial diversity to enhance soil functions may improve the success of direct revegetation in sulphidic mine tailings. Therefore, it is essential to explore how remediation and initial plant establishment can alter microbial communities, and, which edaphic factors control these changes under field conditions. A long-term revegetation trial was established at a Pb-Zn-Cu tailings impoundment in northwest Queensland. The control and amended and/or revegetated treatments were sampled from the 3-year-old trial. In total, 24 samples were examined using pyrosequencing of 16S rRNA genes and various chemical properties. The results showed that the microbial diversity was positively controlled by soil soluble Si and negatively controlled by soluble S, total Fe and total As, implying that pyrite weathering posed a substantial stress on microbial development in the tailings. All treatments were dominated by typical extremophiles and lithotrophs, typically Truepera, Thiobacillus, Rubrobacter; significant increases in microbial diversity, biomass and frequency of organotrophic genera (typically Nocardioides and Altererythrobacter) were detected in the revegetated and amended treatment. We concluded that appropriate phytostabilization options have the potential to drive the microbial diversity and community structure in the tailings toward those of natural soils, however, inherent environmental stressors may limit such changes. PMID:26268667

When micro meets macro: microbial lipid analysis and ecosystem ecology

NASA Astrophysics Data System (ADS)

Balser, T.; Gutknecht, J.

2008-12-01

There is growing interest in linking soil microbial community composition and activity with large-scale field studies of nutrient cycling or plant community response to disturbances. And while analysis of microbial communities has moved rapidly in the past decade from culture-based to non-culture based techniques, still it must be asked what have we gained from the move? How well does the necessarily micro-scale of microbial analysis allow us to address questions of interest at the macro-scale? Several challenges exist in bridging the scales, and foremost is the question of methodological feasibility. Past microbiological methodologies have not been readily adaptable to the large sample sizes necessary for ecosystem-scale research. As a result, it has been difficult to generate compatible microbial and ecosystem data sets. We describe the use of a modified lipid extraction method to generate microbial community data sets that allow us to match landscape-scale or long-term ecological studies with microbial community data. We briefly discuss the challenges and advantages associated with lipid analysis as an approach to addressing ecosystem ecological studies, and provide examples from our research in ecosystem restoration and recovery following disturbance and climate change.

Distinct Ecological Niche of Anal, Oral, and Cervical Mucosal Microbiomes in Adolescent Women.

PubMed

Smith, Benjamin C; Zolnik, Christine P; Usyk, Mykhaylo; Chen, Zigui; Kaiser, Katherine; Nucci-Sack, Anne; Peake, Ken; Diaz, Angela; Viswanathan, Shankar; Strickler, Howard D; Schlecht, Nicolas F; Burk, Robert D

2016-09-01

Human body sites represent ecological niches for microorganisms, each providing variations in microbial exposure, nutrient availability, microbial competition, and host immunological responses. In this study, we investigated the oral, anal, and cervical microbiomes from the same 20 sexually active adolescent females, using culture-independent, next-generation sequencing. DNA from each sample was amplified for the bacterial 16S rRNA gene and sequenced on an Illumina platform using paired-end reads. Across the three anatomical niches, we found significant differences in bacterial community composition and diversity. Overall anal samples were dominated with Prevotella and Bacteriodes , oral samples with Streptococcus and Prevotella , and cervical samples with Lactobacillus . The microbiomes of a few cervical samples clustered with anal samples in weighted principal coordinate analyses, due in part to a higher proportion of Prevotella in those samples. Additionally, cervical samples had the lowest alpha diversity. Our results demonstrate the occurrence of distinct microbial communities across body sites within the same individual.

The effect of temperature change on the microbial diversity and community structure along the chronosequence of the sub-arctic glacier forefield of Styggedalsbreen (Norway).

PubMed

Mateos-Rivera, Alejandro; Yde, Jacob C; Wilson, Bryan; Finster, Kai W; Reigstad, Laila J; Øvreås, Lise

2016-04-01

Microbial communities in the glacier forefield of Styggedalsbreen, Norway, were investigated along a chronosequence from newly exposed soil to vegetated soils using next-generation sequencing of the 16S rRNA gene. In order to monitor the short-term effect of temperature on community successions along the soil gradient, the soil samples were incubated at three different temperatures (5°C, 10°C and 22°C). The microbial community composition along the chronosequence differed according to distance from the glacial terminus and incubation temperature. Samples close to the glacier terminus were dominated by Proteobacteria at 5°C and 10°C, while at 22°C members of Chloroflexi, Acidobacteria and Verrucomicrobia in addition to Proteobacteria accounted for most of the diversity, indicating that sites close to the glacier terminus are more closely related to former subglacial environments. Within the Archaea domain, members of the phylum Euryarchaeota dominated in samples closer to the glacier terminus with a shift to members of the phyla Thaumarchaeota-Crenarchaeota with increased soil age. Our data indicate that composition and diversity of the microbial communities along the glacier forefield depend not only on exposure time but are also to a large degree influenced by soil surface temperature and soil maturation. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Development of a Genome-Proxy Microarray for Profiling Marine Microbial Communities and its Application to a Time Series in Monterey Bay, California

DTIC Science & Technology

2008-09-01

community representation. 12 survey a complex microbial community. Community DNA or rRNA extracted from a sample may require amplification before...restricted to cultivated clades, since not only do many clades have sufficient database representation due to 16S environmental surveys , but such...well developed for standard and comprehensive surveys . Depending on the population being targeted and the identification method, FCM can be a

Microbial communities in bulk fluids and biofilms of an oil facility have similar composition but different structure.

PubMed

Stevenson, Bradley S; Drilling, Heather S; Lawson, Paul A; Duncan, Kathleen E; Parisi, Victoria A; Suflita, Joseph M

2011-04-01

The oil-water-gas environments of oil production facilities harbour abundant and diverse microbial communities that can participate in deleterious processes such as biocorrosion. Several molecular methods, including pyrosequencing of 16S rRNA libraries, were used to characterize the microbial communities from an oil production facility on the Alaskan North Slope. The communities in produced water and a sample from a 'pig envelope' were compared in order to identify specific populations or communities associated with biocorrosion. The 'pigs' are used for physical mitigation of pipeline corrosion and fouling and the samples are enriched in surface-associated solids (i.e. paraffins, minerals and biofilm) and coincidentally, microorganisms (over 10(5) -fold). Throughout the oil production facility, bacteria were more abundant (10- to 150-fold) than archaea, with thermophilic members of the phyla Firmicutes (Thermoanaerobacter and Thermacetogenium) and Synergistes (Thermovirga) dominating the community. However, the structure (relative abundances of taxa) of the microbial community in the pig envelope was distinct due to the increased relative abundances of the genera Thermacetogenium and Thermovirga. The data presented here suggest that bulk fluid is representative of the biofilm communities associated with biocorrosion but that certain populations are more abundant in biofilms, which should be the focus of monitoring and mitigation strategies. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Aquifer environment selects for microbial species cohorts in sediment and groundwater

PubMed Central

Hug, Laura A; Thomas, Brian C; Brown, Christopher T; Frischkorn, Kyle R; Williams, Kenneth H; Tringe, Susannah G; Banfield, Jillian F

2015-01-01

Little is known about the biogeography or stability of sediment-associated microbial community membership because these environments are biologically complex and generally difficult to sample. High-throughput-sequencing methods provide new opportunities to simultaneously genomically sample and track microbial community members across a large number of sampling sites or times, with higher taxonomic resolution than is associated with 16 S ribosomal RNA gene surveys, and without the disadvantages of primer bias and gene copy number uncertainty. We characterized a sediment community at 5 m depth in an aquifer adjacent to the Colorado River and tracked its most abundant 133 organisms across 36 different sediment and groundwater samples. We sampled sites separated by centimeters, meters and tens of meters, collected on seven occasions over 6 years. Analysis of 1.4 terabase pairs of DNA sequence showed that these 133 organisms were more consistently detected in saturated sediments than in samples from the vadose zone, from distant locations or from groundwater filtrates. Abundance profiles across aquifer locations and from different sampling times identified organism cohorts that comprised subsets of the 133 organisms that were consistently associated. The data suggest that cohorts are partly selected for by shared environmental adaptation. PMID:25647349

An endangered oasis of aquatic microbial biodiversity in the Chihuahuan desert

PubMed Central

Souza, Valeria; Espinosa-Asuar, Laura; Escalante, Ana E.; Eguiarte, Luis E.; Farmer, Jack; Forney, Larry; Lloret, Lourdes; Rodríguez-Martínez, Juan M.; Soberón, Xavier; Dirzo, Rodolfo; Elser, James J.

2006-01-01

The Cuatro Cienegas basin in the Chihuahuan desert is a system of springs, streams, and pools. These ecosystems support >70 endemic species and abundant living stromatolites and other microbial communities, representing a desert oasis of high biodiversity. Here, we combine data from molecular microbiology and geology to document the microbial biodiversity of this unique environment. Ten water samples from locations within the Cuatro Cienegas basin and two neighboring valleys as well as three samples of wet sediments were analyzed. The phylogeny of prokaryotic populations in the samples was determined by characterizing cultured organisms and by PCR amplification and sequencing of 16S rRNA genes from total community DNA. The composition of microbial communities was also assessed by determining profiles of terminal restriction site polymorphisms of 16S rRNA genes in total community DNA. There were 250 different phylotypes among the 350 cultivated strains. Ninety-eight partial 16S rRNA gene sequences were obtained and classified. The clones represented 38 unique phylotypes from ten major lineages of Bacteria and one of Archaea. Unexpectedly, 50% of the phylotypes were most closely related to marine taxa, even though these environments have not been in contact with the ocean for tens of millions of years. Furthermore, terminal restriction site polymorphism profiles and geological data suggest that the aquatic ecosystems of Cuatro Cienegas are hydrologically interconnected with adjacent valleys recently targeted for agricultural intensification. The findings underscore the conservation value of desert aquatic ecosystems and the urgent need for study and preservation of freshwater microbial communities. PMID:16618921

Indoor-air microbiome in an urban subway network: diversity and dynamics.

PubMed

Leung, Marcus H Y; Wilkins, David; Li, Ellen K T; Kong, Fred K F; Lee, Patrick K H

2014-11-01

Subway systems are indispensable for urban societies, but microbiological characteristics of subway aerosols are relatively unknown. Previous studies investigating microbial compositions in subways employed methodologies that underestimated the diversity of microbial exposure for commuters, with little focus on factors governing subway air microbiology, which may have public health implications. Here, a culture-independent approach unraveling the bacterial diversity within the urban subway network in Hong Kong is presented. Aerosol samples from multiple subway lines and outdoor locations were collected. Targeting the 16S rRNA gene V4 region, extensive taxonomic diversity was found, with the most common bacterial genera in the subway environment among those associated with skin. Overall, subway lines harbored different phylogenetic communities based on α- and β-diversity comparisons, and closer inspection suggests that each community within a line is dependent on architectural characteristics, nearby outdoor microbiomes, and connectedness with other lines. Microbial diversities and assemblages also varied depending on the day sampled, as well as the time of day, and changes in microbial communities between peak and nonpeak commuting hours were attributed largely to increases in skin-associated genera in peak samples. Microbial diversities within the subway were influenced by temperature and relative humidity, while carbon dioxide levels showed a positive correlation with abundances of commuter-associated genera. This Hong Kong data set and communities from previous studies conducted in the United States formed distinct community clusters, indicating that additional work is required to unravel the mechanisms that shape subway microbiomes around the globe. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Quantification of the effects of ocean acidification on sediment microbial communities in the environment: the importance of ecosystem approaches.

PubMed

Hassenrück, Christiane; Fink, Artur; Lichtschlag, Anna; Tegetmeyer, Halina E; de Beer, Dirk; Ramette, Alban

2016-05-01

To understand how ocean acidification (OA) influences sediment microbial communities, naturally CO2-rich sites are increasingly being used as OA analogues. However, the characterization of these naturally CO2-rich sites is often limited to OA-related variables, neglecting additional environmental variables that may confound OA effects. Here, we used an extensive array of sediment and bottom water parameters to evaluate pH effects on sediment microbial communities at hydrothermal CO2 seeps in Papua New Guinea. The geochemical composition of the sediment pore water showed variations in the hydrothermal signature at seep sites with comparable pH, allowing the identification of sites that may better represent future OA scenarios. At these sites, we detected a 60% shift in the microbial community composition compared with reference sites, mostly related to increases in Chloroflexi sequences. pH was among the factors significantly, yet not mainly, explaining changes in microbial community composition. pH variation may therefore often not be the primary cause of microbial changes when sampling is done along complex environmental gradients. Thus, we recommend an ecosystem approach when assessing OA effects on sediment microbial communities under natural conditions. This will enable a more reliable quantification of OA effects via a reduction of potential confounding effects. © FEMS 2016.

Rapid Response of Eastern Mediterranean Deep Sea Microbial Communities to Oil

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Jiang; Techtmann, Stephen M.; Woo, Hannah L.

Deep marine oil spills like the Deepwater Horizon (DWH) in the Gulf of Mexico have the potential to drastically impact marine systems. Crude oil contamination in marine systems remains a concern, especially for countries around the Mediterranean Sea with off shore oil production. The goal of this study was to investigate the response of indigenous microbial communities to crude oil in the deep Eastern Mediterranean Sea (E. Med.) water column and to minimize potential bias associated with storage and shifts in microbial community structure from sample storage. 16S rRNA amplicon sequencing was combined with GeoChip metagenomic analysis to monitor themore » microbial community changes to the crude oil and dispersant in on-ship microcosms set up immediately after water collection. After 3 days of incubation at 14 °C, the microbial communities from two different water depths: 824 m and 1210 m became dominated by well-known oil degrading bacteria. The archaeal population and the overall microbial community diversity drastically decreased. Similarly, GeoChip metagenomic analysis revealed a tremendous enrichment of genes related to oil biodegradation, which was consistent with the results from the DWH oil spill. These results highlight a rapid microbial adaption to oil contamination in the deep E. Med., and indicate strong oil biodegradation potentia« less

Habitat generalists and specialists in microbial communities across a terrestrial-freshwater gradient

NASA Astrophysics Data System (ADS)

Monard, C.; Gantner, S.; Bertilsson, S.; Hallin, S.; Stenlid, J.

2016-11-01

Observations of distributions of microorganisms and their differences in community composition across habitats provide evidence of biogeographical patterns. However, little is known about the processes controlling transfers across habitat gradients. By analysing the overall microbial community composition (bacteria, fungi, archaea) across a terrestrial-freshwater gradient, the aim of this study was to understand the spatial distribution patterns of populations and identify taxa capable of crossing biome borders. Barcoded 454 pyrosequencing of taxonomic gene markers was used to describe the microbial communities in adjacent soil, freshwater and sediment samples and study the role of biotic and spatial factors in shaping their composition. Few habitat generalists but a high number of specialists were detected indicating that microbial community composition was mainly regulated by species sorting and niche partitioning. Biotic interactions within microbial groups based on an association network underlined the importance of Actinobacteria, Sordariomycetes, Agaricomycetes and Nitrososphaerales in connecting among biomes. Even if dispersion seemed limited, the shore of the lake represented a transition area, allowing populations to cross the biome boundaries. In finding few broadly distributed populations, our study points to biome specialization within microbial communities with limited potential for dispersal and colonization of new habitats along the terrestrial-freshwater continuum.

The ocean sampling day consortium.

PubMed

Kopf, Anna; Bicak, Mesude; Kottmann, Renzo; Schnetzer, Julia; Kostadinov, Ivaylo; Lehmann, Katja; Fernandez-Guerra, Antonio; Jeanthon, Christian; Rahav, Eyal; Ullrich, Matthias; Wichels, Antje; Gerdts, Gunnar; Polymenakou, Paraskevi; Kotoulas, Giorgos; Siam, Rania; Abdallah, Rehab Z; Sonnenschein, Eva C; Cariou, Thierry; O'Gara, Fergal; Jackson, Stephen; Orlic, Sandi; Steinke, Michael; Busch, Julia; Duarte, Bernardo; Caçador, Isabel; Canning-Clode, João; Bobrova, Oleksandra; Marteinsson, Viggo; Reynisson, Eyjolfur; Loureiro, Clara Magalhães; Luna, Gian Marco; Quero, Grazia Marina; Löscher, Carolin R; Kremp, Anke; DeLorenzo, Marie E; Øvreås, Lise; Tolman, Jennifer; LaRoche, Julie; Penna, Antonella; Frischer, Marc; Davis, Timothy; Katherine, Barker; Meyer, Christopher P; Ramos, Sandra; Magalhães, Catarina; Jude-Lemeilleur, Florence; Aguirre-Macedo, Ma Leopoldina; Wang, Shiao; Poulton, Nicole; Jones, Scott; Collin, Rachel; Fuhrman, Jed A; Conan, Pascal; Alonso, Cecilia; Stambler, Noga; Goodwin, Kelly; Yakimov, Michael M; Baltar, Federico; Bodrossy, Levente; Van De Kamp, Jodie; Frampton, Dion Mf; Ostrowski, Martin; Van Ruth, Paul; Malthouse, Paul; Claus, Simon; Deneudt, Klaas; Mortelmans, Jonas; Pitois, Sophie; Wallom, David; Salter, Ian; Costa, Rodrigo; Schroeder, Declan C; Kandil, Mahrous M; Amaral, Valentina; Biancalana, Florencia; Santana, Rafael; Pedrotti, Maria Luiza; Yoshida, Takashi; Ogata, Hiroyuki; Ingleton, Tim; Munnik, Kate; Rodriguez-Ezpeleta, Naiara; Berteaux-Lecellier, Veronique; Wecker, Patricia; Cancio, Ibon; Vaulot, Daniel; Bienhold, Christina; Ghazal, Hassan; Chaouni, Bouchra; Essayeh, Soumya; Ettamimi, Sara; Zaid, El Houcine; Boukhatem, Noureddine; Bouali, Abderrahim; Chahboune, Rajaa; Barrijal, Said; Timinouni, Mohammed; El Otmani, Fatima; Bennani, Mohamed; Mea, Marianna; Todorova, Nadezhda; Karamfilov, Ventzislav; Ten Hoopen, Petra; Cochrane, Guy; L'Haridon, Stephane; Bizsel, Kemal Can; Vezzi, Alessandro; Lauro, Federico M; Martin, Patrick; Jensen, Rachelle M; Hinks, Jamie; Gebbels, Susan; Rosselli, Riccardo; De Pascale, Fabio; Schiavon, Riccardo; Dos Santos, Antonina; Villar, Emilie; Pesant, Stéphane; Cataletto, Bruno; Malfatti, Francesca; Edirisinghe, Ranjith; Silveira, Jorge A Herrera; Barbier, Michele; Turk, Valentina; Tinta, Tinkara; Fuller, Wayne J; Salihoglu, Ilkay; Serakinci, Nedime; Ergoren, Mahmut Cerkez; Bresnan, Eileen; Iriberri, Juan; Nyhus, Paul Anders Fronth; Bente, Edvardsen; Karlsen, Hans Erik; Golyshin, Peter N; Gasol, Josep M; Moncheva, Snejana; Dzhembekova, Nina; Johnson, Zackary; Sinigalliano, Christopher David; Gidley, Maribeth Louise; Zingone, Adriana; Danovaro, Roberto; Tsiamis, George; Clark, Melody S; Costa, Ana Cristina; El Bour, Monia; Martins, Ana M; Collins, R Eric; Ducluzeau, Anne-Lise; Martinez, Jonathan; Costello, Mark J; Amaral-Zettler, Linda A; Gilbert, Jack A; Davies, Neil; Field, Dawn; Glöckner, Frank Oliver

2015-01-01

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world's oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.

Biodiversity of the microbial mat of the Garga hot spring.

PubMed

Rozanov, Alexey Sergeevich; Bryanskaya, Alla Victorovna; Ivanisenko, Timofey Vladimirovich; Malup, Tatyana Konstantinovna; Peltek, Sergey Evgenievich

2017-12-28

Microbial mats are a good model system for ecological and evolutionary analysis of microbial communities. There are more than 20 alkaline hot springs on the banks of the Barguzin river inflows. Water temperature reaches 75 °C and pH is usually 8.0-9.0. The formation of microbial mats is observed in all hot springs. Microbial communities of hot springs of the Baikal rift zone are poorly studied. Garga is the biggest hot spring in this area. In this study, we investigated bacterial and archaeal diversity of the Garga hot spring (Baikal rift zone, Russia) using 16S rRNA metagenomic sequencing. We studied two types of microbial communities: (i) small white biofilms on rocks in the points with the highest temperature (75 °C) and (ii) continuous thick phototrophic microbial mats observed at temperatures below 70 °C. Archaea (mainly Crenarchaeota; 19.8% of the total sequences) were detected only in the small biofilms. The high abundance of Archaea in the sample from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. In the microbial mats, primary products were formed by cyanobacteria of the genus Leptolyngbya. Heterotrophic microorganisms were mostly represented by Actinobacteria and Proteobacteria in all studied samples of the microbial mats. Planctomycetes, Chloroflexi, and Chlorobi were abundant in the middle layer of the microbial mats, while heterotrophic microorganisms represented mostly by Firmicutes (Clostridia, strict anaerobes) dominated in the bottom part. Besides prokaryotes, we detect some species of Algae with help of detection their chloroplasts 16 s rRNA. High abundance of Archaea in samples from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. Metagenomic analysis of microbial communities of the microbial mat of Garga hot spring showed that the three studied points sampled at 70 °C, 55 °C, and 45 °C had similar species composition. Cyanobacteria of the genus Leptolyngbya dominated in the upper layer of the microbial mat. Chloroflexi and Chlorobi were less abundant and were mostly observed in the middle part of the microbial mat. We detected domains of heterotrophic organisms in high abundance (Proteobacteria, Firmicutes, Verrucomicrobia, Planctomicetes, Bacteroidetes, Actinobacteria, Thermi), according to metabolic properties of known relatives, which can form complete cycles of carbon, sulphur, and nitrogen in the microbial mat. The studied microbial mats evolved in early stages of biosphere formation. They can live autonomously, providing full cycles of substances and preventing live activity products poisoning.

Microbial profiling of dental plaque from mechanically ventilated patients

PubMed Central

Twigg, Joshua A.; Lewis, Michael A. O.; Wise, Matt P.; Marchesi, Julian R.; Smith, Ann; Wilson, Melanie J.; Williams, David W.

2016-01-01

Micro-organisms isolated from the oral cavity may translocate to the lower airways during mechanical ventilation (MV) leading to ventilator-associated pneumonia (VAP). Changes within the dental plaque microbiome during MV have been documented previously, primarily using culture-based techniques. The aim of this study was to use community profiling by high throughput sequencing to comprehensively analyse suggested microbial changes within dental plaque during MV. Bacterial 16S rDNA gene sequences were obtained from 38 samples of dental plaque sampled from 13 mechanically ventilated patients and sequenced using the Illumina platform. Sequences were processed using Mothur, applying a 97 % gene similarity cut-off for bacterial species level identifications. A significant ‘microbial shift’ occurred in the microbial community of dental plaque during MV for nine out of 13 patients. Following extubation, or removal of the endotracheal tube that facilitates ventilation, sampling revealed a decrease in the relative abundance of potential respiratory pathogens and a compositional change towards a more predominantly (in terms of abundance) oral microbiota including Prevotella spp., and streptococci. The results highlight the need to better understand microbial shifts in the oral microbiome in the development of strategies to reduce VAP, and may have implications for the development of other forms of pneumonia such as community-acquired infection. PMID:26690690

Microbial profiling of dental plaque from mechanically ventilated patients.

PubMed

Sands, Kirsty M; Twigg, Joshua A; Lewis, Michael A O; Wise, Matt P; Marchesi, Julian R; Smith, Ann; Wilson, Melanie J; Williams, David W

2016-02-01

Micro-organisms isolated from the oral cavity may translocate to the lower airways during mechanical ventilation (MV) leading to ventilator-associated pneumonia (VAP). Changes within the dental plaque microbiome during MV have been documented previously, primarily using culture-based techniques. The aim of this study was to use community profiling by high throughput sequencing to comprehensively analyse suggested microbial changes within dental plaque during MV. Bacterial 16S rDNA gene sequences were obtained from 38 samples of dental plaque sampled from 13 mechanically ventilated patients and sequenced using the Illumina platform. Sequences were processed using Mothur, applying a 97% gene similarity cut-off for bacterial species level identifications. A significant 'microbial shift' occurred in the microbial community of dental plaque during MV for nine out of 13 patients. Following extubation, or removal of the endotracheal tube that facilitates ventilation, sampling revealed a decrease in the relative abundance of potential respiratory pathogens and a compositional change towards a more predominantly (in terms of abundance) oral microbiota including Prevotella spp., and streptococci. The results highlight the need to better understand microbial shifts in the oral microbiome in the development of strategies to reduce VAP, and may have implications for the development of other forms of pneumonia such as community-acquired infection.

Characterization of Microbial Communities in Gas Industry Pipelines

PubMed Central

Zhu, Xiang Y.; Lubeck, John; Kilbane, John J.

2003-01-01

Culture-independent techniques, denaturing gradient gel electrophoresis (DGGE) analysis, and random cloning of 16S rRNA gene sequences amplified from community DNA were used to determine the diversity of microbial communities in gas industry pipelines. Samples obtained from natural gas pipelines were used directly for DNA extraction, inoculated into sulfate-reducing bacterium medium, or used to inoculate a reactor that simulated a natural gas pipeline environment. The variable V2-V3 (average size, 384 bp) and V3-V6 (average size, 648 bp) regions of bacterial and archaeal 16S rRNA genes, respectively, were amplified from genomic DNA isolated from nine natural gas pipeline samples and analyzed. A total of 106 bacterial 16S rDNA sequences were derived from DGGE bands, and these formed three major clusters: beta and gamma subdivisions of Proteobacteria and gram-positive bacteria. The most frequently encountered bacterial species was Comamonas denitrificans, which was not previously reported to be associated with microbial communities found in gas pipelines or with microbially influenced corrosion. The 31 archaeal 16S rDNA sequences obtained in this study were all related to those of methanogens and phylogenetically fall into three clusters: order I, Methanobacteriales; order III, Methanomicrobiales; and order IV, Methanosarcinales. Further microbial ecology studies are needed to better understand the relationship among bacterial and archaeal groups and the involvement of these groups in the process of microbially influenced corrosion in order to develop improved ways of monitoring and controlling microbially influenced corrosion. PMID:12957923

One Step Closer to Mars with Aquaponics: Cultivating Citizen Science in K12 Schools

NASA Technical Reports Server (NTRS)

Kolattukudy, Maria; Puranik, Niyati; Sane, Nishant; Bisht, Kritika; Saffat, Nabeeha; Gupta, Anika; McHugh, Anne; Detweiler, Angela; Bebout, Brad; Everroad, R. Craig

2017-01-01

The Microbial Ecology and Biogeochemistry Research Laboratory at NASA Ames Research Center focuses primarily on the nutrient cycling and diversity of complex microbial communities. NASA is interested in the composition and functioning of microbial mat communities as these processes fundamentally shape the form and function of these analogs for the earliest forms of life on Earth (3.6 billion years ago), and likely will on other planets as well. Aquaponics systems are supported by microbial communities who perform many complex ecosystem services, including cycling nitrogen. Microbes are integral to the stability and productivity of aquaponics systems, which are analogous to microbial communities in food production systems that are essential for building efficient life support systems for long-distance space travel. Students at Meadow Park Middle School created 10 parallel aquaponics systems and took temporal microbial samples to characterize whether any macro-ecology variables impacted or changed the microbial diversity of these systems. Students additionally created a website so that other classrooms can pursue similar projects in their own schools (https://go.nasa.gov/2uJhxmF). Our lab at NASA Ames has sequenced water samples from each of the 10 tanks at 3 timepoints using a MinION sequencer. MPMS students will be involved in the analysis of the bioinformatics data generated through this collaboration. Our ongoing collaboration aims to collect and analyze data in the classroom setting that has utility for research scientists, while involving students as collaborators in the research process.

Microbial utilization of nitrogen in cold core eddies: size does matter

NASA Astrophysics Data System (ADS)

McInnes, A.; Messer, L. F.; Laiolo, L.; Laverock, B.; Laczka, O.; Brown, M. V.; Seymour, J.; Doblin, M.

2016-02-01

As the base of the marine food web, and the first step in the biological carbon pump, understanding changes in microbial community composition is essential for predicting changes in the marine nitrogen (N) cycle. Climate change projections suggest that oligotrophic waters will become more stratified with a concomitant shift in microbial community composition based on changes in N supply. In regions of strong boundary currents, eddies could reduce this limitation through nutrient uplift and other forms of eddy mixing. Understanding the preference for different forms of N by microbes is essential for understanding and predicting shifts in the microbial community. This study aims to understand the utilization of different N species within different microbial size fractions as well as understand the preferred source of N to these groups across varying mesoscale and sub-mesoscale features in the East Australian Current (EAC). In June 2015 we sampled microbial communities from three depths (surface, chlorophyll-a maximum and below the mixed layer), in three mesoscale and sub-mesoscale eddy features, as well as two end-point water masses (coastal and oligotrophic EAC water). Particulate matter was analysed for stable C and N isotopes, and seawater incubations with trace amounts of 15NO3, 15NH4, 15N2, 15Urea and 13C were undertaken. All samples were size fractionated into 0.3-2.0 µm, 2.0-10 µm, and >10 µm size classes, encompassing the majority of microbes in these waters. Microbial community composition was also assessed (pigments, flow cytometry, DNA), as well as physical and chemical parameters, to better understand the drivers of carbon fixation and nitrogen utilization across a diversity of water masses and microbial size classes. We observed that small, young features have a greater abundance of larger size classes. We therefore predict that these microbes will preferentially draw down the recently pulsed NO3. Ultimately, the size and age of a feature will determine the N compound utilization and microbial community composition and as the feature grows in size and age a community succession will lead to differential more diverse N compound utilization.

Microbial communities related to sensory attributes in Korean fermented soy bean paste (doenjang).

PubMed

Kim, Min Jung; Kwak, Han Sub; Jung, Hee Yeon; Kim, Sang Sook

2016-11-01

Various microbial communities play a role in generating the distinctive sensory characteristics of the traditional Korean soybean paste, doenjang. The objective of this study was to investigate the relationship between sensory characteristics and microbial communities in traditional doenjang. The results of the descriptive analysis revealed that some traditional doenjang (T1-T11) exhibited distinctive characteristics, such as fish sauce flavor, meju, bitterness, sourness, and saltiness, whereas the modified samples (M1-M3) demonstrated sweetness, umami, and an alcohol odor. According to the metagenomic analysis based on 16S rRNA gene sequencing, the phylum Firmicutes was the dominant bacterium in most doenjang. At the genus level, lactic acid bacteria (LAB) were frequently found in most doenjang. Among these LAB, the major genera of bacteria were Tetragenococcus in M2 (60.30%), T3 (91.20%), T8 (48.60%), and T9 (60.90%); Enterococcus in T1 (29.40%), T4 (34.10%), and T10 (50.50%); Leuconostoc in T7 (89.10%); and Lactobacillus in T9 (38.3%). The most frequently occurring non-LAB was Bacillus in M3 (50.10%), T5 (46.50%), and T6 (20.50%), and M1 and T2 contained Staphylococcus and Ochrobactrum as their major non-LAB, respectively. The results of a correlation analysis between the sensory attributes from the descriptive analysis and the microbial communities from 454 pyrosequencing provided an overview for the relationship between sensory characteristics and microbial communities. Ochrobactrum, Stenotrophomonas, Rhodobacteraceae, Proteus, and Luteimonas were found in samples that had a strong fish sauce characteristic. The presence of LAB-Tetragenococcus, Enterococcus, Pediococcus, Carnobacterium, and Weissella-was related to sourness. Enterococcus and Enterobacter were found in samples with a matured flavor and a soft mouthfeel, respectively. The overall results of the study demonstrate that microbial communities found in doenjang were closely related to distinct sensory attributes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Multi-scale variation in spatial heterogeneity for microbial community structure in an eastern Virginia agricultural field

NASA Technical Reports Server (NTRS)

Franklin, Rima B.; Mills, Aaron L.

2003-01-01

To better understand the distribution of soil microbial communities at multiple spatial scales, a survey was conducted to examine the spatial organization of community structure in a wheat field in eastern Virginia (USA). Nearly 200 soil samples were collected at a variety of separation distances ranging from 2.5 cm to 11 m. Whole-community DNA was extracted from each sample, and community structure was compared using amplified fragment length polymorphism (AFLP) DNA fingerprinting. Relative similarity was calculated between each pair of samples and compared using geostatistical variogram analysis to study autocorrelation as a function of separation distance. Spatial autocorrelation was found at scales ranging from 30 cm to more than 6 m, depending on the sampling extent considered. In some locations, up to four different correlation length scales were detected. The presence of nested scales of variability suggests that the environmental factors regulating the development of the communities in this soil may operate at different scales. Kriging was used to generate maps of the spatial organization of communities across the plot, and the results demonstrated that bacterial distributions can be highly structured, even within a habitat that appears relatively homogeneous at the plot and field scale. Different subsets of the microbial community were distributed differently across the plot, and this is thought to be due to the variable response of individual populations to spatial heterogeneity associated with soil properties. c2003 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.

Spatially extensive microbial biogeography of the Indian Ocean provides insights into the unique community structure of a pristine coral atoll

NASA Astrophysics Data System (ADS)

Jeffries, Thomas C.; Ostrowski, Martin; Williams, Rohan B.; Xie, Chao; Jensen, Rachelle M.; Grzymski, Joseph J.; Senstius, Svend Jacob; Givskov, Michael; Hoeke, Ron; Philip, Gayle K.; Neches, Russell Y.; Drautz-Moses, Daniela I.; Chénard, Caroline; Paulsen, Ian T.; Lauro, Federico M.

2015-10-01

Microorganisms act both as drivers and indicators of perturbations in the marine environment. In an effort to establish baselines to predict the response of marine habitats to environmental change, here we report a broad survey of microbial diversity across the Indian Ocean, including the first microbial samples collected in the pristine lagoon of Salomon Islands, Chagos Archipelago. This was the first large-scale ecogenomic survey aboard a private yacht employing a ‘citizen oceanography’ approach and tools and protocols easily adapted to ocean going sailboats. Our data highlighted biogeographic patterns in microbial community composition across the Indian Ocean. Samples from within the Salomon Islands lagoon contained a community which was different even from adjacent samples despite constant water exchange, driven by the dominance of the photosynthetic cyanobacterium Synechococcus. In the lagoon, Synechococcus was also responsible for driving shifts in the metatranscriptional profiles. Enrichment of transcripts related to photosynthesis and nutrient cycling indicated bottom-up controls of community structure. However a five-fold increase in viral transcripts within the lagoon during the day, suggested a concomitant top-down control by bacteriophages. Indeed, genome recruitment against Synechococcus reference genomes suggested a role of viruses in providing the ecological filter for determining the β-diversity patterns in this system.

Spatially extensive microbial biogeography of the Indian Ocean provides insights into the unique community structure of a pristine coral atoll.

PubMed

Jeffries, Thomas C; Ostrowski, Martin; Williams, Rohan B; Xie, Chao; Jensen, Rachelle M; Grzymski, Joseph J; Senstius, Svend Jacob; Givskov, Michael; Hoeke, Ron; Philip, Gayle K; Neches, Russell Y; Drautz-Moses, Daniela I; Chénard, Caroline; Paulsen, Ian T; Lauro, Federico M

2015-10-20

Microorganisms act both as drivers and indicators of perturbations in the marine environment. In an effort to establish baselines to predict the response of marine habitats to environmental change, here we report a broad survey of microbial diversity across the Indian Ocean, including the first microbial samples collected in the pristine lagoon of Salomon Islands, Chagos Archipelago. This was the first large-scale ecogenomic survey aboard a private yacht employing a 'citizen oceanography' approach and tools and protocols easily adapted to ocean going sailboats. Our data highlighted biogeographic patterns in microbial community composition across the Indian Ocean. Samples from within the Salomon Islands lagoon contained a community which was different even from adjacent samples despite constant water exchange, driven by the dominance of the photosynthetic cyanobacterium Synechococcus. In the lagoon, Synechococcus was also responsible for driving shifts in the metatranscriptional profiles. Enrichment of transcripts related to photosynthesis and nutrient cycling indicated bottom-up controls of community structure. However a five-fold increase in viral transcripts within the lagoon during the day, suggested a concomitant top-down control by bacteriophages. Indeed, genome recruitment against Synechococcus reference genomes suggested a role of viruses in providing the ecological filter for determining the β-diversity patterns in this system.

Spatially extensive microbial biogeography of the Indian Ocean provides insights into the unique community structure of a pristine coral atoll

PubMed Central

Jeffries, Thomas C.; Ostrowski, Martin; Williams, Rohan B.; Xie, Chao; Jensen, Rachelle M.; Grzymski, Joseph J.; Senstius, Svend Jacob; Givskov, Michael; Hoeke, Ron; Philip, Gayle K.; Neches, Russell Y.; Drautz-Moses, Daniela I.; Chénard, Caroline; Paulsen, Ian T.; Lauro, Federico M.

2015-01-01

Microorganisms act both as drivers and indicators of perturbations in the marine environment. In an effort to establish baselines to predict the response of marine habitats to environmental change, here we report a broad survey of microbial diversity across the Indian Ocean, including the first microbial samples collected in the pristine lagoon of Salomon Islands, Chagos Archipelago. This was the first large-scale ecogenomic survey aboard a private yacht employing a ‘citizen oceanography’ approach and tools and protocols easily adapted to ocean going sailboats. Our data highlighted biogeographic patterns in microbial community composition across the Indian Ocean. Samples from within the Salomon Islands lagoon contained a community which was different even from adjacent samples despite constant water exchange, driven by the dominance of the photosynthetic cyanobacterium Synechococcus. In the lagoon, Synechococcus was also responsible for driving shifts in the metatranscriptional profiles. Enrichment of transcripts related to photosynthesis and nutrient cycling indicated bottom-up controls of community structure. However a five-fold increase in viral transcripts within the lagoon during the day, suggested a concomitant top-down control by bacteriophages. Indeed, genome recruitment against Synechococcus reference genomes suggested a role of viruses in providing the ecological filter for determining the β-diversity patterns in this system. PMID:26481089

Contrasting the microbiomes from forest rhizosphere and deeper bulk soil from an Amazon rainforest reserve.

PubMed

Fonseca, Jose Pedro; Hoffmann, Luisa; Cabral, Bianca Catarina Azeredo; Dias, Victor Hugo Giordano; Miranda, Marcio Rodrigues; de Azevedo Martins, Allan Cezar; Boschiero, Clarissa; Bastos, Wanderley Rodrigues; Silva, Rosane

2018-02-05

Pristine forest ecosystems provide a unique perspective for the study of plant-associated microbiota since they host a great microbial diversity. Although the Amazon forest is one of the hotspots of biodiversity around the world, few metagenomic studies described its microbial community diversity thus far. Understanding the environmental factors that can cause shifts in microbial profiles is key to improving soil health and biogeochemical cycles. Here we report a taxonomic and functional characterization of the microbiome from the rhizosphere of Brosimum guianense (Snakewood), a native tree, and bulk soil samples from a pristine Brazilian Amazon forest reserve (Cuniã), for the first time by the shotgun approach. We identified several fungi and bacteria taxon significantly enriched in forest rhizosphere compared to bulk soil samples. For archaea, the trend was the opposite, with many archaeal phylum and families being considerably more enriched in bulk soil compared to forest rhizosphere. Several fungal and bacterial decomposers like Postia placenta and Catenulispora acidiphila which help maintain healthy forest ecosystems were found enriched in our samples. Other bacterial species involved in nitrogen (Nitrobacter hamburgensis and Rhodopseudomonas palustris) and carbon cycling (Oligotropha carboxidovorans) were overrepresented in our samples indicating the importance of these metabolic pathways for the Amazon rainforest reserve soil health. Hierarchical clustering based on taxonomic similar microbial profiles grouped the forest rhizosphere samples in a distinct clade separated from bulk soil samples. Principal coordinate analysis of our samples with publicly available metagenomes from the Amazon region showed grouping into specific rhizosphere and bulk soil clusters, further indicating distinct microbial community profiles. In this work, we reported significant shifts in microbial community structure between forest rhizosphere and bulk soil samples from an Amazon forest reserve that are probably caused by more than one environmental factors such as rhizosphere and soil depth. Copyright © 2017 Elsevier B.V. All rights reserved.

Impact of Long-Term Diesel Contamination on Soil Microbial Community Structure

PubMed Central

Maphosa, Farai; Morillo, Jose A.; Abu Al-Soud, Waleed; Langenhoff, Alette A. M.; Grotenhuis, Tim; Rijnaarts, Huub H. M.; Smidt, Hauke

2013-01-01

Microbial community composition and diversity at a diesel-contaminated railway site were investigated by pyrosequencing of bacterial and archaeal 16S rRNA gene fragments to understand the interrelationships among microbial community composition, pollution level, and soil geochemical and physical properties. To this end, 26 soil samples from four matrix types with various geochemical characteristics and contaminant concentrations were investigated. The presence of diesel contamination significantly impacted microbial community composition and diversity, regardless of the soil matrix type. Clean samples showed higher diversity than contaminated samples (P < 0.001). Bacterial phyla with high relative abundances in all samples included Proteobacteria, Firmicutes, Actinobacteria, Acidobacteria, and Chloroflexi. High relative abundances of Archaea, specifically of the phylum Euryarchaeota, were observed in contaminated samples. Redundancy analysis indicated that increased relative abundances of the phyla Chloroflexi, Firmicutes, and Euryarchaeota correlated with the presence of contamination. Shifts in the chemical composition of diesel constituents across the site and the abundance of specific operational taxonomic units (OTUs; defined using a 97% sequence identity threshold) in contaminated samples together suggest that natural attenuation of contamination has occurred. OTUs with sequence similarity to strictly anaerobic Anaerolineae within the Chloroflexi, as well as to Methanosaeta of the phylum Euryarchaeota, were detected. Anaerolineae and Methanosaeta are known to be associated with anaerobic degradation of oil-related compounds; therefore, their presence suggests that natural attenuation has occurred under anoxic conditions. This research underscores the usefulness of next-generation sequencing techniques both to understand the ecological impact of contamination and to identify potential molecular proxies for detection of natural attenuation. PMID:23144139

Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH

PubMed Central

Twing, Katrina I.; Brazelton, William J.; Kubo, Michael D. Y.; Hyer, Alex J.; Cardace, Dawn; Hoehler, Tori M.; McCollom, Tom M.; Schrenk, Matthew O.

2017-01-01

Serpentinization is a widespread geochemical process associated with aqueous alteration of ultramafic rocks that produces abundant reductants (H2 and CH4) for life to exploit, but also potentially challenging conditions, including high pH, limited availability of terminal electron acceptors, and low concentrations of inorganic carbon. As a consequence, past studies of serpentinites have reported low cellular abundances and limited microbial diversity. Establishment of the Coast Range Ophiolite Microbial Observatory (California, U.S.A.) allowed a comparison of microbial communities and physicochemical parameters directly within serpentinization-influenced subsurface aquifers. Samples collected from seven wells were subjected to a range of analyses, including solute and gas chemistry, microbial diversity by 16S rRNA gene sequencing, and metabolic potential by shotgun metagenomics, in an attempt to elucidate what factors drive microbial activities in serpentinite habitats. This study describes the first comprehensive interdisciplinary analysis of microbial communities in hyperalkaline groundwater directly accessed by boreholes into serpentinite rocks. Several environmental factors, including pH, methane, and carbon monoxide, were strongly associated with the predominant subsurface microbial communities. A single operational taxonomic unit (OTU) of Betaproteobacteria and a few OTUs of Clostridia were the almost exclusive inhabitants of fluids exhibiting the most serpentinized character. Metagenomes from these extreme samples contained abundant sequences encoding proteins associated with hydrogen metabolism, carbon monoxide oxidation, carbon fixation, and acetogenesis. Metabolic pathways encoded by Clostridia and Betaproteobacteria, in particular, are likely to play important roles in the ecosystems of serpentinizing groundwater. These data provide a basis for further biogeochemical studies of key processes in serpentinite subsurface environments. PMID:28298908

Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH.

PubMed

Twing, Katrina I; Brazelton, William J; Kubo, Michael D Y; Hyer, Alex J; Cardace, Dawn; Hoehler, Tori M; McCollom, Tom M; Schrenk, Matthew O

2017-01-01

Serpentinization is a widespread geochemical process associated with aqueous alteration of ultramafic rocks that produces abundant reductants (H 2 and CH 4 ) for life to exploit, but also potentially challenging conditions, including high pH, limited availability of terminal electron acceptors, and low concentrations of inorganic carbon. As a consequence, past studies of serpentinites have reported low cellular abundances and limited microbial diversity. Establishment of the Coast Range Ophiolite Microbial Observatory (California, U.S.A.) allowed a comparison of microbial communities and physicochemical parameters directly within serpentinization-influenced subsurface aquifers. Samples collected from seven wells were subjected to a range of analyses, including solute and gas chemistry, microbial diversity by 16S rRNA gene sequencing, and metabolic potential by shotgun metagenomics, in an attempt to elucidate what factors drive microbial activities in serpentinite habitats. This study describes the first comprehensive interdisciplinary analysis of microbial communities in hyperalkaline groundwater directly accessed by boreholes into serpentinite rocks. Several environmental factors, including pH, methane, and carbon monoxide, were strongly associated with the predominant subsurface microbial communities. A single operational taxonomic unit (OTU) of Betaproteobacteria and a few OTUs of Clostridia were the almost exclusive inhabitants of fluids exhibiting the most serpentinized character. Metagenomes from these extreme samples contained abundant sequences encoding proteins associated with hydrogen metabolism, carbon monoxide oxidation, carbon fixation, and acetogenesis. Metabolic pathways encoded by Clostridia and Betaproteobacteria, in particular, are likely to play important roles in the ecosystems of serpentinizing groundwater. These data provide a basis for further biogeochemical studies of key processes in serpentinite subsurface environments.

An Integrated Insight into the Relationship between Soil Microbial Community and Tobacco Bacterial Wilt Disease

PubMed Central

Yang, Hongwu; Li, Juan; Xiao, Yunhua; Gu, Yabing; Liu, Hongwei; Liang, Yili; Liu, Xueduan; Hu, Jin; Meng, Delong; Yin, Huaqun

2017-01-01

The soil microbial communities play an important role in plant health, however, the relationship between the below-ground microbiome and above-ground plant health remains unclear. To reveal such a relationship, we analyzed soil microbial communities through sequencing of 16S rRNA gene amplicons from 15 different tobacco fields with different levels of wilt disease in the central south part of China. We found that plant health was related to the soil microbial diversity as plants may benefit from the diverse microbial communities. Also, those 15 fields were grouped into ‘healthy’ and ‘infected’ samples based upon soil microbial community composition analyses such as unweighted paired-group method with arithmetic means (UPGMA) and principle component analysis, and furthermore, molecular ecological network analysis indicated that some potential plant-beneficial microbial groups, e.g., Bacillus and Actinobacteria could act as network key taxa, thus reducing the chance of plant soil-borne pathogen invasion. In addition, we propose that a more complex soil ecology network may help suppress tobacco wilt, which was also consistent with highly diversity and composition with plant-beneficial microbial groups. This study provides new insights into our understanding the relationship between the soil microbiome and plant health. PMID:29163453

The microbial community structure in petroleum-contaminated sediments corresponds to geophysical signatures

USGS Publications Warehouse

Allen, J.P.; Atekwana, E.A.; Duris, J.W.; Werkema, D.D.; Rossbach, S.

2007-01-01

The interdependence between geoelectrical signatures at underground petroleum plumes and the structures of subsurface microbial communities was investigated. For sediments contaminated with light non-aqueousphase liquids, anomalous high conductivity values have been observed. Vertical changes in the geoelectrical properties of the sediments were concomitant with significant changes in the microbial community structures as determined by the construction and evaluation of 16S rRNA gene libraries. DNA sequencing of clones from four 16S rRNA gene libraries from different depths of a contaminated field site and two libraries from an uncontaminated background site revealed spatial heterogeneity in the microbial community structures. Correspondence analysis showed that the presence of distinct microbial populations, including the various hydrocarbon-degrading, syntrophic, sulfate-reducing, and dissimilatory-iron-reducing populations, was a contributing factor to the elevated geoelectrical measurements. Thus, through their growth and metabolic activities, microbial populations that have adapted to the use of petroleum as a carbon source can strongly influence their geophysical surroundings. Since changes in the geophysical properties of contaminated sediments parallel changes in the microbial community compositions, it is suggested that geoelectrical measurements can be a cost-efficient tool to guide microbiological sampling for microbial ecology studies during the monitoring of natural or engineered bioremediation processes. Copyright ?? 2007, American Society for Microbiology. All Rights Reserved.

Noma Affected Children from Niger Have Distinct Oral Microbial Communities Based on High-Throughput Sequencing of 16S rRNA Gene Fragments

PubMed Central

Whiteson, Katrine L.; Lazarevic, Vladimir; Tangomo-Bento, Manuela; Girard, Myriam; Maughan, Heather; Pittet, Didier; Francois, Patrice; Schrenzel, Jacques

2014-01-01

We aim to understand the microbial ecology of noma (cancrum oris), a devastating ancient illness which causes severe facial disfigurement in>140,000 malnourished children every year. The cause of noma is still elusive. A chaotic mix of microbial infection, oral hygiene and weakened immune system likely contribute to the development of oral lesions. These lesions are a plausible entry point for unidentified microorganisms that trigger gangrenous facial infections. To catalog bacteria present in noma lesions and identify candidate noma-triggering organisms, we performed a cross-sectional sequencing study of 16S rRNA gene amplicons from sixty samples of gingival fluid from twelve healthy children, twelve children suffering from noma (lesion and healthy sites), and twelve children suffering from Acute Necrotizing Gingivitis (ANG) (lesion and healthy sites). Relative to healthy individuals, samples taken from lesions in diseased mouths were enriched with Spirochaetes and depleted for Proteobacteria. Samples taken from healthy sites of diseased mouths had proportions of Spirochaetes and Proteobacteria that were similar to healthy control individuals. Samples from noma mouths did not have a higher abundance of Fusobacterium, casting doubt on its role as a causative agent of noma. Microbial communities sampled from noma and ANG lesions were dominated by the same Prevotella intermedia OTU, which was much less abundant in healthy sites sampled from the same mouths. Multivariate analysis confirmed that bacterial communities in healthy and lesion sites were significantly different. Several OTUs in the Orders Erysipelotrichales, Clostridiales, Bacteroidales, and Spirochaetales were identified as indicators of noma, suggesting that one or more microbes within these Orders is associated with the development of noma lesions. Future studies should include longitudinal sampling of viral and microbial components of this community, before and early in noma lesion development. PMID:25474262

Microbiome analysis of dairy cows fed pasture or total mixed ration diets.

PubMed

de Menezes, Alexandre B; Lewis, Eva; O'Donovan, Michael; O'Neill, Brendan F; Clipson, Nicholas; Doyle, Evelyn M

2011-11-01

Understanding rumen microbial ecology is essential for the development of feed systems designed to improve livestock productivity, health and for methane mitigation strategies from cattle. Although rumen microbial communities have been studied previously, few studies have applied next-generation sequencing technologies to that ecosystem. The aim of this study was to characterize changes in microbial community structure arising from feeding dairy cows two widely used diets: pasture and total mixed ration (TMR). Bacterial, archaeal and protozoal communities were characterized by terminal restriction fragment length polymorphism of the amplified SSU rRNA gene and statistical analysis showed that bacterial and archaeal communities were significantly affected by diet, whereas no effect was observed for the protozoal community. Deep amplicon sequencing of the 16S rRNA gene revealed significant differences in the bacterial communities between the diets and between rumen solid and liquid content. At the family level, some important groups of rumen bacteria were clearly associated with specific diets, including the higher abundance of the Fibrobacteraceae in TMR solid samples and members of the propionate-producing Veillonelaceae in pasture samples. This study will be relevant to the study of rumen microbial ecology and livestock feed management. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Namib Desert Soil Microbial Community Diversity, Assembly, and Function Along a Natural Xeric Gradient.

PubMed

Scola, Vincent; Ramond, Jean-Baptiste; Frossard, Aline; Zablocki, Olivier; Adriaenssens, Evelien M; Johnson, Riegardt M; Seely, Mary; Cowan, Don A

2018-01-01

The hyperarid Namib desert is a coastal desert in southwestern Africa and one of the oldest and driest deserts on the planet. It is characterized by a west/east increasing precipitation gradient and by regular coastal fog events (extending up to 75 km inland) that can also provide soil moisture. In this study, we evaluated the role of this natural aridity and xeric gradient on edaphic microbial community structure and function in the Namib desert. A total of 80 individual soil samples were collected at 10-km intervals along a 190-km transect from the fog-dominated western coastal region to the eastern desert boundary. Seventeen physicochemical parameters were measured for each soil sample. Soil parameters reflected the three a priori defined climatic/xeric zones along the transect ("fog," "low rain," and "high rain"). Microbial community structures were characterized by terminal restriction fragment length polymorphism fingerprinting and shotgun metaviromics, and their functional capacities were determined by extracellular enzyme activity assays. Both microbial community structures and activities differed significantly between the three xeric zones. The deep sequencing of surface soil metavirome libraries also showed shifts in viral composition along the xeric transect. While bacterial community assembly was influenced by soil chemistry and stochasticity along the transect, variations in community "function" were apparently tuned by xeric stress.

Comparison of DNA preservation methods for environmental bacterial community samples.

PubMed

Gray, Michael A; Pratte, Zoe A; Kellogg, Christina A

2013-02-01

Field collections of environmental samples, for example corals, for molecular microbial analyses present distinct challenges. The lack of laboratory facilities in remote locations is common, and preservation of microbial community DNA for later study is critical. A particular challenge is keeping samples frozen in transit. Five nucleic acid preservation methods that do not require cold storage were compared for effectiveness over time and ease of use. Mixed microbial communities of known composition were created and preserved by DNAgard(™), RNAlater(®), DMSO-EDTA-salt (DESS), FTA(®) cards, and FTA Elute(®) cards. Automated ribosomal intergenic spacer analysis and clone libraries were used to detect specific changes in the faux communities over weeks and months of storage. A previously known bias in FTA(®) cards that results in lower recovery of pure cultures of Gram-positive bacteria was also detected in mixed community samples. There appears to be a uniform bias across all five preservation methods against microorganisms with high G + C DNA. Overall, the liquid-based preservatives (DNAgard(™), RNAlater(®), and DESS) outperformed the card-based methods. No single liquid method clearly outperformed the others, leaving method choice to be based on experimental design, field facilities, shipping constraints, and allowable cost. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Diversity is the question, not the answer

DOE PAGES

Shade, Ashley

2016-09-16

Local diversity (within-sample or alpha diversity) is often implicated as a cause of success or failure of a microbial community. However, the relationships between diversity and emergent properties of a community, such as its stability, productivity or invasibility, are much more nuanced. In this paper, I argue that diversity without context provides limited insights into the mechanisms underpinning community patterns. I provide examples from traditional and microbial ecology to discuss common complications and assumptions about within-sample diversity that may prevent us from digging deeper into the more specific mechanisms underpinning community outcomes. I suggest that measurement of diversity should servemore » as a starting point for further inquiry of ecological mechanisms rather than an 'answer' to community outcomes.« less

[Prokaryotic community of subglacial bottom sediments of Antarctic Lake Untersee: detection by cultural and direct microscopic techniques].

PubMed

Muliukin, A L; Demkina, E V; Manucharova, N A; Akimov, V N; Andersen, D; McKay, C; Gal'chenko, V F

2014-01-01

The heterotrophic mesophilic component was studied in microbial communities of the samples of frozen regolith collected from the glacier near Lake Untersee collected in 2011 during the joint Russian-American expedition to central Dronning Maud Land (Eastern Antarctica). Cultural techniques revealed high bacterial numbers in the samples. For enumeration of viable cells, the most probable numbers (MPN) method proved more efficient than plating on agar media. Fluorescent in situ hybridization with the relevant oligonucleotide probes revealed members of the groups Eubacteria (Actinobacteria, Firmicutes) and Archaea. Application of the methods of cell resuscitation, such as the use of diluted media and prevention of oxidative stress, did not result in a significant increase in the numbers of viable cells retrieved form subglacial sediment samples. Our previous investigations demonstrated the necessity for special procedures for efficient reactivation of the cells from microbial communities of preserved fossil soil and permafrost samples collected in the Arctic zone. The differences in response to the special resuscitation procedures may reflect the differences in the physiological and morphological state of bacterial cells in microbial communities subject to continuous or periodic low temperatures and dehydration.

Adaptation of soil microbial community structure and function to chronic metal contamination at an abandoned Pb-Zn mine.

PubMed

Epelde, Lur; Lanzén, Anders; Blanco, Fernando; Urich, Tim; Garbisu, Carlos

2015-01-01

Toxicity of metals released from mine tailings may cause severe damage to ecosystems. A diversity of microorganisms, however, have successfully adapted to such sites. In this study, our objective was to advance the understanding of the indigenous microbial communities of mining-impacted soils. To this end, a metatranscriptomic approach was used to study a heavily metal-contaminated site along a metal concentration gradient (up to 3220 000 and 97 000 mg kg(-1) of Cd, Pb and Zn, respectively) resulting from previous mining. Metal concentration, soil pH and amount of clay were the most important factors determining the structure of soil microbial communities. Interestingly, evenness of the microbial communities, but not its richness, increased with contamination level. Taxa with high metabolic plasticity like Ktedonobacteria and Chloroflexi were found with higher relative abundance in more contaminated samples. However, several taxa belonging to the phyla Actinobacteria and Acidobacteria followed opposite trends in relation to metal pollution. Besides, functional transcripts related to transposition or transfer of genetic material and membrane transport, potentially involved in metal resistance mechanisms, had a higher expression in more contaminated samples. Our results provide an insight into microbial communities in long-term metal-contaminated environments and how they contrast to nearby sites with lower contamination. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Wastewater treatment plant effluent introduces recoverable shifts in microbial community composition in urban streams

NASA Astrophysics Data System (ADS)

Ledford, S. H.; Price, J. R.; Ryan, M. O.; Toran, L.; Sales, C. M.

2017-12-01

New technologies are allowing for intense scrutiny of the impact of land use on microbial communities in stream networks. We used a combination of analytical chemistry, real-time polymerase chain reaction (qPCR) and targeted amplicon sequencing for a preliminary study on the impact of wastewater treatment plant effluent discharge on urban streams. Samples were collected on two dates above and below treatment plants on the Wissahickon Creek, and its tributary, Sandy Run, in Montgomery County, PA, USA. As expected, effluent was observed to be a significant source of nutrients and human and non-specific fecal associated taxa. There was an observed increase in the alpha diversity at locations immediately below effluent outflows, which contributed many taxa involved in wastewater treatment processes and nutrient cycling to the stream's microbial community. Unexpectedly, modeling of microbial community shifts along the stream was not controlled by concentrations of measured nutrients. Furthermore, partial recovery, in the form of decreasing abundances of bacteria and nutrients associated with wastewater treatment plant processes, nutrient cycling bacteria, and taxa associated with fecal and sewage sources, was observed between effluent sources. Antecedent moisture conditions impacted overall microbial community diversity, with higher diversity occurring after rainfall. These findings hint at resilience in stream microbial communities to recover from wastewater treatment plant effluent and are vital to understanding the impacts of urbanization on microbial stream communities.

Effects of soil water repellency on microbial community structure and functions in Mediterranean pine forests

NASA Astrophysics Data System (ADS)

Lozano, Elena; Grayston, Sue J.; Mataix-Solera, Jorge; Arcenegui, Victoria; Jimenez-Pinilla, Patricia; Mataix-Beneyto, Jorge

2015-04-01

Soil water repellency (SWR) is a property commonly observed in forest areas showing wettable and water repellent patches with high spatial variability. SWR can greatly influence the hydrology and the ecology of forest soils. The capacity of soil microorganisms to degrade different organic compounds depends upon species composition, so this may affect changes in SWR on the microsite scale (such as the presence of soil water repellent patches; Mülleret al., 2010). In the Mediterranean forest context, SWR has been found to be related to microbial community composition. The accumulation of different hydrophobic compounds might be causing the shifts in microbial community structure (Lozano et al., 2014). In this study we investigated the effects of SWR persistence on soil microbial community structure and enzyme activity under Pinus halepensis forest in three different sites: Petrer, Gorga and Jávea (Alicante, E Spain). Soil samples were classified into three different water repellency classes (wettable, slight or strongly water repellent samples) depending on the SWR persistence. The soil microbial community was determined through phospholipid fatty acids (PLFAs). Enzyme activities chosen for this study were cellulase, β-glucosidase and N-acetyl-β-glucosaminide (NAG). The relationships between microbiological community structure and some soil properties such as pH, Glomalin Related Soil Protein, soil organic matter content and soil respiration were also studied. Redundancy analyses and decomposition of the variances were performed to clarify how microbial community composition and enzyme activities are affected by SWR and soil properties. The effect of SWR on microbial community composition differed between locations. This effect was clearer in the Petrer site. Enzyme activity varied considerably depending on SWR persistence. The highest activities were found in slightly SWR samples and the lowest mostly in the strongly water repellent ones. These preliminary results suggest a possible influence of SWR on microbial structure and its activity in soils. References: Lozano, E., García-Orenes, F., Bárcenas-Moreno, G., Jiménez-Pinilla, P., Mataix-Solera, J., Arcenegui, V., Morugán-Coronado, A., Mataix-Beneyto, J., 2014. Relationships between soil water repellency and microbial community composition under different plant species in a Mediterranean semiarid forest. J. Hydrol. Hydromech., 62, 101-107 Müller, K., Deurer, M., Newton, P.C.D., 2010. Is there a link between elevated atmospheric carbon dioxide concentration, soil water repellency and soil carbon mineralization? Agric. Ecosyst. Environ., 139, 98-109. Acknowledgements: to the "Ministerio de Economía and Competitividad" of Spanish Government for finance the POSTFIRE project (CGL2013- 47862-C2-1-R), Generalitat Valenciana for PhD grant, and Spanish Soil Science Society and FUEGORED for their support.

Extractable nitrogen and microbial community structure respond to grassland restoration regardless of historical context and soil composition

PubMed Central

Dickens, Sara Jo M.; Allen, Edith B.; Santiago, Louis S.; Crowley, David

2015-01-01

Grasslands have a long history of invasion by exotic annuals, which may alter microbial communities and nutrient cycling through changes in litter quality and biomass turnover rates. We compared plant community composition, soil chemical and microbial community composition, potential soil respiration and nitrogen (N) turnover rates between invaded and restored plots in inland and coastal grasslands. Restoration increased microbial biomass and fungal : bacterial (F : B) ratios, but sampling season had a greater influence on the F : B ratio than did restoration. Microbial community composition assessed by phospholipid fatty acid was altered by restoration, but also varied by season and by site. Total soil carbon (C) and N and potential soil respiration did not differ between treatments, but N mineralization decreased while extractable nitrate and nitrification and N immobilization rate increased in restored compared with unrestored sites. The differences in soil chemistry and microbial community composition between unrestored and restored sites indicate that these soils are responsive, and therefore not resistant to feedbacks caused by changes in vegetation type. The resilience, or recovery, of these soils is difficult to assess in the absence of uninvaded control grasslands. However, the rapid changes in microbial and N cycling characteristics following removal of invasives in both grassland sites suggest that the soils are resilient to invasion. The lack of change in total C and N pools may provide a buffer that promotes resilience of labile pools and microbial community structure. PMID:25555522

Molecular Analysis of Endolithic Microbial Communities in Volcanic Glasses

NASA Astrophysics Data System (ADS)

di Meo, C. A.; Giovannoni, S.; Fisk, M.

2002-12-01

Terrestrial and marine volcanic glasses become mineralogically and chemically altered, and in many cases this alteration has been attributed to microbial activity. We have used molecular techniques to study the resident microbial communities from three different volcanic environments that may be responsible for this crustal alteration. Total microbial DNA was extracted from rhyolite glass of the 7 million year old Rattlesnake Tuff in eastern Oregon. The DNA was amplified using the polymerase chain reaction (PCR) with bacterial primers targeting the 16S rRNA gene. This 16S rDNA was cloned and screened with restriction fragment length polymorphism (RFLP). Out of 89 total clones screened, 46 belonged to 13 different clone families containing two or more members, while 43 clones were unique. Sequences of eight clones representing the most dominant clone families in the library were 92 to 97% similar to soil bacterial species. In a separate study, young pillow basalts (<20 yrs old) from six different sites along the ridge axis at 9°N, East Pacific Rise were examined for microbial life. Total DNA was extracted from the basalt glass and screened for the presence of both bacteria and archaea using the PCR. Repeated attempts with different primer sets yielded no bacterial genes, whereas archaeal genes were quite abundant. A genetic fingerprinting technique, terminal restriction fragment length polymorphism (T-RFLP), was used to compare the archaeal community compositions among the six different basalts. Filtered deep-sea water samples (~15 L) were examined in parallel to identify any overlap between rock- and seawater-associated archaea. The six rock community profiles were quite similar to each other, and the background water communities were also similar, respectively. Both the rock and water communities shared the same dominant peak. To identify the T-RFLP peaks corresponding to the individual members of the rock and seawater communities, clone libraries of the archaeal 16S rDNA for one basalt sample (Dive 3718) and its corresponding background water sample were constructed. The most abundant archaeal genes were closely related to uncultured Group I marine Crenarchaeota that have been previously identified from similar deep-sea habitats. These archaeal genes collectively correspond to the dominant T-RFLP peak present in both the rock and water samples. In a third study, we investigated the microbial community residing in a Hawaiian Scientific Drilling Program core collected near Hilo, Hawaii. Total microbial DNA was extracted from a depth of 1351 m in the drill core (ambient temperature in the drill hole ~16°C), where petrographic evidence suggested the presence of microbial alteration. Archaeal 16S rRNA genes were amplified, cloned, and twelve clones representing the most abundant groups were sequenced. Eleven out of the twelve clones were 97 to 99% similar to Group I marine Crenarchaeota, while the remaining clone was 95% similar to Euryarchaeota, based on BLAST searches of the GenBank database. Our community-level approach to studying microbes living in volcanic glasses has provided a greater understanding of the microbial communities that potentially alter these materials.

Microbiology Meets Archaeology: Soil Microbial Communities Reveal Different Human Activities at Archaic Monte Iato (Sixth Century BC).

PubMed

Margesin, Rosa; Siles, José A; Cajthaml, Tomas; Öhlinger, Birgit; Kistler, Erich

2017-05-01

Microbial ecology has been recognized as useful in archaeological studies. At Archaic Monte Iato in Western Sicily, a native (indigenous) building was discovered. The objective of this study was the first examination of soil microbial communities related to this building. Soil samples were collected from archaeological layers at a ritual deposit (food waste disposal) in the main room and above the fireplace in the annex. Microbial soil characterization included abundance (cellular phospholipid fatty acids (PLFA), viable bacterial counts), activity (physiological profiles, enzyme activities of viable bacteria), diversity, and community structure (bacterial and fungal Illumina amplicon sequencing, identification of viable bacteria). PLFA-derived microbial abundance was lower in soils from the fireplace than in soils from the deposit; the opposite was observed with culturable bacteria. Microbial communities in soils from the fireplace had a higher ability to metabolize carboxylic and acetic acids, while those in soils from the deposit metabolized preferentially carbohydrates. The lower deposit layer was characterized by higher total microbial and bacterial abundance and bacterial richness and by a different carbohydrate metabolization profile compared to the upper deposit layer. Microbial community structures in the fireplace were similar and could be distinguished from those in the two deposit layers, which had different microbial communities. Our data confirmed our hypothesis that human consumption habits left traces on microbiota in the archaeological evidence; therefore, microbiological residues as part of the so-called ecofacts are, like artifacts, key indicators of consumer behavior in the past.

Putative Effect of Aquifer Recharge on the Abundance and Taxonomic Composition of Endemic Microbial Communities

PubMed Central

Sibley, Cally A.; Hutson, John L.; Mitchell, James G.

2015-01-01

Drought events and the overexploitation of freshwater resources have led to the increased need to manage groundwater reserves. Aquifer storage and recovery (ASR), whereby artificial water is injected into aquifers for storage, is one of the proposed methods by which freshwater supplies can be increased. Microbial clogging following injection, however, is a major issue. Here, during laboratory simulations of ASR, we used flow cytometry and bar-coded pyrosequencing to investigate changes in microbial abundance and community dynamics. Bacterial abundance ranged from 5.0 × 104 to 1.4 × 107 cells ml-1 before the addition of synthetic wastewater. Following wastewater addition, a 25-fold decrease in abundance was observed, coinciding with a 12-fold increase in viral abundance. Taxa shifted from an overrepresentation of Sphingomonadales, Sphingobacteriales, Rhodospirillales, Caulobacterales, Legionellales, Bacillales, Fusobacteriales and Verrucomicrobiales prior to the addition of synthetic wastewater to Burkholderiales, Actinomycetales, Pseudomonadales, Xanthomonadales, Rhodobacterales, Thizobiales and Thiotrichales following the addition of synthetic wastewater. Furthermore, a significant difference in overall taxonomic composition between the groundwater samples before and after the addition of synthetic wastewater was observed, with water samples exhibiting more similarity to sediment samples after wastewater was added. Collectively, these results suggest that ASR may alter the taxonomic composition of endemic microbial communities and that complete profiles of groundwater properties, including microbial community abundance and composition need to be taken into consideration when selecting aquifers for ASR practices. PMID:26083532

The Changing Microbial Community Along the Orca Basin Pycnocline

NASA Astrophysics Data System (ADS)

Hyde, A.; Nigro, L. M.; Montoya, J. P.; Joye, S. B.; Teske, A.

2016-02-01

Orca Basin in the Gulf of Mexico is the largest seafloor brine basin in the world, with a brine depth up to 220 m and an areal extent of 123 km2. Within the chemocline and pycnocline of Orca Basin, salinity, temperature, oxygen concentration, porewater chemistry, and microbial community composition change within approx. 100 meters, from fully oxic and marine saline deepwater conditions at 2150 m to anoxic hypersaline brine at 2250 m depth. Previous surveys of Orca Basin have detected distinct peaks of metal-cycling bacteria, and of archaeal lipids in the Orca Basin chemocline. The steep pycnocline slows down the sinking speed and therefore concentrates organic matter and microbial populations from the water column; it also allows in-situ growth of microbial populations that can take advantage of coexisting electron donors and acceptors. To survey the microbial community structure and stratification in Orca Basin, we performed a high-throughput bacterial 16S rRNA gene sequencing of filter samples from the Orca Basin deep water, chemocline and brine, collected in April 2014 on RV Atlantis. Widely spaced 50 m sample intervals from 1800 to 2350 m depth were complemented with fine-scale sampling every ten meters between 2150 and 2250 m depth, centered on the pycno- and chemocline as evident from CTD data, and with additional samples taken at 2125, 2275, and 2375 m depth. While we expect abundant and diverse chemosynthetic interface bacteria and halophiles, we are also exploring the possibility that the Orca Basin pycnocline preserves and amplifies microbial hydrocarbon signatures in the Gulf of Mexico, as in a long-term particle trap.

The role of macrobiota in structuring microbial communities along rocky shores

DOE PAGES

Pfister, Catherine A.; Gilbert, Jack A.; Gibbons, Sean M.

2014-10-16

Rocky shore microbial diversity presents an excellent system to test for microbial habitat specificity or generality, enabling us to decipher how common macrobiota shape microbial community structure. At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton. While all sampled entities had a core of common OTUs, rare OTUs drove differences among biotic and abiotic substrates. For the mussel Mytilus californianus, the shell surface harbored greater alpha diversity compared to internal tissues of themore » gill and siphon. Strikingly, a 7-year experimental removal of this mussel from tidepools did not significantly alter the microbial community structure of microbes associated with inert surfaces when compared with unmanipulated tidepools. However, bacterial taxa associated with nitrate reduction had greater relative abundance with mussels present, suggesting an impact of increased animal-derived nitrogen on a subset of microbial metabolism. Because the presence of mussels did not affect the structure and diversity of the microbial community on adjacent inert substrates, microbes in this rocky shore environment may be predominantly affected through direct physical association with macrobiota.« less

The role of macrobiota in structuring microbial communities along rocky shores

PubMed Central

Gilbert, Jack A.; Gibbons, Sean M.

2014-01-01

Rocky shore microbial diversity presents an excellent system to test for microbial habitat specificity or generality, enabling us to decipher how common macrobiota shape microbial community structure. At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton. While all sampled entities had a core of common OTUs, rare OTUs drove differences among biotic and abiotic substrates. For the mussel Mytilus californianus, the shell surface harbored greater alpha diversity compared to internal tissues of the gill and siphon. Strikingly, a 7-year experimental removal of this mussel from tidepools did not significantly alter the microbial community structure of microbes associated with inert surfaces when compared with unmanipulated tidepools. However, bacterial taxa associated with nitrate reduction had greater relative abundance with mussels present, suggesting an impact of increased animal-derived nitrogen on a subset of microbial metabolism. Because the presence of mussels did not affect the structure and diversity of the microbial community on adjacent inert substrates, microbes in this rocky shore environment may be predominantly affected through direct physical association with macrobiota. PMID:25337459

Microbial communities and soil fertility in flood irrigated orchards under different management systems in eastern spain

NASA Astrophysics Data System (ADS)

Morugán-Coronado, Alicia; García-Orenes, Fuensanta; Caravaca, Fuensanta; Roldán, Antonio

2016-04-01

Unsuitable land management such as the excessive use of herbicides can lead to a loss of soil fertility and a drastic reduction in the abundance of microbial populations and their functions related to nutrient cycling. Microbial communities are the most sensitive and rapid indicators of perturbations in agroecosystems. A field experiment was performed in an orange-trees orchard (Citrus sinensis) to assess the long-term effect of three different management systems on the soil microbial community biomass, structure and composition (phospholipid fatty acids (PLFAs) total, pattern, and abundance). The three agricultural systems assayed were established 30 years ago: herbicides (Glyphosate (N-(phosphonomethyl)glycine) with inorganic fertilizers (H), intensive ploughing and inorganic fertilizers (NPK 15%) (P) and organic farming (chipped pruned branches and weeds, manure from sheep and goats) (O). Nine soil samples were taken from each system. The results showed that the management practices including herbicides and intensive ploughing had similar results on soil microbial properties, while organic fertilization significantly increased microbial biomass, shifted the structure and composition of the soil microbial community, and stimulated microbial activity, when compared to inorganic fertilization systems; thus, enhancing the sustainability of this agroecosystem under semiarid conditions.

Physical Factors Correlate to Microbial Community Structure and Nitrogen Cycling Gene Abundance in a Nitrate Fed Eutrophic Lagoon.

PubMed

Highton, Matthew P; Roosa, Stéphanie; Crawshaw, Josie; Schallenberg, Marc; Morales, Sergio E

2016-01-01

Nitrogenous run-off from farmed pastures contributes to the eutrophication of Lake Ellesmere, a large shallow lagoon/lake on the east coast of New Zealand. Tributaries periodically deliver high loads of nitrate to the lake which likely affect microbial communities therein. We hypothesized that a nutrient gradient would form from the potential sources (tributaries) creating a disturbance resulting in changes in microbial community structure. To test this we first determined the existence of such a gradient but found only a weak nitrogen (TN) and phosphorous gradient (DRP). Changes in microbial communities were determined by measuring functional potential (quantification of nitrogen cycling genes via nifH , nirS , nosZI , and nosZII using qPCR), potential activity (via denitrification enzyme activity), as well as using changes in total community (via 16S rRNA gene amplicon sequencing). Our results demonstrated that changes in microbial communities at a phylogenetic (relative abundance) and functional level (proportion of the microbial community carrying nifH and nosZI genes) were most strongly associated with physical gradients (e.g., lake depth, sediment grain size, sediment porosity) and not nutrient concentrations. Low nitrate influx at the time of sampling is proposed as a factor contributing to the observed patterns.

Effect of different levels of nitrogen on rhizosphere bacterial community structure in intensive monoculture of greenhouse lettuce.

PubMed

Li, Jian-Gang; Shen, Min-Chong; Hou, Jin-Feng; Li, Ling; Wu, Jun-Xia; Dong, Yuan-Hua

2016-04-28

Pyrosequencing-based analyses revealed significant effects among low (N50), medium (N80), and high (N100) fertilization on community composition involving a long-term monoculture of lettuce in a greenhouse in both summer and winter. The non-fertilized control (CK) treatment was characterized by a higher relative abundance of Actinobacteria, Acidobacteria, and Chloroflexi; however, the average abundance of Firmicutes typically increased in summer, and the relative abundance of Bacteroidetes increased in winter in the N-fertilized treatments. Principle component analysis showed that the distribution of the microbial community was separated by a N gradient with N80 and N100 in the same group in the summer samples, while CK and N50 were in the same group in the winter samples, with the other N-level treatments existing independently. Redundancy analysis revealed that available N, NO3(-)-N, and NH4(+)-N, were the main environmental factors affecting the distribution of the bacterial community. Correlation analysis showed that nitrogen affected the shifts of microbial communities by strongly driving the shifts of Firmicutes, Bacteroidetes, and Proteobacteria in summer samples, and Bacteroidetes, Actinobacteria, and Acidobacteria in winter samples. The study demonstrates a novel example of rhizosphere bacterial diversity and the main factors influencing rizosphere microbial community in continuous vegetable cropping within an intensive greenhouse ecosystem.

Effect of different levels of nitrogen on rhizosphere bacterial community structure in intensive monoculture of greenhouse lettuce

NASA Astrophysics Data System (ADS)

Li, Jian-Gang; Shen, Min-Chong; Hou, Jin-Feng; Li, Ling; Wu, Jun-Xia; Dong, Yuan-Hua

2016-04-01

Pyrosequencing-based analyses revealed significant effects among low (N50), medium (N80), and high (N100) fertilization on community composition involving a long-term monoculture of lettuce in a greenhouse in both summer and winter. The non-fertilized control (CK) treatment was characterized by a higher relative abundance of Actinobacteria, Acidobacteria, and Chloroflexi; however, the average abundance of Firmicutes typically increased in summer, and the relative abundance of Bacteroidetes increased in winter in the N-fertilized treatments. Principle component analysis showed that the distribution of the microbial community was separated by a N gradient with N80 and N100 in the same group in the summer samples, while CK and N50 were in the same group in the winter samples, with the other N-level treatments existing independently. Redundancy analysis revealed that available N, NO3--N, and NH4+-N, were the main environmental factors affecting the distribution of the bacterial community. Correlation analysis showed that nitrogen affected the shifts of microbial communities by strongly driving the shifts of Firmicutes, Bacteroidetes, and Proteobacteria in summer samples, and Bacteroidetes, Actinobacteria, and Acidobacteria in winter samples. The study demonstrates a novel example of rhizosphere bacterial diversity and the main factors influencing rizosphere microbial community in continuous vegetable cropping within an intensive greenhouse ecosystem.

Energy Gradients Structure Microbial Communities Across Sediment Horizons in Deep Marine Sediments of the South China Sea

PubMed Central

Graw, Michael F.; D'Angelo, Grace; Borchers, Matthew; Thurber, Andrew R.; Johnson, Joel E.; Zhang, Chuanlun; Liu, Haodong; Colwell, Frederick S.

2018-01-01

The deep marine subsurface is a heterogeneous environment in which the assembly of microbial communities is thought to be controlled by a combination of organic matter deposition, electron acceptor availability, and sedimentology. However, the relative importance of these factors in structuring microbial communities in marine sediments remains unclear. The South China Sea (SCS) experiences significant variability in sedimentation across the basin and features discrete changes in sedimentology as a result of episodic deposition of turbidites and volcanic ashes within lithogenic clays and siliceous or calcareous ooze deposits throughout the basin's history. Deep subsurface microbial communities were recently sampled by the International Ocean Discovery Program (IODP) at three locations in the SCS with sedimentation rates of 5, 12, and 20 cm per thousand years. Here, we used Illumina sequencing of the 16S ribosomal RNA gene to characterize deep subsurface microbial communities from distinct sediment types at these sites. Communities across all sites were dominated by several poorly characterized taxa implicated in organic matter degradation, including Atribacteria, Dehalococcoidia, and Aerophobetes. Sulfate-reducing bacteria comprised only 4% of the community across sulfate-bearing sediments from multiple cores and did not change in abundance in sediments from the methanogenic zone at the site with the lowest sedimentation rate. Microbial communities were significantly structured by sediment age and the availability of sulfate as an electron acceptor in pore waters. However, microbial communities demonstrated no partitioning based on the sediment type they inhabited. These results indicate that microbial communities in the SCS are structured by the availability of electron donors and acceptors rather than sedimentological characteristics. PMID:29696012

Plants regulate the effects of experimental warming on the soil microbial community in an alpine scrub ecosystem.

PubMed

Ma, Zhiliang; Zhao, Wenqiang; Zhao, Chunzhang; Wang, Dong; Liu, Mei; Li, Dandan; Liu, Qing

2018-01-01

Information on how soil microbial communities respond to warming is still scarce for alpine scrub ecosystems. We conducted a field experiment with two plant treatments (plant removal or undisturbed) subjected to warmed or unwarmed conditions to examine the effects of warming and plant removal on soil microbial community structures during the growing season in a Sibiraea angustata scrubland of the eastern Qinghai-Tibetan Plateau. The results indicate that experimental warming significantly influenced soil microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN), but the warming effects were dependent on the plant treatments and sampling seasons. In the plant-removal plots, warming did not affect most of the microbial variables, while in the undisturbed plots, warming significantly increased the abundances of actinomycete and Gram-positive bacterial groups during the mid-growing season (July), but it did not affect the fungi groups. Plant removal significantly reduced fungal abundance throughout the growing season and significantly altered the soil microbial community structure in July. The interaction between warming and plant removal significantly influenced the soil MBC and MBN and the abundances of total microbes, bacteria and actinomycete throughout the growing season. Experimental warming significantly reduced the abundance of rare taxa, while the interaction between warming and plant removal tended to have strong effects on the abundant taxa. These findings suggest that the responses of soil microbial communities to warming are regulated by plant communities. These results provide new insights into how soil microbial community structure responds to climatic warming in alpine scrub ecosystems.

Plants regulate the effects of experimental warming on the soil microbial community in an alpine scrub ecosystem

PubMed Central

Ma, Zhiliang; Zhao, Wenqiang; Zhao, Chunzhang; Wang, Dong; Liu, Mei; Li, Dandan

2018-01-01

Information on how soil microbial communities respond to warming is still scarce for alpine scrub ecosystems. We conducted a field experiment with two plant treatments (plant removal or undisturbed) subjected to warmed or unwarmed conditions to examine the effects of warming and plant removal on soil microbial community structures during the growing season in a Sibiraea angustata scrubland of the eastern Qinghai–Tibetan Plateau. The results indicate that experimental warming significantly influenced soil microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN), but the warming effects were dependent on the plant treatments and sampling seasons. In the plant-removal plots, warming did not affect most of the microbial variables, while in the undisturbed plots, warming significantly increased the abundances of actinomycete and Gram-positive bacterial groups during the mid-growing season (July), but it did not affect the fungi groups. Plant removal significantly reduced fungal abundance throughout the growing season and significantly altered the soil microbial community structure in July. The interaction between warming and plant removal significantly influenced the soil MBC and MBN and the abundances of total microbes, bacteria and actinomycete throughout the growing season. Experimental warming significantly reduced the abundance of rare taxa, while the interaction between warming and plant removal tended to have strong effects on the abundant taxa. These findings suggest that the responses of soil microbial communities to warming are regulated by plant communities. These results provide new insights into how soil microbial community structure responds to climatic warming in alpine scrub ecosystems. PMID:29668711

Prokaryotic communities differ along a geothermal soil photic gradient.

PubMed

Meadow, James F; Zabinski, Catherine A

2013-01-01

Geothermal influenced soils exert unique physical and chemical limitations on resident microbial communities but have received little attention in microbial ecology research. These environments offer a model system in which to investigate microbial community heterogeneity and a range of soil ecological concepts. We conducted a 16S bar-coded pyrosequencing survey of the prokaryotic communities in a diatomaceous geothermal soil system and compared communities across soil types and along a conspicuous photic depth gradient. We found significant differences between the communities of the two different soils and also predictable differences between samples taken at different depths. Additionally, we targeted three ecologically relevant bacterial phyla, Cyanobacteria, Planctomycetes, and Verrucomicrobia, for clade-wise comparisons with these variables and found strong differences in their abundances, consistent with the autecology of these groups.

The Effect of Sampling and Storage on the Fecal Microbiota Composition in Healthy and Diseased Subjects

PubMed Central

Tedjo, Danyta I.; Jonkers, Daisy M. A. E.; Savelkoul, Paul H.; Masclee, Ad A.; van Best, Niels; Pierik, Marieke J.; Penders, John

2015-01-01

Large-scale cohort studies are currently being designed to investigate the human microbiome in health and disease. Adequate sampling strategies are required to limit bias due to shifts in microbial communities during sampling and storage. Therefore, we examined the impact of different sampling and storage conditions on the stability of fecal microbial communities in healthy and diseased subjects. Fecal samples from 10 healthy controls, 10 irritable bowel syndrome and 8 inflammatory bowel disease patients were collected on site, aliquoted immediately after defecation and stored at -80°C, -20°C for 1 week, at +4°C or room temperature for 24 hours. Fecal transport swabs (FecalSwab, Copan) were collected and stored for 48-72 hours at room temperature. We used pyrosequencing of the 16S gene to investigate the stability of microbial communities. Alpha diversity did not differ between all storage methods and -80°C, except for the fecal swabs. UPGMA clustering and principal coordinate analysis showed significant clustering by test subject (p<0.001) but not by storage method. Bray-Curtis dissimilarity and (un)weighted UniFrac showed a significant higher distance between fecal swabs and -80°C versus the other methods and -80°C samples (p<0.009). The relative abundance of Ruminococcus and Enterobacteriaceae did not differ between the storage methods versus -80°C, but was higher in fecal swabs (p<0.05). Storage up to 24 hours (at +4°C or room temperature) or freezing at -20°C did not significantly alter the fecal microbial community structure compared to direct freezing of samples from healthy subjects and patients with gastrointestinal disorders. PMID:26024217

16S rRNA analysis of diversity of manure microbial community in dairy farm environment

PubMed Central

Miao, Max; Wang, Yi; Settles, Matthew; del Rio, Noelia Silva; Castillo, Alejandro; Souza, Alex; Pereira, Richard

2018-01-01

Dairy farms generate a considerable amount of manure, which is applied in cropland as fertilizer. While the use of manure as fertilizer reduces the application of chemical fertilizers, the main concern with regards to manure application is microbial pollution. Manure is a reservoir of a broad range of microbial populations, including pathogens, which have potential to cause contamination and pose risks to public and animal health. Despite the widespread use of manure fertilizer, the change in microbial diversity of manure under various treatment processes is still not well-understood. We hypothesize that the microbial population of animal waste changes with manure handling used in a farm environment. Consequential microbial risk caused by animal manure may depend on manure handling. In this study, a reconnaissance effort for sampling dairy manure in California Central Valley followed by 16S rRNA analysis of content and diversity was undertaken to understand the microbiome of manure after various handling processes. The microbial community analysis of manure revealed that the population in liquid manure differs from that in solid manure. For instance, the bacteria of genus Sulfuriomonas were unique in liquid samples, while the bacteria of genus Thermos were observed only in solid samples. Bacteria of genus Clostridium were present in both solid and liquid samples. The population among liquid samples was comparable, as was the population among solid samples. These findings suggest that the mode of manure application (i.e., liquid versus solid) could have a potential impact on the microbiome of cropland receiving manure as fertilizers. PMID:29304047

Microbial succession in an inflated lunar/Mars analog habitat during a 30-day human occupation.

PubMed

Mayer, Teresa; Blachowicz, Adriana; Probst, Alexander J; Vaishampayan, Parag; Checinska, Aleksandra; Swarmer, Tiffany; de Leon, Pablo; Venkateswaran, Kasthuri

2016-06-02

For potential future human missions to the Moon or Mars and sustained presence in the International Space Station, a safe enclosed habitat environment for astronauts is required. Potential microbial contamination of closed habitats presents a risk for crewmembers due to reduced human immune response during long-term confinement. To make future habitat designs safer for crewmembers, lessons learned from characterizing analogous habitats is very critical. One of the key issues is that how human presence influences the accumulation of microorganisms in the closed habitat. Molecular technologies, along with traditional microbiological methods, were utilized to catalog microbial succession during a 30-day human occupation of a simulated inflatable lunar/Mars habitat. Surface samples were collected at different time points to capture the complete spectrum of viable and potential opportunistic pathogenic bacterial population. Traditional cultivation, propidium monoazide (PMA)-quantitative polymerase chain reaction (qPCR), and adenosine triphosphate (ATP) assays were employed to estimate the cultivable, viable, and metabolically active microbial population, respectively. Next-generation sequencing was used to elucidate the microbial dynamics and community profiles at different locations of the habitat during varying time points. Statistical analyses confirm that occupation time has a strong influence on bacterial community profiles. The Day 0 samples (before human occupation) have a very different microbial diversity compared to the later three time points. Members of Proteobacteria (esp. Oxalobacteraceae and Caulobacteraceae) and Firmicutes (esp. Bacillaceae) were most abundant before human occupation (Day 0), while other members of Firmicutes (Clostridiales) and Actinobacteria (esp. Corynebacteriaceae) were abundant during the 30-day occupation. Treatment of samples with PMA (a DNA-intercalating dye for selective detection of viable microbial population) had a significant effect on the microbial diversity compared to non-PMA-treated samples. Statistical analyses revealed a significant difference in community structure of samples over time, particularly of the bacteriomes existing before human occupation of the habitat (Day 0 sampling) and after occupation (Day 13, Day 20, and Day 30 samplings). Actinobacteria (mainly Corynebacteriaceae) and Firmicutes (mainly Clostridiales Incertae Sedis XI and Staphylococcaceae) were shown to increase over the occupation time period. The results of this study revealed a strong relationship between human presence and succession of microbial diversity in a closed habitat. Consequently, it is necessary to develop methods and tools for effective maintenance of a closed system to enable safe human habitation in enclosed environments on Earth and beyond.

Longitudinal changes in microbial planktonic communities of a French river in relation to pesticide and nutrient inputs.

PubMed

Pesce, Stéphane; Fajon, Céline; Bardot, Corinne; Bonnemoy, Frédérique; Portelli, Christophe; Bohatier, Jacques

2008-02-18

To determine the effects of anthropic activities on river planktonic microbial populations, monthly water samples were collected for 11 months from two sampling sites characterized by differing nutrient and pesticide levels. The difference in trophic level between the two stations was particularly pronounced from May to November. Total pesticide concentrations were notably higher at the downstream station from April to October with a clear predominance of herbicide residues, especially the glyphosate metabolite aminomethylphosphonic acid (AMPA). From spring, algal biomass and density were favored by the high orthophosphate concentrations recorded at the downstream location. However, isolated drops in algal biomass were recorded at this sampling station, suggesting an adverse effect of herbicides on algal communities. No major difference was observed in bacterial heterotrophic production, density, or activity (CTC reduction) between the two sampling stations. No major variation was detected using the fluorescent in situ hybridization (FISH) method, but shifts in bacterial community composition were recorded by PCR-TTGE analysis at the downstream station following high nutrient and pesticide inputs. However, outside the main anthropic pollution period, the water's chemical properties and planktonic microbial communities were very similar at the two sampling sites, suggesting a high recovery potential for this lotic system.

The microbiota of traumatic, open fracture wounds is associated with mechanism of injury.

PubMed

Bartow-McKenney, Casey; Hannigan, Geoffrey D; Horwinski, Joseph; Hesketh, Patrick; Horan, Annamarie D; Mehta, Samir; Grice, Elizabeth A

2018-05-26

Open fractures are characterized by disruption of the skin and soft tissue, which allows for microbial contamination and colonization. Preventing infection-related complications of open fractures and other acute wounds remains an evolving challenge due to an incomplete understanding of how microbial colonization and contamination influence healing and outcomes. Culture-independent molecular methods are now widely used to study human-associated microbial communities without introducing culture biases. Using such approaches, the objectives of this study were to 1) define the long-term temporal microbial community dynamics of open fracture wounds and 2) examine microbial community dynamics with respect to clinical and demographic factors. Fifty-two subjects with traumatic open fracture wounds (32 blunt and 20 penetrating injuries) were enrolled prospectively and sampled longitudinally from presentation to the emergency department and at each subsequent inpatient or outpatient encounter. Specimens were collected from both the wound center and adjacent skin. Culture-independent sequencing of the 16S ribosomal RNA gene was employed to identify and characterize microbiota. Upon presentation to the emergency department and time points immediately following, sample collection site (wound or adjacent skin) was the most defining feature discriminating microbial profiles. Microbial composition of adjacent skin and wound center converged over time. Mechanism of injury most strongly defined the microbiota after initial convergence. Further analysis controlling for race, gender, and age revealed that mechanism of injury remained a significant discriminating feature throughout the continuum of care. We conclude that the microbial communities associated with open fracture wounds are dynamic in nature until eventual convergence with the adjacent skin community during healing, with mechanism of injury as an important feature affecting both diversity and composition of the microbiota. A more complete understanding of the factors influencing microbial contamination and/or colonization in open fractures is a critical foundation for identifying markers indicative of outcome and deciphering their respective contributions to healing and/or complication. This article is protected by copyright. All rights reserved. © 2018 by the Wound Healing Society.

Gut microbial communities of American pikas (Ochotona princeps): Evidence for phylosymbiosis and adaptations to novel diets.

PubMed

Kohl, Kevin D; Varner, Johanna; Wilkening, Jennifer L; Dearing, M Denise

2018-03-01

Gut microbial communities provide many physiological functions to their hosts, especially in herbivorous animals. We still lack an understanding of how these microbial communities are structured across hosts in nature, especially within a given host species. Studies on laboratory mice have demonstrated that host genetics can influence microbial community structure, but that diet can overwhelm these genetic effects. We aimed to test these ideas in a natural system, the American pika (Ochotona princeps). First, pikas are high-elevation specialists with significant population structure across various mountain ranges in the USA, allowing us to investigate whether similarities in microbial communities match host genetic differences. Additionally, pikas are herbivorous, with some populations exhibiting remarkable dietary plasticity and consuming high levels of moss, which is exceptionally high in fibre and low in protein. This allows us to investigate adaptations to an herbivorous diet, as well as to the especially challenging diet of moss. Here, we inventoried the microbial communities of pika caecal pellets from various populations using 16S rRNA sequencing to investigate structuring of microbial communities across various populations with different natural diets. Microbial communities varied significantly across populations, and differences in microbial community structure were congruent with genetic differences in host population structure, a pattern known as "phylosymbiosis." Several microbial members (Ruminococcus, Prevotella, Oxalobacter and Coprococcus) were detected across all samples, and thus likely represent a "core microbiome." These genera are known to perform a number of services for herbivorous hosts such as fibre fermentation and the degradation of plant defensive compounds, and thus are likely important for herbivory in pikas. Moreover, pikas that feed on moss harboured microbial communities highly enriched in Melainabacteria. This uncultivable candidate phylum has been proposed to ferment fibre for herbivores, and thus may contribute to the ability of some pika populations to consume high amounts of moss. These findings demonstrate that both host genetics and diet can influence the microbial communities of the American pika. These animals may be novel sources of fibre-degrading microbes. Last, we discuss the implications of population-specific microbial communities for conservation efforts in this species. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

Insights into Diversity and Imputed Metabolic Potential of Bacterial Communities in the Continental Shelf of Agatti Island

PubMed Central

Dhar, Sunil Kumar; Jani, Kunal; Apte, Deepak A.; Shouche, Yogesh S.; Sharma, Avinash

2015-01-01

Marine microbes play a key role and contribute largely to the global biogeochemical cycles. This study aims to explore microbial diversity from one such ecological hotspot, the continental shelf of Agatti Island. Sediment samples from various depths of the continental shelf were analyzed for bacterial diversity using deep sequencing technology along with the culturable approach. Additionally, imputed metagenomic approach was carried out to understand the functional aspects of microbial community especially for microbial genes important in nutrient uptake, survival and biogeochemical cycling in the marine environment. Using culturable approach, 28 bacterial strains representing 9 genera were isolated from various depths of continental shelf. The microbial community structure throughout the samples was dominated by phylum Proteobacteria and harbored various bacterioplanktons as well. Significant differences were observed in bacterial diversity within a short region of the continental shelf (1–40 meters) i.e. between upper continental shelf samples (UCS) with lesser depths (i.e. 1–20 meters) and lower continental shelf samples (LCS) with greater depths (i.e. 25–40 meters). By using imputed metagenomic approach, this study also discusses several adaptive mechanisms which enable microbes to survive in nutritionally deprived conditions, and also help to understand the influence of nutrition availability on bacterial diversity. PMID:26066038

Insights into Diversity and Imputed Metabolic Potential of Bacterial Communities in the Continental Shelf of Agatti Island.

PubMed

Kumbhare, Shreyas V; Dhotre, Dhiraj P; Dhar, Sunil Kumar; Jani, Kunal; Apte, Deepak A; Shouche, Yogesh S; Sharma, Avinash

2015-01-01

Marine microbes play a key role and contribute largely to the global biogeochemical cycles. This study aims to explore microbial diversity from one such ecological hotspot, the continental shelf of Agatti Island. Sediment samples from various depths of the continental shelf were analyzed for bacterial diversity using deep sequencing technology along with the culturable approach. Additionally, imputed metagenomic approach was carried out to understand the functional aspects of microbial community especially for microbial genes important in nutrient uptake, survival and biogeochemical cycling in the marine environment. Using culturable approach, 28 bacterial strains representing 9 genera were isolated from various depths of continental shelf. The microbial community structure throughout the samples was dominated by phylum Proteobacteria and harbored various bacterioplanktons as well. Significant differences were observed in bacterial diversity within a short region of the continental shelf (1-40 meters) i.e. between upper continental shelf samples (UCS) with lesser depths (i.e. 1-20 meters) and lower continental shelf samples (LCS) with greater depths (i.e. 25-40 meters). By using imputed metagenomic approach, this study also discusses several adaptive mechanisms which enable microbes to survive in nutritionally deprived conditions, and also help to understand the influence of nutrition availability on bacterial diversity.

Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology.

PubMed

Binga, Erik K; Lasken, Roger S; Neufeld, Josh D

2008-03-01

Microbial ecology is a field that applies molecular techniques to analyze genes and communities associated with a plethora of unique environments on this planet. In the past, low biomass and the predominance of a few abundant community members have impeded the application of techniques such as PCR, microarray analysis and metagenomics to complex microbial populations. In the absence of suitable cultivation methods, it was not possible to obtain DNA samples from individual microorganisms. Recently, a method called multiple displacement amplification (MDA) has been used to circumvent these limitations by amplifying DNA from microbial communities in low-biomass environments, individual cells from uncultivated microbial species and active organisms obtained through stable isotope probing incubations. This review describes the development and applications of MDA, discusses its strengths and limitations and highlights the impact of MDA on the field of microbial ecology. Whole genome amplification via MDA has increased access to the genomic DNA of uncultivated microorganisms and low-biomass environments and represents a 'power tool' in the molecular toolbox of microbial ecologists.

Long-term spatial and temporal microbial community dynamics in a large-scale drinking water distribution system with multiple disinfectant regimes.

PubMed

Potgieter, Sarah; Pinto, Ameet; Sigudu, Makhosazana; du Preez, Hein; Ncube, Esper; Venter, Stephanus

2018-08-01

Long-term spatial-temporal investigations of microbial dynamics in full-scale drinking water distribution systems are scarce. These investigations can reveal the process, infrastructure, and environmental factors that influence the microbial community, offering opportunities to re-think microbial management in drinking water systems. Often, these insights are missed or are unreliable in short-term studies, which are impacted by stochastic variabilities inherent to large full-scale systems. In this two-year study, we investigated the spatial and temporal dynamics of the microbial community in a large, full scale South African drinking water distribution system that uses three successive disinfection strategies (i.e. chlorination, chloramination and hypochlorination). Monthly bulk water samples were collected from the outlet of the treatment plant and from 17 points in the distribution system spanning nearly 150 km and the bacterial community composition was characterised by Illumina MiSeq sequencing of the V4 hypervariable region of the 16S rRNA gene. Like previous studies, Alpha- and Betaproteobacteria dominated the drinking water bacterial communities, with an increase in Betaproteobacteria post-chloramination. In contrast with previous reports, the observed richness, diversity, and evenness of the bacterial communities were higher in the winter months as opposed to the summer months in this study. In addition to temperature effects, the seasonal variations were also likely to be influenced by changes in average water age in the distribution system and corresponding changes in disinfectant residual concentrations. Spatial dynamics of the bacterial communities indicated distance decay, with bacterial communities becoming increasingly dissimilar with increasing distance between sampling locations. These spatial effects dampened the temporal changes in the bulk water community and were the dominant factor when considering the entire distribution system. However, temporal variations were consistently stronger as compared to spatial changes at individual sampling locations and demonstrated seasonality. This study emphasises the need for long-term studies to comprehensively understand the temporal patterns that would otherwise be missed in short-term investigations. Furthermore, systematic long-term investigations are particularly critical towards determining the impact of changes in source water quality, environmental conditions, and process operations on the changes in microbial community composition in the drinking water distribution system. Copyright © 2018 Elsevier Ltd. All rights reserved.

Nutrient gradients in a granular activated carbon biofilter drives bacterial community organization and dynamics.

PubMed

Boon, Nico; Pycke, Benny F G; Marzorati, Massimo; Hammes, Frederik

2011-12-01

The quality of drinking water is ensured by hygienic barriers and filtration steps, such as ozonation and granular activated carbon (GAC) filtration. Apart from adsorption, GAC filtration involves microbial processes that remove biodegradable organic carbon from the ozonated ground or surface water and ensures biological stability of the treated water. In this study, microbial community dynamics in were monitored during the start-up and maturation of an undisturbed pilot-scale GAC filter at 4 depths (10, 45, 80 and 115 cm) over a period of 6 months. New ecological tools, based on 16S rRNA gene-DGGE, were correlated to filter performance and microbial activity and showed that the microbial gradients developing in the filter was of importance. At 10 cm from the top, receiving the freshly ozonated water with the highest concentration of nutrients, the microbial community dynamics were minimal and the species richness remained low. However, the GAC samples at 80-115 cm showed a 2-3 times higher species richness than the 10-45 cm samples. The highest biomass densities were observed at 45-80 cm, which corresponded with maximum removal of dissolved and assimilable organic carbon. Furthermore, the start-up period was clearly distinguishable using the Lorenz analysis, as after 80 days, the microbial community shifted to an apparent steady-state condition with increased evenness. This study showed that GAC biofilter performance is not necessarily correlated to biomass concentration, but rather that an elevated functionality can be the result of increased microbial community richness, evenness and dynamics. Copyright © 2011 Elsevier Ltd. All rights reserved.

Microbial Signatures of Cadaver Gravesoil During Decomposition.

PubMed

Finley, Sheree J; Pechal, Jennifer L; Benbow, M Eric; Robertson, B K; Javan, Gulnaz T

2016-04-01

Genomic studies have estimated there are approximately 10(3)-10(6) bacterial species per gram of soil. The microbial species found in soil associated with decomposing human remains (gravesoil) have been investigated and recognized as potential molecular determinants for estimates of time since death. The nascent era of high-throughput amplicon sequencing of the conserved 16S ribosomal RNA (rRNA) gene region of gravesoil microbes is allowing research to expand beyond more subjective empirical methods used in forensic microbiology. The goal of the present study was to evaluate microbial communities and identify taxonomic signatures associated with the gravesoil human cadavers. Using 16S rRNA gene amplicon-based sequencing, soil microbial communities were surveyed from 18 cadavers placed on the surface or buried that were allowed to decompose over a range of decomposition time periods (3-303 days). Surface soil microbial communities showed a decreasing trend in taxon richness, diversity, and evenness over decomposition, while buried cadaver-soil microbial communities demonstrated increasing taxon richness, consistent diversity, and decreasing evenness. The results show that ubiquitous Proteobacteria was confirmed as the most abundant phylum in all gravesoil samples. Surface cadaver-soil communities demonstrated a decrease in Acidobacteria and an increase in Firmicutes relative abundance over decomposition, while buried soil communities were consistent in their community composition throughout decomposition. Better understanding of microbial community structure and its shifts over time may be important for advancing general knowledge of decomposition soil ecology and its potential use during forensic investigations.

Epifluorescent direct counts of bacteria and viruses from topsoil of various desert dust storm regions

USGS Publications Warehouse

Gonzalez-Martin, Cristina; Teigell-Perez, Nuria; Lyles, Mark; Valladares, Basilio; Griffin, Dale W.

2013-01-01

Topsoil from arid regions is the main source of dust clouds that move through the earth's atmosphere, and microbial communities within these soils can survive long-range dispersion. Microbial abundance and chemical composition were analyzed in topsoil from various desert regions. Statistical analyses showed that microbial direct counts were strongly positively correlated with calcium concentrations and negatively correlated with silicon concentrations. While variance between deserts was expected, it was interesting to note differences between sample sites within a given desert region, illustrating the 'patchy' nature of microbial communities in desert environments.

The soil microbial community composition and soil microbial carbon uptake are more affected by soil type than by different vegetation types (C3 and C4 plants) and seasonal changes

NASA Astrophysics Data System (ADS)

Griselle Mellado Vazquez, Perla; Lange, Markus; Gleixner, Gerd

2016-04-01

This study investigates the influence of different vegetation types (C3 and C4 plants), soil type and seasonal changes on the soil microbial biomass, soil microbial community composition and soil microbial carbon (C) uptake. We collected soil samples in winter (non-growing season) and summer (growing season) in 2012 from an experimental site cropping C3 and C4 plants for 6 years on two different soil types (sandy and clayey). The amount of phospholipid fatty acids (PLFAs) and their compound-specific δ13C values were used to determined microbial biomass and the flow of C from plants to soil microorganisms, respectively. Higher microbial biomass was found in the growing season. The microbial community composition was mainly explained by soil type. Higher amounts of SOC were driving the predominance of G+ bacteria, actinobacteria and cyclic G- bacteria in sandy soils, whereas root biomass was significantly related to the increased proportions of G- bacteria in clayey soils. Plant-derived C in G- bacteria increased significantly in clayey soils in the growing season. This increase was positively and significantly driven by root biomass. Moreover, changes in plant-derived C among microbial groups pointed to specific capabilities of different microbial groups to decompose distinct sources of C. We concluded that soil texture and favorable growth conditions driven by rhizosphere interactions are the most important factors controlling the soil microbial community. Our results demonstrate that a change of C3 plants vs. C4 plants has only a minor effect on the soil microbial community. Thus, such experiments are well suited to investigate soil organic matter dynamics as they allow to trace the C flow from plants into the soil microbial community without changing the community abundance and composition.

Seasonality in ocean microbial communities.

PubMed

Giovannoni, Stephen J; Vergin, Kevin L

2012-02-10

Ocean warming occurs every year in seasonal cycles that can help us to understand long-term responses of plankton to climate change. Rhythmic seasonal patterns of microbial community turnover are revealed when high-resolution measurements of microbial plankton diversity are applied to samples collected in lengthy time series. Seasonal cycles in microbial plankton are complex, but the expansion of fixed ocean stations monitoring long-term change and the development of automated instrumentation are providing the time-series data needed to understand how these cycles vary across broad geographical scales. By accumulating data and using predictive modeling, we gain insights into changes that will occur as the ocean surface continues to warm and as the extent and duration of ocean stratification increase. These developments will enable marine scientists to predict changes in geochemical cycles mediated by microbial communities and to gauge their broader impacts.

Effects of application of corn straw on soil microbial community structure during the maize growing season.

PubMed

Lu, Ping; Lin, Yin-Hua; Yang, Zhong-Qi; Xu, Yan-Peng; Tan, Fei; Jia, Xu-Dong; Wang, Miao; Xu, De-Rong; Wang, Xi-Zhuo

2015-01-01

This study investigated the influence of corn straw application on soil microbial communities and the relationship between such communities and soil properties in black soil. The crop used in this study was maize (Zea mays L.). The five treatments consisted of applying a gradient (50, 100, 150, and 200%) of shattered corn straw residue to the soil. Soil samples were taken from May through September during the 2012 maize growing season. The microbial community structure was determined using phospholipid fatty acid (PLFA) analysis. Our results revealed that the application of corn straw influenced the soil properties and increased the soil organic carbon and total nitrogen. Applying corn straw to fields also influenced the variation in soil microbial biomass and community composition, which is consistent with the variations found in soil total nitrogen (TN) and soil respiration (SR). However, the soil carbon-to-nitrogen ratio had no effect on soil microbial communities. The abundance of PLFAs, TN, and SR was higher in C1.5 than those in other treatments, suggesting that the soil properties and soil microbial community composition were affected positively by the application of corn straw to black soil. A Principal Component Analysis indicated that soil microbial communities were different in the straw decomposition processes. Moreover, the soil microbial communities from C1.5 were significantly different from those of CK (p < 0.05). We also found a high ratio of fungal-to-bacterial PLFAs in black soil and significant variations in the ratio of monounsaturated-to-branched fatty acids with different straw treatments that correlated with SR (p < 0.05). These results indicated that the application of corn straw positively influences soil properties and soil microbial communities and that these properties affect these communities. The individual PLFA signatures were sensitive indicators that reflected the changes in the soil environment condition. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Global-Scale Structure of the Eelgrass Microbiome.

PubMed

Fahimipour, Ashkaan K; Kardish, Melissa R; Lang, Jenna M; Green, Jessica L; Eisen, Jonathan A; Stachowicz, John J

2017-06-15

Plant-associated microorganisms are essential for their hosts' survival and performance. Yet, most plant microbiome studies to date have focused on terrestrial species sampled across relatively small spatial scales. Here, we report the results of a global-scale analysis of microbial communities associated with leaf and root surfaces of the marine eelgrass Zostera marina throughout its range in the Northern Hemisphere. By contrasting host microbiomes with those of surrounding seawater and sediment, we uncovered the structure, composition, and variability of microbial communities associated with eelgrass. We also investigated hypotheses about the assembly of the eelgrass microbiome using a metabolic modeling approach. Our results reveal leaf communities displaying high variability and spatial turnover that mirror their adjacent coastal seawater microbiomes. By contrast, roots showed relatively low compositional turnover and were distinct from surrounding sediment communities, a result driven by the enrichment of predicted sulfur-oxidizing bacterial taxa on root surfaces. Predictions from metabolic modeling of enriched taxa were consistent with a habitat-filtering community assembly mechanism whereby similarity in resource use drives taxonomic cooccurrence patterns on belowground, but not aboveground, host tissues. Our work provides evidence for a core eelgrass root microbiome with putative functional roles and highlights potentially disparate processes influencing microbial community assembly on different plant compartments. IMPORTANCE Plants depend critically on their associated microbiome, yet the structure of microbial communities found on marine plants remains poorly understood in comparison to that for terrestrial species. Seagrasses are the only flowering plants that live entirely in marine environments. The return of terrestrial seagrass ancestors to oceans is among the most extreme habitat shifts documented in plants, making them an ideal testbed for the study of microbial symbioses with plants that experience relatively harsh abiotic conditions. In this study, we report the results of a global sampling effort to extensively characterize the structure of microbial communities associated with the widespread seagrass species Zostera marina , or eelgrass, across its geographic range. Our results reveal major differences in the structure and composition of above- versus belowground microbial communities on eelgrass surfaces, as well as their relationships with the environment and host. Copyright © 2017 Fahimipour et al.

Spatially resolved sampling reveals dynamic microbial communities in rising hydrothermal plumes across a back-arc basin.

PubMed

Sheik, Cody S; Anantharaman, Karthik; Breier, John A; Sylvan, Jason B; Edwards, Katrina J; Dick, Gregory J

2015-06-01

Within hydrothermal plumes, chemosynthetic processes and microbe-mineral interactions drive primary productivity in deep-ocean food webs and may influence transport of elements such as iron. However, the source of microorganisms in plumes and the factors governing how these communities assemble are poorly understood, in part due to lack of data from early stages of plume formation. In this study, we examined microbial community composition of rising hydrothermal plumes from five vent fields along the Eastern Lau Spreading Center. Seafloor and plume microbial communities were significantly dissimilar and shared few phylotypes. Plume communities were highly similar to each other with significant differences in community membership only between Kilo Moana and Mariner, two vents that are separated by extremes in depth, latitude and geochemistry. Systematic sampling of waters surrounding the vents revealed that species richness and phylogenetic diversity was typically highest near the vent orifice, implying mixing of microbial communities from the surrounding habitats. Above-plume background communities were primarily dominated by SAR11, SAR324 and MG-I Archaea, while SUP05, Sulfurovum, Sulfurimonas, SAR324 and Alteromonas were abundant in plume and near-bottom background communities. These results show that the ubiquitous water-column microorganisms populate plume communities, and that the composition of background seawater exerts primary influence on plume community composition, with secondary influence from geochemical and/or physical properties of vents. Many of these pervasive deep-ocean organisms are capable of lithotrophy, suggesting that they are poised to use inorganic electron donors encountered in hydrothermal plumes.

Spatially resolved sampling reveals dynamic microbial communities in rising hydrothermal plumes across a back-arc basin

PubMed Central

Sheik, Cody S; Anantharaman, Karthik; Breier, John A; Sylvan, Jason B; Edwards, Katrina J; Dick, Gregory J

2015-01-01

Within hydrothermal plumes, chemosynthetic processes and microbe–mineral interactions drive primary productivity in deep-ocean food webs and may influence transport of elements such as iron. However, the source of microorganisms in plumes and the factors governing how these communities assemble are poorly understood, in part due to lack of data from early stages of plume formation. In this study, we examined microbial community composition of rising hydrothermal plumes from five vent fields along the Eastern Lau Spreading Center. Seafloor and plume microbial communities were significantly dissimilar and shared few phylotypes. Plume communities were highly similar to each other with significant differences in community membership only between Kilo Moana and Mariner, two vents that are separated by extremes in depth, latitude and geochemistry. Systematic sampling of waters surrounding the vents revealed that species richness and phylogenetic diversity was typically highest near the vent orifice, implying mixing of microbial communities from the surrounding habitats. Above-plume background communities were primarily dominated by SAR11, SAR324 and MG-I Archaea, while SUP05, Sulfurovum, Sulfurimonas, SAR324 and Alteromonas were abundant in plume and near-bottom background communities. These results show that the ubiquitous water-column microorganisms populate plume communities, and that the composition of background seawater exerts primary influence on plume community composition, with secondary influence from geochemical and/or physical properties of vents. Many of these pervasive deep-ocean organisms are capable of lithotrophy, suggesting that they are poised to use inorganic electron donors encountered in hydrothermal plumes. PMID:25489728

Chapter 11. Community analysis-based methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cao, Y.; Wu, C.H.; Andersen, G.L.

2010-05-01

Microbial communities are each a composite of populations whose presence and relative abundance in water or other environmental samples are a direct manifestation of environmental conditions, including the introduction of microbe-rich fecal material and factors promoting persistence of the microbes therein. As shown by culture-independent methods, different animal-host fecal microbial communities appear distinctive, suggesting that their community profiles can be used to differentiate fecal samples and to potentially reveal the presence of host fecal material in environmental waters. Cross-comparisons of microbial communities from different hosts also reveal relative abundances of genetic groups that can be used to distinguish sources. Inmore » increasing order of their information richness, several community analysis methods hold promise for MST applications: phospholipid fatty acid (PLFA) analysis, denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (TRFLP), cloning/sequencing, and PhyloChip. Specific case studies involving TRFLP and PhyloChip approaches demonstrate the ability of community-based analyses of contaminated waters to confirm a diagnosis of water quality based on host-specific marker(s). The success of community-based MST for comprehensively confirming fecal sources relies extensively upon using appropriate multivariate statistical approaches. While community-based MST is still under evaluation and development as a primary diagnostic tool, results presented herein demonstrate its promise. Coupled with its inherently comprehensive ability to capture an unprecedented amount of microbiological data that is relevant to water quality, the tools for microbial community analysis are increasingly accessible, and community-based approaches have unparalleled potential for translation into rapid, perhaps real-time, monitoring platforms.« less

Impact of refined petroleum spills on water quality, macro-invertebrate and microbial communities of a tropical aquatic environment.

PubMed

Chukwu, L O; Nwachukwu, S C U

2005-07-01

Water quality characteristics, benthic macro-invertebrates and microbial communities of three first order streams in South West Nigeria were investigated to assess the effects of refined petroleum five months after spillage. All physical and chemical conditions except temperature and pH were significantly different (P<0.01) at the upstream control stations and impacted stations reflecting the perturbational stress. The benthic macro-invertebrate fauna were dominated by arthropods, but the faunal spectrum was dissimilar at all the stations studied. Sampling stations at the epicentre of the spill showed considerable reduction in faunal compositions and relative abundance. Generally, the microbial density and diversity were highest in both soil and water samples from impacted sites than in control sites. There was a significantly higher proportion (P < 0.05) of hydrocarbon utilizers in soil than in water samples in all stations except in samples from stations (P<0.05).

Bacterial, fungal, and plant communities exhibit no biomass or compositional response to two years of simulated nitrogen deposition in a semiarid grassland: Bacterial, fungal, and plant communities

DOE Office of Scientific and Technical Information (OSTI.GOV)

McHugh, Theresa A.; Morrissey, Ember M.; Mueller, Rebecca C.

Nitrogen (N) deposition affects myriad aspects of terrestrial ecosystem structure and function, and microbial communities may be particularly sensitive to anthropogenic N inputs. However, our understanding of N deposition effects on microbial communities is far from complete, especially for drylands where data are comparatively rare. To address the need for an improved understanding of dryland biological responses to N deposition, we conducted a two-year fertilization experiment in a semiarid grassland on the Colorado Plateau in the southwestern United States. We evaluated effects of varied levels of N inputs on archaeal, bacterial, fungal and chlorophyte community composition within three microhabitats: biologicalmore » soil crusts (biocrusts), soil below biocrusts, and the plant rhizosphere. Surprisingly, N addition did not affect the community composition or diversity of any of these microbial groups; however, microbial community composition varied significantly among sampling microhabitats. Further, while plant richness, diversity, and cover showed no response to N addition, there were strong linkages between plant properties and microbial community structure. Overall, these findings highlight the potential for some dryland communities to have limited biotic ability to retain augmented N inputs, possibly leading to large N losses to the atmosphere and to aquatic systems.« less

Bacterial, fungal, and plant communities exhibit no biomass or compositional response to two years of simulated nitrogen deposition in a semiarid grassland: Bacterial, fungal, and plant communities

DOE PAGES

McHugh, Theresa A.; Morrissey, Ember M.; Mueller, Rebecca C.; ...

2017-03-13

Nitrogen (N) deposition affects myriad aspects of terrestrial ecosystem structure and function, and microbial communities may be particularly sensitive to anthropogenic N inputs. However, our understanding of N deposition effects on microbial communities is far from complete, especially for drylands where data are comparatively rare. To address the need for an improved understanding of dryland biological responses to N deposition, we conducted a two-year fertilization experiment in a semiarid grassland on the Colorado Plateau in the southwestern United States. We evaluated effects of varied levels of N inputs on archaeal, bacterial, fungal and chlorophyte community composition within three microhabitats: biologicalmore » soil crusts (biocrusts), soil below biocrusts, and the plant rhizosphere. Surprisingly, N addition did not affect the community composition or diversity of any of these microbial groups; however, microbial community composition varied significantly among sampling microhabitats. Further, while plant richness, diversity, and cover showed no response to N addition, there were strong linkages between plant properties and microbial community structure. Overall, these findings highlight the potential for some dryland communities to have limited biotic ability to retain augmented N inputs, possibly leading to large N losses to the atmosphere and to aquatic systems.« less

Microbial biomass carbon and enzyme activities of urban soils in Beijing.

PubMed

Wang, Meie; Markert, Bernd; Shen, Wenming; Chen, Weiping; Peng, Chi; Ouyang, Zhiyun

2011-07-01

To promote rational and sustainable use of soil resources and to maintain the urban soil quality, it is essential to assess urban ecosystem health. In this study, the microbiological properties of urban soils in Beijing and their spatial distribution patterns across the city were evaluated based on measurements of microbial biomass carbon and urease and invertase activities of the soils for the purpose of assessing the urban ecosystem health of Beijing. Grid sampling design, normal Kriging technique, and the multiple comparisons among different land use types were used in soil sampling and data treatment. The inherent chemical characteristics of urban soils in Beijing, e.g., soil pH, electronic conductivity, heavy metal contents, total N, P and K contents, and soil organic matter contents were detected. The size and diversity of microbial community and the extent of microbial activity in Beijing urban soils were measured as the microbial biomass carbon content and the ratio of microbial biomass carbon content to total soil organic carbon. The microbial community health measured in terms of microbial biomass carbon, urease, and invertase activities varied with the organic substrate and nutrient contents of the soils and were not adversely affected by the presence of heavy metals at p < 0.01. It was shown that the older and the biologically more stable part of city exhibited higher microbial activity levels than the more recently developed part of the city and the road areas of heavy traffic. It was concluded that the land use patterns in Beijing urban soils influenced the nature and activities of the microbial communities.

High-resolution phylogenetic microbial community profiling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singer, Esther; Bushnell, Brian; Coleman-Derr, Devin

Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger sequencing for microbial community profiling. The transition to new technologies has provided more quantitative information at the expense of taxonomic resolution with implications for inferring metabolic traits in various ecosystems. We applied single-molecule real-time sequencing for microbial community profiling, generating full-length 16S rRNA gene sequences at high throughput, which we propose to name PhyloTags. We benchmarked and validated this approach using a defined microbial community. When further applied to samples from the water column of meromictic Sakinaw Lake, we show that while community structuresmore » at the phylum level are comparable between PhyloTags and Illumina V4 16S rRNA gene sequences (iTags), variance increases with community complexity at greater water depths. PhyloTags moreover allowed less ambiguous classification. Last, a platform-independent comparison of PhyloTags and in silico generated partial 16S rRNA gene sequences demonstrated significant differences in community structure and phylogenetic resolution across multiple taxonomic levels, including a severe underestimation in the abundance of specific microbial genera involved in nitrogen and methane cycling across the Lake's water column. Thus, PhyloTags provide a reliable adjunct or alternative to cost-effective iTags, enabling more accurate phylogenetic resolution of microbial communities and predictions on their metabolic potential.« less

High-resolution phylogenetic microbial community profiling

DOE PAGES

Singer, Esther; Bushnell, Brian; Coleman-Derr, Devin; ...

2016-02-09

Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger sequencing for microbial community profiling. The transition to new technologies has provided more quantitative information at the expense of taxonomic resolution with implications for inferring metabolic traits in various ecosystems. We applied single-molecule real-time sequencing for microbial community profiling, generating full-length 16S rRNA gene sequences at high throughput, which we propose to name PhyloTags. We benchmarked and validated this approach using a defined microbial community. When further applied to samples from the water column of meromictic Sakinaw Lake, we show that while community structuresmore » at the phylum level are comparable between PhyloTags and Illumina V4 16S rRNA gene sequences (iTags), variance increases with community complexity at greater water depths. PhyloTags moreover allowed less ambiguous classification. Last, a platform-independent comparison of PhyloTags and in silico generated partial 16S rRNA gene sequences demonstrated significant differences in community structure and phylogenetic resolution across multiple taxonomic levels, including a severe underestimation in the abundance of specific microbial genera involved in nitrogen and methane cycling across the Lake's water column. Thus, PhyloTags provide a reliable adjunct or alternative to cost-effective iTags, enabling more accurate phylogenetic resolution of microbial communities and predictions on their metabolic potential.« less

Microbial Communities in the Vertical Atmosphere: Effects of Urbanization and the Natural Environment in Four North American Ecosystems

NASA Astrophysics Data System (ADS)

Docherty, K. M.; Lemmer, K. M.; Domingue, K. D.; Spring, A.; Kerber, T. V.; Mooney, M. M.

2017-12-01

Airborne transport of microbial communities is a key component of the global ecosystem because it serves as a mechanism for dispersing microbial life between all surface habitats on the planet. However, most of our understanding of airborne microbial distribution is derived from samples collected near the ground. Little is understood about how the vertical layers of the air may act as a habitat filter or how local terrestrial ecosystems contribute to a vast airborne microbial seedbank. Specifically, urbanization may fundamentally alter the terrestrial sources of airborne microbial biodiversity. To address this question, we conducted airborne sampling at minimally disturbed natural sites and paired urban sites in 4 different North American ecosystems: shortgrass steppe, desert scrub, eastern deciduous forest, and northern mesic forest. All natural area sites were co-located with NEON/Ameriflux tower sites collecting atmospheric data. We developed an airborne sampling platform that uses tethered helikites at 3 replicate locations within each ecosystem to launch remote-controlled sampler payloads. We designed sampler payloads to collect airborne bacteria and fungi from 150, 30 and 2 m above the ground. Payload requirements included: ability to be disinfected and remain contaminant-free during transport, remote open/close functionality, payload weight under 6 lbs and automated collection of weather data. After sampling for 6 hours at each location, we extracted DNA collected by the samplers. We also extracted DNA from soil and plant samples collected from each location, and characterized ground vegetation. We conducted bacterial 16S amplicon-based sequencing using Mi-Seq and sequence analysis using QIIME. We used ArcGIS to determine percent land use coverage. Our results demonstrate that terrestrial ecosystem type is the most important factor contributing to differences in airborne bacterial community composition, and that communities differed by ecosystem. The signature of the specific ecosystem, and whether it was located in a natural or urban area, was evident in both near-surface and higher altitude samples. This suggests that continued urbanization and increases in impervious surface area can fundamentally change sources of atmospheric biodiversity and distribution patterns.

Microbial communities biostimulated by ethanol during uranium (VI) bioremediation in contaminated sediment as shown by stable isotope probing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leigh, Mary Beth; Wu, Wei -Min; Cardenas, Erick

Stable isotope probing (SIP) was used to identify microbes stimulated by ethanol addition in microcosms containing two sediments collected from the bioremediation test zone at the US Department of Energy Oak Ridge site, TN, USA. One sample was highly bioreduced with ethanol while another was less reduced. Microcosms with the respective sediments were amended with 13C labeled ethanol and incubated for 7 days for SIP. Ethanol was rapidly converted to acetate within 24 h accompanied with the reduction of nitrate and sulfate. The accumulation of acetate persisted beyond the 7 d period. Aqueous U did not decline in the microcosmmore » with the reduced sediment due to desorption of U but continuously declined in the less reduced sample. Microbial growth and concomitant 13C-DNA production was detected when ethanol was exhausted and abundant acetate had accumulated in both microcosms. This coincided with U(VI) reduction in the less reduced sample. 13C originating from ethanol was ultimately utilized for growth, either directly or indirectly, by the dominant microbial community members within 7 days of incubation. The microbial community was comprised predominantly of known denitrifiers, sulfate-reducing bacteria and iron (III) reducing bacteria including Desulfovibrio, Sphingomonas, Ferribacterium, Rhodanobacter, Geothrix, Thiobacillus and others, including the known U(VI)-reducing bacteria Acidovorax, Anaeromyxobacter, Desulfovibrio, Geobacter and Desulfosporosinus. As a result, the findings suggest that ethanol biostimulates the U(VI)-reducing microbial community by first serving as an electron donor for nitrate, sulfate, iron (III) and U(VI) reduction, and acetate which then functions as electron donor for U(VI) reduction and carbon source for microbial growth.« less

Development of the human infant intestinal microbiota.

PubMed

Palmer, Chana; Bik, Elisabeth M; DiGiulio, Daniel B; Relman, David A; Brown, Patrick O

2007-07-01

Almost immediately after a human being is born, so too is a new microbial ecosystem, one that resides in that person's gastrointestinal tract. Although it is a universal and integral part of human biology, the temporal progression of this process, the sources of the microbes that make up the ecosystem, how and why it varies from one infant to another, and how the composition of this ecosystem influences human physiology, development, and disease are still poorly understood. As a step toward systematically investigating these questions, we designed a microarray to detect and quantitate the small subunit ribosomal RNA (SSU rRNA) gene sequences of most currently recognized species and taxonomic groups of bacteria. We used this microarray, along with sequencing of cloned libraries of PCR-amplified SSU rDNA, to profile the microbial communities in an average of 26 stool samples each from 14 healthy, full-term human infants, including a pair of dizygotic twins, beginning with the first stool after birth and continuing at defined intervals throughout the first year of life. To investigate possible origins of the infant microbiota, we also profiled vaginal and milk samples from most of the mothers, and stool samples from all of the mothers, most of the fathers, and two siblings. The composition and temporal patterns of the microbial communities varied widely from baby to baby. Despite considerable temporal variation, the distinct features of each baby's microbial community were recognizable for intervals of weeks to months. The strikingly parallel temporal patterns of the twins suggested that incidental environmental exposures play a major role in determining the distinctive characteristics of the microbial community in each baby. By the end of the first year of life, the idiosyncratic microbial ecosystems in each baby, although still distinct, had converged toward a profile characteristic of the adult gastrointestinal tract.

Microbial community dynamics and methane, carbon dioxide, oxygen, and nitrous oxide concentrations in upland forest and riparian soils across a seasonal gradient of fully saturated soils to completely dried soils

NASA Astrophysics Data System (ADS)

Jones, R. T.; McGlynn, B. L.; McDermott, T.; Dore, J. E.

2015-12-01

Gas concentrations (CH4, CO2, N2O, and O2), soil properties (soil water content and pH), and microbial community composition were measured from soils at 32 sites across the Stringer Creek Watershed in the Tenderfoot Creek Experimental Forest 7 times between June 3, 2013 and September 20, 2013. Soils were fully saturated during the initial sampling period and dried down over the course of the summer. Soils and gas were sampled from 5cm and 20cm at each site and also at 50cm at eight riparian sites. In total, 496 individual soil samples were collected. Soil moisture ranged from 3.7% to fully saturated; soil pH ranged from 3.60 to 6.68. Methane concentrations in soils ranged from 0.426 ppm to 218 ppm; Carbon dioxide concentrations ranged from 550 ppm to 42,990 ppm; Nitrous oxide concentrations ranged from 0.220 ppm to 2.111 ppm; Oxygen concentrations ranged from 10.2% to 21.5%. Soil microbial communities were characterized by DNA sequences covering the V4 region of the 16S rRNA gene. DNA sequences were generated (~30,000,000 sequences) from the 496 soil samples using the Illumina MiSeq platform. Operational Taxonomic Units were generated using USEARCH, and representative sequences were taxonomically classified according the Ribosomal Database Project's taxonomy scheme. Analysis of similarity revealed that microbial communities found within a landscape type (high upland forest, low upland forest, riparian) were more similar than among landscape types (R = 0.600; p<0.001). Similarly, communities from unique site x depths were similar across the 7 collection periods (R = 0.646; p<0.001) despite changes in soil moisture. Euclidean distances of soil properties and gas concentrations were compared to Bray-Curtis community dissimilarity matrices using Mantel tests to determine how community structure co-varies with the soil environment and gas concentrations. All variables measured significantly co-varied with microbial community membership (pH: R = 0.712, p < 0.001; CO2: R = 0.578, p < 0.001; O2: R = 0.517, p < 0.001; Soil moisture: R = 0.408, p < 0.001; N2O: R = 0.218, p = 0.003; CH4: R = 0.195, p = 0.008). Despite the rather low co-variation between methane concentrations and microbial community composition, relative abundances of methanotrophic and methanogenic lineages did co-vary strongly with methane concentrations.

Exploring the dynamic links between microbial ecology and redox state of the hyporheic zone: insight from flume experiments

NASA Astrophysics Data System (ADS)

Kaufman, M.; Cardenas, M. B.; Stegen, J.; Graham, E.; Cook, P. L. M.; Kessler, A. J.

2016-12-01

The hyporheic zone (HZ) provides key ecosystem services such as heavy metal sequestration, nutrient uptake and consumption, and habitat for a diverse collection of ecologically and commercially important species. Microbes are responsible for many of the chemical transformations in the HZ. These microbe populations are intimately linked to redox conditions, and recent work has shown that redox conditions in the HZ can be highly dynamic. Here we investigate the dynamic coupling between surface flow conditions, hyporheic redox conditions, and the hyporheic microbiome. Our window into this world is a large experimental flume (5m x 0.7m x 0.3m), prepared and incubated in a way that is relatively common to hyporheic zone research, without a strong attempt to impose a specific microbial community structure. We use computer-controlled flow combined with sand bedforms within the flume to generate a pattern of oxic and anoxic sediment zones, from which we collected sediment and water samples. Dissolved oxygen was mapped with a large planar optode. The samples were analyzed for microbial community composition through 16S rRNA gene sequencing. We compare the population structure between oxic and anoxic zones, showing that the presence of oxygen in the HZ is a strong predictor of microbial composition. Additionally, we compare both the oxic and anoxic community structure from the flume to those of samples taken from natural environments, showing both interesting similarities and differences. In the future, we plan to use time-series sampling to observe the response times of microbial communities subjected to dynamic surface channel flow and redox conditions. This work will yield greater understanding of the role that dynamic rivers play in microbe-provided ecosystem services.

Exploring the dynamic links between microbial ecology and redox state of the hyporheic zone: insight from flume experiments

NASA Astrophysics Data System (ADS)

Kaufman, M.; Cardenas, M. B.; Stegen, J.; Graham, E.; Cook, P. L. M.; Kessler, A. J.

2017-12-01

The hyporheic zone (HZ) provides key ecosystem services such as heavy metal sequestration, nutrient uptake and consumption, and habitat for a diverse collection of ecologically and commercially important species. Microbes are responsible for many of the chemical transformations in the HZ. These microbe populations are intimately linked to redox conditions, and recent work has shown that redox conditions in the HZ can be highly dynamic. Here we investigate the dynamic coupling between surface flow conditions, hyporheic redox conditions, and the hyporheic microbiome. Our window into this world is a large experimental flume (5m x 0.7m x 0.3m), prepared and incubated in a way that is relatively common to hyporheic zone research, without a strong attempt to impose a specific microbial community structure. We use computer-controlled flow combined with sand bedforms within the flume to generate a pattern of oxic and anoxic sediment zones, from which we collected sediment and water samples. Dissolved oxygen was mapped with a large planar optode. The samples were analyzed for microbial community composition through 16S rRNA gene sequencing. We compare the population structure between oxic and anoxic zones, showing that the presence of oxygen in the HZ is a strong predictor of microbial composition. Additionally, we compare both the oxic and anoxic community structure from the flume to those of samples taken from natural environments, showing both interesting similarities and differences. In the future, we plan to use time-series sampling to observe the response times of microbial communities subjected to dynamic surface channel flow and redox conditions. This work will yield greater understanding of the role that dynamic rivers play in microbe-provided ecosystem services.

Relationships among plants, soils and microbial communities along a hydrological gradient in the New Jersey Pinelands, USA

PubMed Central

Yu, Shen; Ehrenfeld, Joan G.

2010-01-01

Background and Aims Understanding the role of different components of hydrology in structuring wetland communities is not well developed. A sequence of adjacent wetlands located on a catenary sequence of soils and receiving the same sources and qualities of water is used to examine specifically the role of water-table median position and variability in affecting plant and microbial community composition and soil properties. Methods Two replicates of three types of wetland found adjacent to each other along a hydrological gradient in the New Jersey Pinelands (USA) were studied. Plant-community and water-table data were obtained within a 100-m2 plot in each community (pine swamp, maple swamp and Atlantic-white-cedar swamp). Monthly soil samples from each plot were analysed for soil moisture, organic matter, extractable nitrogen fractions, N mineralization rate and microbial community composition. Multivariate ordination methods were used to compare patterns among sites within and between data sets. Key Results The maple and pine wetlands were more similar to each other in plant community composition, soil properties and microbial community composition than either was to the cedar swamps. However, maple and pine wetlands differed from each other in water-table descriptors as much as they differed from the cedar swamps. All microbial communities were dominated by Gram-positive bacteria despite hydrologic differences among the sites. Water-table variability was as important as water-table level in affecting microbial communities. Conclusions Water tables affect wetland communities through both median level and variability. Differentiation of both plant and microbial communities are not simple transforms of differences in water-table position, even when other hydrologic factors are kept constant. Rather, soil genesis, a result of both water-table position and geologic history, appears to be the main factor affecting plant and microbial community similarities. PMID:19643908

The Ocean Sampling Day Consortium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kopf, Anna; Bicak, Mesude; Kottmann, Renzo

In this study, Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and theirmore » embedded functional traits.« less

The Ocean Sampling Day Consortium

DOE PAGES

Kopf, Anna; Bicak, Mesude; Kottmann, Renzo; ...

2015-06-19

In this study, Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and theirmore » embedded functional traits.« less

Pyrosequencing-based assessment of microbial community shifts in leachate from animal carcass burial lysimeter.

PubMed

Kim, Hyun Young; Seo, Jiyoung; Kim, Tae-Hun; Shim, Bomi; Cha, Seok Mun; Yu, Seungho

2017-06-01

This study examined the use of microbial community structure as a bio-indicator of decomposition levels. High-throughput pyrosequencing technology was used to assess the shift in microbial community of leachate from animal carcass lysimeter. The leachate samples were collected monthly for one year and a total of 164,639 pyrosequencing reads were obtained and used in the taxonomic classification and operational taxonomy units (OTUs) distribution analysis based on sequence similarity. Our results show considerable changes in the phylum-level bacterial composition, suggesting that the microbial community is a sensitive parameter affected by the burial environment. The phylum classification results showed that Proteobacteria (Pseudomonas) were the most influential taxa in earlier decomposition stage whereas Firmicutes (Clostridium, Sporanaerobacter, and Peptostreptococcus) were dominant in later stage under anaerobic conditions. The result of this study can provide useful information on a time series of leachate profiles of microbial community structures and suggest patterns of microbial diversity in livestock burial sites. In addition, this result can be applicable to predict the decomposition stages under clay loam based soil conditions of animal livestock. Copyright © 2017 Elsevier B.V. All rights reserved.

Deciphering Diversity Indices for a Better Understanding of Microbial Communities.

PubMed

Kim, Bo-Ra; Shin, Jiwon; Guevarra, Robin; Lee, Jun Hyung; Kim, Doo Wan; Seol, Kuk-Hwan; Lee, Ju-Hoon; Kim, Hyeun Bum; Isaacson, Richard

2017-12-28

The past decades have been a golden era during which great tasks were accomplished in the field of microbiology, including food microbiology. In the past, culture-dependent methods have been the primary choice to investigate bacterial diversity. However, using cultureindependent high-throughput sequencing of 16S rRNA genes has greatly facilitated studies exploring the microbial compositions and dynamics associated with health and diseases. These culture-independent DNA-based studies generate large-scale data sets that describe the microbial composition of a certain niche. Consequently, understanding microbial diversity becomes of greater importance when investigating the composition, function, and dynamics of the microbiota associated with health and diseases. Even though there is no general agreement on which diversity index is the best to use, diversity indices have been used to compare the diversity among samples and between treatments with controls. Tools such as the Shannon- Weaver index and Simpson index can be used to describe population diversity in samples. The purpose of this review is to explain the principles of diversity indices, such as Shannon- Weaver and Simpson, to aid general microbiologists in better understanding bacterial communities. In this review, important questions concerning microbial diversity are addressed. Information from this review should facilitate evidence-based strategies to explore microbial communities.

Effect of Saccharomyces boulardii and Mode of Delivery on the Early Development of the Gut Microbial Community in Preterm Infants.

PubMed

Zeber-Lubecka, Natalia; Kulecka, Maria; Ambrozkiewicz, Filip; Paziewska, Agnieszka; Lechowicz, Milosz; Konopka, Ewa; Majewska, Urszula; Borszewska-Kornacka, Maria; Mikula, Michal; Cukrowska, Bozena; Ostrowski, Jerzy

2016-01-01

Recent advances in culture-independent approaches have enabled insights into the diversity, complexity, and individual variability of gut microbial communities. To examine the effect of oral administration of Saccharomyces (S.) boulardii and mode of delivery on the intestinal microbial community in preterm infants. Stool samples were collected from preterm newborns randomly divided into two groups: a probiotic-receiving group (n = 18) or a placebo group (n = 21). Samples were collected before probiotic intake (day 0), and after 2 and 6 weeks of supplementation. The composition of colonizing bacteria was assessed by 16S ribosomal RNA (rRNA) gene sequencing of fecal samples using the Ion 16S Metagenomics Kit and the Ion Torrent Personal Genome Machine platform. A total of 11932257 reads were generated, and were clustered into 459, 187, and 176 operational taxonomic units at 0 days, 2 weeks, and 6 weeks, respectively. Of the 17 identified phyla, Firmicutes Actinobacteria, Proteobacteria, and Bacteroidetes were universal. The microbial community differed at day 0 compared with at 2 weeks and 6 weeks. There was a tendency for increased bacterial diversity at 2 weeks and 6 weeks compared with day 0, and infants with a gestational age of 31 weeks or higher presented increased bacterial diversity prior to S. boulardii administration. Firmicutes and Proteobacteria remained stable during the observation period, whereas Actinobacteria and Bacteroidetes increased in abundance, the latter particularly more sharply in vaginally delivered infants. While the mode of delivery may influence the development of a microbial community, this study had not enough power to detect statistical differences between cohorts supplemented with probiotics, and in a consequence, to speculate on S. boulardii effect on gut microbiome composition in preterm newborns.

Effect of Saccharomyces boulardii and Mode of Delivery on the Early Development of the Gut Microbial Community in Preterm Infants

PubMed Central

Zeber-Lubecka, Natalia; Kulecka, Maria; Ambrozkiewicz, Filip; Paziewska, Agnieszka; Lechowicz, Milosz; Konopka, Ewa; Majewska, Urszula; Borszewska-Kornacka, Maria; Mikula, Michal; Cukrowska, Bozena; Ostrowski, Jerzy

2016-01-01

Background Recent advances in culture-independent approaches have enabled insights into the diversity, complexity, and individual variability of gut microbial communities. Objectives To examine the effect of oral administration of Saccharomyces (S.) boulardii and mode of delivery on the intestinal microbial community in preterm infants. Study Design Stool samples were collected from preterm newborns randomly divided into two groups: a probiotic-receiving group (n = 18) or a placebo group (n = 21). Samples were collected before probiotic intake (day 0), and after 2 and 6 weeks of supplementation. The composition of colonizing bacteria was assessed by 16S ribosomal RNA (rRNA) gene sequencing of fecal samples using the Ion 16S Metagenomics Kit and the Ion Torrent Personal Genome Machine platform. Results A total of 11932257 reads were generated, and were clustered into 459, 187, and 176 operational taxonomic units at 0 days, 2 weeks, and 6 weeks, respectively. Of the 17 identified phyla, Firmicutes Actinobacteria, Proteobacteria, and Bacteroidetes were universal. The microbial community differed at day 0 compared with at 2 weeks and 6 weeks. There was a tendency for increased bacterial diversity at 2 weeks and 6 weeks compared with day 0, and infants with a gestational age of 31 weeks or higher presented increased bacterial diversity prior to S. boulardii administration. Firmicutes and Proteobacteria remained stable during the observation period, whereas Actinobacteria and Bacteroidetes increased in abundance, the latter particularly more sharply in vaginally delivered infants. Conclusion While the mode of delivery may influence the development of a microbial community, this study had not enough power to detect statistical differences between cohorts supplemented with probiotics, and in a consequence, to speculate on S. boulardii effect on gut microbiome composition in preterm newborns. PMID:26918330

[Influence of PCR cycle number on microbial diversity analysis through next generation sequencing].

PubMed

An, Yunhe; Gao, Lijuan; Li, Junbo; Tian, Yanjie; Wang, Jinlong; Zheng, Xuejuan; Wu, Huijuan

2016-08-25

Using of high throughput sequencing technology to study the microbial diversity in complex samples has become one of the hottest issues in the field of microbial diversity research. In this study, the soil and sheep rumen chyme samples were used to extract DNA, respectively. Then the 25 ng total DNA was used to amplify the 16S rRNA V3 region with 20, 25, 30 PCR cycles, and the final sequencing library was constructed by mixing equal amounts of purified PCR products. Finally, the operational taxonomic unit (OUT) amount, rarefaction curve, microbial number and species were compared through data analysis. It was found that at the same amount of DNA template, the proportion of the community composition was not the best with more numbers of PCR cycle, although the species number was much more. In all, when the PCR cycle number is 25, the number of species and proportion of the community composition were the most optimal both in soil or chyme samples.

Microbial diversity at the moderate acidic stage in three different sulfidic mine tailings dumps generating acid mine drainage.

PubMed

Korehi, Hananeh; Blöthe, Marco; Schippers, Axel

2014-11-01

In freshly deposited sulfidic mine tailings the pH is alkaline or circumneutral. Due to pyrite or pyrrhotite oxidation the pH is dropping over time to pH values <3 at which acidophilic iron- and sulfur-oxidizing prokaryotes prevail and accelerate the oxidation processes, well described for several mine waste sites. The microbial communities at the moderate acidic stage in mine tailings are only scarcely studied. Here we investigated the microbial diversity via 16S rRNA gene sequence analysis in eight samples (pH range 3.2-6.5) from three different sulfidic mine tailings dumps in Botswana, Germany and Sweden. In total 701 partial 16S rRNA gene sequences revealed a divergent microbial community between the three sites and at different tailings depths. Proteobacteria and Firmicutes were overall the most abundant phyla in the clone libraries. Acidobacteria, Actinobacteria, Bacteroidetes, and Nitrospira occurred less frequently. The found microbial communities were completely different to microbial communities in tailings at

The influence of in situ chemical oxidation on microbial community composition in groundwater contaminated with chlorinated solvents.

PubMed

Sercu, Bram; Jones, Antony D G; Wu, Cindy H; Escobar, Mauricio H; Serlin, Carol L; Knapp, Timothy A; Andersen, Gary L; Holden, Patricia A

2013-01-01

In situ chemical oxidation with permanganate has become an accepted remedial treatment for groundwater contaminated with chlorinated solvents. This study focuses on the immediate and short-term effects of sodium permanganate (NaMnO(4)) on the indigenous subsurface microbial community composition in groundwater impacted by trichloroethylene (TCE). Planktonic and biofilm microbial communities were studied using groundwater grab samples and reticulated vitreous carbon passive samplers, respectively. Microbial community composition was analyzed by terminal restriction fragment length polymorphism and a high-density phylogenetic microarray (PhyloChip). Significant reductions in microbial diversity and biomass were shown during NaMnO(4) exposure, followed by recovery within several weeks after the oxidant concentrations decreased to <1 mg/L. Bray-Curtis similarities and nonmetric multidimensional scaling showed that microbial community composition before and after NaMnO(4) was similar, when taking into account the natural variation of the microbial communities. Also, 16S rRNA genes of two reductive dechlorinators (Desulfuromonas spp. and Sulfurospirillum spp.) and diverse taxa capable of cometabolic TCE oxidation were detected in similar quantities by PhyloChip across all monitoring wells, irrespective of NaMnO(4) exposure and TCE concentrations. However, minimal biodegradation of TCE was observed in this study, based on oxidized conditions, concentration patterns of chlorinated and nonchlorinated hydrocarbons, geochemistry, and spatiotemporal distribution of TCE-degrading bacteria.

Soil microbial respiration and PICT responses to an industrial and historic lead pollution: a field study.

PubMed

Bérard, Annette; Capowiez, Line; Mombo, Stéphane; Schreck, Eva; Dumat, Camille; Deola, Frédéric; Capowiez, Yvan

2016-03-01

We performed a field investigation to study the long-term impacts of Pb soil contamination on soil microbial communities and their catabolic structure in the context of an industrial site consisting of a plot of land surrounding a secondary lead smelter. Microbial biomass, catabolic profiles, and ecotoxicological responses (PICT) were monitored on soils sampled at selected locations along 110-m transects established on the site. We confirmed the high toxicity of Pb on respirations and microbial and fungal biomasses by measuring positive correlations with distance from the wall factory and negative correlation with total Pb concentrations. Pb contamination also induced changes in microbial and fungal catabolic structure (from carbohydrates to amino acids through carboxylic malic acid). Moreover, PICT measurement allowed to establish causal linkages between lead and its effect on biological communities taking into account the contamination history of the ecosystem at community level. The positive correlation between qCO2 (based on respiration and substrate use) and PICT suggested that the Pb stress-induced acquisition of tolerance came at a greater energy cost for microbial communities in order to cope with the toxicity of the metal. In this industrial context of long-term polymetallic contamination dominated by Pb in a field experiment, we confirmed impacts of this metal on soil functioning through microbial communities, as previously observed for earthworm communities.

The influence of e-waste recycling on the molecular ecological network of soil microbial communities in Pakistan and China.

PubMed

Jiang, Longfei; Cheng, Zhineng; Zhang, Dayi; Song, Mengke; Wang, Yujie; Luo, Chunling; Yin, Hua; Li, Jun; Zhang, Gan

2017-12-01

Primitive electronic waste (e-waste) recycling releases large amounts of organic pollutants and heavy metals into the environment. As crucial moderators of geochemical cycling processes and pollutant remediation, soil microbes may be affected by these contaminants. We collected soil samples heavily contaminated by e-waste recycling in China and Pakistan, and analyzed the indigenous microbial communities. The results of this work revealed that the microbial community composition and diversity, at both whole and core community levels, were affected significantly by polycyclic aromatic hydrocarbons (PAHs), polybrominated diphenyl ethers (PBDEs) and heavy metals (e.g., Cu, Zn, and Pb). The geographical distance showed limited impacts on microbial communities compared with geochemical factors. The constructed ecological network of soil microbial communities illustrated microbial co-occurrence, competition and antagonism across soils, revealing the response of microbes to soil properties and pollutants. Two of the three main modules constructed with core operational taxonomic units (OTUs) were sensitive to nutrition (total organic carbon and total nitrogen) and pollutants. Five key OTUs assigned to Acidobacteria, Proteobacteria, and Nitrospirae in ecological network were identified. This is the first study to report the effects of e-waste pollutants on soil microbial network, providing a deeper understanding of the ecological influence of crude e-waste recycling activities on soil ecological functions. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Functional Potential of Microbial Communities in Hydraulic Fracturing Source Water and Produced Water from Natural Gas Extraction Characterized by Metagenomic Sequencing

PubMed Central

Mohan, Arvind Murali; Bibby, Kyle J.; Lipus, Daniel; Hammack, Richard W.; Gregory, Kelvin B.

2014-01-01

Microbial activity in produced water from hydraulic fracturing operations can lead to undesired environmental impacts and increase gas production costs. However, the metabolic profile of these microbial communities is not well understood. Here, for the first time, we present results from a shotgun metagenome of microbial communities in both hydraulic fracturing source water and wastewater produced by hydraulic fracturing. Taxonomic analyses showed an increase in anaerobic/facultative anaerobic classes related to Clostridia, Gammaproteobacteria, Bacteroidia and Epsilonproteobacteria in produced water as compared to predominantly aerobic Alphaproteobacteria in the fracturing source water. The metabolic profile revealed a relative increase in genes responsible for carbohydrate metabolism, respiration, sporulation and dormancy, iron acquisition and metabolism, stress response and sulfur metabolism in the produced water samples. These results suggest that microbial communities in produced water have an increased genetic ability to handle stress, which has significant implications for produced water management, such as disinfection. PMID:25338024

The functional potential of microbial communities in hydraulic fracturing source water and produced water from natural gas extraction characterized by metagenomic sequencing

DOE PAGES

Mohan, Arvind Murali; Bibby, Kyle J.; Lipus, Daniel; ...

2014-10-22

Microbial activity in produced water from hydraulic fracturing operations can lead to undesired environmental impacts and increase gas production costs. However, the metabolic profile of these microbial communities is not well understood. Here, for the first time, we present results from a shotgun metagenome of microbial communities in both hydraulic fracturing source water and wastewater produced by hydraulic fracturing. Taxonomic analyses showed an increase in anaerobic/facultative anaerobic classes related to Clostridia, Gammaproteobacteria, Bacteroidia and Epsilonproteobacteria in produced water as compared to predominantly aerobic Alphaproteobacteria in the fracturing source water. Thus, the metabolic profile revealed a relative increase in genes responsiblemore » for carbohydrate metabolism, respiration, sporulation and dormancy, iron acquisition and metabolism, stress response and sulfur metabolism in the produced water samples. These results suggest that microbial communities in produced water have an increased genetic ability to handle stress, which has significant implications for produced water management, such as disinfection.« less

The functional potential of microbial communities in hydraulic fracturing source water and produced water from natural gas extraction characterized by metagenomic sequencing.

PubMed

Mohan, Arvind Murali; Bibby, Kyle J; Lipus, Daniel; Hammack, Richard W; Gregory, Kelvin B

2014-01-01

Microbial activity in produced water from hydraulic fracturing operations can lead to undesired environmental impacts and increase gas production costs. However, the metabolic profile of these microbial communities is not well understood. Here, for the first time, we present results from a shotgun metagenome of microbial communities in both hydraulic fracturing source water and wastewater produced by hydraulic fracturing. Taxonomic analyses showed an increase in anaerobic/facultative anaerobic classes related to Clostridia, Gammaproteobacteria, Bacteroidia and Epsilonproteobacteria in produced water as compared to predominantly aerobic Alphaproteobacteria in the fracturing source water. The metabolic profile revealed a relative increase in genes responsible for carbohydrate metabolism, respiration, sporulation and dormancy, iron acquisition and metabolism, stress response and sulfur metabolism in the produced water samples. These results suggest that microbial communities in produced water have an increased genetic ability to handle stress, which has significant implications for produced water management, such as disinfection.

Sampling from living organisms: section 3 in Sampling and experiments with biofilms in the environment: chapter 6

USGS Publications Warehouse

Kellogg, Christina A.

2014-01-01

Living organisms, unlike inanimate surfaces, seem to exert some control over their surface microbiota, in many cases maintaining conserved, species-specific microbial communities. Microbial ecologists seek to characterize and identify these microbes to understand the roles they are playing in the larger organism's biology.

IDENTIFYING THE SIGNATURE OF THE NATURAL ATTENUATION IN THE MICROBIAL ECOLOGY OF HYDROCARBON CONTAMINATED GROUNDWATER USING MOLECULAR METHODS AND &LDQUO;BUG TRAPS&RDQUO;

EPA Science Inventory

These related projects have combined biological molecular methods and a novel passive sampling system (bio-trap) to produce a technology that will allow the active component of any contaminated groundwater microbial community to be investigated. Conventional sampling methods c...

Increased diversity of egg-associated bacteria on brown trout (Salmo trutta) at elevated temperatures.

PubMed

Wilkins, Laetitia G E; Rogivue, Aude; Schütz, Frédéric; Fumagalli, Luca; Wedekind, Claus

2015-11-27

The taxonomic composition of egg-associated microbial communities can play a crucial role in the development of fish embryos. In response, hosts increasingly influence the composition of their associated microbial communities during embryogenesis, as concluded from recent field studies and laboratory experiments. However, little is known about the taxonomic composition and the diversity of egg-associated microbial communities within ecosystems; e.g., river networks. We sampled late embryonic stages of naturally spawned brown trout at nine locations within two different river networks and applied 16S rRNA pyrosequencing to describe their bacterial communities. We found no evidence for a significant isolation-by-distance effect on the composition of bacterial communities, and no association between neutral genetic divergence of fish host (based on 11 microsatellites) and phylogenetic distances of the composition of their associated bacterial communities. We characterized core bacterial communities on brown trout eggs and compared them to corresponding water samples with regard to bacterial composition and its presumptive function. Bacterial diversity was positively correlated with water temperature at the spawning locations. We discuss this finding in the context of the increased water temperatures that have been recorded during the last 25 years in the study area.

Increased diversity of egg-associated bacteria on brown trout (Salmo trutta) at elevated temperatures

PubMed Central

Wilkins, Laetitia G. E.; Rogivue, Aude; Schütz, Frédéric; Fumagalli, Luca; Wedekind, Claus

2015-01-01

The taxonomic composition of egg-associated microbial communities can play a crucial role in the development of fish embryos. In response, hosts increasingly influence the composition of their associated microbial communities during embryogenesis, as concluded from recent field studies and laboratory experiments. However, little is known about the taxonomic composition and the diversity of egg-associated microbial communities within ecosystems; e.g., river networks. We sampled late embryonic stages of naturally spawned brown trout at nine locations within two different river networks and applied 16S rRNA pyrosequencing to describe their bacterial communities. We found no evidence for a significant isolation-by-distance effect on the composition of bacterial communities, and no association between neutral genetic divergence of fish host (based on 11 microsatellites) and phylogenetic distances of the composition of their associated bacterial communities. We characterized core bacterial communities on brown trout eggs and compared them to corresponding water samples with regard to bacterial composition and its presumptive function. Bacterial diversity was positively correlated with water temperature at the spawning locations. We discuss this finding in the context of the increased water temperatures that have been recorded during the last 25 years in the study area. PMID:26611640

Molecular phylogenetic and chemical analyses of the microbial mats in deep-sea cold seep sediments at the northeastern Japan Sea.

PubMed

Arakawa, Shizuka; Sato, Takako; Sato, Rumi; Zhang, Jing; Gamo, Toshitaka; Tsunogai, Urumu; Hirota, Akinari; Yoshida, Yasuhiko; Usami, Ron; Inagaki, Fumio; Kato, Chiaki

2006-08-01

Microbial communities inhabiting deep-sea cold seep sediments at the northeastern Japan Sea were characterized by molecular phylogenetic and chemical analyses. White patchy microbial mats were observed along the fault offshore the Hokkaido Island and sediment samples were collected from two stations at the southern foot of the Shiribeshi seamount (M1 site at a depth of 2,961 m on the active fault) and off the Motta Cape site (M2 site at a depth of 3,064 m off the active fault). The phylogenetic and terminal-restriction fragment polymorphism analyses of PCR-amplified 16S rRNA genes revealed that microbial community structures were different between two sampling stations. The members of ANME-2 archaea and diverse bacterial components including sulfate reducers within Deltaproteobacteria were detected from M1 site, indicating the occurrence of biologically mediated anaerobic oxidation of methane, while microbial community at M2 site was predominantly composed of members of Marine Crenarchaeota group I, sulfate reducers of Deltaproteobacteria, and sulfur oxidizers of Epsilonproteobacteria. Chemical analyses of seawater above microbial mats suggested that concentrations of sulfate and methane at M1 site were largely decreased relative to those at M2 site and carbon isotopic composition of methane at M1 site shifted heavier ((13)C-enriched), the results of which are consistent with molecular analyses. These results suggest that the mat microbial communities in deep-sea cold seep sediments at the northeastern Japan Sea are significantly responsible for sulfur and carbon circulations and the geological activity associated with plate movements serves unique microbial habitats in deep-sea environments.

Comparison of whole-cell fatty acid (MIDI) or phospholipid fatty acid (PLFA) extractants as biomarkers to profile soil microbial communities.

PubMed

Fernandes, Marcelo F; Saxena, Jyotisna; Dick, Richard P

2013-07-01

The whole-cell lipid extraction to profile microbial communities on soils using fatty acid (FA) biomarkers is commonly done with the two extractants associated with the phospholipid fatty acid (PLFA) or Microbial IDentification Inc. (MIDI) methods. These extractants have very different chemistry and lipid separation procedures, but often shown a similar ability to discriminate soils from various management and vegetation systems. However, the mechanism and the chemistry of the exact suite of FAs extracted by these two methods are poorly understood. Therefore, the objective was to qualitatively and quantitatively compare the MIDI and PLFA microbial profiling methods for detecting microbial community shifts due to soil type or management. Twenty-nine soil samples were collected from a wide range of soil types across Oregon and extracted FAs by each method were analyzed by gas chromatography (GC) and GC-mass spectrometry. Unlike PLFA profiles, which were highly related to microbial FAs, the overall MIDI-FA profiles were highly related to the plant-derived FAs. Plant-associated compounds were quantitatively related to particulate organic matter (POM) and qualitatively related to the standing vegetation at sampling. These FAs were negatively correlated to respiration rate normalized to POM (RespPOM), which increased in systems under more intensive management. A strong negative correlation was found between MIDI-FA to PLFA ratios and total organic carbon (TOC). When the reagents used in MIDI procedure were tested for the limited recovery of MIDI-FAs from soil with high organic matter, the recovery of MIDI-FA microbial signatures sharply decreased with increasing ratios of soil to extractant. Hence, the MIDI method should be used with great caution for interpreting changes in FA profiles due to shifts in microbial communities.

Changes in Microbial Community Structure and Soil Biological Properties in Mined Dune Areas During Re-vegetation.

PubMed

Escobar, Indra Elena C; Santos, Vilma M; da Silva, Danielle Karla A; Fernandes, Marcelo F; Cavalcante, Uided Maaze T; Maia, Leonor C

2015-06-01

The aim of this study was to describe the impact of re-vegetation on the restoration of microbial community structure and soil microbiological properties in sand dunes that had been affected by mining activity. Soil samples were collected during the dry and rainy seasons from a chronosequence (1, 9, 21 years) of re-vegetated dunes using a single preserved dune as a reference. The composition of the fatty acid methyl esters and soil microbial properties were evaluated. The results showed that the changes in microbial community structure were related to seasonal variations: biomarkers of Gram-positive bacteria were higher than Gram-negative bacteria during the dry season, showing that this group of organisms is more tolerant to these stressful conditions. The microbial community structure in the natural dune was less affected by seasonal variation compared to the re-vegetated areas, whereas the opposite was observed for microbiological properties. Thus, in general, the proportion of saprobic fungi was higher in the natural dune, whereas Gram-negative bacteria were proportionally more common in the younger areas. Although over time the re-vegetation allows the recovery of the microbial community and the soil functions, these communities and functions are different from those found in the undisturbed areas.

Microbial communities and their predicted metabolic characteristics in deep fracture groundwaters of the crystalline bedrock at Olkiluoto, Finland

NASA Astrophysics Data System (ADS)

Bomberg, Malin; Lamminmäki, Tiina; Itävaara, Merja

2016-11-01

The microbial diversity in oligotrophic isolated crystalline Fennoscandian Shield bedrock fracture groundwaters is high, but the core community has not been identified. Here we characterized the bacterial and archaeal communities in 12 water conductive fractures situated at depths between 296 and 798 m by high throughput amplicon sequencing using the Illumina HiSeq platform. Between 1.7 × 104 and 1.2 × 106 bacterial or archaeal sequence reads per sample were obtained. These sequences revealed that up to 95 and 99 % of the bacterial and archaeal sequences obtained from the 12 samples, respectively, belonged to only a few common species, i.e. the core microbiome. However, the remaining rare microbiome contained over 3- and 6-fold more bacterial and archaeal taxa. The metabolic properties of the microbial communities were predicted using PICRUSt. The approximate estimation showed that the metabolic pathways commonly included fermentation, fatty acid oxidation, glycolysis/gluconeogenesis, oxidative phosphorylation, and methanogenesis/anaerobic methane oxidation, but carbon fixation through the Calvin cycle, reductive TCA cycle, and the Wood-Ljungdahl pathway was also predicted. The rare microbiome is an unlimited source of genomic functionality in all ecosystems. It may consist of remnants of microbial communities prevailing in earlier environmental conditions, but could also be induced again if changes in their living conditions occur.

Subsurface metabolic potential on the Costa Rican Margin

NASA Astrophysics Data System (ADS)

Biddle, J.; Leon, Z. R.; Martino, A. J.; Bousses, K.; House, C. H.

2017-12-01

The distribution of archaea and bacteria and their associated metabolic abilities in the deep subseafloor are poorly understood. In order to explore this, we focused on samples from the Costa Rica margin IODP Expedition 334. The microbial community was analyzed via metagenomics in two different sites at multiple depths. At Site 1378, samples are from 2 meters below the sea floor (mbsf), 33 mbsf and 93 mbsf, and at Site 1379 from 22 mbsf to 45 mbsf. Whole community analysis of conserved gene markers in the metagenome show that the microbial community varies with depth, and drastically differs between the two geographically close sites. Thirty-two genomes were recovered from the metagenomic data with more than 30% completion. Archaea make 49% of all genomes recovered and over 90% of these recovered genomes belong to recently discovered and poorly characterized groups of Archaea. This study explored the relative dynamics of microbial communities in the deep biosphere and presents the metabolic potential of distinct subsurface biosphere archaeal groups.

Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range

PubMed Central

Henderson, Gemma; Cox, Faith; Ganesh, Siva; Jonker, Arjan; Young, Wayne; Abecia, Leticia; Angarita, Erika; Aravena, Paula; Nora Arenas, Graciela; Ariza, Claudia; Attwood, Graeme T.; Mauricio Avila, Jose; Avila-Stagno, Jorge; Bannink, André; Barahona, Rolando; Batistotti, Mariano; Bertelsen, Mads F.; Brown-Kav, Aya; Carvajal, Andres M.; Cersosimo, Laura; Vieira Chaves, Alexandre; Church, John; Clipson, Nicholas; Cobos-Peralta, Mario A.; Cookson, Adrian L.; Cravero, Silvio; Cristobal Carballo, Omar; Crosley, Katie; Cruz, Gustavo; Cerón Cucchi, María; de la Barra, Rodrigo; De Menezes, Alexandre B.; Detmann, Edenio; Dieho, Kasper; Dijkstra, Jan; dos Reis, William L. S.; Dugan, Mike E. R.; Hadi Ebrahimi, Seyed; Eythórsdóttir, Emma; Nde Fon, Fabian; Fraga, Martín; Franco, Francisco; Friedeman, Chris; Fukuma, Naoki; Gagić, Dragana; Gangnat, Isabelle; Javier Grilli, Diego; Guan, Le Luo; Heidarian Miri, Vahideh; Hernandez-Sanabria, Emma; Gomez, Alma Ximena Ibarra; Isah, Olubukola A.; Ishaq, Suzanne; Jami, Elie; Jelincic, Juan; Kantanen, Juha; Kelly, William J.; Kim, Seon-Ho; Klieve, Athol; Kobayashi, Yasuo; Koike, Satoshi; Kopecny, Jan; Nygaard Kristensen, Torsten; Julie Krizsan, Sophie; LaChance, Hannah; Lachman, Medora; Lamberson, William R.; Lambie, Suzanne; Lassen, Jan; Leahy, Sinead C.; Lee, Sang-Suk; Leiber, Florian; Lewis, Eva; Lin, Bo; Lira, Raúl; Lund, Peter; Macipe, Edgar; Mamuad, Lovelia L.; Cuquetto Mantovani, Hilário; Marcoppido, Gisela Ariana; Márquez, Cristian; Martin, Cécile; Martinez, Gonzalo; Eugenia Martinez, Maria; Lucía Mayorga, Olga; McAllister, Tim A.; McSweeney, Chris; Mestre, Lorena; Minnee, Elena; Mitsumori, Makoto; Mizrahi, Itzhak; Molina, Isabel; Muenger, Andreas; Munoz, Camila; Murovec, Bostjan; Newbold, John; Nsereko, Victor; O’Donovan, Michael; Okunade, Sunday; O’Neill, Brendan; Ospina, Sonia; Ouwerkerk, Diane; Parra, Diana; Pereira, Luiz Gustavo Ribeiro; Pinares-Patino, Cesar; Pope, Phil B.; Poulsen, Morten; Rodehutscord, Markus; Rodriguez, Tatiana; Saito, Kunihiko; Sales, Francisco; Sauer, Catherine; Shingfield, Kevin; Shoji, Noriaki; Simunek, Jiri; Stojanović-Radić, Zorica; Stres, Blaz; Sun, Xuezhao; Swartz, Jeffery; Liang Tan, Zhi; Tapio, Ilma; Taxis, Tasia M.; Tomkins, Nigel; Ungerfeld, Emilio; Valizadeh, Reza; van Adrichem, Peter; Van Hamme, Jonathan; Van Hoven, Woulter; Waghorn, Garry; John Wallace, R.; Wang, Min; Waters, Sinéad M.; Keogh, Kate; Witzig, Maren; Wright, Andre-Denis G.; Yamano, Hidehisa; Yan, Tianhai; Yanez-Ruiz, David R.; Yeoman, Carl J.; Zambrano, Ricardo; Zeitz, Johanna; Zhou, Mi; Wei Zhou, Hua; Xia Zou, Cai; Zunino, Pablo; Janssen, Peter H.

2015-01-01

Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific. PMID:26449758

Microbial community response reveals underlying mechanism of industrial-scale manganese sand biofilters used for the simultaneous removal of iron, manganese and ammonia from groundwater.

PubMed

Zhang, Yu; Sun, Rui; Zhou, Aijuan; Zhang, Jiaguang; Luan, Yunbo; Jia, Jianna; Yue, Xiuping; Zhang, Jie

2018-01-08

Most studies have employed aeration-biofiltration process for the simultaneous removal of iron, manganese and ammonia in groundwater. However, what's inside the "black box", i.e., the potential contribution of functional microorganisms behavior and interactions have seldom been investigated. Moreover, little attention has been paid to the correlations between environmental variables and functional microorganisms. In this study, the performance of industrial-scale biofilters for the contaminated groundwater treatment was studied. The effluent were all far below the permitted concentration level in the current drinking water standard. Pyrosequencing illustrated that shifts in microbial community structure were observed in the microbial samples from different depths of filter. Microbial networks showed that the microbial community structure in the middle- and deep-layer samples was similar, in which a wide range of manganese-oxidizing bacteria was identified. By contrast, canonical correlation analysis showed that the bacteria capable of ammonia-oxidizing and nitrification was enriched in the upper-layer, i.e., Propionibacterium, Nitrosomonas, Nitrosomonas and Candidatus Nitrotoga. The stable biofilm on the biofilter media, created by certain microorganisms from the groundwater microflora, played a crucial role in the simultaneous removal of the three pollutants.

Effect of short-term room temperature storage on the microbial community in infant fecal samples.

PubMed

Guo, Yong; Li, Sheng-Hui; Kuang, Ya-Shu; He, Jian-Rong; Lu, Jin-Hua; Luo, Bei-Jun; Jiang, Feng-Ju; Liu, Yao-Zhong; Papasian, Christopher J; Xia, Hui-Min; Deng, Hong-Wen; Qiu, Xiu

2016-05-26

Sample storage conditions are important for unbiased analysis of microbial communities in metagenomic studies. Specifically, for infant gut microbiota studies, stool specimens are often exposed to room temperature (RT) conditions prior to analysis. This could lead to variations in structural and quantitative assessment of bacterial communities. To estimate such effects of RT storage, we collected feces from 29 healthy infants (0-3 months) and partitioned each sample into 5 portions to be stored for different lengths of time at RT before freezing at -80 °C. Alpha diversity did not differ between samples with storage time from 0 to 2 hours. The UniFrac distances and microbial composition analysis showed significant differences by testing among individuals, but not by testing between different time points at RT. Changes in the relative abundance of some specific (less common, minor) taxa were still found during storage at room temperature. Our results support previous studies in children and adults, and provided useful information for accurate characterization of infant gut microbiomes. In particular, our study furnished a solid foundation and justification for using fecal samples exposed to RT for less than 2 hours for comparative analyses between various medical conditions.

First Investigation of Microbial Community Composition in the Bridge (Gadeok Channel) between the Jinhae-Masan Bay and the South Sea of Korea

NASA Astrophysics Data System (ADS)

Lee, Jiyoung; Lim, Jae-Hyun; Park, Junhyung; Youn, Seok-Hyun; Oh, Hyun-Ju; Kim, Ju-Hyoung; Kim, Myung Kyum; Cho, Hyeyoun; Yoon, Joo-Eun; Kim, Soyeon; Markkandan, Kesavan; Park, Ki-Tae; Kim, Il-Nam

2018-02-01

Microbial community composition varies based on seasonal dynamics (summer: strongly stratified water column; autumn: weakly stratified water column; winter: vertically homogeneous water column) and vertical distributions (surface, middle, and bottom depths) in the Gadeok Channel, which is the primary passage to exchange waters and materials between the Jinhae-Masan Bay and the South Sea waters. The microbial community composition was analyzed from June to December 2016 using 16S rRNA gene sequencing. The community was dominated by the phyla Proteobacteria (45%), Bacteroidetes (18%), Cyanobacteria (15%), Verrucomicrobia (6%), and Actinobacteria (6%). Alphaproteobacteria (29%) was the most abundant microbial class, followed by Flavobacteria (15%) and Gammaproteobacteria (15%) in all samples. The composition of the microbial communities was found to vary vertically and seasonally. The orders Flavobacteriales and Stramenopiles showed opposing seasonal patterns; Flavobacteriales was more abundant in August and December while Stramenopiles showed high abundance in June and October at all depths. The genus Synechococcus reached extremely high abundance (14%) in the June surface water column, but was much less abundant in December water columns. Clustering analysis showed that there was a difference in the microbial community composition pattern between the strongly stratified season and well-mixed season. These results indicate that the seasonal dynamics of physicochemical and hydrologic conditions throughout the water column are important parameters in shaping the microbial community composition in the Gadeok Channel.

Comparison of two bioinformatics tools used to characterize the microbial diversity and predictive functional attributes of microbial mats from Lake Obersee, Antarctica.

PubMed

Koo, Hyunmin; Hakim, Joseph A; Morrow, Casey D; Eipers, Peter G; Davila, Alfonso; Andersen, Dale T; Bej, Asim K

2017-09-01

In this study, using NextGen sequencing of the collective 16S rRNA genes obtained from two sets of samples collected from Lake Obersee, Antarctica, we compared and contrasted two bioinformatics tools, PICRUSt and Tax4Fun. We then developed an R script to assess the taxonomic and predictive functional profiles of the microbial communities within the samples. Taxa such as Pseudoxanthomonas, Planctomycetaceae, Cyanobacteria Subsection III, Nitrosomonadaceae, Leptothrix, and Rhodobacter were exclusively identified by Tax4Fun that uses SILVA database; whereas PICRUSt that uses Greengenes database uniquely identified Pirellulaceae, Gemmatimonadetes A1-B1, Pseudanabaena, Salinibacterium and Sinobacteraceae. Predictive functional profiling of the microbial communities using Tax4Fun and PICRUSt separately revealed common metabolic capabilities, while also showing specific functional IDs not shared between the two approaches. Combining these functional predictions using a customized R script revealed a more inclusive metabolic profile, such as hydrolases, oxidoreductases, transferases; enzymes involved in carbohydrate and amino acid metabolisms; and membrane transport proteins known for nutrient uptake from the surrounding environment. Our results present the first molecular-phylogenetic characterization and predictive functional profiles of the microbial mat communities in Lake Obersee, while demonstrating the efficacy of combining both the taxonomic assignment information and functional IDs using the R script created in this study for a more streamlined evaluation of predictive functional profiles of microbial communities. Copyright © 2017 Elsevier B.V. All rights reserved.

Bacterial, fungal, and plant communities exhibit no biomass or compositional response to two years of simulated nitrogen deposition in a semiarid grassland

USGS Publications Warehouse

McHugh, Theresa A.; Morrissey, Ember M.; Mueller, Rebecca C.; Gallegos-Graves, La Verne; Kuske, Cheryl R.; Reed, Sasha C.

2017-01-01

Nitrogen (N) deposition affects myriad aspects of terrestrial ecosystem structure and function, and microbial communities may be particularly sensitive to anthropogenic N inputs. However, our understanding of N deposition effects on microbial communities is far from complete, especially for drylands where data are comparatively rare. To address the need for an improved understanding of dryland biological responses to N deposition, we conducted a two-year fertilization experiment in a semiarid grassland on the Colorado Plateau in the southwestern United States. We evaluated effects of varied levels of N inputs on archaeal, bacterial, fungal and chlorophyte community composition within three microhabitats: biological soil crusts (biocrusts), soil below biocrusts, and the plant rhizosphere. Surprisingly, N addition did not affect the community composition or diversity of any of these microbial groups; however, microbial community composition varied significantly among sampling microhabitats. Further, while plant richness, diversity, and cover showed no response to N addition, there were strong linkages between plant properties and microbial community structure. Overall, these findings highlight the potential for some dryland communities to have limited biotic ability to retain augmented N inputs, possibly leading to large N losses to the atmosphere and to aquatic systems.

Microbes and Microstructure: Dust's Role in the Snowpack Evolution

NASA Astrophysics Data System (ADS)

Lieblappen, R.; Courville, Z.; Fegyveresi, J. M.; Barbato, R.; Thurston, A.

2017-12-01

Dust is a primary vehicle for transporting microbial communities to polar and alpine snowpacks both through wind distribution (dry deposition) and snowfall events (wet deposition). The resulting microbial community diversity in the snowpack may then resemble the source material properties rather than its new habitat. Dust also has a strong influence on the microstructural properties of snow, resulting in changes to radiative and mechanical properties. As local reductions in snowpack albedo lead to enhanced melting and a heterogeneous snow surface, the microbial communities are also impacted. Here we study the impact of the changing microstructure in the snowpack, its influence on microbial function, and the fate of dust particles within the snow matrix. We seek to quantify the changes in respiration and water availability with the onset of melt. Polar samples were collected from the McMurdo Ice Shelf, Antarctica in February, 2017, while alpine samples were collected from Silverton, CO from October to May, 2017 as part of the Colorado Dust on Snow (CDOS) network. At each site, coincident meteorological data provides temperature, wind, and radiative measurements. Samples were collected immediately following dust deposition events and after subsequent snowpack evolution. We used x-ray micro-computed tomography to quantify the microstructural evolution of the snow, while also imaging the microstructural distribution of the dust within the snow. The dust was then collected and analyzed for chemical and microbial activity.

Temporal and spatial changes of microbial community in an industrial effluent receiving area in Hangzhou Bay.

PubMed

Zhang, Yan; Chen, Lujun; Sun, Renhua; Dai, Tianjiao; Tian, Jinping; Zheng, Wei; Wen, Donghui

2016-06-01

Anthropogenic activities usually contaminate water environments, and have led to the eutrophication of many estuaries and shifts in microbial communities. In this study, the temporal and spatial changes of the microbial community in an industrial effluent receiving area in Hangzhou Bay were investigated by 454 pyrosequencing. The bacterial community showed higher richness and biodiversity than the archaeal community in all sediments. Proteobacteria dominated in the bacterial communities of all the samples; Marine_Group_I and Methanomicrobia were the two dominant archaeal classes in the effluent receiving area. PCoA and AMOVA revealed strong seasonal but minor spatial changes in both bacterial and archaeal communities in the sediments. The seasonal changes of the bacterial community were less significant than those of the archaeal community, which mainly consisted of fluctuations in abundance of a large proportion of longstanding species rather than the appearance and disappearance of major archaeal species. Temperature was found to positively correlate with the dominant bacteria, Betaproteobacteria, and negatively correlate with the dominant archaea, Marine_Group_I; and might be the primary driving force for the seasonal variation of the microbial community. Copyright © 2016. Published by Elsevier B.V.

Utilizing novel diversity estimators to quantify multiple dimensions of microbial biodiversity across domains

PubMed Central

2013-01-01

Background Microbial ecologists often employ methods from classical community ecology to analyze microbial community diversity. However, these methods have limitations because microbial communities differ from macro-organismal communities in key ways. This study sought to quantify microbial diversity using methods that are better suited for data spanning multiple domains of life and dimensions of diversity. Diversity profiles are one novel, promising way to analyze microbial datasets. Diversity profiles encompass many other indices, provide effective numbers of diversity (mathematical generalizations of previous indices that better convey the magnitude of differences in diversity), and can incorporate taxa similarity information. To explore whether these profiles change interpretations of microbial datasets, diversity profiles were calculated for four microbial datasets from different environments spanning all domains of life as well as viruses. Both similarity-based profiles that incorporated phylogenetic relatedness and naïve (not similarity-based) profiles were calculated. Simulated datasets were used to examine the robustness of diversity profiles to varying phylogenetic topology and community composition. Results Diversity profiles provided insights into microbial datasets that were not detectable with classical univariate diversity metrics. For all datasets analyzed, there were key distinctions between calculations that incorporated phylogenetic diversity as a measure of taxa similarity and naïve calculations. The profiles also provided information about the effects of rare species on diversity calculations. Additionally, diversity profiles were used to examine thousands of simulated microbial communities, showing that similarity-based and naïve diversity profiles only agreed approximately 50% of the time in their classification of which sample was most diverse. This is a strong argument for incorporating similarity information and calculating diversity with a range of emphases on rare and abundant species when quantifying microbial community diversity. Conclusions For many datasets, diversity profiles provided a different view of microbial community diversity compared to analyses that did not take into account taxa similarity information, effective diversity, or multiple diversity metrics. These findings are a valuable contribution to data analysis methodology in microbial ecology. PMID:24238386

Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity

DOE PAGES

Shade, Ashley; Jones, Stuart E.; Caporaso, J. Gregory; ...

2014-07-15

Microbial communities typically contain many rare taxa that make up the majority of the observed membership, yet the contribution of this microbial “rare biosphere” to community dynamics is unclear. Using 16S rRNA amplicon sequencing of 3,237 samples from 42 time series of microbial communities from nine different ecosystems (air; marine; lake; stream; adult human skin, tongue, and gut; infant gut; and brewery wastewater treatment), we introduce a new method to detect typically rare microbial taxa that occasionally become very abundant (conditionally rare taxa [CRT]) and then quantify their contributions to temporal shifts in community structure. We discovered that CRT mademore » up 1.5 to 28% of the community membership, represented a broad diversity of bacterial and archaeal lineages, and explained large amounts of temporal community dissimilarity (i.e., up to 97% of Bray-Curtis dissimilarity). Most of the CRT were detected at multiple time points, though we also identified “one-hit wonder” CRT that were observed at only one time point. Using a case study from a temperate lake, we gained additional insights into the ecology of CRT by comparing routine community time series to large disturbance events. Our results reveal that many rare taxa contribute a greater amount to microbial community dynamics than is apparent from their low proportional abundances. In conclusion, this observation was true across a wide range of ecosystems, indicating that these rare taxa are essential for understanding community changes over time.« less

Impact of CO 2 on the Evolution of Microbial Communities Exposed to Carbon Storage Conditions, Enhanced Oil Recovery, and CO 2 Leakage

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gulliver, Djuna; Gregory, Kelvin B.; Lowry, Gregorgy V.

Geologic carbon storage (GCS) is a crucial part of a proposed mitigation strategy to reduce the anthropogenic carbon dioxide (CO 2) emissions to the atmosphere. During this process, CO 2 is injected as super critical carbon dioxide (SC-CO 2) in confined deep subsurface storage units, such as saline aquifers and depleted oil reservoirs. The deposition of vast amounts of CO 2 in subsurface geologic formations could unintentionally lead to CO 2 leakage into overlying freshwater aquifers. Introduction of CO 2 into these subsurface environments will greatly increase the CO 22 concentration and will create CO 2 concentration gradients that drivemore » changes in the microbial communities present. While it is expected that altered microbial communities will impact the biogeochemistry of the subsurface, there is no information available on how CO 2 gradients will impact these communities. The overarching goal of this project is to understand how CO 2 exposure will impact subsurface microbial communities at temperatures and pressures that are relevant to GCS and CO 2 leakage scenarios. To meet this goal, unfiltered, aqueous samples from a deep saline aquifer, a depleted oil reservoir, and a fresh water aquifer were exposed to varied concentrations of CO 2 at reservoir pressure and temperature. The microbial ecology of the samples was examined using molecular, DNA-based techniques. The results from these studies were also compared across the sites to determine any existing trends. Results reveal that increasing CO 2 leads to decreased DNA concentrations regardless of the site, suggesting that microbial processes will be significantly hindered or absent nearest the CO 2 injection/leakage plume where CO 2 concentrations are highest. At CO 2 exposures expected downgradient from the CO 2 plume, selected microorganisms emerged as dominant in the CO 2 exposed conditions. Results suggest that the altered microbial community was site specific and highly dependent on pH. The site-dependent results suggest a limited ability to predict the emerging dominant species for other CO 2 exposed environments. This study improves the understanding of how a subsurface microbial community may respond to conditions expected from GCS and CO 2 leakage. This is the first step for understanding how a CO 2-altered microbial community may impact injectivity, permanence of stored CO 2, and subsurface water quality. Future work with microbial communities from new subsurface sites would increase the current understanding of this project. Additionally, incorporation of metagenomic methods would increase understanding of potential microbial processes that may be prevalent in CO 2 exposed environments.« less

Impact of CO 2 on the Evolution of Microbial Communities Exposed to Carbon Storage Conditions, Enhanced Oil Recovery, and CO 2 Leakage

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gulliver, Djuna M.; Gregory, Kelvin B.; Lowry, Gregory V.

Geologic carbon storage (GCS) is a crucial part of a proposed mitigation strategy to reduce the anthropogenic carbon dioxide (CO 2) emissions to the atmosphere. During this process, CO 2 is injected as super critical carbon dioxide (SC-CO 2) in confined deep subsurface storage units, such as saline aquifers and depleted oil reservoirs. The deposition of vast amounts of CO 2 in subsurface geologic formations could unintentionally lead to CO 2 leakage into overlying freshwater aquifers. Introduction of CO 2 into these subsurface environments will greatly increase the CO 2 concentration and will create CO 2 concentration gradients that drivemore » changes in the microbial communities present. While it is expected that altered microbial communities will impact the biogeochemistry of the subsurface, there is no information available on how CO 2 gradients will impact these communities. The overarching goal of this project is to understand how CO 2 exposure will impact subsurface microbial communities at temperatures and pressures that are relevant to GCS and CO 2 leakage scenarios. To meet this goal, unfiltered, aqueous samples from a deep saline aquifer, a depleted oil reservoir, and a fresh water aquifer were exposed to varied concentrations of CO 2 at reservoir pressure and temperature. The microbial ecology of the samples was examined using molecular, DNA-based techniques. The results from these studies were also compared across the sites to determine any existing trends. Results reveal that increasing CO 2 leads to decreased DNA concentrations regardless of the site, suggesting that microbial processes will be significantly hindered or absent nearest the CO 2 injection/leakage plume where CO 2 concentrations are highest. At CO 2 exposures expected downgradient from the CO 2 plume, selected microorganisms emerged as dominant in the CO 2 exposed conditions. Results suggest that the altered microbial community was site specific and highly dependent on pH. The site-dependent results suggest a limited ability to predict the emerging dominant species for other CO 2-exposed environments. This study improves the understanding of how a subsurface microbial community may respond to conditions expected from GCS and CO 2 leakage. This is the first step for understanding how a CO 2-altered microbial community may impact injectivity, permanence of stored CO 2, and subsurface water quality. Future work with microbial communities from new subsurface sites would increase the current understanding of this project. Additionally, incorporation of metagenomic methods would increase understanding of potential microbial processes that may be prevalent in CO 2 exposed environments.« less

Final Scientific/Technical Report, DE-FG02-06ER64171, Integrated Nucleic Acid System for In-Field Monitoring of Microbial Community Dynamics and Metabolic Activity – Subproject to Co-PI Eric E. Roden

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eric E. Roden

2009-07-08

This report summarizes research conducted in conjunction with a project entitled “Integrated Nucleic Acid System for In-Field Monitoring of Microbial Community Dynamics and Metabolic Activity”, which was funded through the Integrative Studies Element of the former NABIR Program (now the Environmental Remediation Sciences Program) within the Office of Biological and Environmental Research. Dr. Darrell Chandler (originally at Argonne National Laboratory, now with Akonni Biosystems) was the overall PI/PD for the project. The overall project goals were to (1) apply a model iron-reducer and sulfate-reducer microarray and instrumentation systems to sediment and groundwater samples from the Scheibe et al. FRC Areamore » 2 field site, UMTRA sediments, and other DOE contaminated sites; (2) continue development and expansion of a 16S rRNA/rDNA¬-targeted probe suite for microbial community dynamics as new sequences are obtained from DOE-relevant sites; and (3) address the fundamental molecular biology and analytical chemistry associated with the extraction, purification and analysis of functional genes and mRNA in environmental samples. Work on the UW subproject focused on conducting detailed batch and semicontinuous culture reactor experiments with uranium-contaminated FRC Area 2 sediment. The reactor experiments were designed to provide coherent geochemical and microbiological data in support of microarray analyses of microbial communities in Area 2 sediments undergoing biostimulation with ethanol. A total of four major experiments were conducted (one batch and three semicontinuous culture), three of which (the batch and two semicontinuous culture) provided samples for DNA microarray analysis. A variety of other molecular analyses (clone libraries, 16S PhyloChip, RT-PCR, and T-RFLP) were conducted on parallel samples from the various experiments in order to provide independent information on microbial community response to biostimulation.« less

Phylogenetic analysis of the fecal microbial community in herbivorous land and marine iguanas of the Galápagos Islands using 16S rRNA-based pyrosequencing.

PubMed

Hong, Pei-Ying; Wheeler, Emily; Cann, Isaac K O; Mackie, Roderick I

2011-09-01

Herbivorous reptiles depend on complex gut microbial communities to effectively degrade dietary polysaccharides. The composition of these fermentative communities may vary based on dietary differences. To explore the role of diet in shaping gut microbial communities, we evaluated the fecal samples from two related host species--the algae-consuming marine iguana (Amblyrhynchus cristatus) and land iguanas (LI) (genus Conolophus) that consume terrestrial vegetation. Marine and LI fecal samples were collected from different islands in the Galápagos archipelago. High-throughput 16S rRNA-based pyrosequencing was used to provide a comparative analysis of fecal microbial diversity. At the phylum level, the fecal microbial community in iguanas was predominated by Firmicutes (69.5±7.9%) and Bacteroidetes (6.2±2.8%), as well as unclassified Bacteria (20.6±8.6%), suggesting that a large portion of iguana fecal microbiota is novel and could be involved in currently unknown functions. Host species differed in the abundance of specific bacterial groups. Bacteroides spp., Lachnospiraceae and Clostridiaceae were significantly more abundant in the marine iguanas (MI) (P-value>1E-9). In contrast, Ruminococcaceae were present at >5-fold higher abundance in the LI than MI (P-value>6E-14). Archaea were only detected in the LI. The number of operational taxonomic units (OTUs) in the LI (356-896 OTUs) was >2-fold higher than in the MI (112-567 OTUs), and this increase in OTU diversity could be related to the complexity of the resident bacterial population and their gene repertoire required to breakdown the recalcitrant polysaccharides prevalent in terrestrial plants. Our findings suggest that dietary differences contribute to gut microbial community differentiation in herbivorous lizards. Most importantly, this study provides a better understanding of the microbial diversity in the iguana gut; therefore facilitating future efforts to discover novel bacterial-associated enzymes that can effectively breakdown a wide variety of complex polysaccharides.

Shift in the Microbial Ecology of a Hospital Hot Water System following the Introduction of an On-Site Monochloramine Disinfection System

PubMed Central

Baron, Julianne L.; Vikram, Amit; Duda, Scott; Stout, Janet E.; Bibby, Kyle

2014-01-01

Drinking water distribution systems, including premise plumbing, contain a diverse microbiological community that may include opportunistic pathogens. On-site supplemental disinfection systems have been proposed as a control method for opportunistic pathogens in premise plumbing. The majority of on-site disinfection systems to date have been installed in hospitals due to the high concentration of opportunistic pathogen susceptible occupants. The installation of on-site supplemental disinfection systems in hospitals allows for evaluation of the impact of on-site disinfection systems on drinking water system microbial ecology prior to widespread application. This study evaluated the impact of supplemental monochloramine on the microbial ecology of a hospital’s hot water system. Samples were taken three months and immediately prior to monochloramine treatment and monthly for the first six months of treatment, and all samples were subjected to high throughput Illumina 16S rRNA region sequencing. The microbial community composition of monochloramine treated samples was dramatically different than the baseline months. There was an immediate shift towards decreased relative abundance of Betaproteobacteria, and increased relative abundance of Firmicutes, Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria and Actinobacteria. Following treatment, microbial populations grouped by sampling location rather than sampling time. Over the course of treatment the relative abundance of certain genera containing opportunistic pathogens and genera containing denitrifying bacteria increased. The results demonstrate the driving influence of supplemental disinfection on premise plumbing microbial ecology and suggest the value of further investigation into the overall effects of premise plumbing disinfection strategies on microbial ecology and not solely specific target microorganisms. PMID:25033448

Shift in the microbial ecology of a hospital hot water system following the introduction of an on-site monochloramine disinfection system.

PubMed

Baron, Julianne L; Vikram, Amit; Duda, Scott; Stout, Janet E; Bibby, Kyle

2014-01-01

Drinking water distribution systems, including premise plumbing, contain a diverse microbiological community that may include opportunistic pathogens. On-site supplemental disinfection systems have been proposed as a control method for opportunistic pathogens in premise plumbing. The majority of on-site disinfection systems to date have been installed in hospitals due to the high concentration of opportunistic pathogen susceptible occupants. The installation of on-site supplemental disinfection systems in hospitals allows for evaluation of the impact of on-site disinfection systems on drinking water system microbial ecology prior to widespread application. This study evaluated the impact of supplemental monochloramine on the microbial ecology of a hospital's hot water system. Samples were taken three months and immediately prior to monochloramine treatment and monthly for the first six months of treatment, and all samples were subjected to high throughput Illumina 16S rRNA region sequencing. The microbial community composition of monochloramine treated samples was dramatically different than the baseline months. There was an immediate shift towards decreased relative abundance of Betaproteobacteria, and increased relative abundance of Firmicutes, Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria and Actinobacteria. Following treatment, microbial populations grouped by sampling location rather than sampling time. Over the course of treatment the relative abundance of certain genera containing opportunistic pathogens and genera containing denitrifying bacteria increased. The results demonstrate the driving influence of supplemental disinfection on premise plumbing microbial ecology and suggest the value of further investigation into the overall effects of premise plumbing disinfection strategies on microbial ecology and not solely specific target microorganisms.

Specific Microbial Communities Associate with the Rhizosphere of Welwitschia mirabilis, a Living Fossil.

PubMed

Valverde, Angel; De Maayer, Pieter; Oberholster, Tanzelle; Henschel, Joh; Louw, Michele K; Cowan, Don

2016-01-01

Welwitschia mirabilis is an ancient and rare plant distributed along the western coast of Namibia and Angola. Several aspects of Welwitschia biology and ecology have been investigated, but very little is known about the microbial communities associated with this plant. This study reports on the bacterial and fungal communities inhabiting the rhizosphere of W. mirabilis and the surrounding bulk soil. Rhizosphere communities were dominated by sequences of Alphaproteobacteria and Euromycetes, while Actinobacteria, Alphaproteobacteria, and fungi of the class Dothideomycetes jointly dominated bulk soil communities. Although microbial communities within the rhizosphere and soil samples were highly variable, very few "species" (OTUs defined at a 97% identity cut-off) were shared between these two environments. There was a small 'core' rhizosphere bacterial community (formed by Nitratireductor, Steroidobacter, Pseudonocardia and three Phylobacteriaceae) that together with Rhizophagus, an arbuscular mycorrhizal fungus, and other putative plant growth-promoting microbes may interact synergistically to promote Welwitschia growth.

Using growth-based methods to determine direct effects of salinity on soil microbial communities

NASA Astrophysics Data System (ADS)

Rath, Kristin; Rousk, Johannes

2015-04-01

Soil salinization is a widespread agricultural problem and increasing salt concentrations in soils have been found to be correlated with decreased microbial activity. A central challenge in microbial ecology is to link environmental factors, such as salinity, to responses in the soil microbial community. That is, it can be difficult to distinguish direct from indirect effects. In order to determine direct salinity effects on the community we employed the ecotoxicological concept of Pollution-Induced Community Tolerance (PICT). This concept is built on the assumption that if salinity had an ecologically relevant effect on the community, it should have selected for more tolerant species and strains, resulting in an overall higher community tolerance to salt in communities from saline soils. Growth-based measures, such as the 3H-leucine incorporation into bacterial protein , provide sensitive tools to estimate community tolerance. They can also provide high temporal resolution in tracking changes in tolerance over time. In our study we used growth-based methods to investigate: i) at what levels of salt exposure and over which time scales salt tolerance can be induced in a non-saline soil, and (ii) if communities from high salinity sites have higher tolerance to salt exposure along natural salinity gradients. In the first part of the study, we exposed a non-saline soil to a range of salinities and monitored the development of community tolerance over time. We found that community tolerance to intermediate salinities up to around 30 mg NaCl per g soil can be induced at relatively short time scales of a few days, providing evidence that microbial communities can adapt rapidly to changes in environmental conditions. In the second part of the study we used soil samples originating from natural salinity gradients encompassing a wide range of salinity levels, with electrical conductivities ranging from 0.1 dS/m to >10 dS/m. We assessed community tolerance to salt by measuring the bacterial growth response to added NaCl in a soil suspension. The bacterial community tolerance to salt increased along the salt gradients with higher in situ soil salinity. In samples from the low-saline end of the gradient, bacterial growth rates in the soil suspension showed a clear concentration-response relationship to NaCl resulting in inhibition curves. This relationship gradually changed toward higher salt concentrations. In soil samples from high salinity sites, bacterial growth was no longer inhibited by adding high concentrations of NaCl to the bacterial soil suspension. In fact, adding NaCl even promoted bacterial growth rates. These results show that salinity played an ecologically significant role in shaping communities at the highly saline end of the gradients and provide evidence for a direct salt effect on the microbial community

Effects of Physiochemical Factors on Prokaryotic Biodiversity in Malaysian Circumneutral Hot Springs.

PubMed

Chan, Chia S; Chan, Kok-Gan; Ee, Robson; Hong, Kar-Wai; Urbieta, María S; Donati, Edgardo R; Shamsir, Mohd S; Goh, Kian M

2017-01-01

Malaysia has a great number of hot springs, especially along the flank of the Banjaran Titiwangsa mountain range. Biological studies of the Malaysian hot springs are rare because of the lack of comprehensive information on their microbial communities. In this study, we report a cultivation-independent census to describe microbial communities in six hot springs. The Ulu Slim (US), Sungai Klah (SK), Dusun Tua (DT), Sungai Serai (SS), Semenyih (SE), and Ayer Hangat (AH) hot springs exhibit circumneutral pH with temperatures ranging from 43°C to 90°C. Genomic DNA was extracted from environmental samples and the V3-V4 hypervariable regions of 16S rRNA genes were amplified, sequenced, and analyzed. High-throughput sequencing analysis showed that microbial richness was high in all samples as indicated by the detection of 6,334-26,244 operational taxonomy units. In total, 59, 61, 72, 73, 65, and 52 bacterial phyla were identified in the US, SK, DT, SS, SE, and AH hot springs, respectively. Generally, Firmicutes and Proteobacteria dominated the bacterial communities in all hot springs. Archaeal communities mainly consisted of Crenarchaeota, Euryarchaeota, and Parvarchaeota. In beta diversity analysis, the hot spring microbial memberships were clustered primarily on the basis of temperature and salinity. Canonical correlation analysis to assess the relationship between the microbial communities and physicochemical variables revealed that diversity patterns were best explained by a combination of physicochemical variables, rather than by individual abiotic variables such as temperature and salinity.

Next-Generation Sequencing of Microbial Communities in the Athabasca River and Its Tributaries in Relation to Oil Sands Mining Activities

PubMed Central

Yergeau, Etienne; Lawrence, John R.; Sanschagrin, Sylvie; Waiser, Marley J.; Korber, Darren R.

2012-01-01

The Athabasca oil sands deposit is the largest reservoir of crude bitumen in the world. Recently, the soaring demand for oil and the availability of modern bitumen extraction technology have heightened exploitation of this reservoir and the potential unintended consequences of pollution in the Athabasca River. The main objective of the present study was to evaluate the potential impacts of oil sands mining on neighboring aquatic microbial community structure. Microbial communities were sampled from sediments in the Athabasca River and its tributaries as well as in oil sands tailings ponds. Bacterial and archaeal 16S rRNA genes were amplified and sequenced using next-generation sequencing technology (454 and Ion Torrent). Sediments were also analyzed for a variety of chemical and physical characteristics. Microbial communities in the fine tailings of the tailings ponds were strikingly distinct from those in the Athabasca River and tributary sediments. Microbial communities in sediments taken close to tailings ponds were more similar to those in the fine tailings of the tailings ponds than to the ones from sediments further away. Additionally, bacterial diversity was significantly lower in tailings pond sediments. Several taxonomic groups of Bacteria and Archaea showed significant correlations with the concentrations of different contaminants, highlighting their potential as bioindicators. We also extensively validated Ion Torrent sequencing in the context of environmental studies by comparing Ion Torrent and 454 data sets and by analyzing control samples. PMID:22923391

Effects of Physiochemical Factors on Prokaryotic Biodiversity in Malaysian Circumneutral Hot Springs

PubMed Central

Chan, Chia S.; Chan, Kok-Gan; Ee, Robson; Hong, Kar-Wai; Urbieta, María S.; Donati, Edgardo R.; Shamsir, Mohd S.; Goh, Kian M.

2017-01-01

Malaysia has a great number of hot springs, especially along the flank of the Banjaran Titiwangsa mountain range. Biological studies of the Malaysian hot springs are rare because of the lack of comprehensive information on their microbial communities. In this study, we report a cultivation-independent census to describe microbial communities in six hot springs. The Ulu Slim (US), Sungai Klah (SK), Dusun Tua (DT), Sungai Serai (SS), Semenyih (SE), and Ayer Hangat (AH) hot springs exhibit circumneutral pH with temperatures ranging from 43°C to 90°C. Genomic DNA was extracted from environmental samples and the V3–V4 hypervariable regions of 16S rRNA genes were amplified, sequenced, and analyzed. High-throughput sequencing analysis showed that microbial richness was high in all samples as indicated by the detection of 6,334–26,244 operational taxonomy units. In total, 59, 61, 72, 73, 65, and 52 bacterial phyla were identified in the US, SK, DT, SS, SE, and AH hot springs, respectively. Generally, Firmicutes and Proteobacteria dominated the bacterial communities in all hot springs. Archaeal communities mainly consisted of Crenarchaeota, Euryarchaeota, and Parvarchaeota. In beta diversity analysis, the hot spring microbial memberships were clustered primarily on the basis of temperature and salinity. Canonical correlation analysis to assess the relationship between the microbial communities and physicochemical variables revealed that diversity patterns were best explained by a combination of physicochemical variables, rather than by individual abiotic variables such as temperature and salinity. PMID:28729863

Challenges and perspectives of metaproteomic data analysis.

PubMed

Heyer, Robert; Schallert, Kay; Zoun, Roman; Becher, Beatrice; Saake, Gunter; Benndorf, Dirk

2017-11-10

In nature microorganisms live in complex microbial communities. Comprehensive taxonomic and functional knowledge about microbial communities supports medical and technical application such as fecal diagnostics as well as operation of biogas plants or waste water treatment plants. Furthermore, microbial communities are crucial for the global carbon and nitrogen cycle in soil and in the ocean. Among the methods available for investigation of microbial communities, metaproteomics can approximate the activity of microorganisms by investigating the protein content of a sample. Although metaproteomics is a very powerful method, issues within the bioinformatic evaluation impede its success. In particular, construction of databases for protein identification, grouping of redundant proteins as well as taxonomic and functional annotation pose big challenges. Furthermore, growing amounts of data within a metaproteomics study require dedicated algorithms and software. This review summarizes recent metaproteomics software and addresses the introduced issues in detail. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

MetaSort untangles metagenome assembly by reducing microbial community complexity

PubMed Central

Ji, Peifeng; Zhang, Yanming; Wang, Jinfeng; Zhao, Fangqing

2017-01-01

Most current approaches to analyse metagenomic data rely on reference genomes. Novel microbial communities extend far beyond the coverage of reference databases and de novo metagenome assembly from complex microbial communities remains a great challenge. Here we present a novel experimental and bioinformatic framework, metaSort, for effective construction of bacterial genomes from metagenomic samples. MetaSort provides a sorted mini-metagenome approach based on flow cytometry and single-cell sequencing methodologies, and employs new computational algorithms to efficiently recover high-quality genomes from the sorted mini-metagenome by the complementary of the original metagenome. Through extensive evaluations, we demonstrated that metaSort has an excellent and unbiased performance on genome recovery and assembly. Furthermore, we applied metaSort to an unexplored microflora colonized on the surface of marine kelp and successfully recovered 75 high-quality genomes at one time. This approach will greatly improve access to microbial genomes from complex or novel communities. PMID:28112173

Microbial community structure of different electrode materials in constructed wetland incorporating microbial fuel cell.

PubMed

Wang, Junfeng; Song, Xinshan; Wang, Yuhui; Abayneh, Befkadu; Ding, Yi; Yan, Denghua; Bai, Junhong

2016-12-01

The microbial fuel cell coupled with constructed wetland (CW-MFC) microcosms were operated under fed-batch mode for evaluating the effect of electrode materials on bioelectricity generation and microbial community composition. Experimental results indicated that the bioenergy output in CW-MFC increased with the substrate concentration; maximum average voltage (177mV) was observed in CW-MFC with carbon fiber felt (CFF). In addition, the four different materials resulted in the formation of significantly different microbial community distribution around the anode electrode. The relative abundance of Proteobacteria in CFF and foamed nickel (FN) was significantly higher than that in stainless steel mesh (SSM) and graphite rod (GR) samples. Notably, the findings indicate that CW-MFC utilizing FN anode electrode could apparently improve relative abundance of Dechloromonas, which has been regarded as a denitrifying and phosphate accumulating microorganism. Copyright © 2016 Elsevier Ltd. All rights reserved.

Groundwater Isolation Governs Chemistry and Microbial Community Structure along Hydrologic Flowpaths

PubMed Central

Ben Maamar, Sarah; Aquilina, Luc; Quaiser, Achim; Pauwels, Hélène; Michon-Coudouel, Sophie; Vergnaud-Ayraud, Virginie; Labasque, Thierry; Roques, Clément; Abbott, Benjamin W.; Dufresne, Alexis

2015-01-01

This study deals with the effects of hydrodynamic functioning of hard-rock aquifers on microbial communities. In hard-rock aquifers, the heterogeneous hydrologic circulation strongly constrains groundwater residence time, hydrochemistry, and nutrient supply. Here, residence time and a wide range of environmental factors were used to test the influence of groundwater circulation on active microbial community composition, assessed by high throughput sequencing of 16S rRNA. Groundwater of different ages was sampled along hydrogeologic paths or loops, in three contrasting hard-rock aquifers in Brittany (France). Microbial community composition was driven by groundwater residence time and hydrogeologic loop position. In recent groundwater, in the upper section of the aquifers or in their recharge zone, surface water inputs caused high nitrate concentration and the predominance of putative denitrifiers. Although denitrification does not seem to fully decrease nitrate concentrations due to low dissolved organic carbon concentrations, nitrate input has a major effect on microbial communities. The occurrence of taxa possibly associated with the application of organic fertilizers was also noticed. In ancient isolated groundwater, an ecosystem based on Fe(II)/Fe(III) and S/SO4 redox cycling was observed down to several 100 of meters below the surface. In this depth section, microbial communities were dominated by iron oxidizing bacteria belonging to Gallionellaceae. The latter were associated to old groundwater with high Fe concentrations mixed to a small but not null percentage of recent groundwater inducing oxygen concentrations below 2.5 mg/L. These two types of microbial community were observed in the three sites, independently of site geology and aquifer geometry, indicating hydrogeologic circulation exercises a major control on microbial communities. PMID:26733990

Long lasting effects of the conversion from natural forest to poplar plantation on soil microbial communities.

PubMed

Vitali, Francesco; Mastromei, Giorgio; Senatore, Giuliana; Caroppo, Cesarea; Casalone, Enrico

2016-01-01

In this study, we evaluate the long-lasting effects on soil microbial communities of a change within a single land-use category, specifically the conversion from natural forest to forest plantation. To minimize the effects of impacts other than land-use (i.e., climatic and anthropogenic), we chose three sites within a Natural Park, with homogeneous orographic and soil texture characteristics. We compared microbial diversity in a total of 156 soil samples from two natural mixed forests and a similar forest converted to poplar plantation about thirty years ago. The diversity and structure of bacterial and fungal communities were investigated by terminal restriction fragments length polymorphism (T-RFLP) analysis of the 16S-rRNA gene and the ITS-rDNA regions, respectively. Bacterial and fungal communities from the forest plantation, compared to those from natural forest soils, showed different community structure and lower α-diversity values, consistently with the significantly higher pH values and lower organic matter content of those soils. β-diversity values, the number of measured and estimated dominant OTUs, and their distribution among the three sites showed that microbial communities from the two natural forests were much more similar to each other than they were to communities from the poplar plantation, suggesting an effect of the forest conversion on the composition and diversity of soil microbial communities. α-diversity in cultivated forest soils had narrower temporal fluctuations than in natural forest soils, suggesting higher temporal stability of microbial communities. Overall, we demonstrated that the conversion from natural forest to forest plantation altered soil microbial communities, changing their structure, lowering their diversity, and causing a spatial and temporal homogenization. Copyright © 2015 Elsevier GmbH. All rights reserved.

A Mosaic of Geothermal and Marine Features Shapes Microbial Community Structure on Deception Island Volcano, Antarctica.

PubMed

Bendia, Amanda G; Signori, Camila N; Franco, Diego C; Duarte, Rubens T D; Bohannan, Brendan J M; Pellizari, Vivian H

2018-01-01

Active volcanoes in Antarctica contrast with their predominantly cold surroundings, resulting in environmental conditions capable of selecting for versatile and extremely diverse microbial communities. This is especially true on Deception Island, where geothermal, marine, and polar environments combine to create an extraordinary range of environmental conditions. Our main goal in this study was to understand how microbial community structure is shaped by gradients of temperature, salinity, and geochemistry in polar marine volcanoes. Thereby, we collected surface sediment samples associated with fumaroles and glaciers at two sites on Deception, with temperatures ranging from 0 to 98°C. Sequencing of the 16S rRNA gene was performed to assess the composition and diversity of Bacteria and Archaea. Our results revealed that Deception harbors a combination of taxonomic groups commonly found both in cold and geothermal environments of continental Antarctica, and also groups normally identified at deep and shallow-sea hydrothermal vents, such as hyperthermophilic archaea. We observed a clear separation in microbial community structure across environmental gradients, suggesting that microbial community structure is strongly niche driven on Deception. Bacterial community structure was significantly associated with temperature, pH, salinity, and chemical composition; in contrast, archaeal community structure was strongly associated only with temperature. Our work suggests that Deception represents a peculiar "open-air" laboratory to elucidate central questions regarding molecular adaptability, microbial evolution, and biogeography of extremophiles in polar regions.

Life in the "plastisphere": microbial communities on plastic marine debris.

PubMed

Zettler, Erik R; Mincer, Tracy J; Amaral-Zettler, Linda A

2013-07-02

Plastics are the most abundant form of marine debris, with global production rising and documented impacts in some marine environments, but the influence of plastic on open ocean ecosystems is poorly understood, particularly for microbial communities. Plastic marine debris (PMD) collected at multiple locations in the North Atlantic was analyzed with scanning electron microscopy (SEM) and next-generation sequencing to characterize the attached microbial communities. We unveiled a diverse microbial community of heterotrophs, autotrophs, predators, and symbionts, a community we refer to as the "Plastisphere". Pits visualized in the PMD surface conformed to bacterial shapes suggesting active hydrolysis of the hydrocarbon polymer. Small-subunit rRNA gene surveys identified several hydrocarbon-degrading bacteria, supporting the possibility that microbes play a role in degrading PMD. Some Plastisphere members may be opportunistic pathogens (the authors, unpublished data) such as specific members of the genus Vibrio that dominated one of our plastic samples. Plastisphere communities are distinct from surrounding surface water, implying that plastic serves as a novel ecological habitat in the open ocean. Plastic has a longer half-life than most natural floating marine substrates, and a hydrophobic surface that promotes microbial colonization and biofilm formation, differing from autochthonous substrates in the upper layers of the ocean.

Functions and Unique Diversity of Genes and Microorganisms Involved in Arsenite Oxidation from the Tailings of a Realgar Mine

PubMed Central

E, Guoji; Wang, Jianing; Wang, Nian; Chen, Xiaoming; Mu, Yao; Li, Hao; Yang, Ye; Liu, Yichen; Wang, Yanxin

2016-01-01

ABSTRACT The tailings of the Shimen realgar mine have unique geochemical features. Arsenite oxidation is one of the major biogeochemical processes that occurs in the tailings. However, little is known about the functional and molecular aspects of the microbial community involved in arsenite oxidation. Here, we fully explored the functional and molecular features of the microbial communities from the tailings of the Shimen realgar mine. We collected six samples of tailings from sites A, B, C, D, E, and F. Microcosm assays indicated that all of the six sites contain both chemoautotrophic and heterotrophic arsenite-oxidizing microorganisms; their activities differed considerably from each other. The microbial arsenite-oxidizing activities show a positive correlation with soluble arsenic concentrations. The microbial communities of the six sites contain 40 phyla of bacteria and 2 phyla of archaea that show extremely high diversity. Soluble arsenic, sulfate, pH, and total organic carbon (TOC) are the key environmental factors that shape the microbial communities. We further identified 114 unique arsenite oxidase genes from the samples; all of them code for new or new-type arsenite oxidases. We also isolated 10 novel arsenite oxidizers from the samples, of which 4 are chemoautotrophic and 6 are heterotrophic. These data highlight the unique diversities of the arsenite-oxidizing microorganisms and their oxidase genes from the tailings of the Shimen realgar mine. To the best of our knowledge, this is the first report describing the functional and molecular features of microbial communities from the tailings of a realgar mine. IMPORTANCE This study focused on the functional and molecular characterizations of microbial communities from the tailings of the Shimen realgar mine. We fully explored, for the first time, the arsenite-oxidizing activities and the functional gene diversities of microorganisms from the tailings, as well as the correlation of the microbial activities/diversities with environmental factors. The findings of this study help us to better understand the diversities of the arsenite-oxidizing bacteria and the geochemical cycle of arsenic in the tailings of the Shimen realgar mine and gain insights into the microbial mechanisms by which the secondary minerals of the tailings were formed. This work also offers a set of unique arsenite-oxidizing bacteria for basic research of the molecular regulation of arsenite oxidation in bacterial cells and for the environmentally friendly bioremediation of arsenic-contaminated groundwater. PMID:27663031

Functions and Unique Diversity of Genes and Microorganisms Involved in Arsenite Oxidation from the Tailings of a Realgar Mine.

PubMed

Zeng, Xian-Chun; E, Guoji; Wang, Jianing; Wang, Nian; Chen, Xiaoming; Mu, Yao; Li, Hao; Yang, Ye; Liu, Yichen; Wang, Yanxin

2016-12-15

The tailings of the Shimen realgar mine have unique geochemical features. Arsenite oxidation is one of the major biogeochemical processes that occurs in the tailings. However, little is known about the functional and molecular aspects of the microbial community involved in arsenite oxidation. Here, we fully explored the functional and molecular features of the microbial communities from the tailings of the Shimen realgar mine. We collected six samples of tailings from sites A, B, C, D, E, and F. Microcosm assays indicated that all of the six sites contain both chemoautotrophic and heterotrophic arsenite-oxidizing microorganisms; their activities differed considerably from each other. The microbial arsenite-oxidizing activities show a positive correlation with soluble arsenic concentrations. The microbial communities of the six sites contain 40 phyla of bacteria and 2 phyla of archaea that show extremely high diversity. Soluble arsenic, sulfate, pH, and total organic carbon (TOC) are the key environmental factors that shape the microbial communities. We further identified 114 unique arsenite oxidase genes from the samples; all of them code for new or new-type arsenite oxidases. We also isolated 10 novel arsenite oxidizers from the samples, of which 4 are chemoautotrophic and 6 are heterotrophic. These data highlight the unique diversities of the arsenite-oxidizing microorganisms and their oxidase genes from the tailings of the Shimen realgar mine. To the best of our knowledge, this is the first report describing the functional and molecular features of microbial communities from the tailings of a realgar mine. This study focused on the functional and molecular characterizations of microbial communities from the tailings of the Shimen realgar mine. We fully explored, for the first time, the arsenite-oxidizing activities and the functional gene diversities of microorganisms from the tailings, as well as the correlation of the microbial activities/diversities with environmental factors. The findings of this study help us to better understand the diversities of the arsenite-oxidizing bacteria and the geochemical cycle of arsenic in the tailings of the Shimen realgar mine and gain insights into the microbial mechanisms by which the secondary minerals of the tailings were formed. This work also offers a set of unique arsenite-oxidizing bacteria for basic research of the molecular regulation of arsenite oxidation in bacterial cells and for the environmentally friendly bioremediation of arsenic-contaminated groundwater. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Hot-Alkaline DNA Extraction Method for Deep-Subseafloor Archaeal Communities

PubMed Central

Terada, Takeshi; Hoshino, Tatsuhiko; Inagaki, Fumio

2014-01-01

A prerequisite for DNA-based microbial community analysis is even and effective cell disruption for DNA extraction. With a commonly used DNA extraction kit, roughly two-thirds of subseafloor sediment microbial cells remain intact on average (i.e., the cells are not disrupted), indicating that microbial community analyses may be biased at the DNA extraction step, prior to subsequent molecular analyses. To address this issue, we standardized a new DNA extraction method using alkaline treatment and heating. Upon treatment with 1 M NaOH at 98°C for 20 min, over 98% of microbial cells in subseafloor sediment samples collected at different depths were disrupted. However, DNA integrity tests showed that such strong alkaline and heat treatment also cleaved DNA molecules into short fragments that could not be amplified by PCR. Subsequently, we optimized the alkaline and temperature conditions to minimize DNA fragmentation and retain high cell disruption efficiency. The best conditions produced a cell disruption rate of 50 to 80% in subseafloor sediment samples from various depths and retained sufficient DNA integrity for amplification of the complete 16S rRNA gene (i.e., ∼1,500 bp). The optimized method also yielded higher DNA concentrations in all samples tested compared with extractions using a conventional kit-based approach. Comparative molecular analysis using real-time PCR and pyrosequencing of bacterial and archaeal 16S rRNA genes showed that the new method produced an increase in archaeal DNA and its diversity, suggesting that it provides better analytical coverage of subseafloor microbial communities than conventional methods. PMID:24441163

Integrated metagenomics and network analysis of soil microbial community of the forest timberline

PubMed Central

Ding, Junjun; Zhang, Yuguang; Deng, Ye; Cong, Jing; Lu, Hui; Sun, Xin; Yang, Caiyun; Yuan, Tong; Van Nostrand, Joy D.; Li, Diqiang; Zhou, Jizhong; Yang, Yunfeng

2015-01-01

The forest timberline responds quickly and markedly to climate changes, rendering it a ready indicator. Climate warming has caused an upshift of the timberline worldwide. However, the impact on belowground ecosystem and biogeochemical cycles remain elusive. To understand soil microbial ecology of the timberline, we analyzed microbial communities via 16s rRNA Illumina sequencing, a microarray-based tool named GeoChip 4.0 and a random matrix theory-based association network approach. We selected 24 sampling sites at two vegetation belts forming the timberline of Shennongjia Mountain in Hubei Province of China, a region with extraordinarily rich biodiversity. We found that temperature, among all of measured environmental parameters, showed the most significant and extensive linkages with microbial biomass, microbial diversity and composition at both taxonomic and functional gene levels, and microbial association network. Therefore, temperature was the best predictor for microbial community variations in the timberline. Furthermore, abundances of nitrogen cycle and phosphorus cycle genes were concomitant with NH4+-N, NO3−-N and total phosphorus, offering tangible clues to the underlying mechanisms of soil biogeochemical cycles. As the first glimpse at both taxonomic and functional compositions of soil microbial community of the timberline, our findings have major implications for predicting consequences of future timberline upshift. PMID:25613225

Noninvasive analysis of microbiome dynamics in the fruit fly Drosophila melanogaster.

PubMed

Fink, Christine; Staubach, Fabian; Kuenzel, Sven; Baines, John F; Roeder, Thomas

2013-11-01

The diversity and structure of the intestinal microbial community has a strong influence on life history. To understand how hosts and microbes interact, model organisms with comparatively simple microbial communities, such as the fruit fly (Drosophila melanogaster), offer key advantages. However, studies of the Drosophila microbiome are limited to a single point in time, because flies are typically sacrificed for DNA extraction. In order to test whether noninvasive approaches, such as sampling of fly feces, could be a means to assess fly-associated communities over time on the same cohort of flies, we compared the microbial communities of fly feces, dissected fly intestines, and whole flies across three different Drosophila strains. Bacterial species identified in either whole flies or isolated intestines were reproducibly found in feces samples. Although the bacterial communities of feces and intestinal samples were not identical, they shared similarities and obviously the same origin. In contrast to material from whole flies and intestines, feces samples were not compromised by Wolbachia spp. infections, which are widespread in laboratory and wild strains. In a proof-of-principle experiment, we showed that simple nutritional interventions, such as a high-fat diet or short-term starvation, had drastic and long-lasting effects on the micobiome. Thus, the analysis of feces can supplement the toolbox for microbiome studies in Drosophila, unleashing the full potential of such studies in time course experiments where multiple samples from single populations are obtained during aging, development, or experimental manipulations.

Characterization of eubacterial and archaeal community diversity in the pit mud of Chinese Luzhou-flavor liquor by nested PCR-DGGE.

PubMed

Ding, Xiao-Fei; Wu, Chong-De; Zhang, Li-Qiang; Zheng, Jia; Zhou, Rong-Qing

2014-02-01

The aim of this study was to investigate and compare the microbial community structures of eubacteria and archaea in the pit mud of Chinese Luzhou-flavor liquor from the wall (C(w)) and bottom (C(b)) of cellar through nested PCR-denaturing gradient gel electrophoresis (DGGE). The Shannon-Wiener index (H) calculated from the DGGE profiles showed that the community diversities of eubacteria and archaea in samples from C(b) were almost higher than that from C(w). In addition, cluster analysis of the DGGE profiles revealed that some differences were found in the microbial community structure in samples from different locations. The closely relative microorganisms of all eubacterial 16S rRNA gene sequences fell into four phyla (Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria), including 12 genera and 2 uncultured eubacteria. Moreover, 37.1% eubacteria were affiliated with Clostridium. Particularly, genus Acinetobacter was absent in all samples from C(b) but present in all samples from C(w). The closely relative microorganisms of all archaeal 16S rRNA gene sequences fell into four genera, which included Methanobrevibacter, Methanoculleus, Methanobacterium and Methanosaeta, while the dominant archaea in samples from C(w) and C(b) were similar. Results presented in this study provide further understanding of the spatial differences in microbial community structure in the pit mud, and is of great importance for the production and quality improvement of Luzhou-flavor liquor.

Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in Alaska.

PubMed

Deng, Jie; Gu, Yunfu; Zhang, Jin; Xue, Kai; Qin, Yujia; Yuan, Mengting; Yin, Huaqun; He, Zhili; Wu, Liyou; Schuur, Edward A G; Tiedje, James M; Zhou, Jizhong

2015-01-01

Understanding the response of permafrost microbial communities to climate warming is crucial for evaluating ecosystem feedbacks to global change. This study investigated soil bacterial and archaeal communities by Illumina MiSeq sequencing of 16S rRNA gene amplicons across a permafrost thaw gradient at different depths in Alaska with thaw progression for over three decades. Over 4.6 million passing 16S rRNA gene sequences were obtained from a total of 97 samples, corresponding to 61 known classes and 470 genera. Soil depth and the associated soil physical-chemical properties had predominant impacts on the diversity and composition of the microbial communities. Both richness and evenness of the microbial communities decreased with soil depth. Acidobacteria, Verrucomicrobia, Alpha- and Gamma-Proteobacteria dominated the microbial communities in the upper horizon, whereas abundances of Bacteroidetes, Delta-Proteobacteria and Firmicutes increased towards deeper soils. Effects of thaw progression were absent in microbial communities in the near-surface organic soil, probably due to greater temperature variation. Thaw progression decreased the abundances of the majority of the associated taxa in the lower organic soil, but increased the abundances of those in the mineral soil, including groups potentially involved in recalcitrant C degradation (Actinomycetales, Chitinophaga, etc.). The changes in microbial communities may be related to altered soil C sources by thaw progression. Collectively, this study revealed different impacts of thaw in the organic and mineral horizons and suggests the importance of studying both the upper and deeper soils while evaluating microbial responses to permafrost thaw. © 2014 John Wiley & Sons Ltd.

PanFP: Pangenome-based functional profiles for microbial communities

DOE PAGES

Jun, Se -Ran; Hauser, Loren John; Schadt, Christopher Warren; ...

2015-09-26

For decades there has been increasing interest in understanding the relationships between microbial communities and ecosystem functions. Current DNA sequencing technologies allows for the exploration of microbial communities in two principle ways: targeted rRNA gene surveys and shotgun metagenomics. For large study designs, it is often still prohibitively expensive to sequence metagenomes at both the breadth and depth necessary to statistically capture the true functional diversity of a community. Although rRNA gene surveys provide no direct evidence of function, they do provide a reasonable estimation of microbial diversity, while being a very cost effective way to screen samples of interestmore » for later shotgun metagenomic analyses. However, there is a great deal of 16S rRNA gene survey data currently available from diverse environments, and thus a need for tools to infer functional composition of environmental samples based on 16S rRNA gene survey data. As a result, we present a computational method called pangenome based functional profiles (PanFP), which infers functional profiles of microbial communities from 16S rRNA gene survey data for Bacteria and Archaea. PanFP is based on pangenome reconstruction of a 16S rRNA gene operational taxonomic unit (OTU) from known genes and genomes pooled from the OTU s taxonomic lineage. From this lineage, we derive an OTU functional profile by weighting a pangenome s functional profile with the OTUs abundance observed in a given sample. We validated our method by comparing PanFP to the functional profiles obtained from the direct shotgun metagenomic measurement of 65 diverse communities via Spearman correlation coefficients. These correlations improved with increasing sequencing depth, within the range of 0.8 0.9 for the most deeply sequenced Human Microbiome Project mock community samples. PanFP is very similar in performance to another recently released tool, PICRUSt, for almost all of survey data analysed here. But, our method is unique in that any OTU building method can be used, as opposed to being limited to closed reference OTU picking strategies against specific reference sequence databases. In conclusion, we developed an automated computational method, which derives an inferred functional profile based on the 16S rRNA gene surveys of microbial communities. The inferred functional profile provides a cost effective way to study complex ecosystems through predicted comparative functional metagenomes and metadata analysis. All PanFP source code and additional documentation are freely available online at GitHub.« less

PanFP: pangenome-based functional profiles for microbial communities.

PubMed

Jun, Se-Ran; Robeson, Michael S; Hauser, Loren J; Schadt, Christopher W; Gorin, Andrey A

2015-09-26

For decades there has been increasing interest in understanding the relationships between microbial communities and ecosystem functions. Current DNA sequencing technologies allows for the exploration of microbial communities in two principle ways: targeted rRNA gene surveys and shotgun metagenomics. For large study designs, it is often still prohibitively expensive to sequence metagenomes at both the breadth and depth necessary to statistically capture the true functional diversity of a community. Although rRNA gene surveys provide no direct evidence of function, they do provide a reasonable estimation of microbial diversity, while being a very cost-effective way to screen samples of interest for later shotgun metagenomic analyses. However, there is a great deal of 16S rRNA gene survey data currently available from diverse environments, and thus a need for tools to infer functional composition of environmental samples based on 16S rRNA gene survey data. We present a computational method called pangenome-based functional profiles (PanFP), which infers functional profiles of microbial communities from 16S rRNA gene survey data for Bacteria and Archaea. PanFP is based on pangenome reconstruction of a 16S rRNA gene operational taxonomic unit (OTU) from known genes and genomes pooled from the OTU's taxonomic lineage. From this lineage, we derive an OTU functional profile by weighting a pangenome's functional profile with the OTUs abundance observed in a given sample. We validated our method by comparing PanFP to the functional profiles obtained from the direct shotgun metagenomic measurement of 65 diverse communities via Spearman correlation coefficients. These correlations improved with increasing sequencing depth, within the range of 0.8-0.9 for the most deeply sequenced Human Microbiome Project mock community samples. PanFP is very similar in performance to another recently released tool, PICRUSt, for almost all of survey data analysed here. But, our method is unique in that any OTU building method can be used, as opposed to being limited to closed-reference OTU picking strategies against specific reference sequence databases. We developed an automated computational method, which derives an inferred functional profile based on the 16S rRNA gene surveys of microbial communities. The inferred functional profile provides a cost effective way to study complex ecosystems through predicted comparative functional metagenomes and metadata analysis. All PanFP source code and additional documentation are freely available online at GitHub ( https://github.com/srjun/PanFP ).

Parameters of microbial respiration in soils of the impact zone of a mineral fertilizer factory

NASA Astrophysics Data System (ADS)

Zhukova, A. D.; Khomyakov, D. M.

2015-08-01

The carbon content in the microbial biomass and the microbial production of CO2 (the biological component of soil respiration) were determined in the upper layer (0-10 cm) of soils in the impact zone of the OJSC Voskresensk Mineral Fertilizers, one of the largest factories manufacturing mineral fertilizers in Russia. Statistical characteristics and schematic distribution of the biological parameters in the soil cover of the impact zone were analyzed. The degree of disturbance of microbial communities in the studied objects varied from weak to medium. The maximum value (0.44) was observed on the sampling plot 4 km away from the factory and 0.5 km away from the place of waste (phosphogypsum) storage. Significantly lower carbon content in the microbial biomass and its specific respiration were recorded in the agrosoddy-podzolic soil as compared with the alluvial soil sampled at the same distance from the plant. The effects of potential soil pollutants (fluorine, sulfur, cadmium, and stable strontium) on the characteristics of soil microbial communities were described with reliable regression equations.

A communal catalogue reveals Earth’s multiscale microbial diversity

DOE PAGES

Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel; ...

2017-11-01

Our growing awareness of the importance and diversity of the microbial world contrasts starkly with our limited understanding of its fundamental structure. Despite remarkable advances in DNA sequence generation, a lack of standardized protocols and common analytical framework impede useful comparison between studies, hindering development of global inferences about microbial life on Earth. Here, we show that with coordinated protocols, exact microbial 16S rRNA gene sequences can be followed across scores of individual studies, revealing patterns of diversity, community structure, and life history strategy at a planetary scale. Using 27,751 crowdsourced environmental samples comprising more than 2.2 billion reads, wemore » find sharp divides between host-associated and free-living communities. We show that the distribution of taxonomic and sequence diversity follows consistent trends across samples types and along gradients of environmental parameters, highlighting some of the global evolutionary patterns and ecological principles that underpin Earth’s microbiome. Here, this dataset provides the most complete environmental survey of our microbial world to date, and serves as a growing reference to provide immediate global context to future microbial surveys.« less

A communal catalogue reveals Earth’s multiscale microbial diversity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel

Our growing awareness of the importance and diversity of the microbial world contrasts starkly with our limited understanding of its fundamental structure. Despite remarkable advances in DNA sequence generation, a lack of standardized protocols and common analytical framework impede useful comparison between studies, hindering development of global inferences about microbial life on Earth. Here, we show that with coordinated protocols, exact microbial 16S rRNA gene sequences can be followed across scores of individual studies, revealing patterns of diversity, community structure, and life history strategy at a planetary scale. Using 27,751 crowdsourced environmental samples comprising more than 2.2 billion reads, wemore » find sharp divides between host-associated and free-living communities. We show that the distribution of taxonomic and sequence diversity follows consistent trends across samples types and along gradients of environmental parameters, highlighting some of the global evolutionary patterns and ecological principles that underpin Earth’s microbiome. Here, this dataset provides the most complete environmental survey of our microbial world to date, and serves as a growing reference to provide immediate global context to future microbial surveys.« less

Molecular Phylogenetic Diversity and Spatial Distribution of Bacterial Communities in Cooling Stage during Swine Manure Composting

PubMed Central

Guo, Yan; Zhang, Jinliang; Yan, Yongfeng; Wu, Jian; Zhu, Nengwu; Deng, Changyan

2015-01-01

Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and subsequent sub-cloning and sequencing were used in this study to analyze the molecular phylogenetic diversity and spatial distribution of bacterial communities in different spatial locations during the cooling stage of composted swine manure. Total microbial DNA was extracted, and bacterial near full-length 16S rRNA genes were subsequently amplified, cloned, RFLP-screened, and sequenced. A total of 420 positive clones were classified by RFLP and near-full-length 16S rDNA sequences. Approximately 48 operational taxonomic units (OTUs) were found among 139 positive clones from the superstratum sample; 26 among 149 were from the middle-level sample and 35 among 132 were from the substrate sample. Thermobifida fusca was common in the superstratum layer of the pile. Some Bacillus spp. were remarkable in the middle-level layer, and Clostridium sp. was dominant in the substrate layer. Among 109 OTUs, 99 displayed homology with those in the GenBank database. Ten OTUs were not closely related to any known species. The superstratum sample had the highest microbial diversity, and different and distinct bacterial communities were detected in the three different layers. This study demonstrated the spatial characteristics of the microbial community distribution in the cooling stage of swine manure compost. PMID:25925066

Microbial community composition and dynamics of moving bed biofilm reactor systems treating municipal sewage.

PubMed

Biswas, Kristi; Turner, Susan J

2012-02-01

Moving bed biofilm reactor (MBBR) systems are increasingly used for municipal and industrial wastewater treatment, yet in contrast to activated sludge (AS) systems, little is known about their constituent microbial communities. This study investigated the community composition of two municipal MBBR wastewater treatment plants (WWTPs) in Wellington, New Zealand. Monthly samples comprising biofilm and suspended biomass were collected over a 12-month period. Bacterial and archaeal community composition was determined using a full-cycle community approach, including analysis of 16S rRNA gene libraries, fluorescence in situ hybridization (FISH) and automated ribosomal intergenic spacer analysis (ARISA). Differences in microbial community structure and abundance were observed between the two WWTPs and between biofilm and suspended biomass. Biofilms from both plants were dominated by Clostridia and sulfate-reducing members of the Deltaproteobacteria (SRBs). FISH analyses indicated morphological differences in the Deltaproteobacteria detected at the two plants and also revealed distinctive clustering between SRBs and members of the Methanosarcinales, which were the only Archaea detected and were present in low abundance (<5%). Biovolume estimates of the SRBs were higher in biofilm samples from one of the WWTPs which receives both domestic and industrial waste and is influenced by seawater infiltration. The suspended communities from both plants were diverse and dominated by aerobic members of the Gammaproteobacteria and Betaproteobacteria. This study represents the first detailed analysis of microbial communities in full-scale MBBR systems and indicates that this process selects for distinctive biofilm and planktonic communities, both of which differ from those found in conventional AS systems.

Linking Spatial Structure and Community-Level Biotic Interactions through Cooccurrence and Time Series Modeling of the Human Intestinal Microbiota.

PubMed

de Muinck, Eric J; Lundin, Knut E A; Trosvik, Pål

2017-01-01

The gastrointestinal (GI) microbiome is a densely populated ecosystem where dynamics are determined by interactions between microbial community members, as well as host factors. The spatial organization of this system is thought to be important in human health, yet this aspect of our resident microbiome is still poorly understood. In this study, we report significant spatial structure of the GI microbiota, and we identify general categories of spatial patterning in the distribution of microbial taxa along a healthy human GI tract. We further estimate the biotic interaction structure in the GI microbiota, both through time series and cooccurrence modeling of microbial community data derived from a large number of sequentially collected fecal samples. Comparison of these two approaches showed that species pairs involved in significant negative interactions had strong positive contemporaneous correlations and vice versa, while for species pairs without significant interactions, contemporaneous correlations were distributed around zero. We observed similar patterns when comparing these models to the spatial correlations between taxa identified in the adherent microbiota. This suggests that colocalization of microbial taxon pairs, and thus the spatial organization of the GI microbiota, is driven, at least in part, by direct or indirect biotic interactions. Thus, our study can provide a basis for an ecological interpretation of the biogeography of the human gut. IMPORTANCE The human gut microbiome is the subject of intense study due to its importance in health and disease. The majority of these studies have been based on the analysis of feces. However, little is known about how the microbial composition in fecal samples relates to the spatial distribution of microbial taxa along the gastrointestinal tract. By characterizing the microbial content both in intestinal tissue samples and in fecal samples obtained daily, we provide a conceptual framework for how the spatial structure relates to biotic interactions on the community level. We further describe general categories of spatial distribution patterns and identify taxa conforming to these categories. To our knowledge, this is the first study combining spatial and temporal analyses of the human gut microbiome. This type of analysis can be used for identifying candidate probiotics and designing strategies for clinical intervention.

Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient

PubMed Central

Fortunato, Caroline S.; Crump, Byron C.

2015-01-01

Microbial communities mediate the biogeochemical cycles that drive ecosystems, and it is important to understand how these communities are affected by changing environmental conditions, especially in complex coastal zones. As fresh and marine waters mix in estuaries and river plumes, the salinity, temperature, and nutrient gradients that are generated strongly influence bacterioplankton community structure, yet, a parallel change in functional diversity has not been described. Metagenomic and metatranscriptomic analyses were conducted on five water samples spanning the salinity gradient of the Columbia River coastal margin, including river, estuary, plume, and ocean, in August 2010. Samples were pre-filtered through 3 μm filters and collected on 0.2 μm filters, thus results were focused on changes among free-living microbial communities. Results from metagenomic 16S rRNA sequences showed taxonomically distinct bacterial communities in river, estuary, and coastal ocean. Despite the strong salinity gradient observed over sampling locations (0 to 33), the functional gene profiles in the metagenomes were very similar from river to ocean with an average similarity of 82%. The metatranscriptomes, however, had an average similarity of 31%. Although differences were few among the metagenomes, we observed a change from river to ocean in the abundance of genes encoding for catabolic pathways, osmoregulators, and metal transporters. Additionally, genes specifying both bacterial oxygenic and anoxygenic photosynthesis were abundant and expressed in the estuary and plume. Denitrification genes were found throughout the Columbia River coastal margin, and most highly expressed in the estuary. Across a river to ocean gradient, the free-living microbial community followed three different patterns of diversity: 1) the taxonomy of the community changed strongly with salinity, 2) metabolic potential was highly similar across samples, with few differences in functional gene abundance from river to ocean, and 3) gene expression was highly variable and generally was independent of changes in salinity. PMID:26536246

Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient.

PubMed

Fortunato, Caroline S; Crump, Byron C

2015-01-01

Microbial communities mediate the biogeochemical cycles that drive ecosystems, and it is important to understand how these communities are affected by changing environmental conditions, especially in complex coastal zones. As fresh and marine waters mix in estuaries and river plumes, the salinity, temperature, and nutrient gradients that are generated strongly influence bacterioplankton community structure, yet, a parallel change in functional diversity has not been described. Metagenomic and metatranscriptomic analyses were conducted on five water samples spanning the salinity gradient of the Columbia River coastal margin, including river, estuary, plume, and ocean, in August 2010. Samples were pre-filtered through 3 μm filters and collected on 0.2 μm filters, thus results were focused on changes among free-living microbial communities. Results from metagenomic 16S rRNA sequences showed taxonomically distinct bacterial communities in river, estuary, and coastal ocean. Despite the strong salinity gradient observed over sampling locations (0 to 33), the functional gene profiles in the metagenomes were very similar from river to ocean with an average similarity of 82%. The metatranscriptomes, however, had an average similarity of 31%. Although differences were few among the metagenomes, we observed a change from river to ocean in the abundance of genes encoding for catabolic pathways, osmoregulators, and metal transporters. Additionally, genes specifying both bacterial oxygenic and anoxygenic photosynthesis were abundant and expressed in the estuary and plume. Denitrification genes were found throughout the Columbia River coastal margin, and most highly expressed in the estuary. Across a river to ocean gradient, the free-living microbial community followed three different patterns of diversity: 1) the taxonomy of the community changed strongly with salinity, 2) metabolic potential was highly similar across samples, with few differences in functional gene abundance from river to ocean, and 3) gene expression was highly variable and generally was independent of changes in salinity.

Bacterial diversity of floor drain biofilms and drain waters in a Listeria monocytogenes contaminated food processing environment.

PubMed

Dzieciol, Monika; Schornsteiner, Elisa; Muhterem-Uyar, Meryem; Stessl, Beatrix; Wagner, Martin; Schmitz-Esser, Stephan

2016-04-16

Sanitation protocols are applied on a daily basis in food processing facilities to prevent the risk of cross-contamination with spoilage organisms. Floor drain water serves along with product-associated samples (slicer dust, brine or cheese smear) as an important hygiene indicator in monitoring Listeria monocytogenes in food processing facilities. Microbial communities of floor drains are representative for each processing area and are influenced to a large degree by food residues, liquid effluents and washing water. The microbial communities of drain water are steadily changing, whereas drain biofilms provide more stable niches. Bacterial communities of four floor drains were characterized using 16S rRNA gene pyrosequencing to better understand the composition and exchange of drain water and drain biofilm communities. Furthermore, the L. monocytogenes contamination status of each floor drain was determined by applying cultivation-independent real-time PCR quantification and cultivation-dependent detection according to ISO11290-1. Pyrosequencing of 16S rRNA genes of drain water and drain biofilm bacterial communities yielded 50,611 reads, which were clustered into 641 operational taxonomic units (OTUs), affiliated to 16 phyla dominated by Proteobacteria, Firmicutes and Bacteroidetes. The most abundant OTUs represented either product- (Lactococcus lactis) or fermentation- and food spoilage-associated phylotypes (Pseudomonas mucidolens, Pseudomonas fragi, Leuconostoc citreum, and Acetobacter tropicalis). The microbial communities in DW and DB samples were distinct in each sample type and throughout the whole processing plant, indicating the presence of indigenous specific microbial communities in each processing compartment. The microbiota of drain biofilms was largely different from the microbiota of the drain water. A sampling approach based on drain water alone may thus only provide reliable information on planktonic bacterial cells but might not allow conclusions on the bacterial composition of the microbiota in biofilms. Copyright © 2016. Published by Elsevier B.V.

Microbial community pattern detection in human body habitats via ensemble clustering framework.

PubMed

Yang, Peng; Su, Xiaoquan; Ou-Yang, Le; Chua, Hon-Nian; Li, Xiao-Li; Ning, Kang

2014-01-01

The human habitat is a host where microbial species evolve, function, and continue to evolve. Elucidating how microbial communities respond to human habitats is a fundamental and critical task, as establishing baselines of human microbiome is essential in understanding its role in human disease and health. Recent studies on healthy human microbiome focus on particular body habitats, assuming that microbiome develop similar structural patterns to perform similar ecosystem function under same environmental conditions. However, current studies usually overlook a complex and interconnected landscape of human microbiome and limit the ability in particular body habitats with learning models of specific criterion. Therefore, these methods could not capture the real-world underlying microbial patterns effectively. To obtain a comprehensive view, we propose a novel ensemble clustering framework to mine the structure of microbial community pattern on large-scale metagenomic data. Particularly, we first build a microbial similarity network via integrating 1920 metagenomic samples from three body habitats of healthy adults. Then a novel symmetric Nonnegative Matrix Factorization (NMF) based ensemble model is proposed and applied onto the network to detect clustering pattern. Extensive experiments are conducted to evaluate the effectiveness of our model on deriving microbial community with respect to body habitat and host gender. From clustering results, we observed that body habitat exhibits a strong bound but non-unique microbial structural pattern. Meanwhile, human microbiome reveals different degree of structural variations over body habitat and host gender. In summary, our ensemble clustering framework could efficiently explore integrated clustering results to accurately identify microbial communities, and provide a comprehensive view for a set of microbial communities. The clustering results indicate that structure of human microbiome is varied systematically across body habitats and host genders. Such trends depict an integrated biography of microbial communities, which offer a new insight towards uncovering pathogenic model of human microbiome.

Microbial community pattern detection in human body habitats via ensemble clustering framework

PubMed Central

2014-01-01

Background The human habitat is a host where microbial species evolve, function, and continue to evolve. Elucidating how microbial communities respond to human habitats is a fundamental and critical task, as establishing baselines of human microbiome is essential in understanding its role in human disease and health. Recent studies on healthy human microbiome focus on particular body habitats, assuming that microbiome develop similar structural patterns to perform similar ecosystem function under same environmental conditions. However, current studies usually overlook a complex and interconnected landscape of human microbiome and limit the ability in particular body habitats with learning models of specific criterion. Therefore, these methods could not capture the real-world underlying microbial patterns effectively. Results To obtain a comprehensive view, we propose a novel ensemble clustering framework to mine the structure of microbial community pattern on large-scale metagenomic data. Particularly, we first build a microbial similarity network via integrating 1920 metagenomic samples from three body habitats of healthy adults. Then a novel symmetric Nonnegative Matrix Factorization (NMF) based ensemble model is proposed and applied onto the network to detect clustering pattern. Extensive experiments are conducted to evaluate the effectiveness of our model on deriving microbial community with respect to body habitat and host gender. From clustering results, we observed that body habitat exhibits a strong bound but non-unique microbial structural pattern. Meanwhile, human microbiome reveals different degree of structural variations over body habitat and host gender. Conclusions In summary, our ensemble clustering framework could efficiently explore integrated clustering results to accurately identify microbial communities, and provide a comprehensive view for a set of microbial communities. The clustering results indicate that structure of human microbiome is varied systematically across body habitats and host genders. Such trends depict an integrated biography of microbial communities, which offer a new insight towards uncovering pathogenic model of human microbiome. PMID:25521415

Effect of Sodium Bisulfite Injection on the Microbial Community Composition in a Brackish-Water-Transporting Pipeline▿†

PubMed Central

Park, Hyung Soo; Chatterjee, Indranil; Dong, Xiaoli; Wang, Sheng-Hung; Sensen, Christoph W.; Caffrey, Sean M.; Jack, Thomas R.; Boivin, Joe; Voordouw, Gerrit

2011-01-01

Pipelines transporting brackish subsurface water, used in the production of bitumen by steam-assisted gravity drainage, are subject to frequent corrosion failures despite the addition of the oxygen scavenger sodium bisulfite (SBS). Pyrosequencing of 16S rRNA genes was used to determine the microbial community composition for planktonic samples of transported water and for sessile samples of pipe-associated solids (PAS) scraped from pipeline cutouts representing corrosion failures. These were obtained from upstream (PAS-616P) and downstream (PAS-821TP and PAS-821LP, collected under rapid-flow and stagnant conditions, respectively) of the SBS injection point. Most transported water samples had a large fraction (1.8% to 97% of pyrosequencing reads) of Pseudomonas not found in sessile pipe samples. The sessile population of PAS-616P had methanogens (Methanobacteriaceae) as the main (56%) community component, whereas Deltaproteobacteria of the genera Desulfomicrobium and Desulfocapsa were not detected. In contrast, PAS-821TP and PAS-821LP had lower fractions (41% and 0.6%) of Methanobacteriaceae archaea but increased fractions of sulfate-reducing Desulfomicrobium (18% and 48%) and of bisulfite-disproportionating Desulfocapsa (35% and 22%) bacteria. Hence, SBS injection strongly changed the sessile microbial community populations. X-ray diffraction analysis of pipeline scale indicated that iron carbonate was present both upstream and downstream, whereas iron sulfide and sulfur were found only downstream of the SBS injection point, suggesting a contribution of the bisulfite-disproportionating and sulfate-reducing bacteria in the scale to iron corrosion. Incubation of iron coupons with pipeline waters indicated iron corrosion coupled to the formation of methane. Hence, both methanogenic and sulfidogenic microbial communities contributed to corrosion of pipelines transporting these brackish waters. PMID:21856836

The Earth Microbiome Project and modeling the planets microbial potential (Invited)

NASA Astrophysics Data System (ADS)

Gilbert, J. A.

2013-12-01

The understanding of Earth's climate and ecology requires multiscale observations of the biosphere, of which microbial life are a major component. However, to acquire and process physical samples of soil, water and air that comprise the appropriate spatial and temporal resolution to capture the immense variation in microbial dynamics, would require a herculean effort and immense financial resources dwarfing even the most ambitious projects to date. To overcome this hurdle we created the Earth Microbiome Project, a crowd-sourced effort to acquire physical samples from researchers around the world that are, importantly, contextualized with physical, chemical and biological data detailing the environmental properties of that sample in the location and time it was acquired. The EMP leverages these existing efforts to target a systematic analysis of microbial taxonomic and functional dynamics across a vast array of environmental parameter gradients. The EMP captures the environmental gradients, location, time and sampling protocol information about every sample donated by our valued collaborators. Physical samples are then processed using a standardized DNA extraction, PCR, and shotgun sequencing protocol to generate comparable data regarding the microbial community structure and function in each sample. To date we have processed >17,000 samples from 40 different biomes. One of the key goals of the EMP is to map the spatiotemporal variability of microbial communities to capture the changes in important functional processes that need to be appropriately expressed in models to provide reliable forecasts of ecosystem phenotype across our changing planet. This is essential if we are to develop economically sound strategies to be good stewards of our Earth. The EMP recognizes that environments are comprised of complex sets of interdependent parameters and that the development of useful predictive computational models of both terrestrial and atmospheric systems requires recognition and accommodation of sources of uncertainty.

Structural and functional diversity of microbial communities from a lake sediment contaminated with trenbolone, an endocrine-disrupting chemical.

PubMed

Radl, Viviane; Pritsch, Karin; Munch, Jean Charles; Schloter, Michael

2005-09-01

Effects of trenbolone (TBOH), a hormone used in cattle production, on the structure and function of microbial communities in a fresh water sediment from a lake in Southern Germany were studied in a microcosm experiment. The microbial community structure and the total gene pool of the sediment, assessed by 16S rRNA/rDNA and RAPD fingerprint analysis, respectively, were not significantly affected by TBOH. In contrast, the N-acetyl-glucosaminidase activity was almost 50% lower in TBOH treated samples (P<0.05). Also, the substrate utilization potential, measured using the BIOLOG system, was reduced after TBOH treatment. Interestingly, this potential did not recover at the end of the experiment, i.e. 19 days after the addition of the chemical. Repeated application of TBOH did not lead to an additional reduction in the substrate utilization potential. Overall results indicate that microbial community function was more sensitive to TBOH treatment than the community structure and the total gene pool.

Pyrosequencing analysis yields comprehensive assessment of microbial communities in pilot-scale two-stage membrane biofilm reactors.

PubMed

Ontiveros-Valencia, Aura; Tang, Youneng; Zhao, He-Ping; Friese, David; Overstreet, Ryan; Smith, Jennifer; Evans, Patrick; Rittmann, Bruce E; Krajmalnik-Brown, Rosa

2014-07-01

We studied the microbial community structure of pilot two-stage membrane biofilm reactors (MBfRs) designed to reduce nitrate (NO3(-)) and perchlorate (ClO4(-)) in contaminated groundwater. The groundwater also contained oxygen (O2) and sulfate (SO4(2-)), which became important electron sinks that affected the NO3(-) and ClO4(-) removal rates. Using pyrosequencing, we elucidated how important phylotypes of each "primary" microbial group, i.e., denitrifying bacteria (DB), perchlorate-reducing bacteria (PRB), and sulfate-reducing bacteria (SRB), responded to changes in electron-acceptor loading. UniFrac, principal coordinate analysis (PCoA), and diversity analyses documented that the microbial community of biofilms sampled when the MBfRs had a high acceptor loading were phylogenetically distant from and less diverse than the microbial community of biofilm samples with lower acceptor loadings. Diminished acceptor loading led to SO4(2-) reduction in the lag MBfR, which allowed Desulfovibrionales (an SRB) and Thiothrichales (sulfur-oxidizers) to thrive through S cycling. As a result of this cooperative relationship, they competed effectively with DB/PRB phylotypes such as Xanthomonadales and Rhodobacterales. Thus, pyrosequencing illustrated that while DB, PRB, and SRB responded predictably to changes in acceptor loading, a decrease in total acceptor loading led to important shifts within the "primary" groups, the onset of other members (e.g., Thiothrichales), and overall greater diversity.

Soil organic carbon (SOC) accumulation in rice paddies under long-term agro-ecosystem experiments in southern China - VI. Changes in microbial community structure and respiratory activity

NASA Astrophysics Data System (ADS)

Liu, D.; Liu, X.; Liu, Y.; Li, L.; Pan, G.; Crowley, D.; Tippkötter, R.

2011-02-01

Biological stabilization within accumulated soil organic carbon (SOC) has not been well understood, while its role in physical and chemical protection as well as of chemical recalcitrance had been addressed in Chinese rice paddies. In this study, topsoil samples were collected and respiratory activity measured in situ following rice harvest under different fertilization treatments of three long-term experimental sites across southern China in 2009. The SOC contents, microbial biomass carbon (SMBC) and nitrogen (SMBN) were analysed using chemical digestion and microbial community structure assessment via clony dilute plate counting methods. While SOC contents were consistently higher under compound chemical fertilization (Comp-Fert) or combined organic and inorganic fertilization (Comb-Fert) compared to N fertilization only (N-Fert), there was significantly higher fungal-bacterial ratio under Comb-Fert than under N-Fert and Comp-Fert. When subtracting the background effect under no fertilization treatment (Non-Fert), the increase both in SMBC and SMBN under fertilization treatment was found very significantly correlated to the increase in SOC over controls across the sites. Also, the ratio of culturable fungal to bacterial population numbers (F/B ratio) was well correlated with soil organic carbon contents in all samples across the sites studied. SOC accumulation favoured a build-up the microbial community with increasing fungal dominance in the rice paddies under fertilization treatments. While soil respiration rates were high under Comb-Fert as a result of enhanced microbial community build-up, the specific soil respiratory activity based on microbial biomass carbon was found in a significantly negatively correlation with the SOC contents for overall samples. Thus, a fungal-dominated microbial community seemed to slow SOC turnover, thereby favouring SOC accumulation under Comp-Fert or under Comb-Fert in the rice paddies. Therefore, the biological stabilization process is of importance in SOC sequestration in the rice paddies, operating with physical and chemical protection and chemical recalcitrance. However, sufficient understanding and prediction of SOM dynamics needs further quantitative characterization of the simultaneous operation of several mechanisms.

Microbial community analysis and biodeterioration of waterlogged archaeological wood from the Nanhai No. 1 shipwreck during storage.

PubMed

Liu, Zijun; Fu, Tongtong; Hu, Cuiting; Shen, Dawa; Macchioni, Nicola; Sozzi, Lorena; Chen, Yue; Liu, Jie; Tian, Xingling; Ge, Qinya; Feng, Zhengteng; Liu, Huiru; Zhang, Zhiguo; Pan, Jiao

2018-05-08

Wooden shipwrecks are a significant part of the underwater cultural heritage. In 2007, the Nanhai No. 1 shipwreck was salvaged from the seabed and moved into the Marine Silk Road Museum, where it is still stored in a water tank. We analysed the microbial communities colonizing the hull surface of the Nanhai No. 1 shipwreck during storage. Six samples exposed to air were collected from different spots of the ship that exhibited obvious microbial plaques. High-throughput sequencing revealed the bacterial community includes both aquatic and terrestrial species, while in the fungal community, Fusarium was the most abundant genus across all samples and accounted for 84.91% to 98.40% of the total community composition. Two Fusarium species were isolated from the samples and were identified as F. solani and F. oxysporum. Both of the isolates were able to degrade cellulose, but only F. solani had the ability to degrade lignin. Antimicrobial efficacy in inhibiting the growth of Fusarium was assessed with five kinds of biocides, and isothiazolinones exhibited specific inhibition of Fusarium growth. These results provide critical background information to protect and reduce the biodegradation and destruction of this important historical shipwreck, and inform efforts to protect other similar artifacts.

Microbial communities at the borehole observatory on the Costa Rica Rift flank (Ocean Drilling Program Hole 896A).

PubMed

Nigro, Lisa M; Harris, Kate; Orcutt, Beth N; Hyde, Andrew; Clayton-Luce, Samuel; Becker, Keir; Teske, Andreas

2012-01-01

The microbiology of subsurface, hydrothermally influenced basaltic crust flanking mid-ocean ridges has remained understudied, due to the difficulty in accessing the subsurface environment. The instrumented boreholes resulting from scientific ocean drilling offer access to samples of the formation fluids circulating through oceanic crust. We analyzed the phylogenetic diversity of bacterial communities of fluid and microbial mat samples collected in situ from the observatory at Ocean Drilling Program Hole 896A, drilled into ~6.5 million-year-old basaltic crust on the flank of the Costa Rica Rift in the equatorial Pacific Ocean. Bacterial 16S rRNA gene sequences recovered from borehole fluid and from a microbial mat coating the outer surface of the fluid port revealed both unique and shared phylotypes. The dominant bacterial clones from both samples were related to the autotrophic, sulfur-oxidizing genus Thiomicrospira. Both samples yielded diverse gamma- and alphaproteobacterial phylotypes, as well as members of the Bacteroidetes, Planctomycetes, and Verrucomicrobia. Analysis of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) genes (cbbL and cbbM) from the sampling port mat and from the borehole fluid demonstrated autotrophic carbon assimilation potential for in situ microbial communities; most cbbL genes were related to those of the sulfur-oxidizing genera Thioalkalivibrio and Thiomicrospira, and cbbM genes were affiliated with uncultured phylotypes from hydrothermal vent plumes and marine sediments. Several 16S rRNA gene phylotypes from the 896A observatory grouped with phylotypes recovered from seawater-exposed basalts and sulfide deposits at inactive hydrothermal vents, but there is little overlap with hydrothermally influenced basaltic boreholes 1026B and U1301A on the Juan de Fuca Ridge flank, suggesting that site-specific characteristics of Hole 896A (i.e., seawater mixing into borehole fluids) affect the microbial community composition.

Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank

PubMed Central

Leite, Márcio F. A.; Pan, Yao; Bloem, Jaap; Berge, Hein ten; Kuramae, Eiko E.

2017-01-01

Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments, which range in Carbon/Nitrogen (C/N) ratio and degradability, on the soil microbiome in a mesocosm study at 32, 69 and 132 days. Soil samples were collected to determine community structure (assessed by 16S and 18S rRNA gene sequences), microbial biomass (fungi and bacteria), microbial activity (leucine incorporation and active hyphal length), and carbon and nitrogen mineralization rates. We considered the microbial soil DNA as the microbial seedbank. High C/N ratio favored fungal presence, while low C/N favored dominance of bacterial populations. Our results suggest that organic amendments shape the soil microbial community structure through a feedback mechanism by which microbial activity responds to changing organic inputs and rearranges composition of the microbial seedbank. We hypothesize that the microbial seedbank composition responds to changing organic inputs according to the resistance and resilience of individual species, while changes in microbial activity may result in increases or decreases in availability of various soil nutrients that affect plant nutrient uptake. PMID:28198425

Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank.

PubMed

Leite, Márcio F A; Pan, Yao; Bloem, Jaap; Berge, Hein Ten; Kuramae, Eiko E

2017-02-15

Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments, which range in Carbon/Nitrogen (C/N) ratio and degradability, on the soil microbiome in a mesocosm study at 32, 69 and 132 days. Soil samples were collected to determine community structure (assessed by 16S and 18S rRNA gene sequences), microbial biomass (fungi and bacteria), microbial activity (leucine incorporation and active hyphal length), and carbon and nitrogen mineralization rates. We considered the microbial soil DNA as the microbial seedbank. High C/N ratio favored fungal presence, while low C/N favored dominance of bacterial populations. Our results suggest that organic amendments shape the soil microbial community structure through a feedback mechanism by which microbial activity responds to changing organic inputs and rearranges composition of the microbial seedbank. We hypothesize that the microbial seedbank composition responds to changing organic inputs according to the resistance and resilience of individual species, while changes in microbial activity may result in increases or decreases in availability of various soil nutrients that affect plant nutrient uptake.

Seasonal induced changes in spinach rhizosphere microbial community structure with varying salinity and drought.

PubMed

Mark Ibekwe, A; Ors, Selda; Ferreira, Jorge F S; Liu, Xuan; Suarez, Donald L

2017-02-01

Salinity is a common problem under irrigated agriculture, especially in low rainfall and high evaporative demand areas of southwestern United States and other semi-arid regions around the world. However, studies on salinity effects on soil microbial communities are relatively few while the effects of irrigation-induced salinity on soil chemical and physical properties and plant growth are well documented. In this study, we examined the effects of salinity, temperature, and temporal variability on soil and rhizosphere microbial communities in sand tanks irrigated with prepared solutions designed to simulate saline wastewater. Three sets of experiments with spinach (Spinacia oleracea L., cv. Racoon) were conducted under saline water during different time periods (early winter, late spring, and early summer). Bacterial 16S V4 rDNA region was amplified utilizing fusion primers designed against the surrounding conserved regions using MiSeq® Illumina sequencing platform. Across the two sample types, bacteria were relatively dominant among three phyla-the Proteobacteria, Cyanobacteria, and Bacteroidetes-accounted for 77.1% of taxa detected in the rhizosphere, while Proteobacteria, Bacteroidetes, and Actinobacteria accounted for 55.1% of taxa detected in soil. The results were analyzed using UniFrac coupled with principal coordinate analysis (PCoA) to compare diversity, abundance, community structure, and specific bacterial groups in soil and rhizosphere samples. Permutational analysis of variance (PERMANOVA) analysis showed that soil temperature (P=0.001), rhizosphere temperature (P=0.001), rhizosphere salinity (P=0.032), and evapotranspiration (P=0.002) significantly affected beta diversity of soil and rhizosphere microbial communities. Furthermore, salinity had marginal effects (P=0.078) on soil beta diversity. However, temporal variability differentially affected rhizosphere microbial communities irrigated with saline wastewater. Therefore, microbial communities in soils impacted by saline irrigation water respond differently to irrigation water quality and season of application due to temporal effects associated with temperature. Published by Elsevier B.V.

Association between degradation of pharmaceuticals and endocrine-disrupting compounds and microbial communities along a treated wastewater effluent gradient in Lake Mead

USGS Publications Warehouse

Blunt, Susanna M.; Sackett, Joshua D.; Rosen, Michael R.; Benotti, Mark J.; Trenholm, Rebecca A.; Vanderford, Brett J.; Hedlund, Brian P.; Moser, Duane P.

2018-01-01

The role of microbial communities in the degradation of trace organic contaminants in the environment is little understood. In this study, the biotransformation potential of 27 pharmaceuticals and endocrine-disrupting compounds was examined in parallel with a characterization of the native microbial community in water samples from four sites variously impacted by urban run-off and wastewater discharge in Lake Mead, Nevada and Arizona, USA. Samples included relatively pristine Colorado River water at the upper end of the lake, nearly pure tertiary-treated municipal wastewater entering via the Las Vegas Wash, and waters of mixed influence (Las Vegas Bay and Boulder Basin), which represented a gradient of treated wastewater effluent impact. Microbial diversity analysis based on 16S rRNA gene censuses revealed the community at this site to be distinct from the less urban-impacted locations, although all sites were similar in overall diversity and richness. Similarly, Biolog EcoPlate assays demonstrated that the microbial community at Las Vegas Wash was the most metabolically versatile and active. Organic contaminants added as a mixture to laboratory microcosms were more rapidly and completely degraded in the most wastewater-impacted sites (Las Vegas Wash and Las Vegas Bay), with the majority exhibiting shorter half-lives than at the other sites or in a bacteriostatic control. Although the reasons for enhanced degradation capacity in the wastewater-impacted sites remain to be established, these data are consistent with the acclimatization of native microorganisms (either through changes in community structure or metabolic regulation) to effluent-derived trace contaminants. This study suggests that in urban, wastewater-impacted watersheds, prior exposure to organic contaminants fundamentally alters the structure and function of microbial communities, which in turn translates into greater potential for the natural attenuation of these compounds compared to more pristine sites.

Association between degradation of pharmaceuticals and endocrine-disrupting compounds and microbial communities along a treated wastewater effluent gradient in Lake Mead.

PubMed

Blunt, Susanna M; Sackett, Joshua D; Rosen, Michael R; Benotti, Mark J; Trenholm, Rebecca A; Vanderford, Brett J; Hedlund, Brian P; Moser, Duane P

2018-05-01

The role of microbial communities in the degradation of trace organic contaminants in the environment is little understood. In this study, the biotransformation potential of 27 pharmaceuticals and endocrine-disrupting compounds was examined in parallel with a characterization of the native microbial community in water samples from four sites variously impacted by urban run-off and wastewater discharge in Lake Mead, Nevada and Arizona, USA. Samples included relatively pristine Colorado River water at the upper end of the lake, nearly pure tertiary-treated municipal wastewater entering via the Las Vegas Wash, and waters of mixed influence (Las Vegas Bay and Boulder Basin), which represented a gradient of treated wastewater effluent impact. Microbial diversity analysis based on 16S rRNA gene censuses revealed the community at this site to be distinct from the less urban-impacted locations, although all sites were similar in overall diversity and richness. Similarly, Biolog EcoPlate assays demonstrated that the microbial community at Las Vegas Wash was the most metabolically versatile and active. Organic contaminants added as a mixture to laboratory microcosms were more rapidly and completely degraded in the most wastewater-impacted sites (Las Vegas Wash and Las Vegas Bay), with the majority exhibiting shorter half-lives than at the other sites or in a bacteriostatic control. Although the reasons for enhanced degradation capacity in the wastewater-impacted sites remain to be established, these data are consistent with the acclimatization of native microorganisms (either through changes in community structure or metabolic regulation) to effluent-derived trace contaminants. This study suggests that in urban, wastewater-impacted watersheds, prior exposure to organic contaminants fundamentally alters the structure and function of microbial communities, which in turn translates into greater potential for the natural attenuation of these compounds compared to more pristine sites. Copyright © 2017. Published by Elsevier B.V.

Changes in the microbial communities during co-composting of digestates☆

PubMed Central

Franke-Whittle, Ingrid H.; Confalonieri, Alberto; Insam, Heribert; Schlegelmilch, Mirko; Körner, Ina

2014-01-01

Anaerobic digestion is a waste treatment method which is of increasing interest worldwide. At the end of the process, a digestate remains, which can gain added value by being composted. A study was conducted in order to investigate microbial community dynamics during the composting process of a mixture of anaerobic digestate (derived from the anaerobic digestion of municipal food waste), green wastes and a screened compost (green waste/kitchen waste compost), using the COMPOCHIP microarray. The composting process showed a typical temperature development, and the highest degradation rates occurred during the first 14 days of composting, as seen from the elevated CO2 content in the exhaust air. With an exception of elevated nitrite and nitrate levels in the day 34 samples, physical–chemical parameters for all compost samples collected during the 63 day process indicated typical composting conditions. The microbial communities changed over the 63 days of composting. According to principal component analysis of the COMPOCHIP microarray results, compost samples from the start of the experiment were found to cluster most closely with the digestate and screened compost samples. The green waste samples were found to group separately. All starting materials investigated were found to yield fewer and lower signals when compared to the samples collected during the composting experiment. PMID:24456768

A novel analysis method for paired-sample microbial ecology experiments

DOE PAGES

Olesen, Scott W.; Vora, Suhani; Techtmann, Stephen M.; ...

2016-05-06

Many microbial ecology experiments use sequencing data to measure a community s response to an experimental treatment. In a common experimental design, two units, one control and one experimental, are sampled before and after the treatment is applied to the experimental unit. The four resulting samples contain information about the dynamics of organisms that respond to the treatment, but there are no analytical methods designed to extract exactly this type of information from this configuration of samples. Here we present an analytical method specifically designed to visualize and generate hypotheses about microbial community dynamics in experiments that have paired samplesmore » and few or no replicates. The method is based on the Poisson lognormal distribution, long studied in macroecology, which we found accurately models the abundance distribution of taxa counts from 16S rRNA surveys. To demonstrate the method s validity and potential, we analyzed an experiment that measured the effect of crude oil on ocean microbial communities in microcosm. Our method identified known oil degraders as well as two clades, Maricurvus and Rhodobacteraceae, that responded to amendment with oil but do not include known oil degraders. Furthermore, our approach is sensitive to organisms that increased in abundance only in the experimental unit but less sensitive to organisms that increased in both control and experimental units, thus mitigating the role of bottle effects .« less

A novel analysis method for paired-sample microbial ecology experiments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Olesen, Scott W.; Vora, Suhani; Techtmann, Stephen M.

Many microbial ecology experiments use sequencing data to measure a community s response to an experimental treatment. In a common experimental design, two units, one control and one experimental, are sampled before and after the treatment is applied to the experimental unit. The four resulting samples contain information about the dynamics of organisms that respond to the treatment, but there are no analytical methods designed to extract exactly this type of information from this configuration of samples. Here we present an analytical method specifically designed to visualize and generate hypotheses about microbial community dynamics in experiments that have paired samplesmore » and few or no replicates. The method is based on the Poisson lognormal distribution, long studied in macroecology, which we found accurately models the abundance distribution of taxa counts from 16S rRNA surveys. To demonstrate the method s validity and potential, we analyzed an experiment that measured the effect of crude oil on ocean microbial communities in microcosm. Our method identified known oil degraders as well as two clades, Maricurvus and Rhodobacteraceae, that responded to amendment with oil but do not include known oil degraders. Furthermore, our approach is sensitive to organisms that increased in abundance only in the experimental unit but less sensitive to organisms that increased in both control and experimental units, thus mitigating the role of bottle effects .« less

Carbon turnover in topsoil and subsoil: The microbial response to root litter additions and different environmental conditions in a reciprocal soil translocation experiment

NASA Astrophysics Data System (ADS)

Preusser, Sebastian; Poll, Christian; Marhan, Sven; Kandeler, Ellen

2017-04-01

At the global scale, soil organic carbon (SOC) represents the largest active terrestrial organic carbon (OC) pool. Carbon dynamics in subsoil, however, vary from those in topsoil with much lower C concentrations in subsoil than in topsoil horizons, although more than 50 % of SOC is stored in subsoils below 30 cm soil depth. In addition, microorganisms in subsoil are less abundant, more heterogeneously distributed and the microbial communities have a lower diversity than those in topsoil. Especially in deeper soil, the impact of changes in habitat conditions on microorganisms involved in carbon cycling are largely unexplored and consequently the understanding of microbial functioning is limited. A reciprocal translocation experiment allowed us to investigate the complex interaction effects of altered environmental and substrate conditions on microbial decomposer communities in both topsoil and subsoil habitats under in situ conditions. We conducted this experiment with topsoil (5 cm soil depth) and subsoil (110 cm) samples of an acid and sandy Dystric Cambisol from a European beech (Fagus sylvatica L.) forest in Lower Saxony, Germany. In total 144 samples were buried into three depths (5 cm, 45 cm and 110 cm) and 13C-labelled root litter was added to expose the samples to different environmental conditions and to increase the substrate availability, respectively. Samples were taken in three month intervals up to a maximum exposure time of one year to follow the temporal development over the experimental period. Analyses included 13Cmic and 13C PLFA measurements to investigate the response of microbial abundance, community structure and 13C-root decomposition activity under the different treatments. Environmental conditions in the respective soil depths such as soil temperature and water content were recorded throughout the experimental period. All microbial groups (gram+ and gram- bacteria, fungi) showed highest relative 13C incorporation in 110 cm depth and samples with root addition had generally higher microbial abundances than those with no root addition. Here, especially fungi benefited from the additional carbon source with highly increased abundances in all incorporation depths. Also the altered environmental conditions in the different incorporation depths significantly influenced the different microbial groups. The steepest decrease with depth was detected in fungal abundance, while bacteria were less affected and increased in relative abundance in soil samples incorporated into subsoil layers. The highest seasonal variability in microbial abundance, however, was determined in 5 cm incorporation depth demonstrating the higher amplitude in micro-climatic and micro-environmental conditions in this near-surface soil habitat. In summary, this experiment demonstrated that carbon quality and quantity are the main factors restricting fungal abundance in deeper soil layers, while bacterial decomposer communities are adapted to a wider range of habitat conditions.

Heterogeneity of interactions of microbial communities in regions of Taihu Lake with different nutrient loadings: A network analysis.

PubMed

Cao, Xinyi; Zhao, Dayong; Xu, Huimin; Huang, Rui; Zeng, Jin; Yu, Zhongbo

2018-06-11

To investigate the differences in the interactions of microbial communities in two regions in Taihu Lake with different nutrient loadings [Meiliang Bay (MLB) and Xukou Bay (XKB)], water samples were collected and both intra- and inter-kingdom microbial community interactions were examined with network analysis. It is demonstrated that all of the bacterioplankton, microeukaryotes and inter-kingdom communities networks in Taihu Lake were non-random. For the networks of bacterioplankton and inter-kingdom community in XKB, higher clustering coefficient and average degree but lower average path length indexes were observed, indicating the nodes in XKB were more clustered and closely connected with plenty edges than those of MLB. The bacterioplankton and inter-kingdom networks were considerably larger and more complex with more module hubs and connectors in XKB compared with those of MLB, whereas the microeukaryotes networks were comparable and had no module hubs or connectors in the two lake zones. The phyla of Acidobacteria, Cyanobacteria and Planctomycetes maintained greater cooperation with other phyla in XKB, rather than competition. The relationships between microbial communities and environmental factors in MLB were weaker. Compared with the microbial community networks of XKB, less modules in networks of MLB were significantly correlated with total phosphorous and total nitrogen.

Microbial communities in natural rubber coagula during maturation: impacts on technological properties of dry natural rubber.

PubMed

Salomez, M; Subileau, M; Vallaeys, T; Santoni, S; Bonfils, F; Sainte-Beuve, J; Intapun, J; Granet, F; Vaysse, L; Dubreucq, É

2018-02-01

To characterize microbial communities present in natural rubber (NR) coagula from Hevea brasiliensis latex during maturation and identify microbial taxa (bacteria and fungi) having an impact on dry NR properties. Microbial community dynamics in NR coagula maturated under controlled conditions were compared and related with the evolution of dry NR properties. The pyrosequencing of 16S (119 837 effective reads) and 18S (131 879 effective reads) rRNA gene regions was performed on 21 samples covering different maturation times and two aeration conditions. Results showed a relatively high bacterial richness (Chao1 estimates of 200-1000) associated with significant bacterial dynamics. Lactic acid bacteria (LAB) were dominant in the first days of maturation. Then, in aerobic conditions, development of Actinobacteria represented by the family Microbacteriaceae was associated with alkalinization of the samples and a higher sensitivity of NR to thermo-oxidation as evaluated by its plasticity retention index (PRI). In anaerobiosis, the reduced development of bacteria, mostly LAB present, was associated with improved NR properties (higher initial plasticity P 0 and PRI). The involvement of micro-organisms in the evolution of dry NR properties during the maturation of NR coagula was confirmed. The importance of the structure and dynamics of microbial communities is specifically highlighted. Natural rubber is a key elastomer for the tyre industry and for a variety of other applications. The majority of raw NR is obtained by natural coagulation of H. brasiliensis latex under the activity of micro-organisms. An improved understanding of the microbial communities involved in the maturation of NR coagula may lead to an improvement in the production process of raw NR to provide a better consistency in NR quality. © 2017 The Society for Applied Microbiology.

Response of the soil microbial community to imazethapyr application in a soybean field.

PubMed

Xu, Jun; Guo, Liqun; Dong, Fengshou; Liu, Xingang; Wu, Xiaohu; Sheng, Yu; Zhang, Ying; Zheng, Yongquan

2013-01-01

The objective of this study was to determine the effects of imazethapyr on soil microbial communities combined with its effect on soybean growth. A short-term field experiment was conducted, and imazethapyr was applied to the soil at three different doses [1-fold, 10-fold, and 50-fold of the recommended field rate (H1, H10, H50)] during the soybean seedling period (with two leaves). Soil sampling was performed after 1, 7, 30, 60, 90, and 120 days of application to determine the imazethapyr concentration and microbial community structure by investigating phospholipid fatty acids (PLFA) and microbial biomass carbon (MBC). The half-lives of the imazethapyr in the field soil varied from 30.1 to 43.3 days. Imazethapyr at H1 was innocuous to soybean plants, but imazethapyr at H10 and H50 led to a significant inhibition in soybean plant height and leaf number. The soil MBC, total PLFA, and bacterial PLFA were decreased by the application of imazethapyr during the initial period and could recover by the end of the experiment. The ratio of Gram-negative/Gram-positive (GN/GP) bacteria during the three treatments went through increases and decreases, and then recovered at the end of the experiment. The fungal PLFA of all three treatments increased during the initial period and then declined, and only the fungal PLFA at H50 recovered by the end of the treatment. A principal component analysis (PCA) of the PLFA clearly separated the treatments and sampling times, and the results demonstrate that imazethapyr alters the microbial community structure. This is the first systemic study reporting the effects of imazethapyr on the soil microbial community structure under soybean field conditions.

Microbial distributions detected by an oligonucleotide microarray across geochemical zones associated with methane in marine sediments from the Ulleung Basin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Briggs, Brandon R; Graw, Michael; Brodie, Eoin L

2013-11-01

The biogeochemical processes that occur in marine sediments on continental margins are complex; however, from one perspective they can be considered with respect to three geochemical zones based on the presence and form of methane: sulfate–methane transition (SMTZ), gas hydrate stability zone (GHSZ), and free gas zone (FGZ). These geochemical zones may harbor distinct microbial communities that are important in biogeochemical carbon cycles. The objective of this study was to describe the microbial communities in sediments from the SMTZ, GHSZ, and FGZ using molecular ecology methods (i.e. PhyloChip microarray analysis and terminal restriction fragment length polymorphism (T-RFLP)) and examining themore » results in the context of non-biological parameters in the sediments. Non-metric multidimensional scaling and multi-response permutation procedures were used to determine whether microbial community compositions were significantly different in the three geochemical zones and to correlate samples with abiotic characteristics of the sediments. This analysis indicated that microbial communities from all three zones were distinct from one another and that variables such as sulfate concentration, hydrate saturation of the nearest gas hydrate layer, and depth (or unmeasured variables associated with depth e.g. temperature, pressure) were correlated to differences between the three zones. The archaeal anaerobic methanotrophs typically attributed to performing anaerobic oxidation of methane were not detected in the SMTZ; however, the marine benthic group-B, which is often found in SMTZ, was detected. Within the GHSZ, samples that were typically closer to layers that contained higher hydrate saturation had indicator sequences related to Vibrio-type taxa. These results suggest that the biogeographic patterns of microbial communities in marine sediments are distinct based on geochemical zones defined by methane.« less

Preliminary characterization of the oral microbiota of Chinese adults with and without gingivitis

PubMed Central

2011-01-01

Background Microbial communities inhabiting human mouth are associated with oral health and disease. Previous studies have indicated the general prevalence of adult gingivitis in China to be high. The aim of this study was to characterize in depth the oral microbiota of Chinese adults with or without gingivitis, by defining the microbial phylogenetic diversity and community-structure using highly paralleled pyrosequencing. Methods Six non-smoking Chinese, three with and three without gingivitis (age range 21-39 years, 4 females and 2 males) were enrolled in the present cross-sectional study. Gingival parameters of inflammation and bleeding on probing were characterized by a clinician using the Mazza Gingival Index (MGI). Plaque (sampled separately from four different oral sites) and salivary samples were obtained from each subject. Sequences and relative abundance of the bacterial 16 S rDNA PCR-amplicons were determined via pyrosequencing that produced 400 bp-long reads. The sequence data were analyzed via a computational pipeline customized for human oral microbiome analyses. Furthermore, the relative abundances of selected microbial groups were validated using quantitative PCR. Results The oral microbiomes from gingivitis and healthy subjects could be distinguished based on the distinct community structures of plaque microbiomes, but not the salivary microbiomes. Contributions of community members to community structure divergence were statistically accessed at the phylum, genus and species-like levels. Eight predominant taxa were found associated with gingivitis: TM7, Leptotrichia, Selenomonas, Streptococcus, Veillonella, Prevotella, Lautropia, and Haemophilus. Furthermore, 98 species-level OTUs were identified to be gingivitis-associated, which provided microbial features of gingivitis at a species resolution. Finally, for the two selected genera Streptococcus and Fusobacterium, Real-Time PCR based quantification of relative bacterial abundance validated the pyrosequencing-based results. Conclusions This methods study suggests that oral samples from this patient population of gingivitis can be characterized via plaque microbiome by pyrosequencing the 16 S rDNA genes. Further studies that characterize serial samples from subjects (longitudinal study design) with a larger population size may provide insight into the temporal and ecological features of oral microbial communities in clinically-defined states of gingivitis. PMID:22152152

Soil microbial diversity in the vicinity of desert shrubs.

PubMed

Saul-Tcherkas, Vered; Unc, Adrian; Steinberger, Yosef

2013-04-01

Water and nutrient availability are the major limiting factors of biological activity in arid and semiarid ecosystems. Therefore, perennial plants have developed different ecophysiological adaptations to cope with harsh conditions. The chemical profile of the root exudates varies among plant species and this can induce variability in associated microbial populations. We examined the influence of two shrubs species, Artemisia sieberi and Noaea mucronata, on soil microbial diversity. Soil samples were collected monthly, from December 2006 to November 2007, near canopies of both shrubs (0-10-cm depth). Samples were used for abiotic tests and determination of soil bacterial diversity. No significant differences were found in the abiotic variables (soil moisture, total organic matter, and total soluble nitrogen (TSN)) between soil samples collected from under the two shrubs during the study period. No obvious differences in the Shannon-Weaver index, evenness values, or total phylogenetic distances were found for the soil microbial communities. However, detailed denaturing gradient gel electrophoresis (DGGE) clustering as well as taxonomic diversity analyses indicated clear shifts in the soil microbial community composition. These shifts were governed by seasonal variability in water availability and, significantly, by plant species type.

Temporal and Spatial Impact of Human Cadaver Decomposition on Soil Bacterial and Arthropod Community Structure and Function

PubMed Central

Singh, Baneshwar; Minick, Kevan J.; Strickland, Michael S.; Wickings, Kyle G.; Crippen, Tawni L.; Tarone, Aaron M.; Benbow, M. Eric; Sufrin, Ness; Tomberlin, Jeffery K.; Pechal, Jennifer L.

2018-01-01

As vertebrate carrion decomposes, there is a release of nutrient-rich fluids into the underlying soil, which can impact associated biological community structure and function. How these changes alter soil biogeochemical cycles is relatively unknown and may prove useful in the identification of carrion decomposition islands that have long lasting, focal ecological effects. This study investigated the spatial (0, 1, and 5 m) and temporal (3–732 days) dynamics of human cadaver decomposition on soil bacterial and arthropod community structure and microbial function. We observed strong evidence of a predictable response to cadaver decomposition that varies over space for soil bacterial and arthropod community structure, carbon (C) mineralization and microbial substrate utilization patterns. In the presence of a cadaver (i.e., 0 m samples), the relative abundance of Bacteroidetes and Firmicutes was greater, while the relative abundance of Acidobacteria, Chloroflexi, Gemmatimonadetes, and Verrucomicrobia was lower when compared to samples at 1 and 5 m. Micro-arthropods were more abundant (15 to 17-fold) in soils collected at 0 m compared to either 1 or 5 m, but overall, micro-arthropod community composition was unrelated to either bacterial community composition or function. Bacterial community structure and microbial function also exhibited temporal relationships, whereas arthropod community structure did not. Cumulative precipitation was more effective in predicting temporal variations in bacterial abundance and microbial activity than accumulated degree days. In the presence of the cadaver (i.e., 0 m samples), the relative abundance of Actinobacteria increased significantly with cumulative precipitation. Furthermore, soil bacterial communities and C mineralization were sensitive to the introduction of human cadavers as they diverged from baseline levels and did not recover completely in approximately 2 years. These data are valuable for understanding ecosystem function surrounding carrion decomposition islands and can be applicable to environmental bio-monitoring and forensic sciences. PMID:29354106

Temporal and Spatial Impact of Human Cadaver Decomposition on Soil Bacterial and Arthropod Community Structure and Function.

PubMed

Singh, Baneshwar; Minick, Kevan J; Strickland, Michael S; Wickings, Kyle G; Crippen, Tawni L; Tarone, Aaron M; Benbow, M Eric; Sufrin, Ness; Tomberlin, Jeffery K; Pechal, Jennifer L

2017-01-01

As vertebrate carrion decomposes, there is a release of nutrient-rich fluids into the underlying soil, which can impact associated biological community structure and function. How these changes alter soil biogeochemical cycles is relatively unknown and may prove useful in the identification of carrion decomposition islands that have long lasting, focal ecological effects. This study investigated the spatial (0, 1, and 5 m) and temporal (3-732 days) dynamics of human cadaver decomposition on soil bacterial and arthropod community structure and microbial function. We observed strong evidence of a predictable response to cadaver decomposition that varies over space for soil bacterial and arthropod community structure, carbon (C) mineralization and microbial substrate utilization patterns. In the presence of a cadaver (i.e., 0 m samples), the relative abundance of Bacteroidetes and Firmicutes was greater, while the relative abundance of Acidobacteria, Chloroflexi, Gemmatimonadetes, and Verrucomicrobia was lower when compared to samples at 1 and 5 m. Micro-arthropods were more abundant (15 to 17-fold) in soils collected at 0 m compared to either 1 or 5 m, but overall, micro-arthropod community composition was unrelated to either bacterial community composition or function. Bacterial community structure and microbial function also exhibited temporal relationships, whereas arthropod community structure did not. Cumulative precipitation was more effective in predicting temporal variations in bacterial abundance and microbial activity than accumulated degree days. In the presence of the cadaver (i.e., 0 m samples), the relative abundance of Actinobacteria increased significantly with cumulative precipitation. Furthermore, soil bacterial communities and C mineralization were sensitive to the introduction of human cadavers as they diverged from baseline levels and did not recover completely in approximately 2 years. These data are valuable for understanding ecosystem function surrounding carrion decomposition islands and can be applicable to environmental bio-monitoring and forensic sciences.

Molecular analysis of the gut microbiota of identical twins with Crohn's disease

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jansson, Janet; Dicksved, Johan; Halfvarson, Jonas

2008-03-14

Increasing evidence suggests that a combination of host genetics and the composition of the gut microbiota are important for development of Crohn's disease (CD). Our aim was to study identical twins with CD to determine microbial factors independently of host genetics. Fecal samples were studied from 10 monozygotic twin pairs with CD (discordant n=6, concordant n=4) and 8 healthy twin pairs. DNA was extracted, 16S rRNA genes were PCR amplified and T-RFLP fingerprints generated using general bacterial and Bacteroides group specific primers. The microbial communities were also profiled based on their % G+C contents. Bacteroides 16S rRNA genes were clonedmore » and sequenced from a subset of the samples. The bacterial diversity in each sample and similarity indices between samples were estimated based on the T-RFLP data using a combination of statistical approaches. Healthy individuals had a significantly higher bacterial diversity compared to individuals with CD. The fecal microbial communities were more similar between healthy twins than between twins with CD, especially when these were discordant for the disease. The microbial community profiles of individuals with ileal CD were significantly different from healthy individuals and those with colonic CD. Also, CD individuals had a lower relative abundance of B. uniformis and higher relative abundances of B. ovatus and B. vulgatus. Our results suggest that genetics and/or environmental exposure during childhood in part determine the gut microbial composition. However, CD is associated with dramatic changes in the gut microbiota and this was particularly evident for individuals with ileal CD.« less

Extraction of Total DNA and RNA from Marine Filter Samples and Generation of a cDNA as Universal Template for Marker Gene Studies.

PubMed

Schneider, Dominik; Wemheuer, Franziska; Pfeiffer, Birgit; Wemheuer, Bernd

2017-01-01

Microbial communities play an important role in marine ecosystem processes. Although the number of studies targeting marker genes such as the 16S rRNA gene has been increased in the last few years, the vast majority of marine diversity is rather unexplored. Moreover, most studies focused on the entire bacterial community and thus disregarded active microbial community players. Here, we describe a detailed protocol for the simultaneous extraction of DNA and RNA from marine water samples and for the generation of cDNA from the isolated RNA which can be used as a universal template in various marker gene studies.

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling

DOE PAGES

Podar, Mircea; Shakya, Migun; D'Amore, Rosalinda; ...

2016-01-14

In the last 5 years, the rapid pace of innovations and improvements in sequencing technologies has completely changed the landscape of metagenomic and metagenetic experiments. Therefore, it is critical to benchmark the various methodologies for interrogating the composition of microbial communities, so that we can assess their strengths and limitations. Here, the most common phylogenetic marker for microbial community diversity studies is the 16S ribosomal RNA gene and in the last 10 years the field has moved from sequencing a small number of amplicons and samples to more complex studies where thousands of samples and multiple different gene regions aremore » interrogated.« less

Metaproteome analysis of endodontic infections in association with different clinical conditions.

PubMed

Provenzano, José Claudio; Siqueira, José F; Rôças, Isabela N; Domingues, Romênia R; Paes Leme, Adriana F; Silva, Márcia R S

2013-01-01

Analysis of the metaproteome of microbial communities is important to provide an insight of community physiology and pathogenicity. This study evaluated the metaproteome of endodontic infections associated with acute apical abscesses and asymptomatic apical periodontitis lesions. Proteins persisting or expressed after root canal treatment were also evaluated. Finally, human proteins associated with these infections were identified. Samples were taken from root canals of teeth with asymptomatic apical periodontitis before and after chemomechanical treatment using either NaOCl or chlorhexidine as the irrigant. Samples from abscesses were taken by aspiration of the purulent exudate. Clinical samples were processed for analysis of the exoproteome by using two complementary mass spectrometry platforms: nanoflow liquid chromatography coupled with linear ion trap quadrupole Velos Orbitrap and liquid chromatography-quadrupole time-of-flight. A total of 308 proteins of microbial origin were identified. The number of proteins in abscesses was higher than in asymptomatic cases. In canals irrigated with chlorhexidine, the number of identified proteins decreased substantially, while in the NaOCl group the number of proteins increased. The large majority of microbial proteins found in endodontic samples were related to metabolic and housekeeping processes, including protein synthesis, energy metabolism and DNA processes. Moreover, several other proteins related to pathogenicity and resistance/survival were found, including proteins involved with adhesion, biofilm formation and antibiotic resistance, stress proteins, exotoxins, invasins, proteases and endopeptidases (mostly in abscesses), and an archaeal protein linked to methane production. The majority of human proteins detected were related to cellular processes and metabolism, as well as immune defense. Interrogation of the metaproteome of endodontic microbial communities provides information on the physiology and pathogenicity of the community at the time of sampling. There is a growing need for expanded and more curated protein databases that permit more accurate identifications of proteins in metaproteomic studies.

Analysis of the Gull Fecal Microbial Community Reveals the Dominance of Catellicoccus marimammalium in Relation to Culturable Enterococci

PubMed Central

Koskey, Amber M.; Fisher, Jenny C.; Traudt, Mary F.; Newton, Ryan J.

2014-01-01

Gulls are prevalent in beach environments and can be a major source of fecal contamination. Gulls have been shown to harbor a high abundance of fecal indicator bacteria (FIB), such as Escherichia coli and enterococci, which can be readily detected as part of routine beach monitoring. Despite the ubiquitous presence of gull fecal material in beach environments, the associated microbial community is relatively poorly characterized. We generated comprehensive microbial community profiles of gull fecal samples using Roche 454 and Illumina MiSeq platforms to investigate the composition and variability of the gull fecal microbial community and to measure the proportion of FIB. Enterococcaceae and Enterobacteriaceae were the two most abundant families in our gull samples. Sequence comparisons between short-read data and nearly full-length 16S rRNA gene clones generated from the same samples revealed Catellicoccus marimammalium as the most numerous taxon among all samples. The identification of bacteria from gull fecal pellets cultured on membrane-Enterococcus indoxyl-β-d-glucoside (mEI) plates showed that the dominant sequences recovered in our sequence libraries did not represent organisms culturable on mEI. Based on 16S rRNA gene sequencing of gull fecal isolates cultured on mEI plates, 98.8% were identified as Enterococcus spp., 1.2% were identified as Streptococcus spp., and none were identified as C. marimammalium. Illumina deep sequencing indicated that gull fecal samples harbor significantly higher proportions of C. marimammalium 16S rRNA gene sequences (>50-fold) relative to typical mEI culturable Enterococcus spp. C. marimammalium therefore can be confidently utilized as a genetic marker to identify gull fecal pollution in the beach environment. PMID:24242244

Microbial community composition and function in the Tonga Trench: from 400m below the sea surface to 9100m water depth and from 0 to 2 m below the seafloor.

NASA Astrophysics Data System (ADS)

Leon Zayas, R. I.; Bartlett, D.; Biddle, J.

2016-12-01

Exploration of the deep ocean has expanded our understanding of oceanic ecosystems including continental margins and mid-ocean ridges, but little is known about the deepest sites on Earth, oceanic trenches. In this study, sediment and water samples were collected from the Tonga Trench at 9100m below sea level. These include four water column samples at depths of 400m, 3000m, 5000m and 9100m, and sediment samples at 0, 1, and 2 meter below the seafloor (mbsf). DNA was extracted and sequencing was performed for the recovery of metagenomic data for all samples. The analysis of the sediment samples from Tonga Trench has provided a new perspective of life in the deep ocean. The data for microbial community composition and metabolic profiles at the surface sediments, 0 mbsf, suggest that the microbes are present and taxonomically similar to the water column microbes, and perform an array of aerobic as well as anaerobic metabolisms, including degradation of organic carbon, oxidative phosphorylation, fermentation, nitrate reduction and sulfur oxidation among others. On the other hand, at 1 and 2 mbsf, the microbial community has diminished richness and diversity when compared to 0 mbsf and is potentially environmentally degraded due to the lack of quality data recoverable. Tonga Trench water column metagenomes are compared to other deep and hadal environments to better understand how different geographical locations, water masses and depth affect microbial community composition, distribution and metabolic potential. To our knowledge, this is the deepest metagenome analyzed to date (9100m), presenting an unprecedented look at one of the deepest environments on our planet.

Predicting effects of climate change on the composition and function of soil microbial communities

NASA Astrophysics Data System (ADS)

Dubinsky, E.; Brodie, E.; Myint, C.; Ackerly, D.; van Nostrand, J.; Bird, J.; Zhou, J.; Andersen, G.; Firestone, M.

2008-12-01

Complex soil microbial communities regulate critical ecosystem processes that will be altered by climate change. A critical step towards predicting the impacts of climate change on terrestrial ecosystems is to determine the primary controllers of soil microbial community composition and function, and subsequently evaluate climate change scenarios that alter these controllers. We surveyed complex soil bacterial and archaeal communities across a range of climatic and edaphic conditions to identify critical controllers of soil microbial community composition in the field and then tested the resulting predictions using a 2-year manipulation of precipitation and temperature using mesocosms of California annual grasslands. Community DNA extracted from field soils sampled from six different ecosystems was assayed for bacterial and archaeal communities using high-density phylogenetic microarrays as well as functional gene arrays. Correlations among the relative abundances of thousands of microbial taxa and edaphic factors such as soil moisture and nutrient content provided a basis for predicting community responses to changing soil conditions. Communities of soil bacteria and archaea were strongly structured by single environmental predictors, particularly variables related to soil water. Bacteria in the Actinomycetales and Bacilli consistently demonstrated a strong negative response to increasing soil moisture, while taxa in a greater variety of lineages responded positively to increasing soil moisture. In the climate change experiment, overall bacterial community structure was impacted significantly by total precipitation but not by plant species. Changes in soil moisture due to decreased rainfall resulted in significant and predictable alterations in community structure. Over 70% of the bacterial taxa in common with the cross-ecosystem study responded as predicted to altered precipitation, with the most conserved response from Actinobacteria. The functional consequences of these predictable changes in community composition were measured with functional arrays that detect genes involved in the metabolism of carbon, nitrogen and other elements. The response of soil microbial communities to altered precipitation can be predicted from the distribution of microbial taxa across moisture gradients.

Effects of interactions between Collembola and soil microbial community on the degradation of glyphosate-based herbicide

NASA Astrophysics Data System (ADS)

Wee, J.; Lee, Y. S.; Son, J.; Kim, Y.; Nam, T. H.; Cho, K.

2017-12-01

Glyphosate is the most widely used herbicide because of its broad spectrum activity and effectiveness, however, little is known about adverse effects on non-target species and their interactions. Therefore, in this study, we investigated the effects of glyphosate on interactions between Collembola and soil microbial community and the effect of Collembola on degradation of glyphosate. The experiment carried out in PS container filled with 30g of soil according to OECD 232 guidelines. Investigating the effects of soil microbial community and Collembola on degradation of glyphosate, we prepared defaunated field soil (only maintaining soil microbial community, sampling in May and September, 2016.) and autoclaved soil with 0, 10, 30 adults of Paronychiurus kimi (Collembola) respectively. Survived adults and hatched juveniles of P. kimi were counted after 28-day exposures in both soils spiked with 100 mg/kg of glyphosate. Glyphosate in soil of 7, 14, 21, 28 days after spiking of glyphosate based herbicide was analyzed by spectrophotometer (Jan et al., 2009). Also soil microbial community structure was investigated using phospholipid fatty acids (PLFAs) composition analysis of soils following the procedures given by the Sherlock Microbial Identification System (MIDI Inc., Newark, DE). Glyphosate (100mg/kg soil) has no effects on reproduction and survival of P. kimi in any soils. Also, glyphosate in soils with Collembola was more rapidly degraded. Rapid increase of soil microbial biomass(PLFAs) was shown in soil with Collembola addition. This result showed that glyphosate affected interactions between Collembola and soil microorganisms, and also soil microbial community affected by Collembola changed degradation of glyphosate.

Modified RNA-seq method for microbial community and diversity analysis using rRNA in different types of environmental samples

PubMed Central

Yan, Yong-Wei; Zou, Bin; Zhu, Ting; Hozzein, Wael N.

2017-01-01

RNA-seq-based SSU (small subunit) rRNA (ribosomal RNA) analysis has provided a better understanding of potentially active microbial community within environments. However, for RNA-seq library construction, high quantities of purified RNA are typically required. We propose a modified RNA-seq method for SSU rRNA-based microbial community analysis that depends on the direct ligation of a 5’ adaptor to RNA before reverse-transcription. The method requires only a low-input quantity of RNA (10–100 ng) and does not require a DNA removal step. The method was initially tested on three mock communities synthesized with enriched SSU rRNA of archaeal, bacterial and fungal isolates at different ratios, and was subsequently used for environmental samples of high or low biomass. For high-biomass salt-marsh sediments, enriched SSU rRNA and total nucleic acid-derived RNA-seq datasets revealed highly consistent community compositions for all of the SSU rRNA sequences, and as much as 46.4%-59.5% of 16S rRNA sequences were suitable for OTU (operational taxonomic unit)-based community and diversity analyses with complete coverage of V1-V2 regions. OTU-based community structures for the two datasets were also highly consistent with those determined by all of the 16S rRNA reads. For low-biomass samples, total nucleic acid-derived RNA-seq datasets were analyzed, and highly active bacterial taxa were also identified by the OTU-based method, notably including members of the previously underestimated genus Nitrospira and phylum Acidobacteria in tap water, members of the phylum Actinobacteria on a shower curtain, and members of the phylum Cyanobacteria on leaf surfaces. More than half of the bacterial 16S rRNA sequences covered the complete region of primer 8F, and non-coverage rates as high as 38.7% were obtained for phylum-unclassified sequences, providing many opportunities to identify novel bacterial taxa. This modified RNA-seq method will provide a better snapshot of diverse microbial communities, most notably by OTU-based analysis, even communities with low-biomass samples. PMID:29016661

Microbial community structure and density under different tree species in an acid forest soil (Morvan, France).

PubMed

Lejon, David P H; Chaussod, Rémi; Ranger, Jacques; Ranjard, Lionel

2005-11-01

Overexploitation of forests to increase wood production has led to the replacement of native forest by large areas of monospecific tree plantations. In the present study, the effects of different monospecific tree cover plantations on density and composition of the indigenous soil microbial community are described. The experimental site of "Breuil-Chenue" in the Morvan (France) was the site of a comparison of a similar mineral soil under Norway spruce (Picea abies), Douglas fir (Pseudotuga menziesii), oak (Quercus sessiflora), and native forest [mixed stand dominated by oak and beech (Fagus sylvatica)]. Sampling was performed during winter (February) at three depths (0-5, 5-10, and 10-15 cm). Abundance of microorganisms was estimated via microbial biomass measurements, using the fumigation-extraction method. The genetic structure of microbial communities was investigated using the bacterial- and fungal-automated ribosomal intergenic spacer analysis (B-ARISA and F-ARISA, respectively) DNA fingerprint. Only small differences in microbial biomass were observed between tree species, the highest values being recorded under oak forest and the lowest under Douglas fir. B- and F-ARISA community profiles of the different tree covers clustered separately, but noticeable similarities were observed for soils under Douglas fir and oak. A significant stratification was revealed under each tree species by a decrease in microbial biomass with increasing depths and by distinct microbial communities for each soil layer. Differences in density and community composition according to tree species and depth were related to soil physicochemical characteristics and organic matter composition.

Impacts of Deepwater Horizon Oil on Marsh Sediment Biogeochemistry in Barataria Bay, LA, USA

NASA Astrophysics Data System (ADS)

Mills, C. T.; Windham-Myers, L.; Waldrop, M. P.; Krabbenhoft, D. P.; Marvin-DiPasquale, M. C.; Orem, W. H.; Piazza, S.; Haw, M.; McFarland, J.; Varonka, M. S.

2012-12-01

Oil from the Deepwater Horizon spill came ashore on many salt marsh islands in Barataria Bay, LA in summer 2010, coating plants and settling on the sediment surface. In coordination with a plant community study of affected marshes, we investigated impacts of oiling on marsh sediment microbial biogeochemistry. Sediment samples (upmost 2 cm) were collected along transects perpendicular and parallel to the shore at three oiled and three non-oiled sites in both July and Oct. 2011. Samples from both collections were analyzed for sediment characteristics, total and methylmercury, and microbial membrane phospholipid fatty acids (PLFAs) which are a proxy for viable microbial cell numbers. Sediment DNA collected in Oct. 2011 was analyzed for bacterial, fungal, and archaeal community composition and abundance as well as various enzyme activities. Select Oct. 2011 samples were assayed to determine the rates of terminal electron accepting processes (oxygen demand, denitrification, iron reduction, sulfate reduction, methanogenesis). All sites had similar sediment characteristics. Impacts on sediment biogeochemistry were greatest at marsh edges, and reduced microbial abundance appeared to be more important than changes in microbial community structure. In July 2011, the mean PLFA concentration in oiled marsh edge sediments (0.15±0.03 μmol g-1; 95% CI; n=9) was substantially lower than for non-oiled sites (0.33±0.08 μmol g-1; n=9). Mean PLFA concentrations for interior marsh samples were more similar for oiled (0.30±0.08 μmol g-1; n=8) and non-oiled (0.37±0.04 μmol g-1; n=9) sites. This PLFA pattern was also observed in Oct. 2011 samples, and other measures of microbial abundance and activity showed similar trends. Cellulase, phosphatase, and chitinase mean activities were nearly twice as great in non-oiled versus oiled edge sites. Lower microbial activity in oiled sites was also inferred by somewhat lower denitrification and sulfate reduction potentials. Conversely, both methanogenesis rates and concentrations of methanogen DNA were somewhat greater in oiled edge samples, suggesting an effect of oiling on terminal electron accepting processes. The mean methylmercury concentration was lower in oiled versus non-oiled edge sites, likely as a result of decreased sulfate-reducer activity. The reduced microbial activity in near-edge sediments of the oiled marsh is likely an indirect effect of reduced plant productivity which supports rhizosphere communities. Both mean above- and below-ground live biomass at oiled edge sites were less than half that at non-oiled edge sites. Some marsh edge samples from the oiled site contained relatively large amounts of oil and we are currently quantifying oil-derived hydrocarbons to understand impacts of the oil itself on sediment biogeochemistry.

Large variability of bathypelagic microbial eukaryotic communities across the world's oceans.

PubMed

Pernice, Massimo C; Giner, Caterina R; Logares, Ramiro; Perera-Bel, Júlia; Acinas, Silvia G; Duarte, Carlos M; Gasol, Josep M; Massana, Ramon

2016-04-01

In this work, we study the diversity of bathypelagic microbial eukaryotes (0.8-20 μm) in the global ocean. Seawater samples from 3000 to 4000 m depth from 27 stations in the Atlantic, Pacific and Indian Oceans were analyzed by pyrosequencing the V4 region of the 18S ribosomal DNA. The relative abundance of the most abundant operational taxonomic units agreed with the results of a parallel metagenomic analysis, suggesting limited PCR biases in the tag approach. Although rarefaction curves for single stations were seldom saturated, the global analysis of all sequences together suggested an adequate recovery of bathypelagic diversity. Community composition presented a large variability among samples, which was poorly explained by linear geographic distance. In fact, the similarity between communities was better explained by water mass composition (26% of the variability) and the ratio in cell abundance between prokaryotes and microbial eukaryotes (21%). Deep diversity appeared dominated by four taxonomic groups (Collodaria, Chrysophytes, Basidiomycota and MALV-II) appearing in different proportions in each sample. Novel diversity amounted to 1% of the pyrotags and was lower than expected. Our study represents an essential step in the investigation of bathypelagic microbial eukaryotes, indicating dominating taxonomic groups and suggesting idiosyncratic assemblages in distinct oceanic regions.

Termite hindguts and the ecology of microbial communities in the sequencing age.

PubMed

Tai, Vera; Keeling, Patrick J

2013-01-01

Advances in high-throughput nucleic acid sequencing have improved our understanding of microbial communities in a number of ways. Deeper sequence coverage provides the means to assess diversity at the resolution necessary to recover ecological and biogeographic patterns, and at the same time single-cell genomics provides detailed information about the interactions between members of a microbial community. Given the vastness and complexity of microbial ecosystems, such analyses remain challenging for most environments, so greater insight can also be drawn from analysing less dynamic ecosystems. Here, we outline the advantages of one such environment, the wood-digesting hindgut communities of termites and cockroaches, and how it is a model to examine and compare both protist and bacterial communities. Beyond the analysis of diversity, our understanding of protist community ecology will depend on using statistically sound sampling regimes at biologically relevant scales, transitioning from discovery-based to experimental ecology, incorporating single-cell microbiology and other data sources, and continued development of analytical tools. © 2013 The Author(s) Journal of Eukaryotic Microbiology © 2013 International Society of Protistologists.

Microbial biogeography of San Francisco Bay sediments

NASA Astrophysics Data System (ADS)

Lee, J. A.; Francis, C. A.

2014-12-01

The largest estuary on the west coast of North America, San Francisco Bay is an ecosystem of enormous biodiversity, and also enormous human impact. The benthos has experienced dredging, occupation by invasive species, and over a century of sediment input as a result of hydraulic mining. Although the Bay's great cultural and ecological importance has inspired numerous surveys of the benthic macrofauna, to date there has been almost no investigation of the microbial communities on the Bay floor. An understanding of those microbial communities would contribute significantly to our understanding of both the biogeochemical processes (which are driven by the microbiota) and the physical processes (which contribute to microbial distributions) in the Bay. Here, we present the first broad survey of bacterial and archaeal taxa in the sediments of the San Francisco Bay. We conducted 16S rRNA community sequencing of bacteria and archaea in sediment samples taken bimonthly for one year, from five sites spanning the salinity gradient between Suisun and Central Bay, in order to capture the effect of both spatial and temporal environmental variation on microbial diversity. From the same samples we also conducted deep sequencing of a nitrogen-cycling functional gene, nirS, allowing an assessment of evolutionary diversity at a much finer taxonomic scale within an important and widespread functional group of bacteria. We paired these sequencing projects with extensive geochemical metadata as well as information about macrofaunal distribution. Our data reveal a diversity of distinct biogeographical patterns among different taxa: clades ubiquitous across sites; clades that respond to measurable environmental drivers; and clades that show geographical site-specificity. These community datasets allow us to test the hypothesis that salinity is a major driver of both overall microbial community structure and community structure of the denitrifying bacteria specifically; and to assess whether patterns of diversity observed at the broadest of taxonomic scales also apply to patterns observed within a single extremely diverse gene (nirS). In sum, this project provides a first look at the forces driving the migration and selection of microbial communities in San Francisco Bay.

Agroforestry management in vineyards: effects on soil microbial communities

NASA Astrophysics Data System (ADS)

Montagne, Virginie; Nowak, Virginie; Guilland, Charles; Gontier, Laure; Dufourcq, Thierry; Guenser, Josépha; Grimaldi, Juliette; Bourgade, Emilie; Ranjard, Lionel

2017-04-01

Some vineyard practices (tillage, chemical weeding or pest management) are generally known to impact the environment with particular negative effects on the diversity and the abundance of soil microorganisms, and cause water and soil pollutions. In an agro-ecological context, innovative cropping systems have been developed to improve ecosystem services. Among them, agroforestry offers strategies of sustainable land management practices. It consists in intercropping trees with annual/perennial/fodder crop on the same plot but it is weakly referenced with grapevine. The present study assesses the effects of intercropped and neighbouring trees on the soil of three agroforestry vineyards, in south-western France regions. More precisely soils of the different plots were sampled and the impact of the distance to the tree or to the neighbouring trees (forest) on soil microbial community has been considered. Indigenous soil microbial communities were characterized by a metagenomic approach that consisted in extracting the molecular microbial biomass, then in calculating the soil fungi/bacteria ratio - obtained by qPCR - and then in characterizing the soil microbial diversity - through Illumina sequencing of 16S and 18S regions. Our results showed a significant difference between the soil of agroforestry vineyards and the soil sampled in the neighbouring forest in terms of microbial abundance and diversity. However, only structure and composition of bacterial community seem to be influenced by the implanted trees in the vine plots. In addition, the comparison of microbial co-occurrence networks between vine and forest plots as well as inside vine plots according to distance to the tree allow revealing a more sensitive impact of agroforestry practices. Altogether, the results we obtained build up the first references for concerning the soil of agroforestry vineyards which will be interpreted in terms of soil quality, functioning and sustainability.

Methanogenesis at low temperatures by microflora of tundra wetland soil.

PubMed

Kotsyurbenko, O R; Nozhevnikova, A N; Soloviova, T I; Zavarzin, G A

1996-01-01

Active methanogenesis from organic matter contained in soil samples from tundra wetland occurred even at 6 degrees C. Methane was the only end product in balanced microbial community with H2/CO2 as a substrate, besides acetate was produced as an intermediate at temperatures below 10 degrees C. The activity of different microbial groups of methanogenic community in the temperature range of 6-28 degrees C was investigated using 5% of tundra soil as inoculum. Anaerobic microflora of tundra wetland fermented different organic compounds with formation of hydrogen, volatile fatty acids (VFA) and alcohols. Methane was produced at the second step. Homoacetogenic and methanogenic bacteria competed for such substrates as hydrogen, formate, carbon monoxide and methanol. Acetogens out competed methanogens in an excess of substrate and low density of microbial population. Kinetic analysis of the results confirmed the prevalence of hydrogen acetogenesis on methanogenesis. Pure culture of acetogenic bacteria was isolated at 6 degrees C. Dilution of tundra soil and supply with the excess of substrate disbalanced the methanoigenic microbial community. It resulted in accumulation of acetate and other VFA. In balanced microbial community obviously autotrophic methanogens keep hydrogen concentration below a threshold for syntrophic degradation of VFA. Accumulation of acetate- and H2/CO2-utilising methanogens should be very important in methanogenic microbial community operating at low temperatures.

Microbial Stimulation and Succession following a Test Well Injection Simulating CO₂ Leakage into a Shallow Newark Basin Aquifer

PubMed Central

O’Mullan, Gregory; Dueker, M. Elias; Clauson, Kale; Yang, Qiang; Umemoto, Kelsey; Zakharova, Natalia; Matter, Juerg; Stute, Martin; Takahashi, Taro; Goldberg, David

2015-01-01

In addition to efforts aimed at reducing anthropogenic production of greenhouse gases, geological storage of CO2 is being explored as a strategy to reduce atmospheric greenhouse gas emission and mitigate climate change. Previous studies of the deep subsurface in North America have not fully considered the potential negative effects of CO2 leakage into shallow drinking water aquifers, especially from a microbiological perspective. A test well in the Newark Rift Basin was utilized in two field experiments to investigate patterns of microbial succession following injection of CO2-saturated water into an isolated aquifer interval, simulating a CO2 leakage scenario. A decrease in pH following injection of CO2 saturated aquifer water was accompanied by mobilization of trace elements (e.g. Fe and Mn), and increased bacterial cell concentrations in the recovered water. 16S ribosomal RNA gene sequence libraries from samples collected before and after the test well injection were compared to link variability in geochemistry to changes in aquifer microbiology. Significant changes in microbial composition, compared to background conditions, were found following the test well injections, including a decrease in Proteobacteria, and an increased presence of Firmicutes, Verrucomicrobia and microbial taxa often noted to be associated with iron and sulfate reduction. The concurrence of increased microbial cell concentrations and rapid microbial community succession indicate significant changes in aquifer microbial communities immediately following the experimental CO2 leakage event. Samples collected one year post-injection were similar in cell number to the original background condition and community composition, although not identical, began to revert toward the pre-injection condition, indicating microbial resilience following a leakage disturbance. This study provides a first glimpse into the in situ successional response of microbial communities to CO2 leakage after subsurface injection in the Newark Basin and the potential microbiological impact of CO2 leakage on drinking water resources. PMID:25635675

A precision multi-sampler for deep-sea hydrothermal microbial mat studies

NASA Astrophysics Data System (ADS)

Breier, J. A.; Gomez-Ibanez, D.; Reddington, E.; Huber, J. A.; Emerson, D.

2012-12-01

A new tool was developed for deep-sea microbial mat studies by remotely operated vehicles and was successfully deployed during a cruise to the hydrothermal vent systems of the Mid-Cayman Rise. The Mat Sampler allows for discrete, controlled material collection from complex microbial structures, vertical-profiling within thick microbial mats and particulate and fluid sample collection from venting seafloor fluids. It has a reconfigurable and expandable sample capacity based on magazines of 6 syringes, filters, or water bottles. Multiple magazines can be used such that 12-36 samples can be collected routinely during a single dive; several times more if the dive is dedicated for this purpose. It is capable of hosting in situ physical, electrochemical, and optical sensors, including temperature and oxygen probes in order to guide sampling and to record critical environmental parameters at the time and point of sample collection. The precision sampling capability of this instrument will greatly enhance efforts to understand the structured, delicate, microbial mat communities that grow in diverse benthic habitats.

Bacterial and archaeal communities in the deep-sea sediments of inactive hydrothermal vents in the Southwest India Ridge

NASA Astrophysics Data System (ADS)

Zhang, Likui; Kang, Manyu; Xu, Jiajun; Xu, Jian; Shuai, Yinjie; Zhou, Xiaojian; Yang, Zhihui; Ma, Kesen

2016-05-01

Active deep-sea hydrothermal vents harbor abundant thermophilic and hyperthermophilic microorganisms. However, microbial communities in inactive hydrothermal vents have not been well documented. Here, we investigated bacterial and archaeal communities in the two deep-sea sediments (named as TVG4 and TVG11) collected from inactive hydrothermal vents in the Southwest India Ridge using the high-throughput sequencing technology of Illumina MiSeq2500 platform. Based on the V4 region of 16S rRNA gene, sequence analysis showed that bacterial communities in the two samples were dominated by Proteobacteria, followed by Bacteroidetes, Actinobacteria and Firmicutes. Furthermore, archaeal communities in the two samples were dominated by Thaumarchaeota and Euryarchaeota. Comparative analysis showed that (i) TVG4 displayed the higher bacterial richness and lower archaeal richness than TVG11; (ii) the two samples had more divergence in archaeal communities than bacterial communities. Bacteria and archaea that are potentially associated with nitrogen, sulfur metal and methane cycling were detected in the two samples. Overall, we first provided a comparative picture of bacterial and archaeal communities and revealed their potentially ecological roles in the deep-sea environments of inactive hydrothermal vents in the Southwest Indian Ridge, augmenting microbial communities in inactive hydrothermal vents.

Merging metagenomics and geochemistry reveals environmental controls on biological diversity and evolution.

PubMed

Alsop, Eric B; Boyd, Eric S; Raymond, Jason

2014-05-28

The metabolic strategies employed by microbes inhabiting natural systems are, in large part, dictated by the physical and geochemical properties of the environment. This study sheds light onto the complex relationship between biology and environmental geochemistry using forty-three metagenomes collected from geochemically diverse and globally distributed natural systems. It is widely hypothesized that many uncommonly measured geochemical parameters affect community dynamics and this study leverages the development and application of multidimensional biogeochemical metrics to study correlations between geochemistry and microbial ecology. Analysis techniques such as a Markov cluster-based measure of the evolutionary distance between whole communities and a principal component analysis (PCA) of the geochemical gradients between environments allows for the determination of correlations between microbial community dynamics and environmental geochemistry and provides insight into which geochemical parameters most strongly influence microbial biodiversity. By progressively building from samples taken along well defined geochemical gradients to samples widely dispersed in geochemical space this study reveals strong links between the extent of taxonomic and functional diversification of resident communities and environmental geochemistry and reveals temperature and pH as the primary factors that have shaped the evolution of these communities. Moreover, the inclusion of extensive geochemical data into analyses reveals new links between geochemical parameters (e.g. oxygen and trace element availability) and the distribution and taxonomic diversification of communities at the functional level. Further, an overall geochemical gradient (from multivariate analyses) between natural systems provides one of the most complete predictions of microbial taxonomic and functional composition. Clustering based on the frequency in which orthologous proteins occur among metagenomes facilitated accurate prediction of the ordering of community functional composition along geochemical gradients, despite a lack of geochemical input. The consistency in the results obtained from the application of Markov clustering and multivariate methods to distinct natural systems underscore their utility in predicting the functional potential of microbial communities within a natural system based on system geochemistry alone, allowing geochemical measurements to be used to predict purely biological metrics such as microbial community composition and metabolism.

Microbial community structure and function in sediments from e-waste contaminated rivers at Guiyu area of China.

PubMed

Liu, Jun; Chen, Xi; Shu, Hao-Yue; Lin, Xue-Rui; Zhou, Qi-Xing; Bramryd, Torleif; Shu, Wen-Sheng; Huang, Li-Nan

2018-04-01

The release of toxic organic pollutants and heavy metals by primitive electronic waste (e-waste) processing to waterways has raised significant concerns, but little is known about their potential ecological effects on aquatic biota especially microorganisms. We characterized the microbial community composition and diversity in sediments sampled along two rivers consistently polluted by e-waste, and explored how community functions may respond to the complex combined pollution. High-throughput 16S rRNA gene sequencing showed that Proteobacteria (particularly Deltaproteobacteria) dominated the sediment microbial assemblages followed by Bacteroidetes, Acidobacteria, Chloroflexi and Firmicutes. PICRUSt metagenome inference provided an initial insight into the metabolic potentials of these e-waste affected communities, speculating that organic pollutants degradation in the sediment might be mainly performed by some of the dominant genera (such as Sulfuricurvum, Thiobacillus and Burkholderia) detected in situ. Statistical analyses revealed that toxic organic compounds contributed more to the observed variations in sediment microbial community structure and predicted functions (24.68% and 8.89%, respectively) than heavy metals (12.18% and 4.68%), and Benzo(a)pyrene, bioavailable lead and electrical conductivity were the key contributors. These results have shed light on the microbial assemblages in e-waste contaminated river sediments, indicating a potential influence of e-waste pollution on the microbial community structure and function in aquatic ecosystems. Copyright © 2017 Elsevier Ltd. All rights reserved.

Impacts of Projected Climate Warming and Wetting on Soil Microbial Communities in Alpine Grassland Ecosystems of the Tibetan Plateau.

PubMed

Zeng, Jun; Shen, Ju-Pei; Wang, Jun-Tao; Hu, Hang-Wei; Zhang, Cui-Jing; Bai, Ren; Zhang, Li-Mei; He, Ji-Zheng

2018-05-01

Climate change is projected to have impacts on precipitation and temperature regimes in drylands of high elevation regions, with especially large effects in the Qinghai-Tibetan Plateau. However, there was limited information about how the projected climate change will impact on the soil microbial community and their activity in the region. Here, we present results from a study conducted across 72 soil samples from 24 different sites along a temperature and precipitation gradient (substituted by aridity index ranging from 0.079 to 0.89) of the Plateau, to assess how changes in aridity affect the abundance, community composition, and diversity of bacteria, ammonia-oxidizers, and denitrifers (nirK/S and nosZ genes-containing communities) as well as nitrogen (N) turnover enzyme activities. We found V-shaped or inverted V-shaped relationships between the aridity index (AI) and soil microbial parameters (gene abundance, community structures, microbial diversity, and N turnover enzyme activities) with a threshold at AI = 0.27. The increasing or decreasing rates of the microbial parameters were higher in areas with AI < 0.27 (alpine steppes) than in mesic areas with 0.27 < AI < 0.89 (alpine meadow and swamp meadow). The results indicated that the projected warming and wetting have a strong impact on soil microbial communities in the alpine steppes.

Biogeography and Metabolic Potential of Soil Microbial Communities Across Local Environmental Gradients Illuminated Through Metagenomics

NASA Astrophysics Data System (ADS)

Sharrar, A.; Diamond, S.; Butterfield, C.; Starr, E.; Thomas, B. C.; Banfield, J. F.

2016-12-01

Soils are extremely heterogeneous and diverse microbial habitats. The distribution of microbes and their metabolic functions in soil is important for carbon and nitrogen cycling and overall ecosystem functioning. Little is known about biogeographical patterns of microbes in soil and how they relate to different environmental gradients. To address this topic, we have obtained metagenomes from 86 soil samples taken at the Eel River Critical Zone Observatory and a nearby meadow in the northern California Angelo Coast Range Reserve over a period of two years. These samples span a variety of environmental parameters, including depth, relief, time since last rainfall, and proximity to root carbon inputs. Phylogenetic diversity and community overlap between these samples was analyzed using ribosomal protein sequence identity and scaffold coverage. Independent of genomic bins, de-replicated ribosomal protein sequences were used to identify thousands of unique organisms between datasets. Despite environmental differences, a subset of these organisms were found in every sample. The dominant phyla in this cosmopolitan subset were Proteobacteria, Actinobacteria, Gemmatimonadetes, Verrucomicrobia, Acidobacteria, and Rokubacteria. Archaea and Nitrospirae were particularly prevalent at depths below 30cm. Patterns of ribosomal protein scaffold coverage across samples was used to compare the similarity of the microbial communities. We found that location was the greatest predictor of community similarity, followed by depth. In a subset of 60 samples taken in the same meadow, sampling plot was a greater predictor of community similarity than time since last rainfall in the same year. In addition, genome-independent analyses revealed differences in the metabolic potential for functions involved in nitrogen and carbon metabolism across environmental gradients. This study will further our understanding of soil biogeography and its relationship to overall biogeochemical cycling.

Estimating and comparing microbial diversity in the presence of sequencing errors

PubMed Central

Chiu, Chun-Huo

2016-01-01

Estimating and comparing microbial diversity are statistically challenging due to limited sampling and possible sequencing errors for low-frequency counts, producing spurious singletons. The inflated singleton count seriously affects statistical analysis and inferences about microbial diversity. Previous statistical approaches to tackle the sequencing errors generally require different parametric assumptions about the sampling model or about the functional form of frequency counts. Different parametric assumptions may lead to drastically different diversity estimates. We focus on nonparametric methods which are universally valid for all parametric assumptions and can be used to compare diversity across communities. We develop here a nonparametric estimator of the true singleton count to replace the spurious singleton count in all methods/approaches. Our estimator of the true singleton count is in terms of the frequency counts of doubletons, tripletons and quadrupletons, provided these three frequency counts are reliable. To quantify microbial alpha diversity for an individual community, we adopt the measure of Hill numbers (effective number of taxa) under a nonparametric framework. Hill numbers, parameterized by an order q that determines the measures’ emphasis on rare or common species, include taxa richness (q = 0), Shannon diversity (q = 1, the exponential of Shannon entropy), and Simpson diversity (q = 2, the inverse of Simpson index). A diversity profile which depicts the Hill number as a function of order q conveys all information contained in a taxa abundance distribution. Based on the estimated singleton count and the original non-singleton frequency counts, two statistical approaches (non-asymptotic and asymptotic) are developed to compare microbial diversity for multiple communities. (1) A non-asymptotic approach refers to the comparison of estimated diversities of standardized samples with a common finite sample size or sample completeness. This approach aims to compare diversity estimates for equally-large or equally-complete samples; it is based on the seamless rarefaction and extrapolation sampling curves of Hill numbers, specifically for q = 0, 1 and 2. (2) An asymptotic approach refers to the comparison of the estimated asymptotic diversity profiles. That is, this approach compares the estimated profiles for complete samples or samples whose size tends to be sufficiently large. It is based on statistical estimation of the true Hill number of any order q ≥ 0. In the two approaches, replacing the spurious singleton count by our estimated count, we can greatly remove the positive biases associated with diversity estimates due to spurious singletons and also make fair comparisons across microbial communities, as illustrated in our simulation results and in applying our method to analyze sequencing data from viral metagenomes. PMID:26855872

Microbial Interactions with Natural Organic Matter Extracted from the Oak Ridge FRC

NASA Astrophysics Data System (ADS)

Wu, X.; Jagadamma, S.; Lancaster, A.; Adams, M. W. W.; Hazen, T.; Justice, N.; Chakraborty, R.

2015-12-01

Natural organic matter (NOM) is central to microbial food webs; however, little is known about the interplay between the physical and chemical characteristics of NOM and its turnover by microbial communities based upon biotic and abiotic parameters (e.g., biogenic precursors, redox state, bioavailability). Microbial activity changes the structures and properties that influence further bioavailability of NOM. To date, our understanding of these interactions is insufficient, and indigenous microbial activities that regulate NOM turnover are poorly resolved. It is critical to identify NOM characteristics to the structure and composition of microbial communities and to the metabolic potential of that community. Towards that end, sediment samples collected from the background area well FW305 (Oak Ridge Field Research Center, Oak Ridge, TN) were tested for NOM extraction methods that used three mild solvents, e.g., phosphate buffered saline (PBS), pyrophosphate, and MilliQ-water. MilliQ-water was finally chosen for extracting sediment samples via shaking and sonication. Groundwater from well FW301 was used as an inoculum to which the extracted NOM was added as carbon sources to feed native microbes. To identify the specific functional groups of extracted NOM that are bioavailable to indigenous microbes, several techniques, including FTIR, LC-MS, EEM, were applied to characterize the extracted NOM as well as the transformed NOM metabolites. 16S rDNA amplicon sequencing was also performed to identify the specific microbial diversity that was enriched and microbial isolates that preferentially grew with these NOM was also cultivated in the lab for future detailed studies.

Microbial Biogeography and Core Microbiota of the Rat Digestive Tract

NASA Astrophysics Data System (ADS)

Li, Dongyao; Chen, Haiqin; Mao, Bingyong; Yang, Qin; Zhao, Jianxin; Gu, Zhennan; Zhang, Hao; Chen, Yong Q.; Chen, Wei

2017-04-01

As a long-standing biomedical model, rats have been frequently used in studies exploring the correlations between gastrointestinal (GI) bacterial biota and diseases. In the present study, luminal and mucosal samples taken along the longitudinal axis of the rat digestive tract were subjected to 16S rRNA gene sequencing-based analysis to determine the baseline microbial composition. Results showed that the community diversity increased from the upper to lower GI segments and that the stratification of microbial communities as well as shift of microbial metabolites were driven by biogeographic location. A greater proportion of lactate-producing bacteria (such as Lactobacillus, Turicibacter and Streptococcus) were found in the stomach and small intestine, while anaerobic Lachnospiraceae and Ruminococcaceae, fermenting carbohydrates and plant aromatic compounds, constituted the bulk of the large-intestinal core microbiota where topologically distinct co-occurrence networks were constructed for the adjacent luminal and mucosal compartments. When comparing the GI microbiota from different hosts, we found that the rat microbial biogeography might represent a new reference, distinct from other murine animals. Our study provides the first comprehensive characterization of the rat GI microbiota landscape for the research community, laying the foundation for better understanding and predicting the disease-related alterations in microbial communities.

Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles

PubMed Central

Xiong, Weili; Olm, Matthew R.; Thomas, Brian C.; Baker, Robyn; Firek, Brian; Morowitz, Michael J.; Hettich, Robert L.

2018-01-01

ABSTRACT During the first weeks of life, microbial colonization of the gut impacts human immune system maturation and other developmental processes. In premature infants, aberrant colonization has been implicated in the onset of necrotizing enterocolitis (NEC), a life-threatening intestinal disease. To study the premature infant gut colonization process, genome-resolved metagenomics was conducted on 343 fecal samples collected during the first 3 months of life from 35 premature infants housed in a neonatal intensive care unit, 14 of whom developed NEC, and metaproteomic measurements were made on 87 samples. Microbial community composition and proteomic profiles remained relatively stable on the time scale of a week, but the proteome was more variable. Although genetically similar organisms colonized many infants, most infants were colonized by distinct strains with metabolic profiles that could be distinguished using metaproteomics. Microbiome composition correlated with infant, antibiotics administration, and NEC diagnosis. Communities were found to cluster into seven primary types, and community type switched within infants, sometimes multiple times. Interestingly, some communities sampled from the same infant at subsequent time points clustered with those of other infants. In some cases, switches preceded onset of NEC; however, no species or community type could account for NEC across the majority of infants. In addition to a correlation of protein abundances with organism replication rates, we found that organism proteomes correlated with overall community composition. Thus, this genome-resolved proteomics study demonstrated that the contributions of individual organisms to microbiome development depend on microbial community context. PMID:29636439

Allometry and Ecology of the Bilaterian Gut Microbiome.

PubMed

Sherrill-Mix, Scott; McCormick, Kevin; Lauder, Abigail; Bailey, Aubrey; Zimmerman, Laurie; Li, Yingying; Django, Jean-Bosco N; Bertolani, Paco; Colin, Christelle; Hart, John A; Hart, Terese B; Georgiev, Alexander V; Sanz, Crickette M; Morgan, David B; Atencia, Rebeca; Cox, Debby; Muller, Martin N; Sommer, Volker; Piel, Alexander K; Stewart, Fiona A; Speede, Sheri; Roman, Joe; Wu, Gary; Taylor, Josh; Bohm, Rudolf; Rose, Heather M; Carlson, John; Mjungu, Deus; Schmidt, Paul; Gaughan, Celeste; Bushman, Joyslin I; Schmidt, Ella; Bittinger, Kyle; Collman, Ronald G; Hahn, Beatrice H; Bushman, Frederic D

2018-03-27

Classical ecology provides principles for construction and function of biological communities, but to what extent these apply to the animal-associated microbiota is just beginning to be assessed. Here, we investigated the influence of several well-known ecological principles on animal-associated microbiota by characterizing gut microbial specimens from bilaterally symmetrical animals ( Bilateria ) ranging from flies to whales. A rigorously vetted sample set containing 265 specimens from 64 species was assembled. Bacterial lineages were characterized by 16S rRNA gene sequencing. Previously published samples were also compared, allowing analysis of over 1,098 samples in total. A restricted number of bacterial phyla was found to account for the great majority of gut colonists. Gut microbial composition was associated with host phylogeny and diet. We identified numerous gut bacterial 16S rRNA gene sequences that diverged deeply from previously studied taxa, identifying opportunities to discover new bacterial types. The number of bacterial lineages per gut sample was positively associated with animal mass, paralleling known species-area relationships from island biogeography and implicating body size as a determinant of community stability and niche complexity. Samples from larger animals harbored greater numbers of anaerobic communities, specifying a mechanism for generating more-complex microbial environments. Predictions for species/abundance relationships from models of neutral colonization did not match the data set, pointing to alternative mechanisms such as selection of specific colonists by environmental niche. Taken together, the data suggest that niche complexity increases with gut size and that niche selection forces dominate gut community construction. IMPORTANCE The intestinal microbiome of animals is essential for health, contributing to digestion of foods, proper immune development, inhibition of pathogen colonization, and catabolism of xenobiotic compounds. How these communities assemble and persist is just beginning to be investigated. Here we interrogated a set of gut samples from a wide range of animals to investigate the roles of selection and random processes in microbial community construction. We show that the numbers of bacterial species increased with the weight of host organisms, paralleling findings from studies of island biogeography. Communities in larger organisms tended to be more anaerobic, suggesting one mechanism for niche diversification. Nonselective processes enable specific predictions for community structure, but our samples did not match the predictions of the neutral model. Thus, these findings highlight the importance of niche selection in community construction and suggest mechanisms of niche diversification. Copyright © 2018 Sherrill-Mix et al.

Mesocosms of aquatic bacterial communities from the Cuatro Cienegas Basin (Mexico): a tool to test bacterial community response to environmental stress.

PubMed

Pajares, Silvia; Bonilla-Rosso, German; Travisano, Michael; Eguiarte, Luis E; Souza, Valeria

2012-08-01

Microbial communities are responsible for important ecosystem processes, and their activities are regulated by environmental factors such as temperature and solar ultraviolet radiation. Here we investigate changes in aquatic microbial community structure, diversity, and evenness in response to changes in temperature and UV radiation. For this purpose, 15 mesocosms were seeded with both microbial mat communities and plankton from natural pools within the Cuatro Cienegas Basin (Mexico). Clone libraries (16S rRNA) were obtained from water samples at the beginning and at the end of the experiment (40 days). Phylogenetic analysis indicated substantial changes in aquatic community composition and structure in response to temperature and UV radiation. Extreme treatments with elevation in temperature or UV radiation reduced diversity in relation to the Control treatments, causing a reduction in richness and increase in dominance, with a proliferation of a few resistant operational taxonomic units. Each phylum was affected differentially by the new conditions, which translates in a differential modification of ecosystem functioning. This suggests that the impact of environmental stress, at least at short term, will reshape the aquatic bacterial communities of this unique ecosystem. This work also demonstrates the possibility of designing manageable synthetic microbial community ecosystems where controlled environmental variables can be manipulated. Therefore, microbial model systems offer a complementary approach to field and laboratory studies of global research problems associated with the environment.

An assessment of microbial communities associated with surface mining-disturbed overburden.

PubMed

Poncelet, Dominique M; Cavender, Nicole; Cutright, Teresa J; Senko, John M

2014-03-01

To assess the microbiological changes that occur during the maturation of overburden that has been disturbed by surface mining of coal, a surface mining-disturbed overburden unit in southeastern Ohio, USA was characterized. Overburden from the same unit that had been disturbed for 37 and 16 years were compared to undisturbed soil from the same region. Overburden and soil samples were collected as shallow subsurface cores from each subregion of the mined area (i.e., land 16 years and 37 years post-mining, and unmined land). Chemical and mineralogical characteristics of overburden samples were determined, as were microbial respiration rates. The composition of microbial communities associated with overburden and soil were determined using culture-independent, nucleic acid-based approaches. Chemical and mineralogical evaluation of overburden suggested that weathering of disturbed overburden gave rise to a setting with lower pH and more oxidized chemical constituents. Overburden-associated microbial biomass and respiration rates increased with time after overburden disturbance. Evaluation of 16S rRNA gene libraries that were produced by "next-generation" sequencing technology revealed that recently disturbed overburden contained an abundance of phylotypes attributable to sulfur-oxidizing Limnobacter spp., but with increasing time post-disturbance, overburden-associated microbial communities developed a structure similar to that of undisturbed soil, but retained characteristics of more recently disturbed overburden. Our results indicate that over time, the biogeochemical weathering of disturbed overburden leads to the development of geochemical conditions and microbial communities that approximate those of undisturbed soil, but that this transition is incomplete after 37 years of overburden maturation.

Microbial Community Structure and Arsenic Biogeochemistry in an Acid Vapor-Formed Spring in Tengchong Geothermal Area, China.

PubMed

Jiang, Zhou; Li, Ping; Jiang, Dawei; Dai, Xinyue; Zhang, Rui; Wang, Yanhong; Wang, Yanxin

2016-01-01

Arsenic biogeochemistry has been studied extensively in acid sulfate-chloride hot springs, but not in acid sulfate hot springs with low chloride. In this study, Zhenzhuquan in Tengchong geothermal area, a representative acid sulfate hot spring with low chloride, was chosen to study arsenic geochemistry and microbial community structure using Illumina MiSeq sequencing. Over 0.3 million 16S rRNA sequence reads were obtained from 6-paired parallel water and sediment samples along its outflow channel. Arsenic oxidation occurred in the Zhenxhuquan pool, with distinctly high ratios of arsenate to total dissolved arsenic (0.73-0.86). Coupled with iron and sulfur oxidation along the outflow channel, arsenic accumulated in downstream sediments with concentrations up to 16.44 g/kg and appeared to significantly constrain their microbial community diversity. These oxidations might be correlated with the appearance of some putative functional microbial populations, such as Aquificae and Pseudomonas (arsenic oxidation), Sulfolobus (sulfur and iron oxidation), Metallosphaera and Acidicaldus (iron oxidation). Temperature, total organic carbon and dissolved oxygen significantly shaped the microbial community structure of upstream and downstream samples. In the upstream outflow channel region, most microbial populations were microaerophilic/anaerobic thermophiles and hyperthermophiles, such as Sulfolobus, Nocardia, Fervidicoccus, Delftia, and Ralstonia. In the downstream region, aerobic heterotrophic mesophiles and thermophiles were identified, including Ktedonobacteria, Acidicaldus, Chthonomonas and Sphingobacteria. A total of 72.41-95.91% unassigned-genus sequences were derived from the downstream high arsenic sediments 16S rRNA clone libraries. This study could enable us to achieve an integrated understanding on arsenic biogeochemistry in acid hot springs.

Mosaic patterns of B-vitamin synthesis and utilization in a natural marine microbial community.

PubMed

Gómez-Consarnau, Laura; Sachdeva, Rohan; Gifford, Scott M; Cutter, Lynda S; Fuhrman, Jed A; Sañudo-Wilhelmy, Sergio A; Moran, Mary Ann

2018-04-16

Aquatic environments contain large communities of microorganisms whose synergistic interactions mediate the cycling of major and trace nutrients, including vitamins. B-vitamins are essential coenzymes that many organisms cannot synthesize. Thus, their exchange among de novo synthesizers and auxotrophs is expected to play an important role in the microbial consortia and explain some of the temporal and spatial changes observed in diversity. In this study, we analyzed metatranscriptomes of a natural marine microbial community, diel sampled quarterly over one year to try to identify the potential major B-vitamin synthesizers and consumers. Transcriptomic data showed that the best-represented taxa dominated the expression of synthesis genes for some B-vitamins but lacked transcripts for others. For instance, Rhodobacterales dominated the expression of vitamin-B 12 synthesis, but not of vitamin-B 7 , whose synthesis transcripts were mainly represented by Flavobacteria. In contrast, bacterial groups that constituted less than 4% of the community (e.g., Verrucomicrobia) accounted for most of the vitamin-B 1 synthesis transcripts. Furthermore, ambient vitamin-B 1 concentrations were higher in samples collected during the day, and were positively correlated with chlorophyll-a concentrations. Our analysis supports the hypothesis that the mosaic of metabolic interdependencies through B-vitamin synthesis and exchange are key processes that contribute to shaping microbial communities in nature. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Ecological guild and enzyme activities of rhizosphere soil microbial communities associated with Bt-maize cultivation under field conditions in North West Province of South Africa.

PubMed

van Wyk, Deidré A B; Adeleke, Rasheed; Rhode, Owen H J; Bezuidenhout, Carlos C; Mienie, Charlotte

2017-09-01

Insecticidal proteins expressed by genetically modified Bt maize may alter the enzymatic and microbial communities associated with rhizosphere soil. This study investigated the structure and enzymatic activity of rhizosphere soil microbial communities associated with field grown Bt and non-Bt maize. Rhizosphere soil samples were collected from Bt and non-Bt fields under dryland and irrigated conditions. Samples were subjected to chemical tests, enzyme analyses, and next generation sequencing. Results showed that nitrate and phosphorus concentrations were significantly higher in non-Bt maize dryland soils, while organic carbon was significantly higher in non-Bt maize irrigated field soil. Acid phosphatase and β-glucosidase activities were significantly reduced in soils under Bt maize cultivation. The species diversity differed between fields and Bt and non-Bt maize soils. Results revealed that Actinobacteria, Proteobacteria, and Acidobacteria were the dominant phyla present in these soils. Redundancy analyses indicated that some chemical properties and enzyme activities could explain differences in bacterial community structures. Variances existed in microbial community structures between Bt and non-Bt maize fields. There were also differences between the chemical and biochemical properties of rhizosphere soils under Bt and non-Bt maize cultivation. These differences could be related to agricultural practices and cultivar type. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Zonation of Microbial Communities by a Hydrothermal Mound in the Atlantis II Deep (the Red Sea).

PubMed

Wang, Yong; Li, Jiang Tao; He, Li Sheng; Yang, Bo; Gao, Zhao Ming; Cao, Hui Luo; Batang, Zenon; Al-Suwailem, Abdulaziz; Qian, Pei-Yuan

2015-01-01

In deep-sea geothermal rift zones, the dispersal of hydrothermal fluids of moderately-high temperatures typically forms subseafloor mounds. Major mineral components of the crust covering the mound are barite and metal sulfides. As a result of the continental rifting along the Red Sea, metalliferous sediments accumulate on the seafloor of the Atlantis II Deep. In the present study, a barite crust was identified in a sediment core from the Atlantis II Deep, indicating the formation of a hydrothermal mound at the sampling site. Here, we examined how such a dense barite crust could affect the local environment and the distribution of microbial inhabitants. Our results demonstrate distinctive features of mineral components and microbial communities in the sediment layers separated by the barite crust. Within the mound, archaea accounted for 65% of the community. In contrast, the sediments above the barite boundary were overwhelmed by bacteria. The composition of microbial communities under the mound was similar to that in the sediments of the nearby Discovery Deep and marine cold seeps. This work reveals the zonation of microbial communities after the formation of the hydrothermal mound in the subsurface sediments of the rift basin.

Zonation of Microbial Communities by a Hydrothermal Mound in the Atlantis II Deep (the Red Sea)

PubMed Central

Wang, Yong; Li, Jiang Tao; He, Li Sheng; Yang, Bo; Gao, Zhao Ming; Cao, Hui Luo; Batang, Zenon; Al-Suwailem, Abdulaziz; Qian, Pei-Yuan

2015-01-01

In deep-sea geothermal rift zones, the dispersal of hydrothermal fluids of moderately-high temperatures typically forms subseafloor mounds. Major mineral components of the crust covering the mound are barite and metal sulfides. As a result of the continental rifting along the Red Sea, metalliferous sediments accumulate on the seafloor of the Atlantis II Deep. In the present study, a barite crust was identified in a sediment core from the Atlantis II Deep, indicating the formation of a hydrothermal mound at the sampling site. Here, we examined how such a dense barite crust could affect the local environment and the distribution of microbial inhabitants. Our results demonstrate distinctive features of mineral components and microbial communities in the sediment layers separated by the barite crust. Within the mound, archaea accounted for 65% of the community. In contrast, the sediments above the barite boundary were overwhelmed by bacteria. The composition of microbial communities under the mound was similar to that in the sediments of the nearby Discovery Deep and marine cold seeps. This work reveals the zonation of microbial communities after the formation of the hydrothermal mound in the subsurface sediments of the rift basin. PMID:26485717

Microbiome succession during ammonification in eelgrass bed sediments.

PubMed

Ettinger, Cassandra L; Williams, Susan L; Abbott, Jessica M; Stachowicz, John J; Eisen, Jonathan A

2017-01-01

Eelgrass ( Zostera marina ) is a marine angiosperm and foundation species that plays an important ecological role in primary production, food web support, and elemental cycling in coastal ecosystems. As with other plants, the microbial communities living in, on, and near eelgrass are thought to be intimately connected to the ecology and biology of eelgrass. Here we characterized the microbial communities in eelgrass sediments throughout an experiment to quantify the rate of ammonification, the first step in early remineralization of organic matter, also known as diagenesis, from plots at a field site in Bodega Bay, CA. Sediment was collected from 72 plots from a 15 month long field experiment in which eelgrass genotypic richness and relatedness were manipulated. In the laboratory, we placed sediment samples ( n  = 4 per plot) under a N 2 atmosphere, incubated them at in situ temperatures (15 °C) and sampled them initially and after 4, 7, 13, and 19 days to determine the ammonification rate. Comparative microbiome analysis using high throughput sequencing of 16S rRNA genes was performed on sediment samples taken initially and at seven, 13 and 19 days to characterize changes in the relative abundances of microbial taxa throughout ammonification. Within-sample diversity of the sediment microbial communities across all plots decreased after the initial timepoint using both richness based (observed number of OTUs, Chao1) and richness and evenness based diversity metrics (Shannon, Inverse Simpson). Additionally, microbial community composition changed across the different timepoints. Many of the observed changes in relative abundance of taxonomic groups between timepoints appeared driven by sulfur cycling with observed decreases in predicted sulfur reducers ( Desulfobacterales ) and corresponding increases in predicted sulfide oxidizers ( Thiotrichales ). None of these changes in composition or richness were associated with variation in ammonification rates. Our results showed that the microbiome of sediment from different plots followed similar successional patterns, which we infer to be due to changes related to sulfur metabolism. These large changes likely overwhelmed any potential changes in sediment microbiome related to ammonification rate. We found no relationship between eelgrass presence or genetic composition and the microbiome. This was likely due to our sampling of bulk sediments to measure ammonification rates rather than sampling microbes in sediment directly in contact with the plants and suggests that eelgrass influence on the sediment microbiome may be limited in spatial extent. More in-depth functional studies associated with eelgrass microbiome will be required in order to fully understand the implications of these microbial communities in broader host-plant and ecosystem functions (e.g., elemental cycling and eelgrass-microbe interactions).

Composition of Hydrothermal Vent Microbial Communities as Revealed by Analyses of Signature Lipids, Stable Carbon Isotopes and Aquificales Cultures

NASA Technical Reports Server (NTRS)

Jahnke, Linda L.; Eder, Wolfgang; Huber, Robert; Hinrichs, Kai-Uwe; Hayes, John M.; Cady, Sherry L.; DesMarais, David J.; Hope, Janet M.; Summons, Roger E.

2001-01-01

Extremely thermophilic microbial communities associated with the siliceous vent walls and outflow channel of Octopus Spring, Yellowstone National Park, have been examined for lipid biomarker and carbon isotopic signatures. These data were compared with that obtained from representatives of three Aquificales genera. Thermocrinis ruber, Thermocrinis sp. HI, Hydrogenobacter thermophilus, Aquifex pyrophilus and Aquifex aeolicus all contained phospholipids composed not only of the usual ester-linked fatty acids, but also ether-linked alkyl moieties. The fatty acids of all cultured organisms were dominated by very distinct pattern of n-C-20:1 and cy-C-21 compounds. The alkyl glycerol ethers were present primarily as C-18:0 monoethers with the exception of the Aquifex spp. in which dialkyl glycerol ethers with a boarder carbon-number distribution were also present. These Aquificales biomarker lipids were the major constituents in the lipid extracts of the Octopus Spring microbial samples. Two natural samples, a microbial biofilm growing in association with deposition of amorphous silica on the vent walls at 92 C, and the well-known "pink-streamer community" (PSC), siliceous filaments of a microbial consortia growing in the outflow channel at 87 C were analyzed. Both the biofilm and PSC samples contained mono- and dialkyl glycerol ethers with a prevalence of C-18 and C-20 alkyls. Phospholipid fatty acids were comprised of both the characteristic. Additional information is contained in the original extended abstract.

A Mosaic of Geothermal and Marine Features Shapes Microbial Community Structure on Deception Island Volcano, Antarctica

PubMed Central

Bendia, Amanda G.; Signori, Camila N.; Franco, Diego C.; Duarte, Rubens T. D.; Bohannan, Brendan J. M.; Pellizari, Vivian H.

2018-01-01

Active volcanoes in Antarctica contrast with their predominantly cold surroundings, resulting in environmental conditions capable of selecting for versatile and extremely diverse microbial communities. This is especially true on Deception Island, where geothermal, marine, and polar environments combine to create an extraordinary range of environmental conditions. Our main goal in this study was to understand how microbial community structure is shaped by gradients of temperature, salinity, and geochemistry in polar marine volcanoes. Thereby, we collected surface sediment samples associated with fumaroles and glaciers at two sites on Deception, with temperatures ranging from 0 to 98°C. Sequencing of the 16S rRNA gene was performed to assess the composition and diversity of Bacteria and Archaea. Our results revealed that Deception harbors a combination of taxonomic groups commonly found both in cold and geothermal environments of continental Antarctica, and also groups normally identified at deep and shallow-sea hydrothermal vents, such as hyperthermophilic archaea. We observed a clear separation in microbial community structure across environmental gradients, suggesting that microbial community structure is strongly niche driven on Deception. Bacterial community structure was significantly associated with temperature, pH, salinity, and chemical composition; in contrast, archaeal community structure was strongly associated only with temperature. Our work suggests that Deception represents a peculiar “open-air” laboratory to elucidate central questions regarding molecular adaptability, microbial evolution, and biogeography of extremophiles in polar regions. PMID:29867810

Microbial Activity and Silica Degradation in Rice Straw

NASA Astrophysics Data System (ADS)

Kim, Esther Jin-kyung

Abundantly available agricultural residues like rice straw have the potential to be feedstocks for bioethanol production. Developing optimized conditions for rice straw deconstruction is a key step toward utilizing the biomass to its full potential. One challenge associated with conversion of rice straw to bioenergy is its high silica content as high silica erodes machinery. Another obstacle is the availability of enzymes that hydrolyze polymers in rice straw under industrially relevant conditions. Microbial communities that colonize compost may be a source of enzymes for bioconversion of lignocellulose to products because composting systems operate under thermophilic and high solids conditions that have been shown to be commercially relevant. Compost microbial communities enriched on rice straw could provide insight into a more targeted source of enzymes for the breakdown of rice straw polysaccharides and silica. Because rice straw is low in nitrogen it is important to understand the impact of nitrogen concentrations on the production of enzyme activity by the microbial community. This study aims to address this issue by developing a method to measure microbial silica-degrading activity and measure the effect of nitrogen amendment to rice straw on microbial activity and extracted enzyme activity during a high-solids, thermophilic incubation. An assay was developed to measure silica-degrading enzyme or silicase activity. This process included identifying methods of enzyme extraction from rice straw, identifying a model substrate for the assay, and optimizing measurement techniques. Rice straw incubations were conducted with five different levels of nitrogen added to the biomass. Microbial activity was measured by respiration and enzyme activity. A microbial community analysis was performed to understand the shift in community structure with different treatments. With increased levels of nitrogen, respiration and cellulose and hemicellulose degrading activity increased. Silicase activity did not change across nitrogen treatments despite a shift in microbial community with varied nitrogen concentration. Samples treated with different nitrogen concentrations had similar levels of diversity, however the microbial community composition differed with added nitrogen. The results demonstrated that adding nitrogen to rice straw during thermophilic decomposition nurtured a more active microbial community and promoted enzyme secretion thus improving the ability to discover enzymes for rice straw deconstruction. These results can inform future experiments for cultivating a unique, thriving compost-derived microbial community that can successfully decompose rice straw. Understanding the silicase activity of microorganisms may alleviate the challenges associated with silica in various feedstocks.

Properties of Soil Pore Space Regulate Pathways of Plant Residue Decomposition and Community Structure of Associated Bacteria

PubMed Central

Negassa, Wakene C.; Guber, Andrey K.; Kravchenko, Alexandra N.; Marsh, Terence L.; Hildebrandt, Britton; Rivers, Mark L.

2015-01-01

Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO2 emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis of amplified 16S–18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75–80% of the added plant residue was decomposed, cumulative CO2 emission constituted 1,200 µm C g-1 soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO2 emission constituted 2,000 µm C g-1 soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO2 emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C decomposition processes. PMID:25909444

Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria

DOE PAGES

Negassa, Wakene C.; Guber, Andrey K.; Kravchenko, Alexandra N.; ...

2015-07-01

Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO₂ emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis ofmore » amplified 16S–18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75–80% of the added plant residue was decomposed, cumulative CO₂ emission constituted 1,200 µm C g⁻¹ soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO₂ emission constituted 2,000 µm C g⁻¹ soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO₂ emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C decomposition processes.« less

Assessment of Cu applications in two contrasting soils-effects on soil microbial activity and the fungal community structure.

PubMed

Keiblinger, Katharina M; Schneider, Martin; Gorfer, Markus; Paumann, Melanie; Deltedesco, Evi; Berger, Harald; Jöchlinger, Lisa; Mentler, Axel; Zechmeister-Boltenstern, Sophie; Soja, Gerhard; Zehetner, Franz

2018-03-01

Copper (Cu)-based fungicides have been used in viticulture to prevent downy mildew since the end of the 19th century, and are still used today to reduce fungal diseases. Consequently, Cu has built up in many vineyard soils, and it is still unclear how this affects soil functioning. The present study aimed to assess the short and medium-term effects of Cu contamination on the soil fungal community. Two contrasting agricultural soils, an acidic sandy loam and an alkaline silt loam, were used for an eco-toxicological greenhouse pot experiment. The soils were spiked with a Cu-based fungicide in seven concentrations (0-5000 mg Cu kg -1 soil) and alfalfa was grown in the pots for 3 months. Sampling was conducted at the beginning and at the end of the study period to test Cu toxicity effects on total microbial biomass, basal respiration and enzyme activities. Fungal abundance was analysed by ergosterol at both samplings, and for the second sampling, fungal community structure was evaluated via ITS amplicon sequences. Soil microbial biomass C as well as microbial respiration rate decreased with increasing Cu concentrations, with EC 50 ranging from 76 to 187 mg EDTA-extractable Cu kg -1 soil. Oxidative enzymes showed a trend of increasing activity at the first sampling, but a decline in peroxidase activity was observed for the second sampling. We found remarkable Cu-induced changes in fungal community abundance (EC 50 ranging from 9.2 to 94 mg EDTA-extractable Cu kg -1 soil) and composition, but not in diversity. A large number of diverse fungi were able to thrive under elevated Cu concentrations, though within the order of Hypocreales several species declined. A remarkable Cu-induced change in the community composition was found, which depended on the soil properties and, hence, on Cu availability.

Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria.

PubMed

Negassa, Wakene C; Guber, Andrey K; Kravchenko, Alexandra N; Marsh, Terence L; Hildebrandt, Britton; Rivers, Mark L

2015-01-01

Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO2 emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis of amplified 16S-18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75-80% of the added plant residue was decomposed, cumulative CO2 emission constituted 1,200 µm C g(-1) soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO2 emission constituted 2,000 µm C g(-1) soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO2 emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C decomposition processes.

Microbial communities in sediment from Zostera marina patches, but not the Z. marina leaf or root microbiomes, vary in relation to distance from patch edge

PubMed Central

Ettinger, Cassandra L.; Voerman, Sofie E.; Lang, Jenna M.; Stachowicz, John J.

2017-01-01

Background Zostera marina (also known as eelgrass) is a foundation species in coastal and marine ecosystems worldwide and is a model for studies of seagrasses (a paraphyletic group in the order Alismatales) that include all the known fully submerged marine angiosperms. In recent years, there has been a growing appreciation of the potential importance of the microbial communities (i.e., microbiomes) associated with various plant species. Here we report a study of variation in Z. marina microbiomes from a field site in Bodega Bay, CA. Methods We characterized and then compared the microbial communities of root, leaf and sediment samples (using 16S ribosomal RNA gene PCR and sequencing) and associated environmental parameters from the inside, edge and outside of a single subtidal Z. marina patch. Multiple comparative approaches were used to examine associations between microbiome features (e.g., diversity, taxonomic composition) and environmental parameters and to compare sample types and sites. Results Microbial communities differed significantly between sample types (root, leaf and sediment) and in sediments from different sites (inside, edge, outside). Carbon:Nitrogen ratio and eelgrass density were both significantly correlated to sediment community composition. Enrichment of certain taxonomic groups in each sample type was detected and analyzed in regard to possible functional implications (especially regarding sulfur metabolism). Discussion Our results are mostly consistent with prior work on seagrass associated microbiomes with a few differences and additional findings. From a functional point of view, the most significant finding is that many of the taxa that differ significantly between sample types and sites are closely related to ones commonly associated with various aspects of sulfur and nitrogen metabolism. Though not a traditional model organism, we believe that Z. marina can become a model for studies of marine plant-microbiome interactions. PMID:28462046

Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Negassa, Wakene C.; Guber, Andrey K.; Kravchenko, Alexandra N.

Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO₂ emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis ofmore » amplified 16S–18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75–80% of the added plant residue was decomposed, cumulative CO₂ emission constituted 1,200 µm C g⁻¹ soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO₂ emission constituted 2,000 µm C g⁻¹ soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO₂ emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C decomposition processes.« less

Comparison of Bacterial Diversity in Azorean and Hawai’ian Lava Cave Microbial Mats

PubMed Central

MARSHALL HATHAWAY, JENNIFER J.; GARCIA, MATTHEW G.; BALASCH, MONICA MOYA; SPILDE, MICHAEL N.; STONE, FRED D.; DAPKEVICIUS, MARIA DE LURDES N. E.; AMORIM, ISABEL R.; GABRIEL, ROSALINA; BORGES, PAULO A. V.; NORTHUP, DIANA E.

2015-01-01

Worldwide, lava caves host colorful microbial mats. However, little is known about the diversity of these microorganisms, or what role they may play in the subsurface ecosystem. White and yellow microbial mats were collected from four lava caves each on the Azorean island of Terceira and the Big Island of Hawai’i, to compare the bacterial diversity found in lava caves from two widely separated archipelagos in two different oceans at different latitudes. Scanning electron microscopy of mat samples showed striking similarities between Terceira and Hawai’ian microbial morphologies. 16S rRNA gene clone libraries were constructed to determine the diversity within these lava caves. Fifteen bacterial phyla were found across the samples, with more Actinobacteria clones in Hawai’ian communities and greater numbers of Acidobacteria clones in Terceira communities. Bacterial diversity in the subsurface was correlated with a set of factors. Geographical location was the major contributor to differences in community composition (at the OTU level), together with differences in the amounts of organic carbon, nitrogen and copper available in the lava rock that forms the cave. These results reveal, for the first time, the similarity among the extensive bacterial diversity found in lava caves in two geographically separate locations and contribute to the current debate on the nature of microbial biogeography. PMID:26924866

High-resolution analyses reveal structural diversity patterns of microbial communities in Chromite Ore Processing Residue (COPR) contaminated soils.

PubMed

Min, Xiaobo; Wang, Yangyang; Chai, Liyuan; Yang, Zhihui; Liao, Qi

2017-09-01

To explore how heavy metal contamination in Chromite Ore Processing Residue (COPR) disposal sites determine the dissimilarities of indigenous microbial communities, 16S rRNA gene MiSeq sequencing and advanced statistical methods were applied. 13 soil samples were collected from three COPR disposal sites in Mouding of southwestern, Shangnan of northwestern and Yima of central China. The results of analyses of variance (ANOVA), similarities (ANOSIM), and non-metric multidimensional scaling (NMDS) showed that the structural diversity of the microbial communities in the samples with high total chromium (Cr) content (more than 300 mg kg -1 ; High group) were significantly lesser than in the Low group (less than 90 mg kg -1 ) regardless of their geographical distribution. But their diversity had virtually rehabilitated under the pressures of long-term metal contamination. Furthermore, the similarity percentage (SIMPER) analysis indicated that the major dissimilarity contributors Micrococcaceae, Delftia, and Streptophyta, possibly having Cr(VI)-resistant and/or Cr(VI)-reducing capability, were dominant in the High group, while Ramlibacter and Gemmatimonas with potential resistances to other heavy metals were prevalent in the Low group. In addition, the multivariate regression tree (MRT), aggregated boosted tree (ABT), and Mantel test revealed that total Cr content affiliated with Cr(VI) was the principal factor shaping the dissimilarities between the soil microbial communities in the COPR sites. Our findings provide a deep insight of the influence of these heavy metals on the microbial communities in the COPR disposal sites and will facilitate bioremediation on such site. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microbial diversity within basement fluids of the sediment-buried Juan de Fuca Ridge flank

PubMed Central

Jungbluth, Sean P; Grote, Jana; Lin, Huei-Ting; Cowen, James P; Rappé, Michael S

2013-01-01

Despite its immense size, logistical and methodological constraints have largely limited microbiological investigations of the subseafloor basement biosphere. In this study, a unique sampling system was used to collect fluids from the subseafloor basaltic crust via a Circulation Obviation Retrofit Kit (CORK) observatory at Integrated Ocean Drilling Program borehole 1301A, located at a depth of 2667 m in the Pacific Ocean on the eastern flank of the Juan de Fuca Ridge. Here, a fluid delivery line directly accesses a 3.5 million years old basalt-hosted basement aquifer, overlaid by 262 m of sediment, which serves as a barrier to direct exchange with bottom seawater. At an average of 1.2 × 104 cells ml−1, microorganisms in borehole fluids were nearly an order of magnitude less abundant than in surrounding bottom seawater. Ribosomal RNA genes were characterized from basement fluids, providing the first snapshots of microbial community structure using a high-integrity fluid delivery line. Interestingly, microbial communities retrieved from different CORKs (1026B and 1301A) nearly a decade apart shared major community members, consistent with hydrogeological connectivity. However, over three sampling years, the dominant gene clone lineage changed from relatives of Candidatus Desulforudis audaxviator within the bacterial phylum Firmicutes in 2008 to the Miscellaneous Crenarchaeotic Group in 2009 and a lineage within the JTB35 group of Gammaproteobacteria in 2010, and statistically significant variation in microbial community structure was observed. The enumeration of different phylogenetic groups of cells within borehole 1301A fluids supported our observation that the deep subsurface microbial community was temporally dynamic. PMID:22791235

Geochemical Influence on Microbial Communities at CO2-Leakage Analog Sites.

PubMed

Ham, Baknoon; Choi, Byoung-Young; Chae, Gi-Tak; Kirk, Matthew F; Kwon, Man Jae

2017-01-01

Microorganisms influence the chemical and physical properties of subsurface environments and thus represent an important control on the fate and environmental impact of CO 2 that leaks into aquifers from deep storage reservoirs. How leakage will influence microbial populations over long time scales is largely unknown. This study uses natural analog sites to investigate the long-term impact of CO 2 leakage from underground storage sites on subsurface biogeochemistry. We considered two sites with elevated CO 2 levels (sample groups I and II) and one control site with low CO 2 content (group III). Samples from sites with elevated CO 2 had pH ranging from 6.2 to 4.5 and samples from the low-CO 2 control group had pH ranging from 7.3 to 6.2. Solute concentrations were relatively low for samples from the control group and group I but high for samples from group II, reflecting varying degrees of water-rock interaction. Microbial communities were analyzed through clone library and MiSeq sequencing. Each 16S rRNA analysis identified various bacteria, methane-producing archaea, and ammonia-oxidizing archaea. Both bacterial and archaeal diversities were low in groundwater with high CO 2 content and community compositions between the groups were also clearly different. In group II samples, sequences classified in groups capable of methanogenesis, metal reduction, and nitrate reduction had higher relative abundance in samples with relative high methane, iron, and manganese concentrations and low nitrate levels. Sequences close to Comamonadaceae were abundant in group I, while the taxa related to methanogens, Nitrospirae , and Anaerolineaceae were predominant in group II. Our findings provide insight into subsurface biogeochemical reactions that influence the carbon budget of the system including carbon fixation, carbon trapping, and CO 2 conversion to methane. The results also suggest that monitoring groundwater microbial community can be a potential tool for tracking CO 2 leakage from geologic storage sites.