Characterisation of the bacterial community structures in the intestine of Lampetra morii.

PubMed

Li, Yingying; Xie, Wenfang; Li, Qingwei

2016-07-01

The metagenomic analysis and 16S rDNA sequencing method were used to investigate the bacterial community in the intestines of Lampetra morii. The bacterial community structure in L. morii intestine was relatively simple. Eight different operational taxonomic units were observed. Chitinophagaceae_unclassified (26.5 %) and Aeromonas spp. (69.6 %) were detected as dominant members at the genus level. The non-dominant genera were as follows: Acinetobacter spp. (1.4 %), Candidatus Bacilloplasma (2.5 %), Enterobacteria spp. (1.5 %), Shewanella spp. (0.04 %), Vibrio spp. (0.09 %), and Yersinia spp. (1.8 %). The Shannon-Wiener (H) and Simpson (1-D) indexes were 0.782339 and 0.5546, respectively. The rarefaction curve representing the bacterial community richness and Shannon-Wiener curve representing the bacterial community diversity reached asymptote, which indicated that the sequence depth were sufficient to represent the majority of species richness and bacterial community diversity. The number of Aeromonas in lamprey intestine was two times higher after stimulation by lipopolysaccharide than PBS. This study provides data for understanding the bacterial community harboured in lamprey intestines and exploring potential key intestinal symbiotic bacteria essential for the L. morii immune response.

Structure of the Bacterial Community in Different Stages of Early Childhood Caries.

PubMed

Ximenes, Marcos; Armas, Rafael Dutra de; Triches, Thaisa Cezária; Cardoso, Mariane; Vieira, Ricardo de Souza

2018-01-15

To characterise in vivo the structure of bacterial communities in decayed and sound primary teeth. Samples of biofilms were collected from three groups of patients with complete and exclusively primary dentition (n = 45): G1: sound teeth (n = 15); G2: enamel lesion (n = 15); G3: dentin lesion (n = 15). DNA was extracted (CTAB 2%) from the biofilm, the partial 16S rRNA gene was amplified with Bacteria Universal Primers (BA338fGC - UN518r) and subjected to DGGE (denaturing gradient gel electrophoresis). Multidimensional scaling and ANOSIM (analysis of similarity) were employed to determine the structure of the bacterial communities. The amplicon richness was determined by averaging amplicons, with the differences between treatments determined with ANOVA, while means were compared using Tukey's test (p < 0.05). Compared to sound teeth, a greater variety of bacterial communities was found in decayed teeth. Despite the differences between the bacterial communities of sound teeth and decayed teeth, the Venn diagram showed that the samples had 38 amplicons in common. Greater amplicon richness was observed in samples of decayed teeth (enamel: 20.5 ± 2.7; dentin: 20.1 ± 2.8) compared with the sound samples (12.0 ± 4.3) (p <0.05), indicating enhanced growth for specific groups of bacteria on decayed teeth. Although there is less bacterial diversity on sound than ECC-decayed teeth, the bacterial communities are very similar.

[Effects of Phyllostachys edulis cultivation on soil bacterial and fungal community structure and diversity].

PubMed

Zhao, Tian Xin; Mao, Xin Wei; Cheng, Min; Chen, Jun Hui; Qin, Hua; Li, Yong Chun; Liang, Chen Fei; Xu, Qiu Fang

2017-11-01

This study examined how soil bacterial and fungal communities responded to the cultivation history of Moso bamboo in Anji and Changxing counties, Huzhou, Zhejiang, China. Soil samples (0-20 and 20-40 cm) were taken from bamboo plantations subjected to different cultivation histories and analyzed the community structures of soil bacterial and fungal by PCR-DGGE methods. It was found that soil bacterial and fungal communities varied greatly with the development of bamboo plantations which converted from Masson pine forest or formed via invading adjacent broadleaf shrub forest. Soil bacterial community structures exhibited a greater response to bamboo cultivation time than fungal community, but bacteria structure of surface soil displayed an ability of resiliency to disturbance and the tendency to recover to the original state. The cultivation time, sampling site and soil layer significantly affected the biodiversity of soil bacteria and fungi, especially the latter two factors. Redundancy analysis (RDA) of soil properties and bacteria or fungi communities showed that there were no accordant factors to drive the alteration of microbial structure, and the first two axes explained less than 65.0% of variance for most of the sampling sites and soil layers, indicating there existed soil parameters besides the five examined that contributed to microbial community alteration.

Bacterial community structure in the drinking water microbiome is governed by filtration processes.

PubMed

Pinto, Ameet J; Xi, Chuanwu; Raskin, Lutgarde

2012-08-21

The bacterial community structure of a drinking water microbiome was characterized over three seasons using 16S rRNA gene based pyrosequencing of samples obtained from source water (a mix of a groundwater and a surface water), different points in a drinking water plant operated to treat this source water, and in the associated drinking water distribution system. Even though the source water was shown to seed the drinking water microbiome, treatment process operations limit the source water's influence on the distribution system bacterial community. Rather, in this plant, filtration by dual media rapid sand filters played a primary role in shaping the distribution system bacterial community over seasonal time scales as the filters harbored a stable bacterial community that seeded the water treatment processes past filtration. Bacterial taxa that colonized the filter and sloughed off in the filter effluent were able to persist in the distribution system despite disinfection of finished water by chloramination and filter backwashing with chloraminated backwash water. Thus, filter colonization presents a possible ecological survival strategy for bacterial communities in drinking water systems, which presents an opportunity to control the drinking water microbiome by manipulating the filter microbial community. Grouping bacterial taxa based on their association with the filter helped to elucidate relationships between the abundance of bacterial groups and water quality parameters and showed that pH was the strongest regulator of the bacterial community in the sampled drinking water system.

Bacterial community structure and function shift along a successional series of tidal flats in the Yellow River Delta

PubMed Central

Lv, Xiaofei; Ma, Bin; Yu, Junbao; Chang, Scott X.; Xu, Jianming; Li, Yunzhao; Wang, Guangmei; Han, Guangxuan; Bo, Guan; Chu, Xiaojing

2016-01-01

Coastal ecosystems play significant ecological and economic roles but are threatened and facing decline. Microbes drive various biogeochemical processes in coastal ecosystems. Tidal flats are critical components of coastal ecosystems; however, the structure and function of microbial communities in tidal flats are poorly understood. Here we investigated the seasonal variations of bacterial communities along a tidal flat series (subtidal, intertidal and supratidal flats) and the factors affecting the variations. Bacterial community composition and diversity were analyzed over four seasons by 16S rRNA genes using the Ion Torrent PGM platform. Bacterial community composition differed significantly along the tidal flat series. Bacterial phylogenetic diversity increased while phylogenetic turnover decreased from subtidal to supratidal flats. Moreover, the bacterial community structure differed seasonally. Canonical correspondence analysis identified salinity as a major environmental factor structuring the microbial community in the sediment along the successional series. Meanwhile, temperature and nitrite concentration were major drivers of seasonal microbial changes. Despite major compositional shifts, nitrogen, methane and energy metabolisms predicted by PICRUSt were inhibited in the winter. Taken together, this study indicates that bacterial community structure changed along the successional tidal flat series and provides new insights on the characteristics of bacterial communities in coastal ecosystems. PMID:27824160

Bacterial community structure and function shift along a successional series of tidal flats in the Yellow River Delta.

PubMed

Lv, Xiaofei; Ma, Bin; Yu, Junbao; Chang, Scott X; Xu, Jianming; Li, Yunzhao; Wang, Guangmei; Han, Guangxuan; Bo, Guan; Chu, Xiaojing

2016-11-08

Coastal ecosystems play significant ecological and economic roles but are threatened and facing decline. Microbes drive various biogeochemical processes in coastal ecosystems. Tidal flats are critical components of coastal ecosystems; however, the structure and function of microbial communities in tidal flats are poorly understood. Here we investigated the seasonal variations of bacterial communities along a tidal flat series (subtidal, intertidal and supratidal flats) and the factors affecting the variations. Bacterial community composition and diversity were analyzed over four seasons by 16S rRNA genes using the Ion Torrent PGM platform. Bacterial community composition differed significantly along the tidal flat series. Bacterial phylogenetic diversity increased while phylogenetic turnover decreased from subtidal to supratidal flats. Moreover, the bacterial community structure differed seasonally. Canonical correspondence analysis identified salinity as a major environmental factor structuring the microbial community in the sediment along the successional series. Meanwhile, temperature and nitrite concentration were major drivers of seasonal microbial changes. Despite major compositional shifts, nitrogen, methane and energy metabolisms predicted by PICRUSt were inhibited in the winter. Taken together, this study indicates that bacterial community structure changed along the successional tidal flat series and provides new insights on the characteristics of bacterial communities in coastal ecosystems.

Phylogenetic structure of soil bacterial communities predicts ecosystem functioning.

PubMed

Pérez-Valera, Eduardo; Goberna, Marta; Verdú, Miguel

2015-05-01

Quantifying diversity with phylogeny-informed metrics helps understand the effects of diversity on ecosystem functioning (EF). The sign of these effects remains controversial because phylogenetic diversity and taxonomic identity may interactively influence EF. Positive relationships, traditionally attributed to complementarity effects, seem unimportant in natural soil bacterial communities. Negative relationships could be attributed to fitness differences leading to the overrepresentation of few productive clades, a mechanism recently invoked to assemble soil bacteria communities. We tested in two ecosystems contrasting in terms of environmental heterogeneity whether two metrics of phylogenetic community structure, a simpler measure of phylogenetic diversity (NRI) and a more complex metric incorporating taxonomic identity (PCPS), correctly predict microbially mediated EF. We show that the relationship between phylogenetic diversity and EF depends on the taxonomic identity of the main coexisting lineages. Phylogenetic diversity was negatively related to EF in soils where a marked fertility gradient exists and a single and productive clade (Proteobacteria) outcompete other clades in the most fertile plots. However, phylogenetic diversity was unrelated to EF in soils where the fertility gradient is less marked and Proteobacteria coexist with other abundant lineages. Including the taxonomic identity of bacterial lineages in metrics of phylogenetic community structure allows the prediction of EF in both ecosystems. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Matrix composition and community structure analysis of a novel bacterial pyrite leaching community.

PubMed

Ziegler, Sibylle; Ackermann, Sonia; Majzlan, Juraj; Gescher, Johannes

2009-09-01

Here we describe a novel bacterial community that is embedded in a matrix of carbohydrates and bio/geochemical products of pyrite (FeS(2)) oxidation. This community grows in stalactite-like structures--snottites--on the ceiling of an abandoned pyrite mine at pH values of 2.2-2.6. The aqueous phase in the matrix contains 200 mM of sulfate and total iron concentrations of 60 mM. Micro-X-ray diffraction analysis showed that jarosite [(K,Na,H(3)O)Fe(3)(SO(4))(2)(OH)(6)] is the major mineral embedded in the snottites. X-ray absorption near-edge structure experiments revealed three different sulfur species. The major signal can be ascribed to sulfate, and the other two features may correspond to thiols and sulfoxides. Arabinose was detected as the major sugar component in the extracellular polymeric substance. Via restriction fragment length polymorphism analysis, a community was found that mainly consists of iron oxidizing Leptospirillum and Ferrovum species but also of bacteria that could be involved in dissimilatory sulfate and dissimilatory iron reduction. Each snottite can be regarded as a complex, self-contained consortium of bacterial species fuelled by the decomposition of pyrite.

Disconnect of microbial structure and function: enzyme activities and bacterial communities in nascent stream corridors.

PubMed

Frossard, Aline; Gerull, Linda; Mutz, Michael; Gessner, Mark O

2012-03-01

A fundamental issue in microbial and general ecology is the question to what extent environmental conditions dictate the structure of communities and the linkages with functional properties of ecosystems (that is, ecosystem function). We approached this question by taking advantage of environmental gradients established in soil and sediments of small stream corridors in a recently created, early successional catchment. Specifically, we determined spatial and temporal patterns of bacterial community structure and their linkages with potential microbial enzyme activities along the hydrological flow paths of the catchment. Soil and sediments were sampled in a total of 15 sites on four occasions spread throughout a year. Denaturing gradient gel electrophoresis (DGGE) was used to characterize bacterial communities, and substrate analogs linked to fluorescent molecules served to track 10 different enzymes as specific measures of ecosystem function. Potential enzyme activities varied little among sites, despite contrasting environmental conditions, especially in terms of water availability. Temporal changes, in contrast, were pronounced and remarkably variable among the enzymes tested. This suggests much greater importance of temporal dynamics than spatial heterogeneity in affecting specific ecosystem functions. Most strikingly, bacterial community structure revealed neither temporal nor spatial patterns. The resulting disconnect between bacterial community structure and potential enzyme activities indicates high functional redundancy within microbial communities even in the physically and biologically simplified stream corridors of early successional landscapes.

Jellyfish modulate bacterial dynamic and community structure.

PubMed

Tinta, Tinkara; Kogovšek, Tjaša; Malej, Alenka; Turk, Valentina

2012-01-01

Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom-forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish-enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to 'jellyfish-associated' and 'free-living' bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into possible changes in

Structure of bacterial communities in soil following cover crop and organic fertilizer incorporation.

PubMed

Fernandez, Adria L; Sheaffer, Craig C; Wyse, Donald L; Staley, Christopher; Gould, Trevor J; Sadowsky, Michael J

2016-11-01

Incorporation of organic material into soils is an important element of organic farming practices that can affect the composition of the soil bacterial communities that carry out nutrient cycling and other functions crucial to crop health and growth. We conducted a field experiment to determine the effects of cover crops and fertilizers on bacterial community structure in agricultural soils under long-term organic management. Illumina sequencing of 16S rDNA revealed diverse communities comprising 45 bacterial phyla in corn rhizosphere and bulk field soil. Community structure was most affected by location and by the rhizosphere effect, followed by sampling time and amendment treatment. These effects were associated with soil physicochemical properties, including pH, moisture, organic matter, and nutrient levels. Treatment differences were apparent in bulk and rhizosphere soils at the time of peak corn growth in the season following cover crop and fertilizer application. Cover crop and fertilizer treatments tended to lower alpha diversity in early season samples. However, winter rye, oilseed radish, and buckwheat cover crop treatments increased alpha diversity in some later season samples compared to a no-amendment control. Fertilizer treatments and some cover crops decreased relative abundance of members of the ammonia-oxidizing family Nitrosomonadaceae. Pelleted poultry manure and Sustane® (a commercial fertilizer) decreased the relative abundance of Rhizobiales. Our data point to a need for future research exploring how (1) cover crops influence bacterial community structure and functions, (2) these effects differ with biomass composition and quantity, and (3) existing soil conditions and microbial community composition influence how soil microbial populations respond to agricultural management practices.

Dynamic Effects of Biochar on the Bacterial Community Structure in Soil Contaminated with Polycyclic Aromatic Hydrocarbons.

PubMed

Song, Yang; Bian, Yongrong; Wang, Fang; Xu, Min; Ni, Ni; Yang, Xinglun; Gu, Chenggang; Jiang, Xin

2017-08-16

Amending soil with biochar is an effective soil remediation strategy for organic contaminants. This study investigated the dynamic effects of wheat straw biochar on the bacterial community structure during remediation by high-throughput sequencing. The wheat straw biochar amended into the soil significantly reduced the bioavailability and toxicity of polycyclic aromatic hydrocarbons (PAHs). Biochar amendment helped to maintain the bacterial diversity in the PAH-contaminated soil. The relationship between the immobilization of PAHs and the soil bacterial diversity fit a quadratic model. Before week 12 of the incubation, the incubation time was the main factor contributing to the changes in the soil bacterial community structure. However, biochar greatly affected the bacterial community structure after 12 weeks of amendment, and the effects were dependent upon the biochar type. Amendment with biochar mainly facilitated the growth of rare bacterial genera (relative abundance of 0.01-1%) in the studied soil. Therefore, the application of wheat straw biochar into PAH-contaminated soil can reduce the environmental risks of PAHs and benefit the soil microbial ecology.

Phospholipid-derived fatty acids and quinones as markers for bacterial biomass and community structure in marine sediments.

PubMed

Kunihiro, Tadao; Veuger, Bart; Vasquez-Cardenas, Diana; Pozzato, Lara; Le Guitton, Marie; Moriya, Kazuyoshi; Kuwae, Michinobu; Omori, Koji; Boschker, Henricus T S; van Oevelen, Dick

2014-01-01

Phospholipid-derived fatty acids (PLFA) and respiratory quinones (RQ) are microbial compounds that have been utilized as biomarkers to quantify bacterial biomass and to characterize microbial community structure in sediments, waters, and soils. While PLFAs have been widely used as quantitative bacterial biomarkers in marine sediments, applications of quinone analysis in marine sediments are very limited. In this study, we investigated the relation between both groups of bacterial biomarkers in a broad range of marine sediments from the intertidal zone to the deep sea. We found a good log-log correlation between concentrations of bacterial PLFA and RQ over several orders of magnitude. This relationship is probably due to metabolic variation in quinone concentrations in bacterial cells in different environments, whereas PLFA concentrations are relatively stable under different conditions. We also found a good agreement in the community structure classifications based on the bacterial PLFAs and RQs. These results strengthen the application of both compounds as quantitative bacterial biomarkers. Moreover, the bacterial PLFA- and RQ profiles revealed a comparable dissimilarity pattern of the sampled sediments, but with a higher level of dissimilarity for the RQs. This means that the quinone method has a higher resolution for resolving differences in bacterial community composition. Combining PLFA and quinone analysis as a complementary method is a good strategy to yield higher resolving power in bacterial community structure.

Coupled cryoconite ecosystem structure-function relationships are revealed by comparing bacterial communities in alpine and Arctic glaciers.

PubMed

Edwards, Arwyn; Mur, Luis A J; Girdwood, Susan E; Anesio, Alexandre M; Stibal, Marek; Rassner, Sara M E; Hell, Katherina; Pachebat, Justin A; Post, Barbara; Bussell, Jennifer S; Cameron, Simon J S; Griffith, Gareth Wyn; Hodson, Andrew J; Sattler, Birgit

2014-08-01

Cryoconite holes are known as foci of microbial diversity and activity on polar glacier surfaces, but are virtually unexplored microbial habitats in alpine regions. In addition, whether cryoconite community structure reflects ecosystem functionality is poorly understood. Terminal restriction fragment length polymorphism and Fourier transform infrared metabolite fingerprinting of cryoconite from glaciers in Austria, Greenland and Svalbard demonstrated cryoconite bacterial communities are closely correlated with cognate metabolite fingerprints. The influence of bacterial-associated fatty acids and polysaccharides was inferred, underlining the importance of bacterial community structure in the properties of cryoconite. Thus, combined application of T-RFLP and FT-IR metabolite fingerprinting promises high throughput, and hence, rapid assessment of community structure-function relationships. Pyrosequencing revealed Proteobacteria were particularly abundant, with Cyanobacteria likely acting as ecosystem engineers in both alpine and Arctic cryoconite communities. However, despite these generalities, significant differences in bacterial community structures, compositions and metabolomes are found between alpine and Arctic cryoconite habitats, reflecting the impact of local and regional conditions on the challenges of thriving in glacial ecosystems. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

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

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

Bacterial community structure in aquifers corresponds to stratigraphy

NASA Astrophysics Data System (ADS)

Beyer, Andrea; Möller, Silke; Neumann, Stefan; Burow, Katja; Gutmann, Falko; Lindner, Julia; Müsse, Steffen; Kothe, Erika; Büchel, Georg

2014-05-01

So far, groundwater microbiology with respect to different host rocks has not been well described in the literature. However, factors influencing the communities would be of interest to provide a tool for mapping groundwater paths. The Thuringian Basin (Germany) studied here, contains formations of the Permian (Zechstein) and also Triassic period of Buntsandstein, Muschelkalk and Keuper, all of which can be found to crop out at the surface in different regions. We analyzed the bacterial community of nine natural springs and sixteen groundwater wells of the respective rock formations as well as core material from the Zechstein salts. For that we sampled in a mine 3 differnet salt rock samples (carnallitite, halite and sylvinitite). To validate the different approaches, similar rock formations were compared and a consistent microbial community for Buntsandstein could be verified. Similary, for Zechstein, the presence of halophiles was seen with cultivation, isolation directly from the rock material and also in groundwater with DNA-dependent approaches. A higher overlap between sandstone- and limestone-derived communities was visible as if compared to the salt formations. Principal component analysis confirmed formation specific patterns for Muschelkalk, Buntsandstein and Zechstein for the bacterial taxa present, with some overlaps. Bacilli and Gammaproteobacteria were the major groups, with the genera Pseudomonas, Marinomonas, Bacillus, Marinobacter and Pseudoalteromonas representing the communities. The bacteria are well adapted to their respective environment with survival strategies including a wide range of salinity which makes them suitable as tracers for fluid movement below the ground. The results indicate the usefulness and robustness of the approach taken here to investigate aquifer community structures in dependence of the stratigraphy of the groundwater reservoir.

Host species and developmental stage, but not host social structure, affects bacterial community structure in socially polymorphic bees.

PubMed

McFrederick, Quinn S; Wcislo, William T; Hout, Michael C; Mueller, Ulrich G

2014-05-01

Social transmission and host developmental stage are thought to profoundly affect the structure of bacterial communities associated with honey bees and bumble bees, but these ideas have not been explored in other bee species. The halictid bees Megalopta centralis and M. genalis exhibit intrapopulation social polymorphism, which we exploit to test whether bacterial communities differ by host social structure, developmental stage, or host species. We collected social and solitary Megalopta nests and sampled bees and nest contents from all stages of host development. To survey these bacterial communities, we used 16S rRNA gene 454 pyrosequencing. We found no effect of social structure, but found differences by host species and developmental stage. Wolbachia prevalence differed between the two host species. Bacterial communities associated with different developmental stages appeared to be driven by environmentally acquired bacteria. A Lactobacillus kunkeei clade bacterium that is consistently associated with other bee species was dominant in pollen provisions and larval samples, but less abundant in mature larvae and pupae. Foraging adults appeared to often reacquire L. kunkeei clade bacteria, likely while foraging at flowers. Environmental transmission appears to be more important than social transmission for Megalopta bees at the cusp between social and solitary behavior. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Experimental warming effects on the bacterial community structure and diversity

NASA Astrophysics Data System (ADS)

Kim, W.; Han, S.; Adams, J.; Son, Y.

2014-12-01

The objective of this study is to investigate the responses of soil bacterial community to future temperature increase by conducting open-field warming experiment. We conducted an open-field experimental warming system using infra-red heater in 2011 and regulated the temperature of warmed plots by 3oC higher than that of control plots constantly. The seeds of Pinus densiflora, Abies holophylla, Abies koreana, Betula costata, Quercus variabilis, Fraxinus rhynchophylla, and Zelkova serrata were planted in each 1 m × 1 m plot (n=3) in April, 2012. We collected soil samples from the rhizosphere of 7 tree species. DNA was extracted and PCR-amplified for the bacterial 16S gene targeting V1-V3 region. The paired-end sequencing was performed at Beijing Genome Institute (BGI, Hong Kong, China) using 2× 100 bp Hiseq2000 (Illumina). This study aimed to answer the following prediction/hypothesis: 1) Experimental warming will change the structure of soil bacterial community, 2) There will be distinct 'indicator group' which response to warming treatment relatively more sensitive than other groups. 3) Warming treatment will enhance the microbial activity in terms of soil respiration. 4) The rhizoplane bacterial communities for each of 7 tree species will show different response pattern to warming treatment. Since the sequence data does not arrive before the submission deadline, therefore, we would like to present the results and discussions on December 2014, AGU Fall Meeting.

Bacterial Community Structure and Physiological State within an Industrial Phenol Bioremediation System

PubMed Central

Whiteley, Andrew S.; Bailey, Mark J.

2000-01-01

The structure of bacterial populations in specific compartments of an operational industrial phenol remediation system was assessed to examine bacterial community diversity, distribution, and physiological state with respect to the remediation of phenolic polluted wastewater. Rapid community fingerprinting by PCR-based denaturing gradient gel electrophoresis (DGGE) of 16S rDNA indicated highly structured bacterial communities residing in all nine compartments of the treatment plant and not exclusively within the Vitox biological reactor. Whole-cell targeting by fluorescent in situ hybridization with specific oligonucleotides (directed to the α, β and γ subclasses of the class Proteobacteria [α-, β-, and γ-Proteobacteria, respectively], the Cytophaga-Flavobacterium group, and the Pseudomonas group) tended to mirror gross changes in bacterial community composition when compared with DGGE community fingerprinting. At the whole-cell level, the treatment compartments were numerically dominated by cells assigned to the Cytophaga-Flavobacterium group and to the γ-Proteobacteria. The α subclass Proteobacteria were of low relative abundance throughout the treatment system whilst the β subclass of the Proteobacteria exhibited local dominance in several of the processing compartments. Quantitative image analyses of cellular fluorescence was used as an indicator of physiological state within the populations probed with rDNA. For cells hybridized with EUB338, the mean fluorescence per cell decreased with increasing phenolic concentration, indicating the strong influence of the primary pollutant upon cellular rRNA content. The γ subclass of the Proteobacteria had a ribosome content which correlated positively with total phenolics and thiocyanate. While members of the Cytophaga-Flavobacterium group were numerically dominant in the processing system, their abundance and ribosome content data for individual populations did not correlate with any of the measured chemical

Bacterial diversity, community structure and potential growth rates along an estuarine salinity gradient

PubMed Central

Campbell, Barbara J; Kirchman, David L

2013-01-01

Very little is known about growth rates of individual bacterial taxa and how they respond to environmental flux. Here, we characterized bacterial community diversity, structure and the relative abundance of 16S rRNA and 16S rRNA genes (rDNA) using pyrosequencing along the salinity gradient in the Delaware Bay. Indices of diversity, evenness, structure and growth rates of the surface bacterial community significantly varied along the transect, reflecting active mixing between the freshwater and marine ends of the estuary. There was no positive correlation between relative abundances of 16S rRNA and rDNA for the entire bacterial community, suggesting that abundance of bacteria does not necessarily reflect potential growth rate or activity. However, for almost half of the individual taxa, 16S rRNA positively correlated with rDNA, suggesting that activity did follow abundance in these cases. The positive relationship between 16S rRNA and rDNA was less in the whole water community than for free-living taxa, indicating that the two communities differed in activity. The 16S rRNA:rDNA ratios of some typically marine taxa reflected differences in light, nutrient concentrations and other environmental factors along the estuarine gradient. The ratios of individual freshwater taxa declined as salinity increased, whereas the 16S rRNA:rDNA ratios of only some typical marine bacteria increased as salinity increased. These data suggest that physical and other bottom-up factors differentially affect growth rates, but not necessarily abundance of individual taxa in this highly variable environment. PMID:22895159

Secondary successional trajectories of structural and catabolic bacterial communities in oil-polluted soil planted with hybrid poplar.

PubMed

Mukherjee, Shinjini; Sipilä, Timo; Pulkkinen, Pertti; Yrjälä, Kim

2015-02-01

Poplars have widely been used for rhizoremediation of a broad range of organic contaminants for the past two decades. Still, there is a knowledge gap regarding the rhizosphere-associated bacterial communities of poplars and their dynamics during the remediation process. It is envisaged that a detailed understanding of rhizosphere-associated microbial populations will greatly contribute to a better design and implementation of rhizoremediation. To investigate the long-term succession of structural and catabolic bacterial communities in oil-polluted soil planted with hybrid poplar, we carried out a 2-year field study. Hybrid aspen (Populus tremula × Populus tremuloides) seedlings were planted in polluted soil excavated from an accidental oil-spill site. Vegetated and un-vegetated soil samples were collected for microbial community analyses at seven different time points during the course of 2 years and sampling time points were chosen to cover the seasonal variation in the boreal climate zone. Bacterial community structure was accessed by means of 16S rRNA gene amplicon pyrosequencing, whereas catabolic diversity was monitored by pyrosequencing of alkane hydroxylase and extradiol dioxygenase genes. We observed a clear succession of bacterial communities on both structural and functional levels from early to late-phase communities. Sphingomonas type extradiol dioxygenases and alkane hydroxylase homologs of Rhodococcus clearly dominated the early-phase communities. The high-dominance/low-diversity functional gene communities underwent a transition to low-dominance/high-diversity communities in the late phase. These results pointed towards increased catabolic capacities and a change from specialist to generalist strategy of bacterial communities during the course of secondary succession. © 2014 John Wiley & Sons Ltd.

Inoculation of a phenanthrene-degrading endophytic bacterium reduces the phenanthrene level and alters the bacterial community structure in wheat.

PubMed

Liu, Juan; Xiang, Yanbing; Zhang, Zhiming; Ling, Wanting; Gao, Yanzheng

2017-06-01

Colonization by polycyclic aromatic hydrocarbon (PAH)-degrading endophytic bacteria (PAHDEB) can reduce the PAH contamination risk in plant. However, little information is available on the impact of PAHDEB colonization on the endophytic bacterial community of inner plant tissues. A phenanthrene-degrading endophytic bacterium (PDEB), Massilia sp. Pn2, was inoculated onto the roots of wheat and subjected to greenhouse container experiments. The endophytic bacterial community structure in wheat was investigated using high-throughput sequencing technology. The majority of endophytic bacteria in wheat were Proteobacteria, and the dominant genus was Pseudomonas. Phenanthrene contamination clearly increased the diversity of endophytic bacteria in wheat. The cultivable endophytic bacteria counts in wheat decreased with increasing the level of phenanthrene contamination; the endophytic bacterial community structure changed correspondingly, and the bacterial richness first increased and then decreased. Inoculation of strain Pn2 reduced the phenanthrene contamination in wheat, enlarged the biomass of wheat roots, changed the bacterial community structure and enhanced the cell counts, diversity and richness of endophytic bacteria in phenanthrene-contaminated wheat in a contamination level-dependent manner. The findings of this investigation provide insight into the responses of endophytic bacterial community in plant to external PAH contamination and PAHDEB colonization.

Adaptations in bacterial catabolic enzyme activity and community structure in membrane-coupled bioreactors fed simple synthetic wastewater.

PubMed

LaPara, Timothy M; Klatt, Christian G; Chen, Ruoyu

2006-02-10

Membrane-coupled bioreactors (MBRs) offer substantial benefits compared to conventional reactor designs for biological wastewater treatment. MBR treatment efficiency, however, has not been optimized because the effects of the MBR on process microbiology are poorly understood. In this study, the structure and function of the microbial communities growing in MBRs fed simple synthetic wastewater were investigated. In four starch-fed MBRs, the bacterial community substantially increased its alpha-glucosidase affinity (>1000-fold), while the leucine aminopeptidase and heptanoate esterase affinities increased slightly (<40-fold) or remained relatively constant. Concomitant to these physiological adaptations, shifts in the bacterial community structure in two of the starch-fed MBRs were detected by PCR-DGGE. Four of the bacterial populations detected by PCR-DGGE were isolated and exhibited specific growth rates in batch culture ranging from 0.009 to 0.22 h(-1). Our results suggest that bacterial communities growing under increasingly stringent nutrient limitation adapt their enzyme activities primarily for the nutrients provided, but that there is also a more subtle response not linked to the substrates included in the feed medium. Our research also demonstrates that MBRs can support relatively complex bacterial communities even on simple feed media.

Effects of storage temperature on bacterial growth rates and community structure in fresh retail sushi.

PubMed

Hoel, S; Jakobsen, A N; Vadstein, O

2017-09-01

This study was conducted to assess the effects of different storage temperatures (4-20°C), on bacterial concentrations, growth rates and community structure in fresh retail sushi, a popular retail product with a claimed shelf life of 2-3 days. The maximum specific growth rate based on aerobic plate count (APC) at 4°C was 0·06 h -1 and displayed a sixfold increase (0·37 h -1 ) at 20°C. Refrigeration resulted in no growth of hydrogen sulphide (H 2 S)-producing bacteria, but this group had the strongest temperature response. The bacterial community structure was determined by PCR/DGGE (denaturing gradient gel electrophoresis). Multivariate analysis based on Bray-Curtis similarities demonstrated that temperature alone was not the major determinant for the bacterial community structure. The total concentration of aerobic bacteria was the variable that most successfully explained the differences between the communities. The dominating organisms, detected by sequencing of DNA bands excised from the DGGE gel, were Brochothrix thermosphacta and genera of lactic acid bacteria (LAB). The relationship between growth rates and storage temperatures clearly demonstrates that these products are sensitive to deviations from optimal storage temperature, possibly resulting in loss of quality during shelf life. Regardless of the storage temperature, the bacterial communities converged towards a similar structure and density, but the storage temperature determined how fast the community reached its carrying capacity. Little information is available on the microbial composition of ready-to-eat food that are prepared with raw fish, subjected to contamination during handling, and susceptible to microbial growth during cold storage. Moreover, the data are a good first possibility to simulate growth of APC, H 2 S-producing bacteria and LAB under different temperature scenarios that might occur during production, distribution or storage. © 2017 The Society for Applied Microbiology.

Effects of field-grown genetically modified Zoysia grass on bacterial community structure.

PubMed

Lee, Yong-Eok; Yang, Sang-Hwan; Bae, Tae-Woong; Kang, Hong-Gyu; Lim, Pyung-Ok; Lee, Hyo-Yeon

2011-04-01

Herbicide-tolerant Zoysia grass has been previously developed through Agrobacterium-mediated transformation. We investigated the effects of genetically modified (GM) Zoysia grass and the associated herbicide application on bacterial community structure by using culture-independent approaches. To assess the possible horizontal gene transfer (HGT) of transgenic DNA to soil microorganisms, total soil DNAs were amplified by PCR with two primer sets for the bar and hpt genes, which were introduced into the GM Zoysia grass by a callus-type transformation. The transgenic genes were not detected from the total genomic DNAs extracted from 1.5 g of each rhizosphere soils of GM and non-GM Zoysia grasses. The structures and diversities of the bacterial communities in rhizosphere soils of GM and non-GM Zoysia grasses were investigated by constructing 16S rDNA clone libraries. Classifier, provided in the RDP II, assigned 100 clones in the 16S rRNA gene sequences library into 11 bacterial phyla. The most abundant phyla in both clone libraries were Acidobacteria and Proteobacteria. The bacterial diversity of the GM clone library was lower than that of the non- GM library. The former contained four phyla, whereas the latter had seven phyla. Phylogenetic trees were constructed to confirm these results. Phylogenetic analyses of the two clone libraries revealed considerable difference from each other. The significance of difference between clone libraries was examined with LIBSHUFF statistics. LIBSHUFF analysis revealed that the two clone libraries differed significantly (P〈0.025), suggesting alterations in the composition of the microbial community associated with GM Zoysia grass.

Structure of the human gastric bacterial community in relation to Helicobacter pylori status.

PubMed

Maldonado-Contreras, Ana; Goldfarb, Kate C; Godoy-Vitorino, Filipa; Karaoz, Ulas; Contreras, Mónica; Blaser, Martin J; Brodie, Eoin L; Dominguez-Bello, Maria G

2011-04-01

The human stomach is naturally colonized by Helicobacter pylori, which, when present, dominates the gastric bacterial community. In this study, we aimed to characterize the structure of the bacterial community in the stomach of patients of differing H. pylori status. We used a high-density 16S rRNA gene microarray (PhyloChip, Affymetrix, Inc.) to hybridize 16S rRNA gene amplicons from gastric biopsy DNA of 10 rural Amerindian patients from Amazonas, Venezuela, and of two immigrants to the United States (from South Asia and Africa, respectively). H. pylori status was determined by PCR amplification of H. pylori glmM from gastric biopsy samples. Of the 12 patients, 8 (6 of the 10 Amerindians and the 2 non-Amerindians) were H. pylori glmM positive. Regardless of H. pylori status, the PhyloChip detected Helicobacteriaceae DNA in all patients, although with lower relative abundance in patients who were glmM negative. The G2-chip taxonomy analysis of PhyloChip data indicated the presence of 44 bacterial phyla (of which 16 are unclassified by the Taxonomic Outline of the Bacteria and Archaea taxonomy) in a highly uneven community dominated by only four phyla: Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Positive H. pylori status was associated with increased relative abundance of non-Helicobacter bacteria from the Proteobacteria, Spirochetes and Acidobacteria, and with decreased abundance of Actinobacteria, Bacteroidetes and Firmicutes. The PhyloChip detected richness of low abundance phyla, and showed marked differences in the structure of the gastric bacterial community according to H. pylori status.

Structure of the human gastric bacterial community in relation to Helicobacter pylori status

PubMed Central

Maldonado-Contreras, Ana; Goldfarb, Kate C; Godoy-Vitorino, Filipa; Karaoz, Ulas; Contreras, Mónica; Blaser, Martin J; Brodie, Eoin L; Dominguez-Bello, Maria G

2011-01-01

The human stomach is naturally colonized by Helicobacter pylori, which, when present, dominates the gastric bacterial community. In this study, we aimed to characterize the structure of the bacterial community in the stomach of patients of differing H. pylori status. We used a high-density 16S rRNA gene microarray (PhyloChip, Affymetrix, Inc.) to hybridize 16S rRNA gene amplicons from gastric biopsy DNA of 10 rural Amerindian patients from Amazonas, Venezuela, and of two immigrants to the United States (from South Asia and Africa, respectively). H. pylori status was determined by PCR amplification of H. pylori glmM from gastric biopsy samples. Of the 12 patients, 8 (6 of the 10 Amerindians and the 2 non-Amerindians) were H. pylori glmM positive. Regardless of H. pylori status, the PhyloChip detected Helicobacteriaceae DNA in all patients, although with lower relative abundance in patients who were glmM negative. The G2-chip taxonomy analysis of PhyloChip data indicated the presence of 44 bacterial phyla (of which 16 are unclassified by the Taxonomic Outline of the Bacteria and Archaea taxonomy) in a highly uneven community dominated by only four phyla: Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Positive H. pylori status was associated with increased relative abundance of non-Helicobacter bacteria from the Proteobacteria, Spirochetes and Acidobacteria, and with decreased abundance of Actinobacteria, Bacteroidetes and Firmicutes. The PhyloChip detected richness of low abundance phyla, and showed marked differences in the structure of the gastric bacterial community according to H. pylori status. PMID:20927139

Arbuscular mycorrhizal fungi inoculation mediated changes in rhizosphere bacterial community structure while promoting revegetation in a semiarid ecosystem.

PubMed

Rodríguez-Caballero, G; Caravaca, F; Fernández-González, A J; Alguacil, M M; Fernández-López, M; Roldán, A

2017-04-15

The main goal of this study was to assess the effect of the inoculation of four autochthonous shrub species with the arbuscular mycorrhizal (AM) fungus Rhizophagus intraradices on the rhizosphere bacterial community and to ascertain whether such an effect is dependent on the host plant species. Additionally, analysis of rhizosphere soil chemical and biochemical properties was performed to find relationships between them and the rhizosphere bacterial communities. Non-metric multidimensional scaling analysis and subsequent permutational multivariate analysis of variance revealed differences in bacterial community composition and structure between non-inoculated and inoculated rhizospheres. Moreover, an influence of the plant species was observed. Different bacterial groups were found to be indicator taxonomic groups of non-inoculated and inoculated rhizospheres, Gemmatimonadetes and Anaerolineaceae, respectively, being the most notable indicators. As shown by distance based redundancy analysis, the shifts in bacterial community composition and structure mediated by the inoculation with the AM fungus were mainly related to changes in plant nutrients and growth parameters, such as the shoot phosphorus content. Our findings suggest that the AM fungal inoculum was able to modify the rhizosphere bacterial community assemblage while improving the host plant performance. Copyright © 2017 Elsevier B.V. All rights reserved.

Bacterial community structure in response to environmental impacts in the intertidal sediments along the Yangtze Estuary, China.

PubMed

Guo, Xing-Pan; Lu, Da-Pei; Niu, Zuo-Shun; Feng, Jing-Nan; Chen, Yu-Ru; Tou, Fei-Yun; Liu, Min; Yang, Yi

2018-01-01

This study was designed to investigate the characteristics of bacterial communities in intertidal sediments along the Yangtze Estuary and their responses to environmental factors. The results showed that bacterial abundance was significantly correlated with salinity, SO 4 2- and total organic carbon, while bacterial diversity was significantly correlated with SO 4 2- and total nitrogen. At different taxonomic levels, both the dominant taxa and their abundances varied among the eight samples, with Proteobacteria being the most dominant phylum in general. Cluster analysis revealed that the bacterial community structure was influenced by river runoff and sewerage discharge. Moreover, SO 4 2- , salinity and total phosphorus were the vital environmental factors that influenced the bacterial community structure. Quantitative PCR and sequencing of sulphate-reducing bacteria indicated that the sulphate reduction process occurs frequently in intertidal sediments. These findings are important to understand the microbial ecology and biogeochemical cycles in estuarine environments. Copyright © 2017 Elsevier Ltd. All rights reserved.

Aspect has a greater impact on alpine soil bacterial community structure than elevation.

PubMed

Wu, Jieyun; Anderson, Barbara J; Buckley, Hannah L; Lewis, Gillian; Lear, Gavin

2017-03-01

Gradients in environmental conditions, including climate factors and resource availability, occur along mountain inclines, providing a 'natural laboratory' to explore their combined impacts on microbial distributions. Conflicting spatial patterns observed across elevation gradients in soil bacterial community structure suggest that they are driven by various interacting factors at different spatial scales. Here, we investigated the relative impacts of non-resource (e.g. soil temperature, pH) and resource conditions (e.g. soil carbon and nitrogen) on the biogeography of soil bacterial communities across broad (i.e. along a 1500 m mountain elevation gradient) and fine sampling scales (i.e. along sunny and shady aspects of a mountain ridge). Our analysis of 16S rRNA gene data confirmed that when sampling across distances of < 1000 m, bacterial community composition was more closely related to the aspect of a site than its elevation. However, despite large differences in climate and resource-availability factors across elevation- and aspect-related gradients, bacterial community composition and richness were most strongly correlated with soil pH. These findings highlight the need to incorporate knowledge of multiple factors, including site aspect and soil pH for the appropriate use of elevation gradients as a proxy to explore the impacts of climate change on microbial community composition. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Soils associated to different tree communities do not elicit predictable responses in lake bacterial community structure and function.

PubMed

Ruiz-González, Clara; Archambault, Esther; Laforest-Lapointe, Isabelle; Del Giorgio, Paul A; Kembel, Steven W; Messier, Christian; Nock, Charles A; Beisner, Beatrix E

2018-06-14

Freshwater bacterioplankton communities are influenced by the inputs of material and bacteria from the surrounding landscape, yet few studies have investigated how different terrestrial inputs affect bacterioplankton. We examined whether the addition of soils collected under various tree species combinations differentially influences lake bacterial communities. Lake water was incubated for 6 days following addition of five different soils. We assessed the taxonomic composition (16S rRNA gene sequencing) and metabolic activity (Biolog Ecoplates) of lake bacteria with and without soil addition, and compared these to initial soil communities. Soil bacterial assemblages showed a strong influence of tree composition, but such community differences were not reflected in the structure of lake communities that developed during the experiment. Bacterial taxa showing the largest abundance increases during incubation were initially present in both lake water and across most soils, and were related to Cytophagales, Burkholderiales and Rhizobiales. No clear metabolic profiles based on inoculum source were found, yet soil-amended communities used 60% more substrate than non-inoculated communities. Overall, we show that terrestrial inputs influence aquatic communities by stimulating the growth and activity of certain ubiquitous taxa distributed across the terrestrial-aquatic continuum, yet different forest soils did not cause predictable changes in lake bacterioplankton assemblages.

Influence of oyster culture on biogeochemistry and bacterial community structure at the sediment-water interface.

PubMed

Azandégbé, Afi; Poly, Franck; Andrieux-Loyer, Françoise; Kérouel, Roger; Philippon, Xavier; Nicolas, Jean-Louis

2012-10-01

Bacterial community structure and some biogeochemical parameters were studied in the sediment of two Pacific oyster farming sites, Aber Benoît (AB) and Rivière d'Auray (RA) in Brittany (France), to examine the ecological impact of oysters and to evaluate the emission of sulfide and ammonia from sediment. At AB, the organic matter accumulated in the sediment beneath the oyster tables was rapidly mineralized, with strong fluxes of ammonia and sulfide that reached 1014 and 215 μmol m(-2) h(-1), respectively, in June 2007. At RA, the fluxes were about half as strong on average and better distributed through the year. The ammonia and sulfide concentrations in the overlying water never reached levels that would be toxic to oysters in either site, nor did hypoxia occur. Total culturable bacteria (TCB) varied greatly according to the temperature: from 1.6 × 10(4) to 9.4 × 10(7) cell g(-1) sediment. Inversely, the bacterial community structure remained surprising stable through the seasons, marginally influenced by the presence of oysters and by temperature. Bacterial communities appeared to be characteristic of the sites, with only one common phylotype, Vibrio aestuarianus, a potential oyster pathogen. These data refine the hypothesis of seawater toxicity to oysters because of ammonia and sulfide fluxes and show that the measured environmental factors had only a weak influence on bacterial community structure. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Interspecific Plant Interactions Reflected in Soil Bacterial Community Structure and Nitrogen Cycling in Primary Succession

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

Knelman, Joseph E.; Graham, Emily B.; Prevéy, Janet S.

Past research demonstrating the importance plant-microbe interactions as drivers of ecosystem succession has focused on how plants condition soil microbial communities, impacting subsequent plant performance and successional trajectories in plant community assembly. These studies, however, largely treat microbial communities as a black box. In this study we sought to examine how emblematic shifts from early-successional Alnus sinuata (alder) to late successional Picea sitchensis (spruce) in primary succession may be reflected in specific belowground changes in bacterial community structure and nitrogen cycling related to the interaction of these two plants. We examined early successional alder-conditioned soils in a glacial forefield tomore » delineate how alders alter the soil microbial community with increasing dominance. Further, we assessed the impact of late-successional spruce plants on these early-successional alder-conditioned microbiomes and related nitrogen cycling through a leachate addition microcosm experiment. We show how increasingly abundant alder select for particular bacterial taxa. Additionally, we found that spruce leachate drives shifts in the relative abundance of major taxa of bacteria in alder-influenced soils, including declines in those that are enriched by alder. We found these effects to be spruce-specific, beyond a general leachate effect. Our work also demonstrates a unique influence of spruce on ammonium availability. Our results show that spruce leachate addition more strongly structures bacterial communities than alders (less dispersion in bacterial community beta diversity). Such insights bolster theory relating the importance of plant-microbe interactions with late-successional plants and interspecific plant interactions more generally.« less

Relationships between soil organic matter, nutrients, bacterial community structure, and the performance of microbial fuel cells.

PubMed

Dunaj, Sara J; Vallino, Joseph J; Hines, Mark E; Gay, Marcus; Kobyljanec, Christine; Rooney-Varga, Juliette N

2012-02-07

Microbial fuel cells (MFCs) offer the potential for generating electricity, mitigating greenhouse gas emissions, and bioremediating pollutants through utilization of a plentiful renewable resource: soil organic carbon. We analyzed bacterial community structure, MFC performance, and soil characteristics in different microhabitats within MFCs constructed from agricultural or forest soils in order to determine how soil type and bacterial dynamics influence MFC performance. Our results indicated that MFCs constructed from agricultural soil had power output about 17 times that of forest soil-based MFCs and respiration rates about 10 times higher than forest soil MFCs. Agricultural soil MFCs had lower C:N ratios, polyphenol content, and acetate concentrations than forest soil MFCs. Bacterial community profile data indicate that the bacterial communities at the anode of the high power MFCs were less diverse than in low power MFCs and were dominated by Deltaproteobacteria, Geobacter, and to a lesser extent, Clostridia, while low-power MFC anode communities were dominated by Clostridia. These results suggest that the presence of organic carbon substrate (acetate) was not the major limiting factor in selecting for highly electrogenic bacterial communities, while the quality of available organic matter may have played a significant role in supporting high performing bacterial communities.

Minerals in soil select distinct bacterial communities in their microhabitats.

PubMed

Carson, Jennifer K; Campbell, Louise; Rooney, Deirdre; Clipson, Nicholas; Gleeson, Deirdre B

2009-03-01

We tested the hypothesis that different minerals in soil select distinct bacterial communities in their microhabitats. Mica (M), basalt (B) and rock phosphate (RP) were incubated separately in soil planted with Trifolium subterraneum, Lolium rigidum or left unplanted. After 70 days, the mineral and soil fractions were separated by sieving. Automated ribosomal intergenic spacer analysis was used to determine whether the bacterial community structure was affected by the mineral, fraction and plant treatments. Principal coordinate plots showed clustering of bacterial communities from different fraction and mineral treatments, but not from different plant treatments. Permutational multivariate anova (permanova) showed that the microhabitats of M, B and RP selected bacterial communities different from each other in unplanted and L. rigidum, and in T. subterraneum, bacterial communities from M and B differed (P<0.046). permanova also showed that each mineral fraction selected bacterial communities different from the surrounding soil fraction (P<0.05). This study shows that the structure of bacterial communities in soil is influenced by the mineral substrates in their microhabitat and that minerals in soil play a greater role in bacterial ecology than simply providing an inert matrix for bacterial growth. This study suggests that mineral heterogeneity in soil contributes to the spatial variation in bacterial communities.

Bacterial community structure in atmospheric particulate matters of different sizes during the haze days in Xi'an, China.

PubMed

Lu, Rui; Li, Yanpeng; Li, Wanxin; Xie, Zhengsheng; Fan, Chunlan; Liu, Pengxia; Deng, Shunxi

2018-05-09

Serious air pollution events have frequently occurred in China associated with the acceleration of urbanization and industrialization in recent years. Exposure to atmospheric particulate matter (PM) of high concentration can lead to adverse effects on human health. Airborne bacteria are important constituents of microbial aerosols and contain lots of pathogens. However, variations in bacterial community structure in atmospheric PM of different sizes (PM 2.5 , PM 10 and TSP) have not yet been explored. In this study, PM samples of different sizes were collected during the hazy days from Jul.2016 to Apr.2017 to determine bacterial diversity and community structure. Samples from soils and leaf surfaces were also collected to determine potential sources of bacterial aerosols. High-throughput sequencing technology was used generate bacterial community profiles, where we determined their diversity and abundances in the samples. Results showed that the dominant bacterial community structures in PM 2.5 , PM 10 and TSP were strongly similar. Compared with non-haze days, the relative abundances of most bacterial pathogens on the haze days did not increase. Meanwhile, temperature, O 3 and NO 2 had more significant effects on bacterial community than the other environmental factors. Source tracking analysis indicated that the airborne bacteria might be not from local environment. It may come from the entire city or other regions by long distance airflow transport. Results of this study improved our understanding of the influence of bioaerosols on human health and the potential sources of airborne microbes. Copyright © 2018 Elsevier B.V. All rights reserved.

Taxonomic profiling of bacterial community structure from coastal sediment of Alang-Sosiya shipbreaking yard near Bhavnagar, India.

PubMed

Patel, Vilas; Munot, Hitendra; Shah, Varun; Shouche, Yogesh S; Madamwar, Datta

2015-12-30

The Alang-Sosiya shipbreaking yard (ASSBY) is considered the largest of its kind in the world, and a major source of anthropogenic pollutants. The aim of this study was to investigate the impact of shipbreaking activities on the bacterial community structure with a combination of culture-dependent and culture-independent approaches. In the culture-dependent approach, 200 bacterial cultures were isolated and analyzed by molecular fingerprinting and 16S ribosomal RNA (r-RNA) gene sequencing, as well as being studied for degradation of polycyclic aromatic hydrocarbons (PAHs). In the culture-independent approach, operational taxonomic units (OTUs) were related to eight major phyla, of which Betaproteobacteria (especially Acidovorax) was predominantly found in the polluted sediments of ASSBY and Gammaproteobacteria in the pristine sediment sample. The statistical approaches showed a significant difference in the bacterial community structure between the pristine and polluted sediments. To the best of our knowledge, this is the first study investigating the effect of shipbreaking activity on the bacterial community structure of the coastal sediment at ASSBY. Copyright © 2015. Published by Elsevier Ltd.

A Dissolved Oxygen Threshold for Shifts in Bacterial Community Structure in a Seasonally Hypoxic Estuary.

PubMed

Spietz, Rachel L; Williams, Cheryl M; Rocap, Gabrielle; Horner-Devine, M Claire

2015-01-01

Pelagic ecosystems can become depleted of dissolved oxygen as a result of both natural processes and anthropogenic effects. As dissolved oxygen concentration decreases, energy shifts from macrofauna to microorganisms, which persist in these hypoxic zones. Oxygen-limited regions are rapidly expanding globally; however, patterns of microbial communities associated with dissolved oxygen gradients are not yet well understood. To assess the effects of decreasing dissolved oxygen on bacteria, we examined shifts in bacterial community structure over space and time in Hood Canal, Washington, USA-a glacial fjord-like water body that experiences seasonal low dissolved oxygen levels known to be detrimental to fish and other marine organisms. We found a strong negative association between bacterial richness and dissolved oxygen. Bacterial community composition across all samples was also strongly associated with the dissolved oxygen gradient, and significant changes in bacterial community composition occurred at a dissolved oxygen concentration between 5.18 and 7.12 mg O2 L(-1). This threshold value of dissolved oxygen is higher than classic definitions of hypoxia (<2.0 mg O2 L(-1)), suggesting that changes in bacterial communities may precede the detrimental effects on ecologically and economically important macrofauna. Furthermore, bacterial taxa responsible for driving whole community changes across the oxygen gradient are commonly detected in other oxygen-stressed ecosystems, suggesting that the patterns we uncovered in Hood Canal may be relevant in other low oxygen ecosystems.

A Dissolved Oxygen Threshold for Shifts in Bacterial Community Structure in a Seasonally Hypoxic Estuary

PubMed Central

Spietz, Rachel L.; Williams, Cheryl M.; Rocap, Gabrielle; Horner-Devine, M. Claire

2015-01-01

Pelagic ecosystems can become depleted of dissolved oxygen as a result of both natural processes and anthropogenic effects. As dissolved oxygen concentration decreases, energy shifts from macrofauna to microorganisms, which persist in these hypoxic zones. Oxygen-limited regions are rapidly expanding globally; however, patterns of microbial communities associated with dissolved oxygen gradients are not yet well understood. To assess the effects of decreasing dissolved oxygen on bacteria, we examined shifts in bacterial community structure over space and time in Hood Canal, Washington, USA−a glacial fjord-like water body that experiences seasonal low dissolved oxygen levels known to be detrimental to fish and other marine organisms. We found a strong negative association between bacterial richness and dissolved oxygen. Bacterial community composition across all samples was also strongly associated with the dissolved oxygen gradient, and significant changes in bacterial community composition occurred at a dissolved oxygen concentration between 5.18 and 7.12 mg O2 L-1. This threshold value of dissolved oxygen is higher than classic definitions of hypoxia (<2.0 mg O2 L-1), suggesting that changes in bacterial communities may precede the detrimental effects on ecologically and economically important macrofauna. Furthermore, bacterial taxa responsible for driving whole community changes across the oxygen gradient are commonly detected in other oxygen-stressed ecosystems, suggesting that the patterns we uncovered in Hood Canal may be relevant in other low oxygen ecosystems. PMID:26270047

Unraveling the Molecular Mechanisms Underlying the Nasopharyngeal Bacterial Community Structure.

PubMed

de Steenhuijsen Piters, Wouter A A; Bogaert, Debby

2016-02-02

The upper respiratory tract is colonized by a diverse array of commensal bacteria that harbor potential pathogens, such as Streptococcus pneumoniae. As long as the local microbial ecosystem-also called "microbiome"-is in balance, these potentially pathogenic bacterial residents cause no harm to the host. However, similar to macrobiological ecosystems, when the bacterial community structure gets perturbed, potential pathogens can overtake the niche and cause mild to severe infections. Recent studies using next-generation sequencing show that S. pneumoniae, as well as other potential pathogens, might be kept at bay by certain commensal bacteria, including Corynebacterium and Dolosigranulum spp. Bomar and colleagues are the first to explore a specific biological mechanism contributing to the antagonistic interaction between Corynebacterium accolens and S. pneumoniae in vitro [L. Bomar, S. D. Brugger, B. H. Yost, S. S. Davies, K. P. Lemon, mBio 7(1):e01725-15, 2016, doi:10.1128/mBio.01725-15]. The authors comprehensively show that C. accolens is capable of hydrolyzing host triacylglycerols into free fatty acids, which display antipneumococcal properties, suggesting that these bacteria might contribute to the containment of pneumococcus. This work exemplifies how molecular epidemiological findings can lay the foundation for mechanistic studies to elucidate the host-microbe and microbial interspecies interactions underlying the bacterial community structure. Next, translation of these results to an in vivo setting seems necessary to unveil the magnitude and importance of the observed effect in its natural, polymicrobial setting. Copyright © 2016 de Steenhuijsen Piters and Bogaert.

Unraveling the Molecular Mechanisms Underlying the Nasopharyngeal Bacterial Community Structure

PubMed Central

de Steenhuijsen Piters, Wouter A. A.

2016-01-01

ABSTRACT The upper respiratory tract is colonized by a diverse array of commensal bacteria that harbor potential pathogens, such as Streptococcus pneumoniae. As long as the local microbial ecosystem—also called “microbiome”—is in balance, these potentially pathogenic bacterial residents cause no harm to the host. However, similar to macrobiological ecosystems, when the bacterial community structure gets perturbed, potential pathogens can overtake the niche and cause mild to severe infections. Recent studies using next-generation sequencing show that S. pneumoniae, as well as other potential pathogens, might be kept at bay by certain commensal bacteria, including Corynebacterium and Dolosigranulum spp. Bomar and colleagues are the first to explore a specific biological mechanism contributing to the antagonistic interaction between Corynebacterium accolens and S. pneumoniae in vitro [L. Bomar, S. D. Brugger, B. H. Yost, S. S. Davies, K. P. Lemon, mBio 7(1):e01725-15, 2016, doi:10.1128/mBio.01725-15]. The authors comprehensively show that C. accolens is capable of hydrolyzing host triacylglycerols into free fatty acids, which display antipneumococcal properties, suggesting that these bacteria might contribute to the containment of pneumococcus. This work exemplifies how molecular epidemiological findings can lay the foundation for mechanistic studies to elucidate the host-microbe and microbial interspecies interactions underlying the bacterial community structure. Next, translation of these results to an in vivo setting seems necessary to unveil the magnitude and importance of the observed effect in its natural, polymicrobial setting. PMID:26838716

Unique hyper-thermal composting process in Kagoshima City forms distinct bacterial community structures.

PubMed

Tashiro, Yukihiro; Tabata, Hanae; Itahara, Asuka; Shimizu, Natsuki; Tashiro, Kosuke; Sakai, Kenji

2016-11-01

A unique compost, Satsuma soil, is produced from three types of wastewater sludge using hyper-thermal processes at temperatures much higher than that of general thermophilic processes in Kagoshima City, Japan. We analyzed the bacterial community structures of this hyper-thermal compost sample and other sludges and composts by a high-throughput barcoded pyrosequencing method targeting the 16S rRNA gene. In total, 621,076 reads were derived from 17 samples and filtered. Artificial sequences were deleted and the reads were clustered based on the operational taxonomic units (OTUs) at 97% similarity. Phylum-level analysis of the hyper-thermal compost revealed drastic changes of the sludge structures (each relative abundance) from Firmicutes (average 47.8%), Proteobacteria (average 22.3%), and Bacteroidetes (average 10.1%) to two main phyla including Firmicutes (73.6%) and Actinobacteria (25.0%) with less Proteobacteria (∼0.3%) and Bacteroidetes (∼0.1%). Furthermore, we determined the predominant species (each relative abundance) of the hyper-thermal compost including Firmicutes related to Staphylococcus cohnii (13.8%), Jeotgalicoccus coquinae (8.01%), and Staphylococcus lentus (5.96%), and Actinobacteria related to Corynebacterium stationis (6.41%), and found that these species were not predominant in wastewater sludge. In contrast, we did not observe any common structures among eight other composts produced, using the hyper-thermal composts as the inoculums, under thermophilic conditions from different materials. Principle coordinate analysis of the hyper-thermal compost indicated a large difference in bacterial community structures from material sludge and other composts. These results suggested that a distinct bacterial community structure was formed by hyper-thermal composting. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Interactions between accumulated copper, bacterial community structure and histamine levels in crayfish meat during storage.

PubMed

Soedarini, Bernadeta; van Gestel, Cornelis A M; van Straalen, Nico M; Widianarko, Budi; Röling, Wilfred F M

2014-08-01

Pollution in aquaculture areas may negatively impact edible species and threaten seafood quality and safety. The aim of this study was to determine the interaction between copper and bacteria in the aquatic habitat and their impact upon crustaceans. Marbled crayfish was chosen as a model of aquatic crustaceans and the influence of metal contamination on bacterial community structure in water used to culture crayfish and in crayfish themselves was investigated. Histamine, an allergen commonly formed by certain groups of bacteria in crustacean edible tissue during storage, was also determined. Copper exposure increased its concentration in crayfish meat by 17.4%, but the copper concentration remained within acceptable food safety limits. Elevated copper levels affected the bacterial community both in the water used to cultivate crayfish and in the marbled crayfish themselves. Cluster analysis of 16S rRNA-gene based microbial community fingerprints revealed that copper impacted the bacterial community in the water and in the crayfish meat. However, copper exposure reduced the formation of histamine in crayfish meat during storage by 66.3%. Copper from the habitat appears to reduce histamine accumulation in crayfish meat during storage by affecting the bacterial community structure of the cultivation water and most likely also in the intestine of the crayfish. From a food safety point of view, copper treatment during the aqua culturing of crustaceans has a positive impact on the postharvest stage. © 2013 Society of Chemical Industry.

Bacterial community structure and abundances of antibiotic resistance genes in heavy metals contaminated agricultural soil.

PubMed

Zhang, Fengli; Zhao, Xiaoxue; Li, Qingbo; Liu, Jia; Ding, Jizhe; Wu, Huiying; Zhao, Zongsheng; Ba, Yue; Cheng, Xuemin; Cui, Liuxin; Li, Hongping; Zhu, Jingyuan

2018-04-01

Soil contamination with heavy metals is a worldwide problem especially in China. The interrelation of soil bacterial community structure, antibiotic resistance genes, and heavy metal contamination in soil is still unclear. Here, seven agricultural areas (G1-G7) with heavy metal contamination were sampled with different distances (741 to 2556 m) to the factory. Denaturing gradient gel electrophoresis (DGGE) and Shannon index were used to analyze bacterial community diversity. Real-time fluorescence quantitative PCR was used to detect the relative abundance of ARGs sul1, sul2, tetA, tetM, tetW, one mobile genetic elements (MGE) inti1. Results showed that all samples were polluted by Cadmium (Cd), and some of them were polluted by lead (Pb), mercury (Hg), arsenic (As), copper (Cu), and zinc (Zn). DGGE showed that the most abundant bacterial species were found in G7 with the lightest heavy metal contamination. The results of the principal component analysis and clustering analysis both showed that G7 could not be classified with other samples. The relative abundance of sul1 was correlated with Cu, Zn concentration. Gene sul2 are positively related with total phosphorus, and tetM was associated with organic matter. Total gene abundances and relative abundance of inti1 both correlated with organic matter. Redundancy analysis showed that Zn and sul2 were significantly related with bacterial community structure. Together, our results indicate a complex linkage between soil heavy metal concentration, bacterial community composition, and some global disseminated ARG abundance.

Simazine biodegradation in soil: analysis of bacterial community structure by in situ hybridization.

PubMed

Caracciolo, Anna Barra; Grenni, Paola; Ciccoli, Roberto; Di Landa, Giuseppe; Cremisini, Carlo

2005-09-01

Pesticide and nitrate contamination of soil and groundwater from agriculture is an environmental and public health concern worldwide. Simazine, 6-chloro-N2,N4-diethyl-1,3,5-triazine-2,4-diamine, is a triazine herbicide used in agriculture for selective weed control with several types of crops and it is frequently applied to soils receiving N-fertilizers. Degradation experiments were performed in the laboratory to assess whether the biodegradation of simazine in soil may be influenced by the presence of urea. Simazine degradation rates under different experimental conditions (presence/absence of urea, microbiologically active/sterilized soil) were assessed together with the formation, degradation and transformation of its main metabolites in soil. Simazine degradation was affected by the presence of urea, in terms both of a smaller half-life (t(1/2)) and of a higher amount of desethyl-simazine formed. The soil bacterial community was also studied. Microbial abundances were determined by epifluorescence direct counting. Moreover in situ hybridization with rRNA-targeted fluorescent oligonucleotide probes was used to analyze the bacterial community structure. Fluorescent in situ hybridization (FISH) was used to detect specific groups of bacteria such as the alpha,beta,gamma-subdivisions of Proteobacteria, Gram-positive bacteria with a high G + C DNA content, Planctomycetes, Betaproteobacterial ammonia-oxidizing bacteria and nitrifying bacteria. The presence of the herbicide and/or urea affected the bacterial community structure, showing that FISH is a valuable tool for determining the response of bacterial populations to different environmental conditions. Copyright 2005 Society of Chemical Industry

Parental material and cultivation determine soil bacterial community structure and fertility.

PubMed

Sun, Li; Gao, Jusheng; Huang, Ting; Kendall, Joshua R A; Shen, Qirong; Zhang, Ruifu

2015-01-01

Microbes are the key components of the soil environment, playing important roles during soil development. Soil parent material provides the foundation elements that comprise the basic nutritional environment for the development of microbial community. After 30 years artificial maturation of cultivation, the soil developments of three different parental materials were evaluated and bacterial community compositions were investigated using the high-throughput sequencing approach. Thirty years of cultivation increased the soil fertility and soil microbial biomass, richness and diversity, greatly changed the soil bacterial communities, the proportion of phylum Actinobacteria decreased significantly, while the relative abundances of the phyla Acidobacteria, Chloroflexi, Gemmatimonadetes, Armatimonadetes and Nitrospira were significantly increased. Soil bacterial communities of parental materials were separated with the cultivated ones, and comparisons of different soil types, granite soil and quaternary red clay soil were similar and different with purple sandy shale soil in both parental materials and cultivated treatments. Bacterial community variations in the three soil types were affected by different factors, and their alteration patterns in the soil development also varied with soil type. Soil properties (except total potassium) had a significant effect on the soil bacterial communities in all three soil types and a close relationship with abundant bacterial phyla. The amounts of nitrogen-fixing bacteria as well as the abundances of the nifH gene in all cultivated soils were higher than those in the parental materials; Burkholderia and Rhizobacte were enriched significantly with long-term cultivation. The results suggested that crop system would not deplete the nutrients of soil parental materials in early stage of soil maturation, instead it increased soil fertility and changed bacterial community, specially enriched the nitrogen-fixing bacteria to accumulate

Mineral Types and Tree Species Determine the Functional and Taxonomic Structures of Forest Soil Bacterial Communities.

PubMed

Colin, Y; Nicolitch, O; Turpault, M-P; Uroz, S

2017-03-01

Although minerals represent important soil constituents, their impact on the diversity and structure of soil microbial communities remains poorly documented. In this study, pure mineral particles with various chemistries (i.e., obsidian, apatite, and calcite) were considered. Each mineral type was conditioned in mesh bags and incubated in soil below different tree stands (beech, coppice with standards, and Corsican pine) for 2.5 years to determine the relative impacts of mineralogy and mineral weatherability on the taxonomic and functional diversities of mineral-associated bacterial communities. After this incubation period, the minerals and the surrounding bulk soil were collected to determine mass loss and to perform soil analyses, enzymatic assays, and cultivation-dependent and -independent analyses. Notably, our 16S rRNA gene pyrosequencing analyses revealed that after the 2.5-year incubation period, the mineral-associated bacterial communities strongly differed from those of the surrounding bulk soil for all tree stands considered. When focusing only on minerals, our analyses showed that the bacterial communities associated with calcite, the less recalcitrant mineral type, significantly differed from those that colonized obsidian and apatite minerals. The cultivation-dependent analysis revealed significantly higher abundances of effective mineral-weathering bacteria on the most recalcitrant minerals (i.e., apatite and obsidian). Together, our data showed an enrichment of Betaproteobacteria and effective mineral-weathering bacteria related to the Burkholderia and Collimonas genera on the minerals, suggesting a key role for these taxa in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems. IMPORTANCE Forests are usually developed on nutrient-poor and rocky soils, while nutrient-rich soils have been dedicated to agriculture. In this context, nutrient recycling and nutrient access are key processes in such environments. Deciphering how soil

Mineral Types and Tree Species Determine the Functional and Taxonomic Structures of Forest Soil Bacterial Communities

PubMed Central

Colin, Y.; Nicolitch, O.; Turpault, M.-P.

2016-01-01

ABSTRACT Although minerals represent important soil constituents, their impact on the diversity and structure of soil microbial communities remains poorly documented. In this study, pure mineral particles with various chemistries (i.e., obsidian, apatite, and calcite) were considered. Each mineral type was conditioned in mesh bags and incubated in soil below different tree stands (beech, coppice with standards, and Corsican pine) for 2.5 years to determine the relative impacts of mineralogy and mineral weatherability on the taxonomic and functional diversities of mineral-associated bacterial communities. After this incubation period, the minerals and the surrounding bulk soil were collected to determine mass loss and to perform soil analyses, enzymatic assays, and cultivation-dependent and -independent analyses. Notably, our 16S rRNA gene pyrosequencing analyses revealed that after the 2.5-year incubation period, the mineral-associated bacterial communities strongly differed from those of the surrounding bulk soil for all tree stands considered. When focusing only on minerals, our analyses showed that the bacterial communities associated with calcite, the less recalcitrant mineral type, significantly differed from those that colonized obsidian and apatite minerals. The cultivation-dependent analysis revealed significantly higher abundances of effective mineral-weathering bacteria on the most recalcitrant minerals (i.e., apatite and obsidian). Together, our data showed an enrichment of Betaproteobacteria and effective mineral-weathering bacteria related to the Burkholderia and Collimonas genera on the minerals, suggesting a key role for these taxa in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems. IMPORTANCE Forests are usually developed on nutrient-poor and rocky soils, while nutrient-rich soils have been dedicated to agriculture. In this context, nutrient recycling and nutrient access are key processes in such environments. Deciphering

Influence of hydraulic regimes on bacterial community structure and composition in an experimental drinking water distribution system.

PubMed

Douterelo, I; Sharpe, R L; Boxall, J B

2013-02-01

Microbial biofilms formed on the inner-pipe surfaces of drinking water distribution systems (DWDS) can alter drinking water quality, particularly if they are mechanically detached from the pipe wall to the bulk water, such as due to changes in hydraulic conditions. Results are presented here from applying 454 pyrosequencing of the 16S ribosomal RNA (rRNA) gene to investigate the influence of different hydrological regimes on bacterial community structure and to study the potential mobilisation of material from the pipe walls to the network using a full scale, temperature-controlled experimental pipeline facility accurately representative of live DWDS. Analysis of pyrosequencing and water physico-chemical data showed that habitat type (water vs. biofilm) and hydraulic conditions influenced bacterial community structure and composition in our experimental DWDS. Bacterial community composition clearly differed between biofilms and bulk water samples. Gammaproteobacteria and Betaproteobacteria were the most abundant phyla in biofilms while Alphaproteobacteria was predominant in bulk water samples. This suggests that bacteria inhabiting biofilms, predominantly species belonging to genera Pseudomonas, Zooglea and Janthinobacterium, have an enhanced ability to express extracellular polymeric substances to adhere to surfaces and to favour co-aggregation between cells than those found in the bulk water. Highest species richness and diversity were detected in 28 days old biofilms with this being accentuated at highly varied flow conditions. Flushing altered the pipe-wall bacterial community structure but did not completely remove bacteria from the pipe walls, particularly under highly varied flow conditions, suggesting that under these conditions more compact biofilms were generated. This research brings new knowledge regarding the influence of different hydraulic regimes on the composition and structure of bacterial communities within DWDS and the implication that this

Highly Heterogeneous Soil Bacterial Communities around Terra Nova Bay of Northern Victoria Land, Antarctica

PubMed Central

Lim, Hyoun Soo; Hong, Soon Gyu; Kim, Ji Hee; Lee, Joohan; Choi, Taejin; Ahn, Tae Seok; Kim, Ok-Sun

2015-01-01

Given the diminished role of biotic interactions in soils of continental Antarctica, abiotic factors are believed to play a dominant role in structuring of microbial communities. However, many ice-free regions remain unexplored, and it is unclear which environmental gradients are primarily responsible for the variations among bacterial communities. In this study, we investigated the soil bacterial community around Terra Nova Bay of Victoria Land by pyrosequencing and determined which environmental variables govern the bacterial community structure at the local scale. Six bacterial phyla, Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Cyanobacteria, and Bacteroidetes, were dominant, but their relative abundance varied greatly across locations. Bacterial community structures were affected little by spatial distance, but structured more strongly by site, which was in accordance with the soil physicochemical compositions. At both the phylum and species levels, bacterial community structure was explained primarily by pH and water content, while certain earth elements and trace metals also played important roles in shaping community variation. The higher heterogeneity of the bacterial community structure found at this site indicates how soil bacterial communities have adapted to different compositions of edaphic variables under extreme environmental conditions. Taken together, these findings greatly advance our understanding of the adaption of soil bacterial populations to this harsh environment. PMID:25799273

[Effect of ground mulch managements on soil bacterial community structure and diversity in the non-irrigated apple orchard in Weibei Loess Plateau].

PubMed

Chen, Yuexing; Wen, Xiaoxia; Sun, Yulin; Zhang, Junli; Lin, Xiaoli; Liao, Yuncheng

2015-07-04

We studied the changes in soil bacterial communities induced by ground mulch managements at different apple growth periods. We adopted the denaturing gradient gel electrophoresis (DGGE) with PCR-amplified 16S rRNA fragments to determine soil bacterial community structure and diversity. Soil bacterial community structure with different ground mulch managements were significantly different. Both the mulch management strategies and apple growth periods affected the predominant groups and their abundance in soil bacterial communities. Grass mulch and cornstalk mulch treatments had higher bacterial diversity and richness than the control at young fruit period and fruit expanding period, whereas film mulch treatment had no significant difference compared with the control. During mature period, bacterial diversity in the control reached its maximum, which may be ascribed to the rapid growth and reproduction of the r-selection bacteria. The clustering and detrended correspondence analysis revealed that differences in soil bacterial communities were closely correlated to apple growth periods and ground mulch managements. Soil samples from the grass mulch and cornstalk mulch treatments clustered together while those mulched with plastic film treatment were similar to the control. The most abundant phylum in soil bacterial community was Proteobacteria followed by Bacteroidetes. Some other phyla were also detected, such as Acidobacteria, Firmicutes, Actinobacteria and Chloroflexi. Mulching with plant (Grass/Cornstalk) had great effects on soil bacterial community structure and enhanced the diversity while film mulch management had no significant effects.

Influence of environmental variables on the structure and composition of soil bacterial communities in natural and constructed wetlands.

PubMed

Arroyo, Paula; Sáenz de Miera, Luis E; Ansola, Gemma

2015-02-15

Bacteria are key players in wetland ecosystems, however many essential aspects regarding the ecology of wetland bacterial communities remain unknown. The present study characterizes soil bacterial communities from natural and constructed wetlands through the pyrosequencing of 16S rDNA genes in order to evaluate the influence of wetland variables on bacterial community composition and structure. The results show that the composition of soil bacterial communities was significantly associated with the wetland type (natural or constructed wetland), the type of environment (lagoon, Typha or Salix) and three continuous parameters (SOM, COD and TKN). However, no clear associations were observed with soil pH. Bacterial diversity values were significantly lower in the constructed wetland with the highest inlet nutrient concentrations. The abundances of particular metabolic groups were also related to wetland characteristics. Copyright © 2014 Elsevier B.V. All rights reserved.

Responses of Baltic Sea Ice and Open-Water Natural Bacterial Communities to Salinity Change

PubMed Central

Kaartokallio, Hermanni; Laamanen, Maria; Sivonen, Kaarina

2005-01-01

To investigate the responses of Baltic Sea wintertime bacterial communities to changing salinity (5 to 26 practical salinity units), an experimental study was conducted. Bacterial communities of Baltic seawater and sea ice from a coastal site in southwest Finland were used in two batch culture experiments run for 17 or 18 days at 0°C. Bacterial abundance, cell volume, and leucine and thymidine incorporation were measured during the experiments. The bacterial community structure was assessed using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified partial 16S rRNA genes with sequencing of DGGE bands from initial communities and communities of day 10 or 13 of the experiment. The sea ice-derived bacterial community was metabolically more active than the open-water community at the start of the experiment. Ice-derived bacterial communities were able to adapt to salinity change with smaller effects on physiology and community structure, whereas in the open-water bacterial communities, the bacterial cell volume evolution, bacterial abundance, and community structure responses indicated the presence of salinity stress. The closest relatives for all eight partial 16S rRNA gene sequences obtained were either organisms found in polar sea ice and other cold habitats or those found in summertime Baltic seawater. All sequences except one were associated with the α- and γ-proteobacteria or the Cytophaga-Flavobacterium-Bacteroides group. The overall physiological and community structure responses were parallel in ice-derived and open-water bacterial assemblages, which points to a linkage between community structure and physiology. These results support previous assumptions of the role of salinity fluctuation as a major selective factor shaping the sea ice bacterial community structure. PMID:16085826

Substrate Type and Free Ammonia Determine Bacterial Community Structure in Full-Scale Mesophilic Anaerobic Digesters Treating Cattle or Swine Manure.

PubMed

Li, Jiabao; Rui, Junpeng; Yao, Minjie; Zhang, Shiheng; Yan, Xuefeng; Wang, Yuanpeng; Yan, Zhiying; Li, Xiangzhen

2015-01-01

The microbial-mediated anaerobic digestion (AD) process represents an efficient biological process for the treatment of organic waste along with biogas harvest. Currently, the key factors structuring bacterial communities and the potential core and unique bacterial populations in manure anaerobic digesters are not completely elucidated yet. In this study, we collected sludge samples from 20 full-scale anaerobic digesters treating cattle or swine manure, and investigated the variations of bacterial community compositions using high-throughput 16S rRNA amplicon sequencing. Clustering and correlation analysis suggested that substrate type and free ammonia (FA) play key roles in determining the bacterial community structure. The COD: [Formula: see text] (C:N) ratio of substrate and FA were the most important available operational parameters correlating to the bacterial communities in cattle and swine manure digesters, respectively. The bacterial populations in all of the digesters were dominated by phylum Firmicutes, followed by Bacteroidetes, Proteobacteria and Chloroflexi. Increased FA content selected Firmicutes, suggesting that they probably play more important roles under high FA content. Syntrophic metabolism by Proteobacteria, Chloroflexi, Synergistetes and Planctomycetes are likely inhibited when FA content is high. Despite the different manure substrates, operational conditions and geographical locations of digesters, core bacterial communities were identified. The core communities were best characterized by phylum Firmicutes, wherein Clostridium predominated overwhelmingly. Substrate-unique and abundant communities may reflect the properties of manure substrate and operational conditions. These findings extend our current understanding of the bacterial assembly in full-scale manure anaerobic digesters.

Bacterial community structure in the hyperarid core of the Atacama Desert, Chile

USGS Publications Warehouse

Drees, Kevin P.; Neilson, Julia W.; Betancourt, Julio L.; Quade, Jay; Henderson, David A.; Pryor, Barry M.; Maier, Raina M.

2006-01-01

Soils from the hyperarid Atacama Desert of northern Chile were sampled along an east-west elevational transect (23.75 to 24.70 degrees S) through the driest sector to compare the relative structure of bacterial communities. Analysis of denaturing gradient gel electrophoresis (DGGE) profiles from each of the samples revealed that microbial communities from the extreme hyperarid core of the desert clustered separately from all of the remaining communities. Bands sequenced from DGGE profiles of two samples taken at a 22-month interval from this core region revealed the presence of similar populations dominated by bacteria from the Gemmatimonadetes and Planctomycetes phyla.

Interactive effects of solar radiation and dissolved organic matter on bacterial activity and community structure

PubMed Central

Pérez, María Teresa; Sommaruga, Ruben

2007-01-01

We studied the interactive effects of dissolved organic matter (DOM) and solar radiation on the activity and community structure of bacteria from an alpine lake. Activity was assessed both at the community level as leucine incorporation rates and at the single-cell level by microautoradiography. Fluorescent in situ hybridization and signal amplification by catalysed reporter deposition (CARD-FISH) was used to track changes in the bacterial community composition. Bacteria-free filtrates of different DOM sources (lake, algae or soil) were incubated either in the dark or exposed to solar radiation. Afterwards, the natural bacterial assemblage was inoculated and the cultures incubated in the dark for 24–48 h. Bacterial activity was enhanced in the first 24 h in the soil and algal DOM amendments kept in the dark. After 48 h, the enhancement effect was greatly reduced. The initial bacterial community was dominated by Betaproteobacteria followed by Actinobacteria. The relative abundance (expressed as a percentage of DAPI-stained cells) of Betaproteobacteria increased first in dark incubated DOM amendments, but after 48 h no significant differences were detected among treatments. In contrast, the relative abundance of Actinobacteria increased in pre-irradiated DOM treatments. Although Betaproteobacteria dominated at the end of the experiment, the relative abundance of their R-BT subgroup differed among treatments. Changes in bacterial community activity were significantly correlated with those of the relative abundance and activity of Betaproteobacteria, whereas the contribution of Actinobacteria to the bulk activity was very modest. Our results indicate a negative effect of DOM photoalteration on the bulk bacterial activity. The magnitude of this effect was time-dependent and related to rapid changes in the bacterial assemblage composition. PMID:17686018

Interactive effects of solar radiation and dissolved organic matter on bacterial activity and community structure.

PubMed

Pérez, María Teresa; Sommaruga, Ruben

2007-09-01

We studied the interactive effects of dissolved organic matter (DOM) and solar radiation on the activity and community structure of bacteria from an alpine lake. Activity was assessed both at the community level as leucine incorporation rates and at the single-cell level by microautoradiography. Fluorescent in situ hybridization and signal amplification by catalysed reporter deposition (CARD-FISH) was used to track changes in the bacterial community composition. Bacteria-free filtrates of different DOM sources (lake, algae or soil) were incubated either in the dark or exposed to solar radiation. Afterwards, the natural bacterial assemblage was inoculated and the cultures incubated in the dark for 24-48 h. Bacterial activity was enhanced in the first 24 h in the soil and algal DOM amendments kept in the dark. After 48 h, the enhancement effect was greatly reduced. The initial bacterial community was dominated by Betaproteobacteria followed by Actinobacteria. The relative abundance (expressed as a percentage of DAPI-stained cells) of Betaproteobacteria increased first in dark incubated DOM amendments, but after 48 h no significant differences were detected among treatments. In contrast, the relative abundance of Actinobacteria increased in pre-irradiated DOM treatments. Although Betaproteobacteria dominated at the end of the experiment, the relative abundance of their R-BT subgroup differed among treatments. Changes in bacterial community activity were significantly correlated with those of the relative abundance and activity of Betaproteobacteria, whereas the contribution of Actinobacteria to the bulk activity was very modest. Our results indicate a negative effect of DOM photoalteration on the bulk bacterial activity. The magnitude of this effect was time-dependent and related to rapid changes in the bacterial assemblage composition.

Structural Variation in the Bacterial Community Associated with Airborne Particulate Matter in Beijing, China, during Hazy and Nonhazy Days.

PubMed

Yan, Dong; Zhang, Tao; Su, Jing; Zhao, Li-Li; Wang, Hao; Fang, Xiao-Mei; Zhang, Yu-Qin; Liu, Hong-Yu; Yu, Li-Yan

2018-05-01

The structural variation of the bacterial community associated with particulate matter (PM) was assessed in an urban area of Beijing during hazy and nonhazy days. Sampling for different PM fractions (PM 2.5 [<2.5 μm], PM 10 [<10 μm], and total suspended particulate) was conducted using three portable air samplers from September 2014 to February 2015. The airborne bacterial community in these samples was analyzed using the Illumina MiSeq platform with bacterium-specific primers targeting the 16S rRNA gene. A total of 1,707,072 reads belonging to 6,009 operational taxonomic units were observed. The airborne bacterial community composition was significantly affected by PM fractions ( R = 0.157, P < 0.01). In addition, the relative abundances of several genera significantly differed between samples with various haze levels; for example, Methylobacillus , Tumebacillus , and Desulfurispora spp. increased in heavy-haze days. Canonical correspondence analysis and permutation tests showed that temperature, SO 2 concentration, relative humidity, PM 10 concentration, and CO concentration were significant factors that associated with airborne bacterial community composition. Only six genera increased across PM 10 samples ( Dokdonella , Caenimonas , Geminicoccus , and Sphingopyxis ) and PM 2.5 samples ( Cellulomonas and Rhizobacter ), while a large number of taxa significantly increased in total suspended particulate samples, such as Paracoccus , Kocuria , and Sphingomonas Network analysis indicated that Paracoccus , Rubellimicrobium , Kocuria , and Arthrobacter were the key genera in the airborne PM samples. Overall, the findings presented here suggest that diverse airborne bacterial communities are associated with PM and provide further understanding of bacterial community structure in the atmosphere during hazy and nonhazy days. IMPORTANCE The results presented here represent an analysis of the airborne bacterial community associated with particulate matter (PM) and

Soil Bacterial Community Structure Responses to Precipitation Reduction and Forest Management in Forest Ecosystems across Germany

PubMed Central

Felsmann, Katja; Baudis, Mathias; Gimbel, Katharina; Kayler, Zachary E.; Ellerbrock, Ruth; Bruehlheide, Helge; Bruckhoff, Johannes; Welk, Erik; Puhlmann, Heike; Weiler, Markus; Gessler, Arthur; Ulrich, Andreas

2015-01-01

Soil microbial communities play an important role in forest ecosystem functioning, but how climate change will affect the community composition and consequently bacterial functions is poorly understood. We assessed the effects of reduced precipitation with the aim of simulating realistic future drought conditions for one growing season on the bacterial community and its relation to soil properties and forest management. We manipulated precipitation in beech and conifer forest plots managed at different levels of intensity in three different regions across Germany. The precipitation reduction decreased soil water content across the growing season by between 2 to 8% depending on plot and region. T-RFLP analysis and pyrosequencing of the 16S rRNA gene were used to study the total soil bacterial community and its active members after six months of precipitation reduction. The effect of reduced precipitation on the total bacterial community structure was negligible while significant effects could be observed for the active bacteria. However, the effect was secondary to the stronger influence of specific soil characteristics across the three regions and management selection of overstorey tree species and their respective understorey vegetation. The impact of reduced precipitation differed between the studied plots; however, we could not determine the particular parameters being able to modify the response of the active bacterial community among plots. We conclude that the moderate drought induced by the precipitation manipulation treatment started to affect the active but not the total bacterial community, which points to an adequate resistance of the soil microbial system over one growing season. PMID:25875835

Soil bacterial community structure responses to precipitation reduction and forest management in forest ecosystems across Germany.

PubMed

Felsmann, Katja; Baudis, Mathias; Gimbel, Katharina; Kayler, Zachary E; Ellerbrock, Ruth; Bruelheide, Helge; Bruehlheide, Helge; Bruckhoff, Johannes; Welk, Erik; Puhlmann, Heike; Weiler, Markus; Gessler, Arthur; Ulrich, Andreas

2015-01-01

Soil microbial communities play an important role in forest ecosystem functioning, but how climate change will affect the community composition and consequently bacterial functions is poorly understood. We assessed the effects of reduced precipitation with the aim of simulating realistic future drought conditions for one growing season on the bacterial community and its relation to soil properties and forest management. We manipulated precipitation in beech and conifer forest plots managed at different levels of intensity in three different regions across Germany. The precipitation reduction decreased soil water content across the growing season by between 2 to 8% depending on plot and region. T-RFLP analysis and pyrosequencing of the 16S rRNA gene were used to study the total soil bacterial community and its active members after six months of precipitation reduction. The effect of reduced precipitation on the total bacterial community structure was negligible while significant effects could be observed for the active bacteria. However, the effect was secondary to the stronger influence of specific soil characteristics across the three regions and management selection of overstorey tree species and their respective understorey vegetation. The impact of reduced precipitation differed between the studied plots; however, we could not determine the particular parameters being able to modify the response of the active bacterial community among plots. We conclude that the moderate drought induced by the precipitation manipulation treatment started to affect the active but not the total bacterial community, which points to an adequate resistance of the soil microbial system over one growing season.

Importance of inoculum properties on the structure and growth of bacterial communities during Recolonisation of humus soil with different pH.

PubMed

Pettersson, Marie; Bååth, Erland

2013-08-01

The relationship between community structure and growth and pH tolerance of a soil bacterial community was studied after liming in a reciprocal inoculum study. An unlimed (UL) humus soil with a pH of 4.0 was fumigated with chloroform for 4 h, after which < 1 % of the initial bacterial activity remained. Half of the fumigated soil was experimentally limed (EL) to a pH of 7.6. Both the UL and the EL soil were then reciprocally inoculated with UL soil or field limed (FL) soil with a pH of 6.2. The FL soil was from a 15-year-old experiment. The structural changes were measured on both bacteria in soil and on bacteria able to grow on agar plates using phospholipids fatty acid (PLFA) and denaturing gradient gel electrophoresis (DGGE) analysis. The developing community pH tolerance and bacterial growth were also monitored over time using thymidine incorporation. The inoculum source had a significant impact on both growth and pH tolerance of the bacterial community in the EL soil. These differences between the EL soil inoculated with UL soil and FL soil were correlated to structural changes, as evidenced by both PLFA and DGGE analyses on the soil. Similar correlations were seen to the fraction of the community growing on agar plates. There were, however, no differences between the soil bacterial communities in the unlimed soils with different inocula. This study showed the connection between the development of function (growth), community properties (pH tolerance) and the structure of the bacterial community. It also highlighted the importance of both the initial properties of the community and the selection pressure after environmental changes in shaping the resulting microbial community.

Impact of Oil on Bacterial Community Structure in Bioturbated Sediments

PubMed Central

Stauffert, Magalie; Cravo-Laureau, Cristiana; Jézéquel, Ronan; Barantal, Sandra; Cuny, Philippe; Gilbert, Franck; Cagnon, Christine; Militon, Cécile; Amouroux, David; Mahdaoui, Fatima; Bouyssiere, Brice; Stora, Georges; Merlin, François-Xavier; Duran, Robert

2013-01-01

Oil spills threaten coastlines where biological processes supply essential ecosystem services. Therefore, it is crucial to understand how oil influences the microbial communities in sediments that play key roles in ecosystem functioning. Ecosystems such as sediments are characterized by intensive bioturbation due to burrowing macrofauna that may modify the microbial metabolisms. It is thus essential to consider the bioturbation when determining the impact of oil on microbial communities. In this study, an experimental laboratory device maintaining pristine collected mudflat sediments in microcosms closer to true environmental conditions – with tidal cycles and natural seawater – was used to simulate an oil spill under bioturbation conditions. Different conditions were applied to the microcosms including an addition of: standardized oil (Blend Arabian Light crude oil, 25.6 mg.g−1 wet sediment), the common burrowing organism Hediste (Nereis) diversicolor and both the oil and H. diversicolor. The addition of H. diversicolor and its associated bioturbation did not affect the removal of petroleum hydrocarbons. After 270 days, 60% of hydrocarbons had been removed in all microcosms irrespective of the H. diversicolor addition. However, 16S-rRNA gene and 16S-cDNA T-RFLP and RT-PCR-amplicon libraries analysis showed an effect of the condition on the bacterial community structure, composition, and dynamics, supported by PerMANOVA analysis. The 16S-cDNA libraries from microcosms where H. diversicolor was added (oiled and un-oiled) showed a marked dominance of sequences related to Gammaproteobacteria. However, in the oiled-library sequences associated to Deltaproteobacteria and Bacteroidetes were also highly represented. The 16S-cDNA libraries from oiled-microcosms (with and without H. diversicolor addition) revealed two distinct microbial communities characterized by different phylotypes associated to known hydrocarbonoclastic bacteria and dominated by

Impact of oil on bacterial community structure in bioturbated sediments.

PubMed

Stauffert, Magalie; Cravo-Laureau, Cristiana; Jézéquel, Ronan; Barantal, Sandra; Cuny, Philippe; Gilbert, Franck; Cagnon, Christine; Militon, Cécile; Amouroux, David; Mahdaoui, Fatima; Bouyssiere, Brice; Stora, Georges; Merlin, François-Xavier; Duran, Robert

2013-01-01

Oil spills threaten coastlines where biological processes supply essential ecosystem services. Therefore, it is crucial to understand how oil influences the microbial communities in sediments that play key roles in ecosystem functioning. Ecosystems such as sediments are characterized by intensive bioturbation due to burrowing macrofauna that may modify the microbial metabolisms. It is thus essential to consider the bioturbation when determining the impact of oil on microbial communities. In this study, an experimental laboratory device maintaining pristine collected mudflat sediments in microcosms closer to true environmental conditions--with tidal cycles and natural seawater--was used to simulate an oil spill under bioturbation conditions. Different conditions were applied to the microcosms including an addition of: standardized oil (Blend Arabian Light crude oil, 25.6 mg.g⁻¹ wet sediment), the common burrowing organism Hediste (Nereis) diversicolor and both the oil and H. diversicolor. The addition of H. diversicolor and its associated bioturbation did not affect the removal of petroleum hydrocarbons. After 270 days, 60% of hydrocarbons had been removed in all microcosms irrespective of the H. diversicolor addition. However, 16S-rRNA gene and 16S-cDNA T-RFLP and RT-PCR-amplicon libraries analysis showed an effect of the condition on the bacterial community structure, composition, and dynamics, supported by PerMANOVA analysis. The 16S-cDNA libraries from microcosms where H. diversicolor was added (oiled and un-oiled) showed a marked dominance of sequences related to Gammaproteobacteria. However, in the oiled-library sequences associated to Deltaproteobacteria and Bacteroidetes were also highly represented. The 16S-cDNA libraries from oiled-microcosms (with and without H. diversicolor addition) revealed two distinct microbial communities characterized by different phylotypes associated to known hydrocarbonoclastic bacteria and dominated by Gammaproteobacteria

Substrate Type and Free Ammonia Determine Bacterial Community Structure in Full-Scale Mesophilic Anaerobic Digesters Treating Cattle or Swine Manure

PubMed Central

Li, Jiabao; Rui, Junpeng; Yao, Minjie; Zhang, Shiheng; Yan, Xuefeng; Wang, Yuanpeng; Yan, Zhiying; Li, Xiangzhen

2015-01-01

The microbial-mediated anaerobic digestion (AD) process represents an efficient biological process for the treatment of organic waste along with biogas harvest. Currently, the key factors structuring bacterial communities and the potential core and unique bacterial populations in manure anaerobic digesters are not completely elucidated yet. In this study, we collected sludge samples from 20 full-scale anaerobic digesters treating cattle or swine manure, and investigated the variations of bacterial community compositions using high-throughput 16S rRNA amplicon sequencing. Clustering and correlation analysis suggested that substrate type and free ammonia (FA) play key roles in determining the bacterial community structure. The COD: NH4+-N (C:N) ratio of substrate and FA were the most important available operational parameters correlating to the bacterial communities in cattle and swine manure digesters, respectively. The bacterial populations in all of the digesters were dominated by phylum Firmicutes, followed by Bacteroidetes, Proteobacteria and Chloroflexi. Increased FA content selected Firmicutes, suggesting that they probably play more important roles under high FA content. Syntrophic metabolism by Proteobacteria, Chloroflexi, Synergistetes and Planctomycetes are likely inhibited when FA content is high. Despite the different manure substrates, operational conditions and geographical locations of digesters, core bacterial communities were identified. The core communities were best characterized by phylum Firmicutes, wherein Clostridium predominated overwhelmingly. Substrate-unique and abundant communities may reflect the properties of manure substrate and operational conditions. These findings extend our current understanding of the bacterial assembly in full-scale manure anaerobic digesters. PMID:26648921

Insight into the effects of different cropping systems on soil bacterial community and tobacco bacterial wilt rate.

PubMed

Niu, Jiaojiao; Chao, Jin; Xiao, Yunhua; Chen, Wu; Zhang, Chao; Liu, Xueduan; Rang, Zhongwen; Yin, Huaqun; Dai, Linjian

2017-01-01

Rotation is an effective strategy to control crop disease and improve plant health. However, the effects of crop rotation on soil bacterial community composition and structure, and crop health remain unclear. In this study, using 16S rRNA gene sequencing, we explored the soil bacterial communities under four different cropping systems, continuous tobacco cropping (control group), tobacco-maize rotation, tobacco-lily rotation, and tobacco-turnip rotation. Results of detrended correspondence analysis and dissimilarity tests showed that soil bacterial community composition and structure changed significantly among the four groups, such that Acidobacteria and Actinobacteria were more abundant in the maize rotation group (16.6 and 11.5%, respectively) than in the control (8.5 and 7.1%, respectively). Compared with the control group (57.78%), maize and lily were effective rotation crops in controlling tobacco bacterial wilt (about 23.54 and 48.67%). On the other hand, tobacco bacterial wilt rate was increased in the turnip rotation (59.62%) relative to the control. Further study revealed that the abundances of several bacterial populations were directly correlated with tobacco bacterial wilt. For example, Acidobacteria and Actinobacteria were significantly negatively correlated to the tobacco bacterial wilt rate, so they may be probiotic bacteria. Canonical correspondence analysis showed that soil pH and calcium content were key factors in determining soil bacterial communities. In conclusion, our study revealed the composition and structure of bacterial communities under four different cropping systems and may unveil molecular mechanisms for the interactions between soil microorganisms and crop health. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Changes in diversity, abundance, and structure of soil bacterial communities in Brazilian Savanna under different land use systems.

PubMed

Rampelotto, Pabulo Henrique; de Siqueira Ferreira, Adão; Barboza, Anthony Diego Muller; Roesch, Luiz Fernando Wurdig

2013-10-01

The Brazilian Savanna, also known as "Cerrado", is the richest and most diverse savanna in the world and has been ranked as one of the main hotspots of biodiversity. The Cerrado is a representative biome in Central Brazil and the second largest biome in species diversity of South America. Nevertheless, large areas of native vegetation have been converted to agricultural land including grain production, livestock, and forestry. In this view, understanding how land use affects microbial communities is fundamental for the sustainable management of agricultural ecosystems. The aim of this work was to analyze and compare the soil bacterial communities from the Brazilian Cerrado associated with different land use systems using high throughput pyrosequencing of 16S rRNA genes. Relevant differences were observed in the abundance and structure of bacterial communities in soils under different land use systems. On the other hand, the diversity of bacterial communities was not relevantly changed among the sites studied. Land use systems had also an important impact on specific bacterial groups in soil, which might change the soil function and the ecological processes. Acidobacteria, Proteobacteria, and Actinobacteria were the most abundant groups in the Brazilian Cerrado. These findings suggest that more important than analyzing the general diversity is to analyze the composition of the communities. Since soil type was the same among the sites, we might assume that land use was the main factor defining the abundance and structure of bacterial communities.

Bacterial community changes in an industrial algae production system.

PubMed

Fulbright, Scott P; Robbins-Pianka, Adam; Berg-Lyons, Donna; Knight, Rob; Reardon, Kenneth F; Chisholm, Stephen T

2018-04-01

While microalgae are a promising feedstock for production of fuels and other chemicals, a challenge for the algal bioproducts industry is obtaining consistent, robust algae growth. Algal cultures include complex bacterial communities and can be difficult to manage because specific bacteria can promote or reduce algae growth. To overcome bacterial contamination, algae growers may use closed photobioreactors designed to reduce the number of contaminant organisms. Even with closed systems, bacteria are known to enter and cohabitate, but little is known about these communities. Therefore, the richness, structure, and composition of bacterial communities were characterized in closed photobioreactor cultivations of Nannochloropsis salina in F/2 medium at different scales, across nine months spanning late summer-early spring, and during a sequence of serially inoculated cultivations. Using 16S rRNA sequence data from 275 samples, bacterial communities in small, medium, and large cultures were shown to be significantly different. Larger systems contained richer bacterial communities compared to smaller systems. Relationships between bacterial communities and algae growth were complex. On one hand, blooms of a specific bacterial type were observed in three abnormal, poorly performing replicate cultivations, while on the other, notable changes in the bacterial community structures were observed in a series of serial large-scale batch cultivations that had similar growth rates. Bacteria common to the majority of samples were identified, including a single OTU within the class Saprospirae that was found in all samples. This study contributes important information for crop protection in algae systems, and demonstrates the complex ecosystems that need to be understood for consistent, successful industrial algae cultivation. This is the first study to profile bacterial communities during the scale-up process of industrial algae systems.

Effect of Sugarcane Burning or Green Harvest Methods on the Brazilian Cerrado Soil Bacterial Community Structure

PubMed Central

Rachid, Caio T. C. C.; Santos, Adriana L.; Piccolo, Marisa C.; Balieiro, Fabiano C.; Coutinho, Heitor L. C.; Peixoto, Raquel S.; Tiedje, James M.; Rosado, Alexandre S.

2013-01-01

Background The Brazilian Cerrado is one of the most important biodiversity reservoirs in the world. The sugarcane cultivation is expanding in this biome and necessitates the study of how it may impact the soil properties of the Cerrado. There is a lack of information especially about the impacts of different sugarcane management on the native bacterial communities of Cerrado soil. Therefore, our objective was to evaluate and compare the soil bacterial community structure of the Cerrado vegetation with two sugarcane systems. Methods We evaluated samples under native vegetation and the impact of the two most commonly used management strategies for sugarcane cultivation (burnt cane and green cane) on this diversity using pyrosequencing and quantitative PCR of the rrs gene (16S rRNA). Results and Conclusions Nineteen different phyla were identified, with Acidobacteria (≈35%), Proteobacteria (≈24%) and Actinobacteria (≈21%) being the most abundant. Many of the sequences were represented by few operational taxonomic units (OTUs, 3% of dissimilarity), which were found in all treatments. In contrast, there were very strong patterns of local selection, with many OTUs occurring only in one sample. Our results reveal a complex bacterial diversity, with a large fraction of microorganisms not yet described, reinforcing the importance of this biome. As possible sign of threat, the qPCR detected a reduction of the bacterial population in agricultural soils compared with native Cerrado soil communities. We conclude that sugarcane cultivation promoted significant structural changes in the soil bacterial community, with Firmicutes phylum and Acidobacteria classes being the groups most affected. PMID:23533619

Effect of sugarcane burning or green harvest methods on the Brazilian Cerrado soil bacterial community structure.

PubMed

Rachid, Caio T C C; Santos, Adriana L; Piccolo, Marisa C; Balieiro, Fabiano C; Coutinho, Heitor L C; Peixoto, Raquel S; Tiedje, James M; Rosado, Alexandre S

2013-01-01

The Brazilian Cerrado is one of the most important biodiversity reservoirs in the world. The sugarcane cultivation is expanding in this biome and necessitates the study of how it may impact the soil properties of the Cerrado. There is a lack of information especially about the impacts of different sugarcane management on the native bacterial communities of Cerrado soil. Therefore, our objective was to evaluate and compare the soil bacterial community structure of the Cerrado vegetation with two sugarcane systems. We evaluated samples under native vegetation and the impact of the two most commonly used management strategies for sugarcane cultivation (burnt cane and green cane) on this diversity using pyrosequencing and quantitative PCR of the rrs gene (16S rRNA). Nineteen different phyla were identified, with Acidobacteria (≈35%), Proteobacteria (≈24%) and Actinobacteria (≈21%) being the most abundant. Many of the sequences were represented by few operational taxonomic units (OTUs, 3% of dissimilarity), which were found in all treatments. In contrast, there were very strong patterns of local selection, with many OTUs occurring only in one sample. Our results reveal a complex bacterial diversity, with a large fraction of microorganisms not yet described, reinforcing the importance of this biome. As possible sign of threat, the qPCR detected a reduction of the bacterial population in agricultural soils compared with native Cerrado soil communities. We conclude that sugarcane cultivation promoted significant structural changes in the soil bacterial community, with Firmicutes phylum and Acidobacteria classes being the groups most affected.

Polymicrobial airway bacterial communities in adult bronchiectasis patients

PubMed Central

2014-01-01

Background Chronic airway infection contributes to the underlying pathogenesis of non-cystic fibrosis bronchiectasis (NCFBr). In contrast to other chronic airway infections, associated with COPD and CF bronchiectasis, where polymicrobial communities have been implicated in lung damage due to the vicious circle of recurrent bacterial infections and inflammation, there is sparse information on the composition of bacterial communities in NCFBr. Seventy consecutive patients were recruited from an outpatient adult NCFBr clinic. Bacterial communities in sputum samples were analysed by culture and pyrosequencing approaches. Bacterial sequences were analysed using partial least square discrimination analyses to investigate trends in community composition and identify those taxa that contribute most to community variation. Results The lower airway in NCFBr is dominated by three bacterial taxa Pasteurellaceae, Streptococcaceae and Pseudomonadaceae. Moreover, the bacterial community is much more diverse than indicated by culture and contains significant numbers of other genera including anaerobic Prevotellaceae, Veillonellaceae and Actinomycetaceae. We found particular taxa are correlated with different clinical states, 27 taxa were associated with acute exacerbations, whereas 11 taxa correlated with stable clinical states. We were unable to demonstrate a significant effect of antibiotic therapy, gender, or lung function on the diversity of the bacterial community. However, presence of clinically significant culturable taxa; particularly Pseudomonas aeruginosa and Haemophilus influenzae correlated with a significant change in the diversity of the bacterial community in the lung. Conclusions We have demonstrated that acute exacerbations, the frequency of exacerbation and episodes of clinical stability are correlated, in some patients, with a significantly different bacterial community structure, that are associated with a presence of particular taxa in the NCFBr lung. Moreover

Architectural Design Drives the Biogeography of Indoor Bacterial Communities

PubMed Central

O’Connor, Timothy K.; Mhuireach, Gwynne; Northcutt, Dale; Kline, Jeff; Moriyama, Maxwell; Brown, G. Z.; Bohannan, Brendan J. M.; Green, Jessica L.

2014-01-01

Background Architectural design has the potential to influence the microbiology of the built environment, with implications for human health and well-being, but the impact of design on the microbial biogeography of buildings remains poorly understood. In this study we combined microbiological data with information on the function, form, and organization of spaces from a classroom and office building to understand how design choices influence the biogeography of the built environment microbiome. Results Sequencing of the bacterial 16S gene from dust samples revealed that indoor bacterial communities were extremely diverse, containing more than 32,750 OTUs (operational taxonomic units, 97% sequence similarity cutoff), but most communities were dominated by Proteobacteria, Firmicutes, and Deinococci. Architectural design characteristics related to space type, building arrangement, human use and movement, and ventilation source had a large influence on the structure of bacterial communities. Restrooms contained bacterial communities that were highly distinct from all other rooms, and spaces with high human occupant diversity and a high degree of connectedness to other spaces via ventilation or human movement contained a distinct set of bacterial taxa when compared to spaces with low occupant diversity and low connectedness. Within offices, the source of ventilation air had the greatest effect on bacterial community structure. Conclusions Our study indicates that humans have a guiding impact on the microbial biodiversity in buildings, both indirectly through the effects of architectural design on microbial community structure, and more directly through the effects of human occupancy and use patterns on the microbes found in different spaces and space types. The impact of design decisions in structuring the indoor microbiome offers the possibility to use ecological knowledge to shape our buildings in a way that will select for an indoor microbiome that promotes our

Comparison of bacterial communities of conventional and A-stage activated sludge systems

PubMed Central

Gonzalez-Martinez, Alejandro; Rodriguez-Sanchez, Alejandro; Lotti, Tommaso; Garcia-Ruiz, Maria-Jesus; Osorio, Francisco; Gonzalez-Lopez, Jesus; van Loosdrecht, Mark C. M.

2016-01-01

The bacterial community structure of 10 different wastewater treatment systems and their influents has been investigated through pyrosequencing, yielding a total of 283486 reads. These bioreactors had different technological configurations: conventional activated sludge (CAS) systems and very highly loaded A-stage systems. A-stage processes are proposed as the first step in an energy producing municipal wastewater treatment process. Pyrosequencing analysis indicated that bacterial community structure of all influents was similar. Also the bacterial community of all CAS bioreactors was similar. Bacterial community structure of A-stage bioreactors showed a more case-specific pattern. A core of genera was consistently found for all influents, all CAS bioreactors and all A-stage bioreactors, respectively, showing that different geographical locations in The Netherlands and Spain did not affect the functional bacterial communities in these technologies. The ecological roles of these bacteria were discussed. Influents and A-stage bioreactors shared several core genera, while none of these were shared with CAS bioreactors communities. This difference is thought to reside in the different operational conditions of the two technologies. This study shows that bacterial community structure of CAS and A-stage bioreactors are mostly driven by solids retention time (SRT) and hydraulic retention time (HRT), as suggested by multivariate redundancy analysis. PMID:26728449

Application of Bioorganic Fertilizer Significantly Increased Apple Yields and Shaped Bacterial Community Structure in Orchard Soil.

PubMed

Wang, Lei; Li, Jing; Yang, Fang; E, Yaoyao; Raza, Waseem; Huang, Qiwei; Shen, Qirong

2017-02-01

Application of bioorganic fertilizers has been reported to improve crop yields and change soil bacterial community structure; however, little work has been done in apple orchard soils where the biological properties of the soils are being degraded due to long-term application of chemical fertilizers. In this study, we used Illumina-based sequencing approach to characterize the bacterial community in the 0-60-cm soil profile under different fertilizer regimes in the Loess Plateau. The experiment includes three treatments: (1) control without fertilization (CK); (2) application of chemical fertilizer (CF); and (3) application of bioorganic fertilizer and organic-inorganic mixed fertilizer (BOF). The results showed that the treatment BOF increased the apple yields by 114 and 67 % compared to the CK and CF treatments, respectively. The treatment BOF also increased the soil organic matter (SOM) by 22 and 16 % compared to the CK and CF treatments, respectively. The Illumina-based sequencing showed that Acidobacteria and Proteobacteria were the predominant phyla and Alphaproteobacteria and Gammaproteobacteria were the most abundant classes in the soil profile. The bacterial richness for ACE was increased after the addition of BOF. Compared to CK and CF treatments, BOF-treated soil revealed higher abundance of Proteobacteria, Alphaproteobacteria and Gammaproteobacteria, Rhizobiales, and Xanthomonadales while Acidobacteria, Gp7, Gp17, and Sphaerobacter were found in lower abundance throughout the soil profile. Bacterial community structure varied with soil depth under different fertilizer treatments, e.g., the bacterial richness, diversity, and the relative abundance of Verruccomicrobia, Candidatus Brocadiales, and Skermanella were decreased with the soil depth in all three treatments. Permutational multivariate analysis showed that the fertilizer regime was the major factor than soil depth in the variations of the bacterial community composition. Two groups, Lysobacter

Bacterial community structure in two permafrost wetlands on the Tibetan Plateau and Sanjiang Plain, China.

PubMed

Yun, Juanli; Ju, Yiwen; Deng, Yongcui; Zhang, Hongxun

2014-08-01

Permafrost wetlands are important methane emission sources and fragile ecosystems sensitive to climate change. Presently, there remains a lack of knowledge regarding bacterial communities, especially methanotrophs in vast areas of permafrost on the Tibetan Plateau in Northwest China and the Sanjiang Plain (SJ) in Northeast China. In this study, 16S rRNA-based quantitative PCR (qPCR) and 454 pyrosequencing were used to identify bacterial communities in soils sampled from a littoral wetland of Lake Namco on the Tibetan Plateau (NMC) and an alluvial wetland on the SJ. Additionally, methanotroph-specific primers targeting particulate methane monooxygenase subunit A gene (pmoA) were used for qPCR and pyrosequencing analysis of methanotrophic community structure in NMC soils. qPCR analysis revealed the presence of 10(10) 16S rRNA gene copies per gram of wet soil in both wetlands, with 10(8) pmoA copies per gram of wet soil in NMC. The two permafrost wetlands showed similar bacterial community compositions, which differed from those reported in other cold environments. Proteobacteria, Actinobacteria , and Chloroflexi were the most abundant phyla in both wetlands, whereas Acidobacteria was prevalent in the acidic wetland SJ only. These four phyla constituted more than 80 % of total bacterial community diversity in permafrost wetland soils, and Methylobacter of type I methanotrophs was overwhelmingly dominant in NMC soils. This study is the first major bacterial sequencing effort of permafrost in the NMC and SJ wetlands, which provides fundamental data for further studies of microbial function in extreme ecosystems under climate change scenarios.

Temporal and spatial influences incur reconfiguration of Arctic heathland soil bacterial community structure.

PubMed

Hill, Richard; Saetnan, Eli R; Scullion, John; Gwynn-Jones, Dylan; Ostle, Nick; Edwards, Arwyn

2016-06-01

Microbial responses to Arctic climate change could radically alter the stability of major stores of soil carbon. However, the sensitivity of plot-scale experiments simulating climate change effects on Arctic heathland soils to potential confounding effects of spatial and temporal changes in soil microbial communities is unknown. Here, the variation in heathland soil bacterial communities at two survey sites in Sweden between spring and summer 2013 and at scales between 0-1 m and, 1-100 m and between sites (> 100 m) were investigated in parallel using 16S rRNA gene T-RFLP and amplicon sequencing. T-RFLP did not reveal spatial structuring of communities at scales < 100 m in any site or season. However, temporal changes were striking. Amplicon sequencing corroborated shifts from r- to K-selected taxon-dominated communities, influencing in silico predictions of functional potential. Network analyses reveal temporal keystone taxa, with a spring betaproteobacterial sub-network centred upon a Burkholderia operational taxonomic unit (OTU) and a reconfiguration to a summer sub-network centred upon an alphaproteobacterial OTU. Although spatial structuring effects may not confound comparison between plot-scale treatments, temporal change is a significant influence. Moreover, the prominence of two temporally exclusive keystone taxa suggests that the stability of Arctic heathland soil bacterial communities could be disproportionally influenced by seasonal perturbations affecting individual taxa. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Bacterial diversity and community structure in lettuce soil are shifted by cultivation time

NASA Astrophysics Data System (ADS)

Liu, Yiqian; Chang, Qing; Guo, Xu; Yi, Xinxin

2017-08-01

Compared with cereal production, vegetable production usually requires a greater degree of management and larger input of nutrients and irrigation, but these systems are not sustainable in the long term. This study aimed to what extent lettuce determine the bacterial community composition in the soil, during lettuce cultivation, pesticides and fertilizers were not apply to soil. Soil samples were collected from depths of 0-20cm and 20-40cm. A highthroughput sequencing approach was employed to investigate bacterial communities in lettuce-cultivated soil samples in a time-dependent manner. The dominant bacteria in the lettuce soil samples were mainly Proteobacteria, Actinobacteria, Chloroflexi, Nitrospirae, Firmicutes, Acidobacteria, Bacteroidetes, Verrucomicrobia, Planctomycetes, Gemmatimo nadetes, Cyanobacteria. Proteobacteria was the most abundant phylum in the 6 soil samples. The relative abundance of Acidobacteria, Firmicutes, Bacteroidetes, Verrucomicrobia and Cyanobacteria decreased through time of lettuce cultivation, but the relative abundance of Proteobacteria, Actinobacteria, Gemmatimonadetes, Chloroflexi, Planctomycetes and Nitrospirae increased over time. In the 0-20cm depth group and the 20-40cm depth soil, a similar pattern was observed that the percentage number of only shared OTUs between the early and late stage was lower than that between the early and middle stage soil, the result showed that lettuce growth can affect structure of soil bacterial communities.

Detecting macroecological patterns in bacterial communities across independent studies of global soils.

PubMed

Ramirez, Kelly S; Knight, Christopher G; de Hollander, Mattias; Brearley, Francis Q; Constantinides, Bede; Cotton, Anne; Creer, Si; Crowther, Thomas W; Davison, John; Delgado-Baquerizo, Manuel; Dorrepaal, Ellen; Elliott, David R; Fox, Graeme; Griffiths, Robert I; Hale, Chris; Hartman, Kyle; Houlden, Ashley; Jones, David L; Krab, Eveline J; Maestre, Fernando T; McGuire, Krista L; Monteux, Sylvain; Orr, Caroline H; van der Putten, Wim H; Roberts, Ian S; Robinson, David A; Rocca, Jennifer D; Rowntree, Jennifer; Schlaeppi, Klaus; Shepherd, Matthew; Singh, Brajesh K; Straathof, Angela L; Bhatnagar, Jennifer M; Thion, Cécile; van der Heijden, Marcel G A; de Vries, Franciska T

2018-02-01

The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries. Whereas previous meta-analysis efforts have focused on bacterial diversity measures or abundances of major taxa, we show that disparate amplicon sequence data can be combined at the taxonomy-based level to assess bacterial community structure. We find that rarer taxa are more important for structuring soil communities than abundant taxa, and that these rarer taxa are better predictors of community structure than environmental factors, which are often confounded across studies. We conclude that combining data from independent studies can be used to explore bacterial community dynamics, identify potential 'indicator' taxa with an important role in structuring communities, and propose hypotheses on the factors that shape bacterial biogeography that have been overlooked in the past.

Soil Parameters Drive the Structure, Diversity and Metabolic Potentials of the Bacterial Communities Across Temperate Beech Forest Soil Sequences.

PubMed

Jeanbille, M; Buée, M; Bach, C; Cébron, A; Frey-Klett, P; Turpault, M P; Uroz, S

2016-02-01

Soil and climatic conditions as well as land cover and land management have been shown to strongly impact the structure and diversity of the soil bacterial communities. Here, we addressed under a same land cover the potential effect of the edaphic parameters on the soil bacterial communities, excluding potential confounding factors as climate. To do this, we characterized two natural soil sequences occurring in the Montiers experimental site. Spatially distant soil samples were collected below Fagus sylvatica tree stands to assess the effect of soil sequences on the edaphic parameters, as well as the structure and diversity of the bacterial communities. Soil analyses revealed that the two soil sequences were characterized by higher pH and calcium and magnesium contents in the lower plots. Metabolic assays based on Biolog Ecoplates highlighted higher intensity and richness in usable carbon substrates in the lower plots than in the middle and upper plots, although no significant differences occurred in the abundance of bacterial and fungal communities along the soil sequences as assessed using quantitative PCR. Pyrosequencing analysis of 16S ribosomal RNA (rRNA) gene amplicons revealed that Proteobacteria, Acidobacteria and Bacteroidetes were the most abundantly represented phyla. Acidobacteria, Proteobacteria and Chlamydiae were significantly enriched in the most acidic and nutrient-poor soils compared to the Bacteroidetes, which were significantly enriched in the soils presenting the higher pH and nutrient contents. Interestingly, aluminium, nitrogen, calcium, nutrient availability and pH appeared to be the best predictors of the bacterial community structures along the soil sequences.

Field-Scale Transplantation Experiment To Investigate Structures of Soil Bacterial Communities at Pioneering Sites▿†

PubMed Central

Lazzaro, Anna; Gauer, Andreas; Zeyer, Josef

2011-01-01

Studies on the effect of environmental conditions on plants and microorganisms are a central issue in ecology, and they require an adequate experimental setup. A strategy often applied in geobotanical studies is based on the reciprocal transplantation of plant species at different sites. We adopted a similar approach as a field-based tool to investigate the relationships of soil bacterial communities with the environment. Soil samples from two different (calcareous and siliceous) unvegetated glacier forefields were reciprocally transplanted and incubated for 15 months between 2009 and 2010. Controls containing local soils were included. The sites were characterized over time in terms of geographical (bedrock, exposition, sunlight, temperature, and precipitation) and physicochemical (texture, water content, soluble and nutrients) features. The incubating local (“home”) and transplanted (“away”) soils were monitored for changes in extractable nutrients and in the bacterial community structure, defined through terminal restriction fragment length polymorphism (T-RFLP) of the 16S rRNA gene. Concentrations of soluble ions in most samples were more significantly affected by seasons than by the transplantation. For example, NO3− showed a seasonal pattern, increasing from 1 to 3 μg NO3− (g soil dry weight)−1 after the melting of snow but decreasing to <1 μg NO3− (g soil dry weight)−1 in autumn. Seasons, and in particular strong precipitation events occurring in the summer of 2010 (200 to 300 mm of rain monthly), were also related to changes of bacterial community structures. Our results show the suitability of this approach to compare responses of bacterial communities to different environmental conditions directly in the field. PMID:21965395

Assessing genetic structure and diversity of airborne bacterial communities by DNA fingerprinting and 16S rDNA clone library

NASA Astrophysics Data System (ADS)

Maron, Pierre-Alain; Lejon, David P. H.; Carvalho, Esmeralda; Bizet, Karine; Lemanceau, Philippe; Ranjard, Lionel; Mougel, Christophe

The density, genetic structure and diversity of airborne bacterial communities were assessed in the outdoor atmosphere. Two air samples were collected on the same location (north of France) at two dates (March 2003 (sample1) and May 2003 (sample 2)). Molecular culture -independent methods were used to characterise airborne bacterial communities regardless of the cell culturability. The automated-ribosomal intergenic spacer analysis (A-RISA) was performed to characterise the community structure in each sample. For both sampling dates, complex A-RISA patterns were observed suggesting a highly diverse community structure, comparable to those found in soil, water or sediment environments. Furthermore, differences in the genetic structure of airborne bacterial communities were observed between samples 1 and 2 suggesting an important variability in time. A clone library of 16S rDNA directly amplified from air DNA of sample 1 was constructed and sequenced to analyse the community composition and diversity. The Proteobacteria group had the greatest representation (60%), with bacteria belonging to the different subdivisions α- (19%), β-(21%), γ-(12%) and δ-(8%). Firmicute and Actinobacteria were also well represented with 14% and 12%, respectively. Most of the identified bacteria are known to be commonly associated with soil or plant environments suggesting that the atmosphere is mainly colonised transiently by microorganisms from local sources, depending on air fluxes.

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.

Response of bacterial community structure to seasonal fluctuation and anthropogenic pollution on coastal water of Alang-Sosiya ship breaking yard, Bhavnagar, India.

PubMed

Patel, Vilas; Munot, Hitendra; Shouche, Yogesh S; Madamwar, Datta

2014-06-01

Bacterial community structure was analyzed from coastal water of Alang-Sosiya ship breaking yard (ASSBY), world's largest ship breaking yard, near Bhavnagar, using 16S rRNA gene sequencing (cultured dependent and culture independent). In clone libraries, total 2324 clones were retrieved from seven samples (coastal water of ASSBY for three seasons along with one pristine coastal water) which were grouped in 525 operational taxonomic units. Proteobacteria was found to be dominant in all samples. In pristine samples, Gammaproteobacteria was found to be dominant, whereas in polluted samples dominancy of Gammaproteobacteria has shifted to Betaproteobacteria and Epsilonproteobacteria. Richness and diversity indices also indicated that bacterial community in pristine sample was the most diverse followed by summer, monsoon and winter samples. To the best of knowledge, this is the first study describing bacterial community structure from coastal water of ASSBY, and it suggests that seasonal fluctuation and anthropogenic pollutions alters the bacterial community structure. Copyright © 2014 Elsevier Ltd. All rights reserved.

Different impacts of manure and chemical fertilizers on bacterial community structure and antibiotic resistance genes in arable soils.

PubMed

Liu, Peng; Jia, Shuyu; He, Xiwei; Zhang, Xuxiang; Ye, Lin

2017-12-01

Both manure and chemical fertilizers are widely used in modern agriculture. However, the impacts of different fertilizers on bacterial community structure and antibiotic resistance genes (ARGs) in arable soils still remain unclear. In this study, high-throughput sequencing and quantitative PCR were employed to investigate the bacterial community structure, ARGs and mobile genetic elements (MGEs) influenced by the application of different fertilizers, including chemical fertilizers, piggery manure and straw ash. The results showed that the application of fertilizers could significantly change the soil bacterial community and the abundance of Gaiella under phylum Actinobacteria was significantly reduced from 12.9% in unfertilized soil to 4.1%-7.4% in fertilized soil (P < 0.05). It was also found that the application of manure could cause a transient effect on soil resistome composition and the relative abundance of ARGs increased from 7.37 ppm to 32.10 ppm. The abundance of aminoglycoside, sulfonamide and tetracycline resistance genes greatly increased after manure fertilization and then gradually returned to normal levels with the decay of some intestinal bacteria carrying ARGs. In contrast, the application of chemical fertilizers and straw ash significantly changed the bacterial community structure but exerted little effect on soil resistome. Overall, the results of this study illustrated the different effects of different fertilizers on the soil resistome and revealed that the changes of soil resistome induced by manure application mainly resulted from alteration of bacteria community rather than the horizontal gene transfer. Copyright © 2017 Elsevier Ltd. All rights reserved.

Assessment of pollution impact on biological activity and structure of seabed bacterial communities in the Port of Livorno (Italy).

PubMed

Iannelli, Renato; Bianchi, Veronica; Macci, Cristina; Peruzzi, Eleonora; Chiellini, Carolina; Petroni, Giulio; Masciandaro, Grazia

2012-06-01

The main objective of this study was to assess the impact of pollution on seabed bacterial diversity, structure and activity in the Port of Livorno. Samples of seabed sediments taken from five selected sites within the port were subjected to chemical analyses, enzymatic activity detection, bacterial count and biomolecular analysis. Five different statistics were used to correlate the level of contamination with the detected biological indicators. The results showed that the port is mainly contaminated by variable levels of petroleum hydrocarbons and heavy metals, which affect the structure and activity of the bacterial population. Irrespective of pollution levels, the bacterial diversity did not diverge significantly among the assessed sites and samples, and no dominance was observed. The type of impact of hydrocarbons and heavy metals was controversial, thus enforcing the supposition that the structure of the bacterial community is mainly driven by the levels of nutrients. The combined use of chemical and biological essays resulted in an in-depth observation and analysis of the existing links between pollution macro-indicators and biological response of seabed bacterial communities. Copyright © 2012 Elsevier B.V. All rights reserved.

Controls on bacterial and archaeal community structure and greenhouse gas production in natural, mined, and restored Canadian peatlands

PubMed Central

Basiliko, Nathan; Henry, Kevin; Gupta, Varun; Moore, Tim R.; Driscoll, Brian T.; Dunfield, Peter F.

2013-01-01

Northern peatlands are important global C reservoirs, largely because of their slow rates of microbial C mineralization. Particularly in sites that are heavily influenced by anthropogenic disturbances, there is scant information about microbial ecology and whether or not microbial community structure influences greenhouse gas production. This work characterized communities of bacteria and archaea using terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis of 16S rRNA and functional genes across eight natural, mined, or restored peatlands in two locations in eastern Canada. Correlations were explored among chemical properties of peat, bacterial and archaeal community structure, and carbon dioxide (CO2) and methane (CH4) production rates under oxic and anoxic conditions. Bacteria and archaea similar to those found in other peat soil environments were detected. In contrast to other reports, methanogen diversity was low in our study, with only 2 groups of known or suspected methanogens. Although mining and restoration affected substrate availability and microbial activity, these land-uses did not consistently affect bacterial or archaeal community composition. In fact, larger differences were observed between the two locations and between oxic and anoxic peat samples than between natural, mined, and restored sites, with anoxic samples characterized by less detectable bacterial diversity and stronger dominance by members of the phylum Acidobacteria. There were also no apparent strong linkages between prokaryote community structure and CH4 or CO2 production, suggesting that different organisms exhibit functional redundancy and/or that the same taxa function at very different rates when exposed to different peat substrates. In contrast to other earlier work focusing on fungal communities across similar mined and restored peatlands, bacterial and archaeal communities appeared to be more resistant or resilient to peat substrate changes brought

A multifactor analysis of fungal and bacterial community structure of the root microbiome of mature Populus deltoides trees

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

Shakya, Migun; Gottel, Neil R; Castro Gonzalez, Hector F

2013-01-01

Bacterial and fungal communities associated with plant roots are central to the host- health, survival and growth. However, a robust understanding of root-microbiome and the factors that drive host associated microbial community structure have remained elusive, especially in mature perennial plants from natural settings. Here, we investigated relationships of bacterial and fungal communities in the rhizosphere and root endosphere of the riparian tree species Populus deltoides, and the influence of soil parameters, environmental properties (host phenotype and aboveground environmental settings), host plant genotype (Simple Sequence Repeat (SSR) markers), season (Spring vs. Fall) and geographic setting (at scales from regional watershedsmore » to local riparian zones) on microbial community structure. Each of the trees sampled displayed unique aspects to it s associated community structure with high numbers of Operational Taxonomic Units (OTUs) specific to an individual trees (bacteria >90%, fungi >60%). Over the diverse conditions surveyed only a small number of OTUs were common to all samples within rhizosphere (35 bacterial and 4 fungal) and endosphere (1 bacterial and 1 fungal) microbiomes. As expected, Proteobacteria and Ascomycota were dominant in root communities (>50%) while other higher-level phylogenetic groups (Chytridiomycota, Acidobacteria) displayed greatly reduced abundance in endosphere compared to the rhizosphere. Variance partitioning partially explained differences in microbiome composition between all sampled roots on the basis of seasonal and soil properties (4% to 23%). While most variation remains unattributed, we observed significant differences in the microbiota between watersheds (Tennessee vs. North Carolina) and seasons (Spring vs. Fall). SSR markers clearly delineated two host populations associated with the samples taken in TN vs. NC, but overall genotypic distances did not have a significant effect on corresponding communities that

A Multifactor Analysis of Fungal and Bacterial Community Structure in the Root Microbiome of Mature Populus deltoides Trees

PubMed Central

Shakya, Migun; Gottel, Neil; Castro, Hector; Yang, Zamin K.; Gunter, Lee; Labbé, Jessy; Muchero, Wellington; Bonito, Gregory; Vilgalys, Rytas; Tuskan, Gerald; Podar, Mircea; Schadt, Christopher W.

2013-01-01

Bacterial and fungal communities associated with plant roots are central to the host health, survival and growth. However, a robust understanding of the root-microbiome and the factors that drive host associated microbial community structure have remained elusive, especially in mature perennial plants from natural settings. Here, we investigated relationships of bacterial and fungal communities in the rhizosphere and root endosphere of the riparian tree species Populus deltoides, and the influence of soil parameters, environmental properties (host phenotype and aboveground environmental settings), host plant genotype (Simple Sequence Repeat (SSR) markers), season (Spring vs. Fall) and geographic setting (at scales from regional watersheds to local riparian zones) on microbial community structure. Each of the trees sampled displayed unique aspects to its associated community structure with high numbers of Operational Taxonomic Units (OTUs) specific to an individual trees (bacteria >90%, fungi >60%). Over the diverse conditions surveyed only a small number of OTUs were common to all samples within rhizosphere (35 bacterial and 4 fungal) and endosphere (1 bacterial and 1 fungal) microbiomes. As expected, Proteobacteria and Ascomycota were dominant in root communities (>50%) while other higher-level phylogenetic groups (Chytridiomycota, Acidobacteria) displayed greatly reduced abundance in endosphere compared to the rhizosphere. Variance partitioning partially explained differences in microbiome composition between all sampled roots on the basis of seasonal and soil properties (4% to 23%). While most variation remains unattributed, we observed significant differences in the microbiota between watersheds (Tennessee vs. North Carolina) and seasons (Spring vs. Fall). SSR markers clearly delineated two host populations associated with the samples taken in TN vs. NC, but overall host genotypic distances did not have a significant effect on corresponding communities that

Cumulative Effects of Short-Term Polymetal Contamination on Soil Bacterial Community Structure

PubMed Central

Ranjard, L.; Lignier, L.; Chaussod, R.

2006-01-01

In this study we evaluated the short-term effects of copper, cadmium, and mercury, added singly or in combination at different doses, on soil bacterial community structure using the bacterial automated ribosomal intergenic spacer analysis (B-ARISA) fingerprinting technique. Principal-component analysis of B-ARISA profiles allowed us to deduce the following order of impact: (Cu + Cd + Hg) >> Hg ≥ Cd > Cu. These results demonstrated that there was a cumulative effect of metal toxicity. Furthermore, the trend of modifications was consistent with the “hump-backed” relationships between biological diversity and disturbance described by Giller et al. (K. E. Giller, E. Witler, and S. P. McGrath, Soil Biol. Biochem. 30:1389-1414, 1998). PMID:16461728

River Flow Impacts Bacterial and Archaeal Community Structure in Surface Sediments in the Northern Gulf of Mexico.

PubMed

Ortmann, Alice C; Brannock, Pamela M; Wang, Lei; Halanych, Kenneth M

2018-04-17

Meiobenthic community structure in the northern Gulf of Mexico has been shown to be driven by geographical differences due to inshore-offshore gradients and location relative to river discharge. Samples collected along three transects spanning Mobile Bay, Alabama, showed significant differences in meiobenthic communities east of the bay compared to those sampled from the west. In contrast, analysis of bacterial and archaeal communities from the same sediment samples shows that the inshore-offshore gradient has minimal impact on their community structure. Significant differences in community structure were observed for Bacteria and Archaea between the east and west samples, but there was no difference in richness or diversity. Grouped by sediment type, higher richness was observed in silty samples compared to sandy samples. Significant differences were also observed among sediment types for community structure with bacteria communities in silty samples having more anaerobic sulfate reducers compared to aerobic heterotrophs, which had higher abundances in sandy sediments. This is likely due to increased organic matter in the silty sediments from the overlying river leading to low oxygen habitats. Most archaeal sequences represented poorly characterized high-level taxa, limiting interpretation of their distributions. Overlap between groups based on transect and sediment characteristics made determining which factor is more important in structuring bacterial and archaeal communities difficult. However, both factors are driven by discharge from the Mobile River. Although inshore-offshore gradients do not affect Bacteria or Archaea to the same extent as the meiobenthic communities, all three groups are strongly affected by sediment characteristics.

Microenvironmental heterogeneity of gut compartments drives bacterial community structure in wood- and humus-feeding higher termites.

PubMed

Mikaelyan, Aram; Meuser, Katja; Brune, Andreas

2017-01-01

Symbiotic digestion of lignocellulose in higher termites (family Termitidae) is accomplished by an exclusively prokaryotic gut microbiota. By deep sequencing of amplified 16S rRNA genes, we had identified diet as the primary determinant of bacterial community structure in a broad selection of termites specialized on lignocellulose in different stages of humification. Here, we increased the resolution of our approach to account for the pronounced heterogeneity in microenvironmental conditions and microbial activities in the major hindgut compartments. The community structure of consecutive gut compartments in each species strongly differed, but that of homologous compartments clearly converged, even among unrelated termites. While the alkaline P1 compartments of all termites investigated contained specific lineages of Clostridiales, the posterior hindgut compartments (P3, P4) differed between feeding groups and were predominantly colonized by putatively fiber-associated lineages of Spirochaetes, Fibrobacteres and the TG3 phylum (wood and grass feeders) or diverse assemblages of Clostridiales and Bacteroidetes (humus and soil feeders). The results underscore that bacterial community structure in termite guts is driven by microenvironmental factors, such as pH, available substrates and gradients of O 2 and H 2 , and inspire investigations on the functional roles of specific bacterial taxa in lignocellulose and humus digestion. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Metamorphosis of a butterfly-associated bacterial community.

PubMed

Hammer, Tobin J; McMillan, W Owen; Fierer, Noah

2014-01-01

Butterflies are charismatic insects that have long been a focus of biological research. They are also habitats for microorganisms, yet these microbial symbionts are little-studied, despite their likely importance to butterfly ecology and evolution. In particular, the diversity and composition of the microbial communities inhabiting adult butterflies remain uncharacterized, and it is unknown how the larval (caterpillar) and adult microbiota compare. To address these knowledge gaps, we used Illumina sequencing of 16S rRNA genes from internal bacterial communities associated with multiple life stages of the neotropical butterfly Heliconius erato. We found that the leaf-chewing larvae and nectar- and pollen-feeding adults of H. erato contain markedly distinct bacterial communities, a pattern presumably rooted in their distinct diets. Larvae and adult butterflies host relatively small and similar numbers of bacterial phylotypes, but few are common to both stages. The larval microbiota clearly simplifies and reorganizes during metamorphosis; thus, structural changes in a butterfly's bacterial community parallel those in its own morphology. We furthermore identify specific bacterial taxa that may mediate larval and adult feeding biology in Heliconius and other butterflies. Although male and female Heliconius adults differ in reproductive physiology and degree of pollen feeding, bacterial communities associated with H. erato are not sexually dimorphic. Lastly, we show that captive and wild individuals host different microbiota, a finding that may have important implications for the relevance of experimental studies using captive butterflies.

Metamorphosis of a Butterfly-Associated Bacterial Community

PubMed Central

Hammer, Tobin J.; McMillan, W. Owen; Fierer, Noah

2014-01-01

Butterflies are charismatic insects that have long been a focus of biological research. They are also habitats for microorganisms, yet these microbial symbionts are little-studied, despite their likely importance to butterfly ecology and evolution. In particular, the diversity and composition of the microbial communities inhabiting adult butterflies remain uncharacterized, and it is unknown how the larval (caterpillar) and adult microbiota compare. To address these knowledge gaps, we used Illumina sequencing of 16S rRNA genes from internal bacterial communities associated with multiple life stages of the neotropical butterfly Heliconius erato. We found that the leaf-chewing larvae and nectar- and pollen-feeding adults of H. erato contain markedly distinct bacterial communities, a pattern presumably rooted in their distinct diets. Larvae and adult butterflies host relatively small and similar numbers of bacterial phylotypes, but few are common to both stages. The larval microbiota clearly simplifies and reorganizes during metamorphosis; thus, structural changes in a butterfly's bacterial community parallel those in its own morphology. We furthermore identify specific bacterial taxa that may mediate larval and adult feeding biology in Heliconius and other butterflies. Although male and female Heliconius adults differ in reproductive physiology and degree of pollen feeding, bacterial communities associated with H. erato are not sexually dimorphic. Lastly, we show that captive and wild individuals host different microbiota, a finding that may have important implications for the relevance of experimental studies using captive butterflies. PMID:24466308

Interspecific Plant Interactions Reflected in Soil Bacterial Community Structure and Nitrogen Cycling in Primary Succession.

PubMed

Knelman, Joseph E; Graham, Emily B; Prevéy, Janet S; Robeson, Michael S; Kelly, Patrick; Hood, Eran; Schmidt, Steve K

2018-01-01

Past research demonstrating the importance plant-microbe interactions as drivers of ecosystem succession has focused on how plants condition soil microbial communities, impacting subsequent plant performance and plant community assembly. These studies, however, largely treat microbial communities as a black box. In this study, we sought to examine how emblematic shifts from early successional Alnus viridus ssp. sinuata (Sitka alder) to late successional Picea sitchensis (Sitka spruce) in primary succession may be reflected in specific belowground changes in bacterial community structure and nitrogen cycling related to the interaction of these two plants. We examined early successional alder-conditioned soils in a glacial forefield to delineate how alders alter the soil microbial community with increasing dominance. Further, we assessed the impact of late-successional spruce plants on these early successional alder-conditioned microbiomes and related nitrogen cycling through a leachate addition microcosm experiment. We show how increasingly abundant alder select for particular bacterial taxa. Additionally, we found that spruce leachate significantly alters the composition of these microbial communities in large part by driving declines in taxa that are enriched by alder, including bacterial symbionts. We found these effects to be spruce specific, beyond a general leachate effect. Our work also demonstrates a unique influence of spruce on ammonium availability. Such insights bolster theory relating the importance of plant-microbe interactions with late-successional plants and interspecific plant interactions more generally.

Interspecific Plant Interactions Reflected in Soil Bacterial Community Structure and Nitrogen Cycling in Primary Succession

PubMed Central

Knelman, Joseph E.; Graham, Emily B.; Prevéy, Janet S.; Robeson, Michael S.; Kelly, Patrick; Hood, Eran; Schmidt, Steve K.

2018-01-01

Past research demonstrating the importance plant–microbe interactions as drivers of ecosystem succession has focused on how plants condition soil microbial communities, impacting subsequent plant performance and plant community assembly. These studies, however, largely treat microbial communities as a black box. In this study, we sought to examine how emblematic shifts from early successional Alnus viridus ssp. sinuata (Sitka alder) to late successional Picea sitchensis (Sitka spruce) in primary succession may be reflected in specific belowground changes in bacterial community structure and nitrogen cycling related to the interaction of these two plants. We examined early successional alder-conditioned soils in a glacial forefield to delineate how alders alter the soil microbial community with increasing dominance. Further, we assessed the impact of late-successional spruce plants on these early successional alder-conditioned microbiomes and related nitrogen cycling through a leachate addition microcosm experiment. We show how increasingly abundant alder select for particular bacterial taxa. Additionally, we found that spruce leachate significantly alters the composition of these microbial communities in large part by driving declines in taxa that are enriched by alder, including bacterial symbionts. We found these effects to be spruce specific, beyond a general leachate effect. Our work also demonstrates a unique influence of spruce on ammonium availability. Such insights bolster theory relating the importance of plant–microbe interactions with late-successional plants and interspecific plant interactions more generally. PMID:29467741

Efficiency of temporary storage of geothermal waters in a lake system: Monitoring the changes of water quality and bacterial community structures.

PubMed

Szirányi, Barbara; Krett, Gergely; Kosáros, Tünde; Janurik, Endre; Pekár, Ferenc; Márialigeti, Károly; Borsodi, Andrea K

2017-12-01

Disposal of used geothermal waters in Hungary often means temporary storage in reservoir lakes to reduce temperature and improve water quality. In this study, the physical and chemical properties and changes in the bacterial community structure of a reservoir lake system in southeast region of Hungary were monitored and compared through 2 years, respectively. The values of biological oxygen demand, concentrations of ammonium ion, total inorganic nitrogen, total phosphorous, and total phenol decreased, whereas oxygen saturation, total organic nitrogen, pH, and conductivity increased during the storage period. Bacterial community structure of water and sediment samples was compared by denaturing gradient gel electrophoresis (DGGE) following the amplification of the 16S rRNA gene. According to the DGGE patterns, greater seasonal than spatial differences of bacterial communities were revealed in both water and sediment of the lakes. Representatives of the genera Arthrospira and Anabaenopsis (cyanobacteria) were identified as permanent and dominant members of the bacterial communities.

Temporal variability of bacterial communities in cryoconite on an alpine glacier.

PubMed

Franzetti, Andrea; Navarra, Federico; Tagliaferri, Ilario; Gandolfi, Isabella; Bestetti, Giuseppina; Minora, Umberto; Azzoni, Roberto Sergio; Diolaiuti, Guglielmina; Smiraglia, Claudio; Ambrosini, Roberto

2017-04-01

Cryoconite holes, that is, small ponds that form on glacier surface, are considered the most biologically active environments on glaciers. Bacterial communities in these environments have been extensively studied, but often through snapshot studies based on the assumption of a general stability of community structure. In this study, the temporal variation of bacterial communities in cryoconite holes on the Forni Glacier (Italian Alps) was investigated by high throughput DNA sequencing. A temporal change of bacterial communities was observed with autotrophic Cyanobacteria populations dominating communities after snowmelt, and heterotrophic Sphingobacteriales populations increasing in abundance later in the season. Bacterial communities also varied according to hole depth and area, amount of organic matter in the cryoconite and oxygen concentration. However, variation in environmental features explained a lower fraction of the variation in bacterial communities than temporal variation. Temporal change along ablation season seems therefore more important than local environmental conditions in shaping bacterial communities of cryoconite of the Forni Glacier. These findings challenge the assumption that bacterial communities of cryoconite holes are stable. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Grazing of leaf-associated Cercomonads (Protists: Rhizaria: Cercozoa) structures bacterial community composition and function.

PubMed

Flues, Sebastian; Bass, David; Bonkowski, Michael

2017-08-01

Preferential food selection in protists is well documented, but we still lack basic understanding on how protist predation modifies the taxonomic and functional composition of bacterial communities. We conducted feeding trials using leaf-associated cercomonad Cercozoa by incubating them on a standardized, diverse bacterial community washed from plant leaves. We used a shotgun metagenomics approach to investigate the taxonomic and functional changes of the bacterial community after five days protist predation on bacteria. Predation-induced shifts in bacterial community composition could be linked to phenotypic protist traits. Protist reproduction rate, morphological plasticity and cell speed were most important in determining bacterial community composition. Analyses of co-occurrence patterns showed less complex correlations between bacterial taxa in the protist-grazed treatments with a higher proportion of positive correlations than in non-grazed controls, suggesting that predation reduced the influence of strong competitors. Protist predation influenced 14 metabolic core functions including membrane transport from which type VI secretion systems were in particular upregulated. In view of the functional importance of bacterial communities in the phyllosphere and rhizosphere of plants, a more detailed understanding of predator-prey interactions, changes in microbial composition and function, and subsequent repercussions on plant performance are clearly required. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Structure and temporal dynamics of the bacterial communities associated to microhabitats of the coral Oculina patagonica.

PubMed

Rubio-Portillo, Esther; Santos, Fernando; Martínez-García, Manuel; de Los Ríos, Asunción; Ascaso, Carmen; Souza-Egipsy, Virginia; Ramos-Esplá, Alfonso A; Anton, Josefa

2016-12-01

Corals are known to contain a diverse microbiota that plays a paramount role in the physiology and health of holobiont. However, few studies have addressed the variability of bacterial communities within the coral host. In this study, bacterial community composition from the mucus, tissue and skeleton of the scleractinian coral Oculina patagonica were investigated seasonally at two locations in the Western Mediterranean Sea, to further understand how environmental conditions and the coral microbiome structure are related. We used denaturing gradient gel electrophoresis in combination with next-generation sequencing and electron microscopy to characterize the bacterial community. The bacterial communities were significantly different among coral compartments, and coral tissue displayed the greatest changes related to environmental conditions and coral health status. Species belonging to the Rhodobacteraceae and Vibrionaceae families form part of O. patagonica tissues core microbiome and may play significant roles in the nitrogen cycle. Furthermore, sequences related to the coral pathogens, Vibrio mediterranei and Vibrio coralliilyticus, were detected not only in bleached corals but also in healthy ones, even during cold months. This fact opens a new view onto unveiling the role of pathogens in the development of coral diseases in the future. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Associations between soil bacterial community structure and nutrient cycling functions in long-term organic farm soils following cover crop and organic fertilizer amendment.

PubMed

Fernandez, Adria L; Sheaffer, Craig C; Wyse, Donald L; Staley, Christopher; Gould, Trevor J; Sadowsky, Michael J

2016-10-01

Agricultural management practices can produce changes in soil microbial populations whose functions are crucial to crop production and may be detectable using high-throughput sequencing of bacterial 16S rRNA. To apply sequencing-derived bacterial community structure data to on-farm decision-making will require a better understanding of the complex associations between soil microbial community structure and soil function. Here 16S rRNA sequencing was used to profile soil bacterial communities following application of cover crops and organic fertilizer treatments in certified organic field cropping systems. Amendment treatments were hairy vetch (Vicia villosa), winter rye (Secale cereale), oilseed radish (Raphanus sativus), buckwheat (Fagopyrum esculentum), beef manure, pelleted poultry manure, Sustane(®) 8-2-4, and a no-amendment control. Enzyme activities, net N mineralization, soil respiration, and soil physicochemical properties including nutrient levels, organic matter (OM) and pH were measured. Relationships between these functional and physicochemical parameters and soil bacterial community structure were assessed using multivariate methods including redundancy analysis, discriminant analysis, and Bayesian inference. Several cover crops and fertilizers affected soil functions including N-acetyl-β-d-glucosaminidase and β-glucosidase activity. Effects, however, were not consistent across locations and sampling timepoints. Correlations were observed among functional parameters and relative abundances of individual bacterial families and phyla. Bayesian analysis inferred no directional relationships between functional activities, bacterial families, and physicochemical parameters. Soil functional profiles were more strongly predicted by location than by treatment, and differences were largely explained by soil physicochemical parameters. Composition of soil bacterial communities was predictive of soil functional profiles. Differences in soil function were

Bacterial density and community structure associated with aggregate size fractions of soil-feeding termite mounds.

PubMed

Fall, S; Nazaret, S; Chotte, J L; Brauman, A

2004-08-01

The building and foraging activities of termites are known to modify soil characteristics such as the heterogeneity. In tropical savannas the impact of the activity of soil-feeding termites ( Cubitermes niokoloensis) has been shown to affect the properties of the soil at the aggregate level by creating new soil microenvironments (aggregate size fractions) [13]. These changes were investigated in greater depth by looking at the microbial density (AODC) and the genetic structure (automated rRNA intergenic spacer analysis: ARISA) of the communities in the different aggregate size fractions (i.e., coarse sand, fine sand, coarse silt, fine silt, and dispersible clays) separated from compartments (internal and external wall) of three Cubitermes niokoloensis mounds. The bacterial density of the mounds was significantly higher (1.5 to 3 times) than that of the surrounding soil. Within the aggregate size fractions, the termite building activity resulted in a significant increase in bacterial density within the coarser fractions (>20 mum). Multivariate analysis of the ARISA profiles revealed that the bacterial genetic structures of unfractionated soil and soil aggregate size fractions of the three mounds was noticeably different from the savanna soil used as a reference. Moreover, the microbial community associated with the different microenvironments in the three termite mounds revealed three distinct clusters formed by the aggregate size fractions of each mound. Except for the 2-20 mum fraction, these results suggest that the mound microbial genetic structure is more dependent upon microbial pool affiliation (the termite mound) than on the soil location (aggregate size fraction). The causes of the specificity of the microbial community structure of termite mound aggregate size fractions are discussed.

Industrial activated sludge exhibit unique bacterial community composition at high taxonomic ranks.

PubMed

Ibarbalz, Federico M; Figuerola, Eva L M; Erijman, Leonardo

2013-07-01

Biological degradation of domestic and industrial wastewater by activated sludge depends on a common process of separation of the diverse self-assembled and self-sustained microbial flocs from the treated wastewater. Previous surveys of bacterial communities indicated the presence of a common core of bacterial phyla in municipal activated sludge, an observation consistent with the concept of ecological coherence of high taxonomic ranks. The aim of this work was to test whether this critical feature brings about a common pattern of abundance distribution of high bacterial taxa in industrial and domestic activated sludge, and to relate the bacterial community structure of industrial activated sludge with relevant operational parameters. We have applied 454 pyrosequencing of 16S rRNA genes to evaluate bacterial communities in full-scale biological wastewater treatment plants sampled at different times, including seven systems treating wastewater from different industries and one plant that treats domestic wastewater, and compared our datasets with the data from municipal wastewater treatment plants obtained by three different laboratories. We observed that each industrial activated sludge system exhibited a unique bacterial community composition, which is clearly distinct from the common profile of bacterial phyla or classes observed in municipal plants. The influence of process parameters on the bacterial community structure was evaluated using constrained analysis of principal coordinates (CAP). Part of the differences in the bacterial community structure between industrial wastewater treatment systems were explained by dissolved oxygen and pH. Despite the ecological relevance of floc formation for the assembly of bacterial communities in activated sludge, the wastewater characteristics are likely to be the major determinant that drives bacterial composition at high taxonomic ranks. Copyright © 2013 Elsevier Ltd. All rights reserved.

Bacterial community structure and variation in a full-scale seawater desalination plant for drinking water production.

PubMed

Belila, A; El-Chakhtoura, J; Otaibi, N; Muyzer, G; Gonzalez-Gil, G; Saikaly, P E; van Loosdrecht, M C M; Vrouwenvelder, J S

2016-05-01

Microbial processes inevitably play a role in membrane-based desalination plants, mainly recognized as membrane biofouling. We assessed the bacterial community structure and diversity during different treatment steps in a full-scale seawater desalination plant producing 40,000 m(3)/d of drinking water. Water samples were taken over the full treatment train consisting of chlorination, spruce media and cartridge filters, de-chlorination, first and second pass reverse osmosis (RO) membranes and final chlorine dosage for drinking water distribution. The water samples were analyzed for water quality parameters (total bacterial cell number, total organic carbon, conductivity, pH, etc.) and microbial community composition by 16S rRNA gene pyrosequencing. The planktonic microbial community was dominated by Proteobacteria (48.6%) followed by Bacteroidetes (15%), Firmicutes (9.3%) and Cyanobacteria (4.9%). During the pretreatment step, the spruce media filter did not impact the bacterial community composition dominated by Proteobacteria. In contrast, the RO and final chlorination treatment steps reduced the Proteobacterial relative abundance in the produced water where Firmicutes constituted the most dominant bacterial group. Shannon and Chao1 diversity indices showed that bacterial species richness and diversity decreased during the seawater desalination process. The two-stage RO filtration strongly reduced the water conductivity (>99%), TOC concentration (98.5%) and total bacterial cell number (>99%), albeit some bacterial DNA was found in the water after RO filtration. About 0.25% of the total bacterial operational taxonomic units (OTUs) were present in all stages of the desalination plant: the seawater, the RO permeates and the chlorinated drinking water, suggesting that these bacterial strains can survive in different environments such as high/low salt concentration and with/without residual disinfectant. These bacterial strains were not caused by contamination during

Time-dependent effect of graphene on the structure, abundance, and function of the soil bacterial community.

PubMed

Ren, Wenjie; Ren, Gaidi; Teng, Ying; Li, Zhengao; Li, Lina

2015-10-30

The increased application of graphene raises concerns about its environmental impact, but little information is available on the effect of graphene on the soil microbial community. This study evaluated the impact of graphene on the structure, abundance and function of the soil bacterial community based on quantitative real-time polymerase chain reaction (qPCR), pyrosequencing and soil enzyme activities. The results show that the enzyme activities of dehydrogenase and fluorescein diacetate (FDA) esterase and the biomass of the bacterial populations were transiently promoted by the presence of graphene after 4 days of exposure, but these parameters recovered completely after 21 days. Pyrosequencing analysis suggested a significant shift in some bacterial populations after 4 days, and the shift became weaker or disappeared as the exposure time increased to 60 days. During the entire exposure process, the majority of bacterial phylotypes remained unaffected. Some bacterial populations involved in nitrogen biogeochemical cycles and the degradation of organic compounds can be affected by the presence of graphene. Copyright © 2015 Elsevier B.V. All rights reserved.

Sediment bacterial community structures and their predicted functions implied the impacts from natural processes and anthropogenic activities in coastal area.

PubMed

Su, Zhiguo; Dai, Tianjiao; Tang, Yushi; Tao, Yile; Huang, Bei; Mu, Qinglin; Wen, Donghui

2018-06-01

Coastal ecosystem structures and functions are changing under natural and anthropogenic influences. In this study, surface sediment samples were collected from disturbed zone (DZ), near estuary zone (NEZ), and far estuary zone (FEZ) of Hangzhou Bay, one of the most seriously polluted bays in China. The bacterial community structures and predicted functions varied significantly in different zones. Firmicutes were found most abundantly in DZ, highlighting the impacts of anthropogenic activities. Sediment total phosphorus was most influential on the bacterial community structures. Predicted by PICRUSt analysis, DZ significantly exceeded FEZ and NEZ in the subcategory of Xenobiotics Biodegradation and Metabolism; and DZ enriched all the nitrate reduction related genes, except nrfA gene. Seawater salinity and inorganic nitrogen, respectively as the representative natural and anthropogenic factor, performed exact-oppositely in nitrogen metabolism functions. The changes of bacterial community compositions and predicted functions provide a new insight into human-induced pollution impacts on coastal ecosystem. Copyright © 2018 Elsevier Ltd. All rights reserved.

Diet is the primary determinant of bacterial community structure in the guts of higher termites.

PubMed

Mikaelyan, Aram; Dietrich, Carsten; Köhler, Tim; Poulsen, Michael; Sillam-Dussès, David; Brune, Andreas

2015-10-01

The gut microbiota of termites plays critical roles in the symbiotic digestion of lignocellulose. While phylogenetically 'lower termites' are characterized by a unique association with cellulolytic flagellates, higher termites (family Termitidae) harbour exclusively prokaryotic communities in their dilated hindguts. Unlike the more primitive termite families, which primarily feed on wood, they have adapted to a variety of lignocellulosic food sources in different stages of humification, ranging from sound wood to soil organic matter. In this study, we comparatively analysed representatives of different taxonomic lineages and feeding groups of higher termites to identify the major drivers of bacterial community structure in the termite gut, using amplicon libraries of 16S rRNA genes from 18 species of higher termites. In all analyses, the wood-feeding species were clearly separated from humus and soil feeders, irrespective of their taxonomic affiliation, offering compelling evidence that diet is the primary determinant of bacterial community structure. Within each diet group, however, gut communities of termites from the same subfamily were more similar than those of distantly related species. A highly resolved classification using a curated reference database revealed only few genus-level taxa whose distribution patterns indicated specificity for certain host lineages, limiting any possible cospeciation between the gut microbiota and host to short evolutionary timescales. Rather, the observed patterns in the host-specific distribution of the bacterial lineages in termite guts are best explained by diet-related differences in the availability of microhabitats and functional niches. © 2015 John Wiley & Sons Ltd.

Plant secondary metabolite-induced shifts in bacterial community structure and degradative ability in contaminated soil.

PubMed

Uhlik, Ondrej; Musilova, Lucie; Ridl, Jakub; Hroudova, Miluse; Vlcek, Cestmir; Koubek, Jiri; Holeckova, Marcela; Mackova, Martina; Macek, Tomas

2013-10-01

The aim of the study was to investigate how selected natural compounds (naringin, caffeic acid, and limonene) induce shifts in both bacterial community structure and degradative activity in long-term polychlorinated biphenyl (PCB)-contaminated soil and how these changes correlate with changes in chlorobiphenyl degradation capacity. In order to address this issue, we have integrated analytical methods of determining PCB degradation with pyrosequencing of 16S rRNA gene tag-encoded amplicons and DNA-stable isotope probing (SIP). Our model system was set in laboratory microcosms with PCB-contaminated soil, which was enriched for 8 weeks with the suspensions of flavonoid naringin, terpene limonene, and phenolic caffeic acid. Our results show that application of selected plant secondary metabolites resulted in bacterial community structure far different from the control one (no natural compound amendment). The community in soil treated with caffeic acid is almost solely represented by Proteobacteria, Acidobacteria, and Verrucomicrobia (together over 99 %). Treatment with naringin resulted in an enrichment of Firmicutes to the exclusion of Acidobacteria and Verrucomicrobia. SIP was applied in order to identify populations actively participating in 4-chlorobiphenyl catabolism. We observed that naringin and limonene in soil foster mainly populations of Hydrogenophaga spp., caffeic acid Burkholderia spp. and Pseudoxanthomonas spp. None of these populations were detected among 4-chlorobiphenyl utilizers in non-amended soil. Similarly, the degradation of individual PCB congeners was influenced by the addition of different plant compounds. Residual content of PCBs was lowest after treating the soil with naringin. Addition of caffeic acid resulted in comparable decrease of total PCBs with non-amended soil; however, higher substituted congeners were more degraded after caffeic acid treatment compared to all other treatments. Finally, it appears that plant secondary metabolites

Bacterial community structure analysis of sediment in the Sagami River, Japan using a rapid approach based on two-dimensional DNA gel electrophoresis mapping with selective primer pairs.

PubMed

Liu, Guo-hua; Rajendran, Narasimmalu; Amemiya, Takashi; Itoh, Kiminori

2011-11-01

A rapid approach based on two-dimensional DNA gel electrophroesis (2-DGE) mapping with selective primer pairs was employed to analyze bacterial community structure in sediments from upstream, midstream and downstream of Sagami River in Japan. The 2-DGE maps indicated that Alpha- and Delta-proteobacteria were major bacterial populations in the upstream and midstream sediments. Further bacterial community structure analysis showed that richness proportion of Alpha- and Delta-proteobacterial groups reflected a trend toward decreasing from the upstream to downstream sediments. The biomass proportion of bacterial populations in the midstream sediment showed a significantly difference from that in the other sediments, suggesting that there may be an environmental pressure on the midstream bacterial community. Lorenz curves, together with Gini coefficients were successfully applied to the 2-DGE mapping data for resolving evenness of bacterial populations, and showed that the plotted curve from high-resolution 2-DGE mapping became less linear and more an exponential function than that of the 1-DGE methods such as chain length analysis and denaturing gradient gel electrophoresis, suggesting that the 2-DGE mapping may achieve a more detailed evaluation of bacterial community. In conclusion, the 2-DGE mapping combined with the selective primer pairs enables bacterial community structure analysis in river sediment and thus it can also monitor sediment pollution based on the change of bacterial community structure.

Composition and development of oral bacterial communities.

PubMed

Palmer, Robert J

2014-02-01

The oral bacterial microbiome encompasses approximately 700 commonly occurring phylotypes, approximately half of which can be present at any time in any individual. These bacteria are largely indigenous to the oral cavity; this limited habitat range suggests that interactions between the various phylotypes, and between the phylotypes and their environment, are crucial for their existence. Molecular cataloging has confirmed many basic observations on the composition of the oral microbiome that were formulated well before ribosomal RNA-based systematics, but the power and the scope of molecular taxonomy have resulted in the discovery of new phylotypes and, more importantly, have made possible a level of bacterial community analysis that was unachievable with classical methods. Bacterial community structure varies with location within the mouth, and changes in community structure are related to disease initiation and disease progression. Factors that influence the formation and the evolution of communities include selective adherence to epithelial or tooth surfaces, specific cell-to-cell binding as a driver of early community composition, and interorganismal interaction leading to alteration of the local environment, which represents the first step on the road to oral disease. A comprehensive understanding of how these factors interact to drive changes in the composition of the oral microbial community can lead to new strategies for the inhibition of periodontal diseases and dental caries. Published 2013. This article is a US Government work and is in the public domain in the USA.

Effects of remediation on the bacterial community of an acid mine drainage impacted stream.

PubMed

Ghosh, Suchismita; Moitra, Moumita; Woolverton, Christopher J; Leff, Laura G

2012-11-01

Acid mine drainage (AMD) represents a global threat to water resources, and as such, remediation of AMD-impacted streams is a common practice. During this study, we examined bacterial community structure and environmental conditions in a low-order AMD-impacted stream before, during, and after remediation. Bacterial community structure was examined via polymerase chain reaction amplification of 16S rRNA genes followed by denaturing gradient gel electrophoresis. Also, bacterial abundance and physicochemical data (including metal concentrations) were collected and relationships to bacterial community structure were determined using BIO-ENV analysis. Remediation of the study stream altered environmental conditions, including pH and concentrations of some metals, and consequently, the bacterial community changed. However, remediation did not necessarily restore the stream to conditions found in the unimpacted reference stream; for example, bacterial abundances and concentrations of some elements, such as sulfur, magnesium, and manganese, were different in the remediated stream than in the reference stream. BIO-ENV analysis revealed that changes in pH and iron concentration, associated with remediation, primarily explained temporal alterations in bacterial community structure. Although the sites sampled in the remediated stream were in relatively close proximity to each other, spatial variation in community composition suggests that differences in local environmental conditions may have large impacts on the microbial assemblage.

Restructuring of the Aquatic Bacterial Community by Hydric Dynamics Associated with Superstorm Sandy

PubMed Central

Ulrich, Nikea; Rosenberger, Abigail; Brislawn, Colin; Wright, Justin; Kessler, Collin; Toole, David; Solomon, Caroline; Strutt, Steven; McClure, Erin

2016-01-01

ABSTRACT Bacterial community composition and longitudinal fluctuations were monitored in a riverine system during and after Superstorm Sandy to better characterize inter- and intracommunity responses associated with the disturbance associated with a 100-year storm event. High-throughput sequencing of the 16S rRNA gene was used to assess microbial community structure within water samples from Muddy Creek Run, a second-order stream in Huntingdon, PA, at 12 different time points during the storm event (29 October to 3 November 2012) and under seasonally matched baseline conditions. High-throughput sequencing of the 16S rRNA gene was used to track changes in bacterial community structure and divergence during and after Superstorm Sandy. Bacterial community dynamics were correlated to measured physicochemical parameters and fecal indicator bacteria (FIB) concentrations. Bioinformatics analyses of 2.1 million 16S rRNA gene sequences revealed a significant increase in bacterial diversity in samples taken during peak discharge of the storm. Beta-diversity analyses revealed longitudinal shifts in the bacterial community structure. Successional changes were observed, in which Betaproteobacteria and Gammaproteobacteria decreased in 16S rRNA gene relative abundance, while the relative abundance of members of the Firmicutes increased. Furthermore, 16S rRNA gene sequences matching pathogenic bacteria, including strains of Legionella, Campylobacter, Arcobacter, and Helicobacter, as well as bacteria of fecal origin (e.g., Bacteroides), exhibited an increase in abundance after peak discharge of the storm. This study revealed a significant restructuring of in-stream bacterial community structure associated with hydric dynamics of a storm event. IMPORTANCE In order to better understand the microbial risks associated with freshwater environments during a storm event, a more comprehensive understanding of the variations in aquatic bacterial diversity is warranted. This study

Impact of disinfection on drinking water biofilm bacterial community.

PubMed

Mi, Zilong; Dai, Yu; Xie, Shuguang; Chen, Chao; Zhang, Xiaojian

2015-11-01

Disinfectants are commonly applied to control the growth of microorganisms in drinking water distribution systems. However, the effect of disinfection on drinking water microbial community remains poorly understood. The present study investigated the impacts of different disinfectants (chlorine and chloramine) and dosages on biofilm bacterial community in bench-scale pipe section reactors. Illumina MiSeq sequencing illustrated that disinfection strategy could affect both bacterial diversity and community structure of drinking water biofilm. Proteobacteria tended to predominate in chloraminated drinking water biofilms, while Firmicutes in chlorinated and unchlorinated biofilms. The major proteobacterial groups were influenced by both disinfectant type and dosage. In addition, chloramination had a more profound impact on bacterial community than chlorination. Copyright © 2015. Published by Elsevier B.V.

The development of permafrost bacterial communities under submarine conditions

NASA Astrophysics Data System (ADS)

Mitzscherling, Julia; Winkel, Matthias; Winterfeld, Maria; Horn, Fabian; Yang, Sizhong; Grigoriev, Mikhail N.; Wagner, Dirk; Overduin, Pier P.; Liebner, Susanne

2017-07-01

Submarine permafrost is more vulnerable to thawing than permafrost on land. Besides increased heat transfer from the ocean water, the penetration of salt lowers the freezing temperature and accelerates permafrost degradation. Microbial communities in thawing permafrost are expected to be stimulated by warming, but how they develop under submarine conditions is completely unknown. We used the unique records of two submarine permafrost cores from the Laptev Sea on the East Siberian Arctic Shelf, inundated about 540 and 2500 years ago, to trace how bacterial communities develop depending on duration of the marine influence and pore water chemistry. Combined with geochemical analysis, we quantified total cell numbers and bacterial gene copies and determined the community structure of bacteria using deep sequencing of the bacterial 16S rRNA gene. We show that submarine permafrost is an extreme habitat for microbial life deep below the seafloor with changing thermal and chemical conditions. Pore water chemistry revealed different pore water units reflecting the degree of marine influence and stages of permafrost thaw. Millennia after inundation by seawater, bacteria stratify into communities in permafrost, marine-affected permafrost, and seabed sediments. In contrast to pore water chemistry, the development of bacterial community structure, diversity, and abundance in submarine permafrost appears site specific, showing that both sedimentation and permafrost thaw histories strongly affect bacteria. Finally, highest microbial abundance was observed in the ice-bonded seawater unaffected but warmed permafrost of the longer inundated core, suggesting that permafrost bacterial communities exposed to submarine conditions start to proliferate millennia after warming.

Different bacterial communities in ectomycorrhizae and surrounding soil

PubMed Central

Vik, Unni; Logares, Ramiro; Blaalid, Rakel; Halvorsen, Rune; Carlsen, Tor; Bakke, Ingrid; Kolstø, Anne-Brit; Økstad, Ole Andreas; Kauserud, Håvard

2013-01-01

Several eukaryotic symbioses have shown to host a rich diversity of prokaryotes that interact with their hosts. Here, we study bacterial communities associated with ectomycorrhizal root systems of Bistorta vivipara compared to bacterial communities in bulk soil using pyrosequencing of 16S rRNA amplicons. A high richness of Operational Taxonomic Units (OTUs) was found in plant roots (3,571 OTUs) and surrounding soil (3,476 OTUs). The community composition differed markedly between these two environments. Actinobacteria, Armatimonadetes, Chloroflexi and OTUs unclassified at phylum level were significantly more abundant in plant roots than in soil. A large proportion of the OTUs, especially those in plant roots, presented low similarity to Sanger 16S rRNA reference sequences, suggesting novel bacterial diversity in ectomycorrhizae. Furthermore, the bacterial communities of the plant roots were spatially structured up to a distance of 60 cm, which may be explained by bacteria using fungal hyphae as a transport vector. The analyzed ectomycorrhizae presents a distinct microbiome, which likely influence the functioning of the plant-fungus symbiosis. PMID:24326907

Soil quality and bacterial community structure: a case study from the mediterranean region

NASA Astrophysics Data System (ADS)

Anguita-Maeso, Manuel; Miralles*, Isabel; Soriano**, Miguel; Ortega, Raúl; García-Salcedo, José Antonio; Sánchez-Marañon, Manuel

2017-04-01

Bacterial communities play a central role in innumerable processes and functions of soils such as decomposition of organic residues, nutrient cycling, aggregation, and formation of humic substances. We investigated the relationships between bacterial communities, soil profiles, and quality parameters in eight benchmark soils of the Mediterranean calcareous mountain sampled on a local scale. The diversity and composition of prokaryotic community was assessed by 16S rRNA gene amplicon pyrosequencing of DNA from samples of topsoil (10 x 10 x 0.2 m). The bacterial profile content resulted in the identification of groups belonging to 16 phyla and 75 genera. Two-dimensional models using multidimensional scaling (Stress < 0.11), correspondence analysis (Inertia > 71%), and principal component analysis (Variance > 60%) showed a decrease in the abundance of acidobacteria Gp4 and Gp3 while actinobacteria flourished with increasing soil profile development (from Leptosol to Luvisol). This can be attributed to inherent changes in soil quality along pedogenesis such as pH (8.3 to 7.8), organic C (20.0 to 45.2 Mg ha-1), macropososity (0.11 to 0.32 cm3 cm-3), and water stable aggregates (365.8 to 963.4 Mg ha-1). Actinobacteria genera like Aciditerrimonas, Nocardioides, and Solirubrobacter also displayed positive correlations (r > 0.90) with the content of clay and free Ferric forms. Other factors like Re-carbonation, loss of organic matter, and soil compaction probably caused by land use and management, led to a decline in the Chao1 richness and Shannon diversity indices (3625 and 6.3) with respect to native soils (7852 and 7.4). Likewise, Firmicutes and Gemmatimonadetes were tripled and the genera of Proteobacteria and Bacteroidetes decreased. Our data indicate that bacterial community structure depends largely on the soil quality status, both inherent and managed and suggest the bacterial group composition also follows the course of soil genesis. (*) Financial support by Marie

Streptomycin Application Has No Detectable Effect on Bacterial Community Structure in Apple Orchard Soil

PubMed Central

Shade, Ashley; Klimowicz, Amy K.; Spear, Russell N.; Linske, Matthew; Donato, Justin J.; Hogan, Clifford S.; McManus, Patricia S.

2013-01-01

Streptomycin is commonly used to control fire blight disease on apple trees. Although the practice has incited controversy, little is known about its nontarget effects in the environment. We investigated the impact of aerial application of streptomycin on nontarget bacterial communities in soil beneath streptomycin-treated and untreated trees in a commercial apple orchard. Soil samples were collected in two consecutive years at 4 or 10 days before spraying streptomycin and 8 or 9 days after the final spray. Three sources of microbial DNA were profiled using tag-pyrosequencing of 16S rRNA genes: uncultured bacteria from the soil (culture independent) and bacteria cultured on unamended or streptomycin-amended (15 μg/ml) media. Multivariate tests for differences in community structure, Shannon diversity, and Pielou's evenness test results showed no evidence of community response to streptomycin. The results indicate that use of streptomycin for disease management has minimal, if any, immediate effect on apple orchard soil bacterial communities. This study contributes to the profile of an agroecosystem in which antibiotic use for disease prevention appears to have minimal consequences for nontarget bacteria. PMID:23974143

Impacts of Long-Term Irrigation of Domestic Treated Wastewater on Soil Biogeochemistry and Bacterial Community Structure

PubMed Central

Wafula, Denis; White, John R.; Canion, Andy; Jagoe, Charles; Pathak, Ashish

2015-01-01

Freshwater scarcity and regulations on wastewater disposal have necessitated the reuse of treated wastewater (TWW) for soil irrigation, which has several environmental and economic benefits. However, TWW irrigation can cause nutrient loading to the receiving environments. We assessed bacterial community structure and associated biogeochemical changes in soil plots irrigated with nitrate-rich TWW (referred to as pivots) for periods ranging from 13 to 30 years. Soil cores (0 to 40 cm) were collected in summer and winter from five irrigated pivots and three adjacently located nonirrigated plots. Total bacterial and denitrifier gene abundances were estimated by quantitative PCR (qPCR), and community structure was assessed by 454 massively parallel tag sequencing (MPTS) of small-subunit (SSU) rRNA genes along with terminal restriction fragment length polymorphism (T-RFLP) analysis of nirK, nirS, and nosZ functional genes responsible for denitrification of the TWW-associated nitrate. Soil physicochemical analyses showed that, regardless of the seasons, pH and moisture contents (MC) were higher in the irrigated (IR) pivots than in the nonirrigated (NIR) plots; organic matter (OM) and microbial biomass carbon (MBC) were higher as a function of season but not of irrigation treatment. MPTS analysis showed that TWW loading resulted in the following: (i) an increase in the relative abundance of Proteobacteria, especially Betaproteobacteria and Gammaproteobacteria; (ii) a decrease in the relative abundance of Actinobacteria; (iii) shifts in the communities of acidobacterial groups, along with a shift in the nirK and nirS denitrifier guilds as shown by T-RFLP analysis. Additionally, bacterial biomass estimated by genus/group-specific real-time qPCR analyses revealed that higher numbers of total bacteria, Acidobacteria, Actinobacteria, Alphaproteobacteria, and the nirS denitrifier guilds were present in the IR pivots than in the NIR plots. Identification of the nir

Skin and fur bacterial diversity and community structure on American southwestern bats: effects of habitat, geography and bat traits

PubMed Central

Hathaway, Jennifer J.M.; Kimble, Jason C.; Buecher, Debbie C.; Valdez, Ernest W.; Young, Jesse M.; Read, Kaitlyn J.H.; Northup, Diana E.

2017-01-01

Microorganisms that reside on and in mammals, such as bats, have the potential to influence their host’s health and to provide defenses against invading pathogens. However, we have little understanding of the skin and fur bacterial microbiota on bats, or factors that influence the structure of these communities. The southwestern United States offers excellent sites for the study of external bat bacterial microbiota due to the diversity of bat species, the variety of abiotic and biotic factors that may govern bat bacterial microbiota communities, and the lack of the newly emergent fungal disease in bats, white-nose syndrome (WNS), in the southwest. To test these variables, we used 16S rRNA gene 454 pyrosequencing from swabs of external skin and fur surfaces from 163 bats from 13 species sampled from southeastern New Mexico to northwestern Arizona. Community similarity patterns, random forest models, and generalized linear mixed-effects models show that factors such as location (e.g., cave-caught versus surface-netted) and ecoregion are major contributors to the structure of bacterial communities on bats. Bats caught in caves had a distinct microbial community compared to those that were netted on the surface. Our results provide a first insight into the distribution of skin and fur bat bacteria in the WNS-free environment of New Mexico and Arizona. More importantly, it provides a baseline of bat external microbiota that can be explored for potential natural defenses against pathogens. PMID:29093998

Skin and fur bacterial diversity and community structure on American southwestern bats: effects of habitat, geography and bat traits.

PubMed

Winter, Ara S; Hathaway, Jennifer J M; Kimble, Jason C; Buecher, Debbie C; Valdez, Ernest W; Porras-Alfaro, Andrea; Young, Jesse M; Read, Kaitlyn J H; Northup, Diana E

2017-01-01

Microorganisms that reside on and in mammals, such as bats, have the potential to influence their host's health and to provide defenses against invading pathogens. However, we have little understanding of the skin and fur bacterial microbiota on bats, or factors that influence the structure of these communities. The southwestern United States offers excellent sites for the study of external bat bacterial microbiota due to the diversity of bat species, the variety of abiotic and biotic factors that may govern bat bacterial microbiota communities, and the lack of the newly emergent fungal disease in bats, white-nose syndrome (WNS), in the southwest. To test these variables, we used 16S rRNA gene 454 pyrosequencing from swabs of external skin and fur surfaces from 163 bats from 13 species sampled from southeastern New Mexico to northwestern Arizona. Community similarity patterns, random forest models, and generalized linear mixed-effects models show that factors such as location (e.g., cave-caught versus surface-netted) and ecoregion are major contributors to the structure of bacterial communities on bats. Bats caught in caves had a distinct microbial community compared to those that were netted on the surface. Our results provide a first insight into the distribution of skin and fur bat bacteria in the WNS-free environment of New Mexico and Arizona. More importantly, it provides a baseline of bat external microbiota that can be explored for potential natural defenses against pathogens.

Skin and fur bacterial diversity and community structure on American southwestern bats: effects of habitat, geography and bat traits

USGS Publications Warehouse

Winter, Ara S.; Hathaway, Jennifer J. M.; Kimble, Jason C.; Buecher, Debbie C.; Valdez, Ernest W.; Porras-Alfaro, Andrea; Young, Jesse M.; Read, Kaitlyn J. H.; Northup, Diana E.

2017-01-01

Microorganisms that reside on and in mammals, such as bats, have the potential to influence their host’s health and to provide defenses against invading pathogens. However, we have little understanding of the skin and fur bacterial microbiota on bats, or factors that influence the structure of these communities. The southwestern United States offers excellent sites for the study of external bat bacterial microbiota due to the diversity of bat species, the variety of abiotic and biotic factors that may govern bat bacterial microbiota communities, and the lack of the newly emergent fungal disease in bats, white-nose syndrome (WNS), in the southwest. To test these variables, we used 16S rRNA gene 454 pyrosequencing from swabs of external skin and fur surfaces from 163 bats from 13 species sampled from southeastern New Mexico to northwestern Arizona. Community similarity patterns, random forest models, and generalized linear mixed-effects models show that factors such as location (e.g., cave-caught versus surface-netted) and ecoregion are major contributors to the structure of bacterial communities on bats. Bats caught in caves had a distinct microbial community compared to those that were netted on the surface. Our results provide a first insight into the distribution of skin and fur bat bacteria in the WNS-free environment of New Mexico and Arizona. More importantly, it provides a baseline of bat external microbiota that can be explored for potential natural defenses against pathogens.

Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest

PubMed Central

Kembel, Steven W.; O’Connor, Timothy K.; Arnold, Holly K.; Hubbell, Stephen P.; Wright, S. Joseph; Green, Jessica L.

2014-01-01

The phyllosphere—the aerial surfaces of plants, including leaves—is a ubiquitous global habitat that harbors diverse bacterial communities. Phyllosphere bacterial communities have the potential to influence plant biogeography and ecosystem function through their influence on the fitness and function of their hosts, but the host attributes that drive community assembly in the phyllosphere are poorly understood. In this study we used high-throughput sequencing to quantify bacterial community structure on the leaves of 57 tree species in a neotropical forest in Panama. We tested for relationships between bacterial communities on tree leaves and the functional traits, taxonomy, and phylogeny of their plant hosts. Bacterial communities on tropical tree leaves were diverse; leaves from individual trees were host to more than 400 bacterial taxa. Bacterial communities in the phyllosphere were dominated by a core microbiome of taxa including Actinobacteria, Alpha-, Beta-, and Gammaproteobacteria, and Sphingobacteria. Host attributes including plant taxonomic identity, phylogeny, growth and mortality rates, wood density, leaf mass per area, and leaf nitrogen and phosphorous concentrations were correlated with bacterial community structure on leaves. The relative abundances of several bacterial taxa were correlated with suites of host plant traits related to major axes of plant trait variation, including the leaf economics spectrum and the wood density–growth/mortality tradeoff. These correlations between phyllosphere bacterial diversity and host growth, mortality, and function suggest that incorporating information on plant–microbe associations will improve our ability to understand plant functional biogeography and the drivers of variation in plant and ecosystem function. PMID:25225376

Soil-Borne Bacterial Structure and Diversity Does Not Reflect Community Activity in Pampa Biome

PubMed Central

Lupatini, Manoeli; Suleiman, Afnan Khalil Ahmad; Jacques, Rodrigo Josemar Seminoti; Antoniolli, Zaida Inês; Kuramae, Eiko Eurya; de Oliveira Camargo, Flávio Anastácio; Roesch, Luiz Fernando Würdig

2013-01-01

The Pampa biome is considered one of the main hotspots of the world’s biodiversity and it is estimated that half of its original vegetation was removed and converted to agricultural land and tree plantations. Although an increasing amount of knowledge is being assembled regarding the response of soil bacterial communities to land use change, to the associated plant community and to soil properties, our understanding about how these interactions affect the microbial community from the Brazilian Pampa is still poor and incomplete. In this study, we hypothesized that the same soil type from the same geographic region but under distinct land use present dissimilar soil bacterial communities. To test this hypothesis, we assessed the soil bacterial communities from four land-uses within the same soil type by 454-pyrosequencing of 16S rRNA gene and by soil microbial activity analyzes. We found that the same soil type under different land uses harbor similar (but not equal) bacterial communities and the differences were controlled by many microbial taxa. No differences regarding diversity and richness between natural areas and areas under anthropogenic disturbance were detected. However, the measures of microbial activity did not converge with the 16S rRNA data supporting the idea that the coupling between functioning and composition of bacterial communities is not necessarily correlated. PMID:24146873

Soil-borne bacterial structure and diversity does not reflect community activity in Pampa biome.

PubMed

Lupatini, Manoeli; Suleiman, Afnan Khalil Ahmad; Jacques, Rodrigo Josemar Seminoti; Antoniolli, Zaida Inês; Kuramae, Eiko Eurya; de Oliveira Camargo, Flávio Anastácio; Roesch, Luiz Fernando Würdig

2013-01-01

The Pampa biome is considered one of the main hotspots of the world's biodiversity and it is estimated that half of its original vegetation was removed and converted to agricultural land and tree plantations. Although an increasing amount of knowledge is being assembled regarding the response of soil bacterial communities to land use change, to the associated plant community and to soil properties, our understanding about how these interactions affect the microbial community from the Brazilian Pampa is still poor and incomplete. In this study, we hypothesized that the same soil type from the same geographic region but under distinct land use present dissimilar soil bacterial communities. To test this hypothesis, we assessed the soil bacterial communities from four land-uses within the same soil type by 454-pyrosequencing of 16S rRNA gene and by soil microbial activity analyzes. We found that the same soil type under different land uses harbor similar (but not equal) bacterial communities and the differences were controlled by many microbial taxa. No differences regarding diversity and richness between natural areas and areas under anthropogenic disturbance were detected. However, the measures of microbial activity did not converge with the 16S rRNA data supporting the idea that the coupling between functioning and composition of bacterial communities is not necessarily correlated.

Comparative Analysis of Bacterial Community Composition and Structure in Clinically Symptomatic and Asymptomatic Central Venous Catheters

PubMed Central

Stressmann, Franziska A.; Couve-Deacon, Elodie; Chainier, Delphine; Chauhan, Ashwini; Wessel, Aimee; Durand-Fontanier, Sylvaine; Escande, Marie-Christine; Kriegel, Irène; Francois, Bruno; Ploy, Marie-Cécile

2017-01-01

ABSTRACT Totally implanted venous access ports (TIVAPs) are commonly used catheters for the management of acute or chronic pathologies. Although these devices improve health care, repeated use of this type of device for venous access over long periods of time is also associated with risk of colonization and infection by pathogenic bacteria, often originating from skin. However, although the skin microbiota is composed of both pathogenic and nonpathogenic bacteria, the extent and the consequences of TIVAP colonization by nonpathogenic bacteria have rarely been studied. Here, we used culture-dependent and 16S rRNA gene-based culture-independent approaches to identify differences in bacterial colonization of TIVAPs obtained from two French hospitals. To explore the relationships between nonpathogenic organisms colonizing TIVAPs and the potential risk of infection, we analyzed the bacterial community parameters between TIVAPs suspected (symptomatic) or not (asymptomatic) of infection. Although we did not find a particular species assemblage or community marker to distinguish infection risk on an individual sample level, we identified differences in bacterial community composition, diversity, and structure between clinically symptomatic and asymptomatic TIVAPs that could be explored further. This study therefore provides a new view of bacterial communities and colonization patterns in intravascular TIVAPs and suggests that microbial ecology approaches could improve our understanding of device-associated infections and could be a prognostic tool to monitor the evolution of bacterial communities in implants and their potential susceptibility to infections. IMPORTANCE Totally implanted venous access ports (TIVAPs) are commonly used implants for the management of acute or chronic pathologies. Although their use improves the patient’s health care and quality of life, they are associated with a risk of infection and subsequent clinical complications, often leading to

Variation of nonylphenol-degrading gene abundance and bacterial community structure in bioaugmented sediment microcosm.

PubMed

Wang, Zhao; Yang, Yuyin; Sun, Weimin; Dai, Yu; Xie, Shuguang

2015-02-01

Nonylphenol (NP) can accumulate in river sediment. Bioaugmentation is an attractive option to dissipate heavy NP pollution in river sediment. In this study, two NP degraders were isolated from crude oil-polluted soil and river sediment. Microcosms were constructed to test their ability to degrade NP in river sediment. The shift in the proportion of NP-degrading genes and bacterial community structure in sediment microcosms were characterized using quantitative PCR assay and terminal restriction fragment length polymorphism analysis, respectively. Phylogenetic analysis indicated that the soil isolate belonged to genus Stenotrophomonas, while the sediment isolate was a Sphingobium species. Both of them could almost completely clean up a high level of NP in river sediment (150 mg/kg NP) in 10 or 14 days after inoculation. An increase in the proportion of alkB and sMO genes was observed in sediment microcosms inoculated with Stenotrophomonas strain Y1 and Sphingobium strain Y2, respectively. Moreover, bioaugmentation using Sphingobium strain Y2 could have a strong impact on sediment bacterial community structure, while inoculation of Stenotrophomonas strain Y1 illustrated a weak impact. This study can provide some new insights towards NP biodegradation and bioremediation.

Bacterial Communities in the Groundwater of Xikuangshan Antimony Mine, China

NASA Astrophysics Data System (ADS)

Wu, M.; Wang, H.; Wang, N.; Wang, M.

2017-12-01

Xikuangshan (XKS) is the biggest antimony (Sb) mine around the word, which causes serious environmental contamination due to the mining actives. To fully understand the bacterial compositions in the groundwater around the mining area in XKS and their correlation with environmental factors, groundwater samples were collected and subject to 16S rDNA high throughput sequencing. Results indicated that Proteobacteria (especially Gamma-Proteobacteria) dominated bacterial communities in high-Sb groundwater samples, whereas Bacteroidetes predominated in low-Sb groundwater. Furthermore, antimony concentration was found to be the most significant factor shaping bacterial communities (P=0.002) with an explanation of 9.16% of the variation. Other factors such as pH, contents of Mg, Ca and orthophosphate were also observed to significantly correlate with bacterial communities. This was the first report to show the important impact of Sb concentration on bacterial community structure in the groundwater in the mining area. Our results will enhance the understanding of subsurface biogeochemical processes mediated by microbes.

Bacterial community structure and diversity responses to the direct revegetation of an artisanal zinc smelting slag after 5 years.

PubMed

Luo, Youfa; Wu, Yonggui; Wang, Hu; Xing, Rongrong; Zheng, Zhilin; Qiu, Jing; Yang, Lian

2018-05-01

This comparative field study examined the responses of bacterial community structure and diversity to the revegetation of zinc (Zn) smelting waste slag with eight plant species after 5 years. The microbial community structure of waste slag with and without vegetation was evaluated using high-throughput sequencing. The physiochemical properties of Zn smelting slag after revegetation with eight plant rhizospheres for 5 years were improved compared to those of bulk slag. Revegetation significantly increased the microbial community diversity in plant rhizospheres, and at the phylum level, Proteobacteria, Acidobacteria, and Bacteroidetes were notably more abundant in rhizosphere slags than those in bulk waste slag. Additionally, revegetation increased the relative abundance of plant growth-promoting rhizobacteria such as Flavobacterium, Streptomyces, and Arthrobacter as well as symbiotic N 2 fixers such as Bradyrhizobium. Three dominant native plant species (Arundo donax, Broussonetia papyrifera, and Robinia pseudoacacia) greatly increased the quality of the rhizosphere slags. Canonical correspondence analysis showed that the differences in bacterial community structure between the bulk and rhizosphere slags were explained by slag properties, i.e., pH, available copper (Cu) and lead (Pb), moisture, available nitrogen (N), phosphorus (P), and potassium (K), and organic matter (OM); however, available Zn and cadmium (Cd) contents were the slag parameters that best explained the differences between the rhizosphere communities of the eight plant species. The results suggested that revegetation plays an important role in enhancing bacterial community abundance and diversity in rhizosphere slags and that revegetation may also regulate microbiological properties and diversity mainly through changes in heavy metal bioavailability and physiochemical slag characteristics.

Effects of farmhouse hotel and paper mill effluents on bacterial community structures in sediment and surface water of Nanxi River, China.

PubMed

Lu, Xiao-Ming; Lu, Peng-Zhen

2014-11-01

The pyrosequencing technique was used to evaluate bacterial community structures in sediment and surface water samples taken from Nanxi River receiving effluents from a paper mill and a farmhouse hotel, respectively. For each sample, 4,610 effective bacterial sequences were selected and used to do the analysis of diversity and abundance, respectively. Bacterial phylotype richness in the sediment sample without effluent input was higher than the other samples, and the surface water sample with addition of effluent from the paper mill contained the least richness. Effluents from both the paper mill and farmhouse hotel have a potential to reduce the bacterial diversity and abundance in the sediment and surface water, especially it is more significant in the sediment. The effect of the paper mill effluent on the sediment and surface water bacterial communities was more serious than that of the farmhouse hotel effluent. Characterization of microbial community structures in the sediment and surface water from two tributaries of the downstream river indicated that various effluents from the paper mill and farmhouse hotel have the similar potential to decrease the natural variability in riverine microbial ecosystems.

Forest strata drive spatial structure of bacterial and archaeal communities and microbial methane cycling in neotropical bromeliad wetlands

NASA Astrophysics Data System (ADS)

Martinson, Guntars; Brandt, Franziska; Conrad, Ralf

2016-04-01

, and their constrained environmental characteristics shape the spatial structure of archaeal and bacterial communities and microbial methane cycling in neotropical bromeliad wetlands.

Bacterial Community Structure Shifted by Geosmin in Granular Activated Carbon System of Water Treatment Plants.

PubMed

Pham, Ngoc Dung; Lee, Eun-Hee; Chae, Seon-Ha; Cho, Yongdeok; Shin, Hyejin; Son, Ahjeong

2016-01-01

We investigated the relation between the presence of geosmin in water and the bacterial community structure within the granular activated carbon (GAC) system of water treatment plants in South Korea. GAC samples were collected in May and August of 2014 at three water treatment plants (Sungnam, Koyang, and Yeoncho in Korea). Dissolved organic carbon and geosmin were analyzed before and after GAC treatment. Geosmin was found in raw water from Sungnam and Koyang water treatment plants but not in that from Yeoncho water treatment plant. Interestingly, but not surprisingly, the 16S rRNA clone library indicated that the bacterial communities from the Sungnam and Koyang GAC systems were closely related to geosmin-degrading bacteria. Based on the phylogenetic tree and multidimensional scaling plot, bacterial clones from GAC under the influence of geosmin were clustered with Variovorax paradoxus strain DB 9b and Comamonas sp. DB mg. In other words, the presence of geosmin in water might have inevitably contributed to the growth of geosmin degraders within the respective GAC system.

Complexity of Bacterial Communities in a River-Floodplain System (Danube, Austria)

PubMed Central

Besemer, Katharina; Moeseneder, Markus M.; Arrieta, Jesus M.; Herndl, Gerhard J.; Peduzzi, Peter

2005-01-01

Natural floodplains play an essential role in the processing and decomposition of organic matter and in the self-purification ability of rivers, largely due to the activity of bacteria. Knowledge about the composition of bacterial communities and its impact on organic-matter cycling is crucial for the understanding of ecological processes in river-floodplain systems. Particle-associated and free-living bacterial assemblages from the Danube River and various floodplain pools with different hydrological characteristics were investigated using terminal restriction fragment length polymorphism analysis. The particle-associated bacterial community exhibited a higher number of operational taxonomic units (OTUs) and was more heterogeneous in time and space than the free-living community. The temporal dynamics of the community structure were generally higher in isolated floodplain pools. The community structures of the river and the various floodplain pools, as well as those of the particle-associated and free-living bacteria, differed significantly. The compositional dynamics of the planktonic bacterial communities were related to changes in the algal biomass, temperature, and concentrations of organic and inorganic nutrients. The OTU richness of the free-living community was correlated with the concentration and origin of organic matter and the concentration of inorganic nutrients, while no correlation with the OTU richness of the particle-associated assemblage was found. Our results demonstrate the importance of the river-floodplain interactions and the influence of damming and regulation on the bacterial-community composition. PMID:15691909

A geostatistical analysis of small-scale spatial variability in bacterial abundance and community structure in salt marsh creek bank sediments

NASA Technical Reports Server (NTRS)

Franklin, Rima B.; Blum, Linda K.; McComb, Alison C.; Mills, Aaron L.

2002-01-01

Small-scale variations in bacterial abundance and community structure were examined in salt marsh sediments from Virginia's eastern shore. Samples were collected at 5 cm intervals (horizontally) along a 50 cm elevation gradient, over a 215 cm horizontal transect. For each sample, bacterial abundance was determined using acridine orange direct counts and community structure was analyzed using randomly amplified polymorphic DNA fingerprinting of whole-community DNA extracts. A geostatistical analysis was used to determine the degree of spatial autocorrelation among the samples, for each variable and each direction (horizontal and vertical). The proportion of variance in bacterial abundance that could be accounted for by the spatial model was quite high (vertical: 60%, horizontal: 73%); significant autocorrelation was found among samples separated by 25 cm in the vertical direction and up to 115 cm horizontally. In contrast, most of the variability in community structure was not accounted for by simply considering the spatial separation of samples (vertical: 11%, horizontal: 22%), and must reflect variability from other parameters (e.g., variation at other spatial scales, experimental error, or environmental heterogeneity). Microbial community patch size based upon overall similarity in community structure varied between 17 cm (vertical) and 35 cm (horizontal). Overall, variability due to horizontal position (distance from the creek bank) was much smaller than that due to vertical position (elevation) for both community properties assayed. This suggests that processes more correlated with elevation (e.g., drainage and redox potential) vary at a smaller scale (therefore producing smaller patch sizes) than processes controlled by distance from the creek bank. c2002 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.

Land-use changes influence soil bacterial communities in a meadow grassland in Northeast China

NASA Astrophysics Data System (ADS)

Cao, Chengyou; Zhang, Ying; Qian, Wei; Liang, Caiping; Wang, Congmin; Tao, Shuang

2017-10-01

The conversion of natural grassland into agricultural fields is an intensive anthropogenic perturbation commonly occurring in semiarid regions, and this perturbation strongly affects soil microbiota. In this study, the influences of land-use conversion on the soil properties and bacterial communities in the Horqin Grasslands in Northeast China were assessed. This study aimed to investigate (1) how the abundances of soil bacteria changed across land-use types, (2) how the structure of the soil bacterial community was altered in each land-use type, and (3) how these variations were correlated with soil physical and chemical properties. Variations in the diversities and compositions of bacterial communities and the relative abundances of dominant taxa were detected in four distinct land-use systems, namely, natural meadow grassland, paddy field, upland field, and poplar plantation, through the high-throughput Illumina MiSeq sequencing technique. The results indicated that land-use changes primarily affected the soil physical and chemical properties and bacterial community structure. Soil properties, namely, organic matter, pH, total N, total P, available N and P, and microbial biomass C, N, and P, influenced the bacterial community structure. The dominant phyla and genera were almost the same among the land-use types, but their relative abundances were significantly different. The effects of land-use changes on the structure of soil bacterial communities were more quantitative than qualitative.

Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments.

PubMed

Rocha, Lidianne L; Colares, Geórgia B; Nogueira, Vanessa L R; Paes, Fernanda A; Melo, Vânia M M

2016-01-01

We investigated the relationship among environmental variables, composition, and structure of bacterial communities in different habitats in a mangrove located nearby to an oil exploitation area, aiming to retrieve the natural pattern of bacterial communities in this ecosystem. The T-RFLP analysis showed a high diversity of bacterial populations and an increase in the bacterial richness from habitats closer to the sea and without vegetation (S1) to habitats covered by Avicennia schaueriana (S2) and Rhizophora mangle (S3). Environmental variables in S1 and S2 were more similar than in S3; however, when comparing the bacterial compositions, S2 and S3 shared more OTUs between them, suggesting that the presence of vegetation is an important factor in shaping these bacterial communities. In silico analyses of the fragments revealed a high diversity of the class Gammaproteobacteria in the 3 sites, although in general they presented quite different bacterial composition, which is probably shaped by the specificities of each habitat. This study shows that microhabitats inside of a mangrove ecosystem harbor diverse and distinct microbiota, reinforcing the need to conserve these ecosystems as a whole.

Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments

PubMed Central

Rocha, Lidianne L.; Colares, Geórgia B.; Nogueira, Vanessa L. R.; Paes, Fernanda A.; Melo, Vânia M. M.

2016-01-01

We investigated the relationship among environmental variables, composition, and structure of bacterial communities in different habitats in a mangrove located nearby to an oil exploitation area, aiming to retrieve the natural pattern of bacterial communities in this ecosystem. The T-RFLP analysis showed a high diversity of bacterial populations and an increase in the bacterial richness from habitats closer to the sea and without vegetation (S1) to habitats covered by Avicennia schaueriana (S2) and Rhizophora mangle (S3). Environmental variables in S1 and S2 were more similar than in S3; however, when comparing the bacterial compositions, S2 and S3 shared more OTUs between them, suggesting that the presence of vegetation is an important factor in shaping these bacterial communities. In silico analyses of the fragments revealed a high diversity of the class Gammaproteobacteria in the 3 sites, although in general they presented quite different bacterial composition, which is probably shaped by the specificities of each habitat. This study shows that microhabitats inside of a mangrove ecosystem harbor diverse and distinct microbiota, reinforcing the need to conserve these ecosystems as a whole. PMID:26989418

Response of bacterial community structure and function to experimental rainwater additions in a coastal eutrophic embayment

NASA Astrophysics Data System (ADS)

Teira, Eva; Hernando-Morales, Víctor; Martínez-García, Sandra; Figueiras, Francisco G.; Arbones, Belén; Álvarez-Salgado, Xosé Antón

2013-03-01

Although recognized as a potentially important source of both inorganic and organic nutrients, the impact of rainwater on microbial populations from marine planktonic systems has been poorly assessed. The effect of rainwater additions on bacterioplankton metabolism and community composition was evaluated in microcosm experiments enclosing natural marine plankton populations from the Ría de Vigo (NW Spain). The experiments were conducted during three different seasons (spring, autumn and winter) using rainwater collected at three different locations: marine, urban and rural sites. Bacterial abundance and production significantly increased up to 1.3 and 1.8-fold, respectively, after urban rainwater additions in spring, when ambient nutrient concentration was very low. Overall, the increments in bacterial production were higher than those in bacterial respiration, which implies that a higher proportion of carbon consumed by bacteria would be available to higher trophic levels. The response of the different bacterial groups to distinct rainwater types differed between seasons. The most responsive bacterial groups were Betaproteobacteria which significantly increased their abundance after urban (in spring and winter) and marine (in spring) rainwater additions, and Bacteroidetes which positively responded to all rainwater treatments in spring and to urban rainwater in autumn. Gammaproteobacteria and Roseobacter responded only to urban (in spring) and marine (in winter) rainwater treatment, respectively. The responses to rainwater additions were moderate and transient, and the resulting bacterial community structure was not importantly altered.

Responses of bacterial community structure and denitrifying bacteria in biofilm to submerged macrophytes and nitrate

NASA Astrophysics Data System (ADS)

Zhang, Songhe; Pang, Si; Wang, Peifang; Wang, Chao; Guo, Chuan; Addo, Felix Gyawu; Li, Yi

2016-10-01

Submerged macrophytes play important roles in constructed wetlands and natural water bodies, as these organisms remove nutrients and provide large surfaces for biofilms, which are beneficial for nitrogen removal, particularly from submerged macrophyte-dominated water columns. However, information on the responses of biofilms to submerged macrophytes and nitrogen molecules is limited. In the present study, bacterial community structure and denitrifiers were investigated in biofilms on the leaves of four submerged macrophytes and artificial plants exposed to two nitrate concentrations. The biofilm cells were evenly distributed on artificial plants but appeared in microcolonies on the surfaces of submerged macrophytes. Proteobacteria was the most abundant phylum in all samples, accounting for 27.3-64.8% of the high-quality bacterial reads, followed by Chloroflexi (3.7-25.4%), Firmicutes (3.0-20.1%), Acidobacteria (2.7-15.7%), Actinobacteria (2.2-8.7%), Bacteroidetes (0.5-9.7%), and Verrucomicrobia (2.4-5.2%). Cluster analysis showed that bacterial community structure can be significantly different on macrophytes versus from those on artificial plants. Redundancy analysis showed that electrical conductivity and nitrate concentration were positively correlated with Shannon index and operational taxonomic unit (OTU) richness (log10 transformed) but somewhat negatively correlated with microbial density. The relative abundances of five denitrifying genes were positively correlated with nitrate concentration and electrical conductivity but negatively correlated with dissolved oxygen.

Panamanian frog species host unique skin bacterial communities

PubMed Central

Belden, Lisa K.; Hughey, Myra C.; Rebollar, Eria A.; Umile, Thomas P.; Loftus, Stephen C.; Burzynski, Elizabeth A.; Minbiole, Kevin P. C.; House, Leanna L.; Jensen, Roderick V.; Becker, Matthew H.; Walke, Jenifer B.; Medina, Daniel; Ibáñez, Roberto; Harris, Reid N.

2015-01-01

Vertebrates, including amphibians, host diverse symbiotic microbes that contribute to host disease resistance. Globally, and especially in montane tropical systems, many amphibian species are threatened by a chytrid fungus, Batrachochytrium dendrobatidis (Bd), that causes a lethal skin disease. Bd therefore may be a strong selective agent on the diversity and function of the microbial communities inhabiting amphibian skin. In Panamá, amphibian population declines and the spread of Bd have been tracked. In 2012, we completed a field survey in Panamá to examine frog skin microbiota in the context of Bd infection. We focused on three frog species and collected two skin swabs per frog from a total of 136 frogs across four sites that varied from west to east in the time since Bd arrival. One swab was used to assess bacterial community structure using 16S rRNA amplicon sequencing and to determine Bd infection status, and one was used to assess metabolite diversity, as the bacterial production of anti-fungal metabolites is an important disease resistance function. The skin microbiota of the three Panamanian frog species differed in OTU (operational taxonomic unit, ~bacterial species) community composition and metabolite profiles, although the pattern was less strong for the metabolites. Comparisons between frog skin bacterial communities from Panamá and the US suggest broad similarities at the phylum level, but key differences at lower taxonomic levels. In our field survey in Panamá, across all four sites, only 35 individuals (~26%) were Bd infected. There was no clustering of OTUs or metabolite profiles based on Bd infection status and no clear pattern of west-east changes in OTUs or metabolite profiles across the four sites. Overall, our field survey data suggest that different bacterial communities might be producing broadly similar sets of metabolites across frog hosts and sites. Community structure and function may not be as tightly coupled in these skin symbiont

Linking bacterial community structure to advection and environmental impact along a coast-fjord gradient of the Sognefjord, western Norway

NASA Astrophysics Data System (ADS)

Storesund, Julia E.; Sandaa, Ruth-Anne; Thingstad, T. Frede; Asplin, Lars; Albretsen, Jon; Erga, Svein Rune

2017-12-01

Here we present novel data on bacterial assemblages along a coast-fjord gradient in the Sognefjord, the deepest (1308 m) and longest (205 km) ice-free fjord in the world. Data were collected on two cruises, one in November 2012, and one in May 2013. Special focus was on the impact of advective processes and how these are reflected in the autochthonous and allochthonous fractions of the bacterial communities. Both in November and May bacterial community composition, determined by Automated Ribosomal Intergenic Spacer Analyses (ARISA), in the surface and intermediate water appeared to be highly related to bacterial communities originating from freshwater runoff and coastal water, whereas the sources in the basin water were mostly unknown. Additionally, the inner part of the Sognefjord was more influenced by side-fjords than the outer part, and changes in bacterial community structure along the coast-fjord gradient generally showed higher correlation with environmental variables than with geographic distances. High resolution model simulations indicated a surprisingly high degree of temporal and spatial variation in both current speed and direction. This led to a more episodic/discontinuous horizontal current pattern, with several vortices (10-20 km wide) being formed from time to time along the fjord. We conclude that during periods of strong wind forcing, advection led to allochthonous species being introduced to the surface and intermediate layers of the fjord, and also appeared to homogenize community composition in the basin water. We also expect vortices to be active mixing zones where inflowing bacterial populations on the southern side of the fjord are mixed with the outflowing populations on the northern side. On average, retention time of the fjord water was sufficient for bacterial communities to be established.

Bacterial Community Dynamics in Dichloromethane-Contaminated Groundwater Undergoing Natural Attenuation

PubMed Central

Wright, Justin; Kirchner, Veronica; Bernard, William; Ulrich, Nikea; McLimans, Christopher; Campa, Maria F.; Hazen, Terry; Macbeth, Tamzen; Marabello, David; McDermott, Jacob; Mackelprang, Rachel; Roth, Kimberly; Lamendella, Regina

2017-01-01

The uncontrolled release of the industrial solvent methylene chloride, also known as dichloromethane (DCM), has resulted in widespread groundwater contamination in the United States. Here we investigate the role of groundwater bacterial communities in the natural attenuation of DCM at an undisclosed manufacturing site in New Jersey. This study investigates the bacterial community structure of groundwater samples differentially contaminated with DCM to better understand the biodegradation potential of these autochthonous bacterial communities. Bacterial community analysis was completed using high-throughput sequencing of the 16S rRNA gene of groundwater samples (n = 26) with DCM contamination ranging from 0.89 to 9,800,000 μg/L. Significant DCM concentration-driven shifts in overall bacterial community structure were identified between samples, including an increase in the abundance of Firmicutes within the most contaminated samples. Across all samples, a total of 6,134 unique operational taxonomic units (OTUs) were identified, with 16 taxa having strong correlations with increased DCM concentration. Putative DCM degraders such as Pseudomonas, Dehalobacterium and Desulfovibrio were present within groundwater across all levels of DCM contamination. Interestingly, each of these taxa dominated specific DCM contamination ranges respectively. Potential DCM degrading lineages yet to be cited specifically as a DCM degrading organisms, such as the Desulfosporosinus, thrived within the most heavily contaminated groundwater samples. Co-occurrence network analysis revealed aerobic and anaerobic bacterial taxa with DCM-degrading potential were present at the study site. Our 16S rRNA gene survey serves as the first in situ bacterial community assessment of contaminated groundwater harboring DCM concentrations ranging over seven orders of magnitude. Diversity analyses revealed known as well as potentially novel DCM degrading taxa within defined DCM concentration ranges

Bacterial Community Dynamics in Dichloromethane-Contaminated Groundwater Undergoing Natural Attenuation

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

Wright, Justin; Kirchner, Veronica; Bernard, William

The uncontrolled release of the industrial solvent methylene chloride, also known as dichloromethane (DCM), has resulted in widespread groundwater contamination in the United States. Here we investigate the role of groundwater bacterial communities in the natural attenuation of DCM at an undisclosed manufacturing site in New Jersey. Here, we investigate the bacterial community structure of groundwater samples differentially contaminated with DCM to better understand the biodegradation potential of these autochthonous bacterial communities. Bacterial community analysis was completed using high-throughput sequencing of the 16S rRNA gene of groundwater samples (n = 26) with DCM contamination ranging from 0.89 to 9,800,000 μg/L.more » Significant DCM concentration-driven shifts in overall bacterial community structure were identified between samples, including an increase in the abundance of Firmicutes within the most contaminated samples. And across all samples, a total of 6,134 unique operational taxonomic units (OTUs) were identified, with 16 taxa having strong correlations with increased DCM concentration. Putative DCM degraders such as Pseudomonas, Dehalobacterium and Desulfovibrio were present within groundwater across all levels of DCM contamination. Interestingly, each of these taxa dominated specific DCM contamination ranges respectively. Potential DCM degrading lineages yet to be cited specifically as a DCM degrading organisms, such as the Desulfosporosinus, thrived within the most heavily contaminated groundwater samples. Co-occurrence network analysis revealed aerobic and anaerobic bacterial taxa with DCM-degrading potential were present at the study site. Our 16S rRNA gene survey serves as the first in situ bacterial community assessment of contaminated groundwater harboring DCM concentrations ranging over seven orders of magnitude. Diversity analyses revealed known as well as potentially novel DCM degrading taxa within defined DCM concentration ranges

Bacterial Community Dynamics in Dichloromethane-Contaminated Groundwater Undergoing Natural Attenuation

DOE PAGES

Wright, Justin; Kirchner, Veronica; Bernard, William; ...

2017-11-22

The uncontrolled release of the industrial solvent methylene chloride, also known as dichloromethane (DCM), has resulted in widespread groundwater contamination in the United States. Here we investigate the role of groundwater bacterial communities in the natural attenuation of DCM at an undisclosed manufacturing site in New Jersey. Here, we investigate the bacterial community structure of groundwater samples differentially contaminated with DCM to better understand the biodegradation potential of these autochthonous bacterial communities. Bacterial community analysis was completed using high-throughput sequencing of the 16S rRNA gene of groundwater samples (n = 26) with DCM contamination ranging from 0.89 to 9,800,000 μg/L.more » Significant DCM concentration-driven shifts in overall bacterial community structure were identified between samples, including an increase in the abundance of Firmicutes within the most contaminated samples. And across all samples, a total of 6,134 unique operational taxonomic units (OTUs) were identified, with 16 taxa having strong correlations with increased DCM concentration. Putative DCM degraders such as Pseudomonas, Dehalobacterium and Desulfovibrio were present within groundwater across all levels of DCM contamination. Interestingly, each of these taxa dominated specific DCM contamination ranges respectively. Potential DCM degrading lineages yet to be cited specifically as a DCM degrading organisms, such as the Desulfosporosinus, thrived within the most heavily contaminated groundwater samples. Co-occurrence network analysis revealed aerobic and anaerobic bacterial taxa with DCM-degrading potential were present at the study site. Our 16S rRNA gene survey serves as the first in situ bacterial community assessment of contaminated groundwater harboring DCM concentrations ranging over seven orders of magnitude. Diversity analyses revealed known as well as potentially novel DCM degrading taxa within defined DCM concentration ranges

Bacterial community structure in experimental methanogenic bioreactors and search for pathogenic clostridia as community members.

PubMed

Dohrmann, Anja B; Baumert, Susann; Klingebiel, Lars; Weiland, Peter; Tebbe, Christoph C

2011-03-01

Microbial conversion of organic waste or harvested plant material into biogas has become an attractive technology for energy production. Biogas is produced in reactors under anaerobic conditions by a consortium of microorganisms which commonly include bacteria of the genus Clostridium. Since the genus Clostridium also harbors some highly pathogenic members in its phylogenetic cluster I, there has been some concern that an unintended growth of such pathogens might occur during the fermentation process. Therefore this study aimed to follow how process parameters affect the diversity of Bacteria in general, and the diversity of Clostridium cluster I members in particular. The development of both communities was followed in model biogas reactors from start-up during stable methanogenic conditions. The biogas reactors were run with either cattle or pig manures as substrates, and both were operated at mesophilic and thermophilic conditions. The structural diversity was analyzed independent of cultivation using a PCR-based detection of 16S rRNA genes and genetic profiling by single-strand conformation polymorphism (SSCP). Genetic profiles indicated that both bacterial and clostridial communities evolved in parallel, and the community structures were highly influenced by both substrate and temperature. Sequence analysis of 16S rRNA genes recovered from prominent bands from SSCP profiles representing Clostridia detected no pathogenic species. Thus, this study gave no indication that pathogenic clostridia would be enriched as dominant community members in biogas reactors fed with manure.

Bacterial community composition and structure in an Urban River impacted by different pollutant sources.

PubMed

Ibekwe, A Mark; Ma, Jincai; Murinda, Shelton E

2016-10-01

Microbial communities in terrestrial fresh water are diverse and dynamic in composition due to different environmental factors. The goal of this study was to undertake a comprehensive analysis of bacterial composition along different rivers and creeks and correlate these to land-use practices and pollutant sources. Here we used 454 pyrosequencing to determine the total bacterial community composition, and bacterial communities that are potentially of fecal origin, and of relevance to water quality assessment. The results were analyzed using UniFrac coupled with principal coordinate analysis (PCoA) to compare diversity, abundance, and community composition. Detrended correspondence analysis (DCA) and canonical correspondence analysis (CCA) were used to correlate bacterial composition in streams and creeks to different environmental parameters impacting bacterial communities in the sediment and surface water within the watershed. Bacteria were dominated by the phyla Proteobacteria, Bacteroidetes, Acidobacteria, and Actinobacteria, with Bacteroidetes significantly (P<0.001) higher in all water samples than sediment, where as Acidobacteria and Actinobacteria where significantly higher (P<0.05) in all the sediment samples than surface water. Overall results, using the β diversity measures, coupled with PCoA and DCA showed that bacterial composition in sediment and surface water was significantly different (P<0.001). Also, there were differences in bacterial community composition between agricultural runoff and urban runoff based on parsimony tests using 454 pyrosequencing data. Fecal indicator bacteria in surface water along different creeks and channels were significantly correlated with pH (P<0.01), NO2 (P<0.03), and NH4N (P<0.005); and in the sediment with NO3 (P<0.015). Our results suggest that microbial community compositions were influenced by several environmental factors, and pH, NO2, and NH4 were the major environmental factors driving FIB in surface water

Comparison of bacterial community structure and dynamics during the thermophilic composting of different types of solid wastes: anaerobic digestion residue, pig manure and chicken manure.

PubMed

Song, Caihong; Li, Mingxiao; Jia, Xuan; Wei, Zimin; Zhao, Yue; Xi, Beidou; Zhu, Chaowei; Liu, Dongming

2014-09-01

This study investigated the impact of composting substrate types on the bacterial community structure and dynamics during composting processes. To this end, pig manure (PM), chicken manure (CM), a mixture of PM and CM (PM + CM), and a mixture of PM, CM and anaerobic digestion residue (ADR) (PM + CM + ADR) were selected for thermophilic composting. The bacterial community structure and dynamics during the composting process were detected and analysed by polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) coupled with a statistic analysis. The physical-chemical analyses indicated that compared to single-material composting (PM, CM), co-composting (PM + CM, PM + CM + ADR) could promote the degradation of organic matter and strengthen the ability of conserving nitrogen. A DGGE profile and statistical analysis demonstrated that co-composting, especially PM + CM + ADR, could improve the bacterial community structure and functional diversity, even in the thermophilic stage. Therefore, co-composting could weaken the screening effect of high temperature on bacterial communities. Dominant sequencing analyses indicated a dramatic shift in the dominant bacterial communities from single-material composting to co-composting. Notably, compared with PM, PM + CM increased the quantity of xylan-degrading bacteria and reduced the quantity of human pathogens. © 2014 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Comparison of bacterial community structure and dynamics during the thermophilic composting of different types of solid wastes: anaerobic digestion residue, pig manure and chicken manure

PubMed Central

Song, Caihong; Li, Mingxiao; Jia, Xuan; Wei, Zimin; Zhao, Yue; Xi, Beidou; Zhu, Chaowei; Liu, Dongming

2014-01-01

This study investigated the impact of composting substrate types on the bacterial community structure and dynamics during composting processes. To this end, pig manure (PM), chicken manure (CM), a mixture of PM and CM (PM + CM), and a mixture of PM, CM and anaerobic digestion residue (ADR) (PM + CM + ADR) were selected for thermophilic composting. The bacterial community structure and dynamics during the composting process were detected and analysed by polymerase chain reaction–denaturing gradient gel electrophoresis (DGGE) coupled with a statistic analysis. The physical-chemical analyses indicated that compared to single-material composting (PM, CM), co-composting (PM + CM, PM + CM + ADR) could promote the degradation of organic matter and strengthen the ability of conserving nitrogen. A DGGE profile and statistical analysis demonstrated that co-composting, especially PM + CM + ADR, could improve the bacterial community structure and functional diversity, even in the thermophilic stage. Therefore, co-composting could weaken the screening effect of high temperature on bacterial communities. Dominant sequencing analyses indicated a dramatic shift in the dominant bacterial communities from single-material composting to co-composting. Notably, compared with PM, PM + CM increased the quantity of xylan-degrading bacteria and reduced the quantity of human pathogens. PMID:24963997

Comparison of benthic bacterial community composition in nine streams

Treesearch

Xueqing Gao; Ola A. Olapade; Laura G. Leff

2005-01-01

In this study, the abundance of major bacterial taxa (based on fluorescent in situ hybridization, FISH) and the structure of the bacterial community (based on denaturing gradient gel electrophoresis, DGGE) were determined in the benthos of 9 streams in the southeastern and midwestern United States and related to differences in environmental...

Bacterial Diversity and Community Structure in Korean Ginseng Field Soil Are Shifted by Cultivation Time

PubMed Central

Hoang, Van-An; Subramaniyam, Sathiyamoorthy; Kang, Jong-Pyo; Kang, Chang Ho; Yang, Deok-Chun

2016-01-01

Traditional molecular methods have been used to examine bacterial communities in ginseng-cultivated soil samples in a time-dependent manner. Despite these efforts, our understanding of the bacterial community is still inadequate. Therefore, in this study, a high-throughput sequencing approach was employed to investigate bacterial diversity in various ginseng field soil samples over cultivation times of 2, 4, and 6 years in the first and second rounds of cultivation. We used non-cultivated soil samples to perform a comparative study. Moreover, this study assessed changes in the bacterial community associated with soil depth and the health state of the ginseng. Bacterial richness decreased through years of cultivation. This study detected differences in relative abundance of bacterial populations between the first and second rounds of cultivation, years of cultivation, and health states of ginseng. These bacterial populations were mainly distributed in the classes Acidobacteria, Alphaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Sphingobacteria. In addition, we found that pH, available phosphorus, and exchangeable Ca+ seemed to have high correlations with bacterial class in ginseng cultivated soil. PMID:27187071

Bacterial Diversity and Community Structure in Korean Ginseng Field Soil Are Shifted by Cultivation Time.

PubMed

Nguyen, Ngoc-Lan; Kim, Yeon-Ju; Hoang, Van-An; Subramaniyam, Sathiyamoorthy; Kang, Jong-Pyo; Kang, Chang Ho; Yang, Deok-Chun

2016-01-01

Traditional molecular methods have been used to examine bacterial communities in ginseng-cultivated soil samples in a time-dependent manner. Despite these efforts, our understanding of the bacterial community is still inadequate. Therefore, in this study, a high-throughput sequencing approach was employed to investigate bacterial diversity in various ginseng field soil samples over cultivation times of 2, 4, and 6 years in the first and second rounds of cultivation. We used non-cultivated soil samples to perform a comparative study. Moreover, this study assessed changes in the bacterial community associated with soil depth and the health state of the ginseng. Bacterial richness decreased through years of cultivation. This study detected differences in relative abundance of bacterial populations between the first and second rounds of cultivation, years of cultivation, and health states of ginseng. These bacterial populations were mainly distributed in the classes Acidobacteria, Alphaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Sphingobacteria. In addition, we found that pH, available phosphorus, and exchangeable Ca+ seemed to have high correlations with bacterial class in ginseng cultivated soil.

Bacterial Community Succession in Pine-Wood Decomposition.

PubMed

Kielak, Anna M; Scheublin, Tanja R; Mendes, Lucas W; van Veen, Johannes A; Kuramae, Eiko E

2016-01-01

Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here, we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities.

Bacterial Community Succession in Pine-Wood Decomposition

PubMed Central

Kielak, Anna M.; Scheublin, Tanja R.; Mendes, Lucas W.; van Veen, Johannes A.; Kuramae, Eiko E.

2016-01-01

Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here, we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities. PMID:26973611

Distinct bacterial communities across a gradient of vegetation from a preserved Brazilian Cerrado.

PubMed

de Araujo, Ademir Sergio Ferreira; Bezerra, Walderly Melgaço; Dos Santos, Vilma Maria; Rocha, Sandra Mara Barbosa; Carvalho, Nilza da Silva; de Lyra, Maria do Carmo Catanho Pereira; Figueiredo, Marcia do Vale Barreto; de Almeida Lopes, Ângela Celis; Melo, Vania Maria Maciel

2017-04-01

The Cerrado biome in the Sete Cidades National Park, an Ecological Reserve in Northeastern Brazil, has conserved its native biodiversity and presents a variety of plants found in other savannas in Brazil. Despite this finding the soil microbial diversity and community structure are poorly understood. Therefore, we described soil bacterial diversity and distribution along a savanna vegetation gradient taking into account the prevailing environmental factors. The bacterial composition was retrieved by sequencing a fragment of the 16S ribosomal RNA gene. The bacterial operational taxonomic units (OTUs) were assigned to 37 different phyla, 96 classes, and 83 genera. At the phylum level, a core comprised by Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, Verrucomicrobia and Planctomycetes, was detected in all areas of Cerrado. 'Cerrado stricto sensu' and 'Cerradao' share more similarities between edaphic properties and vegetation and also present more similar bacterial communities, while 'Floresta decidual' and 'Campo graminoide' show the largest environmental differences and also more distinct bacterial communities. Proteobacteria (26%), Acidobacteria (21%) and Actinobacteria (21%) were the most abundant phyla within the four areas. All the samples present similar bacteria richness (alpha diversity) and the observed differences among them (beta diversity) were more related to the abundance of specific taxon OTUs compared to their presence or absence. Total organic C, N and P are the main abiotic factors structuring the bacterial communities. In summary, our findings show the bacterial community structure was clearly different across the Cerrado gradient, but that these environments share a bacterial phylum-core comprising Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia and Planctomycetes with other Brazilian savannas.

Bacterial communities in floral nectar.

PubMed

Fridman, Svetlana; Izhaki, Ido; Gerchman, Yoram; Halpern, Malka

2012-02-01

Floral nectar is regarded as the most important reward available to animal-pollinated plants to attract pollinators. Despite the vast amount of publications on nectar properties, the role of nectar as a natural bacterial habitat is yet unexplored. To gain a better understanding of bacterial communities inhabiting floral nectar, culture-dependent and -independent (454-pyrosequencing) methods were used. Our findings demonstrate that bacterial communities in nectar are abundant and diverse. Using culture-dependent method we showed that bacterial communities of nectar displayed significant variation among three plant species: Amygdalus communis, Citrus paradisi and Nicotiana glauca. The dominant class in the nectar bacterial communities was Gammaproteobacteria. About half of the isolates were novel species (< 97% similarities of the 16S rRNA gene with known species). Using 454-pyrosequencing we demonstrated that nectar microbial community are distinct for each of the plant species while there are no significant differences between nectar microbial communities within nectars taken from different plants of the same species. Primary selection of the nectar bacteria is unclear; it may be affected by variations in the chemical composition of the nectar in each plant. The role of the rich and diverse nectar microflora in the attraction-repulsion relationships between the plant and its nectar consumers has yet to be explored. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Bacterial Communities in Boreal Forest Mushrooms Are Shaped Both by Soil Parameters and Host Identity

PubMed Central

Pent, Mari; Põldmaa, Kadri; Bahram, Mohammad

2017-01-01

Despite recent advances in understanding the microbiome of eukaryotes, little is known about microbial communities in fungi. Here we investigate the structure of bacterial communities in mushrooms, including common edible ones, with respect to biotic and abiotic factors in the boreal forest. Using a combination of culture-based and Illumina high-throughput sequencing, we characterized the bacterial communities in fruitbodies of fungi from eight genera spanning four orders of the class Agaricomycetes (Basidiomycota). Our results revealed that soil pH followed by fungal identity are the main determinants of the structure of bacterial communities in mushrooms. While almost half of fruitbody bacteria were also detected from soil, the abundance of several bacterial taxa differed considerably between the two environments. The effect of host identity was significant at the fungal genus and order level and could to some extent be ascribed to the distinct bacterial community of the chanterelle, representing Cantharellales—the earliest diverged group of mushroom-forming basidiomycetes. These data suggest that besides the substantial contribution of soil as a major taxa source of bacterial communities in mushrooms, the structure of these communities is also affected by the identity of the host. Thus, bacteria inhabiting fungal fruitbodies may be non-randomly selected from environment based on their symbiotic functions and/or habitat requirements. PMID:28539921

Camparison of benthic bacterial community composition in nine streams

Treesearch

Xuqing Gao; Ola A. Olapade; Laura G. Leff

2005-01-01

In this study, the abundance of major bacterial taxa (based on fluorescent in situ hybridization, FISH) and the structure of the bacterial community (based on denaturing gradient gel electrophoresis, DGGE) were determined in the benthos of 9 streams in the southeastern and midwestern United States and related to differences in environmental conditions. Taxa examined...

Spatial and Temporal Variation of Archaeal, Bacterial and Fungal Communities in Agricultural Soils

PubMed Central

Pereira e Silva, Michele C.; Dias, Armando Cavalcante Franco; van Elsas, Jan Dirk; Salles, Joana Falcão

2012-01-01

Background Soil microbial communities are in constant change at many different temporal and spatial scales. However, the importance of these changes to the turnover of the soil microbial communities has been rarely studied simultaneously in space and time. Methodology/Principal Findings In this study, we explored the temporal and spatial responses of soil bacterial, archaeal and fungal β-diversities to abiotic parameters. Taking into account data from a 3-year sampling period, we analyzed the abundances and community structures of Archaea, Bacteria and Fungi along with key soil chemical parameters. We questioned how these abiotic variables influence the turnover of bacterial, archaeal and fungal communities and how they impact the long-term patterns of changes of the aforementioned soil communities. Interestingly, we found that the bacterial and fungal β-diversities are quite stable over time, whereas archaeal diversity showed significantly higher fluctuations. These fluctuations were reflected in temporal turnover caused by soil management through addition of N-fertilizers. Conclusions Our study showed that management practices applied to agricultural soils might not significantly affect the bacterial and fungal communities, but cause slow and long-term changes in the abundance and structure of the archaeal community. Moreover, the results suggest that, to different extents, abiotic and biotic factors determine the community assembly of archaeal, bacterial and fungal communities. PMID:23284712

Community-acquired bacterial meningitis.

PubMed

van de Beek, Diederik; Brouwer, Matthijs; Hasbun, Rodrigo; Koedel, Uwe; Whitney, Cynthia G; Wijdicks, Eelco

2016-11-03

Meningitis is an inflammation of the meninges and subarachnoid space that can also involve the brain cortex and parenchyma. It can be acquired spontaneously in the community - community-acquired bacterial meningitis - or in the hospital as a complication of invasive procedures or head trauma (nosocomial bacterial meningitis). Despite advances in treatment and vaccinations, community-acquired bacterial meningitis remains one of the most important infectious diseases worldwide. Streptococcus pneumoniae and Neisseria meningitidis are the most common causative bacteria and are associated with high mortality and morbidity; vaccines targeting these organisms, which have designs similar to the successful vaccine that targets Haemophilus influenzae type b meningitis, are now being used in many routine vaccination programmes. Experimental and genetic association studies have increased our knowledge about the pathogenesis of bacterial meningitis. Early antibiotic treatment improves the outcome, but the growing emergence of drug resistance as well as shifts in the distribution of serotypes and groups are fuelling further development of new vaccines and treatment strategies. Corticosteroids were found to be beneficial in high-income countries depending on the bacterial species. Further improvements in the outcome are likely to come from dampening the host inflammatory response and implementing preventive measures, especially the development of new vaccines.

Diversity and Assembling Processes of Bacterial Communities in Cryoconite Holes of a Karakoram Glacier.

PubMed

Ambrosini, Roberto; Musitelli, Federica; Navarra, Federico; Tagliaferri, Ilario; Gandolfi, Isabella; Bestetti, Giuseppina; Mayer, Christoph; Minora, Umberto; Azzoni, Roberto Sergio; Diolaiuti, Guglielmina; Smiraglia, Claudio; Franzetti, Andrea

2017-05-01

Cryoconite holes are small ponds that form on the surface of glaciers that contain a dark debris, the cryoconite, at the bottom and host active ecological communities. Differences in the structure of bacterial communities have been documented among Arctic and mountain glaciers, and among glaciers in different areas of the world. In this study, we investigated the structure of bacterial communities of cryoconite holes of Baltoro Glacier, a large (62 km in length and 524 km 2 of surface) glacier of the Karakoram, by high-throughput sequencing of the V5-V6 hypervariable regions of the 16S rRNA gene. We found that Betaproteobacteria dominated bacterial communities, with large abundance of genera Polaromonas, probably thanks to its highly versatile metabolism, and Limnohabitans, which may have been favoured by the presence of supraglacial lakes in the area where cryoconite holes were sampled. Variation in bacterial communities among different sampling areas of the glacier could be explained by divergent selective processes driven by variation in environmental conditions, particularly pH, which was the only environmental variable that significantly affected the structure of bacterial communities. This variability may be due to both temporal and spatial patterns of variation in environmental conditions.

Corexit 9500 Enhances Oil Biodegradation and Changes Active Bacterial Community Structure of Oil-Enriched Microcosms.

PubMed

Techtmann, Stephen M; Zhuang, Mobing; Campo, Pablo; Holder, Edith; Elk, Michael; Hazen, Terry C; Conmy, Robyn; Santo Domingo, Jorge W

2017-05-15

To better understand the impacts of Corexit 9500 on the structure and activity levels of hydrocarbon-degrading microbial communities, we analyzed next-generation 16S rRNA gene sequencing libraries of hydrocarbon enrichments grown at 5 and 25°C using both DNA and RNA extracts as the sequencing templates. Oil biodegradation patterns in both 5 and 25°C enrichments were consistent with those reported in the literature (i.e., aliphatics were degraded faster than aromatics). Slight increases in biodegradation were observed in the presence of Corexit at both temperatures. Differences in community structure were observed between treatment conditions in the DNA-based libraries. The 25°C consortia were dominated by Vibrio , Idiomarina , Marinobacter , Alcanivorax , and Thalassospira species, while the 5°C consortia were dominated by several species of the genera Flavobacterium , Alcanivorax , and Oleispira Most of these genera have been linked to hydrocarbon degradation and have been observed after oil spills. Colwellia and Cycloclasticus , known aromatic degraders, were also found in these enrichments. The addition of Corexit did not have an effect on the active bacterial community structure of the 5°C consortia, while at 25°C, a decrease in the relative abundance of Marinobacter was observed. At 25°C, Thalassospira , Marinobacter , and Idiomarina were present at higher relative abundances in the RNA than DNA libraries, suggesting that they were active in degradation. Similarly, Oleispira was greatly stimulated by the addition of oil at 5°C. IMPORTANCE While dispersants such as Corexit 9500 can be used to treat oil spills, there is still debate on the effectiveness on enhancing oil biodegradation and its potential toxic effect on oil-degrading microbial communities. The results of this study provide some insights on the microbial dynamics of hydrocarbon-degrading bacterial populations in the presence of Corexit 9500. Operational taxonomic unit (OTU) analyses

Corexit 9500 Enhances Oil Biodegradation and Changes Active Bacterial Community Structure of Oil-Enriched Microcosms

PubMed Central

Zhuang, Mobing; Campo, Pablo; Holder, Edith; Elk, Michael; Conmy, Robyn

2017-01-01

ABSTRACT To better understand the impacts of Corexit 9500 on the structure and activity levels of hydrocarbon-degrading microbial communities, we analyzed next-generation 16S rRNA gene sequencing libraries of hydrocarbon enrichments grown at 5 and 25°C using both DNA and RNA extracts as the sequencing templates. Oil biodegradation patterns in both 5 and 25°C enrichments were consistent with those reported in the literature (i.e., aliphatics were degraded faster than aromatics). Slight increases in biodegradation were observed in the presence of Corexit at both temperatures. Differences in community structure were observed between treatment conditions in the DNA-based libraries. The 25°C consortia were dominated by Vibrio, Idiomarina, Marinobacter, Alcanivorax, and Thalassospira species, while the 5°C consortia were dominated by several species of the genera Flavobacterium, Alcanivorax, and Oleispira. Most of these genera have been linked to hydrocarbon degradation and have been observed after oil spills. Colwellia and Cycloclasticus, known aromatic degraders, were also found in these enrichments. The addition of Corexit did not have an effect on the active bacterial community structure of the 5°C consortia, while at 25°C, a decrease in the relative abundance of Marinobacter was observed. At 25°C, Thalassospira, Marinobacter, and Idiomarina were present at higher relative abundances in the RNA than DNA libraries, suggesting that they were active in degradation. Similarly, Oleispira was greatly stimulated by the addition of oil at 5°C. IMPORTANCE While dispersants such as Corexit 9500 can be used to treat oil spills, there is still debate on the effectiveness on enhancing oil biodegradation and its potential toxic effect on oil-degrading microbial communities. The results of this study provide some insights on the microbial dynamics of hydrocarbon-degrading bacterial populations in the presence of Corexit 9500. Operational taxonomic unit (OTU) analyses

Effect of reclaimed water effluent on bacterial community structure in the Typha angustifolia L. rhizosphere soil of urbanized riverside wetland, China.

PubMed

Huang, Xingru; Xiong, Wei; Liu, Wei; Guo, Xiaoyu

2017-05-01

In order to evaluate the impact of reclaimed water on the ecology of bacterial communities in the Typha angustifolia L. rhizosphere soil, bacterial community structure was investigated using a combination of terminal restriction fragment length polymorphism and 16S rRNA gene clone library. The results revealed significant spatial variation of bacterial communities along the river from upstream and downstream. For example, a higher relative abundance of γ-Proteobacteria, Firmicutes, Chloroflexi and a lower proportion of β-Proteobacteria and ε-Proteobacteria was detected at the downstream site compared to the upstream site. Additionally, with an increase of the reclaimed water interference intensity, the rhizosphere bacterial community showed a decrease in taxon richness, evenness and diversity. The relative abundance of bacteria closely related to the resistant of heavy-metal was markedly increased, while the bacteria related for carbon/nitrogen/phosphorus/sulfur cycling wasn't strikingly changed. Besides that, the pathogenic bacteria markedly increased in the downstream rhizosphere soil since reclaimed water supplement, while the possible plant growth-promoting rhizobacteria obviously reduced in the downstream sediment. Together these data suggest cause and effect between reclaimed water input into the wetland, shift in bacterial communities through habitat change, and alteration of capacity for biogeochemical cycling of contaminants. Copyright © 2016. Published by Elsevier B.V.

Denitrification in Agriculturally Impacted Streams: Seasonal Changes in Structure and Function of the Bacterial Community

PubMed Central

Manis, Erin; Royer, Todd V.; Johnson, Laura T.; Leff, Laura G.

2014-01-01

Denitrifiers remove fixed nitrogen from aquatic environments and hydrologic conditions are one potential driver of denitrification rate and denitrifier community composition. In this study, two agriculturally impacted streams in the Sugar Creek watershed in Indiana, USA with different hydrologic regimes were examined; one stream is seasonally ephemeral because of its source (tile drainage), whereas the other stream has permanent flow. Additionally, a simulated flooding experiment was performed on the riparian benches of the ephemeral stream during a dry period. Denitrification activity was assayed using the chloramphenicol amended acetylene block method and bacterial communities were examined based on quantitative PCR and terminal restriction length polymorphisms of the nitrous oxide reductase (nosZ) and 16S rRNA genes. In the stream channel, hydrology had a substantial impact on denitrification rates, likely by significantly lowering water potential in sediments. Clear patterns in denitrification rates were observed among pre-drying, dry, and post-drying dates; however, a less clear scenario was apparent when analyzing bacterial community structure suggesting that denitrifier community structure and denitrification rate were not strongly coupled. This implies that the nature of the response to short-term hydrologic changes was physiological rather than increases in abundance of denitrifiers or changes in composition of the denitrifier community. Flooding of riparian bench soils had a short-term, transient effect on denitrification rate. Our results imply that brief flooding of riparian zones is unlikely to contribute substantially to removal of nitrate (NO3 -) and that seasonal drying of stream channels has a negative impact on NO3 - removal, particularly because of the time lag required for denitrification to rebound. This time lag is presumably attributable to the time required for the denitrifiers to respond physiologically rather than a change in abundance or

Soil bacterial community responses to revegetation of moving sand dune in semi-arid grassland.

PubMed

Cao, Chengyou; Zhang, Ying; Cui, Zhenbo; Feng, Shuwei; Wang, Tingting; Ren, Qing

2017-08-01

Grasslands in semi-arid Northern China are widely desertified, thus inducing the formation of a large area of moving sand lands. Revegetation of the sandy land is commonly adopted to restore degraded grasslands. The structure of the soil microbial community might dramatically change during degradation and recovery because microorganisms are one of the major drivers of ecological process through their interactions with plants and soil. Assuming that soil properties are the key determinants of the structure of soil bacterial community within the same soil type, whether the vegetation type causes the significant difference in the structure of soil bacterial community during revegetation and restoration of the degraded grasslands remains poorly understood. Our study aimed to (1) investigate the response of soil bacterial communities to the changes during vegetation degradation and recovery and (2) evaluate whether the soil bacterial communities under plantations return to their native state. We detected the shifts in diversities and compositions of the soil bacterial communities and the relative abundance of dominant bacterial taxa by using the high-throughput Illumina MiSeq sequencing technique in an area covered by 32-year-old Caragana microphylla, Artemisia halodendron, Hedysarum fruticosum, Pinus sylvestris var. mongolica, Populus simonii, and Salix gordejevii sand-fixing plantations and in the native community (NC) dominated by elm, and moving sandy dune (MS). We found that the obtained operational taxonomic units by 16S rRNA gene sequencing and diversity index in MS were all significantly lower than those in NC, and the number and composition of dominant genera were significantly different between NC and MS. Interestingly, the compositions of bacterial communities and the dominant genera in different sand-fixation plantations (C. microphylla, A. halodendron, H. fruticosum, P. sylvestris var. mongolica, P. simonii, and S. gordejevii) were all similar to those of

Effect of physical sediments reworking on hydrocarbon degradation and bacterial community structure in marine coastal sediments.

PubMed

Duran, Robert; Bonin, Patricia; Jezequel, Ronan; Dubosc, Karine; Gassie, Claire; Terrisse, Fanny; Abella, Justine; Cagnon, Christine; Militon, Cecile; Michotey, Valérie; Gilbert, Franck; Cuny, Philippe; Cravo-Laureau, Cristiana

2015-10-01

The present study aimed to examine whether the physical reworking of sediments by harrowing would be suitable for favouring the hydrocarbon degradation in coastal marine sediments. Mudflat sediments were maintained in mesocosms under conditions as closer as possible to those prevailing in natural environments with tidal cycles. Sediments were contaminated with Ural blend crude oil, and in half of them, harrowing treatment was applied in order to mimic physical reworking of surface sediments. Hydrocarbon distribution within the sediment and its removal was followed during 286 days. The harrowing treatment allowed hydrocarbon compounds to penetrate the first 6 cm of the sediments, and biodegradation indexes (such as n-C18/phytane) indicated that biodegradation started 90 days before that observed in untreated control mesocosms. However, the harrowing treatment had a severe impact on benthic organisms reducing drastically the macrofaunal abundance and diversity. In the harrowing-treated mesocosms, the bacterial abundance, determined by 16S rRNA gene Q-PCR, was slightly increased; and terminal restriction fragment length polymorphism (T-RFLP) analyses of 16S rRNA genes showed distinct and specific bacterial community structure. Co-occurrence network and canonical correspondence analyses (CCA) based on T-RFLP data indicated the main correlations between bacterial operational taxonomic units (OTUs) as well as the associations between OTUs and hydrocarbon compound contents further supported by clustered correlation (ClusCor) analysis. The analyses highlighted the OTUs constituting the network structural bases involved in hydrocarbon degradation. Negative correlations indicated the possible shifts in bacterial communities that occurred during the ecological succession.

Bacterial community initial development in proglacial soils of Larsemann hill, East Antarctica

NASA Astrophysics Data System (ADS)

Ma, H.; Yan, W.; Shi, G.; Sun, B.; Zhang, Y.; Xiao, X.

2016-12-01

Glacial forefields are considered ideal places to explore how microbial communities will response to climate-driven environmental changes. Our knowledge of how the bacterial community activities and structure was influenced by changing environment due to glacier retreat is still very limited, especially at the initial stage of glacier retreat. The short gradient soil samples including the ice free and ice covered sites were sampled in the forehead of East Antarctica ice sheet, in Larsemann Hills. By employing the Miseq sequencing methods, 1.8 x104 high-quality sequences were gotten for each sample and the bacterial diversity including abundant bacteria and rare bacteria were studied and compared between the gradient samples. Even though in such an extreme stress condition, the bacterial diversity was high. The coefficient of variance between the five sites of abundant group was 0.886 which was higher than that of the top 20 rare group (0.159) significantly (unpaired t test, p-value<0.0001) suggesting that the abundant bacterial communities were more sensitive to the ice sheet change in the initial stage than rare bacteria did. And the abundant bacteria contributed the community structure more than the rare bacteria did. The rare group acted more like seed bank to keep the community functionality in the forehead of sheet. And the ice thickness was the major factor to affect the abundant bacterial community. Given the fact that Antarctica environment was more sensitive to the global warming, the study about abundant and rare bacteria response to condition change will be helpful to precisely predict community response to climate change in polar region. This finding will improve the understanding about the relationship between community structure and environment condition in extreme stress condition.

Variations in Bacterial Community in a Temperate Lake Associated with an Agricultural Watershed.

PubMed

Song, Liyan; Li, Lei

2016-08-01

Terrestrially derived carbon and nutrients are washed into lakes, providing nutritional drivers for both microbial heterotrophy and phototrophy. Changes in the quantity and diversity of carbon and nutrients exported from watersheds in response to alterations in long-term land use have led to a need for evaluation of the linkage between watershed-exported carbon and nutrients and bacterial community structure in watershed associated lakes. To learn more about these interactions, we investigated Muskrat Lake in Michigan, which has a well-defined moderately sized watershed dominated by agriculture. We measured the water chemistry, characterized the dissolved organic carbon, and determined the structure of the bacterial communities at the inlet and center of this lake (five depths per site) over the summer and fall of 2008. The lake had temporal and rain event-based fluctuations in water chemistry, as well as temporal and rain event-dependent shifts in bacterial communities as measured by terminal restriction fragment length polymorphism. Agricultural watershed inputs were observed in the lake during and after rain events. Terminal restriction fragment length polymorphism and 454 pyrosequencing of the bacterial communities indicated that there were differences over time and that the dominant phylotypes shifted between summer and late fall. Some populations (e.g., Polynucleobacter and Mycobacterium) increased during fall, while others (e.g., Gemmatimonas) diminished. Redundancy and partitioning analyses showed that water chemistry is highly correlated with variations in the bacterial community of the lake, which explained 34 % of the variations in the bacterial community. Dissolved organic carbon had the greatest effects on variations in the Muskrat Lake bacterial community (2 %). The results of this study provide information that will enable a better understanding of the interaction between the bacterial community of lakes and changes in chemical properties as a

Investigation of bacterial communities in peat land of the Gahai Lake natural conservation area

NASA Astrophysics Data System (ADS)

Bai, Yani; Wang, Jinchang; Zhan, Zhigao; Guan, Limei; Jin, Liang; Zheng, Guohua

2017-10-01

Peat is involved in the global carbon cycle and water conservation; therefore, it is implicated in global environmental change. Microorganisms play an important role in the function of peat. To investigate the bacterial communities in peat of Gahai Lake, different locations and depths were sampled and Illumina Miseq sequencing was used to analyze the microbial community. Chemical properties of peat samples were analyzed by China state standard methods (GB methods). The results showed that bacterial communities were affected by depth, with bacterial diversity and community structure at 90 and 120 cm significantly different from that at 10, 30 and 50 cm depth from the peat surface. Chemical properties of peat land including organic matter, total nitrogen and humus content did not significantly influence bacterial community structure in peat, with only one group from genus Rhizomicrobium that was significantly correlated with total nitrogen. A substantial proportion of the bacterial sequences were unclassified (1.4%), which indicates the great application potential of peat in the Gahai Lake natural conservation area in the future.

Effects of ecological engineered oxygenation on the bacterial community structure in an anoxic fjord in western Sweden

PubMed Central

Forth, Michael; Liljebladh, Bengt; Stigebrandt, Anders; Hall, Per O J; Treusch, Alexander H

2015-01-01

Oxygen-depleted bodies of water are becoming increasingly common in marine ecosystems. Solutions to reverse this trend are needed and under development, for example, by the Baltic deep-water OXygenation (BOX) project. In the framework of this project, the Swedish Byfjord was chosen for a pilot study, investigating the effects of an engineered oxygenation on long-term anoxic bottom waters. The strong stratification of the water column of the Byfjord was broken up by pumping surface water into the deeper layers, triggering several inflows of oxygen-rich water and increasing oxygen levels in the lower water column and the benthic zone up to 110 μmol l−1.We used molecular ecologic methods to study changes in bacterial community structure in response to the oxygenation in the Byfjord. Water column samples from before, during and after the oxygenation as well as from two nearby control fjords were analyzed. Our results showed a strong shift in bacterial community composition when the bottom water in the Byfjord became oxic. Initially dominant indicator species for oxygen minimum zones such as members of the SUP05 clade declined in abundance during the oxygenation event and nearly vanished after the oxygenation was accomplished. In contrast, aerobic species like SAR11 that initially were restricted to surface waters could later be detected deep into the water column. Overall, the bacterial community in the formerly anoxic bottom waters changed to a community structure similar to those found in oxic waters, showing that an engineered oxygenation of a large body of anoxic marine water is possible and emulates that of a natural oxygenation event. PMID:25238400

Effects of ecological engineered oxygenation on the bacterial community structure in an anoxic fjord in western Sweden.

PubMed

Forth, Michael; Liljebladh, Bengt; Stigebrandt, Anders; Hall, Per O J; Treusch, Alexander H

2015-03-01

Oxygen-depleted bodies of water are becoming increasingly common in marine ecosystems. Solutions to reverse this trend are needed and under development, for example, by the Baltic deep-water OXygenation (BOX) project. In the framework of this project, the Swedish Byfjord was chosen for a pilot study, investigating the effects of an engineered oxygenation on long-term anoxic bottom waters. The strong stratification of the water column of the Byfjord was broken up by pumping surface water into the deeper layers, triggering several inflows of oxygen-rich water and increasing oxygen levels in the lower water column and the benthic zone up to 110 μmol l(-1).We used molecular ecologic methods to study changes in bacterial community structure in response to the oxygenation in the Byfjord. Water column samples from before, during and after the oxygenation as well as from two nearby control fjords were analyzed. Our results showed a strong shift in bacterial community composition when the bottom water in the Byfjord became oxic. Initially dominant indicator species for oxygen minimum zones such as members of the SUP05 clade declined in abundance during the oxygenation event and nearly vanished after the oxygenation was accomplished. In contrast, aerobic species like SAR11 that initially were restricted to surface waters could later be detected deep into the water column. Overall, the bacterial community in the formerly anoxic bottom waters changed to a community structure similar to those found in oxic waters, showing that an engineered oxygenation of a large body of anoxic marine water is possible and emulates that of a natural oxygenation event.

Influence of straw incorporation with and without straw decomposer on soil bacterial community structure and function in a rice-wheat cropping system.

PubMed

Zhao, Jun; Ni, Tian; Xun, Weibing; Huang, Xiaolei; Huang, Qiwei; Ran, Wei; Shen, Biao; Zhang, Ruifu; Shen, Qirong

2017-06-01

To study the influence of straw incorporation with and without straw decomposer on bacterial community structure and biological traits, a 3-year field experiments, including four treatments: control without fertilizer (CK), chemical fertilizer (NPK), chemical fertilizer plus 7500 kg ha -1 straw incorporation (NPKS), and chemical fertilizer plus 7500 kg ha -1 straw incorporation and 300 kg ha -1 straw decomposer (NPKSD), were performed in a rice-wheat cropping system in Changshu (CS) and Jintan (JT) city, respectively. Soil samples were taken right after wheat (June) and rice (October) harvest in both sites, respectively. The NPKS and NPKSD treatments consistently increased crop yields, cellulase activity, and bacterial abundance in both sampling times and sites. Moreover, the NPKS and NPKSD treatments altered soil bacterial community structure, particularly in the wheat harvest soils in both sites, separating from the CK and NPK treatments. In the rice harvest soils, both NPKS and NPKSD treatments had no considerable impacts on bacterial communities in CS, whereas the NPKSD treatment significantly shaped bacterial communities compared to the other treatments in JT. These practices also significantly shifted the bacterial composition of unique operational taxonomic units (OTUs) rather than shared OTUs. The relative abundances of copiotrophic bacteria (Proteobacteria, Betaproteobacteria, and Actinobacteria) were positively correlated with soil total N, available N, and available P. Taken together, these results indicate that application of straw incorporation with and without straw decomposer could particularly stimulate the copiotrophic bacteria, enhance the soil biological activity, and thus, contribute to the soil productivity and sustainability in agro-ecosystems.

Variability in bacterial community structure during upwelling in the coastal ocean

USGS Publications Warehouse

Kerkhof, L.J.; Voytek, M.A.; Sherrell, Robert M.; Millie, D.; Schofield, O.

1999-01-01

Over the last 30 years, investigations at the community level of marine bacteria and phytoplankton populations suggest they are tightly coupled. However, traditional oceanographic approaches cannot assess whether associations between specific bacteria and phytoplankton exist. Recently, molecular based approaches have been implemented to characterize specific members of different marine bacterial communities. Yet, few molecular-based studies have examined coastal upwelling situations. This is important since upwelling systems provide a unique opportunity for analyzing the association between specific bacteria and specific phytoplankton in the ocean. It is widely believed that upwelling can lead to changes in phytoplankton populations (blooms). Thus, if specific associations exist, we would expect to observe changes in the bacterial population triggered by the bloom. In this paper, we present preliminary data from coastal waters off New Jersey that confirm a shift in bacterial communities during a 1995 upwelling event recorded at a long-term earth observatory (LEO-15) in the Mid-Atlantic Bight. Using PCR amplification and cloning, specific bacterial 16S ribosomal RNA sequences were found which were present in upwelling samples during a phytoplankton bloom, but were not detected in non-bloom samples (surface seawater, offshore sites or sediment samples) collected at the same time or in the same area. These findings are consistent with the notion of specific associations between bacteria and phytoplankton in the ocean. However, further examination of episodic events, such as coastal upwelling, are needed to confirm the existence of specific associations. Additionally, experiments need to be performed to elucidate the mechanisms leading to the specific linkages between a group of bacteria and a group of phytoplankton.

The effect of heavy metal contamination on the bacterial community structure at Jiaozhou Bay, China.

PubMed

Yao, Xie-Feng; Zhang, Jiu-Ming; Tian, Li; Guo, Jian-Hua

In this study, determination of heavy metal parameters and microbiological characterization of marine sediments obtained from two heavily polluted sites and one low-grade contaminated reference station at Jiaozhou Bay in China were carried out. The microbial communities found in the sampled marine sediments were studied using PCR-DGGE (denaturing gradient gel electrophoresis) fingerprinting profiles in combination with multivariate analysis. Clustering analysis of DGGE and matrix of heavy metals displayed similar occurrence patterns. On this basis, 17 samples were classified into two clusters depending on the presence or absence of the high level contamination. Moreover, the cluster of highly contaminated samples was further classified into two sub-groups based on the stations of their origin. These results showed that the composition of the bacterial community is strongly influenced by heavy metal variables present in the sediments found in the Jiaozhou Bay. This study also suggested that metagenomic techniques such as PCR-DGGE fingerprinting in combination with multivariate analysis is an efficient method to examine the effect of metal contamination on the bacterial community structure. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Fire modifies the phylogenetic structure of soil bacterial co-occurrence networks.

PubMed

Pérez-Valera, Eduardo; Goberna, Marta; Faust, Karoline; Raes, Jeroen; García, Carlos; Verdú, Miguel

2017-01-01

Fire alters ecosystems by changing the composition and community structure of soil microbes. The phylogenetic structure of a community provides clues about its main assembling mechanisms. While environmental filtering tends to reduce the community phylogenetic diversity by selecting for functionally (and hence phylogenetically) similar species, processes like competitive exclusion by limiting similarity tend to increase it by preventing the coexistence of functionally (and phylogenetically) similar species. We used co-occurrence networks to detect co-presence (bacteria that co-occur) or exclusion (bacteria that do not co-occur) links indicative of the ecological interactions structuring the community. We propose that inspecting the phylogenetic structure of co-presence or exclusion links allows to detect the main processes simultaneously assembling the community. We monitored a soil bacterial community after an experimental fire and found that fire altered its composition, richness and phylogenetic diversity. Both co-presence and exclusion links were more phylogenetically related than expected by chance. We interpret such a phylogenetic clustering in co-presence links as a result of environmental filtering, while that in exclusion links reflects competitive exclusion by limiting similarity. This suggests that environmental filtering and limiting similarity operate simultaneously to assemble soil bacterial communities, widening the traditional view that only environmental filtering structures bacterial communities. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Dynamics of bacterial and fungal communities associated with eggshells during incubation

PubMed Central

Grizard, Stéphanie; Dini-Andreote, Francisco; Tieleman, B Irene; Salles, Joana F

2014-01-01

Microorganisms are closely associated with eggs and may play a determinant role in embryo survival. Yet, the majority of studies focusing on this association relied on culture-based methodology, eventually leading to a skewed assessment of microbial communities. By targeting the 16S rRNA gene and internal transcribed spacer (ITS) region, we, respectively, described bacterial and fungal communities on eggshells of the homing pigeon Columba livia. We explored their structure, abundance, and composition. Firstly, we showed that sampling technique affected the outcome of the results. While broadly used, the egg swabbing procedure led to a lower DNA extraction efficiency and provided different profiles of bacterial communities than those based on crushed eggshell pieces. Secondly, we observed shifts in bacterial and fungal communities during incubation. At late incubation, bacterial communities showed a reduction in diversity, while their abundance increased, possibly due to the competitive advantage of some species. When compared to their bacterial counterparts, fungal communities also decreased in diversity at late incubation. In that case, however, the decline was associated with a diminution of their overall abundance. Conclusively, our results showed that although incubation might inhibit microbial growth when compared to unincubated eggs, we observed the selective growth of specific bacterial species during incubation. Moreover, we showed that fungi are a substantial component of the microbial communities associated with eggshells and require further investigations in avian ecology. Identifying the functional roles of these microorganisms is likely to provide news insights into the evolutionary strategies that control embryo survival. We aimed to describe the dynamics of bacterial and fungal communities on homing pigeon eggshell surfaces. We investigated these communities at early and late incubation stages. PMID:24772289

Bacterial community structures in air conditioners installed in Japanese residential buildings.

PubMed

Hatayama, Kouta; Oikawa, Yurika; Ito, Hiroyuki

2018-01-01

The bacterial community structures in four Japanese split-type air conditioners were analyzed using a next-generation sequencer. A variety of bacteria were detected in the air filter of an air conditioner installed on the first floor. In the evaporator of this air conditioner, bacteria belonging to the genus Methylobacterium, or the family of Sphingomonadaceae, were predominantly detected. On the other hand, the majority of bacteria detected in the air filters and evaporators of air conditioners installed on the fifth and twelfth floors belonged to the family Enterobacteriaceae. The source of bacteria belonging to the family Enterobacteriaceae may have been aerosols generated by toilet flushing in the buildings. Our results suggested the possibility that the bacterial contamination in the air conditioners was affected by the floor level on which they were installed. The air conditioner installed on the lower floor, near the ground, may have been contaminated by a variety of outdoor bacteria, whereas the air conditioners installed on floors more distant from the ground may have been less contaminated by outdoor bacteria. However, these suppositions may apply only to the specific split-type air conditioners that we analyzed, because our sample size was small.

Diverse bacterial communities exist on canine skin and are impacted by cohabitation and time.

PubMed

Torres, Sheila; Clayton, Jonathan B; Danzeisen, Jessica L; Ward, Tonya; Huang, Hu; Knights, Dan; Johnson, Timothy J

2017-01-01

It has previously been shown that domestic dogs and their household owners share bacterial populations, and that sharing of bacteria between humans is facilitated through the presence of dogs in the household. However, less is known regarding the bacterial communities of dogs, how these communities vary by location and over time, and how cohabitation of dogs themselves influences their bacterial community. Furthermore, the effects of factors such as breed, hair coat length, sex, shedding, and age on the canine skin microbiome is unknown. This study sampled the skin bacterial communities of 40 dogs belonging to 20 households longitudinally across three seasons (spring, summer, and winter). Significant differences in bacterial community structure between samples were identified when stratified by season, but not by dog sex, age, breed, hair type, or skin site. Cohabitating dogs were more likely to share bacteria of the skin than non-cohabitating dogs. Similar to human bacterial microbiomes, dogs' microbiomes were more similar to their own microbiomes over time than to microbiomes of other individuals. Dogs sampled during the same season were also more similar to each other than to dogs from different seasons, irrespective of household. However, there were very few core operational taxonomic units (OTUs) identified across all dogs sampled. Taxonomic classification revealed Propionibacterium acnes and Haemophilus sp. as key members of the dog skin bacterial community, along with Corynebacterium sp. and Staphylococcus epidermidis . This study shows that the skin bacterial community structure of dogs is highly individualized, but can be shared among dogs through cohabitation.

Assessment of bacterial and archaeal community structure in Swine wastewater treatment processes.

PubMed

Da Silva, Marcio Luis Busi; Cantão, Mauricio Egídio; Mezzari, Melissa Paola; Ma, Jie; Nossa, Carlos Wolfgang

2015-07-01

Microbial communities from two field-scale swine wastewater treatment plants (WWTPs) were assessed by pyrosequencing analyses of bacterial and archaeal 16S ribosomal DNA (rDNA) fragments. Effluent samples from secondary (anaerobic covered lagoons and upflow anaerobic sludge blanket [UASB]) and tertiary treatment systems (open-pond natural attenuation lagoon and air-sparged nitrification-denitrification tank followed by alkaline phosphorus precipitation process) were analyzed. A total of 56,807 and 48,859 high-quality reads were obtained from bacterial and archaeal libraries, respectively. Dominant bacterial communities were associated with the phylum Firmicutes, Bacteroidetes, Proteobacteria, or Actinobacteria. Bacteria and archaea diversity were highest in UASB effluent sample. Escherichia, Lactobacillus, Bacteroides, and/or Prevotella were used as indicators of putative pathogen reduction throughout the WWTPs. Satisfactory pathogen reduction was observed after the open-pond natural attenuation lagoon but not after the air-sparged nitrification/denitrification followed by alkaline phosphorus precipitation treatment processes. Among the archaeal communities, 80% of the reads was related to hydrogeno-trophic methanogens Methanospirillum. Enrichment of hydrogenotrophic methanogens detected in effluent samples from the anaerobic covered lagoons and UASB suggested that CO2 reduction with H2 was the dominant methanogenic pathway in these systems. Overall, the results served to improve our current understanding of major microbial communities' changes downgradient from the pen and throughout swine WWTP as a result of different treatment processes.

Diversity and biogeochemical structuring of bacterial communities across the Porangahau ridge accretionary prism, New Zealand

USGS Publications Warehouse

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

2011-01-01

Sediments from the Porangahau ridge, located off the northeastern coast of New Zealand, were studied to describe bacterial community structure in conjunction with differing biogeochemical regimes across the ridge. Low diversity was observed in sediments from an eroded basin seaward of the ridge and the community was dominated by uncultured members of the Burkholderiales. Chloroflexi/GNS and Deltaproteobacteria were abundant in sediments from a methane seep located landward of the ridge. Gas-charged and organic-rich sediments further landward had the highest overall diversity. Surface sediments, with the exception of those from the basin, were dominated by Rhodobacterales sequences associated with organic matter deposition. Taxa related to the Desulfosarcina/Desulfococcus and the JS1 candidates were highly abundant at the sulfate-methane transition zone (SMTZ) at three sites. To determine how community structure was influenced by terrestrial, pelagic and in situ substrates, sequence data were statistically analyzed against geochemical data (e.g. sulfate, chloride, nitrogen, phosphorous, methane, bulk inorganic and organic carbon pools) using the Biota-Environmental matching procedure. Landward of the ridge, sulfate was among the most significant structuring factors. Seaward of the ridge, silica and ammonium were important structuring factors. Regardless of the transect location, methane was the principal structuring factor on SMTZ communities. FEMS Microbiology Ecology ?? 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. No claim to original US government works.

Biofilm bacterial communities in urban drinking water distribution systems transporting waters with different purification strategies.

PubMed

Wu, Huiting; Zhang, Jingxu; Mi, Zilong; Xie, Shuguang; Chen, Chao; Zhang, Xiaojian

2015-02-01

Biofilm formation in drinking water distribution systems (DWDS) has many adverse consequences. Knowledge of microbial community structure of DWDS biofilm can aid in the design of an effective control strategy. However, biofilm bacterial community in real DWDS and the impact of drinking water purification strategy remain unclear. The present study investigated the composition and diversity of biofilm bacterial community in real DWDSs transporting waters with different purification strategies (conventional treatment and integrated treatment). High-throughput Illumina MiSeq sequencing analysis illustrated a large shift in the diversity and structure of biofilm bacterial community in real DWDS. Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Nitrospirae, and Cyanobacteria were the major components of biofilm bacterial community. Proteobacteria (mainly Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria) predominated in each DWDS biofilm, but the compositions of the dominant proteobacterial classes and genera and their proportions varied among biofilm samples. Drinking water purification strategy could shape DWDS biofilm bacterial community. Moreover, Pearson's correlation analysis indicated that Actinobacteria was positively correlated with the levels of total alkalinity and dissolved organic carbon in tap water, while Firmicutes had a significant positive correlation with nitrite nitrogen.

Plants of the fynbos biome harbour host species-specific bacterial communities.

PubMed

Miyambo, Tsakani; Makhalanyane, Thulani P; Cowan, Don A; Valverde, Angel

2016-08-01

The fynbos biome in South Africa is globally recognised as a plant biodiversity hotspot. However, very little is known about the bacterial communities associated with fynbos plants, despite interactions between primary producers and bacteria having an impact on the physiology of both partners and shaping ecosystem diversity. This study reports on the structure, phylogenetic composition and potential roles of the endophytic bacterial communities located in the stems of three fynbos plants (Erepsia anceps, Phaenocoma prolifera and Leucadendron laureolum). Using Illumina MiSeq 16S rRNA sequencing we found that different subpopulations of Deinococcus-Thermus, Alphaproteobacteria, Acidobacteria and Firmicutes dominated the endophytic bacterial communities. Alphaproteobacteria and Actinobacteria were prevalent in P. prolifera, whereas Deinococcus-Thermus dominated in L. laureolum, revealing species-specific host-bacteria associations. Although a high degree of variability in the endophytic bacterial communities within hosts was observed, we also detected a core microbiome across the stems of the three plant species, which accounted for 72% of the sequences. Altogether, it seems that both deterministic and stochastic processes shaped microbial communities. Endophytic bacterial communities harboured putative plant growth-promoting bacteria, thus having the potential to influence host health and growth. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

[Effects of bamboo charcoal on the growth of Trifolium repens and soil bacterial community structure].

PubMed

Li, Song-Hao; He, Dong-Hua; Shen, Qiu-Lan; Xu, Qiu-Fang

2014-08-01

The effects of addition rates (0, 3% and 9%) and particle sizes (0.05, 0.05-1.0 and 1.0-2.0 mm) of bamboo charcoal on the growth of Trifolium repens and soil microbial community structure were investigated. The results showed that bamboo charcoal addition greatly promoted the early growth of T. repens, with the 9% charcoal addition rate being slightly better than the 3% charcoal addition rate. The effects of different particle sizes of bamboo charcoal on the growth of T. repens were not different significantly. Growth promotion declined with time during 120 days after sowing, and disappeared completely after 5 months. DGGE analysis of the bacterial 16S rDNA V3 fragment indicated that bamboo charcoal altered the soil bacterial community structure. The amount and Shannon diversity index of bacteria in the bamboo charcoal addition treatments increased compared with CK. The quantitative analysis showed that the amount of bacteria in the treatment with bamboo charcoal of fine particle (D < 0.05 mm) at the 9% addition rate was significantly higher than in the other treatments. The fine bamboo charcoal had a great effect on soil bacteria amount compared with the charcoal of other sizes at the same addition rate.

Gut bacterial communities across tadpole ecomorphs in two diverse tropical anuran faunas

NASA Astrophysics Data System (ADS)

Vences, Miguel; Lyra, Mariana L.; Kueneman, Jordan G.; Bletz, Molly C.; Archer, Holly M.; Canitz, Julia; Handreck, Svenja; Randrianiaina, Roger-Daniel; Struck, Ulrich; Bhuju, Sabin; Jarek, Michael; Geffers, Robert; McKenzie, Valerie J.; Tebbe, Christoph C.; Haddad, Célio F. B.; Glos, Julian

2016-04-01

Animal-associated microbial communities can play major roles in the physiology, development, ecology, and evolution of their hosts, but the study of their diversity has yet focused on a limited number of host species. In this study, we used high-throughput sequencing of partial sequences of the bacterial 16S rRNA gene to assess the diversity of the gut-inhabiting bacterial communities of 212 specimens of tropical anuran amphibians from Brazil and Madagascar. The core gut-associated bacterial communities among tadpoles from two different continents strongly overlapped, with eight highly represented operational taxonomic units (OTUs) in common. In contrast, the core communities of adults and tadpoles from Brazil were less similar with only one shared OTU. This suggests a community turnover at metamorphosis. Bacterial diversity was higher in tadpoles compared to adults. Distinct differences in composition and diversity occurred among gut bacterial communities of conspecific tadpoles from different water bodies and after experimental fasting for 8 days, demonstrating the influence of both environmental factors and food on the community structure. Communities from syntopic tadpoles clustered by host species both in Madagascar and Brazil, and the Malagasy tadpoles also had species-specific isotope signatures. We recommend future studies to analyze the turnover of anuran gut bacterial communities at metamorphosis, compare the tadpole core communities with those of other aquatic organisms, and assess the possible function of the gut microbiota as a reservoir for protective bacteria on the amphibian skin.

Changes in assembly processes in soil bacterial communities following a wildfire disturbance.

PubMed

Ferrenberg, Scott; O'Neill, Sean P; Knelman, Joseph E; Todd, Bryan; Duggan, Sam; Bradley, Daniel; Robinson, Taylor; Schmidt, Steven K; Townsend, Alan R; Williams, Mark W; Cleveland, Cory C; Melbourne, Brett A; Jiang, Lin; Nemergut, Diana R

2013-06-01

Although recent work has shown that both deterministic and stochastic processes are important in structuring microbial communities, the factors that affect the relative contributions of niche and neutral processes are poorly understood. The macrobiological literature indicates that ecological disturbances can influence assembly processes. Thus, we sampled bacterial communities at 4 and 16 weeks following a wildfire and used null deviation analysis to examine the role that time since disturbance has in community assembly. Fire dramatically altered bacterial community structure and diversity as well as soil chemistry for both time-points. Community structure shifted between 4 and 16 weeks for both burned and unburned communities. Community assembly in burned sites 4 weeks after fire was significantly more stochastic than in unburned sites. After 16 weeks, however, burned communities were significantly less stochastic than unburned communities. Thus, we propose a three-phase model featuring shifts in the relative importance of niche and neutral processes as a function of time since disturbance. Because neutral processes are characterized by a decoupling between environmental parameters and community structure, we hypothesize that a better understanding of community assembly may be important in determining where and when detailed studies of community composition are valuable for predicting ecosystem function.

Changes in assembly processes in soil bacterial communities following a wildfire disturbance

PubMed Central

Ferrenberg, Scott; O'Neill, Sean P; Knelman, Joseph E; Todd, Bryan; Duggan, Sam; Bradley, Daniel; Robinson, Taylor; Schmidt, Steven K; Townsend, Alan R; Williams, Mark W; Cleveland, Cory C; Melbourne, Brett A; Jiang, Lin; Nemergut, Diana R

2013-01-01

Although recent work has shown that both deterministic and stochastic processes are important in structuring microbial communities, the factors that affect the relative contributions of niche and neutral processes are poorly understood. The macrobiological literature indicates that ecological disturbances can influence assembly processes. Thus, we sampled bacterial communities at 4 and 16 weeks following a wildfire and used null deviation analysis to examine the role that time since disturbance has in community assembly. Fire dramatically altered bacterial community structure and diversity as well as soil chemistry for both time-points. Community structure shifted between 4 and 16 weeks for both burned and unburned communities. Community assembly in burned sites 4 weeks after fire was significantly more stochastic than in unburned sites. After 16 weeks, however, burned communities were significantly less stochastic than unburned communities. Thus, we propose a three-phase model featuring shifts in the relative importance of niche and neutral processes as a function of time since disturbance. Because neutral processes are characterized by a decoupling between environmental parameters and community structure, we hypothesize that a better understanding of community assembly may be important in determining where and when detailed studies of community composition are valuable for predicting ecosystem function. PMID:23407312

Interspecific variation of the bacterial community structure in the phyllosphere of the three major plant components of mangrove forests

PubMed Central

Dias, Armando Cavalcante Franco; Taketani, Rodrigo Gouveia; Andreote, Fernando Dini; Luvizotto, Danice Mazzer; da Silva, João Luis; Nascimento, Rosely dos Santos; de Melo, Itamar Soares

2012-01-01

Mangrove forests encompass a group of trees species that inhabit the intertidal zones, where soil is characterized by the high salinity and low availability of oxygen. The phyllosphere of these trees represent the habitat provided on the aboveground parts of plants, supporting in a global scale, a large and complex microbial community. The structure of phyllosphere communities reflects immigration, survival and growth of microbial colonizers, which is influenced by numerous environmental factors in addition to leaf physical and chemical properties. Here, a combination of culture-base methods with PCR-DGGE was applied to test whether local or plant specific factors shape the bacterial community of the phyllosphere from three plant species (Avicenia shaueriana, Laguncularia racemosa and Rhizophora mangle), found in two mangroves. The number of bacteria in the phyllosphere of these plants varied between 3.62 x 104 in A. schaeriana and 6.26 x 103 in R. mangle. The results obtained by PCR-DGGE and isolation approaches were congruent and demonstrated that each plant species harbor specific bacterial communities in their leaves surfaces. Moreover, the ordination of environmental factors (mangrove and plant species), by redundancy analysis (RDA), also indicated that the selection exerted by plant species is higher than mangrove location on bacterial communities at phyllosphere. PMID:24031877

Interspecific variation of the bacterial community structure in the phyllosphere of the three major plant components of mangrove forests.

PubMed

Dias, Armando Cavalcante Franco; Taketani, Rodrigo Gouveia; Andreote, Fernando Dini; Luvizotto, Danice Mazzer; da Silva, João Luis; Nascimento, Rosely Dos Santos; de Melo, Itamar Soares

2012-04-01

Mangrove forests encompass a group of trees species that inhabit the intertidal zones, where soil is characterized by the high salinity and low availability of oxygen. The phyllosphere of these trees represent the habitat provided on the aboveground parts of plants, supporting in a global scale, a large and complex microbial community. The structure of phyllosphere communities reflects immigration, survival and growth of microbial colonizers, which is influenced by numerous environmental factors in addition to leaf physical and chemical properties. Here, a combination of culture-base methods with PCR-DGGE was applied to test whether local or plant specific factors shape the bacterial community of the phyllosphere from three plant species (Avicenia shaueriana, Laguncularia racemosa and Rhizophora mangle), found in two mangroves. The number of bacteria in the phyllosphere of these plants varied between 3.62 x 10(4) in A. schaeriana and 6.26 x 10(3) in R. mangle. The results obtained by PCR-DGGE and isolation approaches were congruent and demonstrated that each plant species harbor specific bacterial communities in their leaves surfaces. Moreover, the ordination of environmental factors (mangrove and plant species), by redundancy analysis (RDA), also indicated that the selection exerted by plant species is higher than mangrove location on bacterial communities at phyllosphere.

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

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.

Impact of oxytetracycline and bacterial bioaugmentation on the efficiency and microbial community structure of a pesticide-degrading biomixture.

PubMed

Castro-Gutiérrez, Víctor; Masís-Mora, Mario; Carazo-Rojas, Elizabeth; Mora-López, Marielos; Rodríguez-Rodríguez, Carlos E

2018-04-01

An experimental study evaluating the effect of bioaugmentation and antibiotic (oxytetracycline) application on pesticide degradation and microbial community structure of a biomixture used in a biopurification system (BPR) was conducted. The bioaugmentation employed a carbofuran-degrading bacterial consortium. The non-bioaugmented biomixture showed excellent performance for removal of atrazine (t 1/2 : 9.9 days), carbendazim (t 1/2 : 3.0 days), carbofuran (t 1/2 : 2.8 days), and metalaxyl (t 1/2 : 2.7 days). Neither the addition of oxytetracycline nor bioaugmentation affected the efficiency of pesticide removal or microbial community (bacterial and fungal) structure, as determined by DGGE analysis. Instead, biomixture aging was mainly responsible for microbial population shifts. Even though the bioaugmentation did not enhance the biomixtures' performance, this matrix showed a high capability to sustain initial stresses related to antibiotic addition; therefore, simultaneous elimination of this particular mixture of pesticides together with oxytetracycline residues is not discouraged.

Terrestrial origin of bacterial communities in complex boreal freshwater networks.

PubMed

Ruiz-González, Clara; Niño-García, Juan Pablo; Del Giorgio, Paul A

2015-08-25

Bacteria inhabiting boreal freshwaters are part of metacommunities where local assemblages are often linked by the flow of water in the landscape, yet the resulting spatial structure and the boundaries of the network metacommunity have never been explored. Here, we reconstruct the spatial structure of the bacterial metacommunity in a complex boreal aquatic network by determining the taxonomic composition of bacterial communities along the entire terrestrial/aquatic continuum, including soil and soilwaters, headwater streams, large rivers and lakes. We show that the network metacommunity has a directional spatial structure driven by a common terrestrial origin of aquatic communities, which are numerically dominated by taxa recruited from soils. Local community assembly is driven by variations along the hydrological continuum in the balance between mass effects and species sorting of terrestrial taxa, and seems further influenced by priority effects related to the spatial sequence of entry of soil bacteria into the network. © 2015 John Wiley & Sons Ltd/CNRS.

Diazotrophic potential among bacterial communities associated with wild and cultivated Agave species.

PubMed

Desgarennes, Damaris; Garrido, Etzel; Torres-Gomez, Miryam J; Peña-Cabriales, Juan J; Partida-Martinez, Laila P

2014-12-01

Agaves are major biotic resources in arid and semi-arid ecosystems. Despite their ecological, economical and cultural relevance, many aspects of the microbial communities associated with agaves are still unknown. Here, we investigated the bacterial communities associated with two Agave species by 16S rRNA- Denaturing gradient gel electrophoresis fingerprinting and sequencing. We also evaluated the effects of biotic and abiotic factors in the structure of the bacterial communities. In parallel, we isolated and characterized diazotrophic bacteria associated with agaves, as Agave soils are characterized by their low nitrogen content. Our results demonstrate that in Agave, the structure of prokaryotic assemblages was mostly influenced by the community group, where the soil, episphere, and endosphere were clearly distinct. Proteobacteria (γ and α), Actinobacteria, and Acidobacteria were the dominant phyla. Bacterial communities in the episphere of agaves were mainly influenced by the host species, whereas in the endosphere were affected by the season. Fifteen bacterial taxa were common and abundant in the endosphere of both Agave species during the dry season. Notably, some of the confirmed diazotrophic strains belonged to this group, suggesting a possible beneficial role in planta. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Pyrosequencing analysis of the bacterial community in drinking water wells.

PubMed

Navarro-Noya, Yendi E; Suárez-Arriaga, Mayra C; Rojas-Valdes, Aketzally; Montoya-Ciriaco, Nina M; Gómez-Acata, Selene; Fernández-Luqueño, Fabián; Dendooven, Luc

2013-07-01

Wells used for drinking water often have a large biomass and a high bacterial diversity. Current technologies are not always able to reduce the bacterial population, and the threat of pathogen proliferation in drinking water sources is omnipresent. The environmental conditions that shape the microbial communities in drinking water sources have to be elucidated, so that pathogen proliferation can be foreseen. In this work, the bacterial community in nine water wells of a groundwater aquifer in Northern Mexico were characterized and correlated to environmental characteristics that might control them. Although a large variation was observed between the water samples, temperature and iron concentration were the characteristics that affected the bacterial community structure and composition in groundwater wells. Small increases in the concentration of iron in water modified the bacterial communities and promoted the growth of the iron-oxidizing bacteria Acidovorax. The abundance of the genera Flavobacterium and Duganella was correlated positively with temperature and the Acidobacteria Gp4 and Gp1, and the genus Acidovorax with iron concentrations in the well water. Large percentages of Flavobacterium and Pseudomonas bacteria were found, and this is of special concern as bacteria belonging to both genera are often biofilm developers, where pathogens survival increases.

Comparative molecular analysis of chemolithoautotrophic bacterial diversity and community structure from coastal saline soils, Gujarat, India

PubMed Central

2012-01-01

Background Soils harbour high diversity of obligate as well as facultative chemolithoautotrophic bacteria that contribute significantly to CO2 dynamics in soil. In this study, we used culture dependent and independent methods to assess the community structure and diversity of chemolithoautotrophs in agricultural and coastal barren saline soils (low and high salinity). We studied the composition and distribution of chemolithoautotrophs by means of functional marker gene cbbL encoding large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase and a phylogenetic marker 16S rRNA gene. The cbbL form IA and IC genes associated with carbon fixation were analyzed to gain insight into metabolic potential of chemolithoautotrophs in three soil types of coastal ecosystems which had a very different salt load and sulphur content. Results In cbbL libraries, the cbbL form IA was retrieved only from high saline soil whereas form IC was found in all three soil types. The form IC cbbL was also amplified from bacterial isolates obtained from all soil types. A number of novel monophyletic lineages affiliated with form IA and IC phylogenetic trees were found. These were distantly related to the known cbbL sequences from agroecosystem, volcanic ashes and marine environments. In 16S rRNA clone libraries, the agricultural soil was dominated by chemolithoautotrophs (Betaproteobacteria) whereas photoautotrophic Chloroflexi and sulphide oxidizers dominated saline ecosystems. Environmental specificity was apparently visible at both higher taxonomic levels (phylum) and lower taxonomic levels (genus and species). The differentiation in community structure and diversity in three soil ecosystems was supported by LIBSHUFF (P = 0.001) and UniFrac. Conclusion This study may provide fundamentally new insights into the role of chemolithoautotrophic and photoautotrophic bacterial diversity in biochemical carbon cycling in barren saline soils. The bacterial communities varied greatly among the

The dynamic bacterial communities of a melting High Arctic glacier snowpack

PubMed Central

Hell, Katherina; Edwards, Arwyn; Zarsky, Jakub; Podmirseg, Sabine M; Girdwood, Susan; Pachebat, Justin A; Insam, Heribert; Sattler, Birgit

2013-01-01

Snow environments can occupy over a third of land surface area, but little is known about the dynamics of snowpack bacteria. The effect of snow melt on bacterial community structure and diversity of surface environments of a Svalbard glacier was examined using analyses of 16S rRNA genes via T-RFLP, qPCR and 454 pyrosequencing. Distinct community structures were found in different habitat types, with changes over 1 week apparent, in particular for the dominant bacterial class present, Betaproteobacteria. The differences observed were consistent with influences from depositional mode (snowfall vs aeolian dusts), contrasting snow with dust-rich snow layers and near-surface ice. Contrary to that, slush as the decompositional product of snow harboured distinct lineages of bacteria, further implying post-depositional changes in community structure. Taxa affiliated to the betaproteobacterial genus Polaromonas were particularly dynamic, and evidence for the presence of betaproteobacterial ammonia-oxidizing bacteria was uncovered, inviting the prospect that the dynamic bacterial communities associated with snowpacks may be active in supraglacial nitrogen cycling and capable of rapid responses to changes induced by snowmelt. Furthermore the potential of supraglacial snowpack ecosystems to respond to transient yet spatially extensive melting episodes such as that observed across most of Greenland's ice sheet in 2012 merits further investigation. PMID:23552623

The dynamic bacterial communities of a melting High Arctic glacier snowpack.

PubMed

Hell, Katherina; Edwards, Arwyn; Zarsky, Jakub; Podmirseg, Sabine M; Girdwood, Susan; Pachebat, Justin A; Insam, Heribert; Sattler, Birgit

2013-09-01

Snow environments can occupy over a third of land surface area, but little is known about the dynamics of snowpack bacteria. The effect of snow melt on bacterial community structure and diversity of surface environments of a Svalbard glacier was examined using analyses of 16S rRNA genes via T-RFLP, qPCR and 454 pyrosequencing. Distinct community structures were found in different habitat types, with changes over 1 week apparent, in particular for the dominant bacterial class present, Betaproteobacteria. The differences observed were consistent with influences from depositional mode (snowfall vs aeolian dusts), contrasting snow with dust-rich snow layers and near-surface ice. Contrary to that, slush as the decompositional product of snow harboured distinct lineages of bacteria, further implying post-depositional changes in community structure. Taxa affiliated to the betaproteobacterial genus Polaromonas were particularly dynamic, and evidence for the presence of betaproteobacterial ammonia-oxidizing bacteria was uncovered, inviting the prospect that the dynamic bacterial communities associated with snowpacks may be active in supraglacial nitrogen cycling and capable of rapid responses to changes induced by snowmelt. Furthermore the potential of supraglacial snowpack ecosystems to respond to transient yet spatially extensive melting episodes such as that observed across most of Greenland's ice sheet in 2012 merits further investigation.

Phyllosphere Bacterial Community of Floating Macrophytes in Paddy Soil Environments as Revealed by Illumina High-Throughput Sequencing

PubMed Central

Xie, Wan-Ying

2014-01-01

The phyllosphere of floating macrophytes in paddy soil ecosystems, a unique habitat, may support large microbial communities but remains largely unknown. We took Wolffia australiana as a representative floating plant and investigated its phyllosphere bacterial community and the underlying driving forces of community modulation in paddy soil ecosystems using Illumina HiSeq 2000 platform-based 16S rRNA gene sequence analysis. The results showed that the phyllosphere of W. australiana harbored considerably rich communities of bacteria, with Proteobacteria and Bacteroidetes as the predominant phyla. The core microbiome in the phyllosphere contained genera such as Acidovorax, Asticcacaulis, Methylibium, and Methylophilus. Complexity of the phyllosphere bacterial communities in terms of class number and α-diversity was reduced compared to those in corresponding water and soil. Furthermore, the bacterial communities exhibited structures significantly different from those in water and soil. These findings and the following redundancy analysis (RDA) suggest that species sorting played an important role in the recruitment of bacterial species in the phyllosphere. The compositional structures of the phyllosphere bacterial communities were modulated predominantly by water physicochemical properties, while the initial soil bacterial communities had limited impact. Taken together, the findings from this study reveal the diversity and uniqueness of the phyllosphere bacterial communities associated with the floating macrophytes in paddy soil environments. PMID:25362067

Plant-plant competition outcomes are modulated by plant effects on the soil bacterial community.

PubMed

Hortal, S; Lozano, Y M; Bastida, F; Armas, C; Moreno, J L; Garcia, C; Pugnaire, F I

2017-12-19

Competition is a key process that determines plant community structure and dynamics, often mediated by nutrients and water availability. However, the role of soil microorganisms on plant competition, and the links between above- and belowground processes, are not well understood. Here we show that the effects of interspecific plant competition on plant performance are mediated by feedbacks between plants and soil bacterial communities. Each plant species selects a singular community of soil microorganisms in its rhizosphere with a specific species composition, abundance and activity. When two plant species interact, the resulting soil bacterial community matches that of the most competitive plant species, suggesting strong competitive interactions between soil bacterial communities as well. We propose a novel mechanism by which changes in belowground bacterial communities promoted by the most competitive plant species influence plant performance and competition outcome. These findings emphasise the strong links between plant and soil communities, paving the way to a better understanding of plant community dynamics and the effects of soil bacterial communities on ecosystem functioning and services.

Consistent effects of nitrogen fertilization on soil bacterial communities in black soils for two crop seasons in China.

PubMed

Zhou, Jing; Jiang, Xin; Wei, Dan; Zhao, Baisuo; Ma, Mingchao; Chen, Sanfeng; Cao, Fengming; Shen, Delong; Guan, Dawei; Li, Jun

2017-06-12

Long-term use of inorganic nitrogen (N) fertilization has greatly influenced the bacterial community in black soil of northeast China. It is unclear how N affects the bacterial community in two successive crop seasons in the same field for this soil type. We sampled soils from a long-term fertilizer experimental field in Harbin city with three N gradients. We applied sequencing and quantitative PCR targeting at the 16S rRNA gene to examine shifts in bacterial communities and test consistent shifts and driving-factors bacterial responses to elevated N additions. N addition decreased soil pH and bacterial 16S rDNA copy numbers, and increased soil N and crop yield. N addition consistently decreased bacterial diversity and altered bacterial community composition, by increasing the relative abundance of Proteobacteria, and decreasing that of Acidobacteria and Nitrospirae in both seasons. Consistent changes in the abundant classes and genera, and the structure of the bacterial communities across both seasons were observed. Our results suggest that increases in N inputs had consistent effects on the richness, diversity and composition of soil bacterial communities across the crop seasons in two continuous years, and the N addition and the subsequent edaphic changes were important factors in shaping bacterial community structures.

Dynamic changes of bacterial community under bioremediation with Sphingobium sp. LY-6 in buprofezin-contaminated soil.

PubMed

Liu, Yuan; Hou, Qianqian; Liu, Wanru; Meng, Yawen; Wang, Guangli

2015-08-01

Buprofezin is a commonly used chemical with satisfactory biological activity against sucking insect pests, but its disposal can cause serious environmental problems. To study the feasibility of remedying contamination by buprofezin, microcosm experiments were carried out to study the effects of various concentrations of buprofezin and Sphingobium sp. LY-6 on soil bacterial communities in soils collected from vegetable fields. In this experiment, the results showed that buprofezin was effectively degraded by Sphingobium sp. LY-6 in incubation soils. Comparing to non-incubated soils, the cumulative degradation ratio of buprofezin was significantly increased, up to the extent of 85 and 51%, in the initial concentration of 10 and 100 mg kg(-1). The abundance and community structure of the bacterial communities were analysed by real-time PCR (qPCR) and terminal-restriction fragment length polymorphism (T-RFLP). The findings suggest that buprofezin had a negative effect on soil bacterial community, and decreases in bacterial abundance were observed in the later part of the incubation period. The bacterial community structure and diversity shifted significantly at each sampling time. In conclusion, the buprofezin-degrading strain LY-6 played a major role in the bioremediation of the buprofezin-contaminated soil and influenced the dynamics and structure of the bacterial community, demonstrating the great potential of exogenous microorganisms for soil remediation.

Assessing the impact of fungicide enostroburin application on bacterial community in wheat phyllosphere.

PubMed

Gu, Likun; Bai, Zhihui; Jin, Bo; Hu, Qing; Wang, Huili; Zhuang, Guoqiang; Zhang, Hongxun

2010-01-01

Fungicides have been used extensively for controlling fungal pathogens of plants. However, little is known regarding the effects that fungicides upon the indigenous bacterial communities within the plant phyllosphere. The aims of this study were to assess the impact of fungicide enostroburin upon bacterial communities in wheat phyllosphere. Culture-independent methodologies of 16S rDNA clone library and 16S rDNA directed polymerase chain reaction with denaturing gradient gel electrophoresis (PCR-DGGE) were used for monitoring the change of bacterial community. The 16S rDNA clone library and PCR-DGGE analysis both confirmed the microbial community of wheat plant phyllosphere were predominantly of the gamma-Proteobacteria phyla. Results from PCR-DGGE analysis indicated a significant change in bacterial community structure within the phyllosphere following fungicide enostroburin application. Bands sequenced within control cultures were predominantly of Pseudomonas genus, but those bands sequenced in the treated samples were predominantly strains of Pantoea genus and Pseudomonas genus. Of interest was the appearance of two DGGE bands following fungicide treatment, one of which had sequence similarities (98%) to Pantoea sp. which might be a competitor of plant pathogens. This study revealed the wheat phyllosphere bacterial community composition and a shift in the bacterial community following fungicide enostroburin application.

Consistent changes in the taxonomic structure and functional attributes of bacterial communities during primary succession.

PubMed

Ortiz-Álvarez, Rüdiger; Fierer, Noah; de Los Ríos, Asunción; Casamayor, Emilio O; Barberán, Albert

2018-02-20

Ecologists have long studied primary succession, the changes that occur in biological communities after initial colonization of an environment. Most of this work has focused on succession in plant communities, laying the conceptual foundation for much of what we currently know about community assembly patterns over time. Because of their prevalence and importance in ecosystems, an increasing number of studies have focused on microbial community dynamics during succession. Here, we conducted a meta-analysis of bacterial primary succession patterns across a range of distinct habitats, including the infant gut, plant surfaces, soil chronosequences, and aquatic environments, to determine whether consistent changes in bacterial diversity, community composition, and functional traits are evident over the course of succession. Although these distinct habitats harbor unique bacterial communities, we were able to identify patterns in community assembly that were shared across habitat types. We found an increase in taxonomic and functional diversity with time while the taxonomic composition and functional profiles of communities became less variable (lower beta diversity) in late successional stages. In addition, we found consistent decreases in the rRNA operon copy number and in the high-efficient phosphate assimilation process (Pst system) suggesting that reductions in resource availability during succession select for taxa adapted to low-resource conditions. Together, these results highlight that, like many plant communities, microbial communities also exhibit predictable patterns during primary succession.

Dietary and developmental shifts in butterfly-associated bacterial communities

PubMed Central

2018-01-01

Bacterial communities associated with insects can substantially influence host ecology, evolution and behaviour. Host diet is a key factor that shapes bacterial communities, but the impact of dietary transitions across insect development is poorly understood. We analysed bacterial communities of 12 butterfly species across different developmental stages, using amplicon sequencing of the 16S rRNA gene. Butterfly larvae typically consume leaves of a single host plant, whereas adults are more generalist nectar feeders. Thus, we expected bacterial communities to vary substantially across butterfly development. Surprisingly, only few species showed significant dietary and developmental transitions in bacterial communities, suggesting weak impacts of dietary transitions across butterfly development. On the other hand, bacterial communities were strongly influenced by butterfly species and family identity, potentially due to dietary and physiological variation across the host phylogeny. Larvae of most butterfly species largely mirrored bacterial community composition of their diets, suggesting passive acquisition rather than active selection. Overall, our results suggest that although butterflies harbour distinct microbiomes across taxonomic groups and dietary guilds, the dramatic dietary shifts that occur during development do not impose strong selection to maintain distinct bacterial communities across all butterfly hosts. PMID:29892359

Bacterial Community Dynamics in Full-Scale Activated Sludge Bioreactors: Operational and Ecological Factors Driving Community Assembly and Performance

PubMed Central

Valentín-Vargas, Alexis; Toro-Labrador, Gladys; Massol-Deyá, Arturo A.

2012-01-01

The assembling of bacterial communities in conventional activated sludge (CAS) bioreactors was thought, until recently, to be chaotic and mostly unpredictable. Studies done over the last decade have shown that specific, and often, predictable random and non-random factors could be responsible for that process. These studies have also motivated a “structure–function” paradigm that is yet to be resolved. Thus, elucidating the factors that affect community assembly in the bioreactors is necessary for predicting fluctuations in community structure and function. For this study activated sludge samples were collected during a one-year period from two geographically distant CAS bioreactors of different size. Combining community fingerprinting analysis and operational parameters data with a robust statistical analysis, we aimed to identify relevant links between system performance and bacterial community diversity and dynamics. In addition to revealing a significant β-diversity between the bioreactors’ communities, results showed that the largest bioreactor had a less dynamic but more efficient and diverse bacterial community throughout the study. The statistical analysis also suggests that deterministic factors, as opposed to stochastic factors, may have a bigger impact on the community structure in the largest bioreactor. Furthermore, the community seems to rely mainly on mechanisms of resistance and functional redundancy to maintain functional stability. We suggest that the ecological theories behind the Island Biogeography model and the species-area relationship were appropriate to predict the assembly of bacterial communities in these CAS bioreactors. These results are of great importance for engineers and ecologists as they reveal critical aspects of CAS systems that could be applied towards improving bioreactor design and operation. PMID:22880016

Local Environmental Factors Drive Divergent Grassland Soil Bacterial Communities in the Western Swiss Alps

PubMed Central

Pinto-Figueroa, Eric; Buri, Aline; Spangenberg, Jorge E.; Adatte, Thierry; Guisan, Antoine; van der Meer, Jan Roelof

2016-01-01

ABSTRACT Mountain ecosystems are characterized by a diverse range of climatic and topographic conditions over short distances and are known to shelter a high biodiversity. Despite important progress, still little is known on bacterial diversity in mountain areas. Here, we investigated soil bacterial biogeography at more than 100 sampling sites randomly stratified across a 700-km2 area with 2,200-m elevation gradient in the western Swiss Alps. Bacterial grassland communities were highly diverse, with 12,741 total operational taxonomic units (OTUs) across 100 sites and an average of 2,918 OTUs per site. Bacterial community structure was correlated with local climatic, topographic, and soil physicochemical parameters with high statistical significance. We found pH (correlated with % CaO and % mineral carbon), hydrogen index (correlated with bulk gravimetric water content), and annual average number of frost days during the growing season to be among the groups of the most important environmental drivers of bacterial community structure. In contrast, bacterial community structure was only weakly stratified as a function of elevation. Contrasting patterns were discovered for individual bacterial taxa. Acidobacteria responded both positively and negatively to pH extremes. Various families within the Bacteroidetes responded to available phosphorus levels. Different verrucomicrobial groups responded to electrical conductivity, total organic carbon, water content, and mineral carbon contents. Alpine grassland bacterial communities are thus highly diverse, which is likely due to the large variety of different environmental conditions. These results shed new light on the biodiversity of mountain ecosystems, which were already identified as potentially fragile to anthropogenic influences and climate change. IMPORTANCE This article addresses the question of how microbial communities in alpine regions are dependent on local climatic and soil physicochemical variables. We benefit

Local Environmental Factors Drive Divergent Grassland Soil Bacterial Communities in the Western Swiss Alps.

PubMed

Yashiro, Erika; Pinto-Figueroa, Eric; Buri, Aline; Spangenberg, Jorge E; Adatte, Thierry; Niculita-Hirzel, Hélène; Guisan, Antoine; van der Meer, Jan Roelof

2016-11-01

Mountain ecosystems are characterized by a diverse range of climatic and topographic conditions over short distances and are known to shelter a high biodiversity. Despite important progress, still little is known on bacterial diversity in mountain areas. Here, we investigated soil bacterial biogeography at more than 100 sampling sites randomly stratified across a 700-km 2 area with 2,200-m elevation gradient in the western Swiss Alps. Bacterial grassland communities were highly diverse, with 12,741 total operational taxonomic units (OTUs) across 100 sites and an average of 2,918 OTUs per site. Bacterial community structure was correlated with local climatic, topographic, and soil physicochemical parameters with high statistical significance. We found pH (correlated with % CaO and % mineral carbon), hydrogen index (correlated with bulk gravimetric water content), and annual average number of frost days during the growing season to be among the groups of the most important environmental drivers of bacterial community structure. In contrast, bacterial community structure was only weakly stratified as a function of elevation. Contrasting patterns were discovered for individual bacterial taxa. Acidobacteria responded both positively and negatively to pH extremes. Various families within the Bacteroidetes responded to available phosphorus levels. Different verrucomicrobial groups responded to electrical conductivity, total organic carbon, water content, and mineral carbon contents. Alpine grassland bacterial communities are thus highly diverse, which is likely due to the large variety of different environmental conditions. These results shed new light on the biodiversity of mountain ecosystems, which were already identified as potentially fragile to anthropogenic influences and climate change. This article addresses the question of how microbial communities in alpine regions are dependent on local climatic and soil physicochemical variables. We benefit from a unique 700

Sulfamethoxazole and COD increase abundance of sulfonamide resistance genes and change bacterial community structures within sequencing batch reactors.

PubMed

Guo, Xueping; Pang, Weihai; Dou, Chunling; Yin, Daqiang

2017-05-01

The abundant microbial community in biological treatment processes in wastewater treatment plants (WWTPs) may potentially enhance the horizontal gene transfer of antibiotic resistance genes with the presence of antibiotics. A lab-scale sequencing batch reactor was designed to investigate response of sulfonamide resistance genes (sulI, sulII) and bacterial communities to various concentrations of sulfamethoxazole (SMX) and chemical oxygen demand (COD) of wastewater. The SMX concentrations (0.001 mg/L, 0.1 mg/L and 10 mg/L) decreased with treatment time and higher SMX level was more difficult to remove. The presence of SMX also significantly reduced the removal efficiency of ammonia nitrogen, affecting the normal function of WWTPs. All three concentrations of SMX raised both sulI and sulII genes with higher concentrations exhibiting greater increases. The abundance of sul genes was positive correlated with treatment time and followed the second-order reaction kinetic model. Interestingly, these two genes have rather similar activity. SulI and sulII gene abundance also performed similar response to COD. Simpson index and Shannon-Weiner index did not show changes in the microbial community diversity. However, the 16S rRNA gene cloning and sequencing results showed the bacterial community structures varied during different stages. The results demonstrated that influent antibiotics into WWTPs may facilitate selection of ARGs and affect the wastewater conventional treatment as well as the bacteria community structures. Copyright © 2017 Elsevier Ltd. All rights reserved.

Bacterial community and arsenic functional genes diversity in arsenic contaminated soils from different geographic locations

PubMed Central

Gu, Yunfu; D. Van Nostrand, Joy; Wu, Liyou; He, Zhili; Qin, Yujia; Zhao, Fang-Jie; Zhou, Jizhong

2017-01-01

To understand how soil microbial communities and arsenic (As) functional genes respond to soil arsenic (As) contamination, five soils contaminated with As at different levels were collected from diverse geographic locations, incubated for 54 days under flooded conditions, and examined by both MiSeq sequencing of 16S rRNA gene amplicons and functional gene microarray (GeoChip 4.0). The results showed that both bacterial community structure and As functional gene structure differed among geographical locations. The diversity of As functional genes correlated positively with the diversity of 16S rRNA genes (P< 0.05). Higher diversities of As functional genes and 16S rRNA genes were observed in the soils with higher available As. Soil pH, phosphate-extractable As, and amorphous Fe content were the most important factors in shaping the bacterial community structure and As transformation functional genes. Geographic location was also important in controlling both the bacterial community and As transformation functional potential. These findings provide insights into the variation of As transformation functional genes in soils contaminated with different levels of As at different geographic locations, and the impact of environmental As contamination on the soil bacterial community. PMID:28475654

Community structure of the metabolically active rumen bacterial and archaeal communities of dairy cows over the transition period

PubMed Central

Zhu, Zhigang; Noel, Samantha Joan; Difford, Gareth Frank; Al-Soud, Waleed Abu; Brejnrod, Asker; Sørensen, Søren Johannes; Lassen, Jan; Løvendahl, Peter; Højberg, Ole

2017-01-01

Dairy cows experience dramatic changes in host physiology from gestation to lactation period and dietary switch from high-forage prepartum diet to high-concentrate postpartum diet over the transition period (parturition +/- three weeks). Understanding the community structure and activity of the rumen microbiota and its associative patterns over the transition period may provide insight for e.g. improving animal health and production. In the present study, rumen samples from ten primiparous Holstein dairy cows were collected over seven weeks spanning the transition period. Total RNA was extracted from the rumen samples and cDNA thereof was subsequently used for characterizing the metabolically active bacterial (16S rRNA transcript amplicon sequencing) and archaeal (qPCR, T-RFLP and mcrA and 16S rRNA transcript amplicon sequencing) communities. The metabolically active bacterial community was dominated by three phyla, showing significant changes in relative abundance range over the transition period: Firmicutes (from prepartum 57% to postpartum 35%), Bacteroidetes (from prepartum 22% to postpartum 18%) and Proteobacteria (from prepartum 7% to postpartum 32%). For the archaea, qPCR analysis of 16S rRNA transcript number, revealed a significant prepartum to postpartum increase in Methanobacteriales, in accordance with an observed increase (from prepartum 80% to postpartum 89%) in relative abundance of 16S rRNA transcript amplicons allocated to this order. On the other hand, a significant prepartum to postpartum decrease (from 15% to 2%) was observed in relative abundance of Methanomassiliicoccales 16S rRNA transcripts. In contrast to qPCR analysis of the 16S rRNA transcripts, quantification of mcrA transcripts revealed no change in total abundance of metabolically active methanogens over the transition period. According to T-RFLP analysis of the mcrA transcripts, two Methanobacteriales genera, Methanobrevibacter and Methanosphaera (represented by the T-RFs 39 and 267

Phyllosphere bacterial community of floating macrophytes in paddy soil environments as revealed by illumina high-throughput sequencing.

PubMed

Xie, Wan-Ying; Su, Jian-Qiang; Zhu, Yong-Guan

2015-01-01

The phyllosphere of floating macrophytes in paddy soil ecosystems, a unique habitat, may support large microbial communities but remains largely unknown. We took Wolffia australiana as a representative floating plant and investigated its phyllosphere bacterial community and the underlying driving forces of community modulation in paddy soil ecosystems using Illumina HiSeq 2000 platform-based 16S rRNA gene sequence analysis. The results showed that the phyllosphere of W. australiana harbored considerably rich communities of bacteria, with Proteobacteria and Bacteroidetes as the predominant phyla. The core microbiome in the phyllosphere contained genera such as Acidovorax, Asticcacaulis, Methylibium, and Methylophilus. Complexity of the phyllosphere bacterial communities in terms of class number and α-diversity was reduced compared to those in corresponding water and soil. Furthermore, the bacterial communities exhibited structures significantly different from those in water and soil. These findings and the following redundancy analysis (RDA) suggest that species sorting played an important role in the recruitment of bacterial species in the phyllosphere. The compositional structures of the phyllosphere bacterial communities were modulated predominantly by water physicochemical properties, while the initial soil bacterial communities had limited impact. Taken together, the findings from this study reveal the diversity and uniqueness of the phyllosphere bacterial communities associated with the floating macrophytes in paddy soil environments. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Quality of Irrigation Water Affects Soil Functionality and Bacterial Community Stability in Response to Heat Disturbance.

PubMed

Frenk, Sammy; Hadar, Yitzhak; Minz, Dror

2018-02-15

Anthropogenic activities alter the structure and function of a bacterial community. Furthermore, bacterial communities structured by the conditions the anthropogenic activities present may consequently reduce their stability in response to an unpredicted acute disturbance. The present mesocosm-scale study exposed soil bacterial communities to different irrigation water types, including freshwater, fertilized freshwater, treated wastewater, and artificial wastewater, and evaluated their response to a disturbance caused by heat. These effectors may be considered deterministic and stochastic forces common in agricultural operations of arid and semiarid regions. Bacterial communities under conditions of high mineral and organic carbon availability (artificial wastewater) differed from the native bacterial community and showed a proteobacterial dominance. These bacterial communities had a lower resistance to the heat treatment disturbance than soils under conditions of low resource availability (high-quality treated wastewater or freshwater). The latter soil bacterial communities showed a higher abundance of operational taxonomic units (OTUs) classified as Bacilli These results were elucidated by soil under conditions of high resource availability, which lost higher degrees of functional potential and had a greater bacterial community composition change. However, the functional resilience, after the disturbance ended, was higher under a condition of high resource availability despite the bacterial community composition shift and the decrease in species richness. The functional resilience was directly connected to the high growth rates of certain Bacteroidetes and proteobacterial groups. A high stability was found in samples that supported the coexistence of both resistant OTUs and fast-growing OTUs. IMPORTANCE This report presents the results of a study employing a hypothesis-based experimental approach to reveal the forces involved in determining the stability of a

Bacterial community shift during the startup of a full-scale oxidation ditch treating sewage.

PubMed

Chen, Yajun; Ye, Lin; Zhao, Fuzheng; Xiao, Lin; Cheng, Shupei; Zhang, Xu-Xiang

2016-10-06

Oxidation ditch (OD) is one of the most widely used processes for treating municipal wastewater. However, the microbial communities in the OD systems have not been well characterized and little information about the shift of bacterial community during the startup process of the OD systems is available. In this study, we investigated the bacterial community changes during the startup period (over 100 days) of a full-scale OD. The results showed that the bacterial community dramatically changed during the startup period. Similar to the activated sludge samples in other studies, Proteobacteria (accounting for 26.3%~48.4%) was the most dominant bacterial phylum in the OD system but its relative abundance declined nearly 40% during the startup process. It was also found that Planctomycetes proliferated greatly (from 4.79% to 13.5%) and finally replaced Bacteroidetes as the second abundant phylum in the OD system. Specifically, some bacteria affiliated with Flavobacterium genus of exhibited remarkable decreasing trends, while bacterial species belonging to OD1 candidate division and Saprospiraceae family were found to increase during the startup process. Despite of the bacterial community shift, the organic matter, nitrogen and phosphorus in the effluent were always in low concentrations, suggesting the functional redundancy of the bacterial community. Moreover, by comparing with the bacterial community in other municipal wastewater treatment bioreactors, some potentially novel bacterial species were found to be present in the OD system. Collectively, this study improved our understandings of bacterial community structure and the microbial ecology during the startup of full-scale wastewater treatment bioreactor.

Bioaugmentation of Hydrogenispora ethanolica LX-B affects hydrogen production through altering indigenous bacterial community structure.

PubMed

Yang, Zhiman; Guo, Rongbo; Shi, Xiaoshuang; He, Shuai; Wang, Lin; Dai, Meng; Qiu, Yanling; Dang, Xiaoxiao

2016-07-01

Bioaugmentation can facilitate hydrogen production from complex organic substrates, but it still is unknown how indigenous microbial communities respond to the added bacteria. Here, using a Hydrogenispora ethanolica LX-B (named as LX-B) bioaugmentation experiments, the distribution of metabolites and the responses of indigenous bacterial communities were investigated via batch cultivation (BC) and repeated batch cultivation (RBC). In BC the LX-B/sludge ratio of 0.12 achieved substantial high hydrogen yield, which was over twice that of control. In RBC one-time bioaugmentation and repeated batch bioaugmentation of LX-B resulted in the hydrogen yield that was average 1.2-fold and 0.8-fold higher than that in control, respectively. This improved hydrogen production performance mainly benefited from a shift in composition of the indigenous bacterial community caused by LX-B bioaugmentation. The findings represented an important step in understanding the relationship between bioaugmentation, a shift in bacterial communities, and altered bioreactor performance. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effect of pine bark on the biotransformation of trinitrotoluene and on the bacterial community structure in a batch experiment.

PubMed

Chusova, Olga; Nolvak, Hiie; Nehrenheim, Emma; Truu, Jaak; Odlare, Monica; Oopkaup, Kristjan; Truu, Marika

2014-01-01

Pine bark, a low-cost industrial residue, has been suggested as a promising substitute for granular activated carbon in the on-site treatment of water contaminated with 2,4,6-trinitrotoluene (TNT). However, the complex organic structure and indigenous microbial community of pine bark have thus far not been thoroughly described in the context of TNT-contaminated water treatment. This two-week batch study examined the removal efficiency ofTNT from water by (1) adsorption on pine bark and (2) simultaneous adsorption on pine bark and biotransformation by specialized TNT-biotransforming microbial inocula. The bacterial community composition of experimental batches, inocula and pine bark, was profiled by Illumina sequencing of the V6 region of the 16S rRNA gene. The results revealed that the inocula and experimental batches were dominated by phylotypes belonging to the Enterobacteriaceae family and that the tested inocula had good potential for TNT biotransformation. The type of applied inocula had the most profound effect on the TNT-transforming bacterial community structure in the experimental batches. The indigenous microbial community of pine bark harboured phylotypes that also have a potential to degrade TNT. Altogether, the combination of a specialized inoculum and pine bark proved to be the most efficient treatment option for TNT-contaminated water.

Nutrient-enhanced n-alkanes biodegradation and succession of bacterial communities

NASA Astrophysics Data System (ADS)

Sun, Yanyu; Wang, Hui; Li, Junde; Wang, Bin; Qi, Cancan; Hu, Xiaoke

2017-11-01

Bioremediation, is an effective and environment-friendly method of cleaning up crude oil pollution after an oil spill. However, the in situ bioremediation of crude oil is usually inhibited by deficiency of inorganic nutrients. To understand the effects of nutrient addition on the bioremediation of crude oil and the succession of bacterial communities during process of bioremediation, microcosms containing oil-contaminated sediments were constructed and biodegradation of crude oil was assessed based on the depletion of different ingredients. We used two culture-independent methods, denaturing gradient gel electrophoresis and a 16S rRNA gene based clone library, to analyze the succession of bacterial communities. The results suggested n-alkanes were degraded after 30 days and that nutrient amendments significantly improved the efficiency of their biodegradation. Moreover, oil contamination and nutrient amendments could dramatically change bacterial community structures. Lower diversity was detected after being contaminated with oil. For instance, bacterial clones affiliated with the phylum Armatimonadetes, Firmicutes, Gemmatimonadetes, and Planctomycetes and the class Deltaproteobacteria and Epsilonproteobacteria could not be identified after 30 days of incubation with crude oil. However, "professional hydrocarbonocastic bacteria" became abundant in samples treated with oil during the bioremediation period, while these clones were almost completely absent from the control plots. Interestingly, bioinformatics analysis showed that even when dramatic differences in oil biodegradation efficiency were observed, bacterial communities in the plots with nutrient amendments were not significantly different from those in plots treated with oil alone. These findings indicated that nutrient amendments could stimulate the process of biodegradation but had less impact on bacterial communities. Overall, nutrient amendments might be able to stimulate the growth of n-alkane degrading

Changes in bacterial community of anthracene bioremediation in municipal solid waste composting soil*

PubMed Central

Zhang, Shu-ying; Wang, Qing-feng; Wan, Rui; Xie, Shu-guang

2011-01-01

Polycyclic aromatic hydrocarbons (PAHs) are common contaminants in a municipal solid waste (MSW) composting site. Knowledge of changes in microbial structure is useful to identify particular PAH degraders. However, the microbial community in the MSW composting soil and its change associated with prolonged exposure to PAHs and subsequent biodegradation remain largely unknown. In this study, anthracene was selected as a model compound. The bacterial community structure was investigated using terminal restriction fragment length polymorphism (TRFLP) and 16S rRNA gene clone library analysis. The two bimolecular tools revealed a large shift of bacterial community structure after anthracene amendment and subsequent biodegradation. Genera Methylophilus, Mesorhizobium, and Terrimonas had potential links to anthracene biodegradation, suggesting a consortium playing an active role. PMID:21887852

The structure and functions of bacterial communities in an agrocenosis

NASA Astrophysics Data System (ADS)

Dobrovol'skaya, T. G.; Khusnetdinova, K. A.; Manucharova, N. A.; Balabko, P. N.

2016-01-01

The most significant factor responsible for the specific taxonomic composition of the bacterial communities in the agrocenosis studied was found to be a part or organ of plants (leaves, flowers, roots, fruits). A stage of plant ontogeny also determines changes of taxa. In the course of the plant growth, eccrisotrophic bacteria are replaced by hydrolytic ones that belong to the group of cellulose-decomposing bacteria. Representatives of the proteobacteria genera that are difficult to identify by phenotypic methods were determined using molecular-biological methods. They were revealed only on oat leaves in the moist period. As the vetch-oat mixture was fertilized with BIOUD-1 (foliar application) in the phyllosphere of both oats and vetch, on all the plant organs, representatives of the Rhodococcus genus as dominants were isolated. This fact was related to the capability of bacteria to decompose the complex aromatic compounds that are ingredients of the fertilizers applied. Another positive effect for plants of the bacterial communities forming in agrocenoses is the presence of bacteria that are antagonists of phytopathogenic bacteria. Thus, in agrocenoses, some interrelationships promoting the growth and reproduction of plants are formed in crop plants and bacteria.

Soil bacterial communities are shaped by temporal and environmental filtering: evidence from a long-term chronosequence.

PubMed

Freedman, Zachary; Zak, Donald R

2015-09-01

Soil microbial communities are abundant, hyper-diverse and mediate global biogeochemical cycles, but we do not yet understand the processes mediating their assembly. Current hypothetical frameworks suggest temporal (e.g. dispersal limitation) and environmental (e.g. soil pH) filters shape microbial community composition; however, there is limited empirical evidence supporting this framework in the hyper-diverse soil environment, particularly at large spatial (i.e. regional to continental) and temporal (i.e. 100 to 1000 years) scales. Here, we present evidence from a long-term chronosequence (4000 years) that temporal and environmental filters do indeed shape soil bacterial community composition. Furthermore, nearly 20 years of environmental monitoring allowed us to control for potentially confounding environmental variation. Soil bacterial communities were phylogenetically distinct across the chronosequence. We determined that temporal and environmental factors accounted for significant portions of bacterial phylogenetic structure using distance-based linear models. Environmental factors together accounted for the majority of phylogenetic structure, namely, soil temperature (19%), pH (17%) and litter carbon:nitrogen (C:N; 17%). However, of all individual factors, time since deglaciation accounted for the greatest proportion of bacterial phylogenetic structure (20%). Taken together, our results provide empirical evidence that temporal and environmental filters act together to structure soil bacterial communities across large spatial and long-term temporal scales. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Relationships between Host Phylogeny, Host Type and Bacterial Community Diversity in Cold-Water Coral Reef Sponges

PubMed Central

Schöttner, Sandra; Hoffmann, Friederike; Cárdenas, Paco; Rapp, Hans Tore; Boetius, Antje; Ramette, Alban

2013-01-01

Cold-water coral reefs are known to locally enhance the diversity of deep-sea fauna as well as of microbes. Sponges are among the most diverse faunal groups in these ecosystems, and many of them host large abundances of microbes in their tissues. In this study, twelve sponge species from three cold-water coral reefs off Norway were investigated for the relationship between sponge phylogenetic classification (species and family level), as well as sponge type (high versus low microbial abundance), and the diversity of sponge-associated bacterial communities, taking also geographic location and water depth into account. Community analysis by Automated Ribosomal Intergenic Spacer Analysis (ARISA) showed that as many as 345 (79%) of the 437 different bacterial operational taxonomic units (OTUs) detected in the dataset were shared between sponges and sediments, while only 70 (16%) appeared purely sponge-associated. Furthermore, changes in bacterial community structure were significantly related to sponge species (63% of explained community variation), sponge family (52%) or sponge type (30%), whereas mesoscale geographic distances and water depth showed comparatively small effects (<5% each). In addition, a highly significant, positive relationship between bacterial community dissimilarity and sponge phylogenetic distance was observed within the ancient family of the Geodiidae. Overall, the high diversity of sponges in cold-water coral reefs, combined with the observed sponge-related variation in bacterial community structure, support the idea that sponges represent heterogeneous, yet structured microbial habitats that contribute significantly to enhancing bacterial diversity in deep-sea ecosystems. PMID:23393586

Phytoplankton-Associated Bacterial Community Composition and Succession during Toxic Diatom Bloom and Non-Bloom Events

PubMed Central

Sison-Mangus, Marilou P.; Jiang, Sunny; Kudela, Raphael M.; Mehic, Sanjin

2016-01-01

Pseudo-nitzschia blooms often occur in coastal and open ocean environments, sometimes leading to the production of the neurotoxin domoic acid that can cause severe negative impacts to higher trophic levels. Increasing evidence suggests a close relationship between phytoplankton bloom and bacterial assemblages, however, the microbial composition and succession during a bloom process is unknown. Here, we investigate the bacterial assemblages before, during and after toxic and non-toxic Pseudo-nitzschia blooms to determine the patterns of bacterial succession in a natural bloom setting. Opportunistic sampling of bacterial community profiles were determined weekly at Santa Cruz Municipal Wharf by 454 pyrosequencing and analyzed together with domoic acid levels, phytoplankton community and biomass, nutrients and temperature. We asked if the bacterial communities are similar between bloom and non-bloom events and if domoic acid or the presence of toxic algal species acts as a driving force that can significantly structure phytoplankton-associated bacterial communities. We found that bacterial diversity generally increases when Pseudo-nitzschia numbers decline. Furthermore, bacterial diversity is higher when the low-DA producing P. fraudulenta dominates the algal bloom while bacterial diversity is lower when high-DA producing P. australis dominates the algal bloom, suggesting that the presence of algal toxin can structure bacterial community. We also found bloom-related succession patterns among associated bacterial groups; Gamma-proteobacteria, were dominant during low toxic P. fraudulenta blooms comprising mostly of Vibrio spp., which increased in relative abundance (6–65%) as the bloom progresses. On the other hand, Firmicutes bacteria comprising mostly of Planococcus spp. (12–86%) dominate during high toxic P. australis blooms, with the bacterial assemblage showing the same bloom-related successional patterns in three independent bloom events. Other environmental

Vegetation-Associated Impacts on Arctic Tundra Bacterial and Microeukaryotic Communities

PubMed Central

Shi, Yu; Xiang, Xingjia; Shen, Congcong; Neufeld, Josh D.; Walker, Virginia K.

2014-01-01

The Arctic is experiencing rapid vegetation changes, such as shrub and tree line expansion, due to climate warming, as well as increased wetland variability due to hydrological changes associated with permafrost thawing. These changes are of global concern because changes in vegetation may increase tundra soil biogeochemical processes that would significantly enhance atmospheric CO2 concentrations. Predicting the latter will at least partly depend on knowing the structure, functional activities, and distributions of soil microbes among the vegetation types across Arctic landscapes. Here we investigated the bacterial and microeukaryotic community structures in soils from the four principal low Arctic tundra vegetation types: wet sedge, birch hummock, tall birch, and dry heath. Sequencing of rRNA gene fragments indicated that the wet sedge and tall birch communities differed significantly from each other and from those associated with the other two dominant vegetation types. Distinct microbial communities were associated with soil pH, ammonium concentration, carbon/nitrogen (C/N) ratio, and moisture content. In soils with similar moisture contents and pHs (excluding wet sedge), bacterial, fungal, and total eukaryotic communities were correlated with the ammonium concentration, dissolved organic nitrogen (DON) content, and C/N ratio. Operational taxonomic unit (OTU) richness, Faith's phylogenetic diversity, and the Shannon species-level index (H′) were generally lower in the tall birch soil than in soil from the other vegetation types, with pH being strongly correlated with bacterial richness and Faith's phylogenetic diversity. Together, these results suggest that Arctic soil feedback responses to climate change will be vegetation specific not just because of distinctive substrates and environmental characteristics but also, potentially, because of inherent differences in microbial community structure. PMID:25362064

Spatial and vertical distribution of bacterial community in the northern South China Sea.

PubMed

Sun, Fu-Lin; Wang, You-Shao; Wu, Mei-Lin; Sun, Cui-Ci; Cheng, Hao

2015-10-01

Microbial communities are highly diverse in coastal oceans and response rapidly with changing environments. Learning about this will help us understand the ecology of microbial populations in marine ecosystems. This study aimed to assess the spatial and vertical distributions of the bacterial community in the northern South China Sea. Multi-dimensional scaling analyses revealed structural differences of the bacterial community among sampling sites and vertical depth. Result also indicated that bacterial community in most sites had higher diversity in 0-75 m depths than those in 100-200 m depths. Bacterial community of samples was positively correlation with salinity and depth, whereas was negatively correlation with temperature. Proteobacteria and Cyanobacteria were the dominant groups, which accounted for the majority of sequences. The α-Proteobacteria was highly diverse, and sequences belonged to Rhodobacterales bacteria were dominant in all characterized sequences. The current data indicate that the Rhodobacterales bacteria, especially Roseobacter clade are the diverse group in the tropical waters.

Changes in soil bacterial community structure as a result of incorporation of Brassica plants compared with continuous planting eggplant and chemical disinfection in greenhouses

PubMed Central

Zheng, Chengyu; Kang, Chunsheng; Yang, Zichao; Yao, Xiaotong; Song, Fengbin; Zhang, Runzhi; Wang, Xuerong; Xu, Ning; Zhang, Chunyi; Li, Wei; Li, Shumin

2017-01-01

Greenhouse eggplant monocropping in China has contributed to the aggravation of soil-borne diseases, reductions in crop quality and yield, and the degradation of physical and chemical soil properties. Crop rotation is one effective way of alleviating the problems of continuous cropping worldwide; however, few studies have reported changes in soil bacterial community structures and physical and chemical soil properties after Brassica vegetables had been rotated with eggplant in greenhouses. In this experiment, mustard-eggplant (BFN) and oilseed rape-eggplant (BFC) rotations were studied to identify changes in the physicochemical properties and bacterial community structure in soil that was previously subject to monocropping. Samples were taken after two types of Brassica plants incorporated into soil for 15 days to compare with continually planted eggplant (control, CN) and chemical disinfection of soil (CF) in greenhouses. MiSeq pyrosequencing was used to analyze soil bacterial diversity and structure in the four different treatments. A total of 55,129 reads were identified, and rarefaction analysis showed that the soil treatments were equally sampled. The bacterial richness of the BFC treatment and the diversity of the BFN treatment were significantly higher than those of the other treatments. Further comparison showed that the bacterial community structures of BFC and BFN treatments were also different from CN and CF treatments. The relative abundance of several dominant bacterial genera in the BFC and BFN treatments (such as Flavobacteria, Stenotrophomonas, Massilia and Cellvibrio, which played different roles in improving soil fertility and advancing plant growth) was distinctly higher than the CN or CF treatments. Additionally, the total organic matter and Olsen-P content of the BFC and BFN treatments were significantly greater than the CN treatment. We conclude that Brassica vegetables-eggplant crop rotations could provide a more effective means of solving

Changes in soil bacterial community structure as a result of incorporation of Brassica plants compared with continuous planting eggplant and chemical disinfection in greenhouses.

PubMed

Li, Tianzhu; Liu, Tongtong; Zheng, Chengyu; Kang, Chunsheng; Yang, Zichao; Yao, Xiaotong; Song, Fengbin; Zhang, Runzhi; Wang, Xuerong; Xu, Ning; Zhang, Chunyi; Li, Wei; Li, Shumin

2017-01-01

Greenhouse eggplant monocropping in China has contributed to the aggravation of soil-borne diseases, reductions in crop quality and yield, and the degradation of physical and chemical soil properties. Crop rotation is one effective way of alleviating the problems of continuous cropping worldwide; however, few studies have reported changes in soil bacterial community structures and physical and chemical soil properties after Brassica vegetables had been rotated with eggplant in greenhouses. In this experiment, mustard-eggplant (BFN) and oilseed rape-eggplant (BFC) rotations were studied to identify changes in the physicochemical properties and bacterial community structure in soil that was previously subject to monocropping. Samples were taken after two types of Brassica plants incorporated into soil for 15 days to compare with continually planted eggplant (control, CN) and chemical disinfection of soil (CF) in greenhouses. MiSeq pyrosequencing was used to analyze soil bacterial diversity and structure in the four different treatments. A total of 55,129 reads were identified, and rarefaction analysis showed that the soil treatments were equally sampled. The bacterial richness of the BFC treatment and the diversity of the BFN treatment were significantly higher than those of the other treatments. Further comparison showed that the bacterial community structures of BFC and BFN treatments were also different from CN and CF treatments. The relative abundance of several dominant bacterial genera in the BFC and BFN treatments (such as Flavobacteria, Stenotrophomonas, Massilia and Cellvibrio, which played different roles in improving soil fertility and advancing plant growth) was distinctly higher than the CN or CF treatments. Additionally, the total organic matter and Olsen-P content of the BFC and BFN treatments were significantly greater than the CN treatment. We conclude that Brassica vegetables-eggplant crop rotations could provide a more effective means of solving

Assessment of the effect of Enteromorpha prolifera on bacterial community structures in aquaculture environment.

PubMed

Lin, Guorong; Sun, Fulin; Wang, Chunzhong; Zhang, Li; Zhang, Xinzhong

2017-01-01

In recent years, Enteromorpha prolifera blooms had serious impacts on costal environments and fisheries in China. Nevertheless, the effects of E. prolifera on microbial ecology remain unknown. In this study, for the first time, an Illumina sequencing analysis was used to investigate bacterial communities in source water, aquaculture ponds with E. prolifera, and an aquaculture pond in which E. prolifera -free. Principal coordinate and phylogenic analyses revealed obvious differences among the bacterial communities in the pond water with and without E. prolifera. Abundant bacterial taxa in the E. prolifera-containing pond were generally absent from the pond without E. prolifera. Interestingly, pond water with E. prolifera was dominated by Actinomycetales (> 50%), as well as by anaerobic bacteria in the underlying sediment (Desulfobacterales and Desulfuromonadales (> 20%). Pond water in which E. prolifera-free was dominated by Rhodobacterales (58.19%), as well as aerobic and facultative anaerobic bacteria in the sediment. In addition, the ecological functions of other dominant bacteria, such as Candidatus Aquiluna, Microcella spp., and Marivita spp., should be studied in depth. Overall, massive growth of E. prolifera will have serious effects on bacterial communities, and, thus, it will have an important impact on the environment. The novel findings in this study will be valuable for understanding green tides.

Temporal changes in soil bacterial and archaeal communities with different fertilizers in tea orchards.

PubMed

Wang, Hua; Yang, Shao-hui; Yang, Jing-ping; Lv, Ya-min; Zhao, Xing; Pang, Ji-liang

2014-11-01

It is important to understand the effects of temporal changes in microbial communities in the acidic soils of tea orchards with different fertilizers. A field experiment involving organic fertilizer (OF), chemical fertilizer (CF), and unfertilized control (CK) treatments was arranged to analyze the temporal changes in the bacterial and archaeal communities at bimonthly intervals based on the 16S ribosomal RNA (rRNA) gene using terminal restriction fragment length polymorphism (T-RFLP) profiling. The abundances of total bacteria, total archaea, and selected functional genes (bacterial and archaeal amoA, bacterial narG, nirK, nirS, and nosZ) were determined by quantitative polymerase chain reaction (qPCR). The results indicate that the structures of bacterial and archaeal communities varied significantly with time and fertilization based on changes in the relative abundance of dominant T-RFs. The abundancy of the detected genes changed with time. The total bacteria, total archaea, and archaeal amoA were less abundant in July. The bacterial amoA and denitrifying genes were less abundant in September, except the nirK gene. The OF treatment increased the abundance of the observed genes, while the CF treatment had little influence on them. The soil temperature significantly affected the bacterial and archaeal community structures. The soil moisture was significantly correlated with the abundance of denitrifying genes. Of the soil chemical properties, soil organic carbon was the most important factor and was significantly correlated with the abundance of the detected genes, except the nirK gene. Overall, this study demonstrated the effects of both temporal alteration and organic fertilizer on the structures of microbial communities and the abundance of genes involved in the nitrogen cycle.

Temporal changes in soil bacterial and archaeal communities with different fertilizers in tea orchards* #

PubMed Central

Wang, Hua; Yang, Shao-hui; Yang, Jing-ping; Lv, Ya-min; Zhao, Xing; Pang, Ji-liang

2014-01-01

It is important to understand the effects of temporal changes in microbial communities in the acidic soils of tea orchards with different fertilizers. A field experiment involving organic fertilizer (OF), chemical fertilizer (CF), and unfertilized control (CK) treatments was arranged to analyze the temporal changes in the bacterial and archaeal communities at bimonthly intervals based on the 16S ribosomal RNA (rRNA) gene using terminal restriction fragment length polymorphism (T-RFLP) profiling. The abundances of total bacteria, total archaea, and selected functional genes (bacterial and archaeal amoA, bacterial narG, nirK, nirS, and nosZ) were determined by quantitative polymerase chain reaction (qPCR). The results indicate that the structures of bacterial and archaeal communities varied significantly with time and fertilization based on changes in the relative abundance of dominant T-RFs. The abundancy of the detected genes changed with time. The total bacteria, total archaea, and archaeal amoA were less abundant in July. The bacterial amoA and denitrifying genes were less abundant in September, except the nirK gene. The OF treatment increased the abundance of the observed genes, while the CF treatment had little influence on them. The soil temperature significantly affected the bacterial and archaeal community structures. The soil moisture was significantly correlated with the abundance of denitrifying genes. Of the soil chemical properties, soil organic carbon was the most important factor and was significantly correlated with the abundance of the detected genes, except the nirK gene. Overall, this study demonstrated the effects of both temporal alteration and organic fertilizer on the structures of microbial communities and the abundance of genes involved in the nitrogen cycle. PMID:25367788

Bacterial community structure across environmental gradients in permafrost thaw ponds: methanotroph-rich ecosystems

PubMed Central

Crevecoeur, Sophie; Vincent, Warwick F.; Comte, Jérôme; Lovejoy, Connie

2015-01-01

Permafrost thawing leads to the formation of thermokarst ponds that potentially emit CO2 and CH4 to the atmosphere. In the Nunavik subarctic region (northern Québec, Canada), these numerous, shallow ponds become well-stratified during summer. This creates a physico-chemical gradient of temperature and oxygen, with an upper oxic layer and a bottom low oxygen or anoxic layer. Our objective was to determine the influence of stratification and related limnological and landscape properties on the community structure of potentially active bacteria in these waters. Samples for RNA analysis were taken from ponds in three contrasting valleys across a gradient of permafrost degradation. A total of 1296 operational taxonomic units were identified by high throughput amplicon sequencing, targeting bacterial 16S rRNA that was reverse transcribed to cDNA. β-proteobacteria were the dominant group in all ponds, with highest representation by the genera Variovorax and Polynucleobacter. Methanotrophs were also among the most abundant sequences at most sites. They accounted for up to 27% of the total sequences (median of 4.9% for all samples), indicating the importance of methane as a bacterial energy source in these waters. Both oxygenic (cyanobacteria) and anoxygenic (Chlorobi) phototrophs were also well-represented, the latter in the low oxygen bottom waters. Ordination analyses showed that the communities clustered according to valley and depth, with significant effects attributed to dissolved oxygen, pH, dissolved organic carbon, and total suspended solids. These results indicate that the bacterial assemblages of permafrost thaw ponds are filtered by environmental gradients, and are complex consortia of functionally diverse taxa that likely affect the composition as well as magnitude of greenhouse gas emissions from these abundant waters. PMID:25926816

Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome

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

Hodkinson, Brendan P; Gottel, Neil R; Schadt, Christopher Warren

2011-01-01

Although common knowledge dictates that the lichen thallus is formed solely by a fungus (mycobiont) that develops a symbiotic relationship with an alga and/or cyanobacterium (photobiont), the non-photoautotrophic bacteria found in lichen microbiomes are increasingly regarded as integral components of lichen thalli. For this study, comparative analyses were conducted on lichen-associated bacterial communities to test for effects of photobiont-types (i.e. green algal vs. cyanobacterial), mycobiont-types and large-scale spatial distances (from tropical to arctic latitudes). Amplicons of the 16S (SSU) rRNA gene were examined using both Sanger sequencing of cloned fragments and barcoded pyrosequencing. Rhizobiales is typically the most abundant andmore » taxonomically diverse order in lichen microbiomes; however, overall bacterial diversity in lichens is shown to be much higher than previously reported. Members of Acidobacteriaceae, Acetobacteraceae, Brucellaceae and sequence group LAR1 are the most commonly found groups across the phylogenetically and geographically broad array of lichens examined here. Major bacterial community trends are significantly correlated with differences in large-scale geography, photobiont-type and mycobiont-type. The lichen as a microcosm represents a structured, unique microbial habitat with greater ecological complexity and bacterial diversity than previously appreciated and can serve as a model system for studying larger ecological and evolutionary principles.« less

Dynamics of Different Bacterial Communities Are Capable of Generating Sustainable Electricity from Microbial Fuel Cells with Organic Waste

PubMed Central

Yamamoto, Shuji; Suzuki, Kei; Araki, Yoko; Mochihara, Hiroki; Hosokawa, Tetsuya; Kubota, Hiroko; Chiba, Yusuke; Rubaba, Owen; Tashiro, Yosuke; Futamata, Hiroyuki

2014-01-01

The relationship between the bacterial communities in anolyte and anode biofilms and the electrochemical properties of microbial fuel cells (MFCs) was investigated when a complex organic waste-decomposing solution was continuously supplied to MFCs as an electron donor. The current density increased gradually and was maintained at approximately 100 to 150 mA m−2. Polarization curve analyses revealed that the maximum power density was 7.4 W m−3 with an internal resistance of 110 Ω. Bacterial community structures in the organic waste-decomposing solution and MFCs differed from each other. Clonal analyses targeting 16S rRNA genes indicated that bacterial communities in the biofilms on MFCs developed to specific communities dominated by novel Geobacter. Multidimensional scaling analyses based on DGGE profiles revealed that bacterial communities in the organic waste-decomposing solution fluctuated and had no dynamic equilibrium. Bacterial communities on the anolyte in MFCs had a dynamic equilibrium with fluctuations, while those of the biofilm converged to the Geobacter-dominated structure. These bacterial community dynamics of MFCs differed from those of control-MFCs under open circuit conditions. These results suggested that bacterial communities in the anolyte and biofilm have a gentle symbiotic system through electron flow, which resulted in the advance of current density from complex organic waste. PMID:24789988

Dynamics of different bacterial communities are capable of generating sustainable electricity from microbial fuel cells with organic waste.

PubMed

Yamamoto, Shuji; Suzuki, Kei; Araki, Yoko; Mochihara, Hiroki; Hosokawa, Tetsuya; Kubota, Hiroko; Chiba, Yusuke; Rubaba, Owen; Tashiro, Yosuke; Futamata, Hiroyuki

2014-01-01

The relationship between the bacterial communities in anolyte and anode biofilms and the electrochemical properties of microbial fuel cells (MFCs) was investigated when a complex organic waste-decomposing solution was continuously supplied to MFCs as an electron donor. The current density increased gradually and was maintained at approximately 100 to 150 mA m(-2). Polarization curve analyses revealed that the maximum power density was 7.4 W m(-3) with an internal resistance of 110 Ω. Bacterial community structures in the organic waste-decomposing solution and MFCs differed from each other. Clonal analyses targeting 16S rRNA genes indicated that bacterial communities in the biofilms on MFCs developed to specific communities dominated by novel Geobacter. Multidimensional scaling analyses based on DGGE profiles revealed that bacterial communities in the organic waste-decomposing solution fluctuated and had no dynamic equilibrium. Bacterial communities on the anolyte in MFCs had a dynamic equilibrium with fluctuations, while those of the biofilm converged to the Geobacter-dominated structure. These bacterial community dynamics of MFCs differed from those of control-MFCs under open circuit conditions. These results suggested that bacterial communities in the anolyte and biofilm have a gentle symbiotic system through electron flow, which resulted in the advance of current density from complex organic waste.

Geo-Chip analysis reveals reduced functional diversity of the bacterial community at a dumping site for dredged Elbe sediment.

PubMed

Störmer, Rebecca; Wichels, Antje; Gerdts, Gunnar

2013-12-15

The dumping of dredged sediments represents a major stressor for coastal ecosystems. The impact on the ecosystem function is determined by its complexity not easy to assess. In the present study, we evaluated the potential of bacterial community analyses to act as ecological indicators in environmental monitoring programmes. We investigated the functional structure of bacterial communities, applying functional gene arrays (GeoChip4.2). The relationship between functional genes and environmental factors was analysed using distance-based multivariate multiple regression. Apparently, both the function and structure of the bacterial communities are impacted by dumping activities. The bacterial community at the dumping centre displayed a significant reduction of its entire functional diversity compared with that found at a reference site. DDX compounds separated bacterial communities of the dumping site from those of un-impacted sites. Thus, bacterial community analyses show great potential as ecological indicators in environmental monitoring. Copyright © 2013 Elsevier Ltd. All rights reserved.

Tropical soil bacterial communities in Malaysia: pH dominates in the equatorial tropics too.

PubMed

Tripathi, Binu M; Kim, Mincheol; Singh, Dharmesh; Lee-Cruz, Larisa; Lai-Hoe, Ang; Ainuddin, A N; Go, Rusea; Rahim, Raha Abdul; Husni, M H A; Chun, Jongsik; Adams, Jonathan M

2012-08-01

The dominant factors controlling soil bacterial community variation within the tropics are poorly known. We sampled soils across a range of land use types--primary (unlogged) and logged forests and crop and pasture lands in Malaysia. PCR-amplified soil DNA for the bacterial 16S rRNA gene targeting the V1-V3 region was pyrosequenced using the 454 Roche machine. We found that land use in itself has a weak but significant effect on the bacterial community composition. However, bacterial community composition and diversity was strongly correlated with soil properties, especially soil pH, total carbon, and C/N ratio. Soil pH was the best predictor of bacterial community composition and diversity across the various land use types, with the highest diversity close to neutral pH values. In addition, variation in phylogenetic structure of dominant lineages (Alphaproteobacteria, Beta/Gammaproteobacteria, Acidobacteria, and Actinobacteria) is also significantly correlated with soil pH. Together, these results confirm the importance of soil pH in structuring soil bacterial communities in Southeast Asia. Our results also suggest that unlike the general diversity pattern found for larger organisms, primary tropical forest is no richer in operational taxonomic units of soil bacteria than logged forest, and agricultural land (crop and pasture) is actually richer than primary forest, partly due to selection of more fertile soils that have higher pH for agriculture and the effects of soil liming raising pH.

Bacterial structures and ecosystem functions in glaciated floodplains: contemporary states and potential future shifts.

PubMed

Freimann, Remo; Bürgmann, Helmut; Findlay, Stuart E G; Robinson, Christopher T

2013-12-01

Glaciated alpine floodplains are responding quickly to climate change through shrinking ice masses. Given the expected future changes in their physicochemical environment, we anticipated variable shifts in structure and ecosystem functioning of hyporheic microbial communities in proglacial alpine streams, depending on present community characteristics and landscape structures. We examined microbial structure and functioning during different hydrologic periods in glacial (kryal) streams and, as contrasting systems, groundwater-fed (krenal) streams. Three catchments were chosen to cover an array of landscape features, including interconnected lakes, differences in local geology and degree of deglaciation. Community structure was assessed by automated ribosomal intergenic spacer analysis and microbial function by potential enzyme activities. We found each catchment to contain a distinct bacterial community structure and different degrees of separation in structure and functioning that were linked to the physicochemical properties of the waters within each catchment. Bacterial communities showed high functional plasticity, although achieved by different strategies in each system. Typical kryal communities showed a strong linkage of structure and function that indicated a major prevalence of specialists, whereas krenal sediments were dominated by generalists. With the rapid retreat of glaciers and therefore altered ecohydrological characteristics, lotic microbial structure and functioning are likely to change substantially in proglacial floodplains in the future. The trajectory of these changes will vary depending on contemporary bacterial community characteristics and landscape structures that ultimately determine the sustainability of ecosystem functioning.

Spatial distribution of marine airborne bacterial communities

PubMed Central

Seifried, Jasmin S; Wichels, Antje; Gerdts, Gunnar

2015-01-01

The spatial distribution of bacterial populations in marine bioaerosol samples was investigated during a cruise from the North Sea to the Baltic Sea via Skagerrak and Kattegat. The analysis of the sampled bacterial communities with a pyrosequencing approach revealed that the most abundant phyla were represented by the Proteobacteria (49.3%), Bacteroidetes (22.9%), Actinobacteria (16.3%), and Firmicutes (8.3%). Cyanobacteria were assigned to 1.5% of all bacterial reads. A core of 37 bacterial OTUs made up more than 75% of all bacterial sequences. The most abundant OTU was Sphingomonas sp. which comprised 17% of all bacterial sequences. The most abundant bacterial genera were attributed to distinctly different areas of origin, suggesting highly heterogeneous sources for bioaerosols of marine and coastal environments. Furthermore, the bacterial community was clearly affected by two environmental parameters – temperature as a function of wind direction and the sampling location itself. However, a comparison of the wind directions during the sampling and calculated backward trajectories underlined the need for more detailed information on environmental parameters for bioaerosol investigations. The current findings support the assumption of a bacterial core community in the atmosphere. They may be emitted from strong aerosolizing sources, probably being mixed and dispersed over long distances. PMID:25800495

Exploring lot-to-lot variation in spoilage bacterial communities on commercial modified atmosphere packaged beef.

PubMed

Säde, Elina; Penttinen, Katri; Björkroth, Johanna; Hultman, Jenni

2017-04-01

Understanding the factors influencing meat bacterial communities is important as these communities are largely responsible for meat spoilage. The composition and structure of a bacterial community on a high-O 2 modified-atmosphere packaged beef product were examined after packaging, on the use-by date and two days after, to determine whether the communities at each stage were similar to those in samples taken from different production lots. Furthermore, we examined whether the taxa associated with product spoilage were distributed across production lots. Results from 16S rRNA amplicon sequencing showed that while the early samples harbored distinct bacterial communities, after 8-12 days storage at 6 °C the communities were similar to those in samples from different lots, comprising mainly of common meat spoilage bacteria Carnobacterium spp., Brochothrix spp., Leuconostoc spp. and Lactococcus spp. Interestingly, abundant operational taxonomic units associated with product spoilage were shared between the production lots, suggesting that the bacteria enable to spoil the product were constant contaminants in the production chain. A characteristic succession pattern and the distribution of common spoilage bacteria between lots suggest that both the packaging type and the initial community structure influenced the development of the spoilage bacterial community. Copyright © 2016 Elsevier Ltd. All rights reserved.

Distinctive bacterial communities in the rhizoplane of four tropical tree species.

PubMed

Oh, Yoon Myung; Kim, Mincheol; Lee-Cruz, Larisa; Lai-Hoe, Ang; Go, Rusea; Ainuddin, N; Rahim, Raha Abdul; Shukor, Noraini; Adams, Jonathan M

2012-11-01

It is known that the microbial community of the rhizosphere is not only influenced by factors such as root exudates, phenology, and nutrient uptake but also by the plant species. However, studies of bacterial communities associated with tropical rainforest tree root surfaces, or rhizoplane, are lacking. Here, we analyzed the bacterial community of root surfaces of four species of native trees, Agathis borneensis, Dipterocarpus kerrii, Dyera costulata, and Gnetum gnemon, and nearby bulk soils, in a rainforest arboretum in Malaysia, using 454 pyrosequencing of the 16S rRNA gene. The rhizoplane bacterial communities for each of the four tree species sampled clustered separately from one another on an ordination, suggesting that these assemblages are linked to chemical and biological characteristics of the host or possibly to the mycorrhizal fungi present. Bacterial communities of the rhizoplane had various similarities to surrounding bulk soils. Acidobacteria, Alphaproteobacteria, and Betaproteobacteria were dominant in rhizoplane communities and in bulk soils from the same depth (0-10 cm). In contrast, the relative abundance of certain bacterial lineages on the rhizoplane was different from that in bulk soils: Bacteroidetes and Betaproteobacteria, which are known as copiotrophs, were much more abundant in the rhizoplane in comparison to bulk soil. At the genus level, Burkholderia, Acidobacterium, Dyella, and Edaphobacter were more abundant in the rhizoplane. Burkholderia, which are known as both pathogens and mutualists of plants, were especially abundant on the rhizoplane of all tree species sampled. The Burkholderia species present included known mutualists of tropical crops and also known N fixers. The host-specific character of tropical tree rhizoplane bacterial communities may have implications for understanding nutrient cycling, recruitment, and structuring of tree species diversity in tropical forests. Such understanding may prove to be useful in both

Two decades of warming increases diversity of a potentially lignolytic bacterial community

PubMed Central

Pold, Grace; Melillo, Jerry M.; DeAngelis, Kristen M.

2015-01-01

As Earth's climate warms, the massive stores of carbon found in soil are predicted to become depleted, and leave behind a smaller carbon pool that is less accessible to microbes. At a long-term forest soil-warming experiment in central Massachusetts, soil respiration and bacterial diversity have increased, while fungal biomass and microbially-accessible soil carbon have decreased. Here, we evaluate how warming has affected the microbial community's capability to degrade chemically-complex soil carbon using lignin-amended BioSep beads. We profiled the bacterial and fungal communities using PCR-based methods and completed extracellular enzyme assays as a proxy for potential community function. We found that lignin-amended beads selected for a distinct community containing bacterial taxa closely related to known lignin degraders, as well as members of many genera not previously noted as capable of degrading lignin. Warming tended to drive bacterial community structure more strongly in the lignin beads, while the effect on the fungal community was limited to unamended beads. Of those bacterial operational taxonomic units (OTUs) enriched by the warming treatment, many were enriched uniquely on lignin-amended beads. These taxa may be contributing to enhanced soil respiration under warming despite reduced readily available C availability. In aggregate, these results suggest that there is genetic potential for chemically complex soil carbon degradation that may lead to extended elevated soil respiration with long-term warming. PMID:26042112

Molecular bacterial community analysis of clean rooms where spacecraft are assembled.

PubMed

Moissl, Christine; Osman, Shariff; La Duc, Myron T; Dekas, Anne; Brodie, Eoin; DeSantis, Todd; Desantis, Tadd; Venkateswaran, Kasthuri

2007-09-01

Molecular bacterial community composition was characterized from three geographically distinct spacecraft-associated clean rooms to determine whether such populations are influenced by the surrounding environment or the maintenance of the clean rooms. Samples were collected from facilities at the Jet Propulsion Laboratory (JPL), Kennedy Space Flight Center (KSC), and Johnson Space Center (JSC). Nine clone libraries representing different surfaces within the spacecraft facilities and three libraries from the surrounding air were created. Despite the highly desiccated, nutrient-bare conditions within these clean rooms, a broad diversity of bacteria was detected, covering all the main bacterial phyla. Furthermore, the bacterial communities were significantly different from each other, revealing only a small subset of microorganisms common to all locations (e.g. Sphingomonas, Staphylococcus). Samples from JSC assembly room surfaces showed the greatest diversity of bacteria, particularly within the Alpha- and Gammaproteobacteria and Actinobacteria. The bacterial community structure of KSC assembly surfaces revealed a high presence of proteobacterial groups, whereas the surface samples collected from the JPL assembly facility showed a predominance of Firmicutes. Our study presents the first extended molecular survey and comparison of NASA spacecraft assembly facilities, and provides new insights into the bacterial diversity of clean room environments .

Structural and functional diversity of soil bacterial and fungal communities following woody plant encroachment in the southern Great Plains

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

Hollister, Emily B; Schadt, Christopher Warren; Palumbo, Anthony Vito

In the southern Great Plains (USA), encroachment of grassland ecosystems by Prosopis glandulosa (honey mesquite) is widespread. Mesquite encroachment alters net primary productivity, enhances stores of C and N in plants and soil, and leads to increased levels of soil microbial biomass and activity. While mesquite's impact on the biogeochemistry of the region is well established, it effects on soil microbial diversity and function are unknown. In this study, soils associated with four plant types (C{sub 3} perennial grasses, C{sub 4} midgrasses, C{sub 4} shortgrasses, and mesquite) from a mesquite-encroached mixed grass prairie were surveyed to in an attempt tomore » characterize the structure, diversity, and functional capacity of their soil microbial communities. rRNA gene cloning and sequencing were used in conjunction with the GeoChip functional gene array to evaluate these potential differences. Mesquite soil supported increased bacterial and fungal diversity and harbored a distinct fungal community relative to other plant types. Despite differences in composition and diversity, few significant differences were detected with respect to the potential functional capacity of the soil microbial communities. These results may suggest that a high level of functional redundancy exists within the bacterial portion of the soil communities; however, given the bias of the GeoChip toward bacterial functional genes, potential functional differences among soil fungi could not be addressed. The results of this study illustrate the linkages shared between above- and belowground communities and demonstrate that soil microbial communities, and in particular soil fungi, may be altered by the process of woody plant encroachment.« less

Fungal networks shape dynamics of bacterial dispersal and community assembly in cheese rind microbiomes.

PubMed

Zhang, Yuanchen; Kastman, Erik K; Guasto, Jeffrey S; Wolfe, Benjamin E

2018-01-23

Most studies of bacterial motility have examined small-scale (micrometer-centimeter) cell dispersal in monocultures. However, bacteria live in multispecies communities, where interactions with other microbes may inhibit or facilitate dispersal. Here, we demonstrate that motile bacteria in cheese rind microbiomes use physical networks created by filamentous fungi for dispersal, and that these interactions can shape microbial community structure. Serratia proteamaculans and other motile cheese rind bacteria disperse on fungal networks by swimming in the liquid layers formed on fungal hyphae. RNA-sequencing, transposon mutagenesis, and comparative genomics identify potential genetic mechanisms, including flagella-mediated motility, that control bacterial dispersal on hyphae. By manipulating fungal networks in experimental communities, we demonstrate that fungal-mediated bacterial dispersal can shift cheese rind microbiome composition by promoting the growth of motile over non-motile community members. Our single-cell to whole-community systems approach highlights the interactive dynamics of bacterial motility in multispecies microbiomes.

Bacterial communities in soil samples from the Mingyong Glacier of southwestern China.

PubMed

Li, Haoyu; Taj, Muhammad Kamran; Ji, Xiuling; Zhang, Qi; Lin, Liangbing; Zhou, Zhimei; Wei, Yunlin

2017-05-01

The present study was an effort to determine the bacterial diversity of soils in Mingyong Glacier located at the Meili Snow Mountains of southwestern China. Mingyong Glacier has different climatic zones within a very narrow area, and bacterial community diversity in this low temperature area remains largely unknown. In this study, soil samples were collected from four different climatic zones: M11A (dry warm valley), M14 (forest), M15 (grass land), and M16 (glacier zones). Phylogenetic analysis based on 16S rRNA gene V6 hypervariable region showed high bacterial abundance in the glacier. The number of Operational Taxonomic Units ranged from 2.24×10 3 to 5.56×10 3 in soil samples. Statistical analysis of 16S rRNA gene clone libraries results showed that bacterial diversity in zones M11A，M14 and M16 are higher than in zone M15. The bacterial community structures are clearly distinguishable, and phylogenetic analysis showed that the predominant phyla were Proteobacteria, Deinococcus-Thermus, Firmicutes, Actinobacteria, and Nitrospirae in Mingyong Glacier. Seventy-nine different orders from four zones have been isolated. Bacterial diversity and distribution of bacterial communities related to the anthropogenic perturbations in zone (M15) were confirmed by diversity index analysis, and the diversity index of other three zones was satisfactory through this analysis software. The results suggest that bacterial diversity and distribution analyses using bacterial 16S rRNA gene V6 hypervariable region were successful, and bacterial communities in this area not only had the same bacterial phyla compared to other glaciers but also had their own rare species.

Determinants of bacterial communities in Canadian agroforestry systems.

PubMed

Banerjee, Samiran; Baah-Acheamfour, Mark; Carlyle, Cameron N; Bissett, Andrew; Richardson, Alan E; Siddique, Tariq; Bork, Edward W; Chang, Scott X

2016-06-01

Land-use change is one of the most important factors influencing soil microbial communities, which play a pivotal role in most biogeochemical and ecological processes. Using agroforestry systems as a model, this study examined the effects of land uses and edaphic properties on bacterial communities in three agroforestry types covering a 270 km soil-climate gradient in Alberta, Canada. Our results demonstrate that land-use patterns exert stronger effects on soil bacterial communities than soil zones in these agroforestry systems. Plots with trees in agroforestry systems promoted greater bacterial abundance and to some extent species richness, which was associated with more nutrient-rich soil resources. While Acidobacteria, Actinobacteria and Alphaproteobacteria were the dominant bacterial phyla and subphyla across land uses, Arthrobacter, Acidobacteria_Gp16, Burkholderia, Rhodanobacter and Rhizobium were the keystone taxa in these agroforestry systems. Soil pH and carbon contents emerged as the major determinants of bacterial community characteristics. We found non-random co-occurrence and modular patterns of soil bacterial communities, and these patterns were controlled by edaphic factors and not their taxonomy. Overall, this study highlights the drivers and co-occurrence patterns of soil microbial communities in agroforestry systems. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Global and local-scale variation in bacterial community structure of snow from the Swiss and Australian Alps.

PubMed

Wunderlin, Tina; Ferrari, Belinda; Power, Michelle

2016-09-01

Seasonally, snow environments cover up to 50% of the land's surface, yet the microbial diversity and ecosystem functioning within snow, particularly from alpine regions are not well described. This study explores the bacterial diversity in snow using next-generation sequencing technology. Our data expand the global inventory of snow microbiomes by focusing on two understudied regions, the Swiss Alps and the Australian Alps. A total biomass similar to cell numbers in polar snow was detected, with 5.2 to 10.5 × 10(3) cells mL(-1) of snow. We found that microbial community structure of surface snow varied by country and site and along the altitudinal range (alpine and sub-alpine). The bacterial communities present were diverse, spanning 25 distinct phyla, but the six phyla Proteobacteria (Alpha- and Betaproteobacteria), Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria and Firmicutes, accounted for 72%-98% of the total relative abundance. Taxa such as Acidobacteriaceae and Methylocystaceae, associated with cold soils, may be part of the atmospherically sourced snow community, while families like Sphingomonadaceae were detected in every snow sample and are likely part of the common snow biome. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Grazers structure the bacterial and algal diversity of aquatic metacommunities.

PubMed

Birtel, Julia; Matthews, Blake

2016-12-01

Consumers can have strong effects on the biotic and abiotic dynamics of spatially-structured ecosystems. In metacommunities, dispersing consumers can alter local assembly dynamics either directly through trophic interactions or indirectly by modifying local environmental conditions. In aquatic systems, very little is known about how key grazers, such as Daphnia, structure the microbial diversity of metacommunities and influence bacterial-mediated ecosystem functions. In an outdoor mesocosm experiment with replicate metacommunities (two 300 L mesocosms), we tested how the presence and absence of Daphnia and the initial density of the microbial community (manipulated via dilution) influenced the diversity and community structure of algae and bacteria, and several ecosystem properties (e.g., pH, dissolved substances) and functions (e.g., enzyme activity, respiration). We found that Daphnia strongly affected the local and regional diversity of both phytoplankton and bacteria, the taxonomic composition of bacterial communities, the biomass of algae, and ecosystem metabolism (i.e., respiration). Diluting the microbial inoculum (0.2-5 μm size fraction) to the metacommunities increased local phytoplankton diversity, decreased bacteria beta-diversity, and changed the relative abundance of bacterial classes. Changes in the rank abundance of different bacterial groups exhibited phylogenetic signal, implying that closely related bacteria species might share similar responses to the presence of Daphnia. © 2016 by the Ecological Society of America.

Effects of triclosan on bacterial community composition and ...

EPA Pesticide Factsheets

Pharmaceuticals and personal care products, including antimicrobials, can be found at trace levels in treated wastewater effluent. Impacts of chemical contaminants on coastal aquatic microbial community structure and pathogen abundance are unknown despite the potential for selection through antimicrobial resistance. In particular, Vibrio, a marine bacterial genus that includes several human pathogens, displays resistance to the ubiquitous antimicrobial compound triclosan. Here we demonstrated through use of natural seawater microcosms that triclosan (at a concentration of ~5 ppm) can induce a significant Vibrio growth response (68–1,700 fold increases) in comparison with no treatment controls for three distinct coastal ecosystems: Looe Key Reef (Florida Keys National Marine Sanctuary), Doctors Arm Canal (Big Pine Key, FL), and Clam Bank Landing (North Inlet Estuary, Georgetown, SC). Additionally, microbial community analysis by 16 S rRNA gene sequencing for Looe Key Reef showed distinct changes in microbial community structure with exposure to 5 ppm triclosan, with increases observed in the relative abundance of Vibrionaceae (17-fold), Pseudoalteromonadaceae (65-fold), Alteromonadaceae (108-fold), Colwelliaceae (430-fold), and Oceanospirillaceae (1,494-fold). While the triclosan doses tested were above concentrations typically observed in coastal surface waters, results identify bacterial families that are potentially resistant to triclosan and/or adapted to u

Responses of Bacterial Communities in Arable Soils in a Rice-Wheat Cropping System to Different Fertilizer Regimes and Sampling Times

PubMed Central

Zhao, Jun; Ni, Tian; Li, Yong; Xiong, Wu; Ran, Wei; Shen, Biao; Shen, Qirong; Zhang, Ruifu

2014-01-01

Soil physicochemical properties, soil microbial biomass and bacterial community structures in a rice-wheat cropping system subjected to different fertilizer regimes were investigated in two seasons (June and October). All fertilizer regimes increased the soil microbial biomass carbon and nitrogen. Both fertilizer regime and time had a significant effect on soil physicochemical properties and bacterial community structure. The combined application of inorganic fertilizer and manure organic-inorganic fertilizer significantly enhanced the bacterial diversity in both seasons. The bacterial communities across all samples were dominated by Proteobacteria, Acidobacteria and Chloroflexi at the phylum level. Permutational multivariate analysis confirmed that both fertilizer treatment and season were significant factors in the variation of the composition of the bacterial community. Hierarchical cluster analysis based on Bray-Curtis distances further revealed that bacterial communities were separated primarily by season. The effect of fertilizer treatment is significant (P = 0.005) and accounts for 7.43% of the total variation in bacterial community. Soil nutrients (e.g., available K, total N, total P and organic matter) rather than pH showed significant correlation with the majority of abundant taxa. In conclusion, both fertilizer treatment and seasonal changes affect soil properties, microbial biomass and bacterial community structure. The application of NPK plus manure organic-inorganic fertilizer may be a sound fertilizer practice for sustainable food production. PMID:24465530

Succession of Bacterial Community Structure and Diversity in Soil along a Chronosequence of Reclamation and Re-Vegetation on Coal Mine Spoils in China

PubMed Central

Li, Yuanyuan; Wen, Hongyu; Chen, Longqian; Yin, Tingting

2014-01-01

The growing concern about the effectiveness of reclamation strategies has motivated the evaluation of soil properties following reclamation. Recovery of belowground microbial community is important for reclamation success, however, the response of soil bacterial communities to reclamation has not been well understood. In this study, PCR-based 454 pyrosequencing was applied to compare bacterial communities in undisturbed soils with those in reclaimed soils using chronosequences ranging in time following reclamation from 1 to 20 year. Bacteria from the Proteobacteria, Chloroflexi, Actinobacteria, Acidobacteria, Planctomycetes and Bacteroidetes were abundant in all soils, while the composition of predominant phyla differed greatly across all sites. Long-term reclamation strongly affected microbial community structure and diversity. Initial effects of reclamation resulted in significant declines in bacterial diversity indices in younger reclaimed sites (1, 8-year-old) compared to the undisturbed site. However, bacterial diversity indices tended to be higher in older reclaimed sites (15, 20-year-old) as recovery time increased, and were more similar to predisturbance levels nearly 20 years after reclamation. Bacterial communities are highly responsive to soil physicochemical properties (pH, soil organic matter, Total N and P), in terms of both their diversity and community composition. Our results suggest that the response of soil microorganisms to reclamation is likely governed by soil characteristics and, indirectly, by the effects of vegetation restoration. Mixture sowing of gramineae and leguminosae herbage largely promoted soil geochemical conditions and bacterial diversity that recovered to those of undisturbed soil, representing an adequate solution for soil remediation and sustainable utilization for agriculture. These results confirm the positive impacts of reclamation and vegetation restoration on soil microbial diversity and suggest that the most important

Vegetation-associated impacts on arctic tundra bacterial and microeukaryotic communities.

PubMed

Shi, Yu; Xiang, Xingjia; Shen, Congcong; Chu, Haiyan; Neufeld, Josh D; Walker, Virginia K; Grogan, Paul

2015-01-01

The Arctic is experiencing rapid vegetation changes, such as shrub and tree line expansion, due to climate warming, as well as increased wetland variability due to hydrological changes associated with permafrost thawing. These changes are of global concern because changes in vegetation may increase tundra soil biogeochemical processes that would significantly enhance atmospheric CO2 concentrations. Predicting the latter will at least partly depend on knowing the structure, functional activities, and distributions of soil microbes among the vegetation types across Arctic landscapes. Here we investigated the bacterial and microeukaryotic community structures in soils from the four principal low Arctic tundra vegetation types: wet sedge, birch hummock, tall birch, and dry heath. Sequencing of rRNA gene fragments indicated that the wet sedge and tall birch communities differed significantly from each other and from those associated with the other two dominant vegetation types. Distinct microbial communities were associated with soil pH, ammonium concentration, carbon/nitrogen (C/N) ratio, and moisture content. In soils with similar moisture contents and pHs (excluding wet sedge), bacterial, fungal, and total eukaryotic communities were correlated with the ammonium concentration, dissolved organic nitrogen (DON) content, and C/N ratio. Operational taxonomic unit (OTU) richness, Faith's phylogenetic diversity, and the Shannon species-level index (H') were generally lower in the tall birch soil than in soil from the other vegetation types, with pH being strongly correlated with bacterial richness and Faith's phylogenetic diversity. Together, these results suggest that Arctic soil feedback responses to climate change will be vegetation specific not just because of distinctive substrates and environmental characteristics but also, potentially, because of inherent differences in microbial community structure. Copyright © 2015, American Society for Microbiology. All Rights

Meteorological factors had more impact on airborne bacterial communities than air pollutants.

PubMed

Zhen, Quan; Deng, Ye; Wang, Yaqing; Wang, Xiaoke; Zhang, Hongxing; Sun, Xu; Ouyang, Zhiyun

2017-12-01

Airborne bacteria have gained increasing attention because they affect ecological balance and pose potential risks on human health. Recently, some studies have focused on the abundance and composition of airborne bacteria under heavy, hazy polluted weather in China, but they reached different conclusions about the comparisons with non-polluted days. In this study, we tested the hypothesis that meteorological factors could have a higher impact on shaping airborne bacterial communities than air pollutants by systematically monitoring the communities for 1year. Total suspended particles in Beijing were sampled for 20 consecutive days in each season of 2015. Bacterial abundance varied from 8.71×10 3 to 2.14×10 7 ribosomal operons per cubic meter according to the quantitative PCR analysis. There were relatively higher bacterial counts in spring and in autumn than in winter and summer. Airborne bacterial communities displayed a strong seasonality, according to the hierarchical cluster analysis. Only two exceptions overtook the seasonal trend, and both occurred in or after violent meteorological changes (sandstorm or rain). Aggregated boosted tree analysis performed on bacterial abundance showed that the dominant factors shaping bacterial communities were meteorological. They were air pressure in winter, air temperature and relative humidity in spring, RH in summer, and vapor pressure in autumn. Variation partition analysis on community structure showed that meteorological factors explained more variations than air pollutants. Therefore, both of the two models verified our hypothesis that the differences in airborne bacterial communities in polluted days or non-polluted days were mainly driven by the discrepancies of meteorological factors rather than by the presence of air pollutants. Copyright © 2017 Elsevier B.V. All rights reserved.

[Algo-bacterial communities of the Kulunda steppe (Altai region, Russia) soda lakes].

PubMed

Samylina, O S; Sapozhnikov, F V; Gaĭnanova, O Iu; Riabova, A V; Nikitin, M A; Sorokin, D Iu

2015-01-01

The composition and macroscopic structure of the floating oxygenic phototrophic communities from Kulunda steppe soda lakes (Petukhovskoe sodovoe, Tanatara VI, and Gorchiny 3) was described based on the data of the 2011 and 2012 expeditions (Winogradsky Institute of Microbiology). The algo-bacterial community with a green alga Ctenocladus circinnatus as an edificator was the typical one. Filamentous Geitlerinema sp. and Nodosilinea sp. were the dominant cyanobacteria. Apart from C. circinnatus, the algological component of the community contained unicellular green algae Dunaliella viridis and cf. Chlorella minutissima, as well as diatoms (Anomeoneis sphaerophora, Brchysira brebissonii, Brachysira zellensis, Mastogloia pusilla var. subcapitata, Nitzschia amphibia, Nitzschia communis, and Nitzschia sp.1). The latter have not been previously identified in the lakes under study. In all lakes, a considerable increase in salinity was found to result in changes in the composition and macroscopic structure of algo-bacterial communities.

Analysis on the Spatial Difference of Bacterial Community Structure in Micro-pressure Air-lift Loop Reactor

NASA Astrophysics Data System (ADS)

Wan, L. G.; Lin, Q.; Bian, D. J.; Ren, Q. K.; Xiao, Y. B.; Lu, W. X.

2018-02-01

In order to reveal the spatial difference of the bacterial community structure in the Micro-pressure Air-lift Loop Reactor, the activated sludge bacterial at five different representative sites in the reactor were studied by denaturing gradient gel electrophoresis (DGGE). The results of DGGE showed that the difference of environmental conditions (such as substrate concentration, dissolved oxygen and PH, etc.) resulted in different diversity and similarity of microbial flora in different spatial locations. The Shannon-Wiener diversity index of the total bacterial samples from five sludge samples varied from 0.92 to 1.28, the biodiversity index was the smallest at point 5, and the biodiversity index was the highest at point 2. The similarity of the flora between the point 2, 3 and 4 was 80% or more, respectively. The similarity of the flora between the point 5 and the other samples was below 70%, and the similarity of point 2 was only 59.2%. Due to the different contribution of different strains to the removal of pollutants, it can give full play to the synergistic effect of bacterial degradation of pollutants, and further improve the efficiency of sewage treatment.

Bacterial Community Profiling of Plastic Litter in the Belgian Part of the North Sea.

PubMed

De Tender, Caroline A; Devriese, Lisa I; Haegeman, Annelies; Maes, Sara; Ruttink, Tom; Dawyndt, Peter

2015-08-18

Bacterial colonization of marine plastic litter (MPL) is known for over four decades. Still, only a few studies on the plastic colonization process and its influencing factors are reported. In this study, seafloor MPL was sampled at different locations across the Belgian part of the North Sea to study bacterial community structure using 16S metabarcoding. These marine plastic bacterial communities were compared with those of sediment and seawater, and resin pellets sampled on the beach, to investigate the origin and uniqueness of plastic bacterial communities. Plastics display great variation of bacterial community composition, while each showed significant differences from those of sediment and seawater, indicating that plastics represent a distinct environmental niche. Various environmental factors correlate with the diversity of MPL bacterial composition across plastics. In addition, intrinsic plastic-related factors such as pigment content may contribute to the differences in bacterial colonization. Furthermore, the differential abundance of known primary and secondary colonizers across the various plastics may indicate different stages of bacterial colonization, and may confound comparisons of free-floating plastics. Our studies provide insights in the factors that shape plastic bacterial colonization and shed light on the possible role of plastic as transport vehicle for bacteria through the aquatic environment.

Nematode grazing promotes bacterial community dynamics in soil at the aggregate level

PubMed Central

Jiang, Yuji; Liu, Manqiang; Zhang, Jiabao; Chen, Yan; Chen, Xiaoyun; Chen, Lijun; Li, Huixin; Zhang, Xue-Xian; Sun, Bo

2017-01-01

Nematode predation has important roles in determining bacterial community composition and dynamics, but the extent of the effects remains largely rudimentary, particularly in natural environment settings. Here, we investigated the complex microbial–microfaunal interactions in the rhizosphere of maize grown in red soils, which were derived from four long-term fertilization regimes. Root-free rhizosphere soil samples were separated into three aggregate fractions whereby the abundance and community composition were examined for nematode and total bacterial communities. A functional group of alkaline phosphomonoesterase (ALP) producing bacteria was included to test the hypothesis that nematode grazing may significantly affect specific bacteria-mediated ecological functions, that is, organic phosphate cycling in soil. Results of correlation analysis, structural equation modeling and interaction networks combined with laboratory microcosm experiments consistently indicated that bacterivorous nematodes enhanced bacterial diversity, and the abundance of bacterivores was positively correlated with bacterial biomass, including ALP-producing bacterial abundance. Significantly, such effects were more pronounced in large macroaggregates than in microaggregates. There was a positive correlation between the most dominant bacterivores Protorhabditis and the ALP-producing keystone 'species' Mesorhizobium. Taken together, these findings implicate important roles of nematodes in stimulating bacterial dynamics in a spatially dependent manner. PMID:28742069

Nematode grazing promotes bacterial community dynamics in soil at the aggregate level.

PubMed

Jiang, Yuji; Liu, Manqiang; Zhang, Jiabao; Chen, Yan; Chen, Xiaoyun; Chen, Lijun; Li, Huixin; Zhang, Xue-Xian; Sun, Bo

2017-12-01

Nematode predation has important roles in determining bacterial community composition and dynamics, but the extent of the effects remains largely rudimentary, particularly in natural environment settings. Here, we investigated the complex microbial-microfaunal interactions in the rhizosphere of maize grown in red soils, which were derived from four long-term fertilization regimes. Root-free rhizosphere soil samples were separated into three aggregate fractions whereby the abundance and community composition were examined for nematode and total bacterial communities. A functional group of alkaline phosphomonoesterase (ALP) producing bacteria was included to test the hypothesis that nematode grazing may significantly affect specific bacteria-mediated ecological functions, that is, organic phosphate cycling in soil. Results of correlation analysis, structural equation modeling and interaction networks combined with laboratory microcosm experiments consistently indicated that bacterivorous nematodes enhanced bacterial diversity, and the abundance of bacterivores was positively correlated with bacterial biomass, including ALP-producing bacterial abundance. Significantly, such effects were more pronounced in large macroaggregates than in microaggregates. There was a positive correlation between the most dominant bacterivores Protorhabditis and the ALP-producing keystone 'species' Mesorhizobium. Taken together, these findings implicate important roles of nematodes in stimulating bacterial dynamics in a spatially dependent manner.

The dual oxidase gene BdDuox regulates the intestinal bacterial community homeostasis of Bactrocera dorsalis

PubMed Central

Yao, Zhichao; Wang, Ailin; Li, Yushan; Cai, Zhaohui; Lemaitre, Bruno; Zhang, Hongyu

2016-01-01

The guts of metazoans are in permanent contact with the microbial realm that includes beneficial symbionts, nonsymbionts, food-borne microbes and life-threatening pathogens. However, little is known concerning how host immunity affects gut bacterial community. Here, we analyze the role of a dual oxidase gene (BdDuox) in regulating the intestinal bacterial community homeostasis of the oriental fruit fly Bactrocera dorsalis. The results showed that knockdown of BdDuox led to an increased bacterial load, and to a decrease in the relative abundance of Enterobacteriaceae and Leuconostocaceae bacterial symbionts in the gut. The resulting dysbiosis, in turn, stimulates an immune response by activating BdDuox and promoting reactive oxygen species (ROS) production that regulates the composition and structure of the gut bacterial community to normal status by repressing the overgrowth of minor pathobionts. Our results suggest that BdDuox plays a pivotal role in regulating the homeostasis of the gut bacterial community in B. dorsalis. PMID:26565723

Field scale molecular analysis for the monitoring of bacterial community structures during on-site diesel bioremediation.

PubMed

Ciric, Lena; Griffiths, Robert I; Philp, James C; Whiteley, Andrew S

2010-07-01

A diesel contaminated groundwater site was surveyed using 16S rRNA gene based analyses to investigate the effect of bioaugmentation on the bacterial communities present. The analyses included the use of denaturing gradient gel electrophoresis (DGGE) to profile microbial community structure and the construction and sequencing of clone libraries in order to identify the organisms present. Community analyses revealed a high degree of similarity in the inoculated compartments during bioaugmentation, not observed once inoculation had ceased. However, it was also shown that there was very little community similarity between the inoculum and the inoculated samples. Instead, the similarity seen during the application of the bioaugmentation treatment was thought to be due to nutrient addition applied along with the inoculum. Furthermore, once the bioaugmentation treatment had ceased the communities around the site became more diverse, suggesting that the hierarchical structure seen during treatment was due to the stimulation of a group of opportunistic indigenous organisms by the nutrients added. The findings not only highlight the importance of monitoring the fate of inocula used in bioaugmentation but also how crucial the process of the selection of species and the culture conditions used in the construction of these consortia. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Structural alterations of faecal and mucosa-associated bacterial communities in irritable bowel syndrome.

PubMed

Durbán, Ana; Abellán, Juan J; Jiménez-Hernández, Nuria; Salgado, Patricia; Ponce, Marta; Ponce, Julio; Garrigues, Vicente; Latorre, Amparo; Moya, Andrés

2012-04-01

Irritable bowel syndrome (IBS) is the most common functional gastrointestinal disorder in western countries. Previous studies on IBS, mostly based on faecal samples, suggest alterations in the intestinal microbiota. However, no consensus has been reached regarding the association between specific bacteria and IBS. We explore the alterations of intestinal bacterial communities in IBS using massive sequencing of amplified 16S rRNA genes. Mucosal biopsies of the ascending and descending colon and faeces from 16 IBS patients and 9 healthy controls were analysed. Strong inter-individual variation was observed in the composition of the bacterial communities in both patients and controls. These communities showed less diversity in IBS cases. There were larger differences in the microbiota composition between biopsies and faeces than between patients and controls. We found a few over-represented and under-represented taxa in IBS cases with respect to controls. The detected alterations varied by site, with no changes being consistent across sample types. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Influence of housing characteristics on bacterial and fungal communities in homes of asthmatic children

PubMed Central

Dannemiller, Karen C.; Gent, Janneane F.; Leaderer, Brian P.; Peccia, Jordan

2015-01-01

Variations in home characteristics, such as moisture and occupancy, affect indoor microbial ecology as well as human exposure to microorganisms. Our objective was to determine how indoor bacterial and fungal community structure and diversity are associated with the broader home environment and its occupants. Next-generation DNA sequencing was used to describe fungal and bacterial communities in house dust sampled from 198 homes of asthmatic children in southern New England. Housing characteristics included number of people/children, level of urbanization, single/multifamily home, reported mold, reported water leaks, air conditioning (AC) use, and presence of pets. Both fungal and bacterial community structure were non-random and demonstrated species segregation (C-score, p<0.00001). Increased microbial richness was associated with the presence of pets, water leaks, longer AC use, suburban (vs. urban) homes, and dust composition measures (p<0.05). The most significant differences in community composition were observed for AC use and occupancy (people, children, and pets) characteristics. Occupant density measures were associated with beneficial bacterial taxa, including Lactobacillus johnsonii as measured by qPCR. A more complete knowledge of indoor microbial communities is useful for linking housing characteristics to human health outcomes. Microbial assemblies in house dust result, in part, from the building’s physical and occupant characteristics. PMID:25833176

Changes in bacterial community after application of three different herbicides.

PubMed

Moretto, Jéssica Aparecida Silva; Altarugio, Lucas Miguel; Andrade, Pedro Avelino; Fachin, Ana Lúcia; Andreote, Fernando Dini; Stehling, Eliana Guedes

2017-07-06

The native soil microbiota is very important to maintain the quality of that environment, but with the intensive use of agrochemicals, changes in microbial biomass and formation of large quantities of toxic waste were observed in soil, groundwater and surface water. Thereby, the goal of this study was to evaluate if the selective pressure exerted by the presence of the herbicides atrazine, diuron and 2,4-D changes the bacterial community structure of an agricultural soil, using denaturing gradient gel electrophoresis technique. According to PERMANOVA analysis, a greater effect of the herbicide persistence time in the soil, the effect of the herbicide class and the effect of interaction between these two factors (persistence time and herbicide class) were observed. In conclusion, the results showed that the selective pressure exerted by the presence of these herbicides altered the composition of the local microbiota, being atrazine and diuron that most significantly affected the bacterial community in soil, and the herbicide 2,4-D was the one that less altered the microbial community and that bacterial community was reestablished first. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Bacterial structures and ecosystem functions in glaciated floodplains: contemporary states and potential future shifts

PubMed Central

Freimann, Remo; Bürgmann, Helmut; Findlay, Stuart EG; Robinson, Christopher T

2013-01-01

Glaciated alpine floodplains are responding quickly to climate change through shrinking ice masses. Given the expected future changes in their physicochemical environment, we anticipated variable shifts in structure and ecosystem functioning of hyporheic microbial communities in proglacial alpine streams, depending on present community characteristics and landscape structures. We examined microbial structure and functioning during different hydrologic periods in glacial (kryal) streams and, as contrasting systems, groundwater-fed (krenal) streams. Three catchments were chosen to cover an array of landscape features, including interconnected lakes, differences in local geology and degree of deglaciation. Community structure was assessed by automated ribosomal intergenic spacer analysis and microbial function by potential enzyme activities. We found each catchment to contain a distinct bacterial community structure and different degrees of separation in structure and functioning that were linked to the physicochemical properties of the waters within each catchment. Bacterial communities showed high functional plasticity, although achieved by different strategies in each system. Typical kryal communities showed a strong linkage of structure and function that indicated a major prevalence of specialists, whereas krenal sediments were dominated by generalists. With the rapid retreat of glaciers and therefore altered ecohydrological characteristics, lotic microbial structure and functioning are likely to change substantially in proglacial floodplains in the future. The trajectory of these changes will vary depending on contemporary bacterial community characteristics and landscape structures that ultimately determine the sustainability of ecosystem functioning. PMID:23842653

Analysis of Structure and Composition of Bacterial Core Communities in Mature Drinking Water Biofilms and Bulk Water of a Citywide Network in Germany

PubMed Central

Henne, Karsten; Kahlisch, Leila; Brettar, Ingrid

2012-01-01

The bacterial core communities of bulk water and corresponding biofilms of a more than 20-year-old drinking water network were compared using 16S rRNA single-strand confirmation polymorphism (SSCP) fingerprints based on extracted DNA and RNA. The structure and composition of the bacterial core community in the bulk water was highly similar (>70%) across the city of Braunschweig, Germany, whereas all biofilm samples contained a unique community with no overlapping phylotypes from bulk water. Biofilm samples consisted mainly of Alphaproteobacteria (26% of all phylotypes), Gammaproteobacteria (11%), candidate division TM6 (11%), Chlamydiales (9%), and Betaproteobacteria (9%). The bulk water community consisted primarily of Bacteroidetes (25%), Betaproteobacteria (20%), Actinobacteria (16%), and Alphaproteobacteria (11%). All biofilm communities showed higher relative abundances of single phylotypes and a reduced richness compared to bulk water. Only biofilm communities sampled at nearby sampling points showed similar communities irrespective of support materials. In all of our bulk water studies, the community composition determined from 16S rRNA was completely different from the 16S rRNA gene-based community composition, whereas in biofilms both molecular fractions resulted in community compositions that were similar to each other. We hypothesize that a higher fraction of active bacterial phylotypes and a better protection from oxidative stress in drinking water biofilms are responsible for this higher similarity. PMID:22389373

Analysis of structure and composition of bacterial core communities in mature drinking water biofilms and bulk water of a citywide network in Germany.

PubMed

Henne, Karsten; Kahlisch, Leila; Brettar, Ingrid; Höfle, Manfred G

2012-05-01

The bacterial core communities of bulk water and corresponding biofilms of a more than 20-year-old drinking water network were compared using 16S rRNA single-strand confirmation polymorphism (SSCP) fingerprints based on extracted DNA and RNA. The structure and composition of the bacterial core community in the bulk water was highly similar (>70%) across the city of Braunschweig, Germany, whereas all biofilm samples contained a unique community with no overlapping phylotypes from bulk water. Biofilm samples consisted mainly of Alphaproteobacteria (26% of all phylotypes), Gammaproteobacteria (11%), candidate division TM6 (11%), Chlamydiales (9%), and Betaproteobacteria (9%). The bulk water community consisted primarily of Bacteroidetes (25%), Betaproteobacteria (20%), Actinobacteria (16%), and Alphaproteobacteria (11%). All biofilm communities showed higher relative abundances of single phylotypes and a reduced richness compared to bulk water. Only biofilm communities sampled at nearby sampling points showed similar communities irrespective of support materials. In all of our bulk water studies, the community composition determined from 16S rRNA was completely different from the 16S rRNA gene-based community composition, whereas in biofilms both molecular fractions resulted in community compositions that were similar to each other. We hypothesize that a higher fraction of active bacterial phylotypes and a better protection from oxidative stress in drinking water biofilms are responsible for this higher similarity.

High-Resolution Melt Analysis for Rapid Comparison of Bacterial Community Compositions

PubMed Central

Hjelmsø, Mathis Hjort; Hansen, Lars Hestbjerg; Bælum, Jacob; Feld, Louise; Holben, William E.

2014-01-01

In the study of bacterial community composition, 16S rRNA gene amplicon sequencing is today among the preferred methods of analysis. The cost of nucleotide sequence analysis, including requisite computational and bioinformatic steps, however, takes up a large part of many research budgets. High-resolution melt (HRM) analysis is the study of the melt behavior of specific PCR products. Here we describe a novel high-throughput approach in which we used HRM analysis targeting the 16S rRNA gene to rapidly screen multiple complex samples for differences in bacterial community composition. We hypothesized that HRM analysis of amplified 16S rRNA genes from a soil ecosystem could be used as a screening tool to identify changes in bacterial community structure. This hypothesis was tested using a soil microcosm setup exposed to a total of six treatments representing different combinations of pesticide and fertilization treatments. The HRM analysis identified a shift in the bacterial community composition in two of the treatments, both including the soil fumigant Basamid GR. These results were confirmed with both denaturing gradient gel electrophoresis (DGGE) analysis and 454-based 16S rRNA gene amplicon sequencing. HRM analysis was shown to be a fast, high-throughput technique that can serve as an effective alternative to gel-based screening methods to monitor microbial community composition. PMID:24610853

Antagonistic interactions are sufficient to explain self-assemblage of bacterial communities in a homogeneous environment: a computational modeling approach

PubMed Central

Zapién-Campos, Román; Olmedo-Álvarez, Gabriela; Santillán, Moisés

2015-01-01

Most of the studies in Ecology have been devoted to analyzing the effects the environment has on individuals, populations, and communities, thus neglecting the effects of biotic interactions on the system dynamics. In the present work we study the structure of bacterial communities in the oligotrophic shallow water system of Churince, Cuatro Cienegas, Mexico. Since the physicochemical conditions of this water system are homogeneous and quite stable in time, it is an excellent candidate to study how biotic factors influence the structure of bacterial communities. In a previous study, the binary antagonistic interactions of 78 bacterial strains, isolated from Churince, were experimentally determined. We employ these data to develop a computer algorithm to simulate growth experiments in a cellular grid representing the pond. Remarkably, in our model, the dynamics of all the simulated bacterial populations is determined solely by antagonistic interactions. Our results indicate that all bacterial strains (even those that are antagonized by many other bacteria) survive in the long term, and that the underlying mechanism is the formation of bacterial community patches. Patches corresponding to less antagonistic and highly susceptible strains are consistently isolated from the highly-antagonistic bacterial colonies by patches of neutral strains. These results concur with the observed features of the bacterial community structure previously reported. Finally, we study how our findings depend on factors like initial population size, differential population growth rates, homogeneous population death rates, and enhanced bacterial diffusion. PMID:26052318

Significance of treated agrowaste residue and autochthonous inoculates (Arbuscular mycorrhizal fungi and Bacillus cereus) on bacterial community structure and phytoextraction to remediate soils contaminated with heavy metals.

PubMed

Azcón, Rosario; Medina, Almudena; Roldán, Antonio; Biró, Borbála; Vivas, Astrid

2009-04-01

In this study, we analyzed the impact of treatments such as Aspergillus niger-treated sugar beet waste (SB), PO4(3-) fertilization and autochthonous inoculants [arbuscular mycorrhizal (AM) fungi and Bacillus cereus], on the bacterial community structure in a soils contaminated with heavy metals as well as, the effectiveness on plant growth (Trifolium repens). The inoculation with AM fungi in SB amended soil, increased plant growth similarly to PO4(3-) addition, and both treatments matched in P acquisition but bacterial biodiversity estimated by denaturing gradient gel electrophoresis of amplified 16S rDNA sequences, was more stimulated by the presence of the AM fungus than by PO4(3-) fertilization. The SB amendment plus AM inoculation increased the microbial diversity by 233% and also changed (by 215%) the structure of the bacterial community. The microbial inoculants and amendment used favoured plant growth and the phytoextraction process and concomitantly modified bacterial community in the rhizosphere; thus they can be used for remediation. Therefore, the understanding of such microbial ecological aspects is important for phytoremediation and the recovery of contaminated soils.

The social structure of microbial community involved in colonization resistance.

PubMed

He, Xuesong; McLean, Jeffrey S; Guo, Lihong; Lux, Renate; Shi, Wenyuan

2014-03-01

It is well established that host-associated microbial communities can interfere with the colonization and establishment of microbes of foreign origins, a phenomenon often referred to as bacterial interference or colonization resistance. However, due to the complexity of the indigenous microbiota, it has been extremely difficult to elucidate the community colonization resistance mechanisms and identify the bacterial species involved. In a recent study, we have established an in vitro mice oral microbial community (O-mix) and demonstrated its colonization resistance against an Escherichia coli strain of mice gut origin. In this study, we further analyzed the community structure of the O-mix by using a dilution/regrowth approach and identified the bacterial species involved in colonization resistance against E. coli. Our results revealed that, within the O-mix there were three different types of bacterial species forming unique social structure. They act as 'Sensor', 'Mediator' and 'Killer', respectively, and have coordinated roles in initiating the antagonistic action and preventing the integration of E. coli. The functional role of each identified bacterial species was further confirmed by E. coli-specific responsiveness of the synthetic communities composed of different combination of the identified players. The study reveals for the first time the sophisticated structural and functional organization of a colonization resistance pathway within a microbial community. Furthermore, our results emphasize the importance of 'Facilitation' or positive interactions in the development of community-level functions, such as colonization resistance.

Bacterial community structure transformed after thermophilically composting human waste in Haiti

PubMed Central

Kramer, Sasha; Roy, Monika; Reid, Francine C.; Dubinsky, Eric A.

2017-01-01

Recycling human waste for beneficial use has been practiced for millennia. Aerobic (thermophilic) composting of sewage sludge has been shown to reduce populations of opportunistically pathogenic bacteria and to inactivate both Ascaris eggs and culturable Escherichia coli in raw waste, but there is still a question about the fate of most fecal bacteria when raw material is composted directly. This study undertook a comprehensive microbial community analysis of composting material at various stages collected over 6 months at two composting facilities in Haiti. The fecal microbiota signal was monitored using a high-density DNA microarray (PhyloChip). Thermophilic composting altered the bacterial community structure of the starting material. Typical fecal bacteria classified in the following groups were present in at least half the starting material samples, yet were reduced below detection in finished compost: Prevotella and Erysipelotrichaceae (100% reduction of initial presence), Ruminococcaceae (98–99%), Lachnospiraceae (83–94%, primarily unclassified taxa remained), Escherichia and Shigella (100%). Opportunistic pathogens were reduced below the level of detection in the final product with the exception of Clostridium tetani, which could have survived in a spore state or been reintroduced late in the outdoor maturation process. Conversely, thermotolerant or thermophilic Actinomycetes and Firmicutes (e.g., Thermobifida, Bacillus, Geobacillus) typically found in compost increased substantially during the thermophilic stage. This community DNA-based assessment of the fate of human fecal microbiota during thermophilic composting will help optimize this process as a sanitation solution in areas where infrastructure and resources are limited. PMID:28570610

Effects of low dose silver nanoparticle treatment on the structure and community composition of bacterial freshwater biofilms.

PubMed

Grün, Alexandra Y; App, Constantin B; Breidenbach, Andreas; Meier, Jutta; Metreveli, George; Schaumann, Gabriele E; Manz, Werner

2018-01-01

The application of engineered silver nanoparticles (AgNPs) in a considerable amount of registered commercial products inevitably will result in the continuous release of AgNPs into the natural aquatic environment. Therefore, native biofilms, as the prominent life form of microorganisms in almost all known ecosystems, will be subjected to AgNP exposure. Despite the exponentially growing research activities worldwide, it is still difficult to assess nanoparticle-mediated toxicity in natural environments. In order to obtain an ecotoxicologically relevant exposure scenario, we performed experiments with artificial stream mesocosm systems approaching low dose AgNP concentrations close to predicted environmental concentrations. Pregrown freshwater biofilms were exposed for 14 days to citrate-stabilized AgNPs at a concentration of 600 μg l-1 in two commonly used sizes (30 and 70 nm). Sublethal effects of AgNP treatment were assessed with regard to biofilm structure by gravimetric measurements (biofilm thickness and density) and by two biomass parameters, chlorophyll a and protein content. The composition of bacterial biofilm communities was characterized by t-RFLP fingerprinting combined with phylogenetic studies based on the 16S gene. After 14 days of treatment, the structural parameters of the biofilm such as thickness, density, and chlorophyll a and protein content were not statistically significantly changed by AgNP exposure. Furthermore, t-RFLP fingerprint analysis showed that the bacterial diversity was not diminished by AgNPs, as calculated by Shannon Wiener and evenness indices. Nevertheless, t-RFLP analysis also indicated that AgNPs led to an altered biofilm community composition as was shown by cluster analysis and multidimensional scaling (MDS) based on the Bray Curtis index. Sequence analysis of cloned 16S rRNA genes further revealed that changes in community composition were related with the displacement of putatively AgNP-sensitive bacterial taxa

Development of bacterial communities in biological soil crusts along a revegetation chronosequence in the Tengger Desert, northwest China

NASA Astrophysics Data System (ADS)

Liu, Lichao; Liu, Yubing; Zhang, Peng; Song, Guang; Hui, Rong; Wang, Zengru; Wang, Jin

2017-08-01

Knowledge of structure and function of microbial communities in different successional stages of biological soil crusts (BSCs) is still scarce for desert areas. In this study, Illumina MiSeq sequencing was used to assess the compositional changes of bacterial communities in different ages of BSCs in the revegetation of Shapotou in the Tengger Desert. The most dominant phyla of bacterial communities shifted with the changed types of BSCs in the successional stages, from Firmicutes in mobile sand and physical crusts to Actinobacteria and Proteobacteria in BSCs, and the most dominant genera shifted from Bacillus, Enterococcus and Lactococcus to RB41_norank and JG34-KF-361_norank. Alpha diversity and quantitative real-time polymerase chain reaction (PCR) analysis indicated that bacterial richness and abundance reached their highest levels after 15 years of BSC development. Redundancy analysis showed that silt + clay content and total K were the prime determinants of the bacterial communities of BSCs. The results suggested that bacterial communities of BSCs recovered quickly with the improved soil physicochemical properties in the early stages of BSC succession. Changes in the bacterial community structure may be an important indicator in the biogeochemical cycling and nutrient storage in early successional stages of BSCs in desert ecosystems.

Influence of housing characteristics on bacterial and fungal communities in homes of asthmatic children.

PubMed

Dannemiller, K C; Gent, J F; Leaderer, B P; Peccia, J

2016-04-01

Variations in home characteristics, such as moisture and occupancy, affect indoor microbial ecology as well as human exposure to microorganisms. Our objective was to determine how indoor bacterial and fungal community structure and diversity are associated with the broader home environment and its occupants. Next-generation DNA sequencing was used to describe fungal and bacterial communities in house dust sampled from 198 homes of asthmatic children in southern New England. Housing characteristics included number of people/children, level of urbanization, single/multifamily home, reported mold, reported water leaks, air conditioning (AC) use, and presence of pets. Both fungal and bacterial community structures were non-random and demonstrated species segregation (C-score, P < 0.00001). Increased microbial richness was associated with the presence of pets, water leaks, longer AC use, suburban (vs. urban) homes, and dust composition measures (P < 0.05). The most significant differences in community composition were observed for AC use and occupancy (people, children, and pets) characteristics. Occupant density measures were associated with beneficial bacterial taxa, including Lactobacillus johnsonii as measured by qPCR. A more complete knowledge of indoor microbial communities is useful for linking housing characteristics to human health outcomes. Microbial assemblies in house dust result, in part, from the building's physical and occupant characteristics. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

[Effects of different catch modes on soil enzyme activities and bacterial community in the rhizosphere of cucumber].

PubMed

Li, Min; Wu, Feng-zhi

2014-12-01

Effects of different catch modes on soil enzyme activities and bacterial community in the rhizosphere of cucumber (Cucumis sativus) were analyzed by conventional chemical method, PCR-denaturing gradient gel electrophoresis (DGGE) and real-time PCR methods. Pot experiment was carried out in the greenhouse for three consecutive years with cucumber as the main crop, and scallion (Allium fistulosum), wheat (Triticum aestivum) and oilseed rape (Brassica campestri) as catch crops. Results showed that, with the increase of crop planting times, soil urease, neutral phosphatase and invertase activities in the wheat treatment were significantly) higher than in the scallion and oilseed rape treatments, and these enzyme activities in the oilseed rape treatment were significantly higher than in the scallion treatment. PCR-DGGR analysis showed that cucumber rhizosphere bacterial community structures were different among treatments. Scallion and wheat treatments maintained relatively higher diversity indices of bacterial community structure. qPCR results showed that the abundance of soil bacterial community in the wheat treatment was significantly higher than in the scallion and oilseed rape treatments. In conclusion, different catch treatments affected soil enzyme activities and bacteria community and changed the soil environment. Wheat used as summer catch crop could maintain relatively higher soil enzyme activities, bacterial community diversity and abundance.

[Changes of bacterial community structure on reusing domestic sewage of Daoxianghujing Hotel to landscape water].

PubMed

Zhu, Jing-nan; Wang, Xiao-dan; Zhai, Zhen-hua; Ma, Wen-lin; Li, Rong-qi; Wang, Xue-lian; Li, Yan-hong

2010-05-01

A 16S rDNA library was used to evaluate the bacterial diversity and identify dominant groups of bacteria in different treatment pools in the domestic sewage system of the Beijing Daoxianghujing Hotel. The results revealed that there were many types of bacteria in the hotel domestic sewage, and the bacterial Shannon-Weaver diversity index was 3.12. In addition, epsilon Proteobacteria was found to be the dominant group with the ratio of 32%. In addition, both the CFB phylum, Fusobacteria, gamma Proteobacteria and Firmicutes were also reached to 9%-15%. After treated with the reclaimed water station, the bacterial Shannon-Weaver diversity index was reduced to 2. 41 and beta Proteobacteria became the dominant group and occupied 73% of the total clones. However, following artificial wetland training, the bacterial Shannon-Weaver diversity index in the sample increased to 3.38, Actinobacteria arrived to 33% and became the most dominant group; Cyanobacteria reached to 26%, and was the second dominant group. But, the control sample comprised 38% Cyanobacteria, and mainly involved in Cyanobium, Synechoccus and Microcystis, with ratios of 47.1%, 17.6% and 8.8%, respectively. Some bacteria of Microcystis aenruginosa were also detected, which probably resulted in the light bloom finally. Therefore, the bacterial diversity and community structures changed in response to treatment of the hotel domestic sewage; there was no cyanobacteria bloom explosion in the treated water. This study will aid in investigation the changes of microbial ecology in different types of water and providing the useful information for enhancing the cyanobacteria blooms control from ecological angle.

The Bacterial Community Structure of Hydrocarbon-Polluted Marine Environments as the Basis for the Definition of an Ecological Index of Hydrocarbon Exposure

PubMed Central

Lozada, Mariana; Marcos, Magalí S.; Commendatore, Marta G.; Gil, Mónica N.; Dionisi, Hebe M.

2014-01-01

The aim of this study was to design a molecular biological tool, using information provided by amplicon pyrosequencing of 16S rRNA genes, that could be suitable for environmental assessment and bioremediation in marine ecosystems. We selected 63 bacterial genera that were previously linked to hydrocarbon biodegradation, representing a minimum sample of the bacterial guild associated with this process. We defined an ecological indicator (ecological index of hydrocarbon exposure, EIHE) using the relative abundance values of these genera obtained by pyrotag analysis. This index reflects the proportion of the bacterial community that is potentially capable of biodegrading hydrocarbons. When the bacterial community structures of intertidal sediments from two sites with different pollution histories were analyzed, 16 of the selected genera (25%) were significantly overrepresented with respect to the pristine site, in at least one of the samples from the polluted site. Although the relative abundances of individual genera associated with hydrocarbon biodegradation were generally low in samples from the polluted site, EIHE values were 4 times higher than those in the pristine sample, with at least 5% of the bacterial community in the sediments being represented by the selected genera. EIHE values were also calculated in other oil-exposed marine sediments as well as in seawater using public datasets from experimental systems and field studies. In all cases, the EIHE was significantly higher in oiled than in unpolluted samples, suggesting that this tool could be used as an estimator of the hydrocarbon-degrading potential of microbial communities. PMID:24964812

The bacterial community structure of hydrocarbon-polluted marine environments as the basis for the definition of an ecological index of hydrocarbon exposure.

PubMed

Lozada, Mariana; Marcos, Magalí S; Commendatore, Marta G; Gil, Mónica N; Dionisi, Hebe M

2014-09-17

The aim of this study was to design a molecular biological tool, using information provided by amplicon pyrosequencing of 16S rRNA genes, that could be suitable for environmental assessment and bioremediation in marine ecosystems. We selected 63 bacterial genera that were previously linked to hydrocarbon biodegradation, representing a minimum sample of the bacterial guild associated with this process. We defined an ecological indicator (ecological index of hydrocarbon exposure, EIHE) using the relative abundance values of these genera obtained by pyrotag analysis. This index reflects the proportion of the bacterial community that is potentially capable of biodegrading hydrocarbons. When the bacterial community structures of intertidal sediments from two sites with different pollution histories were analyzed, 16 of the selected genera (25%) were significantly overrepresented with respect to the pristine site, in at least one of the samples from the polluted site. Although the relative abundances of individual genera associated with hydrocarbon biodegradation were generally low in samples from the polluted site, EIHE values were 4 times higher than those in the pristine sample, with at least 5% of the bacterial community in the sediments being represented by the selected genera. EIHE values were also calculated in other oil-exposed marine sediments as well as in seawater using public datasets from experimental systems and field studies. In all cases, the EIHE was significantly higher in oiled than in unpolluted samples, suggesting that this tool could be used as an estimator of the hydrocarbon-degrading potential of microbial communities.

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.

Soil bacterial community shifts associated with sugarcane straw removal

NASA Astrophysics Data System (ADS)

Pimentel, Laisa; Gumiere, Thiago; Andreote, Fernando; Cerri, Carlos

2017-04-01

In Brazil, the adoption of the mechanical unburned sugarcane harvest potentially increase the quantity of residue left in the field after harvesting. Economically, this material has a high potential for second generation ethanol (2G) production. However, crop residues have an essential role in diverse properties and processes in the soil. The greater part of the uncertainties about straw removal for 2G ethanol production is based on its effects in soil microbial community. In this sense, it is important to identify the main impacts of sugarcane straw removal on soil microbial community. Therefore, we conducted a field study, during one year, in Valparaíso (São Paulo state - Brazil) to evaluate the effects of straw decomposition on soil bacterial community. Specifically, we wanted: i) to compare the rates of straw removal and ii) to evaluate the effects of straw decomposition on soil bacterial groups over one year. The experiment was in a randomized block design with treatments arranged in strip plot. The treatments are different rates of sugarcane straw removal, namely: no removal, 50, 75 and 100% of straw removal. Soil sampling was carried out at 0, 4, 8 and 12 months after the sugarcane harvest (August 2015). Total DNA was extracted from soil using the PowersoilTM DNA Isolation kit. And the abundance of bacterial in each soil sample was estimated via quantification of 16S rRNA gene. The composition of the bacterial communities was estimated via terminal restriction fragment length polymorphism (T-RFLP) analysis, and the T-RF sizes were performed on a 3500 Genetic Analyzer. Finally, the results were examined with GeneMapper 4.1 software. There was bacterial community shifts through the time and among the rates of sugarcane straw removal. Bacterial community was firstly determined by the time scale, which explained 29.16% of total variation. Rates of straw removal explained 11.55% of shifts on bacterial community. Distribution through the time is an important

Perturbation of seafloor bacterial community structure by drilling waste discharge.

PubMed

Nguyen, Tan T; Cochrane, Sabine K J; Landfald, Bjarne

2018-04-01

Offshore drilling operations result in the generation of drill cuttings and localized smothering of the benthic habitats. This study explores bacterial community changes in the in the upper layers of the seafloor resulting from an exploratory drilling operation at 1400m water depth on the Barents Sea continental slope. Significant restructurings of the sediment microbiota were restricted to the sampling sites notably affected by the drilling waste discharge, i.e. at 30m and 50m distances from the drilling location, and to the upper 2cm of the seafloor. Three bacterial groups, the orders Clostridiales and Desulfuromonadales and the class Mollicutes, were almost exclusively confined to the upper two centimeters at 30m distance, thereby corroborating an observed increase in anaerobicity inflicted by the drilling waste deposition. The potential of these phylogenetic groups as microbial bioindicators of the spatial extent and persistence of drilling waste discharge should be further explored. Copyright © 2017 Elsevier Ltd. All rights reserved.

New insights into the spatial variability of biofilm communities and potentially negative bacterial groups in hydraulic concrete structures.

PubMed

Cai, Wei; Li, Yi; Niu, Lihua; Zhang, Wenlong; Wang, Chao; Wang, Peifang; Meng, Fangang

2017-10-15

The composition and distribution characteristics of bacterial communities in biofilms attached to hydraulic concrete structure (HCS) surfaces were investigated for the first time in four reservoirs in the middle and lower reaches of the Yangtze River Basin using 16S rRNA Miseq sequencing. High microbial diversity was found in HCS biofilms, and notable differences were observed in different types of HCS. Proteobacteria, Cyanobacteria and Chloroflexi were the predominant phyla, with respective relative abundances of 35.3%, 25.4% and 13.0%. The three most abundant genera were Leptolyngbya, Anaerolineaceae and Polynucleobacter. The phyla Beta-proteobacteria and Firmicutes and genus Lyngbya were predominant in CGP, whereas the phyla Cyanobacteria and Chloroflexi and genera Leptolyngbya, Anaerolinea and Polynucleobacter survived better in land walls and bank slopes. Dissolved oxygen, ammonia nitrogen and temperature were characterized as the main factors driving the bacterial community composition. The most abundant groups of metabolic functions were also identified as ammonia oxidizers, sulphate reducers, and dehalogenators. Additionally, functional groups related to biocorrosion were found to account for the largest proportion (14.0% of total sequences) in gate piers, followed by those in land walls (11.5%) and bank slopes (10.2%). Concrete gate piers were at the greatest risk of biocorrosion with the most abundant negative bacterial groups, especially for sulphate reducers. Thus, it should be paid high attention to the biocorrosion prevention of concrete gate piers. Overall, this study contributed to the optimization of microbial control and the improvement of the safety management for water conservation structures. Copyright © 2017 Elsevier Ltd. All rights reserved.

Safe-Site Effects on Rhizosphere Bacterial Communities in a High-Altitude Alpine Environment

PubMed Central

Zerbe, Stefan

2014-01-01

The rhizosphere effect on bacterial communities associated with three floristic communities (RW, FI, and M sites) which differed for the developmental stages was studied in a high-altitude alpine ecosystem. RW site was an early developmental stage, FI was an intermediate stage, M was a later more matured stage. The N and C contents in the soils confirmed a different developmental stage with a kind of gradient from the unvegetated bare soil (BS) site through RW, FI up to M site. The floristic communities were composed of 21 pioneer plants belonging to 14 species. Automated ribosomal intergenic spacer analysis showed different bacterial genetic structures per each floristic consortium which differed also from the BS site. When plants of the same species occurred within the same site, almost all their bacterial communities clustered together exhibiting a plant species effect. Unifrac significance value (P < 0.05) on 16S rRNA gene diversity revealed significant differences (P < 0.05) between BS site and the vegetated sites with a weak similarity to the RW site. The intermediate plant colonization stage FI did not differ significantly from the RW and the M vegetated sites. These results pointed out the effect of different floristic communities rhizospheres on their soil bacterial communities. PMID:24995302

pH is the primary determinant of the bacterial community structure in agricultural soils impacted by polycyclic aromatic hydrocarbon pollution

NASA Astrophysics Data System (ADS)

Wu, Yucheng; Zeng, Jun; Zhu, Qinghe; Zhang, Zhenfa; Lin, Xiangui

2017-01-01

Acidification and pollution are two major threats to agricultural ecosystems; however, microbial community responses to co-existed soil acidification and pollution remain less explored. In this study, arable soils of broad pH (4.26-8.43) and polycyclic aromatic hydrocarbon (PAH) gradients (0.18-20.68 mg kg-1) were collected from vegetable farmlands. Bacterial community characteristics including abundance, diversity and composition were revealed by quantitative PCR and high-throughput sequencing. The bacterial 16S rRNA gene copies significantly correlated with soil carbon and nitrogen contents, suggesting the control of nutrients accessibility on bacterial abundance. The bacterial diversity was strongly related to soil pH, with higher diversity in neutral samples and lower in acidic samples. Soil pH was also identified by an ordination analysis as important factor shaping bacterial community composition. The relative abundances of some dominant phyla varied along the pH gradient, and the enrichment of a few phylotypes suggested their adaptation to low pH condition. In contrast, at the current pollution level, PAH showed marginal effects on soil bacterial community. Overall, these findings suggest pH was the primary determinant of bacterial community in these arable soils, indicative of a more substantial influence of acidification than PAH pollution on bacteria driven ecological processes.

Characterization of the bacterial communities of life stages of free living lone star ticks (Amblyomma americanum).

PubMed

Williams-Newkirk, Amanda Jo; Rowe, Lori A; Mixson-Hayden, Tonya R; Dasch, Gregory A

2014-01-01

The lone star tick (Amblyomma americanum) is an abundant and aggressive biter of humans, domestic animals, and wildlife in the southeastern-central USA and an important vector of several known and suspected zoonotic bacterial pathogens. However, the biological drivers of bacterial community variation in this tick are still poorly defined. Knowing the community context in which tick-borne bacterial pathogens exist and evolve is required to fully understand the ecology and immunobiology of the ticks and to design effective public health and veterinary interventions. We performed a metagenomic survey of the bacterial communities of questing A. americanum and tested 131 individuals (66 nymphs, 24 males, and 41 females) from five sites in three states. Pyrosequencing was performed with barcoded eubacterial primers targeting variable 16S rRNA gene regions 5-3. The bacterial communities were dominated by Rickettsia (likely R. amblyommii) and an obligate Coxiella symbiont, together accounting for 6.7-100% of sequences per tick. DNAs from Midichloria, Borrelia, Wolbachia, Ehrlichia, Pseudomonas, or unidentified Bacillales, Enterobacteriaceae, or Rhizobiales groups were also detected frequently. Wolbachia and Midichloria significantly co-occurred in Georgia (p<0.00001), but not in other states. The significance of the Midichloria-Wolbachia co-occurrence is unknown. Among ticks collected in Georgia, nymphs differed from adults in both the composition (p = 0.002) and structure (p = 0.002) of their bacterial communities. Adults differed only in their community structure (p = 0.002) with males containing more Rickettsia and females containing more Coxiella. Comparisons among adult ticks collected in New York and North Carolina supported the findings from the Georgia collection despite differences in geography, collection date, and sample handling, implying that the differences detected are consistent attributes. The data also suggest that some members of the

Spatio-temporal variability of airborne bacterial communities and their correlation with particulate matter chemical composition across two urban areas.

PubMed

Gandolfi, I; Bertolini, V; Bestetti, G; Ambrosini, R; Innocente, E; Rampazzo, G; Papacchini, M; Franzetti, A

2015-06-01

The study of spatio-temporal variability of airborne bacterial communities has recently gained importance due to the evidence that airborne bacteria are involved in atmospheric processes and can affect human health. In this work, we described the structure of airborne microbial communities in two urban areas (Milan and Venice, Northern Italy) through the sequencing, by the Illumina platform, of libraries containing the V5-V6 hypervariable regions of the 16S rRNA gene and estimated the abundance of airborne bacteria with quantitative PCR (qPCR). Airborne microbial communities were dominated by few taxa, particularly Burkholderiales and Actinomycetales, more abundant in colder seasons, and Chloroplasts, more abundant in warmer seasons. By partitioning the variation in bacterial community structure, we could assess that environmental and meteorological conditions, including variability between cities and seasons, were the major determinants of the observed variation in bacterial community structure, while chemical composition of atmospheric particulate matter (PM) had a minor contribution. Particularly, Ba, SO4 (2-) and Mg(2+) concentrations were significantly correlated with microbial community structure, but it was not possible to assess whether they simply co-varied with seasonal shifts of bacterial inputs to the atmosphere, or their variation favoured specific taxa. Both local sources of bacteria and atmospheric dispersal were involved in the assembling of airborne microbial communities, as suggested, to the one side by the large abundance of bacteria typical of lagoon environments (Rhodobacterales) observed in spring air samples from Venice and to the other by the significant effect of wind speed in shaping airborne bacterial communities at all sites.

Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators

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

Wu, C.H.; Sercu, B.; Van De Werhorst, L.C.

2010-03-01

Microbial communities in aquatic environments are spatially and temporally dynamic due to environmental fluctuations and varied external input sources. A large percentage of the urban watersheds in the United States are affected by fecal pollution, including human pathogens, thus warranting comprehensive monitoring. Using a high-density microarray (PhyloChip), we examined water column bacterial community DNA extracted from two connecting urban watersheds, elucidating variable and stable bacterial subpopulations over a 3-day period and community composition profiles that were distinct to fecal and non-fecal sources. Two approaches were used for indication of fecal influence. The first approach utilized similarity of 503 operational taxonomicmore » units (OTUs) common to all fecal samples analyzed in this study with the watershed samples as an index of fecal pollution. A majority of the 503 OTUs were found in the phyla Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. The second approach incorporated relative richness of 4 bacterial classes (Bacilli, Bacteroidetes, Clostridia and a-proteobacteria) found to have the highest variance in fecal and non-fecal samples. The ratio of these 4 classes (BBC:A) from the watershed samples demonstrated a trend where bacterial communities from gut and sewage sources had higher ratios than from sources not impacted by fecal material. This trend was also observed in the 124 bacterial communities from previously published and unpublished sequencing or PhyloChip- analyzed studies. This study provided a detailed characterization of bacterial community variability during dry weather across a 3-day period in two urban watersheds. The comparative analysis of watershed community composition resulted in alternative community-based indicators that could be useful for assessing ecosystem health.« less

Characterization of Coastal Urban Watershed Bacterial Communities Leads to Alternative Community-Based Indicators

PubMed Central

Wu, Cindy H.; Sercu, Bram; Van De Werfhorst, Laurie C.; Wong, Jakk; DeSantis, Todd Z.; Brodie, Eoin L.; Hazen, Terry C.; Holden, Patricia A.; Andersen, Gary L.

2010-01-01

Background Microbial communities in aquatic environments are spatially and temporally dynamic due to environmental fluctuations and varied external input sources. A large percentage of the urban watersheds in the United States are affected by fecal pollution, including human pathogens, thus warranting comprehensive monitoring. Methodology/Principal Findings Using a high-density microarray (PhyloChip), we examined water column bacterial community DNA extracted from two connecting urban watersheds, elucidating variable and stable bacterial subpopulations over a 3-day period and community composition profiles that were distinct to fecal and non-fecal sources. Two approaches were used for indication of fecal influence. The first approach utilized similarity of 503 operational taxonomic units (OTUs) common to all fecal samples analyzed in this study with the watershed samples as an index of fecal pollution. A majority of the 503 OTUs were found in the phyla Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. The second approach incorporated relative richness of 4 bacterial classes (Bacilli, Bacteroidetes, Clostridia and α-proteobacteria) found to have the highest variance in fecal and non-fecal samples. The ratio of these 4 classes (BBC∶A) from the watershed samples demonstrated a trend where bacterial communities from gut and sewage sources had higher ratios than from sources not impacted by fecal material. This trend was also observed in the 124 bacterial communities from previously published and unpublished sequencing or PhyloChip- analyzed studies. Conclusions/Significance This study provided a detailed characterization of bacterial community variability during dry weather across a 3-day period in two urban watersheds. The comparative analysis of watershed community composition resulted in alternative community-based indicators that could be useful for assessing ecosystem health. PMID:20585654

Responses of soil microbial biomass and bacterial community structure to closed-off management (an ecological natural restoration measures): A case study of Dongting Lake wetland, middle China.

PubMed

Dai, Juan; Wu, Haipeng; Zhang, Chang; Zeng, Guangming; Liang, Jie; Guo, Shenglian; Li, Xiaodong; Huang, Lu; Lu, Lunhui; Yuan, Yujie

2016-09-01

Soil microbial biomass (SMB) and bacterial community structure, which are critical to global ecosystem and fundamental ecological processes, are sensitive to anthropogenic activities and environmental conditions. In this study, we examined the possible effects of closed-off management (an ecological natural restoration measures, ban on anthropogenic activity, widely employed for many important wetlands) on SMB, soil bacterial community structure and functional marker genes of nitrogen cycling in Dongting Lake wetland. Soil samples were collected from management area (MA) and contrast area (CA: human activities, such as hunting, fishing and draining, are permitted) in November 2013 and April 2014. Soil properties, microbial biomass carbon (MBC), and bacterial community structure were investigated. Comparison of the values of MA and CA showed that SMB and bacterial community diversity of the MA had a significant increase after 7 years closed-off management. The mean value of Shannon-Weiner diversity index of MA and CA respectively were 2.85 and 2.07. The gene copy numbers of 16S rRNA and nosZ of MA were significant higher than those of CA. the gene copy numbers of ammonia-oxidizing archaea (AOA) and nirK of MA were significant lower than those of CA. However, there was no significant change in the gene copy numbers of ammonia-oxidizing bacteria (AOB) and nirS. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Distinct responses of bacterial communities to agricultural and urban impacts in temperate southern African estuaries

NASA Astrophysics Data System (ADS)

Matcher, G. F.; Froneman, P. W.; Meiklejohn, I.; Dorrington, R. A.

2018-01-01

Worldwide, estuaries are regarded as amongst the most ecologically threatened ecosystems and are increasingly being impacted by urban development, agricultural activities and reduced freshwater inflow. In this study, we examined the influence of different human activities on the diversity and structure of bacterial communities in the water column and sediment in three distinct, temperate permanently open estuarine systems within the same geographic region of southern Africa. The Kariega system is freshwater-deprived and is considered to be relatively pristine; the Kowie estuary is marine-dominated and impacted by urban development, while the Sundays system is fresh-water dominated and impacted by agricultural activity in its catchment. The bacterial communities in all three systems comprise predominantly heterotrophic species belonging to the Bacteroidetes and Proteobacteria phyla with little overlap between bacterioplankton and benthic bacterial communities at the species level. There was overlap between the operational taxonomic units (OTUs) of the Kowie and Kariega, both marine-influenced estuaries. However, lower species richness in the Kowie, likely reflects the impact of human settlements along the estuary. The dominant OTUs in the Sundays River system were distinct from those of the Kariega and Kowie estuaries with an overall decrease in species richness and evenness. This study provides an important snapshot into the microbial population structures of permanently open temperate estuarine systems and the influence of anthropogenic impacts on bacterial diversity and community structure.