Application of ion torrent sequencing to the assessment of the effect of alkali ballast water treatment on microbial community diversity.

PubMed

Fujimoto, Masanori; Moyerbrailean, Gregory A; Noman, Sifat; Gizicki, Jason P; Ram, Michal L; Green, Phyllis A; Ram, Jeffrey L

2014-01-01

The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry. Ballast water samples from a Great Lakes ship were collected from the intake and discharge of both control and NaOH (pH 12) treated tanks and were analyzed in duplicates. One set of duplicates was treated with the membrane-impermeable DNA cross-linking reagent propidium mono-azide (PMA) prior to PCR amplification to differentiate between live and dead microorganisms. Ion Torrent sequencing generated nearly 580,000 reads for 31 bar-coded samples and revealed alterations of the microbial community structure in ballast water that had been treated with NaOH. Rarefaction analysis of the Ion Torrent sequencing data showed that BWT using NaOH significantly decreased microbial community diversity relative to control discharge (p<0.001). UniFrac distance based principal coordinate analysis (PCoA) plots and UPGMA tree analysis revealed that NaOH-treated ballast water microbial communities differed from both intake communities and control discharge communities. After NaOH treatment, bacteria from the genus Alishewanella became dominant in the NaOH-treated samples, accounting for <0.5% of the total reads in intake samples but more than 50% of the reads in the treated discharge samples. The only apparent difference in microbial community structure between PMA-processed and non-PMA samples occurred in intake water samples, which exhibited a significantly higher amount of PMA-sensitive cyanobacteria/chloroplast 16S rRNA than their corresponding non-PMA total DNA samples. The community assembly obtained using Ion Torrent sequencing was comparable to that obtained from a subset of samples that were also subjected to 454 pyrosequencing. This study showed the efficacy of alkali ballast water treatment in reducing ballast water microbial diversity and demonstrated the application of new Ion Torrent sequencing techniques to microbial community studies.

A survey of microbial community diversity in marine sediments impacted by petroleum hydrocarbons from the Gulf of Mexico and Atlantic shorelines, Texas to Florida

USGS Publications Warehouse

Lisle, John T.; Stellick, Sarah H.

2011-01-01

Microbial community genomic DNA was extracted from sediment samples collected along the Gulf of Mexico and Atlantic coasts from Texas to Florida. Sample sites were identified as being ecologically sensitive and (or) as having high potential of being impacted by Macondo-1 (M-1) well oil from the Deepwater Horizon blowout. The diversity within the microbial communities associated with the collected sediments provides a baseline dataset to which microbial community-diversity data from impacted sites could be compared. To determine the microbial community diversity in the samples, genetic fingerprints were generated and compared. Specific sequences within the community genomic DNA were first amplified using the polymerase chain reaction (PCR) with a primer set that provides possible resolution to the species level. A second nested PCR was performed on the primary PCR products using a primer set on which a GC-clamp was attached to one of the primers. The nested PCR products were separated using denaturing-gradient gel electrophoresis (DGGE) that resolves the nested PCR products based on sequence dissimilarities (or similarities), forming a genomic fingerprint of the microbial diversity within the respective samples. Samples with similar fingerprints were grouped and compared to oil-fingerprint data from the same sites (Rosenbauer and others, 2011). The microbial community fingerprints were generally grouped into sites that had been shown to contain background concentrations of non-Deepwater Horizon oil. However, these groupings also included sites where no oil signature was detected. This report represents some of the first information on naturally occurring microbial communities in sediment from shorelines along the Gulf of Mexico and Atlantic coasts from Texas to Florida.

Adolescent Outcomes of Childhood Attention-Deficit/Hyperactivity Disorder in a Diverse Community Sample

ERIC Educational Resources Information Center

Bussing, Regina; Mason, Dana M.; Bell, Lindsay; Porter, Phillip; Garvan, Cynthia

2010-01-01

Objective: To describe adolescent outcomes of childhood attention-deficit/hyperactivity disorder (ADHD) in a diverse community sample. Method: ADHD screening of a school district sample of 1,615 students aged 5 to 11 years was followed by a case-control study 8 years later. High-risk youths meeting full (n = 94) and subthreshold (n = 75) DSM-IV…

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

PubMed

Gülay, Arda; Smets, Barth F

2015-09-01

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

[Community structure and diversity of culturable moderate halophilic bacteria isolated from Qrhan salt lake on Qinghai-Tibet Plateau].

PubMed

Shen, Shuo

2017-04-04

I studied the community structure and diversity of culturable moderate halophilic bacteria isolated from Qrhan Salt Lake. I isolated and cultured the moderate halophilic bacteria on different selective media. After the 16S rRNA gene sequences was amplified and measured, I constructed the phylogenic tree, analyzed the community structure and calculated the diversity indexes according to the 16S rRNA gene information. A total of 421 moderate halophilic bacteria were isolated from water and mud samples in Qrhan Salt Lake. The 16S rRNA gene information showed that 4 potential novel species belonged to the family Bacillaceae. Eighty-three model strains belonged to 3 phylurms 6 families 16 genus. Among them, Bacillus sp., Oceanobacillus sp. and Halomonas sp. were dominant species. Diversity analysis showed that the diversity of strains isolated from water sample was higher than that from mud sample, but the dominance degree of strains isolated from mud sample was higher than that from water sample. The genetic diversity of moderate halophilic bacteria isolated from Qrhan Salt Lake was abundant. Also, there were dominant and novel species of culturable moderate halophilic bacteria in this lake.

Effects of transgenic cry1Ie maize on non-lepidopteran pest abundance, diversity and community composition.

PubMed

Guo, Jingfei; He, Kanglai; Bai, Shuxiong; Zhang, Tiantao; Liu, Yunjun; Wang, Fuxin; Wang, Zhenying

2016-12-01

Non-lepidopteran pests are exposed to, and may be influenced by, Bt toxins when feeding on Bt maize that express insecticidal Cry proteins derived from Bacillus thuringiensis (Bt). In order to assess the potential effects of transgenic cry1Ie maize on non-lepidopteran pest species and ecological communities, a 2-year field study was conducted to compare the non-lepidopteran pest abundance, diversity and community composition between transgenic cry1Ie maize (Event IE09S034, Bt maize) and its near isoline (Zong 31, non-Bt maize) by whole plant inspections. Results showed that Bt maize had no effects on non-lepidopteran pest abundance and diversity (Shannon-Wiener diversity index, Simpson's diversity index, species richness, and Pielou's index). There was a significant effect of year and sampling time on those indices analyzed. Redundancy analysis indicated maize type, sampling time and year totally explained 20.43 % of the variance in the non-lepidopteran pest community composition, but no association was presented between maize type (Bt maize and non-Bt maize) and the variance. Nonmetric multidimensional scaling analysis showed that sampling time and year, rather than maize type had close relationship with the non-lepidopteran pest community composition. These results corroborated the hypothesis that, at least in the short-term, the transgenic cry1Ie maize had negligible effects on the non-lepidopteran pest abundance, diversity and community composition.

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

PubMed

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

2017-01-01

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

Top-down and bottom-up control on bacterial diversity in a western Norwegian deep-silled fjord.

PubMed

Storesund, Julia E; Erga, Svein Rune; Ray, Jessica L; Thingstad, T Frede; Sandaa, Ruth-Anne

2015-07-01

We investigated the relationship between viruses and co-occurring bacterial communities in the Sognefjord, a deep-silled fjord in Western Norway. A combination of flow cytometry and automated ribosomal intergenic spacer analysis (ARISA) was used to assess prokaryote and viral abundances, and bacterial diversity and community composition, respectively, in depth profiles and at two different sampling seasons (November and May). With one exception, bacterial diversity did not vary between samples regardless of depth or season. The virus and prokaryote abundances as well as bacterial community composition, however, varied significantly with season and depth, suggesting a link between the Sognefjord viral community and potential bacterial host community diversity. To our knowledge, these findings provide the first description of microbial communities in the unique Sognefjord ecosystem, and in addition are in agreement with the simple model version of the 'Killing the Winner' theory (KtW), which postulates that microbial community diversity is a feature that is essentially top-down controlled by viruses, while community composition is bottom-up controlled by competition for limiting growth substrates. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Community structure of age-0 fishes in paired mainstem and created shallow-water habitats in the Lower Missouri River

USGS Publications Warehouse

Starks, Trevor A.; Long, James M.; Dzialowski, Andrew R.

2016-01-01

Anthropogenic alterations to aquatic ecosystems have greatly reduced and homogenized riverine habitat, especially those used by larval and juvenile fishes. Creation of shallow-water habitats is used as a restoration technique in response to altered conditions in several studies globally, but only recently in the USA. In the summer of 2012, the U.S. Army Corps of Engineers sampled larval and juvenile fishes at six paired sites (mainstem and constructed chute shallow-water habitats) along a section of the Missouri River between Rulo, NE and St. Louis, MO, USA. From those samples, we enumerated and identified a total of 7622 fishes representing 12 families. Community responses of fishes to created shallow-water habitats were assessed by comparisons of species richness and diversity measures between paired sites and among sampling events. Shannon entropy measures were transformed, and gamma diversity (total diversity) was partitioned into two components, alpha (within community) and beta (between community) diversity using a multiplicative decomposition method. Mantel test results suggest site location, time of sampling event and habitat type were drivers of larval and juvenile community structure. Paired t-test results indicated little to no differences in beta diversity between habitat types; however, chute habitats had significantly higher alpha and gamma diversity as well as increased abundances of Asian carp larvae when compared with mainstem shallow-water habitat. Our results not only show the importance of created shallow-water habitat in promoting stream fish diversity but also highlight the role space and time may play in future restoration and management efforts. 

Ecological and evolutionary consequences of benthic community stasis in the very deep sea (>1500 m)

USGS Publications Warehouse

Buzas, Martin A.; Hayek, Lee-Ann C.; Culver, Stephen J.; Hayward, Bruce W.; Osterman, Lisa E.

2014-01-01

An enigma of deep-sea biodiversity research is that the abyss with its low productivity and densities appears to have a biodiversity similar to that of shallower depths. This conceptualization of similarity is based mainly on per-sample estimates (point diversity, within-habitat, or α-diversity). Here, we use a measure of between-sample within-community diversity (β1H) to examine benthic foraminiferal diversity between 333 stations within 49 communties from New Zealand, the South Atlantic, the Gulf of Mexico, the Norwegian Sea, and the Arctic. The communities are grouped into two depth categories: 200–1500 m and >1500 m. β1H diversity exhibits no evidence of regional differences. Instead, higher values at shallower depths are observed worldwide. At depths of >1500 m the average β1H is zero, indicating stasis or no biodiversity gradient. The difference in β1H-diversity explains why, despite species richness often being greater per sample at deeper depths, the total number of species is greater at shallower depths. The greater number of communities and higher rate of evolution resulting in shorter species durations at shallower depths is also consistent with higher β1H values.

Impact of enzymatic digestion on bacterial community composition in CF airway samples.

PubMed

Williamson, Kayla M; Wagner, Brandie D; Robertson, Charles E; Johnson, Emily J; Zemanick, Edith T; Harris, J Kirk

2017-01-01

Previous studies have demonstrated the importance of DNA extraction methods for molecular detection of Staphylococcus, an important bacterial group in cystic fibrosis (CF). We sought to evaluate the effect of enzymatic digestion (EnzD) prior to DNA extraction on bacterial communities identified in sputum and oropharyngeal swab (OP) samples from patients with CF. DNA from 81 samples (39 sputum and 42 OP) collected from 63 patients with CF was extracted in duplicate with and without EnzD. Bacterial communities were determined by rRNA gene sequencing, and measures of alpha and beta diversity were calculated. Principal Coordinate Analysis (PCoA) was used to assess differences at the community level and Wilcoxon Signed Rank tests were used to compare relative abundance (RA) of individual genera for paired samples with and without EnzD. Shannon Diversity Index (alpha-diversity) decreased in sputum and OP samples with the use of EnzD. Larger shifts in community composition were observed for OP samples (beta-diversity, measured by Morisita-Horn), whereas less change in communities was observed for sputum samples. The use of EnzD with OP swabs resulted in significant increase in RA for the genera Gemella ( p  < 0.01), Streptococcus ( p  < 0.01), and Rothia ( p  < 0.01). Staphylococcus ( p  < 0.01) was the only genus with a significant increase in RA from sputum, whereas the following genera decreased in RA with EnzD: Veillonella ( p  < 0.01), Granulicatella ( p  < 0.01), Prevotella ( p  < 0.01), and Gemella ( p  = 0.02). In OP samples, higher RA of Gram-positive taxa was associated with larger changes in microbial community composition. We show that the application of EnzD to CF airway samples, particularly OP swabs, results in differences in microbial communities detected by sequencing. Use of EnzD can result in large changes in bacterial community composition, and is particularly useful for detection of Staphylococcus in CF OP samples. The enhanced identification of Staphylococcus aureus is a strong indication to utilize EnzD in studies that use OP swabs to monitor CF airway communities.

High Diversity of Myocyanophage in Various Aquatic Environments Revealed by High-Throughput Sequencing of Major Capsid Protein Gene With a New Set of Primers.

PubMed

Hou, Weiguo; Wang, Shang; Briggs, Brandon R; Li, Gaoyuan; Xie, Wei; Dong, Hailiang

2018-01-01

Myocyanophages, a group of viruses infecting cyanobacteria, are abundant and play important roles in elemental cycling. Here we investigated the particle-associated viral communities retained on 0.2 μm filters and in sediment samples (representing ancient cyanophage communities) from four ocean and three lake locations, using high-throughput sequencing and a newly designed primer pair targeting a gene fragment (∼145-bp in length) encoding the cyanophage gp23 major capsid protein (MCP). Diverse viral communities were detected in all samples. The fragments of 142-, 145-, and 148-bp in length were most abundant in the amplicons, and most sequences (>92%) belonged to cyanophages. Additionally, different sequencing depths resulted in different diversity estimates of the viral community. Operational taxonomic units obtained from deep sequencing of the MCP gene covered the majority of those obtained from shallow sequencing, suggesting that deep sequencing exhibited a more complete picture of cyanophage community than shallow sequencing. Our results also revealed a wide geographic distribution of marine myocyanophages, i.e., higher dissimilarities of the myocyanophage communities corresponded with the larger distances between the sampling sites. Collectively, this study suggests that the newly designed primer pair can be effectively used to study the community and diversity of myocyanophage from different environments, and the high-throughput sequencing represents a good method to understand viral diversity.

High Diversity of Myocyanophage in Various Aquatic Environments Revealed by High-Throughput Sequencing of Major Capsid Protein Gene With a New Set of Primers

PubMed Central

Hou, Weiguo; Wang, Shang; Briggs, Brandon R.; Li, Gaoyuan; Xie, Wei; Dong, Hailiang

2018-01-01

Myocyanophages, a group of viruses infecting cyanobacteria, are abundant and play important roles in elemental cycling. Here we investigated the particle-associated viral communities retained on 0.2 μm filters and in sediment samples (representing ancient cyanophage communities) from four ocean and three lake locations, using high-throughput sequencing and a newly designed primer pair targeting a gene fragment (∼145-bp in length) encoding the cyanophage gp23 major capsid protein (MCP). Diverse viral communities were detected in all samples. The fragments of 142-, 145-, and 148-bp in length were most abundant in the amplicons, and most sequences (>92%) belonged to cyanophages. Additionally, different sequencing depths resulted in different diversity estimates of the viral community. Operational taxonomic units obtained from deep sequencing of the MCP gene covered the majority of those obtained from shallow sequencing, suggesting that deep sequencing exhibited a more complete picture of cyanophage community than shallow sequencing. Our results also revealed a wide geographic distribution of marine myocyanophages, i.e., higher dissimilarities of the myocyanophage communities corresponded with the larger distances between the sampling sites. Collectively, this study suggests that the newly designed primer pair can be effectively used to study the community and diversity of myocyanophage from different environments, and the high-throughput sequencing represents a good method to understand viral diversity.

Sediment Enzyme Activities and Microbial Community Diversity in an Oligotrophic Drinking Water Reservoir, Eastern China

PubMed Central

Zhang, Haihan; Huang, Tinglin; Liu, Tingting

2013-01-01

Drinking water reservoir plays a vital role in the security of urban water supply, yet little is known about microbial community diversity harbored in the sediment of this oligotrophic freshwater environmental ecosystem. In the present study, integrating community level physiological profiles (CLPPs), nested polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) and clone sequence technologies, we examined the sediment urease and protease activities, bacterial community functional diversity, genetic diversity of bacterial and fungal communities in sediments from six sampling sites of Zhou cun drinking water reservoir, eastern China. The results showed that sediment urease activity was markedly distinct along the sites, ranged from 2.48 to 11.81 mg NH3-N/(g·24h). The highest average well color development (AWCD) was found in site C, indicating the highest metabolic activity of heterotrophic bacterial community. Principal component analysis (PCA) revealed tremendous differences in the functional (metabolic) diversity patterns of the sediment bacterial communities from different sites. Meanwhile, DGGE fingerprints also indicated spatial changes of genetic diversity of sediment bacterial and fungal communities. The sequence BLAST analysis of all the sediment samples found that Comamonas sp. was the dominant bacterial species harbored in site A. Alternaria alternate, Allomyces macrogynus and Rhizophydium sp. were most commonly detected fungal species in sediments of the Zhou cun drinking water reservoir. The results from this work provide new insights about the heterogeneity of sediment microbial community metabolic activity and genetic diversity in the oligotrophic drinking water reservoir. PMID:24205265

Fungal communities in soils along a vegetative ecotone.

PubMed

Karst, Justine; Piculell, Bridget; Brigham, Christy; Booth, Michael; Hoeksema, Jason D

2013-01-01

We investigated the community composition and diversity of soil fungi along a sharp vegetative ecotone between coastal sage scrub (CSS) and nonnative annual grassland habitat at two sites in coastal California. USA- We pooled soil samples across 29 m transects on either side of the ecotone at each of the two sites, and. using clone libraries of fungal ribosomal DNA, we identified 280 operational taxonomic units (OTUs) from a total 40 g soil. We combined information from partial LSU and ITS sequences and found that the majority of OTUs belonged to the phylum Ascomycota, followed by Basidiomycota. Within the Ascomycota. a quarter of OTUs were Sordariomycetes. 17% were Leotiomycet.es, 16% were Dothideomycetes and the remaining OTUs were distributed among the classes Eurotiomycetes, Pezizomycetes, Lecanoromycetes, Orbiliomycetes and Arthoniomycetes. Within the Basidiomycota. all OTUs but one belonged to the subphylum Agaricomycotina. We also sampled plant communities at the same sites to offer a point of comparison for patterns in richness of fungal communities. Fungal communities had higher alpha and beta diversity than plant communities; fungal communities were approximately 20 times as rich as plant communities and the majority of OTUs were found in single soil samples. Soils harbored a unique mycoflora that did not reveal vegetative boundaries or site differences. High alpha and beta diversity and possible sampling artifacts necessitate extensive sampling to reveal differentiation in these fungal communities.

Estimating and comparing microbial diversity in the presence of sequencing errors

PubMed Central

Chiu, Chun-Huo

2016-01-01

Estimating and comparing microbial diversity are statistically challenging due to limited sampling and possible sequencing errors for low-frequency counts, producing spurious singletons. The inflated singleton count seriously affects statistical analysis and inferences about microbial diversity. Previous statistical approaches to tackle the sequencing errors generally require different parametric assumptions about the sampling model or about the functional form of frequency counts. Different parametric assumptions may lead to drastically different diversity estimates. We focus on nonparametric methods which are universally valid for all parametric assumptions and can be used to compare diversity across communities. We develop here a nonparametric estimator of the true singleton count to replace the spurious singleton count in all methods/approaches. Our estimator of the true singleton count is in terms of the frequency counts of doubletons, tripletons and quadrupletons, provided these three frequency counts are reliable. To quantify microbial alpha diversity for an individual community, we adopt the measure of Hill numbers (effective number of taxa) under a nonparametric framework. Hill numbers, parameterized by an order q that determines the measures’ emphasis on rare or common species, include taxa richness (q = 0), Shannon diversity (q = 1, the exponential of Shannon entropy), and Simpson diversity (q = 2, the inverse of Simpson index). A diversity profile which depicts the Hill number as a function of order q conveys all information contained in a taxa abundance distribution. Based on the estimated singleton count and the original non-singleton frequency counts, two statistical approaches (non-asymptotic and asymptotic) are developed to compare microbial diversity for multiple communities. (1) A non-asymptotic approach refers to the comparison of estimated diversities of standardized samples with a common finite sample size or sample completeness. This approach aims to compare diversity estimates for equally-large or equally-complete samples; it is based on the seamless rarefaction and extrapolation sampling curves of Hill numbers, specifically for q = 0, 1 and 2. (2) An asymptotic approach refers to the comparison of the estimated asymptotic diversity profiles. That is, this approach compares the estimated profiles for complete samples or samples whose size tends to be sufficiently large. It is based on statistical estimation of the true Hill number of any order q ≥ 0. In the two approaches, replacing the spurious singleton count by our estimated count, we can greatly remove the positive biases associated with diversity estimates due to spurious singletons and also make fair comparisons across microbial communities, as illustrated in our simulation results and in applying our method to analyze sequencing data from viral metagenomes. PMID:26855872

Presence of pathogenic Escherichia coli is correlated with bacterial community diversity and composition on pre-harvest cattle hides.

PubMed

Chopyk, Jessica; Moore, Ryan M; DiSpirito, Zachary; Stromberg, Zachary R; Lewis, Gentry L; Renter, David G; Cernicchiaro, Natalia; Moxley, Rodney A; Wommack, K Eric

2016-03-22

Since 1982, specific serotypes of Shiga toxin-producing Escherichia coli (STEC) have been recognized as significant foodborne pathogens acquired from contaminated beef and, more recently, other food products. Cattle are the major reservoir hosts of these organisms, and while there have been advancements in food safety practices and industry standards, STEC still remains prevalent within beef cattle operations with cattle hides implicated as major sources of carcass contamination. To investigate whether the composition of hide-specific microbial communities are associated with STEC prevalence, 16S ribosomal RNA (rRNA) bacterial community profiles were obtained from hide and fecal samples collected from a large commercial feedlot over a 3-month period. These community data were examined amidst an extensive collection of prevalence data on a subgroup of STEC that cause illness in humans, referred to as enterohemorrhagic E. coli (EHEC). Fecal 16S rRNA gene OTUs (operational taxonomic units) were subtracted from the OTUs found within each hide 16S rRNA amplicon library to identify hide-specific bacterial populations. Comparative analysis of alpha diversity revealed a significant correlation between low bacterial diversity and samples positive for the presence of E. coli O157:H7 and/or the non-O157 groups: O26, O111, O103, O121, O45, and O145. This trend occurred regardless of diversity metric or fecal OTU presence. The number of EHEC serogroups present in the samples had a compounding effect on the inverse relationship between pathogen presence and bacterial diversity. Beta diversity data showed differences in bacterial community composition between samples containing O157 and non-O157 populations, with certain OTUs demonstrating significant changes in relative abundance. The cumulative prevalence of the targeted EHEC serogroups was correlated with low bacterial community diversity on pre-harvest cattle hides. Understanding the relationship between indigenous hide bacterial communities and populations may provide strategies to limit EHEC in cattle and provide biomarkers for EHEC risk assessment.

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.

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

PubMed

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

2016-07-01

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

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

PubMed Central

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

2014-01-01

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

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

PubMed Central

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

2016-01-01

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

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

PubMed

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

2009-11-01

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

Dry coniferous forest restoration and understory plant diversity: The importance of community heterogeneity and the scale of observation

Treesearch

Erich Kyle Dodson; David W. Peterson

2010-01-01

Maintaining understory plant species diversity is an important management goal as forest restoration and fuel reduction treatments are applied extensively to dry coniferous forests of western North America. However, understory diversity is a function of both local species richness (number of species in a sample unit) and community heterogeneity (beta diversity) at...

A noninvasive assessment of skin carotenoid status through reflection spectroscopy is a feasible and reliable measure of dietary carotenoid consumption in a diverse community sample

USDA-ARS?s Scientific Manuscript database

Background: Skin carotenoid status, as assessed by reflection spectroscopy (RS), is a promising means of approximating fruit and vegetable consumption. This study’s purpose was to assess the feasibility, reliability, and validity of RS to assess skin carotenoids in a racially diverse community sampl...

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

PubMed

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

2010-02-01

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

Microbial communities of the Lemon Creek Glacier show subtle structural variation yet stable phylogenetic composition over space and time

PubMed Central

Sheik, Cody S.; Stevenson, Emily I.; Den Uyl, Paul A.; Arendt, Carli A.; Aciego, Sarah M.; Dick, Gregory J.

2015-01-01

Glaciers are geologically important yet transient ecosystems that support diverse, biogeochemically significant microbial communities. During the melt season glaciers undergo dramatic physical, geochemical, and biological changes that exert great influence on downstream biogeochemical cycles. Thus, we sought to understand the temporal melt-season dynamics of microbial communities and associated geochemistry at the terminus of Lemon Creek Glacier (LCG) in coastal southern Alaska. Due to late season snowfall, sampling of LCG occurred in three interconnected areas: proglacial Lake Thomas, the lower glacial outflow stream, and the glacier’s terminus. LCG associated microbial communities were phylogenetically diverse and varied by sampling location. However, Betaproteobacteria, Alphaproteobacteria, and Bacteroidetes dominated communities at all sampling locations. Strict anaerobic groups such as methanogens, SR1, and OP11 were also recovered from glacier outflows, indicating anoxic conditions in at least some portions of the LCG subglacial environment. Microbial community structure was significantly correlated with sampling location and sodium concentrations. Microbial communities sampled from terminus outflow waters exhibited day-to-day fluctuation in taxonomy and phylogenetic similarity. However, these communities were not significantly different from randomly constructed communities from all three sites. These results indicate that glacial outflows share a large proportion of phylogenetic overlap with downstream environments and that the observed significant shifts in community structure are driven by changes in relative abundance of different taxa, and not complete restructuring of communities. We conclude that LCG glacial discharge hosts a diverse and relatively stable microbiome that shifts at fine taxonomic scales in response to geochemistry and likely water residence time. PMID:26042114

Genus-Specific Primers for Study of Fusarium Communities in Field Samples

PubMed Central

Edel-Hermann, Véronique; Gautheron, Nadine; Durling, Mikael Brandström; Kolseth, Anna-Karin; Steinberg, Christian; Persson, Paula; Friberg, Hanna

2015-01-01

Fusarium is a large and diverse genus of fungi of great agricultural and economic importance, containing many plant pathogens and mycotoxin producers. To date, high-throughput sequencing of Fusarium communities has been limited by the lack of genus-specific primers targeting regions with high discriminatory power at the species level. In the present study, we evaluated two Fusarium-specific primer pairs targeting translation elongation factor 1 (TEF1). We also present the new primer pair Fa+7/Ra+6. Mock Fusarium communities reflecting phylogenetic diversity were used to evaluate the accuracy of the primers in reflecting the relative abundance of the species. TEF1 amplicons were subjected to 454 high-throughput sequencing to characterize Fusarium communities. Field samples from soil and wheat kernels were included to test the method on more-complex material. For kernel samples, a single PCR was sufficient, while for soil samples, nested PCR was necessary. The newly developed primer pairs Fa+7/Ra+6 and Fa/Ra accurately reflected Fusarium species composition in mock DNA communities. In field samples, 47 Fusarium operational taxonomic units were identified, with the highest Fusarium diversity in soil. The Fusarium community in soil was dominated by members of the Fusarium incarnatum-Fusarium equiseti species complex, contradicting findings in previous studies. The method was successfully applied to analyze Fusarium communities in soil and plant material and can facilitate further studies of Fusarium ecology. PMID:26519387

Detection of forest stand-level spatial structure in ectomycorrhizal fungal communities

Treesearch

Erik A. Lilleskov; Thomas D. Bruns; Thomas R. Horton; D. Lee Taylor; Paul Grogan

2004-01-01

Ectomycorrhizal fungal (EMF) communities are highly diverse at the stand level. To begin to understand what might lead to such diversity, and to improve sampling designs, we investigated the spatial structure of these communities. We used EMF community data from a number of studies carried out in seven mature and one recently fire-initiated forest stand. We applied...

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

O'Brien, Sarah L.; Gibbons, Sean M.; Owens, Sarah M.

Soil microbial communities are essential for ecosystem function, but linking community composition to biogeochemical processes is challenging because of high microbial diversity and large spatial variability of most soil characteristics. We investigated soil bacterial community structure in a switchgrass stand planted on soil with a history of grassland vegetation at high spatial resolution to determine whether biogeographic trends occurred at the centimeter scale. Moreover, we tested whether such heterogeneity, if present, influenced community structure within or among ecosystems. Pronounced heterogeneity was observed at centimeter scales, with abrupt changes in relative abundance of phyla from sample to sample. At the ecosystemmore » scale (> 10 m), however, bacterial community composition and structure were subtly, but significantly, altered by fertilization, with higher alpha diversity in fertilized plots. Moreover, by comparing these data with data from 1772 soils from the Earth Microbiome Project, it was found that 20% diverse globally sourced soil samples, while grassland soils shared approximately 40% of their operational taxonomic units with the current study. By spanning several orders of magnitude, the analysis suggested that extreme patchiness characterized community structure at smaller scales but that coherent patterns emerged at larger length scales.« less

How Does Dung Beetle (Coleoptera: Scarabaeidae) Diversity Vary Along a Rainy Season in a Tropical Dry Forest?

PubMed

Novais, Samuel M A; Evangelista, Lucas A; Reis-Júnior, Ronaldo; Neves, Frederico S

2016-01-01

Dung beetle community dynamics are determined by regional rainfall patterns. However, little is known about the temporal dynamics of these communities in tropical dry forests (TDFs). This study was designed to test the following predictions: 1) Peak diversity of dung beetle species occurs early in the wet season, with a decrease in diversity (α and β) and abundance throughout the season; 2) Nestedness is the primary process determining β-diversity, with species sampled in the middle and the end of the wet season representing subsets of the early wet season community. Dung beetles were collected in a TDF in the northern Minas Gerais state, Brazil over three sampling events (December 2009, February and April 2010). We sampled 2,018 dung beetles belonging to 39 species and distributed among 15 genera. Scarabaeinae α-diversity and abundance were highest in December and equivalent between February and April, while β-diversity among plots increased along the wet season. The importance of nestedness and species turnover varies between pairs of sample periods as the main process of temporal β-diversity. Most species collected in the middle and end of the wet season were found in greater abundance in early wet season. Thus, the dung beetle community becomes more homogeneous at the beginning of the wet season, and as the season advances, higher resource scarcity limits population size, which likely results in a smaller foraging range, increasing β-diversity. Our results demonstrate high synchronism between the dung beetle life cycle and seasonality of environmental conditions throughout the wet season in a TDF, where the onset of rains determines adult emergence for most species. © The Authors 2016. Published by Oxford University Press on behalf of Entomological Society of America.

Energy gradients and the geographic distribution of local ant diversity.

PubMed

Kaspari, Michael; Ward, Philip S; Yuan, May

2004-08-01

Geographical diversity gradients, even among local communities, can ultimately arise from geographical differences in speciation and extinction rates. We evaluated three models--energy-speciation, energy-abundance, and area--that predict how geographic trends in net diversification rates generate trends in diversity. We sampled 96 litter ant communities from four provinces: Australia, Madagascar, North America, and South America. The energy-speciation hypothesis best predicted ant species richness by accurately predicting the slope of the temperature diversity curve, and accounting for most of the variation in diversity. The communities showed a strong latitudinal gradient in species richness as well as inter-province differences in diversity. The former vanished in the temperature-diversity residuals, suggesting that the latitudinal gradient arises primarily from higher diversification rates in the tropics. However, inter-province differences in diversity persisted in those residuals--South American communities remained more diverse than those in North America and Australia even after the effects of temperature were removed.

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

PubMed

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

2014-11-01

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

Downstream Effects of Diversion Dams on Riparian Vegetation Communities in the Routt National Forest, Colorado

NASA Astrophysics Data System (ADS)

Caskey, S. T.; Wohl, E. E.; Dwire, K. A.; Merritt, D. M.; Schnackenberg, L.

2012-12-01

The relationship between riparian vegetation and changes in fluvial processes as a response to flow diversion is not well understood. Water extraction affects the hydrologic flow regime (i.e., magnitude, duration, and frequency of flows) reducing peak and base-flows, which could negatively impact riparian vegetation. Vegetation communities are temporally and spatially variable and are strongly interrelated with alluvial landforms and hydrograph variability. This research compares riparian community characteristics on diverted and undiverted pool-riffle channels and low gradient valleys to examine changes associated with flow diversion in the Routt National Forest (RNF). The RNF is the only under-appropriated area in Colorado, making future water extraction proposals likely. Many small extraction canals siphon water from small, headwater streams in the RNF, but the site-specific or cumulative effects of these diversions on riverine ecosystems have not been investigated. Systematic investigation is necessary, however, to determine whether existing flow diversions have influenced riparian communities and, if so, which communities are most sensitive to diversions. A total of 36 sites were sampled with five channel cross sections established per site, extending into the riparian zone at distance of two times the active channel width, and vegetation was sampled using the line-point intercept method. Preliminary results suggest a shift in vegetation communities from typical riparian species composition to more upland vegetation. The relative sensitivity of these responses are different depending on valley type; low- gradient, unconfined areas are less tolerant of diversion than steeper, confined reaches. Additionally, when stratified by plant assemblage, Salix abundance is significantly reduced downstream of diversion. The results of this study contribute to the collective understanding of mountain headwater riparian vegetation community response to changes in flow regimes and fluvial processes related directly to water extraction by diversion dams.

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.

Community Structure of Lithotrophically-Driven Hydrothermal Microbial Mats from the Mariana Arc and Back-Arc

PubMed Central

Hager, Kevin W.; Fullerton, Heather; Butterfield, David A.; Moyer, Craig L.

2017-01-01

The Mariana region exhibits a rich array of hydrothermal venting conditions in a complex geological setting, which provides a natural laboratory to study the influence of local environmental conditions on microbial community structure as well as large-scale patterns in microbial biogeography. We used high-throughput amplicon sequencing of the bacterial small subunit (SSU) rRNA gene from 22 microbial mats collected from four hydrothermally active locations along the Mariana Arc and back-arc to explore the structure of lithotrophically-based microbial mat communities. The vent effluent was classified as iron- or sulfur-rich corresponding with two distinct community types, dominated by either Zetaproteobacteria or Epsilonproteobacteria, respectively. The Zetaproteobacterial-based communities had the highest richness and diversity, which supports the hypothesis that Zetaproteobacteria function as ecosystem engineers creating a physical habitat within a chemical environment promoting enhanced microbial diversity. Gammaproteobacteria were also high in abundance within the iron-dominated mats and some likely contribute to primary production. In addition, we also compare sampling scale, showing that bulk sampling of microbial mats yields higher diversity than micro-scale sampling. We present a comprehensive analysis and offer new insights into the community structure and diversity of lithotrophically-driven microbial mats from a hydrothermal region associated with high microbial biodiversity. Our study indicates an important functional role of for the Zetaproteobacteria altering the mat habitat and enhancing community interactions and complexity. PMID:28970817

[Research on bacteria microecology in root rot rhizosphere soil of Coptis chinensis produced in Shizhu city].

PubMed

Song, Xu-Hong; Wang, Yu; Li, Long-Yun; Tan, Jun

2017-04-01

Illumina Hiseq 2500 high-throughput sequencing platform was used to study the bacteria richness and diversity, the soil enzyme activities, nutrients in unplanted soil, root-rot and healthy rhizophere soil of Coptis chinensis for deeply discussing the mechanism of the root-rot of C. chinensis. The high-throughput sequencing result showed that the artificial cultivation effected the bacteria community richness and diversity. The bacteria community richness in healthy and diseased rhizosphere soil showed significant lower than that of in unplanted soil (P<0.05) and declined bacteria diversity. The bacteria community richness in root-rot rhizosphere soil increased significantly than that of health and unplanted soil and the diversity was lower significant than that of unplanted soil (P<0.05). The results of soil nutrients and enzyme activities detected that the pH value, available phosphorus and urease activity decreased and the sucrase activity increased significantly (P<0.05). The content of organic carbon and alkaline hydrolysis nitrogen the catalase and urease activity in root rot soil samples was significantly lower than that of healthy soil samples (P<0.05). However, the contents of available phosphorus and available potassium were significantly in root-rot sample higher than that of healthy soil samples (P<0.05). Comprehensive analysis showed that the artificial cultivation declined the bacteria community richness and diversity. The bacteria community richness decreased significantly and the decreased diversity may be the cause of the root-rot. Meanwhile, the decrease of carbon and the catalase activity may be another cause of the root-rot in C. chinensis produced in Shizhu city, Chongqing province. Copyright© by the Chinese Pharmaceutical Association.

L-Lake macroinvertebrate community

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

Specht, W.L.

1996-06-01

To characterize the present benthic macroinvertebrate community of L-Lake, Regions 5 and 7 of the reservoir were sampled in September 1995 at the same locations sampled in 1988 and 1989 during the L-Lake monitoring program. The macroinvertebrate community of 1995 is compared to that of 1988 and 1989. The species composition of L-Lake`s macroinvertebrate community has changed considerably since 1988-1989, due primarily to maturation of the reservoir ecosystem. L-Lake contains a reasonably diverse macroinvertebrate community that is capable of supporting higher trophic levels, including a diverse assemblage of fish species. The L-Lake macroinvertebrate community is similar to those of manymore » other southeastern reservoirs, and there is no indication that the macroinvertebrate community is perturbed by chemical or physical stressors.« less

Exploration of Microbial Diversity and Community Structure of Lonar Lake: The Only Hypersaline Meteorite Crater Lake within Basalt Rock

PubMed Central

Paul, Dhiraj; Kumbhare, Shreyas V.; Mhatre, Snehit S.; Chowdhury, Somak P.; Shetty, Sudarshan A.; Marathe, Nachiket P.; Bhute, Shrikant; Shouche, Yogesh S.

2016-01-01

Lonar Lake is a hypersaline and hyperalkaline soda lake and the only meteorite impact crater in the world situated in basalt rocks. Although culture-dependent studies have been reported, a comprehensive understanding of microbial community composition and structure in Lonar Lake remains elusive. In the present study, microbial community structure associated with Lonar Lake sediment and water samples was investigated using high-throughput sequencing. Microbial diversity analysis revealed the existence of diverse, yet largely consistent communities. Proteobacteria (30%), Actinobacteria (24%), Firmicutes (11%), and Cyanobacteria (5%) predominated in the sequencing survey, whereas Bacteroidetes (1.12%), BD1-5 (0.5%), Nitrospirae (0.41%), and Verrucomicrobia (0.28%) were detected in relatively minor abundances in the Lonar Lake ecosystem. Within the Proteobacteria phylum, the Gammaproteobacteria represented the most abundantly detected class (21–47%) within sediment samples, but only a minor population in the water samples. Proteobacteria and Firmicutes were found at significantly higher abundance (p ≥ 0.05) in sediment samples, whereas members of Actinobacteria, Candidate division TM7 and Cyanobacteria (p ≥ 0.05) were significantly abundant in water samples. Compared to the microbial communities of other hypersaline soda lakes, those of Lonar Lake formed a distinct cluster, suggesting a different microbial community composition and structure. Here we report for the first time, the difference in composition of indigenous microbial communities between the sediment and water samples of Lonar Lake. An improved census of microbial community structure in this Lake ecosystem provides a foundation for exploring microbial biogeochemical cycling and microbial function in hypersaline lake environments. PMID:26834712

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

PubMed

Kamika, I; Azizi, S; Tekere, M

2016-07-01

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

Bacterial diversity characterization in petroleum samples from Brazilian reservoirs

PubMed Central

de Oliveira, Valéria Maia; Sette, Lara Durães; Simioni, Karen Christina Marques; dos Santos Neto, Eugênio Vaz

2008-01-01

This study aimed at evaluating potential differences among the bacterial communities from formation water and oil samples originated from biodegraded and non-biodegraded Brazilian petroleum reservoirs by using a PCR-DGGE based approach. Environmental DNA was isolated and used in PCR reactions with bacterial primers, followed by separation of 16S rDNA fragments in the DGGE. PCR products were also cloned and sequenced, aiming at the taxonomic affiliation of the community members. The fingerprints obtained allowed the direct comparison among the bacterial communities from oil samples presenting distinct degrees of biodegradation, as well as between the communities of formation water and oil sample from the non-biodegraded reservoir. Very similar DGGE band profiles were observed for all samples, and the diversity of the predominant bacterial phylotypes was shown to be low. Cloning and sequencing results revealed major differences between formation water and oil samples from the non-biodegraded reservoir. Bacillus sp. and Halanaerobium sp. were shown to be the predominant components of the bacterial community from the formation water sample, whereas the oil sample also included Alicyclobacillus acidoterrestris, Rhodococcus sp., Streptomyces sp. and Acidithiobacillus ferrooxidans. The PCR-DGGE technique, combined with cloning and sequencing of PCR products, revealed the presence of taxonomic groups not found previously in these samples when using cultivation-based methods and 16S rRNA gene library assembly, confirming the need of a polyphasic study in order to improve the knowledge of the extent of microbial diversity in such extreme environments. PMID:24031244

Tropical Aquatic Archaea Show Environment-Specific Community Composition

PubMed Central

Silveira, Cynthia B.; Cardoso, Alexander M.; Coutinho, Felipe H.; Lima, Joyce L.; Pinto, Leonardo H.; Albano, Rodolpho M.; Clementino, Maysa M.; Martins, Orlando B.; Vieira, Ricardo P.

2013-01-01

The Archaea domain is ubiquitously distributed and extremely diverse, however, environmental factors that shape archaeal community structure are not well known. Aquatic environments, including the water column and sediments harbor many new uncultured archaeal species from which metabolic and ecological roles remain elusive. Some environments are especially neglected in terms of archaeal diversity, as is the case of pristine tropical areas. Here we investigate the archaeal composition in marine and freshwater systems from Ilha Grande, a South Atlantic tropical environment. All sampled habitats showed high archaeal diversity. No OTUs were shared between freshwater, marine and mangrove sediment samples, yet these environments are interconnected and geographically close, indicating environment-specific community structuring. Group II Euryarchaeota was the main clade in marine samples, while the new putative phylum Thaumarchaeota and LDS/RCV Euryarchaeota dominated freshwaters. Group III Euryarchaeota , a rare clade, was also retrieved in reasonable abundance in marine samples. The archaeal community from mangrove sediments was composed mainly by members of mesophilic Crenarchaeota and by a distinct clade forming a sister-group to Crenarchaeota and Thaumarchaeota. Our results show strong environment-specific community structuring in tropical aquatic Archaea, as previously seen for Bacteria. PMID:24086729

Diversity of bacteria and archaea from two shallow marine hydrothermal vents from Vulcano Island.

PubMed

Antranikian, Garabed; Suleiman, Marcel; Schäfers, Christian; Adams, Michael W W; Bartolucci, Simonetta; Blamey, Jenny M; Birkeland, Nils-Kåre; Bonch-Osmolovskaya, Elizaveta; da Costa, Milton S; Cowan, Don; Danson, Michael; Forterre, Patrick; Kelly, Robert; Ishino, Yoshizumi; Littlechild, Jennifer; Moracci, Marco; Noll, Kenneth; Oshima, Tairo; Robb, Frank; Rossi, Mosè; Santos, Helena; Schönheit, Peter; Sterner, Reinhard; Thauer, Rudolf; Thomm, Michael; Wiegel, Jürgen; Stetter, Karl Otto

2017-07-01

To obtain new insights into community compositions of hyperthermophilic microorganisms, defined as having optimal growth temperatures of 80 °C and above, sediment and water samples were taken from two shallow marine hydrothermal vents (I and II) with temperatures of 100 °C at Vulcano Island, Italy. A combinatorial approach of denaturant gradient gel electrophoresis (DGGE) and metagenomic sequencing was used for microbial community analyses of the samples. In addition, enrichment cultures, growing anaerobically on selected polysaccharides such as starch and cellulose, were also analyzed by the combinatorial approach. Our results showed a high abundance of hyperthermophilic archaea, especially in sample II, and a comparable diverse archaeal community composition in both samples. In particular, the strains of the hyperthermophilic anaerobic genera Staphylothermus and Thermococcus, and strains of the aerobic hyperthermophilic genus Aeropyrum, were abundant. Regarding the bacterial community, ε-Proteobacteria, especially the genera Sulfurimonas and Sulfurovum, were highly abundant. The microbial diversity of the enrichment cultures changed significantly by showing a high dominance of archaea, particularly the genera Thermococcus and Palaeococcus, depending on the carbon source and the selected temperature.

Community level patterns in diverse systems: A case study of litter fauna in a Mexican pine-oak forest using higher taxa surrogates and re-sampling methods

NASA Astrophysics Data System (ADS)

Moreno, Claudia E.; Guevara, Roger; Sánchez-Rojas, Gerardo; Téllez, Dianeis; Verdú, José R.

2008-01-01

Environmental assessment at the community level in highly diverse ecosystems is limited by taxonomic constraints and statistical methods requiring true replicates. Our objective was to show how diverse systems can be studied at the community level using higher taxa as biodiversity surrogates, and re-sampling methods to allow comparisons. To illustrate this we compared the abundance, richness, evenness and diversity of the litter fauna in a pine-oak forest in central Mexico among seasons, sites and collecting methods. We also assessed changes in the abundance of trophic guilds and evaluated the relationships between community parameters and litter attributes. With the direct search method we observed differences in the rate of taxa accumulation between sites. Bootstrap analysis showed that abundance varied significantly between seasons and sampling methods, but not between sites. In contrast, diversity and evenness were significantly higher at the managed than at the non-managed site. Tree regression models show that abundance varied mainly between seasons, whereas taxa richness was affected by litter attributes (composition and moisture content). The abundance of trophic guilds varied among methods and seasons, but overall we found that parasitoids, predators and detrivores decreased under management. Therefore, although our results suggest that management has positive effects on the richness and diversity of litter fauna, the analysis of trophic guilds revealed a contrasting story. Our results indicate that functional groups and re-sampling methods may be used as tools for describing community patterns in highly diverse systems. Also, the higher taxa surrogacy could be seen as a preliminary approach when it is not possible to identify the specimens at a low taxonomic level in a reasonable period of time and in a context of limited financial resources, but further studies are needed to test whether the results are specific to a system or whether they are general with regards to land management.

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.

Functional Diversity of Microbial Communities in Sludge-Amended Soils

NASA Astrophysics Data System (ADS)

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

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

Dispersal and neutral sampling mediate contingent effects of disturbance on plant beta-diversity: a meta-analysis.

PubMed

Catano, Christopher P; Dickson, Timothy L; Myers, Jonathan A

2017-03-01

A major challenge in ecology, conservation and global-change biology is to understand why biodiversity responds differently to similar environmental changes. Contingent biodiversity responses may depend on how disturbance and dispersal interact to alter variation in community composition (β-diversity) and assembly mechanisms. However, quantitative syntheses of these patterns and processes across studies are lacking. Using null-models and meta-analyses of 22 factorial experiments in herbaceous plant communities across Europe and North America, we show that disturbance diversifies communities when dispersal is limited, but homogenises communities when combined with increased immigration from the species pool. In contrast to the hypothesis that disturbance and dispersal mediate the strength of niche assembly, both processes altered β-diversity through neutral-sampling effects on numbers of individuals and species in communities. Our synthesis suggests that stochastic effects of disturbance and dispersal on community assembly play an important, but underappreciated, role in mediating biotic homogenisation and biodiversity responses to environmental change. © 2017 John Wiley & Sons Ltd/CNRS.

Prevalence and diversity of avian Haemosporida infecting songbirds in southwest Michigan.

PubMed

Smith, Jamie D; Gill, Sharon A; Baker, Kathleen M; Vonhof, Maarten J

2018-02-01

Avian blood parasites from the genera Plasmodium, Haemoproteus, and Leucocytozoon (Haemosporida) affect hosts in numerous ways. They influence species interactions, host behavior, reproductive success, and cause pathology and mortality in birds. The Great Lakes region of North America has extensive aquatic and wetland habitat and supports a diverse vector community. Here we describe the community of bird-infecting Haemosporida in southwest Michigan and their host associations by measuring parasite prevalence, diversity, and host breadth across a diverse community of avian hosts. Over 700 songbirds of 55 species were screened for Haemosporida infection across southwest Michigan, including 11 species that were targeted for larger sample sizes. In total, 71 parasite lineages infected over 40% of birds. Of these, 42 were novel, yet richness estimates suggest that approximately half of the actual parasite diversity in the host community was observed despite intensive sampling of multiple host species. Parasite prevalence varied among parasite genera (7-24%) and target host species (0-85%), and parasite diversity was consistently high across most target species. Host breadth varied widely across the most prevalent parasite lineages, and we detected around 60% of host species richness for these parasite lineages. We report many new lineages and novel host-parasite associations, but substantial parasite diversity remains undiscovered in the Midwest.

Insights into Diversity and Imputed Metabolic Potential of Bacterial Communities in the Continental Shelf of Agatti Island

PubMed Central

Dhar, Sunil Kumar; Jani, Kunal; Apte, Deepak A.; Shouche, Yogesh S.; Sharma, Avinash

2015-01-01

Marine microbes play a key role and contribute largely to the global biogeochemical cycles. This study aims to explore microbial diversity from one such ecological hotspot, the continental shelf of Agatti Island. Sediment samples from various depths of the continental shelf were analyzed for bacterial diversity using deep sequencing technology along with the culturable approach. Additionally, imputed metagenomic approach was carried out to understand the functional aspects of microbial community especially for microbial genes important in nutrient uptake, survival and biogeochemical cycling in the marine environment. Using culturable approach, 28 bacterial strains representing 9 genera were isolated from various depths of continental shelf. The microbial community structure throughout the samples was dominated by phylum Proteobacteria and harbored various bacterioplanktons as well. Significant differences were observed in bacterial diversity within a short region of the continental shelf (1–40 meters) i.e. between upper continental shelf samples (UCS) with lesser depths (i.e. 1–20 meters) and lower continental shelf samples (LCS) with greater depths (i.e. 25–40 meters). By using imputed metagenomic approach, this study also discusses several adaptive mechanisms which enable microbes to survive in nutritionally deprived conditions, and also help to understand the influence of nutrition availability on bacterial diversity. PMID:26066038

Insights into Diversity and Imputed Metabolic Potential of Bacterial Communities in the Continental Shelf of Agatti Island.

PubMed

Kumbhare, Shreyas V; Dhotre, Dhiraj P; Dhar, Sunil Kumar; Jani, Kunal; Apte, Deepak A; Shouche, Yogesh S; Sharma, Avinash

2015-01-01

Marine microbes play a key role and contribute largely to the global biogeochemical cycles. This study aims to explore microbial diversity from one such ecological hotspot, the continental shelf of Agatti Island. Sediment samples from various depths of the continental shelf were analyzed for bacterial diversity using deep sequencing technology along with the culturable approach. Additionally, imputed metagenomic approach was carried out to understand the functional aspects of microbial community especially for microbial genes important in nutrient uptake, survival and biogeochemical cycling in the marine environment. Using culturable approach, 28 bacterial strains representing 9 genera were isolated from various depths of continental shelf. The microbial community structure throughout the samples was dominated by phylum Proteobacteria and harbored various bacterioplanktons as well. Significant differences were observed in bacterial diversity within a short region of the continental shelf (1-40 meters) i.e. between upper continental shelf samples (UCS) with lesser depths (i.e. 1-20 meters) and lower continental shelf samples (LCS) with greater depths (i.e. 25-40 meters). By using imputed metagenomic approach, this study also discusses several adaptive mechanisms which enable microbes to survive in nutritionally deprived conditions, and also help to understand the influence of nutrition availability on bacterial diversity.

Effect of disopyramide on bacterial diversity in drinking water

NASA Astrophysics Data System (ADS)

Wu, Qing; Zhao, Xiaofei; Tian, Qi; Wang, Lei; Zhao, Xinhua

2018-02-01

Disopyramide was detected in drinking water by LC-MS/MS and the microbial diversity was investigated by PCR and high-throughput sequencing. The results showed that bacteria community structure in drinking water changed a lot when added different concentrations of disopyramide. The results of Shannon index showed that the total number and abundance of bacterial community species in drinking water samples decreased significantly after the addition of disopyramide. However, the number and abundance of community structure did not change with the concentration of disopyramide. Disopyramide inhibits the activity of bacterial community in drinking water and also can reduce the bacterial community diversity in drinking water.

Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity.

PubMed

Rodriguez-R, Luis M; Gunturu, Santosh; Tiedje, James M; Cole, James R; Konstantinidis, Konstantinos T

2018-01-01

Estimations of microbial community diversity based on metagenomic data sets are affected, often to an unknown degree, by biases derived from insufficient coverage and reference database-dependent estimations of diversity. For instance, the completeness of reference databases cannot be generally estimated since it depends on the extant diversity sampled to date, which, with the exception of a few habitats such as the human gut, remains severely undersampled. Further, estimation of the degree of coverage of a microbial community by a metagenomic data set is prohibitively time-consuming for large data sets, and coverage values may not be directly comparable between data sets obtained with different sequencing technologies. Here, we extend Nonpareil, a database-independent tool for the estimation of coverage in metagenomic data sets, to a high-performance computing implementation that scales up to hundreds of cores and includes, in addition, a k -mer-based estimation as sensitive as the original alignment-based version but about three hundred times as fast. Further, we propose a metric of sequence diversity ( N d ) derived directly from Nonpareil curves that correlates well with alpha diversity assessed by traditional metrics. We use this metric in different experiments demonstrating the correlation with the Shannon index estimated on 16S rRNA gene profiles and show that N d additionally reveals seasonal patterns in marine samples that are not captured by the Shannon index and more precise rankings of the magnitude of diversity of microbial communities in different habitats. Therefore, the new version of Nonpareil, called Nonpareil 3, advances the toolbox for metagenomic analyses of microbiomes. IMPORTANCE Estimation of the coverage provided by a metagenomic data set, i.e., what fraction of the microbial community was sampled by DNA sequencing, represents an essential first step of every culture-independent genomic study that aims to robustly assess the sequence diversity present in a sample. However, estimation of coverage remains elusive because of several technical limitations associated with high computational requirements and limiting statistical approaches to quantify diversity. Here we described Nonpareil 3, a new bioinformatics algorithm that circumvents several of these limitations and thus can facilitate culture-independent studies in clinical or environmental settings, independent of the sequencing platform employed. In addition, we present a new metric of sequence diversity based on rarefied coverage and demonstrate its use in communities from diverse ecosystems.

SSU rDNA sequence diversity and seasonally differentiated distribution of nanoplanktonic ciliates in neritic Bohai and Yellow Seas as revealed by T-RFLP.

PubMed

Dong, Jun; Shi, Fei; Li, Han; Zhang, Xiaoming; Hu, Xiaozhong; Gong, Jun

2014-01-01

Nanociliates have been frequently found to be important players in the marine microbial loop, however, little is known about their diversity and distribution in coastal ecosystems. We investigated the molecular diversity and distribution patterns of nanoplanktonic oligotrich and choreotrich (OC) ciliates in surface water of three neritic basins of northern China, the South Yellow Sea (SYS), North Yellow Sea (NYS), and Bohai Sea (BS) in June and November 2011. SSU rRNA gene clone libraries generated from three summertime samples (sites B38, B4 and H8) were analyzed and revealed a large novel ribotype diversity, of which many were low-abundant phylotypes belonging to the subclass Oligotrichia, but divergent from described morphospecies. Based on the data of terminal-restriction fragment length polymorphism (T-RFLP) analysis of all 35 samples, we found that the T-RF richness was generally higher in the SYS than in the BS, and negatively correlated with the molar ratio of P to Si. Overall, multidimensional scaling and permutational multivariate analysis of variance of the community turnover demonstrated a distinct seasonal pattern but no basin-to-basin differentiation across all samples. Nevertheless, significant community differences among basins were recognized in the winter dataset. Mantel tests showed that the environmental factors, P:Si ratio, water temperature and concentration of dissolved oxygen (DO), determined the community across all samples. However, both biogeographic distance and environment shaped the community in winter, with DO being the most important physicochemical factor. Our results indicate that the stoichiometric ratio of P:Si is a key factor, through which the phytoplankton community may be shaped, resulting in a cascade effect on the diversity and community composition of OC nanociliates in the N-rich, Si-limited coastal surface waters, and that the Yellow Sea Warm Current drives the nanociliate community, and possibly the microbial food webs, in the coastal ecosystem in winter.

Bacterial Community Diversity of Oil-Contaminated Soils Assessed by High Throughput Sequencing of 16S rRNA Genes.

PubMed

Peng, Mu; Zi, Xiaoxue; Wang, Qiuyu

2015-09-24

Soil bacteria play a major role in ecological and biodegradable function processes in oil-contaminated soils. Here, we assessed the bacterial diversity and changes therein in oil-contaminated soils exposed to different periods of oil pollution using 454 pyrosequencing of 16S rRNA genes. No less than 24,953 valid reads and 6246 operational taxonomic units (OTUs) were obtained from all five studied samples. OTU richness was relatively higher in contaminated soils than clean samples. Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Planctomycetes and Proteobacteria were the dominant phyla among all the soil samples. The heatmap plot depicted the relative percentage of each bacterial family within each sample and clustered five samples into two groups. For the samples, bacteria in the soils varied at different periods of oil exposure. The oil pollution exerted strong selective pressure to propagate many potentially petroleum degrading bacteria. Redundancy analysis (RDA) indicated that organic matter was the highest determinant factor for explaining the variations in community compositions. This suggests that compared to clean soils, oil-polluted soils support more diverse bacterial communities and soil bacterial community shifts were mainly controlled by organic matter and exposure time. These results provide some useful information for bioremediation of petroleum contaminated soil in the future.

Diversity analysis of gut microbiota in osteoporosis and osteopenia patients.

PubMed

Wang, Jihan; Wang, Yangyang; Gao, Wenjie; Wang, Biao; Zhao, Heping; Zeng, Yuhong; Ji, Yanhong; Hao, Dingjun

2017-01-01

Some evidence suggests that bone health can be regulated by gut microbiota. To better understand this, we performed 16S ribosomal RNA sequencing to analyze the intestinal microbial diversity in primary osteoporosis (OP) patients, osteopenia (ON) patients and normal controls (NC). We observed an inverse correlation between the number of bacterial taxa and the value of bone mineral density. The diversity estimators in the OP and ON groups were increased compared with those in the NC group. Beta diversity analyses based on hierarchical clustering and principal coordinate analysis (PCoA) could discriminate the NC samples from OP and ON samples. Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria constituted the four dominant phyla in all samples. Proportion of Firmicutes was significantly higher and Bacteroidetes was significantly lower in OP samples than that in NC samples ( p  < 0.05), Gemmatimonadetes and Chloroflexi were significantly different between OP and NC group as well as between ON and NC group ( p  < 0.01). A total of 21 genera with proportions above 1% were detected and Bacteroides accounted for the largest proportion in all samples. The Blautia, Parabacteroides and Ruminococcaceae genera differed significantly between the OP and NC group ( p  < 0.05). Linear discriminant analysis (LDA) results showed one phylum community and seven phylum communities were enriched in ON and OP, respectively. Thirty-five genus communities, five genus communities and two genus communities were enriched in OP, ON and NC, respectively. The results of this study indicate that gut microbiota may be a critical factor in osteoporosis development, which can further help us search for novel biomarkers of gut microbiota in OP and understand the interaction between gut microbiota and bone health.

Nested PCR Biases in Interpreting Microbial Community Structure in 16S rRNA Gene Sequence Datasets

PubMed Central

Yu, Guoqin; Fadrosh, Doug; Goedert, James J.; Ravel, Jacques; Goldstein, Alisa M.

2015-01-01

Background Sequencing of the PCR-amplified 16S rRNA gene has become a common approach to microbial community investigations in the fields of human health and environmental sciences. This approach, however, is difficult when the amount of DNA is too low to be amplified by standard PCR. Nested PCR can be employed as it can amplify samples with DNA concentration several-fold lower than standard PCR. However, potential biases with nested PCRs that could affect measurement of community structure have received little attention. Results In this study, we used 17 DNAs extracted from vaginal swabs and 12 DNAs extracted from stool samples to study the influence of nested PCR amplification of the 16S rRNA gene on the estimation of microbial community structure using Illumina MiSeq sequencing. Nested and standard PCR methods were compared on alpha- and beta-diversity metrics and relative abundances of bacterial genera. The effects of number of cycles in the first round of PCR (10 vs. 20) and microbial diversity (relatively low in vagina vs. high in stool) were also investigated. Vaginal swab samples showed no significant difference in alpha diversity or community structure between nested PCR and standard PCR (one round of 40 cycles). Stool samples showed significant differences in alpha diversity (except Shannon’s index) and relative abundance of 13 genera between nested PCR with 20 cycles in the first round and standard PCR (P<0.01), but not between nested PCR with 10 cycles in the first round and standard PCR. Operational taxonomic units (OTUs) that had low relative abundance (sum of relative abundance <0.167) accounted for most of the distortion (>27% of total OTUs in stool). Conclusions Nested PCR introduced bias in estimated diversity and community structure. The bias was more significant for communities with relatively higher diversity and when more cycles were applied in the first round of PCR. We conclude that nested PCR could be used when standard PCR does not work. However, rare taxa detected by nested PCR should be validated by other technologies. PMID:26196512

Nested PCR Biases in Interpreting Microbial Community Structure in 16S rRNA Gene Sequence Datasets.

PubMed

Yu, Guoqin; Fadrosh, Doug; Goedert, James J; Ravel, Jacques; Goldstein, Alisa M

2015-01-01

Sequencing of the PCR-amplified 16S rRNA gene has become a common approach to microbial community investigations in the fields of human health and environmental sciences. This approach, however, is difficult when the amount of DNA is too low to be amplified by standard PCR. Nested PCR can be employed as it can amplify samples with DNA concentration several-fold lower than standard PCR. However, potential biases with nested PCRs that could affect measurement of community structure have received little attention. In this study, we used 17 DNAs extracted from vaginal swabs and 12 DNAs extracted from stool samples to study the influence of nested PCR amplification of the 16S rRNA gene on the estimation of microbial community structure using Illumina MiSeq sequencing. Nested and standard PCR methods were compared on alpha- and beta-diversity metrics and relative abundances of bacterial genera. The effects of number of cycles in the first round of PCR (10 vs. 20) and microbial diversity (relatively low in vagina vs. high in stool) were also investigated. Vaginal swab samples showed no significant difference in alpha diversity or community structure between nested PCR and standard PCR (one round of 40 cycles). Stool samples showed significant differences in alpha diversity (except Shannon's index) and relative abundance of 13 genera between nested PCR with 20 cycles in the first round and standard PCR (P<0.01), but not between nested PCR with 10 cycles in the first round and standard PCR. Operational taxonomic units (OTUs) that had low relative abundance (sum of relative abundance <0.167) accounted for most of the distortion (>27% of total OTUs in stool). Nested PCR introduced bias in estimated diversity and community structure. The bias was more significant for communities with relatively higher diversity and when more cycles were applied in the first round of PCR. We conclude that nested PCR could be used when standard PCR does not work. However, rare taxa detected by nested PCR should be validated by other technologies.

The Bacterial and Fungal Diversity of an Aged PAH- and Heavy Metal-Contaminated Soil is Affected by Plant Cover and Edaphic Parameters.

PubMed

Bourceret, Amélia; Cébron, Aurélie; Tisserant, Emilie; Poupin, Pascal; Bauda, Pascale; Beguiristain, Thierry; Leyval, Corinne

2016-04-01

Industrial wasteland soils with aged PAH and heavy metal contaminations are environments where pollutant toxicity has been maintained for decades. Although the communities may be well adapted to the presence of stressors, knowledge about microbial diversity in such soils is scarce. Soil microbial community dynamics can be driven by the presence of plants, but the impact of plant development on selection or diversification of microorganisms in these soils has not been established yet. To test these hypotheses, aged-contaminated soil samples from a field trial were collected. Plots planted with alfalfa were compared to bare soil plots, and bacterial and fungal diversity and abundance were assessed after 2 and 6 years. Using pyrosequencing of 16S rRNA gene and ITS amplicons, we showed that the bacterial community was dominated by Proteobacteria, Actinobacteria, and Bacteroidetes and was characterized by low Acidobacteria abundance, while the fungal community was mainly represented by members of the Ascomycota. The short-term toxic impact of pollutants usually reduces the microbial diversity, yet in our samples bacterial and fungal species richness and diversity was high suggesting that the community structure and diversity adapted to the contaminated soil over decades. The presence of plants induced higher bacterial and fungal diversity than in bare soil. It also increased the relative abundance of bacterial members of the Actinomycetales, Rhizobiales, and Xanthomonadales orders and of most fungal orders. Multivariate analysis showed correlations between microbial community structure and heavy metal and PAH concentrations over time, but also with edaphic parameters (C/N, pH, phosphorus, and nitrogen concentrations).

Microbial diversity and composition of the sediment in the drinking water reservoir Saidenbach (Saxonia, Germany).

PubMed

Röske, Kerstin; Sachse, René; Scheerer, Carola; Röske, Isolde

2012-02-01

Sediments contain a huge number and diversity of microorganisms that are important for the flux of material and are pivotal to all major biogeochemical cycles. Sediments of reservoirs are affected by a wide spectrum of allochthous and autochthonous influences providing versatile environments along the flow of water within the reservoir. Here we report on the microbial diversity in sediments of the mesotrophic drinking water reservoir Saidenbach, Germany, featuring a pronounced longitudinal gradient in sediment composition in the reservoir system. Three sampling sites were selected along the gradient, and the microbial communities in two sediment depths were characterized using catalysed reporter deposition fluorescence in situ hybridization (CARD-FISH) and a bar-coded pyrosequencing approach. Multivariate statistic was used to reveal relationships between sequence diversity and the environmental conditions. The microbial communities were tremendously diverse with a Shannon index of diversity (H') ranging from 6.7 to 7.1. 18,986 sequences could be classified into 37 phyla including candidate divisions, but the full extent of genetic diversity was not captured. While CARD-FISH gave an overview about the community composition, more detailed information was gained by pyrosequencing. Bacteria were more abundant than Archaea. The dominating phylum in all samples was Proteobacteria, especially Betaproteobacteria and Deltaproteobacteria. Furthermore, sequences of Bacteroidetes, Verrucomicrobia, Acidobacteria, Chlorobi, Nitrospira, Spirochaetes, Gammaproteobacteria, Alphaproteobacteria, Chloroflexi, and Gemmatimonadetes were found. The site ammonium concentration, water content and organic matter content revealed to be strongest environmental predictors explaining the observed significant differences in the community composition between sampling sites. Copyright © 2011 Elsevier GmbH. All rights reserved.

Recruitment and baseline characteristics of the Community of Voices choir study to promote the health and well-being of diverse older adults.

PubMed

Johnson, Julene K; Gregorich, Steven E; Acree, Michael; Nápoles, Anna M; Flatt, Jason D; Pounds, Dana; Pabst, Alexandria; Stewart, Anita L

2017-12-01

To describe the recruitment and baseline results of the Community of Voices study that aims to examine the effect of a community choir intervention on the health and well-being of older adults from diverse racial/ethnic and socioeconomic backgrounds. Using community-based participatory research methods, we recruited adults age 60 and over from 12 Administration on Aging-supported senior centers in San Francisco into a 2-arm cluster-randomized controlled trial of the community choir intervention. Multiple outreach methods were used. We tracked outreach, screening, and recruitment metrics and collected demographics and baseline outcomes via community-based, interviewer-administered surveys and performance measures of cognition, physical function, and psychosocial variables. The study contacted 819 individuals, screened 636, and enrolled 390 diverse older adults over a 42-month, phased recruitment period. The mean age was 71.2 (SD = 7.3), and the majority were women. Two-thirds of the sample are non-white, and 20% of participants reported having financial hardship. Outreach and recruitment methods used in the Community of Voices trial facilitated enrollment of a large proportion of minority and lower-SES older adults in the final sample. Similar recruitment approaches could serve as a model for recruiting diverse racial/ethnic and socioeconomic older adults into research.

Greatest soil microbial diversity found in micro-habitats

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

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

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

Phylogenetic diversity, host-specificity and community profiling of sponge-associated bacteria in the northern Gulf of Mexico.

PubMed

Erwin, Patrick M; Olson, Julie B; Thacker, Robert W

2011-01-01

Marine sponges can associate with abundant and diverse consortia of microbial symbionts. However, associated bacteria remain unexamined for the majority of host sponges and few studies use phylogenetic metrics to quantify symbiont community diversity. DNA fingerprinting techniques, such as terminal restriction fragment length polymorphisms (T-RFLP), might provide rapid profiling of these communities, but have not been explicitly compared to traditional methods. We investigated the bacterial communities associated with the marine sponges Hymeniacidon heliophila and Haliclona tubifera, a sympatric tunicate, Didemnum sp., and ambient seawater from the northern Gulf of Mexico by combining replicated clone libraries with T-RFLP analyses of 16S rRNA gene sequences. Clone libraries revealed that bacterial communities associated with the two sponges exhibited lower species richness and lower species diversity than seawater and tunicate assemblages, with differences in species composition among all four source groups. T-RFLP profiles clustered microbial communities by source; individual T-RFs were matched to the majority (80.6%) of clone library sequences, indicating that T-RFLP analysis can be used to rapidly profile these communities. Phylogenetic metrics of community diversity indicated that the two sponge-associated bacterial communities include dominant and host-specific bacterial lineages that are distinct from bacteria recovered from seawater, tunicates, and unrelated sponge hosts. In addition, a large proportion of the symbionts associated with H. heliophila were shared with distant, conspecific host populations in the southwestern Atlantic (Brazil). The low diversity and species-specific nature of bacterial communities associated with H. heliophila and H. tubifera represent a distinctly different pattern from other, reportedly universal, sponge-associated bacterial communities. Our replicated sampling strategy, which included samples that reflect the ambient environment, allowed us to differentiate resident symbionts from potentially transient or prey bacteria. Pairing replicated clone library construction with rapid community profiling via T-RFLP analyses will greatly facilitate future studies of sponge-microbe symbioses.

Diversity of Ktedonobacteria with Actinomycetes-Like Morphology in Terrestrial Environments

PubMed Central

Yabe, Shuhei; Sakai, Yasuteru; Abe, Keietsu; Yokota, Akira

2017-01-01

Bacteria with an actinomycetes-like morphology have recently been discovered, and the class Ktedonobacteria was created for these bacteria in the phylum Chloroflexi. They may prove to be a valuable resource with the potential to produce unprecedented secondary metabolites. However, our understanding of their diversity, richness, habitat, and ecological significance is very limited. We herein developed a 16S rRNA gene-targeted, Ktedonobacteria-specific primer and analyzed ktedonobacterial amplicons. We investigated abundance, diversity, and community structure in forest and garden soils, sand, bark, geothermal sediment, and compost. Forest soils had the highest diversity among the samples tested (1181–2934 operational taxonomic units [OTUs]; Chao 1 estimate, 2503–5613; Shannon index, 4.21–6.42). A phylogenetic analysis of representative OTUs revealed at least eight groups within unclassified Ktedonobacterales, expanding the known diversity of this order. Ktedonobacterial communities markedly varied among our samples. The common mesic environments (soil, sand, and bark) were dominated by diverse phylotypes within the eight groups. In contrast, compost and geothermal sediment samples were dominated by known ktedonobacterial families (Thermosporotrichaceae and Thermogemmatisporaceae, respectively). The relative abundance of Ktedonobacteria in the communities, based on universal primers, was ≤0.8%, but was 12.9% in the geothermal sediment. These results suggest that unknown diverse Ktedonobacteria inhabit common environments including forests, gardens, and sand at low abundances, as well as extreme environments such as geothermal areas. PMID:28321007

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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

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

USGS Publications Warehouse

Lisle, John T.

2011-01-01

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

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

PubMed Central

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

2014-01-01

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

Host species shapes the co-occurrence patterns rather than diversity of stomach bacterial communities in pikas.

PubMed

Li, Huan; Li, Tongtong; Tu, Bo; Kou, Yongping; Li, Xiangzhen

2017-07-01

The mammalian stomach acts as an important barrier against ingested pathogens into the entire gastrointestinal tract, thereby playing a key role in host health. However, little is known regarding to the stomach microbial compositions in wild mammals and the factors that may influence the community compositions. Using high-throughput sequencing of the 16S rRNA gene, we characterized the stomach bacterial community compositions, diversity, and interactions in two common pika (Ochotona sp.) species in China, including Plateau pikas (Ochotona curzoniae) and Daurian pikas (Ochotona daurica) living in the Qinghai-Tibet Plateau and the Inner Mongolia Grassland, respectively. The bacterial communities can be divided into two distinct phylogenetic clusters. The most dominant bacteria in cluster I were unclassified bacteria. Cluster II was more diverse, predominantly consisting of Bacteroidetes, followed by unclassified bacteria, Firmicutes and Proteobacteria. Three dominant genera (Prevotella, Oscillospira, and Ruminococcus) in pika stomachs were significantly enriched in cluster II. In addition, seasons, host species, and sampling sites as well as body weight and sex had no significant impacts on the composition and diversity of pika stomach communities. Interestingly, Plateau pikas harbored a more complex bacterial network than Daurian pikas, and these two pika species showed different co-occurrence patterns. These results suggested that the pika stomach harbors a diverse but relatively stable and unique bacterial community, which is independent on host (host species, body weight, and sex) and measured environmental factors (sampling sites and seasons). Interestingly, host species shapes the microbial interactions rather than diversity of stomach bacterial communities in pikas, reflecting specific niche adaptation of stomach bacterial communities through species interactions.

High-Density 16S Microarray and Clone Library-Based Microbial Community Composition of the Phoenix Spacecraft Assembly Clean Room

NASA Astrophysics Data System (ADS)

Vaishampayan, Parag; Osman, Shariff; Andersen, Gary; Venkateswaran, Kasthuri

2010-06-01

The bacterial diversity and comparative community structure of a clean room used for assembling the Phoenix spacecraft was characterized throughout the spacecraft assembly process by using 16S rRNA gene cloning/sequencing and DNA microarray (PhyloChip) technologies. Samples were collected from several locations of the clean room at three time points: before Phoenix's arrival (PHX-B), during hardware assembly (PHX-D), and after the spacecraft was removed for launch (PHX-A). Bacterial diversity comprised of all major bacterial phyla of PHX-B was found to be statistically different from PHX-D and PHX-A samples. Due to stringent cleaning and decontamination protocols during assembly, PHX-D bacterial diversity was dramatically reduced when compared to PHX-B and PHX-A samples. Comparative community analysis based on PhyloChip results revealed similar overall trends as were seen in clone libraries, but the high-density phylogenetic microarray detected larger diversity in all sampling events. The decrease in community complexity in PHX-D compared to PHX-B, and the subsequent recurrence of these organisms in PHX-A, speaks to the effectiveness of NASA cleaning protocols. However, the persistence of a subset of bacterial signatures throughout all spacecraft assembly phases underscores the need for continued refinement of sterilization technologies and the implementation of safeguards that monitor and inventory microbial contaminants.

High-density 16S microarray and clone library-based microbial community composition of the Phoenix spacecraft assembly clean room.

PubMed

Vaishampayan, Parag; Osman, Shariff; Andersen, Gary; Venkateswaran, Kasthuri

2010-06-01

The bacterial diversity and comparative community structure of a clean room used for assembling the Phoenix spacecraft was characterized throughout the spacecraft assembly process by using 16S rRNA gene cloning/sequencing and DNA microarray (PhyloChip) technologies. Samples were collected from several locations of the clean room at three time points: before Phoenix's arrival (PHX-B), during hardware assembly (PHX-D), and after the spacecraft was removed for launch (PHX-A). Bacterial diversity comprised of all major bacterial phyla of PHX-B was found to be statistically different from PHX-D and PHX-A samples. Due to stringent cleaning and decontamination protocols during assembly, PHX-D bacterial diversity was dramatically reduced when compared to PHX-B and PHX-A samples. Comparative community analysis based on PhyloChip results revealed similar overall trends as were seen in clone libraries, but the high-density phylogenetic microarray detected larger diversity in all sampling events. The decrease in community complexity in PHX-D compared to PHX-B, and the subsequent recurrence of these organisms in PHX-A, speaks to the effectiveness of NASA cleaning protocols. However, the persistence of a subset of bacterial signatures throughout all spacecraft assembly phases underscores the need for continued refinement of sterilization technologies and the implementation of safeguards that monitor and inventory microbial contaminants.

Composition and diversity of rhizosphere fungal community in Coptis chinensis Franch. continuous cropping fields

PubMed Central

Li, Longyun; Wu, Xiaoli; Wang, Yu

2018-01-01

In this study, effects of continuous cropping on soil properties, enzyme activities, and relative abundance, community composition and diversity of fungal taxa were investigated. Rhizosphere soil from field continuously cropped for one-year, three-year and five-year by Coptis chinensis Franch. was collected and analyzed. Illumina high-throughput sequencing analysis showed that continuous cropping of C. chinensis resulted in a significant and continuous decline in the richness and diversity of soil fungal population. Ascomycota, Zygomycota, Basidiomycota, and Glomeromycota were the dominant phyla of fungi detected in rhizosphere soil. Fungal genera such as Phoma, Volutella, Pachycudonia, Heterodermia, Gibberella, Cladosporium, Trichocladium, and Sporothrix, were more dominant in continuously cropped samples for three-year and five-year compared to that for one-year. By contrast, genera, such as Zygosaccharomyces, Pseudotaeniolina, Hydnum, Umbelopsis, Humicola, Crustoderma, Psilocybe, Coralloidiomyces, Mortierella, Polyporus, Pyrenula, and Monographella showed higher relative abundance in one-year samples than that in three-year and five-year samples. Cluster analysis of the fungal communities from three samples of rhizosphere soil from C. chinensis field revealed that the fungal community composition, diversity, and structure were significantly affected by the continuous cropping. Continuous cropping of C. chinensis also led to significant declines in soil pH, urease, and catalase activities. Redundancy analysis showed that the soil pH had the most significant effect on soil fungal population under continuous cropping of C. chinensis. PMID:29538438

Composition and diversity of rhizosphere fungal community in Coptis chinensis Franch. continuous cropping fields.

PubMed

Song, Xuhong; Pan, Yuan; Li, Longyun; Wu, Xiaoli; Wang, Yu

2018-01-01

In this study, effects of continuous cropping on soil properties, enzyme activities, and relative abundance, community composition and diversity of fungal taxa were investigated. Rhizosphere soil from field continuously cropped for one-year, three-year and five-year by Coptis chinensis Franch. was collected and analyzed. Illumina high-throughput sequencing analysis showed that continuous cropping of C. chinensis resulted in a significant and continuous decline in the richness and diversity of soil fungal population. Ascomycota, Zygomycota, Basidiomycota, and Glomeromycota were the dominant phyla of fungi detected in rhizosphere soil. Fungal genera such as Phoma, Volutella, Pachycudonia, Heterodermia, Gibberella, Cladosporium, Trichocladium, and Sporothrix, were more dominant in continuously cropped samples for three-year and five-year compared to that for one-year. By contrast, genera, such as Zygosaccharomyces, Pseudotaeniolina, Hydnum, Umbelopsis, Humicola, Crustoderma, Psilocybe, Coralloidiomyces, Mortierella, Polyporus, Pyrenula, and Monographella showed higher relative abundance in one-year samples than that in three-year and five-year samples. Cluster analysis of the fungal communities from three samples of rhizosphere soil from C. chinensis field revealed that the fungal community composition, diversity, and structure were significantly affected by the continuous cropping. Continuous cropping of C. chinensis also led to significant declines in soil pH, urease, and catalase activities. Redundancy analysis showed that the soil pH had the most significant effect on soil fungal population under continuous cropping of C. chinensis.

Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons

PubMed Central

Penton, C. Ryan; Gupta, Vadakattu V. S. R.; Yu, Julian; Tiedje, James M.

2016-01-01

We examined the effect of different soil sample sizes obtained from an agricultural field, under a single cropping system uniform in soil properties and aboveground crop responses, on bacterial and fungal community structure and microbial diversity indices. DNA extracted from soil sample sizes of 0.25, 1, 5, and 10 g using MoBIO kits and from 10 and 100 g sizes using a bead-beating method (SARDI) were used as templates for high-throughput sequencing of 16S and 28S rRNA gene amplicons for bacteria and fungi, respectively, on the Illumina MiSeq and Roche 454 platforms. Sample size significantly affected overall bacterial and fungal community structure, replicate dispersion and the number of operational taxonomic units (OTUs) retrieved. Richness, evenness and diversity were also significantly affected. The largest diversity estimates were always associated with the 10 g MoBIO extractions with a corresponding reduction in replicate dispersion. For the fungal data, smaller MoBIO extractions identified more unclassified Eukaryota incertae sedis and unclassified glomeromycota while the SARDI method retrieved more abundant OTUs containing unclassified Pleosporales and the fungal genera Alternaria and Cercophora. Overall, these findings indicate that a 10 g soil DNA extraction is most suitable for both soil bacterial and fungal communities for retrieving optimal diversity while still capturing rarer taxa in concert with decreasing replicate variation. PMID:27313569

Bacterial Diversity in Bentonites, Engineered Barrier for Deep Geological Disposal of Radioactive Wastes.

PubMed

Lopez-Fernandez, Margarita; Cherkouk, Andrea; Vilchez-Vargas, Ramiro; Jauregui, Ruy; Pieper, Dietmar; Boon, Nico; Sanchez-Castro, Ivan; Merroun, Mohamed L

2015-11-01

The long-term disposal of radioactive wastes in a deep geological repository is the accepted international solution for the treatment and management of these special residues. The microbial community of the selected host rocks and engineered barriers for the deep geological repository may affect the performance and the safety of the radioactive waste disposal. In this work, the bacterial population of bentonite formations of Almeria (Spain), selected as a reference material for bentonite-engineered barriers in the disposal of radioactive wastes, was studied. 16S ribosomal RNA (rRNA) gene-based approaches were used to study the bacterial community of the bentonite samples by traditional clone libraries and Illumina sequencing. Using both techniques, the bacterial diversity analysis revealed similar results, with phylotypes belonging to 14 different bacterial phyla: Acidobacteria, Actinobacteria, Armatimonadetes, Bacteroidetes, Chloroflexi, Cyanobacteria, Deinococcus-Thermus, Firmicutes, Gemmatimonadetes, Planctomycetes, Proteobacteria, Nitrospirae, Verrucomicrobia and an unknown phylum. The dominant groups of the community were represented by Proteobacteria and Bacteroidetes. A high diversity was found in three of the studied samples. However, two samples were less diverse and dominated by Betaproteobacteria.

Deciphering Diversity Indices for a Better Understanding of Microbial Communities.

PubMed

Kim, Bo-Ra; Shin, Jiwon; Guevarra, Robin; Lee, Jun Hyung; Kim, Doo Wan; Seol, Kuk-Hwan; Lee, Ju-Hoon; Kim, Hyeun Bum; Isaacson, Richard

2017-12-28

The past decades have been a golden era during which great tasks were accomplished in the field of microbiology, including food microbiology. In the past, culture-dependent methods have been the primary choice to investigate bacterial diversity. However, using cultureindependent high-throughput sequencing of 16S rRNA genes has greatly facilitated studies exploring the microbial compositions and dynamics associated with health and diseases. These culture-independent DNA-based studies generate large-scale data sets that describe the microbial composition of a certain niche. Consequently, understanding microbial diversity becomes of greater importance when investigating the composition, function, and dynamics of the microbiota associated with health and diseases. Even though there is no general agreement on which diversity index is the best to use, diversity indices have been used to compare the diversity among samples and between treatments with controls. Tools such as the Shannon- Weaver index and Simpson index can be used to describe population diversity in samples. The purpose of this review is to explain the principles of diversity indices, such as Shannon- Weaver and Simpson, to aid general microbiologists in better understanding bacterial communities. In this review, important questions concerning microbial diversity are addressed. Information from this review should facilitate evidence-based strategies to explore microbial communities.

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

PubMed

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

2013-01-01

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

Distribution and Diversity of Pathogenic Leptospira Species in Peri-domestic Surface Waters from South Central Chile.

PubMed

Mason, Meghan R; Encina, Carolina; Sreevatsan, Srinand; Muñoz-Zanzi, Claudia

2016-08-01

Leptospirosis is a neglected zoonosis affecting animals and humans caused by infection with Leptospira. The bacteria can survive outside of hosts for long periods of time in soil and water. While identification of Leptospira species from human cases and animal reservoirs are increasingly reported, little is known about the diversity of pathogenic Leptospira species in the environment and how surveillance of the environment might be used for monitoring and controlling disease. Water samples (n = 104) were collected from the peri-domestic environment of 422 households from farms, rural villages, and urban slums participating in a broader study on the eco-epidemiology of leptospirosis in the Los Rios Region, Chile, between October 2010 and April 2012. The secY region of samples, previously detected as pathogenic Leptospira by PCR, was amplified and sequenced. Sequences were aligned using ClustalW in MEGA, and a minimum spanning tree was created in PHYLOViZ using the goeBURST algorithm to assess sequence similarity. Sequences from four clinical isolates, 17 rodents, and 20 reference strains were also included in the analysis. Overall, water samples contained L. interrogans, L. kirschneri, and L. weilii, with descending frequency. All species were found in each community type. The distribution of the species differed by the season in which the water samples were obtained. There was no evidence that community-level prevalence of Leptospira in dogs, rodents, or livestock influenced pathogen diversity in the water samples. This study reports the presence of pathogenic Leptospira in the peri-domestic environment of households in three community types and the differences in Leptospira diversity at the community level. Systematic environmental surveillance of Leptospira can be used for detecting changes in pathogen diversity and to identify and monitor contaminated areas where an increased risk of human infection exists.

Genetic Diversity of Bacterial Communities and Gene Transfer Agents in Northern South China Sea

PubMed Central

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

2014-01-01

Pyrosequencing of the 16S ribosomal RNA gene (rDNA) amplicons was performed to investigate the unique distribution of bacterial communities in northern South China Sea (nSCS) and evaluate community structure and spatial differences of bacterial diversity. Cyanobacteria, Proteobacteria, Actinobacteria, and Bacteroidetes constitute the majority of bacteria. The taxonomic description of bacterial communities revealed that more Chroococcales, SAR11 clade, Acidimicrobiales, Rhodobacterales, and Flavobacteriales are present in the nSCS waters than other bacterial groups. Rhodobacterales were less abundant in tropical water (nSCS) than in temperate and cold waters. Furthermore, the diversity of Rhodobacterales based on the gene transfer agent (GTA) major capsid gene (g5) was investigated. Four g5 gene clone libraries were constructed from samples representing different regions and yielded diverse sequences. Fourteen g5 clusters could be identified among 197 nSCS clones. These clusters were also related to known g5 sequences derived from genome-sequenced Rhodobacterales. The composition of g5 sequences in surface water varied with the g5 sequences in the sampling sites; this result indicated that the Rhodobacterales population could be highly diverse in nSCS. Phylogenetic tree analysis result indicated distinguishable diversity patterns among tropical (nSCS), temperate, and cold waters, thereby supporting the niche adaptation of specific Rhodobacterales members in unique environments. PMID:25364820

Beyond Biodiversity: Fish Metagenomes

PubMed Central

Ardura, Alba; Planes, Serge; Garcia-Vazquez, Eva

2011-01-01

Biodiversity and intra-specific genetic diversity are interrelated and determine the potential of a community to survive and evolve. Both are considered together in Prokaryote communities treated as metagenomes or ensembles of functional variants beyond species limits. Many factors alter biodiversity in higher Eukaryote communities, and human exploitation can be one of the most important for some groups of plants and animals. For example, fisheries can modify both biodiversity and genetic diversity (intra specific). Intra-specific diversity can be drastically altered by overfishing. Intense fishing pressure on one stock may imply extinction of some genetic variants and subsequent loss of intra-specific diversity. The objective of this study was to apply a metagenome approach to fish communities and explore its value for rapid evaluation of biodiversity and genetic diversity at community level. Here we have applied the metagenome approach employing the Barcoding target gene COI as a model sequence in catch from four very different fish assemblages exploited by fisheries: freshwater communities from the Amazon River and northern Spanish rivers, and marine communities from the Cantabric and Mediterranean seas. Treating all sequences obtained from each regional catch as a biological unit (exploited community) we found that metagenomic diversity indices of the Amazonian catch sample here examined were lower than expected. Reduced diversity could be explained, at least partially, by overexploitation of the fish community that had been independently estimated by other methods. We propose using a metagenome approach for estimating diversity in Eukaryote communities and early evaluating genetic variation losses at multi-species level. PMID:21829636

Beyond biodiversity: fish metagenomes.

PubMed

Ardura, Alba; Planes, Serge; Garcia-Vazquez, Eva

2011-01-01

Biodiversity and intra-specific genetic diversity are interrelated and determine the potential of a community to survive and evolve. Both are considered together in Prokaryote communities treated as metagenomes or ensembles of functional variants beyond species limits.Many factors alter biodiversity in higher Eukaryote communities, and human exploitation can be one of the most important for some groups of plants and animals. For example, fisheries can modify both biodiversity and genetic diversity (intra specific). Intra-specific diversity can be drastically altered by overfishing. Intense fishing pressure on one stock may imply extinction of some genetic variants and subsequent loss of intra-specific diversity. The objective of this study was to apply a metagenome approach to fish communities and explore its value for rapid evaluation of biodiversity and genetic diversity at community level. Here we have applied the metagenome approach employing the barcoding target gene coi as a model sequence in catch from four very different fish assemblages exploited by fisheries: freshwater communities from the Amazon River and northern Spanish rivers, and marine communities from the Cantabric and Mediterranean seas.Treating all sequences obtained from each regional catch as a biological unit (exploited community) we found that metagenomic diversity indices of the Amazonian catch sample here examined were lower than expected. Reduced diversity could be explained, at least partially, by overexploitation of the fish community that had been independently estimated by other methods.We propose using a metagenome approach for estimating diversity in Eukaryote communities and early evaluating genetic variation losses at multi-species level.

Experimental Manipulation of Grassland Plant Diversity Induces Complex Shifts in Aboveground Arthropod Diversity

PubMed Central

Hertzog, Lionel R.; Meyer, Sebastian T.; Weisser, Wolfgang W.; Ebeling, Anne

2016-01-01

Changes in producer diversity cause multiple changes in consumer communities through various mechanisms. However, past analyses investigating the relationship between plant diversity and arthropod consumers focused only on few aspects of arthropod diversity, e.g. species richness and abundance. Yet, shifts in understudied facets of arthropod diversity like relative abundances or species dominance may have strong effects on arthropod-mediated ecosystem functions. Here we analyze the relationship between plant species richness and arthropod diversity using four complementary diversity indices, namely: abundance, species richness, evenness (equitability of the abundance distribution) and dominance (relative abundance of the dominant species). Along an experimental gradient of plant species richness (1, 2, 4, 8, 16 and 60 plant species), we sampled herbivorous and carnivorous arthropods using pitfall traps and suction sampling during a whole vegetation period. We tested whether plant species richness affects consumer diversity directly (i), or indirectly through increased productivity (ii). Further, we tested the impact of plant community composition on arthropod diversity by testing for the effects of plant functional groups (iii). Abundance and species richness of both herbivores and carnivores increased with increasing plant species richness, but the underlying mechanisms differed between the two trophic groups. While higher species richness in herbivores was caused by an increase in resource diversity, carnivore richness was driven by plant productivity. Evenness of herbivore communities did not change along the gradient in plant species richness, whereas evenness of carnivores declined. The abundance of dominant herbivore species showed no response to changes in plant species richness, but the dominant carnivores were more abundant in species-rich plant communities. The functional composition of plant communities had small impacts on herbivore communities, whereas carnivore communities were affected by forbs of small stature, grasses and legumes. Contrasting patterns in the abundance of dominant species imply different levels of resource specialization for dominant herbivores (narrow food spectrum) and carnivores (broad food spectrum). That in turn could heavily affect ecosystem functions mediated by herbivorous and carnivorous arthropods, such as herbivory or biological pest control. PMID:26859496

Genetic signatures of ecological diversity along an urbanization gradient.

PubMed

Kelly, Ryan P; O'Donnell, James L; Lowell, Natalie C; Shelton, Andrew O; Samhouri, Jameal F; Hennessey, Shannon M; Feist, Blake E; Williams, Gregory D

2016-01-01

Despite decades of work in environmental science and ecology, estimating human influences on ecosystems remains challenging. This is partly due to complex chains of causation among ecosystem elements, exacerbated by the difficulty of collecting biological data at sufficient spatial, temporal, and taxonomic scales. Here, we demonstrate the utility of environmental DNA (eDNA) for quantifying associations between human land use and changes in an adjacent ecosystem. We analyze metazoan eDNA sequences from water sampled in nearshore marine eelgrass communities and assess the relationship between these ecological communities and the degree of urbanization in the surrounding watershed. Counter to conventional wisdom, we find strongly increasing richness and decreasing beta diversity with greater urbanization, and similar trends in the diversity of life histories with urbanization. We also find evidence that urbanization influences nearshore communities at local (hundreds of meters) rather than regional (tens of km) scales. Given that different survey methods sample different components of an ecosystem, we then discuss the advantages of eDNA-which we use here to detect hundreds of taxa simultaneously-as a complement to traditional ecological sampling, particularly in the context of broad ecological assessments where exhaustive manual sampling is impractical. Genetic data are a powerful means of uncovering human-ecosystem interactions that might otherwise remain hidden; nevertheless, no sampling method reveals the whole of a biological community.

Community composition of root-associated fungi in a Quercus-dominated temperate forest: “codominance” of mycorrhizal and root-endophytic fungi

PubMed Central

Toju, Hirokazu; Yamamoto, Satoshi; Sato, Hirotoshi; Tanabe, Akifumi S; Gilbert, Gregory S; Kadowaki, Kohmei

2013-01-01

In terrestrial ecosystems, plant roots are colonized by various clades of mycorrhizal and endophytic fungi. Focused on the root systems of an oak-dominated temperate forest in Japan, we used 454 pyrosequencing to explore how phylogenetically diverse fungi constitute an ecological community of multiple ecotypes. In total, 345 operational taxonomic units (OTUs) of fungi were found from 159 terminal-root samples from 12 plant species occurring in the forest. Due to the dominance of an oak species (Quercus serrata), diverse ectomycorrhizal clades such as Russula, Lactarius, Cortinarius, Tomentella, Amanita, Boletus, and Cenococcum were observed. Unexpectedly, the root-associated fungal community was dominated by root-endophytic ascomycetes in Helotiales, Chaetothyriales, and Rhytismatales. Overall, 55.3% of root samples were colonized by both the commonly observed ascomycetes and ectomycorrhizal fungi; 75.0% of the root samples of the dominant Q. serrata were so cocolonized. Overall, this study revealed that root-associated fungal communities of oak-dominated temperate forests were dominated not only by ectomycorrhizal fungi but also by diverse root endophytes and that potential ecological interactions between the two ecotypes may be important to understand the complex assembly processes of belowground fungal communities. PMID:23762515

Parametric scaling from species to growth-form diversity: an interesting analogy with multifractal functions.

PubMed

Ricotta, Carlo; Pacini, Alessandra; Avena, Giancarlo

2002-01-01

We propose a measure of divergence from species to life-form diversity aimed at summarizing the ecological similarity among different plant communities without losing information on traditional taxonomic diversity. First, species and life-form relative abundances within a given plant community are determined. Next, using Rényi's generalized entropy, the diversity profiles of the analyzed community are computed both from species and life-form relative abundances. Finally, the speed of decrease from species to life-form diversity is obtained by combining the outcome of both profiles. Interestingly, the proposed measure shows some formal analogies with multifractal functions developed in statistical physics for the analysis of spatial patterns. As an application for demonstration, a small data set from a plant community sampled in the archaeological site of Paestum (southern Italy) is used.

Community Structure of Decapod Inhabit Dead Coral Pocillopora sp. in Pemuteran, Bali

NASA Astrophysics Data System (ADS)

Pertiwi, N. P. D.; Malik, M. D. A.; Kholilah, N.; Kurniasih, E. M.; Sembiring, A.; Anggoro, A. W.; Ambariyanto; Meyer, C.

2018-02-01

Decapod is one of the cryptic fauna associated with coral reefs, which play an important role and accounts for a major part of the biodiversity in the reef ecosystem. However, this biodiversity is largely overlooked and assessment regarding this biodiversity has not been conducted thoroughly due to lack of resources and the difficulties of sample collection. This research used semi-quantitative sampling methods to assess the community structure of decapod species inhabit dead Pocillopora sp. in Pemuteran, Bali. Two dead coral head of Pocillopora sp. were used as pilot study and sampled at the 8-12 m depth. All decapod found were collected and identify into family level. The result showed 214 decapods found consisting 12 families, with Xanthidae as the most abundant family. Community Index which consisting diversity, uniformity, and dominancy, indicated medium diversity, stable uniformity, and low dominancy of decapod community. This result also indicated no dominancy between families of decapod. Meanwhile, Species Density Index showed the value of 84.58 ± 2.04 individual per m3, with mean diversity of 7.05 ± 2.04 individual per m3 for each family.

The Biogeography of Endorheic Soda Lakes in the Western United States

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Study protocol for a cluster randomized trial of the Community of Voices choir intervention to promote the health and well-being of diverse older adults.

PubMed

Johnson, Julene K; Nápoles, Anna M; Stewart, Anita L; Max, Wendy B; Santoyo-Olsson, Jasmine; Freyre, Rachel; Allison, Theresa A; Gregorich, Steven E

2015-10-13

Older adults are the fastest growing segment of the United States population. There is an immediate need to identify novel, cost-effective community-based approaches that promote health and well-being for older adults, particularly those from diverse racial/ethnic and socioeconomic backgrounds. Because choral singing is multi-modal (requires cognitive, physical, and psychosocial engagement), it has the potential to improve health outcomes across several dimensions to help older adults remain active and independent. The purpose of this study is to examine the effect of a community choir program (Community of Voices) on health and well-being and to examine its costs and cost-effectiveness in a large sample of diverse, community-dwelling older adults. In this cluster randomized controlled trial, diverse adults age 60 and older were enrolled at Administration on Aging-supported senior centers and completed baseline assessments. The senior centers were randomly assigned to either start the choir immediately (intervention group) or wait 6 months to start (control). Community of Voices is a culturally tailored choir program delivered at the senior centers by professional music conductors that reflects three components of engagement (cognitive, physical, and psychosocial). We describe the nature of the study including the cluster randomized trial study design, sampling frame, sample size calculation, methods of recruitment and assessment, and primary and secondary outcomes. The study involves conducting a randomized trial of an intervention as delivered in "real-world" settings. The choir program was designed using a novel translational approach that integrated evidence-based research on the benefits of singing for older adults, community best practices related to community choirs for older adults, and the perspective of the participating communities. The practicality and relatively low cost of the choir intervention means it can be incorporated into a variety of community settings and adapted to diverse cultures and languages. If successful, this program will be a practical and acceptable community-based approach for promoting health and well-being of older adults. ClinicalTrials.gov NCT01869179 registered 9 January 2013.

Broad Surveys of DNA Viral Diversity Obtained through Viral Metagenomics of Mosquitoes

PubMed Central

Ng, Terry Fei Fan; Willner, Dana L.; Lim, Yan Wei; Schmieder, Robert; Chau, Betty; Nilsson, Christina; Anthony, Simon; Ruan, Yijun; Rohwer, Forest; Breitbart, Mya

2011-01-01

Viruses are the most abundant and diverse genetic entities on Earth; however, broad surveys of viral diversity are hindered by the lack of a universal assay for viruses and the inability to sample a sufficient number of individual hosts. This study utilized vector-enabled metagenomics (VEM) to provide a snapshot of the diversity of DNA viruses present in three mosquito samples from San Diego, California. The majority of the sequences were novel, suggesting that the viral community in mosquitoes, as well as the animal and plant hosts they feed on, is highly diverse and largely uncharacterized. Each mosquito sample contained a distinct viral community. The mosquito viromes contained sequences related to a broad range of animal, plant, insect and bacterial viruses. Animal viruses identified included anelloviruses, circoviruses, herpesviruses, poxviruses, and papillomaviruses, which mosquitoes may have obtained from vertebrate hosts during blood feeding. Notably, sequences related to human papillomaviruses were identified in one of the mosquito samples. Sequences similar to plant viruses were identified in all mosquito viromes, which were potentially acquired through feeding on plant nectar. Numerous bacteriophages and insect viruses were also detected, including a novel densovirus likely infecting Culex erythrothorax. Through sampling insect vectors, VEM enables broad survey of viral diversity and has significantly increased our knowledge of the DNA viruses present in mosquitoes. PMID:21674005

Phytoplankton Community Structure in 2011-2013 Compared to the Extratropical Warming Event of 2014-2015

NASA Astrophysics Data System (ADS)

Du, X.; Peterson, W. T.

2018-02-01

Coastal waters of the Northern California Current experienced "normal" ocean conditions in 2011-2012, weak upwelling in 2013-2014, then suddenly warmed in September 2014. The response of phytoplankton community structure to contrasting ocean conditions was determined from samples collected off Newport, Oregon. Cluster analysis identified three prominent phytoplankton community types: one that occurred during the upwelling season characterized by the highest abundance and diversity of diatoms, a preupwelling/relaxation community characterized by lower abundance, lowest diversity of diatoms and dinoflagellates, and another one associated with the warm anomalies from September 2014 through 2015 with reduced diatom abundance and diversity but the highest dinoflagellate diversity. The changes of diatom and dinoflagellate community were correlated with local factors (silicate, silicate: nitrate ratios, temperature, and salinity), and with the Pacific Decadal Oscillation.

High bacterial diversity of biological soil crusts in water tracks over permafrost in the high arctic polar desert.

PubMed

Steven, Blaire; Lionard, Marie; Kuske, Cheryl R; Vincent, Warwick F

2013-01-01

In this study we report the bacterial diversity of biological soil crusts (biocrusts) inhabiting polar desert soils at the northern land limit of the Arctic polar region (83° 05 N). Employing pyrosequencing of bacterial 16S rRNA genes this study demonstrated that these biocrusts harbor diverse bacterial communities, often as diverse as temperate latitude communities. The effect of wetting pulses on the composition of communities was also determined by collecting samples from soils outside and inside of permafrost water tracks, hill slope flow paths that drain permafrost-affected soils. The intermittent flow regime in the water tracks was correlated with altered relative abundance of phylum level taxonomic bins in the bacterial communities, but the alterations varied between individual sampling sites. Bacteria related to the Cyanobacteria and Acidobacteria demonstrated shifts in relative abundance based on their location either inside or outside of the water tracks. Among cyanobacterial sequences, the proportion of sequences belonging to the family Oscillatoriales consistently increased in relative abundance in the samples from inside the water tracks compared to those outside. Acidobacteria showed responses to wetting pulses in the water tracks, increasing in abundance at one site and decreasing at the other two sites. Subdivision 4 acidobacterial sequences tended to follow the trends in the total Acidobacteria relative abundance, suggesting these organisms were largely responsible for the changes observed in the Acidobacteria. Taken together, these data suggest that the bacterial communities of these high latitude polar biocrusts are diverse but do not show a consensus response to intermittent flow in water tracks over high Arctic permafrost.

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

PubMed

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

2013-01-01

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

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

PubMed Central

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

2013-01-01

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

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

PubMed

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

2014-11-01

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

Analysis of spatial patterns informs community assembly and sampling requirements for Collembola in forest soils

NASA Astrophysics Data System (ADS)

Dirilgen, Tara; Juceviča, Edite; Melecis, Viesturs; Querner, Pascal; Bolger, Thomas

2018-01-01

The relative importance of niche separation, non-equilibrial and neutral models of community assembly has been a theme in community ecology for many decades with none appearing to be applicable under all circumstances. In this study, Collembola species abundances were recorded over eleven consecutive years in a spatially explicit grid and used to examine (i) whether observed beta diversity differed from that expected under conditions of neutrality, (ii) whether sampling points differed in their relative contributions to overall beta diversity, and (iii) the number of samples required to provide comparable estimates of species richness across three forest sites. Neutrality could not be rejected for 26 of the forest by year combinations. However, there is a trend toward greater structure in the oldest forest, where beta diversity was greater than predicted by neutrality on five of the eleven sampling dates. The lack of difference in individual- and sample-based rarefaction curves also suggests randomness in the system at this particular scale of investigation. It seems that Collembola communities are not spatially aggregated and assembly is driven primarily by neutral processes particularly in the younger two sites. Whether this finding is due to small sample size or unaccounted for environmental variables cannot be determined. Variability between dates and sites illustrates the potential of drawing incorrect conclusions if data are collected at a single site and a single point in time.

Negative Effects of an Exotic Grass Invasion on Small-Mammal Communities

PubMed Central

Freeman, Eric D.; Sharp, Tiffanny R.; Larsen, Randy T.; Knight, Robert N.; Slater, Steven J.; McMillan, Brock R.

2014-01-01

Exotic invasive species can directly and indirectly influence natural ecological communities. Cheatgrass (Bromus tectorum) is non-native to the western United States and has invaded large areas of the Great Basin. Changes to the structure and composition of plant communities invaded by cheatgrass likely have effects at higher trophic levels. As a keystone guild in North American deserts, granivorous small mammals drive and maintain plant diversity. Our objective was to assess potential effects of invasion by cheatgrass on small-mammal communities. We sampled small-mammal and plant communities at 70 sites (Great Basin, Utah). We assessed abundance and diversity of the small-mammal community, diversity of the plant community, and the percentage of cheatgrass cover and shrub species. Abundance and diversity of the small-mammal community decreased with increasing abundance of cheatgrass. Similarly, cover of cheatgrass remained a significant predictor of small-mammal abundance even after accounting for the loss of the shrub layer and plant diversity, suggesting that there are direct and indirect effects of cheatgrass. The change in the small-mammal communities associated with invasion of cheatgrass likely has effects through higher and lower trophic levels and has the potential to cause major changes in ecosystem structure and function. PMID:25269073

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

PubMed Central

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

2016-01-01

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

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

PubMed

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

2016-09-29

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

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

PubMed Central

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

2014-01-01

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

Analysis of the influence of living environment and age on vaginal fungal microbiome in giant pandas (Ailuropoda melanoleuca) by high throughput sequencing.

PubMed

Chen, Danyu; Li, Caiwu; Feng, Lan; Zhang, Zhizhong; Zhang, Heming; Cheng, Guangyang; Li, Desheng; Zhang, Guiquan; Wang, Hongning; Chen, Yanxi; Feng, Mingfu; Wang, Chengdong; Wu, Honglin; Deng, Linhua; Ming, He; Yang, Xin

2018-02-01

A recent study has described the normal vaginal bacterial community in giant pandas, but there is a lack of knowledge of the fungal community residing in the vagina of giant pandas. In order to comprehensively understand the vaginal fungal microbial diversity and abundance in giant pandas, high throughput sequencing was used to analyse the ITS1 region, based on thirteen samples taken from the pandas' vaginas, which were grouped by sampling points and age. The results showed that the most abundant phyla were Basidiomycota (73.37%), followed by Ascomycota (20.04%), Zygomycota (5.23%), Glomeromycota (0.014%) and Chytridiomycota (0.006%). At the genus level, Guehomyces (37.92%) was the most abundant, followed by Cladosporium (9.072%), Trichosporon (6.2%) and Mucor (4.97%). Furthermore, Candida only accounted for a low percentage of the vaginal fungal community. With the saturation of rarefaction curves and fungal diversity indices, the samples from Dujiangyan and Chungking Safari Park (DC group) showed a higher fungal species richness and diversity than other living environments. Shannon diversity indices showed significant difference between group WL (Wolong nature reserve) and DC (P < .05). Additionally, a higher diversity was found in ten to fifteen years old (Group 2) than other groups. Group 2 and Group 3 displayed significant differences in the diversities of their vaginal fungal communities (P < .05). These data that has been collected from this research will be helpful for further study to improve the reproductive status of giant pandas. Copyright © 2018 Elsevier Ltd. All rights reserved.

Bacterial Communities in Malagasy Soils with Differing Levels of Disturbance Affecting Botanical Diversity

PubMed Central

Blasiak, Leah C.; Schmidt, Alex W.; Andriamiarinoro, Honoré; Mulaw, Temesgen; Rasolomampianina, Rado; Applequist, Wendy L.; Birkinshaw, Chris; Rejo-Fienena, Félicitée; Lowry, Porter P.; Schmidt, Thomas M.; Hill, Russell T.

2014-01-01

Madagascar is well-known for the exceptional biodiversity of its macro-flora and fauna, but the biodiversity of Malagasy microbial communities remains relatively unexplored. Understanding patterns of bacterial diversity in soil and their correlations with above-ground botanical diversity could influence conservation planning as well as sampling strategies to maximize access to bacterially derived natural products. We present the first detailed description of Malagasy soil bacterial communities from a targeted 16S rRNA gene survey of greater than 290,000 sequences generated using 454 pyrosequencing. Two sampling plots in each of three forest conservation areas were established to represent different levels of disturbance resulting from human impact through agriculture and selective exploitation of trees, as well as from natural impacts of cyclones. In parallel, we performed an in-depth characterization of the total vascular plant morphospecies richness within each plot. The plots representing different levels of disturbance within each forest did not differ significantly in bacterial diversity or richness. Changes in bacterial community composition were largest between forests rather than between different levels of impact within a forest. The largest difference in bacterial community composition with disturbance was observed at the Vohibe forest conservation area, and this difference was correlated with changes in both vascular plant richness and soil pH. These results provide the first survey of Malagasy soil bacterial diversity and establish a baseline of botanical diversity within important conservation areas. PMID:24465484

Application of denaturing high-performance liquid chromatography for monitoring sulfate-reducing bacteria in oil fields.

PubMed

Priha, Outi; Nyyssönen, Mari; Bomberg, Malin; Laitila, Arja; Simell, Jaakko; Kapanen, Anu; Juvonen, Riikka

2013-09-01

Sulfate-reducing bacteria (SRB) participate in microbially induced corrosion (MIC) of equipment and H2S-driven reservoir souring in oil field sites. Successful management of industrial processes requires methods that allow robust monitoring of microbial communities. This study investigated the applicability of denaturing high-performance liquid chromatography (DHPLC) targeting the dissimilatory sulfite reductase ß-subunit (dsrB) gene for monitoring SRB communities in oil field samples from the North Sea, the United States, and Brazil. Fifteen of the 28 screened samples gave a positive result in real-time PCR assays, containing 9 × 10(1) to 6 × 10(5) dsrB gene copies ml(-1). DHPLC and denaturing gradient gel electrophoresis (DGGE) community profiles of the PCR-positive samples shared an overall similarity; both methods revealed the same samples to have the lowest and highest diversity. The SRB communities were diverse, and different dsrB compositions were detected at different geographical locations. The identified dsrB gene sequences belonged to several phylogenetic groups, such as Desulfovibrio, Desulfococcus, Desulfomicrobium, Desulfobulbus, Desulfotignum, Desulfonatronovibrio, and Desulfonauticus. DHPLC showed an advantage over DGGE in that the community profiles were very reproducible from run to run, and the resolved gene fragments could be collected using an automated fraction collector and sequenced without a further purification step. DGGE, on the other hand, included casting of gradient gels, and several rounds of rerunning, excising, and reamplification of bands were needed for successful sequencing. In summary, DHPLC proved to be a suitable tool for routine monitoring of the diversity of SRB communities in oil field samples.

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

USGS Publications Warehouse

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

2012-01-01

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

16S rRNA Gene-Based Metagenomic Analysis of Ozark Cave Bacteria.

PubMed

Oliveira, Cássia; Gunderman, Lauren; Coles, Cathryn A; Lochmann, Jason; Parks, Megan; Ballard, Ethan; Glazko, Galina; Rahmatallah, Yasir; Tackett, Alan J; Thomas, David J

2017-09-01

The microbial diversity within cave ecosystems is largely unknown. Ozark caves maintain a year-round stable temperature (12-14 °C), but most parts of the caves experience complete darkness. The lack of sunlight and geological isolation from surface-energy inputs generate nutrient-poor conditions that may limit species diversity in such environments. Although microorganisms play a crucial role in sustaining life on Earth and impacting human health, little is known about their diversity, ecology, and evolution in community structures. We used five Ozark region caves as test sites for exploring bacterial diversity and monitoring long-term biodiversity. Illumina MiSeq sequencing of five cave soil samples and a control sample revealed a total of 49 bacterial phyla, with seven major phyla: Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, Chloroflexi, Bacteroidetes, and Nitrospirae. Variation in bacterial composition was observed among the five caves studied. Sandtown Cave had the lowest richness and most divergent community composition. 16S rRNA gene-based metagenomic analysis of cave-dwelling microbial communities in the Ozark caves revealed that species abundance and diversity are vast and included ecologically, agriculturally, and economically relevant taxa.

Increased diversity of egg-associated bacteria on brown trout (Salmo trutta) at elevated temperatures.

PubMed

Wilkins, Laetitia G E; Rogivue, Aude; Schütz, Frédéric; Fumagalli, Luca; Wedekind, Claus

2015-11-27

The taxonomic composition of egg-associated microbial communities can play a crucial role in the development of fish embryos. In response, hosts increasingly influence the composition of their associated microbial communities during embryogenesis, as concluded from recent field studies and laboratory experiments. However, little is known about the taxonomic composition and the diversity of egg-associated microbial communities within ecosystems; e.g., river networks. We sampled late embryonic stages of naturally spawned brown trout at nine locations within two different river networks and applied 16S rRNA pyrosequencing to describe their bacterial communities. We found no evidence for a significant isolation-by-distance effect on the composition of bacterial communities, and no association between neutral genetic divergence of fish host (based on 11 microsatellites) and phylogenetic distances of the composition of their associated bacterial communities. We characterized core bacterial communities on brown trout eggs and compared them to corresponding water samples with regard to bacterial composition and its presumptive function. Bacterial diversity was positively correlated with water temperature at the spawning locations. We discuss this finding in the context of the increased water temperatures that have been recorded during the last 25 years in the study area.

Increased diversity of egg-associated bacteria on brown trout (Salmo trutta) at elevated temperatures

PubMed Central

Wilkins, Laetitia G. E.; Rogivue, Aude; Schütz, Frédéric; Fumagalli, Luca; Wedekind, Claus

2015-01-01

The taxonomic composition of egg-associated microbial communities can play a crucial role in the development of fish embryos. In response, hosts increasingly influence the composition of their associated microbial communities during embryogenesis, as concluded from recent field studies and laboratory experiments. However, little is known about the taxonomic composition and the diversity of egg-associated microbial communities within ecosystems; e.g., river networks. We sampled late embryonic stages of naturally spawned brown trout at nine locations within two different river networks and applied 16S rRNA pyrosequencing to describe their bacterial communities. We found no evidence for a significant isolation-by-distance effect on the composition of bacterial communities, and no association between neutral genetic divergence of fish host (based on 11 microsatellites) and phylogenetic distances of the composition of their associated bacterial communities. We characterized core bacterial communities on brown trout eggs and compared them to corresponding water samples with regard to bacterial composition and its presumptive function. Bacterial diversity was positively correlated with water temperature at the spawning locations. We discuss this finding in the context of the increased water temperatures that have been recorded during the last 25 years in the study area. PMID:26611640

Diversity and community structure of pelagic cnidarians in the Celebes and Sulu Seas, southeast Asian tropical marginal seas

NASA Astrophysics Data System (ADS)

Grossmann, Mary M.; Nishikawa, Jun; Lindsay, Dhugal J.

2015-06-01

The Sulu Sea is a semi-isolated, marginal basin surrounded by high sills that greatly reduce water inflow at mesopelagic depths. For this reason, the entire water column below 400 m is stable and homogeneous with respect to salinity (ca. 34.00) and temperature (ca. 10 °C). The neighbouring Celebes Sea is more open, and highly influenced by Pacific waters at comparable depths. The abundance, diversity, and community structure of pelagic cnidarians was investigated in both seas in February 2000. Cnidarian abundance was similar in both sampling locations, but species diversity was lower in the Sulu Sea, especially at mesopelagic depths. At the surface, the cnidarian community was similar in both marginal seas, but, at depth, community structure was dependent first on sampling location and then on depth within each Sea. Cnidarians showed different patterns of dominance at the two sampling locations, with Sulu Sea communities often dominated by species that are rare elsewhere in the Indo-Pacific. Mesopelagic and bathypelagic species recorded in the Sulu Sea did not have significantly different vertical distributions in the Celebes Sea. However, some deep mesopelagic genera were absent from the Sulu Sea in the sampled depth range. These results suggest that a combination of environmental and physiological parameters determine the distribution and dominance of pelagic cnidarians.

Utilizing novel diversity estimators to quantify multiple dimensions of microbial biodiversity across domains

PubMed Central

2013-01-01

Background Microbial ecologists often employ methods from classical community ecology to analyze microbial community diversity. However, these methods have limitations because microbial communities differ from macro-organismal communities in key ways. This study sought to quantify microbial diversity using methods that are better suited for data spanning multiple domains of life and dimensions of diversity. Diversity profiles are one novel, promising way to analyze microbial datasets. Diversity profiles encompass many other indices, provide effective numbers of diversity (mathematical generalizations of previous indices that better convey the magnitude of differences in diversity), and can incorporate taxa similarity information. To explore whether these profiles change interpretations of microbial datasets, diversity profiles were calculated for four microbial datasets from different environments spanning all domains of life as well as viruses. Both similarity-based profiles that incorporated phylogenetic relatedness and naïve (not similarity-based) profiles were calculated. Simulated datasets were used to examine the robustness of diversity profiles to varying phylogenetic topology and community composition. Results Diversity profiles provided insights into microbial datasets that were not detectable with classical univariate diversity metrics. For all datasets analyzed, there were key distinctions between calculations that incorporated phylogenetic diversity as a measure of taxa similarity and naïve calculations. The profiles also provided information about the effects of rare species on diversity calculations. Additionally, diversity profiles were used to examine thousands of simulated microbial communities, showing that similarity-based and naïve diversity profiles only agreed approximately 50% of the time in their classification of which sample was most diverse. This is a strong argument for incorporating similarity information and calculating diversity with a range of emphases on rare and abundant species when quantifying microbial community diversity. Conclusions For many datasets, diversity profiles provided a different view of microbial community diversity compared to analyses that did not take into account taxa similarity information, effective diversity, or multiple diversity metrics. These findings are a valuable contribution to data analysis methodology in microbial ecology. PMID:24238386

Composition of soil microbiome along elevation gradients in southwestern highlands of Saudi Arabia.

PubMed

Yasir, Muhammad; Azhar, Esam I; Khan, Imran; Bibi, Fehmida; Baabdullah, Rnda; Al-Zahrani, Ibrahim A; Al-Ghamdi, Ahmed K

2015-03-14

Saudi Arabia is mostly barren except the southwestern highlands that are susceptible to environmental changes, a hotspot for biodiversity, but poorly studied for microbial diversity and composition. In this study, 454-pyrosequencing of 16S rRNA gene hypervariable region V6 was used to analyze soil bacterial community along elevation gradients of the southwestern highlands. In general, lower percentage of total soil organic matter (SOM) and nitrogen were detected in the analyzed soil samples. Total 33 different phyla were identified across the samples, including dominant phyla Proteobacteria, Actinobacteria and Acidobacteria. Representative OTUs were grouped into 329 and 508 different taxa at family and genus level taxonomic classification, respectively. The identified OTUs unique to each sample were very low irrespective of the altitude. Jackknifed principal coordinates analysis (PCoA) revealed, overall differences in the bacterial community were more related to the quantity of specific OTUs than to their diversity among the studied samples. Bacterial diversity and soil physicochemical properties did not show consistent changes along the elevation gradients. The large number of OTUs shared between the studied samples suggest the presence of a core soil bacterial community in the southwestern highlands of Saudi Arabia.

Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons

DOE PAGES

Penton, C. Ryan; Gupta, Vadakattu V. S. R.; Yu, Julian; ...

2016-06-02

We examined the effect of different soil sample sizes obtained from an agricultural field, under a single cropping system uniform in soil properties and aboveground crop responses, on bacterial and fungal community structure and microbial diversity indices. DNA extracted from soil sample sizes of 0.25, 1, 5, and 10 g using MoBIO kits and from 10 and 100 g sizes using a bead-beating method (SARDI) were used as templates for high-throughput sequencing of 16S and 28S rRNA gene amplicons for bacteria and fungi, respectively, on the Illumina MiSeq and Roche 454 platforms. Sample size significantly affected overall bacterial and fungalmore » community structure, replicate dispersion and the number of operational taxonomic units (OTUs) retrieved. Richness, evenness and diversity were also significantly affected. The largest diversity estimates were always associated with the 10 g MoBIO extractions with a corresponding reduction in replicate dispersion. For the fungal data, smaller MoBIO extractions identified more unclassified Eukaryota incertae sedis and unclassified glomeromycota while the SARDI method retrieved more abundant OTUs containing unclassified Pleosporales and the fungal genera Alternaria and Cercophora. Overall, these findings indicate that a 10 g soil DNA extraction is most suitable for both soil bacterial and fungal communities for retrieving optimal diversity while still capturing rarer taxa in concert with decreasing replicate variation.« less

Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons

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

Penton, C. Ryan; Gupta, Vadakattu V. S. R.; Yu, Julian

We examined the effect of different soil sample sizes obtained from an agricultural field, under a single cropping system uniform in soil properties and aboveground crop responses, on bacterial and fungal community structure and microbial diversity indices. DNA extracted from soil sample sizes of 0.25, 1, 5, and 10 g using MoBIO kits and from 10 and 100 g sizes using a bead-beating method (SARDI) were used as templates for high-throughput sequencing of 16S and 28S rRNA gene amplicons for bacteria and fungi, respectively, on the Illumina MiSeq and Roche 454 platforms. Sample size significantly affected overall bacterial and fungalmore » community structure, replicate dispersion and the number of operational taxonomic units (OTUs) retrieved. Richness, evenness and diversity were also significantly affected. The largest diversity estimates were always associated with the 10 g MoBIO extractions with a corresponding reduction in replicate dispersion. For the fungal data, smaller MoBIO extractions identified more unclassified Eukaryota incertae sedis and unclassified glomeromycota while the SARDI method retrieved more abundant OTUs containing unclassified Pleosporales and the fungal genera Alternaria and Cercophora. Overall, these findings indicate that a 10 g soil DNA extraction is most suitable for both soil bacterial and fungal communities for retrieving optimal diversity while still capturing rarer taxa in concert with decreasing replicate variation.« less

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

Insights into global diatom distribution and diversity in the world's ocean.

PubMed

Malviya, Shruti; Scalco, Eleonora; Audic, Stéphane; Vincent, Flora; Veluchamy, Alaguraj; Poulain, Julie; Wincker, Patrick; Iudicone, Daniele; de Vargas, Colomban; Bittner, Lucie; Zingone, Adriana; Bowler, Chris

2016-03-15

Diatoms (Bacillariophyta) constitute one of the most diverse and ecologically important groups of phytoplankton. They are considered to be particularly important in nutrient-rich coastal ecosystems and at high latitudes, but considerably less so in the oligotrophic open ocean. The Tara Oceans circumnavigation collected samples from a wide range of oceanic regions using a standardized sampling procedure. Here, a total of ∼12 million diatom V9-18S ribosomal DNA (rDNA) ribotypes, derived from 293 size-fractionated plankton communities collected at 46 sampling sites across the global ocean euphotic zone, have been analyzed to explore diatom global diversity and community composition. We provide a new estimate of diversity of marine planktonic diatoms at 4,748 operational taxonomic units (OTUs). Based on the total assigned ribotypes, Chaetoceros was the most abundant and diverse genus, followed by Fragilariopsis, Thalassiosira, and Corethron We found only a few cosmopolitan ribotypes displaying an even distribution across stations and high abundance, many of which could not be assigned with confidence to any known genus. Three distinct communities from South Pacific, Mediterranean, and Southern Ocean waters were identified that share a substantial percentage of ribotypes within them. Sudden drops in diversity were observed at Cape Agulhas, which separates the Indian and Atlantic Oceans, and across the Drake Passage between the Atlantic and Southern Oceans, indicating the importance of these ocean circulation choke points in constraining diatom distribution and diversity. We also observed high diatom diversity in the open ocean, suggesting that diatoms may be more relevant in these oceanic systems than generally considered.

Insights into global diatom distribution and diversity in the world’s ocean

PubMed Central

Malviya, Shruti; Scalco, Eleonora; Audic, Stéphane; Vincent, Flora; Veluchamy, Alaguraj; Poulain, Julie; Wincker, Patrick; Iudicone, Daniele; de Vargas, Colomban; Bittner, Lucie; Zingone, Adriana; Bowler, Chris

2016-01-01

Diatoms (Bacillariophyta) constitute one of the most diverse and ecologically important groups of phytoplankton. They are considered to be particularly important in nutrient-rich coastal ecosystems and at high latitudes, but considerably less so in the oligotrophic open ocean. The Tara Oceans circumnavigation collected samples from a wide range of oceanic regions using a standardized sampling procedure. Here, a total of ∼12 million diatom V9-18S ribosomal DNA (rDNA) ribotypes, derived from 293 size-fractionated plankton communities collected at 46 sampling sites across the global ocean euphotic zone, have been analyzed to explore diatom global diversity and community composition. We provide a new estimate of diversity of marine planktonic diatoms at 4,748 operational taxonomic units (OTUs). Based on the total assigned ribotypes, Chaetoceros was the most abundant and diverse genus, followed by Fragilariopsis, Thalassiosira, and Corethron. We found only a few cosmopolitan ribotypes displaying an even distribution across stations and high abundance, many of which could not be assigned with confidence to any known genus. Three distinct communities from South Pacific, Mediterranean, and Southern Ocean waters were identified that share a substantial percentage of ribotypes within them. Sudden drops in diversity were observed at Cape Agulhas, which separates the Indian and Atlantic Oceans, and across the Drake Passage between the Atlantic and Southern Oceans, indicating the importance of these ocean circulation choke points in constraining diatom distribution and diversity. We also observed high diatom diversity in the open ocean, suggesting that diatoms may be more relevant in these oceanic systems than generally considered. PMID:26929361

Molecular Phylogenetic Diversity and Spatial Distribution of Bacterial Communities in Cooling Stage during Swine Manure Composting

PubMed Central

Guo, Yan; Zhang, Jinliang; Yan, Yongfeng; Wu, Jian; Zhu, Nengwu; Deng, Changyan

2015-01-01

Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and subsequent sub-cloning and sequencing were used in this study to analyze the molecular phylogenetic diversity and spatial distribution of bacterial communities in different spatial locations during the cooling stage of composted swine manure. Total microbial DNA was extracted, and bacterial near full-length 16S rRNA genes were subsequently amplified, cloned, RFLP-screened, and sequenced. A total of 420 positive clones were classified by RFLP and near-full-length 16S rDNA sequences. Approximately 48 operational taxonomic units (OTUs) were found among 139 positive clones from the superstratum sample; 26 among 149 were from the middle-level sample and 35 among 132 were from the substrate sample. Thermobifida fusca was common in the superstratum layer of the pile. Some Bacillus spp. were remarkable in the middle-level layer, and Clostridium sp. was dominant in the substrate layer. Among 109 OTUs, 99 displayed homology with those in the GenBank database. Ten OTUs were not closely related to any known species. The superstratum sample had the highest microbial diversity, and different and distinct bacterial communities were detected in the three different layers. This study demonstrated the spatial characteristics of the microbial community distribution in the cooling stage of swine manure compost. PMID:25925066

Acidobacteria appear to dominate the microbiome of two sympatric Caribbean Sponges and one Zoanthid.

PubMed

O'Connor-Sánchez, Aileen; Rivera-Domínguez, Adán J; Santos-Briones, César de los; López-Aguiar, Lluvia K; Peña-Ramírez, Yuri J; Prieto-Davo, Alejandra

2014-12-10

Marine invertebrate-associated microbial communities are interesting examples of complex symbiotic systems and are a potential source of biotechnological products. In this work, pyrosequencing-based assessment from bacterial community structures of sediments, two sponges, and one zoanthid collected in the Mexican Caribbean was performed. The results suggest that the bacterial diversity at the species level is higher in the sediments than in the animal samples. Analysis of bacterial communities' structure showed that about two thirds of the bacterial diversity in all the samples belongs to the phyla Acidobacteria and Proteobacteria. The genus Acidobacterium appears to dominate the bacterial community in all the samples, reaching almost 80% in the sponge Hyrtios. Our evidence suggests that the sympatric location of these benthonic species may lead to common bacterial structure features among their bacterial communities. The results may serve as a first insight to formulate hypotheses that lead to more extensive studies of sessile marine organisms' microbiomes from the Mexican Caribbean.

Dynamics of soil diazotrophic community structure, diversity, and functioning during the cropping period of cotton (Gossypium hirsutum).

PubMed

Rai, Sandhya; Singh, Dileep Kumar; Annapurna, Kannepalli

2015-01-01

The soil sampled at different growth stages along the cropping period of cotton were analyzed using various molecular tools: restriction fragment length polymorphism (RFLP), terminal restriction length polymorphism (T-RFLP), and cloning-sequencing. The cluster analysis of the diazotrophic community structure of early sampled soil (0, 15, and 30 days) was found to be more closely related to each other than the later sampled one. Phylogenetic and diversity analysis of sequences obtained from the first (0 Day; C0) and last soil sample (180 day; C180) confirmed the data. The phylogenetic analysis revealed that C0 was having more unique sequences than C180 (presence of γ-Proteobacteria exclusively in C0). A relatively higher richness of diazotrophic community sequences was observed in C0 (S(ACE) : 30.76; S(Chao1) : 20.94) than C180 (S(ACE) : 18.00; S(Chao1) : 18.00) while the evenness component of Shannon diversity index increased from C0 (0.97) to C180 (1.15). The impact of routine agricultural activities was more evident based on diazotrophic activity (measured by acetylene reduction assay) than its structure and diversity. The nitrogenase activity of C0 (1264.85 ± 35.7 ηmol of ethylene production g(-1) dry soil h(-1) ) was statistically higher when compared to all other values (p < 0.05). There was no correlation found between diazotrophic community structure/diversity and N2 fixation rates. Thus, considerable functional redundancy of nifH was concluded to be existing at the experimental site. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Diversity of halophilic bacteria isolated from Rambla Salada, Murcia (Spain).

PubMed

Luque, Rocío; Béjar, Victoria; Quesada, Emilia; Llamas, Inmaculada

2014-12-01

In this study we analyzed the diversity of the halophilic bacteria community from Rambla Salada during the years 2006 and 2007. We collected a total of 364 strains, which were then identified by means of phenotypic tests and by the hypervariable V1-V3 region of the 16S rRNA sequences (around 500 bp). The ribosomal data showed that the isolates belonged to Proteobacteria (72.5%), Firmicutes (25.8%), Actinobacteria (1.4%), and Bacteroidetes (0.3%) phyla, with Gammaproteobacteria the predominant class. Halomonas was the most abundant genus (41.2% isolates) followed by Marinobacter (12.9% isolates) and Bacillus (12.6% isolates). In addition, 9 strains showed <97% sequence identity with validly described species and may well represent new taxa. The diversity of the bacterial community analyzed with the DOTUR package determined 139 operational taxonomic units at 3% genetic distance level. Rarefaction curves and diversity indexes demonstrated that our collection of isolates adequately represented all the bacterial community at Rambla Salada that can be grown under the conditions used in this work. We found that the sampling season influenced the composition of the bacterial community, and bacterial diversity was higher in 2007; this fact could be related to lower salinity at this sampling time.

The endohelminth fauna of barbel ( Barbus barbus) correlates with water quality of the Danube River in Bulgaria.

PubMed

Nachev, M; Sures, B

2009-04-01

Infection of barbel with 10 species of metazoan parasites including 3 trematodes, 3 acanthocephalans and 4 nematodes was observed in fish collected from 3 localities in the Bulgarian part of the river Danube between summer 2004 and summer 2007. The composition as well as the diversity characteristics of the parasite communities were analysed seasonally and showed a clear correlation with the composition of the invertebrate fauna and water quality. The most prevalent species was the acanthocephalan Pomphorhynchus laevis, which was also the dominant species of the intestinal component communities at all sampling sites. The second most frequent parasite at all Danube localities was Rhabdochona hellichi, which occurred in significantly higher numbers at the less polluted sites. Overall, the diversity of helminth communities increased with decreasing levels of nutrients and pollutants at all sampling sites. Therefore, the composition and diversity of parasite communities may be used to characterize ecosystem health and integrity.

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

NASA Astrophysics Data System (ADS)

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

2005-12-01

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

Child Sexual Abuse Consequences in Community Samples of Latino and European American Adolescents

ERIC Educational Resources Information Center

Newcomb, Michael D.; Munoz, David T.; Carmona, Jennifer Vargas

2009-01-01

Objective: Research investigating the impact of child sexual abuse (CSA) in community samples of adolescents has been limited. This study aims to identify sexual abuse among ethnically diverse high school adolescents of both genders and evaluate their psycho-emotional consequences. Method: Through the use of self-report instruments, a sample of…

Fine grained compositional analysis of Port Everglades Inlet microbiome using high throughput DNA sequencing.

PubMed

O'Connell, Lauren; Gao, Song; McCorquodale, Donald; Fleisher, Jay; Lopez, Jose V

2018-01-01

Similar to natural rivers, manmade inlets connect inland runoff to the ocean. Port Everglades Inlet (PEI) is a busy cargo and cruise ship port in South Florida, which can act as a source of pollution to surrounding beaches and offshore coral reefs. Understanding the composition and fluctuations of bacterioplankton communities ("microbiomes") in major port inlets is important due to potential impacts on surrounding environments. We hypothesize seasonal microbial fluctuations, which were profiled by high throughput 16S rRNA amplicon sequencing and analysis. Surface water samples were collected every week for one year. A total of four samples per month, two from each sampling location, were used for statistical analysis creating a high sampling frequency and finer sampling scale than previous inlet microbiome studies. We observed significant differences in community alpha diversity between months and seasons. Analysis of composition of microbiomes (ANCOM) tests were run in QIIME 2 at genus level taxonomic classification to determine which genera were differentially abundant between seasons and months. Beta diversity results yielded significant differences in PEI community composition in regard to month, season, water temperature, and salinity. Analysis of potentially pathogenic genera showed presence of Staphylococcus and Streptococcus . However, statistical analysis indicated that these organisms were not present in significantly high abundances throughout the year or between seasons. Significant differences in alpha diversity were observed when comparing microbial communities with respect to time. This observation stems from the high community evenness and low community richness in August. This indicates that only a few organisms dominated the community during this month. August had lower than average rainfall levels for a wet season, which may have contributed to less runoff, and fewer bacterial groups introduced into the port surface waters. Bacterioplankton beta diversity differed significantly by month, season, water temperature, and salinity. The 2013-2014 dry season (October-April), was warmer and wetter than historical averages. This may have driven significant differences in beta diversity. Increased nitrogen and phosphorous concentrations were observed in these dry season months, possibly creating favorable bacterial growth conditions. Potentially pathogenic genera were present in the PEI. However their relatively low, non-significant abundance levels highlight their relatively low risk for public health concerns. This study represents the first to sample a large port at this sampling scale and sequencing depth. These data can help establish the inlet microbial community baseline and supplement the vital monitoring of local marine and recreational environments, all the more poignant in context of local reef disease outbreaks and worldwide coral reef collapse in wake of a harsh 2014-16 El Niño event.

Biogeographic patterns of soil diazotrophic communities across six forests in the North America.

PubMed

Tu, Qichao; Deng, Ye; Yan, Qingyun; Shen, Lina; Lin, Lu; He, Zhili; Wu, Liyou; Van Nostrand, Joy D; Buzzard, Vanessa; Michaletz, Sean T; Enquist, Brian J; Weiser, Michael D; Kaspari, Michael; Waide, Robert B; Brown, James H; Zhou, Jizhong

2016-06-01

Soil diazotrophs play important roles in ecosystem functioning by converting atmospheric N2 into biologically available ammonium. However, the diversity and distribution of soil diazotrophic communities in different forests and whether they follow biogeographic patterns similar to macroorganisms still remain unclear. By sequencing nifH gene amplicons, we surveyed the diversity, structure and biogeographic patterns of soil diazotrophic communities across six North American forests (126 nested samples). Our results showed that each forest harboured markedly different soil diazotrophic communities and that these communities followed traditional biogeographic patterns similar to plant and animal communities, including the taxa-area relationship (TAR) and latitudinal diversity gradient. Significantly higher community diversity and lower microbial spatial turnover rates (i.e. z-values) were found for rainforests (~0.06) than temperate forests (~0.1). The gradient pattern of TARs and community diversity was strongly correlated (r(2)  > 0.5) with latitude, annual mean temperature, plant species richness and precipitation, and weakly correlated (r(2)  < 0.25) with pH and soil moisture. This study suggests that even microbial subcommunities (e.g. soil diazotrophs) follow general biogeographic patterns (e.g. TAR, latitudinal diversity gradient), and indicates that the metabolic theory of ecology and habitat heterogeneity may be the major underlying ecological mechanisms shaping the biogeographic patterns of soil diazotrophic communities. © 2016 John Wiley & Sons Ltd.

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

PubMed Central

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

2017-01-01

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

High Bacterial Diversity of Biological Soil Crusts in Water Tracks over Permafrost in the High Arctic Polar Desert

DOE PAGES

Steven, Blaire; Lionard, Marie; Kuske, Cheryl R.; ...

2013-08-13

In this paper we report the bacterial diversity of biological soil crusts (biocrusts) inhabiting polar desert soils at the northern land limit of the Arctic polar region (83° 05 N). Employing pyrosequencing of bacterial 16S rRNA genes this study demonstrated that these biocrusts harbor diverse bacterial communities, often as diverse as temperate latitude communities. The effect of wetting pulses on the composition of communities was also determined by collecting samples from soils outside and inside of permafrost water tracks, hill slope flow paths that drain permafrost-affected soils. The intermittent flow regime in the water tracks was correlated with altered relativemore » abundance of phylum level taxonomic bins in the bacterial communities, but the alterations varied between individual sampling sites. Bacteria related to the Cyanobacteria and Acidobacteria demonstrated shifts in relative abundance based on their location either inside or outside of the water tracks. Among cyanobacterial sequences, the proportion of sequences belonging to the family Oscillatoriales consistently increased in relative abundance in the samples from inside the water tracks compared to those outside. Acidobacteria showed responses to wetting pulses in the water tracks, increasing in abundance at one site and decreasing at the other two sites. Subdivision 4 acidobacterial sequences tended to follow the trends in the total Acidobacteria relative abundance, suggesting these organisms were largely responsible for the changes observed in the Acidobacteria. Finally, taken together, these data suggest that the bacterial communities of these high latitude polar biocrusts are diverse but do not show a consensus response to intermittent flow in water tracks over high Arctic permafrost.« less

High Bacterial Diversity of Biological Soil Crusts in Water Tracks over Permafrost in the High Arctic Polar Desert

PubMed Central

Steven, Blaire; Lionard, Marie; Kuske, Cheryl R.; Vincent, Warwick F.

2013-01-01

In this study we report the bacterial diversity of biological soil crusts (biocrusts) inhabiting polar desert soils at the northern land limit of the Arctic polar region (83° 05 N). Employing pyrosequencing of bacterial 16S rRNA genes this study demonstrated that these biocrusts harbor diverse bacterial communities, often as diverse as temperate latitude communities. The effect of wetting pulses on the composition of communities was also determined by collecting samples from soils outside and inside of permafrost water tracks, hill slope flow paths that drain permafrost-affected soils. The intermittent flow regime in the water tracks was correlated with altered relative abundance of phylum level taxonomic bins in the bacterial communities, but the alterations varied between individual sampling sites. Bacteria related to the Cyanobacteria and Acidobacteria demonstrated shifts in relative abundance based on their location either inside or outside of the water tracks. Among cyanobacterial sequences, the proportion of sequences belonging to the family Oscillatoriales consistently increased in relative abundance in the samples from inside the water tracks compared to those outside. Acidobacteria showed responses to wetting pulses in the water tracks, increasing in abundance at one site and decreasing at the other two sites. Subdivision 4 acidobacterial sequences tended to follow the trends in the total Acidobacteria relative abundance, suggesting these organisms were largely responsible for the changes observed in the Acidobacteria. Taken together, these data suggest that the bacterial communities of these high latitude polar biocrusts are diverse but do not show a consensus response to intermittent flow in water tracks over high Arctic permafrost. PMID:23967218

Phylogenetic structure of arbuscular mycorrhizal fungal communities along an elevation gradient.

PubMed

Egan, Cameron P; Callaway, Ragan M; Hart, Miranda M; Pither, Jason; Klironomos, John

2017-04-01

Despite the importance of arbuscular mycorrhizal (AM) fungi within terrestrial ecosystems, we know little about how natural AM fungal communities are structured. To date, the majority of studies examining AM fungal community diversity have focused on single habitats with similar environmental conditions, with relatively few studies having assessed the diversity of AM fungi over large-scale environmental gradients. In this study, we characterized AM fungal communities in the soil along a high-elevation gradient in the North American Rocky Mountains. We focused on phylogenetic patterns of AM fungal communities to gain insight into how AM fungal communities are naturally assembled. We found that alpine AM fungal communities had lower phylogenetic diversity relative to lower elevation communities, as well as being more heterogeneous in composition than either treeline or subalpine communities. AM fungal communities were phylogenetically clustered at all elevations sampled, suggesting that environmental filtering, either selection by host plants or fungal niches, is the primary ecological process structuring communities along the gradient.

Changes in the Bacterial Community of Soil from a Neutral Mine Drainage Channel

PubMed Central

Pereira, Letícia Bianca; Vicentini, Renato; Ottoboni, Laura M. M.

2014-01-01

Mine drainage is an important environmental disturbance that affects the chemical and biological components in natural resources. However, little is known about the effects of neutral mine drainage on the soil bacteria community. Here, a high-throughput 16S rDNA pyrosequencing approach was used to evaluate differences in composition, structure, and diversity of bacteria communities in samples from a neutral drainage channel, and soil next to the channel, at the Sossego copper mine in Brazil. Advanced statistical analyses were used to explore the relationships between the biological and chemical data. The results showed that the neutral mine drainage caused changes in the composition and structure of the microbial community, but not in its diversity. The Deinococcus/Thermus phylum, especially the Meiothermus genus, was in large part responsible for the differences between the communities, and was positively associated with the presence of copper and other heavy metals in the environmental samples. Other important parameters that influenced the bacterial diversity and composition were the elements potassium, sodium, nickel, and zinc, as well as pH. The findings contribute to the understanding of bacterial diversity in soils impacted by neutral mine drainage, and demonstrate that heavy metals play an important role in shaping the microbial population in mine environments. PMID:24796430

Disturbance, neutral theory, and patterns of beta diversity in soil communities.

PubMed

Maaß, Stefanie; Migliorini, Massimo; Rillig, Matthias C; Caruso, Tancredi

2014-12-01

Beta diversity describes how local communities within an area or region differ in species composition/abundance. There have been attempts to use changes in beta diversity as a biotic indicator of disturbance, but lack of theory and methodological caveats have hampered progress. We here propose that the neutral theory of biodiversity plus the definition of beta diversity as the total variance of a community matrix provide a suitable, novel, starting point for ecological applications. Observed levels of beta diversity (BD) can be compared to neutral predictions with three possible outcomes: Observed BD equals neutral prediction or is larger (divergence) or smaller (convergence) than the neutral prediction. Disturbance might lead to either divergence or convergence, depending on type and strength. We here apply these ideas to datasets collected on oribatid mites (a key, very diverse soil taxon) under several regimes of disturbances. When disturbance is expected to increase the heterogeneity of soil spatial properties or the sampling strategy encompassed a range of diverging environmental conditions, we observed diverging assemblages. On the contrary, we observed patterns consistent with neutrality when disturbance could determine homogenization of soil properties in space or the sampling strategy encompassed fairly homogeneous areas. With our method, spatial and temporal changes in beta diversity can be directly and easily monitored to detect significant changes in community dynamics, although the method itself cannot inform on underlying mechanisms. However, human-driven disturbances and the spatial scales at which they operate are usually known. In this case, our approach allows the formulation of testable predictions in terms of expected changes in beta diversity, thereby offering a promising monitoring tool.

Community structure and diversity of tropical forest mammals: data from a global camera trap network.

PubMed

Ahumada, Jorge A; Silva, Carlos E F; Gajapersad, Krisna; Hallam, Chris; Hurtado, Johanna; Martin, Emanuel; McWilliam, Alex; Mugerwa, Badru; O'Brien, Tim; Rovero, Francesco; Sheil, Douglas; Spironello, Wilson R; Winarni, Nurul; Andelman, Sandy J

2011-09-27

Terrestrial mammals are a key component of tropical forest communities as indicators of ecosystem health and providers of important ecosystem services. However, there is little quantitative information about how they change with local, regional and global threats. In this paper, the first standardized pantropical forest terrestrial mammal community study, we examine several aspects of terrestrial mammal species and community diversity (species richness, species diversity, evenness, dominance, functional diversity and community structure) at seven sites around the globe using a single standardized camera trapping methodology approach. The sites-located in Uganda, Tanzania, Indonesia, Lao PDR, Suriname, Brazil and Costa Rica-are surrounded by different landscape configurations, from continuous forests to highly fragmented forests. We obtained more than 51 000 images and detected 105 species of mammals with a total sampling effort of 12 687 camera trap days. We find that mammal communities from highly fragmented sites have lower species richness, species diversity, functional diversity and higher dominance when compared with sites in partially fragmented and continuous forest. We emphasize the importance of standardized camera trapping approaches for obtaining baselines for monitoring forest mammal communities so as to adequately understand the effect of global, regional and local threats and appropriately inform conservation actions.

Microbial analysis in primary and persistent endodontic infections by using pyrosequencing.

PubMed

Hong, Bo-Young; Lee, Tae-Kwon; Lim, Sang-Min; Chang, Seok Woo; Park, Joonhong; Han, Seung Hyun; Zhu, Qiang; Safavi, Kamran E; Fouad, Ashraf F; Kum, Kee Yeon

2013-09-01

The aim of this study was to investigate the bacterial community profile of intracanal microbiota in primary and persistent endodontic infections associated with asymptomatic chronic apical periodontitis by using GS-FLX Titanium pyrosequencing. The null hypothesis was that there is no difference in diversity of overall bacterial community profiles between primary and persistent infections. Pyrosequencing analysis from 10 untreated and 8 root-filled samples was conducted. Analysis from 18 samples yielded total of 124,767 16S rRNA gene sequences (with a mean of 6932 reads per sample) that were taxonomically assigned into 803 operational taxonomic units (3% distinction), 148 genera, and 10 phyla including unclassified. Bacteroidetes was the most abundant phylum in both primary and persistent infections. There were no significant differences in bacterial diversity between the 2 infection groups (P > .05). The bacterial community profile that was based on dendrogram showed that bacterial population in both infections was not significantly different in their structure and composition (P > .05). The present pyrosequencing study demonstrates that persistent infections have as diverse bacterial community as primary infections. Copyright © 2013 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

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 .

The ecology and diversity of microbial eukaryotes in geothermal springs.

PubMed

Oliverio, Angela M; Power, Jean F; Washburne, Alex; Cary, S Craig; Stott, Matthew B; Fierer, Noah

2018-04-16

Decades of research into the Bacteria and Archaea living in geothermal spring ecosystems have yielded great insight into the diversity of life and organismal adaptations to extreme environmental conditions. Surprisingly, while microbial eukaryotes (protists) are also ubiquitous in many environments, their diversity across geothermal springs has mostly been ignored. We used high-throughput sequencing to illuminate the diversity and structure of microbial eukaryotic communities found in 160 geothermal springs with broad ranges in temperature and pH across the Taupō Volcanic Zone in New Zealand. Protistan communities were moderately predictable in composition and varied most strongly across gradients in pH and temperature. Moreover, this variation mirrored patterns observed for bacterial and archaeal communities across the same spring samples, highlighting that there are similar ecological constraints across the tree of life. While extreme pH values were associated with declining protist diversity, high temperature springs harbored substantial amounts of protist diversity. Although protists are often overlooked in geothermal springs and other extreme environments, our results indicate that such environments can host distinct and diverse protistan communities.

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

PubMed

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

2016-11-01

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

Ecospaces occupied by Homo erectus and Homo sapiens in insular Southeast Asia in the Pleistocene

NASA Astrophysics Data System (ADS)

Hertler, Christine; Haupt, Susanne; Volmer, Rebekka; Bruch, Angela

2014-05-01

Hominins migrated to the islands of the Sunda Shelf multiple times. At least two immigration events are evident, an early immigration of Homo erectus in the late Early Pleistocene and a second immigration of Homo sapiens during the Late Pleistocene. Regional environments changed considerably in the Pleistocene. Expansion patterns among hominins are at least co-determined by their ecologies and environmental change. We examine these expansion patterns on the basis of habitat reconstructions. Mammalian communities provide a geographically extensive record and permit to assess hominin ecospaces. Although chronological resolution is low, they represent the most complete record of habitat changes associated with hominin expansion patterns. In order to reconstruct and compare hominin ecospaces on a quantitative scale, we set up a reference sample consisting of mammalian communities of 117 national parks in South Asia and Sub-Saharan Africa. The diversity of such communities is assessed by ecological profiling of specialized herbivore taxa. Moreover, datasets on climate and vegetation correlate with the diversity structure of such specialized herbivore communities. Reconstructing the diversity structure of communities at key sites in Pleistocene Southeast Asia permits to infer features of the climatic and vegetation framework associated with different hominin taxa. Our results show that Homo erectus and Homo sapiens did not occupy similar ecospaces. The ecospace of Homo erectus is characterized by comparatively low diversity among frugivorous and folivorous taxa, while obligate grazers are part of the assemblages. Specialized herbivore communities with such a diversity structure occur at present in East Africa, while they are absent in Southeast Asia. In the reference sample, this type of ecospace corresponds to seasonal wetlands. Although Homo sapiens still inhabits this type of environment in Southeast Asia, his ecospace is wider. Homo sapiens is associated with specialized herbivore communities dominated by frugivorous and folivorous taxa. Specialized herbivore communities with such a diversity structure occur at present in rainforests on the Sunda Shelf.

Sexual Knowledge, Attitudes, and Behaviors of an Ethnically Diverse Sample of Community College Students in Metropolitan New York.

ERIC Educational Resources Information Center

DeMarzo, Jenine

This study investigated the association among select socio-cultural variables and sexual knowledge, attitudes, and behaviors with a diverse population of metropolitan New York community college students. The Sexual Knowledge, Attitude, and Behavior Test survey instrument was administered to 338 students between the ages of 17 and 26 in their…

The indirect impact of long-term overbrowsing on insects in the Allegheny National Forest region of Pennsylvania

Treesearch

Michael J. Chips; Ellen H. Yerger; Arpad Hervanek; Tim Nuttle; Alex Royo; Jonathan N. Pruitt; Terrence P. McGlynn; Cynthia L. Riggall; Walter P. Carson

2015-01-01

Overbrowsing has created depauperate plant communities throughout the eastern deciduous forest. We hypothesized these low-diversity plant communities are associated with lower insect diversity. We compared insects inside and outside a 60-year-old fenced deer exclosure where plant species richness is 5x higher inside versus outside. We sampled aboveground and litter...

Spatial and Temporal Variation in DeSoto Canyon Macrofaunal Community Structure

NASA Astrophysics Data System (ADS)

Baco-Taylor, A.; Shantharam, A. K.

2016-02-01

Sediment-dwelling macrofauna (polychaetes, bivalves, and assorted crustaceans ≥ 300 µm) have long served as biological indicators of ecosystem stress. As part of evaluating the 2010 impact from the Deepwater Horizon blowout, we sampled 12 sites along and transverse to the DeSoto Canyon axis, Gulf of Mexico, as well as 2 control sites outside the Canyon. Sites ranged in depth from 479-2310 m. Three of the sites (PCB06, S36, and XC4) were sampled annually from 2012-2014. We provide an overview of the macrofauna community structure of canyon and non-canyon sites, as well as trends in community structure and diversity at the time-series sites. Compositionally, polychaetes dominated the communities, followed by tanaid crustaceans and bivalves. The total number of individuals was not significantly correlated with depth while the total number of taxa and species richness were. Rarefaction shows the deepest station, XC4 (2310 m) had the lowest diversity while NT800 (a non-canyon control at 800m) had the highest. Multivariate analysis shows the canyon assemblages fall into eight clusters with the non-canyon stations forming a separate ninth cluster, indicating a detectable difference in canyon and non-canyon communities. Time series stations show an increase in diversity from 2012-2014 with a strong overlap in community structure in 2013 and 2014 samples. Environmental analysis, via BEST, using data from 10 canyon sites and the controls, indicated depth in combination with latitude explain the most variation in macrofaunal community structure.

Soil drying procedure affects the DNA quantification of Lactarius vinosus but does not change the fungal community composition.

PubMed

Castaño, Carles; Parladé, Javier; Pera, Joan; Martínez de Aragón, Juan; Alday, Josu G; Bonet, José Antonio

2016-11-01

Drying soil samples before DNA extraction is commonly used for specific fungal DNA quantification and metabarcoding studies, but the impact of different drying procedures on both the specific fungal DNA quantity and the fungal community composition has not been analyzed. We tested three different drying procedures (freeze-drying, oven-drying, and room temperature) on 12 different soil samples to determine (a) the soil mycelium biomass of the ectomycorrhizal species Lactarius vinosus using qPCR with a specifically designed TaqMan® probe and (b) the fungal community composition and diversity using the PacBio® RS II sequencing platform. Mycelium biomass of L. vinosus was significantly greater in the freeze-dried soil samples than in samples dried at oven and room temperature. However, drying procedures had no effect on fungal community composition or on fungal diversity. In addition, there were no significant differences in the proportions of fungi according to their functional roles (moulds vs. mycorrhizal species) in response to drying procedures. Only six out of 1139 operational taxonomic units (OTUs) had increased their relative proportions after soil drying at room temperature, with five of these OTUs classified as mould or yeast species. However, the magnitude of these changes was small, with an overall increase in relative abundance of these OTUs of approximately 2 %. These results suggest that DNA degradation may occur especially after drying soil samples at room temperature, but affecting equally nearly all fungi and therefore causing no significant differences in diversity and community composition. Despite the minimal effects caused by the drying procedures at the fungal community composition, freeze-drying resulted in higher concentrations of L. vinosus DNA and prevented potential colonization from opportunistic species.

Benthic protists: the under-charted majority.

PubMed

Forster, Dominik; Dunthorn, Micah; Mahé, Fréderic; Dolan, John R; Audic, Stéphane; Bass, David; Bittner, Lucie; Boutte, Christophe; Christen, Richard; Claverie, Jean-Michel; Decelle, Johan; Edvardsen, Bente; Egge, Elianne; Eikrem, Wenche; Gobet, Angélique; Kooistra, Wiebe H C F; Logares, Ramiro; Massana, Ramon; Montresor, Marina; Not, Fabrice; Ogata, Hiroyuki; Pawlowski, Jan; Pernice, Massimo C; Romac, Sarah; Shalchian-Tabrizi, Kamran; Simon, Nathalie; Richards, Thomas A; Santini, Sébastien; Sarno, Diana; Siano, Raffaele; Vaulot, Daniel; Wincker, Patrick; Zingone, Adriana; de Vargas, Colomban; Stoeck, Thorsten

2016-08-01

Marine protist diversity inventories have largely focused on planktonic environments, while benthic protists have received relatively little attention. We therefore hypothesize that current diversity surveys have only skimmed the surface of protist diversity in marine sediments, which may harbor greater diversity than planktonic environments. We tested this by analyzing sequences of the hypervariable V4 18S rRNA from benthic and planktonic protist communities sampled in European coastal regions. Despite a similar number of OTUs in both realms, richness estimations indicated that we recovered at least 70% of the diversity in planktonic protist communities, but only 33% in benthic communities. There was also little overlap of OTUs between planktonic and benthic communities, as well as between separate benthic communities. We argue that these patterns reflect the heterogeneity and diversity of benthic habitats. A comparison of all OTUs against the Protist Ribosomal Reference database showed that a higher proportion of benthic than planktonic protist diversity is missing from public databases; similar results were obtained by comparing all OTUs against environmental references from NCBI's Short Read Archive. We suggest that the benthic realm may therefore be the world's largest reservoir of marine protist diversity, with most taxa at present undescribed. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Effort versus reward: preparing samples for fungal community characterization in high-throughput sequencing surveys of soils

USDA-ARS?s Scientific Manuscript database

Next generation fungal amplicon sequencing is being used with increasing frequency to study fungal diversity in various ecosystems; however, the influence of sample preparation on the characterization of fungal community is poorly understood. We investigated the effects of four procedural modificati...

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

PubMed

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

2017-07-05

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

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.

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

NASA Astrophysics Data System (ADS)

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

2013-09-01

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

Characterization of rhizosphere and endophytic bacterial communities from leaves, stems and roots of medicinal Stellera chamaejasme L.

PubMed

Jin, Hui; Yang, Xiao-Yan; Yan, Zhi-Qiang; Liu, Quan; Li, Xiu-Zhuang; Chen, Ji-Xiang; Zhang, Deng-Hong; Zeng, Li-Ming; Qin, Bo

2014-07-01

A diverse array of bacteria that inhabit the rhizosphere and different plant organs play a crucial role in plant health and growth. Therefore, a general understanding of these bacterial communities and their diversity is necessary. Using the 16S rRNA gene clone library technique, the bacterial community structure and diversity of the rhizosphere and endophytic bacteria in Stellera chamaejasme compartments were compared and clarified for the first time. Grouping of the sequences obtained showed that members of the Proteobacteria (43.2%), Firmicutes (36.5%) and Actinobacteria (14.1%) were dominant in both samples. Other groups that were consistently found, albeit at lower abundance, were Bacteroidetes (2.1%), Chloroflexi (1.9%), and Cyanobacteria (1.7%). The habitats (rhizosphere vs endophytes) and organs (leaf, stem and root) structured the community, since the Wilcoxon signed rank test indicated that more varied bacteria inhabited the rhizosphere compared to the organs of the plant. In addition, correspondence analysis also showed that differences were apparent in the bacterial communities associated with these distinct habitats. Moreover, principal component analysis revealed that the profiles obtained from the rhizosphere and roots were similar, whereas leaf and stem samples clustered together on the opposite side of the plot from the rhizosphere and roots. Taken together, these results suggested that, although the communities associated with the rhizosphere and organs shared some bacterial species, the associated communities differed in structure and diversity. Copyright © 2014 Elsevier GmbH. All rights reserved.

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

PubMed Central

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

2017-01-01

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

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

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

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

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

Fungal diversity in deep-sea sediments associated with asphalt seeps at the Sao Paulo Plateau

NASA Astrophysics Data System (ADS)

Nagano, Yuriko; Miura, Toshiko; Nishi, Shinro; Lima, Andre O.; Nakayama, Cristina; Pellizari, Vivian H.; Fujikura, Katsunori

2017-12-01

We investigated the fungal diversity in a total of 20 deep-sea sediment samples (of which 14 samples were associated with natural asphalt seeps and 6 samples were not associated) collected from two different sites at the Sao Paulo Plateau off Brazil by Ion Torrent PGM targeting ITS region of ribosomal RNA. Our results suggest that diverse fungi (113 operational taxonomic units (OTUs) based on clustering at 97% sequence similarity assigned into 9 classes and 31 genus) are present in deep-sea sediment samples collected at the Sao Paulo Plateau, dominated by Ascomycota (74.3%), followed by Basidiomycota (11.5%), unidentified fungi (7.1%), and sequences with no affiliation to any organisms in the public database (7.1%). However, it was revealed that only three species, namely Penicillium sp., Cadophora malorum and Rhodosporidium diobovatum, were dominant, with the majority of OTUs remaining a minor community. Unexpectedly, there was no significant difference in major fungal community structure between the asphalt seep and non-asphalt seep sites, despite the presence of mass hydrocarbon deposits and the high amount of macro organisms surrounding the asphalt seeps. However, there were some differences in the minor fungal communities, with possible asphalt degrading fungi present specifically in the asphalt seep sites. In contrast, some differences were found between the two different sampling sites. Classification of OTUs revealed that only 47 (41.6%) fungal OTUs exhibited >97% sequence similarity, in comparison with pre-existing ITS sequences in public databases, indicating that a majority of deep-sea inhabiting fungal taxa still remain undescribed. Although our knowledge on fungi and their role in deep-sea environments is still limited and scarce, this study increases our understanding of fungal diversity and community structure in deep-sea environments.

Community Structure Comparisons of Hydrothermal Vent Microbial Mats Along the Mariana Arc and Back-arc

NASA Astrophysics Data System (ADS)

Hager, K. W.; Fullerton, H.; Moyer, C. L.

2015-12-01

Hydrothermal vents along the Mariana Arc and back-arc represent a hotspot of microbial diversity that has not yet been fully recognized. The Mariana Arc and back-arc contain hydrothermal vents with varied vent effluent chemistry and temperature, which translates to diverse community composition. We have focused on iron-rich sites where the dominant primary producers are iron oxidizing bacteria. Because microbes from these environments have proven elusive in culturing efforts, we performed culture independent analysis among different microbial communities found at these hydrothermal vents. Terminal-restriction fragment length polymorphism (T-RFLP) and Illumina sequencing of small subunit ribosomal gene amplicons were used to characterize community members and identify samples for shotgun metagenomics. Used in combination, these methods will better elucidate the composition and characteristics of the bacterial communities at these hydrothermal vent systems. The overarching goal of this study is to evaluate and compare taxonomic and metabolic diversity among different communities of microbial mats. We compared communities collected on a fine scale to analyze the bacterial community based on gross mat morphology, geography, and nearby vent effluent chemistry. Taxa richness and evenness are compared with rarefaction curves to visualize diversity. As well as providing a survey of diversity this study also presents a juxtaposition of three methods in which ribosomal small subunit diversity is compared with T-RFLP, next generation amplicon sequencing, and metagenomic shotgun sequencing.

Fungal diversity in deep-sea sediments of a hydrothermal vent system in the Southwest Indian Ridge

NASA Astrophysics Data System (ADS)

Xu, Wei; Gong, Lin-feng; Pang, Ka-Lai; Luo, Zhu-Hua

2018-01-01

Deep-sea hydrothermal sediment is known to support remarkably diverse microbial consortia. In deep sea environments, fungal communities remain less studied despite their known taxonomic and functional diversity. High-throughput sequencing methods have augmented our capacity to assess eukaryotic diversity and their functions in microbial ecology. Here we provide the first description of the fungal community diversity found in deep sea sediments collected at the Southwest Indian Ridge (SWIR) using culture-dependent and high-throughput sequencing approaches. A total of 138 fungal isolates were cultured from seven different sediment samples using various nutrient media, and these isolates were identified to 14 fungal taxa, including 11 Ascomycota taxa (7 genera) and 3 Basidiomycota taxa (2 genera) based on internal transcribed spacers (ITS1, ITS2 and 5.8S) of rDNA. Using illumina HiSeq sequencing, a total of 757,467 fungal ITS2 tags were recovered from the samples and clustered into 723 operational taxonomic units (OTUs) belonging to 79 taxa (Ascomycota and Basidiomycota contributed to 99% of all samples) based on 97% sequence similarity. Results from both approaches suggest that there is a high fungal diversity in the deep-sea sediments collected in the SWIR and fungal communities were shown to be slightly different by location, although all were collected from adjacent sites at the SWIR. This study provides baseline data of the fungal diversity and biogeography, and a glimpse to the microbial ecology associated with the deep-sea sediments of the hydrothermal vent system of the Southwest Indian Ridge.

Distribution and Diversity of Pathogenic Leptospira Species in Peri-domestic Surface Waters from South Central Chile

PubMed Central

Mason, Meghan R.; Encina, Carolina; Sreevatsan, Srinand; Muñoz-Zanzi, Claudia

2016-01-01

Background Leptospirosis is a neglected zoonosis affecting animals and humans caused by infection with Leptospira. The bacteria can survive outside of hosts for long periods of time in soil and water. While identification of Leptospira species from human cases and animal reservoirs are increasingly reported, little is known about the diversity of pathogenic Leptospira species in the environment and how surveillance of the environment might be used for monitoring and controlling disease. Methods and Findings Water samples (n = 104) were collected from the peri-domestic environment of 422 households from farms, rural villages, and urban slums participating in a broader study on the eco-epidemiology of leptospirosis in the Los Rios Region, Chile, between October 2010 and April 2012. The secY region of samples, previously detected as pathogenic Leptospira by PCR, was amplified and sequenced. Sequences were aligned using ClustalW in MEGA, and a minimum spanning tree was created in PHYLOViZ using the goeBURST algorithm to assess sequence similarity. Sequences from four clinical isolates, 17 rodents, and 20 reference strains were also included in the analysis. Overall, water samples contained L. interrogans, L. kirschneri, and L. weilii, with descending frequency. All species were found in each community type. The distribution of the species differed by the season in which the water samples were obtained. There was no evidence that community-level prevalence of Leptospira in dogs, rodents, or livestock influenced pathogen diversity in the water samples. Conclusions This study reports the presence of pathogenic Leptospira in the peri-domestic environment of households in three community types and the differences in Leptospira diversity at the community level. Systematic environmental surveillance of Leptospira can be used for detecting changes in pathogen diversity and to identify and monitor contaminated areas where an increased risk of human infection exists. PMID:27529550

A water-quality assessment of the Feather Creek watershed, Vermillion County, Indiana

USGS Publications Warehouse

Eikenberry, Stephen E.

1977-01-01

Navicula sp and Scenedesmus sp dominated the phydoplankton community at the site sampled and indicated an environment lacking in organic enrichment. Cladaphora sp dominated the periphyton community sampled. Benthic invertebrates sampled were mostly caddis flies (Cheumatopsyche sp) and midges (Orthocladius sp) and had a diversity index of 2.3, which indicates some organic enrichment of the stream.

The challenge of accurately documenting bee species richness in agroecosystems: bee diversity in eastern apple orchards

PubMed Central

Russo, Laura; Park, Mia; Gibbs, Jason; Danforth, Bryan

2015-01-01

Bees are important pollinators of agricultural crops, and bee diversity has been shown to be closely associated with pollination, a valuable ecosystem service. Higher functional diversity and species richness of bees have been shown to lead to higher crop yield. Bees simultaneously represent a mega-diverse taxon that is extremely challenging to sample thoroughly and an important group to understand because of pollination services. We sampled bees visiting apple blossoms in 28 orchards over 6 years. We used species rarefaction analyses to test for the completeness of sampling and the relationship between species richness and sampling effort, orchard size, and percent agriculture in the surrounding landscape. We performed more than 190 h of sampling, collecting 11,219 specimens representing 104 species. Despite the sampling intensity, we captured <75% of expected species richness at more than half of the sites. For most of these, the variation in bee community composition between years was greater than among sites. Species richness was influenced by percent agriculture, orchard size, and sampling effort, but we found no factors explaining the difference between observed and expected species richness. Competition between honeybees and wild bees did not appear to be a factor, as we found no correlation between honeybee and wild bee abundance. Our study shows that the pollinator fauna of agroecosystems can be diverse and challenging to thoroughly sample. We demonstrate that there is high temporal variation in community composition and that sites vary widely in the sampling effort required to fully describe their diversity. In order to maximize pollination services provided by wild bee species, we must first accurately estimate species richness. For researchers interested in providing this estimate, we recommend multiyear studies and rarefaction analyses to quantify the gap between observed and expected species richness. PMID:26380684

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

USDA-ARS?s Scientific Manuscript database

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

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

USDA-ARS?s Scientific Manuscript database

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

Predicting Children's Depressive Symptoms from Community and Individual Risk Factors

ERIC Educational Resources Information Center

Dallaire, Danielle H.; Cole, David A.; Smith, Thomas M.; Ciesla, Jeffrey A.; LaGrange, Beth; Jacquez, Farrah M.; Pineda, Ashley Q.; Truss, Alanna E.; Folmer, Amy S.

2008-01-01

Community, demographic, familial, and personal risk factors of childhood depressive symptoms were examined from an ecological theoretical approach using hierarchical linear modeling. Individual-level data were collected from an ethnically diverse (73% African-American) community sample of 197 children and their parents; community-level data were…

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

PubMed

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

2017-09-01

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

Community analysis of the abundance and diversity of mosquito species (Diptera: Culicidae) in three European countries at different latitudes.

PubMed

Möhlmann, Tim W R; Wennergren, Uno; Tälle, Malin; Favia, Guido; Damiani, Claudia; Bracchetti, Luca; Koenraadt, Constantianus J M

2017-10-23

Studies on mosquito species diversity in Europe often focus on a specific habitat, region or country. Moreover, different trap types are used for these sampling studies, making it difficult to compare and validate results across Europe. To facilitate comparisons of trapping sites and community analysis, the present study used two trap types for monitoring mosquito species diversity in three habitat types for three different countries in Europe. Mosquitoes were trapped using Biogents Sentinel (BGS), and Mosquito Magnet Liberty Plus (MMLP) traps at a total of 27 locations in Sweden, the Netherlands and Italy, comprising farm, peri-urban and wetland habitats. From July 2014 to June 2015 all locations were sampled monthly, except for the winter months. Indices of species richness, evenness and diversity were calculated, and community analyses were carried out with non-metric multidimensional scaling (NMDS) techniques. A total of 11,745 female mosquitoes were trapped during 887 collections. More than 90% of the mosquitoes belonged to the genera Culex and Aedes, with Culex pipiens being the most abundant species. The highest mosquito diversity was found in Sweden. Within Sweden, species diversity was highest in wetland habitats, whereas in the Netherlands and Italy this was highest at farms. The NMDS analyses showed clear differences in mosquito communities among countries, but not among habitat types. The MMLP trapped a higher diversity of mosquito species than the BGS traps. Also, MMLP traps trapped higher numbers of mosquitoes, except for the genera Culex and Culiseta in Italy. A core mosquito community could be identified for the three countries, with Culex pipiens as the most abundant species. Differences in mosquito species communities were more defined by the three countries included in the study than by the three habitat types. Differences in mosquito community composition across countries may have implications for disease emergence and further spread throughout Europe. Future research should, therefore, focus on how field data of vector communities can be incorporated into models, to better assess the risk of mosquito-borne disease outbreaks.

16S rRNA Gene-Based Metagenomic Analysis of Ozark Cave Bacteria

PubMed Central

Oliveira, Cássia; Gunderman, Lauren; Coles, Cathryn A.; Lochmann, Jason; Parks, Megan; Ballard, Ethan; Glazko, Galina; Rahmatallah, Yasir; Tackett, Alan J.; Thomas, David J.

2018-01-01

The microbial diversity within cave ecosystems is largely unknown. Ozark caves maintain a year-round stable temperature (12–14 °C), but most parts of the caves experience complete darkness. The lack of sunlight and geological isolation from surface-energy inputs generate nutrient-poor conditions that may limit species diversity in such environments. Although microorganisms play a crucial role in sustaining life on Earth and impacting human health, little is known about their diversity, ecology, and evolution in community structures. We used five Ozark region caves as test sites for exploring bacterial diversity and monitoring long-term biodiversity. Illumina MiSeq sequencing of five cave soil samples and a control sample revealed a total of 49 bacterial phyla, with seven major phyla: Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, Chloroflexi, Bacteroidetes, and Nitrospirae. Variation in bacterial composition was observed among the five caves studied. Sandtown Cave had the lowest richness and most divergent community composition. 16S rRNA gene-based metagenomic analysis of cave-dwelling microbial communities in the Ozark caves revealed that species abundance and diversity are vast and included ecologically, agriculturally, and economically relevant taxa. PMID:29551950

Flow cytometric monitoring of bacterioplankton phenotypic diversity predicts high population-specific feeding rates by invasive dreissenid mussels.

PubMed

Props, Ruben; Schmidt, Marian L; Heyse, Jasmine; Vanderploeg, Henry A; Boon, Nico; Denef, Vincent J

2018-02-01

Species invasion is an important disturbance to ecosystems worldwide, yet knowledge about the impacts of invasive species on bacterial communities remains sparse. Using a novel approach, we simultaneously detected phenotypic and derived taxonomic change in a natural bacterioplankton community when subjected to feeding pressure by quagga mussels, a widespread aquatic invasive species. We detected a significant decrease in diversity within 1 h of feeding and a total diversity loss of 11.6 ± 4.1% after 3 h. This loss of microbial diversity was caused by the selective removal of high nucleic acid populations (29 ± 5% after 3 h). We were able to track the community diversity at high temporal resolution by calculating phenotypic diversity estimates from flow cytometry (FCM) data of minute amounts of sample. Through parallel FCM and 16S rRNA gene amplicon sequencing analysis of environments spanning a broad diversity range, we showed that the two approaches resulted in highly correlated diversity measures and captured the same seasonal and lake-specific patterns in community composition. Based on our results, we predict that selective feeding by invasive dreissenid mussels directly impacts the microbial component of the carbon cycle, as it may drive bacterioplankton communities toward less diverse and potentially less productive states. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Comparison of Bacterial Diversity in Azorean and Hawai’ian Lava Cave Microbial Mats

PubMed Central

MARSHALL HATHAWAY, JENNIFER J.; GARCIA, MATTHEW G.; BALASCH, MONICA MOYA; SPILDE, MICHAEL N.; STONE, FRED D.; DAPKEVICIUS, MARIA DE LURDES N. E.; AMORIM, ISABEL R.; GABRIEL, ROSALINA; BORGES, PAULO A. V.; NORTHUP, DIANA E.

2015-01-01

Worldwide, lava caves host colorful microbial mats. However, little is known about the diversity of these microorganisms, or what role they may play in the subsurface ecosystem. White and yellow microbial mats were collected from four lava caves each on the Azorean island of Terceira and the Big Island of Hawai’i, to compare the bacterial diversity found in lava caves from two widely separated archipelagos in two different oceans at different latitudes. Scanning electron microscopy of mat samples showed striking similarities between Terceira and Hawai’ian microbial morphologies. 16S rRNA gene clone libraries were constructed to determine the diversity within these lava caves. Fifteen bacterial phyla were found across the samples, with more Actinobacteria clones in Hawai’ian communities and greater numbers of Acidobacteria clones in Terceira communities. Bacterial diversity in the subsurface was correlated with a set of factors. Geographical location was the major contributor to differences in community composition (at the OTU level), together with differences in the amounts of organic carbon, nitrogen and copper available in the lava rock that forms the cave. These results reveal, for the first time, the similarity among the extensive bacterial diversity found in lava caves in two geographically separate locations and contribute to the current debate on the nature of microbial biogeography. PMID:26924866

The Choice of PCR Primers Has Great Impact on Assessments of Bacterial Community Diversity and Dynamics in a Wastewater Treatment Plant

PubMed Central

Fredriksson, Nils Johan; Hermansson, Malte; Wilén, Britt-Marie

2013-01-01

Assessments of bacterial community diversity and dynamics are fundamental for the understanding of microbial ecology as well as biotechnological applications. We show that the choice of PCR primers has great impact on the results of analyses of diversity and dynamics using gene libraries and DNA fingerprinting. Two universal primer pairs targeting the 16S rRNA gene, 27F&1492R and 63F&M1387R, were compared and evaluated by analyzing the bacterial community in the activated sludge of a large-scale wastewater treatment plant. The two primer pairs targeted distinct parts of the bacterial community, none encompassing the other, both with similar richness. Had only one primer pair been used, very different conclusions had been drawn regarding dominant phylogenetic and putative functional groups. With 27F&1492R, Betaproteobacteria would have been determined to be the dominating taxa while 63F&M1387R would have described Alphaproteobacteria as the most common taxa. Microscopy and fluorescence in situ hybridization analysis showed that both Alphaproteobacteria and Betaproteobacteria were abundant in the activated sludge, confirming that the two primer pairs target two different fractions of the bacterial community. Furthermore, terminal restriction fragment polymorphism analyses of a series of four activated sludge samples showed that the two primer pairs would have resulted in different conclusions about community stability and the factors contributing to changes in community composition. In conclusion, different PCR primer pairs, although considered universal, target different ranges of bacteria and will thus show the diversity and dynamics of different fractions of the bacterial community in the analyzed sample. We also show that while a database search can serve as an indicator of how universal a primer pair is, an experimental assessment is necessary to evaluate the suitability for a specific environmental sample. PMID:24098498

Contrasting diversity of testate amoebae communities in Sphagnum and brown-moss dominated patches in relation to shell counts.

PubMed

Lizoňová, Zuzana; Horsák, Michal

2017-04-01

Ecological studies of peatland testate amoebae are generally based on totals of 150 individuals per sample. However, the suitability of this standard has never been assessed for alkaline habitats such as spring fens. We explored the differences in testate amoeba diversity between Sphagnum and brown-moss microhabitats at a mire site with a highly diversified moss layer which reflects the small-scale heterogeneity in groundwater chemistry. Relationships between sampling efficiency and sample completeness were explored using individual-based species accumulation curves and the effort required to gain an extra species was assessed. Testate amoeba diversity differed substantially between microhabitats, with brown mosses hosting on average twice as many species and requiring greater shell totals to reach comparable sample analysis efficiency as for Sphagnum. Thus, for samples from alkaline conditions an increase in shell totals would be required and even an overall doubling up to 300 individuals might be considered for reliable community description. Our small-scale data are likely not robust enough to provide an ultimate solution for the optimization of shell totals. However, the results proved that testate amoebae communities from acidic and alkaline environments differ sharply in both species richness and composition and they might call for different methodological approaches. Copyright © 2017 Elsevier GmbH. All rights reserved.

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

PubMed

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

2016-07-01

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

Predictors of elevational biodiversity gradients change from single taxa to the multi-taxa community level

PubMed Central

Peters, Marcell K.; Hemp, Andreas; Appelhans, Tim; Behler, Christina; Classen, Alice; Detsch, Florian; Ensslin, Andreas; Ferger, Stefan W.; Frederiksen, Sara B.; Gebert, Friederike; Haas, Michael; Helbig-Bonitz, Maria; Hemp, Claudia; Kindeketa, William J.; Mwangomo, Ephraim; Ngereza, Christine; Otte, Insa; Röder, Juliane; Rutten, Gemma; Schellenberger Costa, David; Tardanico, Joseph; Zancolli, Giulia; Deckert, Jürgen; Eardley, Connal D.; Peters, Ralph S.; Rödel, Mark-Oliver; Schleuning, Matthias; Ssymank, Axel; Kakengi, Victor; Zhang, Jie; Böhning-Gaese, Katrin; Brandl, Roland; Kalko, Elisabeth K.V.; Kleyer, Michael; Nauss, Thomas; Tschapka, Marco; Fischer, Markus; Steffan-Dewenter, Ingolf

2016-01-01

The factors determining gradients of biodiversity are a fundamental yet unresolved topic in ecology. While diversity gradients have been analysed for numerous single taxa, progress towards general explanatory models has been hampered by limitations in the phylogenetic coverage of past studies. By parallel sampling of 25 major plant and animal taxa along a 3.7 km elevational gradient on Mt. Kilimanjaro, we quantify cross-taxon consensus in diversity gradients and evaluate predictors of diversity from single taxa to a multi-taxa community level. While single taxa show complex distribution patterns and respond to different environmental factors, scaling up diversity to the community level leads to an unambiguous support for temperature as the main predictor of species richness in both plants and animals. Our findings illuminate the influence of taxonomic coverage for models of diversity gradients and point to the importance of temperature for diversification and species coexistence in plant and animal communities. PMID:28004657

[Microbial diversity of salt lakes in Badain Jaran desert].

PubMed

Li, Lu; Hao, Chunbo; Wang, Lihua; Pei, Lixin

2015-04-04

We characterized procaryotic biodiversity, community structure and the relationship between the community structure and environmental factors of salt lakes in Badain Jaran desert, Inner Mongolia, China. We constructed 16S rRNA gene clone libraries by molecular biology techniques to analyze the procaryotic phylogenetic relationships, and used R language to compare the community structure of haloalkalophiles in the salt lakes. Water in this region has a high salinity ranging from 165 to 397 g/L. The water is strongly alkaline with pH value above 10. The microbial diversity and community structure of the salt lakes are obviously different. The diversity of bacteria is more abundant than that of archaea. The main categories of bacteria in the samples are Gammaproteobacteria, Bacteroidetes, Alphaproteobacteria, Firmicute and Verrucomicrobia, whereas all archaea only belong to Halobacteriaceae of Euryarchaeota. Salinity is the most important environmental factor influencing the bacterial community structure, whereas the archaea community structure was influenced comprehensively by multiple environmental factors.

Functional & phylogenetic diversity of copepod communities

NASA Astrophysics Data System (ADS)

Benedetti, F.; Ayata, S. D.; Blanco-Bercial, L.; Cornils, A.; Guilhaumon, F.

2016-02-01

The diversity of natural communities is classically estimated through species identification (taxonomic diversity) but can also be estimated from the ecological functions performed by the species (functional diversity), or from the phylogenetic relationships among them (phylogenetic diversity). Estimating functional diversity requires the definition of specific functional traits, i.e., phenotypic characteristics that impact fitness and are relevant to ecosystem functioning. Estimating phylogenetic diversity requires the description of phylogenetic relationships, for instance by using molecular tools. In the present study, we focused on the functional and phylogenetic diversity of copepod surface communities in the Mediterranean Sea. First, we implemented a specific trait database for the most commonly-sampled and abundant copepod species of the Mediterranean Sea. Our database includes 191 species, described by seven traits encompassing diverse ecological functions: minimal and maximal body length, trophic group, feeding type, spawning strategy, diel vertical migration and vertical habitat. Clustering analysis in the functional trait space revealed that Mediterranean copepods can be gathered into groups that have different ecological roles. Second, we reconstructed a phylogenetic tree using the available sequences of 18S rRNA. Our tree included 154 of the analyzed Mediterranean copepod species. We used these two datasets to describe the functional and phylogenetic diversity of copepod surface communities in the Mediterranean Sea. The replacement component (turn-over) and the species richness difference component (nestedness) of the beta diversity indices were identified. Finally, by comparing various and complementary aspects of plankton diversity (taxonomic, functional, and phylogenetic diversity) we were able to gain a better understanding of the relationships among the zooplankton community, biodiversity, ecosystem function, and environmental forcing.

A Jungle in There: Bacteria in Belly Buttons are Highly Diverse, but Predictable

PubMed Central

Hulcr, Jiri; Latimer, Andrew M.; Henley, Jessica B.; Rountree, Nina R.; Fierer, Noah; Lucky, Andrea; Lowman, Margaret D.; Dunn, Robert R.

2012-01-01

The belly button is one of the habitats closest to us, and yet it remains relatively unexplored. We analyzed bacteria and arachaea from the belly buttons of humans from two different populations sampled within a nation-wide citizen science project. We examined bacterial and archaeal phylotypes present and their diversity using multiplex pyrosequencing of 16S rDNA libraries. We then tested the oligarchy hypothesis borrowed from tropical macroecology, namely that the frequency of phylotypes in one sample of humans predicts its frequency in another independent sample. We also tested the predictions that frequent phylotypes (the oligarchs) tend to be common when present, and tend to be more phylogenetically clustered than rare phylotypes. Once rarefied to four hundred reads per sample, bacterial communities from belly buttons proved to be at least as diverse as communities known from other skin studies (on average 67 bacterial phylotypes per belly button). However, the belly button communities were strongly dominated by a few taxa: only 6 phylotypes occurred on >80% humans. While these frequent bacterial phylotypes (the archaea were all rare) are a tiny part of the total diversity of bacteria in human navels (<0.3% of phylotypes), they constitute a major portion of individual reads (∼1/3), and are predictable among independent samples of humans, in terms of both the occurrence and evolutionary relatedness (more closely related than randomly drawn equal sets of phylotypes). Thus, the hypothesis that “oligarchs” dominate diverse assemblages appears to be supported by human-associated bacteria. Although it remains difficult to predict which species of bacteria might be found on a particular human, predicting which species are most frequent (or rare) seems more straightforward, at least for those species living in belly buttons. PMID:23144827

Factors influencing ruminal bacterial community diversity and composition and microbial fibrolytic enzyme abundance in lactating dairy cows with a focus on the role of active dry yeast.

PubMed

AlZahal, Ousama; Li, Fuyong; Guan, Le Luo; Walker, Nicola D; McBride, Brian W

2017-06-01

The objective of the current study was to employ a DNA-based sequencing technology to study the effect of active dry yeast (ADY) supplementation, diet type, and sample location within the rumen on rumen bacterial community diversity and composition, and to use an RNA-based method to study the effect of ADY supplementation on rumen microbial metabolism during high-grain feeding (HG). Our previous report demonstrated that the supplementation of lactating dairy cows with ADY attenuated the effect of subacute ruminal acidosis. Therefore, we used samples from that study, where 16 multiparous, rumen-cannulated lactating Holstein cows were randomly assigned to 1 of 2 dietary treatments: ADY (Saccharomyces cerevisiae strain Y1242, 80 billion cfu/animal per day) or control (carrier only). Cows received a high-forage diet (77:23, forage:concentrate), then were abruptly switched to HG (49:51, forage:concentrate). Rumen bacterial community diversity and structure were highly influenced by diet and sampling location (fluid, solids, epimural). The transition to HG reduced bacterial diversity, but epimural bacteria maintained a greater diversity than fluid and solids. Analysis of molecular variance indicated a significant separation due to diet × sampling location, but not due to treatment. Across all samples, the analysis yielded 6,254 nonsingleton operational taxonomic units (OTU), which were classified into several phyla: mainly Firmicutes, Bacteroidetes, Fibrobacteres, Tenericutes, and Proteobacteria. High forage and solids were dominated by OTU from Fibrobacter, whereas HG and fluid were dominated by OTU from Prevotella. Epimural samples, however, were dominated in part by Campylobacter. Active dry yeast had no effect on bacterial community diversity or structure. The phylum SR1 was more abundant in all ADY samples regardless of diet or sampling location. Furthermore, on HG, OTU2 and OTU3 (both classified into Fibrobacter succinogenes) were more abundant with ADY in fluid and solids than control samples. This increase with ADY was paralleled by a reduction in prominent Prevotella OTU. Metatranscriptomic profiling of rumen microbiome conducted on random samples from the HG phase showed that ADY increased the abundance of the cellulase endo-β-1,4-glucanase and had a tendency to increase the hemicellulase α-glucuronidase. In conclusion, the shift from high forage to HG and sampling location had a more significant influence on ruminal bacterial community abundance and structure compared with ADY. However, evidence suggested that ADY can increase the abundance of some dominant anaerobic OTU belonging to F. succinogenes and phylum SR1. Further, microbial mRNA-based evidence suggested that ADY can increase the abundance of a specific microbial fibrolytic enzymes. The Authors. Published by the Federation of Animal Science Societies and Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).

Feeding Practices and Styles Used by a Diverse Sample of Low-Income Parents of Preschool-age Children

ERIC Educational Resources Information Center

Ventura, Alison K.; Gromis, Judy C.; Lohse, Barbara

2010-01-01

Objective: To describe the feeding practices and styles used by a diverse sample of low-income parents of preschool-age children. Design: Thirty- to 60-minute meetings involving a semistructured interview and 2 questionnaires administered by the interviewer. Setting: Low-income communities in Philadelphia, PA. Participants: Thirty-two parents of…

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

NASA Astrophysics Data System (ADS)

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

2008-12-01

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

Analysis of Lung Microbiota in Bronchoalveolar Lavage, Protected Brush and Sputum Samples from Subjects with Mild-To-Moderate Cystic Fibrosis Lung Disease

PubMed Central

Hogan, Deborah A.; Willger, Sven D.; Dolben, Emily L.; Hampton, Thomas H.; Stanton, Bruce A.; Morrison, Hilary G.; Sogin, Mitchell L.; Czum, Julianna; Ashare, Alix

2016-01-01

Individuals with cystic fibrosis (CF) often acquire chronic lung infections that lead to irreversible damage. We sought to examine regional variation in the microbial communities in the lungs of individuals with mild-to-moderate CF lung disease, to examine the relationship between the local microbiota and local damage, and to determine the relationships between microbiota in samples taken directly from the lung and the microbiota in spontaneously expectorated sputum. In this initial study, nine stable, adult CF patients with an FEV1>50% underwent regional sampling of different lobes of the right lung by bronchoalveolar lavage (BAL) and protected brush (PB) sampling of mucus plugs. Sputum samples were obtained from six of the nine subjects immediately prior to the procedure. Microbial community analysis was performed on DNA extracted from these samples and the extent of damage in each lobe was quantified from a recent CT scan. The extent of damage observed in regions of the right lung did not correlate with specific microbial genera, levels of community diversity or composition, or bacterial genome copies per ml of BAL fluid. In all subjects, BAL fluid from different regions of the lung contained similar microbial communities. In eight out of nine subjects, PB samples from different regions of the lung were also similar in microbial community composition, and were similar to microbial communities in BAL fluid from the same lobe. Microbial communities in PB samples were more diverse than those in BAL samples, suggesting enrichment of some taxa in mucus plugs. To our knowledge, this study is the first to examine the microbiota in different regions of the CF lung in clinically stable individuals with mild-to-moderate CF-related lung disease. PMID:26943329

[Study on Microbial Diversity of Peri-implantitis Subgingival by High-throughput Sequencing].

PubMed

Li, Zhi-jie; Wang, Shao-guo; Li, Yue-hong; Tu, Dong-xiang; Liu, Shi-yun; Nie, Hong-bing; Li, Zhi-qiang; Zhang, Ju-mei

2015-07-01

To study microbial diversity of peri-implantitis subgingival with high-throughput sequencing, and investigate microbiological etiology of peri-implantitis. Subgingival plaques were sampled from the patients with peri-implantitis (D group) and non-peri-implantitis subjects (N group). The microbiological diversity of the subgingival plaques was detected by sequencing V4 region of 16S rRNA with Illumina Miseq platform. The diversity of the community structure was analyzed using Mothur software. A total of 156 507 gene sequences were detected in nine samples and 4 402 operational taxonomic units (OTUs) were found. Selenomonas, Pseudomonas, and Fusobacterium were dominant bacteria in D group, while Fusobacterium, Veillonella and Streptococcus were dominant bacteria in N group. Differences between peri-implantitis and non-peri-implantitis bacterial communities were observed at all phylogenetic levels by LEfSe, which was also found in PcoA test. The occurrence of peri-implantitis is not only related to periodontitis pathogenic microbe, but also related with the changes of oral microbial community structure. Treponema, Herbaspirillum, Butyricimonas and Phaeobacte may be closely related to the occurrence and development of peri-implantitis.

Large variability of bathypelagic microbial eukaryotic communities across the world's oceans.

PubMed

Pernice, Massimo C; Giner, Caterina R; Logares, Ramiro; Perera-Bel, Júlia; Acinas, Silvia G; Duarte, Carlos M; Gasol, Josep M; Massana, Ramon

2016-04-01

In this work, we study the diversity of bathypelagic microbial eukaryotes (0.8-20 μm) in the global ocean. Seawater samples from 3000 to 4000 m depth from 27 stations in the Atlantic, Pacific and Indian Oceans were analyzed by pyrosequencing the V4 region of the 18S ribosomal DNA. The relative abundance of the most abundant operational taxonomic units agreed with the results of a parallel metagenomic analysis, suggesting limited PCR biases in the tag approach. Although rarefaction curves for single stations were seldom saturated, the global analysis of all sequences together suggested an adequate recovery of bathypelagic diversity. Community composition presented a large variability among samples, which was poorly explained by linear geographic distance. In fact, the similarity between communities was better explained by water mass composition (26% of the variability) and the ratio in cell abundance between prokaryotes and microbial eukaryotes (21%). Deep diversity appeared dominated by four taxonomic groups (Collodaria, Chrysophytes, Basidiomycota and MALV-II) appearing in different proportions in each sample. Novel diversity amounted to 1% of the pyrotags and was lower than expected. Our study represents an essential step in the investigation of bathypelagic microbial eukaryotes, indicating dominating taxonomic groups and suggesting idiosyncratic assemblages in distinct oceanic regions.

Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity

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

Parfrey, Laura Wegener; Walters, William A.; Lauber, Christian L.

2014-06-19

Eukaryotic microbes (protists) residing in the vertebrate gut influence host health and disease, but their diversity and distribution in healthy hosts is poorly understood. Protists found in the gut are typically considered parasites, but many are commensal and some are beneficial. Further, the hygiene hypothesis predicts that association with our co-evolved microbial symbionts may be important to overall health. It is therefore imperative that we understand the normal diversity of our eukaryotic gut microbiota to test for such effects and avoid eliminating commensal organisms. We assembled a dataset of healthy individuals from two populations, one with traditional, agrarian lifestyles andmore » a second with modern, westernized lifestyles, and characterized the human eukaryotic microbiota via high-throughput sequencing. To place the human gut microbiota within a broader context our dataset also includes gut samples from diverse mammals and samples from other aquatic and terrestrial environments. We curated the SILVA ribosomal database to reflect current knowledge of eukaryotic taxonomy and employ it as a phylogenetic framework to compare eukaryotic diversity across environment. We show that adults from the non-western population harbor a diverse community of protists, and diversity in the human gut is comparable to that in other mammals. However, the eukaryotic microbiota of the western population appears depauperate. The distribution of symbionts found in mammals reflects both host phylogeny and diet. Eukaryotic microbiota in the gut are less diverse and more patchily distributed than bacteria. More broadly, we show that eukaryotic communities in the gut are less diverse than in aquatic and terrestrial habitats, and few taxa are shared across habitat types, and diversity patterns of eukaryotes are correlated with those observed for bacteria. These results outline the distribution and diversity of microbial eukaryotic communities in the mammalian gut and across environments.« less

Membership and Behavior of Ultra-Low-Diversity Pathogen Communities Present in the Gut of Humans during Prolonged Critical Illness

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

Zaborin, Alexander; Smith, Daniel; Garfield, Kevin

We analyzed the 16S rRNA amplicon composition in fecal samples of selected patients during their prolonged stay in an intensive care unit (ICU) and observed the emergence of ultra-low-diversity communities (1 to 4 bacterial taxa) in 30% of the patients. Bacteria associated with the genera Enterococcus and Staphylococcus and the family Enterobacteriaceae comprised the majority of these communities. The composition of cultured species from stool samples correlated to the 16S rRNA analysis and additionally revealed the emergence of Candida albicans and Candida glabrata in ~75% of cases. Four of 14 ICU patients harbored 2-member pathogen communities consisting of one Candidamore » taxon and one bacterial taxon. Bacterial members displayed a high degree of resistance to multiple antibiotics. The virulence potential of the 2-member communities was examined in C. elegans during nutrient deprivation and exposure to opioids in order to mimic local conditions in the gut during critical illness. Under conditions of nutrient deprivation, the bacterial members attenuated the virulence of fungal members, leading to a “commensal lifestyle.” However, exposure to opioids led to a breakdown in this commensalism in 2 of the ultra-low-diversity communities. Application of a novel antivirulence agent (phosphate-polyethylene glycol [Pi-PEG]) that creates local phosphate abundance prevented opioid-induced virulence among these pathogen communities, thus rescuing the commensal lifestyle. To conclude, the gut microflora in critically ill patients can consist of ultra-low-diversity communities of multidrug-resistant pathogenic microbes. Local environmental conditions in gut may direct pathogen communities to adapt to either a commensal style or a pathogenic style.« less

Membership and Behavior of Ultra-Low-Diversity Pathogen Communities Present in the Gut of Humans during Prolonged Critical Illness

DOE PAGES

Zaborin, Alexander; Smith, Daniel; Garfield, Kevin; ...

2014-09-23

We analyzed the 16S rRNA amplicon composition in fecal samples of selected patients during their prolonged stay in an intensive care unit (ICU) and observed the emergence of ultra-low-diversity communities (1 to 4 bacterial taxa) in 30% of the patients. Bacteria associated with the genera Enterococcus and Staphylococcus and the family Enterobacteriaceae comprised the majority of these communities. The composition of cultured species from stool samples correlated to the 16S rRNA analysis and additionally revealed the emergence of Candida albicans and Candida glabrata in ~75% of cases. Four of 14 ICU patients harbored 2-member pathogen communities consisting of one Candidamore » taxon and one bacterial taxon. Bacterial members displayed a high degree of resistance to multiple antibiotics. The virulence potential of the 2-member communities was examined in C. elegans during nutrient deprivation and exposure to opioids in order to mimic local conditions in the gut during critical illness. Under conditions of nutrient deprivation, the bacterial members attenuated the virulence of fungal members, leading to a “commensal lifestyle.” However, exposure to opioids led to a breakdown in this commensalism in 2 of the ultra-low-diversity communities. Application of a novel antivirulence agent (phosphate-polyethylene glycol [Pi-PEG]) that creates local phosphate abundance prevented opioid-induced virulence among these pathogen communities, thus rescuing the commensal lifestyle. To conclude, the gut microflora in critically ill patients can consist of ultra-low-diversity communities of multidrug-resistant pathogenic microbes. Local environmental conditions in gut may direct pathogen communities to adapt to either a commensal style or a pathogenic style.« less

Barcoded NS31/AML2 primers for sequencing of arbuscular mycorrhizal communities in environmental samples1

PubMed Central

Morgan, Benjamin S. T.; Egerton-Warburton, Louise M.

2017-01-01

Premise of the study: Arbuscular mycorrhizal fungi (AMF) are globally important root symbioses that enhance plant growth and nutrition and influence ecosystem structure and function. To better characterize levels of AMF diversity relevant to ecosystem function, deeper sequencing depth in environmental samples is needed. In this study, Illumina barcoded primers and a bioinformatics pipeline were developed and applied to study AMF diversity and community structure in environmental samples. Methods: Libraries of small subunit ribosomal RNA fragment amplicons were amplified from environmental DNA using a single-step PCR reaction with barcoded NS31/AML2 primers. Amplicons were sequenced on an Illumina MiSeq sequencer using version 2, 2 × 250-bp paired-end chemistry, and analyzed using QIIME and RDP Classifier. Results: Sequencing captured 196 to 6416 operational taxonomic units (OTUs; depending on clustering parameters) representing nine AMF genera. Regardless of clustering parameters, ∼20 OTUs dominated AMF communities (78–87% reads) with the remaining reads distributed among other OTUs. Analyses also showed significant biogeographic differences in AMF communities and that community composition could be linked to specific edaphic factors. Discussion: Barcoded NS31/AML2 primers and Illumina MiSeq sequencing provide a powerful approach to address AMF diversity and variations in fungal assemblages across host plants, ecosystems, and responses to environmental drivers including global change. PMID:28924511

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

PubMed

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

2016-04-01

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

Long lasting effects of the conversion from natural forest to poplar plantation on soil microbial communities.

PubMed

Vitali, Francesco; Mastromei, Giorgio; Senatore, Giuliana; Caroppo, Cesarea; Casalone, Enrico

2016-01-01

In this study, we evaluate the long-lasting effects on soil microbial communities of a change within a single land-use category, specifically the conversion from natural forest to forest plantation. To minimize the effects of impacts other than land-use (i.e., climatic and anthropogenic), we chose three sites within a Natural Park, with homogeneous orographic and soil texture characteristics. We compared microbial diversity in a total of 156 soil samples from two natural mixed forests and a similar forest converted to poplar plantation about thirty years ago. The diversity and structure of bacterial and fungal communities were investigated by terminal restriction fragments length polymorphism (T-RFLP) analysis of the 16S-rRNA gene and the ITS-rDNA regions, respectively. Bacterial and fungal communities from the forest plantation, compared to those from natural forest soils, showed different community structure and lower α-diversity values, consistently with the significantly higher pH values and lower organic matter content of those soils. β-diversity values, the number of measured and estimated dominant OTUs, and their distribution among the three sites showed that microbial communities from the two natural forests were much more similar to each other than they were to communities from the poplar plantation, suggesting an effect of the forest conversion on the composition and diversity of soil microbial communities. α-diversity in cultivated forest soils had narrower temporal fluctuations than in natural forest soils, suggesting higher temporal stability of microbial communities. Overall, we demonstrated that the conversion from natural forest to forest plantation altered soil microbial communities, changing their structure, lowering their diversity, and causing a spatial and temporal homogenization. Copyright © 2015 Elsevier GmbH. All rights reserved.

Analysis of copper tolerant rhizobacteria from the industrial belt of Gujarat, western India for plant growth promotion in metal polluted agriculture soils.

PubMed

Sharaff, Murali; Kamat, Shalmali; Archana, G

2017-04-01

Agricultural sites irrigated for long term with water polluted by industrial effluents containing heavy metals might adversely affect the soil microbial communities and crop yield. Hence it is important to study rhizobacterial communities and their metal tolerance in such affected agricultural fields to restore soil fertility and ecosystem. Present work deals with the study of rhizobacterial communities from plants grown in copper (Cu) contaminated agricultural fields along the industrial zone of Gujarat, India and are compared with communities from a Cu mine site. Microbial communities from rhizosphere soil samples varied in the magnitude of their Cu tolerance index indicating differences in long term pollution effects. Culture dependent denaturing gradient gel electrophoresis (CD-DGGE) of bacterial communities revealed the diverse composition at the sampling sites and a reduced total diversity due to Cu toxicity. Analysis of 16S rRNA gene diversity of Cu tolerant rhizobacteria revealed the predominance of Enterobacter spp. and Pseudomonas spp. under Cu stress conditions. Cu tolerant bacterial isolates that were able to promote growth of mung bean plants in vitro under Cu stress were obtained from these samples. Cu tolerant rhizobacterium P36 identified as Enterobacter sp. exhibited multiple plant growth promoting traits and significantly alleviated Cu toxicity to mung bean plants by reducing the accumulation of Cu in plant roots and promoted the plant growth in CuSO 4 amended soils. Copyright © 2016 Elsevier Inc. All rights reserved.

Diversity of Bacterial Communities in Container Habitats of Mosquitoes

PubMed Central

Ponnusamy, Loganathan; Xu, Ning; Stav, Gil; Wesson, Dawn M.; Schal, Coby

2010-01-01

We investigated the bacterial diversity of microbial communities in water-filled, human-made and natural container habitats of the mosquitoes Aedes aegypti and Aedes albopictus in suburban landscapes of New Orleans, Louisiana in 2003. We collected water samples from three classes of containers, including tires (n=12), cemetery urns (n=23), and miscellaneous containers that included two tree holes (n=19). Total genomic DNA was extracted from water samples, and 16S ribosomal DNA fragments (operational taxonomic units, OTUs) were amplified by PCR and separated by denaturing gradient gel electrophoresis (DGGE). The bacterial communities in containers represented diverse DGGE-DNA banding patterns that were not related to the class of container or to the local spatial distribution of containers. Mean richness and evenness of OTUs were highest in water samples from tires. Bacterial phylotypes were identified by comparative sequence analysis of 90 16S rDNA DGGE band amplicons. The majority of sequences were placed in five major taxa: Alpha-, Beta- and Gammaproteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, and an unclassified group; Proteobacteria and Bacteroidetes were the predominant heterotrophic bacteria in containers. The bacterial communities in human-made containers consisted mainly of undescribed species, and a phylogenetic analysis based on 16S rRNA sequences suggested that species composition was independent of both container type and the spatial distribution of containers. Comparative PCR-based, cultivation-independent rRNA surveys of microbial communities associated with mosquito habitats can provide significant insight into community organization and dynamics of bacterial species. PMID:18373113

Metabarcoding analysis of strongylid nematode diversity in two sympatric primate species.

PubMed

Pafčo, Barbora; Čížková, Dagmar; Kreisinger, Jakub; Hasegawa, Hideo; Vallo, Peter; Shutt, Kathryn; Todd, Angelique; Petrželková, Klára J; Modrý, David

2018-04-12

Strongylid nematodes in large terrestrial herbivores such as great apes, equids, elephants, and humans tend to occur in complex communities. However, identification of all species within strongylid communities using traditional methods based on coproscopy or single nematode amplification and sequencing is virtually impossible. High-throughput sequencing (HTS) technologies provide opportunities to generate large amounts of sequence data and enable analyses of samples containing a mixture of DNA from multiple species/genotypes. We designed and tested an HTS approach for strain-level identification of gastrointestinal strongylids using ITS-2 metabarcoding at the MiSeq Illumina platform in samples from two free-ranging non-human primate species inhabiting the same environment, but differing significantly in their host traits and ecology. Although we observed overlapping of particular haplotypes, overall the studied primate species differed in their strongylid nematode community composition. Using HTS, we revealed hidden diversity in the strongylid nematode communities in non-human primates, more than one haplotype was found in more than 90% of samples and coinfections of more than one putative species occurred in 80% of samples. In conclusion, the HTS approach on strongylid nematodes, preferably using fecal samples, represents a time and cost-efficient way of studying strongylid communities and provides a resolution superior to traditional approaches.

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

NASA Astrophysics Data System (ADS)

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

2012-10-01

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

High-throughput sequencing-based analysis of endogenetic fungal communities inhabiting the Chinese Cordyceps reveals unexpectedly high fungal diversity

PubMed Central

Xia, Fei; Chen, Xin; Guo, Meng-Yuan; Bai, Xiao-Hui; Liu, Yan; Shen, Guang-Rong; Li, Yu-Ling; Lin, Juan; Zhou, Xuan-Wei

2016-01-01

Chinese Cordyceps, known in Chinese as “DongChong XiaCao”, is a parasitic complex of a fungus (Ophiocordyceps sinensis) and a caterpillar. The current study explored the endogenetic fungal communities inhabiting Chinese Cordyceps. Samples were collected from five different geographical regions of Qinghai and Tibet, and the nuclear ribosomal internal transcribed spacer-1 sequences from each sample were obtained using Illumina high-throughput sequencing. The results showed that Ascomycota was the dominant fungal phylum in Chinese Cordyceps and its soil microhabitat from different sampling regions. Among the Ascomycota, 65 genera were identified, and the abundant operational taxonomic units showed the strongest sequence similarity to Ophiocordyceps, Verticillium, Pseudallescheria, Candida and Ilyonectria Not surprisingly, the genus Ophiocordyceps was the largest among the fungal communities identified in the fruiting bodies and external mycelial cortices of Chinese Cordyceps. In addition, fungal communities in the soil microhabitats were clustered separately from the external mycelial cortices and fruiting bodies of Chinese Cordyceps from different sampling regions. There was no significant structural difference in the fungal communities between the fruiting bodies and external mycelial cortices of Chinese Cordyceps. This study revealed an unexpectedly high diversity of fungal communities inhabiting the Chinese Cordyceps and its microhabitats. PMID:27625176

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

PubMed Central

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

2013-01-01

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

Biodiversity effects of the predation gauntlet

NASA Astrophysics Data System (ADS)

Stier, Adrian C.; Stallings, Christopher D.; Samhouri, Jameal F.; Albins, Mark A.; Almany, Glenn R.

2017-06-01

The ubiquity of trophic downgrading has led to interest in the consequences of mesopredator release on prey communities and ecosystems. This issue is of particular concern for reef-fish communities, where predation is a key process driving ecological and evolutionary dynamics. Here, we synthesize existing experiments that have isolated the effects of mesopredators to quantify the role of predation in driving changes in the abundance and biodiversity of recently settled reef fishes. On average, predators reduced prey abundance through generalist foraging behavior, which, through a statistical sampling artifact, caused a reduction in alpha diversity and an increase in beta diversity. Thus, the synthesized experiments provide evidence that predation reduces overall abundance within prey communities, but—after accounting for sampling effects—does not cause disproportionate effects on biodiversity.

Gut microbial ecology of lizards: insights into diversity in the wild, effects of captivity, variation across gut regions and transmission.

PubMed

Kohl, Kevin D; Brun, Antonio; Magallanes, Melisa; Brinkerhoff, Joshua; Laspiur, Alejandro; Acosta, Juan Carlos; Caviedes-Vidal, Enrique; Bordenstein, Seth R

2017-02-01

Animals maintain complex associations with a diverse microbiota living in their guts. Our understanding of the ecology of these associations is extremely limited in reptiles. Here, we report an in-depth study into the microbial ecology of gut communities in three syntopic and viviparous lizard species (two omnivores: Liolaemus parvus and Liolaemus ruibali and an herbivore: Phymaturus williamsi). Using 16S rRNA gene sequencing to inventory various bacterial communities, we elucidate four major findings: (i) closely related lizard species harbour distinct gut bacterial microbiota that remain distinguishable in captivity; a considerable portion of gut bacterial diversity (39.1%) in nature overlap with that found on plant material, (ii) captivity changes bacterial community composition, although host-specific communities are retained, (iii) faecal samples are largely representative of the hindgut bacterial community and thus represent acceptable sources for nondestructive sampling, and (iv) lizards born in captivity and separated from their mothers within 24 h shared 34.3% of their gut bacterial diversity with their mothers, suggestive of maternal or environmental transmission. Each of these findings represents the first time such a topic has been investigated in lizard hosts. Taken together, our findings provide a foundation for comparative analyses of the faecal and gastrointestinal microbiota of reptile hosts. © 2016 John Wiley & Sons Ltd.

Detection of forest stand-level spatial structure in ectomycorrhizal fungal communities.

PubMed

Lilleskov, Erik A; Bruns, Thomas D; Horton, Thomas R; Taylor, D; Grogan, Paul

2004-08-01

Ectomycorrhizal fungal (EMF) communities are highly diverse at the stand level. To begin to understand what might lead to such diversity, and to improve sampling designs, we investigated the spatial structure of these communities. We used EMF community data from a number of studies carried out in seven mature and one recently fire-initiated forest stand. We applied various measures of spatial pattern to characterize distributions at EMF community and species levels: Mantel tests, Mantel correlograms, variance/mean and standardized variograms. Mantel tests indicated that in four of eight sites community similarity decreased with distance, whereas Mantel correlograms also found spatial autocorrelation in those four plus two additional sites. In all but one of these sites elevated similarity was evident only at relatively small spatial scales (< 2.6 m), whereas one exhibited a larger scale pattern ( approximately 25 m). Evenness of biomass distribution among cores varied widely among taxa. Standardized variograms indicated that most of the dominant taxa showed patchiness at a scale of less than 3 m, with a range from 0 to < or =17 m. These results have implications for both sampling scale and intensity to achieve maximum efficiency of community sampling. In the systems we examined, cores should be at least 3 m apart to achieve the greatest sampling efficiency for stand-level community analysis. In some cases even this spacing may result in reduced sampling efficiency arising from patterns of spatial autocorrelation. Interpretation of the causes and significance of these patterns requires information on the genetic identity of individuals in the communities.

Community Audit of Social, Civil, and Activity Domains in Diverse Environments (CASCADDE)

PubMed Central

Knapp, Emily A.; Nau, Claudia; Brandau, Sy; DeWalle, Joseph; Hirsch, Annemarie G.; Bailey-Davis, Lisa; Schwartz, Brian S.; Glass, Thomas A.

2017-01-01

There are currently no direct observation environmental audit tools that measure diverse aspects of the obesity-related environment efficiently and reliably in a variety of geographical settings. The goal was to develop a new instrument to reliably characterize the overall properties and features of rural, suburban, and urban settings along multiple dimensions. The Community Audit of Social, Civil, and Activity Domains in Diverse Environments (CASCADDE) is an iPad-based instrument that incorporates global positioning system coordinates and photography and is comprised of 214 items yielding 7 summary indices. A comprehensive spatial sampling strategy, training manual, and supporting data analysis code were also developed. Random geospatial sampling using GIS was used to captured features of the community as a whole. A single auditor collected 510 observation points in 30 communities (2013–2015). This analysis was done in 2015–2016. Correlation coefficients were used to compare items and indices to each other and to standard measures. Multilevel unconditional means models were used to calculate intraclass correlation coefficients (ICC) to determine if there was significant variation between communities. Results suggest that CASCADDE measures aspects of communities not previously captured by secondary data sources. Additionally, 7 summary indices capture meaningful differences between communities based on 15 observations per community. Community audit tools such as CASCADDE complement secondary data sources and have the potential to offer new insights about the mechanisms through which communities affect obesity and other health outcomes. PMID:28209283

Community Audit of Social, Civil, and Activity Domains in Diverse Environments (CASCADDE).

PubMed

Knapp, Emily A; Nau, Claudia; Brandau, Sy; DeWalle, Joseph; Hirsch, Annemarie G; Bailey-Davis, Lisa; Schwartz, Brian S; Glass, Thomas A

2017-04-01

There are currently no direct observation environmental audit tools that measure diverse aspects of the obesity-related environment efficiently and reliably in a variety of geographic settings. The goal was to develop a new instrument to reliably characterize the overall properties and features of rural, suburban, and urban settings along multiple dimensions. The Community Audit of Social, Civil, and Activity Domains in Diverse Environments (CASCADDE) is an iPad-based instrument that incorporates GPS coordinates and photography and comprises 214 items yielding seven summary indices. A comprehensive spatial sampling strategy, training manual, and supporting data analysis code were also developed. Random geospatial sampling using GIS was used to capture features of the community as a whole. A single auditor collected 510 observation points in 30 communities (2013-2015). This analysis was done in 2015-2016. Correlation coefficients were used to compare items and indices to each other and to standard measures. Multilevel unconditional means models were used to calculate intraclass correlation coefficients to determine if there was significant variation between communities. Results suggest that CASCADDE measures aspects of communities not previously captured by secondary data sources. Additionally, seven summary indices capture meaningful differences between communities based on 15 observations per community. Community audit tools such as CASCADDE complement secondary data sources and have the potential to offer new insights about the mechanisms through which communities affect obesity and other health outcomes. Copyright © 2017 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.

Characterization of bacterial community associated to biofilms of corroded oil pipelines from the southeast of Mexico.

PubMed

Neria-González, Isabel; Wang, En Tao; Ramírez, Florina; Romero, Juan M; Hernández-Rodríguez, César

2006-06-01

Microbial communities associated to biofilms promote corrosion of oil pipelines. The community structure of bacteria in the biofilm formed in oil pipelines is the basic knowledge to understand the complexity and mechanisms of metal corrosion. To assess bacterial diversity, biofilm samples were obtained from X52 steel coupons corroded after 40 days of exposure to normal operation and flow conditions. The biofilm samples were directly used to extract metagenomic DNA, which was used as template to amplify 16S ribosomal gene by PCR. The PCR products of 16S ribosomal gene were also employed as template for sulfate-reducing bacteria (SRB) specific nested-PCR and both PCR products were utilized for the construction of gene libraries. The V3 region of the 16S rRNA gene was also amplified to analyse the bacterial diversity by analysis of denaturing gradient gel electrophoresis (DGGE). Ribosomal library and DGGE profiles exhibited limited bacterial diversity, basically including Citrobacter spp., Enterobacter spp. and Halanaerobium spp. while Desulfovibrio alaskensis and a novel clade within the genus Desulfonatronovibrio were detected from the nested PCR library. The biofilm samples were also taken for the isolation of SRB. Desulfovibrio alaskensis and Desulfovibrio capillatus, as well as some strains related to Citrobacter were isolated. SRB consists in a very small proportion of the community and Desulfovibrio spp. were the relatively abundant groups among the SRB. This is the first study directly exploring bacterial diversity in corrosive biofilms associated to steel pipelines subjected to normal operation conditions.

Application of Molecular Techniques To Elucidate the Influence of Cellulosic Waste on the Bacterial Community Structure at a Simulated Low-Level-Radioactive-Waste Site▿ †

PubMed Central

Field, Erin K.; D'Imperio, Seth; Miller, Amber R.; VanEngelen, Michael R.; Gerlach, Robin; Lee, Brady D.; Apel, William A.; Peyton, Brent M.

2010-01-01

Low-level-radioactive-waste (low-level-waste) sites, including those at various U.S. Department of Energy sites, frequently contain cellulosic waste in the form of paper towels, cardboard boxes, or wood contaminated with heavy metals and radionuclides such as chromium and uranium. To understand how the soil microbial community is influenced by the presence of cellulosic waste products, multiple soil samples were obtained from a nonradioactive model low-level-waste test pit at the Idaho National Laboratory. Samples were analyzed using 16S rRNA gene clone libraries and 16S rRNA gene microarray (PhyloChip) analyses. Both methods revealed changes in the bacterial community structure with depth. In all samples, the PhyloChip detected significantly more operational taxonomic units, and therefore relative diversity, than the clone libraries. Diversity indices suggest that diversity is lowest in the fill and fill-waste interface (FW) layers and greater in the wood waste and waste-clay interface layers. Principal-coordinate analysis and lineage-specific analysis determined that the Bacteroidetes and Actinobacteria phyla account for most of the significant differences observed between the layers. The decreased diversity in the FW layer and increased members of families containing known cellulose-degrading microorganisms suggest that the FW layer is an enrichment environment for these organisms. These results suggest that the presence of the cellulosic material significantly influences the bacterial community structure in a stratified soil system. PMID:20305022

Grain-dependent responses of mammalian diversity to land use and the implications for conservation set-aside.

PubMed

Wearn, Oliver R; Carbone, Chris; Rowcliffe, J Marcus; Bernard, Henry; Ewers, Robert M

2016-07-01

Diversity responses to land-use change are poorly understood at local scales, hindering our ability to make forecasts and management recommendations at scales which are of practical relevance. A key barrier in this has been the underappreciation of grain-dependent diversity responses and the role that β-diversity (variation in community composition across space) plays in this. Decisions about the most effective spatial arrangement of conservation set-aside, for example high conservation value areas, have also neglected β-diversity, despite its role in determining the complementarity of sites. We examined local-scale mammalian species richness and β-diversity across old-growth forest, logged forest, and oil palm plantations in Borneo, using intensive camera- and live-trapping. For the first time, we were able to investigate diversity responses, as well as β-diversity, at multiple spatial grains, and across the whole terrestrial mammal community (large and small mammals); β-diversity was quantified by comparing observed β-diversity with that obtained under a null model, in order to control for sampling effects, and we refer to this as the β-diversity signal. Community responses to land use were grain dependent, with large mammals showing reduced richness in logged forest compared to old-growth forest at the grain of individual sampling points, but no change at the overall land-use level. Responses varied with species group, however, with small mammals increasing in richness at all grains in logged forest compared to old-growth forest. Both species groups were significantly depauperate in oil palm. Large mammal communities in old-growth forest became more heterogeneous at coarser spatial grains and small mammal communities became more homogeneous, while this pattern was reversed in logged forest. Both groups, however, showed a significant β-diversity signal at the finest grain in logged forest, likely due to logging-induced environmental heterogeneity. The β-diversity signal in oil palm was weak, but heterogeneity at the coarsest spatial grain was still evident, likely due to variation in landscape forest cover. Our findings suggest that the most effective spatial arrangement of set-aside will involve trade-offs between conserving large and small mammals. Greater consideration in the conservation and management of tropical landscapes needs to be given to β-diversity at a range of spatial grains. © 2016 by the Ecological Society of America.

Microbial diversity and carbon cycling in San Francisco Bay wetlands

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

Theroux, Susanna; Hartman, Wyatt; He, Shaomei

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

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.

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.

Communities of Arbuscular Mycorrhizal Fungi Detected in Forest Soil Are Spatially Heterogeneous but Do Not Vary throughout the Growing Season

PubMed Central

Davison, John; Öpik, Maarja; Zobel, Martin; Vasar, Martti; Metsis, Madis; Moora, Mari

2012-01-01

Despite the important ecosystem role played by arbuscular mycorrhizal fungi (AMF), little is known about spatial and temporal variation in soil AMF communities. We used pyrosequencing to characterise AMF communities in soil samples (n = 44) from a natural forest ecosystem. Fungal taxa were identified by BLAST matching of reads against the MaarjAM database of AMF SSU rRNA gene diversity. Sub-sampling within our dataset and experimental shortening of a set of long reads indicated that our approaches to taxonomic identification and diversity analysis were robust to variations in pyrosequencing read length and numbers of reads per sample. Different forest plots (each 10×10 m and separated from one another by 30 m) contained significantly different soil AMF communities, and the pairwise similarity of communities decreased with distance up to 50 m. However, there were no significant changes in community composition between different time points in the growing season (May-September). Spatial structure in soil AMF communities may be related to the heterogeneous vegetation of the natural forest study system, while the temporal stability of communities suggests that AMF in soil represent a fairly constant local species pool from which mycorrhizae form and disband during the season. PMID:22879900

Tropical Estuarine Macrobenthic Communities Are Structured by Turnover Rather than Nestedness

PubMed Central

Medeiros, Carlinda Raílly; Hepp, Luiz Ubiratan; Patrício, Joana; Molozzi, Joseline

2016-01-01

Turnover (i.e., species substitution) and nestedness (i.e., subsets of species from more diverse locations), the two main mechanisms used to explain the beta diversity of biological communities, have different implications for biodiversity conservation. To better understand how these mechanisms contribute to beta diversity, we tested the following hypotheses: (i) greater dissimilarity in community composition occurs between estuarine zones than other hierarchical level studied; (ii) beta diversity in these communities develops by turnover in estuaries with a lower degree of anthropogenic impact, but by nestedness in estuaries with a greater degree of anthropogenic impact; and (iii) the structuring mechanism is independent of season. We studied two tropical estuaries (dry and wet seasons) that vary in terms of land-use of the drainage basins. Subtidal benthic macroinvertebrates were sampled along the estuarine gradient in each of the two estuaries. The additive partitioning approach to species diversity was used to determine the hierarchical scale with the greatest dissimilarity in community composition. General beta diversity was measured using the Sorensen dissimilarity index, partitioning the turnover and nestedness components. The greatest dissimilarity in the composition of the communities occurred between the zones along the estuarine gradient in both seasons (dry = 58.6%; wet = 46.3%). In the estuary with a lower degree of anthropogenic influence, benthic macroinvertebrate diversity was generated by turnover regardless of the season. In the estuary with a greater degree of anthropogenic impact, beta diversity was structured by turnover during the dry season and a combination of both mechanisms during the wet season. We conclude that turnover is the principal mechanism responsible for beta diversity in benthic macroinvertebrate communities in tropical estuaries. PMID:27584726

Tropical Estuarine Macrobenthic Communities Are Structured by Turnover Rather than Nestedness.

PubMed

Medeiros, Carlinda Raílly; Hepp, Luiz Ubiratan; Patrício, Joana; Molozzi, Joseline

2016-01-01

Turnover (i.e., species substitution) and nestedness (i.e., subsets of species from more diverse locations), the two main mechanisms used to explain the beta diversity of biological communities, have different implications for biodiversity conservation. To better understand how these mechanisms contribute to beta diversity, we tested the following hypotheses: (i) greater dissimilarity in community composition occurs between estuarine zones than other hierarchical level studied; (ii) beta diversity in these communities develops by turnover in estuaries with a lower degree of anthropogenic impact, but by nestedness in estuaries with a greater degree of anthropogenic impact; and (iii) the structuring mechanism is independent of season. We studied two tropical estuaries (dry and wet seasons) that vary in terms of land-use of the drainage basins. Subtidal benthic macroinvertebrates were sampled along the estuarine gradient in each of the two estuaries. The additive partitioning approach to species diversity was used to determine the hierarchical scale with the greatest dissimilarity in community composition. General beta diversity was measured using the Sorensen dissimilarity index, partitioning the turnover and nestedness components. The greatest dissimilarity in the composition of the communities occurred between the zones along the estuarine gradient in both seasons (dry = 58.6%; wet = 46.3%). In the estuary with a lower degree of anthropogenic influence, benthic macroinvertebrate diversity was generated by turnover regardless of the season. In the estuary with a greater degree of anthropogenic impact, beta diversity was structured by turnover during the dry season and a combination of both mechanisms during the wet season. We conclude that turnover is the principal mechanism responsible for beta diversity in benthic macroinvertebrate communities in tropical estuaries.

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

PubMed

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

2016-04-26

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

Invasive plants have scale-dependent effects on diversity by altering species-area relationships.

PubMed

Powell, Kristin I; Chase, Jonathan M; Knight, Tiffany M

2013-01-18

Although invasive plant species often reduce diversity, they rarely cause plant extinctions. We surveyed paired invaded and uninvaded plant communities from three biomes. We reconcile the discrepancy in diversity loss from invaders by showing that invaded communities have lower local richness but steeper species accumulation with area than that of uninvaded communities, leading to proportionately fewer species loss at broader spatial scales. We show that invaders drive scale-dependent biodiversity loss through strong neutral sampling effects on the number of individuals in a community. We also show that nonneutral species extirpations are due to a proportionately larger effect of invaders on common species, suggesting that rare species are buffered against extinction. Our study provides a synthetic perspective on the threat of invasions to biodiversity loss across spatial scales.

Vertical Structure of Phyllosphere Fungal Communities in a Tropical Forest in Thailand Uncovered by High-Throughput Sequencing.

PubMed

Izuno, Ayako; Kanzaki, Mamoru; Artchawakom, Taksin; Wachrinrat, Chongrak; Isagi, Yuji

2016-01-01

Phyllosphere fungi harbor a tremendous species diversity and play important ecological roles. However, little is known about their distribution patterns within forest ecosystems. We examined how species diversity and community composition of phyllosphere fungi change along a vertical structure in a tropical forest in Thailand. Fungal communities in 144 leaf samples from 19 vertical layers (1.28-34.4 m above ground) of 73 plant individuals (27 species) were investigated by metabarcoding analysis using Ion Torrent sequencing. In total, 1,524 fungal operational taxonomic units (OTUs) were detected among 890,710 reads obtained from the 144 leaf samples. Taxonomically diverse fungi belonging to as many as 24 orders of Ascomycota and 21 orders of Basidiomycota were detected, most of which inhabited limited parts of the lowest layers closest to the forest floor. Species diversity of phyllosphere fungi was the highest in the lowest layers closest to the forest floor, decreased with increasing height, and lowest in the canopy; 742 and 55 fungal OTUs were detected at the lowest and highest layer, respectively. On the layers close to the forest floor, phyllosphere fungal communities were mainly composed of low frequency OTUs and largely differentiated among plant individuals. Conversely, in the canopy, fungal communities consisted of similar OTUs across plant individuals, and as many as 86.1%-92.7% of the OTUs found in the canopy (≥22 m above ground) were also distributed in the lower layers. Overall, our study showed the variability of phyllosphere fungal communities along the vertical gradient of plant vegetation and environmental conditions, suggesting the significance of biotic and abiotic variation for the species diversity of phyllosphere fungi.

[Effects of environmental factors on β diversity of zooplankton community in thermal discharge seawaters near Guohua Power Plant in Xiangshan Bay, Zhejiang, China].

PubMed

Zhu, Yi-feng; Dai, Mei-xia; Zhou, Xiao-hong; Lin, Xia; Mao, Shuo-qian; Yan, Xiao-jun

2015-08-01

Zooplankton samples were seasonally collected at 10 stations in thermal discharge seawaters near Guohua Power Plant in Xiangshan Bay. The abundance data from these samples were pooled and further combined with field environmental factors, then generalised dissimilarity modelling (GDM) was used to explore the effects of environmental factors on β diversity of zooplankton community. The results showed that altogether 95 species of zooplankton belonging to 14 taxa were found. In these taxa, small zooplankton with 62.6% of abundance was the main taxa, while copepods dominated in adult groups, which abundance accounted for 35.3%. According to Whittaker's definition and additive partition, a diversity accounted for 36.3% and β diversity 63.7%. Environmental factors explained 43.8% of β diversity, and geographical distance between sampling sites had no effect on β diversity. However, there were still 19.9% of β diversity remained to be explained. After GDM fitting, there were nine environmental variables affecting zooplankton β diversity and explaining 68.8% of β diversity. The variables contributing to β diversity from high to low were seasonal water temperature, dissolved oxygen, seawater temperature increment, conductivity, suspended particulate matter, salinity, transparency, water depth and redox potential, respectively. Seasonal water temperature, dissolved oxygen and seawater temperature increment were the most important factors for driving β diversity changes, and accounted for 23.9%, 13.7% and 9.7% of absolute contribution to the interpretable portion of the β diversity, respectively. When seasonal water temperature, dissolved oxygen and seawater temperature increment were below 25 °C, greater than 5 mg · L(-1) and over 1 °C, respectively, β diversity rapidly increased with the increasing variable gradients. Furthermore, other predictors had little effect on β diversity.

Effect of Increasing Nitrogen Deposition on Soil Microbial Communities

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

Xiao, Shengmu; Xue, Kai; He, Zhili

2010-05-17

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

Pepino (Solanum muricatum) planting increased diversity and abundance of bacterial communities in karst area

NASA Astrophysics Data System (ADS)

Hu, Jinxiang; Yang, Hui; Long, Xiaohua; Liu, Zhaopu; Rengel, Zed

2016-02-01

Soil nutrients and microbial communities are the two key factors in revegetation of barren environments. Ecological stoichiometry plays an important role in ecosystem function and limitation, but the relationships between above- and belowground stoichiometry and the bacterial communities in a typical karst region are poorly understood. We used pepino (Solanum muricatum) to examine the stoichiometric traits between soil and foliage, and determine diversity and abundance of bacteria in the karst soil. The soil had a relatively high pH, low fertility, and coarse texture. Foliar N:P ratio and the correlations with soil nitrogen and phosphorus suggested nitrogen limitation. The planting of pepino increased soil urease activity and decreased catalase activity. Higher diversity of bacteria was determined in the pepino rhizosphere than bulk soil using a next-generation, Illumina-based sequencing approach. Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes were the dominant phyla in all samples, accounting for more than 80% of the reads. On a genus level, all 625 detected genera were found in all rhizosphere and bulk soils, and 63 genera showed significant differences among samples. Higher Shannon and Chao 1 indices in the rhizosphere than bulk soil indicated that planting of pepino increased diversity and abundance of bacterial communities in karst area.

Ecological Drivers of Biogeographic Patterns of Soil Archaeal Community

PubMed Central

Zheng, Yuan-Ming; Cao, Peng; Fu, Bojie; Hughes, Jane M.; He, Ji-Zheng

2013-01-01

Knowledge about the biogeography of organisms has long been a focus in ecological research, including the mechanisms that generate and maintain diversity. In this study, we targeted a microbial group relatively underrepresented in the microbial biogeographic literature, the soil Archaea. We surveyed the archaeal abundance and community composition using real-time quantitative PCR and T-RFLP approaches for 105 soil samples from 2 habitat types to identify the archaeal distribution patterns and factors driving these patterns. Results showed that the soil archaeal community was affected by spatial and environmental variables, and 79% and 51% of the community variation was explained in the non-flooded soil (NS) and flooded soil (FS) habitat, respectively, showing its possible biogeographic distribution. The diversity patterns of soil Archaea across the landscape were influenced by a combination of stochastic and deterministic processes. The contribution from neutral processes was higher than that from deterministic processes associated with environmental variables. The variables pH, sample depth and longitude played key roles in determining the archaeal distribution in the NS habitat, while sampling depth, longitude and NH4 +-N were most important in the FS habitat. Overall, there might be similar ecological drivers in the soil archaeal community as in macroorganism communities. PMID:23717418

Anthropogenic disturbance equalizes diversity levels in arbuscular mycorrhizal fungal communities.

PubMed

García de León, David; Davison, John; Moora, Mari; Öpik, Maarja; Feng, Huyuan; Hiiesalu, Inga; Jairus, Teele; Koorem, Kadri; Liu, Yongjun; Phosri, Cherdchai; Sepp, Siim-Kaarel; Vasar, Martti; Zobel, Martin

2018-03-24

The arbuscular mycorrhizal (AM) symbiosis is a key plant-microbe interaction in sustainable functioning ecosystems. Increasing anthropogenic disturbance poses a threat to AM fungal communities worldwide, but there is little empirical evidence about its potential negative consequences. In this global study, we sequenced AM fungal DNA in soil samples collected from pairs of natural (undisturbed) and anthropogenic (disturbed) plots in two ecosystem types (10 naturally wooded and six naturally unwooded ecosystems). We found that ecosystem type had stronger directional effects than anthropogenic disturbance on AM fungal alpha and beta diversity. However, disturbance increased alpha and beta diversity at sites where natural diversity was low and decreased diversity at sites where natural diversity was high. Cultured AM fungal taxa were more prevalent in anthropogenic than natural plots, probably due to their efficient colonization strategies and ability to recover from disturbance. We conclude that anthropogenic disturbance does not have a consistent directional effect on AM fungal diversity; rather, disturbance equalizes levels of diversity at large scales and causes changes in community functional structure. © 2018 John Wiley & Sons Ltd.

Improved imputation accuracy in Hispanic/Latino populations with larger and more diverse reference panels: applications in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL)

PubMed Central

Nelson, Sarah C.; Stilp, Adrienne M.; Papanicolaou, George J.; Taylor, Kent D.; Rotter, Jerome I.; Thornton, Timothy A.; Laurie, Cathy C.

2016-01-01

Imputation is commonly used in genome-wide association studies to expand the set of genetic variants available for analysis. Larger and more diverse reference panels, such as the final Phase 3 of the 1000 Genomes Project, hold promise for improving imputation accuracy in genetically diverse populations such as Hispanics/Latinos in the USA. Here, we sought to empirically evaluate imputation accuracy when imputing to a 1000 Genomes Phase 3 versus a Phase 1 reference, using participants from the Hispanic Community Health Study/Study of Latinos. Our assessments included calculating the correlation between imputed and observed allelic dosage in a subset of samples genotyped on a supplemental array. We observed that the Phase 3 reference yielded higher accuracy at rare variants, but that the two reference panels were comparable at common variants. At a sample level, the Phase 3 reference improved imputation accuracy in Hispanic/Latino samples from the Caribbean more than for Mainland samples, which we attribute primarily to the additional reference panel samples available in Phase 3. We conclude that a 1000 Genomes Project Phase 3 reference panel can yield improved imputation accuracy compared with Phase 1, particularly for rare variants and for samples of certain genetic ancestry compositions. Our findings can inform imputation design for other genome-wide association studies of participants with diverse ancestries, especially as larger and more diverse reference panels continue to become available. PMID:27346520

Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes

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

Gihring, Thomas; Green, Stefan; Schadt, Christopher Warren

2011-01-01

Technologies for massively parallel sequencing are revolutionizing microbial ecology and are vastly increasing the scale of ribosomal RNA (rRNA) gene studies. Although pyrosequencing has increased the breadth and depth of possible rRNA gene sampling, one drawback is that the number of reads obtained per sample is difficult to control. Pyrosequencing libraries typically vary widely in the number of sequences per sample, even within individual studies, and there is a need to revisit the behaviour of richness estimators and diversity indices with variable gene sequence library sizes. Multiple reports and review papers have demonstrated the bias in non-parametric richness estimators (e.g.more » Chao1 and ACE) and diversity indices when using clone libraries. However, we found that biased community comparisons are accumulating in the literature. Here we demonstrate the effects of sample size on Chao1, ACE, CatchAll, Shannon, Chao-Shen and Simpson's estimations specifically using pyrosequencing libraries. The need to equalize the number of reads being compared across libraries is reiterated, and investigators are directed towards available tools for making unbiased diversity comparisons.« less

The Contribution of DNA Metabarcoding to Fungal Conservation: Diversity Assessment, Habitat Partitioning and Mapping Red-Listed Fungi in Protected Coastal Salix repens Communities in the Netherlands

PubMed Central

Geml, József; Gravendeel, Barbara; van der Gaag, Kristiaan J.; Neilen, Manon; Lammers, Youri; Raes, Niels; Semenova, Tatiana A.; de Knijff, Peter; Noordeloos, Machiel E.

2014-01-01

Western European coastal sand dunes are highly important for nature conservation. Communities of the creeping willow (Salix repens) represent one of the most characteristic and diverse vegetation types in the dunes. We report here the results of the first kingdom-wide fungal diversity assessment in S. repens coastal dune vegetation. We carried out massively parallel pyrosequencing of ITS rDNA from soil samples taken at ten sites in an extended area of joined nature reserves located along the North Sea coast of the Netherlands, representing habitats with varying soil pH and moisture levels. Fungal communities in Salix repens beds are highly diverse and we detected 1211 non-singleton fungal 97% sequence similarity OTUs after analyzing 688,434 ITS2 rDNA sequences. Our comparison along a north-south transect indicated strong correlation between soil pH and fungal community composition. The total fungal richness and the number OTUs of most fungal taxonomic groups negatively correlated with higher soil pH, with some exceptions. With regard to ecological groups, dark-septate endophytic fungi were more diverse in acidic soils, ectomycorrhizal fungi were represented by more OTUs in calcareous sites, while detected arbuscular mycorrhizal genera fungi showed opposing trends regarding pH. Furthermore, we detected numerous red listed species in our samples often from previously unknown locations, indicating that some of the fungal species currently considered rare may be more abundant in Dutch S. repens communities than previously thought. PMID:24937200

Aerobic and anaerobic methanotrophic communities in urban landscape wetland.

PubMed

Chen, Sili; Chen, Jianfei; Chang, Sha; Yi, Hao; Huang, Dawei; Xie, Shuguang; Guo, Qingwei

2018-01-01

Both aerobic methane-oxidizing bacteria (MOB) and nitrite-dependent anaerobic methane oxidation (n-damo) organisms can be important methane sinks in a wetland. However, the influences of the vegetation type on aerobic MOB and n-damo communities in wetland, especially in constructed wetland, remain poorly understood. The present study investigated the influences of the vegetation type on both aerobic MOB and n-damo organisms in a constructed urban landscape wetland. Sediments were collected from eight sites vegetated with different plant species. The abundance (1.19-3.27 × 10 7 pmoA gene copies per gram dry sediment), richness (Chao1 estimator = 16.3-81.5), diversity (Shannon index = 2.10-3.15), and structure of the sediment aerobic MOB community were found to vary considerably with sampling site. In contrast, n-damo community abundance (8.74 × 10 5 -4.80 × 10 6 NC10 16S rRNA gene copies per gram dry sediment) changed slightly with the sampling site. The richness (Chao1 estimator = 1-11), diversity (Shannon index = 0-0.78), and structure of the NC10 16S rRNA gene-based n-damo community illustrated slight site-related changes, while the spatial changes of the pmoA gene-based n-damo community richness (Chao1 estimator = 1-8), diversity (Shannon index = 0-0.99), and structure were considerable. The vegetation type could have a profound impact on the wetland aerobic MOB community and had a stronger influence on the pmoA-based n-damo community than on the NC10 16S-based one in urban wetland. Moreover, the aerobic MOB community had greater abundance and higher richness and diversity than the n-damo community. Methylocystis (type II MOB) predominated in urban wetland, while no known type I MOB species was detected. In addition, the ratio of total organic carbon to total nitrogen (C/N) might be a determinant of sediment n-damo community diversity and aerobic MOB richness.

When is the best time to sample aquatic macroinvertebrates in ponds for biodiversity assessment?

PubMed

Hill, M J; Sayer, C D; Wood, P J

2016-03-01

Ponds are sites of high biodiversity and conservation value, yet there is little or no statutory monitoring of them across most of Europe. There are clear and standardised protocols for sampling aquatic macroinvertebrate communities in ponds, but the most suitable time(s) to undertake the survey(s) remains poorly specified. This paper examined the aquatic macroinvertebrate communities from 95 ponds within different land use types over three seasons (spring, summer and autumn) to determine the most appropriate time to undertake sampling to characterise biodiversity. The combined samples from all three seasons provided the most comprehensive record of the aquatic macroinvertebrate taxa recorded within ponds (alpha and gamma diversity). Samples collected during the autumn survey yielded significantly greater macroinvertebrate richness (76% of the total diversity) than either spring or summer surveys. Macroinvertebrate diversity was greatest during autumn in meadow and agricultural ponds, but taxon richness among forest and urban ponds did not differ significantly temporally. The autumn survey provided the highest measures of richness for Coleoptera, Hemiptera and Odonata. However, richness of the aquatic insect order Trichoptera was highest in spring and lowest in autumn. The results illustrate that multiple surveys, covering more than one season, provide the most comprehensive representation of macroinvertebrate biodiversity. When sampling can only be undertaken on one occasion, the most appropriate time to undertake surveys to characterise the macroinvertebrate community biodiversity is during autumn, although this may need to be modified if other floral and faunal groups need to be incorporated into the sampling programme.

Comparing Ecological and Genetic Diversity Within the Marine Diatom Genus Pseudo-nitzschia: A Multiregional Synthesis

NASA Astrophysics Data System (ADS)

Hubbard, K.; Bruzek, S.

2016-02-01

The globally distributed marine diatom genus Pseudo-nitzschia consists of approximately 40 species, more than half of which occur in US coastal waters. Here, sensitive genetic tools targeting a variable portion of the internal transcribed spacer 1 (ITS1) region of the rRNA gene were used to assess Pseudo-nitzschia spp. diversity in more than 600 environmental DNA samples collected from US Atlantic, Pacific, and Gulf of Mexico waters. Community-based approaches employed genus-specific primers for environmental DNA fingerprinting and targeted sequencing. For the Gulf of Mexico samples especially, a nested PCR approach (with or without degenerate primers) improved resolution of species diversity. To date, more than 40 unique ITS1 amplicon sizes have been repeatedly observed in ITS1 fingerprints. Targeted sequencing of environmental DNA as well as single chains isolated from live samples indicate that many of these represent novel and known inter- and intra-specific Pseudo-nitzschia diversity. A few species (e.g., P. pungens, P. cuspidata) occur across all three regions, whereas other species and intraspecific variants occurred at local to regional spatial scales only. Generally, species frequently co-occur in complex assemblages, and transitions in Pseudo-nitzschia community composition occur seasonally, prior to bloom initiation, and across (cross-shelf, latitudinal, and vertical) environmental gradients. These observations highlight the dynamic nature of diatom community composition in the marine environment and the importance of classifying diversity at relevant ecological and/or taxonomic scales.

Learner Characteristics and Writing Performance in a Community College English as a Second Language Course: Some Unexpected Findings

ERIC Educational Resources Information Center

Lambert, Olga D.

2015-01-01

This study investigates the relationships between individual learner characteristics and gain in writing performance as measured by a standardized writing assessment in a sample of community college academic English as a Second Language (ESL) students in the United States. The ethnically and linguistically diverse convenience sample included 76…

Bacterial, Archaeal, and Eukaryotic Diversity across Distinct Microhabitats in an Acid Mine Drainage

PubMed Central

Mesa, Victoria; Gallego, Jose L. R.; González-Gil, Ricardo; Lauga, Béatrice; Sánchez, Jesús; Méndez-García, Celia; Peláez, Ana I.

2017-01-01

Acid mine drainages are characterized by their low pH and the presence of dissolved toxic metallic species. Microorganisms survive in different microhabitats within the ecosystem, namely water, sediments, and biofilms. In this report, we surveyed the microbial diversity within all domains of life in the different microhabitats at Los Rueldos abandoned mercury underground mine (NW Spain), and predicted bacterial function based on community composition. Sediment samples contained higher proportions of soil bacteria (AD3, Acidobacteria), as well as Crenarchaeota and Methanomassiliicoccaceae archaea. Oxic and hypoxic biofilm samples were enriched in bacterial iron oxidizers from the genus Leptospirillum, order Acidithiobacillales, class Betaproteobacteria, and archaea from the class Thermoplasmata. Water samples were enriched in Cyanobacteria and Thermoplasmata archaea at a 3–98% of the sunlight influence, whilst Betaproteobacteria, Thermoplasmata archaea, and Micrarchaea dominated in acid water collected in total darkness. Stalactites hanging from the Fe-rich mine ceiling were dominated by the neutrophilic iron oxidizer Gallionella and other lineages that were absent in the rest of the microhabitats (e.g., Chlorobi, Chloroflexi). Eukaryotes were detected in biofilms and open-air water samples, and belonged mainly to clades SAR (Alveolata and Stramenopiles), and Opisthokonta (Fungi). Oxic and hypoxic biofilms displayed higher proportions of ciliates (Gonostomum, Oxytricha), whereas water samples were enriched in fungi (Paramicrosporidium and unknown microbial Helotiales). Predicted function through bacterial community composition suggested adaptive evolutive convergence of function in heterogeneous communities. Our study showcases a broad description of the microbial diversity across different microhabitats in the same environment and expands the knowledge on the diversity of microbial eukaryotes in AMD habitats. PMID:28955322

Microbiological quality and bacterial diversity of the tropical oyster Crassostrea rhizophorae in a monitored farming system and from natural stocks.

PubMed

Silva Neta, M T; Maciel, B M; Lopes, A T S; Marques, E L S; Rezende, R P; Boehs, G

2015-12-02

Microbiological evaluation is one of the most important parameters for analyzing the viability of an oyster farming system, which addresses public health and ecological concerns. Here, the microbiological quality of the oyster Crassostrea rhizophorae cultivated in a monitored environment and from natural beds in Bahia, northeastern Brazil, was determined. Bacterial diversity in oysters was measured by polymerase chain reaction-denaturing gradient gel electrophoresis. Sequence analysis revealed that most bacterial species showed similarity with uncultured or unidentified bacteria from environmental samples, and were clustered into the phylum Proteobacteria. Diverse bacteria from cultivated (monitored) oyster samples were grouped in the same cluster with a high similarity index (above 79%). Microbiological analyses revealed that these oysters did not contain pathogens. These results reflect the natural balance of the microbial communities essential to the maintenance of health and in inhibiting pathogen colonization in the oyster. On the other hand, bacterial diversity of samples from native stocks in extractive areas displayed a similarity index varying between 55 and 77%, and all samples were clustered separately from each other and from the cluster of samples derived from the cultivation area. Microbiological analyses showed that oysters from the extractive area were not fit for human consumption. This reflected a different composition of the microbial community in this area, probably resulting from anthropic impact. Our study also demonstrated that low temperatures and high rainfall limits the bacterial concentration in tropical oysters. This is the first study analyzing the total bacterial community profiles of the oyster C. rhizophorae.

Red imported fire ant impacts on upland arthropods in Southern Mississippi

USGS Publications Warehouse

Epperson, D.M.; Allen, Craig R.

2010-01-01

Red imported fire ants (Solenopsis invicta) have negative impacts on a broad array of invertebrate species. We investigated the impacts of fire ants on the upland arthropod community on 20???40 ha study sites in southern Mississippi. Study sites were sampled from 19972000 before, during, and after fire ant bait treatments to reduce fire ant populations. Fire ant abundance was assessed with bait transects on all sites, and fire ant population indices were estimated on a subset of study sites. Species richness and diversity of other ant species was also assessed from bait transects. Insect biomass and diversity was determined from light trap samples. Following treatments, fire ant abundance and population indices were significantly reduced, and ant species diversity and richness were greater on treated sites. Arthropod biomass, species diversity and species richness estimated from light trap samples were negatively correlated with fire ant abundance, but there were no observable treatment effects. Solenopsis invicta has the potential to negatively impact native arthropod communities resulting in a potential loss of both species and function.

Contrasting diversity patterns of soil mites and nematodes in secondary succession

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

Kardol, Paul; Newton, Jeffrey S.; Bezemer, T Martijn

2009-01-01

Soil biodiversity has been recognized as a key feature of ecosystem functioning and stability. However, soil biodiversity is strongly impaired by agriculture and relatively little is known on how and at what spatial and temporal scales soil biodiversity is restored after the human disturbances have come to an end. Here, a multi-scale approach was used to compare diversity patterns of soil mites and nematodes at four stages (early, mid, late, reference site) along a secondary succession chronosequence from abandoned arable land to heath land. In each field four soil samples were taken during four successive seasons. We determined soil diversitymore » within samples ({alpha}-diversity), between samples ({beta}-diversity) and within field sites ({gamma}-diversity). The patterns of {alpha}- and {gamma}-diversity developed similarly along the chronosequence for oribatid mites, but not for nematodes. Nematode {alpha}-diversity was highest in mid- and late-successional sites, while {gamma}-diversity was constant along the chronosequence. Oribatid mite {beta}-diversity was initially high, but decreased thereafter, whereas nematode {beta}-diversity increased when succession proceeded; indicating that patterns of within-site heterogeneity diverged for oribatid mites and nematodes. The spatio-temporal diversity patterns after land abandonment suggest that oribatid mite community development depends predominantly on colonization of new taxa, whereas nematode community development depends on shifts in dominance patterns. This would imply that at old fields diversity patterns of oribatid mites are mainly controlled by dispersal, whereas diversity patterns of nematodes are mainly controlled by changing abiotic or biotic soil conditions. Our study shows that the restoration of soil biodiversity along secondary successional gradients can be both scale- and phylum-dependent.« less

Root-associated fungi of Vaccinium carlesii in subtropical forests of China: intra- and inter-annual variability and impacts of human disturbances

PubMed Central

Zhang, Yanhua; Ni, Jian; Tang, Fangping; Pei, Kequan; Luo, Yiqi; Jiang, Lifen; Sun, Lifu; Liang, Yu

2016-01-01

Ericoid mycorrhiza (ERM) are expected to facilitate establishment of ericaceous plants in harsh habitats. However, diversity and driving factors of the root-associated fungi of ericaceous plants are poorly understood. In this study, hair-root samples of Vaccinium carlesii were taken from four forest types: old growth forests (OGF), secondary forests with once or twice cutting (SEC I and SEC II), and Cunninghamia lanceolata plantation (PLF). Fungal communities were determined using high-throughput sequencing, and impacts of human disturbances and the intra- and inter-annual variability of root-associated fungal community were evaluated. Diverse fungal taxa were observed and our results showed that (1) Intra- and inter-annual changes in root-associated fungal community were found, and the Basidiomycota to Ascomycota ratio was related to mean temperature of the sampling month; (2) Human disturbances significantly affected structure of root-associated fungal community of V. carlesii, and two secondary forest types were similar in root-associated fungal community and were closer to that of the old growth forest; (3) Plant community composition, edaphic parameters, and geographic factors significantly affected root-associated fungal communities of V. carlesii. These results may be helpful in better understanding the maintenance mechanisms of fungal diversity associated with hair roots of ERM plants under human disturbances. PMID:26928608

A Multipronged, Adaptive Approach for the Recruitment of Diverse Community-Residing Elders with Memory Impairment: The MIND at Home Experience.

PubMed

Samus, Quincy M; Amjad, Halima; Johnston, Deirdre; Black, Betty S; Bartels, Stephen J; Lyketsos, Constantine G

2015-07-01

To provide a critical review of a multipronged recruitment approach used to identify, recruit, and enroll a diverse community-based sample of persons with memory disorders into an 18-month randomized, controlled dementia care coordination trial. Descriptive analysis of a recruitment approach comprised five strategies: community liaison ("gatekeepers") method, letters sent from trusted community organizations, display and distribution of study materials in the community, research registries, and general community outreach and engagement activities. Participants were 55 community organizations and 63 staff of community organizations in Baltimore, Maryland. Participant referral sources, eligibility, enrollment status, demographics, and loss to follow-up were tracked in a relational access database. In total, 1,275 referrals were received and 303 socioeconomically, cognitively, and racially diverse community-dwelling persons with cognitive disorders were enrolled. Most referrals came from letters sent from community organizations directly to clients on the study's behalf (39%) and referrals from community liaison organizations (29%). African American/black enrollees were most likely to come from community liaison organizations. A multipronged, adaptive approach led to the successful recruitment of diverse community-residing elders with memory impairment for an intervention trial. Key factors for success included using a range of evidence-supported outreach strategies, forming key strategic community partnerships, seeking regular stakeholder input through all research phases, and obtaining "buy-in" from community stakeholders by aligning study objectives with perceived unmet community needs. Copyright © 2015 American Association for Geriatric Psychiatry. Published by Elsevier Inc. All rights reserved.

Biological Characterization of Microenvironments in a Hypersaline Cold Spring Mars Analog

PubMed Central

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

2017-01-01

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

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

PubMed

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

2017-01-01

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

Global Diversity of Desert Hypolithic Cyanobacteria.

PubMed

Lacap-Bugler, Donnabella C; Lee, Kevin K; Archer, Stephen; Gillman, Len N; Lau, Maggie C Y; Leuzinger, Sebastian; Lee, Charles K; Maki, Teruya; McKay, Christopher P; Perrott, John K; de Los Rios-Murillo, Asunción; Warren-Rhodes, Kimberley A; Hopkins, David W; Pointing, Stephen B

2017-01-01

Global patterns in diversity were estimated for cyanobacteria-dominated hypolithic communities that colonize ventral surfaces of quartz stones and are common in desert environments. A total of 64 hypolithic communities were recovered from deserts on every continent plus a tropical moisture sufficient location. Community diversity was estimated using a combined t-RFLP fingerprinting and high throughput sequencing approach. The t-RFLP analysis revealed desert communities were different from the single non-desert location. A striking pattern also emerged where Antarctic desert communities were clearly distinct from all other deserts. Some overlap in community similarity occurred for hot, cold and tundra deserts. A further observation was that the producer-consumer ratio displayed a significant negative correlation with growing season, such that shorter growing seasons supported communities with greater abundance of producers, and this pattern was independent of macroclimate. High-throughput sequencing of 16S rRNA and nif H genes from four representative samples validated the t-RFLP study and revealed patterns of taxonomic and putative diazotrophic diversity for desert communities from the Taklimakan Desert, Tibetan Plateau, Canadian Arctic and Antarctic. All communities were dominated by cyanobacteria and among these 21 taxa were potentially endemic to any given desert location. Some others occurred in all but the most extreme hot and polar deserts suggesting they were relatively less well adapted to environmental stress. The t-RFLP and sequencing data revealed the two most abundant cyanobacterial taxa were Phormidium in Antarctic and Tibetan deserts and Chroococcidiopsis in hot and cold deserts. The Arctic tundra displayed a more heterogenous cyanobacterial assemblage and this was attributed to the maritime-influenced sampling location. The most abundant heterotrophic taxa were ubiquitous among samples and belonged to the Acidobacteria, Actinobacteria, Bacteroidetes, and Proteobacteria. Sequencing using nitrogenase gene-specific primers revealed all putative diazotrophs were Proteobacteria of the orders Burkholderiales, Rhizobiales, and Rhodospirillales. We envisage cyanobacterial carbon input to the system is accompanied by nitrogen fixation largely from non-cyanobacterial taxa. Overall the results indicate desert hypoliths worldwide are dominated by cyanobacteria and that growing season is a useful predictor of their abundance. Differences in cyanobacterial taxa encountered may reflect their adaptation to different moisture availability regimes in polar and non-polar deserts.

Ammonia-Oxidizing Archaea Show More Distinct Biogeographic Distribution Patterns than Ammonia-Oxidizing Bacteria across the Black Soil Zone of Northeast China.

PubMed

Liu, Junjie; Yu, Zhenhua; Yao, Qin; Sui, Yueyu; Shi, Yu; Chu, Haiyan; Tang, Caixian; Franks, Ashley E; Jin, Jian; Liu, Xiaobing; Wang, Guanghua

2018-01-01

Black soils (Mollisols) of northeast China are highly productive and agriculturally important for food production. Ammonia-oxidizing microbes play an important role in N cycling in the black soils. However, the information related to the composition and distribution of ammonia-oxidizing microbes in the black soils has not yet been addressed. In this study, we used the amoA gene to quantify the abundance and community composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) across the black soil zone. The amoA abundance of AOA was remarkably larger than that of AOB, with ratios of AOA/AOB in the range from 3.1 to 91.0 across all soil samples. The abundance of AOA amoA was positively correlated with total soil C content ( p < 0.001) but not with soil pH ( p > 0.05). In contrast, the abundance of AOB amoA positively correlated with soil pH ( p = 0.009) but not with total soil C. Alpha diversity of AOA did not correlate with any soil parameter, however, alpha diversity of AOB was affected by multiple soil factors, such as soil pH, total P, N, and C, available K content, and soil water content. Canonical correspondence analysis indicated that the AOA community was mainly affected by the sampling latitude, followed by soil pH, total P and C; while the AOB community was mainly determined by soil pH, as well as total P, C and N, water content, and sampling latitude, which highlighted that the AOA community was more geographically distributed in the black soil zone of northeast China than AOB community. In addition, the pairwise analyses showed that the potential nitrification rate (PNR) was not correlated with alpha diversity but weakly positively with the abundance of the AOA community ( p = 0.048), whereas PNR significantly correlated positively with the richness ( p = 0.003), diversity ( p = 0.001) and abundance ( p < 0.001) of the AOB community, which suggested that AOB community might make a greater contribution to nitrification than AOA community in the black soils when ammonium is readily available.

Ammonia-Oxidizing Archaea Show More Distinct Biogeographic Distribution Patterns than Ammonia-Oxidizing Bacteria across the Black Soil Zone of Northeast China

PubMed Central

Liu, Junjie; Yu, Zhenhua; Yao, Qin; Sui, Yueyu; Shi, Yu; Chu, Haiyan; Tang, Caixian; Franks, Ashley E.; Jin, Jian; Liu, Xiaobing; Wang, Guanghua

2018-01-01

Black soils (Mollisols) of northeast China are highly productive and agriculturally important for food production. Ammonia-oxidizing microbes play an important role in N cycling in the black soils. However, the information related to the composition and distribution of ammonia-oxidizing microbes in the black soils has not yet been addressed. In this study, we used the amoA gene to quantify the abundance and community composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) across the black soil zone. The amoA abundance of AOA was remarkably larger than that of AOB, with ratios of AOA/AOB in the range from 3.1 to 91.0 across all soil samples. The abundance of AOA amoA was positively correlated with total soil C content (p < 0.001) but not with soil pH (p > 0.05). In contrast, the abundance of AOB amoA positively correlated with soil pH (p = 0.009) but not with total soil C. Alpha diversity of AOA did not correlate with any soil parameter, however, alpha diversity of AOB was affected by multiple soil factors, such as soil pH, total P, N, and C, available K content, and soil water content. Canonical correspondence analysis indicated that the AOA community was mainly affected by the sampling latitude, followed by soil pH, total P and C; while the AOB community was mainly determined by soil pH, as well as total P, C and N, water content, and sampling latitude, which highlighted that the AOA community was more geographically distributed in the black soil zone of northeast China than AOB community. In addition, the pairwise analyses showed that the potential nitrification rate (PNR) was not correlated with alpha diversity but weakly positively with the abundance of the AOA community (p = 0.048), whereas PNR significantly correlated positively with the richness (p = 0.003), diversity (p = 0.001) and abundance (p < 0.001) of the AOB community, which suggested that AOB community might make a greater contribution to nitrification than AOA community in the black soils when ammonium is readily available. PMID:29497404

Global Diversity of Desert Hypolithic Cyanobacteria

PubMed Central

Lacap-Bugler, Donnabella C.; Lee, Kevin K.; Archer, Stephen; Gillman, Len N.; Lau, Maggie C.Y.; Leuzinger, Sebastian; Lee, Charles K.; Maki, Teruya; McKay, Christopher P.; Perrott, John K.; de los Rios-Murillo, Asunción; Warren-Rhodes, Kimberley A.; Hopkins, David W.; Pointing, Stephen B.

2017-01-01

Global patterns in diversity were estimated for cyanobacteria-dominated hypolithic communities that colonize ventral surfaces of quartz stones and are common in desert environments. A total of 64 hypolithic communities were recovered from deserts on every continent plus a tropical moisture sufficient location. Community diversity was estimated using a combined t-RFLP fingerprinting and high throughput sequencing approach. The t-RFLP analysis revealed desert communities were different from the single non-desert location. A striking pattern also emerged where Antarctic desert communities were clearly distinct from all other deserts. Some overlap in community similarity occurred for hot, cold and tundra deserts. A further observation was that the producer-consumer ratio displayed a significant negative correlation with growing season, such that shorter growing seasons supported communities with greater abundance of producers, and this pattern was independent of macroclimate. High-throughput sequencing of 16S rRNA and nifH genes from four representative samples validated the t-RFLP study and revealed patterns of taxonomic and putative diazotrophic diversity for desert communities from the Taklimakan Desert, Tibetan Plateau, Canadian Arctic and Antarctic. All communities were dominated by cyanobacteria and among these 21 taxa were potentially endemic to any given desert location. Some others occurred in all but the most extreme hot and polar deserts suggesting they were relatively less well adapted to environmental stress. The t-RFLP and sequencing data revealed the two most abundant cyanobacterial taxa were Phormidium in Antarctic and Tibetan deserts and Chroococcidiopsis in hot and cold deserts. The Arctic tundra displayed a more heterogenous cyanobacterial assemblage and this was attributed to the maritime-influenced sampling location. The most abundant heterotrophic taxa were ubiquitous among samples and belonged to the Acidobacteria, Actinobacteria, Bacteroidetes, and Proteobacteria. Sequencing using nitrogenase gene-specific primers revealed all putative diazotrophs were Proteobacteria of the orders Burkholderiales, Rhizobiales, and Rhodospirillales. We envisage cyanobacterial carbon input to the system is accompanied by nitrogen fixation largely from non-cyanobacterial taxa. Overall the results indicate desert hypoliths worldwide are dominated by cyanobacteria and that growing season is a useful predictor of their abundance. Differences in cyanobacterial taxa encountered may reflect their adaptation to different moisture availability regimes in polar and non-polar deserts. PMID:28559886

A six-year grazing exclusion changed plant species diversity of a Stipa breviflora desert steppe community, northern China.

PubMed

Wang, Xing; Yang, Xinguo; Wang, Lei; Chen, Lin; Song, Naiping; Gu, Junlong; Xue, Yi

2018-01-01

Excluding grazers is one of most efficient ways to restore degraded grasslands in desert-steppe communities, but may negatively affect the recovery of plant species diversity. However, diversity differences between grazed and fenced grasslands in desert-steppe are poorly known. In a Stipa breviflora desert steppe community in Northern China, we established six plots to examine spatial patterns of plant species diversity under grazed and fenced conditions, respectively. We addressed three aspects of species diversity: (1) The logistic, exponential and power models were used to describe the species-area curve (SAR). Species richness, abundance and Shannon diversity values change differently with increasing sampling areas inside and outside of the fence. The best fitted model for SAR was the logistic model. Excluding grazers had a significant impact on the shape of SAR. (2) Variograms was applied to examine the spatial characteristics of plant species diversity. We found strong spatial autocorrelations in the diversity variables both inside and outside the fence. After grazing exclusion, the spatial heterogeneity decreased in species richness, increased in abundance and did not change in Shannon diversity. (3) We used variance partitioning to determine the relative contributions of spatial and environmental factors to plant species diversity patterns. Environmental factors explained the largest proportion of variation in species diversity, while spatial factors contributed little. Our results suggest that grazing enclosures decreased species diversity patterns and the spatial pattern of the S. breviflora desert steppe community was predictable.

A six-year grazing exclusion changed plant species diversity of a Stipa breviflora desert steppe community, northern China

PubMed Central

Wang, Xing; Yang, Xinguo; Wang, Lei; Chen, Lin; Gu, Junlong; Xue, Yi

2018-01-01

Excluding grazers is one of most efficient ways to restore degraded grasslands in desert-steppe communities, but may negatively affect the recovery of plant species diversity. However, diversity differences between grazed and fenced grasslands in desert-steppe are poorly known. In a Stipa breviflora desert steppe community in Northern China, we established six plots to examine spatial patterns of plant species diversity under grazed and fenced conditions, respectively. We addressed three aspects of species diversity: (1) The logistic, exponential and power models were used to describe the species-area curve (SAR). Species richness, abundance and Shannon diversity values change differently with increasing sampling areas inside and outside of the fence. The best fitted model for SAR was the logistic model. Excluding grazers had a significant impact on the shape of SAR. (2) Variograms was applied to examine the spatial characteristics of plant species diversity. We found strong spatial autocorrelations in the diversity variables both inside and outside the fence. After grazing exclusion, the spatial heterogeneity decreased in species richness, increased in abundance and did not change in Shannon diversity. (3) We used variance partitioning to determine the relative contributions of spatial and environmental factors to plant species diversity patterns. Environmental factors explained the largest proportion of variation in species diversity, while spatial factors contributed little. Our results suggest that grazing enclosures decreased species diversity patterns and the spatial pattern of the S. breviflora desert steppe community was predictable. PMID:29456890

The community distribution of bacteria and fungi on ancient wall paintings of the Mogao Grottoes

PubMed Central

Ma, Yantian; Zhang, He; Du, Ye; Tian, Tian; Xiang, Ting; Liu, Xiande; Wu, Fasi; An, Lizhe; Wang, Wanfu; Gu, Ji-Dong; Feng, Huyuan

2015-01-01

In this study, we compared the microbial communities colonising ancient cave wall paintings of the Mogao Grottoes exhibiting signs of biodeterioration. Ten samples were collected from five different caves built during different time periods and analysed using culture-independent and culture-dependent methods. The clone library results revealed high microbial diversity, including the bacterial groups Firmicutes, Proteobacteria, Actinobacteria, Acidobacteria, Cyanobacteria, Bacteroidetes, Gemmatimonadetes, Planctomycetes, and Chloroflexi and the fungal groups Euascomycetes, Dothideomycetes, Eurotiomycetes, Sordariomycetes, Saccharomycetes, Plectomycetes, Pezizomycetes, Zygomycota, and Basidiomycota. The bacterial community structures differed among the samples, with no consistent temporal or spatial trends. However, the fungal community diversity index correlated with the building time of the caves independent of environmental factors (e.g., temperature or relative humidity). The enrichment cultures revealed that many culturable strains were highly resistant to various stresses and thus may be responsible for the damage to cave paintings in the Mogao Grottoes. PMID:25583346

The community distribution of bacteria and fungi on ancient wall paintings of the Mogao Grottoes.

PubMed

Ma, Yantian; Zhang, He; Du, Ye; Tian, Tian; Xiang, Ting; Liu, Xiande; Wu, Fasi; An, Lizhe; Wang, Wanfu; Gu, Ji-Dong; Feng, Huyuan

2015-01-13

In this study, we compared the microbial communities colonising ancient cave wall paintings of the Mogao Grottoes exhibiting signs of biodeterioration. Ten samples were collected from five different caves built during different time periods and analysed using culture-independent and culture-dependent methods. The clone library results revealed high microbial diversity, including the bacterial groups Firmicutes, Proteobacteria, Actinobacteria, Acidobacteria, Cyanobacteria, Bacteroidetes, Gemmatimonadetes, Planctomycetes, and Chloroflexi and the fungal groups Euascomycetes, Dothideomycetes, Eurotiomycetes, Sordariomycetes, Saccharomycetes, Plectomycetes, Pezizomycetes, Zygomycota, and Basidiomycota. The bacterial community structures differed among the samples, with no consistent temporal or spatial trends. However, the fungal community diversity index correlated with the building time of the caves independent of environmental factors (e.g., temperature or relative humidity). The enrichment cultures revealed that many culturable strains were highly resistant to various stresses and thus may be responsible for the damage to cave paintings in the Mogao Grottoes.

Bacterial community profile of contaminated soils in a typical antimony mining site.

PubMed

Wang, Ningning; Zhang, Suhuan; He, Mengchang

2018-01-01

The soils around the world's largest antimony mine have been contaminated by high concentrations of Sb and As, which might influence microbial diversity in the surrounding soils. The ecological effects of bioavailable Sb and As on the composition and diversity of microbial community in soils remain unknown. In this study, the relative abundance, taxonomic diversity and composition of bacterial community in soils from a typical Sb mine area, and the relationship between the bacterial community and bioavailable concentrations as well as environmental factors have been investigated comprehensively using high-throughput sequencing (HTS) and diffusive gradients in thin films (DGT). The results indicated that Proteobacteria, Acidobacteria, Chloroflexi, Bacteroidetes, Actinobacteria, Gemmatimonadetes, and Cyanobacteria were the dominant bacterial populations at phylum level in all soil samples, accounting for more than 80% of the bacteria sequenced. The abundance and diversity of bacterial community vary along a metal contamination gradient. Redundancy discriminate analysis (RDA) revealed that 74.74% of bacterial community variation in the contaminated soils was explained by six environmental factors (pH, Sb DGT , As DGT , potential ecological risk index (RI), TC, TN), among which pH, Sb DGT , and As DGT were dominant factors influencing the composition and diversity of bacteria. This study contributes to our understanding of microbial diversity in a local ecosystem and introduces the option of studying bioavailable Sb and As using DGT.

Spatial variability of particle-attached and free-living bacterial diversity in surface waters from the Mackenzie River to the Beaufort Sea (Canadian Arctic)

NASA Astrophysics Data System (ADS)

Ortega-Retuerta, E.; Joux, F.; Jeffrey, W. H.; Ghiglione, J.-F.

2012-12-01

We explored the patterns of total and active bacterial community structure in a gradient covering surface waters from the Mackenzie River to the coastal Beaufort Sea, Canadian Arctic Ocean, with a particular focus on free-living vs. particle-attached communities. Capillary electrophoresis-single strand conformation polymorphism (CE-SSCP) showed significant differences when comparing river, coast and open sea bacterial community structures. In contrast to the river and coastal waters, total (16S rDNA-based) and active (16S rRNA-based) communities in the open sea samples were not significantly different, suggesting that most present bacterial groups were equally active in this area. Additionally, we observed significant differences between particle-attached (PA) and free-living (FL) bacterial communities in the open sea, but similar structure in the two fractions for coastal and river samples. Direct multivariate statistical analyses showed that total community structure was mainly driven by salinity (proxy of DOC and CDOM), suspended particles, amino acids and chlorophyll a. 16S rRNA genes pyrosequencing of selected samples confirmed these significant differences from river to sea and also between PA and FL fractions only in open sea samples, and PA samples generally showed higher diversity (Shannon, Simpson and Chao indices) than FL samples. At the class level, Opitutae was most abundant in the PA fraction of the sea sample, followed by Flavobacteria and Gammaproteobacteria, while the FL sea sample was dominated by Alphaproteobacteria. Finally, the coast and river samples, both PA and FL fractions, were dominated by Betaproteobacteria, Alphaproteobacteria and Actinobacteria. These results highlight the coexistence of particle specialists and generalists and the role of particle quality in structuring bacterial communities in the area. These results may also serve as a~basis to predict further changes in bacterial communities should climate change lead to further increases in river discharge and related particles load.

Ecological effects of roads on the plant diversity of coastal wetland in the Yellow River Delta.

PubMed

Li, Yunzhao; Yu, Junbao; Ning, Kai; Du, Siyao; Han, Guangxuan; Qu, Fanzhu; Wang, Guangmei; Fu, Yuqin; Zhan, Chao

2014-01-01

The 26 sample sites in 7 study plots adjacent to asphalt road and earth road in coastal wetland in the Yellow River Delta were selected to quantify plant diversity using quadrat sampling method in plant bloom phase of July and August 2012. The indice of β T and Jaccard's coefficient were applied to evaluate the species diversity. The results showed that the plant diversities and alien plants were high in the range of 0-20 m to the road verge. There were more exotics and halophytes in plots of asphalt roadside than that of earth roadside. However, proportion of halophytes in habitats of asphalt roadsides was lower than that of earth roadside. By comparing β-diversity, there were more common species in the asphalt roadsides than that in the earth roadsides. The similarity of plant communities in studied plots of asphalt roadsides and earth roadsides increased with increasing the distance to road verge. The effect range of roads for plant diversity in study region was about 20 m to road verge. Our results indicate that the construction and maintenance of roads in wetland could increase the plant species diversities of communities and risk of alien species invasion.

Microfungal oasis in an oligotrophic desert: diversity patterns and community structure in three freshwater systems of Cuatro Ciénegas, Mexico

PubMed Central

Gasca-Pineda, Jaime; Rosique-Gil, Edmundo; Eguiarte, Luis E.; Espinosa-Asuar, Laura

2016-01-01

The Cuatro Ciénegas Basin (CCB) comprises several oligotrophic aquatic ecosystems limited by phosphorus. These aquatic systems are dominated by a high prokaryotic diversity, shaped by the stress of low nutrient supplies and interspecific competition. Although fungi constitute a diverse and important component of microbial diversity, the microfungal diversity in the CCB remains to be unveiled. With the aim to explore microfungal diversity and ecological patterns in this area, we present the first investigation analyzing cultivable taxa from sediment and water, as well as lignocellulolytic taxa obtained from incubated submerged plant debris, and wood panels in three contrasting freshwater systems in the CCB: Churince, Becerra and Pozas Rojas. We chose a culture-based approach to analyze sediment and water samples in order to obtain fungal cultures, providing opportunities for a posteriori studies, and the possibility of ex situ preservation of the diversity. We evaluated sequence data from the nuclear ribosomal internal transcribed spacer including the 5.8 rDNA region for 126 isolates, revealing 37 OTUs. These OTUs were phylogenetically affiliated to several genera in the fungal phyla: Zygomycota, Basidiomycota, and Ascomycota. We recorded two OTUs with saline affinity, agreeing with previous findings on the prokaryotic communities with ancestral marine resemblances. All the studied systems showed moderate diversity levels, however discrepancies among the diversity indexes were observed, due to the occurrence of abundant taxa in the samples. Our results indicated that lignocellulolytic microfungal communities are dominated by transient fungal taxa, as resident species were not recorded perhaps as a result of the long-term strong competition with the highly adapted prokaryotic community. Moreover, the obtained microfungal taxa occurred mostly on the resident plant debris, rather than submerged wood panels, perhaps as a result of the high adaptation to specific environmental conditions. In conclusion, the CCB possess a moderate taxonomical diversity compared to other arid environments, probably as a result of high selective pressures. Nonetheless, due to high spatial and temporal heterogeneity, the functional fungal diversity was considerable as predicted by the intermediate disturbance hypothesis. Decisively, the assessment of microfungal diversity freshwater systems is relevant, since this ecological group of microorganisms represents an important indicator of trophic complexity and biotic interactions among microbial communities, having important implications for understanding eukaryotic survival at the oligotrophic limit for life. PMID:27280070

Filter forensics: microbiota recovery from residential HVAC filters.

PubMed

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

2018-01-30

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

A phylogenetic perspective on species diversity, β-diversity and biogeography for the microbial world.

PubMed

Barberán, Albert; Casamayor, Emilio O

2014-12-01

There is an increasing interest to combine phylogenetic data with distributional and ecological records to assess how natural communities arrange under an evolutionary perspective. In the microbial world, there is also a need to go beyond the problematic species definition to deeply explore ecological patterns using genetic data. We explored links between evolution/phylogeny and community ecology using bacterial 16S rRNA gene information from a high-altitude lakes district data set. We described phylogenetic community composition, spatial distribution, and β-diversity and biogeographical patterns applying evolutionary relatedness without relying on any particular operational taxonomic unit definition. High-altitude lakes districts usually contain a large mosaic of highly diverse small water bodies and conform a fine biogeographical model of spatially close but environmentally heterogeneous ecosystems. We sampled 18 lakes in the Pyrenees with a selection criteria focused on capturing the maximum environmental variation within the smallest geographical area. The results showed highly diverse communities nonrandomly distributed with phylogenetic β-diversity patterns mainly shaped by the environment and not by the spatial distance. Community similarity based on both bacterial taxonomic composition and phylogenetic β-diversity shared similar patterns and was primarily structured by similar environmental drivers. We observed a positive relationship between lake area and phylogenetic diversity with a slope consistent with highly dispersive planktonic organisms. The phylogenetic approach incorporated patterns of common ancestry into bacterial community analysis and emerged as a very convenient analytical tool for direct inter- and intrabiome biodiversity comparisons and sorting out microbial habitats with potential application in conservation studies. © 2014 John Wiley & Sons Ltd.

Species diversity of culturable endophytic fungi from Brazilian mangrove forests.

PubMed

de Souza Sebastianes, Fernanda Luiza; Romão-Dumaresq, Aline Silva; Lacava, Paulo Teixeira; Harakava, Ricardo; Azevedo, João Lúcio; de Melo, Itamar Soares; Pizzirani-Kleiner, Aline Aparecida

2013-08-01

This study aimed to perform a comparative analysis of the diversity of endophytic fungal communities isolated from the leaves and branches of Rhizophora mangle, Avicennia schaueriana and Laguncularia racemosa trees inhabiting two mangroves in the state of São Paulo, Brazil [Cananeia and Bertioga (oil spill-affected and unaffected)] in the summer and winter. Three hundred and forty-three fungi were identified by sequencing the ITS1-5.8S-ITS2 region of rDNA. Differences were observed in the frequencies of fungi isolated from the leaves and branches of these three different plant species sampled from the Bertioga oil spill-affected and the oil-unaffected mangrove sites in the summer and winter; these differences indicate a potential impact on fungal diversity in the study area due to the oil spill. The molecular identification of the fungi showed that the fungal community associated with these mangroves is composed of at least 34 different genera, the most frequent of which were Diaporthe, Colletotrichum, Fusarium, Trichoderma and Xylaria. The Shannon and the Chao1 indices [H'(95 %) = 4.00, H'(97 %) = 4.22, Chao1(95 %) = 204 and Chao1(97 %) = 603] indicated that the mangrove fungal community possesses a vast diversity and richness of endophytic fungi. The data generated in this study revealed a large reservoir of fungal genetic diversity inhabiting these Brazilian mangrove forests and highlighted substantial differences between the fungal communities associated with distinct plant tissues, plant species, impacted sites and sampling seasons.

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

PubMed

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

2016-09-01

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

Fungal communities from the calcareous deep-sea sediments in the Southwest India Ridge revealed by Illumina sequencing technology.

PubMed

Zhang, Likui; Kang, Manyu; Huang, Yangchao; Yang, Lixiang

2016-05-01

The diversity and ecological significance of bacteria and archaea in deep-sea environments have been thoroughly investigated, but eukaryotic microorganisms in these areas, such as fungi, are poorly understood. To elucidate fungal diversity in calcareous deep-sea sediments in the Southwest India Ridge (SWIR), the internal transcribed spacer (ITS) regions of rRNA genes from two sediment metagenomic DNA samples were amplified and sequenced using the Illumina sequencing platform. The results revealed that 58-63 % and 36-42 % of the ITS sequences (97 % similarity) belonged to Basidiomycota and Ascomycota, respectively. These findings suggest that Basidiomycota and Ascomycota are the predominant fungal phyla in the two samples. We also found that Agaricomycetes, Leotiomycetes, and Pezizomycetes were the major fungal classes in the two samples. At the species level, Thelephoraceae sp. and Phialocephala fortinii were major fungal species in the two samples. Despite the low relative abundance, unidentified fungal sequences were also observed in the two samples. Furthermore, we found that there were slight differences in fungal diversity between the two sediment samples, although both were collected from the SWIR. Thus, our results demonstrate that calcareous deep-sea sediments in the SWIR harbor diverse fungi, which augment the fungal groups in deep-sea sediments. This is the first report of fungal communities in calcareous deep-sea sediments in the SWIR revealed by Illumina sequencing.

Harnessing Reddit to Understand the Written-Communication Challenges Experienced by Individuals With Mental Health Disorders: Analysis of Texts From Mental Health Communities.

PubMed

Park, Albert; Conway, Mike

2018-04-10

Mental disorders such as depression, bipolar disorder, and schizophrenia are common, incapacitating, and have the potential to be fatal. Despite the prevalence and gravity of mental disorders, our knowledge concerning everyday challenges associated with them is relatively limited. One of the most studied deficits related to everyday challenges is language impairment, yet we do not know how mental disorders can impact common forms of written communication, for example, social media. The aims of this study were to investigate written communication challenges manifest in online mental health communities focusing on depression, bipolar disorder, and schizophrenia, as well as the impact of participating in these online mental health communities on written communication. As the control, we selected three online health communities focusing on positive emotion, exercising, and weight management. We examined lexical diversity and readability, both important features for measuring the quality of writing. We used four well-established readability metrics that consider word frequencies and syntactic complexity to measure writers' written communication ability. We then measured the lexical diversity by calculating the percentage of unique words in posts. To compare lexical diversity and readability among communities, we first applied pairwise independent sample t tests, followed by P value adjustments using the prespecified Hommel procedure to adjust for multiple comparison. To measure the changes, we applied linear least squares regression to the readability and lexical diversity scores against the interaction sequence for each member, followed by pairwise independent sample t tests and P value adjustments. Given the large sample of members, we also report effect sizes and 95% CIs for the pairwise comparisons. On average, members of depression, bipolar disorder, and schizophrenia communities showed indications of difficulty expressing their ideas compared with three other online health communities. Our results also suggest that participating in these platforms has the potential to improve members' written communication. For example, members of all three mental health communities showed statistically significant improvement in both lexical diversity and readability compared with members of the OHC focusing on positive emotion. We provide new insights into the written communication challenges faced by individuals suffering from depression, bipolar disorder, and schizophrenia. A comparison with three other online health communities suggests that written communication in mental health communities is significantly more difficult to read, while also consisting of a significantly less diverse lexicon. We contribute practical suggestions for utilizing our findings in Web-based communication settings to enhance members' communicative experience. We consider these findings to be an important step toward understanding and addressing everyday written communication challenges among individuals suffering from mental disorders. ©Albert Park, Mike Conway. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 10.04.2018.

Atmospheric Deposition-Carried Zn and Cd from a Zinc Smelter and Their Effects on Soil Microflora as Revealed by 16S rDNA

PubMed Central

Shen, Feng; Li, Yanxia; Zhang, Min; Awasthi, Mukesh Kumar; Ali, Amjad; Li, Ronghua; Wang, Quan; Zhang, Zengqiang

2016-01-01

In this study, we investigated the influence of heavy metals (HM) on total soil bacterial population and its diversity pattern from 10 km distance of a Zinc smelter in Feng County, Qinling Mountain, China. We characterized and identified the bacterial community in a HM polluted soil using 16S rDNA technology. Out results indicated that the maximum soil HM concentration and the minimum bacterial population were observed in S2 soil, whereas bacterial diversity raised with the sampling distance increased. The bacterial communities were dominated by the phyla Proteobacteria, Acidobacteria and Actinobacteria in cornfield soils, except Fimicutes phylum which dominated in hilly area soil. The soil CEC, humic acid (HA)/fulvic acid (FA) and microbial OTUs increased with the sampling distance increased. Shewanella, Halomonas and Escherichia genera were highly tolerant to HM stress in both cultivated and non-cultivated soil. Finally, we found a consistent correlation of bacterial diversity with total HM and SOM along the sampling distance surrounding the zinc smelter, which could provide a new insight into the bacterial community-assisted and phytoremediation of HM contaminated soils. PMID:27958371

Plant Rhizosphere Selection of Plasmodiophorid Lineages from Bulk Soil: The Importance of “Hidden” Diversity

PubMed Central

Bass, David; van der Gast, Christopher; Thomson, Serena; Neuhauser, Sigrid; Hilton, Sally; Bending, Gary D.

2018-01-01

Microbial communities closely associated with the rhizosphere can have strong positive and negative impacts on plant health and growth. We used a group-specific amplicon approach to investigate local scale drivers in the diversity and distribution of plasmodiophorids in rhizosphere/root and bulk soil samples from oilseed rape (OSR) and wheat agri-systems. Plasmodiophorids are plant- and stramenopile-associated protists including well known plant pathogens as well as symptomless endobiotic species. We detected 28 plasmodiophorid lineages (OTUs), many of them novel, and showed that plasmodiophorid communities were highly dissimilar and significantly divergent between wheat and OSR rhizospheres and between rhizosphere and bulk soil samples. Bulk soil communities were not significantly different between OSR and wheat systems. Wheat and OSR rhizospheres selected for different plasmodiophorid lineages. An OTU corresponding to Spongospora nasturtii was positively selected in the OSR rhizosphere, as were two genetically distinct OTUs. Two novel lineages related to Sorosphaerula veronicae were significantly associated with wheat rhizosphere samples, indicating unknown plant-protist relationships. We show that group-targeted eDNA approaches to microbial symbiont-host ecology reveal significant novel diversity and enable inference of differential activity and potential interactions between sequence types, as well as their presence. PMID:29503632

Atmospheric Deposition-Carried Zn and Cd from a Zinc Smelter and Their Effects on Soil Microflora as Revealed by 16S rDNA

NASA Astrophysics Data System (ADS)

Shen, Feng; Li, Yanxia; Zhang, Min; Awasthi, Mukesh Kumar; Ali, Amjad; Li, Ronghua; Wang, Quan; Zhang, Zengqiang

2016-12-01

In this study, we investigated the influence of heavy metals (HM) on total soil bacterial population and its diversity pattern from 10 km distance of a Zinc smelter in Feng County, Qinling Mountain, China. We characterized and identified the bacterial community in a HM polluted soil using 16S rDNA technology. Out results indicated that the maximum soil HM concentration and the minimum bacterial population were observed in S2 soil, whereas bacterial diversity raised with the sampling distance increased. The bacterial communities were dominated by the phyla Proteobacteria, Acidobacteria and Actinobacteria in cornfield soils, except Fimicutes phylum which dominated in hilly area soil. The soil CEC, humic acid (HA)/fulvic acid (FA) and microbial OTUs increased with the sampling distance increased. Shewanella, Halomonas and Escherichia genera were highly tolerant to HM stress in both cultivated and non-cultivated soil. Finally, we found a consistent correlation of bacterial diversity with total HM and SOM along the sampling distance surrounding the zinc smelter, which could provide a new insight into the bacterial community-assisted and phytoremediation of HM contaminated soils.

Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents.

PubMed

Blaser, Martin J; Dominguez-Bello, Maria G; Contreras, Monica; Magris, Magda; Hidalgo, Glida; Estrada, Isidoro; Gao, Zhan; Clemente, Jose C; Costello, Elizabeth K; Knight, Rob

2013-01-01

The human skin harbors complex bacterial communities. Prior studies showing high inter-individual variation focused on subjects from developed countries. We therefore compared cutaneous bacterial communities of Amerindians in the Venezuelan Amazon with subjects in the United States. Forearm skin specimens were studied from healthy Amerindians in Platanillal village in Amazonas State, and from healthy persons in New York and Colorado. All skin sampling used similar swab/buffer techniques. Multiplexed V2-targeted 16S rRNA gene pyrosequencing yielded high quality sequences from 112 samples. The results show 20 phyla, with three (Proteobacteria, Firmicutes, Actinobacteria) predominating. US residents and Venezuelan Amerindians had significantly different forearm skin bacterial community compositions, with United States dominated by Propionibacterium. Among the Amerindians, there was a deep split based on bacterial community membership, with 30 and 42 samples, respectively, falling into each of the two groups, not associated with age, gender, or body mass index. One Amerindian group had diversity similar to the United States, but was dominated by Staphylococcus rather than Propionibacterium. The other Amerindian group was significantly more diverse and even than the US or the other Amerindian group, and featured a broad range of Proteobacteria. The results provide evidence that ethnicity, lifestyle and/or geography are associated with the structure of human cutaneous bacterial communities.

In God We Trust: Qualitative Findings on Finances, Family, and Faith from a Diverse Sample of U.S. Families

ERIC Educational Resources Information Center

Marks, Loren D.; Dollahite, David C.; Baumgartner, Jennifer

2010-01-01

Employing qualitative interviews with a diverse national sample of 184 religious families (N = 445 individuals), we present an in-depth look at how participants (a) view and frame their faith-based financial giving, (b) how they contribute to and receive from their faith communities, and (c) how the blending of faith and finances influences their…

A non-invasive assessment of skin carotenoid status through reflection spectroscopy is a feasible, reliable and potentially valid measure of fruit and vegetable consumption in a diverse community sample

USDA-ARS?s Scientific Manuscript database

This study assessed the feasibility, reliability and validity of reflection spectroscopy (RS) to assess skin carotenoids in a racially diverse sample. Study 1 was a cross-sectional study of corner store customers (n= 479) in Eastern North Carolina USA who completed the National Cancer Institute Frui...

Can mangrove plantation enhance the functional diversity of macrobenthic community in polluted mangroves?

PubMed

Leung, Jonathan Y S; Cheung, Napo K M

2017-03-15

Mangrove plantation is widely applied to re-establish the plant community in degraded mangroves, but its effectiveness to restore the ecological functions of macrobenthic community remains poorly known, especially when pollution may overwhelm its potential positive effect. Here, we tested the effect of mangrove plantation on the ecological functions of macrobenthic community in a polluted mangrove by analyzing biological traits of macrobenthos and calculating functional diversity. Mangrove plantation was shown to enhance the functional diversity and restore the ecological functions of macrobenthic community, depending on seasonality. Given the polluted sediment, however, typical traits of opportunistic species (e.g. small and short-lived) prevailed in all habitats and sampling times. We conclude that mangrove plantation can help diversify the ecological functions of macrobenthic community, but its effectiveness is likely reduced by pollution. From the management perspective, therefore, pollution sources must be stringently regulated and mangrove plantation should be conducted to fully recover degraded mangroves. Copyright © 2017 Elsevier Ltd. All rights reserved.

Fire regime, not time-since-fire, affects soil fungal community diversity and composition in temperate grasslands.

PubMed

Egidi, Eleonora; McMullan-Fisher, Sapphire; Morgan, John W; May, Tom; Zeeman, Ben; Franks, Ashley E

2016-09-01

Frequent burning is commonly undertaken to maintain diversity in temperate grasslands of southern Australia. How burning affects below-ground fungal community diversity remains unknown. We show, using a fungal rDNA metabarcoding approach (Illumina MiSeq), that the fungal community composition was influenced by fire regime (frequency) but not time-since-fire. Fungal community composition was resilient to direct fire effects, most likely because grassland fires transfer little heat to the soil. Differences in the fungal community composition due to fire regime was likely due to associated changes that occur in vegetation with recurrent fire, via the break up of obligate symbiotic relationships. However, fire history only partially explains the observed dissimilarity in composition among the soil samples, suggesting a distinctiveness in composition in each grassland site. The importance of considering changes in soil microbe communities when managing vegetation with fire is highlighted. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

First Insights into the Viral Communities of the Deep-sea Anoxic Brines of the Red Sea.

PubMed

Antunes, André; Alam, Intikhab; Simões, Marta Filipa; Daniels, Camille; Ferreira, Ari J S; Siam, Rania; El-Dorry, Hamza; Bajic, Vladimir B

2015-10-01

The deep-sea brines of the Red Sea include some of the most extreme and unique environments on Earth. They combine high salinities with increases in temperature, heavy metals, hydrostatic pressure, and anoxic conditions, creating unique settings for thriving populations of novel extremophiles. Despite a recent increase of studies focusing on these unusual biotopes, their viral communities remain unexplored. The current survey explores four metagenomic datasets obtained from different brine-seawater interface samples, focusing specifically on the diversity of their viral communities. Data analysis confirmed that the particle-attached viral communities present in the brine-seawater interfaces were diverse and generally dominated by Caudovirales, yet appearing distinct from sample to sample. With a level of caution, we report the unexpected finding of Phycodnaviridae, which infects algae and plants, and trace amounts of insect-infecting Iridoviridae. Results from Kebrit Deep revealed stratification in the viral communities present in the interface: the upper-interface was enriched with viruses associated with typical marine bacteria, while the lower-interface was enriched with haloviruses and halophages. These results provide first insights into the unexplored viral communities present in deep-sea brines of the Red Sea, representing one of the first steps for ongoing and future sampling efforts and studies. Copyright © 2015 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

Reduction of Racial Disparities in Prostate Cancer

DTIC Science & Technology

2006-12-01

hyperplasia, interstitial cystitis/chronic pelvic pain, prostatitis, hypogonadism/androgen deficiency, erectile dysfunction , female sexual...socioeconomically diverse, community-based sample of adults aged 30–79 years in Boston, Massachusetts. This report gives estimates from the 2301 men in...survey is designed to estimate the prevalence of symptoms of urological disorders in a multi-ethnic, community-based sample of adults aged 30−79 years

Surface-water quality, Oneida Reservation and vicinity, Wisconsin, 1997-98

USGS Publications Warehouse

Schmidt, Morgan A.; Scudder, Barbara C.; Richards, Kevin D.

2000-01-01

Assessments of the benthic algal community provided relative results as did invertebrate community assessments. Shannon-Wiener diversity values for diatoms indicate that algal communities are under minor stress in four of five streams sampled and under moderate stress in Dutchman Creek. A pollution index based on the percentages of diatoms that are pollution sensitive and pollution tolerant revealed that pollution at Dutchman Creek likely is moderate; pollution at the other four sampled creeks is either minor or nonexistent in terms of effects on the diatom community.

Nearly a decade-long repeatable seasonal diversity patterns of bacterioplankton communities in the eutrophic Lake Donghu (Wuhan, China)

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

Yan, Qingyun; Stegen, James C.; Yu, Yuhe

Uncovering which environmental factors have the greatest influence on community diversity patterns and how ecological processes govern community turnover are key questions related to understanding community assembly mechanisms. Although we have good understanding of plant and animal community assembly, the mechanisms regulating diversity patterns of aquatic bacterial communities in lake ecosystems remains poorly understood. Here we present nearly a decade-long time-series study of bacterioplankton communities from the eutrophic Lake Donghu (Wuhan, China) using 16S rRNA gene amplicon sequencing. We found strong repeatable seasonal patterns for the overall community, common (detected in more than 50% samples) and dominant bacterial taxa (relativemore » abundance > 1%). Moreover, community composition tracked the seasonal temperature gradient, indicating that temperature is an important environmental factor controlling observed diversity patterns. Total phosphorus also contributed significantly to the seasonal shifts in bacterioplankton composition. However, any spatial pattern across the main lake areas was overwhelmed by temporal variability in this eutrophic lake system. Phylogenetic analysis further indicated that 75%-82% of community turnover was governed by homogeneous selection, suggesting that the bacterioplankton communities are mainly controlled by niche-based processes. However, dominant niches available within seasons might be occupied by similar combinations of bacterial taxa with modest dispersal rates throughout this lake system. This study gives us important insights into community assembly and seasonal turnover of lake bacterioplankton, it may be also useful to predict temporal patterns of other planktonic communities.« less

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

PubMed Central

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

2018-01-01

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

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

PubMed Central

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

2010-01-01

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

Herbicides induce change in metabolic and genetic diversity of bacterial community from a cold oligotrophic lake.

PubMed

Aguayo, P; González, C; Barra, R; Becerra, J; Martínez, M

2014-03-01

Pristine cold oligotrophic lakes show unique physical and chemical characteristics with permanent fluctuation in temperature and carbon source availability. Incorporation of organic toxic matters to these ecosystems could alter the bacterial community composition. Our goal was to assess the effects of simazine (Sz) and 2,4 dichlorophenoxyacetic acid (2,4-D) upon the metabolic and genetic diversity of the bacterial community in sediment samples from a pristine cold oligotrophic lake. Sediment samples were collected in winter and summer season, and microcosms were prepared using a ration 1:10 (sediments:water). The microcosms were supplemented with 0.1 mM 2,4-D or 0.5 mM Sz and incubated for 20 days at 10 °C. Metabolic diversity was evaluated by using the Biolog Ecoplate™ system and genetic diversity by 16S rDNA amplification followed by denaturing gradient gel electrophoresis analysis. Total bacterial counts and live/dead ratio were determined by epifluorescence microscopy. The control microcosms showed no significant differences (P > 0.05) in both metabolic and genetic diversity between summer and winter samples. On the other hand, the addition of 2,4-D or Sz to microcosms induces statistical significant differences (P < 0.05) in metabolic and genetic diversity showing the prevalence of Actinobacteria group which are usually not detected in the sediments of these non-contaminated lacustrine systems. The obtained results suggest that contaminations of cold pristine lakes with organic toxic compounds of anthropic origin alter their homeostasis by inhibiting specific susceptible bacterial groups. The concomitant increase of usually low representative bacterial groups modifies the bacterial composition commonly found in this pristine lake.

Pig Farmers' Homes Harbor More Diverse Airborne Bacterial Communities Than Pig Stables or Suburban Homes.

PubMed

Vestergaard, Ditte V; Holst, Gitte J; Basinas, Ioannis; Elholm, Grethe; Schlünssen, Vivi; Linneberg, Allan; Šantl-Temkiv, Tina; Finster, Kai; Sigsgaard, Torben; Marshall, Ian P G

2018-01-01

Airborne bacterial communities are subject to conditions ill-suited to microbial activity and growth. In spite of this, air is an important transfer medium for bacteria, with the bacteria in indoor air having potentially major consequences for the health of a building's occupants. A major example is the decreased diversity and altered composition of indoor airborne microbial communities as a proposed explanation for the increasing prevalence of asthma and allergies worldwide. Previous research has shown that living on a farm confers protection against development of asthma and allergies, with airborne bacteria suggested as playing a role in this protective effect. However, the composition of this beneficial microbial community has still not been identified. We sampled settled airborne dust using a passive dust sampler from Danish pig stables, associated farmers' homes, and from suburban homes (267 samples in total) and carried out quantitative PCR measurements of bacterial abundance and MiSeq sequencing of the V3-V4 region of bacterial 16S rRNA genes found in these samples. Airborne bacteria had a greater diversity and were significantly more abundant in pig stables and farmers' homes than suburban homes (Wilcoxon rank sum test P < 0.05). Moreover, bacterial taxa previously suggested to contribute to a protective effect had significantly higher relative and absolute abundance in pig stables and farmers' homes than in suburban homes (ALDEx2 with P < 0.05), including Firmicutes, Peptostreptococcaceae, Prevotellaceae, Lachnospiraceae, Ruminococcaceae, Ruminiclostridium , and Lactobacillus . Pig stables had significantly lower airborne bacterial diversity than farmers' homes, and there was no discernable direct transfer of airborne bacteria from stable to home. This study identifies differences in indoor airborne bacterial communities that may be an important component of this putative protective effect, while showing that pig stables themselves do not appear to directly contribute to the airborne bacterial communities in the homes of farmers. These findings improve our understanding of the role of airborne bacteria in the increasing prevalence of asthma and allergy.

Microbial Community Changes in Response to Ethanol or Methanol Amendments for U(VI) Reduction

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

Vishnivetskaya, Tatiana A; Brandt, Craig C; Madden, Andrew

2010-01-01

Microbial community responses to ethanol, methanol and methanol + humics amendments in relationship to uranium bioremediation were studied in laboratory microcosm experiments using sediments and ground water from a uranium-contaminated site in Oak Ridge, Tennessee. Ethanol addition always resulted in uranium reduction at rate of 0.8-1.0 mol l-1 d-1 while methanol addition did so occasionally at rate 0.95 mol l-1 d-1. The type of carbon source added, the duration of incubation, and the sampling site influenced the bacterial community structure upon incubation. Analysis of 16S rRNA gene clone libraries indicated (1) bacterial communities found in ethanol- and methanol-amended samples withmore » U(VI) reduction were similar due to presence of -Proteobacteria, and -Proteobacteria (members of the families Burkholderiaceae, Comamonadaceae, Oxalobacteraceae, and Rhodocyclaceae); (2) methanol-amended samples without U(VI) reduction exhibited the lowest diversity and the bacterial community contained 69.2-92.8% of the family Methylophilaceae; and (3) the addition of humics resulted in an increase of phylogenetic diversity of -Proteobacteria (Rodoferax, Polaromonas, Janthinobacterium, Methylophilales, unclassified) and Firmicutes (Desulfosporosinus, Clostridium).« less

Fine-scale phylogenetic architecture of a complex bacterial community.

PubMed

Acinas, Silvia G; Klepac-Ceraj, Vanja; Hunt, Dana E; Pharino, Chanathip; Ceraj, Ivica; Distel, Daniel L; Polz, Martin F

2004-07-29

Although molecular data have revealed the vast scope of microbial diversity, two fundamental questions remain unanswered even for well-defined natural microbial communities: how many bacterial types co-exist, and are such types naturally organized into phylogenetically discrete units of potential ecological significance? It has been argued that without such information, the environmental function, population biology and biogeography of microorganisms cannot be rigorously explored. Here we address these questions by comprehensive sampling of two large 16S ribosomal RNA clone libraries from a coastal bacterioplankton community. We show that compensation for artefacts generated by common library construction techniques reveals fine-scale patterns of community composition. At least 516 ribotypes (unique rRNA sequences) were detected in the sample and, by statistical extrapolation, at least 1,633 co-existing ribotypes in the sampled population. More than 50% of the ribotypes fall into discrete clusters containing less than 1% sequence divergence. This pattern cannot be accounted for by interoperon variation, indicating a large predominance of closely related taxa in this community. We propose that such microdiverse clusters arise by selective sweeps and persist because competitive mechanisms are too weak to purge diversity from within them.

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.

[Influence of PCR cycle number on microbial diversity analysis through next generation sequencing].

PubMed

An, Yunhe; Gao, Lijuan; Li, Junbo; Tian, Yanjie; Wang, Jinlong; Zheng, Xuejuan; Wu, Huijuan

2016-08-25

Using of high throughput sequencing technology to study the microbial diversity in complex samples has become one of the hottest issues in the field of microbial diversity research. In this study, the soil and sheep rumen chyme samples were used to extract DNA, respectively. Then the 25 ng total DNA was used to amplify the 16S rRNA V3 region with 20, 25, 30 PCR cycles, and the final sequencing library was constructed by mixing equal amounts of purified PCR products. Finally, the operational taxonomic unit (OUT) amount, rarefaction curve, microbial number and species were compared through data analysis. It was found that at the same amount of DNA template, the proportion of the community composition was not the best with more numbers of PCR cycle, although the species number was much more. In all, when the PCR cycle number is 25, the number of species and proportion of the community composition were the most optimal both in soil or chyme samples.

Endophytic bacterial community of grapevine leaves influenced by sampling date and phytoplasma infection process

PubMed Central

2014-01-01

Background Endophytic bacteria benefit host plant directly or indirectly, e.g. by biocontrol of the pathogens. Up to now, their interactions with the host and with other microorganisms are poorly understood. Consequently, a crucial step for improving the knowledge of those relationships is to determine if pathogens or plant growing season influence endophytic bacterial diversity and dynamic. Results Four healthy, four phytoplasma diseased and four recovered (symptomatic plants that spontaneously regain a healthy condition) grapevine plants were sampled monthly from June to October 2010 in a vineyard in north-western Italy. Metagenomic DNA was extracted from sterilized leaves and the endophytic bacterial community dynamic and diversity were analyzed by taxon specific real-time PCR, Length-Heterogeneity PCR and genus-specific PCR. These analyses revealed that both sampling date and phytoplasma infection influenced the endophytic bacterial composition. Interestingly, in June, when the plants are symptomless and the pathogen is undetectable (i) the endophytic bacterial community associated with diseased grapevines was different from those in the other sampling dates, when the phytoplasmas are detectable inside samples; (ii) the microbial community associated with recovered plants differs from that living inside healthy and diseased plants. Interestingly, LH-PCR database identified bacteria previously reported as biocontrol agents in the examined grapevines. Of these, Burkholderia, Methylobacterium and Pantoea dynamic was influenced by the phytoplasma infection process and seasonality. Conclusion Results indicated that endophytic bacterial community composition in grapevine is correlated to both phytoplasma infection and sampling date. For the first time, data underlined that, in diseased plants, the pathogen infection process can decrease the impact of seasonality on community dynamic. Moreover, based on experimental evidences, it was reasonable to hypothesize that after recovery the restructured microbial community could maintain the main structure between seasons. PMID:25048741

Endophytic bacterial community of grapevine leaves influenced by sampling date and phytoplasma infection process.

PubMed

Bulgari, Daniela; Casati, Paola; Quaglino, Fabio; Bianco, Piero A

2014-07-21

Endophytic bacteria benefit host plant directly or indirectly, e.g. by biocontrol of the pathogens. Up to now, their interactions with the host and with other microorganisms are poorly understood. Consequently, a crucial step for improving the knowledge of those relationships is to determine if pathogens or plant growing season influence endophytic bacterial diversity and dynamic. Four healthy, four phytoplasma diseased and four recovered (symptomatic plants that spontaneously regain a healthy condition) grapevine plants were sampled monthly from June to October 2010 in a vineyard in north-western Italy. Metagenomic DNA was extracted from sterilized leaves and the endophytic bacterial community dynamic and diversity were analyzed by taxon specific real-time PCR, Length-Heterogeneity PCR and genus-specific PCR. These analyses revealed that both sampling date and phytoplasma infection influenced the endophytic bacterial composition. Interestingly, in June, when the plants are symptomless and the pathogen is undetectable (i) the endophytic bacterial community associated with diseased grapevines was different from those in the other sampling dates, when the phytoplasmas are detectable inside samples; (ii) the microbial community associated with recovered plants differs from that living inside healthy and diseased plants. Interestingly, LH-PCR database identified bacteria previously reported as biocontrol agents in the examined grapevines. Of these, Burkholderia, Methylobacterium and Pantoea dynamic was influenced by the phytoplasma infection process and seasonality. Results indicated that endophytic bacterial community composition in grapevine is correlated to both phytoplasma infection and sampling date. For the first time, data underlined that, in diseased plants, the pathogen infection process can decrease the impact of seasonality on community dynamic. Moreover, based on experimental evidences, it was reasonable to hypothesize that after recovery the restructured microbial community could maintain the main structure between seasons.

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

PubMed Central

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. PMID:28051171

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.

Investigation into the effect of high concentrations of volatile fatty acids in anaerobic digestion on methanogenic communities

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

Franke-Whittle, Ingrid H., E-mail: ingrid.whittle@uibk.ac.at; Walter, Andreas; Ebner, Christian

Highlights: • Different methanogenic communities in mesophilic and thermophilic reactors. • High VFA levels do not cause major changes in archaeal communities. • Real-time PCR indicated greater diversity than ANAEROCHIP microarray. - Abstract: A study was conducted to determine whether differences in the levels of volatile fatty acids (VFAs) in anaerobic digester plants could result in variations in the indigenous methanogenic communities. Two digesters (one operated under mesophilic conditions, the other under thermophilic conditions) were monitored, and sampled at points where VFA levels were high, as well as when VFA levels were low. Physical and chemical parameters were measured, andmore » the methanogenic diversity was screened using the phylogenetic microarray ANAEROCHIP. In addition, real-time PCR was used to quantify the presence of the different methanogenic genera in the sludge samples. Array results indicated that the archaeal communities in the different reactors were stable, and that changes in the VFA levels of the anaerobic digesters did not greatly alter the dominating methanogenic organisms. In contrast, the two digesters were found to harbour different dominating methanogenic communities, which appeared to remain stable over time. Real-time PCR results were inline with those of microarray analysis indicating only minimal changes in methanogen numbers during periods of high VFAs, however, revealed a greater diversity in methanogens than found with the array.« less

Investigating niche partitioning of ectomycorrhizal fungi in specialized rooting zones of the monodominant leguminous tree Dicymbe corymbosa.

PubMed

Smith, Matthew E; Henkel, Terry W; Williams, Gwendolyn C; Aime, M Catherine; Fremier, Alexander K; Vilgalys, Rytas

2017-07-01

Temperate ectomycorrhizal (ECM) fungi show segregation whereby some species dominate in organic layers and others favor mineral soils. Weak layering in tropical soils is hypothesized to decrease niche space and therefore reduce the diversity of ectomycorrhizal fungi. The Neotropical ECM tree Dicymbe corymbosa forms monodominant stands and has a distinct physiognomy with vertical crown development, adventitious roots and massive root mounds, leading to multi-stemmed trees with spatially segregated rooting environments: aerial litter caches, aerial decayed wood, organic root mounds and mineral soil. We hypothesized that these microhabitats host distinct fungal assemblages and therefore promote diversity. To test our hypothesis, we sampled D. corymbosa ectomycorrhizal root tips from the four microhabitats and analyzed community composition based on pyrosequencing of fungal internal transcribed spacer (ITS) barcode markers. Several dominant fungi were ubiquitous but analyses nonetheless suggested that communities in mineral soil samples were statistically distinct from communities in organic microhabitats. These data indicate that distinctive rooting zones of D. corymbosa contribute to spatial segregation of the fungal community and likely enhance fungal diversity. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

[Effect of flooding time on community structure and abundance of Geobacteraceae in paddy soil].

PubMed

You, Jiaohua; Xia, Shuhong; Wang, Baoli; Qu, Dong

2011-06-01

The dynamic characteristics of community structure and relative abundance of Geobacteraceae were investigated to understand their response to microbial iron (III) reducing in flooded paddy soil. The paddy soil was incubated anaerobically and the amount of Fe(II) was determined during the flooding incubation. We retrieved Geobacteraceae sequences from clone libraries constructed for different time points (1 h and day 1, 5, 10, 20 and 30) after flooding of the paddy soil. The diversity and community structure were analyzed by using RFLP method, and the relative abundance of Geobacteraceae was detected by real-time PCR. Microbial reduction of iron (III) changed greatly in early time and was stable after incubated for 20 d in paddy soil. The largest iron reduction potential was 10.16 mg/g with a Vmax of 1.064 mg/(g x d) at the time of 4.84 d whereas this process achieved plateau after 20 days flooding. Diversity of Geobacteraceae, given by alpha indices, fluctuated during the flooding incubation. Two peaks of diversity were observed in treatments of 5 d and 20 d respectively, while significant low diversity appeared in samples of 10 d and 30 d. Beta indices described the differences between community structures of Geobacteraceae and hence reflected the variation of the flooding situation over time. In all samples, 10 RFLP-based preponderant types were found, which fell into clade 1 and clade 2 of Geobacteraceae. The relative abundance of Geobacteraceae was the lowest in 1 d (1.20% ) and the highest in 20 d (4.54%). The dynamic variation of Geobacteraceae diversity, community structure and abundance are closely related to microbial iron (III) reducing in flooding paddy soil.

Comparison of benthos and plankton for Waukegan Harbor Area of Concern, Illinois, and Burns Harbor-Port of Indiana non-Area of Concern, Indiana, in 2015

USGS Publications Warehouse

Eikenberry, Barbara C. Scudder; Olds, Hayley T.; Burns, Daniel J.; Dobrowolski, Edward G.; Schmude, Kurt L.

2017-06-06

During two seasonal sampling events in spring (June) and fall (August) of 2015, the U.S. Geological Survey collected benthos (benthic invertebrates) and plankton (zooplankton and phytoplankton) at three sites each in the Waukegan Harbor Area of Concern (AOC) in Illinois and in Burns Harbor-Port of Indiana, a non-AOC comparison site in Indiana. The study was done in cooperation with the U.S. Environmental Protection Agency and the Illinois Department of Natural Resources. Samples were collected concurrently for physical and chemical parameters (specific conductance, temperature, pH, dissolved oxygen, chlorophyll-a, total and volatile suspended solids in water samples; particle size and volatile-on-ignition solids of sediment in dredge samples). The purpose of the study was to assess whether or not aquatic communities at the AOC were degraded in comparison to communities at the non-AOC, which was presumed to be less impaired than the AOC. Benthos were collected by using Hester-Dendy artificial substrate samplers and a Ponar® dredge sampler to collect composited grabs of bottom sediment; zooplankton were collected by using tows from depth to the surface with a 63-micrometer mesh plankton net; phytoplankton were collected by using whole water samples composited from set depth intervals. Aquatic communities at the AOC and the non-AOC were compared by use of univariate statistical analyses with metrics such as taxa richness (number of unique taxa), diversity, and a multimetric Index of Biotic Integrity (IBI, for artificial-substrate samples only) as well as by use of multivariate statistical analyses of taxa relative abundances.Although benthos communities at Waukegan Harbor AOC were not rated as degraded in comparison to the non-AOC, metrics for zooplankton and phytoplankton communities did show some impairment for the 2015 sampling. Across seasons, benthos richness and diversity were significantly higher and rated as less degraded at the AOC compared to the non-AOC; however, benthos IBIs were not significantly different. Multivariate comparisons revealed that the benthos communities in the AOC and non-AOC were significantly different, but these comparisons do not address current degradation in either harbor. The dominant taxa in dredge samples were oligochaete worms in both harbors, but there were differences in the relative abundances of Dreissena as well as oligochaete and midge taxa. Although zooplankton richness and diversity in the AOC were lower and rated as more degraded in spring, these metrics were rated as less degraded in fall compared to the non-AOC, effectively balancing out so that there was no difference across seasons. Multivariate comparisons also indicated that zooplankton communities in the AOC were significantly different from those in the non-AOC for spring only but not across seasons, possibly because of lower water temperatures in spring at Waukegan Harbor than at the non-AOC site. The spring zooplankton community in Waukegan Harbor was dominated in density and biomass by the rotifer Synchaeta. Across seasons, diatom richness was significantly higher and rated as less degraded in the AOC than the non-AOC because of spring values, whereas soft algae richness was significantly lower and rated as more degraded in the AOC because of fall values. Spring richness of combined phytoplankton (soft algae and diatoms) was significantly higher in the AOC than in the non-AOC. Neither diatom diversity nor soft algae diversity differed significantly between the harbors, but combined phytoplankton diversity across seasons, if replicates were included, was significantly lower and rated as more degraded in the AOC than in the non-AOC. Multivariate tests indicated that the combined phytoplankton communities in the harbors were not significantly different across seasons. Significant differences were not found between harbors for chlorophyll-a, suspended solids, algal densities, or biomass.

Simulated tri-trophic networks reveal complex relationships between species diversity and interaction diversity

PubMed Central

Lumpkin, Will; Hurtado, Paul J.; Dyer, Lee A.

2018-01-01

Most of earth’s biodiversity is comprised of interactions among species, yet it is unclear what causes variation in interaction diversity across space and time. We define interaction diversity as the richness and relative abundance of interactions linking species together at scales from localized, measurable webs to entire ecosystems. Large-scale patterns suggest that two basic components of interaction diversity differ substantially and predictably between different ecosystems: overall taxonomic diversity and host specificity of consumers. Understanding how these factors influence interaction diversity, and quantifying the causes and effects of variation in interaction diversity are important goals for community ecology. While previous studies have examined the effects of sampling bias and consumer specialization on determining patterns of ecological networks, these studies were restricted to two trophic levels and did not incorporate realistic variation in species diversity and consumer diet breadth. Here, we developed a food web model to generate tri-trophic ecological networks, and evaluated specific hypotheses about how the diversity of trophic interactions and species diversity are related under different scenarios of species richness, taxonomic abundance, and consumer diet breadth. We investigated the accumulation of species and interactions and found that interactions accumulate more quickly; thus, the accumulation of novel interactions may require less sampling effort than sampling species in order to get reliable estimates of either type of diversity. Mean consumer diet breadth influenced the correlation between species and interaction diversity significantly more than variation in both species richness and taxonomic abundance. However, this effect of diet breadth on interaction diversity is conditional on the number of observed interactions included in the models. The results presented here will help develop realistic predictions of the relationships between consumer diet breadth, interaction diversity, and species diversity within multi-trophic communities, which is critical for the conservation of biodiversity in this period of accelerated global change. PMID:29579077

Simulated tri-trophic networks reveal complex relationships between species diversity and interaction diversity.

PubMed

Pardikes, Nicholas A; Lumpkin, Will; Hurtado, Paul J; Dyer, Lee A

2018-01-01

Most of earth's biodiversity is comprised of interactions among species, yet it is unclear what causes variation in interaction diversity across space and time. We define interaction diversity as the richness and relative abundance of interactions linking species together at scales from localized, measurable webs to entire ecosystems. Large-scale patterns suggest that two basic components of interaction diversity differ substantially and predictably between different ecosystems: overall taxonomic diversity and host specificity of consumers. Understanding how these factors influence interaction diversity, and quantifying the causes and effects of variation in interaction diversity are important goals for community ecology. While previous studies have examined the effects of sampling bias and consumer specialization on determining patterns of ecological networks, these studies were restricted to two trophic levels and did not incorporate realistic variation in species diversity and consumer diet breadth. Here, we developed a food web model to generate tri-trophic ecological networks, and evaluated specific hypotheses about how the diversity of trophic interactions and species diversity are related under different scenarios of species richness, taxonomic abundance, and consumer diet breadth. We investigated the accumulation of species and interactions and found that interactions accumulate more quickly; thus, the accumulation of novel interactions may require less sampling effort than sampling species in order to get reliable estimates of either type of diversity. Mean consumer diet breadth influenced the correlation between species and interaction diversity significantly more than variation in both species richness and taxonomic abundance. However, this effect of diet breadth on interaction diversity is conditional on the number of observed interactions included in the models. The results presented here will help develop realistic predictions of the relationships between consumer diet breadth, interaction diversity, and species diversity within multi-trophic communities, which is critical for the conservation of biodiversity in this period of accelerated global change.

[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.

Aligning molecular studies of mycorrhizal fungal diversity with ecologically important levels of diversity in ecosystems

PubMed Central

Sanders, Ian R; Rodriguez, Alia

2016-01-01

Arbuscular mycorrhizal fungi (AMF) occur in the roots of most plants and are an ecologically important component of the soil microbiome. Richness of AMF taxa is a strong driver of plant diversity and productivity, thus providing a rationale for characterizing AMF diversity in natural ecosystems. Consequently, a large number of molecular studies on AMF community composition are currently underway. Most published studies, at best, only address species or genera-level resolution. However, several experimental studies indicate that variation in plant performance is large among plants colonised by different individuals of one AMF species. Thus, there is a potential disparity between how molecular community ecologists are currently describing AMF diversity and the level of AMF diversity that may actually be ecologically relevant. We propose a strategy to find many polymorphic loci that can define within-species genetic variability within AMF, or at any level of resolution desired within the Glomermycota. We propose that allele diversity at the intraspecific level could then be measured for target AMF groups, or at other levels of resolution, in environmental DNA samples. Combining the use of such markers with experimental studies on AMF diversity would help to elucidate the most important level(s) of AMF diversity in plant communities. Our goal is to encourage ecologists who are trying to explain how mycorrhizal fungal communities are structured to take an approach that could also yield meaningful information that is relevant to the diversity, functioning and productivity of ecosystems. PMID:27128992

Microbes on mountainsides: Contrasting elevational patterns of bacterial and plant diversity

PubMed Central

Bryant, Jessica A.; Lamanna, Christine; Morlon, Hélène; Kerkhoff, Andrew J.; Enquist, Brian J.; Green, Jessica L.

2008-01-01

The study of elevational diversity gradients dates back to the foundation of biogeography. Although elevational patterns of plant and animal diversity have been studied for centuries, such patterns have not been reported for microorganisms and remain poorly understood. Here, in an effort to assess the generality of elevational diversity patterns, we examined soil bacterial and plant diversity along an elevation gradient. To gain insight into the forces that structure these patterns, we adopted a multifaceted approach to incorporate information about the structure, diversity, and spatial turnover of montane communities in a phylogenetic context. We found that observed patterns of plant and bacterial diversity were fundamentally different. While bacterial taxon richness and phylogenetic diversity decreased monotonically from the lowest to highest elevations, plants followed a unimodal pattern, with a peak in richness and phylogenetic diversity at mid-elevations. At all elevations bacterial communities had a tendency to be phylogenetically clustered, containing closely related taxa. In contrast, plant communities did not exhibit a uniform phylogenetic structure across the gradient: they became more overdispersed with increasing elevation, containing distantly related taxa. Finally, a metric of phylogenetic beta-diversity showed that bacterial lineages were not randomly distributed, but rather exhibited significant spatial structure across the gradient, whereas plant lineages did not exhibit a significant phylogenetic signal. Quantifying the influence of sample scale in intertaxonomic comparisons remains a challenge. Nevertheless, our findings suggest that the forces structuring microorganism and macroorganism communities along elevational gradients differ. PMID:18695215

Phytoplankton Community Structure, Biomass and Diversity on the Louisiana Continental Shelf

EPA Science Inventory

Phytoplankton communities on the Louisiana continental shelf (LCS) respond to nutrient loading from the Mississippi and Atchafalaya River Basin (MARB). Enhanced phytoplankton biomass is a source of organic matter contributing to the development of seasonal hypoxia. Samples were ...

Abiotic factors shape microbial diversity in Sonoran Desert soils.

PubMed

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

2012-11-01

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

Abiotic Factors Shape Microbial Diversity in Sonoran Desert Soils

PubMed Central

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

2012-01-01

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

Metagenomic Insights into the Evolution, Function, and Complexity of the Planktonic Microbial Community of Lake Lanier, a Temperate Freshwater Ecosystem ▿†

PubMed Central

Oh, Seungdae; Caro-Quintero, Alejandro; Tsementzi, Despina; DeLeon-Rodriguez, Natasha; Luo, Chengwei; Poretsky, Rachel; Konstantinidis, Konstantinos T.

2011-01-01

Lake Lanier is an important freshwater lake for the southeast United States, as it represents the main source of drinking water for the Atlanta metropolitan area and is popular for recreational activities. Temperate freshwater lakes such as Lake Lanier are underrepresented among the growing number of environmental metagenomic data sets, and little is known about how functional gene content in freshwater communities relates to that of other ecosystems. To better characterize the gene content and variability of this freshwater planktonic microbial community, we sequenced several samples obtained around a strong summer storm event and during the fall water mixing using a random whole-genome shotgun (WGS) approach. Comparative metagenomics revealed that the gene content was relatively stable over time and more related to that of another freshwater lake and the surface ocean than to soil. However, the phylogenetic diversity of Lake Lanier communities was distinct from that of soil and marine communities. We identified several important genomic adaptations that account for these findings, such as the use of potassium (as opposed to sodium) osmoregulators by freshwater organisms and differences in the community average genome size. We show that the lake community is predominantly composed of sequence-discrete populations and describe a simple method to assess community complexity based on population richness and evenness and to determine the sequencing effort required to cover diversity in a sample. This study provides the first comprehensive analysis of the genetic diversity and metabolic potential of a temperate planktonic freshwater community and advances approaches for comparative metagenomics. PMID:21764968

Multitrophic functional diversity predicts ecosystem functioning in experimental assemblages of estuarine consumers.

PubMed

Lefcheck, Jonathan S; Duffy, J Emmett

2015-11-01

The use of functional traits to explain how biodiversity affects ecosystem functioning has attracted intense interest, yet few studies have a priori altered functional diversity, especially in multitrophic communities. Here, we manipulated multivariate functional diversity of estuarine grazers and predators within multiple levels of species richness to test how species richness and functional diversity predicted ecosystem functioning in a multitrophic food web. Community functional diversity was a better predictor than species richness for the majority of ecosystem properties, based on generalized linear mixed-effects models. Combining inferences from eight traits into a single multivariate index increased prediction accuracy of these models relative to any individual trait. Structural equation modeling revealed that functional diversity of both grazers and predators was important in driving final biomass within trophic levels, with stronger effects observed for predators. We also show that different species drove different ecosystem responses, with evidence for both sampling effects and complementarity. Our study extends experimental investigations of functional trait diversity to a multilevel food web, and demonstrates that functional diversity can be more accurate and effective than species richness in predicting community biomass in a food web context.

Subtle Ecological Gradient in the Tropics Triggers High Species-Turnover in a Local Geographical Scale

PubMed Central

Nguyen, Dinh T.

2016-01-01

Our perception of diversity, including both alpha- and beta-diversity components, depends on spatial scale. Studies of spatial variation of the latter are just starting, with a paucity of research on beta-diversity patterns at smaller scales. Understanding these patterns and the processes shaping the distribution of diversity is critical to describe this diversity, but it is paramount in conservation too. Here, we investigate the diversity and structure of a tropical community of herbivorous beetles at a reduced local scale of some 10 km2, evaluating the effect of a small, gradual ecological change on this structure. We sampled leaf beetles in the Núi Chúa National Park (S Vietnam), studying changes in alpha- and beta-diversity across an elevation gradient up to 500 m, encompassing the ecotone between critically endangered lowland dry deciduous forest and mixed evergreen forest at higher elevations. Leaf beetle diversity was assessed using several molecular tree-based species delimitation approaches (with mtDNA cox1 data), species richness using rarefaction and incidence-based diversity indexes, and beta-diversity was investigated decomposing the contribution of species turnover and nestedness. We documented 155 species in the area explored and species-richness estimates 1.5–2.0x higher. Species diversity was similar in both forest types and changes in alpha-diversity along the elevation gradient showed an expected local increase of diversity in the ecotone. Beta-diversity was high among forest paths (average Sørensen's dissimilarity = 0.694) and, tentatively fixing at 300 m the boundary between otherwise continuous biomes, demonstrated similarly high beta-diversity (Sørensen's dissimilarity = 0.581), with samples clustering according to biome/elevation. Highly relevant considering the local scale of the study, beta-diversity had a high contribution of species replacement among locales (54.8%) and between biomes (79.6%), suggesting environmental heterogeneity as the dominant force shaping diversity at such small scale, directly and indirectly on the plant communities. Protection actions in the Park, especially these addressed at the imperative conservation of dry forest, must ponder the small scale at which processes shape species diversity and community structure for inconspicuous, yet extraordinarily diverse organisms such as the leaf beetles. PMID:27276228

Ecological drivers and habitat associations of estuarine bivalves

PubMed Central

Tunberg, Björn G.; Johnston, Cora A.; Barshis, Daniel J.

2015-01-01

Community composition of the infaunal bivalve fauna of the St. Lucie Estuary and southern Indian River Lagoon, eastern Florida was sampled quarterly for 10 years as part of a long-term benthic monitoring program. A total of 38,514 bivalves of 137 taxa were collected and identified. We utilized this data, along with sediment samples and environmental measurements gathered concurrently, to assess the community composition, distribution, and ecological drivers of the infaunal bivalves of this estuary system. Salinity had the strongest influence on bivalve assemblage across the 15 sites, superseding the influences of sediment type, water turbidity, temperature and other environmental parameters. The greatest diversity was found in higher salinity euhaline sites, while the greatest abundance of individual bivalves was found in medium salinity mixohaline sites, the lowest diversity and abundances were found in the low salinity oligohaline sites, demonstrating a strong positive association between salinity and diversity/abundance. Water management decisions for the estuary should incorporate understanding of the role of salinity on bivalve diversity, abundance, and ecosystem function. PMID:26587338

Ecological drivers and habitat associations of estuarine bivalves.

PubMed

McKeon, C Seabird; Tunberg, Björn G; Johnston, Cora A; Barshis, Daniel J

2015-01-01

Community composition of the infaunal bivalve fauna of the St. Lucie Estuary and southern Indian River Lagoon, eastern Florida was sampled quarterly for 10 years as part of a long-term benthic monitoring program. A total of 38,514 bivalves of 137 taxa were collected and identified. We utilized this data, along with sediment samples and environmental measurements gathered concurrently, to assess the community composition, distribution, and ecological drivers of the infaunal bivalves of this estuary system. Salinity had the strongest influence on bivalve assemblage across the 15 sites, superseding the influences of sediment type, water turbidity, temperature and other environmental parameters. The greatest diversity was found in higher salinity euhaline sites, while the greatest abundance of individual bivalves was found in medium salinity mixohaline sites, the lowest diversity and abundances were found in the low salinity oligohaline sites, demonstrating a strong positive association between salinity and diversity/abundance. Water management decisions for the estuary should incorporate understanding of the role of salinity on bivalve diversity, abundance, and ecosystem function.

Bacterial microbiota of Kazakhstan cheese revealed by single molecule real time (SMRT) sequencing and its comparison with Belgian, Kalmykian and Italian artisanal cheeses.

PubMed

Li, Jing; Zheng, Yi; Xu, Haiyan; Xi, Xiaoxia; Hou, Qiangchuan; Feng, Shuzhen; Wuri, Laga; Bian, Yanfei; Yu, Zhongjie; Kwok, Lai-Yu; Sun, Zhihong; Sun, Tiansong

2017-01-09

In Kazakhstan, traditional artisanal cheeses have a long history and are widely consumed. The unique characteristics of local artisanal cheeses are almost completely preserved. However, their microbial communities have rarely been reported. The current study firstly generated the Single Molecule, Real-Time (SMRT) sequencing bacterial diversity profiles of 6 traditional artisanal cheese samples of Kazakhstan origin, followed by comparatively analyzed the microbiota composition between the current dataset and those from cheeses originated from Belgium, Russian Republic of Kalmykia (Kalmykia) and Italy. Across the Kazakhstan cheese samples, a total of 238 bacterial species belonging to 14 phyla and 140 genera were identified. Lactococcus lactis (28.93%), Lactobacillus helveticus (26.43%), Streptococcus thermophilus (12.18%) and Lactobacillus delbrueckii (12.15%) were the dominant bacterial species for these samples. To further evaluate the cheese bacterial diversity of Kazakhstan cheeses in comparison with those from other geographic origins, 16S rRNA datasets of 36 artisanal cheeses from Belgium, Russian Republic of Kalmykia (Kalmykia) and Italy were retrieved from public databases. The cheese bacterial microbiota communities were largely different across sample origins. By principal coordinate analysis (PCoA) and multivariate analysis of variance (MANOVA), the structure of the Kazakhstan artisanal cheese samples was found to be different from those of the other geographic origins. Furthermore, the redundancy analysis (RDA) identified 16 bacterial OTUs as the key variables responsible for such microbiota structural difference. Our results together suggest that the diversity of bacterial communities in different groups is stratified by geographic region. This study does not only provide novel information on the bacterial microbiota of traditional artisanal cheese of Kazakhstan at species level, but also interesting insights into the bacterial diversity of artisanal cheeses of various geographical origins.

The Effects of Environmental Factors on Marine Micro-Phytoplankton Community Composition in the Summertime Western North Atlantic Ocean During WACS II.

NASA Astrophysics Data System (ADS)

Stone, J. T.; Vaillancourt, R. D.

2016-02-01

Micro-phytoplankton community composition was determined along a section in the western North Atlantic Ocean between waters near Bermuda and the New England continental shelf during the Western Atlantic Climate Study II (WACS II) from May 18, 2014 to June 6, 2014. Seawater samples were collected from the underway line (z = 5 meters) of the RV Knorr and preserved in both Lugol's and formalin preservatives. The concentrations of centric diatoms, pennate diatoms, dinoflagellates and dictyophytes were determined using light microscopy of preserved samples settled in Utermöhl chambers. Cell abundance data were compared with the temperature and salinity of the surface seawater to determine statistical relationships between environmental factors and phytoplankton community composition. The micro-phytoplankton concentrations were lowest around the Sargasso Sea. Diatom concentrations varied along the transect from the Sargasso Sea. Dinoflagellates were the only group of micro-phytoplankton in this study to have a clear pattern in their distribution. Dinoflagellates were most numerous in the northern-most waters and were absent in the southern-most point of the study, in the Sargasso Sea. The most abundant species of diatoms observed were in the genera Pseudo-Nitzschia and Leptocylindrus. The most abundant species of dinoflagellate were of the genus Protoperidinium. Many of the samples with the highest species richness were closer to the coast and more northern than the samples with low species richness, however the Simpson's diversity indices varied amongst regions. While many of the samples were diverse, the lowest of which was in the Sargasso Sea, there was no clear pattern of species diversity with respect to the distance from the coast. Dinoflagellates, centric diatoms, pennate diatoms, dictyophytes and diversity indices were significantly weakly correlated with temperature, while dinoflagellates were significantly strongly correlated with salinity.

Bacterial communities in the collection and chlorinated distribution sections of a drinking water system in Budapest, Hungary.

PubMed

Homonnay, Zalán G; Török, György; Makk, Judit; Brumbauer, Anikó; Major, Eva; Márialigeti, Károly; Tóth, Erika

2014-07-01

Bacterial communities of a bank-filtered drinking water system were investigated by aerobic cultivation and clone library analysis. Moreover, bacterial communities were compared using sequence-aided terminal restriction fragment length polymorphism (T-RFLP) fingerprinting at ten characteristic points located at both the collecting and the distributing part of the water supply system. Chemical characteristics of the samples were similar, except for the presence of chlorine residuals in the distribution system and increased total iron concentration in two of the samples. Assimilable organic carbon (AOC) concentration increased within the collection system, it was reduced by chlorination and it increased again in the distribution system. Neither fecal indicators nor pathogens were detected by standard cultivation techniques. Chlorination reduced bacterial diversity and heterotrophic plate counts. Community structures were found to be significantly different before and after chlorination: the diverse communities in wells and the collection system were dominated by chemolithotrophic (e.g., Gallionella and Nitrospira) and oligocarbophilic-heterotrophic bacteria (e.g., Sphingomonas, Sphingopyxis, and Bradyrhizobium). After chlorination in the distribution system, the most characteristic bacterium was related to the facultative methylotrophic Methylocella spp. Communities changed within the distribution system too, Mycobacterium spp. or Sphingopyxis spp. became predominant in certain samples. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

PubMed Central

Cui, Henglin; Yang, Kun; Pagaling, Eulyn

2013-01-01

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

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

NASA Astrophysics Data System (ADS)

Zhang, X.; Hu, B.

2017-12-01

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

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.

Modified RNA-seq method for microbial community and diversity analysis using rRNA in different types of environmental samples

PubMed Central

Yan, Yong-Wei; Zou, Bin; Zhu, Ting; Hozzein, Wael N.

2017-01-01

RNA-seq-based SSU (small subunit) rRNA (ribosomal RNA) analysis has provided a better understanding of potentially active microbial community within environments. However, for RNA-seq library construction, high quantities of purified RNA are typically required. We propose a modified RNA-seq method for SSU rRNA-based microbial community analysis that depends on the direct ligation of a 5’ adaptor to RNA before reverse-transcription. The method requires only a low-input quantity of RNA (10–100 ng) and does not require a DNA removal step. The method was initially tested on three mock communities synthesized with enriched SSU rRNA of archaeal, bacterial and fungal isolates at different ratios, and was subsequently used for environmental samples of high or low biomass. For high-biomass salt-marsh sediments, enriched SSU rRNA and total nucleic acid-derived RNA-seq datasets revealed highly consistent community compositions for all of the SSU rRNA sequences, and as much as 46.4%-59.5% of 16S rRNA sequences were suitable for OTU (operational taxonomic unit)-based community and diversity analyses with complete coverage of V1-V2 regions. OTU-based community structures for the two datasets were also highly consistent with those determined by all of the 16S rRNA reads. For low-biomass samples, total nucleic acid-derived RNA-seq datasets were analyzed, and highly active bacterial taxa were also identified by the OTU-based method, notably including members of the previously underestimated genus Nitrospira and phylum Acidobacteria in tap water, members of the phylum Actinobacteria on a shower curtain, and members of the phylum Cyanobacteria on leaf surfaces. More than half of the bacterial 16S rRNA sequences covered the complete region of primer 8F, and non-coverage rates as high as 38.7% were obtained for phylum-unclassified sequences, providing many opportunities to identify novel bacterial taxa. This modified RNA-seq method will provide a better snapshot of diverse microbial communities, most notably by OTU-based analysis, even communities with low-biomass samples. PMID:29016661

Bacterial Diversity and Nitrogen Utilization Strategies in the Upper Layer of the Northwestern Pacific Ocean.

PubMed

Li, Yuan-Yuan; Chen, Xiao-Huang; Xie, Zhang-Xian; Li, Dong-Xu; Wu, Peng-Fei; Kong, Ling-Fen; Lin, Lin; Kao, Shuh-Ji; Wang, Da-Zhi

2018-01-01

Nitrogen (N) is a primary limiting nutrient for bacterial growth and productivity in the ocean. To better understand bacterial community and their N utilization strategy in different N regimes of the ocean, we examined bacterial diversity, diazotrophic diversity, and N utilization gene expressions in the northwestern Pacific Ocean (NWPO) using a combination of high-throughput sequencing and real-time qPCR methods. 521 and 204 different operational taxonomic units (OTUs) were identified in the 16s rRNA and nifH libraries from nine surface samples. Of the 16s rRNA gene OTUs, 11.9% were observed in all samples while 3.5 and 15.9% were detected only in N-sufficient and N-deficient samples. Proteobacteria, Cyanobacteria and Bacteroidetes dominated the bacterial community. Prochlorococcus and Pseudoalteromonas were the most abundant at the genus level in N-deficient regimes, while SAR86, Synechococcus and SAR92 were predominant in the Kuroshio-Oyashio confluence region. The distribution of the nifH gene presented great divergence among sampling stations: Cyanobacterium_UCYN-A dominated the N-deficient stations, while clusters related to the Alpha-, Beta- , and Gamma-Proteobacteria were abundant in other stations. Temperature was the main factor that determined bacterial community structure and diversity while concentration of NO X -N was significantly correlated with structure and distribution of N 2 -fixing microorganisms. Expression of the ammonium transporter was much higher than that of urea transporter subunit A ( urtA ) and ferredoxin-nitrate reductase , while urtA had an increased expression in N-deficient surface water. The predicted ammonium transporter and ammonium assimilation enzymes were most abundant in surface samples while urease and nitrogenase were more abundant in the N-deficient regions. These findings underscore the fact that marine bacteria have evolved diverse N utilization strategies to adapt to different N habitats, and that urea metabolism is of vital ecological importance in N-deficient regimes.

Estimating the Prevalence of Potential Enteropathogenic Escherichia coli and Intimin Gene Diversity in a Human Community by Monitoring Sanitary Sewage

PubMed Central

Yang, Kun; Pagaling, Eulyn

2014-01-01

Presently, the understanding of bacterial enteric diseases in the community and their virulence factors relies almost exclusively on clinical disease reporting and examination of clinical pathogen isolates. This study aimed to investigate the feasibility of an alternative approach that monitors potential enteropathogenic Escherichia coli (EPEC) and enterohemorrhagic E. coli (EHEC) prevalence and intimin gene (eae) diversity in a community by directly quantifying and characterizing target virulence genes in the sanitary sewage. The quantitative PCR (qPCR) quantification of the eae, stx1, and stx2 genes in sanitary sewage samples collected over a 13-month period detected eae in all 13 monthly sewage samples at significantly higher abundance (93 to 7,240 calibrator cell equivalents [CCE]/100 ml) than stx1 and stx2, which were detected sporadically. The prevalence level of potential EPEC in the sanitary sewage was estimated by calculating the ratio of eae to uidA, which averaged 1.0% (σ = 0.4%) over the 13-month period. Cloning and sequencing of the eae gene directly from the sewage samples covered the majority of the eae diversity in the sewage and detected 17 unique eae alleles belonging to 14 subtypes. Among them, eae-β2 was identified to be the most prevalent subtype in the sewage, with the highest detection frequency in the clone libraries (41.2%) and within the different sampling months (85.7%). Additionally, sewage and environmental E. coli isolates were also obtained and used to determine the detection frequencies of the virulence genes as well as eae genetic diversity for comparison. PMID:24141131

Elevational Gradients in β-Diversity Reflect Variation in the Strength of Local Community Assembly Mechanisms across Spatial Scales

PubMed Central

Tello, J. Sebastián; Myers, Jonathan A.; Macía, Manuel J.; Fuentes, Alfredo F.; Cayola, Leslie; Arellano, Gabriel; Loza, M. Isabel; Torrez, Vania; Cornejo, Maritza; Miranda, Tatiana B.; Jørgensen, Peter M.

2015-01-01

Despite long-standing interest in elevational-diversity gradients, little is known about the processes that cause changes in the compositional variation of communities (β-diversity) across elevations. Recent studies have suggested that β-diversity gradients are driven by variation in species pools, rather than by variation in the strength of local community assembly mechanisms such as dispersal limitation, environmental filtering, or local biotic interactions. However, tests of this hypothesis have been limited to very small spatial scales that limit inferences about how the relative importance of assembly mechanisms may change across spatial scales. Here, we test the hypothesis that scale-dependent community assembly mechanisms shape biogeographic β-diversity gradients using one of the most well-characterized elevational gradients of tropical plant diversity. Using an extensive dataset on woody plant distributions along a 4,000-m elevational gradient in the Bolivian Andes, we compared observed patterns of β-diversity to null-model expectations. β-deviations (standardized differences from null values) were used to measure the relative effects of local community assembly mechanisms after removing sampling effects caused by variation in species pools. To test for scale-dependency, we compared elevational gradients at two contrasting spatial scales that differed in the size of local assemblages and regions by at least an order of magnitude. Elevational gradients in β-diversity persisted after accounting for regional variation in species pools. Moreover, the elevational gradient in β-deviations changed with spatial scale. At small scales, local assembly mechanisms were detectable, but variation in species pools accounted for most of the elevational gradient in β-diversity. At large spatial scales, in contrast, local assembly mechanisms were a dominant force driving changes in β-diversity. In contrast to the hypothesis that variation in species pools alone drives β-diversity gradients, we show that local community assembly mechanisms contribute strongly to systematic changes in β-diversity across elevations. We conclude that scale-dependent variation in community assembly mechanisms underlies these iconic gradients in global biodiversity. PMID:25803846

Diversity and Distribution Characteristics of Viruses in Soils of a Marine-Terrestrial Ecotone in East China.

PubMed

Yu, Dan-Ting; Han, Li-Li; Zhang, Li-Mei; He, Ji-Zheng

2018-02-01

A substantial gap remains in our understanding of the abundance, diversity, and ecology of viruses in soil although some advances have been achieved in recent years. In this study, four soil samples according to the salinity gradient from shore to inland in East China have been characterized. Results showed that spherical virus particles represented the largest viral component in all of the four samples. The viromes had remarkably different taxonomic compositions, and most of the sequences were derived from single-stranded DNA viruses, especially from families Microviridae and Circoviridae. Compared with viromes from other aquatic and sediment samples, the community compositions of our four soil viromes resembled each other, meanwhile coastal sample virome closely congregated with sediment and hypersaline viromes, and high salinity paddy soil sample virome was similar with surface sediment virome. Phylogenetic analysis of functional genes showed that four viromes have high diversity of the subfamily Gokushovirinae in family Microviridae and most of Circoviridae replicase protein sequences grouped within the CRESS-DNA viruses. This work provided an initial outline of the viral communities in marine-terrestrial ecotone and will improve our understanding of the ecological functions of soil viruses.

Size-fractionated diversity of eukaryotic microbial communities in the Eastern Tropical North Pacific oxygen minimum zone.

PubMed

Duret, Manon T; Pachiadaki, Maria G; Stewart, Frank J; Sarode, Neha; Christaki, Urania; Monchy, Sébastien; Srivastava, Ankita; Edgcomb, Virginia P

2015-05-01

Oxygen minimum zones (OMZs) caused by water column stratification appear to expand in parts of the world's ocean, with consequences for marine biogeochemical cycles. OMZ formation is often fueled by high surface primary production, and sinking organic particles can be hotspots of interactions and activity within microbial communities. This study investigated the diversity of OMZ protist communities in two biomass size fractions (>30 and 30-1.6 μm filters) from the world's largest permanent OMZ in the Eastern Tropical North Pacific. Diversity was quantified via Illumina MiSeq sequencing of V4 region of 18S SSU rRNA genes in samples spanning oxygen gradients at two stations. Alveolata and Rhizaria dominated the two size fractions at both sites along the oxygen gradient. Community composition at finer taxonomic levels was partially shaped by oxygen concentration, as communities associated with versus anoxic waters shared only ∼32% of operational taxonomic unit (OTU) (97% sequence identity) composition. Overall, only 9.7% of total OTUs were recovered at both stations and under all oxygen conditions sampled, implying structuring of the eukaryotic community in this area. Size-fractionated communities exhibited different taxonomical features (e.g. Syndiniales Group I in the 1.6-30 μm fraction) that could be explained by the microniches created on the surface-originated sinking particles. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

New PCR primers targeting hydrazine synthase and cytochrome c biogenesis proteins in anammox bacteria.

PubMed

Zhou, Zhichao; Chen, Jing; Meng, Han; Dvornyk, Volodymyr; Gu, Ji-Dong

2017-02-01

PCR primers targeting genes encoding the two proteins of anammox bacteria, hydrazine synthase and cytochrome c biogenesis protein, were designed and tested in this study. Three different ecotypes of samples, namely ocean sediments, coastal wetland sediments, and wastewater treatment plant (WWTP) samples, were used to assess the primer efficiency and the community structures of anammox bacteria retrieved by 16S ribosomal RNA (rRNA) and the functional genes. Abundances of hzsB gene of anammox bacteria in South China Sea (SCS) samples were significantly correlated with 16S rRNA gene by qPCR method. And hzsB and hzsC gene primer pair hzsB364f-hzsB640r and hzsC745f-hzsC862r in combination with anammox bacterial 16S rRNA gene primers were recommended for quantifying anammox bacteria. Congruent with 16S rRNA gene-based community study, functional gene hzsB could also delineate the coastal-ocean distributing pattern, and seawater depth was positively associated with the diversity and abundance of anammox bacteria from shallow- to deep-sea. Both hzsC and ccsA genes could differentiate marine samples between deep and shallow groups of the Scalindua sp. clades. As for WWTP samples, non-Scalindua anammox bacteria reflected by hzsB, hzsC, ccsA, and ccsB gene-based libraries showed a similar distribution pattern with that by 16S rRNA gene. NH 4 + and NH 4 + /Σ(NO 3 - + NO 2 - ) positively correlated with anammox bacteria gene diversity, but organic matter contents correlated negatively with anammox bacteria gene diversity in SCS. Salinity was positively associated with diversity indices of hzsC and ccsB gene-harboring anammox bacteria communities and could potentially differentiate the distribution patterns between shallow- and deep-sea sediment samples. SCS surface sediments harbored considerably diverse community of Scalindua. A new Mai Po clade representing coastal estuary wetland anammox bacteria group based on 16S rRNA gene phylogeny is proposed. Existence of anammox bacteria within wider coverage of genera in Mai Po wetland indicates this unique niche is very complex, and species of anammox bacteria are niche-specific with different physiological properties towards substrates competing and chemical tolerance capability.

Phylogenetic congruence of lichenised fungi and algae is affected by spatial scale and taxonomic diversity.

PubMed

Buckley, Hannah L; Rafat, Arash; Ridden, Johnathon D; Cruickshank, Robert H; Ridgway, Hayley J; Paterson, Adrian M

2014-01-01

The role of species' interactions in structuring biological communities remains unclear. Mutualistic symbioses, involving close positive interactions between two distinct organismal lineages, provide an excellent means to explore the roles of both evolutionary and ecological processes in determining how positive interactions affect community structure. In this study, we investigate patterns of co-diversification between fungi and algae for a range of New Zealand lichens at the community, genus, and species levels and explore explanations for possible patterns related to spatial scale and pattern, taxonomic diversity of the lichens considered, and the level sampling replication. We assembled six independent datasets to compare patterns in phylogenetic congruence with varied spatial extent of sampling, taxonomic diversity and level of specimen replication. For each dataset, we used the DNA sequences from the ITS regions of both the fungal and algal genomes from lichen specimens to produce genetic distance matrices. Phylogenetic congruence between fungi and algae was quantified using distance-based redundancy analysis and we used geographic distance matrices in Moran's eigenvector mapping and variance partitioning to evaluate the effects of spatial variation on the quantification of phylogenetic congruence. Phylogenetic congruence was highly significant for all datasets and a large proportion of variance in both algal and fungal genetic distances was explained by partner genetic variation. Spatial variables, primarily at large and intermediate scales, were also important for explaining genetic diversity patterns in all datasets. Interestingly, spatial structuring was stronger for fungal than algal genetic variation. As the spatial extent of the samples increased, so too did the proportion of explained variation that was shared between the spatial variables and the partners' genetic variation. Different lichen taxa showed some variation in their phylogenetic congruence and spatial genetic patterns and where greater sample replication was used, the amount of variation explained by partner genetic variation increased. Our results suggest that the phylogenetic congruence pattern, at least at small spatial scales, is likely due to reciprocal co-adaptation or co-dispersal. However, the detection of these patterns varies among different lichen taxa, across spatial scales and with different levels of sample replication. This work provides insight into the complexities faced in determining how evolutionary and ecological processes may interact to generate diversity in symbiotic association patterns at the population and community levels. Further, it highlights the critical importance of considering sample replication, taxonomic diversity and spatial scale in designing studies of co-diversification.

Dynamic genetic features of eukaryotic plankton diversity in the Nakdong River estuary of Korea

NASA Astrophysics Data System (ADS)

Lee, Jee Eun; Chung, Ik Kyo; Lee, Sang-Rae

2017-07-01

Estuaries are environments where freshwater and seawater mix and they display various salinity profiles. The construction of river barrages and dams has rapidly changed these environments and has had a wide range of impacts on plankton communities. To understand the dynamics of such communities, researchers need accurate and rapid techniques for detecting plankton species. We evaluated the diversity of eukaryotic plankton over a salinity gradient by applying a metagenomics tool at the Nakdong River estuary in Korea. Environmental samples were collected on three dates during summer and autumn of 2011 at the Eulsukdo Bridge at the mouth of that river. Amplifying the 18S rDNA allowed us to analyze 456 clones and 122 phylotypes. Metagenomic sequences revealed various taxonomic groups and cryptic genetic variations at the intra- and inter-specific levels. By analyzing the same station at each sampling date, we observed that the phylotypes presented a salinity-related pattern of diversity in assemblages. The variety of species within freshwater samples reflected the rapid environmental changes caused by freshwater inputs. Dinophyceae phylotypes accounted for the highest proportion of overall diversity in the seawater samples. Euryhaline diatoms and dinoflagellates were observed in the freshwater, brackish and seawater samples. The biological data for species composition demonstrate the transitional state between freshwater and seawater. Therefore, this metagenomics information can serve as a biological indicator for tracking changes in aquatic environments.

Fungal communities in gardens of the leafcutter ant Atta cephalotes in forest and cabruca agrosystems of southern Bahia State (Brazil).

PubMed

Reis, Bárbara Monique Dos Santos; Silva, Aline; Alvarez, Martín Roberto; Oliveira, Tássio Brito de; Rodrigues, Andre

2015-12-01

Leaf-cutting ants interact with several fungi in addition to the fungal symbiont they cultivate for food. Here, we assessed alien fungal communities in colonies of Atta cephalotes. Fungus garden fragments were sampled from colonies in the Atlantic Rainforest and in a cabruca agrosystem in the state of Bahia (Brazil) in two distinct periods to evaluate whether differences in nest habitat influence the diversity of fungi in the ant colonies. We recovered a total of 403 alien fungi isolates from 628 garden fragments. The prevalent taxa found in these samples were Escovopsis sp. (26 %), Escovopsioides nivea (24 %), and Trichoderma spirale (10.9 %). Fungal diversity was similar between the colonies sampled in both areas suggesting that ants focus on reducing loads of alien fungi in the fungus gardens instead of avoiding specific fungi. However, fungal taxa composition differed between colonies sampled in the two areas and between the sampling periods. These differences are likely explained by the availability of plant substrates available for foraging over habitats and periods. Ordination analysis further supported that sampling period was the main attribute for community structuring but also revealed that additional factors may explain the structuring of fungal communities in colonies of A. cephalotes. Copyright © 2015 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Decrease in fungal biodiversity along an available phosphorous gradient in arable Andosol soils in Japan.

PubMed

Bao, Zhihua; Matsushita, Yuko; Morimoto, Sho; Hoshino, Yuko Takada; Suzuki, Chika; Nagaoka, Kazunari; Takenaka, Makoto; Murakami, Hiroharu; Kuroyanagi, Yukiko; Urashima, Yasufumi; Sekiguchi, Hiroyuki; Kushida, Atsuhiko; Toyota, Koki; Saito, Masanori; Tsushima, Seiya

2013-06-01

Andosols comprise one of the most important soil groups for agricultural activities in Japan because they cover about 46.5% of arable upland fields. In this soil group, available phosphorus (P) is accumulated by application of excessive fertilizer, but little is known about the influence of increasing P availability on microbial community diversity at large scales. We collected soil samples from 9 agro-geographical sites with Andosol soils across an available P gradient (2048.1-59.1 mg P2O5·kg(-1)) to examine the influence of P availability on the fungal community diversity. We used polymerase chain reaction - denaturing gradient gel electrophoresis to analyze the fungal communities based on 18S rRNA genes. Statistical analyses revealed a high negative correlation between available P and fungal diversity (H'). Fungal diversity across all sites exhibited a significant hump-shaped relationship with available P (R(2) = 0.38, P < 0.001). In addition, the composition of the fungal community was strongly correlated with the available P gradient. The ribotype F6, which was positively correlated with available P, was closely related to Mortierella. The results show that both the diversity and the composition of the fungal community were influenced by available P concentrations in Andosols, at a large scale. This represents an important step toward understanding the processes responsible for the maintenance of fungal diversity in Andosolic soils.

Characterization of the microbial community composition and the distribution of Fe-metabolizing bacteria in a creek contaminated by acid mine drainage.

PubMed

Sun, Weimin; Xiao, Enzong; Krumins, Valdis; Dong, Yiran; Xiao, Tangfu; Ning, Zengping; Chen, Haiyan; Xiao, Qingxiang

2016-10-01

A small watershed heavily contaminated by long-term acid mine drainage (AMD) from an upstream abandoned coal mine was selected to study the microbial community developed in such extreme system. The watershed consists of AMD-contaminated creek, adjacent contaminated soils, and a small cascade aeration unit constructed downstream, which provide an excellent contaminated site to study the microbial response in diverse extreme AMD-polluted environments. The results showed that the innate microbial communities were dominated by acidophilic bacteria, especially acidophilic Fe-metabolizing bacteria, suggesting that Fe and pH are the primary environmental factors in governing the indigenous microbial communities. The distribution of Fe-metabolizing bacteria showed distinct site-specific patterns. A pronounced shift from diverse communities in the upstream to Proteobacteria-dominated communities in the downstream was observed in the ecosystem. This location-specific trend was more apparent at genus level. In the upstream samples (sampling sites just below the coal mining adit), a number of Fe(II)-oxidizing bacteria such as Alicyclobacillus spp., Metallibacterium spp., and Acidithrix spp. were dominant, while Halomonas spp. were the major Fe(II)-oxidizing bacteria observed in downstream samples. Additionally, Acidiphilium, an Fe(III)-reducing bacterium, was enriched in the upstream samples, while Shewanella spp. were the dominant Fe(III)-reducing bacteria in downstream samples. Further investigation using linear discriminant analysis (LDA) effect size (LEfSe), principal coordinate analysis (PCoA), and unweighted pair group method with arithmetic mean (UPGMA) clustering confirmed the difference of microbial communities between upstream and downstream samples. Canonical correspondence analysis (CCA) and Spearman's rank correlation indicate that total organic carbon (TOC) content is the primary environmental parameter in structuring the indigenous microbial communities, suggesting that the microbial communities are shaped by three major environmental parameters (i.e., Fe, pH, and TOC). These findings were beneficial to a better understanding of natural attenuation of AMD.

Distinct soil bacterial communities revealed under a diversely managed agroecosystem

USDA-ARS?s Scientific Manuscript database

Land-use change and management are normally enacted to manipulate environments to improve conditions that relate to production, remediation, and accommodation. However, soil microbial community complexity after manipulations is still difficult to quantify. In this study, replicate soil samples we...

Measures of phylogenetic differentiation provide robust and complementary insights into microbial communities.

PubMed

Parks, Donovan H; Beiko, Robert G

2013-01-01

High-throughput sequencing techniques have made large-scale spatial and temporal surveys of microbial communities routine. Gaining insight into microbial diversity requires methods for effectively analyzing and visualizing these extensive data sets. Phylogenetic β-diversity measures address this challenge by allowing the relationship between large numbers of environmental samples to be explored using standard multivariate analysis techniques. Despite the success and widespread use of phylogenetic β-diversity measures, an extensive comparative analysis of these measures has not been performed. Here, we compare 39 measures of phylogenetic β diversity in order to establish the relative similarity of these measures along with key properties and performance characteristics. While many measures are highly correlated, those commonly used within microbial ecology were found to be distinct from those popular within classical ecology, and from the recently recommended Gower and Canberra measures. Many of the measures are surprisingly robust to different rootings of the gene tree, the choice of similarity threshold used to define operational taxonomic units, and the presence of outlying basal lineages. Measures differ considerably in their sensitivity to rare organisms, and the effectiveness of measures can vary substantially under alternative models of differentiation. Consequently, the depth of sequencing required to reveal underlying patterns of relationships between environmental samples depends on the selected measure. Our results demonstrate that using complementary measures of phylogenetic β diversity can further our understanding of how communities are phylogenetically differentiated. Open-source software implementing the phylogenetic β-diversity measures evaluated in this manuscript is available at http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity.

Response of soil bacterial communities to lead and zinc pollution revealed by Illumina MiSeq sequencing investigation.

PubMed

Xu, Xihui; Zhang, Zhou; Hu, Shunli; Ruan, Zhepu; Jiang, Jiandong; Chen, Chen; Shen, Zhenguo

2017-01-01

Soil provides a critical environment for microbial community development. However, microorganisms may be sensitive to substances such as heavy metals (HMs), which are common soil contaminants. This study investigated bacterial communities using 16S ribosomal RNA (rRNA) gene fragment sequencing in geographic regions with and without HM pollution to elucidate the effects of soil properties and HMs on bacterial communities. No obvious changes in the richness or diversity of bacterial communities were observed between samples from mining and control areas. Significant differences in bacterial richness and diversity were detected between samples from different geographic regions, indicating that the basic soil characteristics were the most important factors affecting bacterial communities other than HMs. However, the abundances of several phyla and genera differed significantly between mining and control samples, suggesting that Zn and Pb pollution may impact the soil bacterial community composition. Moreover, regression analyses showed that the relative abundances of these phyla and genera were correlated significantly with the soil-available Zn and Pb contents. Redundancy analysis indicated that the soil K, ammoniacal nitrogen (NH 4 + -N), total Cu, and available Zn and Cu contents were the most important factors. Our results not only suggested that the soil bacteria were sensitive to HM stresses but also indicated that other soil properties may affect soil microorganisms to a greater extent.

Soil microbial diversity in the vicinity of desert shrubs.

PubMed

Saul-Tcherkas, Vered; Unc, Adrian; Steinberger, Yosef

2013-04-01

Water and nutrient availability are the major limiting factors of biological activity in arid and semiarid ecosystems. Therefore, perennial plants have developed different ecophysiological adaptations to cope with harsh conditions. The chemical profile of the root exudates varies among plant species and this can induce variability in associated microbial populations. We examined the influence of two shrubs species, Artemisia sieberi and Noaea mucronata, on soil microbial diversity. Soil samples were collected monthly, from December 2006 to November 2007, near canopies of both shrubs (0-10-cm depth). Samples were used for abiotic tests and determination of soil bacterial diversity. No significant differences were found in the abiotic variables (soil moisture, total organic matter, and total soluble nitrogen (TSN)) between soil samples collected from under the two shrubs during the study period. No obvious differences in the Shannon-Weaver index, evenness values, or total phylogenetic distances were found for the soil microbial communities. However, detailed denaturing gradient gel electrophoresis (DGGE) clustering as well as taxonomic diversity analyses indicated clear shifts in the soil microbial community composition. These shifts were governed by seasonal variability in water availability and, significantly, by plant species type.

Characterization of the prokaryotic diversity through a stratigraphic permafrost core profile from the Qinghai-Tibet Plateau.

PubMed

Hu, Weigang; Zhang, Qi; Tian, Tian; Li, Dingyao; Cheng, Gang; Mu, Jing; Wu, Qingbai; Niu, Fujun; An, Lizhe; Feng, Huyuan

2016-05-01

Permafrost on the Qinghai-Tibet Plateau is one of the most sensitive regions to climate warming, thus characterizing its microbial diversity and community composition may be important for understanding their potential responses to climate changes. Here, we investigated the prokaryotic diversity in a 10-m-long permafrost core from the Qinghai-Tibet Plateau by restriction fragment length polymorphism analysis targeting the 16S rRNA gene. We detected 191 and 17 bacterial and archaeal phylotypes representing 14 and 2 distinct phyla, respectively. Proteobacteria was the dominant bacterial phylum, while archaeal communities were characterized by a preponderance of Thaumarchaeota. Some of prokaryotic phylotypes were closely related to characterized species involved in carbon and nitrogen cycles, including nitrogen fixation, methane oxidation and nitrification. However, the majority of the phylotypes were only distantly related to known taxa at order or species level, suggesting the potential of novel diversity. Additionally, both bacterial α diversity and community composition changed significantly with sampling depth, where these communities mainly distributed according to core horizons. Arthrobacter-related phylotypes presented at high relative abundance in two active layer soils, while the deeper permafrost soils were dominated by Psychrobacter-related clones. Changes in bacterial community composition were correlated with most measured soil variables, such as carbon and nitrogen contents, pH, and conductivity.

Spatial variability of particle-attached and free-living bacterial diversity in surface waters from the Mackenzie River to the Beaufort Sea (Canadian Arctic)

NASA Astrophysics Data System (ADS)

Ortega-Retuerta, E.; Joux, F.; Jeffrey, W. H.; Ghiglione, J. F.

2013-04-01

We explored the patterns of total and active bacterial community structure in a gradient covering surface waters from the Mackenzie River to the coastal Beaufort Sea in the Canadian Arctic Ocean, with a particular focus on free-living (FL) vs. particle-attached (PA) communities. Capillary electrophoresis-single-strand conformation polymorphism (CE-SSCP) showed significant differences when comparing river, coast and open sea bacterial community structures. In contrast to the river and coastal waters, total (16S rDNA-based) and active (16S rRNA-based) communities in the open sea samples were not significantly different, suggesting that most present bacterial groups were equally active in this area. Additionally, we observed significant differences between PA and FL bacterial community structure in the open sea, but similar structure in the two fractions for coastal and river samples. Direct multivariate statistical analyses showed that total community structure was mainly driven by salinity (a proxy of dissolved organic carbon and chromophoric dissolved organic matter), suspended particles, amino acids and chlorophyll a. Pyrosequencing of 16S rRNA genes from selected samples confirmed significant differences between river, coastal and sea samples. The PA fraction was only different (15.7% similarity) from the FL one in the open sea sample. Furthermore, PA samples generally showed higher diversity (Shannon, Simpson and Chao indices) than FL samples. At the class level, Opitutae was most abundant in the PA fraction of the sea sample, followed by Flavobacteria and Gammaproteobacteria, while the FL sea sample was dominated by Alphaproteobacteria. Finally, for the coast and river samples and both PA and FL fractions, Betaproteobacteria, Alphaproteobacteria and Actinobacteria were dominant. These results highlight the coexistence of particle specialists and generalists and the role of particle quality in structuring bacterial communities in the area. These results may also serve as a basis to predict further changes in bacterial communities should climate change lead to further increases in river discharge and related particle loads.

Microbial community in persistent apical periodontitis: a 16S rRNA gene clone library analysis.

PubMed

Zakaria, M N; Takeshita, T; Shibata, Y; Maeda, H; Wada, N; Akamine, A; Yamashita, Y

2015-08-01

To characterize the microbial composition of persistent periapical lesions of root filled teeth using a molecular genetics approach. Apical lesion samples were collected from 12 patients (23-80 years old) who visited the Kyushu University Hospital for apicectomy with persistent periapical lesions associated with root filled teeth. DNA was directly extracted from each sample and the microbial composition was comprehensively analysed using clone library analysis of the 16S rRNA gene. Enterococcus faecalis, Candida albicans and specific fimA genotypes of Porphyromonas gingivalis were confirmed using polymerase chain reaction (PCR) analysis with specific primers. Bacteria were detected in all samples, and the dominant findings were P. gingivalis (19.9%), Fusobacterium nucleatum (11.2%) and Propionibacterium acnes (9%). Bacterial diversity was greater in symptomatic lesions than in asymptomatic ones. In addition, the following bacteria or bacterial combinations were characteristic to symptomatic lesions: Prevotella spp., Treponema spp., Peptostreptococcaceae sp. HOT-113, Olsenella uli, Slackia exigua, Selemonas infelix, P. gingivalis with type IV fimA, and a combination of P. gingivalis, F. nucleatum, and Peptostreptococcaceae sp. HOT-113 and predominance of Streptococcus spp. On the other hand, neither Enterococcus faecalis nor C. albicans were detected in any of the samples. Whilst a diverse bacterial species were observed in the persistent apical lesions, some characteristic patterns of bacterial community were found in the symptomatic lesions. The diverse variation of community indicates that bacterial combinations as a community may cause persistent inflammation in periapical tissues rather than specific bacterial species. © 2014 International Endodontic Journal. Published by John Wiley & Sons Ltd.

Geochemical and physical drivers of microbial community structure in hot spring ecosystems

NASA Astrophysics Data System (ADS)

Havig, J. R.; Hamilton, T. L.; Boyd, E. S.; Meyer-Dombard, D. R.; Shock, E.

2012-12-01

Microbial communities in natural systems are typically characterized using samples collected from a single time point, thereby neglecting the temporal dynamics that characterize natural systems. The composition of these communities obtained from single point samples is then related to the geochemistry and physical parameters of the environment. Since most microbial life is adapted to a relatively narrow ecological niche (multiplicity of physical and chemical parameters that characterize a local habitat), these assessments provide only modest insight into the controls on community composition. Temporal variation in temperature or geochemical composition would be expected to add another dimension to the complexity of niche space available to support microbial diversity, with systems that experience greater variation supporting a greater biodiversity until a point where the variability is too extreme. . Hot springs often exhibit significant temporal variation, both in physical as well as chemical characteristics. This is a result of subsurface processes including boiling, phase separation, and differential mixing of liquid and vapor phase constituents. These characteristics of geothermal systems, which vary significantly over short periods of time, provide ideal natural laboratories for investigating how i) the extent of microbial community biodiversity and ii) the composition of those communities are shaped by temporal fluctuations in geochemistry. Geochemical and molecular samples were collected from 17 temporally variable hot springs across Yellowstone National Park, Wyoming. Temperature measurements using data-logging thermocouples, allowing accurate determination of temperature maximums, minimums, and ranges for each collection site, were collected in parallel, along with multiple geochemical characterizations as conditions varied. There were significant variations in temperature maxima (54.5 to 90.5°C), minima (12.5 to 82.5°C), and range (3.5 to 77.5°C) for the hot spring environments that spanned ranges of pH values (2.2 to 9.0) and geochemical compositions. We characterized the abundance, composition, and phylogenetic diversity of bacterial and archaeal 16S rRNA gene assemblages in sediment/biofilm samples collected from each site. 16S data can be used as proxy for metabolic dissimilarity. We predict that temporally fluctuating environments should provide additional complexity to the system (additional niche space) capable of supporting additional taxa, which should lead to greater 16S rRNA gene diversity. However, systems with too much variability should collapse the diversity. Thus, one would expect an optimal system for variability, with respect to 16S phylogenetic diversity. Community ecology tools were then applied to model the relative influence of physical and chemical characteristics (including temperature dynamics) on the local biodiversity. The results reveal unique insight into the role of temporal environmental variation in the development of biodiverse communities and provide a platform for predicting the response of an ecosystem to temperature perturbation.

Ecological Effects of Roads on the Plant Diversity of Coastal Wetland in the Yellow River Delta

PubMed Central

Li, Yunzhao; Du, Siyao; Han, Guangxuan; Qu, Fanzhu; Wang, Guangmei; Fu, Yuqin; Zhan, Chao

2014-01-01

The 26 sample sites in 7 study plots adjacent to asphalt road and earth road in coastal wetland in the Yellow River Delta were selected to quantify plant diversity using quadrat sampling method in plant bloom phase of July and August 2012. The indice of β T and Jaccard's coefficient were applied to evaluate the species diversity. The results showed that the plant diversities and alien plants were high in the range of 0–20 m to the road verge. There were more exotics and halophytes in plots of asphalt roadside than that of earth roadside. However, proportion of halophytes in habitats of asphalt roadsides was lower than that of earth roadside. By comparing β-diversity, there were more common species in the asphalt roadsides than that in the earth roadsides. The similarity of plant communities in studied plots of asphalt roadsides and earth roadsides increased with increasing the distance to road verge. The effect range of roads for plant diversity in study region was about 20 m to road verge. Our results indicate that the construction and maintenance of roads in wetland could increase the plant species diversities of communities and risk of alien species invasion. PMID:25147872

Bacterial communities in Great Barrier Reef calcareous sediments: Contrasting 16S rDNA libraries from nearshore and outer shelf reefs

NASA Astrophysics Data System (ADS)

Uthicke, S.; McGuire, K.

2007-03-01

Bacterial communities in eight 16S rDNA clone libraries from calcareous sediments were investigated to provide an assessment of the bacterial diversity on sediments of the Great Barrier Reef (GBR) and to investigate differences due to decreased water quality. Sample effort was spread across two locations on each of four coral reefs, with two reefs located nearshore and two reefs on the outer shelf to allow robust statistical comparison of nearshore reefs (subjected to enhanced runoff) and outer shelf reefs (pristine conditions). Out of 221 non-chimeric sequences, 189 (85.5%) were unique and only one sequence occurred in more than one library. Rarefaction analyses and coverage calculations indicated that only a small fraction of the diversity was sampled. Cluster analyses and comparison to published sequences indicated that sequences retrieved belonged to the α, γ and δ subdivision of the Proteobacteria (6.8, 29.4 and 13.6% of the total, respectively), Cytophaga-Flavobacteria-Bacteroidetes (CFB) group (20.4%), Cyanobacteria (5.4%), Planctomycetaceae (7.7%), Verrucomicrobiaceae (6.8%), Acidobacteriaceae (2.7%). Analysis of Similarity (ANOSIM, based on grouping all retrieved sequences into 9 phylogenetic groups) indicated that subtle differences do exist in the community composition between nearshore and outer shelf reefs. Similarity percentage analysis (SIMPER) indicated that Acidobacteriaceae and Cyanobacteriaceae were the main contributors to the dissimilarity. A significant difference between bacteria on nearshore and outer shelf reefs also existed on the molecular level ( FST = 0.008, p = 0.007 for all samples, 0.006, p = 0.022 when repeated sequences within libraries were removed). Thus, bacterial communities on carbonate sediments investigated were highly diverse and differences in community composition may provide important leads for the search for indicator species or communities for water quality differences.

Community mapping and respondent-driven sampling of gay and bisexual men’s communities in Vancouver, Canada

PubMed Central

Forrest, Jamie I; Stevenson, Benjamin; Rich, Ashleigh; Michelow, Warren; Pai, Jayaram; Jollimore, Jody; Raymond, H. Fisher; Moore, David; Hogg, Robert S; Roth, Eric A

2014-01-01

Literature suggests formative research is vital for those using respondent-driven sampling (RDS) to study hidden populations of interest. However, few authors have described in detail how different qualitative methodologies can address the objectives of formative research for understanding the social network properties of the study population, selecting seeds, and adapting survey logistics to best fit the population. In this paper we describe the use of community mapping exercises as a tool within focus groups to collect data on social and sexual network characteristics of gay and bisexual men in the metropolitan area of Vancouver, Canada. Three key themes emerged from analyzing community maps along with other formative research data: (a) connections between physical spaces and social networks of gay and bisexual men, (b) diversity in communities, and (c) substance use connected with formation of sub-communities. We discuss how these themes informed the planning and operations of a longitudinal epidemiological cohort study recruited by RDS. We argue that using community mapping within formative research is a valuable qualitative tool for characterizing network structures of a diverse and differentiated population of gay and bisexual men in a highly developed urban setting. PMID:24512070

Community stability within the St. Marys River fish community: Evidence from trawl surveys

USGS Publications Warehouse

Schaeffer, Jeffrey S.; Bowen, Anjanette K.; Fielder, David G.

2017-01-01

A trawl survey was conducted in the Saint Marys River during 2010–2011 and we compared our results to a prior trawl survey conducted during 1979–1983 to look for long-term changes in the fish community, especially in terms of changes induced by invasive species. We found no substantive temporal differences in fish density, fish biomass, or fish diversity; lower trawl biomass during 2010–2011 was likely a result of day versus night trawling. The Saint Marys River remains a center of high fish diversity, invasive species remain rare, and the system continues to exhibit overall long-term stability. Trawling captured a wide range of fish species, but was likely not an effective stock assessment tool for managed game fish because catch rates were low or variable for all game species except yellow perch. Trawling appeared to be an effective tool for sampling connecting channel diversity, especially when large numbers of individuals are needed for directed studies, but annual sampling would be needed to use data to assess recruitment.

Shifts in phylogenetic diversity of archaeal communities in mangrove sediments at different sites and depths in southeastern Brazil.

PubMed

Mendes, Lucas William; Taketani, Rodrigo Gouvêa; Navarrete, Acácio Aparecido; Tsai, Siu Mui

2012-06-01

This study focused on the structure and composition of archaeal communities in sediments of tropical mangroves in order to obtain sufficient insight into two Brazilian sites from different locations (one pristine and another located in an urban area) and at different depth levels from the surface. Terminal restriction fragment length polymorphism (T-RFLP) of PCR-amplified 16S rRNA gene fragments was used to scan the archaeal community structure, and 16S rRNA gene clone libraries were used to determine the community composition. Redundancy analysis of T-RFLP patterns revealed differences in archaeal community structure according to location, depth and soil attributes. Parameters such as pH, organic matter, potassium and magnesium presented significant correlation with general community structure. Furthermore, phylogenetic analysis revealed a community composition distributed differently according to depth where, in shallow samples, 74.3% of sequences were affiliated with Euryarchaeota and 25.7% were shared between Crenarchaeota and Thaumarchaeota, while for the deeper samples, 24.3% of the sequences were affiliated with Euryarchaeota and 75.7% with Crenarchaeota and Thaumarchaeota. Archaeal diversity measurements based on 16S rRNA gene clone libraries decreased with increasing depth and there was a greater difference between depths (<18% of sequences shared) than sites (>25% of sequences shared). Taken together, our findings indicate that mangrove ecosystems support a diverse archaeal community; it might possibly be involved in nutrient cycles and are affected by sediment properties, depth and distinct locations. Copyright © 2012 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Fungal Endophytes of Alpinia officinarum Rhizomes: Insights on Diversity and Variation across Growth Years, Growth Sites, and the Inner Active Chemical Concentration

PubMed Central

Shubin, Li; Juan, Huang; RenChao, Zhou; ShiRu, Xu; YuanXiao, Jin

2014-01-01

In the present study, the terminal-restriction fragment length polymorphism (T-RFLP) technique, combined with the use of a clone library, was applied to assess the baseline diversity of fungal endophyte communities associated with rhizomes of Alpinia officinarum Hance, a medicinal plant with a long history of use. A total of 46 distinct T-RFLP fragment peaks were detected using HhaI or MspI mono-digestion-targeted, amplified fungal rDNA ITS sequences from A. officinarum rhizomes. Cloning and sequencing of representative sequences resulted in the detection of members of 10 fungal genera: Pestalotiopsis, Sebacina, Penicillium, Marasmius, Fusarium, Exserohilum, Mycoleptodiscus, Colletotrichum, Meyerozyma, and Scopulariopsis. The T-RFLP profiles revealed an influence of growth year of the host plant on fungal endophyte communities in rhizomes of this plant species; whereas, the geographic location where A. officinarum was grown contributed to only limited variation in the fungal endophyte communities of the host tissue. Furthermore, non-metric multidimensional scaling (NMDS) analysis across all of the rhizome samples showed that the fungal endophyte community assemblages in the rhizome samples could be grouped according to the presence of two types of active indicator chemicals: total volatile oils and galangin. Our present results, for the first time, address a diverse fungal endophyte community is able to internally colonize the rhizome tissue of A. officinarum. The diversity of the fungal endophytes found in the A. officinarum rhizome appeared to be closely correlated with the accumulation of active chemicals in the host plant tissue. The present study also provides the first systematic overview of the fungal endophyte communities in plant rhizome tissue using a culture-independent method. PMID:25536070

Fungal endophytes of Alpinia officinarum rhizomes: insights on diversity and variation across growth years, growth sites, and the inner active chemical concentration.

PubMed

Shubin, Li; Juan, Huang; RenChao, Zhou; ShiRu, Xu; YuanXiao, Jin

2014-01-01

In the present study, the terminal-restriction fragment length polymorphism (T-RFLP) technique, combined with the use of a clone library, was applied to assess the baseline diversity of fungal endophyte communities associated with rhizomes of Alpinia officinarum Hance, a medicinal plant with a long history of use. A total of 46 distinct T-RFLP fragment peaks were detected using HhaI or MspI mono-digestion-targeted, amplified fungal rDNA ITS sequences from A. officinarum rhizomes. Cloning and sequencing of representative sequences resulted in the detection of members of 10 fungal genera: Pestalotiopsis, Sebacina, Penicillium, Marasmius, Fusarium, Exserohilum, Mycoleptodiscus, Colletotrichum, Meyerozyma, and Scopulariopsis. The T-RFLP profiles revealed an influence of growth year of the host plant on fungal endophyte communities in rhizomes of this plant species; whereas, the geographic location where A. officinarum was grown contributed to only limited variation in the fungal endophyte communities of the host tissue. Furthermore, non-metric multidimensional scaling (NMDS) analysis across all of the rhizome samples showed that the fungal endophyte community assemblages in the rhizome samples could be grouped according to the presence of two types of active indicator chemicals: total volatile oils and galangin. Our present results, for the first time, address a diverse fungal endophyte community is able to internally colonize the rhizome tissue of A. officinarum. The diversity of the fungal endophytes found in the A. officinarum rhizome appeared to be closely correlated with the accumulation of active chemicals in the host plant tissue. The present study also provides the first systematic overview of the fungal endophyte communities in plant rhizome tissue using a culture-independent method.

Understanding Loan Use and Debt Burden among Low-Income and Minority Students at a Large Urban Community College

ERIC Educational Resources Information Center

Luna-Torres, Maria; McKinney, Lyle; Horn, Catherine; Jones, Sara

2018-01-01

This study examined a sample of community college students from a diverse, large urban community college system in Texas. To gain a deeper understanding about the effects of background characteristics on student borrowing behaviors and enrollment outcomes, the study employed descriptive statistics and regression techniques to examine two separate…

Community Violence Exposure and Adolescent Substance Use: Does Monitoring and Positive Parenting Moderate Risk in Urban Communities?

ERIC Educational Resources Information Center

Lee, Rosalyn

2012-01-01

This study investigates whether monitoring and positive parenting moderate the relationship between community violence exposure (CVE) and youth substance use. Analyses utilized a subsample (N = 2197) of a cross-sectional, ethnically diverse, urban school district sample. Dependent variables were any past year alcohol or drug use (AOD) and binge…

Relative importance of local habitat complexity and regional factors for assemblages of oribatid mites (Acari: Oribatida) in Sphagnum peat bogs.

PubMed

Minor, M A; Ermilov, S G; Philippov, D A; Prokin, A A

2016-11-01

We investigated communities of oribatid mites in five peat bogs in the north-west of the East European plain. We aimed to determine the extent to which geographic factors (latitude, separation distance), local environment (Sphagnum moss species, ground water level, biogeochemistry) and local habitat complexity (diversity of vascular plants and bryophytes in the surrounding plant community) influence diversity and community composition of Oribatida. There was a significant north-to-south increase in Oribatida abundance. In the variance partitioning, spatial factors explained 33.1 % of variability in abundance across samples; none of the environmental factors were significant. Across all bogs, Oribatida species richness and community composition were similar in Sphagnum rubellum and Sphagnum magellanicum, but significantly different and less diverse in Sphagnum cuspidatum. Sphagnum microhabitat explained 52.2 % of variability in Oribatida species richness, whereas spatial variables explained only 8.7 %. There was no distance decay in community similarity between bogs with increased geographical distance. The environmental variables explained 34.9 % of the variance in community structure, with vascular plants diversity, bryophytes diversity, and ground water level all contributing significantly; spatial variables explained 15.1 % of the total variance. Overall, only 50 % of the Oribatida community variance was explained by the spatial structure and environmental variables. We discuss relative importance of spatial and local environmental factors, and make general inferences about the formation of fauna in Sphagnum bogs.

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

PubMed

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

2016-03-22

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

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.

In four shallow and mesophotic tropical reef sponges from Guam the microbial community largely depends on host identity

PubMed Central

Steinert, Georg; Taylor, Michael W.; Deines, Peter; Simister, Rachel L.; de Voogd, Nicole J.; Hoggard, Michael

2016-01-01

Sponges (phylum Porifera) are important members of almost all aquatic ecosystems, and are renowned for hosting often dense and diverse microbial communities. While the specificity of the sponge microbiota seems to be closely related to host phylogeny, the environmental factors that could shape differences within local sponge-specific communities remain less understood. On tropical coral reefs, sponge habitats can span from shallow areas to deeper, mesophotic sites. These habitats differ in terms of environmental factors such as light, temperature, and food availability, as well as anthropogenic impact. In order to study the host specificity and potential influence of varying habitats on the sponge microbiota within a local area, four tropical reef sponges, Rhabdastrella globostellata, Callyspongia sp., Rhaphoxya sp., and Acanthella cavernosa, were collected from exposed shallow reef slopes and a deep reef drop-off. Based on 16S rRNA gene pyrosequencing profiles, beta diversity analyses revealed that each sponge species possessed a specific microbiota that was significantly different to those of the other species and exhibited attributes that are characteristic of high- and/or low-microbial-abundance sponges. These findings emphasize the influence of host identity on the associated microbiota. Dominant sponge- and seawater-associated bacterial phyla were Chloroflexi, Cyanobacteria, and Proteobacteria. Comparison of individual sponge taxa and seawater samples between shallow and deep reef sites revealed no significant variation in alpha diversity estimates, while differences in microbial beta diversity (variation in community composition) were significant for Callyspongia sp. sponges and seawater samples. Overall, the sponge-associated microbiota is significantly shaped by host identity across all samples, while the effect of habitat differentiation seems to be less predominant in tropical reef sponges. PMID:27114882

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 from a unique 700-km2 study region in the western Swiss Alps region, which has been exhaustively studied for macro-organismal and fungal ecology, and for topoclimatic modeling of future ecological trends, but without taking into account soil bacterial diversity. Here, we present an in-depth biogeographical characterization of the bacterial community diversity in this alpine region across 100 randomly stratified sites, using 56 environmental variables. Our exhaustive sampling ensured the detection of ecological trends with high statistical robustness. Our data both confirm previously observed general trends and show many new detailed trends for a wide range of bacterial taxonomic groups and environmental parameters. PMID:27542929

Diverse Vaginal Microbiomes in Reproductive-Age Women with Vulvovaginal Candidiasis

PubMed Central

Liu, Mu-Biao; Xu, Su-Rong; He, Yan; Deng, Guan-Hua; Sheng, Hua-Fang; Huang, Xue-Mei; Ouyang, Cai-Yan; Zhou, Hong-Wei

2013-01-01

Vulvovaginal candidiasis (VVC) is one of the most prevalent vaginal infectious diseases, and there are controversial reports regarding the diversity of the associated vaginal microbiota. We determined the vaginal microbial community in patients with VVC, bacterial vaginosis (BV), and mixed infection of VVC and BV using Illumina sequencing of 16S rRNA tags. Our results revealed for the first time the highly variable patterns of the vaginal microbiome from VVC patients. In general, the alpha-diversity results of species richness and evenness showed the following order: normal control < VVC only < mixed BV and VVC infection < BV only. The beta-diversity comparison of community structures also showed an intermediate composition of VVC between the control and BV samples. A detailed comparison showed that, although the control and BV communities had typical patterns, the vaginal microbiota of VVC is complex. The mixed BV and VVC infection group showed a unique pattern, with a relatively higher abundance of Lactobacillus than the BV group and higher abundance of Prevotella, Gardnerella, and Atopobium than the normal control. In contrast, the VVC-only group could not be described by any single profile, ranging from a community structure similar to the normal control (predominated with Lactobacillus) to BV-like community structures (abundant with Gardnerella and Atopobium). Treatment of VVC resulted in inconsistent changes of the vaginal microbiota, with four BV/VVC samples recovering to a higher Lactobacillus level, whereas many VVC-only patients did not. These results will be useful for future studies on the role of vaginal microbiota in VVC and related infectious diseases. PMID:24265786

Diverse vaginal microbiomes in reproductive-age women with vulvovaginal candidiasis.

PubMed

Liu, Mu-Biao; Xu, Su-Rong; He, Yan; Deng, Guan-Hua; Sheng, Hua-Fang; Huang, Xue-Mei; Ouyang, Cai-Yan; Zhou, Hong-Wei

2013-01-01

Vulvovaginal candidiasis (VVC) is one of the most prevalent vaginal infectious diseases, and there are controversial reports regarding the diversity of the associated vaginal microbiota. We determined the vaginal microbial community in patients with VVC, bacterial vaginosis (BV), and mixed infection of VVC and BV using Illumina sequencing of 16S rRNA tags. Our results revealed for the first time the highly variable patterns of the vaginal microbiome from VVC patients. In general, the alpha-diversity results of species richness and evenness showed the following order: normal control < VVC only < mixed BV and VVC infection < BV only. The beta-diversity comparison of community structures also showed an intermediate composition of VVC between the control and BV samples. A detailed comparison showed that, although the control and BV communities had typical patterns, the vaginal microbiota of VVC is complex. The mixed BV and VVC infection group showed a unique pattern, with a relatively higher abundance of Lactobacillus than the BV group and higher abundance of Prevotella, Gardnerella, and Atopobium than the normal control. In contrast, the VVC-only group could not be described by any single profile, ranging from a community structure similar to the normal control (predominated with Lactobacillus) to BV-like community structures (abundant with Gardnerella and Atopobium). Treatment of VVC resulted in inconsistent changes of the vaginal microbiota, with four BV/VVC samples recovering to a higher Lactobacillus level, whereas many VVC-only patients did not. These results will be useful for future studies on the role of vaginal microbiota in VVC and related infectious diseases.

Assessment of beetle diversity, community composition and potential threats to forestry using kairomone-baited traps.

PubMed

Olivier-Espejel, S; Hurley, B P; Garnas, J

2017-02-01

Traps designed to capture insects during normal movement/dispersal, or via attraction to non-specific (plant) volatile lures, yield by-catch that carries valuable information about patterns of community diversity and composition. In order to identify potential native/introduced pests and detect predictors of colonization of non-native pines, we examined beetle assemblages captured in intercept panel traps baited with kairomone lures used during a national monitoring of the woodwasp, Sirex noctilio, in Southern Africa. We identified 50 families and 436 morphospecies of beetles from nine sites sampled in both 2008 and 2009 and six areas in 2007 (trap catch pooled by region) across a latitudinal and elevational gradient. The most diverse groups were mainly those strongly associated with trees, known to include damaging pests. While native species dominated the samples in terms of richness, the dominant species was the introduced bark beetle Orthotomicus erosus (Curculionidae: Scolytinae) (22 ± 34 individuals/site). Four Scolytinae species without previous records in South Africa, namely Coccotrypes niger, Hypocryphalus robustus (formerly Hypocryphalus mangiferae), Hypothenemus birmanus and Xyleborus perforans, were captured in low abundances. Communities showed temporal stability within sites and strong biogeographic patterns across the landscape. The strongest single predictors of community composition were potential evaporation, latitude and maximum relative humidity, while the strongest multifactor model contained elevation, potential evaporation and maximum relative humidity. Temperature, land use variables and distance to natural areas did not significantly correlate with community composition. Non-phytophagous beetles were also captured and were highly diverse (32 families) perhaps representing important beneficial insects.

Characterization of eubacterial and archaeal community diversity in the pit mud of Chinese Luzhou-flavor liquor by nested PCR-DGGE.

PubMed

Ding, Xiao-Fei; Wu, Chong-De; Zhang, Li-Qiang; Zheng, Jia; Zhou, Rong-Qing

2014-02-01

The aim of this study was to investigate and compare the microbial community structures of eubacteria and archaea in the pit mud of Chinese Luzhou-flavor liquor from the wall (C(w)) and bottom (C(b)) of cellar through nested PCR-denaturing gradient gel electrophoresis (DGGE). The Shannon-Wiener index (H) calculated from the DGGE profiles showed that the community diversities of eubacteria and archaea in samples from C(b) were almost higher than that from C(w). In addition, cluster analysis of the DGGE profiles revealed that some differences were found in the microbial community structure in samples from different locations. The closely relative microorganisms of all eubacterial 16S rRNA gene sequences fell into four phyla (Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria), including 12 genera and 2 uncultured eubacteria. Moreover, 37.1% eubacteria were affiliated with Clostridium. Particularly, genus Acinetobacter was absent in all samples from C(b) but present in all samples from C(w). The closely relative microorganisms of all archaeal 16S rRNA gene sequences fell into four genera, which included Methanobrevibacter, Methanoculleus, Methanobacterium and Methanosaeta, while the dominant archaea in samples from C(w) and C(b) were similar. Results presented in this study provide further understanding of the spatial differences in microbial community structure in the pit mud, and is of great importance for the production and quality improvement of Luzhou-flavor liquor.

Gut Microbial Diversity in Antibiotic-Naive Children After Systemic Antibiotic Exposure: A Randomized Controlled Trial.

PubMed

Doan, Thuy; Arzika, Ahmed M; Ray, Kathryn J; Cotter, Sun Y; Kim, Jessica; Maliki, Ramatou; Zhong, Lina; Zhou, Zhaoxia; Porco, Travis C; Vanderschelden, Benjamin; Keenan, Jeremy D; Lietman, Thomas M

2017-05-01

Antibiotic exposure can alter the gut microbiome. We evaluate the effects of azithromycin on the gut microbiome diversity of children from an antibiotic-naive community in Niger. A population-based sample of 80 children aged 1-60 months in the Dosso region of Niger was randomized to receive a single dose of either oral azithromycin or placebo. Fecal samples were collected immediately before treatment and 5 days after treatment for 16S rRNA gene sequencing. The prespecified outcome was α-diversity (inverse Simpson's α-diversity index), with secondary outcomes of β and γ Simpson's and Shannon's diversities. At 5 days after treatment, 40 children aged 1-60 months were analyzed in the azithromycin-treated group and 40 children in the placebo-treated group. Diversity of the gut microbiome was significantly lower in the treated group (inverse Simpson's α-diversity, 5.03; 95% confidence interval [CI], 4.08-6.14) than in the placebo group (6.91; 95% CI, 5.82-8.21; P = .03). Similarly, the Shannon's α-diversity was lower in the treated group (10.60; 95% CI, 8.82-12.36) than the placebo group (15.42; 95% CI, 13.24-17.80; P = .004). Simpson's community-level (γ) diversity decreased with azithromycin exposure from 17.72 (95% CI, 13.80-20.21) to 10.10 (95% CI, 7.80-11.40; P = .00008), although β-diversity was not significantly reduced (2.56, 95% CI, 1.88-3.12; to 2.01, 95% CI, 1.46-2.51; P = .26). Oral administration of azithromycin definitively decreases the diversity of the gut microbiome of children in an antibiotic-naive community. NCT02048007. Published by Oxford University Press for the Infectious Diseases Society of America 2017. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Diversity and Composition of Airborne Fungal Community Associated with Particulate Matters in Beijing during Haze and Non-haze 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

2016-01-01

To assess the diversity and composition of airborne fungi associated with particulate matters (PMs) in Beijing, China, a total of 81 PM samples were collected, which were derived from PM2.5, PM10 fractions, and total suspended particles during haze and non-haze days. The airborne fungal community in these samples was analyzed using the Illumina Miseq platform with fungi-specific primers targeting the internal transcribed spacer 1 region of the large subunit rRNA gene. A total of 797,040 reads belonging to 1633 operational taxonomic units were observed. Of these, 1102 belonged to Ascomycota, 502 to Basidiomycota, 24 to Zygomycota, and 5 to Chytridiomycota. The dominant orders were Pleosporales (29.39%), Capnodiales (27.96%), Eurotiales (10.64%), and Hypocreales (9.01%). The dominant genera were Cladosporium, Alternaria, Fusarium, Penicillium, Sporisorium, and Aspergilus. Analysis of similarities revealed that both particulate matter sizes (R = 0.175, p = 0.001) and air quality levels (R = 0.076, p = 0.006) significantly affected the airborne fungal community composition. The relative abundance of many fungal genera was found to significantly differ among various PM types and air quality levels. Alternaria and Epicoccum were more abundant in total suspended particles samples, Aspergillus in heavy-haze days and PM2.5 samples, and Malassezia in PM2.5 samples and heavy-haze days. Canonical correspondence analysis and permutation tests showed that temperature (p < 0.01), NO2 (p < 0.01), PM10 (p < 0.01), SO2(p < 0.01), CO (p < 0.01), and relative humidity (p < 0.05) were significant factors that determine airborne fungal community composition. The results suggest that diverse airborne fungal communities are associated with particulate matters and may provide reliable data for studying the responses of human body to the increasing level of air pollution in Beijing.

Diversity and Composition of Airborne Fungal Community Associated with Particulate Matters in Beijing during Haze and Non-haze Days

PubMed Central

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

2016-01-01

To assess the diversity and composition of airborne fungi associated with particulate matters (PMs) in Beijing, China, a total of 81 PM samples were collected, which were derived from PM2.5, PM10 fractions, and total suspended particles during haze and non-haze days. The airborne fungal community in these samples was analyzed using the Illumina Miseq platform with fungi-specific primers targeting the internal transcribed spacer 1 region of the large subunit rRNA gene. A total of 797,040 reads belonging to 1633 operational taxonomic units were observed. Of these, 1102 belonged to Ascomycota, 502 to Basidiomycota, 24 to Zygomycota, and 5 to Chytridiomycota. The dominant orders were Pleosporales (29.39%), Capnodiales (27.96%), Eurotiales (10.64%), and Hypocreales (9.01%). The dominant genera were Cladosporium, Alternaria, Fusarium, Penicillium, Sporisorium, and Aspergilus. Analysis of similarities revealed that both particulate matter sizes (R = 0.175, p = 0.001) and air quality levels (R = 0.076, p = 0.006) significantly affected the airborne fungal community composition. The relative abundance of many fungal genera was found to significantly differ among various PM types and air quality levels. Alternaria and Epicoccum were more abundant in total suspended particles samples, Aspergillus in heavy-haze days and PM2.5 samples, and Malassezia in PM2.5 samples and heavy-haze days. Canonical correspondence analysis and permutation tests showed that temperature (p < 0.01), NO2 (p < 0.01), PM10 (p < 0.01), SO2(p < 0.01), CO (p < 0.01), and relative humidity (p < 0.05) were significant factors that determine airborne fungal community composition. The results suggest that diverse airborne fungal communities are associated with particulate matters and may provide reliable data for studying the responses of human body to the increasing level of air pollution in Beijing. PMID:27148180

Characterization of Bioaerosol Bacterial Communities During Hazy and Foggy Weather in Qingdao, China

NASA Astrophysics Data System (ADS)

Qi, Jianhua; Li, Mengzhe; Zhen, Yu; Wu, Lijing

2018-06-01

This study was conducted to evaluate the impact of hazy and foggy weather on the bacterial communities in bioaerosols, for which samples were collected from the Qingdao coastal region on sunny, foggy, and hazy days in January and March 2013. Bacterial community compositions were determined using polymerase chain reaction denaturing gradient gel electrophoresis (PCRDGGE). The bacterial community diversity was found to be high on foggy and hazy days, and the dominant species differed during hazy weather. The Shannon-Wiener index revealed that the bacterial community diversity of coarse particles was higher than that of fine particles in the bioaerosols. The bacterial community diversity of fine particles significantly correlated with relative humidity (RH; r 2 = 0.986). The cluster analysis results indicated that the bacterial communities on sunny days differed from those on hazy and foggy days. Compared with sunny days, the bacterial communities in the fine particles during hazy weather exhibited greater changes than those in the coarse particles. Most of the sequenced bacteria were found to be closely affiliated with uncultured bacteria. During hazy weather, members of the classes Bacilli and Gammaproteobacteria ( Pseudomonas and Acinetobacter) were dominant. The DGGE analysis revealed that Proteobacteria and Firmicutes were the predominant phyla, and their relative percentages to all the measured species changed significantly on hazy days, particularly in the fine particles. Haze and fog had a significant impact on the bacterial communities in bioaerosols, and the bacterial community diversity varied on different hazy days.

Internalized Homophobia and Relationship Quality among Lesbians, Gay Men, and Bisexuals

ERIC Educational Resources Information Center

Frost, David M.; Meyer, Ilan H.

2009-01-01

The authors examined the associations between internalized homophobia, outness, community connectedness, depressive symptoms, and relationship quality among a diverse community sample of 396 lesbian, gay, and bisexual (LGB) individuals. Structural equation models showed that internalized homophobia was associated with greater relationship problems…

Contrasting Relationships between Functional and Species Diversity in Subarctic and Subtropical Copepod Communities across the western North Pacific

NASA Astrophysics Data System (ADS)

Garcia-Comas, C.; Chiba, S.; Sugisaki, H.; Hashioka, T.; Smith, S. L.

2016-02-01

Understanding how species coexist in rich communities and the role of biodiversity on ecosystem-functioning is a long-standing challenge in ecology. Comparing functional diversity to species diversity may shed light on these questions. Here, we analyze copepod species data from the ODATE collection: 3142 samples collected over a period of 40 years, which includes a 10 o x 10o area of the Oyashio-Kuroshio Transition System, east of Japan (western North Pacific). The area hosts species characteristic of subarctic and subtropical communities. 163 copepod species were classified into five categorical functional traits (i.e., size, food, reproduction, thermal affinity and coastal-offshore habitat), following online databases and local taxonomic keys. We observe a general opposite hump-shaped relationship of species evenness (lower at mid-point) and functional diversity (Rao's Q) (higher at mid-point) with species richness. Subtropical Kuroshio communities tend to be richer with higher species evenness, and yet subarctic and transition waters tend to host communities of higher functional diversity. The distribution of trait values within each functional trait was further examined in relation to the Species Abundances Distribution (SAD). In subtropical communities, the distribution of trait values in the species ranking is homogenous, mirroring the frequency of those trait values in the entire community. In contrast, in subarctic communities the distribution of trait values differs along the species rank, with dominant species having favorable trait values more often than expected by chance (i.e., based on the overall frequency of that trait value in the entire community). Our results suggest that subtropical communities may be niche-saturated towards the most adapted trait values, so that merely having the most adapted trait value confers no strong competitive advantage to a species.

Community assessment techniques and the implications for rarefaction and extrapolation with Hill numbers.

PubMed

Cox, Kieran D; Black, Morgan J; Filip, Natalia; Miller, Matthew R; Mohns, Kayla; Mortimor, James; Freitas, Thaise R; Greiter Loerzer, Raquel; Gerwing, Travis G; Juanes, Francis; Dudas, Sarah E

2017-12-01

Diversity estimates play a key role in ecological assessments. Species richness and abundance are commonly used to generate complex diversity indices that are dependent on the quality of these estimates. As such, there is a long-standing interest in the development of monitoring techniques, their ability to adequately assess species diversity, and the implications for generated indices. To determine the ability of substratum community assessment methods to capture species diversity, we evaluated four methods: photo quadrat, point intercept, random subsampling, and full quadrat assessments. Species density, abundance, richness, Shannon diversity, and Simpson diversity were then calculated for each method. We then conducted a method validation at a subset of locations to serve as an indication for how well each method captured the totality of the diversity present. Density, richness, Shannon diversity, and Simpson diversity estimates varied between methods, despite assessments occurring at the same locations, with photo quadrats detecting the lowest estimates and full quadrat assessments the highest. Abundance estimates were consistent among methods. Sample-based rarefaction and extrapolation curves indicated that differences between Hill numbers (richness, Shannon diversity, and Simpson diversity) were significant in the majority of cases, and coverage-based rarefaction and extrapolation curves confirmed that these dissimilarities were due to differences between the methods, not the sample completeness. Method validation highlighted the inability of the tested methods to capture the totality of the diversity present, while further supporting the notion of extrapolating abundances. Our results highlight the need for consistency across research methods, the advantages of utilizing multiple diversity indices, and potential concerns and considerations when comparing data from multiple sources.

The vesicomyid bivalve habitat at cold seeps supports heterogeneous and dynamic macrofaunal assemblages

NASA Astrophysics Data System (ADS)

Guillon, Erwan; Menot, Lénaïck; Decker, Carole; Krylova, Elena; Olu, Karine

2017-02-01

The high biodiversity found at cold seeps, despite elevated concentrations of methane and hydrogen sulfide, is attributed to multiple sources of habitat heterogeneity. In addition to geological and geochemical processes, biogenic habitats formed by large symbiont-bearing taxa, such as bivalves and siboglinid tubeworms, or by microbial mats drive the biodiversity of small-sized fauna. However, because these habitat-forming species also depend on geochemical gradients, the respective influence of abiotic and biotic factors in structuring associated macrofaunal communities is often unresolved. The giant pockmark Regab located at 3200 m depth on the Congo margin is characterized by different fluid-flow regimes, providing a mosaic of the most common biogenic habitats encountered at seeps: microbial mats, mussel beds, and vesicomyid clam beds; the latter being distributed along a gradient of environmental conditions from the center to the periphery of the pockmark. Here, we examined the structure of macrofaunal communities in biogenic habitats formed in soft sediment to (1) determine the influence of the habitats on the associated macrofaunal communities (inter-habitat comparison), (2) describe how macrofaunal communities vary among vesicomyid clam beds (intra-habitat comparison) and (3) assess the inter-annual variation in vesicomyid beds based on repeated sampling at a three-year interval. The highest densities were found in the microbial mat communities in intermediate fluid-flow areas, but they had low diversity - also observed in the sediment close to mussel beds. In contrast, vesicomyid beds harbored the highest diversity. The vesicomyid beds did not show a homogeneous macrofaunal community across sampled areas; instead, density and composition of macrofauna varied according to the location of the beds inside the pockmark. The clam bed sampled in the most active, central part of the pockmark resembled bacterial mat communities by the presence of highly sulfide-tolerant species living at the sediment surface, along with vesicomyid juveniles. This similarity suggests a gradual change in community composition from mats to clam beds. Inter-annual comparisons of the different clam beds highlighted that the most active central site had a more variable community than its peripheral counterparts. Finally, a rapid shift in community structure, particularly in polychaete families, in experimentally reduced oxygen concentrations in the central part of Regab, suggests that high beta-diversity communities can withstand intense variation in geochemical conditions. These community dynamics are likely related to the diversity and to the plasticity of the vesicomyids themselves, because they can cope with high spatial and temporal environmental variability at a very local scale.

Spatial patterns of littoral zooplankton assemblages along a salinity gradient in a brackish sea: A functional diversity perspective

NASA Astrophysics Data System (ADS)

Helenius, Laura K.; Leskinen, Elina; Lehtonen, Hannu; Nurminen, Leena

2017-11-01

The distribution patterns and diversity of littoral zooplankton are both key baseline information for understanding the functioning of coastal ecosystems, and for identifying the mechanisms by which the impacts of recently increased eutrophication are transferred through littoral food webs. In this study, zooplankton community structure and diversity along a shallow coastal area of the northern Baltic Sea were determined in terms of horizontal environmental gradients. Spatial heterogeneity of the zooplankton community was examined along the gradient. Altogether 31 sites in shallow sandy bays on the coast of southwest Finland were sampled in the summer periods of 2009 and 2010 for zooplankton and environmental variables (surface water temperature, salinity, turbidity, wave exposure, macrophyte coverage, chlorophyll a and nutrients). Zooplankton diversity was measured as both taxonomic as well as functional diversity, using trait-based classification of planktonic crustaceans. Salinity, and to a lesser extent turbidity and temperature, were found to be the main predictors of the spatial patterns and functional diversity of the zooplankton community. Occurrence of cyclopoid copepods, as well as abundances of the calanoid copepod genus Acartia and the rotifer genus Keratella were found to be key factors in differentiating sites along the gradient. As far as we know, this is the first extensive study of functional diversity in Baltic Sea coastal zooplankton communities.

Abundance, diversity and community composition of free-living protozoa on vegetable sprouts.

PubMed

Chavatte, N; Lambrecht, E; Van Damme, I; Sabbe, K; Houf, K

2016-05-01

Interactions with free-living protozoa (FLP) have been implicated in the persistence of pathogenic bacteria on food products. In order to assess the potential involvement of FLP in this contamination, detailed knowledge on their occurrence, abundance and diversity on food products is required. In the present study, enrichment and cultivation methods were used to inventory and quantify FLP on eight types of commercial vegetable sprouts (alfalfa, beetroot, cress, green pea, leek, mung bean, red cabbage and rosabi). In parallel, total aerobic bacteria and Escherichia coli counts were performed. The vegetable sprouts harbored diverse communities of FLP, with Tetrahymena (ciliate), Bodo saltans and cercomonads (flagellates), and Acanthamoeba and Vannella (amoebae) as the dominant taxa. Protozoan community composition and abundance significantly differed between the sprout types. Beetroot harbored the most abundant and diverse FLP communities, with many unique species such as Korotnevella sp., Vannella sp., Chilodonella sp., Podophrya sp. and Sphaerophrya sp. In contrast, mung bean sprouts were species-poor and had low FLP numbers. Sampling month and company had no significant influence, suggesting that seasonal and local factors are of minor importance. Likewise, no significant relationship between protozoan community composition and bacterial load was observed. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

PubMed Central

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

2015-01-01

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

The structure of microbial community in aggregates of a typical chernozem aggregates under contrasting variants of its agricultural use

NASA Astrophysics Data System (ADS)

Ivanova, E. A.; Kutovaya, O. V.; Tkhakakhova, A. K.; Chernov, T. I.; Pershina, E. V.; Markina, L. G.; Andronov, E. E.; Kogut, B. M.

2015-11-01

The taxonomic structure of microbiomes in aggregates of different sizes from typical chernozems was investigated using sequencing of the 16S rRNA gene. The aggregate fractions of <0.25, 2-5, and >7 mm obtained by sieving of the soil samples at natural moisture were used for analysis. The highest prokaryote biomass (bacteria, archaea) was determined in the fractions <0.25 and aggregates 2-5 mm; the bacterial and archaeal biomass decreased in the following series: fallow > permanent black fallow > permanent winter wheat. The greatest number of fungi was recorded in the fraction <0.25 mm from the soils of the permanent black fallow and in all the studied aggregate fractions in the variant with permanent wheat. The system of agricultural use affected more significantly the structure of the prokaryote community in the chernozem than the size of aggregate fractions did. The most diverse microbial community was recorded in the soil samples of the fallow; the statistically significant maximums of the Shannon diversity indices and indices of phylogenetic diversity (PD) were recorded in the fractions <0.25 and 2-5 mm from the fallow soil. On the whole, the fine soil fractions (<0.25 mm) were characterized by higher diversity indices in comparison with those of the coarser aggregate fractions.

Prokaryotic communities in pit mud from different-aged cellars used for the production of Chinese strong-flavored liquor.

PubMed

Tao, Yong; Li, Jiabao; Rui, Junpeng; Xu, Zhancheng; Zhou, Yan; Hu, Xiaohong; Wang, Xiang; Liu, Menghua; Li, Daping; Li, Xiangzhen

2014-04-01

Chinese strong-flavored liquor (CSFL) accounts for more than 70% of all Chinese liquor production. Microbes in pit mud play key roles in the fermentation cellar for the CSFL production. However, microbial diversity, community structure, and cellar-age-related changes in pit mud are poorly understood. Here, we investigated the prokaryotic community structure and diversity in pit-mud samples with different cellar ages (1, 10, 25, and 50 years) using the pyrosequencing technique. Results indicated that prokaryotic diversity increased with cellar age until the age reached 25 years and that prokaryotic community structure changed significantly between three cellar ages (1, 10, and 25 years). Significant correlations between prokaryotic communities and environmental variables (pH, NH4(+), lactic acid, butyric acid, and caproic acid) were observed. Overall, our study results suggested that the long-term brewing operation shapes unique prokaryotic community structure and diversity as well as pit-mud chemistry. We have proposed a three-phase model to characterize the changes of pit-mud prokaryotic communities. (i) Phase I is an initial domestication period. Pit mud is characterized by abundant Lactobacillus and high lactic acid and low pH levels. (ii) Phase II is a transition period. While Lactobacillus abundance decreases dramatically, that of Bacteroidetes and methanogens increases. (iii) Phase III is a relative mature period. The prokaryotic community shows the highest diversity and capability to produce more caproic acid as a precursor for synthesis of ethyl caproate, the main flavor component in CSFL. This research provides scientific evidence to support the practical experience that old fermentation cellars produce high-quality liquor.

Flooding greatly affects the diversity of arbuscular mycorrhizal fungi communities in the roots of wetland plants.

PubMed

Wang, Yutao; Huang, Yelin; Qiu, Qiu; Xin, Guorong; Yang, Zhongyi; Shi, Suhua

2011-01-01

The communities of arbuscular mycorrhizal fungi (AMF) colonizing the roots of three mangrove species were characterized along a tidal gradient in a mangrove swamp. A fragment, designated SSU-ITS-LSU, including part of the small subunit (SSU), the entire internal transcribed spacer (ITS) and part of the large subunit (LSU) of rDNA from samples of AMF-colonized roots was amplified, cloned and sequenced using AMF-specific primers. Similar levels of AMF diversity to those observed in terrestrial ecosystems were detected in the roots, indicating that the communities of AMF in wetland ecosystems are not necessarily low in diversity. In total, 761 Glomeromycota sequences were obtained, which grouped, according to phylogenetic analysis using the SSU-ITS-LSU fragment, into 23 phylotypes, 22 of which belonged to Glomeraceae and one to Acaulosporaceae. The results indicate that flooding plays an important role in AMF diversity, and its effects appear to depend on the degree (duration) of flooding. Both host species and tide level affected community structure of AMF, indicating the presence of habitat and host species preferences.

Flooding Greatly Affects the Diversity of Arbuscular Mycorrhizal Fungi Communities in the Roots of Wetland Plants

PubMed Central

Wang, Yutao; Huang, Yelin; Qiu, Qiu; Xin, Guorong; Yang, Zhongyi; Shi, Suhua

2011-01-01

The communities of arbuscular mycorrhizal fungi (AMF) colonizing the roots of three mangrove species were characterized along a tidal gradient in a mangrove swamp. A fragment, designated SSU-ITS-LSU, including part of the small subunit (SSU), the entire internal transcribed spacer (ITS) and part of the large subunit (LSU) of rDNA from samples of AMF-colonized roots was amplified, cloned and sequenced using AMF-specific primers. Similar levels of AMF diversity to those observed in terrestrial ecosystems were detected in the roots, indicating that the communities of AMF in wetland ecosystems are not necessarily low in diversity. In total, 761 Glomeromycota sequences were obtained, which grouped, according to phylogenetic analysis using the SSU-ITS-LSU fragment, into 23 phylotypes, 22 of which belonged to Glomeraceae and one to Acaulosporaceae. The results indicate that flooding plays an important role in AMF diversity, and its effects appear to depend on the degree (duration) of flooding. Both host species and tide level affected community structure of AMF, indicating the presence of habitat and host species preferences. PMID:21931734

Neutral processes and species sorting in benthic microalgal community assembly: effects of tidal resuspension.

PubMed

Plante, Craig J; Fleer, Virginia; Jones, Martin L

2016-10-01

Benthic microalgae (BMA) provide vital food resources for heterotrophs and stabilize sediments with their extracellular secretions. A central goal in ecology is to understand how processes such as species interactions and dispersal, contribute to observed patterns of species abundance and distribution. Our objectives were to assess the effects of sediment resuspension on microalgal community structure. We tested whether taxa-abundance distributions could be predicted using neutral community models (NCMs) and also specific hypotheses about passive migration: (i) As migration decreases in sediment patches, BMA α-diversity will decrease, and (ii) As migration decreases, BMA community dissimilarity (β-diversity) will increase. Co-occurrence indices (checkerboard score and variance ratio) were also computed to test for deterministic factors, such as competition and niche differentiation, in shaping communities. Two intertidal sites (mudflat and sand bar) differing in resuspension regime were sampled throughout the tidal cycle. Fluorometry and denaturing gradient gel electrophoresis were utilized to investigate diatom community structure. Observed taxa-abundances fit those predicted from NCMs reasonably well (R 2 of 0.68-0.93), although comparisons of observed local communities to artificial randomly assembled communities rejected the null hypothesis that diatom communities were assembled solely by stochastic processes. No co-occurrence tests indicated a significant role for competitive exclusion or niche partitioning in microalgal community assembly. In general, predictions about relationships between migration and species diversity were supported for local community dynamics. BMA at low tide (lowest migration) exhibited reduced α-diversity as compared to periods of immersion at both mudflat and sand bar sites. β-diversity was higher during low tide emersion on the mudflat, but did not differ temporally at the sand bar site. In between-site metacommunity comparisons, low- and high-resuspension sites exhibited distinct community compositions while the low-energy mudflats contained higher microalgal biomass and greater α-diversity. To our knowledge this is the first study to test the relevance of neutral processes in structuring marine microalgal communities. Our results demonstrate a prominent role for stochastic factors in structuring local BMA community assembly, although unidentified nonrandom processes also appear to play some role. High passive migration, in particular, appears to help maintain species diversity and structure communities in both sand and muddy habitats. © 2016 Phycological Society of America.

Community phylogenetic analysis of moderately thermophilic cyanobacterial mats from China, the Philippines and Thailand.

PubMed

Hongmei, Jing; Aitchison, Jonathan C; Lacap, Donnabella C; Peerapornpisal, Yuwadee; Sompong, Udomluk; Pointing, Stephen B

2005-08-01

Most community molecular studies of thermophilic cyanobacterial mats to date have focused on Synechococcus occurring at temperatures of approximately 50-65 degrees C. These reveal that molecular diversity exceeds that indicated by morphology, and that phylogeographic lineages exist. The moderately thermophilic and generally filamentous cyanobacterial mat communities occurring at lower temperatures have not previously been investigated at the community molecular level. Here we report community diversity in mats of 42-53 degrees C recovered from previously unstudied geothermal locations. Separation of 16S rRNA gene-defined genotypes from community DNA was achieved by DGGE. Genotypic diversity was greater than morphotype diversity in all mats sampled, although genotypes generally corresponded to observed morphotypes. Thirty-six sequences were recovered from DGGE bands. Phylogenetic analyses revealed these to form novel thermophilic lineages distinct from their mesophilic counterparts, within Calothrix, Cyanothece, Fischerella, Phormidium, Pleurocapsa, Oscillatoria and Synechococcus. Where filamentous cyanobacterial sequences belonging to the same genus were recovered from the same site, these were generally closely affiliated. Location-specific sequences were observed for some genotypes recovered from geochemically similar yet spatially separated sites, thus providing evidence for phylogeographic lineages that evolve in isolation. Other genotypes were more closely affiliated to geographically remote counterparts from similar habitats suggesting that adaptation to certain niches is also important.

Local and Regional Diversity Reveals Dispersal Limitation and Drift as Drivers for Groundwater Bacterial Communities from a Fractured Granite Formation

PubMed Central

Beaton, E. D.; Stevenson, Bradley S.; King-Sharp, Karen J.; Stamps, Blake W.; Nunn, Heather S.; Stuart, Marilyne

2016-01-01

Microorganisms found in terrestrial subsurface environments make up a large proportion of the Earth’s biomass. Biogeochemical cycles catalyzed by subsurface microbes have the potential to influence the speciation and transport of radionuclides managed in geological repositories. To gain insight on factors that constrain microbial processes within a formation with restricted groundwater flow we performed a meta-community analysis on groundwater collected from multiple discrete fractures underlying the Chalk River Laboratories site (located in Ontario, Canada). Bacterial taxa were numerically dominant in the groundwater. Although these were mainly uncultured, the closest cultivated representatives were from the phenotypically diverse Betaproteobacteria, Deltaproteobacteria, Bacteroidetes, Actinobacteria, Nitrospirae, and Firmicutes. Hundreds of taxa were identified but only a few were found in abundance (>1%) across all assemblages. The remainder of the taxa were low abundance. Within an ecological framework of selection, dispersal and drift, the local and regional diversity revealed fewer taxa within each assemblage relative to the meta-community, but the taxa that were present were more related than predicted by chance. The combination of dispersion at one phylogenetic depth and clustering at another phylogenetic depth suggest both niche (dispersion) and filtering (clustering) as drivers of local assembly. Distance decay of similarity reveals apparent biogeography of 1.5 km. Beta diversity revealed greater influence of selection at shallow sampling locations while the influences of dispersal limitation and randomness were greater at deeper sampling locations. Although selection has shaped each assemblage, the spatial scale of groundwater sampling favored detection of neutral processes over selective processes. Dispersal limitation between assemblages combined with local selection means the meta-community is subject to drift, and therefore, likely reflects the differential historical events that have influenced the current bacterial composition. Categorizing the study site into smaller regions of interest of more closely spaced fractures, or of potentially hydraulically connected fractures, might improve the resolution of an analysis to reveal environmental influences that have shaped these bacterial communities. PMID:27999569

Local and Regional Diversity Reveals Dispersal Limitation and Drift as Drivers for Groundwater Bacterial Communities from a Fractured Granite Formation.

PubMed

Beaton, E D; Stevenson, Bradley S; King-Sharp, Karen J; Stamps, Blake W; Nunn, Heather S; Stuart, Marilyne

2016-01-01

Microorganisms found in terrestrial subsurface environments make up a large proportion of the Earth's biomass. Biogeochemical cycles catalyzed by subsurface microbes have the potential to influence the speciation and transport of radionuclides managed in geological repositories. To gain insight on factors that constrain microbial processes within a formation with restricted groundwater flow we performed a meta-community analysis on groundwater collected from multiple discrete fractures underlying the Chalk River Laboratories site (located in Ontario, Canada). Bacterial taxa were numerically dominant in the groundwater. Although these were mainly uncultured, the closest cultivated representatives were from the phenotypically diverse Betaproteobacteria, Deltaproteobacteria, Bacteroidetes, Actinobacteria, Nitrospirae, and Firmicutes. Hundreds of taxa were identified but only a few were found in abundance (>1%) across all assemblages. The remainder of the taxa were low abundance. Within an ecological framework of selection, dispersal and drift, the local and regional diversity revealed fewer taxa within each assemblage relative to the meta-community, but the taxa that were present were more related than predicted by chance. The combination of dispersion at one phylogenetic depth and clustering at another phylogenetic depth suggest both niche (dispersion) and filtering (clustering) as drivers of local assembly. Distance decay of similarity reveals apparent biogeography of 1.5 km. Beta diversity revealed greater influence of selection at shallow sampling locations while the influences of dispersal limitation and randomness were greater at deeper sampling locations. Although selection has shaped each assemblage, the spatial scale of groundwater sampling favored detection of neutral processes over selective processes. Dispersal limitation between assemblages combined with local selection means the meta-community is subject to drift, and therefore, likely reflects the differential historical events that have influenced the current bacterial composition. Categorizing the study site into smaller regions of interest of more closely spaced fractures, or of potentially hydraulically connected fractures, might improve the resolution of an analysis to reveal environmental influences that have shaped these bacterial communities.

The helminth community of the skink Chalcides sexlineatus from Gran Canaria (Canary Islands).

PubMed

Roca, V; Carretero, M A; Jorge, F; Perera, A; Ferrero, A; Rodríguez-Reina, S

2012-06-01

A survey of the gastrointestinal helminth communities of a population of Chalcides sexlineatus Steindachner, a small skink endemic to Gran Canaria island (Canary Archipelago, Spain), was conducted to determine the prevalence, abundance and species diversity of intestinal parasites in these reptiles. Only three parasite species were found, one cestode, Oochoristica agamae Baylis, 1919 and two nematodes, Parapharyngodon micipsae (Seurat, 1917) and Pharyngodonidae gen. sp. Helminth infracommunities of C. sexlineatus showed low values of abundance and species richness and diversity, being more similar to the helminth community of Tarentola boettgeri boettgeri (Steindachner) rather than those of Gallotia stehlini (Schenkel), both syntopic with the sampled host.

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

PubMed Central

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

2014-01-01

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

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

PubMed Central

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

2014-01-01

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

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

PanFP: Pangenome-based functional profiles for microbial communities

DOE PAGES

Jun, Se -Ran; Hauser, Loren John; Schadt, Christopher Warren; ...

2015-09-26

For decades there has been increasing interest in understanding the relationships between microbial communities and ecosystem functions. Current DNA sequencing technologies allows for the exploration of microbial communities in two principle ways: targeted rRNA gene surveys and shotgun metagenomics. For large study designs, it is often still prohibitively expensive to sequence metagenomes at both the breadth and depth necessary to statistically capture the true functional diversity of a community. Although rRNA gene surveys provide no direct evidence of function, they do provide a reasonable estimation of microbial diversity, while being a very cost effective way to screen samples of interestmore » for later shotgun metagenomic analyses. However, there is a great deal of 16S rRNA gene survey data currently available from diverse environments, and thus a need for tools to infer functional composition of environmental samples based on 16S rRNA gene survey data. As a result, we present a computational method called pangenome based functional profiles (PanFP), which infers functional profiles of microbial communities from 16S rRNA gene survey data for Bacteria and Archaea. PanFP is based on pangenome reconstruction of a 16S rRNA gene operational taxonomic unit (OTU) from known genes and genomes pooled from the OTU s taxonomic lineage. From this lineage, we derive an OTU functional profile by weighting a pangenome s functional profile with the OTUs abundance observed in a given sample. We validated our method by comparing PanFP to the functional profiles obtained from the direct shotgun metagenomic measurement of 65 diverse communities via Spearman correlation coefficients. These correlations improved with increasing sequencing depth, within the range of 0.8 0.9 for the most deeply sequenced Human Microbiome Project mock community samples. PanFP is very similar in performance to another recently released tool, PICRUSt, for almost all of survey data analysed here. But, our method is unique in that any OTU building method can be used, as opposed to being limited to closed reference OTU picking strategies against specific reference sequence databases. In conclusion, we developed an automated computational method, which derives an inferred functional profile based on the 16S rRNA gene surveys of microbial communities. The inferred functional profile provides a cost effective way to study complex ecosystems through predicted comparative functional metagenomes and metadata analysis. All PanFP source code and additional documentation are freely available online at GitHub.« less

PanFP: pangenome-based functional profiles for microbial communities.

PubMed

Jun, Se-Ran; Robeson, Michael S; Hauser, Loren J; Schadt, Christopher W; Gorin, Andrey A

2015-09-26

For decades there has been increasing interest in understanding the relationships between microbial communities and ecosystem functions. Current DNA sequencing technologies allows for the exploration of microbial communities in two principle ways: targeted rRNA gene surveys and shotgun metagenomics. For large study designs, it is often still prohibitively expensive to sequence metagenomes at both the breadth and depth necessary to statistically capture the true functional diversity of a community. Although rRNA gene surveys provide no direct evidence of function, they do provide a reasonable estimation of microbial diversity, while being a very cost-effective way to screen samples of interest for later shotgun metagenomic analyses. However, there is a great deal of 16S rRNA gene survey data currently available from diverse environments, and thus a need for tools to infer functional composition of environmental samples based on 16S rRNA gene survey data. We present a computational method called pangenome-based functional profiles (PanFP), which infers functional profiles of microbial communities from 16S rRNA gene survey data for Bacteria and Archaea. PanFP is based on pangenome reconstruction of a 16S rRNA gene operational taxonomic unit (OTU) from known genes and genomes pooled from the OTU's taxonomic lineage. From this lineage, we derive an OTU functional profile by weighting a pangenome's functional profile with the OTUs abundance observed in a given sample. We validated our method by comparing PanFP to the functional profiles obtained from the direct shotgun metagenomic measurement of 65 diverse communities via Spearman correlation coefficients. These correlations improved with increasing sequencing depth, within the range of 0.8-0.9 for the most deeply sequenced Human Microbiome Project mock community samples. PanFP is very similar in performance to another recently released tool, PICRUSt, for almost all of survey data analysed here. But, our method is unique in that any OTU building method can be used, as opposed to being limited to closed-reference OTU picking strategies against specific reference sequence databases. We developed an automated computational method, which derives an inferred functional profile based on the 16S rRNA gene surveys of microbial communities. The inferred functional profile provides a cost effective way to study complex ecosystems through predicted comparative functional metagenomes and metadata analysis. All PanFP source code and additional documentation are freely available online at GitHub ( https://github.com/srjun/PanFP ).

Molecular diversity of bacterial communities from subseafloor rock samples in a deep-water production basin in Brazil.

PubMed

von der Weid, Irene; Korenblum, Elisa; Jurelevicius, Diogo; Rosado, Alexandre Soares; Dino, Rodolfo; Sebastian, Gina Vasquez; Seldin, Lucy

2008-01-01

The deep subseafloor rock in oil reservoirs represents a unique environment in which a high oilcontamination and very low biomass can be observed. Sampling this environment has been a challenge owing to the techniques used for drilling and coring. In this study, the facilities developed by the Brazilian oil company PETROBRAS for accessing deep subsurface oil reservoirs were used to obtain rock samples at 2,822-2,828 m below the ocean floor surface from a virgin field located in the Atlantic Ocean, Rio de Janeiro. To address the bacterial diversity of these rock samples, PCR amplicons were obtained using the DNA from four core sections and universal primers for 16S rRNA and for APS reductase (aps) genes. Clone libraries were generated from these PCR fragments and 87 clones were sequenced. The phylogenetic analyses of the 16S rDNA clone libraries showed a wide distribution of types in the domain bacteria in the four core samples, and the majority of the clones were identified as belonging to Betaproteobacteria. The sulfate-reducing bacteria community could only be amplified by PCR in one sample, and all clones were identified as belonging to Gammaproteobacteria. For the first time, the bacterial community was assessed in such deep subsurface environment.

Molecular profiling of fungal communities in moisture damaged buildings before and after remediation--a comparison of culture-dependent and culture-independent methods.

PubMed

Pitkäranta, Miia; Meklin, Teija; Hyvärinen, Anne; Nevalainen, Aino; Paulin, Lars; Auvinen, Petri; Lignell, Ulla; Rintala, Helena

2011-10-21

Indoor microbial contamination due to excess moisture is an important contributor to human illness in both residential and occupational settings. However, the census of microorganisms in the indoor environment is limited by the use of selective, culture-based detection techniques. By using clone library sequencing of full-length internal transcribed spacer region combined with quantitative polymerase chain reaction (qPCR) for 69 fungal species or assay groups and cultivation, we have been able to generate a more comprehensive description of the total indoor mycoflora. Using this suite of methods, we assessed the impact of moisture damage on the fungal community composition of settled dust and building material samples (n = 8 and 16, correspondingly). Water-damaged buildings (n = 2) were examined pre- and post- remediation, and compared with undamaged reference buildings (n = 2). Culture-dependent and independent methods were consistent in the dominant fungal taxa in dust, but sequencing revealed a five to ten times higher diversity at the genus level than culture or qPCR. Previously unknown, verified fungal phylotypes were detected in dust, accounting for 12% of all diversity. Fungal diversity, especially within classes Dothideomycetes and Agaricomycetes tended to be higher in the water damaged buildings. Fungal phylotypes detected in building materials were present in dust samples, but their proportion of total fungi was similar for damaged and reference buildings. The quantitative correlation between clone library phylotype frequencies and qPCR counts was moderate (r = 0.59, p < 0.01). We examined a small number of target buildings and found indications of elevated fungal diversity associated with water damage. Some of the fungi in dust were attributable to building growth, but more information on the material-associated communities is needed in order to understand the dynamics of microbial communities between building structures and dust. The sequencing-based method proved indispensable for describing the true fungal diversity in indoor environments. However, making conclusions concerning the effect of building conditions on building mycobiota using this methodology was complicated by the wide natural diversity in the dust samples, the incomplete knowledge of material-associated fungi fungi and the semiquantitative nature of sequencing based methods.

Diversity of endolithic fungal communities in dolomite and limestone rocks from Nanjiang Canyon in Guizhou karst area, China.

PubMed

Tang, Yuan; Lian, Bin

2012-06-01

The endolithic environment, the tiny pores and cracks in rocks, buffer microbial communities from a number of physical stresses, such as desiccation, rapid temperature variations, and UV radiation. Considerable knowledge has been acquired about the diversity of microorganisms in these ecosystems, but few culture-independent studies have been carried out on the diversity of fungi to date. Scanning electron microscopy of carbonate rock fragments has revealed that the rock samples contain certain kinds of filamentous fungi. We evaluated endolithic fungal communities from bare dolomite and limestone rocks collected from Nanjiang Canyon (a typical karst canyon in China) using culture-independent methods. Results showed that Ascomycota was absolutely dominant both in the dolomite and limestone fungal clone libraries. Basidiomycota and other eukaryotic groups (Bryophyta and Chlorophyta) were only detected occasionally or at low frequencies. The most common genus in the investigated carbonate rocks was Verrucaria. Some other lichen-forming fungi (e.g., Caloplaca, Exophiala, and Botryolepraria), Aspergillus, and Penicillium were also identified from the rock samples. The results provide a cross-section of the endolithic fungal communities in carbonate rocks and help us understand more about the role of microbes (fungi and other rock-inhabiting microorganisms) in rock weathering and pedogenesis.

Effects of isolation on ant assemblages depend on microhabitat

USGS Publications Warehouse

Chen, Xuan; Adams, Benjamin; Layne, Michael; Swarzenski, Christopher M.; Norris, David O.; Hooper-Bui, Linda

2017-01-01

How isolation affects biological communities is a fundamental question in ecology and conservation biology. Local diversity (α) and regional diversity (γ) are consistently lower in insular areas. The pattern of species turnover (β diversity) and the influence of isolation on competitive interactions are less predictable. Differences in communities across microhabitats within an isolated patch could contribute to the variability in patterns related to isolation. Trees form characteristically dense and sparse patches (low vs. high isolation) in floating marshes in coastal Louisiana, and canopy and root areas around these trees could support distinct ant communities. Consequently, trees in floating marshes provide an ideal environment to study the effects of isolation on community assemblages in different microhabitats. We sampled ant communities in 120 trees during the summer of 2016. We found ant α diversity was not different between the canopy and roots, and the magnitude and directional effects of isolation on ants were inconsistent between the canopy and root areas. In the roots of sparse sites, ant diversity (α, β, and γ) was lower, species composition was changed, and the signature of interspecific competition was more prominent compared to dense sites. In the canopy, however, significant differences between dense and sparse sites were only detected in α and γ diversity, and ant species co‐occurrence was not significantly different from a random distribution. The inconsistent responses of ants in canopy and root areas to isolation may be due to the differences of species pool size, environmental harshness, and species interactions between strata. In addition, these findings indicate that communities in distinct microenvironments can respond differentially to habitat isolation. We suggest incorporating organisms from different microhabitats into future research to better understand the influence of isolation on the assembly of biological communities.

[Community composition and diversity of endophytic fungi from roots of Sinopodophyllum hexandrum in forest of Upper-north mountain of Qinghai province].

PubMed

Ning, Yi; Li, Yan-Ling; Zhou, Guo-Ying; Yang, Lu-Cun; Xu, Wen-Hua

2016-04-01

High throughput sequencing technology is also called Next Generation Sequencing (NGS), which can sequence hundreds and thousands sequences in different samples at the same time. In the present study, the culture-independent high throughput sequencing technology was applied to sequence the fungi metagenomic DNA of the fungal internal transcribed spacer 1(ITS 1) in the root of Sinopodophyllum hexandrum. Sequencing data suggested that after the quality control, 22 565 reads were remained. Cluster similarity analysis was done based on 97% sequence similarity, which obtained 517 OTUs for the three samples (LD1, LD2 and LD3). All the fungi which identified from all the reads of OTUs based on 0.8 classification thresholds using the software of RDP classifier were classified as 13 classes, 35 orders, 44 family, 55 genera. Among these genera, the genus of Tetracladium was the dominant genera in all samples(35.49%, 68.55% and 12.96%).The Shannon's diversity indices and the Simpson indices of the endophytic fungi in the samples ranged from 1.75-2.92, 0.11-0.32, respectively.This is the first time for applying high through put sequencing technol-ogyto analyze the community composition and diversity of endophytic fungi in the medicinal plant, and the results showed that there were hyper diver sity and high community composition complexity of endophytic fungi in the root of S. hexandrum. It is also proved that the high through put sequencing technology has great advantage for analyzing ecommunity composition and diversity of endophtye in the plant. Copyright© by the Chinese Pharmaceutical Association.

Diversity, Abundance and Community Structure of Benthic Macro- and Megafauna on the Beaufort Shelf and Slope

PubMed Central

Nephin, Jessica; Juniper, S. Kim; Archambault, Philippe

2014-01-01

Diversity and community patterns of macro- and megafauna were compared on the Canadian Beaufort shelf and slope. Faunal sampling collected 247 taxa from 48 stations with box core and trawl gear over the summers of 2009–2011 between 50 and 1,000 m in depth. Of the 80 macrofaunal and 167 megafaunal taxa, 23% were uniques, present at only one station. Rare taxa were found to increase proportional to total taxa richness and differ between the shelf ( 100 m) where they tended to be sparse and the slope where they were relatively abundant. The macrofauna principally comprised polychaetes with nephtyid polychaetes dominant on the shelf and maldanid polychaetes (up to 92% in relative abundance/station) dominant on the slope. The megafauna principally comprised echinoderms with Ophiocten sp. (up to 90% in relative abundance/station) dominant on the shelf and Ophiopleura sp. dominant on the slope. Macro- and megafauna had divergent patterns of abundance, taxa richness ( diversity) and diversity. A greater degree of macrofaunal than megafaunal variation in abundance, richness and diversity was explained by confounding factors: location (east-west), sampling year and the timing of sampling with respect to sea-ice conditions. Change in megafaunal abundance, richness and diversity was greatest across the depth gradient, with total abundance and richness elevated on the shelf compared to the slope. We conclude that megafaunal slope taxa were differentiated from shelf taxa, as faunal replacement not nestedness appears to be the main driver of megafaunal diversity across the depth gradient. PMID:25007347

Diversity, abundance and community structure of benthic macro- and megafauna on the Beaufort shelf and slope.

PubMed

Nephin, Jessica; Juniper, S Kim; Archambault, Philippe

2014-01-01

Diversity and community patterns of macro- and megafauna were compared on the Canadian Beaufort shelf and slope. Faunal sampling collected 247 taxa from 48 stations with box core and trawl gear over the summers of 2009-2011 between 50 and 1,000 m in depth. Of the 80 macrofaunal and 167 megafaunal taxa, 23% were uniques, present at only one station. Rare taxa were found to increase proportional to total taxa richness and differ between the shelf (< 100 m) where they tended to be sparse and the slope where they were relatively abundant. The macrofauna principally comprised polychaetes with nephtyid polychaetes dominant on the shelf and maldanid polychaetes (up to 92% in relative abundance/station) dominant on the slope. The megafauna principally comprised echinoderms with Ophiocten sp. (up to 90% in relative abundance/station) dominant on the shelf and Ophiopleura sp. dominant on the slope. Macro- and megafauna had divergent patterns of abundance, taxa richness (α diversity) and β diversity. A greater degree of macrofaunal than megafaunal variation in abundance, richness and β diversity was explained by confounding factors: location (east-west), sampling year and the timing of sampling with respect to sea-ice conditions. Change in megafaunal abundance, richness and β diversity was greatest across the depth gradient, with total abundance and richness elevated on the shelf compared to the slope. We conclude that megafaunal slope taxa were differentiated from shelf taxa, as faunal replacement not nestedness appears to be the main driver of megafaunal β diversity across the depth gradient.

Biogeography and Metabolic Potential of Soil Microbial Communities Across Local Environmental Gradients Illuminated Through Metagenomics

NASA Astrophysics Data System (ADS)

Sharrar, A.; Diamond, S.; Butterfield, C.; Starr, E.; Thomas, B. C.; Banfield, J. F.

2016-12-01

Soils are extremely heterogeneous and diverse microbial habitats. The distribution of microbes and their metabolic functions in soil is important for carbon and nitrogen cycling and overall ecosystem functioning. Little is known about biogeographical patterns of microbes in soil and how they relate to different environmental gradients. To address this topic, we have obtained metagenomes from 86 soil samples taken at the Eel River Critical Zone Observatory and a nearby meadow in the northern California Angelo Coast Range Reserve over a period of two years. These samples span a variety of environmental parameters, including depth, relief, time since last rainfall, and proximity to root carbon inputs. Phylogenetic diversity and community overlap between these samples was analyzed using ribosomal protein sequence identity and scaffold coverage. Independent of genomic bins, de-replicated ribosomal protein sequences were used to identify thousands of unique organisms between datasets. Despite environmental differences, a subset of these organisms were found in every sample. The dominant phyla in this cosmopolitan subset were Proteobacteria, Actinobacteria, Gemmatimonadetes, Verrucomicrobia, Acidobacteria, and Rokubacteria. Archaea and Nitrospirae were particularly prevalent at depths below 30cm. Patterns of ribosomal protein scaffold coverage across samples was used to compare the similarity of the microbial communities. We found that location was the greatest predictor of community similarity, followed by depth. In a subset of 60 samples taken in the same meadow, sampling plot was a greater predictor of community similarity than time since last rainfall in the same year. In addition, genome-independent analyses revealed differences in the metabolic potential for functions involved in nitrogen and carbon metabolism across environmental gradients. This study will further our understanding of soil biogeography and its relationship to overall biogeochemical cycling.

Microbial diversity and community structure in an antimony-rich tailings dump.

PubMed

Xiao, Enzong; Krumins, Valdis; Dong, Yiran; Xiao, Tangfu; Ning, Zengping; Xiao, Qingxiang; Sun, Weimin

2016-09-01

To assess the impact of antimony (Sb) on microbial community structure, 12 samples were taken from an Sb tailings pile in Guizhou Province, Southwest China. All 12 samples exhibited elevated Sb concentrations, but the mobile and bioaccessible fractions were small in comparison to total Sb concentrations. Besides the geochemical analyses, microbial communities inhabiting the tailing samples were characterized to investigate the interplay between the microorganisms and environmental factors in mine tailings. In all samples, Proteobacteria and Actinobacteria were the most dominant phyla. At the genus level, Thiobacillus, Limnobacter, Nocardioides, Lysobacter, Phormidium, and Kaistobacter demonstrated relatively high abundances. The two most abundant genera, Thiobacillus and Limnobacter, are characterized as sulfur-oxidizing bacteria and thiosulfate-oxidizing bacteria, respectively, while the genus Lysobacter contains arsenic (As)-resistant bacteria. Canonical correspondence analysis (CCA) indicates that TOC and the sulfate to sulfide ratio strongly shaped the microbial communities, suggesting the influence of the environmental factors in the indigenous microbial communities.

Functions and Unique Diversity of Genes and Microorganisms Involved in Arsenite Oxidation from the Tailings of a Realgar Mine

PubMed Central

E, Guoji; Wang, Jianing; Wang, Nian; Chen, Xiaoming; Mu, Yao; Li, Hao; Yang, Ye; Liu, Yichen; Wang, Yanxin

2016-01-01

ABSTRACT The tailings of the Shimen realgar mine have unique geochemical features. Arsenite oxidation is one of the major biogeochemical processes that occurs in the tailings. However, little is known about the functional and molecular aspects of the microbial community involved in arsenite oxidation. Here, we fully explored the functional and molecular features of the microbial communities from the tailings of the Shimen realgar mine. We collected six samples of tailings from sites A, B, C, D, E, and F. Microcosm assays indicated that all of the six sites contain both chemoautotrophic and heterotrophic arsenite-oxidizing microorganisms; their activities differed considerably from each other. The microbial arsenite-oxidizing activities show a positive correlation with soluble arsenic concentrations. The microbial communities of the six sites contain 40 phyla of bacteria and 2 phyla of archaea that show extremely high diversity. Soluble arsenic, sulfate, pH, and total organic carbon (TOC) are the key environmental factors that shape the microbial communities. We further identified 114 unique arsenite oxidase genes from the samples; all of them code for new or new-type arsenite oxidases. We also isolated 10 novel arsenite oxidizers from the samples, of which 4 are chemoautotrophic and 6 are heterotrophic. These data highlight the unique diversities of the arsenite-oxidizing microorganisms and their oxidase genes from the tailings of the Shimen realgar mine. To the best of our knowledge, this is the first report describing the functional and molecular features of microbial communities from the tailings of a realgar mine. IMPORTANCE This study focused on the functional and molecular characterizations of microbial communities from the tailings of the Shimen realgar mine. We fully explored, for the first time, the arsenite-oxidizing activities and the functional gene diversities of microorganisms from the tailings, as well as the correlation of the microbial activities/diversities with environmental factors. The findings of this study help us to better understand the diversities of the arsenite-oxidizing bacteria and the geochemical cycle of arsenic in the tailings of the Shimen realgar mine and gain insights into the microbial mechanisms by which the secondary minerals of the tailings were formed. This work also offers a set of unique arsenite-oxidizing bacteria for basic research of the molecular regulation of arsenite oxidation in bacterial cells and for the environmentally friendly bioremediation of arsenic-contaminated groundwater. PMID:27663031

Functions and Unique Diversity of Genes and Microorganisms Involved in Arsenite Oxidation from the Tailings of a Realgar Mine.

PubMed

Zeng, Xian-Chun; E, Guoji; Wang, Jianing; Wang, Nian; Chen, Xiaoming; Mu, Yao; Li, Hao; Yang, Ye; Liu, Yichen; Wang, Yanxin

2016-12-15

The tailings of the Shimen realgar mine have unique geochemical features. Arsenite oxidation is one of the major biogeochemical processes that occurs in the tailings. However, little is known about the functional and molecular aspects of the microbial community involved in arsenite oxidation. Here, we fully explored the functional and molecular features of the microbial communities from the tailings of the Shimen realgar mine. We collected six samples of tailings from sites A, B, C, D, E, and F. Microcosm assays indicated that all of the six sites contain both chemoautotrophic and heterotrophic arsenite-oxidizing microorganisms; their activities differed considerably from each other. The microbial arsenite-oxidizing activities show a positive correlation with soluble arsenic concentrations. The microbial communities of the six sites contain 40 phyla of bacteria and 2 phyla of archaea that show extremely high diversity. Soluble arsenic, sulfate, pH, and total organic carbon (TOC) are the key environmental factors that shape the microbial communities. We further identified 114 unique arsenite oxidase genes from the samples; all of them code for new or new-type arsenite oxidases. We also isolated 10 novel arsenite oxidizers from the samples, of which 4 are chemoautotrophic and 6 are heterotrophic. These data highlight the unique diversities of the arsenite-oxidizing microorganisms and their oxidase genes from the tailings of the Shimen realgar mine. To the best of our knowledge, this is the first report describing the functional and molecular features of microbial communities from the tailings of a realgar mine. This study focused on the functional and molecular characterizations of microbial communities from the tailings of the Shimen realgar mine. We fully explored, for the first time, the arsenite-oxidizing activities and the functional gene diversities of microorganisms from the tailings, as well as the correlation of the microbial activities/diversities with environmental factors. The findings of this study help us to better understand the diversities of the arsenite-oxidizing bacteria and the geochemical cycle of arsenic in the tailings of the Shimen realgar mine and gain insights into the microbial mechanisms by which the secondary minerals of the tailings were formed. This work also offers a set of unique arsenite-oxidizing bacteria for basic research of the molecular regulation of arsenite oxidation in bacterial cells and for the environmentally friendly bioremediation of arsenic-contaminated groundwater. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Applications of Ecophylogenetics to Benthic Communities in the Northern Gulf of Mexico: Do Functional Traits Follow Phylogeny?

NASA Astrophysics Data System (ADS)

Gadeken, K.; Dorgan, K. M.; Moore, J.; Berke, S. K.

2016-02-01

Evolutionary relationships may shed light on observed patterns of diversity and functional traits when viewed through the lens of phylogeny. The potential for phylogenetic information to be used to explain patterns in community structure, such as niche partitioning and responses to stress, is extensive. Differential distribution of related species with similar functional traits suggests niche partitioning, and local redundancy in functional traits may indicate the potential for interspecific competition. In this study, we investigated phylogenetic and functional diversity as a function of habitat for sites with varying levels of oil contamination in the Northern Gulf of Mexico. Our study was conducted in a shallow benthic community at the Chandeleur Islands, a group of uninhabited barrier islands. Infauna were sampled from seagrass (Halodule wrightii) and bare sediment at three sites along the island chain that experienced variable levels of oil impact from the Deepwater Horizon oil spill. Individuals were preserved and 18S and COI genes sequenced, and a phylogenetic tree was constructed of the local community using maximum likelihood. Phylogenetic diversity and evenness were quantified. Ecologically important functional traits were then compiled into respective distance matrices, evaluated through different functional diversity indices, and assessed for correlation with the phylogeny. This integration of functional and phylogenetic diversity has the potential to provide greater insight into factors driving community structure than either metric alone. Determining relevant metrics of diversity is critical to understanding the ecological effects of major disturbances such as oil spills.

Ant community change across a ground vegetation gradient in north Florida's longleaf pine flatwoods

PubMed Central

Lubertazzi, David; Tschinkel, Walter R.

2003-01-01

Ant communities in longleaf pine habitats are poorly known and hence the naturally occurring ant assemblages of a large portion of southeastern North America are not well understood. This study examined the diverse ant community found in the longleaf pine flatwoods of north Florida and tested how ant diversity changes along a herbaceous ground cover gradient. Restoring the ground cover to its original floral composition is an important focus of longleaf pine conservation and hence it is important to understand how native faunal communities vary with ground cover variation. Using 4 sampling methods, we characterized the ant community and analyzed its within-habitat variation among 12 study sites. We found the highest plot species richness (55 species) and within-habitat species richness (72 species) ever recorded for North American ants. The ants formed three distinct communities. The low-diversity arboreal and subterranean assemblages varied little across forest stands while the diversity of the species-rich ground foraging ant community was negatively correlated with percent herbaceous cover. The imported fire ant, Solenopsis invicta (monogyne form), was unexpectedly found to be abundant in high herbaceous cover sites. Floral restoration of the pine flatwoods, which is increasing the proportion of herbaceous cover, is likely to cause an increase in the abundance of the imported fire ant. Abbreviation: ANF Apalachicola National Forest PMID:15841237

Deep-Sea Macrobenthos Community Structure Proximal to the 2010 Macondo Well Blowout (2010-2011)

NASA Astrophysics Data System (ADS)

Briggs, K. B.; Brunner, C. A.; Yeager, K. M.

2017-12-01

Macrobenthos, polycyclic aromatic hydrocarbons (PAH) and sedimentary organic carbon (SOC) were sampled by multicorer in the vicinity of the Deepwater Horizon well head in October 2010 and 2011 to assess the effects of the April 2010 spill. Four stations were sampled east of the well head, four stations were sampled west of the well head, and "control" stations were sampled 58 and 65 km to the southwest. The macrobenthos community, as expected for continental slope/bathyal (water depth 1160-1760 m) benthos, was highly diverse. Polychaetes dominated at all stations, with either crustaceans or mollusks comprising the next most abundant taxon. The stations within five km of the well head showed slightly lower diversity than the more distal stations six months after the blowout. Compared to the "control" station, proportions of suspension feeders were generally depressed at stations with high PAH concentrations. Anomalously high values for abundance and diversity (and PAH) were found at one station 20 km west of the well head. The median body size of macrobenthos was negatively correlated with total PAH concentration, with 74% of the variation in median size explained by variation in PAH, when the anomalous station was excluded. Macrobenthos abundance did not appear to be influenced by SOC. Abundance and diversity of the macrobenthos was generally higher 18 months after the blowout, with measured PAH concentrations diminished to below background level.

The diversity of ant communities (Hymenoptera: Formicidae) and their connections with other arthropods from three temperate forests of Central Mexico.

PubMed

Guzmán-Mendoza, Rafael; Castaño-Meneses, Gabriela; Nuñez-Palenius, Hector Gordon

2016-06-01

Ants have been considered useful for bioindication because of their ecological characteristics. Nonetheless, among the characteristics of a bioindicator group, there must be a consistent and replicable response to disturbance. In this sense, divergent reactions have been found, even between taxons narrowly related. The objective of this work was to compare the diversity of the ant communities in three different temperate forests with different levels of disturbance, and to correlate their abundance and diversity of species, with that found in other arthropod communities of the same forests. The work was carried out in three municipalities in the North of the State of Mexico, where three types of different forests were identified by their degree of disturbance. These types include: 1) primary forest (PF), with typical species of a conserved forest; 2) mixed forest (MF), with species of a conserved forest and a reforestation effort; and 3) reforested forest (RF), with species used in reforestation efforts and indicative of disturbance. In each sample, an area of 2 500 m2 was selected. Each area had 16 pitfalls apiece and they were placed 10 m away from each other. Samples were collected twice; one from February through March 2009 (dry season) and another from August through September 2010 (rainy season), which produced a total of 192 traps. Obtained specimens were identified at the most taxonomically specific level. All data captured was transformed to √n + 0.5 and diversity index levels of Shannon and Simpson were calculated, as well as richness of species for ants, beetles, grasshoppers, true bugs, and spiders. The values of richness, diversity, and abundance were correlated with the Pearson coefficient, and to evaluate possible causal relationships between these, a path analysis was performed. Results suggested an important influence of the site over ant communities, and values of richness, abundance and diversity were correlated with the communities of spiders, beetles, grasshoppers and true bugs, but not for all the sites studied. Responses to environmental changes are not only on the numeric proportions of abundance, richness and diversity, but also in the indirect and casual ecological interactions. Finally, the data seems to indicate that the responses of the ants to the environmental changes are not necessarily reflected on other organisms’ communities, so the ants’ role as bioindicators can be limited.

Factors Determining Forest Diversity and Biomass on a Tropical Volcano, Mt. Rinjani, Lombok, Indonesia

PubMed Central

Dossa, Gbadamassi G. O.; Paudel, Ekananda; Fujinuma, Junichi; Yu, Haiying; Chutipong, Wanlop; Zhang, Yuan; Paz, Sherryl; Harrison, Rhett D.

2013-01-01

Tropical volcanoes are an important but understudied ecosystem, and the relationships between plant species diversity and compositional change and elevation may differ from mountains created by uplift, because of their younger and more homogeneous soils. We sampled vegetation over an altitudinal gradient on Mt. Rinjani, Lombok, Indonesia. We modeled alpha- (plot) and beta- (among plot) diversity (Fisher's alpha), compositional change, and biomass against elevation and selected covariates. We also examined community phylogenetic structure across the elevational gradient. We recorded 902 trees and shrubs among 92 species, and 67 species of ground-cover plants. For understorey, subcanopy and canopy plants, an increase in elevation was associated with a decline in alpha-diversity, whereas data for ground-cover plants suggested a hump-shaped pattern. Elevation was consistently the most important factor in determining alpha-diversity for all components. The alpha-diversity of ground-cover vegetation was also negatively correlated with leaf area index, which suggests low light conditions in the understorey may limit diversity at lower elevations. Beta-diversity increased with elevation for ground-cover plants and declined at higher elevations for other components of the vegetation. However, statistical power was low and we could not resolve the relative importance to beta-diversity of different factors. Multivariate GLMs of variation in community composition among plots explained 67.05%, 27.63%, 18.24%, and 19.80% of the variation (deviance) for ground-cover, understorey, subcanopy and canopy plants, respectively, and demonstrated that elevation was a consistently important factor in determining community composition. Above-ground biomass showed no significant pattern with elevation and was also not significantly associated with alpha-diversity. At lower elevations communities had a random phylogenetic structure, but from 1600 m communities were phylogenetically clustered. This suggests a greater role of environmental filtering at higher elevations, and thus provides a possible explanation for the observed decline in diversity with elevation. PMID:23935842

Effects of Ice-Algal Aggregate Export on the Connectivity of Bacterial Communities in the Central Arctic Ocean

PubMed Central

Rapp, Josephine Z.; Fernández-Méndez, Mar; Bienhold, Christina; Boetius, Antje

2018-01-01

In summer 2012, Arctic sea ice declined to a record minimum and, as a consequence of the melting, large amounts of aggregated ice-algae sank to the seafloor at more than 4,000 m depth. In this study, we assessed the composition, turnover and connectivity of bacterial and microbial eukaryotic communities across Arctic habitats from sea ice, algal aggregates and surface waters to the seafloor. Eukaryotic communities were dominated by diatoms, dinoflagellates and other alveolates in all samples, and showed highest richness and diversity in sea-ice habitats (∼400–500 OTUs). Flavobacteriia and Gammaproteobacteria were the predominant bacterial classes across all investigated Arctic habitats. Bacterial community richness and diversity peaked in deep-sea samples (∼1,700 OTUs). Algal aggregate-associated bacterial communities were mainly recruited from the sea-ice community, and were transported to the seafloor with the sinking ice algae. The algal deposits at the seafloor had a unique community structure, with some shared sequences with both the original sea-ice community (22% OTU overlap), as well as with the deep-sea sediment community (17% OTU overlap). We conclude that ice-algal aggregate export does not only affect carbon export from the surface to the seafloor, but may change microbial community composition in central Arctic habitats with potential effects for benthic ecosystem functioning in the future. PMID:29875749

Microbial biogeography of San Francisco Bay sediments

NASA Astrophysics Data System (ADS)

Lee, J. A.; Francis, C. A.

2014-12-01

The largest estuary on the west coast of North America, San Francisco Bay is an ecosystem of enormous biodiversity, and also enormous human impact. The benthos has experienced dredging, occupation by invasive species, and over a century of sediment input as a result of hydraulic mining. Although the Bay's great cultural and ecological importance has inspired numerous surveys of the benthic macrofauna, to date there has been almost no investigation of the microbial communities on the Bay floor. An understanding of those microbial communities would contribute significantly to our understanding of both the biogeochemical processes (which are driven by the microbiota) and the physical processes (which contribute to microbial distributions) in the Bay. Here, we present the first broad survey of bacterial and archaeal taxa in the sediments of the San Francisco Bay. We conducted 16S rRNA community sequencing of bacteria and archaea in sediment samples taken bimonthly for one year, from five sites spanning the salinity gradient between Suisun and Central Bay, in order to capture the effect of both spatial and temporal environmental variation on microbial diversity. From the same samples we also conducted deep sequencing of a nitrogen-cycling functional gene, nirS, allowing an assessment of evolutionary diversity at a much finer taxonomic scale within an important and widespread functional group of bacteria. We paired these sequencing projects with extensive geochemical metadata as well as information about macrofaunal distribution. Our data reveal a diversity of distinct biogeographical patterns among different taxa: clades ubiquitous across sites; clades that respond to measurable environmental drivers; and clades that show geographical site-specificity. These community datasets allow us to test the hypothesis that salinity is a major driver of both overall microbial community structure and community structure of the denitrifying bacteria specifically; and to assess whether patterns of diversity observed at the broadest of taxonomic scales also apply to patterns observed within a single extremely diverse gene (nirS). In sum, this project provides a first look at the forces driving the migration and selection of microbial communities in San Francisco Bay.

Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity

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

Roux, Simon; Emerson, Joanne B.; Eloe-Fadrosh, Emiley A.

BackgroundViral metagenomics (viromics) is increasingly used to obtain uncultivated viral genomes, evaluate community diversity, and assess ecological hypotheses. While viromic experimental methods are relatively mature and widely accepted by the research community, robust bioinformatics standards remain to be established. Here we usedin silicomock viral communities to evaluate the viromic sequence-to-ecological-inference pipeline, including (i) read pre-processing and metagenome assembly, (ii) thresholds applied to estimate viral relative abundances based on read mapping to assembled contigs, and (iii) normalization methods applied to the matrix of viral relative abundances for alpha and beta diversity estimates. ResultsTools specifically designed for metagenomes, specifically metaSPAdes, MEGAHIT, andmore » IDBA-UD, were the most effective at assembling viromes. Read pre-processing, such as partitioning, had virtually no impact on assembly output, but may be useful when hardware is limited. Viral populations with 2–5 × coverage typically assembled well, whereas lesser coverage led to fragmented assembly. Strain heterogeneity within populations hampered assembly, especially when strains were closely related (average nucleotide identity, or ANI ≥97%) and when the most abundant strain represented <50% of the population. Viral community composition assessments based on read recruitment were generally accurate when the following thresholds for detection were applied: (i) ≥10 kb contig lengths to define populations, (ii) coverage defined from reads mapping at ≥90% identity, and (iii) ≥75% of contig length with ≥1 × coverage. Finally, although data are limited to the most abundant viruses in a community, alpha and beta diversity patterns were robustly estimated (±10%) when comparing samples of similar sequencing depth, but more divergent (up to 80%) when sequencing depth was uneven across the dataset. In the latter cases, the use of normalization methods specifically developed for metagenomes provided the best estimates. ConclusionsThese simulations provide benchmarks for selecting analysis cut-offs and establish that an optimized sample-to-ecological-inference viromics pipeline is robust for making ecological inferences from natural viral communities. Continued development to better accessing RNA, rare, and/or diverse viral populations and improved reference viral genome availability will alleviate many of viromics remaining limitations.« less

Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity

DOE PAGES

Roux, Simon; Emerson, Joanne B.; Eloe-Fadrosh, Emiley A.; ...

2017-09-21

BackgroundViral metagenomics (viromics) is increasingly used to obtain uncultivated viral genomes, evaluate community diversity, and assess ecological hypotheses. While viromic experimental methods are relatively mature and widely accepted by the research community, robust bioinformatics standards remain to be established. Here we usedin silicomock viral communities to evaluate the viromic sequence-to-ecological-inference pipeline, including (i) read pre-processing and metagenome assembly, (ii) thresholds applied to estimate viral relative abundances based on read mapping to assembled contigs, and (iii) normalization methods applied to the matrix of viral relative abundances for alpha and beta diversity estimates. ResultsTools specifically designed for metagenomes, specifically metaSPAdes, MEGAHIT, andmore » IDBA-UD, were the most effective at assembling viromes. Read pre-processing, such as partitioning, had virtually no impact on assembly output, but may be useful when hardware is limited. Viral populations with 2–5 × coverage typically assembled well, whereas lesser coverage led to fragmented assembly. Strain heterogeneity within populations hampered assembly, especially when strains were closely related (average nucleotide identity, or ANI ≥97%) and when the most abundant strain represented <50% of the population. Viral community composition assessments based on read recruitment were generally accurate when the following thresholds for detection were applied: (i) ≥10 kb contig lengths to define populations, (ii) coverage defined from reads mapping at ≥90% identity, and (iii) ≥75% of contig length with ≥1 × coverage. Finally, although data are limited to the most abundant viruses in a community, alpha and beta diversity patterns were robustly estimated (±10%) when comparing samples of similar sequencing depth, but more divergent (up to 80%) when sequencing depth was uneven across the dataset. In the latter cases, the use of normalization methods specifically developed for metagenomes provided the best estimates. ConclusionsThese simulations provide benchmarks for selecting analysis cut-offs and establish that an optimized sample-to-ecological-inference viromics pipeline is robust for making ecological inferences from natural viral communities. Continued development to better accessing RNA, rare, and/or diverse viral populations and improved reference viral genome availability will alleviate many of viromics remaining limitations.« less

Bat community species richness and composition in a restinga protected area in Southeastern Brazil.

PubMed

Oprea, M; Esbérard, C E L; Vieira, T B; Mendes, P; Pimenta, V T; Brito, D; Ditchfield, A D

2009-11-01

In Brazil, restingas are under severe human-induced impacts resulting in habitat degradation and loss and remain one of the less frequently studied ecosystems. The main objectives of the present study are to describe the bat community in a restinga in Paulo Cesar Vinha State Park, Guarapari municipality, state of Espírito Santo, southeastern Brazil. Fieldwork was conducted twice a month from August 2004 to September 2005. A total sampling effort of 40,300 m(2)/h, represents the largest sampling effort for sampling bats in restingas to date. Bats were sampled in five different vegetational types in the area. Captured bats were processed recording information on species, sex, age, forearm length and weight. Shannon Diversity and Jaccard indexes were used to analyse diversity and similarity among habitats in the Park. A total of 554 captures belonging to 14 species and two families were obtained. Noctilio leporinus was recorded through direct observation and an ultra-sound detector also registered the presence of individuals from the family Molossidae, without being possible to distinguish it at specific level. Frugivores were the most representative guild. Richness was higher in Clusia shrubs (11 species) and Caraís lagoon (10 species). Shannon diversity index was estimated at H' = 1.43 for the overall sample, with Caraís lagoon representing the most diverse habitat (H' = 1.60). The greater similarity (J = 0.714) was observed for the two areas under high human influence.

Anodic microbial community diversity as a predictor of the power output of microbial fuel cells.

PubMed

Stratford, James P; Beecroft, Nelli J; Slade, Robert C T; Grüning, André; Avignone-Rossa, Claudio

2014-03-01

The relationship between the diversity of mixed-species microbial consortia and their electrogenic potential in the anodes of microbial fuel cells was examined using different diversity measures as predictors. Identical microbial fuel cells were sampled at multiple time-points. Biofilm and suspension communities were analysed by denaturing gradient gel electrophoresis to calculate the number and relative abundance of species. Shannon and Simpson indices and richness were examined for association with power using bivariate and multiple linear regression, with biofilm DNA as an additional variable. In simple bivariate regressions, the correlation of Shannon diversity of the biofilm and power is stronger (r=0.65, p=0.001) than between power and richness (r=0.39, p=0.076), or between power and the Simpson index (r=0.5, p=0.018). Using Shannon diversity and biofilm DNA as predictors of power, a regression model can be constructed (r=0.73, p<0.001). Ecological parameters such as the Shannon index are predictive of the electrogenic potential of microbial communities. Copyright © 2014 Elsevier Ltd. All rights reserved.

Phylogenetic diversity and biogeography of the Mamiellophyceae lineage of eukaryotic phytoplankton across the oceans.

PubMed

Monier, Adam; Worden, Alexandra Z; Richards, Thomas A

2016-08-01

High-throughput diversity amplicon sequencing of marine microbial samples has revealed that members of the Mamiellophyceae lineage are successful phytoplankton in many oceanic habitats. Indeed, these eukaryotic green algae can dominate the picoplanktonic biomass, however, given the broad expanses of the oceans, their geographical distributions and the phylogenetic diversity of some groups remain poorly characterized. As these algae play a foundational role in marine food webs, it is crucial to assess their global distribution in order to better predict potential changes in abundance and community structure. To this end, we analyzed the V9-18S small subunit rDNA sequences deposited from the Tara Oceans expedition to evaluate the diversity and biogeography of these phytoplankton. Our results show that the phylogenetic composition of Mamiellophyceae communities is in part determined by geographical provenance, and do not appear to be influenced - in the samples recovered - by water depth, at least at the resolution possible with the V9-18S. Phylogenetic classification of Mamiellophyceae sequences revealed that the Dolichomastigales order encompasses more sequence diversity than other orders in this lineage. These results indicate that a large fraction of the Mamiellophyceae diversity has been hitherto overlooked, likely because of a combination of size fraction, sequencing and geographical limitations. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Phylogenetic analysis of a spontaneous cocoa bean fermentation metagenome reveals new insights into its bacterial and fungal community diversity.

PubMed

Illeghems, Koen; De Vuyst, Luc; Papalexandratou, Zoi; Weckx, Stefan

2012-01-01

This is the first report on the phylogenetic analysis of the community diversity of a single spontaneous cocoa bean box fermentation sample through a metagenomic approach involving 454 pyrosequencing. Several sequence-based and composition-based taxonomic profiling tools were used and evaluated to avoid software-dependent results and their outcome was validated by comparison with previously obtained culture-dependent and culture-independent data. Overall, this approach revealed a wider bacterial (mainly γ-Proteobacteria) and fungal diversity than previously found. Further, the use of a combination of different classification methods, in a software-independent way, helped to understand the actual composition of the microbial ecosystem under study. In addition, bacteriophage-related sequences were found. The bacterial diversity depended partially on the methods used, as composition-based methods predicted a wider diversity than sequence-based methods, and as classification methods based solely on phylogenetic marker genes predicted a more restricted diversity compared with methods that took all reads into account. The metagenomic sequencing analysis identified Hanseniaspora uvarum, Hanseniaspora opuntiae, Saccharomyces cerevisiae, Lactobacillus fermentum, and Acetobacter pasteurianus as the prevailing species. Also, the presence of occasional members of the cocoa bean fermentation process was revealed (such as Erwinia tasmaniensis, Lactobacillus brevis, Lactobacillus casei, Lactobacillus rhamnosus, Lactococcus lactis, Leuconostoc mesenteroides, and Oenococcus oeni). Furthermore, the sequence reads associated with viral communities were of a restricted diversity, dominated by Myoviridae and Siphoviridae, and reflecting Lactobacillus as the dominant host. To conclude, an accurate overview of all members of a cocoa bean fermentation process sample was revealed, indicating the superiority of metagenomic sequencing over previously used techniques.

A communal catalogue reveals Earth’s multiscale microbial diversity

DOE PAGES

Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel; ...

2017-11-01

Our growing awareness of the importance and diversity of the microbial world contrasts starkly with our limited understanding of its fundamental structure. Despite remarkable advances in DNA sequence generation, a lack of standardized protocols and common analytical framework impede useful comparison between studies, hindering development of global inferences about microbial life on Earth. Here, we show that with coordinated protocols, exact microbial 16S rRNA gene sequences can be followed across scores of individual studies, revealing patterns of diversity, community structure, and life history strategy at a planetary scale. Using 27,751 crowdsourced environmental samples comprising more than 2.2 billion reads, wemore » find sharp divides between host-associated and free-living communities. We show that the distribution of taxonomic and sequence diversity follows consistent trends across samples types and along gradients of environmental parameters, highlighting some of the global evolutionary patterns and ecological principles that underpin Earth’s microbiome. Here, this dataset provides the most complete environmental survey of our microbial world to date, and serves as a growing reference to provide immediate global context to future microbial surveys.« less

A communal catalogue reveals Earth’s multiscale microbial diversity

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

Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel

Our growing awareness of the importance and diversity of the microbial world contrasts starkly with our limited understanding of its fundamental structure. Despite remarkable advances in DNA sequence generation, a lack of standardized protocols and common analytical framework impede useful comparison between studies, hindering development of global inferences about microbial life on Earth. Here, we show that with coordinated protocols, exact microbial 16S rRNA gene sequences can be followed across scores of individual studies, revealing patterns of diversity, community structure, and life history strategy at a planetary scale. Using 27,751 crowdsourced environmental samples comprising more than 2.2 billion reads, wemore » find sharp divides between host-associated and free-living communities. We show that the distribution of taxonomic and sequence diversity follows consistent trends across samples types and along gradients of environmental parameters, highlighting some of the global evolutionary patterns and ecological principles that underpin Earth’s microbiome. Here, this dataset provides the most complete environmental survey of our microbial world to date, and serves as a growing reference to provide immediate global context to future microbial surveys.« less

Trauma and Psychological Distress among Ethnically Diverse Community College Students

ERIC Educational Resources Information Center

Edman, Jeanne L.; Watson, Susan B.; Patron, David J.

2016-01-01

An association has been found between traumatic experiences and psychological distress; however, the impact of ethnicity on psychological distress is less clear. The present study examined the relationship between traumatic experiences and measures of psychological distress among a multiethnic sample of community college students. A total of 389…

From Schoolhouse to Statehouse: Community Organizing for Public School Reform.

ERIC Educational Resources Information Center

Kamber, Thomas

This report reviews the activities, strategies, successes, and problems of diverse school reform efforts across a 14-state sample of community organizations. In 1999 and 2000, interviewers visited over 40 organizations and conducted telephone interviews with dozens of other organizations involved in education reform. They met with directors,…

Diversity and Distribution of Aquatic Fungal Communities in the Ny-Ålesund Region, Svalbard (High Arctic): Aquatic Fungi in the Arctic.

PubMed

Zhang, Tao; Wang, Neng-Fei; Zhang, Yu-Qin; Liu, Hong-Yu; Yu, Li-Yan

2016-04-01

We assessed the diversity and distribution of fungi in 13 water samples collected from four aquatic environments (stream, pond, melting ice water, and estuary) in the Ny-Ålesund Region, Svalbard (High Arctic) using 454 pyrosequencing with fungi-specific primers targeting the internal transcribed spacer (ITS) region of the ribosomal rRNA gene. Aquatic fungal communities in this region showed high diversity, with a total of 43,061 reads belonging to 641 operational taxonomic units (OTUs) being found. Of these OTUs, 200 belonged to Ascomycota, 196 to Chytridiomycota, 120 to Basidiomycota, 13 to Glomeromycota, and 10 to early diverging fungal lineages (traditional Zygomycota), whereas 102 belonged to unknown fungi. The major orders were Helotiales, Eurotiales, and Pleosporales in Ascomycota; Chytridiales and Rhizophydiales in Chytridiomycota; and Leucosporidiales and Sporidiobolales in Basidiomycota. The common fungal genera Penicillium, Rhodotorula, Epicoccum, Glaciozyma, Holtermanniella, Betamyces, and Phoma were identified. Interestingly, the four aquatic environments in this region harbored different aquatic fungal communities. Salinity, conductivity, and temperature were important factors in determining the aquatic fungal diversity and community composition. The results suggest the presence of diverse fungal communities and a considerable number of potentially novel fungal species in Arctic aquatic environments, which can provide reliable data for studying the ecological and evolutionary responses of fungi to climate change in the Arctic ecosystem.

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

PubMed Central

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

2013-01-01

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

Contrasting clonal structure among Pocillopora (Scleractinia) communities at two environmentally distinct sites in the Gulf of California

NASA Astrophysics Data System (ADS)

Pinzón, J. H.; Reyes-Bonilla, H.; Baums, I. B.; LaJeunesse, T. C.

2012-09-01

The contributions of sexual versus asexual reproduction are thought to play an important role in the abundance and ecological success of corals, especially in marginal habitats. Pocillopora corals are distributed throughout the Indo-Pacific and dominate shallow hard-bottom communities in the eastern Pacific where broad seasonal fluctuations in temperature and water turbidity create suboptimal conditions for reef community development. Previous work had revealed three genetic clades in the eastern Pacific that show little correspondence with colony morphology; the broad distribution of type 1 extends into the subtropical southern Gulf of California. Here we examine genetic and clonal structure of two type 1 communities separated by 10 km with microsatellite data. Samples were collected randomly in six 10 m radius circular plots (20 colonies per plot, 3 plots per site). Sites differed in their relative clonality because clonemates (ramets) from a single clone (genet) dominated a large portion (90.9 m long) of the protected leeward side of Gaviota Island (Number of genets/Number of samples = 0.35; observed Genotypic diversity/expected Genotypic diversity = 0.087), while an exposed community at the entrance to La Paz Bay, Punta Galeras, exhibited high genotypic diversity ( N g / N = 0.85; G o / G e = 0.714). Gene flow was unrestricted between sites indicating these communities comprised a single population. The relative proportion of asexual colonies found between community aggregations of Pocillopora in the Gulf of California differed significantly and suggests factors at local, not regional, scales affect these patterns. The possibility that heterogeneity in clonal structure is common throughout the eastern Pacific and across the west Indo-Pacific requires further study. Finally, since morphological variation in Pocillopora has been underappreciated and is in need of taxonomic revision, the use of a consistent field-sampling protocol and high-resolution makers will advance ecological research and aid in the conservation of these corals.

Bacterial Communities Associated with Host-Adapted Populations of Pea Aphids Revealed by Deep Sequencing of 16S Ribosomal DNA

PubMed Central

Gauthier, Jean-Pierre; Outreman, Yannick; Mieuzet, Lucie; Simon, Jean-Christophe

2015-01-01

Associations between microbes and animals are ubiquitous and hosts may benefit from harbouring microbial communities through improved resource exploitation or resistance to environmental stress. The pea aphid, Acyrthosiphon pisum, is the host of heritable bacterial symbionts, including the obligate endosymbiont Buchnera aphidicola and several facultative symbionts. While obligate symbionts supply aphids with key nutrients, facultative symbionts influence their hosts in many ways such as protection against natural enemies, heat tolerance, color change and reproduction alteration. The pea aphid also encompasses multiple plant-specialized biotypes, each adapted to one or a few legume species. Facultative symbiont communities differ strongly between biotypes, although bacterial involvement in plant specialization is uncertain. Here, we analyse the diversity of bacterial communities associated with nine biotypes of the pea aphid complex using amplicon pyrosequencing of 16S rRNA genes. Combined clustering and phylogenetic analyses of 16S sequences allowed identifying 21 bacterial OTUs (Operational Taxonomic Unit). More than 98% of the sequencing reads were assigned to known pea aphid symbionts. The presence of Wolbachia was confirmed in A. pisum while Erwinia and Pantoea, two gut associates, were detected in multiple samples. The diversity of bacterial communities harboured by pea aphid biotypes was very low, ranging from 3 to 11 OTUs across samples. Bacterial communities differed more between than within biotypes but this difference did not correlate with the genetic divergence between biotypes. Altogether, these results confirm that the aphid microbiota is dominated by a few heritable symbionts and that plant specialization is an important structuring factor of bacterial communities associated with the pea aphid complex. However, since we examined the microbiota of aphid samples kept a few generations in controlled conditions, it may be that bacterial diversity was underestimated due to the possible loss of environmental or transient taxa. PMID:25807173

Soil pretreatment and fast cell lysis for direct polymerase chain reaction from forest soils for terminal restriction fragment length polymorphism analysis of fungal communities

Treesearch

Fei Cheng; Lin Hou; Keith Woeste; Zhengchun Shang; Xiaobang Peng; Peng Zhao; Shuoxin Zhang

2016-01-01

Humic substances in soil DNA samples can influence the assessment of microbial diversity and community composition. Using multiple steps during or after cell lysis adds expenses, is time-consuming, and causes DNA loss. A pretreatment of soil samples and a single step DNA extraction may improve experimental results. In order to optimize a protocol for obtaining high...

Coral-Associated Bacterial Diversity Is Conserved across Two Deep-Sea Anthothela Species

PubMed Central

Lawler, Stephanie N.; Kellogg, Christina A.; France, Scott C.; Clostio, Rachel W.; Brooke, Sandra D.; Ross, Steve W.

2016-01-01

Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4–V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont. PMID:27092120

Coral-associated bacterial diversity is conserved across two deep-sea Anthothela species

USGS Publications Warehouse

Lawler, Stephanie N.; Kellogg, Christina A.; France, Scott C; Clostio, Rachel W; Brooke, Sandra D.; Ross, Steve W.

2016-01-01

Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4-V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont.

Pig Farmers’ Homes Harbor More Diverse Airborne Bacterial Communities Than Pig Stables or Suburban Homes

PubMed Central

Vestergaard, Ditte V.; Holst, Gitte J.; Basinas, Ioannis; Elholm, Grethe; Schlünssen, Vivi; Linneberg, Allan; Šantl-Temkiv, Tina; Finster, Kai; Sigsgaard, Torben; Marshall, Ian P. G.

2018-01-01

Airborne bacterial communities are subject to conditions ill-suited to microbial activity and growth. In spite of this, air is an important transfer medium for bacteria, with the bacteria in indoor air having potentially major consequences for the health of a building’s occupants. A major example is the decreased diversity and altered composition of indoor airborne microbial communities as a proposed explanation for the increasing prevalence of asthma and allergies worldwide. Previous research has shown that living on a farm confers protection against development of asthma and allergies, with airborne bacteria suggested as playing a role in this protective effect. However, the composition of this beneficial microbial community has still not been identified. We sampled settled airborne dust using a passive dust sampler from Danish pig stables, associated farmers’ homes, and from suburban homes (267 samples in total) and carried out quantitative PCR measurements of bacterial abundance and MiSeq sequencing of the V3–V4 region of bacterial 16S rRNA genes found in these samples. Airborne bacteria had a greater diversity and were significantly more abundant in pig stables and farmers’ homes than suburban homes (Wilcoxon rank sum test P < 0.05). Moreover, bacterial taxa previously suggested to contribute to a protective effect had significantly higher relative and absolute abundance in pig stables and farmers’ homes than in suburban homes (ALDEx2 with P < 0.05), including Firmicutes, Peptostreptococcaceae, Prevotellaceae, Lachnospiraceae, Ruminococcaceae, Ruminiclostridium, and Lactobacillus. Pig stables had significantly lower airborne bacterial diversity than farmers’ homes, and there was no discernable direct transfer of airborne bacteria from stable to home. This study identifies differences in indoor airborne bacterial communities that may be an important component of this putative protective effect, while showing that pig stables themselves do not appear to directly contribute to the airborne bacterial communities in the homes of farmers. These findings improve our understanding of the role of airborne bacteria in the increasing prevalence of asthma and allergy. PMID:29765370

Community differentiation of the cutaneous microbiota in psoriasis.

PubMed

Alekseyenko, Alexander V; Perez-Perez, Guillermo I; De Souza, Aieska; Strober, Bruce; Gao, Zhan; Bihan, Monika; Li, Kelvin; Methé, Barbara A; Blaser, Martin J

2013-12-23

Psoriasis is a common chronic inflammatory disease of the skin. We sought to characterize and compare the cutaneous microbiota of psoriatic lesions (lesion group), unaffected contralateral skin from psoriatic patients (unaffected group), and similar skin loci in matched healthy controls (control group) in order to discern patterns that govern skin colonization and their relationship to clinical diagnosis. Using high-throughput 16S rRNA gene sequencing, we assayed the cutaneous bacterial communities of 51 matched triplets and characterized these samples using community data analysis techniques. Intragroup Unifrac β diversity revealed increasing diversity from control to unaffected to lesion specimens. Likewise, principal coordinates analysis (PCoA) revealed separation of the lesion samples from unaffected and control along the first axis, suggesting that psoriasis is a major contributor to the observed diversity. The taxonomic richness and evenness decreased in both lesion and unaffected communities compared to control. These differences are explained by the combined increased abundance of the four major skin-associated genera (Corynebacterium, Propionibacterium, Staphylococcus, and Streptococcus), which present a potentially useful predictor for clinical skin type. Psoriasis samples also showed significant univariate decreases in relative abundances and strong classification performance of Cupriavidus, Flavisolibacter, Methylobacterium, and Schlegelella genera versus controls. The cutaneous microbiota separated into two distinct clusters, which we call cutaneotypes: (1) Proteobacteria-associated microbiota, and (2) Firmicutes-associated and Actinobacteria-associated microbiota. Cutaneotype 2 is enriched in lesion specimens compared to control (odds ratio 3.52 (95% CI 1.44 to 8.98), P <0.01). Our results indicate that psoriasis induces physiological changes both at the lesion site and at the systemic level, which select for specific differential microbiota among the assayed clinical skin types. These differences in microbial community structure in psoriasis patients are potentially of pathophysiologic and diagnostic significance.

Effect of Saccharomyces boulardii and Mode of Delivery on the Early Development of the Gut Microbial Community in Preterm Infants.

PubMed

Zeber-Lubecka, Natalia; Kulecka, Maria; Ambrozkiewicz, Filip; Paziewska, Agnieszka; Lechowicz, Milosz; Konopka, Ewa; Majewska, Urszula; Borszewska-Kornacka, Maria; Mikula, Michal; Cukrowska, Bozena; Ostrowski, Jerzy

2016-01-01

Recent advances in culture-independent approaches have enabled insights into the diversity, complexity, and individual variability of gut microbial communities. To examine the effect of oral administration of Saccharomyces (S.) boulardii and mode of delivery on the intestinal microbial community in preterm infants. Stool samples were collected from preterm newborns randomly divided into two groups: a probiotic-receiving group (n = 18) or a placebo group (n = 21). Samples were collected before probiotic intake (day 0), and after 2 and 6 weeks of supplementation. The composition of colonizing bacteria was assessed by 16S ribosomal RNA (rRNA) gene sequencing of fecal samples using the Ion 16S Metagenomics Kit and the Ion Torrent Personal Genome Machine platform. A total of 11932257 reads were generated, and were clustered into 459, 187, and 176 operational taxonomic units at 0 days, 2 weeks, and 6 weeks, respectively. Of the 17 identified phyla, Firmicutes Actinobacteria, Proteobacteria, and Bacteroidetes were universal. The microbial community differed at day 0 compared with at 2 weeks and 6 weeks. There was a tendency for increased bacterial diversity at 2 weeks and 6 weeks compared with day 0, and infants with a gestational age of 31 weeks or higher presented increased bacterial diversity prior to S. boulardii administration. Firmicutes and Proteobacteria remained stable during the observation period, whereas Actinobacteria and Bacteroidetes increased in abundance, the latter particularly more sharply in vaginally delivered infants. While the mode of delivery may influence the development of a microbial community, this study had not enough power to detect statistical differences between cohorts supplemented with probiotics, and in a consequence, to speculate on S. boulardii effect on gut microbiome composition in preterm newborns.

Effect of Saccharomyces boulardii and Mode of Delivery on the Early Development of the Gut Microbial Community in Preterm Infants

PubMed Central

Zeber-Lubecka, Natalia; Kulecka, Maria; Ambrozkiewicz, Filip; Paziewska, Agnieszka; Lechowicz, Milosz; Konopka, Ewa; Majewska, Urszula; Borszewska-Kornacka, Maria; Mikula, Michal; Cukrowska, Bozena; Ostrowski, Jerzy

2016-01-01

Background Recent advances in culture-independent approaches have enabled insights into the diversity, complexity, and individual variability of gut microbial communities. Objectives To examine the effect of oral administration of Saccharomyces (S.) boulardii and mode of delivery on the intestinal microbial community in preterm infants. Study Design Stool samples were collected from preterm newborns randomly divided into two groups: a probiotic-receiving group (n = 18) or a placebo group (n = 21). Samples were collected before probiotic intake (day 0), and after 2 and 6 weeks of supplementation. The composition of colonizing bacteria was assessed by 16S ribosomal RNA (rRNA) gene sequencing of fecal samples using the Ion 16S Metagenomics Kit and the Ion Torrent Personal Genome Machine platform. Results A total of 11932257 reads were generated, and were clustered into 459, 187, and 176 operational taxonomic units at 0 days, 2 weeks, and 6 weeks, respectively. Of the 17 identified phyla, Firmicutes Actinobacteria, Proteobacteria, and Bacteroidetes were universal. The microbial community differed at day 0 compared with at 2 weeks and 6 weeks. There was a tendency for increased bacterial diversity at 2 weeks and 6 weeks compared with day 0, and infants with a gestational age of 31 weeks or higher presented increased bacterial diversity prior to S. boulardii administration. Firmicutes and Proteobacteria remained stable during the observation period, whereas Actinobacteria and Bacteroidetes increased in abundance, the latter particularly more sharply in vaginally delivered infants. Conclusion While the mode of delivery may influence the development of a microbial community, this study had not enough power to detect statistical differences between cohorts supplemented with probiotics, and in a consequence, to speculate on S. boulardii effect on gut microbiome composition in preterm newborns. PMID:26918330

Cultivation and diversity of fungi buried in the Baltic Sea sediments

NASA Astrophysics Data System (ADS)

Xiao, N.

2015-12-01

@font-face { "ＭＳ 明朝"; }@font-face { "Century"; }@font-face { "Century"; }@font-face { "@ＭＳ 明朝"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0mm 0mm 0.0001pt; text-align: justify; font-size: 12pt; ; }.MsoChpDefault { ; }div.WordSection1 { page: WordSection1; } Studies on molecular biological and cultivation have been done for the prokaryotic microbial community in the deep biosphere. Compare to the prokaryotic community, few attempts have been done for eukaryotic microbial community. Here we report the study on fungi buried in deep-subsurface sediments by approaches of both cultivation and molecular diversity survey. Cultivation targeting fungi has been done using a sequential sediment samples obtained from the Baltic Sea, Landsort Deep site during the IODP expedition 347. 6 culture media with different nutrition and salt concentration have been tried for the fungi cultivation. 50 isolates of fungi were obtained from the sediment samples. The surface sediments showed richness of fungi strains but not for the deep sediments. Internal Transcribed Spacer (ITS) regions of RNA genes were amplified and for the identification of the isolates. The isolates were classified to 11 different genera. Pseudeurotium bakeri was the dominant strain throughout the glacial and interglacial sediments. We also found different representative fungal strains from glacial and interglacial sediments, suggesting the cultivated strains are buried from different sources. The survey of fungal diversity was done by sequencing the 18S RNA genes in the total DNA extracted from selected sediment samples. Fungi community showed different cluster in the glacial and interglacial sediments.Our results revealed the presence and activity of fungi in the deep biosphere of the Baltic sea and provided evidence of fungal community response to the climate change.

Plant community succession in modern Yellow River Delta, China*

PubMed Central

Zhang, Gao-sheng; Wang, Ren-qing; Song, Bai-min

2007-01-01

Data were collected in different successional stages using a simultaneous sampling method and analyzed through quantitative classification method. Three large groups and 12 classes were made to represent the community patterns of three succession stages and 12 succession communities. The succession series of plant community in the study area was as follows: saline bare land→community Suaeda salsa→community Tamarix chinensis→grassland. Succession degree and succession process of 12 succession communities were calculated. Most of these communities were in the lower succession stage, however, community Phragmites communis+Glycine soja and community Imperata cylindrica+G. soja were close to the succession stage of grassland climax. Five species diversity indices were used to study the changes in species richness, species evenness and diversity during succession of community. Heterogeneity index and richness index increased gradually during the community succession process, but species evenness tended to decrease with succession development. The relation between succession and environment was studied by ordination technique, and the results showed that the soil salt content was an important factor to halarch succession of the modern Yellow River Delta. It affected community structure, species composition and succession process. PMID:17657854

DGGE and multivariate analysis of a yeast community in spontaneous cocoa fermentation process.

PubMed

Ferreira, A C R; Marques, E L S; Dias, J C T; Rezende, R P

2015-12-28

Cocoa bean is the main raw material used in the production of chocolate. In southern Bahia, Brazil, cocoa farming and processing is an important economic activity. The fermentation of cocoa is the processing stage that yields important chocolate flavor precursors and complex microbial involvement is essential for this process. In this study, PCR-denaturing gradient gel electrophoreses (DGGE) was used to investigate the diversity of yeasts present during the spontaneous fermentation of cocoa in southern Bahia. The DGGE analysis revealed a richness of 8 to 13 distinct bands of varied intensities among the samples; and samples taken at 24, 36, and 48 h into the fermentation process were found to group with 70% similarity and showed the greatest diversity of bands. Hierarchical clustering showed that all samples had common operational taxonomic units (OTUs) and the highest number of OTUs was found in the 48 h sample. Variations in pH and temperature observed within the fermenting mass over time possibly had direct effects on the composition of the existing microbial community. The findings reported here indicate that a heterogeneous yeast community is involved in the complex cocoa fermentation process, which is known to involve a succession of specialized microorganisms.

Microbial diversity of supra- and subgingival biofilms on freshly colonized titanium implant abutments in the human mouth.

PubMed

Heuer, W; Stiesch, M; Abraham, W R

2011-02-01

Supra- and subgingival biofilm formation is considered to be mainly responsible for early implant failure caused by inflammations of periimplant tissues. Nevertheless, little is known about the complex microbial diversity and interindividual similarities around dental implants. An atraumatic assessment was made of the diversity of microbial communities around titanium implants by single strand conformation polymorphism (SSCP) analysis of the 16S rRNA gene amplicons as well as subsequent sequence analysis. Samples of adherent supra- and subgingival periimplant biofilms were collected from ten patients. Additionally, samples of sulcusfluid were taken at titanium implant abutments and remaining teeth. The bacteria in the samples were characterized by SSCP and sequence analysis. A high diversity of bacteria varying between patients and within one patient at different locations was found. Bacteria characteristic for sulcusfluid and supra- and subgingival biofilm communities were identified. Sulcusfluid of the abutments showed higher abundance of Streptococcus species than from residual teeth. Prevotella and Rothia species frequently reported from the oral cavity were not detected at the abutments suggesting a role as late colonizers. Different niches in the human mouth are characterized by specific groups of bacteria. Implant abutments are a very valuable approach to study dental biofilm development in vivo.

Characterization of Metabolically Active Bacterial Populations in Subseafloor Nankai Trough Sediments above, within, and below the Sulfate–Methane Transition Zone

PubMed Central

Mills, Heath J.; Reese, Brandi Kiel; Shepard, Alicia K.; Riedinger, Natascha; Dowd, Scot E.; Morono, Yuki; Inagaki, Fumio

2012-01-01

A remarkable number of microbial cells have been enumerated within subseafloor sediments, suggesting a biological impact on geochemical processes in the subseafloor habitat. However, the metabolically active fraction of these populations is largely uncharacterized. In this study, an RNA-based molecular approach was used to determine the diversity and community structure of metabolically active bacterial populations in the upper sedimentary formation of the Nankai Trough seismogenic zone. Samples used in this study were collected from the slope apron sediment overlying the accretionary prism at Site C0004 during the Integrated Ocean Drilling Program Expedition 316. The sediments represented microbial habitats above, within, and below the sulfate–methane transition zone (SMTZ), which was observed approximately 20 m below the seafloor (mbsf). Small subunit ribosomal RNA were extracted, quantified, amplified, and sequenced using high-throughput 454 pyrosequencing, indicating the occurrence of metabolically active bacterial populations to a depth of 57 mbsf. Transcript abundance and bacterial diversity decreased with increasing depth. The two communities below the SMTZ were similar at the phylum level, however only a 24% overlap was observed at the genus level. Active bacterial community composition was not confined to geochemically predicted redox stratification despite the deepest sample being more than 50 m below the oxic/anoxic interface. Genus-level classification suggested that the metabolically active subseafloor bacterial populations had similarities to previously cultured organisms. This allowed predictions of physiological potential, expanding understanding of the subseafloor microbial ecosystem. Unique community structures suggest very diverse active populations compared to previous DNA-based diversity estimates, providing more support for enhancing community characterizations using more advanced sequencing techniques. PMID:22485111

Patterns of microbial diversity along a salinity gradient in the Guerrero Negro solar saltern, Baja CA Sur, Mexico

PubMed Central

Dillon, Jesse G.; Carlin, Mark; Gutierrez, Abraham; Nguyen, Vivian; McLain, Nathan

2013-01-01

The goal of this study was to use environmental sequencing of 16S rRNA and bop genes to compare the diversity of planktonic bacteria and archaea across ponds with increasing salinity in the Exportadora de Sal (ESSA) evaporative saltern in Guerrero Negro, Baja CA S., Mexico. We hypothesized that diverse communities of heterotrophic bacteria and archaea would be found in the ESSA ponds, but that bacterial diversity would decrease relative to archaea at the highest salinities. Archaeal 16S rRNA diversity was higher in Ponds 11 and 12 (370 and 380 g l−1 total salts, respectively) compared to Pond 9 (180 g l−1 total salts). Both Pond 11 and 12 communities had high representation (47 and 45% of clones, respectively) by Haloquadratum walsbyi-like (99% similarity) lineages. The archaeal community in Pond 9 was dominated (79%) by a single uncultured phylotype with 99% similarity to sequences recovered from the Sfax saltern in Tunisia. This pattern was mirrored in bop gene diversity with greater numbers of highly supported phylotypes including many Haloquadratum-like sequences from the two highest salinity ponds. In Pond 9, most bop sequences, were not closely related to sequences in databases. Bacterial 16S rRNA diversity was higher than archaeal in both Pond 9 and Pond 12 samples, but not Pond 11, where a non-Salinibacter lineage within the Bacteroidetes >98% similar to environmental clones recovered from Lake Tuz in Turkey and a saltern in Chula Vista, CA was most abundant (69% of community). This OTU was also the most abundant in Pond 12, but only represented 14% of clones in the more diverse pond. The most abundant OTU in Pond 9 (33% of community) was 99% similar to an uncultured gammaproteobacterial clone from the Salton Sea. Results suggest that the communities of saltern bacteria and archaea vary even in ponds with similar salinity and further investigation into the ecology of diverse, uncultured halophile communities is warranted. PMID:24391633

Infaunal Benthic Communities from the Inner Shelf off Southwestern Africa Are Characterised by Generalist Species

PubMed Central

Steffani, Nina; Sedick, Safiyya; Rogers, John; Gibbons, Mark John

2015-01-01

Infaunal communities of benthic macro-organisms (≥ 1mm length) were studied from 81 samples collected across nine sites to the north and south of the Orange River in the Benguela upwelling ecosystem in 2003, with a view to describing communities and understanding the drivers of regional community structure, as well as to document diversity and to examine geographic affinities. Although the fauna was dominated by polychaetes and peracarid crustaceans, patterns in community structure could only weakly be explained by the measured environment (~35%). This is attributed to the generalist nature of the species recovered, which were widely distributed amongst different sediments, water-depths and latitudes. The fauna is dominated by species that enjoy a widespread regional and global distribution and is characterised by relatively low diversity, which is discussed. PMID:26618477

Culture-independent analysis of hydrocarbonoclastic bacterial communities in environmental samples during oil-bioremediation.

PubMed

Dashti, Narjes; Ali, Nedaa; Salamah, Samar; Khanafer, Majida; Al-Shamy, Ghada; Al-Awadhi, Husain; Radwan, Samir S

2018-04-15

To analyze microbial communities in environmental samples, this study combined Denaturing Gradient Gel Electrophoresis of amplified 16S rRNA-genes in total genomic DNA extracts from those samples with gene sequencing. The environmental samples studied were oily seawater and soil samples, that had been bioaugmented with natural materials rich in hydrocarbonoclastic bacteria. This molecular approach revealed much more diverse bacterial taxa than the culture-dependent method we had used in an earlier study for the analysis of the same samples. The study described the dynamics of bacterial communities during bioremediation. The main limitation associated with this molecular approach, namely of not distinguishing hydrocarbonoclastic taxa from others, was overcome by consulting the literature for the hydrocarbonoclastic potential of taxa related to those identified in this study. By doing so, it was concluded that the hydrocarbonoclastic bacterial taxa were much more diverse than those captured by the culture-dependent approach. The molecular analysis also revealed the frequent occurrence of nifH-genes in the total genomic DNA extracts of all the studied environmental samples, which reflects a nitrogen-fixation potential. Nitrogen fertilization is long known to enhance microbial oil-bioremediation. The study revealed that bioaugmentation using plant rhizospheres or soil with long history of oil-pollution was more effective in oil-removal in the desert soil than in seawater microcosms. © 2018 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Phylogenetic diversity of culturable fungi in the Heshang Cave, central China

PubMed Central

Man, Baiying; Wang, Hongmei; Xiang, Xing; Wang, Ruicheng; Yun, Yuan; Gong, Linfeng

2015-01-01

Caves are nutrient-limited and dark subterranean ecosystems. To date, attention has been focused on geological research of caves in China, whilst indigenous microbial diversity has been insufficiently characterized. Here, we report the fungal diversity in the pristine, oligotrophic, karst Heshang Cave, central China, using a culture-dependent method coupled with the analysis of the fungal rRNA-ITS gene sequences. A total of 194 isolates were obtained with six different media from 14 sampling sites of sediments, weathered rocks, and bat guanos. Phylogenetic analysis clustered the 194 sequenced isolates into 33 genera within 15 orders of three phyla, Ascomycota, Basidiomycota, and Zygomycota, indicating a high degree of fungal diversity in the Heshang Cave. Notably, 16 out of the 36 fungal genera were also frequently observed in solution caves around the world and 23 genera were previously found in carbonate cave, indicating potential similarities among fungal communities in cave ecosystems. However, 10 genera in this study were not reported previously in any solution caves, thus expanding our knowledge about fungal diversity in cave ecosystems. Moreover, culturable fungal diversity varied from one habitat to another within the cave, being the highest in sediments, followed by weathered rocks and bat guanos as indicated by α-diversity indexes. At the genus level, Penicillium accounted for 40, 54, and 52% in three habitats of sediments, weathered rocks, and bat guanos, respectively. Trichoderma, Paecilomyces, and Aspergillus accounted for 9, 22, and 37% in the above habitats, correspondingly. Despite of the dominance of Penicillium in all samples, β-diversity index indicated significant differences between each two fungal communities in the three habitats in view of both the composition and abundance. Our study is the first report on fungal communities in a natural pristine solution cave system in central China and sheds light on fungal diversity and functions in cave ecosystems. PMID:26539184

Altitudinal Patterns of Species Diversity and Phylogenetic Diversity across Temperate Mountain Forests of Northern China.

PubMed

Zhang, Wenxin; Huang, Dizhou; Wang, Renqing; Liu, Jian; Du, Ning

2016-01-01

The spatial patterns of biodiversity and their underlying mechanisms have been an active area of research for a long time. In this study, a total of 63 samples (20m × 30m) were systematically established along elevation gradients on Mount Tai and Mount Lao, China. We explored altitudinal patterns of plant diversity in the two mountain systems. In order to understand the mechanisms driving current diversity patterns, we used phylogenetic approaches to detect the spatial patterns of phylogenetic diversity and phylogenetic structure along two elevation gradients. We found that total species richness had a monotonically decreasing pattern and tree richness had a unimodal pattern along the elevation gradients in the two study areas. However, altitudinal patterns in shrub richness and herbs richness were not consistent on the two mountains. At low elevation, anthropogenic disturbances contributed to the increase of plant diversity, especially for shrubs and herbs in understory layers, which are more sensitive to changes in microenvironment. The phylogenetic structure of plant communities exhibited an inverted hump-shaped pattern along the elevation gradient on Mount Tai, which demonstrates that environmental filtering is the main driver of plant community assembly at high and low elevations and inter-specific competition may be the main driver of plant community assembly in the middle elevations. However, the phylogenetic structure of plant communities did not display a clear pattern on Mount Lao where the climate is milder. Phylogenetic beta diversity and species beta diversity consistently increased with increasing altitudinal divergence in the two study areas. However, the altitudinal patterns of species richness did not completely mirror phylogenetic diversity patterns. Conservation areas should be selected taking into consideration the preservation of high species richness, while maximizing phylogenetic diversity to improve the potential for diversification in the future.

Prokaryotic Communities in Pit Mud from Different-Aged Cellars Used for the Production of Chinese Strong-Flavored Liquor

PubMed Central

Tao, Yong; Li, Jiabao; Rui, Junpeng; Xu, Zhancheng; Zhou, Yan; Hu, Xiaohong; Wang, Xiang; Liu, Menghua; Li, Daping

2014-01-01

Chinese strong-flavored liquor (CSFL) accounts for more than 70% of all Chinese liquor production. Microbes in pit mud play key roles in the fermentation cellar for the CSFL production. However, microbial diversity, community structure, and cellar-age-related changes in pit mud are poorly understood. Here, we investigated the prokaryotic community structure and diversity in pit-mud samples with different cellar ages (1, 10, 25, and 50 years) using the pyrosequencing technique. Results indicated that prokaryotic diversity increased with cellar age until the age reached 25 years and that prokaryotic community structure changed significantly between three cellar ages (1, 10, and 25 years). Significant correlations between prokaryotic communities and environmental variables (pH, NH4+, lactic acid, butyric acid, and caproic acid) were observed. Overall, our study results suggested that the long-term brewing operation shapes unique prokaryotic community structure and diversity as well as pit-mud chemistry. We have proposed a three-phase model to characterize the changes of pit-mud prokaryotic communities. (i) Phase I is an initial domestication period. Pit mud is characterized by abundant Lactobacillus and high lactic acid and low pH levels. (ii) Phase II is a transition period. While Lactobacillus abundance decreases dramatically, that of Bacteroidetes and methanogens increases. (iii) Phase III is a relative mature period. The prokaryotic community shows the highest diversity and capability to produce more caproic acid as a precursor for synthesis of ethyl caproate, the main flavor component in CSFL. This research provides scientific evidence to support the practical experience that old fermentation cellars produce high-quality liquor. PMID:24487528

Bacterial diversity among four healthcare-associated institutes in Taiwan.

PubMed

Chen, Chang-Hua; Lin, Yaw-Ling; Chen, Kuan-Hsueh; Chen, Wen-Pei; Chen, Zhao-Feng; Kuo, Han-Yueh; Hung, Hsueh-Fen; Tang, Chuan Yi; Liou, Ming-Li

2017-08-15

Indoor microbial communities have important implications for human health, especially in health-care institutes (HCIs). The factors that determine the diversity and composition of microbiomes in a built environment remain unclear. Herein, we used 16S rRNA amplicon sequencing to investigate the relationships between building attributes and surface bacterial communities among four HCIs located in three buildings. We examined the surface bacterial communities and environmental parameters in the buildings supplied with different ventilation types and compared the results using a Dirichlet multinomial mixture (DMM)-based approach. A total of 203 samples from the four HCIs were analyzed. Four bacterial communities were grouped using the DMM-based approach, which were highly similar to those in the 4 HCIs. The α-diversity and β-diversity in the naturally ventilated building were different from the conditioner-ventilated building. The bacterial source composition varied across each building. Nine genera were found as the core microbiota shared by all the areas, of which Acinetobacter, Enterobacter, Pseudomonas, and Staphylococcus are regarded as healthcare-associated pathogens (HAPs). The observed relationship between environmental parameters such as core microbiota and surface bacterial diversity suggests that we might manage indoor environments by creating new sanitation protocols, adjusting the ventilation design, and further understanding the transmission routes of HAPs.

Beta diversity at different spatial scales: plant communities in organic and conventional agriculture.

PubMed

Gabriel, Doreen; Roschewitz, Indra; Tscharntke, Teja; Thies, Carsten

2006-10-01

Biodiversity studies that guide agricultural subsidy policy have generally compared farming systems at a single spatial scale: the field. However, diversity patterns vary across spatial scales. Here, we examined the effects of farming system (organic vs. conventional) and position in the field (edge vs. center) on plant species richness in wheat fields at three spatial scales. We quantified alpha-, beta-, and gamma-diversity at the microscale in 800 plots, at the mesoscale in 40 fields, and at the macroscale in three regions using the additive partitioning approach, and evaluated the relative contribution of beta-diversity at each spatial scale to total observed species richness. We found that alpha-, beta-, and gamma-diversity were higher in organic than conventional fields and higher at the field edge than in the field center at all spatial scales. In both farming systems, beta-diversity at the meso- and macroscale explained most of the overall species richness (up to 37% and 25%, respectively), indicating considerable differences in community composition among fields and regions due to environmental heterogeneity. The spatial scale at which beta-diversity contributed the most to overall species richness differed between rare and common species. Total richness of rare species (present in < or = 5% of total samples) was mainly explained by differences in community composition at the meso- and macroscale (up to 27% and 48%, respectively), but only in organic fields. Total richness of common species (present in > or = 25% of total samples) was explained by differences in community composition at the micro- and mesoscale (up to 29% and 47%, respectively), i.e., among plots and fields, independent of farming system. Our results show that organic farming made the greatest contribution to total species richness at the meso (among fields) and macro (among regions) scale due to environmental heterogeneity. Hence, agri-environment schemes should exploit this large-scale contribution of beta-diversity by tailoring schemes at regional scales to maximize dissimilarity between conservation areas using geographic information systems rather than focusing entirely at the classical local-field scale, which is the current practice.

The Core Gut Microbiome of the American Cockroach, Periplaneta americana, Is Stable and Resilient to Dietary Shifts.

PubMed

Tinker, Kara A; Ottesen, Elizabeth A

2016-11-15

The omnivorous cockroach Periplaneta americana hosts a diverse hindgut microbiota encompassing hundreds of microbial species. In this study, we used 16S rRNA gene sequencing to examine the effect of diet on the composition of the P. americana hindgut microbial community. Results show that the hindgut microbiota of P. americana exhibit a highly stable core microbial community with low variance in compositions between individuals and minimal community change in response to dietary shifts. This core hindgut microbiome is shared between laboratory-hosted and wild-caught individuals, although wild-caught specimens exhibited a higher diversity of low-abundance microbes that were lost following extended cultivation under laboratory conditions. This taxonomic stability strongly contrasts with observations of the gut microbiota of mammals, which have been shown to be highly responsive to dietary change. A comparison of P. americana hindgut samples with human fecal samples indicated that the cockroach hindgut community exhibited higher alpha diversity but a substantially lower beta diversity than the human gut microbiome. This suggests that cockroaches have evolved unique mechanisms for establishing and maintaining a diverse and stable core microbiome. The gut microbiome plays an important role in the overall health of its host. A healthy gut microbiota typically assists with defense against pathogens and the digestion and absorption of nutrients from food, while dysbiosis of the gut microbiota has been associated with reduced health. In this study, we examined the composition and stability of the gut microbiota from the omnivorous cockroach Periplaneta americana. We found that P. americana hosts a diverse core gut microbiome that remains stable after drastic long-term changes in diet. While other insects, notably ant and bee species, have evolved mechanisms for maintaining a stable association with specific gut microbiota, these insects typically host low-diversity gut microbiomes and consume specialized diets. In contrast, P. americana hosts a gut microbiota that is highly species rich and consumes a diverse solid diet, suggesting that cockroaches have evolved unique mechanisms for developing and maintaining a stable gut microbiota. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Soil macroinvertebrate communities across a productivity gradient in deciduous forests of eastern North America

Treesearch

Evelyn S. Wenk; Mac A. Callaham; Joseph O' Brien; Paul J. Hanson

2016-01-01

Within the temperate, deciduous forests of the eastern US, diverse soil-fauna communities are structured by a combination of environmental gradients and interactions with other biota. The introduction of non-native soil taxa has altered communities and soil processes, and adds another degree of variability to these systems. We sampled soil macroinvertebrate abundance...

Assessment of the microbial diversity of Brazilian kefir grains by PCR-DGGE and pyrosequencing analysis.

PubMed

Leite, A M O; Mayo, B; Rachid, C T C C; Peixoto, R S; Silva, J T; Paschoalin, V M F; Delgado, S

2012-09-01

The microbial diversity and community structure of three different kefir grains from different parts of Brazil were examined via the combination of two culture-independent methods: PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and pyrosequencing. PCR-DGGE showed Lactobacillus kefiranofaciens and Lactobacillus kefiri to be the major bacterial populations in all three grains. The yeast community was dominated by Saccharomyces cerevisiae. Pyrosequencing produced a total of 14,314 partial 16S rDNA sequence reads from the three grains. Sequence analysis grouped the reads into three phyla, of which Firmicutes was dominant. Members of the genus Lactobacillus were the most abundant operational taxonomic units (OTUs) in all samples, accounting for up to 96% of the sequences. OTUs belonging to other lactic and acetic acid bacteria genera, such as Lactococcus, Leuconostoc, Streptococcus and Acetobacter, were also identified at low levels. Two of the grains showed identical DGGE profiles and a similar number of OTUs, while the third sample showed the highest diversity by both techniques. Pyrosequencing allowed the identification of bacteria that were present in small numbers and rarely associated with the microbial community of this complex ecosystem. Copyright © 2012 Elsevier Ltd. All rights reserved.

Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics

PubMed Central

Jovel, Juan; Patterson, Jordan; Wang, Weiwei; Hotte, Naomi; O'Keefe, Sandra; Mitchel, Troy; Perry, Troy; Kao, Dina; Mason, Andrew L.; Madsen, Karen L.; Wong, Gane K.-S.

2016-01-01

The advent of next generation sequencing (NGS) has enabled investigations of the gut microbiome with unprecedented resolution and throughput. This has stimulated the development of sophisticated bioinformatics tools to analyze the massive amounts of data generated. Researchers therefore need a clear understanding of the key concepts required for the design, execution and interpretation of NGS experiments on microbiomes. We conducted a literature review and used our own data to determine which approaches work best. The two main approaches for analyzing the microbiome, 16S ribosomal RNA (rRNA) gene amplicons and shotgun metagenomics, are illustrated with analyses of libraries designed to highlight their strengths and weaknesses. Several methods for taxonomic classification of bacterial sequences are discussed. We present simulations to assess the number of sequences that are required to perform reliable appraisals of bacterial community structure. To the extent that fluctuations in the diversity of gut bacterial populations correlate with health and disease, we emphasize various techniques for the analysis of bacterial communities within samples (α-diversity) and between samples (β-diversity). Finally, we demonstrate techniques to infer the metabolic capabilities of a bacteria community from these 16S and shotgun data. PMID:27148170

Microbial composition of the Korean traditional food "kochujang" analyzed by a massive sequencing technique.

PubMed

Nam, Young-Do; Park, So-lim; Lim, Seong-Il

2012-04-01

Kochujang is a traditional Korean fermented food that is made with red pepper, glutinous rice, salt, and soybean. Kochujang is fermented by naturally occurring microorganisms through which it obtains various health-promoting properties. In this study, the bacterial diversities of 9 local and 2 commercial brands of kochujang were analyzed with a barcoded pyrosequencing technique targeting the hyper-variable regions V1/V2 of the 16S rRNA gene. Through the analysis of 13524 bacterial pyrosequences, 223 bacterial species were identified, most of which converged on the phylum Firmicutes (average 93.1%). All of the kochujang samples were largely populated (>90.9% of abundance) by 12 bacterial families, and Bacillaceae showed the highest abundance in all but one sample. Bacillus subtilis and B. licheniformis were the most dominant bacterial species and were broadly distributed among the kochujang samples. Each sample contained a high abundance of region-specific bacterial species, such as B. sonorensis, B. pumilus, Weissella salipiscis, and diverse unidentified Bacillus species. Phylotype- and phylogeny-based community comparison analysis showed that the microbial communities of the two commercial brands were different from those of the local brands. Moreover, each local brand kochujang sample had region-specific microbial community reflecting the manufacturing environment. © 2012 Institute of Food Technologists®

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 water sample filtration or from DNA extraction protocols. Control measurements for sample contamination are important for clean water studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Species area relationships in mediterranean-climate plant communities

USGS Publications Warehouse

Keeley, Jon E.; Fotheringham, C.J.

2003-01-01

Aim To determine the best-fit model of species–area relationships for Mediterranean-type plant communities and evaluate how community structure affects these species–area models.Location Data were collected from California shrublands and woodlands and compared with literature reports for other Mediterranean-climate regions.Methods The number of species was recorded from 1, 100 and 1000 m2 nested plots. Best fit to the power model or exponential model was determined by comparing adjusted r2 values from the least squares regression, pattern of residuals, homoscedasticity across scales, and semi-log slopes at 1–100 m2 and 100–1000 m2. Dominance–diversity curves were tested for fit to the lognormal model, MacArthur's broken stick model, and the geometric and harmonic series.Results Early successional Western Australia and California shrublands represented the extremes and provide an interesting contrast as the exponential model was the best fit for the former, and the power model for the latter, despite similar total species richness. We hypothesize that structural differences in these communities account for the different species–area curves and are tied to patterns of dominance, equitability and life form distribution. Dominance–diversity relationships for Western Australian heathlands exhibited a close fit to MacArthur's broken stick model, indicating more equitable distribution of species. In contrast, Californian shrublands, both postfire and mature stands, were best fit by the geometric model indicating strong dominance and many minor subordinate species. These regions differ in life form distribution, with annuals being a major component of diversity in early successional Californian shrublands although they are largely lacking in mature stands. Both young and old Australian heathlands are dominated by perennials, and annuals are largely absent. Inherent in all of these ecosystems is cyclical disequilibrium caused by periodic fires. The potential for community reassembly is greater in Californian shrublands where only a quarter of the flora resprout, whereas three quarters resprout in Australian heathlands.Other Californian vegetation types sampled include coniferous forests, oak savannas and desert scrub, and demonstrate that different community structures may lead to a similar species–area relationship. Dominance–diversity relationships for coniferous forests closely follow a geometric model whereas associated oak savannas show a close fit to the lognormal model. However, for both communities, species–area curves fit a power model. The primary driver appears to be the presence of annuals. Desert scrub communities illustrate dramatic changes in both species diversity and dominance–diversity relationships in high and low rainfall years, because of the disappearance of annuals in drought years.Main conclusions Species–area curves for immature shrublands in California and the majority of Mediterranean plant communities fit a power function model. Exceptions that fit the exponential model are not because of sampling error or scaling effects, rather structural differences in these communities provide plausible explanations. The exponential species–area model may arise in more than one way. In the highly diverse Australian heathlands it results from a rapid increase in species richness at small scales. In mature California shrublands it results from very depauperate richness at the community scale. In both instances the exponential model is tied to a preponderance of perennials and paucity of annuals. For communities fit by a power model, coefficients z and log c exhibit a number of significant correlations with other diversity parameters, suggesting that they have some predictive value in ecological communities.

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

Jun, Se -Ran; Hauser, Loren John; Schadt, Christopher Warren

For decades there has been increasing interest in understanding the relationships between microbial communities and ecosystem functions. Current DNA sequencing technologies allows for the exploration of microbial communities in two principle ways: targeted rRNA gene surveys and shotgun metagenomics. For large study designs, it is often still prohibitively expensive to sequence metagenomes at both the breadth and depth necessary to statistically capture the true functional diversity of a community. Although rRNA gene surveys provide no direct evidence of function, they do provide a reasonable estimation of microbial diversity, while being a very cost effective way to screen samples of interestmore » for later shotgun metagenomic analyses. However, there is a great deal of 16S rRNA gene survey data currently available from diverse environments, and thus a need for tools to infer functional composition of environmental samples based on 16S rRNA gene survey data. As a result, we present a computational method called pangenome based functional profiles (PanFP), which infers functional profiles of microbial communities from 16S rRNA gene survey data for Bacteria and Archaea. PanFP is based on pangenome reconstruction of a 16S rRNA gene operational taxonomic unit (OTU) from known genes and genomes pooled from the OTU s taxonomic lineage. From this lineage, we derive an OTU functional profile by weighting a pangenome s functional profile with the OTUs abundance observed in a given sample. We validated our method by comparing PanFP to the functional profiles obtained from the direct shotgun metagenomic measurement of 65 diverse communities via Spearman correlation coefficients. These correlations improved with increasing sequencing depth, within the range of 0.8 0.9 for the most deeply sequenced Human Microbiome Project mock community samples. PanFP is very similar in performance to another recently released tool, PICRUSt, for almost all of survey data analysed here. But, our method is unique in that any OTU building method can be used, as opposed to being limited to closed reference OTU picking strategies against specific reference sequence databases. In conclusion, we developed an automated computational method, which derives an inferred functional profile based on the 16S rRNA gene surveys of microbial communities. The inferred functional profile provides a cost effective way to study complex ecosystems through predicted comparative functional metagenomes and metadata analysis. All PanFP source code and additional documentation are freely available online at GitHub.« less

Compositional changes in bee and wasp communities along Neotropical mountain altitudinal gradient.

PubMed

Perillo, Lucas Neves; Neves, Frederico de Siqueira; Antonini, Yasmine; Martins, Rogério Parentoni

2017-01-01

Climate conditions tend to differ along an altitudinal gradient, resulting in some species groups' patterns of lower species richness with increasing altitude. While this pattern is well understood for tropical mountains, studies investigating possible determinants of variation in beta-diversity at its different altitudes are scarce. We sampled bee and wasp communities (Hymenoptera: Aculeata) along an altitudinal gradient (1,000-2,000 m.a.s.l.) in a tropical mountainous region of Brazil. Trap nests and Moericke traps were established at six sampling points, with 200 m difference in altitude between each point. We obtained average climate data (1970-2000) from Worldclim v2 for altitudes at each sampling site. Nest traps captured 17 bee and wasp species from six families, and Moericke traps captured 124 morphospecies from 13 families. We found a negative correlation between altitude and species richness and abundance. Temperature, precipitation, water vapor pressure, and wind speed influenced species richness and abundance, and were correlated with altitude. β-diversity was primarily determined by species turnover as opposed to nestedness, and Aculeate community similarity was higher for more similar altitudinal ranges. Moericke traps seem to be more efficient for altitudinal surveys compared to nest traps. We found high occurrence of singleton and doubleton species at all altitudes, highlighting the need for long-term studies to efficiently assess hymenopteran diversity in these environments.

Potential link between plant and fungal distributions in a dipterocarp rainforest: community and phylogenetic structure of tropical ectomycorrhizal fungi across a plant and soil ecotone.

PubMed

Peay, Kabir G; Kennedy, Peter G; Davies, Stuart J; Tan, Sylvester; Bruns, Thomas D

2010-01-01

*Relatively little is known about diversity or structure of tropical ectomycorrhizal communities or their roles in tropical ecosystem dynamics. In this study, we present one of the largest molecular studies to date of an ectomycorrhizal community in lowland dipterocarp rainforest. *We sampled roots from two 0.4 ha sites located across an ecotone within a 52 ha forest dynamics plot. Our plots contained > 500 tree species and > 40 species of ectomycorrhizal host plants. Fungi were identified by sequencing ribosomal RNA genes. *The community was dominated by the Russulales (30 species), Boletales (17), Agaricales (18), Thelephorales (13) and Cantharellales (12). Total species richness appeared comparable to molecular studies of temperate forests. Community structure changed across the ecotone, although it was not possible to separate the role of environmental factors vs host plant preferences. Phylogenetic analyses were consistent with a model of community assembly where habitat associations are influenced by evolutionary conservatism of functional traits within ectomycorrhizal lineages. *Because changes in the ectomycorrhizal fungal community parallel those of the tree community at this site, this study demonstrates the potential link between the distribution of tropical tree diversity and the distribution of tropical ectomycorrhizal diversity in relation to local-scale edaphic variation.

Urban-development-induced Changes in the Diversity and Composition of the Soil Bacterial Community in Beijing.

PubMed

Yan, Bing; Li, Junsheng; Xiao, Nengwen; Qi, Yue; Fu, Gang; Liu, Gaohui; Qiao, Mengping

2016-12-09

Numerous studies have implicated urbanization as a major cause of loss of biodiversity. Most of them have focused on plants and animals, even though soil microorganisms make up a large proportion of that biodiversity. However, it is unclear how the soil bacterial community is affected by urban development. Here, paired-end Illumina sequencing of the 16 S rRNA gene at V4 region was performed to study the soil microbial community across Beijing's built-up area. Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Verrucomicrobia, Planctomycetes, and Chloroflexi were the dominant phyla in all samples, but the relative abundance of these phyla differed significantly across these concentric zones. The diversity and composition of the soil bacterial community were found to be closely correlated with soil pH. Variance partitioning analysis suggested that urban ring roads contributed 5.95% of the bacterial community variation, and soil environmental factors explained 17.65% of the variation. The results of the current work indicate that urban development can alter the composition and diversity of the soil microbial community, and showed pH to be a key factor in the shaping of the composition of the soil bacterial community. Urban development did have a strong impact on the bacterial community of urban soil in Beijing.

Characterization of soil bacterial, archaeal and fungal communities inhabiting archaeological human-impacted layers at Monte Iato settlement (Sicily, Italy).

PubMed

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

2018-01-30

Microbial communities in human-impacted soils of ancient settlements have been proposed to be used as ecofacts (bioindicators) of different ancient anthropogenic activities. In this study, bacterial, archaeal and fungal communities inhabiting soil of three archaic layers, excavated at the archaeological site on Monte Iato (Sicily, Italy) and believed to have been created in a chronological order in archaic times in the context of periodic cultic feasts, were investigated in terms of (i) abundance (phospholipid fatty acid (PLFA) analysis and quantitative PCR)), (ii) carbon(C)-source consumption patterns (Biolog-Ecoplates) and (iii) diversity and community composition (Illumina amplicon sequencing). PLFA analyses demonstrated the existence of living bacteria and fungi in the soil samples of all three layers. The upper layer showed increased levels of organic C, which were not concomitant with an increment in the microbial abundance. In taxonomic terms, the results indicated that bacterial, archaeal and fungal communities were highly diverse, although differences in richness or diversity among the three layers were not detected for any of the communities. However, significantly different microbial C-source utilization patterns and structures of bacterial, archaeal and fungal communities in the three layers confirmed that changing features of soil microbial communities reflect different past human activities.

Urban-development-induced Changes in the Diversity and Composition of the Soil Bacterial Community in Beijing

NASA Astrophysics Data System (ADS)

Yan, Bing; Li, Junsheng; Xiao, Nengwen; Qi, Yue; Fu, Gang; Liu, Gaohui; Qiao, Mengping

2016-12-01

Numerous studies have implicated urbanization as a major cause of loss of biodiversity. Most of them have focused on plants and animals, even though soil microorganisms make up a large proportion of that biodiversity. However, it is unclear how the soil bacterial community is affected by urban development. Here, paired-end Illumina sequencing of the 16 S rRNA gene at V4 region was performed to study the soil microbial community across Beijing’s built-up area. Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Verrucomicrobia, Planctomycetes, and Chloroflexi were the dominant phyla in all samples, but the relative abundance of these phyla differed significantly across these concentric zones. The diversity and composition of the soil bacterial community were found to be closely correlated with soil pH. Variance partitioning analysis suggested that urban ring roads contributed 5.95% of the bacterial community variation, and soil environmental factors explained 17.65% of the variation. The results of the current work indicate that urban development can alter the composition and diversity of the soil microbial community, and showed pH to be a key factor in the shaping of the composition of the soil bacterial community. Urban development did have a strong impact on the bacterial community of urban soil in Beijing.

Fungal Communities Including Plant Pathogens in Near Surface Air Are Similar across Northwestern Europe.

PubMed

Nicolaisen, Mogens; West, Jonathan S; Sapkota, Rumakanta; Canning, Gail G M; Schoen, Cor; Justesen, Annemarie F

2017-01-01

Information on the diversity of fungal spores in air is limited, and also the content of airborne spores of fungal plant pathogens is understudied. In the present study, a total of 152 air samples were taken from rooftops at urban settings in Slagelse, DK, Wageningen NL, and Rothamsted, UK together with 41 samples from above oilseed rape fields in Rothamsted. Samples were taken during 10-day periods in spring and autumn, each sample representing 1 day of sampling. The fungal content of samples was analyzed by metabarcoding of the fungal internal transcribed sequence 1 (ITS1) and by qPCR for specific fungi. The metabarcoding results demonstrated that season had significant effects on airborne fungal communities. In contrast, location did not have strong effects on the communities, even though locations were separated by up to 900 km. Also, a number of plant pathogens had strikingly similar patterns of abundance at the three locations. Rooftop samples were more diverse than samples taken above fields, probably reflecting greater mixing of air from a range of microenvironments for the rooftop sites. Pathogens that were known to be present in the crop were also found in air samples taken above the field. This paper is one of the first detailed studies of fungal composition in air with the focus on plant pathogens and shows that it is possible to detect a range of pathogens in rooftop air samplers using metabarcoding.

Clustering behavior in microbial communities from acute endodontic infections.

PubMed

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

2012-02-01

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

Effects of reclamation years on composition and diversity of soil bacterial communities in Northwest China.

PubMed

Cheng, Zhibo; Zhang, Fenghua; Gale, William Jeffrey; Wang, Weichao; Sang, Wen; Yang, Haichang

2018-01-01

The objective of this study was to evaluate bacterial community structure and diversity in soil aggregate fractions when salinized farmland was reclaimed after >27 years of abandonment and then farmed again for 1, 5, 10, and 15 years. Illumina MiSeq high-throughput sequencing was performed to characterize the soil bacterial communities in 5 aggregate size classes in each treatment. The results indicated that reclamation significantly increased macro-aggregation (>0.25 mm), as well as soil organic C, available N, and available P. The 10-year field had the largest proportion (93.9%) of soil in the macro-aggregate size classes (i.e., >0.25 mm) and the highest soil electrical conductivity. The 5 most dominant phyla in the soil samples were Proteobacteria, Actinobacteria, Gemmatimonadetes, Acidobacteria, and Bacteroidetes. The phylogenetic diversity, Chao1, and Shannon indices increased after the abandoned land was reclaimed for farming, reaching maximums in the 15-year field. Among aggregate size classes, the 1-0.25 mm aggregates generally had the highest phylogenetic diversity, Chao1, and Shannon indices. Soil organic C and soil electrical conductivity were the main environmental factors affecting the soil bacterial communities. The composition and structure of the bacterial communities also varied significantly depending on soil aggregate size and time since reclamation.

The impacts of Cenozoic climate and habitat changes on small mammal diversity of North America

NASA Astrophysics Data System (ADS)

Samuels, Joshua X.; Hopkins, Samantha S. B.

2017-02-01

Through the Cenozoic, paleoclimate records show general trends of global cooling and increased aridity, and environments in North America shifted from predominantly forests to more open habitats. Paleobotanical records indicate grasses were present on the continent in the Eocene; however, paleosol and phytolith studies indicate that open habitats did not arise until the late Eocene or even later in the Oligocene. Studies of large mammalian herbivores have documented changes in ecomorphology and community structure through time, revealing that shifts in mammalian morphology occurred millions of years after the environmental changes thought to have triggered them. Smaller mammals, like rodents and lagomorphs, should more closely track climate and habitat changes due to their shorter generation times and smaller ranges, but these animals have received much less study. To examine changes in smaller mammals through time, we have assembled and analyzed an ecomorphological database of all North American rodent and lagomorph species. Analyses of these data found that rodent and lagomorph community structure changed dramatically through the Cenozoic, and shifts in diversity and ecology correspond closely with the timing of habitat changes. Cenozoic rodent and lagomorph species diversity is strongly biased by sampling of localities, but sampling-corrected diversity reveals diversity dynamics that, after an initial density-dependent diversification in the Eocene, track habitat changes and the appearance of new ecological adaptations. As habitats became more open and arid through time, rodent and lagomorph crown heights increased while burrowing, jumping, and cursorial adaptations became more prevalent. Through time, open-habitat specialists were added during periods of diversification, while closed-habitat taxa were disproportionately lost in subsequent diversity declines. While shifts among rodents and lagomorphs parallel changes in ungulate communities, they started millions of years earlier than in larger mammals. This is likely a consequence of the smaller mammals' greater sensitivity to environmental changes and more rapid evolution. These results highlight the importance of examining understudied members of vertebrate faunas for understanding the evolution of terrestrial communities through time.

Microbial Communities and Functional Genes Associated with Soil Arsenic Contamination and the Rhizosphere of the Arsenic-Hyperaccumulating Plant Pteris vittata L. ▿ †

PubMed Central

Xiong, Jinbo; Wu, Liyou; Tu, Shuxin; Van Nostrand, Joy D.; He, Zhili; Zhou, Jizhong; Wang, Gejiao

2010-01-01

To understand how microbial communities and functional genes respond to arsenic contamination in the rhizosphere of Pteris vittata, five soil samples with different arsenic contamination levels were collected from the rhizosphere of P. vittata and nonrhizosphere areas and investigated by Biolog, geochemical, and functional gene microarray (GeoChip 3.0) analyses. Biolog analysis revealed that the uncontaminated soil harbored the greatest diversity of sole-carbon utilization abilities and that arsenic contamination decreased the metabolic diversity, while rhizosphere soils had higher metabolic diversities than did the nonrhizosphere soils. GeoChip 3.0 analysis showed low proportions of overlapping genes across the five soil samples (16.52% to 45.75%). The uncontaminated soil had a higher heterogeneity and more unique genes (48.09%) than did the arsenic-contaminated soils. Arsenic resistance, sulfur reduction, phosphorus utilization, and denitrification genes were remarkably distinct between P. vittata rhizosphere and nonrhizosphere soils, which provides evidence for a strong linkage among the level of arsenic contamination, the rhizosphere, and the functional gene distribution. Canonical correspondence analysis (CCA) revealed that arsenic is the main driver in reducing the soil functional gene diversity; however, organic matter and phosphorus also have significant effects on the soil microbial community structure. The results implied that rhizobacteria play an important role during soil arsenic uptake and hyperaccumulation processes of P. vittata. PMID:20833780

Microbial community structure and diversity within hypersaline Keke Salt Lake environments.

PubMed

Han, Rui; Zhang, Xin; Liu, Jing; Long, Qifu; Chen, Laisheng; Liu, Deli; Zhu, Derui

2017-11-01

Keke Salt Lake is located in the Qaidamu Basin of China. It is a unique magnesium sulfate-subtype hypersaline lake that exhibits a halite domain ecosystem, yet its microbial diversity has remained unstudied. Here, the microbial community structure and diversity was investigated via high-throughput sequencing of the V3-V5 regions of 16S rRNA genes. A high diversity of operational taxonomic units was detected for Bacteria and Archaea (734 and 747, respectively), comprising 21 phyla, 43 classes, and 201 genera of Bacteria and 4 phyla, 4 classes, and 39 genera of Archaea. Salt-saturated samples were dominated by the bacterial genera Bacillus (51.52%-58.35% relative abundance), Lactococcus (9.52%-10.51%), and Oceanobacillus (8.82%-9.88%) within the Firmicutes phylum (74.81%-80.99%), contrasting with other hypersaline lakes. The dominant Archaea belonged to the Halobacteriaceae family, and in particular, the genera (with an abundance of >10% of communities) Halonotius, Halorubellus, Halapricum, Halorubrum, and Natronomonas. Additionally, we report the presence of Nanohaloarchaeota and Woesearchaeota in Qinghai-Tibet Plateau lakes, which has not been previously documented. Total salinity (especially Mg 2+ , Cl - , Na + , and K + ) mostly correlated with taxonomic distribution across samples. These results expand our understanding of microbial resource utilization within hypersaline lakes and the potential adaptations of dominant microorganisms that allow them to inhabit such environments.

An approach to bioassessment of water quality using diversity measures based on species accumulative curves.

PubMed

Xu, Guangjian; Zhang, Wei; Xu, Henglong

2015-02-15

Traditional community-based bioassessment is time-consuming because they rely on full species-abundance data of a community. To improve bioassessment efficiency, the feasibility of the diversity measures based on species accumulative curves for bioassessment of water quality status was studied based on a dataset of microperiphyton fauna. The results showed that: (1) the species accumulative curves well fitted the Michaelis-Menten equation; (2) the β- and γ-diversity, as well as the number of samples to 50% of the maximum species number (Michaelis-Menten constant K), can be statistically estimated based on the formulation; (3) the rarefied α-diversity represented a significant negative correlation with the changes in the nutrient NH4-N; and (4) the estimated β-diversity and the K constant were significantly positively related to the concentration of NH4-N. The results suggest that the diversity measures based on species accumulative curves might be used as a potential bioindicator of water quality in marine ecosystems. Copyright © 2014 Elsevier Ltd. All rights reserved.

Mixed cropping regimes promote the soil fungal community under zero tillage.

PubMed

Silvestro, L B; Biganzoli, F; Stenglein, S A; Forjan, H; Manso, L; Moreno, M V

2018-07-01

Fungi of yield soils represent a significant portion of the microbial biomass and reflect sensitivity to changes in the ecosystem. Our hypothesis was that crops included in cropping regimes under the zero tillage system modify the structure of the soil fungi community. Conventional and molecular techniques provide complementary information for the analysis of diversity of fungal species and successful information to accept our hypothesis. The composition of the fungal community varied according to different crops included in the cropping regimes. However, we detected other factors as sources of variation among them, season and sampling depth. The mixed cropping regimes including perennial pastures and one crop per year promote fungal diversity and species with potential benefit to soil and crop. The winter season and 0-5 cm depth gave the largest evenness and fungal diversity. Trichoderma aureoviride and Rhizopus stolonifer could be used for monitoring changes in soil under zero tillage.

Airborne and Grain Dust Fungal Community Compositions Are Shaped Regionally by Plant Genotypes and Farming Practices

PubMed Central

Pellissier, Loïc; Oppliger, Anne; Hirzel, Alexandre H.; Savova-Bianchi, Dessislava; Mbayo, Guilain; Mascher, Fabio; Kellenberger, Stefan

2016-01-01

Chronic exposure to airborne fungi has been associated with different respiratory symptoms and pathologies in occupational populations, such as grain workers. However, the homogeneity in the fungal species composition of these bioaerosols on a large geographical scale and the different drivers that shape these fungal communities remain unclear. In this study, the diversity of fungi in grain dust and in the aerosols released during harvesting was determined across 96 sites at a geographical scale of 560 km2 along an elevation gradient of 500 m by tag-encoded 454 pyrosequencing of the internal transcribed spacer (ITS) sequences. Associations between the structure of fungal communities in the grain dust and different abiotic (farming system, soil characteristics, and geographic and climatic parameters) and biotic (wheat cultivar and previous crop culture) factors were explored. These analyses revealed a strong relationship between the airborne and grain dust fungal communities and showed the presence of allergenic and mycotoxigenic species in most samples, which highlights the potential contribution of these fungal species to work-related respiratory symptoms of grain workers. The farming system was the major driver of the alpha and beta phylogenetic diversity values of fungal communities. In addition, elevation and soil CaCO3 concentrations shaped the alpha diversity, whereas wheat cultivar, cropping history, and the number of freezing days per year shaped the taxonomic beta diversity of these communities. PMID:26826229

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-km 2 study region in the western Swiss Alps region, which has been exhaustively studied for macro-organismal and fungal ecology, and for topoclimatic modeling of future ecological trends, but without taking into account soil bacterial diversity. Here, we present an in-depth biogeographical characterization of the bacterial community diversity in this alpine region across 100 randomly stratified sites, using 56 environmental variables. Our exhaustive sampling ensured the detection of ecological trends with high statistical robustness. Our data both confirm previously observed general trends and show many new detailed trends for a wide range of bacterial taxonomic groups and environmental parameters. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Parental Opinion Concerning School Sexuality Education in a Culturally Diverse Population in the USA

ERIC Educational Resources Information Center

Heller, Janet R.; Johnson, Helen L.

2013-01-01

This study aimed to expand upon previous research related to parental opinion concerning school sexuality education by sampling a culturally diverse, low-income population that has been traditionally under-represented in the literature. A total of 191 parents attending an urban community college completed a written questionnaire about what topics…

Prevalence and Sociodemographic Correlates of Lifetime Substance Use among a Rural and Diverse Sample of Adolescents

ERIC Educational Resources Information Center

McDermott, Michael J.; Drescher, Christopher F.; Smitherman, Todd A.; Tull, Matthew T.; Heiden, Laurie; Damon, John D.; Hight, Terry L.; Young, John

2013-01-01

Background: Data are limited regarding the prevalence of substance use among adolescents in rural and ethnically diverse communities. This study examined rates and sociodemographic correlates of lifetime substance use among adolescents in Mississippi, a rural state that is the poorest in the country (21.3% poverty rate) and has the largest…

The Effect of Art Therapy on Cognitive Performance among Ethnically Diverse Older Adults

ERIC Educational Resources Information Center

Pike, Amanda Alders

2013-01-01

This study examined the effect of art therapy on the cognitive performance of a multisite, ethnically diverse sample ("N" = 91) of older adults. Participants were recruited from several U.S. facilities that included a community center, a retirement center, an adult daycare, an assisted living facility, and a skilled nursing facility.…

[Dynamics of bacterial community during the bloom caused by Skeletonema costatum and Akashiwo sanguinea in Xiamen sea area].

PubMed

Li, Yi; Yang, Caiyun; Li, Dong; Tian, Yun; Zheng, Tianling

2012-10-04

To investigate the dynamics of bacterial community in Xiamen sea during the bloom mainly caused by Skeletonema costatum and Akashiwo sanguine in August 2011. Bacterial community structures of samples from two bloom sites and one non-bloom site were evaluated by PCR-DGGE (Denaturing gradient gel electrophoresis, DGGE). The genetic diversity of bacterial community was analyzed based on the DGGE fingerprint. The correlation between bacterial community and environmental parameters was studied by Canoco. The bacterial community was largely related to pH and N/P during the start-up stage of the bloom; while in the demise stage, it was mostly correlated to salinity and temperature. According to the results of sequence analysis of DGGE dominant bands, Gammaproteobacteria accounted for 47.7% during the bloom and Pseudoalteromonas, Pseudomonas, Alteromonas, Hydrogenophaga, Actibacter and Oleibacter were dominant genus in bacterial community. The Shannon-Weaver diversity index showed that the diversity of bacterial community in bloom site increased firstly and then decreased during this bloom. Hydrogenophaga was dominant in the start-up stage of bloom, while Pseudomonas and Pseudoalteromonas were dominant in the demise stage of bloom. The diversity of attached bacteria and free-living bacteria in bloom sites reached maximum in the same day (the concentration of algae was high) , both of them changed greatly during the bloom while the environment factors which correlated with the two communities were different. It is the first report about dynamics of bacterial community during the bloom caused by several algae together. This work is helpful to understand the dynamics of bacterial community during the bloom, and provides a theoretical basis for bloom's control in the future.

Biogeographical distribution and diversity of bacterial communities in surface sediments of the South China Sea.

PubMed

Li, Tao; Wang, Peng

2013-05-01

This paper aims at an investigation of the features of bacterial communities in surface sediments of the South China Sea (SCS). In particular, biogeographical distribution patterns and the phylogenetic diversity of bacteria found in sediments collected from a coral reef platform, a continental slope, and a deep-sea basin were determined. Bacterial diversity was measured by an observation of 16S rRNA genes, and 18 phylogenetic groups were identified in the bacterial clone library. Planctomycetes, Deltaproteobacteria, candidate division OP11, and Alphaproteobacteria made up the majority of the bacteria in the samples, with their mean bacterial clones being 16%, 15%, 12%, and 9%, respectively. By comparison, the bacterial communities found in the SCS surface sediments were significantly different from other previously observed deep-sea bacterial communities. This research also emphasizes the fact that geographical factors have an impact on the biogeographical distribution patterns of bacterial communities. For instance, canonical correspondence analyses illustrated that the percentage of sand weight and water depth are important factors affecting the bacterial community composition. Therefore, this study highlights the importance of adequately determining the relationship between geographical factors and the distribution of bacteria in the world's seas and oceans.

Characterization of juvenile maritime pine (Pinus pinaster Ait.) ectomycorrhizal fungal community using morphotyping, direct sequencing and fruitbodies sampling.

PubMed

Pestaña Nieto, Montserrat; Santolamazza Carbone, Serena

2009-02-01

Using ectomycorrhizal root tip morphotyping (anatomical and morphological identification), molecular analysis (internal transcribed spacer region amplification and sequencing), and fruitbody sampling, we assessed diversity and composition of the ectomycorrhizal fungal community colonizing juvenile Pinus pinaster Ait. under natural conditions in NW Spain. Overall, we found 15 Basidiomycetes and two Ascomycetes. Members of the family Thelephoraceae represented up to 59.4% of the samples. The most frequent species was Tomentella sublilacina followed by Thelephora terrestris, Russula drimeia, Suillus bovinus, and Paxillus involutus, while the less frequent were Pseudotomentella tristis, Lactarius subdulcis, Russula ochroleuca, and Entoloma conferendum. From October 2007 to June 2008, we sampled 208 sporocarps belonging to seven genera and nine species: Thelephora terrestris, Paxillus involutus, Suillus bovinus, Xerocomus badius, Scleroderma verrucosum, Amanita gemmata, A. rubescens, Amanita sp., and Russula sp. The species belonging to the genus Amanita, X. badius and S. verrucosum were not found on root samples. By comparing our results with a bibliographic review of papers published from 1922 to 2006, we found five genera and six species which have not been previously reported in symbiosis with P. pinaster. This is the first time that the diversity of the ectomycorrhizal fungal community associated with P. pinaster was investigated using molecular techniques. Considering that only 38% of the genera found by sequencing were found as fruitbodies, we conclude that integrating morphotyping and sporocarps surveys with molecular analysis of ectomycorrhizas is important to documenting the ectomycorrhizal fungus community.

Environmentalism and community: connections and implications for social action

Treesearch

Benjamin J. Marcus; Allen M. Omoto; Patricia L. Winter

2011-01-01

This qualitative study explored conceptualizations of environmentalism and community, as well as the connections of ethnicity to these concepts in a small but diverse sample. Semistructured interviews were conducted with eight participants and included a conceptual content cognitive mapping procedure. The resulting maps were examined for themes and ideas about the key...

Global diversity and biogeography of deep-sea pelagic prokaryotes.

PubMed

Salazar, Guillem; Cornejo-Castillo, Francisco M; Benítez-Barrios, Verónica; Fraile-Nuez, Eugenio; Álvarez-Salgado, X Antón; Duarte, Carlos M; Gasol, Josep M; Acinas, Silvia G

2016-03-01

The deep-sea is the largest biome of the biosphere, and contains more than half of the whole ocean's microbes. Uncovering their general patterns of diversity and community structure at a global scale remains a great challenge, as only fragmentary information of deep-sea microbial diversity exists based on regional-scale studies. Here we report the first globally comprehensive survey of the prokaryotic communities inhabiting the bathypelagic ocean using high-throughput sequencing of the 16S rRNA gene. This work identifies the dominant prokaryotes in the pelagic deep ocean and reveals that 50% of the operational taxonomic units (OTUs) belong to previously unknown prokaryotic taxa, most of which are rare and appear in just a few samples. We show that whereas the local richness of communities is comparable to that observed in previous regional studies, the global pool of prokaryotic taxa detected is modest (~3600 OTUs), as a high proportion of OTUs are shared among samples. The water masses appear to act as clear drivers of the geographical distribution of both particle-attached and free-living prokaryotes. In addition, we show that the deep-oceanic basins in which the bathypelagic realm is divided contain different particle-attached (but not free-living) microbial communities. The combination of the aging of the water masses and a lack of complete dispersal are identified as the main drivers for this biogeographical pattern. All together, we identify the potential of the deep ocean as a reservoir of still unknown biological diversity with a higher degree of spatial complexity than hitherto considered.

Global diversity and biogeography of deep-sea pelagic prokaryotes

PubMed Central

Salazar, Guillem; Cornejo-Castillo, Francisco M; Benítez-Barrios, Verónica; Fraile-Nuez, Eugenio; Álvarez-Salgado, X Antón; Duarte, Carlos M; Gasol, Josep M; Acinas, Silvia G

2016-01-01

The deep-sea is the largest biome of the biosphere, and contains more than half of the whole ocean's microbes. Uncovering their general patterns of diversity and community structure at a global scale remains a great challenge, as only fragmentary information of deep-sea microbial diversity exists based on regional-scale studies. Here we report the first globally comprehensive survey of the prokaryotic communities inhabiting the bathypelagic ocean using high-throughput sequencing of the 16S rRNA gene. This work identifies the dominant prokaryotes in the pelagic deep ocean and reveals that 50% of the operational taxonomic units (OTUs) belong to previously unknown prokaryotic taxa, most of which are rare and appear in just a few samples. We show that whereas the local richness of communities is comparable to that observed in previous regional studies, the global pool of prokaryotic taxa detected is modest (~3600 OTUs), as a high proportion of OTUs are shared among samples. The water masses appear to act as clear drivers of the geographical distribution of both particle-attached and free-living prokaryotes. In addition, we show that the deep-oceanic basins in which the bathypelagic realm is divided contain different particle-attached (but not free-living) microbial communities. The combination of the aging of the water masses and a lack of complete dispersal are identified as the main drivers for this biogeographical pattern. All together, we identify the potential of the deep ocean as a reservoir of still unknown biological diversity with a higher degree of spatial complexity than hitherto considered. PMID:26251871

Ectomycorrhizal diversity and community structure in stands of Quercus oleoides in the seasonally dry tropical forests of Costa Rica

NASA Astrophysics Data System (ADS)

Desai, Nikhilesh S.; Wilson, Andrew W.; Powers, Jennifer S.; Mueller, Gregory M.; Egerton-Warburton, Louise M.

2016-12-01

Most conservation efforts in seasonally dry tropical forests have overlooked less obvious targets for conservation, such as mycorrhizal fungi, that are critical to plant growth and ecosystem structure. We documented the diversity of ectomycorrhizal (EMF) and arbuscular mycorrhizal (AMF) fungal communities in Quercus oleoides (Fagaceae) in Guanacaste province, Costa Rica. Soil cores and sporocarps were collected from regenerating Q. oleoides plots differing in stand age (early vs late regeneration) during the wet season. Sequencing of the nuclear ribosomal ITS region in EMF root tips and sporocarps identified 37 taxa in the Basidiomycota; EMF Ascomycota were uncommon. The EMF community was dominated by one species (Thelephora sp. 1; 70% of soil cores), more than half of all EMF species were found only once in an individual soil core, and there were few conspecific taxa. Most EMF taxa were also restricted to either Early or Late plots. Levels of EMF species richness and diversity, and AMF root colonization were similar between plots. Our results highlight the need for comprehensive spatiotemporal samplings of EMF communities in Q. oleoides to identify and prioritize rare EMF for conservation, and document their genetic and functional diversity.

Microbial composition in microcosms amended with natural and mineral fertilizers under different water regimes

NASA Astrophysics Data System (ADS)

Brad, Traian; Chiriac, Cecilia; Szekeres, Edina; Coman, Cristian; Rudi, Knut; Sandor, Mignon

2017-04-01

Twenty microcosm enclosures containing two types of soil (i.e. a rich Chernozemic and a poorer soil) were fertilized with mineral (NPK-complex) and organic (Gülle, manure and a green fertilizer) materials and placed under dry and wet water regimes. After 10, 20 and 30 days of the experiment, soil samples were analyzed for the structure and composition of microbial communities using next generation sequencing techniques (Illumina) and statistical analysis. The differences between bacteria communities in different soil types, and in different fertilization and hydric treatments were analyzed using quantitative phylogenetic distances and the ANOSIM test. The two types of soil especially selected for the structure of microbial communities, while moisture and the type of fertilizer appeared to have a smaller influence on microbial diversity in microcosms. The alpha-diversity indices (species richness, evenness and phylogenetic diversity) had higher values for the poorer soil compared to the rich Chernozemic soil. For both soil types, the highest bacteria diversity values were obtained after fertilization with manure. The microbial communities in the analyzed soils were complex and dominated by sequences belonging to Actinobacteria, Proteobacteria, Acidobacteria and Firmicutes.

Implications of invasion by Juniperus virginiana on small mammals in the southern Great Plains

USGS Publications Warehouse

Horncastle, V.J.; Hellgren, E.C.; Mayer, P.M.; Ganguli, A.C.; Engle, David M.; Leslie, David M.

2005-01-01

Changes in landscape cover in the Great Plains are resulting from the range expansion and invasion of eastern red cedar (Juniperus virginiana). By altering the landscape and local vegetation, red cedar is changing the structure and function of habitat for small mammals. We examined effects of invasion by eastern red cedar on small mammals in 3 plant communities (tallgrass prairie, old field, and cross-timbers forest) in the cross-timbers ecoregion in Oklahoma. We sampled small mammals seasonally from May 2001 to August 2002 by using Sherman live traps and mark-recapture techniques on 3.24-ha, 450-trap grids in each plant community. We sampled vegetation in two hundred twenty-five 12 x 12-m cells within each grid. The structure of the small-mammal community differed among the 3 habitat types, with higher species diversity and richness in the tallgrass-prairie and old-field sites. Overall, the small-mammal community shifted along a gradient of increasing eastern red cedar. In the old-field and tallgrass-prairie plots, occurrence of grassland mammals decreased with increasing red cedar, whereas only 1 woodland mammal species increased. In the cross-timbers forest site, percent woody cover (<1 m in height), rather than cover of red cedar, was the most important factor affecting woodland mammal species. Examination of our data suggests that an increase in overstory cover from 0% to 30% red cedar can change a species-rich prairie community to a depauperate community dominated by 1 species, Peromyscus leucopus. Losses in species diversity and changes in mammal distribution paralleled those seen in avian communities invaded by eastern red cedar. Our results highlight ecological effects of invasion by eastern red cedar on diversity and function at multiple trophic levels. ?? 2005 American Society of Mammalogists.

Bacterial community characterization and biogeochemistry of sediments from a tropical upwelling system (Cabo Frio, Southeastern Brazil)

NASA Astrophysics Data System (ADS)

Castelo-Branco, R.; Barreiro, A.; Silva, F. S.; Carvalhal-Gomes, S. B. V.; Fontana, L. F.; Mendonça-Filho, J. G.; Vasconcelos, V.

2016-11-01

The Cabo Frio Upwelling System is one of the largest and most productive areas in southeastern Brazil. Although it is well-known that bacterial communities play a crucial role in the biogeochemical cycles and food chain of marine ecosystems, little is known regarding the microbial communities in the sediments of this upwelling region. In this research, we address the effect of different hydrological conditions on the biogeochemistry of sediments and the diversity of bacterial communities. Biogeochemistry profiles of sediments from four sampling stations along an inner-outer transect on the continental shelf were evaluated and denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene fragments was used to study the bacterial community composition in these sediments. Our sequencing analysis of excised bands identified Alpha- and Gammaproteobacteria, Bacteroidetes and bacteria belonging to the Firmicutes phyla as the phylogenetic groups, indicating the existence of great diversity in these marine sediments. In this multidisciplinary study, the use of multivariate analysis was crucial for understanding how biogeochemical profiles influence bacterial community distribution. A Principal Component Analysis (PCA) indicated that the biogeochemical variables exhibited a clear spatial pattern that is mainly related to hydrological conditions. A Correspondence Analysis (CA) revealed an important association between certain taxonomic groups and specific sampling locations. Canonical Correspondence Analysis (CCA) demonstrated that the biogeochemistry influences the structure of the bacterial community in sediments. Among the bacterial groups identified, the most taxonomically diverse classes (Alphaproteobacteria and Gammaproteobacteria) were found to be distributed regardless of any studied biogeochemical variables influences, whereas other groups responded to biogeochemical conditions which, in turn, were influenced by hydrological conditions. This finding was observed for members of the two classes in the Bacteroidetes phylum, which were associated with either proteins or carbohydrates.

The same but different: equally megadiverse but taxonomically variant spider communities along an elevational gradient

NASA Astrophysics Data System (ADS)

Malumbres-Olarte, Jagoba; Crespo, Luís; Cardoso, Pedro; Szűts, Tamás; Fannes, Wouter; Pape, Thomas; Scharff, Nikolaj

2018-04-01

Spatial variation in biodiversity is one of the key pieces of information for the delimitation and prioritisation of protected areas. This information is especially important when the protected area includes different climatic and habitat conditions and communities, such as those along elevational gradients. Here we test whether the megadiverse communities of spiders along an elevational gradient change according to two diversity models - a monotonic decrease or a hump-shaped pattern in species richness. We also measure compositional variation along and within elevations, and test the role of the preference of microhabitat (vegetation strata) and the functional (guild) structure of species in the changes. We sampled multiple spider communities using standardised and optimised sampling in three forest types, each at a different elevation along a climatic gradient. The elevational transects were at increasing horizontal distances (between 0.1 and 175 km) in the Udzungwa Mountains, Eastern Arc Mountains, Tanzania. The number of species was similar between plots and forest types, and therefore the pattern did not match either diversity model. However, species composition changed significantly with a gradual change along elevations. Although the number of species per microhabitat and guild also remained similar across elevations, the number of individuals varied, e.g. at higher elevations low canopy vegetation was inhabited by more spiders, and the spiders belonging to guilds that typically use this microhabitat were more abundant. Our findings reflex the complex effects of habitat-microhabitat interactions on spider communities at the individual, species and guild levels. If we aim to understand and conserve some of the most diverse communities in the world, researchers and managers may need to place more attention to small scale and microhabitat characteristics upon which communities depend.

Zooming-in on floral nectar: a first exploration of nectar-associated bacteria in wild plant communities.

PubMed

Alvarez-Pérez, Sergio; Herrera, Carlos M; de Vega, Clara

2012-06-01

Floral nectar of some animal-pollinated plants usually harbours highly adapted yeast communities which can profoundly alter nectar characteristics and, therefore, potentially have significant impacts on plant reproduction through their effects on insect foraging behaviour. Bacteria have also been occasionally observed in floral nectar, but their prevalence, phylogenetic diversity and ecological role within plant-pollinator-yeast systems remains unclear. Here we present the first reported survey of bacteria in floral nectar from a natural plant community. Culturable bacteria occurring in a total of 71 nectar samples collected from 27 South African plant species were isolated and identified by 16S rRNA gene sequencing. Rarefaction-based analyses were used to assess operational taxonomic units (OTUs) richness at the plant community level using nectar drops as sampling units. Our results showed that bacteria are common inhabitants of floral nectar of South African plants (53.5% of samples yielded growth), and their communities are characterized by low species richness (18 OTUs at a 16S rRNA gene sequence dissimilarity cut-off of 3%) and moderate phylogenetic diversity, with most isolates belonging to the Gammaproteobacteria. Furthermore, isolates showed osmotolerance, catalase activity and the ability to grow under microaerobiosis, three traits that might help bacteria to overcome important factors limiting their survival and/or growth in nectar. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Bacterial Community Composition of South China Sea Sediments through Pyrosequencing-Based Analysis of 16S rRNA Genes

PubMed Central

Zhu, Daochen; Tanabe, Shoko-Hosoi; Yang, Chong; Zhang, Weimin; Sun, Jianzhong

2013-01-01

Background Subseafloor sediments accumulate large amounts of organic and inorganic materials that contain a highly diverse microbial ecosystem. The aim of this study was to survey the bacterial community of subseafloor sediments from the South China Sea. Methodology/Principal Findings Pyrosequencing of over 265,000 amplicons of the V3 hypervariable region of the 16S ribosomal RNA gene was performed on 16 sediment samples collected from multiple locations in the northern region of the South China Sea from depths ranging from 35 to 4000 m. A total of 9,726 operational taxonomic units (OTUs; between 695 and 2819 unique OTUs per sample) at 97% sequence similarity level were generated. In total, 40 bacterial phyla including 22 formally described phyla and 18 candidate phyla, with Proteobacteria, Firmicutes, Planctomycetes, Actinobacteria and Chloroflexi being most diverse, were identified. The most abundant phylotype, accounting for 42.6% of all sequences, belonged to Gammaproteobacteria, which possessed absolute predominance in the samples analyzed. Among the 18 candidate phyla, 12 were found for the first time in the South China Sea. Conclusions This study provided a novel insight into the composition of bacterial communities of the South China Sea subseafloor. Furthermore, abundances and community similarity analysis showed that the compositions of the bacterial communities are very similar at phylum level at different depths from 35-4000 m. PMID:24205246

Bacterial community composition of South China Sea sediments through pyrosequencing-based analysis of 16S rRNA genes.

PubMed

Zhu, Daochen; Tanabe, Shoko-Hosoi; Yang, Chong; Zhang, Weimin; Sun, Jianzhong

2013-01-01

Subseafloor sediments accumulate large amounts of organic and inorganic materials that contain a highly diverse microbial ecosystem. The aim of this study was to survey the bacterial community of subseafloor sediments from the South China Sea. Pyrosequencing of over 265,000 amplicons of the V3 hypervariable region of the 16S ribosomal RNA gene was performed on 16 sediment samples collected from multiple locations in the northern region of the South China Sea from depths ranging from 35 to 4000 m. A total of 9,726 operational taxonomic units (OTUs; between 695 and 2819 unique OTUs per sample) at 97% sequence similarity level were generated. In total, 40 bacterial phyla including 22 formally described phyla and 18 candidate phyla, with Proteobacteria, Firmicutes, Planctomycetes, Actinobacteria and Chloroflexi being most diverse, were identified. The most abundant phylotype, accounting for 42.6% of all sequences, belonged to Gammaproteobacteria, which possessed absolute predominance in the samples analyzed. Among the 18 candidate phyla, 12 were found for the first time in the South China Sea. This study provided a novel insight into the composition of bacterial communities of the South China Sea subseafloor. Furthermore, abundances and community similarity analysis showed that the compositions of the bacterial communities are very similar at phylum level at different depths from 35-4000 m.

Effectiveness of Winkler Litter Extraction and Pitfall Traps in Sampling Ant Communities and Functional Groups in a Temperate Forest.

PubMed

Mahon, Michael B; Campbell, Kaitlin U; Crist, Thomas O

2017-06-01

Selection of proper sampling methods for measuring a community of interest is essential whether the study goals are to conduct a species inventory, environmental monitoring, or a manipulative experiment. Insect diversity studies often employ multiple collection methods at the expense of researcher time and funding. Ants (Formicidae) are widely used in environmental monitoring owing to their sensitivity to ecosystem changes. When sampling ant communities, two passive techniques are recommended in combination: pitfall traps and Winkler litter extraction. These recommendations are often based on studies from highly diverse tropical regions or when a species inventory is the goal. Studies in temperate regions often focus on measuring consistent community response along gradients of disturbance or among management regimes; therefore, multiple sampling methods may be unnecessary. We compared the effectiveness of pitfalls and Winkler litter extraction in an eastern temperate forest for measuring ant species richness, composition, and occurrence of ant functional groups in response to experimental manipulations of two key forest ecosystem drivers, white-tailed deer and an invasive shrub (Amur honeysuckle). We found no significant effect of sampling method on the outcome of the ecological experiment; however, we found differences between the two sampling methods in the resulting ant species richness and functional group occurrence. Litter samples approximated the overall combined species richness and composition, but pitfalls were better at sampling large-bodied (Camponotus) species. We conclude that employing both methods is essential only for species inventories or monitoring ants in the Cold-climate Specialists functional group. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Analysis of Composition and Structure of Coastal to Mesopelagic Bacterioplankton Communities in the Northern Gulf of Mexico

PubMed Central

King, Gary M.; Smith, Conor B.; Tolar, Bradley; Hollibaugh, James T.

2013-01-01

16S rRNA gene amplicons were pyrosequenced to assess bacterioplankton community composition, diversity, and phylogenetic community structure for 17 stations in the northern Gulf of Mexico (nGoM) sampled in March 2010. Statistical analyses showed that samples from depths ≤100 m differed distinctly from deeper samples. SAR 11 α-Proteobacteria and Bacteroidetes dominated communities at depths ≤100 m, which were characterized by high α-Proteobacteria/γ-Proteobacteria ratios (α/γ > 1.7). Thaumarchaeota, Firmicutes, and δ-Proteobacteria were relatively abundant in deeper waters, and α/γ ratios were low (<1). Canonical correlation analysis indicated that δ- and γ-Proteobacteria, Thaumarchaeota, and Firmicutes correlated positively with depth; α-Proteobacteria and Bacteroidetes correlated positively with temperature and dissolved oxygen; Actinobacteria, β-Proteobacteria, and Verrucomicrobia correlated positively with a measure of suspended particles. Diversity indices did not vary with depth or other factors, which indicated that richness and evenness elements of bacterioplankton communities might develop independently of nGoM physical-chemical variables. Phylogenetic community structure as measured by the net relatedness (NRI) and nearest taxon (NTI) indices also did not vary with depth. NRI values indicated that most of the communities were comprised of OTUs more distantly related to each other in whole community comparisons than expected by chance. NTI values derived from phylogenetic distances of the closest neighbor for each OTU in a given community indicated that OTUs tended to occur in clusters to a greater extent than expected by chance. This indicates that “habitat filtering” might play an important role in nGoM bacterioplankton species assembly, and that such filtering occurs throughout the water column. PMID:23346078

Molecular techniques revealed highly diverse microbial communities in natural marine biofilms on polystyrene dishes for invertebrate larval settlement.

PubMed

Lee, On On; Chung, Hong Chun; Yang, Jiangke; Wang, Yong; Dash, Swagatika; Wang, Hao; Qian, Pei-Yuan

2014-07-01

Biofilm microbial communities play an important role in the larval settlement response of marine invertebrates. However, the underlying mechanism has yet to be resolved, mainly because of the uncertainties in characterizing members in the communities using traditional 16S rRNA gene-based molecular methods and in identifying the chemical signals involved. In this study, pyrosequencing was used to characterize the bacterial communities in intertidal and subtidal marine biofilms developed during two seasons. We revealed highly diverse biofilm bacterial communities that varied with season and tidal level. Over 3,000 operational taxonomic units with estimates of up to 8,000 species were recovered in a biofilm sample, which is by far the highest number recorded in subtropical marine biofilms. Nineteen phyla were found, of which Cyanobacteria and Proteobacteria were the most dominant one in the intertidal and subtidal biofilms, respectively. Apart from these, Actinobacteria, Bacteroidetes, and Planctomycetes were the major groups recovered in both intertidal and subtidal biofilms, although their relative abundance varied among samples. Full-length 16S rRNA gene clone libraries were constructed for the four biofilm samples and showed similar bacterial compositions at the phylum level to those revealed by pyrosequencing. Laboratory assays confirmed that cyrids of the barnacle Balanus amphitrite preferred to settle on the intertidal rather than subtidal biofilms. This preference was independent of the biofilm bacterial density or biomass but was probably related to the biofilm community structure, particularly, the Proteobacterial and Cyanobacterial groups.

Restoration with pioneer plants changes soil properties and remodels the diversity and structure of bacterial communities in rhizosphere and bulk soil of copper mine tailings in Jiangxi Province, China.

PubMed

Sun, Xiaoyan; Zhou, Yanling; Tan, Yinjing; Wu, Zhaoxiang; Lu, Ping; Zhang, Guohua; Yu, Faxin

2018-05-25

To unravel the ecological function played by pioneer plants in the practical restoration of mine tailings, it is vital to explore changes of soil characteristics and microbial communities in rhizosphere and bulk soil following the adaptation and survival of plants. In the present study, the diversity and structure of rhizospheric bacterial communities of three pioneer plants in copper mine tailings were investigated by Illumina MiSeq sequencing, and the effects of pioneer plants on soil properties were also evaluated. Significant soil improvement was detected in rhizospheric samples, and Alnus cremastogyne showed higher total organic matter, total nitrogen, and available phosphorus than two other herbaceous plants. Microbial diversity indices in rhizosphere and bulk soil of reclaimed tailings were significantly higher than bare tailings, even the soil properties of bulk soil in reclaimed tailings were not significantly different from those of bare tailings. A detailed taxonomic composition analysis demonstrated that Alphaproteobacteria and Deltaproteobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes showed significantly higher relative abundance in rhizosphere and bulk soil. In contrast, Gammaproteobacteria and Firmicutes were abundant in bare tailings, in which Bacillus, Pseudomonas, and Lactococcus made up the majority of the bacterial community (63.04%). Many species within known heavy metal resistance and nutrient regulatory microorganism were identified in reclaimed tailings, and were more abundant among rhizospheric microbes. Hierarchical clustering and principal coordinate analysis (PCoA) analysis demonstrated that the bacterial profiles in the rhizosphere clustered strictly together according to plant types, and were distinguishable from bulk soil. However, we also identified a large shared OTUs that occurred repeatedly and was unaffected by highly diverse soil properties in rhizosphere and bulk samples. Redundancy analysis indicated that water content and Cu and As concentrations were the main environmental regulators of microbial composition. These results suggest that the interactive effect of pioneer plants and harsh soil environmental conditions remodel the specific bacterial communities in rhizosphere and bulk soil in mine tailings. And A. cremastogyne might be approximate candidate for phytoremediation of mine tailings for better soil amelioration effect and relative higher diversity of bacterial community in rhizosphere.

Characterization of the nasal and oral microbiota of detection dogs.

PubMed

Isaiah, Anitha; Hoffmann, Aline Rodrigues; Kelley, Russ; Mundell, Paul; Steiner, Jörg M; Suchodolski, Jan S

2017-01-01

Little is known about physiological factors that affect the sense of olfaction in dogs. The objectives of this study were to describe the canine nasal and oral microbiota in detection dogs. We sought to determine the bacterial composition of the nasal and oral microbiota of a diverse population of detection canines. Nasal and oral swabs were collected from healthy dogs (n = 81) from four locations-Alabama, Georgia, California, and Texas. Nasal and oral swabs were also collected from a second cohort of detection canines belonging to three different detection job categories: explosive detection dogs (SP-E; n = 22), patrol and narcotics detection dogs (P-NDD; n = 15), and vapor wake dogs (VWD-E; n = 9). To understand if the nasal and oral microbiota of detection canines were variable, sample collection was repeated after 7 weeks in a subset of dogs. DNA was extracted from the swabs and used for 454-pyrosequencing of the16S rRNA genes. Nasal samples had a significantly lower diversity than oral samples (P<0.01). Actinobacteria and Proteobacteria were higher in nasal samples, while Bacteroidetes, Firmicutes, Fusobacteria, and Tenericutes were higher in oral samples. Bacterial diversity was not significantly different based on the detection job. No significant difference in beta diversity was observed in the nasal samples based on the detection job. In oral samples, however, ANOSIM suggested a significant difference in bacterial communities based on job category albeit with a small effect size (R = 0.1079, P = 0.02). Analysis of the composition of bacterial communities using LEfSe showed that within the nasal samples, Cardiobacterium and Riemerella were higher in VWD-E dogs, and Sphingobacterium was higher in the P-NDD group. In the oral samples Enterococcus and Capnocytophaga were higher in the P-NDD group. Gemella and Aggregatibacter were higher in S-PE, and Pigmentiphaga, Chryseobacterium, Parabacteroides amongst others were higher within the VWD-E group. Our initial data also shows that there is a temporal variation in alpha diversity in nasal samples in detection canines.

Characterization of the nasal and oral microbiota of detection dogs

PubMed Central

Hoffmann, Aline Rodrigues; Kelley, Russ; Mundell, Paul; Steiner, Jörg M.

2017-01-01

Little is known about physiological factors that affect the sense of olfaction in dogs. The objectives of this study were to describe the canine nasal and oral microbiota in detection dogs. We sought to determine the bacterial composition of the nasal and oral microbiota of a diverse population of detection canines. Nasal and oral swabs were collected from healthy dogs (n = 81) from four locations—Alabama, Georgia, California, and Texas. Nasal and oral swabs were also collected from a second cohort of detection canines belonging to three different detection job categories: explosive detection dogs (SP-E; n = 22), patrol and narcotics detection dogs (P-NDD; n = 15), and vapor wake dogs (VWD-E; n = 9). To understand if the nasal and oral microbiota of detection canines were variable, sample collection was repeated after 7 weeks in a subset of dogs. DNA was extracted from the swabs and used for 454-pyrosequencing of the16S rRNA genes. Nasal samples had a significantly lower diversity than oral samples (P<0.01). Actinobacteria and Proteobacteria were higher in nasal samples, while Bacteroidetes, Firmicutes, Fusobacteria, and Tenericutes were higher in oral samples. Bacterial diversity was not significantly different based on the detection job. No significant difference in beta diversity was observed in the nasal samples based on the detection job. In oral samples, however, ANOSIM suggested a significant difference in bacterial communities based on job category albeit with a small effect size (R = 0.1079, P = 0.02). Analysis of the composition of bacterial communities using LEfSe showed that within the nasal samples, Cardiobacterium and Riemerella were higher in VWD-E dogs, and Sphingobacterium was higher in the P-NDD group. In the oral samples Enterococcus and Capnocytophaga were higher in the P-NDD group. Gemella and Aggregatibacter were higher in S-PE, and Pigmentiphaga, Chryseobacterium, Parabacteroides amongst others were higher within the VWD-E group. Our initial data also shows that there is a temporal variation in alpha diversity in nasal samples in detection canines. PMID:28934260

Physical Activity among Rural Older Adults with Diabetes

ERIC Educational Resources Information Center

Arcury, Thomas A.; Snively, Beverly M.; Bell, Ronny A.; Smith, Shannon L.; Stafford, Jeanette M.; Wetmore-Arkader, Lindsay K.; Quandt, Sara A.

2006-01-01

Purpose: This analysis describes physical activity levels and factors associated with physical activity in an ethnically diverse (African American, Native American, white) sample of rural older adults with diabetes. Method: Data were collected using a population-based, cross-sectional stratified random sample survey of 701 community-dwelling…

Bacterial and fungal community composition and functioning of two different peatlands in China

NASA Astrophysics Data System (ADS)

Wang, Meng; Tian, Jianqing; Bu, Zhaojun; Chen, Huai; Zhu, Qiuan; Peng, Changhui

2017-04-01

Peatlands are important carbon sinks which store one third of the global soil carbon ( 550 Gt) with only 3% of the land surface. The slow rate of organic matter decomposition associated with low microbial diversity and limited functioning under cold, acidic and anoxic condition is of critical importance in controlling biogeochemical cycles in northern peatlands. To evaluate the variation in microbial community composition and functionality can advance our understanding of the underlying mechanisms of the biogeochemical processes and interactions. However, there is still a lack of information for Chinese peatlands. Here, we sampled peat profiles at three different depths (10-20, 30-40 and 60-70 cm) from two typical peatlands in China: a rich fen in Qinghai-Tibet Plateau (QTP) and a poor fen in the Changbai Mountains (CBM). We investigated the bacterial (16S rRNA) and fungal (ITS2) community composition and diversity with high-throughput sequencing and predicted the metagenome functioning with PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States). The results showed that Proteobacteria, Acidobacteria and Actinobacteria were the most abundant bacterial phyla in the upper peat layer (10-20 cm) for both sites, with increasing abundance of Chloroflexi and Bacteroidetes down to the saturated zone (60-70 cm in CMB; 30-40 and 60-70 cm in QTP). For fungi, Ascomycota, Ciliophora and Basidiomycota were the most abundant phyla in both sites, with decreasing Ciliophora abundance down to the saturated zone. The α-diversity of both bacterial and fungal showed a decreasing trend with depth in QTP, with the largest diversity occurring at the depth of 30-40 cm in CMB. Regardless of sampling sites, the bacterial communities at the depth of 60-70 cm were more similar than the other depths. The fungal community was clustered into two groups, corresponding to two sampling sites. The variation in fungal community with depth was larger in QTP than in CBM. The predicted abundances of KEGG orthologs (KOs) assigned to the metabolism of amino acid, lipid and xenobiotics, as well as environmental adaptation, were decreased with depth in CBM, with energy metabolism showing the opposite trend. In contrast, the KO abundances of amino acid and lipid metabolism and environmental adaptation were the highest in the middle layer (30-40 cm) in QTP, where the KO abundance of energy metabolism was the lowest. In general, the difference in predicted metagenome functioning between sites was less obvious than between depths. These results highlight the important role of hydrology in shaping the microbial community in minerotrophic peatlands. The effect of environmental drivers on microbial diversity and functioning may be mediated by shifting in hydrological dynamics (e.g. land use change and desiccation) which should be considered under future global change condition.

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

Wrighton, Kelly C.; Castelle, Cindy; Wilkins, Michael J.

Fermentation-based metabolism is an important ecosystem function often associated with environments rich in organic carbon, such as wetlands, sewage sludge, and the mammalian gut. The diversity of microorganisms and pathways involved in carbon and hydrogen cycling in sediments and aquifers and the impacts of these processes on other biogeochemical cycles remain poorly understood. Here we used metagenomics and proteomics to characterize microbial communities sampled from an aquifer adjacent to the Colorado River at Rifle, Colorado, USA, and document interlinked microbial roles in geochemical cycling. The organic carbon content in the aquifer was elevated via two acetate-based biostimulation treatments. Samples weremore » collected at three time points, with the objective of extensive genome recovery to enable metabolic reconstruction of the community. Fermentative community members include genomes from a new phylum (ACD20), phylogenetically novel members of the Chloroflexi and Bacteroidetes, as well as candidate phyla genomes (OD1, BD1-5, SR1, WWE3, ACD58, TM6, PER, and OP11). These organisms have the capacity to produce hydrogen, acetate, formate, ethanol, butyrate, and lactate, activities supported by proteomic data. The diversity and expression of hydrogenases suggests the importance of hydrogen currency in the subsurface. Our proteogenomic data further indicate the consumption of fermentation intermediates by Proteobacteria can be coupled to nitrate, sulfate, and iron reduction. Thus, fermentation carried out by previously unstudied members of sediment microbial communities may be an important driver of diverse subsurface biogeochemical cycles.« less

Pyrosequencing analysis yields comprehensive assessment of microbial communities in pilot-scale two-stage membrane biofilm reactors.

PubMed

Ontiveros-Valencia, Aura; Tang, Youneng; Zhao, He-Ping; Friese, David; Overstreet, Ryan; Smith, Jennifer; Evans, Patrick; Rittmann, Bruce E; Krajmalnik-Brown, Rosa

2014-07-01

We studied the microbial community structure of pilot two-stage membrane biofilm reactors (MBfRs) designed to reduce nitrate (NO3(-)) and perchlorate (ClO4(-)) in contaminated groundwater. The groundwater also contained oxygen (O2) and sulfate (SO4(2-)), which became important electron sinks that affected the NO3(-) and ClO4(-) removal rates. Using pyrosequencing, we elucidated how important phylotypes of each "primary" microbial group, i.e., denitrifying bacteria (DB), perchlorate-reducing bacteria (PRB), and sulfate-reducing bacteria (SRB), responded to changes in electron-acceptor loading. UniFrac, principal coordinate analysis (PCoA), and diversity analyses documented that the microbial community of biofilms sampled when the MBfRs had a high acceptor loading were phylogenetically distant from and less diverse than the microbial community of biofilm samples with lower acceptor loadings. Diminished acceptor loading led to SO4(2-) reduction in the lag MBfR, which allowed Desulfovibrionales (an SRB) and Thiothrichales (sulfur-oxidizers) to thrive through S cycling. As a result of this cooperative relationship, they competed effectively with DB/PRB phylotypes such as Xanthomonadales and Rhodobacterales. Thus, pyrosequencing illustrated that while DB, PRB, and SRB responded predictably to changes in acceptor loading, a decrease in total acceptor loading led to important shifts within the "primary" groups, the onset of other members (e.g., Thiothrichales), and overall greater diversity.

Prokaryotic diversity and community composition in the Salar de Uyuni, a large scale, chaotropic salt flat.

PubMed

dC Rubin, Sergio S; Marín, Irma; Gómez, Manuel J; Morales, Eduardo A; Zekker, Ivar; San Martín-Uriz, Patxi; Rodríguez, Nuria; Amils, Ricardo

2017-09-01

Salar de Uyuni (SdU), with a geological history that reflects 50 000 years of climate change, is the largest hypersaline salt flat on Earth and is estimated to be the biggest lithium reservoir in the world. Its salinity reaches saturation levels for NaCl, a kosmotropic salt, and high concentrations of MgCL 2 and LiCl, both salts considered important chaotrophic stressors. In addition, extreme temperatures, anoxic conditions, high UV irradiance, high albedo and extremely low concentrations of phosphorous, make SdU a unique natural extreme environment in which to contrast hypotheses about limiting factors of life diversification. Geophysical studies of brines from different sampling stations show that water activity is rather constant along SdU. Geochemical measurements show significant differences in magnesium concentration, ranging from 0.2 to 2M. This work analyses the prokaryotic diversity and community structure at four SdU sampling stations, selected according to their location and ionic composition. Prokaryotic communities were composed of both Archaea (with members of the classes Halobacteria, Thermoplasmata and Nanohaloarchaea, from the Euryarchaeota and Nanohaloarcheota phyla respectively) and Bacteria (mainly belonging to Bacteroidetes and Proteobacteria phyla). The important differences in composition of microbial communities inversely correlate with Mg 2+ concentration, suggesting that prokaryotic diversity at SdU is chaotropic dependent. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Differences in soil micro-eukaryotic communities over soil pH gradients are strongly driven by parasites and saprotrophs.

PubMed

Dupont, A Ö C; Griffiths, R I; Bell, T; Bass, D

2016-06-01

A recent large-scale assessment of bacterial communities across a range of UK soil types showed that bacterial community structure was strongly determined by soil pH. We analysed a data set of eukaryotic 454 sequencing 18S rDNA from the surveyed samples and showed significant differences in eukaryotic assemblages according to pH class, mostly between low pH and higher pH soils. Soil eukaryote communities (per sample) differed most at the taxonomic rank approximating to order level. Taxonomies assigned with the Protist Ribosomal Reference and the Silva 119 databases were taxonomically inconsistent, mostly due to differing 18S annotations, although general structure and composition according to pH were coherent. A relatively small number of lineages, mostly putative parasitic protists and fungi, drive most differences between pH classes, with weaker contributions from bacterivores and autotrophs. Overall, soil parasites included a large diversity of alveolates, in particular apicomplexans. Phylogenetic analysis of alveolate lineages demonstrates a large diversity of unknown gregarines, novel perkinsids, coccidians, colpodellids and uncharacterized alveolates. Other novel and/or divergent lineages were revealed across the eukaryote tree of life. Our study provides an in-depth taxonomic evaluation of micro-eukaryotic diversity, and reveals novel lineages and insights into their relationships with environmental variables across soil gradients. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Organic farming increases richness of fungal taxa in the wheat phyllosphere.

PubMed

Karlsson, Ida; Friberg, Hanna; Kolseth, Anna-Karin; Steinberg, Christian; Persson, Paula

2017-07-01

Organic farming is often advocated as an approach to mitigate biodiversity loss on agricultural land. The phyllosphere provides a habitat for diverse fungal communities that are important for plant health and productivity. However, it is still unknown how organic farming affects the diversity of phyllosphere fungi in major crops. We sampled wheat leaves from 22 organically and conventionally cultivated fields in Sweden, paired based on their geographical location and wheat cultivar. Fungal communities were described using amplicon sequencing and real-time PCR. Species richness was higher on wheat leaves from organically managed fields, with a mean of 54 operational taxonomic units (OTUs) compared with 40 OTUs for conventionally managed fields. The main components of the fungal community were similar throughout the 350-km-long sampling area, and seven OTUs were present in all fields: Zymoseptoria, Dioszegia fristingensis, Cladosporium, Dioszegia hungarica, Cryptococcus, Ascochyta and Dioszegia. Fungal abundance was highly variable between fields, 10 3 -10 5 internal transcribed spacer copies per ng wheat DNA, but did not differ between cropping systems. Further analyses showed that weed biomass was the strongest explanatory variable for fungal community composition and OTU richness. These findings help provide a more comprehensive understanding of the effect of organic farming on the diversity of organism groups in different habitats within the agroecosystem. © 2017 The Authors Molecular Ecology Published by John Wiley & Sons Ltd.

Temporal variations in the abundance and composition of biofilm communities colonizing drinking water distribution pipes.

PubMed

Kelly, John J; Minalt, Nicole; Culotti, Alessandro; Pryor, Marsha; Packman, Aaron

2014-01-01

Pipes that transport drinking water through municipal drinking water distribution systems (DWDS) are challenging habitats for microorganisms. Distribution networks are dark, oligotrophic and contain disinfectants; yet microbes frequently form biofilms attached to interior surfaces of DWDS pipes. Relatively little is known about the species composition and ecology of these biofilms due to challenges associated with sample acquisition from actual DWDS. We report the analysis of biofilms from five pipe samples collected from the same region of a DWDS in Florida, USA, over an 18 month period between February 2011 and August 2012. The bacterial abundance and composition of biofilm communities within the pipes were analyzed by heterotrophic plate counts and tag pyrosequencing of 16S rRNA genes, respectively. Bacterial numbers varied significantly based on sampling date and were positively correlated with water temperature and the concentration of nitrate. However, there was no significant relationship between the concentration of disinfectant in the drinking water (monochloramine) and the abundance of bacteria within the biofilms. Pyrosequencing analysis identified a total of 677 operational taxonomic units (OTUs) (3% distance) within the biofilms but indicated that community diversity was low and varied between sampling dates. Biofilms were dominated by a few taxa, specifically Methylomonas, Acinetobacter, Mycobacterium, and Xanthomonadaceae, and the dominant taxa within the biofilms varied dramatically between sampling times. The drinking water characteristics most strongly correlated with bacterial community composition were concentrations of nitrate, ammonium, total chlorine and monochloramine, as well as alkalinity and hardness. Biofilms from the sampling date with the highest nitrate concentration were the most abundant and diverse and were dominated by Acinetobacter.

Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea

PubMed Central

Herlemann, Daniel PR; Labrenz, Matthias; Jürgens, Klaus; Bertilsson, Stefan; Waniek, Joanna J; Andersson, Anders F

2011-01-01

Salinity is a major factor controlling the distribution of biota in aquatic systems, and most aquatic multicellular organisms are either adapted to life in saltwater or freshwater conditions. Consequently, the saltwater–freshwater mixing zones in coastal or estuarine areas are characterized by limited faunal and floral diversity. Although changes in diversity and decline in species richness in brackish waters is well documented in aquatic ecology, it is unknown to what extent this applies to bacterial communities. Here, we report a first detailed bacterial inventory from vertical profiles of 60 sampling stations distributed along the salinity gradient of the Baltic Sea, one of world's largest brackish water environments, generated using 454 pyrosequencing of partial (400 bp) 16S rRNA genes. Within the salinity gradient, bacterial community composition altered at broad and finer-scale phylogenetic levels. Analogous to faunal communities within brackish conditions, we identified a bacterial brackish water community comprising a diverse combination of freshwater and marine groups, along with populations unique to this environment. As water residence times in the Baltic Sea exceed 3 years, the observed bacterial community cannot be the result of mixing of fresh water and saltwater, but our study represents the first detailed description of an autochthonous brackish microbiome. In contrast to the decline in the diversity of multicellular organisms, reduced bacterial diversity at brackish conditions could not be established. It is possible that the rapid adaptation rate of bacteria has enabled a variety of lineages to fill what for higher organisms remains a challenging and relatively unoccupied ecological niche. PMID:21472016

Regional synchrony in full-scale activated sludge bioreactors due to deterministic microbial community assembly

PubMed Central

Griffin, James S; Wells, George F

2017-01-01

Seasonal community structure and regionally synchronous population dynamics have been observed in natural microbial ecosystems, but have not been well documented in wastewater treatment bioreactors. Few studies of community dynamics in full-scale activated sludge systems facing similar meteorological conditions have been done to compare the importance of deterministic and neutral community assembly mechanisms. We subjected weekly activated sludge samples from six regional full-scale bioreactors at four wastewater treatment plants obtained over 1 year to Illumina sequencing of 16S ribosomal RNA genes, resulting in a library of over 17 million sequences. All samples derived from reactors treating primarily municipal wastewater. Despite variation in operational characteristics and location, communities displayed temporal synchrony at the individual operational taxonomic unit (OTU), broad phylogenetic affiliation and community-wide scale. Bioreactor communities were dominated by 134 abundant and highly regionally synchronized OTU populations that accounted for over 50% of the total reads. Non-core OTUs displayed abundance-dependent population synchrony. Alpha diversity varied by reactor, but showed a highly reproducible and synchronous seasonal fluctuation. Community similarity was dominated by seasonal changes, but individual reactors maintained minor stable differences after 1 year. Finally, the impacts of mass migration driven by direct biomass transfers between reactors was investigated, but had no significant effect on community similarity or diversity in the sink community. Our results show that population dynamics in activated sludge bioreactors are consistent with niche-driven assembly guided by seasonal temperature fluctuations. PMID:27996980

Intertidal nematode communities in the Mekong estuaries of Vietnam and their potential for biomonitoring.

PubMed

Quang, Ngo Xuan; Chau, Nguyen Ngoc; Smol, Nic; Prozorova, Larisa; Vanreusel, Ann

2016-02-01

Nematode communities in eight Mekong estuaries were investigated during the dry season. The aim of the study was to identify the structure and the diversity of the communities in relation to the main environmental characteristics. In each estuary, three to four intertidal sampling stations were identified at regular distances from the mouth to up to 45 km land inward. The nematode communities showed a strong correlation with sediment composition and to a lesser degree with chlorophyll a concentrations. Multivariate analysis resulted in the identification of four types of communities. We identified two types of Desmodora communities in the sandy mouth stations and two types of Parodontophora communities in the silty sand stations. One of the silt associated communities showed a preference for higher chlorophyll a concentrations, resulting in higher densities and higher diversity, mainly of monhysterid species. Because of the strong association between community structure and sediment composition, nematodes are a meaningful tool for monitoring changes in their environment. In case their community deviates from what is expected based on sediment, it may serve as an early warning for disturbance.

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

NASA Astrophysics Data System (ADS)

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

2015-10-01

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

Standard filtration practices may significantly distort planktonic microbial diversity estimates.

PubMed

Padilla, Cory C; Ganesh, Sangita; Gantt, Shelby; Huhman, Alex; Parris, Darren J; Sarode, Neha; Stewart, Frank J

2015-01-01

Fractionation of biomass by filtration is a standard method for sampling planktonic microbes. It is unclear how the taxonomic composition of filtered biomass changes depending on sample volume. Using seawater from a marine oxygen minimum zone, we quantified the 16S rRNA gene composition of biomass on a prefilter (1.6 μm pore-size) and a downstream 0.2 μm filter over sample volumes from 0.05 to 5 L. Significant community shifts occurred in both filter fractions, and were most dramatic in the prefilter community. Sequences matching Vibrionales decreased from ~40 to 60% of prefilter datasets at low volumes (0.05-0.5 L) to less than 5% at higher volumes, while groups such at the Chromatiales and Thiohalorhabdales followed opposite trends, increasing from minor representation to become the dominant taxa at higher volumes. Groups often associated with marine particles, including members of the Deltaproteobacteria, Planctomycetes, and Bacteroidetes, were among those showing the greatest increase with volume (4 to 27-fold). Taxon richness (97% similarity clusters) also varied significantly with volume, and in opposing directions depending on filter fraction, highlighting potential biases in community complexity estimates. These data raise concerns for studies using filter fractionation for quantitative comparisons of aquatic microbial diversity, for example between free-living and particle-associated communities.

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

PubMed

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

2015-10-20

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

Bacterial composition in a metropolitan drinking water distribution system utilizing different source waters.

PubMed

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

2015-03-01

We investigated the bacterial composition of water samples from two service areas within a drinking water distribution system (DWDS), each associated with a different primary source of water (groundwater, GW; surface water, SW) and different treatment process. Community analysis based on 16S rRNA gene clone libraries indicated that Actinobacteria (Mycobacterium spp.) and α-Proteobacteria represented nearly 43 and 38% of the total sequences, respectively. Sequences closely related to Legionella, Pseudomonas, and Vibrio spp. were also identified. In spite of the high number of sequences (71%) shared in both areas, multivariable analysis revealed significant differences between the GW and SW areas. While the dominant phylotypes where not significantly contributing in the ordination of samples, the populations associated with the core of phylotypes (1-10% in each sample) significantly contributed to the differences between both service areas. Diversity indices indicate that the microbial community inhabiting the SW area is more diverse and contains more distantly related species coexisting with local assemblages as compared with the GW area. The bacterial community structure of SW and GW service areas were dissimilar, suggesting that their respective source water and/or water quality parameters shaped by the treatment processes may contribute to the differences in community structure observed.

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

PubMed Central

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

2015-01-01

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

Evaluation of DNA extraction methods for the analysis of microbial community in biological activated carbon.

PubMed

Zheng, Lu; Gao, Naiyun; Deng, Yang

2012-01-01

It is difficult to isolate DNA from biological activated carbon (BAC) samples used in water treatment plants, owing to the scarcity of microorganisms in BAC samples. The aim of this study was to identify DNA extraction methods suitable for a long-term, comprehensive ecological analysis of BAC microbial communities. To identify a procedure that can produce high molecular weight DNA, maximizes detectable diversity and is relatively free from contaminants, the microwave extraction method, the cetyltrimethylammonium bromide (CTAB) extraction method, a commercial DNA extraction kit, and the ultrasonic extraction method were used for the extraction of DNA from BAC samples. Spectrophotometry, agarose gel electrophoresis and polymerase chain reaction (PCR)-restriction fragment length polymorphisms (RFLP) analysis were conducted to compare the yield and quality of DNA obtained using these methods. The results showed that the CTAB method produce the highest yield and genetic diversity of DNA from BAC samples, but DNA purity was slightly less than that obtained with the DNA extraction-kit method. This study provides a theoretical basis for establishing and selecting DNA extraction methods for BAC samples.

Diversity and Seasonal Dynamics of an Assemblage of Sarcophagid Diptera in a Gradient of Urbanization

PubMed Central

Mulieri, Pablo R.; Patitucci, Luciano D.; Schnack, Juan A; Mariluis, Juan C.

2011-01-01

Sarcophagid species inhabiting different locations in a rural-urban gradient were surveyed in the east central Argentine district of the Almirante Brown, Buenos Aires province. The main objectives of this research were to identify the most prevalent sarcophagid species and to describe community richness and diversity according to the degree of urbanization and the environmental variables measured in three locations within a rural-urban gradient sampled during two years from May 2005 to April 2007. Spatial and seasonal variations were the main factors involved in structuring the sarcophagid communities. Diversity was lower in urbanized areas than in rural ones. Bait and microhabitat preferences (sunny or shady places) and seasonal fluctuations were described for 17 sarcophagid species. PMID:21870984

Spatial distribution of vanadium and microbial community responses in surface soil of Panzhihua mining and smelting area, China.

PubMed

Cao, Xuelong; Diao, Muhe; Zhang, Baogang; Liu, Hui; Wang, Song; Yang, Meng

2017-09-01

Spatial distribution of vanadium in surface soils from different processing stages of vanadium-bearing titanomagnetite in Panzhihua mining and smelting area (China) as well as responses of microbial communities including bacteria and fungi to vanadium were investigated by fieldwork and laboratory incubation experiment. The vanadium contents in this region ranged from 149.3 to 4793.6 mg kg -1 , exceeding the soil background value of vanadium in China (82 mg kg -1 ) largely. High-throughput DNA sequencing results showed bacterial communities from different manufacturing locations were quite diverse, but Bacteroidetes and Proteobacteria were abundant in all samples. The contents of organic matter, available P, available S and vanadium had great influences on the structures of bacterial communities in soils. Bacterial communities converged to similar structure after long-term (240 d) cultivation with vanadium containing medium, dominating by bacteria which can tolerate or reduce toxicities of heavy metals. Fungal diversities decreased after cultivation, but Ascomycota and Ciliophora were still the most abundant phyla as in the original soil samples. Results in this study emphasize the urgency of investigating vanadium contaminations in soils and provide valuable information on how vanadium contamination influences bacterial and fungal communities. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

PubMed

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

2011-03-01

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

Spatial diversity of bacterioplankton communities in surface water of northern South China Sea.

PubMed

Li, Jialin; Li, Nan; Li, Fuchao; Zou, Tao; Yu, Shuxian; Wang, Yinchu; Qin, Song; Wang, Guangyi

2014-01-01

The South China Sea is one of the largest marginal seas, with relatively frequent passage of eddies and featuring distinct spatial variation in the western tropical Pacific Ocean. Here, we report a phylogenetic study of bacterial community structures in surface seawater of the northern South China Sea (nSCS). Samples collected from 31 sites across large environmental gradients were used to construct clone libraries and yielded 2,443 sequences grouped into 170 OTUs. Phylogenetic analysis revealed 23 bacterial classes with major components α-, β- and γ-Proteobacteria, as well as Cyanobacteria. At class and genus taxon levels, community structure of coastal waters was distinctively different from that of deep-sea waters and displayed a higher diversity index. Redundancy analyses revealed that bacterial community structures displayed a significant correlation with the water depth of individual sampling sites. Members of α-Proteobacteria were the principal component contributing to the differences of the clone libraries. Furthermore, the bacterial communities exhibited heterogeneity within zones of upwelling and anticyclonic eddies. Our results suggested that surface bacterial communities in nSCS had two-level patterns of spatial distribution structured by ecological types (coastal VS. oceanic zones) and mesoscale physical processes, and also provided evidence for bacterial phylogenetic phyla shaped by ecological preferences.

High-throughput nucleotide sequence analysis of diverse bacterial communities in leachates of decomposing pig carcasses

PubMed Central

Yang, Seung Hak; Lim, Joung Soo; Khan, Modabber Ahmed; Kim, Bong Soo; Choi, Dong Yoon; Lee, Eun Young; Ahn, Hee Kwon

2015-01-01

The leachate generated by the decomposition of animal carcass has been implicated as an environmental contaminant surrounding the burial site. High-throughput nucleotide sequencing was conducted to investigate the bacterial communities in leachates from the decomposition of pig carcasses. We acquired 51,230 reads from six different samples (1, 2, 3, 4, 6 and 14 week-old carcasses) and found that sequences representing the phylum Firmicutes predominated. The diversity of bacterial 16S rRNA gene sequences in the leachate was the highest at 6 weeks, in contrast to those at 2 and 14 weeks. The relative abundance of Firmicutes was reduced, while the proportion of Bacteroidetes and Proteobacteria increased from 3–6 weeks. The representation of phyla was restored after 14 weeks. However, the community structures between the samples taken at 1–2 and 14 weeks differed at the bacterial classification level. The trend in pH was similar to the changes seen in bacterial communities, indicating that the pH of the leachate could be related to the shift in the microbial community. The results indicate that the composition of bacterial communities in leachates of decomposing pig carcasses shifted continuously during the study period and might be influenced by the burial site. PMID:26500442

Connectivity between surface and deep waters determines prokaryotic diversity in the North Atlantic Deep Water

PubMed Central

Frank, Alexander H.; Garcia, Juan A. L.; Herndl, Gerhard J.

2016-01-01

Summary To decipher the influence of depth stratification and surface provincialism on the dark ocean prokaryotic community composition, we sampled the major deep‐water masses in the eastern North Atlantic covering three biogeographic provinces. Their diversity was evaluated using ordination and canonical analysis of 454 pyrotag sequences. Variance partitioning suggested that 16% of the variation in the bacterial community composition was based on depth stratification while 9% of the variation was due to geographic location. General linear mixed effect models showed that the community of the subsurface waters was connected to the dark ocean prokaryotic communities in different biogeographic provinces. Cluster analysis indicated that some prokaryotic taxa are specific to distinct regions in bathypelagic water masses. Taken together, our data suggest that the dark ocean prokaryotic community composition of the eastern North Atlantic is primed by the formation and the horizontal transport of water masses. PMID:26914787

Biological support media influence the bacterial biofouling community in reverse osmosis water reclamation demonstration plants.

PubMed

Ferrera, Isabel; Mas, Jordi; Taberna, Elisenda; Sanz, Joan; Sánchez, Olga

2015-01-01

The diversity of the bacterial community developed in different stages of two reverse osmosis (RO) water reclamation demonstration plants designed in a wastewater treatment plant (WWTP) in Tarragona (Spain) was characterized by applying 454-pyrosequencing of the 16S rRNA gene. The plants were fed by secondary treated effluent to a conventional pretreatment train prior to the two-pass RO system. Plants differed in the material used in the filtration process, which was sand in one demonstration plant and Scandinavian schists in the second plant. The results showed the presence of a highly diverse and complex community in the biofilms, mainly composed of members of the Betaproteobacteria and Bacteroidetes in all stages, with the presence of some typical wastewater bacteria, suggesting a feed water origin. Community similarities analyses revealed that samples clustered according to filter type, highlighting the critical influence of the biological supporting medium in biofilm community structure.

Core-satellite populations and seasonality of water meter biofilms in a metropolitan drinking water distribution system

PubMed Central

Ling, Fangqiong; Hwang, Chiachi; LeChevallier, Mark W; Andersen, Gary L; Liu, Wen-Tso

2016-01-01

Drinking water distribution systems (DWDSs) harbor the microorganisms in biofilms and suspended communities, yet the diversity and spatiotemporal distribution have been studied mainly in the suspended communities. This study examined the diversity of biofilms in an urban DWDS, its relationship with suspended communities and its dynamics. The studied DWDS in Urbana, Illinois received conventionally treated and disinfected water sourced from the groundwater. Over a 2-year span, biomass were sampled from household water meters (n=213) and tap water (n=20) to represent biofilm and suspended communities, respectively. A positive correlation between operational taxonomic unit (OTU) abundance and occupancy was observed. Examined under a ‘core-satellite' model, the biofilm community comprised 31 core populations that encompassed 76.7% of total 16 S rRNA gene pyrosequences. The biofilm communities shared with the suspended community highly abundant and prevalent OTUs, which related to methano-/methylotrophs (i.e., Methylophilaceae and Methylococcaceae) and aerobic heterotrophs (Sphingomonadaceae and Comamonadaceae), yet differed by specific core populations and lower diversity and evenness. Multivariate tests indicated seasonality as the main contributor to community structure variation. This pattern was resilient to annual change and correlated to the cyclic fluctuations of core populations. The findings of a distinctive biofilm community assemblage and methano-/methyltrophic primary production provide critical insights for developing more targeted water quality monitoring programs and treatment strategies for groundwater-sourced drinking water systems. PMID:26251872

Core-satellite populations and seasonality of water meter biofilms in a metropolitan drinking water distribution system.

PubMed

Ling, Fangqiong; Hwang, Chiachi; LeChevallier, Mark W; Andersen, Gary L; Liu, Wen-Tso

2016-03-01

Drinking water distribution systems (DWDSs) harbor the microorganisms in biofilms and suspended communities, yet the diversity and spatiotemporal distribution have been studied mainly in the suspended communities. This study examined the diversity of biofilms in an urban DWDS, its relationship with suspended communities and its dynamics. The studied DWDS in Urbana, Illinois received conventionally treated and disinfected water sourced from the groundwater. Over a 2-year span, biomass were sampled from household water meters (n=213) and tap water (n=20) to represent biofilm and suspended communities, respectively. A positive correlation between operational taxonomic unit (OTU) abundance and occupancy was observed. Examined under a 'core-satellite' model, the biofilm community comprised 31 core populations that encompassed 76.7% of total 16 S rRNA gene pyrosequences. The biofilm communities shared with the suspended community highly abundant and prevalent OTUs, which related to methano-/methylotrophs (i.e., Methylophilaceae and Methylococcaceae) and aerobic heterotrophs (Sphingomonadaceae and Comamonadaceae), yet differed by specific core populations and lower diversity and evenness. Multivariate tests indicated seasonality as the main contributor to community structure variation. This pattern was resilient to annual change and correlated to the cyclic fluctuations of core populations. The findings of a distinctive biofilm community assemblage and methano-/methyltrophic primary production provide critical insights for developing more targeted water quality monitoring programs and treatment strategies for groundwater-sourced drinking water systems.

Variation between the oral and faecal microbiota in a free-living passerine bird, the great tit (Parus major).

PubMed

Kropáčková, Lucie; Pechmanová, Hana; Vinkler, Michal; Svobodová, Jana; Velová, Hana; Těšičký, Martin; Martin, Jean-François; Kreisinger, Jakub

2017-01-01

The gastrointestinal tract of vertebrates is inhabited by diverse bacterial communities that induce marked effects on the host physiology and health status. The composition of the gastrointestinal microbiota is characterized by pronounced taxonomic and functional variability among different regions of the vertebrate gastrointestinal tract. Despite the relatively solid knowledge on the among-region variations of the gastrointestinal microbiota in model mammalian species, there are only a few studies concerning among-region variations of the gastrointestinal microbiota in free-living non-mammalian vertebrate taxa. We used Illumina MiSeq sequencing of bacterial 16S rRNA amplicons to compare the diversity as well as taxonomic composition of bacterial communities in proximal vs. distal parts of the gastrointestinal tract (represented by oral swabs and faecal samples, respectively) in a wild passerine bird, the great tit (Parus major). The diversity of the oral microbiota was significantly higher compared to the faecal microbiota, whereas interindividual variation was higher in faecal than in oral samples. We also observed a pronounced difference in taxonomic content between the oral and faecal microbiota. Bacteria belonging to the phyla Proteobacteria, Firmicutes and Actinobacteria typically dominated in both oral and faecal samples. A high abundance of bacteria belonging to Tenericutes was observed only in faecal samples. Surprisingly, we found only a slight correlation between the faecal and oral microbiota at the within-individual level, suggesting that the microbial composition in these body sites is shaped by independent regulatory processes. Given the independence of these two communities at the individual level, we propose that simultaneous sampling of the faecal and oral microbiota will extend our understanding of host vs. microbiota interactions in wild populations.

Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein

PubMed Central

Hopkins, Max; Kailasan, Shweta; Cohen, Allison; Roux, Simon; Tucker, Kimberly Pause; Shevenell, Amelia; Agbandje-McKenna, Mavis; Breitbart, Mya

2014-01-01

The small single-stranded DNA (ssDNA) bacteriophages of the subfamily Gokushovirinae were traditionally perceived as narrowly targeted, niche-specific viruses infecting obligate parasitic bacteria, such as Chlamydia. The advent of metagenomics revealed gokushoviruses to be widespread in global environmental samples. This study expands knowledge of gokushovirus diversity in the environment by developing a degenerate PCR assay to amplify a portion of the major capsid protein (MCP) gene of gokushoviruses. Over 500 amplicons were sequenced from 10 environmental samples (sediments, sewage, seawater and freshwater), revealing the ubiquity and high diversity of this understudied phage group. Residue-level conservation data generated from multiple alignments was combined with a predicted 3D structure, revealing a tendency for structurally internal residues to be more highly conserved than surface-presenting protein–protein or viral–host interaction domains. Aggregating this data set into a phylogenetic framework, many gokushovirus MCP clades contained samples from multiple environments, although distinct clades dominated the different samples. Antarctic sediment samples contained the most diverse gokushovirus communities, whereas freshwater springs from Florida were the least diverse. Whether the observed diversity is being driven by environmental factors or host-binding interactions remains an open question. The high environmental diversity of this previously overlooked ssDNA viral group necessitates further research elucidating their natural hosts and exploring their ecological roles. PMID:24694711

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

PubMed

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

2012-01-01

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

Experimental Incubations Elicit Profound Changes in Community Transcription in OMZ Bacterioplankton

PubMed Central

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

2012-01-01

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

First Investigation of the Microbiology of the Deepest Layer of Ocean Crust

PubMed Central

Mason, Olivia U.; Nakagawa, Tatsunori; Rosner, Martin; Van Nostrand, Joy D.; Zhou, Jizhong; Maruyama, Akihiko; Fisk, Martin R.; Giovannoni, Stephen J.

2010-01-01

The gabbroic layer comprises the majority of ocean crust. Opportunities to sample this expansive crustal environment are rare because of the technological demands of deep ocean drilling; thus, gabbroic microbial communities have not yet been studied. During the Integrated Ocean Drilling Program Expeditions 304 and 305, igneous rock samples were collected from 0.45-1391.01 meters below seafloor at Hole 1309D, located on the Atlantis Massif (30 °N, 42 °W). Microbial diversity in the rocks was analyzed by denaturing gradient gel electrophoresis and sequencing (Expedition 304), and terminal restriction fragment length polymorphism, cloning and sequencing, and functional gene microarray analysis (Expedition 305). The gabbroic microbial community was relatively depauperate, consisting of a low diversity of proteobacterial lineages closely related to Bacteria from hydrocarbon-dominated environments and to known hydrocarbon degraders, and there was little evidence of Archaea. Functional gene diversity in the gabbroic samples was analyzed with a microarray for metabolic genes (“GeoChip”), producing further evidence of genomic potential for hydrocarbon degradation - genes for aerobic methane and toluene oxidation. Genes coding for anaerobic respirations, such as nitrate reduction, sulfate reduction, and metal reduction, as well as genes for carbon fixation, nitrogen fixation, and ammonium-oxidation, were also present. Our results suggest that the gabbroic layer hosts a microbial community that can degrade hydrocarbons and fix carbon and nitrogen, and has the potential to employ a diversity of non-oxygen electron acceptors. This rare glimpse of the gabbroic ecosystem provides further support for the recent finding of hydrocarbons in deep ocean gabbro from Hole 1309D. It has been hypothesized that these hydrocarbons might originate abiotically from serpentinization reactions that are occurring deep in the Earth's crust, raising the possibility that the lithic microbial community reported here might utilize carbon sources produced independently of the surface biosphere. PMID:21079766

First investigation of the microbiology of the deepest layer of ocean crust.

PubMed

Mason, Olivia U; Nakagawa, Tatsunori; Rosner, Martin; Van Nostrand, Joy D; Zhou, Jizhong; Maruyama, Akihiko; Fisk, Martin R; Giovannoni, Stephen J

2010-11-05

The gabbroic layer comprises the majority of ocean crust. Opportunities to sample this expansive crustal environment are rare because of the technological demands of deep ocean drilling; thus, gabbroic microbial communities have not yet been studied. During the Integrated Ocean Drilling Program Expeditions 304 and 305, igneous rock samples were collected from 0.45-1391.01 meters below seafloor at Hole 1309D, located on the Atlantis Massif (30 °N, 42 °W). Microbial diversity in the rocks was analyzed by denaturing gradient gel electrophoresis and sequencing (Expedition 304), and terminal restriction fragment length polymorphism, cloning and sequencing, and functional gene microarray analysis (Expedition 305). The gabbroic microbial community was relatively depauperate, consisting of a low diversity of proteobacterial lineages closely related to Bacteria from hydrocarbon-dominated environments and to known hydrocarbon degraders, and there was little evidence of Archaea. Functional gene diversity in the gabbroic samples was analyzed with a microarray for metabolic genes ("GeoChip"), producing further evidence of genomic potential for hydrocarbon degradation--genes for aerobic methane and toluene oxidation. Genes coding for anaerobic respirations, such as nitrate reduction, sulfate reduction, and metal reduction, as well as genes for carbon fixation, nitrogen fixation, and ammonium-oxidation, were also present. Our results suggest that the gabbroic layer hosts a microbial community that can degrade hydrocarbons and fix carbon and nitrogen, and has the potential to employ a diversity of non-oxygen electron acceptors. This rare glimpse of the gabbroic ecosystem provides further support for the recent finding of hydrocarbons in deep ocean gabbro from Hole 1309D. It has been hypothesized that these hydrocarbons might originate abiotically from serpentinization reactions that are occurring deep in the Earth's crust, raising the possibility that the lithic microbial community reported here might utilize carbon sources produced independently of the surface biosphere.

The Patterns and Drivers of Bacterial and Fungal β-Diversity in a Typical Dryland Ecosystem of Northwest China.

PubMed

Wang, Jianming; Zhang, Tianhan; Li, Liping; Li, Jingwen; Feng, Yiming; Lu, Qi

2017-01-01

Dryland ecosystems cover more than 30% of the terrestrial area of China, while processes that shape the biogeographic patterns of bacterial and fungal β-diversity have rarely been evaluated synchronously. To compare the biogeographic patterns and its drivers of bacterial and fungal β-diversity, we collected 62 soil samples from a typical dryland region of northwest China. We assessed bacterial and fungal communities by sequencing bacterial 16S rRNA gene and fungal ITS data. Meanwhile, the β-diversity was decomposed into two components: species replacement (species turnover) and nestedness to further explore the bacterial and fungal β-diversity patterns and its causes. The results show that both bacterial and fungal β-diversity were derived almost entirely from species turnover rather than from species nestedness. Distance-decay relationships confirmed that the geographic patterns of bacterial and fungal β-diversity were significantly different. Environmental factors had the dominant influence on both the bacterial and fungal β-diversity and species turnover, however, the role of geographic distance varied across bacterial and fungal communities. Furthermore, both bacterial and fungal nestedness did not significantly respond to the environmental and geographic distance. Our findings suggest that the different response of bacterial and fungal species turnover to dispersal limitation and other, unknown processes may result in different biogeographic patterns of bacterial and fungal β-diversity in the drylands of northwest China. Together, we highlight that the drivers of β-diversity patterns vary between bacterial and fungal communities, and microbial β-diversity are driven by multiple factors in the drylands of northwest China.