Diversity Patterns Of Microbial Communities Research Articles

Diversity patterns and ecological assembly mechanisms of bacterial communities in the northeastern Indian Ocean epipelagic waters during the northeast monsoon

Disentangling microbial community diversity patterns and assembly mechanisms is critical for understanding ecological processes and evaluating biogeochemical cycling in ecosystems. However, the diversity patterns and assembly mechanism of the microbial communities in the epipelagic waters in the northeastern Indian Ocean (NEIO) on the spatial scale are still unclear. In this study, we investigated the spatial dynamics, geographic distribution pattern, and assembly process of the bacterial community using 532 samples collected from the epipelagic waters in the NEIO during the northeast monsoon. The results indicate that the bacterial richness and Bray-Curtis dissimilarity exhibited the strongest correlations with depth compared to the latitudinal and longitudinal scales. The dissolved oxygen was identified as the most important environmental factor affecting the bacterial richness and Bray-Curtis dissimilarity compared to temperature and salinity. The distance–decay relationship (DDR) of the bacterial community strengthened with increasing water depth. Turnover was the predominant β-diversity component influencing the spatial changes in the whole bacterial community. The dispersal limitation of the stochastic process and homogeneous selection of the deterministic process governed the bacterial ecological assembly process of the whole bacterial community. Abundant and rare subcommunities differed in terms of the niche breath, composition changes. The abundant subcommunities exhibited a much wider niche breath than the rare subcommunities. Regarding the abundant subcommunity species changes, the contributions of the turnover and nestedness varied with the water depth and oceanic region. In contrast, turnover was the major β-diversity component regarding the changes in the rare species. These data improve our understanding of the ecological processes of bacterial community assemblages in the NEIO.

Distinct diversity patterns and assembly mechanisms of prokaryotic microbial sub-community in the water column of deep-sea cold seeps

Methane leakage from deep-sea cold seeps has a major impact on marine ecosystems. Microbes sequester methane in the water column of cold seeps and can be divided into abundant and rare groups. Both abundant and rare groups play an important role in cold seep ecosystems, and the environmental heterogeneity in cold seeps may enhance conversion between taxa with different abundances. Yet, the environmental stratification and assembly mechanisms of these microbial sub-communities remain unclear. We investigated the diversities and assembly mechanisms in microbial sub-communities with distinct abundance in the deep-sea cold seep water column, from 400 m to 1400 m. We found that bacterial β-diversity, as measured by Sørensen dissimilarities, exhibited a significant species turnover pattern that was influenced by several environmental factors including depth, temperature, SiO32−, and salinity. In contrast, archaeal β-diversity showed a relatively high percentage of nestedness pattern, which was driven by the levels of soluble reactive phosphate and SiO32−. During the abundance dependency test, abundant taxa of both bacteria and archaea showed a significant species turnover, while the rare taxa possessed a higher percentage of nestedness. Stochastic processes were prominent in shaping the prokaryotic community, but deterministic processes were more pronounced for the abundant taxa than rare ones. Furthermore, the metagenomics results revealed that the abundances of methane oxidation, sulfur oxidation, and nitrogen fixation-related genes and related microbial groups were significantly higher in the bottom water. Our results implied that the carbon, sulfur, and nitrogen cycles were potentially strongly coupled in the bottom water. Overall, the results obtained in this study highlight taxonomic and abundance-dependent microbial community diversity patterns and assembly mechanisms in the water column of cold seeps, which will help understand the impacts of fluid seepage from the sea floor on the microbial community in the water column and further provide guidance for the management of cold seep ecosystem under future environmental pressures.

Evaluating the Reproducibility of Amplicon Sequencing Data Derived from Deep-Sea Cold Seep Sediment-Associated Microbiota.

Benefiting from the rapid developments and wide applications of high-throughput sequencing, great advancements have been made in investigating microbiota, which are highly diverse and play key roles in both element cycling and the energy flow of ecosystems. There have been inherent limitations of amplicon sequencing that could introduce uncertainty and raise concerns about the accuracy and reproducibility of this technology. However, studies focusing on the reproducibility of amplicon sequencing are limited, especially in characterizing microbial communities in deep-sea sediments. To evaluate reproducibility, 118 deep-sea sediment samples were used for 16S rRNA gene sequencing in technical replicates (repeated measurements of the same sample) that demonstrate the variability of amplicon sequencing. The average occurrence-based overlaps were 35.98% and 27.02% between two and among three technical replicates, respectively, whereas their abundance-based overlaps reached 84.88% and 83.16%, respectively. Although variations of alpha and beta diversity indices were found between/among technical replicates, alpha diversity indices were similar across samples, and the average beta diversity indices were much smaller for technical replicates than among samples. Moreover, clustering methods (i.e., operational taxonomic units [OTUs] and amplicon sequence variants [ASVs]) were shown to have little impact on the alpha and beta diversity patterns of microbial communities. Taken together, although there are variations between/among technical replicates, amplicon sequencing is still a powerful tool with which to reveal diversity patterns of microbiota in deep-sea sediments. IMPORTANCE The reproducibility of amplicon sequencing is vital for whether the diversities of microbial communities could be accurately estimated. Thus, reproducibility influences the drawing of sound ecological conclusions. Nevertheless, few studies have focused on the reproducibility of microbial communities that are characterized by amplicon sequencing, and studies focusing on microbiota in deep-sea sediments have been especially lacking. In this study, we evaluated the reproducibility of amplicon sequencing targeting microbiota in deep-sea sediments of cold seep. Our results revealed that there were variations between/among technical replicates and that amplicon sequencing was still a powerful tool with which to characterize the diversities of microbial communities in deep-sea sediments. This study provides valuable guidelines for the reproducibility evaluation of future work in experimental design and interpretation.

Distinct ecological mechanisms drive the spatial scaling of abundant and rare microbial taxa in a coastal sediment

AbstractAimRevealing the ecological mechanisms driving the diversity patterns of microbial communities across space and through time is an essential issue in microbial biogeography. This study links microbial spatial scaling with ecological mechanisms, aiming to provide novel mechanistic insights into the biogeographic patterns followed by different types of microbes.LocationBeibu Gulf, a semi‐enclosed oceanic bay located on the southern coast of China.TaxonBacteria, which were further classified as abundant and rare taxa.MethodsBy employing high throughput sequencing, two typical spatial scaling models, diversity‐area (DAR) and distance‐decay relationships (DDR), were investigated for the abundant and rare microbial communities in a coastal sediment ecosystem. Both alpha‐ and beta‐diversity indices were extended to Hill numbers to verify the contribution of abundant and rare taxa to DAR and DDR. The iCAMP approach was used to quantify the contribution of different ecological processes in structuring microbial communities.ResultsStrong spatial scaling patterns were observed for the whole communities and the rare subcommunities but only weak patterns for the abundant subcommunities. Rare subcommunities were mainly responsible for the observed spatial scaling patterns, as confirmed by extending spatial scaling diversity metrics to Hill numbers. Both environmental heterogeneity and local community assembly mechanisms drove the spatial scaling of microbial communities. Strong ecological drift and dispersal limitation underlay the spatial scaling of rare subcommunities, whereas high homogeneous selection weakened the spatial scaling of abundant subcommunities.Main ConclusionsRare taxa were mainly responsible for the biogeographic patterns followed by sediment microbial communities in the Beibu Gulf. Distinct ecological mechanisms underlay the different biogeographic patterns followed by abundant and rare subcommunities.

Global beta diversity patterns of microbial communities in the surface and deep ocean

AbstractAimDispersal and environmental gradients shape marine microbial communities, yet the relative importance of these factors across taxa with distinct sizes and dispersal capacity in different ocean layers is unknown. Here, we report a comparative analysis of surface and deep ocean microbial beta diversity and examine how these patterns are tied to oceanic distance and environmental gradients.LocationTropical and subtropical oceans (30°N–40°S).Time period2010–2011.Major taxa studiedProkaryotes and picoeukaryotes (eukaryotes between 0.2 and 3 μm).MethodsBeta diversity was calculated from metabarcoding data on prokaryotic and picoeukaryotic microbes collected during the Malaspina expedition across the tropical and subtropical oceans. Mantel correlations were used to determine the relative contribution of environment and oceanic distance driving community beta diversity.ResultsMean community similarity across all sites for prokaryotes was 38.9% in the surface and 51.4% in the deep ocean, compared to mean similarity of 25.8 and 12.1% in the surface and deep ocean, respectively, for picoeukaryotes. Higher dispersal rates and smaller body sizes of prokaryotes relative to picoeukaryotes likely contributed to the significantly higher community similarity for prokaryotes compared with picoeukaryotes. The ecological mechanisms determining the biogeography of microbes varied across depth. In the surface ocean, the environmental differences in space were a more important factor driving microbial distribution compared with the oceanic distance, defined as the shortest path between two sites avoiding land. In the deep ocean, picoeukaryote communities were slightly more structured by the oceanic distance, while prokaryotes were shaped by the combined action of oceanic distance and environmental filtering.Main conclusionsHorizontal gradients in microbial community assembly differed across ocean depths, as did mechanisms shaping them. In the deep ocean, the oceanic distance and environment played significant roles driving microbial spatial distribution, while in the surface the influence of the environment was stronger than oceanic distance.

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

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.

High-resolution analyses reveal structural diversity patterns of microbial communities in Chromite Ore Processing Residue (COPR) contaminated soils

To explore how heavy metal contamination in Chromite Ore Processing Residue (COPR) disposal sites determine the dissimilarities of indigenous microbial communities, 16S rRNA gene MiSeq sequencing and advanced statistical methods were applied. 13 soil samples were collected from three COPR disposal sites in Mouding of southwestern, Shangnan of northwestern and Yima of central China. The results of analyses of variance (ANOVA), similarities (ANOSIM), and non-metric multidimensional scaling (NMDS) showed that the structural diversity of the microbial communities in the samples with high total chromium (Cr) content (more than 300 mg kg−1; High group) were significantly lesser than in the Low group (less than 90 mg kg−1) regardless of their geographical distribution. But their diversity had virtually rehabilitated under the pressures of long-term metal contamination. Furthermore, the similarity percentage (SIMPER) analysis indicated that the major dissimilarity contributors Micrococcaceae, Delftia, and Streptophyta, possibly having Cr(VI)-resistant and/or Cr(VI)-reducing capability, were dominant in the High group, while Ramlibacter and Gemmatimonas with potential resistances to other heavy metals were prevalent in the Low group. In addition, the multivariate regression tree (MRT), aggregated boosted tree (ABT), and Mantel test revealed that total Cr content affiliated with Cr(VI) was the principal factor shaping the dissimilarities between the soil microbial communities in the COPR sites. Our findings provide a deep insight of the influence of these heavy metals on the microbial communities in the COPR disposal sites and will facilitate bioremediation on such site.

Genetic diversity patterns of microbial communities in a subtropical riverine ecosystem (Jiulong River, southeast China)

Prokaryotic and eukaryotic microbes are key organisms in aquatic ecosystems and play pivotal roles in the biogeochemical cycles, but little is known about genetic diversity of these communities in subtropical rivers. In this study, microbial planktonic communities were determined by using denaturing gradient gel electrophoresis (DGGE) analysis from the Jiulong River, southeast China, and their relationships with local environmental factors were studied. The Betaproteobacteria (26%) and Dinophyceae (26%) were the most dominant taxa in prokaryotic and eukaryotic clones derived from DGGE bands, respectively. Further, both cluster and ordination analyses of prokaryotic and eukaryotic DGGE fingerprinting resulted in three identical groups from the 15 sites, which were closely related with the environmental factors. Partial redundancy analysis (partial RDA) revealed that agricultural pollution (phosphorus and nitrogen) and saltwater intrusion (conductivity and salinity) were the main factors impacting microbial community composition, by explaining more than two-thirds of the total variation in both prokaryotic (67.0%) and eukaryotic (70.5%) communities. Moreover, the robust and quantifiable relationship between DGGE results and environmental variables indicated that the community-level molecular fingerprinting techniques could support the physicochemical assessment of riverine water quality and ecosystem health.

Predictive microbial ecology

Predictive microbial ecology