Patterns In Bacterial Community Composition Research Articles

Spatial patterns of bacterial community composition within Lake Erie sediments

Lake Erie is a large freshwater ecosystem with three distinct basins that exhibit an east-to-west gradient of increasing productivity, as well as allochthonous inputs of nutrients and xenobiotics. To evaluate microbial community composition throughout this ecosystem, 435 16S rDNA environmental clones were sequenced from 11 sediment samples throughout the Western, Central, and Eastern basins, as well as the hypoxic “dead zone” of Lake Erie in the hypolimnetic region of the Central basin. Rank abundance distributions of bacterial taxa within each location revealed that Gamma- and Betaproteobacteria, microbes capable of metabolizing a wide range of organic matter pools, comprised a greater fraction of the microbial community within inshore sites of the Central and Western basins compared to the Eastern basin. While geophysical characteristics of the three major basins and the dead zone did not drive significant differences in species diversity, Fast UniFrac analyses revealed microbial community spatial structuring, with the Central basin showing higher phylogenetic uniqueness of bacterial lineages. Principal component analyses based on phylogenetic distances consistently grouped the dead zone with the Central basin and highlighted the distinctiveness of microbial communities from the Eastern basin. Results from this study provide evidence for the local adaptation of microbial communities and the potential role of riverine inputs in modulating taxonomic composition of lacustrine bacterial communities. These results are consistent with previous functional studies on microbial metabolism, which showed that differences in geochemistry across the three basins of Lake Erie play an important role in the local adaptation of microbial communities.

Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates

Much of the phylogenetic diversity in microbial systems arises from rare taxa that comprise the long tail of taxon rank distribution curves. This vast diversity presents a challenge to testing hypotheses about the effects of perturbations on microbial community composition because variability of rare taxa among environmental replicates may be sufficiently large that it would require a prohibitive degree of sequencing to discern differences between samples. In this study we used pyrosequencing of 16S rRNA tags to examine the diversity and within-site variability of salt marsh sediment bacteria. Our goal was to determine whether pyrosequencing could produce similar patterns in community composition among replicate environmental samples from the same location. We hypothesized that repeated sampling from the same location would produce different snapshots of the rare community due to incomplete sequencing of the taxonomically rich rare biosphere. We demonstrate that the salt marsh sediments we sampled contain a remarkably diverse array of bacterial taxa and, in contrast to our hypothesis, repeated sampling from within the same site produces reliably similar patterns in bacterial community composition, even among rare organisms. These results demonstrate that deep sequencing of 16s tags is well suited to distinguish site-specific similarities and differences among rare taxa and is a valuable tool for hypothesis testing in microbial ecology.

Carbon, Metals, and Grain Size Correlate with Bacterial Community Structure in Sediments of a High Arsenic Aquifer

Bacterial communities can exert significant influence on the biogeochemical cycling of arsenic (As). This has globally important implications since As in drinking water affects the health of over 100 million people worldwide, including in the Ganges–Brahmaputra Delta region of Bangladesh where geogenic arsenic in groundwater can reach concentrations of more than 10 times the World Health Organization’s limit. Thus, the goal of this research was to investigate patterns in bacterial community composition across gradients in sediment texture and chemistry in an aquifer with elevated groundwater As concentrations in Araihazar, Bangladesh. We characterized the bacterial community by pyrosequencing 16S rRNA genes from aquifer sediment samples collected at three locations along a groundwater flow path at a range of depths between 1.5 and 15 m. We identified significant differences in bacterial community composition between locations in the aquifer. In addition, we found that bacterial community structure was significantly related to sediment grain size, and sediment carbon (C), manganese (Mn), and iron (Fe) concentrations. Deltaproteobacteria and Chloroflexi were found in higher proportions in silty sediments with higher concentrations of C, Fe, and Mn. By contrast, Alphaproteobacteria and Betaproteobacteria were in higher proportions in sandy sediments with lower concentrations of C and metals. Based on the phylogenetic affiliations of these taxa, these results may indicate a shift to more Fe-, Mn-, and humic substance-reducers in the high C and metal sediments. It is well-documented that C, Mn, and Fe may influence the mobility of groundwater arsenic, and it is intriguing that these constituents may also structure the bacterial community.

Regional patterns of bacterial community composition and biogeochemical properties in the southern North Sea

The German Bight of the North Sea is characterized by intertidal flats, with high loads of suspended particulate matter (SPM) and estuarine inputs of organic matter, as well as pelagic off- shore regions. Due to tidal and wind-induced currents, the hydrography of this area is highly dynamic. In order to examine how these properties affect the regional distribution and composition of the bacterioplankton we conducted 2 surveys, in June 2002 and June 2003; in these surveys we assessed the composition of the free-living (FL) and particle-associated (PA) bacterial communities together with hydrographic properties (salinity, temperature) and biogeochemical properties (SPM, particulate organic carbon, chlorophyll, phytoplankton composition). The bacterial community com- position was determined by denaturing gradient gel electrophoretic (DGGE) analysis of 16S rRNA gene fragments, PCR-amplified by Bacteria-, Alphaproteobacteria- and Bacteroidetes-specific primer sets, and sequencing of excised bands. The results, and a multidimensional scaling (MDS) analysis of the DGGE banding patterns, showed distinct differences in the bacterial community com- position of the FL and PA fractions and also between the inshore and offshore stations. A canonical correspondence analysis (CCA), including the DGGE banding patterns, temperature, salinity and biogeochemical parameters, further showed that the community patterns and the inshore and off- shore gradients can be explained to a great extent by the hydrographic and biogeochemical condi- tions. Several prominent bands, identified as phylotypes affiliated to the Roseobacter clade, persisted throughout all 10 stations visited, whereas other phylotypes occurred only at distinct stations, inshore and offshore.

Linking the patterns of change in composition and function in bacterioplankton successions along environmental gradients

The connections that exist between the composition of bacterial communities and their functional attributes are still a matter of intense debate, despite over a decade of intense studies. Here we explored three different facets of the links that may exist between bacterioplankton compositional and functional successions that occurred along the water flow path in a complex watershed in southern Quebec. We analyzed the correlation between composition and function in terms of their absolute patterns, and in terms of their rates of change relative to transit time in environmental transitions, and relative to shifts in resources along the same transitions. Our results showed that the absolute patterns in bacterial community composition (BCC, using DGGE [denaturing gradient gel electrophoresis] profiles) and functional capacities (FC, using BIOLOG profiles) were not correlated, but that the rates of change in BCC and FC along the transitions were strongly correlated to each other. Further, we observed that the strength and shape of the relationship between the changes in BCC and FC varied relative to the type and intensity of gradient considered. Collectively, these results showed that BCC and FC are strongly related but in a very dynamic manner, such that their absolute patterns do not appear to be connected. This in turn suggests a high level of functional redundancy that occurs both within the existing community and in the meta-community from which phylotypes are selected to occupy the new niches that are created along the transitions.

Characterizing seasonal changes in physicochemistry and bacterial community composition in hyporheic sediments

The hyporheic zone of stream ecosystems is a critical habitat for microbial communities. However, the factors influencing hyporheic bacterial communities along spatial and seasonal gradients remain poorly understood. We sought to characterize patterns in bacterial community composition among the sediments of a small stream in southern Ontario, Canada. We used sampling cores to collect monthly hyporheic water and sediment microbial communities in 2006 and 2007. We described bacterial communities terminal-restriction fragment length polymorphism (TRFLP) and tested for spatial and seasonal relationships with physicochemical parameters using multivariate statistics. Overall, the hyporheic zone appears to be a DOC, oxygen, and nitrogen sink. Microbial communities were distinct from those at the streambed surface and from soil collected in the adjacent watershed. In the sediments, microbial communities were distinct between the fall, spring, and summer seasons, and bacterial communities were more diverse at streambed surface and near-surface sites compared with deeper sites. Moreover, bacterial communities were similar between consecutive fall seasons despite shifting throughout the year, suggesting recurring community assemblages associated with season and location in the hyporheic zone. Using canonical correspondence analysis, seasonal patterns in microbial community composition and environmental parameters were correlated in the following way: temperature was related to summer communities; DOC (likely from biofilm and allochthonous inputs) influenced most fall communities; and nitrogen associated strongly with winter and spring communities. Our results also suggest that labile DOC entering the hyporheic zone occurred in concert with shifts in the bacterial community. Generally, seasonal patterns in hyporheic physicochemistry and microbial biodiversity remain largely unexplored. Therefore, we highlight the importance of seasonal and spatial resolution when assessing surface- and groundwater interactions in stream ecosystems.

Tempo-spatial patterns of bacterial community composition in the western North Pacific Ocean

In the western North Pacific, where subarctic Oyashio waters encounter subtropical Kuroshio waters, phylotype composition of heterotrophic bacteria was estimated by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified bacterial 16S ribosomal DNA. Total bacterial abundance was also measured by flow cytometry. The study area was divided into four water masses: coastal, Oyashio, Kuroshio, and the Kuroshio–Oyashio transition. Abundances of heterotrophic bacteria in the Oyashio, Kuroshio, and Kuroshio–Oyashio transition regions ranged from 0.2 × 10 5 cells mL − 1 to 1.4 × 10 5 cells mL − 1 and were not significantly different, except in the Oyashio region during September. Bacterial compositions were distinct in each water mass. Furthermore, phylotype distributions differed between surface and subsurface waters in the Kuroshio–Oyashio transition region. Out of 61 DGGE bands obtained, 41 were successfully identified as 31 phylotypes: 22 Gammaproteobacteria, 4 Alphaproteobacteria, 2 unknown bacteria, 2 cyanobacteria, and 1 plastid. Although the Gammaproteobacteria OM60 clade was eurytopic in the study area, Psychrobacter glacincola and the uncultured Gammaproteobacteria SAR92 clade were often observed in the Oyashio region. Overall, our results indicated that Gammaproteobacteria were predominant in the bacterial community, which was influenced by the hydrographic properties of each water mass in the study area.

Differentiated free-living and sediment-attached bacterial community structure inside and outside denitrification hotspots in the river–groundwater interface

This study assessed the functional significance of attached and free-living bacterial communities involved in the process of denitrification in a shallow aquifer of a riparian zone (Garonne River, SW France). Denitrification enzyme activity (DEA), bacterial density (BD) and bacterial community composition (BCC) were measured in two aquifer compartments: the groundwater and the sandy fraction of the sediment deposit. Samples were collected in wells located inside (IHD) and outside (OHD) identified hotspots of denitrification. Despite high BD values (up to 1.14 × 1012 cells m−3), DEA was not detected in the water compartment (< 0.32 mg N–N2O m−3 d−1). The sandy fraction showed detectable DEA (up to 1,389 mg N–N2O m−3 d−1) and, consistent with BD pattern, higher DEA values were measured in IHD zones than in OHD zones. The BCC assessed by 16S rDNA polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) partly supported this result: attached and free-living communities were significantly different (< 30% similarity) but patterns of BCC did not cluster according to IHD and OHD zones. Targeting the denitrifying communities by means of a culture enrichment step prior to 16S rDNA PCR-DGGE showed that the free-living and sediment attached communities differed. Most sequences obtained from DGGE profiles of denitrifying communities were affiliated to Proteobacteria and showed low genetic distance with taxa that have already been detected in aquifers (e.g., Azoarcus sp., Acidovorax sp. and Pseudomonas spp.). This study confirms that in the aquifer the sediment-attached fraction exhibits different functions (DEA) from free-living communities and suggests that this functional difference is related to the communities’ structure.

Links between bacterial production, amino-acid utilization and community composition in productive lakes

Influence of distribution and abundance of bacterial taxa on ecosystem function are poorly understood for natural microbial communities. We related 16S rRNA-based terminal restriction fragment length polymorphism to bacterial production and arginine uptake kinetics to test if functional features of bacterioplankton in four lakes could be predicted from community composition. Maximum arginine uptake rate (arginine V(max)) ranged from 10% to 100% of bacterial production. Owing to high growth efficiencies on arginine (63-77%), the bacterial community could potentially saturate its carbon demand using this single organic substrate, for example, during sudden surges of free amino acids. However, due to low in situ concentrations of arginine in these lakes (<0.9 microg l(-1)), actual uptake rates at ambient concentrations rarely exceeded 10% of V(max). Bacterial production and arginine V(max) could be predicted from a subset of bacterial ribotypes, tentatively affiliated with several bacterial divisions (Cyanobacteria, Actinobacteria, Bacteroidetes and Proteobacteria). Multivariate statistical analysis indicates that there were both highly important and less important ribotypes for the prediction of bacterial production and arginine V(max). These populations were either negatively or positively related to the respective functional feature, indicating contrasting ecological roles. Our study provides a statistically robust demonstration that, apart from environmental conditions, patterns in bacterial community composition can also be used to predict lake ecosystem function.

High predictability of the seasonal dynamics of a species‐like Polynucleobacter population in a freshwater lake

One of the key questions in microbial ecology is if seasonal patterns of bacterial community composition (BCC) observed in one year repeat in the following years. We have investigated if the recorded annual dynamics of a species-like Polynucleobacter (subcluster PnecB) population allowed the prediction of the population dynamics in another year. The abundance of PnecB bacteria in the pelagic of temperate Lake Mondsee was investigated by fluorescence in situ hybridization (FISH) over three consecutive years. The PnecB bacteria formed a persistent population, and were present in the entire water body of the lake. Two of the three investigated years differed strongly in summer temperatures and precipitation, which resulted in markedly different growth conditions. But despite of these different environmental conditions, the PnecB population demonstrated remarkably similar seasonal dynamics in the three investigated years. Water temperature was the best predictor of the population dynamics during the first half of the annual cycles. Statistical analysis also indicated influences of phytoplankton and metazooplankton successions on the PnecB population dynamics. Furthermore, 65 lakes and ponds were investigated for the presence of PnecB bacteria. They were detected in the majority (78%) of circum-neutral and alkaline freshwater habitats, but not in any investigated acidic or saline habitat.

Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers

In order to identify patterns in bacterial community composition in freshwater habitats, we analyzed the available database of 16S rDNA sequences from freshwater plankton, including 24 new sequences from Parker River (Massachusetts, USA), 42 from Lake Soyang (South Korea) and 148 from Lake IJssel (The Netherlands). At this point, combined diversity studies using random cloning have deposited 689 bacterial and 75 plastid 16S rDNA sequences from the water column of rivers and lakes in North America, Europe and Asia. Systematic comparisons with the global data- base showed that the majority of the bacterial sequences were most closely related to other fresh- water clones or isolates, while relatively few were closest to sequences recovered from soils or marine habitats. This habitat-specific clustering suggests that the clustered 16S rDNA sequences represent species or groups of species that are indigenous to freshwater. We have discerned 34 phylogenetic clusters of closely related sequences that are either restricted to freshwater or dominated by fresh- water sequences. Of these clusters, 23 contained no cultivated organisms. These putative freshwater clusters were found among the alpha-, beta- and gamma-Proteobacteria, the Cytophaga-Flavobac- terium-Bacteroides group, the Cyanobacteria, the Actinobacteria, the Verrucomicrobia, the green non-sulfur bacteria and candidate division OP10. This study shows that rivers and lakes have a specific planktonic bacterial community distinct from bacteria in neighboring environments such as soil and sediments. It also points out that these planktonic bacteria are distributed in diverse fresh- water ecosystems around the world.