Biogeography of bacterioplankton in lakes and streams of an Arctic tundra catchment

Watershed Urbanization Linked to Differences in Stream Bacterial Community Composition

Urbanization strongly influences headwater stream chemistry and hydrology, but little is known about how these conditions impact bacterial community composition. We predicted that urbanization would impact bacterial community composition, but that stream water column bacterial communities would be most strongly linked to urbanization at a watershed-scale, as measured by impervious cover, while sediment bacterial communities would correlate with environmental conditions at the scale of stream reaches. To test this hypothesis, we determined bacterial community composition in the water column and sediment of headwater streams located across a gradient of watershed impervious cover using high-throughput 16S rRNA gene amplicon sequencing. Alpha diversity metrics did not show a strong response to catchment urbanization, but beta diversity was significantly related to watershed impervious cover with significant differences also found between water column and sediment samples. Samples grouped primarily according to habitat—water column vs. sediment—with a significant response to watershed impervious cover nested within each habitat type. Compositional shifts for communities in urbanized streams indicated an increase in taxa associated with human activity including bacteria from the genus Polynucleobacter, which is widespread, but has been associated with eutrophic conditions in larger water bodies. Another indicator of communities in urbanized streams was an OTU from the genus Gallionella, which is linked to corrosion of water distribution systems. To identify changes in bacterial community interactions, bacterial co-occurrence networks were generated from urban and forested samples. The urbanized co-occurrence network was much smaller and had fewer co-occurrence events per taxon than forested equivalents, indicating a loss of keystone taxa with urbanization. Our results suggest that urbanization has significant impacts on the community composition of headwater streams, and suggest that processes driving these changes in urbanized water column vs. sediment environments are distinct.

Identifying the core seed bank of a complex boreal bacterial metacommunity

Seed banks are believed to contribute to compositional changes within and across microbial assemblages, but the application of this concept to natural communities remains challenging. Here we describe the core seed bank of a bacterial metacommunity from a boreal watershed, using the spatial distribution of bacterial operational taxonomic units (OTUs) across 223 heterogeneous terrestrial, aquatic and phyllosphere bacterial assemblages. Taxa were considered potential seeds if they transitioned from rare to abundant somewhere within the metacommunity and if they were ubiquitous and able to persist under unfavorable conditions, the latter assessed by checking their presence in three deeply sequenced samples (one soil, one river and one lake, 2.2-3 million reads per sample). We show that only a small fraction (13%) of all detected OTUs constitute a metacommunity seed bank that is shared between all terrestrial and aquatic communities, but not by phyllosphere assemblages, which seem to recruit from a different taxa pool. Our results suggest directional recruitment driven by the flow of water in the landscape, since most aquatic sequences were associated to OTUs found in a single deeply-sequenced soil sample, but only 45% of terrestrial sequences belonged to OTUs found in the two deeply-sequenced aquatic communities. Finally, we hypothesize that extreme rarity, and its interplay with water residence time and growth rates, may further constrain the size of the potential seed bank.

Competition and niche separation of pelagic bacteria in freshwater habitats

Freshwater bacterioplankton assemblages are composed of sympatric populations that can be delineated, for example, by ribosomal RNA gene relatedness and that differ in key ecophysiological properties. They may be free-living or attached, specialized for particular concentrations or subsets of substrates, or invest a variable amount of their resources in defence traits against protistan predators and viruses. Some may be motile and tactic whereas others are not, with far-reaching implications for their respective life styles and niche partitioning. The co-occurrence of competitors with overlapping growth requirements has profound consequences for the stability of community functions; it can to some extent be explained by habitat factors such as the microscale complexity and spatiotemporal variability of the lacustrine environments. On the other hand, the composition and diversity of freshwater microbial assemblages also reflects non-equilibrium states, dispersal and the stochasticity of community assembly processes. This review synoptically discusses the competition and niche separation of heterotrophic bacterial populations (defined at various levels of phylogenetic resolution) in the pelagic zone of inland surface waters from a variety of angles, focusing on habitat heterogeneity and the resulting biogeographic distribution patterns, the ecophysiological adaptations to the substrate field and the interactions of prokaryotes with predators and viruses.

Patterns of variation in diversity of the Mississippi river microbiome over 1,300 kilometers

We examined the downriver patterns of variation in taxonomic diversity of the Mississippi River bacterioplankton microbiome along 1,300 river kilometers, or approximately one third the total length of the river. The study section included portions of the Upper, Middle, and Lower Mississippi River, confluences with five tributaries draining distinct sub-basins, river cities, and extended stretches without major inputs to the Mississippi. The composition and proportional abundance of dominant bacterial phyla was distinct for free-living and particle-associated cells, and constant along the entire reach, except for a substantial but transient disturbance near the city of Memphis, Tennessee. At a finer scale of taxonomic resolution (operational taxonomic units, OTUs), however, there were notable patterns in downriver variation in bacterial community alpha diversity (richness within a site) and beta diversity (variation in composition among sites). There was a strong and steady increase downriver in alpha diversity of OTUs on suspended particles, suggesting an increase in particle niche heterogeneity, and/or particle colonization. Relatively large shifts in beta diversity of free-living and particle-associated communities occurred following major tributary confluences and transiently at Memphis, while in long stretches between these points diversity typically varied more gradually. We conclude that the Mississippi River possesses a bacterioplankton microbiome distinct in diversity from other large river microbiomes in the Mississippi River Basin, that at major river confluences or urban point sources its OTU diversity may shift abruptly and substantially, presumably by immigration of distinct external microbiomes, but that where environmental conditions are more stable along the downriver gradient, microbiome diversity tends to vary gradually, presumably by a process of successional change in community composition.

Bacterioplankton community responses to key environmental variables in plateau freshwater lake ecosystems: A structural equation modeling and change point analysis

Elevated environmental pressures negatively affect the bacterial community structure. However, little knowledge about the nonlinear responses of spatially related environmental variable across multiple plateau lake ecosystems on bacterioplankton communities has been gathered. Here, we used 454 pyrosequencing of 16S rRNA genes to study the associations of bacterial communities in terms of environmental characteristics as well as the potentially ecological threshold-inducing shifts of the bacterial community structure along the key environmental variables based on hypothesized structural equation models and the SEGMENTED method in 21 plateau lakes. Our results showed that water transparency was the major driving force and that total nitrogen was more significant than total phosphorus in determining the taxon composition of the bacterioplankton community. Significant community threshold estimates for bacterioplankton were observed at 7.36 for pH and 25.6% for the percentage of the agricultural area, while the remarkable change point of the cyanobacteria community structure responding to pH was at 7.74. Furthermore, the findings indicated that increasing nutrient loads can induce a distinct shift in dominance from Proteobacteria to Cyanobacteria, as well as a sharp decrease and adjacent increase when crossing the change point for Actinobacteria and Bacteroidetes along the gradient of the agricultural area.

Relative importance of advective flow versus environmental gradient in shaping aquatic ammonium oxidizers near the Three Gorges Dam of the Yangtze River, China

Construction of a dam in a large river alters its hydrodynamic condition and geochemical gradient, but the effect of such anthropogenic activity on microbial ecology remains poorly understood. To assess this effect, we investigated the relative importance of advective flow versus environmental condition in shaping ammonia oxidizing bacteria (AOB) and archaea (AOA) community from 110 km upstream to the Three Gorges Dam (TGD) of the Yangtze River, China. Water physicochemical conditions, including turbidity, conductivity, redox state and nutrient level, were fairly constant from 110 to 45 km upstream of the TGD, but significantly oscillated near the dam. AOB and AOA in the Yangtze River were dominated by Nitrosospira- and Nitrosopumilus-affiliated clusters, respectively, and these compositions were invariant throughout the sampled 110 km flow path, suggesting that AOB and AOA communities in the river were largely transported from upstream by advection with minor local and transient inputs from surrounding soils and tributaries. However, the abundance of AOB and AOA was influenced by local geochemical conditions, possibly via the growth/decay mechanisms. The source of AOB in the Yangtze River appeared to be derived from soil near the headwater, but its abundance was enhanced during downstream transport, likely due to survival and growth.

Upstream Freshwater and Terrestrial Sources Are Differentially Reflected in the Bacterial Community Structure along a Small Arctic River and Its Estuary

Glacier melting and altered precipitation patterns influence Arctic freshwater and coastal ecosystems. Arctic rivers are central to Arctic water ecosystems by linking glacier meltwaters and precipitation with the ocean through transport of particulate matter and microorganisms. However, the impact of different water sources on the microbial communities in Arctic rivers and estuaries remains unknown. In this study we used 16S rRNA gene amplicon sequencing to assess a small river and its estuary on the Disko Island, West Greenland (69°N). Samples were taken in August when there is maximum precipitation and temperatures are high in the Disko Bay area. We describe the bacterial community through a river into the estuary, including communities originating in a glacier and a proglacial lake. Our results show that water from the glacier and lake transports distinct communities into the river in terms of diversity and community composition. Bacteria of terrestrial origin were among the dominating OTUs in the main river, while the glacier and lake supplied the river with water containing fewer terrestrial organisms. Also, more psychrophilic taxa were found in the community supplied by the lake. At the river mouth, the presence of dominant bacterial taxa from the lake and glacier was unnoticeable, but these taxa increased their abundances again further into the estuary. On average 23% of the estuary community consisted of indicator OTUs from different sites along the river. Environmental variables showed only weak correlations with community composition, suggesting that hydrology largely influences the observed patterns.

Meltwater export of prokaryotic cells from the Greenland ice sheet

Microorganisms are flushed from the Greenland Ice Sheet (GrIS) where they may contribute towards the nutrient cycling and community compositions of downstream ecosystems. We investigate meltwater microbial assemblages as they exit the GrIS from a large outlet glacier, and as they enter a downstream river delta during the record melt year of 2012. Prokaryotic abundance, flux and community composition was studied, and factors affecting community structures were statistically considered. The mean concentration of cells exiting the ice sheet was 8.30 × 10⁴ cells mL^-1 and we estimate that ∼1.02 × 10²¹ cells were transported to the downstream fjord in 2012, equivalent to 30.95 Mg of carbon. Prokaryotic microbial assemblages were dominated by Proteobacteria, Bacteroidetes, and Actinobacteria. Cell concentrations and community compositions were stable throughout the sample period, and were statistically similar at both sample sites. Based on our observations, we argue that the subglacial environment is the primary source of the river-transported microbiota, and that cell export from the GrIS is dependent on discharge. We hypothesise that the release of subglacial microbiota to downstream ecosystems will increase as freshwater flux from the GrIS rises in a warming world.

Effects of dispersal and selection on stochastic assembly in microbial communities

Stochastic processes can play an important role in microbial community assembly. Dispersal limitation is one process that can increase stochasticity and obscure relationships between environmental variables and microbial community composition, but the relationship between dispersal, selection and stochasticity has not been described in a comprehensive way. We examine how dispersal and its interactions with drift and selection alter the consistency with which microbial communities assemble using a realistic, individual-based model of microbial decomposers. Communities were assembled under different environmental conditions and dispersal rates in repeated simulations, and we examined the compositional difference among replicate communities colonizing the same type of leaf litter ('within-group distance'), as well as between-group deterministic selection. Dispersal rates below 25% turnover per year resulted in high within-group distance among communities and no significant environmental effects. As dispersal limitation was alleviated, both within- and between-group distance decreased, but despite this homogenization, deterministic environmental effects remained significant. In addition to direct effects of dispersal rate, stochasticity of community composition was influenced by an interaction between dispersal and selection strength. Specifically, communities experiencing stronger selection (less favorable litter chemistries) were more stochastic, possibly because lower biomass and richness intensified drift or priority effects. Overall, we show that dispersal rate can significantly alter patterns of community composition. Partitioning the effects of dispersal, selection and drift based on static patterns of microbial composition will be difficult, if not impossible. Experiments will be required to tease apart these complex interactions between assembly processes shaping microbial communities.

Interactions between hydrology and water chemistry shape bacterioplankton biogeography across boreal freshwater networks

Disentangling the mechanisms shaping bacterioplankton communities across freshwater ecosystems requires considering a hydrologic dimension that can influence both dispersal and local sorting, but how the environment and hydrology interact to shape the biogeography of freshwater bacterioplankton over large spatial scales remains unexplored. Using Illumina sequencing of the 16S ribosomal RNA gene, we investigate the large-scale spatial patterns of bacterioplankton across 386 freshwater systems from seven distinct regions in boreal Québec. We show that both hydrology and local water chemistry (mostly pH) interact to shape a sequential structuring of communities from highly diverse assemblages in headwater streams toward larger rivers and lakes dominated by fewer taxa. Increases in water residence time along the hydrologic continuum were accompanied by major losses of bacterial richness and by an increased differentiation of communities driven by local conditions (pH and other related variables). This suggests that hydrology and network position modulate the relative role of environmental sorting and mass effects on community assembly by determining both the time frame for bacterial growth and the composition of the immigrant pool. The apparent low dispersal limitation (that is, the lack of influence of geographic distance on the spatial patterns observed at the taxonomic resolution used) suggests that these boreal bacterioplankton communities derive from a shared bacterial pool that enters the networks through the smallest streams, largely dominated by mass effects, and that is increasingly subjected to local sorting of species during transit along the hydrologic continuum.

Snowmelt-driven changes in dissolved organic matter and bacterioplankton communities in the Heilongjiang watershed of China

Bacterioplankton plays a significant role in the circulation of materials and ecosystem function in the biosphere. Dissolved organic matter (DOM) from dead plant material and surface soil leaches into water bodies when snow melts. In our study, water samples from nine sampling sites along the Heilongjiang watershed were collected in February and June 2014 during which period snowmelt occurred. The goal of this study was to characterize changes in DOM and bacterioplankton community composition (BCC) associated with snowmelt, the effects of DOM, environmental and geographical factors on the distribution of BCC and interactions of aquatic bacterioplankton populations with different sources of DOM in the Heilongjiang watershed. BCC was measured by denaturing gradient gel electrophoresis (DGGE). DOM was measured by excitation-emission matrix (EEM) fluorescence spectroscopy. Bacterioplankton exhibited a distinct seasonal change in community composition due to snowmelt at all sampling points except for EG. Redundancy analysis (RDA) indicated that BCC was more closely related to DOM (Components 1 and 4, dissolved organic carbon, biochemical oxygen demand and chlorophyll a) and environmental factors (water temperature and nitrate nitrogen) than geographical factors. Furthermore, DOM had a greater impact on BCC than environmental factors (29.80 vs. 15.90% of the variation). Overall, spring snowmelt played an important role in altering the quality and quantity of DOM and BCC in the Heilongjiang watershed.

Weak Coherence in Abundance Patterns Between Bacterial Classes and Their Constituent OTUs Along a Regulated River

Deductions about the ecology of high taxonomic bacterial ranks (i.e., phylum, class, order) are often based on their abundance patterns, yet few studies have quantified how accurately variations in abundance of these bacterial groups represent the dynamics of the taxa within them. Using 454-pyrosequencing of the 16S rRNA gene, we investigated whether the changes in abundance of six dominant bacterial classes (Actinobacteria, Beta-/Alpha-/Gamma-proteobacteria, Flavobacteria, and Sphingobacteria) along a large dam-regulated river are reflected by those of their constituent Operational Taxonomic Units (OTUs; 97% similarity level). The environmental impact generated by the reservoirs promoted clear compositional shifts in all bacterial classes that resulted from changes in the abundance of individual OTUs rather than from the appearance of new taxa along the river. Abundance patterns at the class level represented the dynamics of only a small but variable proportion of their constituting OTUs, which were not necessarily the most abundant ones. Within most classes, we detected sub-groups of OTUs showing contrasting responses to reservoir-induced environmental changes. Overall, we show that the patterns observed at the class level fail to capture the dynamics of a significant fraction of their constituent members, calling for caution when the ecological attributes of high-ranks are to be interpreted.

Hydrologic linkages drive spatial structuring of bacterial assemblages and functioning in alpine floodplains

Microbial community assembly and microbial functions are affected by a number of different but coupled drivers such as local habitat characteristics, dispersal rates, and species interactions. In groundwater systems, hydrological flow can introduce spatial structure and directional dependencies among these drivers. We examined the importance of hydrology in structuring bacterial communities and their function within two alpine floodplains during different hydrological states. Piezometers were installed in stream sediments and surrounding riparian zones to assess hydrological flows and also were used as incubation chambers to examine bacterial community structures and enzymatic functions along hydrological flow paths. Spatial eigenvector models in conjunction with models based on physico-chemical groundwater characteristics were used to evaluate the importance of hydrologically-driven processes influencing bacterial assemblages and their enzymatic activities. Our results suggest a strong influence (up to 40% explained variation) of hydrological connectivity on enzymatic activities. The effect of hydrology on bacterial community structure was considerably less strong, suggesting that assemblages demonstrate large functional plasticity/redundancy. Effect size varied between hydrological periods but flow-related mechanisms always had the most power in explaining both bacterial structure and functioning. Changes in hydrology should be considered in models predicting ecosystem functioning and integrated into ecosystem management strategies for floodplains.

Seasonal and spatial patterns of microbial diversity along a trophic gradient in the interconnected lakes of the Osterseen Lake District, Bavaria

The Osterseen Lake District in Bavaria consists of 19 small interconnected lakes that exhibit a pronounced trophic gradient from eutrophic to oligotrophic. It therefore presents a unique model system to address ecological questions regarding niche adaptation and Baas Becking's long standing hypothesis of "everything is everywhere, but the environment selects." Here, we present the first assessment of the microbial diversity in these lakes. We sampled the lakes in August and December and used 454 pyrosequencing of 16S rRNA amplicons to analyze the microbial diversity. The diversity patterns between lakes and seasons were compared and the bacterial community composition was correlated with key chemical and physical parameters. Distinct patterns of bacterial diversity only emerged at the level of individual OTUs (operational taxonomic units), but not at the level of the major bacterial phyla. This emphasizes the high functional and physiological diversity among bacterial species within a phylum and calls for analysis of biodiversity at the level of OTUs in order to understand fine-scale biogeography. We were able to identify a number of cosmopolitan OTUs as well as specialist OTUs that were restricted to certain lakes or seasons, suggesting adaptation to specific ecological niches.

Spatiotemporal dynamics and determinants of planktonic bacterial and microeukaryotic communities in a Chinese subtropical river

The spatiotemporal distribution of microbial diversity, community composition, and their major drivers are fundamental issues in microbial ecology. In this study, the planktonic bacterial and microeukaryotic communities of the Jiulong River were investigated across both wet and dry seasons by using denaturing gradient gel electrophoresis (DGGE). We found evidence of temporal change between wet and dry seasons and distinct spatial patterns of bacterial and microeukaryotic communities. Both bacterial and microeukaryotic communities were strongly correlated with temperature, NH4-N, PO4-P, and chlorophyll a, and these environmental factors were significant but incomplete predictors of microbial community composition. Local environmental factors combined with spatial and temporal factors strongly controlled both bacterial and microeukaryotic communities in complex ways, whereas the direct influence of spatial and temporal factors appeared to be relatively small. Path analysis revealed that the microeukaryotic community played key roles in shaping bacterial community composition, perhaps through grazing effects and multiple interactions. Both Betaproteobacteria and Actinobacteria were the most dominant and diverse taxa in bacterial communities, while the microeukaryotic communities were dominated by Ciliophora (zooplankton) and Chlorophyta (phytoplankton). Our results demonstrated that both bacterial and microeukaryotic communities along the Jiulong River displayed a distinct spatiotemporal pattern; however, microeukaryotic communities exhibited a stronger distance-decay relationship than bacterial communities and their spatial patterns were mostly driven by local environmental variables rather than season or spatial processes of the river. Therefore, we have provided baseline data to support further research on river microbial food webs and integrating different microbial groups into river models.

Quantifying the effects of geographical and environmental factors on distribution of stream bacterioplankton within nature reserves of Fujian, China

Bacterioplankton are important components of freshwater ecosystems and play essential roles in ecological functions and processes; however, little is known about their geographical distribution and the factors influencing their ecology, especially in stream ecosystems. To examine how geographical and environmental factors affect the composition of bacterioplankton communities, we used denaturing gradient gel electrophoresis and clone sequencing to survey bacterioplankton communities in 31 samples of streamwater from seven nature reserves in Fujian province, southeast China. Our results revealed that dominant bacterioplankton communities exhibited a distinct geographical pattern. Further, we provided evidence for distance decay relationships in bacterioplankton community similarity and found similar community gradients in response to elevation and latitude. Both redundancy analyses and Mantel tests showed that bacterioplankton community composition was significantly correlated with both environmental (electrical conductivity, total phosphorus, and PO4-P) and geographical factors (latitude, longitude, and elevation). Variance partitioning further showed that the joint effect of geographical and environmental factors explained the largest proportion of the variation in distribution of bacterioplankton communities (13.6 %), followed by purely geographical factors (11.2 %), and purely environmental factors (0.6 %). The Betaproteobacteria were the most common taxa in the streams, followed by Firmicutes and Gammaproteobacteria. Therefore, our results suggest that the biogeographical patterns of stream bacterioplankton communities across the Fujian nature reserves are more influenced by geographical factors than by local physicochemical properties.

Bacterial diversity along a 2600 km river continuum

The bacterioplankton diversity in large rivers has thus far been under‐sampled despite the importance of streams and rivers as components of continental landscapes. Here, we present a comprehensive dataset detailing the bacterioplankton diversity along the midstream of the Danube River and its tributaries. Using 16S rRNA‐gene amplicon sequencing, our analysis revealed that bacterial richness and evenness gradually declined downriver in both the free‐living and particle‐associated bacterial communities. These shifts were also supported by beta diversity analysis, where the effects of tributaries were negligible in regards to the overall variation. In addition, the river was largely dominated by bacteria that are commonly observed in freshwaters. Dominated by the acI lineage, the freshwater SAR11 (LD12) and the Polynucleobacter group, typical freshwater taxa increased in proportion downriver and were accompanied by a decrease in soil and groundwater‐affiliated bacteria. Based on views of the meta‐community and River Continuum Concept, we interpret the observed taxonomic patterns and accompanying changes in alpha and beta diversity with the intention of laying the foundation for a unified concept for river bacterioplankton diversity.

Stream microbial diversity in response to environmental changes: review and synthesis of existing research

The importance of microbial activity to ecosystem function in aquatic ecosystems is well established, but microbial diversity has been less frequently addressed. This review and synthesis of 100s of published studies on stream microbial diversity shows that factors known to drive ecosystem processes, such as nutrient availability, hydrology, metal contamination, contrasting land-use and temperature, also cause heterogeneity in bacterial diversity. Temporal heterogeneity in stream bacterial diversity was frequently observed, reflecting the dynamic nature of both stream ecosystems and microbial community composition. However, within-stream spatial differences in stream bacterial diversity were more commonly observed, driven specifically by different organic matter (OM) compartments. Bacterial phyla showed similar patterns in relative abundance with regard to compartment type across different streams. For example, surface water contained the highest relative abundance of Actinobacteria, while epilithon contained the highest relative abundance of Cyanobacteria and Bacteroidetes. This suggests that contrasting physical and/or nutritional habitats characterized by different stream OM compartment types may select for certain bacterial lineages. When comparing the prevalence of physicochemical effects on stream bacterial diversity, effects of changing metal concentrations were most, while effects of differences in nutrient concentrations were least frequently observed. This may indicate that although changing nutrient concentrations do tend to affect microbial diversity, other environmental factors are more likely to alter stream microbial diversity and function. The common observation of connections between ecosystem process drivers and microbial diversity suggests that microbial taxonomic turnover could mediate ecosystem-scale responses to changing environmental conditions, including both microbial habitat distribution and physicochemical factors.

Isolating the effects of storm events on arctic aquatic bacteria: temperature, nutrients, and community composition as controls on bacterial productivity

Storm events can pulse nutrients and carbon from soils and provide an important subsidy to food webs in oligotrophic streams and lakes. Bacterial nutrient limitation and the potential response of stream aquatic bacteria to storm events was investigated in arctic tundra environments by manipulating both water temperature and inorganic nutrient concentrations in short (up to 4 days) and long duration (up to 2 weeks) laboratory mesocosm experiments. Inorganic N and P additions increased bacterial production (¹⁴C-labeled leucine uptake) up to seven times over controls, and warmer incubation temperatures increased the speed of this response to added nutrients. Bacterial cell numbers also increased in response to temperature and nutrient additions with cell-specific carbon uptake initially increasing and then declining after 2 days. Bacterial community composition (BCC; determined by means of 16S denaturing gradient gel electrophoresis fingerprinting) shifted rapidly in response to changes in incubation temperature and the addition of nutrients, within 2 days in some cases. While the bacteria in these habitats responded to nutrient additions with rapid changes in productivity and community composition, water temperature controlled the speed of the metabolic response and affected the resultant change in bacterial community structure, constraining the potential responses to pulsed nutrient subsidies associated with storm events. In all cases, at higher nutrient levels and temperatures the effect of initial BCC on bacterial activity was muted, suggesting a consistent, robust interaction of temperature, and nutrients controlling activity in these aquatic systems.

Spatial distribution of bacterial communities driven by multiple environmental factors in a beach wetland of the largest freshwater lake in China

The spatial distributions of bacterial communities may be driven by multiple environmental factors. Thus, understanding the relationships between bacterial distribution and environmental factors is critical for understanding wetland stability and the functioning of freshwater lakes. However, little research on the bacterial communities in deep sediment layers exists. In this study, thirty clone libraries of 16S rRNA were constructed from a beach wetland of the Poyang Lake along both horizontal (distance to the water-land junction) and vertical (sediment depth) gradients to assess the effects of sediment properties on bacterial community structure and diversity. Our results showed that bacterial diversity increased along the horizontal gradient and decreased along the vertical gradient. The heterogeneous sediment properties along gradients substantially affected the dominant bacterial groups at the phylum and species levels. For example, the NH⁺₄ concentration decreased with increasing depth, which was positively correlated with the relative abundance of Alphaproteobacteria. The changes in bacterial diversity and dominant bacterial groups showed that the top layer had a different bacterial community structure than the deeper layers. Principal component analysis revealed that both gradients, not each gradient independently, contributed to the shift in the bacterial community structure. A multiple linear regression model explained the changes in bacterial diversity and richness along the depth and distance gradients. Overall, our results suggest that spatial gradients associated with sediment properties shaped the bacterial communities in the Poyang Lake beach wetland.

Catchment-scale biogeography of riverine bacterioplankton

Lotic ecosystems such as rivers and streams are unique in that they represent a continuum of both space and time during the transition from headwaters to the river mouth. As microbes have very different controls over their ecology, distribution and dispersion compared with macrobiota, we wished to explore biogeographical patterns within a river catchment and uncover the major drivers structuring bacterioplankton communities. Water samples collected across the River Thames Basin, UK, covering the transition from headwater tributaries to the lower reaches of the main river channel were characterised using 16S rRNA gene pyrosequencing. This approach revealed an ecological succession in the bacterial community composition along the river continuum, moving from a community dominated by Bacteroidetes in the headwaters to Actinobacteria-dominated downstream. Location of the sampling point in the river network (measured as the cumulative water channel distance upstream) was found to be the most predictive spatial feature; inferring that ecological processes pertaining to temporal community succession are of prime importance in driving the assemblages of riverine bacterioplankton communities. A decrease in bacterial activity rates and an increase in the abundance of low nucleic acid bacteria relative to high nucleic acid bacteria were found to correspond with these downstream changes in community structure, suggesting corresponding functional changes. Our findings show that bacterial communities across the Thames basin exhibit an ecological succession along the river continuum, and that this is primarily driven by water residence time rather than the physico-chemical status of the river.

Bacterial community composition in three freshwater reservoirs of different alkalinity and trophic status

In order to investigate the factors controlling the bacterial community composition (BCC) in reservoirs, we sampled three freshwater reservoirs with contrasted physical and chemical characteristics and trophic status. The BCC was analysed by 16S rRNA gene amplicon 454 pyrosequencing. In parallel, a complete dataset of environmental parameters and phytoplankton community composition was also collected. BCC in the analysed reservoirs resembled that of epilimnetic waters of natural freshwater lakes with presence of Actinobacteria, Alpha- and Betaproteobacteria, Cytophaga–Flavobacteria–Bacteroidetes (CFB) and Verrucomicrobia groups. Our results evidenced that the retrieved BCC in the analysed reservoirs was strongly influenced by pH, alkalinity and organic carbon content, whereas comparatively little change was observed among layers in stratified conditions.

Bacterial community structure and dissolved organic matter in repeatedly flooded subsurface karst water pools

Bacterial diversity, community assembly, and the composition of the dissolved organic matter (DOM) were studied in three temporary subsurface karst pools with different flooding regimes. We tested the hypothesis that microorganisms introduced to the pools during floods faced environmental filtering toward a 'typical' karst water community, and we investigated whether DOM composition was related to floodings and the residence time of water in stagnant pools. As predicted, longer water residence consistently led to a decline of bacterial diversity. The microbial assemblages in the influx water harbored more 'exotic' lineages with large distances to known genotypes, yet these initial communities already appeared to be shaped by selective processes. β-Proteobacterial operational taxonomic units (OTUs) closely related to microbes from subsurface or surface aquatic environments were mainly responsible for the clustering of samples according to water residence time in the pools. By contrast, several Cytophagaceae and Flavobacteriaceae OTUs were related to different floodings, which were also the main determinants of DOM composition. A subset of compounds distinguishable by molecular mass and O/C content were characteristic for individual floods. Moreover, there was a transformation of DOM in stagnant pools toward smaller and more aromatic compounds, potentially also reflecting microbial utilization.

Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics

This study explored the short-term planktonic microbial community structure and resilience in Lake Lanier (GA, USA) while simultaneously evaluating the technical aspects of identifying taxa via 16S rRNA gene amplicon and metagenomic sequence data. 16S rRNA gene amplicons generated from four temporally discrete samples were sequenced with 454 GS-FLX-Ti yielding ∼40,000 rRNA gene sequences from each sample and representing ∼300 observed OTUs. Replicates obtained from the same biological sample clustered together but several biases were observed, linked to either the PCR or sequencing-preparation steps. In comparisons with companion whole-community shotgun metagenome datasets, the estimated number of OTUs at each timepoint was concordant, but 1.5 times and ∼10 times as many phyla and genera, respectively, were identified in the metagenomes. Our analyses showed that the 16S rRNA gene captures broad shifts in community diversity over time, but with limited resolution and lower sensitivity compared to metagenomic data. We also identified OTUs that showed marked shifts in abundance over four close timepoints separated by perturbations and tracked these taxa in the metagenome vs. 16S rRNA amplicon data. A strong summer storm had less of an effect on community composition than did seasonal mixing, which revealed a distinct succession of organisms. This study provides insights into freshwater microbial communities and advances the approaches for assessing community diversity and dynamics in situ.

Evidence for dissolved organic matter as the primary source and sink of photochemically produced hydroxyl radical in arctic surface waters

Hydroxyl radical (˙OH) is an indiscriminate oxidant that reacts at near-diffusion-controlled rates with organic carbon. Thus, while ˙OH is expected to be an important oxidant of dissolved organic matter (DOM) and other recalcitrant compounds, the role of ˙OH in the oxidation of these compounds in aquatic ecosystems is not well known due to the poorly constrained sources and sinks of ˙OH, especially in pristine (unpolluted) natural waters. We measured the rates of ˙OH formation and quenching across a range of surface waters in the Arctic varying in concentrations of expected sources and sinks of ˙OH. Photochemical formation of ˙OH was observed in all waters tested, with rates of formation ranging from 2.6 ± 0.6 to 900 ± 100 × 10(-12) M s(-1). Steady-state concentrations ranged from 2 ± 1 to 290 ± 60 × 10(-17) M, and overlapped with previously reported values in surface waters. While iron-mediated photo-Fenton reactions likely contributed to the observed ˙OH production, several lines of evidence suggest that DOM was the primary source and sink of photochemically produced ˙OH in pristine arctic surface waters. DOM from first-order or headwater streams was more efficient in producing ˙OH than what has previously been reported for DOM, and ˙OH formation decreased with increasing residence time of DOM in sunlit surface waters. Despite the ubiquitous formation of ˙OH in arctic surface waters observed in this study, photochemical ˙OH formation was estimated to contribute ≤4% to the observed photo-oxidation of DOM; however, key uncertainties in this estimate must be addressed before ruling out the role of ˙OH in the oxidation of DOM in these waters.

Metacommunity dynamics of bacteria in an arctic lake: the impact of species sorting and mass effects on bacterial production and biogeography

To understand mechanisms linking ecosystem processes and microbial diversity in freshwater ecosystems, bacterial productivity and the metacommunity dynamics of species sorting and mass effects were investigated in an 18 ha headwater lake in northern Alaska. On most sampling dates, the phylogenetic composition of bacterial communities in inflowing streams (inlets) was strikingly different than that in the lake and the outflowing stream (outlet) (16S DGGE fingerprinting), demonstrating the shift in composition that occurs as these communities transit the lake. Outlet and downstream communities were also more productive than inlet and upstream communities ((14)C-leucine incorporation). Inlet bacteria transplanted to the outlet stream in dialysis bags were equally or less productive than control bacteria, suggesting that the inlet bacteria are capable of growing under lake conditions, but do not remain abundant because of species sorting in the lake. Outlet bacteria (representative of epilimnetic bacteria) transplanted to the inlet stream were less productive than control bacteria, suggesting that lake bacteria are not as well adapted to growing under inlet conditions. Based on water density, inlet stream water and bacteria generally entered the lake at the base of the epilimnion. However, during low to medium flow in the inlet stream the residence time of the epilimnion was too long relative to bacterial doubling times for these allochthonous bacteria to have a mass effect on the composition of outlet bacteria. The highest community similarity between inlet and outlet bacteria was detected after a large rain event in 2003, with over 61% similarity (average non-storm similarities were 39 ± 8%). While mass effects may be important during large storm events, species sorting appears to be the predominant mechanism structuring bacterial communities within the lake, leading to the assembly of a lake community that has lost some ability to function in stream habitats.

Patterns in the composition of microbial communities from a subtropical river: effects of environmental, spatial and temporal factors

Microbes are key components of aquatic ecosystems and play crucial roles in global biogeochemical cycles. However, the spatiotemporal dynamics of planktonic microbial community composition in riverine ecosystems are still poorly understood. In this study, we used denaturing gradient gel electrophoresis of PCR-amplified 16S and 18S rRNA gene fragments and multivariate statistical methods to explore the spatiotemporal patterns and driving factors of planktonic bacterial and microbial eukaryotic communities in the subtropical Jiulong River, southeast China. Both bacterial and microbial eukaryotic communities varied significantly in time and were spatially structured according to upper stream, middle-lower stream and estuary. Among all the environmental factors measured, water temperature, conductivity, PO₄-P and TN/TP were best related to the spatiotemporal distribution of bacterial community, while water temperature, conductivity, NO_x-N and transparency were closest related to the variation of eukaryotic community. Variation partitioning, based on partial RDA, revealed that environmental factors played the most important roles in structuring the microbial assemblages by explaining 11.3% of bacterial variation and 17.5% of eukaryotic variation. However, pure spatial factors (6.5% for bacteria and 9.6% for eukaryotes) and temporal factors (3.3% for bacteria and 5.5% for eukaryotes) also explained some variation in microbial distribution, thus inherent spatial and temporal variation of microbial assemblages should be considered when assessing the impact of environmental factors on microbial communities.

Surface exposure to sunlight stimulates CO2 release from permafrost soil carbon in the Arctic

Recent climate change has increased arctic soil temperatures and thawed large areas of permafrost, allowing for microbial respiration of previously frozen C. Furthermore, soil destabilization from melting ice has caused an increase in thermokarst failures that expose buried C and release dissolved organic C (DOC) to surface waters. Once exposed, the fate of this C is unknown but will depend on its reactivity to sunlight and microbial attack, and the light available at the surface. In this study we manipulated water released from areas of thermokarst activity to show that newly exposed DOC is >40% more susceptible to microbial conversion to CO(2) when exposed to UV light than when kept dark. When integrated over the water column of receiving rivers, this susceptibility translates to the light-stimulated bacterial activity being on average from 11% to 40% of the total areal activity in turbid versus DOC-colored rivers, respectively. The range of DOC lability to microbes seems to depend on prior light exposure, implying that sunlight may act as an amplification factor in the conversion of frozen C stores to C gases in the atmosphere.

Bacterial and archaeal community structure in the surface microlayer of high mountain lakes examined under two atmospheric aerosol loading scenarios

Bacteria and Archaea of the air-water surface microlayer (neuston) and plankton from three high mountain lakes (Limnological Observatory of the Pyrenees, Spain) were analysed by 16S rRNA gene 454 pyrosequencing (V6 region) in two dates with different atmospheric aerosol loading conditions: (1) under a Saharan dust plume driven by southern winds; and (2) under northern winds with oceanic influence. In general, bacterial communities were richer than archaea, with estimated total richness of c. 2500 OTUs for Bacteria and c. 900 OTUs for Archaea equivalent to a sequencing effort of c. 250,000 and c. 20,000 sequences, respectively. The dominant bacterial OTU was affiliated to Actinobacteria. Archaea were one to two orders of magnitude less abundant than bacteria but were more evenly distributed. Apparently, Bacteroidetes and Thaumarchaeota sequences were preferentially found at the neuston, but no consistent pattern in either total microbial abundance or richness was found in any sample. However, we observed more marked changes in microbial relative abundances between neuston and plankton in the dust-influenced scenario. Higher community dissimilarities between neuston and plankton were also found during the Saharan dust episode, and such differences were higher for Bacteria than for Archaea. Nonetheless, relatively few (< 0.05%) of the neuston sequences matched previously identified airborne microorganisms, and none became important in the dates analysed.

Spatial and temporal scales of aquatic bacterial beta diversity

Understanding characteristic variation in aquatic bacterial community composition (BCC) across space and time can inform us about processes driving community assembly and the ability of bacterial communities to respond to perturbations. In this study, we synthesize BCC data from north temperate lakes to evaluate our current understanding of how BCC varies across multiple scales in time and space. A hierarchy of average similarity emerged with the highest similarity found among samples collected within the same lake, especially within the same basin, followed by similarity among samples collected through time within the same lake, and finally similarity among samples collected from different lakes. Using decay of similarity across time and space, we identified equivalent temporal (1 day) and spatial (10 m) scales of BCC variation. Finally, we identify an intriguing pattern of contrasting patterns of intra- and inter-annual BCC variation in two lakes. We argue our synthesis of spatio-temporal variation of aquatic BCC informs expectations for the response of aquatic bacterial communities to perturbation and environmental change. However, further long-term temporal observations will be needed to develop a general understanding of inter-annual BCC variation and our ability to use aquatic BCC as a sensitive metric of environmental change.

Microbial biogeography of arctic streams: exploring influences of lithology and habitat

Terminal restriction fragment length polymorphism and 16S rRNA gene sequencing were used to explore the community composition of bacterial communities in biofilms on sediments (epipssamon) and rocks (epilithon) in stream reaches that drain watersheds with contrasting lithologies in the Noatak National Preserve, Alaska. Bacterial community composition varied primarily by stream habitat and secondarily by lithology. Positive correlations were detected between bacterial community structure and nutrients, base cations, and dissolved organic carbon. Our results showed significant differences at the stream habitat, between epipssamon and epilithon bacterial communities, which we expected. Our results also showed significant differences at the landscape scale that could be related to different lithologies and associated stream biogeochemistry. These results provide insight into the bacterial community composition of little known and pristine arctic stream ecosystems and illustrate how differences in the lithology, soils, and vegetation community of the terrestrial environment interact to influence stream bacterial taxonomic richness and composition.

Temporal variability in the diversity and composition of stream bacterioplankton communities

Bacterioplankton in freshwater streams play a critical role in stream nutrient cycling. Despite their ecological importance, the temporal variability in the structure of stream bacterioplankton communities remains understudied. We investigated the composition and temporal variability of stream bacterial communities and the influence of physicochemical parameters on these communities. We used barcoded pyrosequencing to survey bacterial communities in 107 streamwater samples collected from four locations in the Colorado Rocky Mountains from September 2008 to November 2009. The four sampled locations harboured distinct communities yet, at each sampling location, there was pronounced temporal variability in both community composition and alpha diversity levels. These temporal shifts in bacterioplankton community structure were not seasonal; rather, their diversity and composition appeared to be driven by intermittent changes in various streamwater biogeochemical conditions. Bacterial communities varied independently of time, as indicated by the observation that communities in samples collected close together in time were no more similar than those collected months apart. The temporal turnover in community composition was higher than observed in most previously studied microbial, plant or animal communities, highlighting the importance of stochastic processes and disturbance events in structuring these communities over time. Detailed temporal sampling is important if the objective is to monitor microbial community dynamics in pulsed ecosystems like streams.

Microbial diversity in arctic freshwaters is structured by inoculation of microbes from soils

Microbes are transported in hydrological networks through many environments, but the nature and dynamics of underlying microbial metacommunities and the impact of downslope inoculation on patterns of microbial diversity across landscapes are unknown. Pyrosequencing of small subunit ribosomal RNA gene hypervariable regions to characterize microbial communities along a hydrological continuum in arctic tundra showed a pattern of decreasing diversity downslope, with highest species richness in soil waters and headwater streams, and lowest richness in lake water. In a downstream lake, 58% and 43% of the bacterial and archaeal taxa, respectively, were also detected in diverse upslope communities, including most of the numerically dominant lake taxa. In contrast, only 18% of microbial eukaryotic taxa in the lake were detected upslope. We suggest that patterns of diversity in surface waters are structured by initial inoculation from microbial reservoirs in soils followed by a species-sorting process during downslope dispersal of both common and rare microbial taxa. Our results suggest that, unlike for metazoans, a substantial portion of bacterial and archaeal diversity in surface freshwaters may originate in complex soil environments.

Local and regional factors influencing bacterial community assembly

The classical view states that microbial biogeography is not affected by dispersal barriers or historical events, but only influenced by the local contemporary habitat conditions (species sorting). This has been challenged during recent years by studies suggesting that also regional factors such as mass effect, dispersal limitation and neutral assembly are important for the composition of local bacterial communities. Here we summarize results from biogeography studies in different environments, i.e. in marine, freshwater and soil as well in human hosts. Species sorting appears to be the most important mechanism. However, this result might be biased since this is the mechanism that is easiest to measure, detect and interpret. Hence, the importance of regional factors may have been underestimated. Moreover, our survey indicates that different assembly mechanisms might be important for different parts of the total community, differing, for example, between generalists and specialists, and between taxa of different dispersal ability and motility. We conclude that there is a clear need for experimental studies, first, to clearly separate regional and local factors in order to study their relative importance, and second, to test whether there are differences in assembly mechanisms depending on different taxonomic or functional groups.

Freshwater bacterioplankton richness in oligotrophic lakes depends on nutrient availability rather than on species-area relationships

A central goal in ecology is to grasp the mechanisms that underlie and maintain biodiversity and patterns in its spatial distribution can provide clues about those mechanisms. Here, we investigated what might determine the bacterioplankton richness (BR) in lakes by means of 454 pyrosequencing of the 16S rRNA gene. We further provide a BR estimate based upon a sampling depth and accuracy, which, to our knowledge, are unsurpassed for freshwater bacterioplankton communities. Our examination of 22,669 sequences per lake showed that freshwater BR in fourteen nutrient-poor lakes was positively influenced by nutrient availability. Our study is, thus, consistent with the finding that the supply of available nutrients is a major driver of species richness; a pattern that may well be universally valid to the world of both micro- and macro-organisms. We, furthermore, observed that BR increased with elevated landscape position, most likely as a consequence of differences in nutrient availability. Finally, BR decreased with increasing lake and catchment area that is negative species-area relationships (SARs) were recorded; a finding that re-opens the debate about whether positive SARs can indeed be found in the microbial world and whether positive SARs can in fact be pronounced as one of the few 'laws' in ecology.

Temporal variation of β-diversity and assembly mechanisms in a bacterial metacommunity

The turnover of community composition across space, β-diversity, is influenced by different assembly mechanisms, which place varying weight on local habitat factors, such as environmental conditions and species interactions, and regional factors such as dispersal and history. Several assembly mechanisms may function simultaneously; however, little is known about how their importance changes over time and why. Here, we implemented a field survey where we sampled a bacterial metacommunity consisting of 17 rock pools located at the Swedish Baltic Sea coast at 11 occasions during 1 year. We determined to which extent communities were structured by different assembly mechanisms using variation partitioning and studied changes in β-diversity across environmental gradients over time. β-Diversity was highest at times of high overall productivity and environmental heterogeneity in the metacommunity, at least partly due to species sorting, that is, selection of taxa by the prevailing environmental conditions. In contrast, dispersal-driven assembly mechanisms were primarily detected at times when β-diversity was relatively low. There were no indications for strong and persistent differences in community composition or β-diversity between permanent and temporary pools, indicating that the physical disturbance regime is of relatively minor importance. In summary, our study clearly suggests that there are temporal differences in the relative importance of different assembly mechanisms related to abiotic factors and shows that the temporal variability of those factors is important for a more complete understanding of bacterial metacommunity dynamics.

Diversity and composition of the bacterial community of Poyang Lake (China) as determined by 16S rRNA gene sequence analysis

Poyang Lake is the largest fresh water lake in China. In this study, the objective was to examine the diversity of bacterial community in this environment. The phylogenetic composition of bacterioplankton communities from two sites and two dates (northern and southern sub-basins in October 2006 and in May 2007, respectively) in the water column of Poyang Lake were investigated by partially sequencing cloned 16SrRNA genes. Moreover, restriction fragment length polymorphism (RFLP) was applied in the 16SrRNA gene clones. In total, four clone libraries were constructed and 347 clones were screened by RFLP, yielding 153 operational taxonomic units, which mainly belonged to the proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Verrucomicrobia and Planctomycetes. Our results showed that Beta-proteobacteria was the most significant lineage, with dominant numbers of operational taxonomic units in the northern October 2006, southern October 2006 and May 2007 libraries. The highest bacterial diversity occurred in the library from the southern sub-basin in May 2007 and the lowest in the library from the northern sub-basin in May 2007. Horizontal and temporal differences associated with the concentration of total phosphorus, water temperature and pH suggested that the trophic state and the physicochemical properties of lake play key roles in sustaining bacterial community composition structure.

Species sorting affects bacterioplankton community composition as determined by 16S rDNA and 16S rRNA fingerprints

To understand the mechanisms determining community composition, it is essential to distinctively unravel the importance of local from that of regional processes. In this effort, the mechanisms underlying bacterioplankton community assembly were analysed in eight lakes of short water residence time (WRT) during a four-season sampling campaign. Bacterioplankton community composition (BCC) was determined using terminal-restriction fragment length polymorphism (t-RFLP) on the 16S rRNA gene (16S rDNA) and 16S rRNA. The relationship between similarity in BCC between a lake and its major inlet on the one hand and cell import per cell production rate from the inlet to the lake epilimnion on the other was used as a measure of the importance of cell dispersal (mass effects) for community assembly. Low similarities in BCC between lakes and their inlets were observed even at short WRTs, and the degree of similarity correlated better with the environmental conditions in lakes and streams than with cell import per cell production rates. Thus, mass effects seemed less important for local lake BCC in comparison to environmental habitat characteristics (species sorting). Analyses of 16S rDNA and 16S rRNA community fingerprints yielded similar results, indicating that species-sorting dynamics exerted an equally important effect on both the abundant and active fraction within the studied bacterioplankton communities.

Bacterial community composition of stream biofilms in spatially variable-flow environments

Streams are highly heterogeneous ecosystems, in terms of both geomorphology and hydrodynamics. While flow is recognized to shape the physical architecture of benthic biofilms, we do not yet understand what drives community assembly and biodiversity of benthic biofilms in the heterogeneous flow landscapes of streams. Within a metacommunity ecology framework, we experimented with streambed landscapes constructed from bedforms in large-scale flumes to illuminate the role of spatial flow heterogeneity in biofilm community composition and biodiversity in streams. Our results show that the spatial variation of hydrodynamics explained a remarkable percentage (up to 47%) of the variation in community composition along bedforms. This suggests species sorting as a model of metacommunity dynamics in stream biofilms, though natural biofilm communities will clearly not conform to a single model offered by metacommunity ecology. The spatial variation induced by the hydrodynamics along the bedforms resulted in a gradient of bacterial beta diversity, measured by a range of diversity and similarity indices, that increased with bedform height and hence with spatial flow heterogeneity at the flume level. Our results underscore the necessity to maintain small-scale physical heterogeneity for community composition and biodiversity of biofilms in stream ecosystems.

Comparison of the structure and composition of bacterial communities from temperate and tropical freshwater ecosystems

We used a partial 16S rRNA sequencing approach to compare the structure and composition of the bacterial communities in three large, deep subalpine lakes in France with those of communities in six shallow tropical reservoirs in Burkina Faso. Despite the very different characteristics of these ecosystems, we found that their bacterial communities share the same composition in regard to the relative proportions of the different phyla, suggesting that freshwater environmental conditions lead to convergence in this composition. In the same way, we found no significant difference in the richness and diversity of the bacterial communities in France and Burkina Faso. We defined core and satellite operational taxonomic units (OTUs) (sequences sharing at least 98% identity) on the basis of their abundance and their geographical distribution. The core OTUs were found either ubiquitously or only in temperate or tropical and subtropical areas, and they contained more than 70% of all the sequences retrieved in this study. In contrast, satellite OTUs were characterized by having a more restricted geographical distribution and by lower abundance. Finally, the bacterial community composition of these freshwater ecosystems in France and Burkina Faso was markedly different, showing that the history of these ecosystems and regional environmental parameters have a greater impact on the relative abundances of the different OTUs in each bacterial community than the local environmental conditions.

Salt marsh sediment bacteria: their distribution and response to external nutrient inputs

A primary focus among microbial ecologists in recent years has been to understand controls on the distribution of microorganisms in various habitats. Much less attention has been paid to the way that environmental disturbance interacts with processes that regulate bacterial community composition. We determined how human disturbance affected the distribution and community structure of salt marsh sediment bacteria by using denaturing gradient gel electrophoresis of 16S rRNA in five different habitats in each of four salt marshes located in northeastern Massachusetts, USA. Two of the four marsh creeks were experimentally enriched 15 x above background by the addition of nitrogen and phosphorus fertilizers for two or more growing seasons. Our results indicate that extrinsic factors acting at broad scales do not influence the distribution of salt marsh sediment bacteria. Intrinsic factors, controlled by local-scale environmental heterogeneity, do play a role in structuring these sediment microbial communities, although nutrient enrichment did not have a consequential effect on the microbial community in most marsh habitats. Only in one habitat, a region of the marsh creek wall that is heavily colonized by filamentous algae, did we see any effect of fertilization on the microbial community structure. When similar habitats were compared among marshes, there was considerable convergence in the microbial community composition during the growing season. Environmental factors that correlated best with microbial community composition varied with habitat, suggesting that habitat-specific intrinsic forces are primarily responsible for maintaining microbial diversity in salt marsh sediments.

Bacterial 'cosmopolitanism' and importance of local environmental factors for community composition in remote high-altitude lakes

In October 2004, plankton samples were collected from six permanent lakes located between 4960 and 5440 m a.s.l. in the Mount Everest region (Nepal) to assess how spatial and local environmental factors affect natural bacterial community composition. Fingerprinting analysis of the bacterial 16S rRNA gene fragment was done by denaturing gradient gel electrophoresis (DGGE).The number of DGGE bands (range: 12-23) was not correlated with lake area or remoteness, but there was a strong negative correlation with the ratio of catchment to lake area (r = -0.826, P < 0.05), suggesting that hydraulic retention time affects the establishment of the bacterial community in these seepage lakes.Most dominant sequences belonged to Betaproteobacteria except in two lakes where members of Bacteroidetes made the largest relative contribution. Up to 81% of the phylotypes had high similarity (>98 to 100%) in partial 16S rRNA gene sequence to those reported from other alpine lakes and glaciers around the world, suggesting the presence of 'cosmopolitan' bacteria.An analysis based on dissimilarity matrices and the Mantel test revealed the existence of dissimilarities in bacterial community composition related to geographical distance over a small spatial scale (<6 km), but determined by local environmental constraints.Our results suggest that several bacterial phylotypes are ubiquitous in the freshwater aquatic realm, but taxon sorting by local environmental constraints is important.