Contrasting community assembly processes structure lotic bacteria metacommunities along the river continuum

The heterogeneous nature of lotic habitats plays an important role in the complex ecological and evolutionary processes that structure the microbial communities within them. Due to such complexity, our understanding of lotic microbial ecology still lacks conceptual frameworks for the ecological processes that shape these communities. We explored how bacterial community composition and underlying ecological assembly processes differ between lotic habitats by examining community composition and inferring community assembly processes across four major habitat types (free-living, particle-associated, biofilm on benthic stones and rocks, and sediment). This was conducted at 12 river sites from headwater streams to the main river in the River Thames, UK. Our results indicate that there are distinct differences in the bacterial communities between four major habitat types, with contrasting ecological processes shaping their community assembly processes. While the mobile free-living and particle-associated communities were consistently less diverse than the fixed sediment and biofilm communities, the latter two communities displayed higher homogeneity across the sampling sites. This indicates that the relative influence of deterministic environmental filtering is elevated in sediment and biofilm communities compared with free-living and particle-associated communities, where stochastic processes play a larger role.     

Community differentiation of bacterioplankton in the epipelagic layer in the South China Sea

The South China Sea (SCS) is the largest marginal sea in the western tropical Pacific Ocean and is characterized by complex physicochemical environments. To date, the biogeographic patterns of the microbial communities have rarely been reported at a basin scale in the SCS. In this study, the bacterial assemblages inhabiting the epipelagic zone across 110°E to 119°E along 14°N latitude were uncovered. The vertical stratification of both bacterial taxa and their potential functions were revealed. These results suggest that the water depth‐specific environment is a driver of the vertical bacterioplankton distribution. Moreover, the bacterial communities were different between the eastern stations and the western stations, where the environmental conditions were distinct. However, the mesoscale eddy did not show an obvious effect on the bacterial community due to the large distance between the sampling site and the center of the eddy. In addition to the water depth and longitudinal location of the samples, the heterogeneity of the phosphate and salinity concentrations also significantly contributed to the variance in the epipelagic bacterial community in the SCS. To the best of our knowledge, this study is the first to report that the variability in epipelagic bacterioplankton is driven by the physicochemical environment at the basin scale in the SCS. Our results emphasize that the ecological significance of bacterioplankton can be better understood by considering the relationship between the biogeographic distribution of bacteria and the oceanic dynamics processes.     

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

Uncovering which environmental factors govern community diversity patterns and how ecological processes drive community turnover are key questions related to understand the community assembly. However, the ecological mechanisms regulating long‐term variations of bacterioplankton communities in lake ecosystems remain poorly understood. Here we present nearly a decade‐long study of bacterioplankton communities from the eutrophic Lake Donghu (Wuhan, China) using 16S rRNA gene amplicon sequencing with MiSeq platform. We found strong repeatable seasonal diversity patterns in terms of both common (detected in more than 50% samples) and dominant (relative abundance >1%) bacterial taxa turnover. Moreover, community composition tracked the seasonal temperature gradient, indicating that temperature is a key environmental factor controlling observed diversity patterns. Total phosphorus also contributed significantly to the seasonal shifts in bacterioplankton composition. However, any spatial pattern of bacterioplankton communities across the main lake areas within season was overwhelmed by their temporal variabilities. Phylogenetic analysis further indicated that 75%–82% of community turnover was governed by homogeneous selection due to consistent environmental conditions within seasons, suggesting that the microbial communities in Lake Donghu are mainly controlled by niche‐based processes. Therefore, dominant niches available within seasons might be occupied by similar combinations of bacterial taxa with modest dispersal rates throughout different lake areas.     

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.     

典型农田退耕后土壤真菌与细菌群落的演替

土壤真菌和细菌作为地下生态系统的重要组成部分,其群落的恢复状况是评价农田退耕还林生态效益的重要指标。以云南省维西县典型退耕还林农田为对象,利用高通量测序等方法比较了不同退耕年限的农田土壤中真菌和细菌群落随植被演替的变化特征。结果发现,农田撂荒后土壤细菌多样性先显著降低后缓慢上升,真菌多样性变化不明显;地上部植被由草本经灌丛再向林地演替的过程中,土壤真菌的群落组成随植被变化呈现明显的改变,主要体现在粪壳菌纲(Sordariomycetes)所占比例的减少(由30%减至10%左右)和伞菌纲(Agaricomycetes)所占比例的增加(由5%以下增至20%以上);而细菌的群落组成无明显变化。聚类分析的结果显示,真菌的群落组成变化与植物群落的演替规律更为同步。不同演替阶段的退耕农田土壤真菌和细菌群落均明显区别于未经扰动的天然林,表明人为扰动对土壤微生物群落的影响可能在较长时间内持续存在。研究揭示了云南典型农田退耕后地下土壤真菌和细菌群落随植被演替的变化特征,为全面评价该地区退耕还林的生态效益提供了数据支撑。     

Fungal community demonstrates stronger dispersal limitation and less network connectivity than bacterial community in sediments along a large river

Despite the essential functions of sedimentary bacterial and fungal communities in biogeochemical cycling, little is known about their biogeographic patterns and driving processes in large rivers. Here we investigated the biogeographic assemblies and co-occurrence patterns of sedimentary bacterial and fungal communities in the Jinsha River, one of the largest rivers in southwestern China. The mainstream of river was divided into upstream, midstream and downstream. The results showed that both bacterial and fungal communities differed significantly among three sections. For both communities, their composition variations in all sites or each river section were controlled by the combination of dispersal limitation and environmental selection, and dispersal limitation was the dominant factor. Compared with bacteria, fungi had stronger dispersal limitation. Co-occurrence network analyses revealed higher network connectivity but a lower proportion of positive interaction in the bacterial than fungal network at all sites. In particular, the keystone species belonging to bacterial phyla Proteobacteria and Firmicutes and fungal phyla Ascomycota and Chytridiomycota may play critical roles in maintaining community function. Together, these observations indicate that fungi have a stronger dispersal limitation influence and less network connectivity than bacteria, implying different community assembly mechanisms and ecological functions between bacteria and fungi in large rivers.     

Assembly processes and source tracking of planktonic and benthic bacterial communities in the Yellow River estuary

Estuaries connect rivers with the ocean and are considered transition regions due to the continuous inputs from rivers. Microbiota from different sources converge and undergo succession in these transition regions, but their assembly mechanisms along environmental gradients remain unclear. Here, we found that salinity had a stronger effect on planktonic than on benthic microbial communities, and the dominant planktonic bacteria changed more distinctly than the dominant benthic bacteria with changes in salinity. The planktonic bacteria in the brackish water came mainly from seawater, which was confirmed in the laboratory, whereas the benthic bacteria were weakly affected by salinity, which appeared to be a mixture of the bacteria from riverine and oceanic sediments. Benthic bacterial community assembly in the sediments was mainly controlled by homogeneous selection and almost unaffected by changes in salinity, the dominant assemblage processes for planktonic bacteria changed dramatically along the salinity gradient, from homogeneous selection in freshwater to drift in seawater. Our results highlight that salinity is the key driver of estuarine microbial succession and that salinity is more important in shaping planktonic than benthic bacterial communities in the Yellow River estuary.     

Succession of bacterial community structure along the Changjiang River determined by denaturing gradient gel electrophoresis and clone library analysis

Bacterial community structure along the Changjiang River (which is more than 2,500 km long) was studied by using denaturing gradient gel electrophoresis (DGGE) and clone library analysis of PCR-amplified 16S ribosomal DNA (rDNA) with universal bacterial primer sets. DGGE profiles and principal-component analysis (PCA) demonstrated that the bacterial community gradually changed from upstream to downstream in both 1998 and 1999. Bacterial diversity, as determined by the Shannon index (H'), gradually decreased from upstream to downstream. The PCA plots revealed that the differences in the bacterial communities among riverine stations were not appreciable compared with the differences in two adjacent lakes, Lake Dongting and Lake Poyang. The relative stability of the bacterial communities at the riverine stations was probably due to the buffering action of the large amount of water flowing down the river. Clone library analysis of 16S rDNA revealed that the dominant bacterial groups changed from beta-proteobacteria and the Cytophaga-Flexibacter-Bacteroides group upstream to high-G+C-content gram-positive bacteria downstream and also that the bacterial community structure differed among the stations in the river and the lakes. The results obtained in this study should provide a reference for future changes caused by construction of the Three Gorges Dam.     

Landscape‐scale spatial abundance distributions discriminate core from random components of boreal lake bacterioplankton

Aquatic bacterial communities harbour thousands of coexisting taxa. To meet the challenge of discriminating between a ‘core’ and a sporadically occurring ‘random’ component of these communities, we explored the spatial abundance distribution of individual bacterioplankton taxa across 198 boreal lakes and their associated fluvial networks (188 rivers). We found that all taxa could be grouped into four distinct categories based on model statistical distributions (normal like, bimodal, logistic and lognormal). The distribution patterns across lakes and their associated river networks showed that lake communities are composed of a core of taxa whose distribution appears to be linked to in‐lake environmental sorting (normal‐like and bimodal categories), and a large fraction of mostly rare bacteria (94% of all taxa) whose presence appears to be largely random and linked to downstream transport in aquatic networks (logistic and lognormal categories). These rare taxa are thus likely to reflect species sorting at upstream locations, providing a perspective of the conditions prevailing in entire aquatic networks rather than only in lakes.     

Annual Patterns in Bacterioplankton Community Variability in a Humic Lake

Bacterioplankton community composition (BCC) was monitored in a shallow humic lake in northern Wisconsin, USA, over 3 years using automated ribosomal intergenic spacer analysis (ARISA). Comparison of ARISA profiles of bacterial communities over time indicated that BCC was highly variable on a seasonal and annual scale. Nonmetric multidimensional scaling (MDS) analysis indicated little similarity in BCC from year to year. Nevertheless, annual patterns in bacterioplankton community diversity were observed. Trends in bacterioplankton community diversity were correlated to annual patterns in community succession observed for phytoplankton and zooplankton populations, consistent with the notion that food web interactions affect bacterioplankton community structure in this humic lake. Bacterioplankton communities experience a dramatic drop in richness and abundance each year in early summer, concurrent with an increase in the abundance of both mixotrophic and heterotrophic flagellates. A second drop in richness, but not abundance, is observed each year in late summer, coinciding with an intense bloom of the nonphagotrophic dinoflagellate Peridinium limbatum. A relationship between bacterial community composition, size, and abundance and the population dynamics of Daphnia was also observed. The noted synchrony between these major population and species shifts suggests that linkages across trophic levels play a role in determining the annual time course of events for the microbial and metazoan components of the plankton.     

Experimental manipulations of microbial food web interactions in a humic lake: shifting biological drivers of bacterial community structure

A previous multiyear study observed correlations between bacterioplankton community composition (BCC) and abundance and the dynamics of phytoplankton populations and bacterivorous grazers in a humic lake. These observations generated hypotheses about the importance of trophic interactions (both top-down and bottom-up) for structuring bacterial communities in this lake, which were tested using two multifactorial food web manipulation experiments that separately manipulated the intensity of grazing and the composition of the phytoplankton community. Our results, combined with field observations, suggest that a hierarchy of drivers structures bacterial communities in this lake. While other studies have noted links between aggregate measures of phytoplankton and bacterioplankton communities, we demonstrate here correlations between succession of phytoplankton assemblages and BCC as assessed by automated ribosomal intergenic spacer analysis (ARISA). We used a novel approach linking community ARISA data to phylogenetic assignments from sequence analysis of 16S rRNA gene clone libraries to examine the responses of specific bacterial phylotypes to the experimental manipulations. The synchronous dynamics of these populations suggests that primary producers may mediate BCC and diversity through labile organic matter production, which evolves in quality and quantity during phytoplankton succession. Superimposed on this resource-mediated control of BCC are brief periods of intense bacterivory that impact bacterial abundance and composition.     

Phylogenetic analysis suggests that habitat filtering is structuring marine bacterial communities across the globe

The phylogenetic structure and community composition were analysed in an existing data set of marine bacterioplankton communities to elucidate the evolutionary and ecological processes dictating the assembly. The communities were sampled from coastal waters at nine locations distributed worldwide and were examined through the use of comprehensive clone libraries of 16S ribosomal RNA genes. The analyses show that the local communities are phylogenetically different from each other and that a majority of them are phylogenetically clustered, i.e. the species (operational taxonomic units) were more related to each other than expected by chance. Accordingly, the local communities were assembled non-randomly from the global pool of available bacterioplankton. Further, the phylogenetic structures of the communities were related to the water temperature at the locations. In agreement with similar studies, including both macroorganisms and bacteria, these results suggest that marine bacterial communities are structured by “habitat filtering”, i.e. through non-random colonization and invasion determined by environmental characteristics. Different bacterial types seem to have different ecological niches that dictate their survival in different habitats. Other eco-evolutionary processes that may contribute to the observed phylogenetic patterns are discussed. The results also imply a mapping between phenotype and phylogenetic relatedness which facilitates the use of community phylogenetic structure analysis to infer ecological and evolutionary assembly processes.     

Contrasted effects of diversity and immigration on ecological insurance in marine bacterioplankton communities

The ecological insurance hypothesis predicts a positive effect of species richness on ecosystem functioning in a variable environment. This effect stems from temporal and spatial complementarity among species within metacommunities coupled with optimal levels of dispersal. Despite its importance in the context of global change by human activities, empirical evidence for ecological insurance remains scarce and controversial. Here we use natural aquatic bacterial communities to explore some of the predictions of the spatial and temporal aspects of the ecological insurance hypothesis. Addressing ecological insurance with bacterioplankton is of strong relevance given their central role in fundamental ecosystem processes. Our experimental set up consisted of water and bacterioplankton communities from two contrasting coastal lagoons. In order to mimic environmental fluctuations, the bacterioplankton community from one lagoon was successively transferred between tanks containing water from each of the two lagoons. We manipulated initial bacterial diversity for experimental communities and immigration during the experiment. We found that the abundance and production of bacterioplankton communities was higher and more stable (lower temporal variance) for treatments with high initial bacterial diversity. Immigration was only marginally beneficial to bacterial communities, probably because microbial communities operate at different time scales compared to the frequency of perturbation selected in this study, and of their intrinsic high physiologic plasticity. Such local "physiological insurance" may have a strong significance for the maintenance of bacterial abundance and production in the face of environmental perturbations.     

罗氏沼虾育苗期浮游细菌群落演替模式、驱动因素及其生物标志物

为了探究罗氏沼虾(Macrobrachium rosenbergii)育苗期浮游细菌群落的时间动态和组装机制,对3个苗种厂的全育苗周期进行持续追踪,利用16S rRNA扩增子测序评估了罗氏沼虾幼苗发育过程中浮游细菌群落的动态演替、环境驱动因素、微生物标志物和共现网络。细菌群落的α-多样性在育苗期呈U型分布规律,群落相似性遵循时间衰减模式,群落周转率为0.011。随着虾苗的发育,微杆菌科(Microbacteriaceae)(放线菌门:Actinobacteria)和冷形菌科(Cryomorphaceae)(拟杆菌门:Bacteroidetes)的相对丰度显著增加(P<0.05),而拟杆菌门中的黄杆菌科(Flavobacteriaceae)和藏红花黄色线菌科(Crocinitomicaceae)的比重下降。pH是影响浮游细菌群落多样性和组成的最主要的环境驱动因素。利用随机森林分析,鉴定了12个幼苗发育相关的微生物标志物,其中伯克氏菌科(Burkholderiaceae)和圆杆菌科(Cyclobacteriaceae)分别是育苗早期(1—2d)和中期(8—10d)的指示性类群,而腐螺...     

Succession of Bacterial Community Structure along the Changjiang River Determined by Denaturing Gradient Gel Electrophoresis and Clone Library Analysis

Bacterial community structure along the Changjiang River (which is more than 2,500 km long) was studied by using denaturing gradient gel electrophoresis (DGGE) and clone library analysis of PCR-amplified 16S ribosomal DNA (rDNA) with universal bacterial primer sets. DGGE profiles and principal-component analysis (PCA) demonstrated that the bacterial community gradually changed from upstream to downstream in both 1998 and 1999. Bacterial diversity, as determined by the Shannon index (H′), gradually decreased from upstream to downstream. The PCA plots revealed that the differences in the bacterial communities among riverine stations were not appreciable compared with the differences in two adjacent lakes, Lake Dongting and Lake Poyang. The relative stability of the bacterial communities at the riverine stations was probably due to the buffering action of the large amount of water flowing down the river. Clone library analysis of 16S rDNA revealed that the dominant bacterial groups changed from β-proteobacteria and the Cytophaga-Flexibacter-Bacteroides group upstream to high-G+C-content gram-positive bacteria downstream and also that the bacterial community structure differed among the stations in the river and the lakes. The results obtained in this study should provide a reference for future changes caused by construction of the Three Gorges Dam.     

Bacterial and phytoplankton responses to nutrient amendments in a boreal lake differ according to season and to taxonomic resolution

Nutrient limitation and resource competition in bacterial and phytoplankton communities may appear different when considering different levels of taxonomic resolution. Nutrient amendment experiments conducted in a boreal lake on three occasions during one open water season revealed complex responses in overall bacterioplankton and phytoplankton abundance and biovolume. In general, bacteria were dominant in spring, while phytoplankton was clearly the predominant group in autumn. Seasonal differences in the community composition of bacteria and phytoplankton were mainly related to changes in observed taxa, while the differences across nutrient treatments within an experiment were due to changes in relative contributions of certain higher- and lower-level phylogenetic groups. Of the main bacterioplankton phyla, only Actinobacteria had a treatment response that was visible even at the phylum level throughout the season. With increasing resolution (from 75 to 99% sequence similarity) major responses to nutrient amendments appeared using 454 pyrosequencing data of 16S rRNA amplicons. This further revealed that OTUs (defined by 97% sequence similarity) annotated to the same highly resolved freshwater groups appeared to occur during different seasons and were showing treatment-dependent differentiation, indicating that OTUs within these groups were not ecologically coherent. Similarly, phytoplankton species from the same genera responded differently to nutrient amendments even though biovolumes of the majority of taxa increased when both nitrogen and phosphorus were added simultaneously. The bacterioplankton and phytoplankton community compositions showed concurrent trajectories that could be seen in synchronous succession patterns over the season. Overall, our data revealed that the response of both communities to nutrient changes was highly dependent on season and that contradictory results may be obtained when using different taxonomic resolutions.     

Bacterial Community Composition in Central European Running Waters Examined by Temperature Gradient Gel Electrophoresis and Sequence Analysis of 16S rRNA Genes

The bacterial community composition in small streams and a river in central Germany was examined by temperature gradient gel electrophoresis (TGGE) with PCR products of 16S rRNA gene fragments and sequence analysis. Complex TGGE band patterns suggested high levels of diversity of bacterial species in all habitats of these environments. Cluster analyses demonstrated distinct differences among the communities in stream and spring water, sandy sediments, biofilms on stones, degrading leaves, and soil. The differences between stream water and sediment were more significant than those between sites within the same habitat along the stretch from the stream source to the mouth. TGGE data from an entire stream course suggest that, in the upper reach of the stream, a special suspended bacterial community is already established and changes only slightly downstream. The bacterial communities in water and sediment in an acidic headwater with a pH below 5 were highly similar to each other but deviated distinctly from the communities at the other sites. As ascertained by nucleotide sequence analysis, stream water communities were dominated by Betaproteobacteria (one-third of the total bacteria), whereas sediment communities were composed mainly of Betaproteobacteria and members of the Fibrobacteres/Acidobacteria group (each accounting for about 25% of bacteria). Sequences obtained from bacteria from water samples indicated the presence of typical cosmopolitan freshwater organisms. TGGE bands shared between stream and soil samples, as well as sequences found in bacteria from stream samples that were related to those of soil bacteria, demonstrated the occurrence of some species in both stream and soil habitats. Changes in bacterial community composition were correlated with geographic distance along a stream, but in comparisons of different streams and rivers, community composition was correlated only with environmental conditions.     

Coherent dynamics and association networks among lake bacterioplankton taxa

Bacteria have important roles in freshwater food webs and in the cycling of elements in the ecosystem. Yet specific ecological features of individual phylogenetic groups and interactions among these are largely unknown. We used 454 pyrosequencing of 16S rRNA genes to study associations of different bacterioplankton groups to environmental characteristics and their co-occurrence patterns over an annual cycle in a dimictic lake. Clear seasonal succession of the bacterioplankton community was observed. After binning of sequences into previously described and highly resolved phylogenetic groups (tribes), their temporal dynamics revealed extensive synchrony and associations with seasonal events such as ice coverage, ice-off, mixing and phytoplankton blooms. Coupling between closely and distantly related tribes was resolved by time-dependent rank correlations, suggesting ecological coherence that was often dependent on taxonomic relatedness. Association networks with the abundant freshwater Actinobacteria and Proteobacteria in focus revealed complex interdependencies within bacterioplankton communities and contrasting linkages to environmental conditions. Accordingly, unique ecological features can be inferred for each tribe and reveal the natural history of abundant cultured and uncultured freshwater bacteria.     

The Temporal Scaling of Bacterioplankton Composition: High Turnover and Predictability during Shrimp Cultivation

The spatial distribution of microbial communities has recently been reliably documented in the form of a distance–similarity decay relationship. In contrast, temporal scaling, the pattern defined by the microbial similarity–time relationships (STRs), has received far less attention. As a result, it is unclear whether the spatial and temporal variations of microbial communities share a similar power law. In this study, we applied the 454 pyrosequencing technique to investigate temporal scaling in patterns of bacterioplankton community dynamics during the process of shrimp culture. Our results showed that the similarities decreased significantly (P?=?0.002) with time during the period over which the bacterioplankton community was monitored, with a scaling exponent of w?=?0.400. However, the diversities did not change dramatically. The community dynamics followed a gradual process of succession relative to the parent communities, with greater similarities between samples from consecutive sampling points. In particular, the variations of the bacterial communities from different ponds shared similar successional trajectories, suggesting that bacterial temporal dynamics are predictable to a certain extent. Changes in bacterial community structure were significantly correlated with the combination of Chl a, TN, PO₄ ^3-, and the C/N ratio. In this study, we identified predictable patterns in the temporal dynamics of bacterioplankton community structure, demonstrating that the STR of the bacterial community mirrors the spatial distance–similarity decay model.