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Contemporary environmental factors such as temperature and pH are generally identified as primary influences on microbial diversity, while the role of geological processes remain understudied. Here, we investigated the diversity and community composition of bacteria and fungi along an elevational gradient from703 to 4514 m on Mt. Kilimanjaro, East Africa. We further examined the effects of contemporary environment and geological processes such as weathering on microbial communities and diversities. For community composition, bacteria and fungi showed clear differentiation along elevations and their community dissimilarities increased with elevational distance indicating elevational distance-decay relationships. Multiple variables such as weathering, climate and chemical factors were significantly associated with microbial communities and showed greater effects on bacterial than fungal communities. Specifically, soil pH mainly shaped bacterial communities, while mean annual temperature for fungi, followed by other variables such as weathering processes. For Shannon diversity, bacteria and fungi showed significant hump-shaped elevational patterns with the peak values at 1857 and 1436 m, respectively. Shannon diversity was mainly affected by soil weathering accounting for 8.9% of the total variance for bacteria, while jointly by weathering and climate accounted for 14.3% of fungi. For the community uniqueness, represented by local contribution to beta diversity (LCBD), there were U-shaped patterns for both taxonomic groups. LCBD was mainly explained by the joint effects of chemical and climate variables which accounted for 51.1% and 33.4% for bacteria and fungi, respectively. Our results highlight the effects of soil weathering processes on diversity and community composition for bacteria and fungi. Thus, the integration of weathering with contemporary environments could provide new insights into microbial elevational diversity patterns., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Bacteria are diverse and play important roles in biogeochemical cycling of aquatic ecosystems, but the global distribution patterns of bacterial communities in lake sediments across different climate zones are still obscure. Here we integrated the high-throughput sequencing data of 750 sediment samples from published literature to investigate the distribution of bacterial communities in different climate zones and the potential driving mechanisms. The obtained results indicated that the diversity and richness of bacterial community were notably higher in temperate and cold zones than those in other climate zones. In addition, the bacterial community composition varied significantly in different climate zones, which further led to changes in bacterial functional groups. Specifically, the relative abundance of nitrogen cycling functional groups in polar zones was notably higher compared to other climate zones. Regression analysis revealed that climate (mean annual precipitation, MAP; and mean annual temperature, MAT), vegetation, and geography together determined the diversity pattern of sediment bacterial community on a global scale. The results of partial least squares path modeling further demonstrated that climate was the most significant factor affecting the composition and diversity of bacterial communities, and MAP was the most important climate factor affecting the composition of bacteria community (R 2  = 0.443, P < 0.001). It is worth noting that a strong positive correlation was observed between the abundance of the dominant bacterial group uncultured&#95;f&#95;Anaerolineaceae and the normalized difference vegetation index (NDVI; P < 0.001), suggesting that vegetation could affect bacterial community diversity by influencing dominant bacterial taxa. This study enhances our understanding of the global diversity patterns and biogeography of sediment bacteria., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Environmental microplastics (MPs) vary in abundance, shape, size, color, and polymer type in freshwater ecosystems, yet their impact on bacterial community assembly in natural lakes is unclear. Here, we examined MPs and bacterial compositions in water and sediments of Taihu Lake, China, to reveal the influence of complex MPs on the bacterial community assembly. The results showed that the complexity index of MPs significantly influenced the turnover and nestedness components of bacterial communities. In the colder season, MP complexity was significantly correlated with the turnover componentin sediments (R 2 = 0.19, P < 0.0001), with turnover increasing as MP complexity increased. Conversely, under warmer season, MP complexity was significantly correlated with turnover and nestedness components. Additionally, the interaction effect of environmental and MP factors affected almost all components of beta diversity, particularly in cold water and sediment, with impacts on nestedness of 0.17 and 0.12, respectively, and should thus not be ignored. Our findings indicate for the first time that complex MPs significantly influence the assembly of bacterial communities in lake systems. The impact varies across seasons and future warming may exacerbate this effect, rendering it more uncertain and complex., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Climate change is altering species distribution and modifying interactions in microbial communities. Understanding microbial community structure and their interactions is crucial to interpreting ecosystem responses to climate change. Here, we examined the assemblages of stream bacteria and fungi, and the associations between the two groups along elevational gradients in two regions with contrasting precipitation and temperature, that is the Galong and Qilian mountains of the Tibetan Plateau. In the wetter and warmer region, the species richness significantly increased and decreased with elevation for bacteria and fungi, respectively, while were nonsignificant in the drier and colder region. Their bipartite network structure was also different by showing significant increases in connectance and nestedness towards higher elevations only in the wetter and warmer region. In addition, these correlation network structure generally exhibited similar positive association with species richness in the wetter and warmer region and the drier and colder region. In the wetter and warmer region, climatic change along elevation was more important in determining connectance and nestedness, whereas microbial species richness exerted a stronger influence on network structure and robustness in the drier and colder region. These findings indicate substantial forthcoming changes in microbial diversity and network structure in warming climates, especially in wetter and warmer regions on Earth, advancing the understanding of microbial bipartite interactions' response to climate change., (© 2024 John Wiley & Sons Ltd.)

Microbial communities are crucial for water quality and biogeochemical cycling in freshwaters. Microbes secrete extracellular enzymes to decompose organic matter for their needs of nutrients and scarce elements. Yet, there is a lack of knowledge on microbial metabolic limitations in freshwaters, especially in lake sediments. Here, we examined the carbon, nitrogen, and phosphorus-acquiring extracellular enzyme activities and the bacterial and fungal communities of 30 sediments across Xingkai Lake, the largest freshwater lake in Northeast Asia. We further analyzed the microbial metabolic limitations via extracellular enzyme stoichiometry and explored the direct and indirect effects of abiotic and biotic factors on the limitations. We found that microbial metabolisms were primarily limited by phosphorus in Xingkai Lake. For instance, microbial carbon and phosphorus limitations were closely correlated to abiotic factors like water depth, total dissolved solids, sediment total carbon, and conductivity. The metabolic limitations were also affected by biotic factors, such as showing positive relationships with the alpha and beta diversity of bacteria, and with the beta diversity of fungi. In addition, community compositions of bacteria and fungi were mainly correlated to abiotic factors such as total carbon and dissolved organic carbon, respectively. Collectively, microbial metabolic limitations were affected directly or indirectly by abiotic factors and microbial communities. Our findings indicate that microbial metabolic limitations are not only driven by bacteria and fungi but also by abiotic factors such as water depth and total nitrogen, and thus provide empirical evidence for effective management of freshwater lakes under climate warming and intensified human activities., (© 2024. The Author(s).)

Ecological interactions are important for maintaining biodiversity and ecosystem functions. Particularly in stream biofilms, little is known about the distributional patterns of different taxonomic groups and their potential interactions along elevational gradients. Here, we investigated the bacterial and fungal community structures of stream biofilms across elevational gradients on Mount Kilimanjaro, and explored patterns of their distribution, diversity, community structures, and taxa co-occurrence. We found that fungal and bacterial richness were more convergent at higher elevations, while their community structures became significantly more divergent. Inferred network complexity and stability significantly decreased with increasing elevation for fungi, while an opposite trend was observed for bacteria. Further quantitative analyses showed that network structures of bacteria and fungi were more divergent as elevation increased. This pattern was strongly associated with shifts in abiotic factors, such as mean annual temperatures, water PO 4 3- -P, and stream width. By constructing bipartite networks, we showed the fungal-bacterial network to be less redundant, more clustering, and unstable with increasing elevation. Abiotic factors (e.g., temperatures and stream width) and microbial community properties (i.e., structure and composition) significantly explained the dynamic changes in fungal-bacterial network properties. Taken together, this study provides evidence for the interplay of biotic and abiotic factors structuring potential microbial interactions in stream biofilms along a mountainside elevational gradient., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Understanding the environmental and biological mechanisms shaping latitudinal patterns in microbial diversity is challenging in the field of ecology. Although multiple hypotheses have been proposed to explain these patterns, a consensus has rarely been reached. Here, we conducted a large-scale field survey and microcosm experiments to investigate how environmental heterogeneity and putative trophic interactions (exerted by protist-bacteria associations and T4-like virus-bacteria associations) affect soil bacterial communities along a latitudinal gradient. We found that the microbial latitudinal diversity was kingdom dependent, showing decreasing, clumped, and increasing trends in bacteria, protists, and T4-like viruses, respectively. Climatic and edaphic drivers played predominant roles in structuring the bacterial communities; the intensity of the climatic effect increased sharply from 30°N to 32°N, whereas the intensity of the edaphic effect remained stable. Biotic associations were also essential in shaping the bacterial communities, with protist-bacteria associations showing a quadratic distribution, whereas virus-bacteria associations were significant only at high latitudes. The microcosm experiments further revealed that the temperature component, which is affiliated with climate conditions, is the primary regulator of trophic associations along the latitudinal gradient. Overall, our study highlights a previously underestimated mechanism of how the putative biotic interactions influence bacterial communities and their response to environmental gradients., (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)

Species attributes such as abundance and traits are important determinant components for ecosystem functions (EFs), while their influences on distinct functions remain understudied. Here, we linked 753 treehole bacterial communities to two distinct types of EFs, including the three broad functions of respiration, metabolic activity and cell yield and the four narrow functions related to specific organic matter degradation. Towards high occurrence of phylotypes or traits, the dependency of broad EFs on species abundance or traits increased, whereas the dependency of narrow functions decreased. Among the immense number of bacterial phylotypes, the relative abundance of only 5.05% of phylotypes (that is, 542 phylotypes), but accounting for 68.60% of total abundance, were significantly related to both distinct EFs ranging from 2 to 7 functions, the level of which was used to quantify species functional generality. Such 'low species number, high relative abundance and strong functional generality' features for these 542 phylotypes could be further potentially linked to their enriched functional genes involved in cellular processes including nutrient acquisition, environmental adaptation and cell growth. Our study highlights the key role of a handful of microbial species in determining and anticipating distinct EFs by explicitly considering their abundance and trait attributes., (© 2021 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Microbial elevational diversity patterns have been extensively studied, but their shaping mechanisms remain to be explored. Here, we examined soil bacterial and fungal diversity and community compositions across a 3.4 km elevational gradient (consists of five elevations) on Mt. Kilimanjaro located in East Africa. Bacteria and fungi had different diversity patterns across this extensive mountain gradient-bacterial diversity had a U shaped pattern while fungal diversity monotonically decreased. Random forest analysis revealed that pH (12.61% importance) was the most important factor affecting bacterial diversity, whereas mean annual temperature (9.84% importance) had the largest impact on fungal diversity, which was consistent with results obtained from mixed-effects model. Meanwhile, the diversity patterns and drivers of those diversity patterns differ among taxonomic groups (phyla/classes) within bacterial or fungal communities. Taken together, our study demonstrated that bacterial and fungal diversity and community composition responded differently to climate and edaphic properties along an extensive mountain gradient, and suggests that the elevational diversity patterns across microbial groups are determined by distinct environmental variables. These findings enhanced our understanding of the formation and maintenance of microbial diversity along elevation, as well as microbial responses to climate change in montane ecosystems., (© 2020 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Understanding the role of climatic variation on biodiversity is of chief importance due to the ongoing biodiversity loss and climate change. Freshwaters, one of the most threatened ecosystems in the world, offer a valuable context to study biodiversity patterns of distinct organism groups in relation to climatic variation. In the Tibetan Plateau biodiversity hotspot - Hengduan Mountain region, we studied the effects of climate and local physico-chemical factors on stream microorganisms (i.e. bacteria) and macroorganisms (i.e. macroinvertebrates) in two parallel catchments with contrasting precipitation and temperature, that is, the Nujiang and Lancang Rivers. Diversities and community structures were better explained by climatic and local environmental variables in the drier and colder catchment and at higher elevations, than in the warmer and wetter conditions and at lower elevations. This suggests that communities may be more strongly assembled by deterministic processes in the former, comparatively harsher conditions, compared to the latter, more benign conditions. Macroinvertebrates were more strongly affected by climatic and local environmental factors compared to bacteria, but the diversities and community structures of the two groups showed spatially similar responses to overall abiotic variation, being especially evident with their community structures' responses to climate. Furthermore, bacterial and macroinvertebrate diversities were positively correlated in the drier and colder catchment, implying that these biologically and ecologically distinct organism groups are likely to be driven by similar processes in areas with such climatic conditions. We conclude that changes in climatic and local environmental conditions may affect the diversity of macroorganisms more strongly than that of microorganisms, at least in subtropical mountainous stream ecosystems studied here, but simultaneous responses of both groups to environmental changes can also be expected., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Taihu Lake is one of the largest freshwater lakes in China and serves as an important source for drinking water. This lake is suffering from eutrophication, cyanobacterial blooms and fecal pollution, and the inflow Tiaoxi River is one of the main contributors. The goal here was to characterize the bacterial community structure of Tiaoxi River water by next-generation sequencing (NGS), paying attention to bacteria that are either fecal-associated or pathogenic, and to examine the relationship between environmental parameters and bacterial community structure. Water samples collected from 15 locations in three seasons, and fecal samples collected from different hosts and wastewater samples were used for bacterial community analysis. The phyla Proteobacteria, Actinobacteria, Bacteroidetes, and Cyanobacteria were predominant in most of the water samples tested. In fecal samples, Bacteroidetes, Firmicutes, and Proteobacteria were abundant, while wastewater samples were dominated by Proteobacteria, Bacteroidetes, Acidobacteria, and Chloroflexi. The cluster analysis and principal coordinate analysis indicated that bacterial community structure was significantly different between water, fecal and sewage samples. Shared OTUs between water samples and chicken, pig, and human fecal samples ranged from 4.5 to 9.8% indicating the presence of avian, pig and human fecal contamination in Tiaoxi River. At genus level, five bacterial genera of fecal origin and sequences of seven potential pathogens were detected in many locations and their presence was correlated well with the land use pattern. The sequencing data revealed that Faecalibacterium could be a potential target for human-associated microbial source-tracking qPCR assays. Our results suggest that pH, conductivity, and temperature were the main environmental factors in shaping the bacterial community based on redundancy analysis. Overall, NGS is a valuable tool for preliminary investigation of environmental samples to identify the potential human health risk, providing specific information about fecal and potentially pathogenic bacteria that can be followed up by specific methods., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Urbanization is increasing worldwide and is happening at a rapid rate in China in line with economic development. Urbanization can lead to major changes in freshwater environments through multiple chemical and microbial contaminants. We assessed the impact of urbanization on physicochemical characteristics and microbial loading in canals in Suzhou, a city that has experienced rapid urbanization in recent decades. Nine sampling locations covering three urban intensity classes (high, medium and low) in Suzhou were selected for field studies and three locations in Huangshan (natural reserve) were included as pristine control locations. Water samples were collected for physicochemical, microbiological and molecular analyses. Compared to medium and low urbanization sites, there were statistically significant higher levels of nutrients and total and thermotolerant coliforms (or fecal coliforms) in highly urbanized locations. The effect of urbanization was also apparent in the abundances of human-associated fecal markers and bacterial pathogens in water samples from highly urbanized locations. These results correlated well with land use types and anthropogenic activities at the sampling sites. The overall results indicate that urbanization negatively impacts water quality, providing high levels of nutrients and a microbial load that includes fecal markers and pathogens.

Microbial biogeography is gaining increasing attention due to recent molecular methodological advance. However, the diversity patterns and their environmental determinants across taxonomic scales are still poorly studied. By sampling along an extensive elevational gradient in subarctic ponds of Finland and Norway, we examined the diversity patterns of aquatic bacteria and fungi from whole community to individual taxa across taxonomic coverage and taxonomic resolutions. We further quantified cross-phylum congruence in multiple biodiversity metrics and evaluated the relative importance of climate, catchment and local pond variables as the hierarchical drivers of biodiversity across taxonomic scales. Bacterial community showed significantly decreasing elevational patterns in species richness and evenness, and U-shaped patterns in local contribution to beta diversity (LCBD). Conversely, no significant species richness and evenness patterns were found for fungal community. Elevational patterns in species richness and LCBD, but not in evenness, were congruent across bacterial phyla. When narrowing down the taxonomic scope towards higher resolutions, bacterial diversity showed weaker and more complex elevational patterns. Taxonomic downscaling also indicated a notable change in the relative importance of biodiversity determinants with stronger local environmental filtering, but decreased importance of climatic variables. This suggested that niche conservatism of temperature preference was phylogenetically deeper than that of water chemistry variables. Our results provide novel perspectives for microbial biogeography and highlight the importance of taxonomic scale dependency and hierarchical drivers when modelling biodiversity and species distribution responses to future climatic scenarios., (© 2018 John Wiley & Sons Ltd.)

Range size is invariably limited and understanding range size variation is an important objective in ecology. However, microbial range size across geographical gradients remains understudied, especially on mountainsides. Here, the patterns of range size of stream microbes (i.e., bacteria and diatoms) and macroorganisms (i.e., macroinvertebrates) along elevational gradients in Asia and Europe were examined. In bacteria, elevational range size showed non-significant phylogenetic signals. In all taxa, there was a positive relationship between niche breadth and species elevational range size, driven by local environmental and climatic variables. No taxa followed the elevational Rapoport's rule. Climate variability explained the most variation in microbial mean elevational range size, whereas local environmental variables were more important for macroinvertebrates. Seasonal and annual climate variation showed negative effects, while daily climate variation had positive effects on community mean elevational range size for all taxa. The negative correlation between range size and species richness suggests that understanding the drivers of range is key for revealing the processes underlying diversity. The results advance the understanding of microbial species thermal barriers by revealing the importance of seasonal and diurnal climate variation, and highlight that aquatic and terrestrial biota may differ in their response to short- and long-term climate variability., (© 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.)

The spatial structure and underlying assembly mechanisms of bacterial communities have been studied widely across aquatic systems, focusing primarily on isolated sites, such as different lakes, ponds and streams. Here, our main aim was to determine the underlying mechanisms for bacterial biofilm assembly within a large, highly connected lake system in Northern Finland using associative methods based on taxonomic and phylogenetic alpha- and beta-diversity and a large number of abiotic and biotic variables. Furthermore, null model approaches were used to quantify the relative importance of different community assembly processes. We found that spatial variation in bacterial communities within the lake was structured by different assembly processes, including stochasticity, species sorting and potentially even dispersal limitation. Species sorting by abiotic environmental conditions explained more of the taxonomic and particularly phylogenetic turnover in community composition compared with that by biotic variables. Finally, we observed clear differences in alpha diversity (species richness and phylogenetic diversity), which were to a stronger extent determined by abiotic compared with biotic factors, but also by dispersal effects. In summary, our study shows that the biodiversity of bacterial biofilm communities within a lake ecosystem is driven by within-habitat gradients in abiotic conditions and by stochastic and deterministic dispersal processes.

The distribution patterns of bacterial communities along elevational gradients remain unexplored in aquatic ecosystems. This study investigated the diversity and community composition of bacteria in the sediments of lakes along a mountainside elevational gradient from 525 to 4 490 m in western China. The bacterial alpha diversity (taxonomic richness and phylogenetic diversity) at different sediment depths decreased monotonically with the increasing elevation, and the beta diversity (dissimilarity between lakes) increased significantly with the increasing elevation distance. Both elevation and chemical variables including pH and carbon/nitrogen ratio were identified as major factors affecting the bacterial diversity. Especially, bacterial alpha/beta diversity was significantly related to both chemical and elevational gradients in the surface sediments, whereas elevation overwhelmed chemical factors in influencing the bacterial alpha/beta diversity in the subsurface sediments. Phylogenetic structure analysis demonstrated that environmental filtering was the most important process affecting the bacterial community assembly along the elevational gradient, and the strength of environmental filtering increased towards high elevations. In summary, we observed for the first time a monotonically decreasing elevational pattern in bacterial diversity of freshwater lake sediments, which is mainly driven by elevation associated environmental factors., (© 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Climate change and anthropogenic factors can alter biodiversity and can lead to changes in community structure and function. Despite the potential impacts, no long-term records of climatic influences on microbial communities exist. The Tibetan Plateau is a highly sensitive region that is currently undergoing significant alteration resulting from both climate change and increased human activity. Ice cores from glaciers in this region serve as unique natural archives of bacterial abundance and community composition, and contain concomitant records of climate and environmental change. We report high-resolution profiles of bacterial density and community composition over the past half century in ice cores from three glaciers on the Tibetan Plateau. Statistical analysis showed that the bacterial community composition in the three ice cores converged starting in the 1990s. Changes in bacterial community composition were related to changing precipitation, increasing air temperature and anthropogenic activities in the vicinity of the plateau. Collectively, our ice core data on bacteria in concert with environmental and anthropogenic proxies indicate that the convergence of bacterial communities deposited on glaciers across a wide geographical area and situated in diverse habitat types was likely induced by climatic and anthropogenic drivers., (© 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Background: As the largest low-latitude permafrost region, the Tibetan Plateau (TP) is an important part of the earth's terrestrial ecosystem and one of the most vulnerable areas to climate change and human activities. However, to the best of our knowledge, the bacterial communities in TP soils and their roles in biogeochemical cycles remain limited., Results: In this study, we report the bacterial community structure and function as well as their correlation with environmental factors in TP major ecosystems (farmland, alpine meadow and oligosaline lake) by using metagenomic approaches. Compared with other soil samples in various environments, TP soils share a core set of microorganisms with a distinct abundance and composition. Among TP soil samples, the taxonomic and functional composition of bacterial communities among the upper (3-5 cm) and lower (18-20 cm) soils of farmland sites were highly similar, whereas the dissimilarities within alpine meadow samples were significantly greater than among farmland samples. A similar pattern was observed in elements cycles and pathways associated with adaption to environment and land use types. Canonical correlation analysis revealed that the bacterial communities in most of farmland and alpine meadow soil samples were also significantly correlated with geogenic variables. Specifically, the root-nodule bacteria are negatively correlated with the soil moisture and pH, while Thiobacillus associated with sulfur cycles show potential responses to low temperature and intense UV radiation., Conclusions: These findings indicate that the bacterial community structure and functions in TP soils were influenced by both human activities and soil environmental properties, and that the bacterial communities appeared to be more homogenized in the farmland soils compared with pristine alpine meadows.

The processes underlying the phylogenetic structure of the biotic communities are typically scale-dependent and thus often poorly resolved. Illustrated by the study of macroorganisms, it is suggested that the relative influence of ecological processes on the phylogenetic structure of the communities can be inferred by the geographical definition of the species pools. However, given the high dispersal ability of microbes, the spatial delineation of the species pool may not be that practical for microbial taxa. This idea is supported by the observational data on bacteria along an elevational gradient. Significant negative values of standardized effect size of the mean nearest taxon distance were consistently observed for different sized species pools considered. Reviewing the reports on microbial phylogenetic structure so far, we suggested that the 'habitat species pools' are perhaps more important for microbes than spatial delineated 'regional species pools'., (© 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.)

It is widely accepted that biodiversity is lower in more extreme environments. In this study, we sought to determine whether this trend, well documented for macroorganisms, also holds at the microbial level for bacteria. We used denaturing gradient gel electrophoresis (DGGE) with phylum-specific primers to quantify the taxon richness (i.e., the DGGE band numbers) of the bacterioplankton communities of 32 pristine Tibetan lakes that represent a broad salinity range (freshwater to hypersaline). For the lakes investigated, salinity was found to be the environmental variable with the strongest influence on the bacterial community composition. We found that the bacterial taxon richness in freshwater habitats increased with increasing salinity up to a value of 1‰. In saline systems (systems with >1‰ salinity), the expected decrease of taxon richness along a gradient of further increasing salinity was not observed. These patterns were consistently observed for two sets of samples taken in two different years. A comparison of 16S rRNA gene clone libraries revealed that the bacterial community of the lake with the highest salinity was characterized by a higher recent accelerated diversification than the community of a freshwater lake, whereas the phylogenetic diversity in the hypersaline lake was lower than that in the freshwater lake. These results suggest that different evolutionary forces may act on bacterial populations in freshwater and hypersaline lakes on the Tibetan Plateau, potentially resulting in different community structures and diversity patterns.

Although organic-aggregate-associated bacteria play a pivotal role in microbial food webs and in the cycling of major elements, their community composition and diversity have not been extensively studied, especially in shallow freshwater systems. This study is among the first to explore intra-lake horizontal heterogeneity of organic-aggregate-associated bacterial community composition (OABC) in the large, shallow, and eutrophic Lake Taihu. During November 2006, samples were collected at four locations representing different trophic states and food web structures. Regional variability of OABC and diversity were studied by amplified ribosomal DNA restriction analysis and comparative analysis of four large 16S ribosomal RNA clone libraries. Our results demonstrate that OABC were numerically dominated by members of the beta-proteobacteria (19.2-38.6%), Bacteroidetes (3.6-20.0%), and alpha-proteobacteria (11.5-19.2%) groups. The dominance of the Bacteroidetes group was related to algae-based aggregates. Horizontal heterogeneity of OABC exists within habitats, suggesting that the trophic state of the water and the physicochemical properties of organic aggregates (OA) play a key role. Diverse bacterial communities found on OA were substantially different from free-living ones. Comparative statistical analyses of the habitats of OA-associated bacteria highlight the potential ecological importance of the exchange between OABC and the surrounding planktonic community. Lastly, we found at least 45% of sequences closely related to ones previously found in soils, sludge, sediments, and other habitats. This demonstrates that microorganisms from terrestrial and sediment habitats are an important component of OA.

While there have been a vast number of studies on bacterial alpha diversity in the shallow terrestrial subsurface, beta diversity - how the bacterial community composition changes with spatial distance - has received surprisingly limited attention. Here, bacterial beta diversity and its controlling factors are investigated by denaturing gradient gel electrophoresis and cloning of samples from a 700-cm-long sediment core, the lower half of which consisted of marine-originated sediments. According to canonical correspondence analysis with variation partitioning, contemporary environmental variables explain beta diversity in a greater proportion than depth. However, we also found that community similarity decayed significantly with spatial distance and the slopes of the distance-decay relationships are relatively high. The high beta diversity indicates that the bacterial distribution patterns are not only controlled by contemporary environments, but also related to historical events, that is, dispersal or depositional history. This is highlighted by the different beta diversity patterns among studied sediment layers. We thus conclude that the high beta diversity in the shallow terrestrial subsurface is a trade-off between historical events and environmental heterogeneity. Furthermore, we suggest that the high beta diversity of bacteria is likely to be recapitulated in other terrestrial sites because of the great frequency of high geochemical and/or historical variations along depth.

Although biodiversity and ecosystem functions are strongly shaped by contemporary environments, such as climate and local biotic and abiotic attributes, relatively little is known about how they depend on long-term geological processes. Here, along a 3000-m elevational gradient with tectonic faults on the Tibetan Plateau (that is, Galongla Mountain in Medog County, China), we study the joint effects of geological and contemporary environments on biological communities, such as the diversity and community composition of plants and soil bacteria, and ecosystem functions. We find that these biological communities and ecosystem functions generally show consistent elevational breakpoints at 2000-2800 m, which coincide with Indus-Yalu suture zone fault and are similar to the elevational breakpoints of soil bacteria on another mountain range 1000 km away. Mean annual temperature, soil pH and moisture are the primary contemporary determinants of biodiversity and ecosystem functions, which support previous findings. However, compared with the models excluding geological processes, inclusion of geological effects, such as parent rock and weathering, increases 67.9 and 35.9% of the explained variations in plant and bacterial communities, respectively. Such inclusion increases 27.6% of the explained variations in ecosystem functions. The geological processes thus provide additional links to ecosystem properties, which are prominent but show divergent effects on biodiversity and ecosystem functions: parent rock and weathering exert considerable direct effects on biodiversity, whereas indirectly influence ecosystem functions via interactions with biodiversity and contemporary environments. Thus, the integration of geological processes with environmental gradients could enhance our understanding of biodiversity and, ultimately, ecosystem functioning across different climatic zones.

To further understand the diversity and dynamics of SRB in response to substrate amendment, we sequenced genes coding for the dissimilatory sulfite reductase (dsrA) in groundwater samples collected after an emulsified vegetable oil (EVO) amendment, which sustained U(VI)-reducing conditions for one year in a fast-flowing aquifer. EVO amendment significantly altered the composition of groundwater SRB communities. Sequences having no closely related-described species dominated (80%) the indigenous SRB communities in nonamended wells. After EVO amendment, Desulfococcus, Desulfobacterium, and Desulfovibrio, known for long-chain-fatty-acid, short-chain-fatty-acid and H2 oxidation and U(VI) reduction, became dominant accounting for 7 ± 2%, 21 ± 8%, and 55 ± 8% of the SRB communities, respectively. Succession of these SRB at different bioactivity stages based on redox substrates/products (acetate, SO4-2, U(VI), NO3-, Fe(II), and Mn(II)) was observed. Desulfovibrio and Desulfococcus dominated SRB communities at 4-31 days, whereas Desulfobacterium became dominant at 80-140 days. By the end of the experiment (day 269), the abundance of these SRB decreased but the overall diversity of groundwater SRB was still higher than non-EVO controls. Up to 62% of the SRB community changes could be explained by groundwater geochemical variables, including those redox substrates/products. A significant (P < 0.001) correlation was observed between groundwater U(VI) concentrations and Desulfovibrio abundance. Our results showed that the members of SRB and their dynamics were correlated significantly with slow EVO biodegradation, electron donor production and maintenance of U(VI)-reducing conditions in the aquifer.

Knowledge about elevational β diversity patterns and processes is limited for microorganisms, especially in sensitive aquatic ecosystems at high latitudes. Our aim is to investigate elevational β diversity patterns and underlying assembly processes for three biofilm microbial groups in subarctic freshwater ponds.We sampled 89 ponds covering an elevational gradient from 10 to 1038 m above sea level in subarctic Finland and Norway. The microbial groups studied included benthic diatoms, cyanobacteria, and bacteria (i.e., bacteria other than cyanobacteria). We expected to find elevational distance decay in community similarity, driven primarily by variation in the local environment. We further tested whether the level of β diversity decreased towards higher elevations, and whether the relative influence of deterministic and stochastic processes on community assembly changed along the elevational gradient, with increasing effect of deterministic processes at higher elevations under more extreme environmental conditions. As statistical methods, we used generalised dissimilarity modelling, Mantel tests, and a null model with Raup–Crick dissimilarities.For all microbial groups, community dissimilarities increased with increasing environmental or elevational distances. The pure effects of environment were significant for all groups, and pH was the most important variable affecting community dissimilarities. Mean community dissimilarities generally decreased with elevation for all microbial groups. The communities were influenced by both deterministic and stochastic processes, the former of which was stronger towards higher elevations. The influence of deterministic processes was strongest for bacteria. Generally, the communities under deterministic control were more similar to each other than expected by chance.Elevational β diversity patterns of subarctic pond microorganisms primarily reflected environmental effects, showing decreasing β diversity towards high elevations owing to stronger environmental filtering. The relative effects of deterministic or stochastic assembly processes varied among microbial groups, highlighting the need for including multiple groups when studying biodiversity patterns and underlying ecological processes. [ABSTRACT FROM AUTHOR]

Islands provide ideal model systems to examine the factors influencing biodiversity, yet knowledge of microbial biodiversity on islands remains scarce. We collected a dataset from 101 rock pools along a freshwater to brackish water transition on islands of the Baltic Sea and investigated the patterns and drivers of community composition and species richness of diatoms, cyanobacteria and non-cyanobacteria bacteria among islands. We also examined whether environmental heterogeneity increased beta diversity and species richness within islands. Among islands, the patterns in community composition were concordant among the microbial groups, with distinct changes along the freshwater–brackish gradient. The patterns in species richness were context-dependent for each microbial group. In general, richness patterns were most strongly associated with nutrient concentrations or the distances to potential sources of immigrants, whereas no positive relationships between ecosystem size and richness were found. Within islands, environmental heterogeneity was positively correlated with the beta diversity of each microbial group, but not species richness. Our findings provide novel insights into the factors influencing microbial biodiversity. The results suggest that island microbial biodiversity patterns are influenced by species sorting and dispersal-related mechanisms and highlight the importance of environmental heterogeneity for beta diversity. [ABSTRACT FROM AUTHOR]

Aim: Community variation (i.e. beta diversity) along geographical gradients is of substantial interest in ecology and biodiversity reserves in the face of global changes. However, the generality in beta diversity patterns and underlying processes remains less studied across trophic levels and geographical regions. We documented beta diversity patterns and underlying ecological processes of stream bacteria, diatoms and macroinvertebrates along six elevational gradients. Locations: Asia and Europe. Methods: We examined stream communities using molecular and morphological methods. We characterised community uniqueness with local contributions to beta diversity (LCBD), and investigated the drivers of its geographic patterns using Mid‐Domain Effect (MDE), coenocline simulation, Raup‐Crick null model approach, and through comparisons to environmental factors. MDE is a stochastic model by considering species elevational range, while coenocline simulation is a deterministic model by considering species niche optima and tolerance. The null model provides possible underlying mechanisms of community assembly with the degree to which deterministic processes create communities deviating from those of null expectations. Results: Across all taxa, we revealed a general U‐shaped LCBD‐elevation relationship, suggesting higher uniqueness of community composition at both elevational ends. This pattern was confirmed and could be explained by both stochastic and deterministic models, that is, MDE and coenocline simulation, respectively, and was supported by the dominance of species replacement. Temperature was the main environmental factor underlying elevational patterns in LCBD. The generalists with broad niche breadths were key in maintaining community uniqueness, and the higher relative importance of deterministic processes resulted in stronger U‐shaped patterns regardless of taxonomic group. Conclusions: Our synthesis across both mountains and taxonomic groups clearly shows that there are consistent elevational patterns in LCBD among taxonomic groups, and that these patterns are explained by similar ecological mechanisms, producing a more complete picture for understanding and bridging the spatial variation in biodiversity under changing climate. [ABSTRACT FROM AUTHOR]

Water-depth biodiversity gradient, one of the typical biogeographical patterns on Earth, is understudied for bacteria in freshwater ecosystems, and thus left the underlying mechanisms poorly understood especially for benthic bacteria. Here, we investigated the water-depth distribution of surface sediment bacterial phyla and their driving factors in Lake Lugu, a plateau lake in Southwest China. Our results revealed that the relative abundance of 11 dominant bacterial phyla showed various water-depth patterns, such as increasing, decreasing, hump-shaped, and U-shaped patterns. These patterns across phyla were consistent with their different niche positions of water depth, while the occupancy-abundance relationships were not dependent on phylum attributes. Consistently, phylum abundance was best explained by water depth; other physical and chemical factors, such as metal ion concentrations, SiO2, and pH, can also explain the variations in some bacterial phyla. Chemical variables were the main drivers of the dominant bacterial phyla. However, biotic variables also showed substantial importance for some phyla, such as Planctomycetes, Actinobacteria, and WS3. This work could provide new insights into the general water-depth patterns and underlying mechanisms of the relative abundance of bacterial phyla in freshwater ecosystems. [ABSTRACT FROM AUTHOR]

Abstract As bilayer vesicular corpuscles secreted by different living cells, exosomes can be found in diverse body fluids and are rich in lipids, proteins, nucleic acids and other complicated components. Exosomes offer a potent mechanism for participation in intercellular transportation, such as targeted transmission of inclusions to nearby or distant cells or tissues, and assistance in intercellular information communication to change physiological functions and properties. Exosomes take part in antigen presentation for activation of immune cells and stimulate the release of inflammatory factors and the expression of immune molecules, thus modulating the immune responses of host cells. In the microbial infection of host cells, exosomes can strengthen innate and specific immune responses and thereby the immune resistance against the invading microbes through natural killer cells, macrophages and activated T cells by the presentation of pathogens including viral factors and bacteria, but exosomes are also capable of immunosuppression during pathogens infection. Exosomes are considerably valuable in research and clinical defense of microbial infection, given their biological activities in intercellular transportation, information communication and cell-mediated immunity modulation after microbial infection. [ABSTRACT FROM AUTHOR]

Understanding biodiversity patterns and the role of biotic attributes in governing these patterns remains one of the most important challenges in ecology. Here, taking water depth in Lake Lugu as a typical geographical gradient, we studied how these different taxa, that is bacteria, diatoms and chironomids, respond to the water depth and environmental gradients using molecular and morphological methods. We further evaluated the relative importance of water depth, environmental variables and biotic attributes in explaining biological characteristics, such as biomass, species richness, and community composition. The biomass of chironomids and the richness of bacteria and chironomids showed a nonlinearly decreasing pattern associated with increased water depth, while biomass and species richness of diatoms showed U-shaped and hump-shaped patterns, respectively. The three taxonomic groups all showed increasing dissimilarity with water depth changes, and there was clear cross-taxon congruence among the variations in community composition. Abiotic variables were pivotal in structuring biological characteristics; however, the biotic attributes also explained a unique portion of their variations. This suggests that biotic interactions significantly influenced the patterns of biomass, species richness, and community compositions along the water depth gradient for the three taxonomic groups studied. Our results provide new evidence that biotic attributes could help in predicting the biodiversity of aquatic communities along geographical gradients, such as water depth. Unlabelled Image • Biodiversity show clear water-depth patterns, but distinct patterns for diatoms. • Diatoms are U-shaped or hump-shaped, while decreasing for bacteria and chironomids. • There is cross-taxon congruence among community compositions for the three taxa. • Biotic attributes can explain diversity, although environmental filtering is pivotal. [ABSTRACT FROM AUTHOR]

Community variation (i.e., beta diversity) along geographical gradients is a well-known ecological pattern, but the corresponding variation in beta diversity components (e.g., species turnover and nestedness) and underlying drivers remain poorly understood. Based on two alternative approaches (that is, the beta diversity partitioning proposed by Baselga and the Local Contributions to Beta Diversity (LCBD) partitioning proposed by Legendre), we examined the patterns of beta diversity components of lacustrine benthos, from bacteria to diatoms and chironomids, in the surface sediments along a 100-m water-depth gradient in Lugu Lake. We further quantified the relative importance of spatial, environmental and biotic variables in explaining water-depth patterns in beta diversity. Based on the Baselga's framework, there was a taxonomic dependency for the patterns of beta diversity components with water-depth, showing a significant species turnover pattern for bacteria, while diatoms and chironomids showed significant nestedness. This dependency was also evident in the patterns of community uniqueness with water-depth because based on Legendre's framework, the LCBD decreased with water depth for bacteria whereas increased with depth for diatoms. The total beta diversity and species turnover of bacteria could be explained by the pure effects of spatial, environmental and biotic variables. A total of 26.8% and 23.6% of the nestedness component of diatoms and chironomids was explained by environmental variables, respectively, while species turnover was mostly related to spatial variables. Bacteria total LCBD and species replacement were driven only by environmental variables. For diatoms and chironomids, however, most of the total LCBD and its two components were explained by spatial variables, and biotic variables were most important for the diatom replacement component. Our findings provide insights into the mechanisms responsible for community organizations along water-depth gradients from the perspective of beta diversity components. Unlabelled Image • Beta diversity components are taxonomically dependent along water-depth gradients. • Bacteria show depth-decay in turnover, while diatoms or chironomids in nestedness. • Uniqueness decrease towards deep water for bacteria, while increase for diatoms. • Depth is most important for beta diversity components across three organisms. • Biotic and abiotic factors explain beta diversity, while the latter more important. [ABSTRACT FROM AUTHOR]