Interactions between SDBS and Hydrilla verticillata - epiphytic biofilm in wetland receiving STPs effluents: Nutrients removal and epiphytic microbial assembly

The fate and effects of sodium dodecyl benzene sulfonate (SDBS) in sewage treatment plants (STPs) effluents on nutrients and submerged macrophytes are far from clear in wetlands. This study conducted a 24-day experiment to investigate changes in nutrients and epiphytic biofilm of Hydrilla verticillata in wetlands receiving effluents with 0.5, 2 and 5 mg L-1 SDBS. The decrease of SDBS in overlying water followed pseudo-first-order kinetic equation, with over 80 % of SDBS removal achieved. 2 and 5 mg L-1 SDBS decreased nutrient removal efficiency, induced oxidative stress response and damaged cells of H. verticillata. SDBS altered bacterial and eukaryotic community diversity. 0.5 mg L-1 SDBS can promote carbon fixation and methane oxidation of microorganisms. Network analysis revealed that 0.5 mg L-1 SDBS decreased the stability of epiphytic ecosystems. Mantel tests indicated significant influences of SDBS, temperature, and total nitrogen on epiphytic microbial communities.

Assembly and maintenance of phyllosphere microbial diversity during rubber tree leaf senescence

Phyllosphere microorganisms execute important ecological functions including supporting host plant growth, enhancing host resistance to abiotic stresses, and promoting plant diversity. How leaf developmental stages affect plant-microbiome interactions and phyllosphere microbial community assembly and diversity is poorly understood. In this study, we utilized amplicon sequencing of 16S rRNA and ITS genes to investigate the composition and diversity of microbial communities across different leaf developmental stages of rubber trees. Our findings reveal that endophytic microbial communities, particularly bacterial communities, are more influenced by leaf senescence than by epiphytic communities. The high abundance of metabolism genes in the endosphere of yellow leaves contributes to the degradation and nutrient relocation processes. Nutrient loss leads to a higher abundance of α-Proteobacteria (r-selected microorganisms) in the yellow leaf endosphere, thereby promoting stochastic community assembly. As leaves age, the proportion of microorganisms entering the inner layer of leaves increases, consequently enhancing the diversity of microorganisms in the inner layer of leaves. These results offer insights into the mechanisms governing community assembly and diversity of leaf bacteria and fungi, thereby advancing our understanding of the evolving functions of microbial communities during leaf senescence in general, and for an important tropical crop species in particular.

Distinct multitrophic biodiversity composition and community organization in a freshwater lake and a hypersaline lake on the Tibetan Plateau

Alpine lakes play pivotal roles in plateau hydrological processes but are highly sensitive to climate change, yet we lack comprehensive knowledge of their multitrophic biodiversity patterns. Here, we compared the biodiversity characteristics of diverse taxonomic groups across water depths and in surface sediments from a freshwater lake and a hypersaline lake on the northwestern Tibetan Plateau. Using multi-marker environmental DNA metabarcoding, we detected 134 cyanobacteria, 443 diatom, 1,519 invertebrate, and 28 vertebrate taxa. Each group had a substantially different community composition in the two lakes, and differences were also found between water and sediments within each lake. Cooccurrence network analysis revealed higher network complexity, lower modularity, and fewer negative cohesions in the hypersaline lake, suggesting that high salinity may destabilize ecological networks. Our results provide the first holistic view of Tibetan lake biodiversity under contrasting salinity levels and reveal structural differences in the ecological networks that may impact ecosystem resilience.

Elucidating potential bioindicators from insights in the diversity and assembly processes of prokaryotic and eukaryotic communities in the Mekong River

Drivers for spatio-temporal distribution patterns of overall planktonic prokaryotes and eukaryotes in riverine ecosystems are generally not fully understood. This study employed amplicon metabarcoding to investigate the distributions and assembly mechanisms of bacterial and eukaryotic communities in the Mekong River. The prevailing bacteria taxa were found to be Betaproteobacteria, Actinobacteria, and Bacteroidetes, while the dominant eukaryotic organisms were cryptophytes, chlorophytes, and diatoms. The community assemblages were influenced by a combination of stochastic and deterministic processes. Drift (DR) and dispersal limitation (DL), signifying the stochastic mechanism, were the main processes shaping the overall prokaryotic and eukaryotic communities. However, homogeneous selection (HoS), indicating deterministic mechanism, played a major role in the assembly process of core prokaryotic communities, especially in the wet season. In contrast, the core eukaryotic communities including Opisthokonta, Sar, and Chlorophyta were dominated by stochastic processes. The significance of HoS within prokaryotic communities was also found to exhibit a decreasing trend from the upstream sampling sites (Chiang Saen and Chiang Khan, Nong Khai) towards the downstream sites (Mukdahan, and Khong Chiam) of the Mekong River. The environmental gradients resulting from the site-specific variations and the gradual decrease in elevation along the river may have a potential influence on the role of HoS in community assembly. Crucial environmental factors that shape the phylogenetic structure within distinct bins of the core prokaryotic communities including water depth, temperature, chloride, sodium, and sulphate were identified, as inferred by their correlation with the beta Net Relatedness Index (betaNRI) during the wet season. Overall, these findings enhance understanding of the complex mechanisms governing the spatio-temporal dynamics of prokaryotic and eukaryotic communities in the Mekong River. Finally, insights gained from this study could provide information on further use of specific core bacteria as microbial-based bioindicators that are effective for the assessment and conservation of the Mekong River ecosystem.

Lakes-scale pattern of eukaryotic phytoplankton diversity and assembly process shaped by electrical conductivity in central Qinghai-Tibet Plateau

Phytoplankton are the main primary producers in aquatic ecosystems and play an important role in food web and geochemical cycles. Its diversity, community structure, and assembly process are influenced by several factors. Alpine lake ecosystems are relatively weak and extremely sensitive to global climate change. However, the impact of climate change on phytoplankton in Qinghai-Tibet Plateau lakes and their responses are still unclear. In this study, we analyzed the diversity, environmental drivers, and assembly process of phytoplankton community in the central QTP lakes. The phytoplankton of these lakes can be primarily distinguished into freshwater and brackish types, with significant differences in species diversity and community dissimilarity. Both shared nearly same key environmental factors that significantly affecting phytoplankton such as EC, and brackish lakes were also positively correlative with TN. Stochastic process was predominant in phytoplankton assembly. Additionally, freshwater and brackish lakes were dominated by dispersal limitation and heterogeneous selection respectively. Alpine lakes had significant EC thresholds, and their diversity and assembly processes changed significantly around the thresholds. The present findings have important implications for understanding and predicting the response of lake phytoplankton communities to climate change and for making decisions to protect the ecological resources of alpine lakes.

Assembly mechanisms of microbial communities in plastisphere related to species taxonomic types and habitat niches

A lot of plastic floats are presented in the kelp cultivation zone, enabling us to effectively evaluate the differences between surface water (SW) and plastic-attached (PA) microbial communities. In this study, we explored the microbial communities (both bacteria and protists) in SW and PA niches during the kelp cultivation activities. Effects of habitat niches on the diversity and composition of microbial communities were found. Beta partitioning and core taxa analyses showed species turnover and local species pool governed the microbial community assembly, and they contributed more to bacteria and protists, respectively. Based on the results of null model, bacterial communities presented a more deterministic and homogeneous assembly compared to protistan communities. Moreover, microbial communities in PA niche had higher species turnover and homogenizing assembly compared to the SW niche. The results of this study supplemented the theory of microbial community assembly and expanded our understanding of protists in plastisphere.

Bacterial and Microeukaryotic Community Compositions and Their Assembly Processes in Lakes on the Eastern Qinghai-Tibet Plateau

Bacterial and microeukaryotic community compositions and their assembly processes have remained challenging and remained unclear in lake ecosystems on the Qinghai-Tibet Plateau (QTP). We revealed the diversity and community compositions, driving factors, ecological assembly processes, and co-occurrence networks of bacterial and microeukaryotic communities in water bodies of the eight lake ecosystems across the Eastern QTP. The results demonstrated that the predominant bacteria in most samples were Proteobacteria, with an average relative abundance of 41.78%, whereas the most abundant of microeukaryotes differed among the sample sites. The redundancy analysis revealed that latitude and pH were the most important driving factors in shaping the bacterial and microeukaryotic community compositions. Homogeneous selection (56.40%) was the dominant process in assembling the bacterial communities, whereas dispersal limitation (67.24%) was the major process in governing the microeukaryotic communities. Furthermore, dissolved organic carbon and salinity were the major factors mediating the balance of deterministic and stochastic assembly processes in the bacterial and microeukaryotic communities. Both the bacterial and microeukaryotic community co-occurrence networks exhibited topological features of modularity and non-random topological features. The results offer insights into the mechanisms underpinning bacterial and microeukaryotic diversities and communities in the lake ecosystems on the QTP.

Patterns of bacterial distance decay and community assembly in different land-use types as influenced by tillage management and soil layers

Land use and cover change are major factors driving global change and greatly impact terrestrial organisms, especially soil microbial diversity. Little is known, however, about bacterial diversity, distribution patterns and assembly processes across different land use types. In this study, therefore, we conducted a large-scale field survey of 48 sampling sites, encompassing different land use types in Xuancheng city, China, with different degrees of soil disturbance and different soil horizons. The distance-decay relationships (DDRs), assembly processes and the spatial patterns of soil bacterial communities were investigated based on high-throughput sequencing data. We found that the DDRs might be weakened by anthropogenic disturbances, which were not observed in tilled soils, while a decreasing trend was observed along the soil horizon in untilled soils. The relative importance of environmental factors and geographic distance varied with soil tillage. Specifically, bacterial communities in tilled soils were driven by non-spatially autocorrelated environmental factors, while untilled soils were more susceptible to geographic distance. In addition, the heterogeneity of soil properties, as well as the differences in soil bacterial niche width and niche overlap, determined the assembly processes of the bacterial community, resulting in opposite trends along the soil layers in tilled and untilled soils. These findings expand the current understanding of the biogeography of soil bacterial communities across different land use types.

Salinity-triggered homogeneous selection constrains the microbial function and stability in lakes

Climate change and anthropogenic exploitation have led to the gradual salinization of inland waters worldwide. However, the impacts of this process on the prokaryotic plankton communities and their role in biogeochemical cycles in the inland lake are poorly known. Here, we take a space-for-time substitution approach, using 16S rRNA gene amplicon sequencing and metagenomic sequencing. We analyzed the prokaryotic plankton communities of 11 lakes in northwest China, with average water salinities ranging from 0.002 to 14.370%. The results demonstrated that, among the various environmental parameters, salinity was the most important driver of prokaryotic plankton β-diversity (Mantel test, r = 0.53, P < 0.001). (1) Under low salinity, prokaryotic planktons were assembled by stochastic processes and employed diverse halotolerant strategies, including the synthesis and uptake of compatible solutes and extrusion of Na+ or Li+ in exchange for H+. Under elevated salinity pressure, strong homogeneous selection meant that only planktonic prokaryotes showing an energetically favorable halotolerant strategy employing an Mnh-type Na+/H+ antiporter remained. (2) The decreasing taxonomic diversity caused by intense environmental filtering in high-salinity lakes impaired functional diversity related to substance metabolism. The prokaryotes enhanced the TCA cycle, carbon fixation, and low-energy-consumption amino acid biosynthesis in high-salinity lakes. (3) Elevated salinity pressure decreased the negative:positive cohesion and the modularity of the molecular ecology networks for the planktonic prokaryotes, indicating a precarious microbial network. Our findings provide new insights into plankton ecology and are helpful for the protecting of the biodiversity and function of inland lakes against the background of salinization. KEY POINTS: • Increased salinity enhances homogeneous selection in the microbial assembly. • Elevated salinity decreases the microbial co-occurrence networks stability. • High salinity damages the microbial function diversity.

Untangling microbiota diversity and assembly patterns in the world's longest underground culvert water diversion canal

The long-distance underground box culvert water transport system (LUBWT) is a crucial link between the source of drinking water and the consumers. It must ensure the stability of water quality during transportation. However, uncontrollable microbial growth can develop in the water delivery system during the long delivery process, posing a risk to health and safety. Therefore, we applied 16 s and 18 s gene sequence analysis in order to study microbial communities in box culvert waters sampled in 2021, as well as a molecular ecological network-based approach to decipher microbial interactions and stability. Our findings revealed that, in contrast to natural freshwater ecosystems, micro-eukaryotes in LUBWT have complex interactions such as predation, parasitism, and symbiosis due to their semi-enclosed box culvert environment. Total nitrogen may be the primary factor affecting bacterial community interactions in addition to temperature. Moreover, employing stability indicators such as robustness and vulnerability, we also found that microbial stability varied significantly from season to season, with summer having the higher stability of microbial communities. Not only that but also the stability of the micronuclei also varied greatly during water transport, which might also be related to the complex interactions among the micro-eukaryotes. To summarize, our study reveals the microbial interactions and stability in LUBWT, providing essential ecological knowledge to ensure the safety of LUBWT's water quality.

Differential distribution patterns and assembly processes of soil microbial communities under contrasting vegetation types at distinctive altitudes in the Changbai Mountain

Diversity patterns and community assembly of soil microorganisms are essential for understanding soil biodiversity and ecosystem processes. Investigating the impacts of environmental factors on microbial community assembly is crucial for comprehending the functions of microbial biodiversity and ecosystem processes. However, these issues remain insufficiently investigated in related studies despite their fundamental significance. The present study aimed to assess the diversity and assembly of soil bacterial and fungal communities to altitude and soil depth variations in mountain ecosystems by using 16S and ITS rRNA gene sequence analyses. In addition, the major roles of environmental factors in determining soil microbial communities and assembly processes were further investigated. The results showed a U-shaped pattern of the soil bacterial diversity at 0-10  cm soil depth along altitudes, reaching a minimum value at 1800 m, while the fungal diversity exhibited a monotonically decreasing trend with increasing altitude. At 10-20  cm soil depth, the soil bacterial diversity showed no apparent changes along altitudinal gradients, while the fungal Chao1 and phylogenetic diversity (PD) indices exhibited hump-shaped patterns with increasing altitude, reaching a maximum value at 1200 m. Soil bacterial and fungal communities were distinctively distributed with altitude at the same depth of soil, and the spatial turnover rates in fungi was greater than in bacteria. Mantel tests suggested soil physiochemical and climate variables significantly correlated with the β diversity of microbial community at two soil depths, suggesting both soil and climate heterogeneity contributed to the variation of bacterial and fungal community. Correspondingly, a novel phylogenetic null model analysis demonstrated that the community assembly of soil bacterial and fungal communities were dominated by deterministic and stochastic processes, respectively. The assembly processes of bacterial community were significantly related to the soil DOC and C:N ratio, while the fungal community assembly processes were significantly related to the soil C:N ratio. Our results provide a new perspective to assess the responses of soil microbial communities to variations with altitude and soil depth.

Distribution patterns and community assembly processes of eukaryotic microorganisms along an altitudinal gradient in the middle reaches of the Yarlung Zangbo River

Eukaryotic microorganisms play an important role in the biogeochemical cycles of rivers. Dynamic hydrological processes in rivers are thought to influence the assembly processes of eukaryotic microbes, as well as affecting local geomorphology. These processes have not been extensively studied for eukaryotic river microbes in extreme environments on the Tibetan Plateau. This study used 18S rDNA gene amplification sequencing, a neutral community model, and a null model to analyze the spatial and temporal dynamics and assembly processes of eukaryotic microbial communities in the middle reaches of the Yarlung Zangbo River. We conducted analyses across wet and dry seasons, as well as varying altitudinal gradients. Our results showed that the diversity, structure, and taxonomic composition of eukaryotic microbial communities varied more with altitude than season, and the diversity of the communities first increased, then decreased, with increasing elevation. Distance-decay analysis showed that the correlation between eukaryotic microbial communities and environmental distance was stronger than the correlation between the microbial communities and geographical distance. Deterministic processes (homogeneous selection) dominated the construction of eukaryotic microbial communities, and water temperature, pH, and total phosphorus were the primary environmental factors that influenced the construction of eukaryotic microbial communities. These results expand our understanding of the characteristics of eukaryotic microbial communities in rivers on the Tibetan Plateau and provide clues to understanding the mechanisms that maintain eukaryotic microbial diversity in extreme environments.

Environmental DNA sequencing reveals the regional difference in diversity and community assembly mechanisms of eukaryotic plankton in coastal waters

The diversity and community assembly mechanisms of eukaryotic plankton in coastal waters is so far not clear. In this study, we selected the coastal waters of Guangdong-Hong Kong-Macao Greater Bay Area, which is a highly developed region in China, as the research area. By use of high-throughput sequencing technologies, the diversity and community assembly mechanisms of eukaryotic marine plankton were studied in which a total of 7,295 OTUs were obtained, and 2,307 species were annotated by doing environmental DNA survey of 17 sites consist of surface and bottom layer. Ultimately, the analysis reveals that the species abundance of bottom layer is, by and large, higher than that in the surface layer. In the bottom, Arthropoda is the first largest group, accounting for more than 20% while Arthropoda and Bacillariophyta are dominant groups in surface waters accounting for more than 40%. It is significant of the variance in alpha-diversity between sampling sites, and the difference of alpha-diversity between bottom sites is greater than that of surface sites. The result suggests that the environmental factors that have significant influence on alpha-diversity are total alkalinity and offshore distance for surface sites, and water depth and turbidity for bottom sites. Likewise, the plankton communities obey the typical distance-decay pattern. Analysis about community assembly mechanisms reveals that, overall, dispersal limitation is the major pattern of community formation, which accounts for more than 83% of the community formation processes, suggesting that stochastic processes are the crucial assembly mechanism of the eukaryotic plankton community in the study area.

Ecological processes differ in community assembly of Archaea, Bacteria and Eukaryotes in a biogeographical survey of groundwater habitats in the Quebec region (Canada)

Aquifers are inhabited by microorganisms from the three major domains of life: Archaea, Eukaryotes and Bacteria. Although interest in the processes that govern the assembly of these microbial communities is growing, their study is almost systematically limited to one of the three domains of life. Archaea, Bacteria and Eukaryotes are however interconnected and essential to understand the functioning of their living ecosystems. We, therefore, conducted a spatial study of the distribution of microorganisms by sampling 35 wells spread over an area of 10,000 km² in the Quebec region (Canada). The obtained data allowed us to define the impact of geographic distance and geochemical water composition on the microbial communities. A null model approach was used to infer the relative influence of stochastic and determinist ecological processes on the assembly of the microbial community from all three domains. We found that the organisms from these three groups are mainly governed by stochastic mechanisms. However, this apparent similarity does not reflect the differences in the processes that govern the phyla assembly. The results obtained highlight the importance of considering all the microorganisms without neglecting their individual specificities.

Depth induced assembly discrepancy of multitrophic microbial communities affect microbial nitrogen transformation processes in river cross-sections

Understanding how the structures and functions of bacterial and microeukaryotic communities vary within cross-sections will improve managements aimed at restoring river ecological functions. However, no comprehensive investigation has examined how microbial community characteristics vary within cross-sections, which makes the accurate calculation and prediction of microbial metabolic processing of substances in rivers difficult. Here, the distributions, co-occurrence networks, and assemblies of bacterial and microeukaryotic communities and their feedback to nitrogen transformation in cross-sections of the Yangtze River were studied by coupling ecological theory, biogeochemistry, and DNA meta-barcoding methods. The study found that depth in cross-sections was the primary driving factor regulating the composition of sediment bacterial and microeukaryotic communities. Co-occurrence network analysis indicated that the effect of bacteria on the co-occurrence network decreased and the network become more simplified and instability with depth in river cross-sections. Quantified using the β-nearest taxon index, the H2 layer sediment (depth 10-20 m) displayed the largest variation in selection processes for microbial assemblies, while homogeneous selection and homogenizing dispersal contributed most to the bacterial and microeukaryotic assemblies in the H3 layer (depth >20 m). Cross-sectional depth and denitrification genes had a significant quadratic correlation, with the highest microbial nitrogen-removal potential occurring in the H2 layer sediment. Structural equation models showed that the sediment nitrogen distributions were regulated by distinct environmental pathways at different depths, and that the H2 layer sediment was primary driven by bacterial community. In this layer, river cross-sectional depth influenced nitrogen transformation by regulating the distribution of sediment particle sizes, which then influenced the assembly of the multitrophic microbial communities. This study will improve river management by clarifying the importance of cross-sectional depth to the ecological function of rivers.

Environmental factors and stochasticity affect the fungal community structures in the water and sediments of Hulun Lake, China

Aquatic fungi form both morphologically and ecologically diverse communities. However, lake ecosystems are frequently overlooked as fungal habitats, despite the potentially important role of fungi in matter cycling and energy flow. Hulun Lake is a typical example of a seasonal glacial lake; however, previous studies have only focused on bacteria in this ecosystem. Therefore, in the current study, internal transcribed spacer ribosomal RNA (ITS rRNA) gene high-throughput sequencing was used to investigate the fungal communities in paired water and sediment samples from the Hulun Lake Basin in China. A significant difference was found between the fungal communities of the two sample types. Across all samples, we identified nine phyla, 30 classes, 78 orders, 177 families, and 307 genera. The dominant phyla in the lake were Ascomycota, Basidiomycota and Chytridiomycota. Our results show that both water and sediments have very high connectivity, are dominated by positive interactions, and have similar interaction patterns. The fungal community structures were found to be significantly affected by environmental factors (temperature, chemical oxygen demand, electrical conductivity, total phosphorus, and pH). In addition, the dispersal limitations of the fungi affected the structure of the fungal communities, and it was revealed that stochasticity is more important than deterministic mechanisms in influencing the structure and function of fungal communities. This study provides unique theoretical support for the study of seasonally frozen lake fungal communities and a scientific basis for the future management and protection of Hulun Lake.

Contrasting assembly mechanisms explain the biogeographic patterns of benthic bacterial and fungal communities on the Tibetan Plateau

The Tibetan Plateau characterized by high altitude and low temperature, where a great number of lakes are located, is a hotspot of global biodiversity research. Both bacterial and fungal communities are vital participants of biogeochemical cycling in lake ecosystems. However, we know very little about the large-scale biogeographic patterns and the underlying assembly mechanisms of lake benthic microbial communities on the Tibetan Plateau. To investigate the biogeographic patterns and their underlying assembly mechanisms of benthic bacterial and fungal communities, we collected sediment samples from 11 lakes on the Tibetan Plateau (maximum geographic distance between lakes over 1100 km). Benthic community diversity and composition were determined using the high-throughput sequencing technique. Our results indicated that there were contrasting distance-decay relationships between benthic bacterial and fungal communities on a regional scale. Benthic bacterial communities showed a significant distance-decay relationship, whereas no significant relationship was observed for benthic fungal communities. Deterministic processes dominated the bacterial community assembly, whereas fungal community assembly was more stochastic. pH was a dominant factor in influencing the geographic distribution of benthic microbial communities. Co-occurrence network analysis revealed that bacterial communities showed higher complexity and greater stability than those of the fungal communities. Taken together, this study contributes to a novel understanding of the assembly mechanisms underlying the biogeographic distribution of plateau benthic bacterial and fungal communities at a large scale.

Untangling microbial diversity and assembly patterns in rare earth element mine drainage in South China

Ion-adsorption rare earth element (REE) deposits are the main reservoirs of REEs worldwide, and are widely exploited in South China. Microbial diversity is essential for maintaining the performance and function of mining ecosystems. Investigating the ecological patterns underlying the REE mine microbiome is essential to understand ecosystem responses to environmental changes and to improve the bioremediation of mining areas. We applied 16S rRNA and ITS gene sequence analyses to investigate the composition characteristics of prokaryotic (bacteria, archaea) and fungal communities in a river impacted by REE acid mine drainage (REE-AMD). The river formed a unique micro-ecosystem, including the main prokaryotic taxa of Proteobacteria, Acidobacteria, Crenarchaeota, and Euryarchaeota, as well as the main fungal taxa of Ascomycota, Basidiomycota, and Chytridiomycota. Analysis of microbial diversity showed that, unlike prokaryotic communities that responded drastically to pollution disturbances, fungal communities were less affected by REE-AMD, but fluctuated significantly in different seasons. Ecological network analysis revealed that fungal communities have lower connectivity and centrality, and higher modularity than prokaryotic networks, indicating that fungal communities have more stable network structures. The introduction of REE-AMD mainly reduced the complexity of the community network and the number of keystone species, while the proportion of negative prokaryotic-fungal associations in the network increased. Ecological process analysis revealed that, compared to the importance of environmental selection for prokaryotes, stochastic processes might have contributed primarily to fungal communities in REE mining areas. These findings confirm that the different assembly mechanisms of prokaryotic and fungal communities are key to the differences in their responses to environmental perturbations. The findings also provide the first insights into microbiota assembly patterns in REE-AMD and important ecological knowledge for the formation and development of microbial communities in REE mining areas.

Comparison of assembly process and co-occurrence pattern between planktonic and benthic microbial communities in the Bohai Sea

Unraveling the mechanisms structuring microbial community is a central goal in microbial ecology, but a detailed understanding of how community assembly processes relate to living habitats is still lacking. Here, via 16S rRNA gene amplicon sequencing, we investigated the assembly process of microbial communities in different habitats [water verse sediment, free-living (FL) verse particle-associated (PA)] and their impacts on the inter-taxa association patterns in the coastal Bohai Sea, China. The results showed clear differences in the composition and diversity of microbial communities among habitats, with greater dissimilarities between water column and sediment than between FL and PA communities. The microbial community assembly was dominated by dispersal limitation, ecological drift, and homogeneous selection, but their relative importance varied in different habitats. The planktonic communities were mainly shaped by dispersal limitation and ecological drift, whereas homogeneous selection played a more important role in structuring the benthic communities. Furthermore, the assembly mechanisms differed between FL and PA communities, especially in the bottom water with a greater effect of ecological drift and dispersal limitation on the FL and PA fractions, respectively. Linking assembly process to co-occurrence pattern showed that the relative contribution of deterministic processes (mainly homogeneous selection) increased under closer co-occurrence relationships. By contrast, stochastic processes exerted a higher effect when there were less inter-taxa connections. Overall, our findings demonstrate contrasting ecological processes underpinning microbial community distribution in different habitats including different lifestyles, which indicate complex microbial dynamic patterns in coastal systems with high anthropogenic perturbations.

Anthropogenic activities and geographic locations regulate microbial diversity, community assembly and species sorting in Canadian and Indian freshwater lakes

Freshwater lakes are important reservoirs and sources of drinking water globally. However, the microbiota, which supports the functionality of these ecosystems is threatened by the influx of nutrients, heavy metals and other toxic chemical substances from anthropogenic activities. The influence of these factors on the diversity, assembly mechanisms and co-occurrence patterns of bacterial communities in freshwater lakes is not clearly understood. Hence, samples were collected from six different impacted lakes in Canada and India and examined by 454-pyrosequencing technology. The trophic status of these lakes was determined using specific chemical parameters. Our results revealed that bacterial diversity and community composition was altered by both the lake water chemistry and geographic distance. Anthropogenic activities pervasively influenced species distribution. Dispersal limitation (32.3%), homogenous selection (31.8%) and drift (20%) accounted for the largest proportions of the bacterial community assembly mechanisms. Homogenous selection increased in lakes with higher nutrient concentration, while stochasticity reduced. Community functional profiles revealed that deterministic processes dominated the assembly mechanisms of phylotypes with higher potential for biodegradation, while stochasticity dominated the assembly of phylotypes with potential for antimicrobial resistance. Bacteroidota (44%) and Proteobacteria (34%) were the most abundant phyla. Co-occurrence network analysis revealed that complexity increased in more impacted lakes, while competition and the nature of anthropogenic activity contributed to species sorting. Overall, this study demonstrates that bacterial community changes in freshwater lakes are linked to anthropogenic activities, with corresponding consequences on the distribution of phylotypes of environmental and human health interest.

Context-dependent role of abiotic and biotic factors structuring nematode communities along two environmental gradients

Although abiotic environmental factors have been historically regarded as the dominant deterministic process in microbial community assembly, recent studies indicate that biotic interactions may be equally significant. However, the extent to which both processes are important in assembly of belowground communities is unknown. Along two environmental gradients: alkalinity (ranging from pH ~7 to ~11) and habitat type (lakes, shorelines, and prairies around lakes) present in the Western Nebraska Sandhills, we used 18S rRNA gene marker metabarcoding and statistical analyses, including generalized dissimilarity modelling (GDM), to evaluate the dynamics between abiotic and biotic factors that might play a role in nematode community assembly. Lakes supported the least diverse and prairies the most diverse communities with completely distinct compositions. We also observed a potential role of alkalinity in shaping these communities but only in lakes. Generally, GDMs indicated the influence of both abiotic and biotic factors. However, their relative importance in explaining community variability was dependent on the habitat. Biotic factors influenced the lake communities most, followed by shorelines and prairies, explaining ~47%, 27% and 8% of the variation, respectively. In contrast, the role of abiotic factors was relatively similar in lakes, shorelines and prairies (~15%, 18% and 14% of the variation, respectively). Most variation in the shorelines (62%) and prairies (82%) remained unexplained, suggesting the potential importance of factors associated with specific traits or a stronger role of stochastic processes. Nevertheless, our findings suggest both deterministic processes are important in nematode community assembly, but their specific contributions are context-dependent.

Aridity Threshold Induces Abrupt Change of Soil Abundant and Rare Bacterial Biogeography in Dryland Ecosystems

Aridity, which is increasing worldwide due to climate change, affects the biodiversity and functions of dryland ecosystems. Whether aridification leads to gradual (or abrupt) and systemic (or specific) changes in the biogeography of abundant and rare microbial species is largely unknown. Here, we investigated stress-adaptive changes (aridity-driven, ranging from 0.65 to 0.94) and biogeographic patterns of abundant and rare bacterial communities in different habitats, including agricultural field, forest, wetland, grassland, and desert, in desert oasis transition zones in northern China. We observed abrupt changes at the breakpoint of aridity values (0.92), characterized by diversity (α-diversity and β-diversity), species coexistence, community assembly processes, and phylogenetic niche conservatism. Specifically, when aridity was <0.92, increasing aridity led to more deterministic assembly and species coexistences for the abundant subcommunity, whereas the reverse was observed for the rare subcommunity. The phylogenetic niche conservatism for both subcommunities increased slowly with aridity. When aridity was >0.92, the systemic responses of abundant and rare taxa changed dramatically in a consistent direction, such that both subcommunities rapidly tended to have a more deterministic assembly, species coexistence, and stronger phylogenetic niche conservatism with increasing aridity. In addition, the change rates of abundant taxa were higher than those of rare taxa, indicating the more sensitive responses of abundant taxa along aridity variation. This finding has important implications for understanding the impact of aridity on the structure and function of abundant and rare soil taxa and how diversity maintenance is associated with soil microbiota responding to global change. The abrupt threshold of soil bacteria found can be used for buffering and for building effective adaptation and mitigation measures aimed at maintaining the capacity of drylands for basic ecosystem functioning. IMPORTANCE Aridity, which is increasing worldwide due to climate change, affects the biodiversity and functions of dryland ecosystems. We provided the first statistical evidence for abrupt changes of species coexistence, ecological processes, and niche conservation of abundant and rare soil bacteria triggered by diversity to abrupt increases in aridity. The abrupt threshold of soil bacterial community response to aridity is spatially heterogeneous at the local scale and should be specified according to local conditions for buffering and for building effective adaptation and mitigation measures aimed at maintaining the capacity of drylands for basic ecosystem functioning.

Nitrogen rather than phosphorus driving the biogeographic patterns of abundant bacterial taxa in a eutrophic plateau lake

Eutrophication of freshwater lakes is an important cause of global water pollution. In this study, the composition and biogeographic distribution of both abundant and rare sedimentary bacterial taxa and their relationship with nutrients were assessed in Erhai Lake, a subtropical plateau lake. Proteobacteria (48.3%) and Nitrospirae (11.7%) dominated the composition of abundant taxa, while the rare taxa were dominated by Proteobacteria (25.8%) and Chloroflexi (14.1%). The abundant bacterial taxa had strong energy metabolism, whereas the rare bacterial taxa had strong xenobiotics biodegradation and metabolism. These results indicated different compositions and functions existed between abundant and rare taxa. Total nitrogen (TN) was the most influential factor shaping the biogeographic patterns of both abundant and rare taxa. Phosphorus was not the deterministic factor, although nitrogen and phosphorus were the main contributors to eutrophication. Total organic carbon and pH also contributed to the biogeographic patterns of both abundant and rare taxa. In the eutrophic plateau lake sediments, abundant taxa, rather than rare taxa, played a dominant role in maintaining the community structure and ecological function of the bacterial community. The TN gradient was an important factor that affected the biogeographic distribution and assembly processes of abundant taxa. This study sheds light on the role of TN in shaping the biogeographic distribution and assembly processes of abundant taxa in eutrophic lakes.

Contrasting Community Assembly Mechanisms Underlie Similar Biogeographic Patterns of Surface Microbiota in the Tropical North Pacific Ocean

Marine microbiota are critical components of global biogeochemical cycles. However, the biogeographic patterns and ecological processes that structure them remain poorly understood, especially in the oligotrophic ocean. In this study, we used high-throughput sequencing of 16S and 18S rRNA genes to investigate the distribution patterns of bacterial and microeukaryotic communities and their assembly mechanisms in the surface waters of the tropical North Pacific Ocean. The fact that both the bacterial and the microeukaryotic communities showed similar distribution patterns (i.e., similar distance-decay patterns) and were clustered according to their geographic origin (i.e., the western tropical North Pacific and central tropical North Pacific) suggested that there was a significant biogeographic pattern of microbiota in the North Pacific Ocean. Indices of alpha diversity such as species richness, phylogenetic diversity, and the Shannon diversity index also differed significantly between regions. The correlations were generally similar between spatial and environmental variables and the alpha and beta diversities of bacteria and microeukaryotes across the entire region. The relative importance of ecological processes differed between bacteria and microeukaryotes: ecological drift was the principal mechanism that accounted for the structure of bacterial communities; heterogeneous selection, dispersal limitation, and ecological drift collectively explained much of the turnover of the microeukaryote communities.

IMPORTANCE Bacteria and microeukaryotes are extremely diverse groups in the ocean, where they regulate elemental cycling and energy flow. Studies of marine microbial ecology have benefited greatly from the rapid progress that has been made in genomic sequencing and theoretical microbial ecology. However, the spatial distribution of marine bacteria and microeukaryotes and the nature of the assembly mechanisms that determine their distribution patterns in oligotrophic marine waters are poorly understood. In this study, we used high-throughput sequencing methods to identify the distribution patterns and ecological processes of bacteria and microeukaryotes in an oligotrophic, tropical ocean. Our study showed that contrasting community assembly mechanisms underlaid similar biogeographic patterns of surface bacterial and microeukaryotic communities in the tropical North Pacific Ocean.

How habitat heterogeneity shapes bacterial and protistan communities in temperate coastal areas near estuaries

In this study, we investigated microbial communities (bacteria and protist) in two coastal areas near the estuaries of the Liaohe (LH) River and Yalujiang (YLJ) River in the Northwestern Pacific Ocean. Due to the existence of Liaodong Peninsula and different levels of urbanization, geographical segregation and significant environmental heterogeneity were observed between these two areas. There were significantly different regional species pools and biogeographic patterns for both bacterial and protistan communities between LH and YLJ coastal areas. Species turnover was the main mechanism driving β-diversity patterns of both bacterial and protistan communities in each area. In addition, the contributed ratio of nestedness to the β-diversity patterns was significantly higher for protists compared to bacteria. Variation in regional species pools was found to be the dominant driver of differences of bacterial and protistan communities between the LH and YLJ coastal areas. For a single-studied area, local community assembly mechanisms, including heterogeneous selection and dispersal limitation, were found to shape the bacterial and protistan communities through calculation of the β-deviation index. Among them, the relative importance of heterogeneous selection and dispersal limitation on the community assembly varied according to microorganism type and habitat.

Community Assembly and Co-occurrence Patterns Underlying the Core and Satellite Bacterial Sub-communities in the Tibetan Lakes

Microbial communities normally comprise a few core species and large numbers of satellite species. These two sub-communities have different ecological and functional roles in natural environments, but knowledge on the assembly processes and co-occurrence patterns of the core and satellite species in Tibetan lakes is still sparse. Here, we investigated the ecological processes and co-occurrence relationships of the core and satellite bacterial sub-communities in the Tibetan lakes via 454 sequencing of 16S rRNA gene. Our studies indicated that the core and satellite bacterial sub-communities have similar dominant phyla (Proteobacteria, Bacteroidetes, and Actinobacteria). But the core sub-communities were less diverse and exhibited a stronger distance-decay relationship than the satellite sub-communities. In addition, topological properties of nodes in the network demonstrated that the core sub-communities had more complex and stable co-occurrence associations and were primarily driven by stochastic processes (58.19%). By contrast, the satellite sub-communities were mainly governed by deterministic processes (62.17%). Overall, this study demonstrated the differences in the core and satellite sub-community assembly and network stability, suggesting the importance of considering species traits to understand the biogeographic distribution of bacterial communities in high-altitude lakes.

Protistan-Bacterial Microbiota Exhibit Stronger Species Sorting and Greater Network Connectivity Offshore than Nearshore across a Coast-to-Basin Continuum

Little is known regarding how community assembly and species association vary with habitat and depth. Here, we examined the assembly and association of protistan and bacterial communities across a coast-shelf-slope-basin gradient of the South China Sea using high-throughput sequencing of the V3 and V4 regions of the rRNA gene transcript. Our study revealed that homogenizing dispersal and drift exerted an influence on protistan communities comparable to that on bacterial communities. In contrast, selection and dispersal limitation exerted contrasting effects on the two microbial communities. Community assembly was governed to a greater degree by selection than by dispersal limitation in the bacterial community, and this was much lower in the protistan community. Moreover, this organismal assembly pattern was robust with habitat and depth. However, the relative importance of selection to dispersal limitation varied with habitat and depth in both communities, where horizontally it was higher offshore than nearshore and vertically it was lower in the bottom or deep chlorophyll maximum (DCM) than on the surface. The offshore possessed more microbial network complexity and more associations among microbial taxa than the nearshore, and vertically, the bottom possessed more complexity than the surface and the DCM. Moreover, temperature is strongly associated with the composition and co-occurrence of microbial communities, implying that temperature plays a dominant role in the selection of the protistan-bacterial microbiome across a coast-to-basin continuum. This study contributes to our understanding of the assembly mechanism and species association of protistan-bacterial microbiota across multiple habitats and depths.

IMPORTANCE Microbial organisms play a crucial role in global nutrient cycling. Few studies have attempted to simultaneously investigate the community assembly of microeukaryotes and prokaryotes and their association patterns in oceanic waters. This is especially true regarding how they vary with habitats and depths despite the fact that they are essential for developing a more holistic understanding of marine ecosystems. This study revealed the differential actions of selection and dispersal limitation and species association across a coast-to-basin continuum on the marine protistan-bacterial microbiome. Moreover, temperature was identified as a crucial factor driving the structure and co-occurrence of protistan and bacterial communities. The results emphasize that the differences in community assembly and association patterns between nearshore and offshore of the main constituents of the ocean microbiota should be considered to understand their current and future configurations. This is especially crucial in the context of climate change, as the response of ocean microbiota to nearshore and offshore temperature changes remains unknown.

Untangling Microbiota Diversity and Assembly Patterns in the World's Largest Water Diversion Canal

Large water diversion projects are important constructions for reallocation of human-essential water resources. Deciphering microbiota dynamics and assembly mechanisms underlying canal water ecosystem services especially during long-distance diversion is a prerequisite for water quality monitoring, biohazard warning and sustainable management. Using a 1432-km canal of the South-to-North Water Diversion Projects as a model system, we answer three central questions: how bacterial and micro-eukaryotic communities spatio-temporally develop, how much ecological stochasticity contributes to microbiota assembly, and which immigrating populations better survive and navigate across the canal. We applied quantitative ribosomal RNA gene sequence analyses to investigate canal water microbial communities sampled over a year, as well as null model- and neutral model-based approaches to disentangle the microbiota assembly processes. Our results showed clear microbiota dynamics in community composition driven by seasonality more than geographic location, and seasonally dependent influence of environmental parameters. Overall, bacterial community was largely shaped by deterministic processes, whereas stochasticity dominated micro-eukaryotic community assembly. We defined a local growth factor (LGF) and demonstrated its innovative use to quantitatively infer microbial proliferation, unraveling taxonomically dependent population response to local environmental selection across canal sections. Using LGF as a quantitative indicator of immigrating capacities, we also found that most micro-eukaryotic populations (82%) from the source water sustained growth in the canal and better acclimated to the hydrodynamical water environment than bacteria (67%). Taxa inferred to largely propagate include Limnohabitans sp. and Cryptophyceae, potentially contributing to water auto-purification. Combined, our work poses first and unique insights into the microbiota assembly patterns and dynamics in the world's largest water diversion canal, providing important ecological knowledge for long-term sustainable water quality maintenance in such a giant engineered system.

Highly comparable metabarcoding results from MGI-Tech and Illumina sequencing platforms

With the developments in DNA nanoball sequencing technologies and the emergence of new platforms, there is an increasing interest in their performance in comparison with the widely used sequencing-by-synthesis methods. Here, we test the consistency of metabarcoding results from DNBSEQ-G400RS (DNA nanoball sequencing platform by MGI-Tech) and NovaSeq 6000 (sequencing-by-synthesis platform by Illumina) platforms using technical replicates of DNA libraries that consist of COI gene amplicons from 120 soil DNA samples. By subjecting raw sequencing data from both platforms to a uniform bioinformatics processing, we found that the proportion of high-quality reads passing through the filtering steps was similar in both datasets. Per-sample operational taxonomic unit (OTU) and amplicon sequence variant (ASV) richness patterns were highly correlated, but sequencing data from DNBSEQ-G400RS harbored a higher number of OTUs. This may be related to the lower dominance of most common OTUs in DNBSEQ data set (thus revealing higher richness by detecting rare taxa) and/or to a lower effective read quality leading to generation of spurious OTUs. However, there was no statistical difference in the ASV and post-clustered ASV richness between platforms, suggesting that additional denoising step in the ASV workflow had effectively removed the 'noisy' reads. Both OTU-based and ASV-based composition were strongly correlated between the sequencing platforms, with essentially interchangeable results. Therefore, we conclude that DNBSEQ-G400RS and NovaSeq 6000 are both equally efficient high-throughput sequencing platforms to be utilized in studies aiming to apply the metabarcoding approach, but the main benefit of the former is related to lower sequencing cost.

Microbial community and abiotic effects on aquatic bacterial communities in north temperate lakes

The aquatic bacterial community (BC) plays a vital role in determining the nature and rate of ecosystem function. However, the biotic and abiotic factors influencing BC structure and function are largely unknown. Hence, the current study characterizes the impact of biotic and abiotic factors on aquatic bacterial biodiversity to determine whether the dominant effects are biotic or abiotic by partitioning their relative effects across temperate Canadian lakes. We collected water samples from sixty southern Ontario lakes and characterized their BC and microbial eukaryotic community (MEC) compositions using high throughput metabarcode sequencing of 16S and 18S rRNA gene fragments. The diversity and richness of aquatic BCs differed considerably among our study lakes, and those differences were explained by environmental, spatial, and biotic (MEC) factors (31%, 23%, and 23% of variance explained, respectively). The relatively large contribution from biotic and abiotic factors (54%), relative to spatial effects, shows deterministic processes prevail in shaping BC assembly in freshwater lakes. However, spatial effects also contributed significantly, highlighting the role of stochastic processes (ecological drift and coupled with limited dispersal) in shaping BC structure. Furthermore, our co-occurrence network analysis showed strong positive and negative interactions within and between the BCs and MECs, indicating mutualistic or antagonistic co-occurrence patterns relationships play important roles in driving the variation in BC composition among our sampled lakes. Considered together, our community analyses show that deterministic and stochastic processes combined contribute to determining the aquatic BC composition, and hence likely function as well, across a broad array of temperate freshwater lakes.

Changes in protist communities in drainages across the Pearl River Delta under anthropogenic influence

Drainages in the Pearl River Delta urban agglomeration (PRDUA) host vital aquatic ecosystems and face enormous pressures from human activities in one of the largest urban agglomerations in the world. Despite being crucial components of aquatic ecosystems, the interactions and assembly processes of the protistan community are rarely explored in areas with serious anthropogenic disturbance. To elucidate the mechanisms of these processes, we used environmental DNA sequencing of 18S rDNA to investigate the influence of environmental factors and species interactions on the protistan community and its assembly in drainages of the PRDUA during summer. The protistan community showed a high level of diversity and a marked spatial pattern in this region. Community assembly was driven primarily by stochastic processes based on the Sloan neutral community model, explaining 74.28%, 75.82%, 73.67%, 74.40% and 51.24% of community variations in the BJ (Beijiang), XJ (Xijiang), PRD (Pearl River Delta), PRE (Pearl River Estuary) areas and in total, respectively. Meanwhile, environmental variables including temperature, pH, dissolved oxygen, transparency, nutrients and land use were strongly correlated with the composition and assembly of the protistan community, explaining 40.40% of variation in the protistan community. Furthermore, the bacterial community was simultaneously analysed by the 16S rDNA sequencing. Co-occurrence network analysis revealed that species interactions within bacteria (81.41% positive) or protists (82.80% positive), and those between bacteria and protists (50% positive and 50% negative) impacted the protistan community assembly. In summary, stochastic processes dominated, whereas species interactions and environmental factors also played important roles in shaping the protistan communities in drainages across the PRDUA. This study provides insights into the ecological patterns, assembly processes and species interactions underlying protistan dynamics in urban aquatic ecosystems experiencing serious anthropogenic disturbance.

Bacteria in the lakes of the Tibetan Plateau and polar regions

The Tibetan Plateau, also termed 'the Third Pole' harbors the largest number of high-altitude lakes in the world. Due to the presence of extreme conditions such as low temperature and oligotrophy, the lakes of the Tibetan Plateau share environmental features in common with lakes in the polar regions. However, the extent to which these environments are analogous, or indeed whether they harbor similar microbial communities or a high level of endemic species is poorly understood. Here we compared high-throughput 16S rRNA gene sequencing data from the lakes of the three different regions in order to characterize their taxonomic diversity, the community composition and biogeography. Our results showed despite the similarity in environmental conditions, the spatial distribution of the bacterial communities was distinct with only 3.1% of all operational taxonomic units (OTUs) being present in all three regions (although these OTUs did account for a considerable proportion of the total sequences, 36.4%). Sequences belonging to Burkholderiales and Actinomycetales dominated the shared OTUs across all three regions. Scale dependent distance decay patterns provided evidence of dispersal limitation. Climatic variables and dispersal limitation were apparently both important in controlling the spatial distribution of bacterial communities across regions. This work expands our understanding of the diversity and biogeography of lake bacterial communities across the Tibetan Plateau and provides insights into how they compare to those of the Antarctic and Arctic.

Aquatic Bacterial Diversity, Community Composition and Assembly in the Semi-Arid Inner Mongolia Plateau: Combined Effects of Salinity and Nutrient Levels

Due to the recent decades of climate change and intensive human activities, endorheic lakes are threatened by both salinization and eutrophication. However, knowledge of the aquatic bacterial community's response to simultaneous increasing salinity and trophic status is still poor. To address this knowledge gap, we collected 40 surface water samples from five lakes and six rivers on the semi-arid Inner Mongolia Plateau, and investigated their bacterial communities using 16S rRNA gene-targeted amplicon sequencing. We found that bacterial species diversity significantly decreased from the mesotrophic freshwater river habitat to the eutrophic high-brackish lake habitat; salinity was more important than trophic status in explaining this decreased diversity. Salinity was the most important environmental factor in shaping community composition, while increased nitrogen loading was more important in structuring predicted functional composition. Within the lake habitats, the impact of environmental filtering on bacterial community assembly increased with the increasing salinity. The results suggested that the elevated salinity and nutrients have combined effects on the aquatic bacterial community, resulting in dramatic declines in species diversity, and promoted the importance of deterministic processes in community assembly. Our findings provide new insights into bacterial communities' responses to the intensified climate-driven and anthropogenic environmental changes in aquatic ecosystems.