Community assembly processes underlying phytoplankton and bacterioplankton across a hydrologic change in a human-impacted river

Biogeographic patterns of meio- and micro-eukaryotic communities in dam-induced river-reservoir systems

Although the Three Gorges Dam (TGD) is the world's largest hydroelectric dam, little is known about the spatial-temporal patterns and community assembly mechanisms of meio- and micro-eukaryotes and its two subtaxa (zooplankton and zoobenthos). This knowledge gap is particularly evident across various habitats and during different water-level periods, primarily arising from the annual regular dam regulation. To address this inquiry, we employed mitochondrial cytochrome c oxidase I (COI) gene-based environmental DNA (eDNA) metabarcoding technology to systematically analyze the biogeographic pattern of the three communities within the Three Gorges Reservoir (TGR). Our findings reveal distinct spatiotemporal characteristics and complementary patterns in the distribution of meio- and micro-eukaryotes. The three communities showed similar biogeographic patterns and assembly processes. Notably, the diversity of these three taxa gradually decreased along the river. Their communities were less shaped by stochastic processes, which gradually decreased along the longitudinal riverine-transition-lacustrine gradient. Hence, deterministic factors, such as seasonality, environmental, and spatial variables, along with species interactions, likely play a pivotal role in shaping these communities. Environmental factors primarily drive seasonal variations in these communities, while hydrological conditions, represented as spatial distance, predominantly influence spatial variations. These three communities followed the distance-decay pattern. In winter, compared to summer, both the decay and species interrelationships are more pronounced. Taken together, this study offers fresh insights into the composition and diversity patterns of meio- and micro-eukaryotes at the spatial-temporal level. It also uncovers the mechanisms behind community assembly in various environmental niches within the dam-induced river-reservoir systems. KEY POINTS: • Distribution and diversity of meio- and micro-eukaryotes exhibit distinct spatiotemporal patterns in the TGR. • Contribution of stochastic processes in community assembly gradually decreases along the river. • Deterministic factors and species interactions shape meio- and micro-eukaryotic community.

Unveiling the hidden impact: How human disturbances threaten aquatic microorganisms in cities

Urban activity emissions have important ecological significance to bacterial communities' spatial and temporal distribution and the mechanism of bacterial community construction. The mechanism of bacterial community construction is the key to community structure and lifestyle, and the influence of this aspect has not been thoroughly studied. This study analyzed the response of bacteria in water and sediment in different seasons to urban activities in Jinsha River. The results showed that the influence of urban activities on bacterial community structure in sediment was greater than that in water. The input of pollution in different regions changed the diversity and abundance of water and sediments bacteria and promoted bacterial community reconstruction to a certain extent. Co-network analysis found that many metal-mediated species are core species within the same module and can be used to mitigate pollution caused by metal or organic pollutants due to interspecific solid interactions. Different potential pollution sources around urban rivers affect the metabolic function of bacteria in aquatic ecosystems and promote the detoxification function of bacteria in different media. The results of this study supplement our understanding of the characteristics of microbial communities in urban river systems and provide clues for understanding the maintenance mechanism of microbial diversity in multi-pollution environments.

Modeling freshwater plankton community dynamics with static and dynamic interactions using graph convolution embedded long short-term memory

Given the frequent association between freshwater plankton and water quality degradation, several predictive models have been devised to understand and estimate their dynamics. However, the significance of biotic and abiotic interactions has been overlooked. In this study, we aimed to address the importance of the interaction term in predicting plankton community dynamics by applying graph convolution embedded long short-term memory networks (GC-LSTM) models, which can incorporate interaction terms as graph signals. Temporal graph series comprising plankton genera or environmental drivers as node features and their relationships for edge features from two distinct water bodies, a reservoir and a river, were utilized to develop these models. To assess the predictability, the performances of the GC-LSTM models on community dynamics were compared those of LSTM and GCN models at various lead times. Moreover, GNNExplainer was used to examine the global and local importance of the nodes and edges for all predictions and specific predictions, respectively. The GC-LSTM models outperformed the LSTM models, consistently showing higher prediction accuracy. Although all the models exhibited performance degradation at longer lead times, the GC-LSTM models consistently demonstrated better performance regarding each graph signal and plankton genus. GNNExplainer yielded interpretable explanations for important genera and interaction pairs among communities, revealing consistent importance patterns across different lead times at both global and local scales. These findings underscore the potential of the proposed modeling approach for forecasting community dynamics and emphasize the critical role of graph signals with interaction terms in plankton communities.

Dispersal limitation determines the ecological processes that regulate the seasonal assembly of bacterial communities in a subtropical river

Bacteria play a crucial role in pollutant degradation, biogeochemical cycling, and energy flow within river ecosystems. However, the underlying mechanisms governing bacterial community assembly and their response to environmental factors at seasonal scales in subtropical rivers remain poorly understood. In this study, we conducted 16S rRNA gene amplicon sequencing on water samples from the Liuxi River to investigate the composition, assembly processes, and co-occurrence relationships of bacterial communities during the wet season and dry season. The results demonstrated that seasonal differences in hydrochemistry significantly influenced the composition of bacterial communities. A more heterogeneous community structure and increased alpha diversity were observed during the dry season. Water temperature emerged as the primary driver for seasonal changes in bacterial communities. Dispersal limitation predominantly governed community assembly, however, during the dry season, its contribution increased due to decreased immigration rates. Co-occurrence network analysis reveals that mutualism played a prevailing role in shaping bacterial community structure. Compared to the wet season, the network of bacterial communities exhibited higher modularity, competition, and keystone species during the dry season, resulting in a more stable community structure. Although keystone species displayed distinct seasonal variations, Proteobacteria and Actinobacteria were consistently abundant keystone species maintaining network structure in both seasons. Our findings provide insights into how bacterial communities respond to seasonal environmental changes, uncovering underlying mechanisms governing community assembly in subtropical rivers, which are crucial for the effective management and conservation of riverine ecosystems.

Higher genotypic diversity and distinct assembly mechanism of free-living Symbiodiniaceae assemblages than sympatric coral-endosymbiotic assemblages in a tropical coral reef

While in hospite Symbiodiniaceae dinoflagellates are essential for coral health, ambient free-living counterparts are crucial for coral recruitment and resilience. Comparing free-living and in hospite Symbiodiniaceae communities can potentially provide insights into endosymbiont acquisition and recurrent recruitment in bleaching recovery. In this study, we studied coral-endosymbiotic and ambient free-living Symbiodiniaceae communities in the South China Sea. We collected samples from 183 coral and ambient plankton samples and conducted metabarcoding to investigate the diversity distribution, driving factors, and assembly mechanisms of the two groups of Symbiodiniaceae. Results revealed Cladocopium C1 and Durusdinium D1 as dominant genotypes. We detected a higher genotypic diversity in free-living than in hospite symbiodiniacean communities, but with shared dominant genotypes. This indicates a genetically diverse pool of Symbiodiniaceae available for recruitment by corals. Strikingly, we found that the cooler area had more Symbiodiniaceae thermosensitive genotypes, whereas the warmer area had more Symbiodiniaceae thermotolerant genotypes. Furthermore, in hospite and free-living Symbiodiniaceae communities were similarly affected by environmental factors, but shaped by different assembly mechanisms. The in hospite communities were controlled mainly by deterministic processes, whereas the ambient communities by stochastic processes. This study sheds light on the genetic diversity of source environmental Symbiodiniaceae and differential assembly mechanisms influencing Symbiodiniaceae inside and outside corals.IMPORTANCESymbiodiniaceae dinoflagellates play a pivotal role as key primary producers within coral reef ecosystems. Coral-endosymbiotic Symbiodiniaceae communities have been extensively studied, but relatively little work has been reported on the free-living Symbiodiniaceae community. Conducting a comparative analysis between sympatric coral-endosymbiotic and free-living Symbiodiniaceae communities can potentially enhance the understanding of how endosymbiont communities change in response to changing environments and the mechanisms driving these changes. Our findings shed light on the genetic diversity of source environmental Symbiodiniaceae and differential assembly mechanisms shaping free-living and in hospite Symbiodiniaceae communities, with implications in evaluating the adaptive and resilient capacity of corals in response to future climate change.

Precipitation input increases biodiversity of planktonic communities in the Qinghai-Tibet Plateau

Planktonic communities in aquatic ecosystems are crucial water quality indicators, with their growth dependent on runoff chemical and hydraulic characteristics (e.g., nutrient availability and turbidity). Previous studies have indicated that runoff components (i.e., proportions of precipitation, groundwater, snowmelt, etc.) play a vital role in regulating runoff characteristics, potentially affecting planktonic communities. However, the response of these communities to runoff components, particularly in mountainous regions, remains underexplored. In this study, we conducted four sampling campaigns from 2017 to 2020 in a watershed on the Qinghai-Tibet Plateau. Combined with laboratory incubation experiments, we examined the impact of various runoff components on the diversity and abundance of phytoplankton and zooplankton. We found that a higher proportion of precipitation in runoff contributed to an increase in the diversity of plankton communities. Laboratory experiments with unified water samples incubated with different runoff components demonstrated that the significant influence of precipitation on planktonic diversity primarily stems from the influx of abundant exogenous particulate material into rivers. Using a path analysis, we further confirmed that the impact of precipitation on diversity is primarily through chemical pathways, notably by increasing nutrient concentrations. Our study enhances our understanding of the interactions between the hydrological cycle and aquatic ecosystems, offering valuable insights for effectively maintaining and managing these natural environments.

Seasonality regulates the distinct assembly patterns of microeukaryotic plankton communities in the Three Gorges Reservoir, China

The hydrographic and environmental factors along the Three Gorges Reservoir (TGR) have been significantly altered since the Three Gorges Dam (TGD) began working in 2006. Here, we collected 54 water samples, and then measured the environmental factors, followed by sequencing of the 18S rRNA gene and subsequent analysis of community assembly mechanisms. The findings indicated that the majority of environmental variables (such as AN, TP, Chl-a, CODMn, and Cu) exhibited both temporal and spatial variations due to the influences of the TGD. The distribution of different environmental factors and microeukaryotic plankton communities is influenced by the changing seasons. The community structure in TGR showed variations across three seasons, possibly due to variations in their environmental preferences, inherent dissimilarities, and seasonal succession. Furthermore, different communities exhibited a comparable distance-decay trend, suggesting that distinct taxa are likely to exhibit a similar spatial distribution. In addition, the community formation in TGR was influenced by both deterministic and stochastic factors, with the balance between them being mainly controlled by the season. Specifically, deterministic processes could explain 33.9-51.1% of community variations, while stochastic processes could contribute 23.5-32.2%. The findings of this research demonstrated that the varying ecological processes' significance relied on environmental gradients, geographical scale, and ecological conditions. This could offer a fresh outlook on comprehending the composition, assembly mechanisms, and distribution patterns of microeukaryotic plankton in reservoir ecosystems.

Integrated evaluation of the impact of water diversion on water quality index and phytoplankton assemblages of eutrophic lake: A case study of Yilong Lake

Water diversion has been widely utilized to enhance lake water quality and mitigate cyanobacterial blooms. However, previous studies have mainly focused on investigating the effects of water diversion on water quality or aquatic ecological health. Consequently, there is limited research investigating the combined impact of water diversion on the water quality and the ecological health of eutrophic lakes, and whether the WQI and phytoplankton assemblages demonstrate similar patterns following water diversion. In this study, the effects of water diversion on the ecosystem health of eutrophic lakes were comprehensively evaluated based on the WQI indices and phytoplankton assemblages during the NWDP-21 and WDP-22. The results showed that the annual mean of WQI increased from 52.02 to 54.36 after water diversion, which improved the water quality of the lake, especially NH3-N and TN decreased by 58.6% and 15.2%, respectively. The phytoplankton assemblages changed significantly before and after water diversion, and we observed that the total biomass of phytoplankton decreased by 12.3% and phytoplankton diversity indices (Shannon-Wiener diversity, Pielou evenness, and Simpson index) increased by 8.6%-8.9% after water diversion, with an improvement in the connectivity and stability of the phytoplankton. Notably, enhanced adaptations of rare sub-communities for resource use in water diversion environments, and water diversion inhibited the dispersal ability of dominant functional groups, and the effects of hydrological disturbances on the structure of phytoplankton assemblage favored the ecological health of eutrophic lakes. VPA analysis further reveals that water diversion alters the drivers of phytoplankton functional group biomass and phytoplankton diversity. The results of the PLS-PM analysis clarify that water diversion indirectly impacts the total phytoplankton biomass and phytoplankton diversity primarily by modifying light availability. Significant correlations are observed between the dominant functional groups biomass and diversity indices of WQI. The trends in changes observed in water quality indices and phytoplankton following water diversion align with the evaluation of water ecological health. This study provides valuable guidance for the ecological management of the diversion project in Yilong Lake and serves as a reference for similar projects in other lakes.

Strategies for regulating the intensity of different cyanobacterial blooms: Insights from the dynamics and stability of bacterioplankton communities

The occurrence of cyanobacterial blooms is increasing in frequency and magnitude due to climate change and human activities, which poses a direct threat to drinking water security. The impacts of abiotic and biotic factors on the development of blooms have been well studied; however, control strategies for different bloom intensities have rarely been explored from the perspective of the dynamics and stability of bacterioplankton communities. Here, a network analysis was used to investigate the interactions and stability of microbial communities during different periods of R. raciborskii bloom in an inland freshwater lake. The abundance and diversity of rare taxa were significantly higher than that of abundant taxa throughout the bloom cycle. At the pre-bloom (PB) stage, microbial interactions among the different bacterial groups were weak but strongly negatively correlated, indicating low robustness and weak disturbance resistance within the community. However, community stability was better, and microbial interactions became more complicated at the high-bloom (HB) and low-bloom (LB) stages. Interestingly, rare taxa were significantly responsible for community stability and connectivity despite their low relative abundance. The Mantel test revealed that Secchi depth (SD), orthophosphate (PO43--P), and dissolved oxygen (DO) were significantly positively correlated with abundant taxa, rare taxa and PB. DO was significantly positively correlated with HB, intermediate taxa, and rare taxa, while water temperature (WT), N/P and total nitrogen (TN) were significantly positively correlated with LB, abundant taxa, intermediate taxa, and rare taxa. These findings suggest that reducing the PO43--P concentration at the PB stage may be an effective approach to preventing the development of R. raciborskii blooms, while regulating rare taxa at the HB and LB stages may be a key factor in controlling R. raciborskii blooms.

Seasonal variation and human impacts of the river biofilm bacterial communities in the Shiting River in southeastern China

Bacterial communities in epilithic biofilm plays an important role in biogeochemistry processes in freshwater ecosystems. Nevertheless, our understanding of the geographical and seasonal variations of the composition of bacterial communities in the biofilm of gravels on river bed is still limited. Various anthropogenic activities also influence the biofilm bacteria in gravel rivers. By taking the Shiting River in the upper Yangtze River basin in Sichuan Province as an example, we studied the geographical and seasonal variations of epilithic bacteria and the impacts of weirs and other human activities (e.g., sewage pollution). The river has experienced severe degradation since the Ms 8.0 Wenchuan Earthquake, and weirs were constructed to prevent bed erosion. We collected epilithic biofilms samples at 17 sites along ~ 30 km river reach of the Shiting River in the autumn of 2021 and the summer of 2022, respectively. We applied 16S rRNA gene high-throughput sequencing technology and Functional Annotation of Prokaryotic Taxa (FAPROTAX) to analyze the seasonal and biogeographic patterns and potential functions of the biofilm bacterial communities. The results showed that epilithic bacteria from the two surveys exhibited variation in community composition, bacterial diversity and potential functions. The bacteria samples collected in the autumn have much higher alpha diversity and richness than those collected in the summer. Bacterial richness and diversity were lower downstream of the weirs than upstream. Low diversity was observed at a sampling site influenced by sewage inflow, which contains high level of nitrogen-related chemicals.

Interactions between water quality and microbes in epiphytic biofilm and superficial sediment of lake in trophic agriculture area

Epiphytic and superficial sediment biofilm-dwelling microbial communities play a pivotal role in water quality regulation and biogeochemical cycling in shallow lakes. However, the interactions are far from clear between water physicochemical parameters and microbial community on aquatic plants and in surface sediments of lake in trophic agriculture area. This study employed Illumina sequencing, Partial Least Squares Path Modeling (PLS-PM), and physico-chemical analytical methods to explore the interactions between water quality and microbes (bacteria and eukaryotes) in three substrates of trophic shallow Lake Cyohoha North, Rwanda. The Lake Cyohoha was significantly polluted with total phosphorus (TP), total nitrogen (TN), nitrate nitrogen (NO3-N), and ammonia nitrogen (NH3-N) in the wet season compared to the dry season. PLS-PM revealed a strong positive correlation (+0.9301) between land use types and physico-chemical variables in the rainy season. In three substrates of the trophic lake, Proteobacteria, Cyanobacteria, Firmicutes, and Actinobacteria were dominant phyla in the bacterial communities, and Rotifers, Platyhelminthes, Gastrotricha, and Ascomycota dominated in microeukaryotic communities. As revealed by null and neutral models, stochastic processes predominantly governed the assembly of bacterial and microeukaryotic communities in biofilms and surface sediments. Network analysis revealed that the microbial interconnections in Ceratophyllum demersum were more stable and complex compared to those in Eichhornia crassipes and sediments. Co-occurrence network analysis (|r| > 0.7, p < 0.05) revealed that there were complex interactions among physicochemical parameters and microbes in epiphytic and sediment biofilms, and many keystone microbes on three substrates played important role in nutrients removal, food web and microbial community stable. These findings emphasize that eutrophic water influence the structure, composition, and interactions of microbes in epiphytic and surface sediment biofilms, and provided new insights into the interconnections between water quality and microbial community in presentative substrates in tropical lacustrine ecosystems in agriculturally polluted areas. The study provides useful information for water quality protection and aquatic plants restoration for policy making and catchment management.

Spatiotemporal assembly and functional composition of planktonic microeukaryotic communities along productivity gradients in a subtropical lake

Microeukaryotes play crucial roles in the microbial loop of freshwater ecosystems, functioning both as primary producers and bacterivorous consumers. However, understanding the assembly of microeukaryotic communities and their functional composition in freshwater lake ecosystems across diverse environmental gradients remains limited. Here, we utilized amplicon sequencing of 18S rRNA gene and multivariate statistical analyses to examine the spatiotemporal and biogeographical patterns of microeukaryotes in water columns (at depths of 0.5, 5, and 10 m) within a subtropical lake in eastern China, covering a 40 km distance during spring and autumn of 2022. Our results revealed that complex and diverse microeukaryotic communities were dominated by Chlorophyta (mainly Chlorophyceae), Fungi, Alveolata, Stramenopiles, and Cryptophyta lineages. Species richness was higher in autumn than in spring, forming significant hump-shaped relationships with chlorophyll a concentration (Chl-a, an indicator of phytoplankton biomass). Microeukaryotic communities exhibited significant seasonality and distance-decay patterns. By contrast, the effect of vertical depth was negligible. Stochastic processes mainly influenced the assembly of microeukaryotic communities, explaining 63, 67, and 55% of community variation for spring, autumn, and both seasons combined, respectively. Trait-based functional analysis revealed the prevalence of heterotrophic and phototrophic microeukaryotic plankton with a trade-off along N:P ratio, Chl-a, and dissolved oxygen (DO) gradients. Similarly, the mixotrophic proportions were significantly and positively correlated with Chl-a and DO concentrations. Overall, our findings may provide useful insights into the assembly patterns of microeukaryotes in lake ecosystem and how their functions respond to environmental changes.

Deciphering microbiomes dozens of meters under our feet and their edaphoclimatic and spatial drivers

Microbes inhabiting deep soil layers are known to be different from their counterpart in topsoil yet remain under investigation in terms of their structure, function, and how their diversity is shaped. The microbiome of deep soils (>1 m) is expected to be relatively stable and highly independent from climatic conditions. Much less is known, however, on how these microbial communities vary along climate gradients. Here, we used amplicon sequencing to investigate bacteria, archaea, and fungi along fifteen 18-m depth profiles at 20-50-cm intervals across contrasting aridity conditions in semi-arid forest ecosystems of China's Loess Plateau. Our results showed that bacterial and fungal α diversity and bacterial and archaeal community similarity declined dramatically in topsoil and remained relatively stable in deep soil. Nevertheless, deep soil microbiome still showed the functional potential of N cycling, plant-derived organic matter degradation, resource exchange, and water coordination. The deep soil microbiome had closer taxa-taxa and bacteria-fungi associations and more influence of dispersal limitation than topsoil microbiome. Geographic distance was more influential in deep soil bacteria and archaea than in topsoil. We further showed that aridity was negatively correlated with deep-soil archaeal and fungal richness, archaeal community similarity, relative abundance of plant saprotroph, and bacteria-fungi associations, but increased the relative abundance of aerobic ammonia oxidation, manganese oxidation, and arbuscular mycorrhizal in the deep soils. Root depth, complexity, soil volumetric moisture, and clay play bridging roles in the indirect effects of aridity on microbes in deep soils. Our work indicates that, even microbial communities and nutrient cycling in deep soil are susceptible to changes in water availability, with consequences for understanding the sustainability of dryland ecosystems and the whole-soil in response to aridification. Moreover, we propose that neglecting soil depth may underestimate the role of soil moisture in dryland ecosystems under future climate scenarios.

Response mechanism of sediment endogenous phosphorus release to functional microorganisms and its cyanobacterial growth and disappearance effects

Endogenous phosphorus (P) release from lake sediments is an important factor in the eutrophication of overlying waters, as P is the limiting nutrient salt affecting cyanobacterial growth. Microorganisms are also key to the evolution of cyanobacterial growth and disappearance, as they can influence the release of endogenous P. Meanwhile, endogenous phosphorus can also have an impact on microbial structure. However, there is a lack of studies on the response mechanisms between endogenous P release and microorganisms, as well as the exploration of endogenous P release on the whole cyanobacterial growth and disappearance evolution process. In this study, metagenome sequencing was used to characterize the microbial community structure at different times and to explain the P cycle from the perspective of functional genes. The results showed that the number of sediment microorganisms (genes) gradually increased with the P release capacity, and the outbreak with the strongest P release capacity possessed the most abundant microorganisms (genes). Proteobacteria with P solubilizing functions were consistently the most abundant phylum in all four periods and were positively correlated with P release potential assessment factors EPC0, EPC0F, and NAP. Functional genes affect the P cycle by acting primarily on inorganic P solubilization, organic P mineralization, and P transport. These P-functional genes are mainly found in Proteobacteria, Acidobacteria, Chloroflexi, and Actinobacteria microorganisms. In addition, the P form in the sediments was dominated by IP, with the highest concentration (704.86 mg/kg) occurring during the dormant period. Sediments from this period acted as a strong P "sink", creating a precondition for cyanobacterial recovery and outbreaks to provide a source of P. The results of this study can provide a theoretical basis for controlling endogenous P release at the microscopic level of cyanobacterial growth and disappearance.

Dynamics of the sedimentary bacterial communities in a plain river network: similar coalescence patterns with bacterioplankton communities driven by distinct assembly processes

IMPORTANCE

Microorganisms play important roles in driving the biogeochemical cycles within river ecosystems. It has been suggested that hydrologic conditions could influence microbial communities in rivers, but their specific effects on the behaviours of microbial coalescence have not been thoroughly investigated. In this study, the dynamics of sedimentary bacterial communities within a plain river network were analyzed by amplicon sequencing followed by several ecological models to uncover the underlying assembly processes. Additionally, a comparative analysis between bacterioplankton communities and sedimentary bacterial communities was performed to unveil their coalescence patterns. The results suggested that similar coalescence patterns between sedimentary bacterial and bacterioplankton communities were driven by distinct assembly processes under dynamic hydrological conditions. These findings enhanced our understanding of microbial diversity features within river ecosystems.

Differences in pathogenic community assembly processes and their interactions with bacterial communities in river and lake ecosystems

Pathogenic bacterial infections caused by water quality degradation are one of the most widespread environmental problems. Clarifying the structure of pathogens and their assembly mechanisms in lake ecosystems is vital to prevent the infestation of waterborne pathogens and maintain human health. However, the composition and assembly mechanisms of pathogenic bacterial communities in river and lake ecosystems are still poorly understood. In this study, we collected 17 water and 17 sediment samples from Lake Chaohu and its 11 inflow rivers. Sequencing of 16S rRNA genes was used to study bacterial pathogen communities. The results of the study showed that there was a significant difference (P < 0.05) in the composition of the pathogen community between riverine and lake habitats. Acinetobacter (36.49%) was the dominant bacterium in the river, whereas Flavobacterium (21.6%) was the most abundant bacterium in the lake. Deterministic processes (i.e., environmental filtering and species interaction) drove the assembly of pathogenic bacterial communities in the lake habitat, while stochastic processes shaped river pathogenic bacterial communities. Spearman correlation analysis showed that the α-diversity of bacterial communities was linearly and negatively linked to the relative abundance of pathogens. Having a higher bacterial community diversity had a suppressive effect on pathogen abundance. In addition, co-occurrence network analysis showed that bacterial communities were tightly linked to pathogenic bacteria. Pseudomonas aeruginosa and Salmonella enterica were identified as keystone species in an inflow water sampling network (W_FR), reducing the complexity of the network. These results provide a reference for assessments of water quality safety and pathogenic bacteria posing risks to human health in large freshwater lakes.

Unraveling the rate-limiting step in microorganisms' mediation of denitrification and phosphorus absorption/transport processes in a highly regulated river-lake system

River-lake ecosystems are indispensable hubs for water transfers and flow regulation engineering, which have frequent and complex artificial hydrological regulation processes, and the water quality is often unstable. Microorganisms usually affect these systems by driving the nutrient cycling process. Thus, understanding the key biochemical rate-limiting steps under highly regulated conditions was critical for the water quality stability of river-lake ecosystems. This study investigated how the key microorganisms and genes involving nitrogen and phosphorus cycling contributed to the stability of water by combining 16S rRNA and metagenomic sequencing using the Dongping river-lake system as the case study. The results showed that nitrogen and phosphorus concentrations were significantly lower in lake zones than in river inflow and outflow zones (p < 0.05). Pseudomonas, Acinetobacter, and Microbacterium were the key microorganisms associated with nitrate and phosphate removal. These microorganisms contributed to key genes that promote denitrification (nirB/narG/narH/nasA) and phosphorus absorption and transport (pstA/pstB/pstC/pstS). Partial least squares path modeling (PLS-PM) revealed that environmental factors (especially flow velocity and COD concentration) have a significant negative effect on the key microbial abundance (p < 0.001). Our study provides theoretical support for the effective management and protection of water transfer and the regulation function of the river-lake system.

Copper and temperature shaped abundant and rare community assembly respectively in the Yellow River

Untangling assembly and microbial interaction of abundant and rare microbiota in aquatic ecosystem is pivotal for understanding how community assembly respond to environmental variables and co-occurrence patterns. Here, we explored the assembly mechanisms, their drivers, and species co-occurrence of abundant and rare microbiomes in the Yellow River using 16S rRNA gene sequencing in Lanzhou, China. Here, abundant community was ubiquitous across all sites, whereas rare community was uneven distributed. The richness and community dissimilarity of rare taxa were significantly greater than those of abundant ones. Stochastic processes structured the rare community assembly in spring and winter, while deterministic processes shaped the abundant and rare community assembly in other seasons and all sites. Copper and water temperature mediated the balance between deterministic and stochastic processes of abundant and rare community, respectively. A few abundant taxa with closer relationships frequently occupied central positions and had a great effect on other co-occurrences in the network, while the majority of keystone microbiota were rare microbiome and played a considerable part in maintaining the network structure. Our study provides some ecological proposals for water quality management and ecological stability of the Yellow River. KEY POINTS: • Deterministic process dominated abundant and rare community assembly. • Cu and TW mediated the balance of abundant and rare community assembly respectively. • Abundant taxa had a greater effect on other co-occurrences in the network.

Local-Scale Damming Impact on the Planktonic Bacterial and Eukaryotic Assemblages in the upper Yangtze River

Dam construction and impoundment cause discontinuities in the natural biophysical gradients in rivers. These discontinuities may alter distinctive habitats and different microbial community assembly mechanisms upstream and downstream of dams, which reflect the potential impacts of damming on riverine aquatic ecosystems. In this study, we investigated the planktonic microbial assemblages of three large dams in the upper Yangtze River by using high-throughput sequencing. The results revealed that the alpha diversity indexes increased downstream of the dams. In addition, more eukaryotic ASVs solely occurred downstream of the dams, which indicated that a large proportion of eukaryotes appeared downstream of the dams. The nonmetric multidimensional scaling analysis indicated that there was no obvious geographic clustering of the planktonic microbial assemblages among the different locations or among the different dams. However, the dam barriers changed dam-related variables (maximum dam height and water level) and local environmental variables (water temperature, DOC, etc.) that could possibly affect the assembly of the planktonic microbial communities that are closest to the dams. A co-occurrence network analysis demonstrated that the keystone taxa of the planktonic bacteria and eukaryotes decreased downstream of the dams. In particular, the keystone taxa of the eukaryotes disappeared downstream of the dams. The robustness analysis indicated that the natural connectivity of the microbial networks decreased more rapidly upstream of the dams, and the downstream eukaryotic network was more stable. In conclusion, damming has a greater impact on planktonic eukaryotes than on bacteria in near-dam areas, and planktonic microbial assemblages were more susceptible to the environmental changes. Our study provides a better understanding of the ecological effects of river damming.

Geographic patterns of microbial traits of river basins in China

River microbiotas contribute to critical geochemical processes and ecological functions of rivers but are sensitive to variations of environmental drivers. Understanding the geographic pattern of river microbial traits in biogeochemical processes can provide important insights into river health. Many studies have characterized river microbial traits in specific situations, but the geographic patterns of these traits and environmental drivers at a large scale are unknown. We reanalyzed 4505 raw 16S rRNA sequences samples for microbiota from river basins in China. The results indicated differences in the diversity, composition, and structure of microbiotas across diverse river basins. Microbial diversity and functional potential in the river basins decreased over time in northern China and increased in southern China due to niche differentiation, e.g., the Yangtze River basin was the healthiest ecosystem. River microbiotas were mainly involved in the cycling of carbon and nitrogen in the river ecosystems and participated in potential organic metabolic functions. Anthropogenic pollutants discharge was the most critical environmental driver for the microbial traits, e.g., antibiotic discharge, followed by climate change. The prediction by machine-learning models indicated that the continuous discharge of antibiotics and climate change led to high ecological risks for the rivers. Our study provides guidelines for improving the health of river ecosystems and for the formulation of strategies to restore the rivers.

Deterministic Processes Shape Abundant and Rare Bacterial Communities in Drinking Water

The deep mechanisms shaping bacterial assembly are a crucial challenge in drinking water ecosystem. However, much less is known about seasonal diversity distributions and assembly mechanisms of abundant and rare bacteria in drinking water. The combination of environmental variables and high-throughput 16S rRNA gene sequencing was conducted to examine the composition, assembly, co-occurrence patterns of abundant and rare bacteria from five drinking water sites across four seasons in one year in China. The results indicated that abundant taxa were mainly composed of Rhizobiales_UG1, Sphingomonadales_UG1, and Comamonadaceae, while rare taxa were Sphingomonadales_UG1, Rhizobiales_UG2, and Rhizobiales_UG1. The richness of rare bacteria was greater than that of abundant ones, and the richness had no differences among seasons. The beta diversity was significantly discrepant in abundant and rare communities and among seasons. Deterministic mechanism accounted for a larger contribution to abundant taxa than rare taxa. Furthermore, water temperature had higher effects on abundant microbiome than rare ones. Co-occurrence network analysis indicated that abundant taxa that occupied frequently in central positions had stronger effect on co-occurrence network. In our study, these results collectively suggested that rare bacteria respond to environmental variables with an analogical pattern to abundant counterparts (similar community assembly), but their ecological diversities, driving forces, and co-occurrence patterns were not equivalent in drinking water.

Biogeographic Patterns and Community Assembly Processes of Bacterioplankton and Potential Pathogens in Subtropical Estuaries in China

Microbial communities in coastal waters are diverse and dynamic and play important roles in ecosystem functions and services. Despite the ecological impact of bacterioplankton or pathogens, little is known about whether bacterioplankton and pathogen communities exhibit similar patterns. Here, using 16S RNA gene amplicon sequencing, the geographic patterns and assembly processes of bacterioplankton and pathogen communities in 30 subtropical estuaries were studied. Results showed that the estuarine bacterioplankton communities mainly consisted of Proteobacteria (49.06%), Actinobacteria (17.62%), and Bacteroidetes (16.33%), among which 31 pathogen genera (186 amplicon sequence variants [ASVs]) were identified. Under the influence of salinity, bacterioplankton and pathogens showed similar biogeographic patterns. Redundancy and correlation analyses indicated that the bacterioplankton communities were strongly correlated with estuarine environmental factors, but potential pathogens were less influenced. Co-occurrence network analysis revealed a close relationship between bacterioplankton and potential pathogens, with two pathogens identified as connectors (i.e., ASV340 [Clostridium perfringens] and ASV1624 [Brevundimonas diminuta]), implying potential impacts of pathogens on structure, function, and stability of estuarine bacterioplankton communities. Null-model analysis revealed that deterministic processes (heterogeneous selection) dominated bacterioplankton community assembly, while stochastic processes (undominated effect) shaped the potential pathogen community. Our findings illustrate the biogeographic patterns and community assembly mechanisms of bacterioplankton and pathogens in estuaries, which should provide guidance and a reference for the control of potential pathogenic bacteria. IMPORTANCE Bacterioplankton play an important role in estuarine ecosystem functions and services; however, potentially pathogenic bacteria may exhibit infectivity and pose a serious threat to environmental and human health. In this study, geographic patterns and assembly processes of bacterioplankton communities in 30 subtropical estuaries were explored, and potential pathogenic bacteria in the estuaries were detected and profiled. Our results demonstrate here that bacterioplankton and pathogens show similar biogeographic patterns under the influence of salinity. Interestingly, heterogeneous selection dominated bacterioplankton assembly, while stochasticity dominated pathogen assembly. This study provides important information for future risk assessment of potential pathogenic bacteria as well as management in estuarine ecosystems.

Lake morphological characteristics and climatic factors affect long-term trends of phytoplankton community in the Rotorua Te Arawa lakes, New Zealand during 23 years observation

Monitoring the long-term dynamics of lake phytoplankton can help understand their natural temporal variability, as well as assess potential impacts of interventions aimed at improving lake ecological condition. However, investigating long-term changes in lake ecosystems has received scant attention. In the present study, we analyzed a long-term dataset of phytoplankton communities collected from 1990 to 2013 from eleven of the 12 Rotorua Te Arawa lakes in New Zealand, to explore their responses to changing abiotic conditions. We used a sequential algorithm to examine the likelihood of regime shifts in abiotic and biotic factors during the study period that could be attributable to lake interventions. Our analysis suggests that lake interventions have improved the abiotic factors, whereas the response of biotic factors was less clear. Total phosphorus levels were implicated in the decline in lake condition, including in two lakes subject to lake interventions, and in four control lakes. Both abiotic and biotic factors showed diverse trends (e.g., increase, decrease or no change), and abiotic factors had more regime shifts than biotic factors. Shifts in biotic indices also displayed time lags to shifts in abiotic factors. Long-term responses of abiotic and biotic factors were also influenced by lake morphological characteristics and climatic variables. This latter finding underscores the importance of considering lake morphological characteristics and climate changes when planning management practices. A sound understanding of resilience and threshold of phytoplankton shifts to environmental changes are needed to assess the effectiveness of previous management strategies and prioritize the future conservation efforts toward water quality goals.

Hydrodynamics-driven community coalescence determines ecological assembly processes and shifts bacterial network stability in river bends

Community coalescence, i.e., the mixing and merging of microbial communities and their surrounding environments, is prevalent in various ecosystems and potentially acts on ecological processes. River bends are distinguished by significant cross-stream velocities and spiral flow. The flow in river bends causes the mixing of microbial communities, thus making the resultant community (after mixing) different from its precursors (before mixing) through ecological processes. However, so far, no studies have explored the effect of community coalescence on ecological processes and network stability under the hydrodynamic processes of river bends. Here, we explored bacterial community assembly and community coalescence in river bends by coupling hydrodynamic profiling, aqueous biogeochemistry, DNA sequencing, and ecological theory. The results showed that the water flow dominated the community coalescence by regulating the movement of suspended sediments. The main ecological process determining the bacterial community compositions in water was the dispersal process, whereas in sediments it was the selection process. Furthermore, the negative cohesion results showed that community coalescence determined the stability of bacterial networks through competition and predation. This study depicted the bacterial community coalescence in river bends and highlighted their associations with network stability, which might provide new insights into bacterial community assembly and coalescence under complex hydrodynamics in the aquatic environment.

Community assembly patterns and processes of microbiome responses to habitats and Mytilopsis sallei invasion in the tidal zones of the Pearl River Estuary

The sustainability of estuarine ecosystem functions depends on the stabilization of microbial ecological processes. However, due to the unique and variable habitat characteristics of estuarine areas, in-depth studies on ecological processes such as the spatial distribution and assembly patterns of microbial community structure are lacking. As methods to elucidate this structure, we used 16S rDNA, 18S rDNA and ITS sequencing technologies to study the composition, diversity, spatial pattern and aggregation mechanism of the bacterial, protist and fungal communities in the tidal zones of the Pearl River Estuary (PRETZ). The abundance of bacterial communities was much higher than that of protists and fungi, and the spatial pattern was obvious in PRETZ. The application of neutral and null models revealed the assembly process of three microbial communities dominated by stochastic processes. Among the stochastic processes, undominated processes (64.03 %, 62.45 %, and 59.29 %) were the most critical processes in the assembly of bacterial, fungal and protist communities. Meanwhile, environmental variables, geographic locations, and biological factors were associated with the composition and assembly of bacterial, protist, and fungal communities. Among the environmental variables, dissolved oxygen and salinity were the main predictors that jointly affected the differences in the community structure of the three microorganisms, and geographic location was the second predictor affecting the community structure of the three microorganisms and had a more pronounced effect on the diversity and network structure of the bacterial and fungal communities. However, biological factors exerted a weaker effect on the microbial community structure than spatial factors and only affected bacteria and protists; the invasive species Mytilopsis sallei only affected the process of protist community assembly. In addition, environmental variables affected the relative importance of stochastic processes. In summary, the formation of microbial communities in the PRETZ was affected by random processes, environmental variables, geographic location, and invasive species.

Early warning of red tides using bacterial and eukaryotic communities in nearshore waters

Anthropogenic discharge activities have increased nutrient pollution in coastal areas, leading to algal blooms and microbial community changes. Particularly, microbial communities could easily be affected with variation in nutrient pollution, and thus offered a promising strategy to predict early red tides warning via microbial community-levels variation and their keystone taxa hysteretic responses to nutrient pollution. Herein high-throughput sequencing technology from 52 samples were used to explore the variation of microbial communities and find the significant tipping points with aggravating nutrient conditions in Xiaoping Island coastal area. Results indicated that bacterial and microeukaryote communities were generally spatial and seasonal heterogeneity and were influenced by the different nutrient conditions. Procrustes test results showed that the comprehensive index of organics polluting (OPI), total nitrogen (TN), inorganic nitrogen (DIN), and total phosphorus (TP) were significantly correlated with the composition of bacteria and microeukaryotes. A SEGMENTED analysis revealed that the threshold of TN, DIN, and NH₄-N for bacterial community were 0.23 ± 0.091 mg/L, 0.21 ± 0.084 mg/L, 0.09 ± 0.057 mg/L, respectively. Tipping points for TN, DIN, and NH₄-N agreed with the concentration during Ceratium tripos and Skeletonema costatum blooms. Co-occurrence network results found that Planktomarina, Acinetobacter, and Verrucomicrobiaceae were keystone and OPI-discriminatory taxa. The abundant changes of Planktomarina at station A1 were significantly correlated with the development of C. tripos blooms (r = 0.55, p < 0.05), and also significantly correlated with TN, DIN, and NO₃-N (r≥|0.55|, p < 0.05). The abundant changes of Acinetobacter and Verrucomicrobiaceae at station C1 were significantly correlated with the development of C. tripos blooms (r ≥ 0.77, p < 0.05), and also significantly correlated with PO₄-P (r ≥ 0.64, p < 0.05). The dynamic abundance of keystone taxa showed that the trend of rapid changes could be monitored 1.5 months before the occurrence of red tide. Therefore, this study provides an assessment method for early warning of red tide occurrence and factors that trigger red tide.

Seasonal variation of phytoplankton community assembly processes in Tibetan Plateau floodplain

Uncovering the mechanisms underlying phytoplankton community assembly remains a major challenge in freshwater ecology. The roles of environmental filtering and spatial processes in shaping phytoplankton metacommunity in Tibetan floodplain ecosystems under various hydrological conditions are still unclear. Here, multivariate statistics and a null model approach were used to compare the spatiotemporal patterns and assembly processes of phytoplankton communities in the river-oxbow lake system of Tibetan Plateau floodplain between non-flood and flood periods. The results showed that phytoplankton communities had significant seasonal and habitat variations, with the seasonal variations being more remarkable. Phytoplankton density, biomass, and alpha diversity were distinctly lower in the flood than non-flood period. The habitat differences (rivers vs. oxbow lakes) in phytoplankton community were less pronounced during the flood than non-flood period, most likely due to the increased hydrological connectivity. There was a significant distance-decay relationship only in lotic phytoplankton communities, and such relationship was stronger in the non-flood than flood period. Variation partitioning and PER-SIMPER analysis showed that the relative role of environmental filtering and spatial processes affecting phytoplankton assemblages varied across hydrological periods, with environmental filtering dominating in the non-flood period and spatial processes in the flood period. These results suggest that the flow regime plays a key role in balancing environmental and spatial factors in shaping phytoplankton communities. This study contributes to a deeper understanding of ecological phenomena in highland floodplains and provides a theoretical basis for floodplain ecosystem maintenance and ecological health management.

Environmental DNA metabarcoding reveals the impacts of anthropogenic pollution on multitrophic aquatic communities across an urban river of western China

Anthropogenic activities are intensively affecting the structure and function of biological communities in river ecosystems. The effects of anthropogenic pollution on single-trophic community have been widely explored, but their effects on the structures and co-occurrence patterns of multitrophic communities remain largely unknown. In this study, we collected 13 water samples from the Neijiang River in Chengdu City of China, and identified totally 2352 bacterial, 207 algal, 204 macroinvertebrate, and 33 fish species based on the eDNA metabarcoding to systematically investigate the responses of multitrophic communities to environmental stressors. We observed significant variations in bacterial, algal, and macroinvertebrate community structures (except fish) with the pollution levels in the river. Network analyses indicated a more intensive interspecific co-occurrence pattern at high pollution level. Although taxonomic diversity of the multitrophic communities varied insignificantly, phylogenetic diversities of fish and algae showed significantly positive and negative associations with the pollution levels, respectively. We demonstrated the primary role of environmental filtering in driving the structures of bacteria, algae, and macroinvertebrates, while the fish was more controlled by dispersal limitation. Nitrogen was identified as the most important factor impacting the multitrophic community, where bacterial composition was mostly associated with NO₃^--N, algal spatial differentiation with TN, and macroinvertebrate and fish with NH₄⁺-N. Further partial least-squares path model confirmed more important effect of environmental variables on the relative abundance of bacteria and algae, while macroinvertebrate and fish communities were directly driven by the algae-mediated pathway in the food web. Our study highlighted the necessity of integrated consideration of multitrophic biodiversity for riverine pollution management, and emphasized the importance of controlling nitrogen inputs targeting a healthy ecosystem.

Denitrifying anaerobic methane-oxidizing bacteria in river networks of the Taihu Basin: Community dynamics and assembly process

Denitrifying anaerobic methane-oxidizing bacteria (DAMO bacteria) plays an important role in reducing methane emissions from river ecosystems. However, the assembly process of their communities underlying different hydrologic seasons remains unclarified. In this study, the dynamics of DAMO bacterial communities in river networks of the Taihu Basin were investigated by amplicon sequencing across wet, normal, and dry seasons followed by multiple statistical analyses. Phylogenetic analysis showed that Group B was the major subgroup of DAMO bacteria and significant dynamics for their communities were observed across different seasons (constrained principal coordinate analysis, p = 0.001). Furthermore, the neutral community model and normalized stochasticity ratio model were applied to reveal the underlying assembly process. Stochastic process and deterministic process dominated the assembly process in wet season and normal season, respectively and similar contributions of deterministic and stochastic processes were observed in dry season. Meanwhile, abundant (relative abundance >0.1%) and rare (relative abundance <0.01%) DAMO bacterial communities were found to be shaped via distinct assembly processes. Deterministic and stochastic processes played a considerable role in shaping abundant DAMO bacterial communities, while deterministic process mainly shaped rare DAMO bacterial communities. Results of this study revealed the dynamics of DAMO bacterial communities in river networks and provided a theoretical basis for further understanding of the assembly process.

The scale-dependence of spatial distribution of reservoir plankton communities in subtropical and tropical China

Distance-decay relationships (DDRs) represent a very useful approach to describing the spatial distribution of biological communities. However, plankton DDR patterns and community assembly mechanisms are still poorly understood at different spatial scales in reservoir ecosystems. We collected phytoplankton, zooplankton and water samples in 24 reservoirs from subtropical and tropical China from July to August 2018. We examined DDR patterns across three distinct spatial scales, i.e., within-reservoir, within-drainage (but between reservoirs) and between drainages. We tested whether the rate of change (i.e., slope) of DDRs is consistent across different spatial scales. We assessed the relative importance of spatial and environmental variables in shaping the community distribution of plankton and quantitatively distinguished the community assembly mechanisms. We observed significant DDR curves in phytoplankton and zooplankton communities, in which slopes of the DDRs were steepest at the smallest spatial scale. Both spatial and environmental factors had significant impacts on DDR and dispersal assembly was a slightly stronger process in reservoir phytoplankton and zooplankton community assembly than niche-based process. We conclude that DDRs of reservoir phytoplankton and zooplankton vary with spatial scale. Our data shed light on how spatial and environmental variables contribute to plankton community assembly together. However, we revealed that dispersal process contributes to the biogeography of reservoir plankton slightly more strongly than environmental filtering. Collectively, this study enhances the understanding of plankton biogeography and distribution at multiple spatial scales.

New insights into cyanobacterial blooms and the response of associated microbial communities in freshwater ecosystems

Cyanobacterial blooms are important environmental problems in aquatic ecosystems. Researchers have found that cyanobacterial blooms cannot be completely prevented by controlling and/or eliminating pollutants (nutrients). Thus, more in-depth basic research on the mechanism of cyanobacterial blooms is urgently needed. Cyanobacteria, being primordial microorganisms, provide habitats and have various forms of interactions (reciprocity and competition) with microorganisms, thus having a significant impact on themselves. However, little is known about how environmental conditions and microbial communities in both water and sediment jointly affect cyanobacterial blooms or about the co-occurrence patterns and interactions of microbial communities. We investigated changes in environmental factors and microbial communities in water and sediment during different cyanobacterial blooms and revealed their interacting effects on cyanobacteria. Cyanobacteria had greater competitive and growth advantages than other microorganisms and had antagonistic and aggressive effects on them when resources (such as nutrients) were abundant. Furthermore, microbial networks from cyanobacterial degradation periods may be more complex and stable than those from bloom periods, with more positive links among the microbial networks, suggesting that microbial community structures strengthen interconnections with each other to degrade cyanobacteria. In addition, we found that sediment-enriched cyanobacteria play a key role in cyanobacterial blooms, and sediment microorganisms promote the nutrient release, further promoting cyanobacterial blooms in the water bodies. The study contributes to further our understanding of the mechanisms for cyanobacterial blooms and microbial community structural composition, co-occurrence patterns, and responses to cyanobacteria. These results can contribute to future management strategies for controlling cyanobacterial blooms in freshwater ecosystems.

Drivers of Spatiotemporal Eukaryote Plankton Distribution in a Trans-Basin Water Transfer Canal in China

Planktonic eukaryotes are important components of aquatic ecosystems, and analyses of the whole eukaryotic planktonic community composition and function have far-reaching significance for water resource management. We aimed to understand the spatiotemporal variation and drivers of eukaryotic plankton distribution in the Middle Route Project of the South-to-North Water Diversion in Henan Province, China. Specifically, we examined planktonic assemblages and water quality at five stations along the canal and another one located before the dam in March, June, September, and December 2019. High-throughput sequencing revealed that the eukaryotic plankton community was primarily composed of 53 phyla, 200 genera, and 277 species, with Cryptophyta, Ciliophora, and norank_k_Cryptophyta being the dominant phyla. Redundancy analysis of the eukaryotic community and environmental factors showed that five vital factors affecting eukaryotic plankton distribution were oxidation-reduction potential, nitrate nitrogen, pH, total phosphorus, and water flow velocity. Furthermore, the geographical distribution of eukaryotic communities was consistent with the distance decay model. Importantly, environmental selection dominantly shaped the geographical distribution of the eukaryotic community. In summary, our study elucidates the ecological response of planktonic eukaryotes by identifying the diversity and ecological distribution of planktonic eukaryotes in trans-basin diversion channels.

Temporal heterogeneity of bacterial communities and their responses to Raphidiopsis raciborskii blooms

To elucidate the interspecies connectivity between cyanobacteria and other bacteria (noncyanobacteria), microbial diversity and composition were investigated through high-throughput sequencing (HTS) in a drinking water reservoir in Chongqing city, Southwest China, during Raphidiopsis raciborskii blooms. Significant temporal changes were observed in microbial community composition during the sampling period, primarily reflected by variations in relative bacterial abundance. The modularity analysis of the network demonstrated that the bacterial community forms co-occurrence/exclusion patterns in response to variations in environmental factors. Moreover, five modules involved in the dynamic phases of the R. raciborskii bloom were categorized into the Pre-Bloom, Bloom, Post-Bloom, and Non-Bloom Groups. The reservoir was eutrophic (i.e., the average concentrations of total nitrogen (TN) and total phosphorus (TP) were 2.32 and 0.07 mg L^-1, respectively) during the investigation; however, Pearson's correlation coefficient showed that R. raciborskii was not significantly correlated with nitrogen and phosphorus. However, other environmental factors, such as water temperature, pH, and the permanganate index, were positively correlated with R. raciborskii. Importantly, Proteobacteria (α-, γ-Proteobacteria), Acidobacteria, Chloroflexi, and Firmicutes were preferentially associated with increased R. raciborskii blooms. These results suggested that the transition of R. raciborskii bloom-related microbial modules and their keystone species could be crucial in the development and collapse of R. raciborskii blooms and could provide a fundamental basis for understanding the linkage between the structure and function of the microbial community during bloom dynamics.

Microeukaryotic Community Shifting Along a Lentic-Lotic Continuum

As an important regulator of ecosystem functions in river systems, microeukaryotes play an important role in energy and material conversion, yet little is known about the shift along a lentic-lotic continuum. In this study, the 18S rRNA genes sequencing was used to identify the microeukaryotic communities at 82 sites along a lentic-lotic continuum with the aim of understanding the impact of upstream inlet river on microeukaryotic communities in Baiyang Lake (BYD) and its downstream. Our results showed that the upstream inlet river affected the diversity and community composition of microeukaryotes in BYD and downstream rivers, and environmental variables greatly affected the composition of microeukaryotic community. The community composition in BYD had lower variabilities. Co-occurrence network analysis revealed that the network was non-random and clearly parsed into three modules, and different modules were relatively more abundant to a particular area. As keystone taxa, some nodes of the upstream microeukaryotic network played an important role in structuring network and maintaining the stability of the ecosystem. In BYD and downstream, the microeukaryotic network was highly fragmented, and the loss of keystone taxa would have an adverse impact on the integrity and function of the microeukaryotic community. Microeukaryotes had strong tendencies to co-occur, which may contribute to the stability and resilience of microeukaryotic communities. Overall, these findings extend the current understanding of the diversity and community composition of microeukaryotic along a lentic-lotic continuum.

Small Run-of-River Dams Affect Taxonomic and Functional β-Diversity, Community Assembly Process of Benthic Diatoms

Being increasingly constructed worldwide, dams are a main driver of flow regime change and biodiversity decline. Although small run-of-river dams have exceeded the number of large dams, their impacts on taxonomic and functional β-diversity as well as community assembly process of aquatic organisms have been largely neglected. Ninety sites within twenty three small run-of-river dams in the Xiangxi River were selected, and the hydrological and physicochemical variables for each site were measured. We analyzed the traits and β-diversity of benthic diatoms, and explored the key driving mechanism of benthic diatom community assembly. Our results indicated that the construction of small run-of-river dams could affect the β-diversity of benthic diatoms and the mechanism of community assembly. Specifically, we found that small run-of-river dams could change the relative contribution of nestedness components to the trait-based β-diversity of benthic diatoms, but generally the taxonomy-based β-diversity was relatively higher than the trait-based β-diversity. Furthermore, the community assembly process of benthic diatoms was also affected. In areas affected directly by small run-of-river dams, dispersal assembly was the key mechanism for community assembly. Compared to unregulated habitats, the dispersal assembly process between the impacted and the unregulated habitats has been enhanced. We advocate that this study can be expanded to other organisms (such as macroinvertebrates, phytoplankton, fish) in future to fully understand impacts of small run-of-river dams on biodiversity from a multi-trophic level aspect. Based on our results, we suggest that maintaining genetic and ecological connectivity based on an effective impact assessment in dry seasons is a potential solution to mitigate the impacts of such dams, as key to adaptive management and sustainability.

Coupled effects of landscape structures and water chemistry on bacterioplankton communities at multi-spatial scales

Bacterioplankton communities in rivers are strongly influenced by the surrounding landscape, yet the relationships between land use and bacterioplankton communities at multi-spatial scales and the mechanisms that shape bacterioplankton communities remain unclear. Here, we collected surface water samples from 14 tributaries of the Yuan River, a secondary tributary of the Yangtze River, which has been heavily impacted by human activities. We characterized the bacterioplankton communities by high-throughput sequencing techniques, and managed to identify the mechanisms governing bacterioplankton community assembly. The results showed that, in general, both landscape compositions and landscape configurations had significant effects on bacterial communities, and the effects were greater at the buffer scale than at the sub-basin scale. Additionally, there was no distinct distance-decay pattern for the effects of landscape structures on bacterial communities from the near-distance (100 m) to the long-distance (1000 m) buffer zones, with the maximal effects occurring in the 1000 m circular buffer (wet season) and 500 m riparian buffer (dry season) zone, respectively. Land use influenced the bacterioplankton community both directly through exogenous inputs (mass effect) and indirectly by affecting water chemistry (species sorting). Variance partitioning analyses showed that the total explanations of bacterial community variations by water chemistry and the intersections of water chemistry and land use (56.2% in wet season and 50.4% in dry season) were higher than that of land use alone (6.1% in wet season and 25.4% in dry season). These suggest that mass effects and species sorting jointly shaped bacterial community assembly, but that the effects of species sorting outweighed those of mass effects. Nevertheless, more biotic and abiotic factors need to be considered to better understand the microbial assembly mechanisms in anthropogenically influenced riverine ecosystems.

Similar geographic patterns but distinct assembly processes of abundant and rare bacterioplankton communities in river networks of the Taihu Basin

Bacterioplankton play an important role in the biogeochemical cycling in rivers. The dynamics of hydrologic conditions in rivers were believed to affect geographic pattern and assembly process of these microorganisms, which have not been widely investigated. In this study, the geographic pattern and assembly process of bacterioplankton community in river networks of the Taihu Basin were systematically explored using amplicon sequencing of the 16S rRNA gene. The results showed that the diversity, structure,  and taxonomic composition of bacterioplankton community all exhibited significant temporal variation during wet, normal, and dry seasons (p<0.01). The neutral community model and null model were applied to reveal the assembly process of bacterioplankton community. The stochastic process and deterministic process both shaped the bacterioplankton community with greater influence of deterministic process. In addition, the abundant and rare bacterioplankton communities were comparatively analyzed. The abundant and rare bacterioplankton communities exhibited similar temporal dynamics (principal coordinates analysis) and spatial variations (distance-decay relationship), indicating similar geographic patterns. Meanwhile, distinct assembly processes were observed for the abundant and rare bacterioplankton communities. Stochastic process (dispersal limitation) shaped the abundant bacterioplankton community while deterministic process (heterogeneous selection) dominated the assembly process of rare bacterioplankton community. Mantel test, redundancy analysis, and correlation analysis together indicated that pH and dissolved oxygen were the major environmental attributes that affected thestructure and assembly process of bacterioplankton community. These results expanded our understanding of the geographic pattern, assembly process, and driving factors of bacterioplankton community in river networks and provided clues for the underlying mechanisms.

Urbanization reduces resource use efficiency of phytoplankton community by altering the environment and decreasing biodiversity

Urbanization often exerts multiple effects on aquatic and terrestrial organisms, including changes in biodiversity, species composition and ecosystem functions. However, the impacts of urbanization on river phytoplankton in subtropical urbanizing watersheds remain largely unknown. Here, we explored the effects of urbanization on phytoplankton community structure (i.e., biomass, community composition and diversity) and function (i.e., resource use efficiency) in a subtropical river at watershed scale in southeast China over 6 years. A total of 318 phytoplankton species belonging into 120 genera and 7 phyla were identified from 108 samples. Bacillariophyta biomass showed an increasing trend with increasing urbanization level. The phytoplankton community shifted from Chlorophyta dominance in rural upstream waters to Bacillariophyta dominance in urbanized downstream waters. Furthermore, phytoplankton diversity and resource use efficiency (RUE = phytoplankton biomass/total phosphorus) were significantly decreased with increasing urbanization level from upstream to downstream. Phytoplankton RUE exhibited a significant positive correlation with species richness, but a negative correlation with phytoplankton evenness. The variation in environmental factors (turbidity, total nitrogen, NH₄⁺-N, total phosphorus, PO₄^3--P and percentage urbanized area) was significantly correlated with phytoplankton diversity and RUE. Overall, our results revealed the influence of urbanization on phytoplankton community structure and ecosystem function was due to its altering the environmental conditions. Therefore, human-driven urbanization may play crucial roles in shaping the structure and function of phytoplankton communities in subtropical rivers, and the mechanism of this process can provide important information for freshwater sustainable uses, watershed management and conservation.

Disentangling the Ecological Processes Shaping the Latitudinal Pattern of Phytoplankton Communities in the Pacific Ocean

Phytoplankton diversity and community compositions vary across spaces and are fundamentally affected by several deterministic (e.g., environmental selection) and stochastic (e.g., ecological drift) processes. How this suite of different processes regulates the biogeography of phytoplankton remains to be comprehensively explored. Using high-throughput sequencing data and null model analysis, we revealed the ecological processes shaping the latitudinal community structure of three major phytoplankton groups (i.e., diatoms, Synechococcus, and haptophytes) across the Pacific Ocean (70°N, 170°W to 35°S, 170°W). At the basin scale, heterogeneous selection (selection under heterogeneous environmental conditions) dominated the assembly processes of all phytoplankton groups; however, its relative importance varied greatly at the climatic zonal scale, explaining the distinct latitudinal α- and β-diversity among phytoplankton groups. Assembly processes in Synechococcus and haptophyte communities were mainly controlled by physical and nutrient factors, respectively. High temperature drove Synechococcus communities to be more deterministic with higher diversity, while haptophyte communities were less environmentally selected at low latitudes due to their wide niche breadth and mixotrophic lifestyle. Diatom communities were overwhelmingly dominated by the selection process but with low correlation of measured environmental factors to their community compositions. This could be attributed to the high growth rate of diatoms, as indicated by their lower site occupation frequency than predicted in the neutral community model. Our study showed that heterogeneous selection is the main force that shaped the biogeography of three key phytoplankton groups in the Pacific Ocean, with a latitudinal variation of relative importance due to the distinct traits among phytoplankton.

IMPORTANCE Phytoplankton are diverse and abundant as primary producers in the ocean, with diversity and community compositions varying spatially. How fundamental processes (e.g., selection, dispersal, and drift) regulate their global biogeography remains to be comprehensively explored. In this study, we disentangled the ecological processes of three key phytoplankton groups (i.e., diatoms, Synechococcus, and haptophytes) along the same latitudinal gradients in the Pacific Ocean. Heterogeneous selection, by promoting species richness and reducing similarity between communities, was the dominant process shaping the communities of each phytoplankton group at the basin scale. However, its relative importance varied greatly among different phytoplankton groups in different climate zones, explaining the uneven latitudinal α- and β-diversity. We also highlight the importance of identifying key factors mediating the relative importance of assembly processes in phytoplankton communities, which will enhance our understanding of their biogeography in the ocean and future patterns under climate changes.

Implications of flow regulation for habitat conditions and phytoplankton populations of the Nakdong River, South Korea

Anthropogenic regulation of hydrographs is a widespread approach to river management; however, the effects of river regulation on habitat conditions and aquatic communities have rarely been studied. In this study, we analyzed the physical, chemical, and biological data from the lower Nakdong River in South Korea from 2005 to 2009 before weir construction and from 2012 to 2016 after weir construction. A partial least square path model (PLS-PM) was applied to delineate the complex interrelationships of diatoms and cyanobacteria with physicochemical parameters, nutrients, zooplankton grazing, and hydrological parameters. Inferential modeling using the hybrid evolutionary algorithm (HEA) allowed the identification of differences in the importance and threshold conditions of population dynamics drivers of diatoms and cyanobacteria before and after flow regulation. The annually averaged trajectories of limnological variables displayed significant shifts in seasonality and magnitudes of phytoplankton, zooplankton, and nutrient concentrations between the two periods. The results of PLS-PM indicated that, after flow regulation, diatoms and cyanobacteria were directly affected by nutrients and zooplankton densities and the path coefficients of hydrological parameters decreased or even were insignificant. The inferential models suggested that diatom dynamics were essentially shaped by threshold conditions of water temperature (WT) and pH before regulation, but mainly by those of rotifers (below 51.1 ind. L^-1) after regulation. As for cyanobacteria dynamics, WT was identified as a critical threshold condition before and after regulation, and the threshold of PO₄^- concentration above 145.4 L^-1 was identified as the reason for occasional blooms during the post-regulation period. Overall, the results suggest that flow regulation gradually alters habitat conditions typically of rivers to those of stagnant waters. These findings must be taken into account for sustainable management strategies of regulated rivers.

Geo-climatic factors weaken the effectiveness of phytoplankton diversity as a water quality indicator in a large sediment-laden river

The study aims to determine whether phytoplankton diversity can be used as an indicator of water quality in large-scale sediment-laden rivers with heterogeneous environmental conditions. We hypothesized that environmental factors, such as sediment load, water surface slope, and precipitation, may impact the effectiveness of using phytoplankton diversity as a water quality indicator. To test this hypothesis, the Yellow River was selected for phytoplankton diversity and water quality assessments. We measured water quality parameters, calculated phytoplankton diversity indices, and collected data on geo-climatic variables at 130 sampling points in the Yellow River mainstream over two seasons (spring and autumn) in 2019. The results of the water quality assessment based on phytoplankton diversity indices were compared with those based on water quality index (WQI). Correlation analysis, multiple stepwise regression, distance-based redundancy analysis, and regression modeling were used to explore the biogeographical patterns and drivers of phytoplankton diversity. According to the WQI, the water quality gradually deteriorated from the source to the estuary of the river. Three biodiversity indices (Margalef, Pielou, and Shannon-Wiener) indicated that the water quality varied dynamically in the middle reaches of the river. The actual relationships between the biodiversity indices and WQI did not fit well with the standard curves of water quality classification based on the respective biodiversity indices and WQI. Variation partitioning analysis indicated that water quality parameters, such as sediment and nutrient load, were the dominant drivers of variation in phytoplankton diversity in most cases, with the contribution ranging from 11.0% to 25.7%. Geo-climatic factors, such as water surface slope and annual mean precipitation, also affected phytoplankton diversity, with the contribution reaching 27.8%. Therefore, in sediment-laden rivers with a large geographical span and complex environment, phytoplankton diversity cannot be used as a suitable water quality indicator, albeit it can reflect habitat changes to a certain extent.

How sediment bacterial community shifts along the urban river located in mining city

Bacterial communities play critical roles in biogeochemical cycles and serve as sensitive indicators of environmental fluctuation. However, the influence of mineral resource exploitation on shaping the bacterial communities in the urban river is still ambiguous. In this study, high-throughput sequencing was used to determine the spatial distribution of the sediment bacterial communities along an urban river in the famous mining city Panzhihua of China. The results showed that mineral resource exploitation had a significant impact on the urban river bacterial community structure but not on the bacterial ecological functions. Distinct families of bacteria often associated with nutrients (i.e., Comamonadaceae and Sphingomonadaceae) and metal contaminants (i.e., Rhodobacteraceae) were more predominant in the residential and mining area, respectively. Relative to dispersal dynamics, environmentally induced species sorting may primarily influence bacterial community structure. Heavy metals and sediment physicochemical properties had both similar and significant influence on shaping bacterial community structure. Among heavy metals, essential metal elements explained more rates of bacterial variation than toxic metals at moderate contaminant levels. Moreover, the bacteria with multiple metal resistances identified in culture-dependent experiments were probably not suitable for indicating heavy metal contamination in field research. Thus, several sensitive bacterial genera such as Rhodobacter, Hylemonella, and Dechloromonas were identified as potential bioindicators to monitor metals (iron and titanium) and nutrients (phosphorus and organic carbon) in the river ecosystem of the Panzhihua region. Together, these results profiled the coupling effect of urbanization and mineral resource utilization on shaping sediment bacterial communities in urban rivers.

Characteristics of phytoplankton-zooplankton communities and the roles in the transmission of antibiotic resistance genes under the pressure of river contamination

Insight into the distribution of antibiotic resistance genes (ARGs) in phytoplankton-zooplankton communities (PZCs) is essential for the management and control of antibiotic resistance in aquatic ecosystems. This study characterized the profiles of PZCs and their carried ARGs in a typical urban river and ranked the factors (water physicochemical parameters, PZCs, bacterial abundance, and mobile genetic elements) influencing the dynamic of ARG profiles by the partial least squares path modeling. Results showed Cyanobacteria, Bacillariophyta and Chlorophyta were dominant phyla of phytoplankton, and Rotifera was with the highest abundance in zooplankton. River contamination markedly altered the structure of PZCs, increasing the abundance of phytoplankton and zooplankton, decreasing the diversity of phytoplankton while elevating in zooplankton. PZCs harbored large amounts of ARGs with average relative abundance of 2.35 × 10^-2/copies nearly an order magnitude higher than the living water and most ARGs exhibited significant accumulation in PZCs with the aggravated environmental pollution. The partial least squares path modeling predicted the water parameters as the most important factor mainly playing indirect effects on ARGs via PZCs and bacterial communities, followed by mobile genetic elements as the most essential direct factor for ARGs profiles. Besides, PZCs were also important drivers for the carried ARGs via direct effects on the ARGs' composition and indirect effects on host bacterial communities of ARGs and their mobile genetic elements. The present study fills the gaps in knowledge about the distribution of ARGs in PZCs and provided a new perspective to decipher the key roles of PZCs in the maintenance and dissemination of ARGs in urban river ecosystems.

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.

Environmental filtering dominates bacterioplankton community assembly in a highly urbanized estuarine ecosystem

Estuaries are important in terms of biodiversity, biogeochemical function, and ecological balance due to their intense land-sea interactions. The sustainability of estuarine ecosystem function relies on a good understanding of the ecological processes related to microbial communities. However, microbial community assembly in such ecosystems is still not well understood. Here, based on 16S rRNA sequencing, we investigated the bacterioplankton community structure in the Pearl River Estuarine system during the wet and dry seasons. Results showed that there were significant seasonal and spatial variations in the bacterioplankton communities of the estuary, with seasonal variations being more remarkable. Multiple bacterioplankton with different abundances in the wet and dry seasons were observed, e.g., the class Actinobacteria and Oxyphotobacteria were enriched in the wet season, whereas Alphaproteobacteria and Saccharimonadia were more abundant in the dry season. Both variation partitioning and null model analysis revealed that environmental filtering dominated the bacterioplankton community assembly in the Pearl River Estuary. Water physical properties (e.g., salinity and temperature), nutrient content (e.g., nitrate), and upstream land use (e.g., urban land cover) together determined the distribution of the bacterioplankton composition in this highly urbanized estuarine ecosystem. These findings would help improve our understanding of the bacterioplankton communities in estuarine ecosystems and provide a theoretical foundation for estuarine ecological health management.

Responses of abundant and rare bacterioplankton to temporal change in a subtropical urban reservoir

Investigation of bacterial community dynamics across different time scales is important for understanding how environmental conditions drive community change over time. Bacterioplankton from the surface waters of a subtropical urban reservoir in southeast China were analyzed through high-frequency sampling over 13 months to compare patterns and ecological processes between short (0‒8 weeks), medium (9‒24 weeks) and long (25‒53 weeks) time intervals. We classified the bacterial community into different subcommunities: abundant taxa (AT); conditionally rare taxa (CRT); rare taxa (RT). CRT contributed > 65% of the alpha-diversity, and temporal change of beta-diversities was more pronounced for AT and CRT than RT. The bacterial community exhibited a directional change in the short- and medium-time intervals and a convergent dynamic during the long-time interval due to a seasonal cycle. Cyanobacteria exhibited a strong succession pattern than other phyla. CRT accounted for > 76% of the network nodes in three stations. The bacteria-environment relationship and deterministic processes were stronger for large sample size at station G (n = 116) than small sample size at stations C (n = 12) and L (n = 22). These findings suggest that a high-frequency sampling approach can provide a better understanding on the time scales at which bacterioplankton can change fast between being abundant or rare, thus providing the facts about environmental factors driving microbial community dynamics. Patterns and processes in alpha- and beta-diversities and community assembly of bacterioplankton differ among different time intervals (short-, medium- and long-time intervals) and different subcommunities (abundant, conditionally rare and rare taxa) in a subtropical urban reservoir, demonstrating the importance of temporal scale and high-frequency sampling in microbial community ecology.

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

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