Distinct Bacterial Communities in Wet and Dry Seasons During a Seasonal Water Level Fluctuation in the Largest Freshwater Lake (Poyang Lake) in China

Rainfall seasonality shapes microbial assembly and niche characteristics in Yunnan Plateau lakes, China

Microorganisms are crucial components of freshwater ecosystems. Understanding the microbial community assembly processes and niche characteristics in freshwater ecosystems, which are poorly understood, is crucial for evaluating microbial ecological roles. The Yunnan Plateau lakes in China represent a freshwater ecosystem that is experiencing eutrophication due to anthropogenic activities. Here, variation in the assembly and niche characteristics of both prokaryotic and microeukaryotic communities was explored in Yunnan Plateau lakes across two seasons (dry season and rainy season) to determine the impacts of rainfall and environmental conditions on the microbial community and niche. The results showed that the environmental heterogeneity of the lakes decreased in the rainy season compared to the dry season. The microbial (bacterial and microeukaryotic) α-diversity significantly decreased during the rainy season. Deterministic processes were found to dominate microbial community assembly in both seasons. β-Diversity decomposition analysis revealed that microbial community compositional dissimilarities were dominated by species replacement processes. The co-occurrence networks indicated reduced species complexity for microbes and a destabilized network for prokaryotes prior to rainfall, while the opposite was found for microeukaryotes following rainfall. Microbial niche breadth decreased significantly in the rainy season. In addition, lower prokaryotic niche overlap, but greater microeukaryotic niche overlap, was observed after rainfall. Rainfall and environmental conditions significantly affected the microbial community assembly and niche characteristics. It can be concluded that rainfall and external pollutant input during the seasonal transition alter the lake environment, thereby regulating the microbial community and niche in these lakes. Our findings offer new insight into microbiota assembly and niche patterns in plateau lakes, further deepening the understanding of freshwater ecosystem functioning.

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.

Microbial community and extracellular polymeric substance dynamics in arid-zone temporary pan ecosystems

Microbial extracellular polymeric substances (EPS) are an important component in sediment ecology. However, most research is highly skewed towards the northern hemisphere and in more permanent systems. This paper investigates EPS (i.e., carbohydrates and proteins) dynamics in arid Austral zone temporary pans sediments. Colorimetric methods and sequence-based metagenomics techniques were employed in a series of small temporary pan ecosystems characterised by alternating wet and dry hydroperiods. Microbial community patterns of distribution were evaluated between seasons (hot-wet and cool-dry) and across depths (and inferred inundation period) based on estimated elevation. Carbohydrates generally occurred in relatively higher proportions than proteins; the carbohydrate:protein ratio was 2.8:1 and 1.6:1 for the dry and wet season respectively, suggesting that EPS found in these systems was largely diatom produced. The wet- hydroperiods (Carbohydrate mean 102 μg g-1; Protein mean 65 μg g-1) supported more EPS production as compared to the dry- hydroperiods (Carbohydrate mean 73 μg g-1; Protein mean 26 μg g-1). A total of 15,042 Unique Amplicon Sequence Variants (ASVs) were allocated to 51 bacterial phyla and 1127 genera. The most abundant genera had commonality in high temperature tolerance, with Firmicutes, Actinobacteria and Proteobacteria in high abundances. Microbial communities were more distinct between seasons compared to within seasons which further suggested that the observed metagenome functions could be seasonally driven. This study's findings implied that there were high levels of denitrification by mostly nitric oxide reductase and nitrite reductase enzymes. EPS production was high in the hot-wet season as compared to relatively lower rates of nitrification in the cool-dry season by ammonia monooxygenases. Both EPS quantities and metagenome functions were highly associated with availability of water, with high rates being mainly associated with wet- hydroperiods compared to dry- hydroperiods. These data suggest that extended dry periods threaten microbially mediated processes in temporary wetlands, with implications to loss of biodiversity by desiccation.

Bacterial and fungal community structures in Hulun Lake are regulated by both stochastic processes and environmental factors

Microorganisms are a crucial component of lake ecosystems and significant contributors to biogeochemical cycles. However, the understanding of how primary microorganism groups (e.g., bacteria and fungi) are distributed and constructed within different lake habitats is lacking. We investigated the bacterial and fungal communities of Hulun Lake using high-throughput sequencing techniques targeting 16S rRNA and Internal Transcribed Spacer 2 genes, including a range of ecological and statistical methodologies. Our findings reveal that environmental factors have high spatial and temporal variability. The composition and community structures vary significantly depending on differences in habitats. Variance partitioning analysis showed that environmental and geographical factors accounted for <20% of the community variation. Canonical correlation analysis showed that among the environmental factors, temperature, pH, and dissolved oxygen had strong control over microbial communities. However, the microbial communities (bacterial and fungal) were primarily controlled by the dispersal limitations of stochastic processes. This study offers fresh perspectives regarding the maintenance mechanism of bacterial and fungal biodiversity in lake ecosystems, especially regarding the responses of microbial communities under identical environmental stress.IMPORTANCELake ecosystems are an important part of the freshwater ecosystem. Lake microorganisms play an important role in material circulation and energy flow owing to their unique enzymatic and metabolic capacity. In this study, we observed that bacterial and fungal communities varied widely in the water and sediments of Hulun Lake. The primary factor affecting their formation was identified as dispersal limitation during stochastic processes. Environmental and geographical factors accounted for <20% of the variation in bacterial and fungal communities, with pH, temperature, and dissolved oxygen being important environmental factors. Our findings provide new insights into the responses of bacteria and fungi to the environment, shed light on the ecological processes of community building, and deepen our understanding of lake ecosystems. The results of this study provide a reference for lake management and conservation, particularly with respect to monitoring and understanding microbial communities in response to environmental changes.

Spatiotemporal successions of N, S, C, Fe, and As cycling genes in groundwater of a wetland ecosystem: Enhanced heterogeneity in wet season

Microorganisms in wetland groundwater play an essential role in driving global biogeochemical cycles. However, largely due to the dynamics of spatiotemporal surface water-groundwater interaction, the spatiotemporal successions of biogeochemical cycling in wetland groundwater remain poorly delineated. Herein, we investigated the seasonal coevolution of hydrogeochemical variables and microbial functional genes involved in nitrogen, carbon, sulfur, iron, and arsenic cycling in groundwater within a typical wetland, located in Poyang Lake Plain, China. During the dry season, the microbial potentials for dissimilatory nitrate reduction to ammonium and ammonification were dominant, whereas the higher potentials for nitrogen fixation, denitrification, methane metabolism, and carbon fixation were identified in the wet season. A likely biogeochemical hotspot was identified in the area located in the low permeable aquifer near the lake, characterized by reducing conditions and elevated levels of Fe2+ (6.65-17.1 mg/L), NH4+ (0.57-3.98 mg/L), total organic carbon (1.02-1.99 mg/L), and functional genes. In contrast to dry season, higher dissimilarities of functional gene distribution were observed in the wet season. Multivariable statistics further indicated that the connection between the functional gene compositions and hydrogeochemical variables becomes less pronounced as the seasons transition from dry to wet. Despite this transition, Fe2+ remained the dominant driving force on gene distribution during both seasons. Gene-based co-occurrence network displayed reduced interconnectivity among coupled C-N-Fe-S cycles from the dry to the wet season, underpinning a less complex and more destabilizing occurrence pattern. The rising groundwater level may have contributed to a reduction in the stability of functional microbial communities, consequently impacting ecological functions. Our findings shed light on microbial-driven seasonal biogeochemical cycling in wetland groundwater.

Diazotrophic community in the sediments of Poyang Lake in response to water level fluctuations

Water level fluctuations (WLFs) are typical characteristic of floodplain lakes and dominant forces regulating the structure and function of lacustrine ecosystems. The sediment diazotrophs play important roles in contributing bioavailable nitrogen to the aquatic environment. However, the relationship between the diazotrophic community and WLFs in floodplain lakes is unknown. In this paper, we carried out a comprehensive investigation on the alpha diversity, abundance, composition and co-occurrence network of the sediment diazotrophs during different water level phases in Poyang Lake. There were no regular variation patterns in the alpha diversity and abundance of the sediment diazotrophs with the water level phase transitions. The relative abundance of some diazotrophic phyla (including Alphaproteobacteria, Deltaproteobacteri, Euryarchaeota, and Firmicutes) and genera (including Geobacter, Deferrisoma, Desulfuromonas, Rivicola, Paraburkholderia, Methylophilus, Methanothrix, Methanobacterium, and Clostridium) was found to change with the water level phase transitions. The results of ANOSIM, PerMANOVA, and DCA at the OTU level showed that the diazotrophic community structure in the low water level phase was significantly different from that in the two high water level phases, while there was no significant difference between the two high water level phases. These results indicated that the diazotrophic community was affected by the declining water level in terms of the composition, while the rising water level contributed to the recoveries of the diazotrophic community. The diazotrophs co-occurrence network was disrupted by the declining water level, but it was strengthened by the rising water level. Moreover, redundancy analysis showed that the variation of the diazotrophic community composition was mostly related to sediment total nitrogen (TN) and total phosphorous (TP). Interestingly, the levels of sediment TN and TP were also found to vary with the water level phase transitions. Therefore, it might be speculated that the WLFs may influence the sediment TN and TP, and in turn influence the diazotrophic community composition. These data can contribute to broadening our understanding of the ecological impacts of WLFs and the nitrogen fixation process in floodplain lakes.

Spatio-temporal variation of toxin-producing gene abundance in Microcystis aeruginosa from Poyang Lake

Microcystis aeruginosa (M. aeruginosa) causes massive blooms in eutrophic freshwater and releases microcystin. Poyang Lake is the largest freshwater lake in China and has kept a mid-nutrient level in recent years. However, there is little research on microcystin production in Poyang Lake. In this study, water and sediment samples from ten sampling sites in Poyang Lake were collected from May to December in 2020, and from January to April in 2021 respectively. Microcystis genes (mcyA, mcyB, 16 s rDNA) were quantified by real-time fluorescence quantitative PCR analysis, and then the spatial and temporal variation of mcy genes, physicochemical factors, and bacterial population structure in the lake was analyzed. The relationship between the abundance of mcy genes and physicochemical factors in water column was also revealed. Results indicated that the microcystin-producing genes mcyA and mcyB showed significant differences in spatial and temporal levels as well, which is closely related to the physicochemical factors especially the water temperature (p < 0.05) and the nitrogen content (p < 0.05). The abundance of mcy genes in the sediment in December affected the abundance of mcy genes in the water column in the next year, while the toxic Microcystis would accumulate in the sediment. In addition to the toxic Microcystis, we also found a large number of non-toxic Microcystis in the water column and sediment, and the ratio of toxic to non-toxic species can also affect the toxicity production of M. aeruginosa. Overall, the results showed that M. aeruginosa toxin-producing genes in Poyang Lake distributed spatially and temporally which related to the physicochemical factors of Poyang Lake.

Deterministic factors modulating assembly of groundwater microbial community in a nitrogen-contaminated and hydraulically-connected river-lake-floodplain ecosystem

The river-lake-floodplain system (RLFS) undergoes intensive surface-groundwater mass and energy exchanges. Some freshwater lakes are groundwater flow-through systems, serving as sinks for nitrogen (N) entering the lake. Despite the threat of cross-nitrogen contamination, the assembly of the microbial communities in the RLFS was poorly understood. Herein, the distribution, co-occurrence, and assembly pattern of microbial community were investigated in a nitrogen-contaminated and hydraulically-connected RLFS. The results showed that nitrate was widely distributed with greater accumulation on the south than on the north side, and ammonia was accumulated in the groundwater discharge area (estuary and lakeshore). The heterotrophic nitrifying bacteria and aerobic denitrifying bacteria were distributed across the entire area. In estuary and lakeshore with low levels of oxidation-reduction potential (ORP) and high levels of total organic carbon (TOC) and ammonia, dissimilatory nitrate reduction to ammonium (DNRA) bacteria were enriched. The bacterial community had close cooperative relationships, and keystone taxa harbored nitrate reduction potentials. Combined with multivariable statistics and self-organizing map (SOM) results, ammonia, TOC, and ORP acted as drivers in the spatial evolution of the bacterial community, coincidence with the predominant deterministic processes and unique niche breadth for microbial assembly. This study provides novel insight into the traits and assembly of bacterial communities and potential nitrogen cycling capacities in RLFS groundwater.

Response of the nitrogen processing bacterial community to water level fluctuation and nitrate availability in an intact marsh soil column

Wetlands are known to experience fluctuations in water levels and receive exogenous nitrogen inputs that affect various organisms, including soil microorganisms. To study the impact of these factors on microbial diversity, we collected intact soil columns from a Phragmites australis-dominated site in the Qixing River National Nature Reserve in Northeast China. In a laboratory experiment, we simulated water level fluctuations and exogenous nitrogen inputs to the soil columns and examined the associated changes in the relative abundance of 51 bacterial genera involved in nitrogen cycling processes. Our findings revealed that different bacterial genera exhibited varying relative abundances across treatments. Specifically, Massilia showed the highest total relative abundance at the genus level, while Planctomyces had the second highest, and Campylobacter had the lowest abundance. The DESeq2 model, based on negative binomial distribution, revealed that the tags of bacterial genera were significantly correlated with soil depth, but not with water levels or nitrogen concentrations. However, the addition of a 30 mg/L nitrate solution caused a decrease in the relative abundances of bacterial genera with decreasing water levels, while a 60 mg/L concentration of nitrogen resulted in a decrease and then an increase in the relative abundances of bacterial genera with decreasing water levels. Our study provides valuable insights into the response of nitrogen-cycling bacteria to changes in different environmental conditions.

Transformation of Biofilm to Carbon Sinks after Prolonged Droughts Linked with Algal Biodiversity Change

Global climate change significantly increased the duration of droughts in intermittent rivers, impacting benthic microbial-mediated biogeochemical processes. However, the impact of prolonged droughts on the carbon contribution of intermittent rivers remains poorly understood. In this study, we investigated the potential effects of varying drought gradients (ranging from 20 to 130 days) on benthic biofilms community structure (algae, bacteria, and fungi) and their carbon metabolism functions (ecosystem metabolism and carbon dioxide (CO2) emission fluxes) using mesocosm experiments. Our findings indicate that longer drought durations lead to reduced alpha diversity and community heterogeneity, tighter interdomain networks, and an increased role of stochastic processes in community assembly, with a discernible threshold at around 60 days. Concurrently, the biofilm transforms into a carbon sink following a drought period of 60 days, as evidenced by the transformation of CO2 emission fluxes from 633.25 ± 194.69 to -349.61 ± 277.79 mg m-2 h-1. Additionally, the partial least-squares path model revealed that the resilience of algal communities and network stability may drive biofilm's transformation into a carbon sink, primarily through the heightened resilience of autotrophic metabolism. This study underscores the significance of the carbon contribution from intermittent rivers, as the shift in carbon metabolism functions with increasing droughts could lead to skewed estimations of current riverine carbon fluxes.

Functional gene transcription variation in bacterial metatranscriptomes in large freshwater Lake Ecosystems: Implications for ecosystem and human health

Little is known regarding the temporal and spatial functional variation of freshwater bacterial community (BC) under non-bloom conditions, especially in winter. To address this, we used metatranscriptomics to assess bacterial gene transcription variation among three sites across three seasons. Our metatranscriptome data for freshwater BCs at three public beaches (Ontario, Canada) sampled in the winter (no ice), summer and fall (2019) showed relatively little spatial, but a strong temporal variation. Our data showed high transcriptional activity in summer and fall but surprisingly, 89% of the KEGG pathway genes and 60% of the selected candidate genes (52 genes) associated with physiological and ecological activity were still active in freezing temperatures (winter). Our data also supported the possibility of an adaptively flexible gene expression response of the freshwater BC to low temperature conditions (winter). Only 32% of the bacterial genera detected in the samples were active, indicating that the majority of detected taxa were non-active (dormant). We also identified high seasonal variation in the abundance and activity of taxa associated with health risks (i.e., Cyanobacteria and waterborne bacterial pathogens). This study provides a baseline for further characterization of freshwater BCs, health-related microbial activity/dormancy and the main drivers of their functional variation (such as rapid human-induced environmental change and climate change).

Nitrogen species and microbial community coevolution along groundwater flowpath in the southwest of Poyang Lake area, China

Nitrate and ammonia overload in groundwater can lead to eutrophication of surface water in areas where surface water is recharged by groundwater. However, this process remained elusive due to the complicated groundwater N cycling, which is governed by the co-evolution of hydrogeochemical conditions and N-cycling microbial communities. Herein, this process was studied along a generalized groundwater flowpath in Ganjing Delta, Poyang Lake area, China. From groundwater recharge to the discharge area near the lake, oxidation-reduction potential (ORP), NO₃-N, and NO₂-N decreased progressively, while NH₃-N, total organic carbon (TOC), Fe²⁺, sulfide, and TOC/NO₃^- ratio accumulated in the lakeside samples. The anthropogenic influences such as sewage and agricultural activities drove the nitrate distribution, as observed by Cl^- vs. NO₃^-/Cl^- ratio and isotopic composition of nitrate. The hydrogeochemical evolution was intimately coupled with the changes in microbial communities. Variations in microbial community structures was significantly explained by Fe²⁺, NH₃-N, and sulfide, while TOC/NO₃^- controlled the distribution of predicted N cycling gene. The absence of NH₃-N in groundwater upstream was accompanied by the enrichment in Acinetobacter capable of nitrification and aerobic denitrification. These two processes were also supported by Ca²⁺ + Mg²⁺ vs. HCO₃^- ratio and isotopic composition of NO₃^-. The DNRA process downstream was revealed by both the presence of DNRA-capable microbes such as Arthrobacter and the isotopic composition of NH₄⁺ in environments with high concentrations of NH₃-N, TOC/NO₃^-, Fe²⁺, and sulfide. This coupled evolution of N cycling and microbial community sheds new light on the N biogeochemical cycle in areas where surface water is recharged by groundwater.

Succession and environmental response of sediment bacterial communities in the Liao River Estuary at the centenary scale

Microbial community succession in turbulent estuarine environments is key to the understanding of microbial community development in estuaries. Centennial-scale sediment core samples collected from the Liao River Estuary (LRE) channel bar and side beaches were studied for geochemistry and 16S rRNA gene-based bacterial analyses. The results showed that bacterial community composition significantly differed between the sediments of the two sides of the channel bar, with Campilobacterota and Bacteroidota being dominant bacterial phyla in the tributary (T1, T2) and mainstream (MS1, MS2) sediment, respectively. Co-occurrence network of the bacterial community at the genus level showed more centralized and compacted topological features in tributary with weaker hydrodynamic, and the keystone taxas were Halioglobus, Luteolibacter, and Lutibacter in the bacterial community. The bacterial network structure had more edges and larger average degree in LRE sediments from the stage of the year 2016-2009 and the stage before 1939, which was possibly related to hydrodynamic conditions and nutrients. Stochastic processes (dispersal limitation) were the key factors driving bacterial community assembly in the LRE sediments. In addition, total organic carbon (TOC), total sulfur (TS), and grain size were the main deterministic factors affecting the change of bacterial community structure. Relative microbial abundance has the potential to indicate geologically historical environmental changes. This study provided a new perspective to reveal the succession and response of bacterial communities under frequent fluctuation environments.

First report on the bacterial community composition, diversity, and functions in Ramsar site of Central Himalayas, Nepal

Wetland bacterial communities are highly sensitive to altered hydrology and the associated change in water physicochemical and biological properties leading to shifts in community composition and diversity, hence affecting the ecological roles. However, relevant studies are lacking in the wetlands of central Himalayas Nepal. Thus, we aimed to explore the variation of bacterial communities, diversity, and ecologic functions in the wet and dry periods of a wetland (designed as Ramsar site, Ramsar no 2257) by using 16S rRNA gene-based Illumina MiSeq sequencing. We reported a pronounced variation in water physicochemical and biological properties (temperature, pH, Chla, DOC, and TN), bacterial diversity, and community composition. Bacterial communities in the dry season harbored significantly higher alpha diversity, while significantly higher richness and abundance were reflected in the wet season. Our results uncovered the effect of nutrients on bacterial abundance, richness, and community composition. Fourteen percent of the total OTUs were shared in two hydrological periods, and the largest portion of unique OTUs (58%) was observed in the dry season. Planctomycetes and Bacteroidetes dominated the wet season exclusive OTUs; meanwhile, Actinobacteria dominated the dry season exclusive OTUs. Bacteria in these wetlands exhibited divergent ecological functions during the dry and wet seasons. By disclosing the variation of water bacterial communities in different hydrologic periods and their relationship with environmental factors, this first-hand work in the Ramsar site of Nepal will develop a baseline dataset for the scientific community that will assist in understanding the wetland's microbial ecology and biogeography.

Eukaryotes contribute more than bacteria to the recovery of freshwater ecosystem functions under different drought durations

Global climate change mostly impacts river ecosystems by affecting microbial biodiversity and ecological functions. Considering the high functional redundancy of microorganisms, the unknown relationship between biodiversity and ecosystem functions obstructs river ecological research, especially under the influence of increasing weather extremes, such as in intermittent rivers and ephemeral streams (IRES). Herein, dry-wet alternation experiments were conducted in artificial stream channels for 25 and 90 days of drought, both followed by 20 days of rewetting. The dynamic recovery of microbial biodiversity and ecosystem functions (represented by ecosystem metabolism and denitrification rate) were determined to analyse biodiversity-ecosystem-function (BEF) relationships after different drought durations. There was a significant difference between bacterial and eukaryotic biodiversity recovery after drought. Eukaryotic biodiversity was more sensitive to drought duration than bacterial, and the eukaryotic network was more stable under dry-wet alternations. Based on the establishment of partial least squares path models, we found that eukaryotic biodiversity has a stronger effect on ecosystem functions than bacteria after long-term drought. Indeed, this work represents a significant step forward for further research on the ecosystem functions of IRES, especially emphasizing the importance of eukaryotic biodiversity in the BEF relationship.

Seasonal succession of microbial community co-occurrence patterns and community assembly mechanism in coal mining subsidence lakes

Coal mining subsidence lakes are classic hydrologic characteristics created by underground coal mining and represent severe anthropogenic disturbances and environmental challenges. However, the assembly mechanisms and diversity of microbial communities shaped by such environments are poorly understood yet. In this study, we explored aquatic bacterial community diversity and ecological assembly processes in subsidence lakes during winter and summer using 16S rRNA gene sequencing. We observed that clear bacterial community structure was driven by seasonality more than by habitat, and the α-diversity and functional diversity of the bacterial community in summer were significantly higher than in winter (p < 0.001). Canonical correspondence analysis indicated that temperature and chlorophyll-a were the most crucial contributing factors influencing the community season variations in subsidence lakes. Specifically, temperature and chlorophyll-a explained 18.26 and 14.69% of the community season variation, respectively. The bacterial community variation was driven by deterministic processes in winter but dominated by stochastic processes in summer. Compared to winter, the network of bacterial communities in summer exhibited a higher average degree, modularity, and keystone taxa (hubs and connectors in a network), thereby forming a highly complex and stable community structure. These results illustrate the clear season heterogeneity of bacterial communities in subsidence lakes and provide new insights into revealing the effects of seasonal succession on microbial assembly processes in coal mining subsidence lake ecosystems.

Seasonal and spatial variability of zooplankton diversity in the Poyang Lake Basin using DNA metabarcoding

Freshwater ecosystems face multiple threats to their stability globally. Poyang Lake is the largest lake in China, but its habitat has been seriously degraded because of human activities and natural factors (e.g. climate change), resulting in a decline in freshwater biodiversity. Zooplankton are useful indicators of environmental stressors because they are sensitive to external perturbations. DNA metabarcoding is an approach that has gained significant traction by aiding ecosystem conservation and management. Here, the seasonal and spatial variability in the zooplankton diversity were analyzed in the Poyang Lake Basin using DNA metabarcoding. The results showed that the community structure of zooplankton exhibited significant seasonal and spatial variability using DNA metabarcoding, where the community structure was correlated with turbidity, water temperature, pH, total phosphorus, and chlorophyll-a. These results indicated habitat variations affected by human activities and seasonal change could be the main driving factors for the variations of zooplankton community. This study also provides an important reference for the management of aquatic ecosystem health and conservation of aquatic biodiversity.

The Seasonal Patterns, Ecological Function and Assembly Processes of Bacterioplankton Communities in the Danjiangkou Reservoir, China

As the water source for the Middle Route Project of the South-to-North Water Diversion Project (MR-SNWD) of China, the Danjiangkou Reservoir (DJR) is in the process of ecosystem reassembly, but the composition, function, and assembly mechanisms of bacterioplankton communities are not yet clear. In this study, the composition, distribution characteristics and influencing factors of bacterioplankton communities were analyzed by high-throughput sequencing (HTS); PICRUSt2 was used to predict community function; a molecular ecological network was used to analyze bacterioplankton interactions; and the assembly process of bacterioplankton communities was estimated with a neutral model. The results indicated that the communities, function and interaction of bacterioplankton in the DJR had significant annual and seasonal variations and that the seasonal differences were greater than that the annual differences. Excessive nitrogen (N) and phosphorus (P) nutrients in the DJR are the most important factors affecting water quality in the reservoir, N and P nutrients are the main factors affecting bacterial communities. Season is the most important factor affecting bacterioplankton N and P cycle functions. Ecological network analysis indicated that the average clustering coefficient and average connectivity of the spring samples were lower than those of the autumn samples, while the number of modules for the spring samples was higher than that for the autumn samples. The neutral model explained 66.3%, 63.0%, 63.0%, and 70.9% of the bacterioplankton community variations in samples in the spring of 2018, the autumn of 2018, the spring of 2019, and the autumn of 2019, respectively. Stochastic processes dominate bacterioplankton community assembly in the DJR. This study revealed the composition, function, interaction, and assembly of bacterioplankton communities in the DJR, providing a reference for the protection of water quality and the ecological functions of DJR bacterioplankton.

The Effects of Water Level Fluctuation on Zooplankton Communities in Shahu Lake Based on DNA Metabarcoding and Morphological Methods

Background: The water level of Poyang Lake (China) fluctuates seasonally. Shahu Lake, a smaller body of water connected to Poyang Lake during the wet season, is separated in the dry season. Due to a special fishing method termed ‘lake enclosed in autumn’, the water level is lowered and reaches its lowest point in January, which is <0.5 m deep in the middle of the lake. Our research investigated the effect of water level changes on the zooplankton community composition in Shahu Lake. Methods: We used both DNA metabarcoding method (MBC) (18S rRNA gene V4 region) and morphological method (MOI) to track the zooplankton community structure over four seasons in Shahu Lake (China). Results: Totals of 90 and 98 species of zooplankton were detected by MOI and MBC, respectively, with rotifers being the main zooplankton component. The α-diversity index of both methods increased from spring to summer and decreased from summer to autumn, reaching the lowest value in winter. NMDS and a cluster analysis showed that all zooplankton communities detected by MOI and MBC were significantly separated by season. The zooplankton community in winter was separated from that of the other three seasons, but the summer and autumn communities were more similar. Conclusions: Changes in the water level had significant effects on the zooplankton community composition. We found that MBC was more able to detect the differences in the zooplankton composition than MOI. MBC also had more advantages in copepod recognition. In our study, 37 species of copepods were detected by MBC, but only 11 species were detected by MOI. We concluded that MBC should be used to research the seasonal variations of zooplankton.

Factors affecting seasonal variation of microbial community structure in Hulun Lake, China

Microbial communities play an important role in water quality regulation and biogeochemical cycling in freshwater ecosystems. However, there is a lack of research on the seasonal variation in lake water microorganisms in cold environments. In this study, 16S rRNA gene high-throughput sequencing was used to explore the microbial community and its influencing factors in Hulun Lake water during different seasons. The results showed that Proteobacteria, Actinobacteria, and Bacteroidetes were the most important phyla in the microbial community of Hulun Lake, but they had significant seasonal differences in their distribution. In addition, significant seasonal differences were observed in the α diversity of microorganisms, with bacterial diversity being higher in winter than in summer. Changes in environmental variables were significantly correlated with changes in the microbial community, and the rapid changes in temperature, pH, and dissolved oxygen are potentially the major factors influencing seasonal bacterial diversity trends. The findings of the present study enhance our understanding of the microbial communities in alpine lake ecosystems and are of great significance for the management and protection of lake ecosystems.

Characteristics of and Influencing Factors of Hydrochemistry and Carbon/Nitrogen Variation in the Huangzhouhe River Basin, a World Natural Heritage Site

In karst areas, the characteristics of water chemistry and carbon and nitrogen are of great significance to basic research. The contents of Ca²⁺, Mg²⁺, K⁺, Na⁺, HCO₃^-, SO₄^2-, NO₃^-, Cl^-, dissolved organic carbon (DOC), and total nitrogen (TN) in water samples from 18 rivers and 14 springs in the Huangzhouhe River Basin were determined. The results showed that the water chemistry type in the Huangzhouhe River Basin is HCO₃-Ca-Mg. The chemical composition is mainly affected by dolomite weathering and also by ion exchange and other human activities. The river and spring DIC remain at the same level in the upper and middle reaches and decrease in the lower reaches. The NO₃-N and TN of river water and TN of spring water increase in the middle reaches, while NO₃-N of spring water decreases in the lower reaches. The DOC in the basin increases with the increase of SO₄^2- and Cl^-, mainly due to the human influence of agricultural and domestic sewage. In the basin, the NO₃-N and TN in spring water are larger, and the DOC in river water is larger, mainly because there are more phytoplankton and human activities in the river water. The carbon and nitrogen in the Huangzhouhe River Basin are mainly HCO₃^- and NO₃^- ions. The evaluation of pH, Cl^-, NO₃-N, SO₄^2-, and TDS shows that the water quality is good and the ecological environment is good.

Phosphorus cycling in freshwater lake sediments: Influence of seasonal water level fluctuations

Freshwater lakes experience drastic water level fluctuations because of climate change and human activities. However, the influence of such fluctuations on phosphorus cycling in sediments has rarely been investigated. We conducted a geochemical investigation on the phosphorus cycle in a shallow freshwater lake, Dongting Lake; under the influence of human activities and climate change, its water regime undergoes drastic changes. Irrespective of the permanent inundation zone (PIZ) or seasonal inundation zone (SIZ), the phosphorus cycle in sediments was found to be dominated by the reductive dissolution of iron (Fe) (oxyhydr)oxides, degradation of organic matters, and conversion between authigenic phosphorus (Ca-P) and detrital phosphorus in individual seasons. From winter to summer, with increasing water level, the content of Fe-bound phosphorus and organic phosphorus increase due to the deposition of suspended matter, thus increasing total phosphorus in PIZ. Moreover, the rising water level also reduces the dissolved oxygen content and promotes the reductive dissolution of Fe (oxyhydr)oxides. The mineralization of increased organic matter can release CO₂ and reduce pH in the vicinity, which can further result in the acidic dissolution of detrital apatite. In turn, most of the released phosphorus can be adsorbed or co-precipitated with calcium minerals, resulting in the significant increase of Ca-P. The mechanisms of phosphorus transformation in SIZ are similar to those in PIZ, but most of the increased organic matter and total P in a core from SIZ are attributable to the decomposition of plant matter. Therefore, the water level rise not only changes the conservative speciation of phosphorus in sediments to active speciation, but also triggers the release of phosphorus adsorbed to oxides and further increases the risk of phosphorus release from sediments to overlying water. Thus, our findings have major implications for freshwater shallow lakes and their P-driven productivity.

Spatial and seasonal variations of sediment bacterial communities in a river-bay system in South China

River-bay systems are transitional areas that hold important roles in biogeochemical processes between continents and oceans. However, composition and structure of microbial communities shaped by such environments have not been clear yet. In this study, we used high-throughput sequencing of 16S rRNA genes to analyze the diversity and composition of sediment bacterial communities from the Shenzhen river-bay system during dry and wet seasons. The results showed that sediment bacterial community structure was varied according to habitats (river vs. estuary) and seasons (wet season vs. dry season). The alpha diversity of sediment bacterial community was significantly higher in the dry season than in the wet season, while no significant difference of alpha diversity was found between river and estuary. Neutral community model revealed a significant influence of stochastic processes on sediment bacterial community assembly, especially in the wet season. However, the beta nearest-taxon index indicated that deterministic processes were more responsible for the assembly of sediment bacterial community. Additionally, redundancy analysis suggested strong links between sediment bacterial communities and environmental factors in Shenzhen river-bay system, with the environmental factors explaining 63.5% of the bacterial community variation. Specifically, NH₄⁺, pH, and salinity were the three most important contributing factors that shaped the sediment bacterial communities. Overall, this study provides a valuable reference to get insights into the spatiotemporal pattern of sediment bacterial communities in a typical river-bay system. KEY POINTS: • Stochastic processes contribute sediment bacterial community assembly. • Deterministic processes dominate sediment bacterial community assembly. • Environmental factors shape sediment bacterial communities.

Total Arsenic, pH, and Sulfate Are the Main Environmental Factors Affecting the Microbial Ecology of the Water and Sediments in Hulun Lake, China

Bacteria have the metabolic potential to produce a diverse array of secondary metabolites, which have important roles in biogeochemical cycling processes. However, for Hulun Lake and the rivers that enter into it, the bacterial community structures and their effects have not previously been widely studied, limiting our ecological understanding of this habitat. To address this, we have analyzed the bacterial communities in the water ecosystem of the Hulun Lake Basin. 16S rRNA high-throughput sequencing identified 64 phyla, 165 classes, 218 orders, 386 families, and 740 genera of bacteria across all samples. The dominant phyla in the central area of the lake were Proteobacteria, Actinobacteria, Firmicutes, and Cyanobacteria, while in all other areas, Proteobacteria, Actinobacteria, and Bacteroidetes were dominant. The microbial community structures were significantly affected by environmental factors [arsenic (As), pH, and sulfate (SO4 2-)] and their location in the lake. The species richness in the sediments of Hulun Lake was higher than in the water, and this ecosystem harbored the highest proportion of unclassified sequences, representing unclassified bacteria. This study provides basic data for future investigations into the Hulun lake ecosystem and for water microbial monitoring and protection measures.

Seasonal Water Level Fluctuation and Concomitant Change of Nutrients Shift Microeukaryotic Communities in a Shallow Lake

Seasonal water level fluctuations (WLFs) impose dramatic influences on lake ecosystems. The influences of WLFs have been well studied for many lake biotas but the microeukaryotic community remains one of the least-explored features. This study employed high-throughput 18S rRNA gene sequencing to investigate the spatiotemporal patterns of microeukaryotic communities in the dry and wet seasons with concomitant change of nutrients in Poyang Lake, which experiences huge seasonal WLFs. The results showed that the dry season and wet season had distinct microeukaryotic community compositions and structures. In the dry season, Ciliophora (13.86–40.98%) and Cryptomonas (3.69–18.64%) were the dominant taxa, and the relative abundance of these taxa were significant higher in the dry season than wet season. Ochrophyta (6.88–45.67%) and Chlorophyta (6.31–22.10%) was the dominant taxa of microeukaryotic communities in the wet season. The seasonal variation of microeukaryotic communities was strongly correlated to seasonal nutrient variations. Microeukaryotic communities responded significantly to dissolved organic carbon, total nitrogen, nitrate, and soluble reactive phosphorus in the dry season, and correlated to nitrate and total phosphorus in the wet season. The microeukaryotic community showed different modular structures in two seasons, and nutrient variations were the key factors influencing seasonal variations of the modular structures. Moreover, microeukaryotic community networks based on different seasons indicated that the microeukaryotic community co-occurrence patterns were not constant but varied largely associating with the nitrogen and phosphorus variations under the effects of WLFs. Our results are important for understanding how microeukaryotic communities respond to nutrient variation under seasonal water level fluctuation.

Impact of Temperature, Nutrients and Heavy Metals on Bacterial Diversity and Ecosystem Functioning Studied by Freshwater Microcosms and High-Throughput DNA Sequencing

Microbial communities are fundamental components in freshwater, and community shifts in ecosystem structure are indicative of changing environmental conditions. This study aimed at investigating the influence of key environmental parameters on bacterial diversity and ecosystem functioning (i.e. organic matter breakdown) in laboratory freshwater microcosms. The effects of varying temperatures (5, 20 and 35 °C), nutrients (representing low, medium and high urbanization) and heavy metals Copper (Cu) and Zinc (Zn) on bacterial diversity and organic matter (OM) breakdown were studied by using leaf bags and capsules filled with polycaprolactonediol-2000 (PCP-2000), respectively. The leaf-associated bacterial diversity was determined by next-generation sequencing of SSU rRNA gene amplicons. The results showed that bacterial diversity increased at high temperature (35 °C) with more operational taxonomic units (OTUs) as compared to medium (20 °C) or low (5 °C) temperatures, whereas nutrient variation had fewer effects on the bacterial community structure. In contrast, the presence of heavy metals, especially high concentrations (100 μM) of Cu, reduced the number of OTUs in the leaf-associated bacterial community. The higher temperatures and nutrient levels accelerated PCP-2000 breakdown rate, but this was impeded by a high concentration (100 μM) of Cu in the short term, though no effect of Zn on breakdown rate was observed. The overall results indicate that temperature and variated heavy metals are among the key factors that affect bacterial diversity and ecosystem functioning in freshwater systems.

Microbial community structure and functional properties in permanently and seasonally flooded areas in Poyang Lake

Water level fluctuations are an inherent feature regulating the ecological structures and functions of lakes. It is vital to understand the effects of water level fluctuations on bacterial communities and metabolic characteristics in freshwater lakes in a changing world. However, information on the microbial community structure and functional properties in permanently and seasonally flooded areas are lacking. Poyang Lake is a typical seasonal lake linked to the Yangtze River and is significantly affected by water level fluctuations. Bottom water was collected from 12 sampling sites: seven inundated for the whole year (inundated areas) and five drained during the dry season (emerged areas). High-throughput 16S rRNA gene sequencing was used to identify the bacterial communities. The results showed that the taxonomic structure and potential functions of the bacterial communities were significantly different between the inundated and emerged areas. Cyanobacteria was dominant in both areas, but the relative abundance of Cyanobacteria was much higher in the emerged areas than in the inundated areas. Bacterial communities were taxonomically sensitive in the inundated areas and functionally sensitive in the emerged areas. Nitrogen, phosphorus, and dissolved organic carbon concentrations and their ratios, as well as dissolved oxygen, played important roles in promoting the bacterial taxonomic and functional compositional patterns in both areas. According to the metabolic predictions based on 16S rRNA gene sequences, the relative abundance of functional genes related to assimilatory nitrate reduction in the emerged areas was higher than in the inundated areas, and the relative abundance of functional genes related to dissimilatory nitrate reduction in the inundated areas was higher. These differences might have been caused by the nitrogen differences between the permanently and seasonally flooded areas caused by intra-annual water level fluctuations. The relative abundance of functional genes associated with denitrification was not significantly different in the inundated and emerged areas. This study improved our knowledge of bacterial community structure and nitrogen metabolic processes in permanently and seasonally flooded areas caused by water level fluctuations in a seasonal lake.

Rare Species Shift the Structure of Bacterial Communities Across Sphagnum Compartments in a Subalpine Peatland

Sphagnum-associated microbiomes are crucial to Sphagnum growth and peatland ecological functions. However, roles of rare species in bacterial communities across Sphagnum compartments are poorly understood. Here the structures of rare taxa (RT) and conditionally abundant and rare taxa (CART) from Sphagnum palustre peat (SP), S. palustre ectosphere (Ecto) and S. palustre endosphere (Endo) were investigated in the Dajiuhu Peatland, central China. Our results showed that plant compartment effects significantly altered the diversities and structures of bacterial communities. The Observed species and Simpson indices of RT and CART in alpha diversity significantly increased from Endo to SP, with those of Ecto in-between. The variations of community dissimilarities of RT and CART among compartments were consistent with those of whole bacterial communities (WBC). Network analysis indicated a non-random co-occurrence pattern of WBC and all keystone species are affiliated with RT and CART, indicating their important role in sustaining the WBC. Furthermore, the community structures of RT and CART in SP were significantly shaped by water table and total nitrogen content, which coincided with the correlations between WBC and environmental factors. Collectively, our results for the first time confirm the importance of rare species to bacterial communities through structural and predicted functional analyses, which expands our understanding of rare species in Sphagnum-associated microbial communities in subalpine peatlands.