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

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.

Disentangling the assembly patterns and drivers of microbial communities during thermal stratification and mixed periods in a deep-water reservoir

Effect of periodic thermal stratification in deep-water reservoirs on aquatic ecosystems has been a research hotspot. Nevertheless, there is limited information on the response patterns of microbial communities to environmental changes under such specialized conditions. To fill this gap, samples were collected from a typical deep-water reservoir during the thermal stratification period (SP) and mixed period (MP). Three crucial questions were answered: 1) How microbial communities develop with stratified to mixed succession, 2) how the relative importance of stochastic and deterministic processes to microbial community assembly, shifted in two periods, and 3) how environmental variables drive microbial co-occurrence networks and functional group alteration. We used Illumina Miseq high-throughput sequencing to investigate the dynamics of the microbial community over two periods, constructed molecular ecological networks (MENs), and unraveled assembly processes based on null and neutral models. The results indicated that a total of 33.9 % and 27.7 % of bacterial taxa, and 23.1 % and 19.4 % of fungal taxa were enriched in the stratified and mixed periods, respectively. Nitrate, water temperature, and total phosphorus drove the variation of microbial community structure. During the thermal stratification period, stochastic processes (dispersal limitation) and deterministic processes (variable selection) dominated the assembly of bacterial and fungal communities, followed by a shift to stochastic processes dominated by dispersal limitation in two communities. The MENs results revealed that thermal stratification-induced environmental stresses increased the complexity of microbial networks but decreased its robustness, resulting in more vulnerable ecological networks. Therefore, this work provides critical ecological insights for the longevity and sustainability of water quality management in an artificially regulated engineered system.

Deciphering assembly processes, network complexity and stability of potential pathogenic communities in two anthropogenic coastal regions of a highly urbanized estuary

The existence of potential pathogens may lead to severe water pollution, disease transmission, and the risk of infectious diseases, posing threats to the stability of aquatic ecosystems and human health. In-depth research on the dynamic of potential pathogenic communities is of significant importance, it can provide crucial support for assessing the health status of aquatic ecosystems, maintaining ecological balance, promoting sustainable economic development, and safeguarding human health. Nevertheless, the current understanding of the distribution and geographic patterns of potential pathogens in coastal ecosystems remains rather limited. Here, we investigated the diversity, assembly, and co-occurrence network of potential pathogenic communities in two anthropogenic coastal regions, i.e., the eight mouths (EPR) and nearshore region (NSE), of the Pearl River Estuary (PRE) and a total of 11 potential pathogenic types were detected. The composition and diversity of potential pathogenic communities exhibited noteworthy distinctions between the EPR and NSE, with 6 shared potential pathogenic families. Additionally, in the NSE, a significant pattern of geographic decay was observed, whereas in the EPR, the pattern of geographic decay was not significant. Based on the Stegen null model, it was noted that undominant processes (53.36%/69.24%) and heterogeneous selection (27.35%/25.19%) dominated the assembly of potential pathogenic communities in EPR and NSE. Co-occurrence network analysis showed higher number of nodes, a lower average path length and graph diameter, as well as higher level of negative co-occurrences and modularity in EPR than those in NSE, indicating more complex and stable correlations between potential pathogens in EPR. These findings lay the groundwork for the effective management of potential pathogens, offering essential information for ecosystem conservation and public health considerations in the anthropogenic coastal regions.

Recovery mechanism of heterotrophic ammonia assimilation system under chromium hexavalent stress

Heterotrophic ammonia assimilation (HAA), an innovative technology for high-salinity wastewater treatment, demonstrates self-recovery capability following Cr (VI) stress. This study investigated the inhibitory effects and self-restoration mechanisms of Cr (VI) at various stress levels. The removal efficiencies of NH4+-N and Cr (VI) in the HAA gradually decreased with increasing influent Cr (VI) concentration. Exposure to Cr (VI) increased the amounts of high-molecular-weight proteins in soluble microbial products and stimulated the generation of extracellular polymeric substances. Heterotrophic functional microorganisms with Cr (VI) tolerance, such as Marinobacter and Planktosalinus, were enriched. An assimilation pathway gene (glnA) and a Cr (VI)-related gene (atoB) were also upregulated. After ceasing Cr (VI) addition, the HAA system demonstrated a 17.1 % increase in the removal efficiency of NH4+-N, which was attributable to its self-recovery ability. This study provides a scientific and theoretical foundation for the HAA process in resisting the impact of heavy-metal-containing wastewater and self-recovery.

Unveiling the overlooked microbial niches thriving on building exteriors

Rapid urbanization in the Asia-Pacific region is expected to place two-thirds of its population in concrete-dominated urban landscapes by 2050. While diverse architectural facades define the unique appearance of these urban systems. There remains a significant gap in our understanding of the composition, assembly, and ecological potential of microbial communities on building exteriors. Here, we examined bacterial and protistan communities on building surfaces along an urbanization gradient (urban, suburban and rural regions), investigating their spatial patterns and the driving factors behind their presence. A total of 55 bacterial and protist phyla were identified. The bacterial community was predominantly composed of Proteobacteria (33.7% to 67.5%). The protistan community exhibited a prevalence of Opisthokonta and Archaeplastida (17.5% to 82.1% and 1.8% to 61.2%, respectively). The composition and functionality of bacterial communities exhibited spatial patterns correlated with urbanization. In urban buildings, factors such as facade type, light exposure, and building height had comparatively less impact on bacterial composition compared to suburban and rural areas. The highest bacterial diversity and lowest Weighted Average Community Identity (WACI) were observed on suburban buildings, followed by rural buildings. In contrast, protists did not show spatial distribution characteristics related to facade type, light exposure, building height and urbanization level. The distinct spatial patterns of protists were primarily shaped by community diffusion and the bottom-up regulation exerted by bacterial communities. Together, our findings suggest that building exteriors serve as attachment points for local microbial metacommunities, offering unique habitats where bacteria and protists exhibit independent adaptive strategies closely tied to the overall ecological potential of the community.

The ecological role of microbiome at community-, taxonomic - and genome-levels in black-odorous waters

Black-odorous waters (BOWs) are heavily polluted waters where microbial information remains elusive mechanistically. Based on gene amplicon and metagenomics sequencing, a comprehensive study was conducted to investigate the microbial communities in urban and rural BOWs. The results revealed that microbial communities' assembly in urban and rural BOWs was predominantly governed by stochastic factors at the community level. At the taxonomic level, there were 62 core species (58.48%) in water and 207 core species (44.56%) in sediment across urban and rural areas. Notably, significant differences were observed in the functional genetic composition of BOWs between urban and rural areas. Specifically, rural areas exhibited an enhanced abundance of genes involved in nitrogen fixation, Fe2+ transport, and sulfate reduction. Conversely, urban areas showed higher abundances of some genes associated with carbon fixation, nitrification and denitrification. A sulfur-centered ecological model of microbial communities was constructed by integrating data from the three levels of analysis, and 14 near-complete draft genomes were generated, representing a substantial portion of the microbial community (35.04% in rural BOWs and 29.97% in urban BOWs). This research provides significant insights into the sustainable management and preservation of aquatic ecosystems affected by BOWs.

Effects of running time on biological activated carbon filters: water purification performance and microbial community evolution

Ozone-biologically activated carbon (BAC) filtration is an advanced treatment process that can be applied to remove recalcitrant organic micro-pollutants in drinking water treatment plants (DWTPs). In this study, we continuously monitored a new and an old BAC filter in a DWTP for 1 year to compare their water purification performance and microbial community evolution. The results revealed that, compared with the new filter, the use of the old BAC filter facilitated a slightly lower rate of dissolved organic carbon (DOC) removal. In the case of the new BAC filter, we recorded general increases in the biomass and microbial diversity of the biofilm with a prolongation of operating time, with the biomass stabilizing after 7 months. For both new and old BAC filters, Proteobacteria and Acidobacteria were the dominant bacterial phyla. At the genus level, the microbial community gradually shifted over the course of operation from a predominance of Herminiimonas and Hydrogenophaga to one predominated by Bradyrhizbium, Bryobacter, Hyphomicrobium, and Pedomicrobium, with Bradyrhizobium being established as the most abundant genus in the old BAC filter. Regarding spatial distribution, we detected reductions in the biomass and number of operational taxonomic units with increasing biofilm depth, whereas there was a corresponding increase in microbial diversity. However, compared with the effects of time, the influence of depth on the composition of the biofilm microbial community was considerably smaller. Furthermore, co-occurrence network analysis revealed that the microbial community network of the new filter after 11 months of operation was the most tightly connected, although its modular coefficient was the lowest of those assessed. We speculate that the positive and negative interactions within the network may be attributable to symbiotic or competitive relationships among species. Moreover, there may have been a significant negative interaction between SWB02 and Acidovorax, plausibly associated with a competition for substrates.

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.

Environmental DNA metabarcoding reveals the effect of environmental selection on phytoplankton community structure along a subtropical river

The Dongjiang River, a major tributary of the Pearl River system that supplies water to more than 40 million people in Guangdong Province and neighboring regions of China, harbors rich biodiversity, including many endemic and endangered species. However, human activities such as urbanization, agriculture, and industrialization have posed serious threats to its water quality and biodiversity. To assess the status and drivers of phytoplankton diversity, which is a key indicator of aquatic ecosystem health, this study used Environmental DNA (eDNA) metabarcoding combined with machine learning methods to explore spatial variations in the composition and structure of phytoplankton communities along the Dongjiang River, including its estuary. The results showed that phytoplankton diversity exhibited spatial distribution patterns, with higher community structure similarity and lower network complexity in the upstream than in the downstream regions. Environmental selection was the main mechanism shaping phytoplankton community composition, with natural factors driving the dominance of Pyrrophyta, Ochrophyta, and Cryptophyta in the upstream regions and estuaries. In contrast, the downstream regions was influenced by high concentrations of pollutants, resulting in increased abundance of Cryptophyta. The random forest model identified temperature, dissolved oxygen, chlorophyll a, NO2-, and NH4+ as the main factors influencing the primary phytoplankton communities and could be used to predict changes during wet periods. This study provides valuable insights into the factors influencing phytoplankton diversity and community composition in the Dongjiang River, and demonstrates the application value of eDNA metabarcoding technique in large-scale, long-distance river biodiversity monitoring.

Predation has a significant impact on the complexity and stability of microbial food webs in subalpine lakes

IMPORTANCE

As an important part of microbial food webs, protists transfer organic carbon and nutrients to higher trophic levels in aquatic ecosystems. Protist predation often influences the abundance and composition of bacterial communities. However, we still do not understand whether and how predation affects the complexity and stability of microbial food webs. This study assessed the seasonal dynamic characteristics and driving factors of microbial food webs in terms of complexity and stability. Our findings have implications for future surveys to reveal the effects of climate and environmental changes.

Novel strategy for treating high salinity oilfield produced water: Pyrite-activated peroxymonosulfate coupled with heterotrophic ammonia assimilation

Existing conventional biological treatment techniques face numerous limitations in effectively removing total petroleum hydrocarbons (TPHs) and ammonia (NH4+-N) from oilfield-produced water (OPW), highlighting the pressing need for innovative pre-oxidation and biological treatment processes. In this study, a pyrite-activated peroxymonosulfate (PMS)-coupled heterotrophic ammonia assimilation (HAA) system was established to achieve satisfactory system performance for OPW treatment. Pyrite sustained-release Fe2+-activated PMS was used to produce SO4•- and •OH, and 71.0 % of TPHs were effectively removed from the oil wastewater. The average TPHs and NH4+-N removal efficiencies in the test group with pre-oxidation were 96.9 and 98.3 %, compared to 46.5 and 77.1 % in the control group, respectively. The maximum fluorescence intensities of tryptophan protein and aromatic protein in the test group declined by 83.7 %. Fourier transform ion cyclotron resonance mass spectrometry revealed that pre-oxidation degraded more long-chain hydrocarbons and aromatic family compound, whereas the HAA process produced more proteins and carbohydrates. Pyrite-PMS promoted the enrichment of ammonia-assimilating bacteria, alleviating the explosive increase in extracellular polymeric substances and reducing sludge settleability. The low cost, efficiency, green chemistry principles, and synergies of this approach make it a powerful solution for practical OPW treatment to reduce environmental impacts and promote sustainable wastewater treatment.

Phytoplankton Communities Miniaturization Driven by Extreme Weather in Subtropical Estuary under Climate Changes

Estuarine ecosystems are subject to extreme weather and climatic events, particularly global climate change. To characterize the effects of extreme weather, such as heavy precipitation and cold waves, on phytoplankton communities, four seasonal cruises were conducted in the subtropical Pearl River Estuary. Among the main phytoplankton taxa, small (pico- and nano-sized) phytoplankton accounted for approximately 50% and 70% in the upstream estuary. In spring, summer, and autumn, small-sized phytoplankton communities were dominated by Chlorophyta (20-45%), Ochrophyta (Bacillariophyceae; 25-40%), and Dinoflagellata (20-25%), associated with high phytoplankton network stability and river discharge. In winter, small phytoplankton communities were dominated by Cryptophyta (50%), Dinoflagellata (25%), and Ochrophyta (Bacillariophyceae; 10%), which were associated with low network stability and temperature. Low light and high nutrient conditions induced by large river discharge favored the growth of the smallest known brackish Chlorophyta, such as Ostreococcus tauri. Low temperatures provided a competitive advantage for the survival of the small-sized cryptophyte genus Teleaulax, especially in the upstream estuary during the 2020/2021 extreme cold wave period. Our findings highlight the impact of extreme weather induced by climatic events on the miniaturization of phytoplankton communities in subtropical estuaries by altering temperature, light availability, and nutrient dynamics.

Flow backward alleviated the river algal blooms

Mechanistic understanding and prediction of river algal blooms remain challenging. It is generally believed that these blooms are formed by the slowdown of water dynamics in tributaries due to the support of the main stream. However, few studies have investigated the impact of flow backward caused by the difference in water dynamics between the main stream and tributaries. Here, we focus on the eutrophication issue in the middle-lower reaches of the Han River, which is affected by the Middle Route of the South-to-North Water Diversion Project (SNWDP), the largest inter-basin water transfer project in Asia. We discover that the reversal of the Yangtze River water level could effectively alleviate the occurrence of Han River water blooms. The Yangtze River frequently back flows into the lower reaches of the Han River, with the probability of such events increasing as it nears the confluence (20 km from the Yangtze: 9.5 %, 10 km: 19.0 %, 8 km: 28.6 %). This flow backward carries nutrients that reduce the nitrogen to phosphorus ration (N:P), leading to a shift in the nutrient structure of the Han River. This change is concomitant with a significant decline in algae biomass (Chlorophyll-a = 11.19 µg·L-1 and algae density = 0.41×107 cells·L-1 under natural flow, Chlorophyll-a = 5.19 µg·L-1 and algae density = 0.18×107 cells·L-1 under flow backward), as well as a weakening of the correlation (R) between diatom density and chlorophyll-a concentration, i.e., R = 0.38 (p>0.05) under flow backward conditions versus R = 0.72 (p<0.01) under natural flow conditions. As phosphorus limitation typically suppresses algae growth, the correlation between diatom density and chlorophyll-a concentration can help to reveal the dominance of diatoms, with stronger correlations indicating greater diatom dominance. Consequently, our study provides evidence that the flow backward can alleviate river algal blooms by weakening the growth advantage of diatoms. This study could prove valuable in investigating the eutrophication mechanism within the complex hydrodynamic conditions of rivers. SYNOPSIS: Flow backward caused by the water level difference between the main streams and tributary alleviated the occurrence of river algal blooms in the confluence area.

Distinct stochastic processes drive bacterial community assembly and co-occurrence patterns with common antibiotic resistance genes in two highly urbanised coastal ecosystems of the Pearl River Estuary

To comprehensively elucidate the ecology of the bacterial community and antibiotic resistance genes (ARGs) in urbanised coastal ecosystems, this study investigated the variations of bacterial community and five common types of ARGs, the impacting factors and assembly of bacterial community, as well as their co-occurrence relationships in two ecosystems of the Pearl River Estuary (PRE). The bacterial community composition and structure of the nearshore ecosystem (NSE) and the eight mouths of the PRE (EPR) markedly differed, with 38 phyla shared between these two ecosystems. The abundances of 10 ARGs and bacterial community diversity were significantly higher in the EPR than NSE. Moreover, 67.82% and 27.82% of the variation in the bacterial community was explained by spatial (44.42%/8.63%) and environmental (23.40%/19.19%) variables in the NSE and EPR, respectively. Significant distance-decay patterns were observed, and distinct stochastic processes (undominated processes or dispersal limitation) dominated bacterial community assembly in the NSE and EPR. Furthermore, co-occurrence patterns showed significant positive correlations between 48/182 ASVs belonging to 6/15 bacterial phyla and 8/11 ARGs in the NSE/EPR, with six common dominant hosts. These results clarify the drivers and mechanism shaping the bacterial community, providing further proof for potential ARG bacterial hosts in urbanised estuarine ecosystems.

Water quality determines protist taxonomic and functional group composition in a high-altitude wetland of international importance

Alpine wetland is a natural laboratory for studying the Earth's third polar ecosphere. Protist communities are key components of wetland ecosystems which are extremely vulnerable to environmental change. It is of great importance to study the protist community in relation to environment, which might be the key to understand the ecosystem of the alpine wetlands under global change. In this study, we investigated the composition of protist communities across the Mitika Wetland, a unique alpine wetland hosting tremendous endemic diversity. Using 18S rRNA gene high-throughput sequencing, we evaluated how protist taxonomic and functional group composition is structured by seasonal climate and environmental variation. We found a high relative abundance of Ochrophyta, Ciliophora, and Cryptophyta, each of which showcased a unique spatial pattern in the wet and dry seasons. The proportion of consumers, parasites and phototrophs groups were stable among the functional zones and also between the seasons, with consumers dominating communities in terms of richness, while phototrophic taxa dominated in terms of relative abundance. Protist and each functional group were rather regulated by deterministic than stochastic processes, with water quality having a strong control on communities. Salinity and pH were the most important environmental factors at shaping protistan community. The protist co-occurrence network dominated by the positive edge indicating the communities resisted extreme environmental conditions through close cooperation, and more consumers were determined as the keystones in wet season and more phototrophic taxa in dry season. Our results provided the baseline of the protist taxonomic and functional group composition in the highest wetland, and highlighted environmental selections drive protist distribution, implying the alpine wetland ecosystem are sensitive to climate changes and human activities.

Mechanistic insights into dissolved organic matter-driven protistan and bacterial community dynamics influenced by vegetation restoration

Vegetation restoration projects can not only improve water quality by absorbing and transferring pollutants and nutrients from non-vegetation sources, but also protect biodiversity by providing habitat for biological growth. However, the mechanism of the protistan and bacterial assembly processes in the vegetation restoration project were rarely explored. To address this, based on 18 S rRNA and 16 S rRNA high-throughput sequencing, we investigated the mechanism of protistan and bacterial community assembly processes, environmental conditions, and microbial interactions in the rivers with (out) vegetation restoration. The results indicated that the deterministic process dominated the protistan and bacterial community assembly (94.29% and 92.38%), influenced by biotic and abiotic factors. For biotic factors, microbial network connectivity was higher in the vegetation zone (average degree = 20.34) than in the bare zone (average degree = 11.00). For abiotic factors, the concentration of dissolved organic carbon ([DOC]) was the most important environmental factor affecting the microbial community composition. [DOC] was lower significantly in vegetation zone (18.65 ± 6.34 mg/L) than in the bare zone (28.22 ± 4.82 mg/L). In overlying water, vegetation restoration upregulated the protein-like fluorescence components (C1 and C2) by 1.26 and 1.01-folds and downregulated the terrestrial humic-like fluorescence components (C3 and C4) by 0.54 and 0.55-folds, respectively. The different DOM components guided bacteria and protists to select different interactive relationships. The protein-like DOM components led to bacterial competition, whereas the humus-like DOM components resulted in protistan competition. Finally, the structural equation model was established to explain that DOM components can affect protistan and bacterial diversity by providing substrates, facilitating microbial interactions, and promoting nutrient input. In general, our study provides insights into the responses of vegetation restored ecosystems to the dynamics and interactives in the anthropogenically influenced river and evaluates the ecological restoration performance of vegetation restoration from a molecular biology perspective.

Response of prokaryotic, eukaryotic and algal communities to heavy rainfall in a reservoir supplied with reclaimed water

The global climate change made the heavy rainfall happen more frequently, and the non-point source pollution caused by it would exacerbate the risk to the water ecological environment. In this study, we took a reservoir (Shahe reservoir, Beijing, China) supplied with reclaimed water as an exapmle to investigate how spatiotemporal changes in the quantity and diversity of prokaryotic, eukaryotic, and algal communities respond to heavy rainfall. Results showed that heavy rainfall could directly impact the composition of the prokaryotic community by introducing amounts of runoff closely associated bacterium especially for the human potential pathogens such as Aliarcobacter, Aeromonas and Pseudomonas in the Shahe reservoir area. While the eukaryotic community was rather stable, and the development and changes in algal communities occurred in the last few days after heavy rainfall. The microbial source tracking through FEAST indicated that Nansha river (S) was the major contributor to the development of all the three concerned communities in the reservoir. The co-occurrence analysis showed that the modules with the highest cumulative abundance in each community were all strongly and positively connected with Chl-a, pH, turbidity, COD and TOC, but negatively correlated with NO₃-N (p < 0.01). The network analysis showed that the eukaryotes played a key role in the interaction network among the three communities, and were more likely to interact with algae and prokaryotes. It was suggested that the controlling of human potential pathogens associated with prokaryotic community should be emphasized at the beginning of the heavy rainfall, but the prevention of the eutrophication bloom should be another focus after the heavy rainfall. This study provided valuable information concerning the role of heavy rainfall on the water ecological environment from the perspective of microbial community.

A meta-analysis reveals that geographical factors drive the bacterial community variation in Chinese lakes

The biogeographical distribution of plants and animals has been extensively studied, however, the biogeographical patterns and the factors that influence bacterial communities in lakes over large scales are yet to be fully understood, even though they play critical roles in biogeochemical cycles. Here, bacterial community compositional data, geographic information, and environmental factors were integrated for 326 Chinese lakes based on previously published studies to determine the underlying factors that shape bacterial diversity among Chinese lakes. The composition of bacterial communities significantly varied among the three primary climatic regions of China (Northern China, NC; Southern China, SC; and the Tibetan Plateau, TIP), and across two different lake habitats (waters and sediments). Sediment bacterial communities exhibited significantly higher alpha-diversity and distance-decay relationships compared to water communities. The results indicate that the "scale-dependent patterns" of controlling factors, primarily influenced by geographical factors, become increasingly pronounced as the spatial scale increases. At a national scale, geographical factors exerted a dominant influence on both the water and sediment communities across all lakes, as geographical barriers restrict the dispersal of individuals. At smaller spatial scales, temperature-driven selection effects played a greater role in shaping water bacterial community variation in the NC, SC, and TIP, while geographical factors had a stronger association with sediment bacterial community variation in the lakes of the three regions. This synthesis offers novel insights into the ecological factors that determine the distribution of bacteria in Chinese lakes.

Environmental DNA metabarcoding reveals the influence of human activities on microeukaryotic plankton along the Chinese coastline

Microeukaryotic plankton, with its extremely diverse taxa, is a key component in both the marine food web and biogeochemical cycling. Coastal seas, which are home to the numerous microeukaryotic plankton that underpin the functions of these aquatic ecosystems, are often impacted by human activities. However, understanding the biogeographical patterns of diversity and community structure of microeukaryotic plankton and the role that major shaping factors play at the continent scale is still a challenge in coastal ecology. Here, the biogeographic patterns of biodiversity, community structure, and co-occurrence patterns were investigated by environmental DNA (eDNA) based approaches. Unlike most eDNA studies, we combined several methods (in silico PCR, mock and environmental communities) to systematically evaluate the specificity and coverage of primers to overcome the limitation of marker selection on biodiversity recovery. The 1380F/1510R primer set showed the best performance for the amplification of coastal plankton with the highest coverage, sensitivity, and resolution. We showed a unimodal pattern for planktonic alpha diversity with latitude (P < 0.001), and nutrient-related factors (NO₃N, NO₂N, and NH₄N) were the leading predictors for spatial patterning. Significant regional biogeographic patterns and potential drivers for planktonic communities were found across coastal regions. All communities generally fitted the regional distance-decay relationship (DDR) model with the strongest spatial turnover rate was found in the Yalujiang (YLJ) estuary (P < 0.001). The environmental factors, especially inorganic nitrogen and heavy metals (HMs), had the greatest impact on planktonic community similarity in the Beibu Bay (BB) and East China Sea (ECS). Furthermore, we observed spatial plankton co-occurrence patterns, and the networked topology and structure were strongly driven by potential anthropogenic activity factors (nutrients and HMs). Overall, our study provided a systematic approach for metabarcode primer selection in eDNA-based biodiversity monitoring and revealed that the spatial pattern of the microeukaryotic plankton community was mainly controlled by regional human activity-related factors.

Exposure to benzalkonium chloride disinfectants promotes antibiotic resistance in sewage sludge microbiomes

Disinfectants are routinely used in human environments to control and prevent the transmission of microbial disease, and this is particularly true during the current COVID-19 crisis. However, it remains unclear whether the increased disinfectant loadings to wastewater treatment plants facilitate the dissemination of antibiotic resistance genes (ARGs) in sewage sludge microbiomes. Here, we investigated the impacts of benzalkonium chlorides (BACs), widely used disinfectants, on ARGs profiles and microbial community structures in sewage sludge by using high-throughput quantitative PCR and Illumina sequencing. A total of 147 unique ARGs and 39 mobile genetic elements (MGEs) were detected in all sewage sludge samples. Our results show that exposure to BACs disinfectants at environmentally relevant concentrations significantly promotes both the diversity and absolute abundance of ARGs in sludge microbiomes, indicating the co-selection of ARGs by BACs disinfectants. The enrichment of ARGs abundance varied from 2.15-fold to 3.63-fold compared to controls. In addition, BACs exposure significantly alters bacterial and protistan communities, resulting in dysbiosis of the sludge microbiota. The Mantel test and Procrustes analysis confirm that bacterial communities are significantly correlated with ARGs profiles under BACs treatments. The structural equation model explains 83.8 % of the total ARGs variation and further illustrates that the absolute abundance of MGEs exerts greater impacts on the variation of absolute abundance of ARGs than microbial communities under BACs exposure, suggesting BACs may promote antibiotic resistance by enhancing the horizontal gene transfer of ARGs across sludge microbiomes. Collectively, our results provide new insights into the proliferation of antibiotic resistance through disinfectant usage during the pandemic and highlight the necessity to minimize the environmental release of disinfectants into the non-target environment for combating antibiotic resistance.

Phytoplankton and Microzooplankton Community Structure and Assembly Mechanisms in Northwestern Pacific Ocean Estuaries with Environmental Heterogeneity and Geographic Segregation

Phytoplankton and microzooplankton are crucial players in marine ecosystems and first responders to environmental changes, but their community structures and how they are shaped by environmental conditions have rarely been studied simultaneously. In this study, we conducted an eDNA metabarcoding sequencing combined with multiple statistical methods to simultaneously analyze the phytoplankton and microzooplankton in Liaohe (LH) and Yalujiang (YLJ) estuaries. The major objective was to examine how plankton community structure and assembly mechanism may differ between two estuaries with similar latitudinal position and climate but geographical segregation and differential level of urbanization (more in LH). Clear differences in diversity and composition of phytoplankton and microzooplankton communities between LH and YLJ estuaries were observed. Richness of phytoplankton was significantly higher in LH than YLJ, while richness of microzooplankton was higher in YLJ. The magnitude of intrahabitat variations in phytoplankton communities was significantly stronger than that of microzooplankton. Some phytoplankton and microzooplankton taxa also showed interhabitat differences in their relative abundances. Phytoplankton showed a stronger geographic distance-decay of similarity than microzooplankton, while significant environmental distance-decay of similarity in microzooplankton was found in the less urbanized YLJ estuary. Community assembly of phytoplankton was, based on the neutral community models, driven primarily by stochastic processes, while deterministic processes contributed more for microzooplankton. Furthermore, we detected wider habitat niche breadths and stronger dispersal abilities in phytoplankton than in microzooplankton. These results suggest that passive dispersal shapes the phytoplankton community whereas environmental selection shapes the microzooplankton community. IMPORTANCE Understanding the underlying mechanisms shaping a metacommunity is useful to management for improving the ecosystem function. The research presented in the manuscript mainly tried to address the effects of habitat geography and environmental conditions on the phytoplankton and microzooplankton communities, and the underlying mechanisms of community assembly in temperate estuaries. In order to achieve this purpose, we developed a metabarcoding sequencing method based on 18S rRNA gene. The phytoplankton and microzooplankton communities from two estuaries with similar latitude and climatic conditions but obvious geographical segregation and significant environmental heterogeneity were investigated. The results of our study could lay a solid foundation for ascertaining phytoplankton and microzooplankton communities in estuaries with obvious environmental heterogeneity and geographic segregation and mechanisms underlying community assembly.

Response mechanism of meiofaunal communities to multi-type of artificial reef habitats from the perspective of high-throughput sequencing technology

Multiple types of artificial reefs have been widely deployed in the coast of northern Yellow Sea, which can enhance fishery resources, restore coastal habitats and improve the marine environment. Meiofauna plays important ecological roles in marine ecosystem, but the response mechanism of meiofaunal community to different types of artificial reef is still poorly understood. In this study, we characterized the meiofaunal communities of concrete artificial reef habitat (CAR), rocky artificial reef habitat (RAR), ship artificial reef habitat (SAR) and adjacent natural habitat (NH) using 18S rRNA gene high-throughput sequencing technology, and explored the relationship of community-environment. The results showed that the diversity and community structure of meiofauna differed significantly on both spatial and temporal scales. Spatial differences were mainly contributed to the flow field effects and biological effects generated by artificial habitats, while temporal differences were driven by temperature (T) and dissolved oxygen (DO). The dominant taxa of meiofauna included arthropods, annelids, platyhelminths and nematodes. Platyhelminths were mainly positively influenced by artificial habitats but annelids were the opposite. Co-occurrence network analysis revealed that NH was more sensitive to environmental change than artificial habitat, while the performance of CAR and SAR were more stable. These results indicated that meiofauna can respond accordingly to different types of artificial habitats, and could be superimposed over the normal seasonal effects. The current study could provide fundamental data for understanding the response mechanism of meiofaunal community to different types of artificial habitats and a reference for assessments of the impact of artificial reefs on the marine 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.

Trophic State Drives the Diversity of Protists in a Tropical River (New River, Belize)

Land use disrupts the ecosystem functioning of freshwater systems and significantly affects trophic state. Consequently, biodiversity is severely affected by changes to the ecosystem. Microbial eukaryotes (i.e., protists) play an essential role in ecosystem functioning, contributing to biogeochemical processes, nutrient cycling, and food webs. Protist composition is a useful biological quality parameter for monitoring aquatic ecosystems and determining aquatic system health. In this study, we investigated the effects of land usage and trophic state on the communities of microbial eukaryotes in the New River (Belize, C.A.). Land use and trophic state both significantly affected protist community compositions, with impacted and mesotrophic sampled sites having higher biodiversity when compared to other sites. Autotrophic organisms dominated indirectly impacted and eutrophic sites, while impacted and mesotrophic sites had proportional ratios of autotrophic and heterotrophic organisms. Our study highlights the significant effects of trophic gradients on protistan community composition, even at the local scales.

Microbial network complexity drives non-linear shift in biodiversity-nutrient cycling in a saline urban reservoir

Aquatic biodiversity is important in mediating ecosystem functioning, contributing to ecosystem sustainability and human wellbeing. However, how microbial network complexity affects the biodiversity-nutrient cycling relationship in saline freshwater ecosystems remains underexplored. Using high-resolution time-series data, we examined the relationships between microeukaryotic-bacterial community network complexity, biodiversity and multi-nutrient cycling in an urban reservoir undergoing a freshwater salinization-desalinization cycle. We found that low microbial diversity enhanced ecosystem multi-nutrient cycling under high salinity stress. In addition, multi-nutrient cycling declined with increased network complexity. Further, we found a non-linear relationship between salinity-induced shifts in the complexity of the microbial network and biodiversity-nutrient cycling (BNC) relationship of keystone taxa, i.e. the strength of the BNC relationship first became weak and then strong with increased network complexity. Together, these results highlighted the significant insight that there is not always positive relationship between biodiversity/network complexity and multi-nutrient cycling, even between network complexity and BNC relationship in real-world ecosystems, suggesting that preserving microbial association is important in aquatic health managing and evaluating the freshwater salinization problem.

Microbial community assembly and co-occurrence relationship in sediments of the river-dominated estuary and the adjacent shelf in the wet season

In the estuarine ecosystem, microbial community plays a vital role in controlling biogeochemical processes. However, there is currently limited comprehensive study on the deterministic and stochastic processes that drive the microbial community assembly in the estuaries and adjacent shelves. In this study, we systematically investigated the co-occurrence relationship and microbial community assembly in the sediments along a large river-dominated estuary to shelf in the northern South China Sea during the wet season. The sampling sites were divided into estuary, transection, and shelf sections based on their salinity values. The microbial co-occurrence networks, hierarchical partitioning-based canonical analysis, null model, neutral community model, and the Mantel test were used to investigate the community assembly. Results suggested that microbial community in the estuary section exhibited more interactions and a higher positive interaction ratio than those in the transition and shelf sections. Stochastic processes dominated community assembly in the study, with homogenizing dispersal contributing the most. The estuary exhibited a higher degree of heterogeneous selection than the transition and shelf sections, whereas homogeneous selection showed an opposite trend. Only the estuary section showed dispersal limitation and undominated processes. The river inflow and the resulting environmental heterogeneity were believed to be the key regulators of the community assembly in the studied area. Our study improved the understanding of how microbial community assembly in estuaries and adjacent shelves.

Community assembly of microbial habitat generalists and specialists in urban aquatic ecosystems explained more by habitat type than pollution gradient

Urban freshwater ecosystems have important ecosystem functions, provide habitats for diverse microbial communities and are susceptible to multiple interconnected factors such as environmental pollution. Despite the ecological significance of bacteria and microeukaryotes, little is known about how their community assembly responds to various environmental factors across water and sediment habitats and ecological processes shaping them. Here, environmental DNA-based approaches were used to investigate the community assembly processes of bacteria and microeukaryotes (including habitat generalists and specialists) in urban water and sediment across an urban-pollution gradient in Wuhan, central China. The diversity, community composition and potential function of bacteria and microeukaryotes showed significantly stronger variation between water and sediment than across an urban pollution gradient. Although, bacterial and microeukaryotic community assemblies were dominated by strong selection processes in both water and sediment habitats, but a contrasting community assembly mechanism was identified between habitat generalists and specialists. Bacterial and microeukaryotic communities showed a greater response to physicochemical variability in water, while a strong distance-decay relationship was found in sediment. Further, cross-kingdom microbial network analysis revealed strong modular associations of bacteria and microeukaryotes, meanwhile, microeukaryotic habitat specialists might be keystone, but generalists have higher proportion of connections in the networks. This study provides significant insights into the response of bacteria and microeukaryotes to different urban pollutions between water and sediment, and the ecological processes structuring microbial community dynamics across habitat types under anthropogenic disturbances.

Composition and spatial-temporal dynamics of phytoplankton community shaped by environmental selection and interactions in the Jiaozhou Bay

The Jiaozhou Bay as a model marine ecosystem in China has been intensively investigated over the last 90 years. However, detailed phytoplankton community composition, spatial-temporal dynamics, and its assembly mechanism were still unclear. To address these, we systematically examined the composition and spatial-temporal dynamics of phytoplankton in the Jiaozhou Bay through high-throughput sequencing of 18S rDNA V4. Analysis of 468 samples from 12 sampling sites over one full year revealed much higher phytoplankton diversity than previous reports, and strong seasonal succession patterns. Some phytoplankton also showed spatial variations, although the phytoplankton community didn't show significant distance-decay pattern. Environmental factors (especially temperature), species-species interrelationships and unique resting stages were uncovered to be the main contributors instead of stochastic process in shaping the phytoplankton community assembly. The overwhelming positive correlations between phytoplankton and other protists suggested that coevolution might be critical in this marine ecosystem. Complementary distributions of different amplicon sequence variants (ASVs) of same genera, such as Skeletonema marinoi (ASV_2) and Skeletonema tropicum (ASV_263) of the genus Skeletonema, suggested that phytoplankton have evolved differentially to exploit a wide range of ecological niches. This study laid a solid foundation for asertaining phytoplankton composition and spatial-temporal dynamics in temperate seawaters and mechanisms underlying phytoplankton community assembly, allowing in-depth studies of marine ecology.

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

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