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

Assessment of planktonic community diversity and stability in lakes and reservoirs based on eDNA metabarcoding--A case study of Minghu National Wetland Park, China

To evaluate the potential differences in plankton diversity and stability within freshwater lake and reservoir ecosystems, this study employed eDNA metabarcoding to analyze the diversity, assembly mechanisms, stability, and environmental drivers of plankton communities in natural water (Y region) and artificial lake water (M region) at Liupanshui Minghu National Wetland Park, Guizhou Province, China. The study revealed notable regional variations in plankton diversity and assembly mechanisms. Specifically, Shannon, Simpson, and Pielou's evenness indices were higher in the M region, suggesting a more complex species composition compared to the Y region. Analysis of community assembly mechanisms indicated that both regions were influenced by a combination of stochastic and deterministic processes, with stochastic processes serving as the dominant driver. Through LEfSe analysis, Random Forest predictions, and molecular ecological network evaluations, certain OTUs identified as "dual-characteristic" species were consistently highlighted. These species may play a critical role in shaping community composition and contributing to stability. Environmental drivers further clarified these differences. Redundancy analysis (RDA) demonstrated that TDS was the primary factor driving regional differences in key zooplankton species, while EC and DO were significant factors influencing the distribution of key phytoplankton species. Stability assessments, which combined molecular ecological network analysis and the coefficient of variation in species population density, revealed higher stability in the Y region. This indicates that the natural water system (Y region) has a greater resistance to disturbances compared to the artificial system in the M region. The findings provide fundamental support for assessing the health of aquatic ecosystems, as well as for the effective monitoring and biodiversity conservation of lake and reservoir ecosystems.

As a reservoir of antibiotic resistance genes and pathogens, the hydrodynamic characteristics drive their distribution patterns in Lake Victoria

Antibiotic resistance genes (ARGs) and pathogenic bacteria pose significant challenges to human health, and hydrodynamic processes complicate their transmission mechanisms in lake ecosystems, particularly in tropical regions. Lake Victoria supports abundant water resources and provides livelihoods for millions of people, yet the environmental behavior of ARGs and pathogenic bacteria remains unclear. Herein, the novel insights into the co-occurrence patterns and transmission mechanisms of ARGs and pathogenic bacteria in Lake Victoria was investigated via molecular techniques and a hydrodynamic model. The results showed that as a large reservoir of ARGs and pathogenic bacteria, a total of 172 ARG subtypes and 93 pathogenic bacteria were identified in Lake Victoria. ARGs were spread through mobile genetic elements (tnpA4 and int2), enhancing the antibiotic resistance and virulence factors (secretion systems, regulatory factors, and toxins) of various pathogenic bacteria. The hydrodynamic model indicated that surface wind-driven currents and bottom compensatory flows shaped the outward dispersion of ARGs and pathogenic bacteria from the gulf. The NCM model suggested that water exchange accelerated the diffusion of antibiotics and pathogens, likely enhancing the deterministic assembly process of ARGs and the stochastic assembly process of pathogens. The PLS-PM model revealed that hydrodynamics directly influenced the accumulation of ARGs and pathogenic bacteria, and subsequently affected the diffusion and distribution patterns of ARGs and pathogens by facilitating the propagation of MGEs. Our study overcomes the limitations associated with lake and microenvironmental scale, providing insights and understanding into the transmission mechanisms of ARGs and pathogenic bacteria.

Seasonal lake ice cover drives the restructuring of bacteria-archaea and bacteria-fungi interdomain ecological networks across diverse habitats

The coexistence of different microbial communities is fundamental to the sustainability of many ecosystems, yet our understanding of the relationships among microbial communities in plateau cold-region lakes affected by seasonal ice cover remains limited. This research involved investigating three lakes in the Inner Mongolia segment of the Yellow River basin during frozen and unfrozen periods in two habitats: water bodies and sediments. The research examined the composition and function of bacteria, archaea, and fungi across different times and habitats within the basin, their response to environmental variables in water and sediment, and inter-domain interactions between bacteria-archaea and bacteria-fungi were compared using interdomain ecological network (IDEN). The findings indicate significant variations in the structures of bacterial, archaeal, and fungal communities across different periods and habitats, with the pH of the water body being a crucial environmental variable affecting microbial community composition. In the frozen period, the functionality of microbial communities, especially in terms of energy metabolism, was significantly impacted, with water bodies experiencing more pronounced effects than sediments. Archaea and fungi significantly contribute to the stability of bacterial communities across various habitats, especially in ice-covered conditions, where stronger associations between bacterial communities, archaea, and fungi promote the microbial communities' adaptability to cold stress. Furthermore, our results indicate that the primary environmental variable influencing the structure of IDENs is the nutrient salt content in both water bodies and sediments. This study broadens our understanding of the responses and feedback mechanisms of inter-domain microbial interactions in lakes influenced by seasonal ice cover.

Influence of microbial agents-loaded biochar on bacterial community assembly and heavy metals morphology in sewage sludge compost: Insights from community stability and complexity

Enhancing the passivation of heavy metals and increasing organic matter content during the composting of sewage sludge poses significant challenges for maximizing its utilization value. Results indicated that in the control, biochar, microbial agents and microbial agents-loaded biochar (BCLMA) groups, BCLMA addition led to a higher composting temperature, with increases of 17-62% in humic acid, 25-73% in germination index, and 30-35% in organic matter consumption. And the residual fraction of Cu, Zn, Cr and Cd were increased by 30%, 12%, 22% and 17%, respectively. Furthermore, BCLMA promotes community cohesion, robustness, and microbial nutrient cycling, and increases the relative abundance of heavy metals-degrading bacteria (Acinetobacter and Corynebacterium) and resistance genes. Structural equation model analysis revealed that heavy metal passivation is attributed to improved community cohesion and robustness, which facilitates the proliferation of heavy metal-resistant microorganisms. These results indicate that community robustness and cohesion are critical for mitigating the heavy metals bioavailability.

Climate and biological factors jointly shape microbial community structure in the Yarlung Zangbo River during the dry season

Microorganisms are crucial components of aquatic ecosystems, playing key roles in biogeochemical cycles. Understanding microbial diversity and community assembly mechanisms is essential for river management and sustainable utilization of freshwater resources. However, the role of inter-microbial taxonomic group relationships in shaping community structures within high-altitude river ecosystems is unclear. This study utilizes high-throughput sequencing and bioinformatics analysis to describe the spatial dynamics of fungal and bacterial communities in the Yarlung Zangbo River at a broad environmental scale and to elucidate their community assembly mechanisms. The results indicate a significant distance-decay pattern in the fungal (p < 0.001) and bacterial (p < 0.001) communities of the Yarlung Zangbo River, with substantial differences in microbial taxonomic composition, diversity, and community structure across different regions (fungi ANOSIM R = 0.20, bacteria ANOSIM R = 0.63). Homogeneous selection predominated the community assembly of fungi (average: 67.4 %) and bacteria (average: 74.5 %) in aquatic environments. As altitude decreases, the influence of deterministic processes on fungal communities increases, while their influence on bacterial communities decreases. At the basin scale, the community structures of fungi and bacteria are mainly influenced by the degree of functional or ecological niche differentiation of another taxonomic group, as well as the hydrothermal conditions of the basin that vary with longitude. This study enhances the understanding of fungal and bacterial biogeographic patterns and community assembly mechanisms in plateau rivers, providing new perspectives for microbial ecological research in these ecosystems.

Similar but different assembly processes of bacterial and micro-eukaryotic communities in an urban river

Bacteria and micro-eukaryotes play important roles in river ecological systems. The processes that govern bacterial and micro-eukaryotic communities in urban rivers are still uncertain. The spatiotemporal characteristics and assembly processes of bacterial and micro-eukaryotic communities in the Xiangjianghe River were explored using 16 S and 18 S rRNA gene amplicon sequencing in the present study. The results indicate that the bacterial and micro-eukaryotic community composition exhibited distinct temporal and spatial variation. The topological characteristics of co-occurrence networks demonstrate that the bacterial and micro-eukaryotic community coexistence patterns vary significantly between the four seasons. Water temperature (WT) and oxidation-reduction potential (ORP) were detected as the most critical factors affecting bacterial and micro-eukaryotic community structure. The stochastic process (dispersal limitation) was the dominant assembly process for bacteria and micro-eukaryotes in all seasons. Deterministic and stochastic processes influenced the bacteria and micro-eukaryotes differently. Compared to bacteria, the values of niche breadth were relatively lower, and the proportion of deterministic processes was relatively higher in micro-eukaryotes. These results expand our understanding of spatiotemporal patterns, assembly mechanisms, and influencing factors of bacterial and micro-eukaryotic communities in urban rivers.

Different wetting states in riparian sediment ecosystems: Response to microplastics exposure

Climate change alters the wetting state of riparian sediments, impacting microbial community response and biogeochemical processes. Microplastics (MPs) invade nearly all ecosystems on earth, posing a significant environmental risk. However, little is known about the response mechanism of MP exposure in sediment ecosystems with different wetting states under alternating seasonal rain and drought conditions. In this study, sediments with three different wetting states were selected to explore the differential response of ecosystems to PLA MP exposure. We observed that PLA MP exposure directly affected biogeochemical processes in sediment ecosystems and induced significant changes in microbial communities. PLA MP exposure was found to alter the composition of key species and microbial functional groups in the ecosystem, resulting in a more complex, interconnected, but less stable microbial network. Our findings showed that PLA MP exposure enhances the contribution of stochastic processes, for example the dispersal limitation increasing from 7.41 % to 54.32 %, indicating that sediment ecosystems strive to buffer disturbances from PLA MP exposure. In addition, 87 pathogenic species were detected in our samples, with PLA MPs acting as vectors for their transmission, potentially amplifying ecosystem disturbance. Importantly, we revealed that submerged sediments may present a greater environmental risk, while alternating wet and dry sediments demonstrate greater resistance and resilience to PLA MPs pollution. Overall, this study sheds light on how sediment ecosystems respond to MP exposure, and highlights differences in sediment response mechanisms across wetting states.

Accelerated stochastic processes of plankton community assembly due to tidal restriction by seawall construction in the Yangtze River Estuary

Seawall construction has complex ecological impacts. However, the ecological mechanisms within plankton communities under tidal restriction resulting from seawall construction remain unexplored. Using environmental DNA (eDNA) metabarcoding, this study examined the impact of seawall construction on the assembly process of planktonic eukaryote and bacteria communities from the unrestricted area and the tide-restricted area in the Chongming Dongtan Nature Reserve of Yangtze River Estuary. While environmental heterogeneity did not exert a significant influence on alpha diversity of plankton, it had a significant impact on community structure. Variation partitioning analysis (VPA) and neutral community model indicated that neither environmental nor spatial factors were predominant drivers of plankton community composition and structure, instead, they were influenced by stochastic processes. Moreover, it was observed that the relative significance of stochastic processes in the tide-restricted area exceeded that in the unrestricted area. High habitat uniformity and water connectivity resulting from seawall construction may facilitate homogenization and spread among high-abundance groups. The results have significant implications for understanding the mechanisms underlying succession and composition, and for improving ecological assessment and remediation efforts in areas impacted by tidal restriction.

Mechanisms Driving Seasonal Succession and Community Assembly in Sediment Microbial Communities Across the Dali River Basin, the Loess Plateau, China

Microorganisms are instrumental in river ecosystems and participate in biogeochemical cycles. It is thought that dynamic hydrological processes in rivers influence microbial community assembly, but the seasonal succession and community assembly of river sediments on the Loess Plateau remain unclear. This study used high-throughput sequencing technology (16S and ITS) and the neutral community model to analyze seasonal succession and the assembly processes associated with microbial communities in the Dali River, a tributary of the Yellow River on the Loess Plateau. The results showed that sediment bacterial and fungal community diversity indexes in non-flood season were 1.03-3.15 times greater than those in flood season. There were obvious variations between non-flood and flood seasons in sediment microorganisms. The similarities among all, abundant, and rare microbial communities decreased as geographical distance increased. Proteobacteria (52.5-99.6%) and Ascomycota (22.0-34.2%) were the primary microbial phyla in all, abundant, and rare microbial communities. Sediment ammonia nitrogen, water temperature, and sediment organic carbon significantly affected (p < 0.05) the structure of all, abundant, and rare sediment microorganism communities. The ecological networks for the bacterial community of non-flood season and fungal community of flood season had complex topological parameters. The bacterial community in river sediments was driven by deterministic processes, while the fungal community was dominated by stochastic processes. These results expanded understanding about sediment microbial community characteristics in rivers on the Loess Plateau and provided insights into the assembly processes and the factors driving microbial communities in river networks.

Assessing the Risks of Potential Pathogens and Antibiotic Resistance Genes Among Heterogeneous Habitats in a Temperate Estuary Wetland: a Meta-analysis

Temperate estuary wetlands act as natural filters for microbiological contamination and have a profound impact on "One Health." However, knowledge of microbiological ecology security across the different habitats in temperate estuarine wetlands remains limited. This study employed meta-analysis to explore the characteristics of bacterial communities, potential pathogens, and antibiotic resistance genes (ARGs) across three heterogeneous habitats (water, soil, and sediment) within the Liaohe Estuary landscape. The diversity and composition of the three bacterial communities differed with biogeography, temperature, and pH, with the highest α-diversity showing a significantly negative correlation along latitude in soil. Furthermore, aminoglycosides were significantly enriched in water and soil, while dihydrofolate was more likely to be enriched in soil. The potential pathogens, Pseudoalteromonas and Planococcus, were dominant in water and sediment, while Stenotrophomonas was the dominant bacterium in soil. The network topology parameter revealed interspecific interactions within the community. PLS-PM highlights the main direct factors affecting the abundance of potential pathogens and the spread of ARGs, while temperature and pH indirectly influence these potential pathogens. This study advances our understanding of bacterial communities in estuarine wetlands, while highlighting the need for effective monitoring to mitigate the risks associated with potential pathogens and ARGs in these ecosystems.

Evidence of sewage discharge on the coalescence mechanism of aquatic microbial communities during high amplitude hydrological periods

Microbial community coalescence is a ubiquitous ecological process in various ecosystems. However, limited research has addressed the effects of the coalescence on microbial ecological processes and network structure, particularly in the context of sewage discharge during high amplitude hydrological periods. Employing 16S rRNA sequencing and species source tracking analysis, we investigated the coalescence pattern of bacterioplankton in the Chishui river and sewage across various hydrological periods. The results demonstrated that the downstream bacterioplankton mainly originated from the upstream water body, and the sewage discharge from the wastewater treatment plants (WWTPs) had less impact on the downstream bacterioplankton. In the low-water period, the bacterioplankton community showed significant coalescence, and the specialist species and functional taxa gathered in the downstream. Bacterioplankton displayed distinct ecological succession patterns after community coalescence, with notable variations in the abundance of dominant group. Bacterioplankton community assembly was dominated by stochastic processes in river and the sewage over different hydrological periods. The ecological networks exhibited the highest complexity in the high-water period, whereas their stability was most pronounced in the low-water period. Species diversity, as opposed to functional and phylogenetic diversity, might be a more accurate indicator to predict changes in microbial network structure. Our findings will provide new perspectives on the mechanisms of aquatic microbial community coalescence in natural environments.

Differential insights into the distribution characteristics of bacterial communities and their response to typical pollutants in the sediment and soil of large drinking water reservoir

In this study, a large drinking water reservoir (Fengshuba Reservoir) was chosen as a representative case, and the bacterial communities in the sediments and soils of Water-level fluctuating zone (WLFZ) as well as their responses to heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) were systematically investigated. The results indicated that the abundance and diversity of the bacterial community obviously changed with seasonal hydrological variations in sediments, and the absolute abundance and composition of bacteria community differed significantly between the sediment phase and soil phase. Bacteria with the ability to degrade pollutants rapidly proliferate and gain ascendancy in the soil phase, with Burkholderia-Caballeronia-Paraburkholderia (B-C-P) and Bradyrhizobium forming the core of the largest community. Furthermore, Co-occurrence network analysis indicated that a more stable bacterial community composition in the sediment phase. The community assembly pattern of bacteria in sediments exhibit a higher degree of stochasticity than that observed in soils of the WLFZ. Furthermore, the Spearman correlations found that the interaction between physicochemical factors, HMs, and PAHs with bacteria community was stronger in the soils of WLFZ. In total, the structural equation models indicated that PAHs were the main driver in altering the deterministic process of bacterial community in the sediment, while HMs and physicochemical factors had a greater effect on the bacteria community in the WLFZ. This study systematically revealed the differential characteristics of bacterial community and their response to typical pollutants between the sediments and soils of large drinking water reservoir.

Stronger biogeographical pattern of bacterioplankton communities than biofilm communities along a riverine ecosystem: A local scale study of the Kaidu river in the arid and semi-arid northwest of China

Although the biogeographical pattern and mechanisms underlying microbial assembly have been well-explored in lentic ecosystems, the relevant scenarios in lotic ecosystems remain poorly understood. By sequencing the bacterial communities in bacterioplankton and biofilm, our study detected their distance-decay relationship (DDR), and the balance between deterministic and stochastic processes, along the Kaidu river in an arid and semi-arid region of northwest China. Our results revealed that bacterioplankton and biofilm had significantly contrasting community structures. The bacterioplankton communities showed a gradually decreasing trend in alpha-diversity from the headwater to the river mouth, contrasting with the alpha-diversity of biofilm communities which was constant along the river length. Both bacterioplankton and biofilm showed significant DDRs along the 500-km river corridor with the slope of the bacterioplankton DDR being steeper than that of the biofilm DDR, which implies a stronger biogeography of bacterioplankton than biofilm. Relative to biofilm communities, the species interactions formed a denser and more complex network in the bacterioplankton communities than in the biofilm communities. Our results also revealed that there was a transition of community assembly from deterministic to stochastic processes upstream to downstream, although both the bacterioplankton and biofilm communities were mainly regulated by deterministic processes within the entire river. All these empirical results expand our knowledge of microbial ecology in an arid and semi-arid lotic ecosystem.

Seasonal dynamics of environmental heterogeneity augment microbial interactions by regulating community structure in different trophic lakes

Understanding how environmental heterogeneity drives microbial communities in lakes is essential for developing effective strategies to manage and restore aquatic ecosystems. However, the mechanisms by which environmental heterogeneity influences microbial community structure, network patterns, and interactions remain largely unexplored. To bridge this gap, we collected 84 water samples from four typical lakes in China (Fuxian, Tianmu, Taihu, and Xingyun) representing a range of trophic levels, across wet and dry seasons. We assessed environmental heterogeneity using 14 water quality parameters, analyzed community structure with Jaccard and Bray-Curtis dissimilarity indices, and developed a comprehensive index to elucidate microbial network complexity. Our study reveals three key findings: (1) Environmental heterogeneity was significantly greater in dry season compared to wet season across all lakes (P < 0.05). (2) Increased environmental heterogeneity led to higher bacterioplankton community dissimilarity, with greater β-diversity observed in dry season (P < 0.05). (3) Shifts in community structure due to increased environmental heterogeneity further enhanced microbial interactions, as evidenced by more complex and interconnected co-occurrence networks in the dry season. In summary, our study demonstrates that environmental heterogeneity significantly impacts bacterioplankton community structure and subsequently enhances microbial interactions. These findings underscore the importance of considering environmental heterogeneity in lake ecosystem management, as it plays a crucial role in regulating microbial community dynamics and interactions.

Bacterial community and antibiotic resistance genes assembly processes were shaped by different mechanisms in the deep-sea basins of the Western Pacific Ocean

As the intrinsic property of microorganisms, antibiotic resistance genes (ARGs) are fundamentally coupled to microbially-linked biogeochemical processes within ecosystems. However, human activities often obscure the natural distribution of ARGs through deterministic selective pressures. The deep-sea basin of the western Pacific Ocean is one of the least disturbed areas globally by human activities, providing a natural laboratory to investigate the intrinsic mechanisms governing ARGs in natural environments. In this study, we analyzed bacterial community and ARG diversity in 15 surface sediment samples from three deep-sea basins in the western Pacific Ocean. The relative abundance of ARGs in the surface sediments ranged from 3.10 × 10-3 to 5.37 × 10-2 copies/16S rRNA copies, with multidrug and β-lactam resistance genes dominated in all samples (49.06%-100%). The bacteria were mainly dominated by the Proteobacteria. The principal coordinate analysis (PCoA) showed significant spatial heterogeneity of ARGs and bacteria among the three basins. Null model, neutral community models (NCM), and normalized stochasticity ratio (NST) indicated that bacterial community was dominated by stochastic assembly, driven by geographic barriers leading to independent evolution. Conversely, the NST revealed that the ARGs profile was mainly shaped by deterministic processes. Environmental factors are more crucial than geographical factors and bacterial community for ARG occurrence among the selected factors. Meanwhile, we found that the spread of ARGs was mainly through vertical gene transfer in the pre-antibiotic era. The disparity between the assembly processes of bacterial community and ARGs may be attributed to the fact that ARG hosts were not the dominant bacteria in the community. This study first reported the distribution and assembly processes of ARGs and bacterial community in surface sediments of the western Pacific.

Spatiotemporal distributions, co-occurrence networks, and assembly mechanisms of the bacterial community in sediments of the Yangtze River: comprehensive insights into abundant and rare taxa

Sediments are key reservoirs for rare bacterial biospheres that provide broad ecological services and resilience in riverine ecosystems. Compared with planktons, there is a lack of knowledge regarding the ecological differences between abundant and rare taxa in benthic bacteria along a large river. Here, we offer comprehensive insights into the spatiotemporal distributions, co-occurrence networks, and assembly processes of three divided categories namely always rare taxa (ART), conditionally rare taxa (CRT), and conditionally rare and abundant taxa (CRAT) in sediments covering a distance of 4,300 km in the Yangtze River. Our study demonstrated that ART/CRT contributed greatly to the higher Chao-1 index, Shannon-Wiener index, and phylogenetic alpha diversity of benthic bacteria in autumn than in spring. ART showed high overall beta diversity, and CRT/CRAT exhibited more significant distance-decay patterns than ART in both seasons, mainly corresponding to macroscopic landform types. CRT predominated the nonrandom co-occurrence network, with 97% of the keystone species mostly affiliated with Acidobacteriota flourishing in the lower-reach plain. Two selection processes had the greatest influences on the assembly of CRT (74.7-77.6%), whereas CRAT were driven primarily by dispersal limitation (74.9-86.8%) and ART were driven by heterogeneous selection (33.9-48.5%) and undominated stochasticity (32.7-36.5%). Natural factors such as river flow and channel slope exhibited more significant correlations with community variation than nutrients in all three groups, and total organic carbon mediated the balance among the distinct assembly processes of the ART and CRT in both seasons. Taken together, these results provide an improved ecological understanding of the discrepancy in biogeographic patterns between abundant and rare bacterial taxa in the sediments of Asia's largest river.

Key bacterial taxa with specific metabolisms and life history strategies sustain soil microbial network stability exposed to carbendazim and deoxynivalenol

Co-contamination of carbendazim (CBD) and deoxynivalenol (DON) is common in agricultural soils, yet their ecological impact on soil microbiome remains poorly assessed. Here, we investigated the influence of CBD and DON on the structure, function, and co-occurrence networks of soil microbiome. The combined treatment of CBD and DON significantly exacerbated the negative impacts on soil microbial diversity, functional diversity, and microbial network stability compared to individual treatments. Specifically, Lysobacter, Gemmatimonas, Nitrospira, Massilia, and Bacillus were identified as indicator species for CBD and DON. Simultaneously, the abundance of genes involved in key ecological functions, such as nitrification (amoA) and organic phosphorus mineralization (phoAD), was significantly reduced. Notably, key bacterial taxa Nitrospira and Gemmatimonas, with K-life history strategy and capabilities for nitrification and organic nitrogen mineralization, played crucial roles in promoting positive interactions in networks. Furthermore, variance partitioning analysis (VPA) and structural equation modeling (SEM) demonstrated that the abundance and niche breadth of key bacterial taxa were the primary drivers of microbial network stability. In conclusion, our study provides new insights into how soil microbiomes and networks respond to pesticides and mycotoxins, aiding in a more comprehensive assessment of exposure risks.

Riverine bacterial communities are more shaped by species sorting in intensive urban and agricultural watersheds

Bacterial communities play a crucial role in maintaining the stability of river ecosystems and driving biogeochemical cycling, exhibiting high sensitivity to environmental change. However, understanding the spatial scale effects and assembly mechanisms of riverine bacterial communities under distinct anthropogenic disturbances remains a challenge. Here, we investigated bacterial communities across three distinct watersheds [i.e., intensive urban (UW), intensive agricultural (AW), and natural (NW)] in both dry and wet seasons. We explored biogeographic patterns of bacterial communities and the influence of landscape patterns at multi-spatial scales and water chemistry on bacterial communities. Results showed that α diversity was significantly lower in UW and AW compared to NW, particularly in the dry season. A gradient of β diversity with NW > UW > AW was observed across both seasons (p < 0.05). Pseudomonadota, Bacteroidota, and Actinobacteriota were the most abundant phyla across all watersheds, with specific taxa enriched in each watershed (i.e., the class Actinobacteria was significant enrichment in UW and AW, and Clostridia in NW). The influence of landscape patterns on bacterial communities was significantly lower in human-disturbed watersheds, particularly in UW, where this influence also varied slightly from near riparian buffers to sub-watershed. Homogeneous selection and drift jointly dominated the bacterial community assembly across all watersheds, with homogeneous selection exhibiting a greater influence in UW and AW. Landscape patterns explained less variance in bacterial communities in UW and AW than in NW, and more variance was explained by water chemistry (particularly in UW). These suggest that the stronger influence of species sorting in UW and AW was driven by more allochthonous inputs of water chemistry (greater environmental stress). These findings provide a theoretical foundation for a deeper understanding of riverine bacterial community structure, spatial scale effects, and ecological management under different anthropogenic activities.

Revealing the distribution characteristics and key driving factors of dissolved organic matter in Baiyangdian Lake inflow rivers from different seasons and sources

The river course is a transitional area connecting the source and receiving water bodies. The dissolved organic matter (DOM) in the river course is an important factor affecting the aquatic environment and ecological health. However, there are shortcomings in studying the differences and quantitative contributions of river DOM in different seasons and sources. In this study, ultraviolet-visible (UV-vis) and three-dimensional fluorescence spectra were used to characterize the optical properties, analyze the spatiotemporal changes, and establish the quantitative relationship between environmental factors and DOM in the inflow rivers of Baiyangdian Lake. The results showed that the relative DOM concentrations in summer and autumn were significantly higher than those in the other seasons (P < 0.001) and that the DOM source (SR < 1) was mainly exogenous. The fluorescence abundance of protein-like substances (C1 + C2 + C3) was the highest in spring, whereas that of humus C4 was the highest in autumn. Moreover, the inflow rivers exhibited strong autogenetic characteristics (BIX > 1) throughout the year. Self-organizing maps (SOM) indicated that the main driving factors of water quality were NO3--N in spring, autumn, and winter and DO, pH, and chemical oxygen demand (COD) in summer. Random forest analysis showed that the fluorescent components (C1-C4) were closely related to the migration and transformation of nitrogen, and pH and nitrogen were the main predictors of each component. The Mantel test and structural equation model (SEM) showed that temperature and NO3--N significantly influenced the DOM concentration, components, and molecular properties in different seasons. Moreover, the river source also affected the distribution mechanism of DOM in the water body. Our study comprehensively analyzed the response of DOM in inflow rivers in different seasons and water sources, providing a basis for further understanding the driving mechanisms of water quality.

Impact of extreme rainfall and flood events on harmful cyanobacterial communities and ecological safety in the Baiyangdian Lake Basin, China

Globally, climate change has intensified extreme rainfall events, leading to substantial hydrological changes in aquatic ecosystems. These changes, in turn, have increased the frequency of harmful algal blooms, particularly those of cyanobacteria. This study examines cyanobacterial community dynamics in the Baiyangdian Lake Basin, China, after heavy rainfall and flooding events. The aim was to clarify how such extreme hydrological events affect cyanobacterial populations in floodplain ecosystems and assess related ecological risks. The results demonstrated a significant increase in cyanobacterial diversity, exemplified by an increase of the Shannon diversity index from an average of 1.72 to 2.1 (p < 0.05). Following heavy rainfall and subsequent flooding, the average relative abundance of cyanobacteria in the microbial community increased from 7.59 % to 9.62 %, along a notable rise in the abundance of harmful cyanobacteria. The community structure exhibited notable differences after flooding, showing an increase in species richness, but a decrease in community tightness and clustering, as well as a reduction in niche overlap among harmful cyanobacteria. Environmental factors such as dissolved oxygen, water temperature, and pH were identified as crucial predictors of harmful cyanobacterial community differences and abundance variations resulting from flooding. These findings provide a critical framework for predicting ecological risks associated with the expansion of bloom-forming cyanobacteria in large shallow lake basins, particularly under intensified rainfall and flooding events. This insight is essential to anticipate potential ecological disruptions in sensitive aquatic ecosystems.

Ignored microbial-induced taste and odor in drinking water reservoirs: Novel insight into actinobacterial community structure, assembly, and odor-producing potential

The presence of actinobacteria in reservoirs can lead to taste and odor issues, posing potential risks to the safety of drinking water supply. However, the response of actinobacterial communities to environmental factors in drinking water reservoirs remains largely unexplored. To address this gap, this study investigated the community structure and metabolic characteristics of odor-producing actinobacteria in water reservoirs across northern and southern China. The findings revealed differences in the actinobacterial composition across the reservoirs, with Mycobacterium sp. and Candidatus Nanopelagicus being the most prevalent genera. Notably, water temperature, nutrient levels, and metal concentrations were associated with differences in actinobacterial communities, with stochastic processes playing a major role in shaping the community assembly. In addition, three strains of odor-producing actinobacteria were cultured in raw reservoir water, namely Streptomyces antibioticus LJH21, Streptomyces sp. ZEU13, and Streptomyces sp. PQK19, with peak ATP concentrations of 51 nmol/L, 66 nmol/L, and 70 nmol/L, respectively, indicating that odor-producing actinobacteria could remain metabolically active under poor nutrient pressure. Additionally, Streptomyces antibioticus LJH21 produced the highest concentration of geosmin at 24.4 ng/L. These findings enhance our understanding of regional variances and reproductive metabolic mechanisms of actinobacteria in drinking water reservoirs, providing a solid foundation for improving drinking water quality control, especially for taste and odor.

Analysis of bacterial community structure, functional variation, and assembly mechanisms in multi-media habitats of lakes during the frozen period

Ice, water, and sediment represent three interconnected habitats in lake ecosystems, and bacteria are crucial for maintaining ecosystem equilibrium and elemental cycling across these habitats. However, the differential characteristics and driving mechanisms of bacterial community structures in the ice, water, and sediments of seasonally frozen lakes remain unclear. In this study, high-throughput sequencing technology was used to analyze and compare the structure, function, network characteristics, and assembly mechanisms of bacterial communities in the ice, water, and sediment of Wuliangsuhai, a typical cold region in Inner Mongolia. The results showed that the bacterial communities in the ice and water phases had similar diversity and composition, with Proteobacteria, Bacteroidota, Actinobacteria, Campilobacterota, and Cyanobacteria as dominant phyla. The bacterial communities in sediments displayed significant differences from ice and water, with Chloroflexi, Proteobacteria, Firmicutes, Desulfobacterota, and Acidobacteriota being the dominant phyla. Notably, the bacterial communities in water exhibited higher spatial variability in their distribution than those in ice and sediment. This study also revealed that during the frozen period, the bacterial community species in the ice, water, and sediment media were dominated by cooperative relationships. Community assembly was primarily influenced by stochastic processes, with dispersal limitation and drift identified as the two most significant factors within this process. However, heterogeneous selection also played a significant role in the community composition. Furthermore, functions related to nitrogen, phosphorus, sulfur, carbon, and hydrogen cycling vary among bacterial communities in ice, water, and sediment. These findings elucidate the intrinsic mechanisms driving variability in bacterial community structure and changes in water quality across different media phases (ice, water, and sediment) in cold-zone lakes during the freezing period, offering new insights for water environmental protection and ecological restoration efforts in such environments.

Differential microbiome features in lake-river systems of Taihu basin in response to water flow disturbance

Introduction

In riverine ecosystems, dynamic interplay between hydrological conditions, such as flow rate, water level, and rainfall, significantly shape the structure and function of bacterial and microeukaryotic communities, with consequences for biogeochemical cycles and ecological stability. Lake Taihu, one of China's largest freshwater lakes, frequently experiences cyanobacterial blooms primarily driven by nutrient over-enrichment and hydrological changes, posing severe threats to water quality, aquatic life, and surrounding human populations. This study explored how varying water flow disturbances influence microbial diversity and community assembly within the interconnected river-lake systems of the East and South of Lake Taihu (ET&ST). The Taipu River in the ET region accounts for nearly one-third of Lake Taihu's outflow, while the ST region includes the Changdougang and Xiaomeigang rivers, which act as inflow rivers. These two rivers not only channel water into Lake Taihu but can also cause the backflow of lake water into the rivers, creating distinct river-lake systems subjected to different intensities of water flow disturbances.

Methods

Utilizing high-throughput sequencing, we selected 22 sampling sites in the ET and ST interconnected river-lake systems and conducted seasonally assessments of bacterial and microeukaryotic community dynamics. We then compared differences in microbial diversity, community assembly, and co-occurrence networks between the two regions under varying hydrological regimes.

Results and discussion

This study demonstrated that water flow intensity and temperature disturbances significantly influenced diversity, community structure, community assembly, ecological niches, and coexistence networks of bacterial and eukaryotic microbes. In the ET region, where water flow disturbances were stronger, microbial richness significantly increased, and phylogenetic relationships were closer, yet variations in community structure were greater than in the ST region, which experienced milder water flow disturbances. Additionally, migration and dispersal rates of microbes in the ET region, along with the impact of dispersal limitations, were significantly higher than in the ST region. High flow disturbances notably reduced microbial niche width and overlap, decreasing the complexity and stability of microbial coexistence networks. Moreover, path analysis indicated that microeukaryotic communities exhibited a stronger response to water flow disturbances than bacterial communities. Our findings underscore the critical need to consider the effects of hydrological disturbance on microbial diversity, community assembly, and coexistence networks when developing strategies to manage and protect river-lake ecosystems, particularly in efforts to control cyanobacterial blooms in Lake Taihu.

Assembly process and co-occurrence network of microbial community in response to free ammonia gradient distribution

Microorganisms are crucial components of the aquatic ecosystem due to their immense diversity and abundance. They are vital in sustaining ecological services, especially in maintaining essential biogeochemical cycles. Recent years have seen a substantial increase in surplus nitrogenous pollutants in aquatic ecosystems due to the heightened occurrence of anthropogenic activities. Elevated levels of free ammonia (FA, NH3), stemming from the discharge of excess nitrogenous pollutants, have caused notable fluctuations in aquatic ecosystems, leading to water eutrophication and various ecological challenges. The impact of these oscillations on microbial communities in aquatic ecosystems has not been extensively studied. This study employed 16S rRNA gene amplicon sequencing to systematically investigate the dynamics, co-occurrence networks, and assembly processes of microbial communities and their subcommunities (abundant, moderate, and rare) in the Luanhe River Diversion Project in China. Our findings indicate that NH3 concentration significantly influences the dynamics of microbial communities, with a notable decrease in community Richness and Phylogenetic Distance alongside increased community dissimilarity under higher NH3 conditions. The analysis revealed that certain microbial groups, particularly Actinobacteriaota, were notably more prevalent in environments with elevated NH3 levels, suggesting their potential resilience or adaptive responses to NH3 stress. Additionally, through co-occurrence network analysis, we observed dynamic changes in network topology and increased connectedness under NH3 stress. Key nodes, identified as connectors and module hubs, played crucial roles in maintaining network structure, particularly Cyanobacteria and Actinobacteriaota. Furthermore, stochastic processes, particularly drift and dispersal limitation, predominantly shaped the microbial communities. Within the three subcommunities, the impact of drift became more pronounced as the effect of dispersal limitation diminished. Overall, elucidating the dynamics of microbial communities in aquatic ecosystems exposed to NH3 can enhance our comprehension of the ecological mechanisms of microbial communities and provide new insights into the conservation of microbial community diversity and ecological functions.

IMPORTANCE

The research presented in this paper explores how varying concentrations of free ammonia impact microbial communities in aquatic ecosystems. By employing advanced gene sequencing techniques, the study reveals significant changes in microbial diversity and network structures in response to increased ammonia levels. Key findings indicate that high ammonia concentrations lead to a decrease in microbial richness and diversity while increasing community dissimilarity. Notably, certain microbial groups, like Actinobacteria, show resilience to ammonia stress. This research enhances our understanding of how pollution affects microbial ecosystems and underscores the importance of maintaining balanced ammonia levels to preserve microbial diversity and ecosystem health.

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.

Exploring seasonal variations, assembly dynamics, and relationships of bacterial communities in different habitats of marine ranching

Offshore coastal marine ranching ecosystems provide habitat for diverse and active bacterial communities. In this study, 16S rRNA gene sequencing and multiple bioinformatics methods were applied to investigate assembly dynamics and relationships in different habitats. The higher number of edges in the water network, more balanced ratio of positive and negative links, and more keystone species included in the co-occurrence network of water. Stochastic processes dominated in shaping gut and sediment community assembly (R2 < 0.5), while water bacterial community assembly were dominated by deterministic processes (R2 > 0.5). Dissimilarity-overlap curve model indicated that the communities in different habitats have general dynamics and interspecific interaction (P < 0.001). Bacterial source-tracking analysis revealed that the gut was more similar to the sediment than the water bacterial communities. In summary, this study provides basic data for the ecological study of marine ranching through the study of bacterial community dynamics.

Distinct strategies of the habitat generalists and specialists in the Arctic sediments: Assembly processes, co-occurrence patterns, and environmental implications

Microorganisms could be classified as habitat generalists and specialists according to their niche breadth, uncovering their survival strategy is a crucial topic in ecology. Here, differences in environmental adaptation, community assemblies, co-occurrence patterns, and ecological functions between generalists and specialists were explored in the Arctic marine sediments. Compared to specialists, generalists showed lower alpha diversity but stronger environmental adaption, and dispersal limitation contributed more to the community assembly of specialists (74 %) than generalists (46 %). Furthermore, the neutral theory model demonstrated that generalists (m = 0.20) had a higher immigration rate than specialists (m = 0.02), but specialists exhibited more complex co-occurrence patterns than generalists. Our results also found that generalists may play more important roles in C, N, S metabolism but are weaker in carbon fixation and xenobiotic biodegradation and metabolism. This study would broaden our understanding of bacterial generalists' and specialists' survival strategies, and further reveal their ecological functions in marine sediments.

Assembly mechanism and stability of zooplankton communities affected by China's south-to-north water diversion project

Water diversion can effectively alleviate water resource shortages and improve water environmental conditions, while also causing unknown ecological consequences, in particular, the assembly mechanism of zooplankton communities in the affected areas will become more complex after long-term water transfer. Taking Nansi Lake, the second largest impounded lake along the eastern route of China's South to North Water Diversion Project (SNWDP), as an example, the composition and diversity of zooplankton communities in the lake area and estuaries during the water diversion period (WDP) and non-water diversion period (NWDP) were studied. The potential assembly process of zooplankton communities was further explored, and the stability of communities in different regions during different periods was compared. The related results indicated that the changes in water quality conditions induced by water diversion had a relatively weak impact on the zooplankton communities. In the assembly mechanism of zooplankton communities, stochastic process played a more important role during both WDP or NWDP, and the proportion of deterministic process was relatively higher during NWDP, which may be related to the greater role of total nitrogen (TN) in the assembly of the zooplankton communities. The network analysis and cohesion calculation results showed that the stability of the zooplankton communities in the lake area sites was higher than that in the estuary sites, and the stability during NWDP was higher than that during WDP. In sum, the stability of zooplankton communities displayed a degree of change affected by water diversion activities, but the community assembly was not significantly influenced by the water quality fluctuations after about relatively long-term water diversion. This study provides an in-depth understanding of the ecological effects of water diversion on the biological communities in the affected lake, which is beneficial to the management and regulation of long-term water diversion projects.

Distinct ecological niches and community dynamics: understanding free-living and particle-attached bacterial communities in an oligotrophic deep lake

Oligotrophic deep-water lakes are unique and sensitive ecosystems with limited nutrient availability. Understanding bacterial communities within these lakes is crucial for assessing ecosystem health, biogeochemical cycling, and responses to environmental changes. In this study, we investigated the seasonal and vertical dynamics of both free-living (FL) and particle-attached (PA) bacteria in Lake Fuxian, a typical oligotrophic deep freshwater lake in southeast China. Our findings revealed distinct seasonal and vertical dynamics of FL and PA bacterial communities, driven by similar physiochemical environmental factors. PA bacteria exhibited higher α- and β-diversity and were enriched with Proteobacteria, Cyanobacteria, Firmicutes, Patescibacteria, Planctomycetota, and Verrucomicrobiota, while FL bacteria were enriched with Actinobacteria and Bacteroidota. FL bacteria showed enrichment in putative functions related to chemoheterotrophy and aerobic anoxygenic photosynthesis, whereas the PA fraction was enriched with intracellular parasites (mainly contributed by Rickettsiales, Chlamydiales, and Legionellales) and nitrogen metabolism functions. Deterministic processes predominantly shaped the assembly of both FL and PA bacterial communities, with stochastic processes playing a greater role in the FL fraction. Network analysis revealed extensive species interactions, with a higher proportion of positively correlated edges in the PA network, indicating mutualistic or cooperative interactions. Cyanobium, Comamonadaceae, and Roseomonas were identified as keystone taxa in the PA network, underscoring potential cooperation between autotrophic and heterotrophic bacteria in organic particle microhabitats. Overall, the disparities in bacterial diversity, community composition, putative function, and network characteristics between FL and PA fractions highlight their adaptation to distinct ecological niches within these unique lake ecosystems.IMPORTANCEUnderstanding the diversity of microbial communities, their assembly mechanisms, and their responses to environmental changes is fundamental to the study of aquatic microbial ecology. Oligotrophic deep-water lakes are fragile ecosystems with limited nutrient resources, rendering them highly susceptible to environmental fluctuations. Examining different bacterial types within these lakes offers valuable insights into the intricate mechanisms governing community dynamics and adaptation strategies across various scales. In our investigation of oligotrophic deep freshwater Lake Fuxian in China, we explored the seasonal and vertical dynamics of two bacterial types: free-living (FL) and particle-attached (PA). Our findings unveiled distinct patterns in the diversity, composition, and putative functions of these bacteria, all shaped by environmental factors. Understanding these subtleties provides insight into bacterial interactions, thereby influencing the overall ecosystem functioning. Ultimately, our research illuminates the adaptation and roles of FL and PA bacteria within these unique lake environments, contributing significantly to our broader comprehension of ecosystem stability and health.

The roles of rare and abundant microbial species in the primary succession of biological soil crusts are differentiated in metal tailings ponds with different states

Tailings ponds formed by long-term accumulation of mineral processing waste have become a global environmental problem. Even worse, tailings ponds are often simply abandoned or landfilled after they cease to be used. This allows pollution to persist and continue to spread in the environment. The significance of primary succession mediated by biological soil crusts for tailings pond remediation has been illustrated by previous studies. However, the process of primary succession may not be the same at different stages during the lifetime of tailings ponds. Therefore, we investigated the environmental differences and the successional characteristics of microbial communities in the primary successional stage of tailings ponds at three different states. The results showed that the primary succession process positively changed the environment of tailings ponds in any state of tailings ponds. The primary successional stage determined the environmental quality more than the state of the tailings pond. In the recently abandoned tailings ponds, abundant species were more subjected to heavy metal stress, while rare species were mainly limited by nutrient content. We found that as the succession progressed, rare species gradually acquired their own community space and became more responsive to environmental stresses. Rare species played an important role in microbial keystone species groups.

Bacterial abundant taxa exhibit stronger environmental adaption than rare taxa in the Arctic Ocean sediments

Marine bacteria influence Earth's environmental dynamics in fundamental ways by controlling the biogeochemistry and productivity of the oceans. However, little is known about the survival strategies of their abundant and rare taxa, especially in polar marine environments. Here, bacterial environmental adaptation, community assembly processes, and co-occurrence patterns between abundant and rare taxa were compared in the Arctic Ocean sediments. Results indicated that the diversity of rare taxa is significantly higher than that of abundant taxa, whereas the distance-decay rate of rare taxa community similarity is over 1.5 times higher than that of abundant taxa. Furthermore, abundant taxa exhibited broader environmental breadth and stronger phylogenetic signals compared to rare taxa. Additionally, the community assembly processes of the abundant taxa were predominantly governed by 81% dispersal limitation, while rare taxa were primarily influenced by 48% heterogeneous selection. The co-occurrence network further revealed the abundant taxa formed a more complex network to enhance their environmental adaptability. This study revealed the differences in environmental responses and community assembly processes between bacterial abundant and rare taxa in polar ocean sediments, providing some valuable insights for understanding their environmental adaptation strategies in marine ecosystems.

Deciphering the environmental adaptation and functional trait of core and noncore bacterial communities in impacted coral reef seawater

Microorganisms play pivotal roles in different biogeochemical cycles within coral reef waters. Nevertheless, our comprehension of the microbially mediated processes following environmental perturbation is still limited. To gain a deeper insight into the environmental adaptation and nutrient cycling, particularly within core and noncore bacterial communities, it is crucial to understand reef ecosystem functioning. In this study, we delved into the microbial community structure and function of seawater in a coral reef under different degrees of anthropogenic disturbance. To achieve this, we harnessed the power of 16S rRNA gene high-throughput sequencing and metagenomics techniques. The results showed that a continuous temporal succession but little spatial heterogeneity in the bacterial communities of core and noncore taxa and functional profiles involved in nitrogen (N) and phosphorus (P) cycling. Eutrophication state (i.e., nutrient concentration and turbidity) and temperature played pivotal roles in shaping both the microbial community composition and functional traits of coral reef seawater. Within this context, the core subcommunity exhibited a remarkably broader habitat niche breadth, stronger phylogenetic signal and lower environmental sensitivity when compared to the noncore taxa. Null model analysis further revealed that the core subcommunity was governed primarily by stochastic processes, while deterministic processes played a more significant role in shaping the noncore subcommunity. Furthermore, our observations indicated that changes in function related to N cycling were correlated to the variations in noncore taxa, while core taxa played a more substantial role in critical processes such as P cycling. Collectively, these findings facilitated our knowledge about environmental adaptability of core and noncore bacterial taxa and shed light on their respective roles in maintaining diverse nutrient cycling within coral reef ecosystems.

Molecular insights into linkages among free-floating macrophyte-derived organic matter, the fate of antibiotic residues, and antibiotic resistance genes

Macrophyte rhizospheric dissolved organic matter (ROM) served as widespread abiotic components in aquatic ecosystems, and its effects on antibiotic residues and antibiotic resistance genes (ARGs) could not be ignored. However, specific influencing mechanisms for ROM on the fate of antibiotic residues and expression of ARGs still remained unclear. Herein, laboratory hydroponic experiments for water lettuce (Pistia stratiotes) were carried out to explore mutual interactions among ROM, sulfamethoxazole (SMX), bacterial community, and ARGs expression. Results showed ROM directly affect SMX concentrations through the binding process, while CO and N-H groups were main binding sites for ROM. Dynamic changes of ROM molecular composition diversified the DOM pool due to microbe-mediated oxidoreduction, with enrichment of heteroatoms (N, S, P) and decreased aromaticity. Microbial community analysis showed SMX pressure significantly stimulated the succession of bacterial structure in both bulk water and rhizospheric biofilms. Furthermore, network analysis further confirmed ROM bio-labile compositions as energy sources and electron shuttles directly influenced microbial structure, thereby facilitating proliferation of antibiotic resistant bacteria (Methylotenera, Sphingobium, Az spirillum) and ARGs (sul1, sul2, intl1). This investigation will provide scientific supports for the control of antibiotic residues and corresponding ARGs in aquatic ecosystems.

Responses of microbial communities subjected to hydrodynamically induced disturbances in an organic contaminated site

Organic contaminated sites have gained significant attention as a prominent contributor to shallow groundwater contamination. However, limited knowledge exists regarding the impact of hydrodynamic effects on microbially mediated contaminant degradation at such sites. In this study, we investigated the distribution characteristics and community structure of prokaryotic microorganisms at the selected site during both wet and dry seasons, with a particular focus on their environmental adaptations. The results revealed significant seasonal variations (P < 0.05) in the α-diversity of prokaryotes within groundwater. The dry season showed more exclusive OTUs than the wet season. The response of prokaryotic metabolism to organic pollution pressure in different seasons was explored by PICRUSt2, and enzymes associated with the degradation of organic pollutants were identified based on the predicted functions. The results showed that hormesis was considered as an adaptive response of microbial communities under pollution stress. In addition, structural equation models demonstrated that groundwater level fluctuations can, directly and indirectly, affect the abundance and diversity of prokaryotes through other factors such as oxidation reduction potential (ORP), dissolved oxygen (DO), and naphthalene (Nap). Overall, our findings imply that the taxonomic composition and functional properties of prokaryotes in groundwater in organic contaminated sites is influenced by the interaction between seasonal variations and characteristics of organic pollution. The results provide new insights into microbiological processes in groundwater systems in organic contaminated sites.

Rare resistome rather than core resistome exhibited higher diversity and risk along the Yangtze River

As important freshwater ecosystems, the occurrence and distribution of antibiotic resistance genes (ARGs) in rivers are relevant to public health. However, studies investigating ARGs of different environmental media in river ecosystems are limited. In this study, we analyzed the ARGs of microbes in free-living setting, particle-associated setting, sediment and bank soil of the Yangtze River using metagenomics. Twenty-six ARGs were found in all samples regardless of media (core resistome) with a diversity of 8.6 %-34.7 %, accounting for 22.7 %-89.2 % of the relative abundance of the overall ARGs. The core resistome of the Yangtze River was dominated by multidrug resistance genes consisting mainly of efflux pumps and bacitracin resistance genes. The rare resistome was dominated by multidrug, sulfonamide, and aminoglycoside resistance genes. The core resistome was more prevalent in chromosomes, implying that these ARGs with low diversity and high relative abundance may be intrinsic to microbes in the Yangtze River. The rare resistome was more prevalent in plasmids, suggesting these ARGs with high diversity and low relative abundance were acquired under environmental stresses and had transfer potential. Additionally, we found that core and rare resistome were mainly carried by specific bacteria. Noteworthily, twenty-two ARGs of high clinical concern were identified in rare resistome, especially aac(6')-I, sul1, and tetM, which were plasmid-borne and hosted by clinically relevant pathogens. Both core and rare resistome hosts showed the highest niche breadths in particle-associated setting compared to other media, and particle-associated setting could provide more stable and ideal conditions for resistome hosts to survive. This study elucidated the genetic locations of ARGs and the community assembly mechanisms of ARG hosts in freshwater environments.

Dynamics of bacterioplankton communities in the estuary areas of the Taihu Lake: Distinct ecological mechanisms of abundant and rare communities

As the crucial confluences of rivers and lakes, the estuary areas with varied hydrodynamic exchanges intensively affect the bacterioplankton communities, whereas the ecological characteristics of the bacterioplankton in the areas have not been well understood. Here, the distribution patterns and assembly mechanisms of bacterioplankton communities in the estuary areas of the Taihu Lake were investigated using high-throughput sequencing and multivariate statistical analyses. Our results showed obvious seasonal variations in bacterioplankton diversity and community composition, which had significant correlations with water temperature. Neutral and null models together revealed that stochastic processes (especially dispersal limitation) were the major processes in shaping the communities across different seasons. By contrast, heterogeneous selection in deterministic processes exhibited increased impacts on community assembly during summer and autumn, which was significantly related to the comprehensive water quality index (WQI) rather than any single factor. In this study, rare communities displayed more pronounced seasonal dynamics compared to abundant communities, likely due to their sensitivity towards environmental factors. Accordingly, the heterogeneous selection of deterministic processes largely shaped the rare communities. These results enriched our understanding of the assembly mechanisms of bacterioplankton communities in estuary areas and emphasized the specific co-occurrence patterns of abundant and rare communities.

Community assembly patterns and processes of bacteria in a field-scale aquaculture wastewater treatment system

Microbial communities are responsible for the biological treatment of wastewater, however, our comprehension of their diversity, assembly patterns, and functions remains limited. In this study, we analyzed bacterial communities in both water and sediment samples. These samples were gathered from a novel field-scale aquaculture wastewater treatment system (FAWTS), which employs a multi-stage purification process to eliminate nutrients from pond culture wastewater. Significant variations were observed in bacterial diversity and composition across various ponds within the system and at different stages of the culture. Notably, the bacterial community in the FAWTS displayed a distinct species abundance distribution. The influence of dispersal-driven processes on shaping FAWTS communities was found to be relatively weak. The utilization of neutral and null models unveiled that the assembly of microbial communities was primarily governed by stochastic processes. Moreover, environmental factors variables such as total nitrogen (TN), dissolved oxygen (DO), and temperature were found to be associated with both the composition and assembly of bacterial communities, influencing the relative significance of stochastic processes. Furthermore, we discovered a close relationship between that bacterial community composition and system functionality. These findings hold significant implications for microbial ecologists and environmental engineers, as they can collaboratively refine operational strategies while preserving biodiversity. This, in turn, promotes the stability and efficiency of the FAWTS. In summary, our study contributes to an enhanced mechanistic understanding of microbial community diversity, assembly patterns, and functionality within the FAWTS, offering valuable insights into both microbial ecology and wastewater treatment processes.

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

IMPORTANCE

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

Seasonal changes driving shifts in microbial community assembly and species coexistence in an urban river

Microbial communities play a vital role in urban river biogeochemical cycles. However, the seasonal variations in microbial community characteristics, particularly phylogenetic group-based community assembly and species coexistence, have not been extensively investigated. Here, we systematically explored the microbiome characteristics and assembly mechanisms of urban rivers in different seasons using 16S rRNA gene sequencing and multivariate statistical methods. The results indicated that the microbial community presented significant temporal heterogeneity in different seasons, and the diversity decreased from spring to winter. The phylogenetic group-based microbial community assembly was governed by dispersal limitation and drift in spring, summer, and autumn but was structured by homogeneous selection in winter. Moreover, the main functions of nitrification, denitrification, and methanol oxidation were susceptible to dispersal limitation and drift processes, whereas sulfate respiration and aromatic compound degradation were controlled by dispersal limitation and homogeneous selection. Network analyses indicated that network complexity decreased and then increased with seasonal changes, while network stability showed the opposite trend, suggesting that higher complexity and diversity reduced community stability. Temperature was determined to be the primary driver of microbial community structure and assembly processes in different seasons based on canonical correspondence analysis and linear regression analysis. In conclusion, seasonal variation drives the dynamics of microbial community assembly and species coexistence patterns in urban rivers. This study provides new insights into the generation and maintenance of microbial community diversity in urban rivers under seasonal change conditions.

Effects of Cascade Reservoirs on Spatiotemporal Dynamics of the Sedimentary Bacterial Community: Co-occurrence Patterns, Assembly Mechanisms, and Potential Functions

Dam construction as an important anthropogenic activity significantly influences ecological processes in altered freshwater bodies. However, the effects of multiple cascade dams on microbial communities have been largely overlooked. In this study, the spatiotemporal distribution, co-occurrence relationships, assembly mechanisms, and functional profiles of sedimentary bacterial communities were systematically investigated in 12 cascade reservoirs across two typical karst basins in southwest China over four seasons. A significant spatiotemporal heterogeneity was observed in bacterial abundance and diversity. Co-occurrence patterns in the Wujiang Basin exhibited greater edge counts, graph density, average degree, robustness, and reduced modularity, suggesting more intimate and stronger ecological interactions among species than in the Pearl River Basin. Furthermore, Armatimonadota and Desulfobacterota, identified as keystone species, occupied a more prominent niche than the dominant species. A notable distance-decay relationship between geographical distance and community dissimilarities was identified in the Pearl River Basin. Importantly, in the Wujiang Basin, water temperature emerged as the primary seasonal variable steering the deterministic process of bacterial communities, whereas 58.5% of the explained community variance in the neutral community model (NCM) indicated that stochastic processes governed community assembly in the Pearl River Basin. Additionally, principal component analysis (PCA) revealed more pronounced seasonal dynamics in nitrogen functional compositions than spatial variation in the Wujiang Basin. Redundancy analysis (RDA) results indicated that in the Wujiang Basin, environmental factors and in Pearl River Basin, geographical distance, reservoir age, and hydraulic retention time (HRT), respectively, influenced the abundance of nitrogen-related genes. Notably, these findings offer novel insights: building multiple cascade reservoirs could lead to a cascading decrease in biodiversity and resilience in the river-reservoir ecosystem.

Distinct diversity patterns and assembly mechanisms of prokaryotic microbial sub-community in the water column of deep-sea cold seeps

Methane leakage from deep-sea cold seeps has a major impact on marine ecosystems. Microbes sequester methane in the water column of cold seeps and can be divided into abundant and rare groups. Both abundant and rare groups play an important role in cold seep ecosystems, and the environmental heterogeneity in cold seeps may enhance conversion between taxa with different abundances. Yet, the environmental stratification and assembly mechanisms of these microbial sub-communities remain unclear. We investigated the diversities and assembly mechanisms in microbial sub-communities with distinct abundance in the deep-sea cold seep water column, from 400 m to 1400 m. We found that bacterial β-diversity, as measured by Sørensen dissimilarities, exhibited a significant species turnover pattern that was influenced by several environmental factors including depth, temperature, SiO32-, and salinity. In contrast, archaeal β-diversity showed a relatively high percentage of nestedness pattern, which was driven by the levels of soluble reactive phosphate and SiO32-. During the abundance dependency test, abundant taxa of both bacteria and archaea showed a significant species turnover, while the rare taxa possessed a higher percentage of nestedness. Stochastic processes were prominent in shaping the prokaryotic community, but deterministic processes were more pronounced for the abundant taxa than rare ones. Furthermore, the metagenomics results revealed that the abundances of methane oxidation, sulfur oxidation, and nitrogen fixation-related genes and related microbial groups were significantly higher in the bottom water. Our results implied that the carbon, sulfur, and nitrogen cycles were potentially strongly coupled in the bottom water. Overall, the results obtained in this study highlight taxonomic and abundance-dependent microbial community diversity patterns and assembly mechanisms in the water column of cold seeps, which will help understand the impacts of fluid seepage from the sea floor on the microbial community in the water column and further provide guidance for the management of cold seep ecosystem under future environmental pressures.

Hydrological disturbances enhance stochastic assembly processes and decrease network stability of algae communities in a highland floodplain system

Floodplains are hotspots for biodiversity research and conservation worldwide. Hydrological disturbances can profoundly influence the ecological processes and functions of floodplain systems by altering key biological groups such as algae communities. However, the impacts of flood disturbance on the assembly processes and co-occurrence patterns of algae communities in floodplain ecosystems are still unclear. To ascertain the response patterns of algae communities to flood disturbance, we characterized planktonic and benthic algae communities in 144 water and sediment samples collected from the Tibetan floodplain during non-flood and flood periods based on 23S ribosomal RNA gene sequencing. Results showed that planktonic algae exhibited higher diversity and greater compositional variations compared with benthic communities after flood disturbance. Flooding promoted algae community homogenization at horizontal (rivers vs. oxbow lakes) and vertical levels (water vs. sediment). Stochastic processes governed the assembly of distinct algae communities, and their ecological impacts were enhanced in response to flooding. In the non-flood period, dispersal limitation (81.78 %) was the primary ecological process driving algae community assembly. In the flood period, the relative contribution of ecological drift (72.91 %) to algae community assembly markedly increased, with dispersal limitation (22.61 %) being less important. Flooding reduced the interactions among algae taxa, resulting in lower network complexity and stability. Compared with the planktonic algae subnetworks, the benthic subnetworks showed greater stability in the face of flooding. Findings of this study broaden our understanding of how algae communities respond to hydrological disturbances from an ecological perspective and could be useful for the management of highland floodplain ecosystems.

Distinct mechanisms shape prokaryotic community assembly across different land-use intensification

Changes in land-use intensity can have a far-reaching impact on river water quality and prokaryotic community composition. While research has been conducted to investigate the assembly mechanism of prokaryotic communities, the contributions of neutral theory and niche theory to prokaryotic community assembly under different land-use intensities remain unknown. In this study, a total of 251 sampling sites were set up in the Yangtze River basin to explore the assembly mechanism under different land-use intensities. Briefly, a "source" landscape can generate pollution, whereas a "sink" landscape can prevent pollution. Firstly, our result showed that higher land-use intensity might disturb the balance between the "source" and "sink" landscape patterns, resulting in water quality deterioration. Then the prokaryotic community assembly was classified into five ecological processes, namely homogeneous selection, homogenizing dispersal, undominated processes, dispersal limitation, and variable selection. The higher land-use intensity was found to strengthen the homogeneous selection, leading to the homogenization of the community at the whole basin scale. Finally, our findings demonstrated that the Yangtze River Basin's prokaryotic community displayed a distance-decay pattern when land-use intensity was low, with a greater contribution from neutral theory to its assembly. On the other hand, with a higher land-use intensity, the degradation of the aquatic environment increased the impacts of environmental filtering on the prokaryotic community, and niche theory played a stronger role in its assembly. Our findings show how land-use intensity influence the formation of prokaryotic communities, which will be an invaluable guide for managing land use and understanding the prokaryotic community assembly mechanisms in the Yangtze River Basin.

Planktonic and epilithic prokaryota community compositions in a large temperate river reflect climate change related seasonal shifts

In freshwaters, microbial communities are of outstanding importance both from ecological and public health perspectives, however, they are threatened by the impact of global warming. To reveal how different prokaryotic communities in a large temperate river respond to environment conditions related to climate change, the present study provides the first detailed insight into the composition and spatial and year-round temporal variations of planktonic and epilithic prokaryotic community. Microbial diversity was studied using high-throughput next generation amplicon sequencing. Sampling was carried out monthly in the midstream and the littoral zone of the Danube, upstream and downstream from a large urban area. Result demonstrated that river habitats predominantly determine the taxonomic composition of the microbiota; diverse and well-differentiated microbial communities developed in water and epilithon, with higher variance in the latter. The composition of bacterioplankton clearly followed the prolongation of the summer resulting from climate change, while the epilithon community was less responsive. Rising water temperatures was associated with increased abundances of many taxa (such as phylum Actinobacteria, class Gammaproteobacteria and orders Synechococcales, Alteromonadales, Chitinophagales, Pseudomonadales, Rhizobiales and Xanthomonadales), and the composition of the microbiota also reflected changes of several further environmental factors (such as turbidity, TOC, electric conductivity, pH and the concentration of phosphate, sulphate, nitrate, total nitrogen and the dissolved oxygen). The results indicate that shift in microbial community responding to changing environment may be of crucial importance in the decomposition of organic compounds (including pollutants and xenobiotics), the transformation and accumulation of heavy metals and the occurrence of pathogens or antimicrobial resistant organisms.

Soil edaphic factors and climate seasonality explain the turnover of methanotrophic communities in riparian wetlands

Aerobic CH4-oxidizing bacteria (methanotrophs) represent a biological model system for the removal of atmospheric CH4, which is sensitive to the dynamics of water tables. However, little attention has been given to the turnover of methanotrophic communities across wet and dry periods in riparian wetlands. Here, by sequencing the pmoA gene, we investigated the turnover of soil methanotrophic communities across wet and dry periods in typical riparian wetlands that experience intensive agricultural practices. The results demonstrated that the methanotrophic abundance and diversity were significantly higher in the wet period than in the dry period, probably owing to the climatic seasonal succession and associated variation in soil edaphic factors. The co-occurrence patterns of the interspecies association analysis demonstrated that the key ecological clusters (i.e., Mod#1, Mod#2, Mod#4, Mod#5) showed contrasting correlations with soil edaphic properties between wet and dry periods. The linear regression slope of the relationships between the relative abundance of Mod#1 and the carbon to nitrogen ratio was higher in the wet period than in the dry period, whereas the linear regression slope of the relationships between the relative abundance of Mod#2 and soil nitrogen content (i.e., dissolved organic nitrogen, nitrate, and total nitrogen) was higher in the dry period than in the wet period. Moreover, Stegen's null model combined with phylogenetic group-based assembly analysis demonstrated that the methanotrophic community exhibited a higher proportion of drift (55.0%) and a lower contribution of dispersal limitation (24.5%) in the wet period than in the dry period (43.8% and 35.7%, respectively). Overall, these findings demonstrate that the turnover of methanotrophic communities across wet and dry periods were soil edaphic factors and climate dependent.

Responses of compositions, functions, and assembly processes of bacterial and microeukaryotic communities to long-range voyages in simulated ballast water

Ballast water is one of the main vectors for the spread of harmful organisms among geologically isolated waters. However, the successional processes of microbial functions and assembly processes in ballast water during the long-term shipping voyage remain unclear. In this study, the compositions, ecological functions, community assembly, and potential environmental drivers of bacteria and microeukaryotes were investigated in simulated ballast water microcosms for 120 days. The results showed that the diversity and compositions of the bacterial and microeukaryotic communities varied significantly in the initial 40 days (T0∼T40 samples) and then gradually converged. The relative abundance of Proteobacteria showed a distinct tendency to decrease (87.90%-41.44%), while that of Ascomycota exhibited an increasing trend (6.35%-62.12%). The functional groups also varied significantly over time and could be related to the variations of the microbial community. The chemoheterotrophy and aerobic chemoheterotrophy functional groups for bacteria decreased from 44.80% to 28.02% and from 43.77% to 25.39%, respectively. Additionally, co-occurrence network analysis showed that the structures of the bacterial community in T60∼T120 samples were more stable than those in T0∼T40 samples. Stochastic processes also significantly affected the community assembly of bacteria and microeukaryotes. pH played the most significant role in driving the structures and assembly processes of the bacterial and microeukaryotic communities. The results of this study could aid in the understanding of variations in the functions and ecological processes of bacterial and microeukaryotic communities in ballast water over time and provide a theoretical basis for its management.

Distinct assembly processes and environmental adaptation of abundant and rare archaea in Arctic marine sediments

Revealing the ecological processes and environmental adaptation of abundant and rare archaea is a central, but poorly understood, topic in ecology. Here, abundant and rare archaeal diversity, community assembly processes and co-occurrence patterns were comparatively analyzed in Arctic marine sediments. Our findings revealed that the rare taxa exhibited significantly higher diversity compared to the abundant taxa. Additionally, the abundant taxa displayed stronger environmental adaptation than the rare taxa. The co-occurrence network analysis demonstrated that the rare taxa developed more interspecies interactions and modules in response to environmental disturbance. Furthermore, the community assembly of abundant and rare taxa in sediments was primarily controlled by stochastic and deterministic processes, respectively. These findings provide valuable insights into the archaeal community assembly processes and significantly contribute to a deeper understanding of the environmental adaptability of abundant and rare taxa in Arctic marine sediments.

Arsenate microbial reducing behavior regulated by the temperature fields in landfills

Attention should be paid to the As(V) reducing behavior in landfills under different temperature fields. In this study, microcosm tests were conducted using enrichment culture from a landfill. The results revealed that the reduction rate of As(V) was significantly affected by the temperature field, with the highest reduction rate observed at 50 °C, followed by 35 °C, 25 °C, and 10 °C. Different As cycling pathways were observed under various temperature fields. At room and medium temperatures, As4S4 was detected, indicating that both biomineralization and methylation processes occurred after As(V) reduction. However, only biogenic methylation was observed under high or low temperatures, indicating that the viability and adaptability of microorganisms varied depending on the temperature field and As contents. Pseudomonas was found to be the primary genus and dominant As(V) reduction bacteria (ARB) in all reactors. The study revealed that Pseudomonas accounted for a significant proportion of arsC genes, ranging from 87.29% to 97.59%, while arsCs genes were predominantly found in Bacillales and Closestridiales, with a contribution ranging from 89.17% to 96.59%. Interestingly, Bacillus and Clostridium were found to possess arsA genes in their metagenome-ssembled genome, resulting in a higher As(V) reducing rate under medium and high temperatures. These findings underscore the importance of temperature in modulating As(V) reducing behavior and As cycling, and could have implications for managing As pollution in landfill sites.

Actinobacteria produce taste and odor in drinking water reservoir: Community composition dynamics, co-occurrence and inactivation models

Taste and odor (T&O) has become a significant concern for drinking water safety. Actinobacteria are believed to produce T&O during the non-algal bloom period; however, this has not been widely investigated. In this study, the seasonal dynamics of the actinobacterial community structure and inactivation of odor-producing actinobacteria were explored. The results indicated that the diversity and community composition of actinobacteria exhibited significant spatiotemporal distribution. Network analysis and structural equation modeling showed that the actinobacterial community occupied a similar environmental niche, and the major environmental attributes exhibited spatiotemporal dynamics, which affected the actinobacterial community. Furthermore, the two genera of odorous actinobacteria were inactivated in drinking water sources using chlorine. Amycolatopsis spp. have a stronger chlorine resistance ability than Streptomyces spp., indicating that chlorine inactivates actinobacteria by first destroying cell membranes and causing the release of intracellular compounds. Finally, we integrated the observed variability in the inactivation rate of actinobacteria into an expanded Chick-Watson model to estimate its effect on inactivation. These findings will deepen our understanding of the seasonal dynamics of actinobacterial community structure in drinking water reservoirs and provide a foundation for reservoir water quality management strategies.

Distinct community assembly processes and habitat specialization driving the biogeographic patterns of abundant and rare bacterioplankton in a brackish coastal lagoon

The ecological diversity patterns and community assembly processes along spatio-temporal scales are least studied in the bacterioplankton sub-communities of brackish coastal lagoons. We examined the biogeographic patterns and relative influences of different assembly processes in structuring the abundant and rare bacterioplankton sub-communities of Chilika, the largest brackish water coastal lagoon of India. Rare taxa demonstrated significantly higher α- and β-diversity and biogeochemical functions than abundant taxa in the high-throughput 16S rRNA gene sequence dataset. The majority of the abundant taxa (91.4 %) were habitat generalists with a wider niche breadth (niche breadth index, B = 11.5), whereas most of the rare taxa (95.2 %) were habitat specialists with a narrow niche breadth (B = 8.9). Abundant taxa exhibited a stronger distance-decay relationship and higher spatial turnover rate than rare taxa. β-diversity partitioning revealed that the contribution of species turnover (72.2-97.8 %) was greater than nestedness (2.2-27.8 %) in causing the spatial variation in both abundant and rare taxa. Null model analyses revealed that the distribution of abundant taxa was mostly structured by stochastic processes (62.8 %), whereas deterministic processes (54.1 %) played a greater role in the rare taxa. However, the balance of these two processes varied across spatio-temporal scales in the lagoon. Salinity was the key deterministic factor controlling the variation of both abundant and rare taxa. Potential interaction networks showed a higher influence of negative interactions, indicating that species exclusion and top-down processes played a greater role in the community assembly. Notably, abundant taxa emerged as keystone taxa across spatio-temporal scales, suggesting their greater influences on other bacterial co-occurrences and network stability. Overall, this study provided detailed mechanistic insights into biogeographic patterns and underlying community assembly processes of the abundant and rare bacterioplankton over spatio-temporal scales in a brackish lagoon.