Groundwater-surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover

The effects of perfluoroalkyl substance pollution on microbial community and key metabolic pathways in the Pearl River Estuary

The extensive use of perfluoroalkyl substances (PFASs) has raised significant concerns regarding their adverse environmental implications. However, the understanding of their behaviors and biological effects in natural estuarine ecosystems remain limited. This study employed a multidisciplinary approach integrating chemical analysis, biological sequencing, and statistical modeling to comprehensively investigate the distribution of PFASs, as well as their intrinsic relationship with microbial community in the Pearl River Estuary (PRE), a rapidly urbanized area. Our findings demonstrate that the total PFAS concentrations ranged from 52-127 ng L-1 in water, and 2-70 μg kg-1 dry weight in sediment, with notably distinct compositions across habitats. Aquatic microbial communities exhibited higher sensitivity to environmental variables, including PFAS concentrations, attributed to increased stochasticity and reduced spatial turnover. Conversely, sediments harbored microbial communities with higher phylogenetic diversity, rendering them less susceptible to PFAS-induced stress. Furthermore, PFAS concentrations significantly affected microbial carbon, nitrogen, and phosphorus cycling, predominantly through indirect alterations in characteristic genus composition. Importantly, noteworthy variations in impacts were observed between perfluorinated carboxylic acids (PFCAs) and perfluorinated sulfonic acids (PFSAs), which might contingent upon C-F bond dissociation energies. The findings shed light on PFAS ecological roles and interaction patterns with microbial communities in human-impacted estuarine environments.

Hydrological characteristics strongly dominate the spatiotemporal variation of bacterioplankton sub-communities in the Yangtze River Estuary

Seasonal variations in river discharge in estuarine ecosystems drive dynamic interactions between freshwater and seawater, significantly impacting the structure and functionality of bacterioplankton sub-communities. Seasonal saltwater intrusion during the dry season intensifies the dynamic variations in water quality and salinity between the northern and southern branches of the Yangtze River Estuary, further complicating the ecological processes governing bacterioplankton communities. Nevertheless, the mechanisms underlying these processes and their effects on distinct bacterioplankton sub-communities remain insufficiently explored. In this study, the composition, functions, and assembly mechanisms of bacterioplankton communities in the Yangtze River Estuary during different hydrological periods were examined using molecular technique and various statistical analysis methods. The results showed that rare sub-communities exhibited the highest α-diversity, abundant and transient sub-communities primarily contributed to the diversity differences across hydrological periods. Saltwater intrusion into the northern branch altered bacterioplankton community and weakened the distance-decay pattern of the transient and rare sub-communities. Additionally, stochastic processes governed the assembly of rare sub-communities, and saltwater intrusion disrupted their migration and dispersal patterns. In contrast, abundant and transient sub-communities maintain their stability by adjusting their ecological strategies in response to salinity changes. Functional analysis indicated that external nutrient inputs and hydrodynamic changes in the wet season promoted community functional diversity and activity, while abundant sub-communities in the dry season were more effective at occupying resources and performing specific functions related to carbon cycling. These findings highlight the relationships between bacterioplankton sub-communities and environmental changes in estuarine ecosystems, underscoring their key roles in biogeochemical cycling.

Carbon Isotope Fractionation of Dissolved Organic Matter Due to •OH-Based Oxidation

•OH-based oxidation plays a crucial role in dissolved organic matter (DOM) transformation and carbon flux, whereas quantifying the contribution of this pathway remains challenging. Here we combined the concentration with the carbon isotope analysis of DOM and its generated CO2 to quantify the contribution of •OH-based oxidation. Results showed that the 13C enrichment factors (ε values) were -8.1‰ to -8.9‰ for benzene ring oxidation in aromatic compounds, -4.2‰ to -28.9‰ for lower-molecular-weight organic acids, and -13.0‰ for DOM from sediment. The fractionation of sediment DOM reflects the average ε value of humic substances and organic acids. These ε values were more negative than those of the photochemical and microbial processes, enabling the identification of DOM transformation mechanisms. Using an end-member mix model, we found that the proportion of •OH-based mineralization in total CO2 emission ranged from 20.9% to 39.8% for 100 g/L sediment oxidation by 5-20 mM H2O2 under pH-neutral condition within 2 h and was only 2% for oxidation by air under the same conditions. We also found that inorganic carbon degassing contributed greatly to CO2 emission during sediment oxidation. This study presents a new isotope-based tool to quantitatively assess the contribution of •OH-based oxidation to the emission of CO2 from DOM.

Microbial community of Nongxiangxing daqu during storage: microbial succession, assembly mechanisms and metabolic functions

BACKGROUND

The storage process of Nongxiangxing daqu is closely related to the quality of the daqu. The role of storage in daqu manufacture remains unclear, and most actual production relies on previous production experience.

RESULTS

With the extension of daqu storage over a period of time, saccharifying activity, liquefying activity, fermenting activity, and esterifying activity reached a peak when stored for 3 to 4 months. Analysis of the flavor compounds showed that 87 flavor components were detected in daqu, and esters and alcohols were the main flavor compounds found. Microbial community analysis suggested that Weissella was the dominant bacterial genus with relative abundance increasing during storage, while Thermomyces was dominant fungal genus with abundance decreasing during storage. Analysis of assembly processes revealed that bacterial assembly was primarily influenced by stochastic processes during storage, whereas fungal assembly was predominantly shaped by deterministic processes. The interactions among microbiota, flavor compounds, and physicochemical parameters were elucidated, suggesting that saccharifying activity was positively correlated with Weissella, Lactobacillus, Kodamaea and Wickerhamomyces, and most of esters were positively correlated with Pediococcus and Clavispora. Microbial community functions were also predicted, highlighting enzymes involved in carbohydrate degradation, flavor formation, and ethanol fermentation. Finally, simulated baijiu fermentation was performed by adding daqu stored for different times, and the results showed that daqu stored for 3 to 4 months was appropriate for baijiu brewing.

CONCLUSION

The results presented in this study may enhance understanding of the impact of storage on daqu quality and, consequently, help to improve it. © 2025 Society of Chemical Industry.

Diazotrophic community difference between specialists and generalists in response to arsenic and antimony contaminations

Diazotrophs are pivotal in bioremediation, particularly in environments contaminated by metal(loid)s. Despite their significance, the specific impacts of such contamination on the diverse functional groups of soil diazotrophs, including both generalists and specialists, are not well understood. Our study examines the influences of antimony and arsenic contamination on the ecological functions of these diazotrophic groups in areas with high (HC) and low (LC) contamination. Utilizing geochemical analyses, nitrogenase gene (nifH) sequencing, and robust statistical approaches, we assessed the composition and distribution patterns of diazotrophs across different contamination levels. Our results show consistent alpha diversity among diazotrophic subcommunities in both HC and LC sites, highlighting their resilience to metal-induced stress. Generalists exhibited significant compositional shifts between HC and LC sites, whereas specialists remained stable. Network analyses revealed that specialists more frequently occupy central roles than generalists, yet metal stress displaces both groups from these positions within the networks. Deterministic processes were identified as the dominant factors influencing community assembly for both subcommunities. While MST values suggested a similar balance of deterministic and stochastic processes between HC and LC sites, the findings indicate that metal(loid) contamination may still contribute to ecological selection, particularly through Sb and As influencing generalist and specialist composition. These results provide valuable insights into the differential responses of generalist and specialist subcommunities to metal contamination, informing improved ecosystem management and bioremediation strategies.

Metabolomic interpretation of bacterial and fungal contribution to per- and polyfluoroalkyl substances interface migration in waterlogged paddy fields

Per- and polyfluoroalkyl substances (PFAS) are widely distributed in paddy soils, and their multi-phase partitioning in soil fractions was proved to be strongly interact with soil microbial community composition and functions. Despite this, soil bacterial and fungal metabolic molecular effects on PFAS water-soil interface migration in waterlogged paddy fields still remain unclear. This study integrated soil untargeted metabolomics with microbial amplicon sequencing to elucidate soil metabolic modulations of 15 PFAS interface release. Inhibition of bacterial and fungal metabolic activity both significantly altered PFAS cross-media translocation (p < 0.05). Gemmatimonadota, Desulfobacterota, Acidobacteriota, Actinobacteriota, and Bacteroidota were vital bacterial taxa affecting PFAS transport, while Basidiobolomycota and Chytridiomycota were vital fungal taxa. Fungi regulated PFAS migration more (R2 = 0.379-0.526) than bacteria (R2 = 0.021-0.030) due to the higher metabolic stability of stochastic-dominated fungi than deterministic-dominated bacteria. At the water-soil interface, the amino acid-like dissolved organic matter (Tyrosine and Tryptophan) contributed most (48.5-58.6 %) to the PFAS multiphase distribution. Untargeted metabolomics further clarified that fungal amino acid-like metabolites, including Phosphoenolpyruvate and Methionine, were key triggers stimulating Tyrosine and Tryptophan biosynthesis (p < 0.001), which were vital in modulating PFAS interface translocation (p < 0.001). These results provide novel insights into soil microbial metabolites' participation in PFAS water-soil interface migration, benefiting PFAS pollution control and agricultural security risk assessment in waterlogged paddy ecosystems.

Slow sand filters with variable filtration rates for rainwater purification: Microecological differences between biofilm and water phases

Slow sand filters (SSFs) have been increasingly applied to rainwater purification in recent years, but the response of SSFs to fluctuating rainfall, as well as the biofilm- and water-phase microecology in SSFs are still poorly understood. This study systematically evaluated the rainwater purification performance of SSFs and compared the bacterial community structure, assembly processes and molecular ecological interactions between the biofilm and water phases. The activated carbon and activated alumina filters exhibited the best performance for NH4+-N (18.82%∼64.00%) and TP (>90%) removal, respectively. As the filtration rate increased from 0.1 m/h to 0.3 m/h, the rainwater purification efficiencies of the three SSFs deteriorated significantly, with the enrichment of Tolumonas, Desulfovibrio and Sulfurospirillum, and reduction in Klebsiella and Enterobacter. The community diversity of biofilm phase was significantly higher than that of water phase, and filtration rate was identified as a key factor in shaping the bacterial community in both phases. The interactions of filtration rate and water quality displayed the best and significant (p < 0.01) explanation for microbiome shift, with the higher values in biofilm phase (34.70%) than in water phase (24.02%). Bacterial community assembly in SSFs was determined by stochastic ecological processes, which played a more important role in water-phase communities, with 86.34% following predictions using a neutral community model. The molecular ecological network of biofilm phase exhibited more complexity, lower modularity and more cooperative relationships than that of water phase. Disadvantaged OTUs occupied core and notable positions in the network, with the highest degree and clustering coefficient. Different keystone species were identified in biofilm- (Runella, Aquabacterium, etc) and water-network (Terrimonas) respectively, despite they processed low relative abundances (<0.1%). These results enhance the understanding of microecology in SSFs, and shed new lights on the improvement and promotion of rainwater biological treatment technology.

Microbial community dynamics in shallow-water grass-type lakes: Habitat succession of microbial ecological assembly and coexistence mechanisms

Aggregation and co-occurrence patterns of microbial communities are the key scientific issues in lake ecology. To explore the mechanisms of microbial ecological assembly and community succession in this unique habitat, 16 samples were collected from eight sites in Wuliangsuhai Lake. Second-generation DNA sequencing was applied to reveal the spatial dynamics of the bacterial community structure and distribution across two environmental media in this nutrient-rich shallow grassland lake and to elucidate the characteristics of the co-occurrence network. This study also examined the effects of environmental filtering and biological interactions on the formation and maintenance of the community composition and diversity. The results highlight habitat heterogeneity in microbial community composition, with no discernible latitudinal diversity patterns. The causal analysis identified electrical conductivity, pH, total nitrogen, and phosphorus as the primary factors driving changes in the bacterial community structure in the water and sediment of grass-type lakes, with TN being the key environmental driver. CL500-3 was identified as a pollution-tolerant species in aquatic environments. g__norank_f_Verrucomicrobiaceae was identified as a pollution-tolerant species in sediment environments. The bacterial communities exhibited a significant distance decay pattern, with a higher spatial turnover rate in water than in sediment. Co-occurrence network analysis revealed greater complexity and stability in the sediment bacterial communities, with three potential keystone species, than in water. The neutral and null model results indicated that the water bacterial communities were more susceptible to dispersal limitation, whereas more complex interactions in sediment increased the role of deterministic processes in community construction. This study proposed the division of aquatic plant regions in freshwater lakes and demonstrated the community characteristics of different habitat types, contributing to a comprehensive understanding of shallow-water bacterial diversity and community structure.

Reconstruction characteristics of gut microbiota from patients with type 1 diabetes affect the phenotypic reproducibility of glucose metabolism in mice

The human microbiota-associated (HMA) mice model, especially the germ-free (GF)-humanized mice, has been widely used to probe the causal relationships between gut microbiota and human diseases such as type 1 diabetes (T1D). However, most studies have not clarified the extent to which the reconstruction of the human donor microbiota in recipient mice correlates with corresponding phenotypic reproducibility. In this study, we transplanted fecal microbiota from five patients with T1D and four healthy people into GF mice, and microbiota from each donor were transplanted into 10 mice. Mice with similar microbiota structure to the donor exhibited better phenotypic reproducibility. The characteristics of the microbial community assembly of donors also influenced the phenotypic reproducibility in mice, and individuals with a higher proportion of stochastic processes showed more severe disorders. Microbes enriched in patients with T1D had a stronger colonization potential in mice with impaired glucose metabolism, and microbiota functional features related to T1D were better reproduced in these mice. This indicates that assembly traits and colonization efficacy of microbiota influence phenotypic reproducibility in GF-humanized mice. Our findings provide important insights for using HMA mice models to explore links between gut microbiota and human diseases.

Amplified impacts of human activities: Non-linear responses of riverine microbial communities to distribution of land use

Rapid global urbanization poses considerable ecological risks to freshwater systems, notably leading to substantial reductions in microbial communities. To assess the impacts of human activities on these communities, we applied the high-throughput amplicon DNA sequencing to examine spatial variations in riverine microbial communities within an urbanized watershed. Coupled with the Geographical Detector Model, the effects of the land use were identified across the watershed. Results show that microbial communities were closely linked to the human-impacted land use patterns. The upstream region, dominated by forest cover (71%), exhibited the highest microbial population (3384 OTUs), whereas the urbanized downstream outlet (91% urban land) showed the lowest microbial population (471 OTUs). Additionally, the spatial distribution of the human-impacted land use appears to abruptly alter microbial pathways along the river. The spatial threshold effect of human-impacted land use is indicated by a Moran's I value exceeding 0.80. Notably, a 300-m buffer zone around different land uses seems to significantly influenced sediment microbial communities. Besides, the influence of land use on microbial communities is intensified by spatial drivers. For instance, agricultural land use was found to impact riverine Parcubacteria communities, with factor detector values increasing by over 30% in 400-500 m buffer zones. These findings provide new insights into the complex relationship between human activity and riverine microbial communities, highlighting important implications for ecosystem management in rapidly urbanization regions.

Functional microbiome assembly in food environments: addressing sustainable development challenges

The global food system faces numerous challenges, creating an urgent need for sustainable reform. Functional microbiome assemblies offer transformative potential by endowing microbial foods with diverse, beneficial characteristics. These assemblies can dynamically influence specific food systems, positioning them as a promising approach for reshaping food production. However, the current applications and types of microbiome assemblies in foods remain limited, with a lack of effective screening and regulatory methods. This review introduces the functions and practical approaches for implementing microbiome assemblies in food systems alongside future directions for enhancing their applications. Several ecological studies evaluated how to regulate functional output and revealed that environmental conditions, which shape the niche for species survival, significantly influenced the functional output of microbiomes. Building on this theoretical foundation, this review presents a model for functional output comprising niche conditions, functional gene codes, and corresponding functional outputs. This model is illustrated with examples to explore sustainable applications and regulatory mechanisms for functional microbiome assemblies. By highlighting the roles of functional outputs in food systems and examining the potential for food environments to induce and modulate microbiome functions, this review provides a roadmap to address emerging challenges in food sustainability.

Variations in the Bacterial, Fungal, and Protist Communities and Their Interactions Within Sediment Affected by the Benthic Organism, Snail Bellamya purificata

In aquatic benthic environments, benthic organisms have been found to regulate important biogeochemical characteristics and perform key ecosystem functions. To further explore the ecological impact of the snail Bellamya purificata's, presence on the benthic environment, we employed high-throughput sequencing technology to investigate its effects on the bacterial, fungal, and protist communities in sediment and their intrinsic interactions. Our findings revealed that B. purificata's presence significantly enhanced the diversity and evenness of the fungal community while simultaneously decreasing the diversity and richness of the protist community, and it also altered the composition and relative abundance of the dominant phyla across the bacterial, fungal, and protist communities. The snail B. purificata considerably altered the co-occurrence networks of the microbial communities, particularly by enhancing the intrinsic complexity of the protist community and by strengthening the interconnections among the protist, bacterial, and fungal communities. Notably, the proportions of specialists within the sediment bacterial, fungal, and protist communities declined due to the snail B. purificata. Its presence also notably expanded the habitat niche breadth for sediment bacteria and protists. In terms of community assembly, B. purificata shifted the fungal community assembly from being dominated by stochastic processes to being dominated by deterministic processes, whereas the protist community assembly shifted from deterministic processes to being dominated by stochastic processes. The mainly altered ecological processes in the fungal and protist assemblies were drift and homogenizing selection. Additionally, the presence of B. purificata resulted in a notable reduction in the sediment ON level and a significant increase in the ammonia, FA, and EN concentrations. Sediment properties, particularly FA and nitrate, were strongly correlated with microbial communities and were key contributors to changes in microbial community dynamics. These research findings not only broadened our understanding of the ecological impacts of B. purificata on benthic microbial communities but also highlighted its substantial potential in enhancing microbial community stability.

Lake ecological restoration of vegetation removal mitigates algal blooms and alters landscape patterns of water and sediment bacteria

Elucidating the influences of ecological restoration measure of lakeshore vegetation removal on water quality and biological community is an important but underestimated subject. We adopted molecular and statistical tools to estimate ecological restoration performance in a plateau lake receiving vegetation removal and simultaneously investigated variabilities of bacterial communities in water and sediment. Significant decreases in lake trophic level and algal bloom degree followed notable decreases in water total nitrogen and total phosphorus after vegetation removal. Non-significant changes in sediment nutrients accompanied remarkable variabilities of abundance and composition of nutrient-cycling functional genes (NCFGs) of sediment bacteria. Taxonomic and phylogenetic α-diversities, functional redundancies, and dispersal potentials of bacteria in water and sediment decreased after vegetation removal, and community successions of water and sediment bacteria were separately significant and non-significant. There were opposite changes in ecological attributes of bacteria in water and sediment in response to vegetation removal, including niche breadth, species replacement, richness difference, community complexity, and community stability. Species replacement rather than richness difference affected more on taxonomic β-diversities of bacteria in water and sediment before and after vegetation removal, and determinism rather than stochasticity dominated bacterial community assemblage. Our results highlighted vegetation removal mitigated algal bloom and affected differently on landscapes of water and sediment bacteria. These findings point to dominant ecological mechanisms underlying landscape shifts in water and sediment bacteria in a disturbed lake receiving vegetation removal and have the potential to guide lake ecological restoration.

Hydrogeochemical differences drive distinct microbial community assembly and arsenic biotransformation in unconfined and confined groundwater of the geothermal system

High‑arsenic (As) groundwater in geothermal aquifers poses a serious threat to public health. Assembly processes governing groundwater microbial community related to As biotransformation are still unexplored in geothermal groundwater across different aquifers. To fill this gap, groundwater microorganisms, community assembly processes, and microbially metabolic coupling of carbon (C), nitrogen (N), phosphorus (P), sulfur (S), and arsenic (As) were investigated in unconfined and confined groundwater in the thermal reservoirs of the Guide Basin. The difference in groundwater hydrogeochemicals led to the heterogeneity of the microbial community and microbially mediated C, N, P, S, and As cycling between unconfined and confined groundwater. Higher temperature and As concentrations, low nutrient supply, and reduced conditions in confined groundwater supported stronger interspecific coexistence and environmental selection, thus promoting the proliferation of As-resistant microorganisms (ARMs) and simplifying the community assemblage. Abundant available nutrient supply and oxidizing conditions supported an increased species diversity and metabolic functionality in unconfined groundwater. S oxidizers, C fixation, and C degradation bacteria potentially contributed to the decreased As concentrations in unconfined groundwater. However, ARMs, ammonification, and anaerobic ammonia-oxidizing bacteria potentially caused As mobilization in confined groundwater. Overall, our results give a comprehensive insight into the interaction between As and microorganisms in geothermal groundwater.

Bacterial and fungal keystone taxa play different roles in maintaining community resistance and driving soil organic carbon dynamics in response to Solidago Canadensis invasion

The invasion of alien plants has significant implications for vegetation structure and diversity, which could lead to changes in the carbon (C) input from vegetation and change the transformation and decomposition processes of C, thereby altering the dynamics of soil organic carbon (SOC) within ecosystems. Whether alien plant invasion increases the SOC stock and changes SOC fractions consistently within regional scales, and the underlying mechanisms driving these SOC dynamics remain poorly understood. This study investigated SOC dynamics by comparing the plots that suffered invasion and non-invasion of Solidago Canadensis across five ecological function areas in Anhui Province, China, considering climate, edaphic factors, vegetation, and soil microbes. The results demonstrated that the impact of S. Canadensis invasion on SOC storage was not consistent at each site in the 0-20 cm soil layer, as indicated by the range of SOC content (5.94-12.45 g kg-1) observed at non-invaded plots. Stable SOC exhibited similar response patterns with SOC to plant invasion, whereas labile SOC did not. In addition, bacterial and fungal communities were shifted in structure at each site by plant invasion. Bacterial communities exhibited greater resistance to S. Canadensis invasion than did fungal communities, as evidenced by three aspects of the resistance indices-community resistance, phylogenetic conservation, and network complexity. The mechanisms driving SOC dynamics under S. Canadensis invasion were explored using structural equation models. This revealed that fungal keystone taxa responsible for community resistance controlled stable SOC fractions. In contrast, bacterial keystone taxa had the opposite effect on labile and stable SOC. Climatic and edaphic factors were also involved in the labile and stable SOC dynamics. Overall, this study provides novel insights into the dynamics of SOC under S. Canadensis invasion on a regional scale.

Ecological processes shaping highly connected bacterial communities along strong environmental gradients

Along the river-sea continuum, microorganisms are directionally dispersed by water flow while being exposed to strong environmental gradients. To compare the two assembly mechanisms that may strongly and differently influence metacommunity dynamics, namely homogenizing dispersal and heterogeneous selection, we characterized the total (16S rRNA gene) and putatively active (16S rRNA transcript) bacterial communities in the Pearl River-South China Sea Continuum, during the wet (summer) and dry (winter) seasons using high-throughput sequencing. Moreover, well-defined sampling was conducted by including freshwater, oligohaline, mesohaline, polyhaline, and marine habitats. We found that heterogeneous selection exceeded homogenizing dispersal in both the total and active fractions of bacterial communities in two seasons. However, homogeneous selection was prevalent (the dominant except in active bacterial communities during summer), which was primarily due to the bacterial communities' tremendous diversity (associated with high rarity) and our specific sampling design. In either summer or winter seasons, homogeneous and heterogeneous selection showed higher relative importance in total and active communities, respectively, implying that the active bacteria were more responsive to environmental gradients than were the total bacteria. In summary, our findings provide insight into the assembly of bacterial communities in natural ecosystems with high spatial connectivity and environmental heterogeneity.

Experimental and modeling insights into mixing-limited reactive transport in heterogeneous porous media: Role of stagnant zones

The understanding of mixing-controlled reactive dynamics in heterogeneous porous media remains limited, presenting significant challenges for modeling subsurface contaminant transport processes and for designing cost-effective environmental remedial efforts. The complexity of accurately observing, measuring, and modeling mixing-limited reactive transport has led to inadequate exploration of these critical processes. This study investigates the mixing and reaction kinetics affected by stagnant zones, which are commonly found in alluvial aquifers-aquitards and fracture-matrix systems. By conducting experiments involving conservative and bimolecular reactive transport through porous media within translucent chambers filled with two sizes of glass beads and under varying flow rates, we explored the effects of grain size and hydrodynamic conditions. Using a high-resolution camera, we monitored the concentration changes of conservative and reactive tracers, with subsequent interpretation through three-dimensional numerical simulations. The outcomes revealed the emergence of distinct mixing interfaces within both mobile and stagnant zones, culminating in a bi-peaked plume formation. Notably, the mixing and reaction times in media containing stagnant zones were found to be approximately 10 times longer than in homogeneous media. These findings, through experimental and modeling efforts, advance our understanding of mixing-limited reactive transport phenomena within heterogeneous media, underscoring the significant role of stagnant zones-a topic previously underexplored.

Hotspots of Dissolved Arsenic Generated from Buried Silt Layers along Fluctuating Rivers

Previous studies along the banks of the tidal Meghna River of the Ganges-Brahmaputra-Meghna Delta demonstrated the active sequestration of dissolved arsenic (As) on newly formed iron oxide minerals (Fe(III)-oxides) within riverbank sands. The sand with high solid-phase As (>500 mg/kg) was located within the intertidal zone where robust mixing occurs with oxygen-rich river water. Here we present new evidence that upwelling groundwater through a buried silt layer generates the dissolved products of reductive dissolution of Fe(III)-oxides, including As, while mobilization of DOC by upwelling groundwater prevents their reconstitution in the intertidal zone by lowering the redox state. A three end-member conservative mixing model demonstrated mixing between riverbank groundwater above the silt layer, upwelling groundwater through the silt layer, and river water. An electrochemical mass balance model confirmed that Fe(III)-oxides were the primary electron acceptor driving the oxidation of DOC sourced from sediment organic carbon in the silt. Thus, the presence of an intercalating silt layer in the riverbanks of tidal rivers can represent a biogeochemical hotspot of As release while preventing its retention in the hyporheic zone.

Microbial Metagenomics Revealed the Diversity and Distribution Characteristics of Groundwater Microorganisms in the Middle and Lower Reaches of the Yangtze River Basin

Groundwater is one of the important freshwater resources on Earth and is closely related to human activities. As a good biological vector, a more diverse repertory of antibiotic resistance genes in the water environment would have a profound impact on human medical health. Therefore, this study conducted a metagenomic sequencing analysis of water samples from groundwater monitoring points in the middle and lower reaches of the Yangtze River to characterize microbial community composition and antibiotic resistance in the groundwater environment. Our results show that different microbial communities and community composition were the driving factors in the groundwater environment, and a diversity of antibiotic resistance genes in the groundwater environment was detected. The main source of antibiotic resistance gene host was determined by correlation tests and analyses. In this study, metagenomics was used for the first time to comprehensively analyze microbial communities in groundwater systems in the middle and lower reaches of the Yangtze River basin. The data obtained from this study serve as an invaluable resource and represent the basic metagenomic characteristics of groundwater microbial communities in the middle and lower reaches of the Yangtze River basin. These findings will be useful tools and provide a basis for future research on water microbial community and quality, greatly expanding the depth and breadth of our understanding of groundwater.

Harnessing elastic instabilities for enhanced mixing and reaction kinetics in porous media

Turbulent flows have been used for millennia to mix solutes; a familiar example is stirring cream into coffee. However, many energy, environmental, and industrial processes rely on the mixing of solutes in porous media where confinement suppresses inertial turbulence. As a result, mixing is drastically hindered, requiring fluid to permeate long distances for appreciable mixing and introducing additional steps to drive mixing that can be expensive and environmentally harmful. Here, we demonstrate that this limitation can be overcome just by adding dilute amounts of flexible polymers to the fluid. Flow-driven stretching of the polymers generates an elastic instability, driving turbulent-like chaotic flow fluctuations, despite the pore-scale confinement that prohibits typical inertial turbulence. Using in situ imaging, we show that these fluctuations stretch and fold the fluid within the pores along thin layers ("lamellae") characterized by sharp solute concentration gradients, driving mixing by diffusion in the pores. This process results in a [Formula: see text] reduction in the required mixing length, a [Formula: see text] increase in solute transverse dispersivity, and can be harnessed to increase the rate at which chemical compounds react by [Formula: see text]-enhancements that we rationalize using turbulence-inspired modeling of the underlying transport processes. Our work thereby establishes a simple, robust, versatile, and predictive way to mix solutes in porous media, with potential applications ranging from large-scale chemical production to environmental remediation.

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.

Microbiome analysis in Asia's largest watershed reveals inconsistent biogeographic pattern and microbial assembly mechanisms in river and lake systems

Microorganisms are critical to the stability of aquatic environments, and understanding the ecological mechanisms of microbial community is essential. However, the distinctions and linkages across biogeographic patterns, ecological processes, and formation mechanisms of microbes in rivers and lakes remain unknown. Accordingly, microbiome-centric analysis was conducted in rivers and lakes in the Yangtze River watershed. Results revealed significant differences in the structure and diversity of microbial communities between rivers and lakes, with rivers showing higher diversity. Lakes exhibited lower community stability, despite higher species interactions. Although deterministic processes dominated microbial community assembly both in rivers and lakes, higher stochastic processes of rare and abundant taxa exhibited in rivers. Spatial factors influenced river microbial community, while environmental factors drove differences in the lake bacterial community. This study deepened the understanding of microbial biogeography and formation mechanisms in large watershed rivers and lakes, highlighting distinct community aggregation patterns between river and lake microorganisms.

The ecology of the sewer systems: Microbial composition, function, assembly, and network in different spatial locations

Microbial induced concrete corrosion (MICC) is the primary deterioration affecting global sewers. Disentangling ecological mechanisms in the sewer system is meaningful for implementing policies to protect sewer pipes using trenchless technology. It is necessary to understand microbial compositions, interaction networks, functions, alongside assembly processes in sewer microbial communities. In this study, sewer wastewater samples and microbial samples from the upper part (UP), middle part (MP) and bottom part (BP) of different pipes were collected for 16S rRNA gene amplicon analysis. It was found that BP harbored distinct microbial communities and the largest proportion of unique species (1141) compared to UP and MP. The community in BP tended to be more clustered. Furthermore, significant differences in microbial functions existed in different spatial locations, including the carbon cycle, nitrogen cycle and sulfur cycle. Active microbial sulfur cycling indicated the corrosion risk of MICC. Among the environmental factors, the oxidation‒reduction potential drove changes in BP, while sulfate managed changes in UP and BP. Stochasticity dominated community assembly in the sewer system. Additionally, the sewer microbial community exhibited numerous positive links. BP possessed a more complex, modular network with higher modularity. These deep insights into microbial ecology in the sewer system may guide engineering safety and disaster prevention in sewer infrastructure.

Higher stochasticity in comammox Nitrospira community assembly in upland soils than the adjacent paddy soils at a regional scale

Understanding the assembly mechanisms of microbial communities, particularly comammox Nitrospira, in agroecosystems is crucial for sustainable agriculture. However, the large-scale distribution and assembly processes of comammox Nitrospira in agricultural soils remain largely elusive. We investigated comammox Nitrospira abundance, community structure, and assembly processes in 16 paired upland peanuts and water-logged paddy soils in south China. Higher abundance, richness, and network complexity of comammox Nitrospira were observed in upland soils than in paddy soils, indicating a preference for upland soils over paddy soils among comammox Nitrospira taxa in agricultural environments. Clade A.2.1 and clade A.1 were the predominant comammox Nitrospira taxa in upland and paddy soils, respectively. Soil pH was the most crucial factor shaping comammox Nitrospira community structure. Stochastic processes were found to predominantly drive comammox Nitrospira community assembly in both upland and paddy soils, with deterministic processes playing a more important role in paddy soils than in upland soils. Overall, our findings demonstrate the higher stochasticity of comammox Nitrospira in upland soils than in the adjacent paddy soils, which may have implications for autotrophic nitrification in acidic agricultural soils.

Fungal communities as dual indicators of river biodiversity and water quality assessment

Given their ecological importance, bioindicators are used for the assessment of the health of river ecosystems. This study explored the fungal compositions and the potential of fungal taxa as bioindicators for indicating the water quality of the Mekong River, as the use of fungal indicators of the Mekong River was not previously well characterized. The Mekong River exhibited dynamic variations in both physicochemical/hydrochemical properties and fungal communities according to seasons and locations. The results revealed the dominance of alkaline earth metal ions and weak acids in the water. The magnesium-bicarbonate water type was found in the dry season, but the water became the chloride-calcium type or mixed type of magnesium-bicarbonate and chloride-calcium in the rainy season at downstream sites. Fungal composition analysis revealed the dominance of Chytridiomycota in the dry season and intermediate periods, and Ascomycota and Basidiomycota in the rainy season. The fungal communities were influenced by stochastic and deterministic assembly processes, mainly homogeneous selection, heterogeneous selection, and dispersal limitation. The extent of environmental filtering implied that some fungal taxa were affected by environmental conditions, suggesting the possibility of identifying certain fungal taxa suitable for being bioindicators of water quality. Subsequently, machine learning with recursive feature elimination identified specific fungal bins mostly consisting of Agaricomycetes (mainly Polyporales, Agaricales, and Auriculariales), Dothideomycetes (mainly Pleosporales), Saccharomycetes (mainly Saccharomycetales), Chytridiomycota, and Rozellomycota as bioindicators that could predict ambient and irrigation water quality with high selectivity and sensitivity. These results thus promote the use of fungal indicators to assess the health of the river.

Assembly dynamics of eukaryotic plankton and bacterioplankton in the Yangtze River estuary: A hybrid community perspective

Estuaries, acting as transitional habitats receiving species introductions from both freshwater and marine sources, undergo significant impacts from global climate changes. Planktonic microorganisms contribute significantly to estuarine biodiversity and ecological stability. These microorganisms primarily fall into three groups: eukaryotic plankton, particle-associated bacteria, and free-living bacteria. Understanding the structural characteristics and interactions within these subcommunities is crucial for comprehending estuarine dynamics. We collected samples from three distinct locations (< 0.1 PSU, 6.6 PSU, and 19 PSU) within the Yangtze River estuary. Samples underwent analysis for physicochemical indicators, while microbial communities were subjected to 16S/18S rRNA amplicon sequencing. Additionally, simulated mixing experiments were conducted using samples of varying salinities. Estuary samples, combined with simulated experiments, were employed to collectively examine the structural characteristics and assembly processes of estuarine microbes. Our research highlights the considerable impact of phylogenetic classification on prokaryotic behavior in these communities. We observed a transition in assembly processes from primarily stochastic for particle-associated bacteria to a predominant influence of homogeneous selection as salinity increased. Particle-associated bacterial communities exhibited a greater influence of stochastic processes compared to free-living bacteria, showcasing higher stability in diversity. The variations in composition and structure of estuarine microbial subcommunities were influenced by diverse environmental factors. Particle-associated bacteria displayed elevated network characterization values and established closer interactions with eukaryotic plankton. Structural equation modeling (SEM) analysis revealed that free-living bacteria displayed a heightened sensitivity to environmental factors and exerted a more significant influence on assembly processes and network characteristics. Simulated mixing in these environments resulted in the loss of species with similar microbial taxonomic relationships. The functioning of bacterioplankton is influenced by salinity and the processes governing their assembly, particularly in relation to different living states. These findings significantly contribute to our understanding of the intricate interplay between prokaryotic and eukaryotic plankton microorganisms in highly dynamic environments, laying a robust foundation for further exploration into the ecological mechanisms governing microbial dynamics in estuaries.

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

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

Environmental stress mediates groundwater microbial community assembly

Community assembly describes how different ecological processes shape microbial community composition and structure. How environmental factors impact community assembly remains elusive. Here we sampled microbial communities and >200 biogeochemical variables in groundwater at the Oak Ridge Field Research Center, a former nuclear waste disposal site, and developed a theoretical framework to conceptualize the relationships between community assembly processes and environmental stresses. We found that stochastic assembly processes were critical (>60% on average) in shaping community structure, but their relative importance decreased as stress increased. Dispersal limitation and 'drift' related to random birth and death had negative correlations with stresses, whereas the selection processes leading to dissimilar communities increased with stresses, primarily related to pH, cobalt and molybdenum. Assembly mechanisms also varied greatly among different phylogenetic groups. Our findings highlight the importance of microbial dispersal limitation and environmental heterogeneity in ecosystem restoration and management.

Bacterial diversity in a continuum from supraglacial habitats to a proglacial lake on the Tibetan Plateau

Mountain glaciers are frequently assessed for their hydrological connectivity from glaciers to proglacial lakes. Ecological process on glacier surfaces and downstream ecosystems have often been investigated separately, but few studies have focused on the connectivity between the different glacial habitats. Therefore, it remains a limited understanding of bacterial community assembly across different habitats along the glacier hydrological continuum. In this study, we sampled along a glacial catchment from supraglacial snow, cryoconite holes, supraglacial runoff, ice-marginal moraine and proglacial lake on the Tibetan Plateau. The bacterial communities in these habitats were analyzed using high-throughput DNA sequencing of the 16S rRNA gene to determine the bacterial composition and assembly. Our results showed that each habitat hosted unique bacterial communities, with higher bacterial α-diversity in transitional habitats (e.g. runoff and ice-marginal moraine). Null model analysis indicated that deterministic processes predominantly shaped bacterial assembly in snow, cryoconite holes and lake, while stochastic process dominantly governed bacterial community in transitional habitats. Collectively, our findings suggest that local environment play a critical role in filtering bacterial community composition within glacier habitats. This study enhances our understanding of microbial assembly process in glacier environments and provides valuable insights into the factors governing bacterial community compositions across different habitats along the glacial hydrological continuum.

Impact of soil inorganic nitrogen on bacterial phylogeny in estuarine intertidal zones: a study of nitrogen metabolism

Here we investigated the potential impacts of soil inorganic nitrogen (SIN) content on the phylogenetic characteristics and ecological functions of soil bacterial communities in estuarine intertidal zones in China, aiming to comprehend the response mechanism of soil microorganisms to variations in SIN content within estuarine wetlands. Our results show that SIN in estuarine areas has a significant spatiotemporal variation on spatial and seasonal scales, in this study and is significantly associated with the phylogenetic diversity and phylogenetic turnover of soil bacterial communities. In addition, the results of the metagenomic analysis showed that the relative abundance of nitrogen-cycling functional genes in bacterial communities did not differ significantly in sampling sites and seasons, and weakly correlated with SIN content. Further, the results based on structural equation modeling (SEM) analysis showed that SIN directly and significantly regulated the phylogenetic characteristics of bacterial communities, thereby indirectly affecting the potential of bacterial nitrogen metabolism. This study emphasizes the key influence of SIN variations on the phylogenetic dissimilarity in soil bacterial communities. Moreover, although there was a weak direct relationship between the functional characteristics of the bacterial nitrogen metabolism and SIN content, the spatiotemporal variation of bacterial nitrogen metabolic potential may be indirectly regulated by SIN content by influencing the phylogenetic diversity in bacterial communities. Our study unravels the pivotal mechanisms through which SIN content influences bacterial communities, thereby offering novel insights into the microbial intricacies governing nitrogen metabolism within estuaries.

Redox gradients drive microbial community assembly patterns and molecular ecological networks in the hyporheic zone of effluent-dominated rivers

The impacts of effluent discharge on receiving waterbodies have been a research hotspot. Nonetheless, limited information is available on the microbial community assembly patterns in the hyporheic zones (HZ) responding to the changes in the microenvironments, e.g., solute transport and redox gradient variations. Using two representative effluent-dominated rivers as model systems, the spatio-temporal bacterial community dynamics and assembly patterns in oxic and suboxic zones in the shallow riverbed sediments were disentangled via null model- and neutral model-based approaches. Bacterial dynamics in community composition were observed driven by environmental filtering, i.e., impacts of environmental variables, more than geographic distances, i.e., the depths of sediments. The communities in samples collected in summer were largely shaped by stochasticity, in which homogeneous selection occupied a higher proportion in oxic (∼39%) than in suboxic zone (∼23%). Deterministic processes contributed to a more complex community structure for samples from oxic zones, whereas weakened the interspecies interactions in suboxic zones. The richness and abundances of non-neutral community were confirmed governing the deterministic assembly in oxic zones. Key species ascribed to 'connectors' and 'network hubs' dominated the community assembly variations in samples collected in winter, and in oxic zones, respectively. Significant positive relationships between β-nearest taxon index and dissolved organic nitrogen (DON) and nitrate highlighted their vital roles in community assembly via deterministic selective pressures in oxic zones. The significance thresholds of nitrogen species for community transition in winter (ΔDON: 2.81 mg-N/L, ΔNO3-: 1.09 mg-N/L) were lower than in summer, probably implying that stricter effluent quality standards should be established in colder seasons. Combined, our work poses first insights on the roles of redox zonation in driving microbial community assembly in HZ, which is of significance in guiding ecological remediation processes in effluent-dominated rivers.

Effects of boundary hydraulics, dissolved oxygen, and dissolved organic carbon on growth and death dynamics of aerobic microbes in riverbed dune-induced hyporheic zones

Surface and groundwater interact in the hyporheic zone beneath and adjacent to rivers in the presence of a diverse microbial community. Heterotrophic bacteria mediate a range of environmentally important reactions, yet few studies have quantified bacterial growth and death dynamics in the hyporheic zone, and none have systematically analyzed their response to variations in hydraulic or chemical conditions. We used MODFLOW and SEAM3D to simulate hydraulics; dissolved oxygen (DO) and dissolved organic carbon (DOC) transport; and aerobic microbial metabolism, growth, and death in hyporheic zones induced by riverbed dunes. We ran simulations both with and without growth/death processes, and varied hydraulic parameters and DO/DOC boundary concentrations. Microbial biomass reached steady state (t = 3 days) in every simulation, at which time there was greater biomass and DOC biodegradation rates in the hyporheic flowcell (300 % and 85 % higher for the base case, respectively) when accounting for microbial growth dynamics. This occurred as microbial biomass tailored its spatial distribution to the availability of DO and DOC, demonstrating the importance of simulating growth/death processes. Biomass generally increased with hyporheic flow cell area as upwelling groundwater decreased. When varying surface water DO and DOC source concentrations relative to the base case, the greatest effect on biomass occurred when increasing DOC and decreasing DO. We determined minimum DO and DOC steady-state concentrations required for microbial growth, but the minimums were not absolute or related by stoichiometry. Increasing DOC created a smaller area of microbes with higher concentrations relative to the base case. Increasing DO slightly increased the area occupied by microbes while keeping the total biomass nearly constant. Overall, microbial growth and death dynamics depend on DO and DOC availability in the hyporheic zone, which is dependent on DOC/DO boundary concentrations and hyporheic flow paths, and in turn the hydraulic interaction between surface water and groundwater.

Unraveling the interplay between antibiotic resistance genes and microbial communities in water and sediments of the intensive tidal flat aquaculture

Tidal flats are formed valuably resources by the interaction of terrestrial and marine processes. Aquaculture on tidal flats has brought significant economic profits, but the over usage of antibiotics has resulted in the prevalence antibiotic resistance genes (ARGs) which pose serious threats to ecosystems. However, ARG abundances and bacterial community assemblies in the overlying water and sediments of tidal flat aquaculture areas have not been fully explored. Thus, antibiotic concentrations, ARG abundances, microbial communities and the influences of environmental factors in the Jiangsu tidal flat aquaculture ponds were investigated using high-throughput sequencing and qPCR. The concentrations of antibiotics at sampling ranged from not detectable to 2322.4 ng g-1, and sulfamethazine and ciprofloxacin were the dominant antibiotics. The sul1 and sul2 abundances were highest and the ARG abundances were higher in sediment than in water. Meanwhile, bacterial community diversities and structures were significantly different (P < 0.05) between water and sediment samples. Network analysis identified Sphingomonadacear, Pseudomonas, and Xanthobacteraceae as potential ARG-carrying pathogens. A positive correlation between ARGs and intI1 indicated that horizontal gene transfer occurred in water, while antibiotics and TN significantly influenced ARG abundances in sediment. Neutral modeling showed that deterministic and stochastic processes contributed most to the bacterial community assemblies of water and sediment samples, respectively. This study comprehensively illustrates the prevalence of ARGs in intensive tidal flat aquaculture regions and provides an effective foundation for the management of antibiotics usage.

River connectivity determines microbial assembly processes and leads to alternative stable states in river networks

River network is a common form of lotic ecosystems. Variances in river connection modes would form networks with significantly different structures, and further affect aquatic organisms. Microbial communities are vital organisms of river networks, they participate in numerous biogeochemical processes. Identifying associations between microbial community and structural features of river networks are essential for maintaining environmental quality. Thus, dendritic (DRN) and trellised river networks (TRN) were studied by combining molecular biological tools, ecological theory and hydrodynamic calculation. Results illustrated that river connectivity, a vital structural feature exhibiting mass transport ability of river network, increased relative importance of homogeneous selection processes in microbial assembly, which would further shape community with alternative stable states. Between the two researched river networks, DRN possessed higher connectivity, which made homogeneous selection as the driving force in community assembly. The microbial communities in DRN were consisted of species occupying similar ecological niche, and exhibited two alternative stable states, which can decrease influences of environmental disturbance on community composition. On the contrary, lower connectivity of TRN decreased proportions of homogeneous selection in community assembly, which further led to species occupying varied ecological niche. The microbial community exhibited only one stable state, and environmental disturbance would cause loss of ecological niche and significantly alter community composition. This study could provide useful information for the optimization of river connection engineering.

Changes in soil stoichiometry, soil organic carbon mineralization and bacterial community assembly processes across soil profiles

Soil organic carbon (SOC) mineralization is essential to biogeochemical recycling in terrestrial ecosystem. However, the microbial mechanisms underlying the nutrient-induced SOC mineralization remain uncertain. Here, we investigated how SOC mineralization was linked to microbial assembly processes as well as soil nutrient availability and stoichiometric ratio in a paddy rice ecosystem at four soil profile levels. Our results showed a sharp decrease in SOC mineralization from topsoil (112.61-146.34 mg CO2 kg-1 day-1) to subsoil (33.51-61.41 mg CO2 kg-1 day-1). High-throughput sequencing showed that both abundance and diversity of specialist microorganisms (Chao1: 1244.30-1341.35) significantly increased along the soil profile, while the generalist microorganisms (Chao1: 427.67-616.15; Shannon: 7.46-7.97) showed the opposite trend. Correspondingly, the proportion of deterministic processes that regulate specialist (9.64-21.59 %) and generalist microorganisms (21.17-53.53 %) increased and decreased from topsoil to subsoil, respectively. Linear regression modeling and partial least squares path modeling indicated that SOC mineralization was primarily controlled by the assembly processes of specialist microorganisms, which was significantly mediated by available soil C:N:P stoichiometry. This study highlighted the importance of soil stoichiometry-mediated bacterial community assembly processes in regulating SOC mineralization. Our results have an important implication for the integration of bacterial community assembly processes into the prediction of SOC dynamics.

Characterizing the transitory groundwater-surface water interaction and its environmental consequence of a riverside karst pool

Exchange between groundwater (GW) and surface water (SW) is a common occurrence in karst water systems through sinking stream disappearance or groundwater emergence. However, the transitory GW-SW interaction caused by river backflowing into a spring is poorly observed and understood. In this study, we present an approach for characterizing the influence of GW-SW interaction in a karst spring by integrating high-resolution hydrology, carefully selected hydrochemistry monitoring and precise microbe measurements. The spring-fed pool water conditions can be distinguished as high, medium, and low-water level periods in a hydrological year. The high-water level accounts for <1 % in a year, while it is associated with the hydrological regimes of backflooding states. The inflow of river backflow was found to be 4.4 times that of the natural discharge of spring water during a rainfall event. The duration of river intrusion into the spring or karst conduit could be assessed by jointly interpreting hydrography and physicochemical signatures, while the lasting environmental consequences should be evaluated together with biotic factors such as Escherichia coli. The GW-SW interaction induced by river backflow has led to the retention of river water in a pool, spring, and karst conduit for 132, 94, and 56 h, respectively. Despite turbidity returning to normal levels after 56 h, E.coli continued to persist for an extended duration. Our study reveals that despite the transient nature of GW-SW induced by river backflow on the hydrograph, they present a lasting risk of contamination from heavy metals, organic matter, and microorganisms. This extended influence can persist within a karst aquifer lacking a hyporheic zone. This research contributes to the quantification of processes involved in transitory GW-SW interaction in a karst spring, and it highlights the underestimation of GW-SW interactions in karst water systems, which might negatively impact water resources management.

Hydrogeochemical changes during artificial groundwater well recharge

Artificial groundwater recharge is a relatively economic and efficient method for solving shortages and uneven spatial-temporal distribution of water resources. Changes in groundwater quality during the recharge process are a key issue that must be addressed. Identifying the hydrogeochemical reactions that occur during recharge can be vital in predicting trends in groundwater quality. However, there are few studies on the evolution of groundwater quality during artificial recharge that comprehensively consider environmental, chemical, organic matter, and microbiological indicators. Based on an artificial groundwater recharge experiment in Xiong'an New Area, this study investigated the hydrogeochemical changes during groundwater recharge through a well. The results indicate that (1) as large amounts of recharge water (RW) were injected, the groundwater level initially rose rapidly, then fluctuated slowly, and finally rose again. (2) Water quality indicators, dissolved organic matter (DOM), and microbial communities were influenced by the mixture of RW and the background groundwater before recharge (BGBR), as well as by water-rock interactions, such as mineral dissolution-precipitation and redox reactions. (3) During well recharge, aerobic respiration, nitrification, denitrification, high-valence manganese (Mn) and iron (Fe) minerals reduction dissolution, and Mn2+ and Fe2+ oxidation-precipitation occurred sequentially. (4) DOM analysis showed that protein-like substances in the BGBR were the main carbon sources for aerobic respiration and denitrification, while humic-like substances carried by the RW significantly enhanced Mn and Fe minerals reduction dissolution. Therefore, RW quality significantly affects groundwater quality after artificial groundwater well recharge. Controlling indicators, such as dissolved oxygen (DO) and DOM, in the RW can effectively reduce harm to groundwater quality after recharge. This study is of theoretical and practical significance for in-depth analysis of the evolution of groundwater quality during artificial well recharge, prediction of trends in groundwater quality during and after recharge and ensuring groundwater quality safety.

Strong bacterial stochasticity and fast fungal turnover in Taihu Lake sediments, China

Understanding the assembly and turnover of microbial communities is crucial for gaining insights into the diversity and functioning of lake ecosystems, a fundamental and central issue in microbial ecology. The ecosystem of Taihu Lake has been significantly jeopardized due to urbanization and industrialization. In this study, we examined the diversity, assembly, and turnover of bacterial and fungal communities in Taihu Lake sediment. The results revealed strong bacterial stochasticity and fast fungal turnover in the sediment. Significant heterogeneity was observed among all sediment samples in terms of environmental factors, especially ORP, TOC, and TN, as well as microbial community composition and alpha diversity. For instance, the fungal richness index exhibited an approximate 3-fold variation. Among the environmental factors, TOC, TN, and pH had a more pronounced influence on the bacterial community composition compared to the fungal community composition. Interestingly, species replacement played a dominant role in microbial beta diversity, with fungi exhibiting a stronger pattern. In contrast, stochastic processes governed the community assembly of both bacteria and fungi, but were more pronounced for bacteria (R2 = 0.7 vs. 0.5). These findings deepen the understanding of microbial assembly and turnover in sediments under environmental stress and provide essential insights for maintaining the multifunctionality of lake ecosystems.

Composition and assembly mechanisms of prokaryotic communities in wetlands, and their relationships with different vegetation and reclamation methods

Coastal wetlands are undergoing substantial transformations globally as a result of increased human activities. However, compared to other ecosystems, diversity and functional characteristics of microbial communities in reclaimed coastal wetlands are not well studied compared to other ecosystems. This is important because it is known that microorganisms can play a crucial role in biogeochemical cycling within coastal wetland ecosystems. Hence, this study utilized the high-throughput sequencing technique to investigate the structure and assembly processes of microbial communities in reclaimed coastal wetlands. The results revealed a substantial change in soil properties following coastal wetland reclamation. Remarkably, the reclaimed soil exhibited significantly lower pH, soil organic carbon (SOC), and total salinity (TS) values (p < 0.05). The dominant phyla included Proteobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, and Planctomycetes among study sites. However, the relative abundance of Proteobacteria increased from un-reclaimed coastal wetlands to reclaimed ones. The Proteobacteria, Chloroflexi, and Acidobacteria showed higher relative abundance in vegetated soil compared to bare soil, while Bacteroidetes and Planctomycetes exhibited the opposite trend. Notably, vegetation types exerted the strongest influence on microbial diversity, surpassing the effects of soil types and depth (F = 34.49, p < 0.001; F = 25.49, p < 0.001; F = 3.173, p < 0.078, respectively). Stochastic assembly processes dominated in un-reclaimed soil, whereas deterministic processes governed the assembly in artificial sea embankment wetlands (SEW). The presence of Spartina alterniflora in all soil types (except SEW soils) indicated stochastic assembly, while Phragmites australis in reclaimed soils pointed toward deterministic microbial assembly. Furthermore, environmental factors such as pH, soil water content (SWC), SOC, total carbon (TC), total nitrogen (TN), total phosphorus (TP), NH4+-N, vegetation types, soil depth, and geographic distance exhibited significant effects on microbial beta diversity indices. Co-occurrence network analysis revealed a stronger association between taxa in SEW compared to land reclaimed from wetlands (LRW) and natural coastal wetlands (NCW). The bottom soil layer exhibited more complex network interactions than the topsoil layer. Besides soil parameters, reclamation and varieties of vegetation were also substantial factors influencing the composition, diversity, and assembly processes of microbial communities in coastal wetlands.

Plant species identity and mycorrhizal type explain the root-associated fungal pathogen community assembly of seedlings based on functional traits in a subtropical forest

Introduction

As a crucial factor in determining ecosystem functioning, interaction between plants and soil-borne fungal pathogens deserves considerable attention. However, little attention has been paid into the determinants of root-associated fungal pathogens in subtropical seedlings, especially the influence of different mycorrhizal plants.

Methods

Using high-throughput sequencing techniques, we analyzed the root-associated fungal pathogen community for 19 subtropical forest species, including 10 ectomycorrhizal plants and 9 arbuscular mycorrhizal plants. We identified the roles of different factors in determining the root-associated fungal pathogen community. Further, we identified the community assembly process at species and mycorrhizal level and managed to reveal the drivers underlying the community assembly.

Results

We found that plant species identity, plant habitat, and plant mycorrhizal type accounted for the variations in fungal pathogen community composition, with species identity and mycorrhizal type showing dominant effects. The relative importance of different community assembly processes, mainly, homogeneous selection and drift, varied with plant species identity. Interestingly, functional traits associated with acquisitive resource-use strategy tended to promote the relative importance of homogeneous selection, while traits associated with conservative resource-use strategy showed converse effect. Drift showed the opposite relationships with functional traits compared with homogeneous selection. Notably, the relative importance of different community assembly processes was not structured by plant phylogeny. Drift was stronger in the pathogen community for ectomycorrhizal plants with more conservative traits, suggesting the predominant role of stochastic gain and loss in the community assembly.

Discussion

Our work demonstrates the determinants of root-associated fungal pathogens, addressing the important roles of plant species identity and plant mycorrhizal type. Furthermore, we explored the community assembly mechanisms of root-associated pathogens and stressed the determinant roles of functional traits, especially leaf phosphorus content (LP), root nitrogen content (RN) and root tissue density (RTD), at species and mycorrhizal type levels, offering new perspectives on the microbial dynamics underlying ecosystem functioning.

Stochastic Processes Derive Gut Fungi Community Assembly of Plateau Pikas (Ochotona curzoniae) along Altitudinal Gradients across Warm and Cold Seasons

Although fungi occupy only a small proportion of the microbial community in the intestinal tract of mammals, they play important roles in host fat accumulation, nutrition metabolism, metabolic health, and immune development. Here, we investigated the dynamics and assembly of gut fungal communities in plateau pikas inhabiting six altitudinal gradients across warm and cold seasons. We found that the relative abundances of Podospora and Sporormiella significantly decreased with altitudinal gradients in the warm season, whereas the relative abundance of Sarocladium significantly increased. Alpha diversity significantly decreased with increasing altitudinal gradient in the warm and cold seasons. Distance-decay analysis showed that fungal community similarities were significantly and negatively correlated with elevation. The co-occurrence network complexity significantly decreased along the altitudinal gradients as the total number of nodes, number of edges, and degree of nodes significantly decreased. Both the null and neutral model analyses showed that stochastic or neutral processes dominated the gut fungal community assembly in both seasons and that ecological drift was the main ecological process explaining the variation in the gut fungal community across different plateau pikas. Homogeneous selection played a weak role in structuring gut fungal community assembly during the warm season. Collectively, these results expand our understanding of the distribution patterns of gut fungal communities and elucidate the mechanisms that maintain fungal diversity in the gut ecosystems of small mammals.

Rethinking Aerobic Respiration in the Hyporheic Zone under Variation in Carbon and Nitrogen Stoichiometry

Hyporheic zones (HZs)─zones of groundwater-surface water mixing─are hotspots for dissolved organic matter (DOM) and nutrient cycling that can disproportionately impact aquatic ecosystem functions. However, the mechanisms affecting DOM metabolism through space and time in HZs remain poorly understood. To resolve this gap, we investigate a recently proposed theory describing trade-offs between carbon (C) and nitrogen (N) limitations as a key regulator of HZ metabolism. We propose that throughout the extent of the HZ, a single process like aerobic respiration (AR) can be limited by both DOM thermodynamics and N content due to highly variable C/N ratios over short distances (centimeter scale). To investigate this theory, we used a large flume, continuous optode measurements of dissolved oxygen (DO), and spatially and temporally resolved molecular analysis of DOM. Carbon and N limitations were inferred from changes in the elemental stoichiometric ratio. We show sequential, depth-stratified relationships of DO with DOM thermodynamics and organic N that change across centimeter scales. In the shallow HZ with low C/N, DO was associated with the thermodynamics of DOM, while deeper in the HZ with higher C/N, DO was associated with inferred biochemical reactions involving organic N. Collectively, our results suggest that there are multiple competing processes that limit AR in the HZ. Resolving this spatiotemporal variation could improve predictions from mechanistic models, either via more highly resolved grid cells or by representing AR colimitation by DOM thermodynamics and organic N.

Dispersal Limitation Controlling the Assembly of the Fungal Community in Karst Caves

As a unique ecosystem, Karst caves harbor an impressive diversity of specific fungi. However, the factors and mechanisms that shape fungal biodiversity in caves remain elusive. In this study, we explored the assembly patterns of fungal communities based on our previous research in eight representative Karst caves in Southwest China. Our results indicated that dispersal limitation plays a crucial role in shaping the overall fungal community as well as specific communities in rock, sediment, and water samples. However, "Undominated" processes contributed more than dispersal limitation in air samples. Interestingly, the dominant assembly processes varied between caves. Consistently, environmental selection had a minor impact on the assembly of fungal communities. Among the examined spatial and environmental variables, latitude, longitude, altitude, and temperature were found to significantly influence fungal communities irrespective of substrate type. These findings provide valuable insights into the ecological factors governing fungal community assembly in Karst caves.

Transformation of dissolved organic matter and related arsenic mobility at a surface water-groundwater interface in the Hetao Basin, China

Porewater arsenic mobility above the groundwater table has been recognized as a potential cause of arsenic-rich groundwater, but the processing pathways of dissolved organic matter (DOM) in that hyporheic zone and their effect on porewater arsenic release remain poorly understood. To address these issues, two porewater profiles were sampled in a surface water-groundwater interaction zone from the Hetao Basin, China, to monitor the porewater geochemistry and DOM molecular characteristics. The results show that the porewater arsenic, Fe(II), and DOC concentrations were all significantly higher than those of the intruding pond water, and were located above the conservative mixing model lines. This indicates a net release of these solutes from the sediment. By comparing the porewater with pond water DOM, we found that the carboxyl-rich alicyclic molecules (CRAM) were selectively preserved, carbohydrates and aliphatics/proteins were preferentially consumed, and low O/C-ratio compounds with high bioproduction index (I_bioprod) and terrestrial index (I_terr) were produced. The transformation of CHO to CHOS compounds also represented a pathway of recalcitrant DOM production. The produced recalcitrant organic compounds mostly contributed to the elevated porewater DOC concentrations, but their contribution decreased along the filtration path. The consumption of labile DOM compounds would be responsible for Fe(III) hydroxide reduction and arsenic release. The generated recalcitrant DOM may also be a driver of porewater arsenic mobility by acting as electron shuttles. This study highlights the importance of the hyporheic zone in shaping shallow groundwater DOM composition and the potential contribution to arsenic enrichment.

Leachate leakage enhances the microbial diversity and richness but decreases Proteobacteria and weakens stable microbial ecosystem in landfill groundwater

Sanitary landfill is the most prevalent and economic method for municipal solid waste disposal, and the resultant groundwater pollution has become an environmental problem due to leachate leakage. The pollution characteristics in groundwater near landfill sites have been extensively investigated, although the succession characteristics and driving mechanisms of microbial communities in leachate-contaminated groundwater and the sensitive microbial indicators for leachate leakage identification remain poorly studied. Herein, results showed that leachate leakage enhanced the microbial diversity and richness and transferred endemic bacteria from landfills into groundwater, producing an average decrease of 17.73% in the relative abundance of Proteobacteria. The key environmental factor driving the evolution of microbial communities in groundwater due to leachate pollution was organic matter, which can explain 16.13% of the changes in microbial community composition. The |βNTI| values of the bacterial communities in all six landfills were <2, and the assembly process of microbial communities was primarily dominated using stochastic processes. Leachate pollution changed the assembly mechanism, transforming the community assembly process from an undominated process to a dispersal limitation process. Leachate pollution reduced the efficiency and stability of microbial communities in groundwater, increasing the vulnerability of the stable microbial ecosystems in groundwater. Notably, microbial indicators are more sensitive to leachate leakage and could accurately identify landfills where leachate leakage occurred and other extraneous pollutants. The phylum Proteobacteria and mcrA could act as appropriate indicators for the identification of leachate leakage. These results provide a novel insight into the monitoring, identification of groundwater pollution and the scientific guidance for appropriate remediation strategies for leachate-contaminated groundwater.

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.

A functional microbiome catalog crowdsourced from North American rivers

Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires understanding the spatial drivers of river microbiomes. However, the unifying microbial processes governing river biogeochemistry are hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we employed a community science effort to accelerate the sampling, sequencing, and genome-resolved analyses of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). This resource profiled the identity, distribution, function, and expression of thousands of microbial genomes across rivers covering 90% of United States watersheds. Specifically, GROWdb encompasses 1,469 microbial species from 27 phyla, including novel lineages from 10 families and 128 genera, and defines the core river microbiome for the first time at genome level. GROWdb analyses coupled to extensive geospatial information revealed local and regional drivers of microbial community structuring, while also presenting a myriad of foundational hypotheses about ecosystem function. Building upon the previously conceived River Continuum Concept 1 , we layer on microbial functional trait expression, which suggests the structure and function of river microbiomes is predictable. We make GROWdb available through various collaborative cyberinfrastructures 2, 3 so that it can be widely accessed across disciplines for watershed predictive modeling and microbiome-based management practices.

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

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

Spatial and temporal changes in the assembly mechanism and co-occurrence network of the chromophytic phytoplankton communities in coastal ecosystems under anthropogenic influences

As a typical semiclosed coastal sea area in China, the ecological environment of Bohai Bay has been significantly disturbed by human activities. As primary producers, the chromophytic phytoplankton are the basis of ecosystems, especially in coastal ecosystems, and changes in the chromophytic phytoplankton community can affect the stability of the entire ecosystem. In this study, we investigated the effects of the human activity-induced spatial and temporal environmental heterogeneity on the community composition, diversity, assembly mechanisms, and co-occurrence networks of chromophytic phytoplankton in Bohai Bay during the wet season and the dry season. The results showed that in both seasons, there was obvious environmental heterogeneity between the nearshore area and the offshore area, and the nearshore areas were more affected by human disturbance. Although higher diversity was supported by the abundance of nutrients in nearshore areas, co-occurrence network analysis revealed that the chromophytic phytoplankton were less closely connected to each other in nearshore areas than in offshore areas due to chemical oxygen demand (COD), eutrophication index (EI), and dissolved inorganic nitrogen (DIN). The nearshore network was less stable than the offshore co-occurrence network in both seasons, which was related to the concentration of dissolved oxygen and COD. Both stochastic and deterministic processes dominated the assembly of the chromophytic phytoplankton communities, with different importance rankings of stochastic and deterministic processes in the nearshore and offshore areas. Drift dominated the assembly of the communities in nearshore areas, while variable selection dominated the assembly of the communities in offshore areas. DIN, EI, and COD, rather than geographic distance, were the main environmental factors affecting the phylogenetic turnover of the chromophytic phytoplankton. Our study showed that environmental heterogeneity caused by human disturbance had a greater impact on the chromophytic phytoplankton communities in Bohai Bay than natural factors such as temperature and salinity.

Enhanced removal of phenanthrene and nutrients in wetland sediment with metallic biochar: Performance and mechanisms

Polycyclic aromatic hydrocarbon (PAHs) are persistent organic pollutants and pose high risk in aquatic environment. The utilization of biochar is a strategy for PAHs-contaminated remediation but is challenging due to the adsorption saturation and reoccurrence of PAHs desorbed back into water. In this study, iron (Fe) and manganese (Mn) were provided as electron acceptors for biochar modification to enhance anaerobic biodegradation of phenanthrene (Phe). Results revealed that, the Mn(Ⅳ) and Fe(Ⅲ) modification improved the removal of Phe by 24.2% and 31.4% than that of biochar, respectively. Additionally, nitrate removal was improved by 19.5% with Fe(Ⅲ) amendment. The Mn-and Fe-biochar decreased Phe contents by 8.7% and 17.4% in sediment, 10.3% and 13.8% in biochar than that of biochar. Much higher DOC contents were observed with Mn- and Fe-biochar, which provided bioavailable carbon source for microbes and contributed to microbial degradation of Phe. The greater degree of humification, higher proportions of humic and fulvic acid like components in metallic biochar participated in electron transport and further enhancing the degradation of PAHs. Microbial analysis proved the high abundance of Phe-degrading bacteria (e.g. PAH-RHD_α, Flavobacterium and Vibrio), nitrogen removal microbes (e.g. amoA, nxrA, and nir), Fe and Mn bioreduction or oxidation (e. g. Bacillus, Thermomonas, Deferribacter) with metallic biochar. Based on the results, the Fe and Mn modification, especially Fe-modified biochar provided well performance for PAHs removal in aquatic sediment.