Temperature and microbial interactions drive the deterministic assembly processes in sediments of hot springs

Spatial scale modulates stochastic and deterministic influence on biogeography of photosynthetic biofilms in Southeast Asian hot springs

Hot springs, with their well-characterized major abiotic variables and island-like habitats, are ideal systems for studying microbial biogeography. Photosynthetic biofilms are a major biological feature of hot springs but despite this large-scale studies are scarce, leaving critical questions about the drivers of spatial turnover unanswered. Here, we analysed 395 photosynthetic biofilms from neutral-alkaline hot springs (39-66 °C, pH 6.4-9.0) across a 2100 km latitudinal gradient in Southeast Asia. The Cyanobacteria-dominated communities were categorized into six biogeographic regions, each characterized by a distinct core microbiome and biotic interactions. We observed a significant decline in the explanatory power of major abiotic variables with increasing spatial scale, from 62.6% locally, 55% regionally, to 26.8% for the inter-regional meta-community. Statistical null models revealed that deterministic environmental filtering predominated at local and regional scales, whereas stochastic ecological drift was more influential at the inter-regional scale. These findings enhance our understanding of the differential contribution of ecological drivers and highlight the importance of spatial scale in shaping biogeographic distributions for microorganisms.

Deciphering the role of traditional flipping crafts in medium-temperature Daqu fermentation: Microbial succession and metabolic phenotypes

Medium-temperature Daqu (MTD) serves as the saccharification and fermentation starter for Nongxiangxing Baijiu. Flipping Daqu (FD) during fermentation is a key craft in traditional MTD preparation. However, the mechanism underlying this flipping craft remains unclear. To address this, we systematically compared FD with non-flipping Daqu (NFD) to elucidate microbial succession dynamics, metabolic phenotypes, and environmental drivers. Our results demonstrated divergent microbial community succession patterns between FD and NFD during the stable fermentation phase (days 9-25). FD exhibited significantly higher enzyme activities and volatile ketone content, along with lower core temperatures compared to NFD. Metabolite production in FD was influenced by both bacteria and fungi, whereas fungi predominantly controlled metabolite production in NFD. Co-occurrence network analysis revealed that the microbial community in FD was simpler yet more stable compared to that in NFD. Microbial succession in MTD was primarily driven by interspecies interactions and environmental factors. Furthermore, deterministic processes and stochastic processes jointly governed microbial assembly both FD and NFD, with temperature, moisture, and acidity as the key driving factors. These findings highlight the pivotal role of the flipping crafts in enhancing microbial functionality and metabolic diversity, offering a theoretical basis for optimizing MTD production and advancing intelligent fermentation systems.

Comparison of plastisphere microbiomes during the degradation of conventional and biodegradable mulching films

Biodegradable mulch films (BDMs) are becoming increasingly popular in agriculture and are emerging as an alternative to conventional polyethylene (PE) films. However, the intricate details surrounding the establishment and growth of microorganisms on BDMs and PE during their degradation in agricultural fields remain unclear. In this study, the succession of bacterial communities in farmland soil and the plastispheres of PE and BDMs were compared through 16S rRNA gene high-throughput sequencing and real-time PCR. The results unveiled noteworthy distinctions in bacterial community structures across different samples. Specifically, the α-diversity in the BDM plastispheres was markedly lower than in the PE plastisphere. Hydrogenophaga and Variovorax genera were abundantly present in the BDM plastisphere, whereas Mycobacterium demonstrated significant enrichment in the PE plastisphere. Functional annotations indicated high abundances of degradation-related and pathogen-related functions in both BDM and PE plastispheres. Furthermore, the BDM plastisphere exhibited lower network complexity and modularity and stronger competitive interactions than the PE plastisphere. The conducted iCAMP analysis showed that stochastic community assembly processes largely govern the PE plastisphere, while deterministic processes prevailed in BDMs and increased significantly over time. These findings shed light on different mulching materials' effects in farmland ecosystems and provide insights into potential ecological risks linked to their usage.

Sediment bacterial biogeography across reservoirs in the Hanjiang river basin, southern China: the predominant influence of eutrophication-induced carbon enrichment

A fundamental goal of reservoir ecosystem management is to understand bacterial biogeographic patterns and the mechanisms shaping them at a regional scale. However, little is known about how eutrophication, a major water quality challenge in reservoirs, influences sediment bacterial biogeographic patterns in subtropical regions. In this study, sediment bacterial communities were sampled from 21 subtropical reservoirs in the Hanjiang river basin, southern China, and spanning trophic states from oligotrophic to eutrophic. Our findings demonstrated that eutrophication-driven changes in total carbon (TC) significantly shaped the regional biogeographic patterns of sediment bacterial communities, weakening the "distance-decay" relationships that typically link bacterial community similarity to geographical distance. TC content exceeding a threshold of 13.2 g·kg-1 resulted in substantial shifts in bacterial community structure. Specifically, high TC levels promoted the dominance of copiotrophic bacteria such as Syntrophales (Deltaproteobacteria), Clostridiaceae (Firmicutes), and VadinHA17 (Bacteroidetes), while oligotrophic taxa like Anaerolineaceae (Chloroflexi) and Nitrospirota were prevalent in low TC sediments. Additionally, higher TC content was associated with increased regional heterogeneity in bacterial community composition. Reservoirs with elevated TC levels exhibited more complex bacterial interaction networks, characterized by stronger niche segregation and higher competition compared to low TC networks. Overall, these findings underscore the pivotal role of sediment TC in shaping bacterial biogeography at a regional scale. They provide valuable insights for predicting ecosystem responses to eutrophication and offer guidance for mitigating the impacts of anthropogenic activities on freshwater ecosystems.

New insights into the assembly processes of biofilm microbiota communities: Taking the world's largest water diversion canal as a case study

Systematic studies on the assembly process and drivers of biofilm microbiota communities are still limited. In this study, we used the artificial concrete channel of the world's largest interbasin water diversion project, the middle route of the South-to-North Water Diversion Project in China, as a model system to investigate the assembly mechanisms of biofilm microbiota communities. Our study revealed that water temperature (p < 0.001) and hydrodynamic disturbance (p < 0.05) significantly influenced biofilm biomass. The bacterial communities exhibited substantial spatial heterogeneity, whereas the eukaryotic communities presented pronounced spatial and seasonal variations (PERMANOVA, p < 0.05). Neutral model and null model analyses indicated that dispersal limitation and homogeneous selection (54.8 %-69.7 % in bacteria and 55.9 %-76.1 % in eukaryotes) predominantly governed community assembly. Deterministic effects such as hydrodynamic conditions and temperature strongly influence eukaryotes (homogeneous selection accounts for 63.9 % of eukaryotes in spring). The metacommunity network could be divided into five primary modules with key nodes, including many species from Proteobacteria, Chlorophyta, Bacillariophyta, and Cyanobacteria. Bacteria, such as Proteobacteria, Chlorophyta, Cyanobacteria, and Bacteroidota, act as connectors and a vital role in maintaining the coexistence of modules. Finally, we confirmed that physicochemical (hydrodynamic conditions, temperature, dissolved oxygen conductivity permanganate index), spatial, and biological factors have significant effects on both bacterial and eukaryotic communities as well as metacommunity networks. Our findings provide new insights into the different assembly processes and drivers of bacterial and eukaryotic communities in biofilms, which is highly important for water quality monitoring and sustainable water diversion.

The co-occurrence patterns and assembly mechanisms of microeukaryotic communities in geothermal ecosystems of the Qinghai-Tibet Plateau

Geothermal spring ecosystems, as extreme habitats, exert significant environmental pressure on their microeukaryotic communities. However, existing studies on the stability of microeukaryotic communities in geothermal ecosystems across different habitats and temperature gradients are still limited. In this study, we used high-throughput 18S rDNA sequencing in combination with environmental factor analysis to investigate the co-occurrence patterns, assembly mechanisms, and responses to environmental changes of microeukaryotic communities in sediment and water samples from 36 geothermal springs across different temperature gradients in southern Tibet. The results show that with increasing temperature, the network stability of microeukaryotic communities in sediments significantly improved, while the stability in water communities decreased. The assembly mechanisms of microeukaryotic communities in both sediment and water were primarily driven by undominant processes within stochastic processes. Latitude and longitude were the key factors influencing changes in sediment community composition, while water temperature and electrical conductivity were the major environmental factors affecting water community composition. Additionally, the stability of the geothermal community network was closely related to its response to external disturbances: sediment communities, being in relatively stable environments, demonstrated higher resistance to disturbances, whereas water communities, influenced by environmental changes such as water flow and precipitation, exhibited greater dynamic variability. These findings not only enhance our understanding of the ecological adaptability of microeukaryotic communities in geothermal springs but also provide valuable insights into how microorganisms in extreme environments respond to external disturbances. This is especially significant for understanding how microeukaryotic communities maintain ecological stability under highly dynamic and stressful environmental conditions.

Diversity, composition, and assembly processes of bacterial communities within per- and polyfluoroalkyl substances (PFAS)-contained urban lake sediments

Per- and polyfluoroalkyl substances (PFAS) are widespread, highly persistent, and bio-accumulative compounds that are increasingly found in the sediments of aquatic systems. Given this accumulation and concerns regarding the environmental impacts of PFAS, their influence on sedimentary bacterial communities remains inadequately studied. Here, we investigated the concentrations of 17 PFAS in sediments from six urban lakes in Nanjing, China, and assessed their effects on the diversity, composition, potential interactions, and assembly mechanisms of sedimentary bacterial communities. Sediment concentrations of PFAS ranged from 4.70 to 5.28 ng·g-1 dry weight. The high concentrations of the short-chain perfluorobutanesulfonic acid (PFBS) suggested its substitution for the long-chain perfluorooctanesulfonic acid (PFOS). As alternatives to long-chain PFAS, short-chain PFAS had similar effects on bacterial communities. The short-chain perfluoropentanoic acid (PFPeA) and the long-chain perfluorotridecanoic acid (PFTrDA) were the most important PFAS related to the ecological patterns of the co-occurrence network and may alter the composition of the sedimentary bacterial communities in the urban lakes. The Anaerolineaceae family represented as keystone bacteria within the PFAS-affected bacterial co-occurrence network. Deterministic processes (65.9 %), particularly homogeneous selection (63.2 %), were the dominant process driving bacterial community assembly. PFAS promoted the phylogenetic clustering and influenced the community dispersal capabilities to shape bacterial community assembly. This study provides a comprehensive analysis of PFAS distribution in sediments across six urban lakes in Nanjing and provides novel insights into the effects of PFAS on sedimentary bacterial communities. Further research is required to elucidate the mechanisms underlying the impacts of PFAS on microbial communities and to evaluate their broader ecological consequences.

Limited Microbial Contribution in Salt Lake Sediment and Water to Each Other's Microbial Communities

Climate change and human activities have led to frequent exchanges of sedimentary and aquatic microorganisms in lakes. However, the ability of these microorganisms to survive in their respective habitats between saline lake sediment and water remains unclear. In this study, we investigated microbial sources and community composition and metabolic functions in sediments and water in Yuncheng Salt Lake using a combination of source tracking and Illumina MiSeq sequencing. The results showed that 0.10-8.47% of the microbial communities in the sediment came from the corresponding water bodies, while 0.12-10.78% of the sedimentary microorganisms contributed to the aquatic microbial populations, and the microbial contributions depended on the salinity difference between sediment and water. Habitat heterogeneity and salinity variations led to the differences in microbial diversity, community composition, and assembly between sediment and water communities. The assembly of sedimentary communities was mainly controlled by stochastic processes (>59%), whereas the assembly of aquatic communities was mainly controlled by deterministic processes (>88%). Furthermore, sediments had a higher potential for metabolic pathways related to specific biogeochemical functions than lake water. These results provide insights into the survival ability of microorganisms and the mechanisms of microbial community assembly under frequent exchange conditions in saline lakes.

Organic matter in geothermal springs and its association with the microbial community

Organic matter (OM) plays an important role in the biogeochemical cycles of carbon, nitrogen, and other elements, shaping the structure of the microbiome and vice versa. However, the molecular composition of OM and its impact on the microbial community in terrestrial geothermal environments remain unclear. In this study, we characterized the OM in water and sediment from a typical geothermal field using ultra-high-resolution Fourier transform ion cyclotron resonance mass spectrometry. By combining high-throughput amplicon sequencing and multivariate analyses, we deciphered the association between OM components and microbial community. A surprisingly high chemodiversity of OM was observed in the waters (11,088 compounds) and sediments (7772 compounds) in geothermal springs. Sulfur-containing organic compounds, a characteristic molecular signature of geothermal springs, accounted for 21 % ± 5 % in waters and 33 % ± 4 % in sediments. Multivariate analyses revealed that both labile and recalcitrant fractions of OM (e.g., carbohydrates intensity and tannins chemodiversity) influenced the structure and function of the microbial community. Co-occurrence networks showed that Proteobacteria and Crenarchaeota accounted for most of the connections with OM in waters (33 % and 15 %, respectively) and sediments (15 % and 12 %, respectively), highlighting their key roles in carbon cycling. This study expands our understanding of the molecular compositions of OM in geothermal springs and highlights its potentially important role in global climate change through microbial carbon cycling.

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.

Plant growth-promoting microorganisms drive K strategists through deterministic processes to alleviate biological stress caused by Fusarium oxysporum

Soybean root rot, caused by soil-borne pathogens such as Fusarium oxysporum, frequently occurs in Northeast China and leads to a decline in soil health and becoming a bottleneck for soybean yield in the region. To address this issue, applying beneficial microorganisms and altering soil microbial community structure have become effective strategies. In this study, the 90-day soybean pot experiment was conducted to explore the assembly process and life strategy selection of bacterial communities in the rhizosphere of healthy (inoculated with Funneliformis mosseae, F group and treated with Pseudomonas putida, P group) and diseased (inoculated with F. oxysporum, O group) soybean plants, as well as the recovery effect of beneficial microorganisms on soil-borne diseases (combined treatments OP and OF). Results indicated that in healthy soils (P and F), microbial community assembly process in the soybean rhizosphere was entirely governed by heterogeneous selection (HeS, 100 %). However, inoculated with P. putida (OP) was primarily driven by stochastic processes (HeS 40 %, dispersal limitation (DL) 60 %), and the F. mosseae treatment (OF) predominantly followed a deterministic process (HeS 89 %, DL 11 %) in diseased soils. Inoculation of plant growth-promoting microorganisms (PGPMs) in diseased soil drove the life strategy of the rhizosphere bacterial community from r- to K-strategy, evident from the lower rRNA operon (rrn) copy numbers (O 3.7, OP 2.1, OF 2.3), higher G+ to G- ratios (O 0.47, OP 0.58, OF 0.57), and a higher abundance of oligotrophs (O 50 %, OP 53 %, OF 54 %). In healthy (P and F) and diseased (O, OP, OF) rhizosphere soils, OTU820, OTU6142, and OTU8841 under the K-strategy, and OTU6032 and OTU6917 under the r-strategy, which served as keystone species, had a significant promoting relationship with plant biomass and defense capabilities ( p ＜0.05). Additionally, inoculation of PGPMs improved autotoxin degradation and positively correlated with bacterial life strategies in both healthy and diseased soils (P, F, OP and OF) ( p ＜0.05). These findings enhance our understanding of soil-microbe interactions and offer new insights and precise control measures for soybean disease management and soil environment remediation.

Redundancy and resilience of microbial community under aniline stress during wastewater treatment

Aniline is one of the most toxic and widespread organic pollutants. Although biological treatment is cost-effective and generates minimal secondary pollution, microbial communities are significantly affected by high aniline concentrations, which result in low degradation efficiency. However, a comprehensive understanding of the microbial community response to aniline stress is lacking. Here, we performed a cyclic experiment with aniline concentrations (200, 600, 1200, 600, and 200 mg/L) to investigate the ability of microbial communities to recover their performance after exposure to high aniline concentrations. At aniline concentrations up to 600 mg/L, the bioreactor exhibited high aniline removal efficiency (almost 100 %). Comamonas, Zoogloea, and Delftia played crucial roles in removing aniline and microbial beta diversity changed. Additionally, alpha diversity and network complexity decreased with increasing aniline concentration, but these metrics recovered to their original levels when the aniline concentration was returned to 200 mg/L. Homogeneous and heterogeneous selection dominated microbial community assembly. Therefore, according to the observed variations in community structure and the recovery of keystones after aniline stress, microbial community redundancy and resilience are pivotal for ensuring system stability. Overall, this study provides valuable insights into the redundancy and resilience of microbial communities under aniline stress and establishes a scientific basis for managing and evaluating wastewater treatment plants.

Bacterial diversity along the geothermal gradients: insights from the high-altitude Himalayan hot spring habitats of Sikkim

Geothermal habitats present a unique opportunity to study microbial adaptation to varying temperature conditions. In such environments, distinct temperature gradients foster diverse microbial communities, each adapted to its optimal niche. However, the complex dynamics of bacterial populations in across these gradients high-altitude hot springs remain largely unexplored. We hypothesize that temperature is a primary driver of microbial diversity, and bacterial richness peaks at intermediate temperatures. To investigate this, we analysed bacterial diversity using 16S rRNA amplicon sequencing across three temperature regions: hot region of 56-65 °C (hot spring), warm region of 35-37 °C (path carrying hot spring water to the river), and cold region of 4-7 °C (river basin). Our findings showed that Bacillota was the most abundant phylum (45.51 %), followed by Pseudomonadota (32.81 %) and Actinomycetota (7.2 %). Bacillota and Chloroflexota flourished in the hot and warm regions, while Pseudomonadota thrived in cooler areas. Core microbiome analysis indicated that species richness was highest in the warm region, declining in both cold and hot regions. Interestingly, an anomaly was observed with Staphylococcus, which was more abundant in cases where ponds were used for bathing and recreation. In contrast, Clostridium was mostly found in cold regions, likely due to its viability in soil and ability to remain dormant as a spore-forming bacterium. The warm region showed the highest bacterial diversity, while richness decreased in both cold and hot regions. This highlights the temperature-dependent nature of microbial communities, with optimal diversity in moderate thermal conditions. The study offers new insights into microbial dynamics in high-altitude geothermal systems.

Vadose-zone characteristic pollutants distribution, microbial community structure and functionality changes in response to long-term leachate pollution of an informal landfill site

The study embarked on a comprehensive examination of the evolution and diversity of microorganisms within long-term leachate pollution environments, with a focus on varying depths and levels of contamination, and its linkage to soil characteristics and the presence of heavy metals. It was observed that microbial diversity presented distinct cross-depth trend, where archaeal communities were found to be particularly sensitive to alterations in soil depth. Noteworthily, Euryarchaeota increased by 4.82 %, 7.64 % and 9.87 % compared with topsoil. The abundance of Tahumarchaeota was successively reduced by 5.79 %, 9.58 %, and 12.66 %. The bacterial community became more sensitive to leachate pollution, and the abundance of Protebacteria in contaminated soil decreased by 10.27 %, while the abundance of Firmicutes increased by 7.46 %. The bacterial genus Gemmobacter, Chitinophaga and Rheinheimera; the archaeal genus Methanomassiliicoccus and Nitrosopumilus; along with the fungal genus Goffeauzyma, Gibberella, and Setophaeosphaeria emerged as pivotal biological markers for their respective domains, underpinning the biogeochemical dynamics of these environments. Furthermore, the study highlighted that geochemical factors, specifically nitrate (NO₃--N) levels and humic acid (HA) fractions, played crucial roles in modulating the composition and metabolic potential of these communities. Predictive analyses of functional potentials suggested that the N functional change of archaea was more pronounced, with anaerobic ammonia oxidation and nitrification decreased by 15.78 % and 14.62 %, respectively. Overall, soil characteristics alone explained 57.9 % of the total variation in the bacterial community structure. For fungal communities within contaminated soil, HMs were the primary contributors, explaining 46.9 % of the variability, while soil depth accounting for 6.4 % of the archaeal variation. This research enriches the understanding of the complex interrelations between heavy metal pollution, soil attributes, and microbial communities, paving the way for informed strategies in managing informal landfill sites effectively.

Glacier Retreat Induces Contrasting Shifts in Bacterial Biodiversity Patterns in Glacial Lake Water and Sediment : Bacterial Communities in Glacial Lakes

Glacial lake ecosystems are experiencing rapid changes due to accelerated glacier retreat. As glaciers recede, their influence on downstream habitats diminishes, potentially affecting the biodiversity of glacial lake microbial communities. However, there remains a knowledge gap regarding how bacterial biodiversity patterns in glacial lakes are altered by diminishing glacial influence. Here, we investigated shifts in bacterial communities in paired water and sediment samples collected from seven glacial lakes on the Tibetan Plateau, using a space-for-time substitution approach to understand the consequences of glacier retreat. Our findings reveal that bacterial diversity in lake water increases significantly with a higher glacier index (GI), whereas sediment bacterial diversity exhibits a negative correlation with GI. Both the water and sediment bacterial communities display significant structural shifts along the GI gradient. Notably, reduced glacial influence decreases the complexity of bacterial co-occurrence networks in lake water but enhances the network complexity in sediment. This divergence in diversity and co-occurrence patterns highlights that water and sediment bacterial communities respond differently to changes in glacial influence in these lake ecosystems. This study provides insights into how diminishing glacial influence impacts the bacterial biodiversity in glacial lake water and sediments, revealing contrasting patterns between the two habitats. These findings emphasize the need for comprehensive monitoring to understand the implications of glacier retreat on these fragile ecosystems.

Microbial community assembly patterns at the species level in different parts of the medium temperature Daqu during fermentation

Medium-temperature Daqu (MT-Daqu) serves as a crucial saccharifying and fermentation agent in the production of strong-flavor Baijiu. Due to the spatial heterogeneity of solid fermentation, significant differences occurred in the fermentation state and appearance features in different parts of Daqu during fermentation. Currently, the understanding of the underlying mechanism behind this phenomenon remains limited. Here, we analyzed the microbial succession and assembly models and driving factors in different parts of MT-Daqu at the species level based on the PacBio single-molecule real-time sequencing technology. The results showed significantly different bacterial and fungal community compositions, successions, and interaction patterns in different parts of MT-Daqu. The bacterial community composition and succession model in the middle layer were similar to those in the core layer, whereas the fungal community composition and succession model in the surface layer were similar to those in the middle layer. The co-occurrence network analysis showed that microbial interaction is stronger in the middle and core layers than in the surface layer. Analyses based on both niche theory and neutral theory models indicated that deterministic processes predominantly governed the microbial community assembly and these processes played an increasingly important role from the surface to the core layer. Random forest analysis revealed that temperature was the primary endogenous factor driving the bacterial and fungal community assembly. The results of this study contribute to a better understanding of the microbial community in MT-Daqu and are helpful for the quality control of MT-Daqu fermentation.

Genotype of pioneer plant Miscanthus is not a key factor in the structure of rhizosphere bacterial community in heavy metal polluted sites

Miscanthus is a common pioneer plant with abundant genetic variation in abandoned mines in southern China. However, the extent to which genetic differentiation among species modulates rhizosphere bacterial communities remains unclear. Miscanthus samples were collected from 26 typical abandoned heavy-metal mines with different soil types in southern China, tested using 14 pairs of simple sequence repeats (SSR) primers, and classified into two genotypes based on Nei's genetic distance. The structure and diversity of rhizosphere bacterial communities were examined using 16 S rRNA sequencing. The results showed that among the factors affecting the rhizosphere bacterial community structure of Miscanthus samples, the role of genotype was not significant, and geographical conditions were the most important factors, followed by pH and total organic carbon (TOC). The process of rhizospheric community assembly varied among different genotypes; however, the recruited species and their abundances were similar. Collectively, we provided an approach based on genetic differentiation to quantify the relative contribution of genotypes to the rhizosphere bacterial community, demonstrating that genotypes contribute less than soil conditions. Our findings provide new insights into the role of host genetics in the ecological processes of plant rhizosphere bacterial communities in abandoned mines and provide theoretical support for microbe-assisted phytoremediation.

Unveiling the deterministic dynamics of microbial meta-metabolism: a multi-omics investigation of anaerobic biodegradation

BACKGROUND

Microbial anaerobic metabolism is a key driver of biogeochemical cycles, influencing ecosystem function and health of both natural and engineered environments. However, the temporal dynamics of the intricate interactions between microorganisms and the organic metabolites are still poorly understood. Leveraging metagenomic and metabolomic approaches, we unveiled the principles governing microbial metabolism during a 96-day anaerobic bioreactor experiment.

RESULTS

During the turnover and assembly of metabolites, homogeneous selection was predominant, peaking at 84.05% on day 12. Consistent dynamic coordination between microbes and metabolites was observed regarding their composition and assembly processes. Our findings suggested that microbes drove deterministic metabolite turnover, leading to consistent molecular conversions across parallel reactors. Moreover, due to the more favorable thermodynamics of N-containing organic biotransformations, microbes preferentially carried out sequential degradations from N-containing to S-containing compounds. Similarly, the metabolic strategy of C18 lipid-like molecules could switch from synthesis to degradation due to nutrient exhaustion and thermodynamical disadvantage. This indicated that community biotransformation thermodynamics emerged as a key regulator of both catabolic and synthetic metabolisms, shaping metabolic strategy shifts at the community level. Furthermore, the co-occurrence network of microbes-metabolites was structured around microbial metabolic functions centered on methanogenesis, with CH4 as a network hub, connecting with 62.15% of total nodes as 1st and 2nd neighbors. Microbes aggregate molecules with different molecular traits and are modularized depending on their metabolic abilities. They established increasingly positive relationships with high-molecular-weight molecules, facilitating resource acquisition and energy utilization. This metabolic complementarity and substance exchange further underscored the cooperative nature of microbial interactions.

CONCLUSIONS

All results revealed three key rules governing microbial anaerobic degradation. These rules indicate that microbes adapt to environmental conditions according to their community-level metabolic trade-offs and synergistic metabolic functions, further driving the deterministic dynamics of molecular composition. This research offers valuable insights for enhancing the prediction and regulation of microbial activities and carbon flow in anaerobic environments. Video Abstract.

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

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

Methanogenic Community Characteristics and Its Influencing Factors in Reservoir Sediments on the Northeastern Qinghai Plateau

Reservoirs are a hotspot for methane emissions, a potent greenhouse gas. However, the microbial basis for methane production in the Qinghai Plateau reservoirs remains unclear. To explore the characteristics of methanogenic communities in reservoir sediments on the northeastern Qinghai Plateau, sediment samples were collected from 18 reservoirs in the Yellow River basin during May 2023 (dry season) and August 2023 (wet season). High-throughput sequencing technology was employed to analyze the community composition, diversity, and co-occurrence network of methanogens. Furthermore, FAPROTAX and Mantel analysis were used to assess the metabolic functions of methanogens and their influencing factors. The results showed that (1) the predominant genera of methanogens were Methanobacterium (28.87%) and Methanosarcina (21.67%). Hydrogenotrophic methanogenesis was the main pathway in the sediments. (2) Significant spatiotemporal differences were observed in the diversity of methanogenic communities (p < 0.05). The composition and diversity of these communities were found to be significantly influenced by temperature, pH, altitude, organic carbon, and total nitrogen (p < 0.05). (3) Methanosarcina, Methanobacterium, and Methanospirillum play crucial roles in maintaining the stability of methanogenic community networks. The co-occurrence network nodes are predominantly positively correlated (99.82%). These results provide data for further studies on carbon cycling in the Qinghai Plateau reservoirs.

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

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

Microeukaryotic plankton community dynamics under ecological water replenishment: Insights from eDNA metabarcoding

Ecological water replenishment (EWR) is an important strategy for river restoration globally, but timely evaluation of its ecological effects at a large spatiotemporal scale to further adjust the EWR schemes is of great challenge. Here, we examine the impact of EWR on microeukaryotic plankton communities in three distinct river ecosystems through environmental DNA (eDNA) metabarcoding. The three ecosystems include a long-term cut-off river, a short-term connected river after EWR, and long-term connected rivers. We analyzed community stability by investigating species composition, stochastic and deterministic dynamics interplay, and ecological network robustness. We found that EWR markedly reduced the diversity and complexity of microeukaryotic plankton, altered their community dynamics, and lessened the variation within the community. Moreover, EWR disrupted the deterministic patterns of community organization, favoring dispersal constraints, and aligning with trends observed in naturally connected rivers. The shift from an isolated to a temporarily connected river appeared to transition community structuring mechanisms from deterministic to stochastic dominance, whereas, in permanently connected rivers, both forces concurrently influenced community assembly. The ecological network in temporarily connected rivers post-EWR demonstrated significantly greater stability and intricacy compared to other river systems. This shift markedly bolstered the resilience of the ecological network. The eDNA metabarcoding insights offer a novel understanding of ecosystem resilience under EWR interventions, which could be critical in assessing the effects of river restoration projects throughout their life cycle.

Distribution patterns of soil bacteria, fungi, and protists emerge from distinct assembly processes across subcommunities

Environmental change exerts a profound effect on soil microbial domains-including bacteria, fungi, and protists-that each perform vital ecological processes. While these microbial domains are ubiquitous and extremely diverse, little is known about how they respond to environmental changes in urban soil ecosystems and what ecological processes shape them. Here we investigated the community assembly processes governing bacteria, fungi, and protists through the lens of four distinct subcommunities: abundant, conditionally rare, conditionally abundant, and rare taxa. We show that transient taxa, including the conditionally rare and conditionally rare or abundant taxa, were the predominant subcommunities. Deterministic processes (e.g., environmental filtering) had major roles in structuring all subcommunities of fungi, as well as conditionally rare and abundant protists. Stochastic processes had strong effects in structuring all subcommunities of bacteria (except rare taxa) and conditionally rare protists. Overall, our study underscores the importance of complementing the traditional taxonomy of microbial domains with the subcommunity approach when investigating microbial communities in urban soil ecosystems.

Microbial difference and its influencing factors in ice-covered lakes on the three poles

Most lakes in the world are permanently or seasonally covered with ice. However, little is known about the distribution of microbes and their influencing factors in ice-covered lakes worldwide. Here we analyzed the microbial community composition in the waters of 14 ice-covered lakes in the Hoh Xil region of northern Qing-Tibetan Plateau (QTP), and conducted a meta-analysis by integrating published microbial community data of ice-covered lakes in the tripolar regions (the Arctic, Antarctica and QTP). The results showed that there were significant differences in microbial diversity, community composition and distribution patterns in the ice-covered tripolar lakes. Microbial diversity and richness were lower in the ice-covered QTP lakes (including the studied lakes in the Hoh Xil region) than those in the Arctic and Antarctica. In the ice-covered lakes of Hoh Xil, prokaryotes are mainly involved in S-metabolic processes, making them more adaptable to extreme environmental conditions. In contrast, prokaryotes in the ice-covered lakes of the Arctic and Antarctica were predominantly involved in carbon/nitrogen metabolic processes. Deterministic (salinity and nutrients) and stochastic processes (dispersal limitation, homogenizing dispersal and drift) jointly determine the geographical distribution patterns of microorganisms in ice-covered lakes, with stochastic processes dominating. These results expand the understanding of microbial diversity, distribution patterns, and metabolic processes in polar ice-covered lakes.

Environmental heterogeneity caused by large-scale cultivation of Pyropia haitanensis shapes multi-group biodiversity distribution in coastal areas

The response of marine biodiversity to mariculture has long been a research focus in marine ecology. However, the effects of seaweed cultivation on biological community assembly are poorly understood, especially in diverse communities with distinct ecological characteristics. In this study, we used environmental DNA metabarcoding to investigate the spatial distribution patterns of bacterial, protistan, and metazoan diversity, aiming to reveal the mechanisms of community assembly in the Pyropia haitanensis cultivation zone along the Fujian coast, China. We found that, compared with the biological communities in control zones, those in P. haitanensis cultivation zones exhibited stronger geographic distance-decay patterns and displayed more complex and stable network structures. Deterministic processes (environmental selection) played a more important role in the assembly of bacterial, protistan, and metazoan communities in P. haitanensis cultivation zones, especially metazoan communities. Variance partitioning analysis showed that environmental variables made greater contributions to the diversity of the three types of communities within the P. haitanensis cultivation zones than in the control zones. Partial least squares path modeling analysis identified nitrate‑nitrogen (NO3-N), pH, particulate organic carbon (POC), and dissolved organic carbon (DOC) as the key environmental variables affecting biodiversity. Overall, the environmental heterogeneity caused by the large-scale cultivation of P. haitanensis could be the crucial factor influencing the composition and structure of various biological communities. Our results highlight the importance of the responses of multi-group organisms to the cultivation of seaweed, and provide insights into the coexistence patterns of biodiversity at the spatial scale.

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

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

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.

Anthropogenic vs. natural habitats: Higher microbial biodiversity pays the trade-off of lower connectivity

Climate change and anthropogenic disturbances are known to influence soil biodiversity. The objectives of this study were to compare the community composition, species coexistence patterns, and ecological assembly processes of soil microbial communities in a paired setting featuring a natural and an anthropogenic ecosystem facing each other at identical climatic, pedological, and vegetational conditions. A transect gradient from forest to seashore allowed for sampling across different habitats within both sites. The field survey was carried out at two adjacent strips of land within the Po River delta lagoon system (Veneto, Italy) one of which is protected within a natural preserve and the other has been converted for decades into a tourist resort. The anthropogenic pressure interestingly led to an increase in the α-diversity of soil microbes but was accompanied by a reduction in β-diversity. The community assembly mechanisms of microbial communities differentiate in natural and anthropic ecosystems: for bacteria, in natural ecosystems deterministic variables and homogeneous selection play a main role (51.92%), while stochastic dispersal limitation (52.15%) is critical in anthropized ecosystems; for fungi, stochastic dispersal limitation increases from 38.1% to 66.09% passing from natural to anthropized ecosystems. We are on calcareous sandy soils and in more natural ecosystems a variation of topsoil pH favors the deterministic selection of bacterial communities, while a divergence of K availability favors stochastic selection. In more anthropized ecosystems, the deterministic variable selection is influenced by the values of SOC. Microbial networks in the natural system exhibited higher numbers of nodes and network edges, as well as higher averages of path length, weighted degree, clustering coefficient, and density than its equivalent sites in the more anthropically impacted environment. The latter on the other hand presented a stronger modularity. Although the influence of stochastic processes increases in anthropized habitats, niche-based selection also proves to impose constraints on communities. Overall, the functionality of the relationships between groups of microorganisms co-existing in communities appeared more relevant to the concept of functional biodiversity in comparison to the plain number of their different taxa. Fewer but functionally more organized lineages displayed traits underscoring a better use of the resources than higher absolute numbers of taxa when those are not equally interconnected in their habitat exploitation. However, considering that network complexity can have important implications for microbial stability and ecosystem multifunctionality, the extinction of complex ecological interactions in anthropogenic habitats may impair important ecosystem services that soils provide us.

SOC bioavailability significantly correlated with the microbial activity mediated by size fractionation and soil morphology in agricultural ecosystems

Despite the fact that physical and chemical processes have been widely proposed to explicate the stabilization mechanisms of soil organic carbon (SOC), thebioavailability of SOC linked to soil physical structure, microbial community structure, and functional genes remains poorly understood. This study aims to investigate the SOC division based on bioavailability differences formed by physical isolation, and to clarify the relationships of SOC bioavailability with soil elements, pore characteristics, and microbial activity. Results revealed that soil element abundances such as SOC, TN, and DOC ranked in the same order as the soil porosity as clay > silt ≥ coarse sand > fine sand in both top and sub soil. In contrast to silt and clay, which had reduced SOC bioavailability, fine sand and coarse sand had dramatically enhanced SOC bioavailability compared to the bulk soil. The bacterial and fungal community structure was significantly influenced by particle size, porosity, and soil elements. Copiotrophic bacteria and functional genes were more prevalent in fine sand than clay, which also contained more oligotrophic bacteria. The SOC bioavailability was positively correlated with abundances of functional genes, C degradation genes, and copiotrophic bacteria, but negatively correlated with abundances of soil elements, porosity, oligotrophic bacteria, and microbial biomass (p < 0.05). This indicated that the soil physical structure divided SOC into pools with varying levels of bioavailability, with sand fractions having more bioavailable organic carbon than finer fractions. Copiotrophic Proteobacteria and oligotrophic Acidobacteria, Firmicutes, and Gemmatimonadetes made up the majority of the bacteria linked to SOC mineralization. Additionally, the fungi Mortierellomycota and Mucoromycota, which are mostly involved in SOC mineralization, may have the potential for oligotrophic metabolism. Our results indicated that particle-size fractionation could influence the SOC bioavailability by restricting SOC accessibility and microbial activity, thus having a significant impact on sustaining soil organic carbon reserves in temperate agricultural ecosystems, and provided a new research direction for organic carbon stability.

Ecological role of reed belts in lakeside zone: Impacts on nutrient retention and bacterial community assembly during Hydrilla verticillata decomposition

Reed belts acting as basic nutrient filters are important parts of lake buffer riparian zones. However, little is known about their impacts on nutrient release and bacterial community during plant litter decomposition. In this study, a field experiment was conducted in west-lake Taihu to monitor the changes in nutrients, bacterial enzymatic activities, and bacterial community in plant debris during Hydrilla verticillata (H. verticillata) decomposition in open water (HvC) and reed belts (HvL) area for 126 days. We found that there was lower temperature but higher nutrient concentrations in overlying water in HvL than HvC. Partial least squares path modeling revealed that environmental parameters in overlying water had important impacts on bacterial activities and nutrient release (such as alkaline phosphatase, cellulase, and soluble sugar) and therefore affected dissolved organic matter components in plant debris. According to Illumina sequencing, 46,003 OTUs from 10 dominant phyla were obtained and Shannon index was higher in HvL than HvC at the same sampling time. Neutral community model explained 49% of bacterial community variance and immigration rate by the estimate of dispersal in HvC (Nm: 27,154) and HvL (Nm: 25,765), respectively. Null model showed stochastic factors governed the bacterial community assembly in HvC (66.67%) and HvL (87.28%). TP and pH were key factors affecting the bacterial community structure at the phylum level. More hubs and complex interactions among bacteria were observed in HvL than HvC. Function analysis showed bacterial community had important role in carbon, organic phosphorus, and nitrogen removal but phosphorus-starvation was detected in debris of H. verticillata. This study provides useful information for understanding the changes in nutrients and bacterial community in litter during H. verticillata decomposition and highlights the role of reed belts on retained plant litter to protect lake from pollution.

Rhizosphere microbial community enrichment processes in healthy and diseased plants: implications of soil properties on biomarkers

Plant health states may influence the distribution of rhizosphere microorganisms, which regulate plant growth and development. In this study, the response of rhizosphere bacteria and fungi of healthy and diseased plants compared to bulk microbes was analyzed using high-throughput sequencing. Plant adaptation strategies of plants under potato virus Y (PVY) infection have been studied from a microbial perspective. The diversity and community structure of bacteria and fungi varied between bulk and rhizosphere soils, but not between healthy and diseased rhizosphere soils. A LEfSe analysis revealed the significant differences between different treatments on bacterial and fungal community compositions and identified Roseiflexaceae, Sphingomonas, and Sphingobium as the bacterial biomarkers of bulk (BCK), healthy rhizosphere (BHS), and diseased rhizosphere (BIS) soils, respectively; Rhodotorula and Ascomycota_unidentified_1_1 were identified as the fungal biomarkers of bulk (FCK) and healthy rhizosphere (FHS) soils. Bacterial networks were found to be more complex and compact than fungal networks and revealed the roles of biomarkers as network keystone taxa. PVY infection further increased the connectedness among microbial taxa to improve rhizosphere microbial community stability and resistance to environmental stress. Additionally, water content (WC) played an apparent influence on bacterial community structure and diversity, and pH showed significant effects on fungal community diversity. WC and pH greatly affected the biomarkers of bacterial rhizosphere communities, whereas the biomarkers of bulk bacterial communities were significantly affected by soil nutrients, especially for Sphingobium. Overall, the rhizosphere microbial community enrichment processes were different between healthy and diseased plants by changing the community compositions and identifying different biomarkers. These findings provide insight into the assemblage of rhizosphere microbial communities and soil physicochemical properties, which contributes to a deeper understanding of the establishment of an artificial core root microbiota to facilitate plant growth and bolstering resistance mechanisms. This knowledge contributes to a deeper understanding of the establishment of an artificial core root microbiota, thereby facilitating plant growth and bolstering resistance mechanisms.

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

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

Distinct Assembly Processes Structure Planktonic Bacterial Communities Among Near- and Offshore Ecosystems in the Yangtze River Estuary

The estuarine system functions as natural filters due to its ability to facilitate material transformation, planktonic bacteria play a crucial role in the cycling of complex nutrients and pollutants within estuaries, and understanding the community composition and assembly therein is crucial for comprehending bacterial ecology within estuaries. Despite extensive investigations into the composition and community assembly of two bacterial fractions (free-living, FLB; particle-attached, PAB), the process by which bacterioplankton communities in these two habitats assemble in the nearshore and offshore zones of estuarine ecosystems remains poorly understood. In this study, we conducted sampling in the Yangtze River Estuary (YRE) to investigate potential variations in the composition and community assembly of FLB and PAB in nearshore and offshore regions. We collected 90 samples of surface, middle, and bottom water from 16 sampling stations and performed 16S rRNA gene amplicon analysis along with environmental factor measurements. The results unveiled that the nearshore communities demonstrated significantly greater species richness and Chao1 indices compared to the offshore communities. In contrast, the nearshore communities had lower values of Shannon and Simpson indices. When compared to the FLB, the PAB exhibit a higher level of biodiversity and abundance. However, no distinct alpha and beta diversity differences were observed between the bottom, middle, and surface water layers. The community assembly analysis indicated that nearshore communities are predominantly shaped by deterministic processes, particularly due to heterogeneous selection of PAB; In contrast, offshore communities are governed more by stochastic processes, largely due to homogenizing dispersal of FLB. Consequently, the findings of this study demonstrate that nearshore and PAB communities exhibit higher levels of species diversity, while stochastic and deterministic processes exert distinct influences on communities among near- and offshore regions. This study further sheds new light on our understanding of the mechanisms governing bacterial communities in estuarine ecosystems.

Depth significantly affects plastisphere microbial evenness, assembly and co-occurrence pattern but not richness and composition

Microplastics have become one of the hot concerns of global marine pollution. In recent years, diversity and abiotic influence factors of plastisphere microbial communities were well documented, but our knowledge of their assembly mechanisms and co-occurrence patterns remains unclear, especially the effects of depth on them. Here, we collected microorganisms on microplastics to investigate how ocean depth affects on microbial diversity, community composition, assembly processes and co-occurrence patterns. Our results indicated that there were similar microbial richness and community compositions but microbial evenness and unique microbes were obviously different in different ocean layers. Our findings also demonstrated that deterministic processes played dominant roles in the assembly of the mesopelagic plastisphere microbial communities, while the bathypelagic microbial community assembly was mainly shaped by stochastic processes. In addition, the co-occurrence networks suggested that the relationships between microorganisms in the mesopelagic layer were more complex and stable than those in the bathypelagic layer. Simultaneously, we also found that Proteobacteria and Actinobacteriota were the most abundant keystones which played important roles in microbial co-occurrence networks at both layers. This study enhanced our understanding of microbial diversity, assembly mechanism, and co-occurrence pattern on plastisphere surfaces, and provided useful insights into microorganisms capable of degrading plastics and microbial remediation.

Iron oxide-supported gold nanoparticle electrode for simultaneous detection of arsenic and sulfide on-site

The environmental behavior of arsenic (As) has garnered significant attention due to its hazardous nature. The fate of As often couples with sulfide, thus co-detecting arsenic and sulfide on-site is crucial for comprehending their geochemical interactions. While electrochemical methods are suitable for on-site chemical analysis, there currently exists no electrode capable of simultaneously detecting both arsenic and sulfide. To address this, we developed a dual-metal electrode consisting of iron oxide-encased carbon cloth loaded with gold nanoparticles (Au/FeOx/CC) using the electrochemical deposition method. This electrode enables square wave stripping voltammetry (SWASV) binary detection of As and sulfide. Comparison experiments reveal that the reaction sites for sulfide primarily reside on FeOx, while the interface synergy of iron oxide and gold nanoparticles enhances the response to arsenite (AsIII). Arsenate (AsV) is directly reduced to As0 on Fe0, obviating the need for an external reducing agent. The electrode achieves detection limits of 1.5 μg/L for AsV, 0.25 μg/L for AsIII, and 11.6 μg/L for sulfide at mild conditions (pH 7.8). Field validation was conducted in the Tengchong geothermal hot spring region, where the electrochemical method exhibited good correlation with the standard methods: Total As (r = 0.978 vs. ICP-MS), AsIII (r = 0.895 vs. HPLC-ICP-MS), and sulfide (r = 0.983 vs. colorimetric method). Principal component analysis and correlation analysis suggest that thioarsenic, could potentially be positive interferents for AsIII. However, this interference can be anticipated and mitigated by monitoring the abundance of sulfide. The study provides new insights and problems for the electrochemical detection of coexisted As and sulfide.

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.

The combination of multiple environmental stressors strongly alters microbial community assembly in aquatic ecosystems

Microorganisms play a critical role in maintaining the delicate balance of ecosystem services. However, the assembly processes that shape microbial communities are vulnerable to a range of environmental stressors, such as climate change, eutrophication, and the use of herbicides. Despite the importance of these stressors, little is known about their cumulative impacts on microbial community assembly in aquatic ecosystems. To address this knowledge gap, we established 48 mesocosm experiments that simulated shallow lake ecosystems and subjected them to warming (including continuous warming (W) and heat waves (H)), glyphosate-based herbicides (G), and nutrient loading (E). Our study revealed that in the control group, both deterministic and stochastic processes codominated the assembly of microbial communities in water, whereas in sediment, the processes were primarily stochastic. Interestingly, the effects of multiple stress factors on assembly in these two habitats were completely opposite. Specifically, stressors promoted the dominance of stochastic processes in water but increased the importance of deterministic processes in sediment. Furthermore, warming amplified the effects of herbicides but exerted an opposite and stronger influence on assembly compared to nutrients, emphasizing the complexity of these mechanisms and the significance of considering multiple stressors. The interaction of some factors significantly affected assembly (p < 0.05), with the effects of WEG being most pronounced in water. Both water and sediment exhibited homogeneous assembly of microbial communities (mean NTI >0), but the phylogenetic clustering of microbial communities in water was more closely related (NTI >2). Our research revealed the response model of microbial community assembly in aquatic ecosystems to multiple environmental stresses, such as agricultural pollution, climate change, and eutrophication, and indicated that microbial community changes in sediment may be an important predictor of lake ecosystem development. This provides scientific evidence that better environmental management can reduce impacts on aquatic ecosystems under the threat of future warming.

Lacustrine plastisphere: Distinct succession and assembly processes of prokaryotic and eukaryotic communities and role of site, time, and polymer types

Microplastics as a carrier can promote microbial diffusion, potentially influencing the ecological functions of microbial communities in aquatic environments. However, our understanding of the assembly mechanism of microbial communities on different microplastic polymers in freshwater lakes during succession is still insufficient, especially for the eukaryotes. Here, the colonization time, site, and polymer types of microplastics were comprehensively considered to investigate the composition and assembly of prokaryotic and eukaryotic communities and their driving factors during the lacustrine plastisphere formation. Results showed that the particle-associated microorganisms in water were the main source of the plastisphere prokaryotes, while the free-living microorganisms in water mainly accounted for the plastisphere eukaryotes. The response of prokaryotic communities to different microplastic polymers was stronger than eukaryotic communities. The assembly of plastisphere prokaryotic communities was dominated by homogenizing processes (mainly homogenous selection), while the assembly of eukaryotic communities was dominated by differentiating processes (mainly dispersal limitation). Colonization time was an important factor affecting the composition of prokaryotic and eukaryotic communities during the formation of the plastisphere. The Chao1 richness of prokaryotic communities in the plastisphere increased with the increase of colonization time, whereas the opposite was true in eukaryotic communities. This differential response of species diversity and composition of prokaryotic and eukaryotic communities in the plastisphere during dynamic succession could lead to their distinct assembly processes. Overall, the results suggest that distinct assembly of microbial communities in the plastisphere may depend more on specific microbial sub-communities and colonization time than polymer types and colonization site.

Bacterial and Microeukaryotic Community Compositions and Their Assembly Processes in Lakes on the Eastern Qinghai-Tibet Plateau

Bacterial and microeukaryotic community compositions and their assembly processes have remained challenging and remained unclear in lake ecosystems on the Qinghai-Tibet Plateau (QTP). We revealed the diversity and community compositions, driving factors, ecological assembly processes, and co-occurrence networks of bacterial and microeukaryotic communities in water bodies of the eight lake ecosystems across the Eastern QTP. The results demonstrated that the predominant bacteria in most samples were Proteobacteria, with an average relative abundance of 41.78%, whereas the most abundant of microeukaryotes differed among the sample sites. The redundancy analysis revealed that latitude and pH were the most important driving factors in shaping the bacterial and microeukaryotic community compositions. Homogeneous selection (56.40%) was the dominant process in assembling the bacterial communities, whereas dispersal limitation (67.24%) was the major process in governing the microeukaryotic communities. Furthermore, dissolved organic carbon and salinity were the major factors mediating the balance of deterministic and stochastic assembly processes in the bacterial and microeukaryotic communities. Both the bacterial and microeukaryotic community co-occurrence networks exhibited topological features of modularity and non-random topological features. The results offer insights into the mechanisms underpinning bacterial and microeukaryotic diversities and communities in the lake ecosystems on the QTP.

Coupling of submerged macrophytes and epiphytic biofilms reduced methane emissions from wetlands: Evidenced by an antibiotic inhibition experiment

Wetlands are the largest natural methane source, but how submerged macrophytes affect methane emission remains controversial. In this study, the impacts of submerged macrophytes on methane fluxes, water purification, and epiphytic microbial community dynamics were investigated in simulated wetlands (with and without Hydrilla verticillata) treated with norfloxacin (NOR) for 24 days. Mean methane fluxes were significantly lower in treatments with Hydrilla verticillata (56.84-90.94 mg/m2/h) than bulks (65.96-113.21 mg/m2/h) (p < 0.05) during the experiment regardless of NOR. The relative conductivity (REC) values, H2O2, and malondialdehyde (MDA) contents increased in plant leaves, while water nutrients removal rates decreased with increasing NOR concentration at the same sampling time. The partial least squares path model analysis revealed that plant physiological indices and water nutrients positively affected methane fluxes (0.72 and 0.49, p < 0.001). According to illumina sequencing results of 16S rRNA and pmoA genes, α-proteobacteria (type II) and γ-proteobacteria (type I) were the dominant methanotroph classes in all epiphytic biofilms. The ratio of type I/type II methanotrophs and pmoA gene abundance in epiphytic biofilm was considerably lower in treatment with 16 mg/L NOR than without it (p < 0.05). pmoA gene abundance was negatively correlated with methane fluxes (p < 0.05). Additionally, the assembly of epiphytic bacterial community was mainly governed by deterministic processes, while stochastic dispersal limitation was the primary assembly process in the epiphytic methanotrophic community under NOR stress. The deterministic process gained more importance with time both in bacterial and methanotrophic community assembly. Network analysis revealed that relationships among bacteria in epiphytic biofilms weakened with time but associations among methanotrophic members were enhanced under NOR stress over time. It could be concluded that submerged macrophytes-epiphytic biofilms symbiotic system exhibited potential prospects to reduce methane emissions from wetlands under reasonable management.

Benthic microbial biogeographic trends in the North Sea are shaped by an interplay of environmental drivers and bottom trawling effort

Microbial composition and diversity in marine sediments are shaped by environmental, biological, and anthropogenic processes operating at different scales. However, our understanding of benthic microbial biogeography remains limited. Here, we used 16S rDNA amplicon sequencing to characterize benthic microbiota in the North Sea from the top centimeter of 339 sediment samples. We utilized spatially explicit statistical models, to disentangle the effects of the different predictors, including bottom trawling intensity, a prevalent industrial fishing practice which heavily impacts benthic ecosystems. Fitted models demonstrate how the geographic interplay of different environmental and anthropogenic drivers shapes the diversity, structure and potential metabolism of benthic microbial communities. Sediment properties were the primary determinants, with diversity increasing with sediment permeability but also with mud content, highlighting different underlying processes. Additionally, diversity and structure varied with total organic matter content, temperature, bottom shear stress and bottom trawling. Changes in diversity associated with bottom trawling intensity were accompanied by shifts in predicted energy metabolism. Specifically, with increasing trawling intensity, we observed a transition toward more aerobic heterotrophic and less denitrifying predicted metabolism. Our findings provide first insights into benthic microbial biogeographic patterns on a large spatial scale and illustrate how anthropogenic activity such as bottom trawling may influence the distribution and abundances of microbes and potential metabolism at macroecological scales.

Linking ecological niches to bacterial community structure and assembly in polluted urban aquatic ecosystems

Introduction

Bacterial communities play crucial roles in the functioning and resilience of aquatic ecosystems, and their responses to water pollution may be assessed from ecological niches. However, our understanding of such response patterns and the underlying ecological mechanisms remains limited.

Methods

In this study, we comprehensively investigated the effects of water pollution on the bacterial structure and assembly within different ecological niches, including water, sediment, submerged plant leaf surfaces, and leaf surfaces, using a 16S high-throughput sequencing approach.

Results

Ecological niches had a greater impact on bacterial community diversity than pollution, with a distinct enrichment of unique dominant phyla in different niches. This disparity in diversity extends to the bacterial responses to water pollution, with a general reduction in α-diversity observed in the niches, excluding leaf surfaces. Additionally, the distinct changes in bacterial composition in response to pollution should be correlated with their predicted functions, given the enrichment of functions related to biogeochemical cycling in plant surface niches. Moreover, our study revealed diverse interaction patterns among bacterial communities in different niches, characterized by relatively simply associations in sediments and intricate or interconnected networks in water and plant surfaces. Furthermore, stochastic processes dominated bacterial community assembly in the water column, whereas selective screening of roots and pollution events increased the impact of deterministic processes.

Discussion

Overall, our study emphasizes the importance of ecological niches in shaping bacterial responses to water pollution. These findings improve our understanding of the complicated microbial response patterns to water pollution and have ecological implications for aquatic ecosystem health.

Microbial community structure and its driving mechanisms in the Hangbu estuary of Chaohu Lake under different sedimentary areas

Estuaries are known for their high ecological diversity and biological productivity. Sediment microorganisms, as crucial components of estuarine ecosystems, play a pivotal role in reflecting the intricate and dynamic ecological niches. However, our research on microbial community characteristics in estuarine ecosystems under different sedimentary types remains limited. In this study, we collected a total of 27 samples from three sampling sites at Hangbu estuary in Chaohu Lake, and three sedimentary areas were classified based on the overlying water flow conditions and sediment particle properties to elucidate their microbial community structure, environmental drivers, assembly processes, and co-occurrence network characteristics. Our results showed significant differences in microbial community composition and diversity among three sedimentary areas. Redundancy analysis indicated that the differences in microbial community composition at the OTU level among the three sedimentary areas were mainly determined by nitrate-nitrogen, temperature, and water content. Phylogenetic bin-based null model analysis revealed that temperature was a key factor influencing deterministic processes among the three sedimentary areas, while stochastic processes predominantly governed the assembly of microbial communities. In addition, co-occurrence network analysis demonstrated that the network in the hydraulically driven sedimentary area of the lake, consisting mainly of medium and fine silt, had the highest complexity, stability, and cohesion, but was missing potential keystone taxa. The remaining two sedimentary areas had 5 and 8 potential keystone taxa, respectively. Overall, our study proposes the delineation of sedimentary types and comprehensively elucidates the microbial community characteristics under different sedimentary areas, providing a new perspective for studying sediment microbial community structure and helping future scholars systematically study ecological dynamics in estuaries.

The Impact of Warming on Assembly Processes and Diversity Patterns of Bacterial Communities in Mesocosms

Bacteria in lake water bodies and sediments play crucial roles in various biogeochemical processes. In this study, we conducted a comprehensive analysis of bacterioplankton and sedimentary bacteria community composition and assembly processes across multiple seasons in 18 outdoor mesocosms exposed to three temperature scenarios. Our findings reveal that warming and seasonal changes play a vital role in shaping microbial diversity, species interactions, and community assembly disparities in water and sediment ecosystems. We observed that the bacterioplankton networks were more fragile, potentially making them susceptible to disturbances, whereas sedimentary bacteria exhibited increased stability. Constant warming and heatwaves had contrasting effects: heatwaves increased stability in both planktonic and sedimentary bacteria communities, but planktonic bacterial networks became more fragile under constant warming. Regarding bacterial assembly, stochastic processes primarily influenced the composition of planktonic and sedimentary bacteria. Constant warming intensified the stochasticity of bacterioplankton year-round, while heatwaves caused a slight shift from stochastic to deterministic in spring and autumn. In contrast, sedimentary bacteria assembly is mainly dominated by drift and remained unaffected by warming. Our study enhances our understanding of how bacterioplankton and sedimentary bacteria communities respond to global warming across multiple seasons, shedding light on the complex dynamics of microbial ecosystems in lakes.

Leaf litter mixtures alter decomposition rate, nutrient retention, and bacterial community composition in a temperate forest

Litter decomposition is a key step in global biogeochemical cycling. In forest ecosystems, litter from different tree spec1ies often decompose together. Although species diversity is widely acknowledged to accelerate decomposition through the regulation of nutrient transfer between litter and decomposer communities, the underlying mechanism remains unclear. To explore the association between the bacterial community and mixed-litter chemical transformation, we conducted a one-year litter mixing decomposition experiment using leaf litter from four dominant tree species in Mount Tai (Eastern China), Robinia pseudoacacia, Quercus acutissima, Pinus tabulaeformis, and Pinus densiflora. Our results showed that: 1) Mass loss of leaf litter mixtures was significantly faster than that of leaf litter monocultures, except for R. pseudoacacia. Litter mixtures without R. pseudoacacia showed non-additive synergistic effects, whereas litter mixtures with R. pseudoacacia exerted additive effects; 2) Litter species in the absence of R. pseudoacacia significantly decreased the nutrient retention rates of litter mixtures compared to those of monocultures; 3) Litter mixtures with or without R. pseudoacacia showing additive and non-additive effects in monocultures had a distinct bacterial community structure; 4) Bacterial community structure was also modified by initial litter traits; carbon (C), nitrogen (N), and phosphorus (P) concentrations in monocultures; N/P and C/N ratios of mixtures with R. pseudoacacia; and the lignin/N ratio of mixtures without R. pseudoacacia. Overall, these findings indicate that tree species diversity controls decomposition and nutrient cycling, implying that an appropriate species community composition is beneficial to maintaining forest ecosystems.

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.

Exploring the bacterial diversity and composition with special emphasis on pathogens in ship ballast water and sediments using full-length 16S rRNA gene sequencing

Accurate detecting bacterial communities in ballast water and sediments supports risk management. This study uses full-length 16S rRNA gene sequencing to investigate the bacterial communities in ballast water and sediments, focusing on detecting pathogens. The results indicate that full-length sequencing more accurately reveals the species diversity. There is a significant difference (P < 0.05) in bacterial communities between ballast water and sediments, despite both being dominated by the Proteobacteria phylum. Thirty human and fish pathogens were identified by full-length sequencing, yet only five pathogens were detected from V3-V4 sequencing. Notably, emerging pathogens such as Citrobacter freundii and Nocardia nova are detected in samples, which are harmful to aquaculture and human health. Several opportunistic pathogens were also identified. In summary, this study provides important insights into the bacterial communities in ballast water and sediments, highlighting the need for strict management.

Stronger effects of simultaneous warming and precipitation increase than the individual factor on soil bacterial community composition and assembly processes in an alpine grassland

Composition and traits of soil microbial communities that closely related to their ecological functions received extensive attention in the context of climate changes. We investigated the responses of soil bacterial community structure, traits, and functional genes to the individual warming, precipitation increases, and the combination of warming and precipitation increases in an alpine grassland in the Qinghai-Tibet Plateau that is experiencing warming and wetting climate change. Soil properties, plant diversity and biomass were measured, and the ecological processes and environmental factors driving bacterial community changes were further explored. Results indicated that the Shannon diversity of soil bacterial communities decreased significantly only under the combination treatment, which might due to the decreased plant diversity. Soil bacterial community composition was significantly correlated with soil pH, and was affected obviously by the combination treatment. At the taxonomic classification, the relative abundance of Xanthobacteraceae and Beijerinckiaceae increased 127.67 and 107.62%, while the relative abundance of Rubrobacteriaceae and Micromonosporaceae decreased 78.29 and 54.72% under the combination treatment. Functional genes related to nitrogen and phosphorus transformation were enhanced in the combination treatment. Furthermore, weighted mean ribosomal operon copy numbers that positively correlated with plant aboveground biomass increased remarkably in the combination treatment, indicating a trend of life-history strategies shift from oligotrophic to copiotrophic. Stochastic processes dominated soil bacterial community, and the proportion of stochasticity increased under the combination treatment. Our study highlights the significant effects of simultaneous warming and precipitation increase on soil bacterial community.

Synergistic effect of biotic and abiotic factors drives microbiota succession and assembly in medium-temperature Daqu

BACKGROUND

The feasibility of fortification techniques to improve the quality of medium-temperature Daqu (MTD) by inoculation functional isolates has been demonstrated. However, it is unclear what is the effect of inoculation on the controllability during the MTD fermentation process. Here, inoculated a single strain of Bacillus licheniformis, and the microbiota composed of Bacillus velezensis and Bacillus subtilis, were used to investigate the synergistic effect of biotic and abiotic factors on the succession and assembly of the MTD microbiota during the process.

RESULTS

The biotic factors promoted the proliferation of microorganisms that arrived early at the MTD. Subsequently, this alteration might inhibit microorganisms that colonized later in the MTD microecosystem, thereby assembling a different but more stable microbial community. Moreover, the biotic factors making bacterial community assembly were dominated by variable selection earlier, whereas the fungal community assembly was dominated mainly by extreme abiotic factors rather than biotic factors. Interestingly, fermentation temperature and moisture were significantly associated with the succession and assembly of the fortified MTD community. Meanwhile, the effect of the environmental variables on endogenous variables was also significant. Thus, changes in endogenous variables could be mitigated by adjusting environmental variables to regulate the process of MTD fermentation.

CONCLUSION

Biotic factors cause rapid changes of the microbiota during the MTD fermentation process, which could be controlled indirectly by regulating environmental variables. Meanwhile, a more stable MTD ecological network might be beneficial for enhancing the stability of MTD quality. © 2023 Society of Chemical Industry.

Identification and relative contributions of environmental driving factors for abundant and rare bacterial taxa to thermal stratification evolution

The thermal stratification of reservoir affects water quality, and water quality evolution is largely driven by microorganisms. However, few studies have been conducted on the response of abundant taxa (AT) and rare taxa (RT) to thermal stratification evolution in reservoirs. Here, using high-throughput absolute quantitative techniques, we examined the classification, phylogenetic diversity patterns, and assembly mechanisms of different subcommunities during different periods and investigated the key environmental factors driving community construction and composition. The results showed that community and phylogenic distances of RT were higher than AT (P < 0.001), and community and phylogenic distances of the different subcommunities were significantly positively correlated with the dissimilarity of environmental factors (P < 0.001). Nitrate (NO₃^--N) was the main driving factor of AT and RT in the water stratification period, and Mn was the main driving factor in the water mixing period (MP) based on redundancy analysis (RDA) and random forest analysis (RF). The interpretation rate of key environmental factors based on the selected indicator species in RT by RF was higher than that of AT, and Xylophilus (10.5%) and Prosthecobacter (0.1%) had the highest average absolute abundance in AT and RT during the water stable stratification period (SSP), whereas Unassigned had the highest abundance during the MP and weak stratification period (WSP). The network of RT and environmental factors was more stable than that of AT, and stratification made the network more complex. NO₃^--N was the main node of the network during the SSP, and manganese (Mn) was the main node during the MP. Dispersal limitation dominated community aggregation, the proportion of AT was higher than that of RT. Structural Equation Model (SEM) showed that NO₃^--N and temperature (T) had the highest direct and total effects on β-diversity of AT and RT for the SP and MP, respectively.