Bacterial Community Assembly Research Articles

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

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

Differences in Biogeographic Patterns and Mechanisms of Assembly in Estuarine Bacterial and Protist Communities.

As transitional ecosystems between land and sea, estuaries are characterized by a unique environment that supports complex and diverse microbial communities. A comprehensive analysis of microbial diversity and ecological processes at different trophic levels is crucial for understanding the ecological functions of estuarine ecosystems. In this study, we systematically analyzed the diversity patterns, community assembly, and environmental adaptability of bacterial and protist communities using high-throughput sequencing techniques. The results revealed a higher alpha diversity for the bacteria than for protists, and the beta diversity pattern was dominated by species turnover in both communities. In addition, the two community assemblages were shown to be dominated by deterministic and stochastic processes, respectively. Furthermore, our results emphasized the influence of the local species pool on microbial communities and the fact that, at larger scales, geographic factors played a more significant role than environmental factors in driving microbial community variation. The study also revealed differences in environmental adaptability among different microbial types. Bacteria exhibited strong adaptability to salinity, while protists demonstrated greater resilience to variations in dissolved oxygen, nitrate, and ammonium concentrations. These results suggested differences in environmental adaptation strategies among microorganisms at different trophic levels, with bacteria demonstrating a more pronounced environmental filtering effect.

Tracing microbial community across endophyte-to-saprotroph continuum of Cinnamomum camphora (L.) Presl leaves considering priority effect of endophyte on litter decomposition

Endophytes typically coexist with plants in symbiosis and transition into the saprobic system as plant tissues senesce, participating in the decomposition process of litter. However, the dynamic changes of endophytic communities during this process and their role in litter decomposition remain unclear. This study tracked the microbial composition across the transition from live leaves to litter in Cinnamomum camphora (L.) Presl (C. camphora), evaluating the contribution of endophytes to litter decomposition by examining microbial diversity, community assembly, and co-occurrence networks along the endophyte-to-saprotroph spectrum. The results revealed increasing bacterial diversity but stable fungal diversity, and the diversity of endogenous microbes is mirrored this in the saprophytic phase. Bacterial community assembly was characterized by deterministic processes during the symbiotic phase, shifted to stochastic processes during the saprophytic phase. In contrast, fungal community assembly was predominantly driven by stochastic processes throughout the continuum. Out of the 49 keystone taxa identified, only Pseudorhodoplanes sinuspersici demonstrated a significant positive correlation with community assembly. All identified bacterial keystone taxa during the saprophytic phase originated from endophytic sources, and around 80% of the fungal keystone taxa in the initial stages of decomposition were similarly endophytic in origin. Additionally, 60% of the dominant bacterial taxa and 28% of the dominant fungal taxa at the commencement of decomposition were of endophytic descent. This suggests that endogenous microbes possess the potential to evolve into both keystone and dominant taxa during the saprophytic phase. Endogenous keystone and dominant microbes both exhibited significant correlations with microbial network, indicating their substantial ecological presence in microbial community. Both endogenous keystone and dominant taxa exerted significant potential influences on litter decomposition. Overall, during the saprophytic phase, endophytes are likely to influence the assemblage of microbial communities, the network structure, and decomposition-related functions. Specifically, it appears that bacterial endophytes may possess a greater adaptability to the decomposition processes of leaf litter compared to their fungal counterparts.

Machine Learning and Multi-Omics Integration to Reveal Biomarkers and Microbial Community Assembly Differences in Abnormal Stacking Fermentation of Sauce-Flavor Baijiu.

Stacking fermentation is critical in sauce-flavor Baijiu production, but winter production often sees abnormal fermentations, like Waistline and Sub-Temp fermentation, affecting yield and quality. This study used three machine learning models (Logistic Regression, KNN, and Random Forest) combined with multi-omics (metagenomics and flavoromics) to develop a classification model for abnormal fermentation. SHAP analysis identified 13 Sub-Temp Fermentation and 9 Waistline microbial biomarkers, along with 9 Sub-Temp Fermentation and 12 Waistline flavor biomarkers. Komagataeibacter and Gluconacetobacter are key for normal fermentation, while Ligilactobacillus and Lactobacillus are critical in abnormal cases. Excessive acid and ester markers caused unbalanced aromas in abnormal fermentations. Additionally, ecological models reveal the bacterial community assembly in abnormal fermentations was influenced by stochastic factors, while the fungal community assembly was influenced by deterministic factors. RDA analysis shows that moisture significantly drove Sub-Temp fermentation. Differential gene analysis and KEGG pathway enrichment identify metabolic pathways for flavor markers. This study provides a theoretical basis for regulating stacking fermentation and ensuring Baijiu quality.

Forest management impacts on soil phosphorus cycling: Insights from metagenomics in Moso bamboo plantations.

Bamboo forests are crucial ecosystems and provide essential ecological and economic services in both tropical and subtropical regions. Soil phosphorus (P), a vital nutrient for plant growth, is fundamental to the productivity and health of bamboo forests. However, the microbial mechanisms through which management practices affect soil P processes in bamboo forests remain poorly understood. This study employed metagenomics to examine alterations in microbial P cycling in Moso bamboo plantations under three distinct management conditions. The results revealed that intensive management (M2, annual fertilization, selective harvesting, and understory vegetation removal) significantly increased soil inorganic P (Pi) by 61.76% and 87.39% compared to extensive management (M1, selective bamboo trunk and shoot harvesting every two years) and non-management (M0), respectively, while decreasing soil organic P (Po) by 50.41% and 41.05%. Forest management significantly altered the bacterial communities: Firmicutes, WPS-2, and Acidobacteriales were represented in M2, Xanthobacteraceae in M1, and Chloroflexi AD3, Acidothermus, and Subgroup_2 in M0. M2 significantly increased the community-level habitat niche breadth and weakened the deterministic process of bacterial community assembly relative to M1 and M0 (p≤0.05). Furthermore, functional metagenomics showed that the total abundance of genes related to Po mineralization, P transportation, and P regulation was significantly lower (p≤0.05) in M2 than in M0 and M1. pstA, pstB, and pstC were more abundant in M2 (p≤0.05), whereas phnN, phnI, phnG, phoA, phoD, phnC, phnD, and phnE were more abundant in M1 (p≤0.05), and phnF was significantly abundant in M0 (p≤0.05). A partial least squares path model indicated that soil bacterial community and P cycling genes had direct effects on Pi and Po, respectively. These findings enhance our understanding of the links between forest management practices and P cycling, providing insights for improving soil functionality and nutrient balance.

Spatial heterogeneity determines the gastrointestinal microbiome signatures and ecological processes that govern bacterial community assembly in sheep.

Sheep's gastrointestinal tract harbors a diverse microbial community crucial for immune system balance, nutrient digestion, and overall health. We explored the microbial community composition, community types (enterotypes), bacterial interactions, and ecological processes in 10 gastrointestinal regions of 36 six-month-old Hu sheep raised under same diets and environmental conditions. Our findings revealed a unique U-shaped pattern of bacterial diversity from the rumen to the rectum, with the lowest diversity in the jejunum. The composition and enterotypes of bacterial communities varied spatially along the gastrointestinal tract, primarily categorized into three distinct groups. The rumen exhibited the highest abundance of bacterial taxa, unique taxa, and unique functions, while the enterotypes in the three regions of the large intestine were consistent. We explored the assembly processes of bacterial communities, elucidating how they find their ecological niches based on their characteristics and environmental demands. The assembly processes in the four-chambered stomach and small intestine resembled random selection, where bacterial positioning depended on luck and chance, while in the large intestine, it appeared more deterministic, with specific bacteria likely selected based on their unique skills and environmental requirements. This study enhances our understanding of microbial coexistence and interactions in complex ecosystems, with implications for improving animal productivity, disease treatment, and the development of novel microbial formulations.

Seasonal Differences and Driving Factors of Microbial Community Structure in Wetlands Along Shores of Daihai Lake

Microorganisms play a crucial role in biogeochemical cycling within wetland ecosystems. Soil-environment-mediated seasonal changes in microbial structure require further investigation. However, the factors driving seasonal variations in the microbial abundance and diversity in the Daihai wetlands remain unclear. This study employed high-throughput sequencing technology to examine the bacterial community structure and diversity in the lakeshore zone of Daihai across different seasons and to explore the seasonal variations in the bacterial community structure and the influence of driving factors. The results indicated that Pseudomonadota and Bacteroidota dominate in spring and Pseudomonadota abundance further increases in summer, while organic-matter-decomposing microorganisms (e.g., Actinobacteriota and Bacteroidota) dominate in autumn. Microbial diversity indices indicated a significantly greater diversity in spring than in summer and autumn (p &lt; 0.05). Changes in environmental variables were strongly associated with bacterial community changes, with variations in total nitrogen, ammonium nitrogen, and soil moisture content being identified as potential key factors influencing seasonal bacterial diversity trends. Furthermore, bacterial community assembly in spring is driven by both stochastic processes and environmental selection, suggesting that abundant nutrients and organic matter promote bacterial diversity. The findings of this study provide a theoretical basis for wetland ecosystem restoration and conservation.

Different Fish Farming Patterns in Paddy Fields Substantially Impact the Bacterial Community Composition, Stability, and Assembly Processes in Paddy Water

Integrated rice–fish farming is an innovative agricultural production pattern that combines rice cultivation with fish farming, enhancing agricultural productivity and ensuring food security. Partitioned rice–fish farming, an advancement of the traditional approach, addresses challenges such as difficulties in fish harvesting and the inconveniences of mechanized operations encountered in paddy fields. To evaluate the environmental impacts of partitioned rice–fish farming on the agricultural ecosystem, we investigated the impacts of partitioned rice–fish farming on the diversity, composition, functionality, co-occurrence networks, and assembly processes of bacterial communities within paddy water. Our results revealed significantly improved Chao1, Observed species, and Pd_faith indices for the bacterial community in the partitioned rice–fish farming system. The relative abundances of the Bacteroidota, Gemmatimonadota, Proteobacteria, and Fluviicola in paddy water were altered by the partitioned system. The partitioned system considerably impacted the bacterial co-occurrence networks within the paddy water, with the planktonic bacterial co-occurrence network in rice cultivation area having more nodes (205) and edges (2085), and its robustness being significantly higher than that of other groups, resulting in a more complex and stable structure of the planktonic bacterial community. In addition, the partitioned system significantly promoted the contribution of stochastic processes to bacterial community assembly in the paddy water, with the main enhanced stochastic processes being homogenizing dispersal and drift. The total proportion of these processes for bacterial community assembly increased from 60% to 70%. Nitrate concentrations in the paddy water were remarkably associated with the water bacterial communities and contributed most to the variations in water bacterial communities. Hence, partitioned rice–fish farming is a feasible and good agricultural production pattern, and from the perspectives of bacterial community diversity and stability it offers both theoretical insights and data-supported foundations for advancing sustainable agricultural practices.

Response and Assembly Process of Soil Microbial Communities Under Different Reclamation Measures

Reclamation is essential for restoring the ecological function of soil in mining areas. However, the microbiological mechanism of soil ecological function reconstruction under different reclamation measures still needs to be clarified. Clarifying the characteristics of soil bacterial and fungal communities, assembly mechanisms, and their relationship with physicochemical properties under different reclamation measures is crucial for reshaping the ecological stability of soil in mining areas. Metagenomic sequencing technology was combined with the null model and neutral model to analyze the differences in soil microbial diversity, community composition, network structure, and community assembly process between the reclaimed natural recovery area （LH） and the reclamation fertilization area （MM）. The results suggested that： ① Compared with that in the LH treatment, the MM treatment significantly increased the soil nutrient content, and the total nitrogen （TN）, total phosphorus （TP）, available phosphorus （AP）, and available potassium （AK） contents increased by 34.70%, 72.72%, 468.98%, and 45.74%, respectively （P&lt;0.05）. ② The dominant bacterial and fungal communities did not change under the LH and MM treatments； however, the abundance of bacterial communities changed significantly. Compared with that in the LH treatment, the relative abundance of Acidobacteria increased significantly by 5.4% in the MM treatment, while the relative abundance of Candidatus Rokubacteria decreased significantly by 235.72% （P&lt;0.05）. Under different reclamation measures, the indicator microorganisms of bacterial and fungal communities changed. ③ Compared with that in the LH treatment, the MM treatment increased the complexity of bacterial networks, decreased the complexity of fungal networks, and increased the number of soil bacterial nodes and links. The reclamation measures transformed the key bacterial groups from Proteobacteria to Candidatus Rokubacteria and Planctomycetes. The key group of fungi was Ascomycota. 4.） The deterministic process dominated the assembly of bacterial and fungal communities. Homogeneous selection contributed the most to the bacterial community assembly in the LH treatment, and heterogeneous selection contributed the most to the MM treatment. The fungal communities were all dominated by heterogeneous selection. These results provide new insights into the soil microbial community structure and ecological function restoration in coal mining subsidence reclamation areas.

Geographic Distribution Pattern Determines Soil Microbial Community Assembly Process in Acanthopanax senticosus Rhizosphere Soil.

The geographic distribution patterns of soil microbial communities associated with cultivated Acanthopanax senticosus plants in Northeast China were investigated. High-throughput sequencing revealed that the diversity and community assembly of bacterial and fungal communities in the inter-root soil varied significantly with geographic location. The study found that bacterial communities were predominantly assembled through stochastic processes at most sites, while fungal communities showed greater variation, with both stochastic and deterministic processes involved. The complexity of bacterial-fungal co-occurrence networks also varied with longitude and latitude, demonstrating both positive and negative interactions. PICRUSt 2.0 and FUNGuild were used to predict the potential functions of soil bacterial and fungal microbiota, respectively, during different land use patterns. The average taxonomic distinctness (AVD) index indicated varying degrees of community stability across sites. Key microbial taxa contributing to community variability were identified through Random Forest modeling, with Bacteriap25 and Sutterellaceae standing out among bacteria, and Archaeorhizomyces and Clavaria among fungi. Soil chemical properties, including pH, TN, TP, EC, and SOC, significantly correlated with microbial diversity, composition, and co-occurrence networks. Structural equation modeling revealed that geographic distribution patterns directly and indirectly influenced soil chemical properties and microbial communities. Overall, the study provides insights into the geographic distribution patterns of soil microbial communities associated with A. senticosus and highlights the need for further research into the underlying mechanisms shaping these patterns.

The Reduction of Nitrogen Fertilizer Rate Shifted Soil Bacterial Community Structure in Rice Paddies

In order to achieve reasonable yield while keeping environmental risks low, nitrogen fertilizer reduction has been adopted for in rice cultivation. The response of the soil microbial community structure to this management is not fully understood. In this study, the treatments comprising conventional farming practices (330 kg ha−1), reduced N application (270 kg ha−1 and 300 kg ha−1, respectively), and a control without N application were set up in order to reveal the effects of N application rate on the soil microbial community composition in rice paddies. It was discovered that Proteobacteria, Acidobacteria, Actinobacteria, and Chloroflexi represented the most abundant bacterial phyla in all samples. The assembly of the soil bacterial community differed among the treatments, with NH4+-N, available phosphorus (AP), and organic matter (OM) as key drivers. The reduction of N application by 20% decreased soil NO3− up to 32% and increased the abundance of the total functional pathways, especially those associated with carbon fixation, N, S, and CH4 metabolism, whereas N reduction by 10% increase soil N accumulation and soil bacterial richness. In summary, a reduction of N fertilizer by up to 20% compared to the amount used in traditional practices could most effectively regulate the soil bacterial community composition and increase the predicted functional groups associated with N transformation, while maintaining lower soil nitrogen contents.

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.

Response of bacterial communities in desert grassland soil profiles to acid mine drainage pollution

Acid mine drainage (AMD) causes serious environmental pollution, which imposes stresses on soil ecosystems. Therefore, it is critical to study the responses of soil bacterial communities to AMD pollution in ecologically fragile desert grasslands. Here, the bacterial community composition, structure, and assembly processes in vertical soil profiles of an AMD contaminated desert grassland were explored using 16S rRNA high-throughput sequencing. The results showed that the surface layers of the profiles exhibited lower pH and higher heavy metals (HMs) content due to AMD influence. The AMD contamination led to reduced bacterial diversity in the surface soil layer of the profiles and significantly changed the bacterial community composition and structure. Gradients in pH, TK, TN, and HMs were the main factors driving bacterial community variability. In contrast to the uncontaminated profile, deterministic processes were important in shaping soil bacterial community in the AMD contaminated profiles. These findings will enhance understanding about the responses of soil bacteria in desert grassland soil to the environmental changes caused by AMD contamination and will improve the remediation of AMD contaminated soil.

Increased antibiotic resistance gene abundance linked to intensive bacterial competition in the phyllosphere across an elevational gradient.

Antibiotic resistance genes (ARGs) are ancient and widespread in natural habitats, providing survival advantages for microbiomes under challenging conditions. In mountain ecosystems, phyllosphere bacterial communities face multiple stress conditions, and the elevational gradients of mountains represent crucial environmental gradients for studying biodiversity distribution patterns. However, the distribution patterns of ARGs in the phyllosphere along elevational gradients, and their correlation with bacterial community structures, remain poorly understood. Here, we applied metagenomic analyses to investigate the abundance and diversity of ARGs in 88 phyllosphere samples collected from Mount Tianmu, a national natural reserve. Our results showed that the abundance of ARGs in the phyllosphere increased along elevational gradients and was dominated by multidrug resistance and efflux pumps. The composition of bacterial communities, rather than plant traits or abiotic factors, significantly affected ARG abundance. Moreover, increased ARG abundance was correlated with greater phylogenetic overdispersion and a greater proportion of negative associations in the bacterial co-occurrence networks, suggesting that bacterial competition primarily shapes phyllosphere resistomes. These findings constitute a major advance in the biodiversity of phyllosphere resistomes along elevations, emphasizing the significant impact of bacterial community structure and assembly on ARG distribution, and are essential for understanding the emergence of ARGs.

Physicochemical properties of acid sulphate soil profoundly influence the composition of rhizobacterial community of rice (Oryza sativa L.)

The soils of kari lands of Kuttanad, the ‘Rice bowl’ of Kerala, India are characterized as acid sulphate as they comprise of pyrite deposits. Productivity in these soils is at stake due to several constraints like high acidity and salinity, metal toxicity, nutrient unavailability, redox fluctuations, besides seasonal flooding. Sustainable management of acid sulphate soil is a critical priority to improve the rice output from these areas. Such soils would harbor unique innate microbial communities with definite abilities which could be exploited further for their sustainable amelioration. Development of inoculant technology with soil and crop specific beneficial microbial agents is expected to boost the production potential of kari soils. However, the soil parameters would impose a great influence on the rhizobacterial community development in these geologically distinct soils. We studied the rhizobacterial communities (at the family level), associated with rice grown in five acid sulphate (Purakkad, Vaikom, Ambalappuzha, Thakazhi and Kallara) as well as one non-acid sulphate (Muhamma) soil series of geographically unique Kuttanad region. We also examined the effects of soil physicochemical attributes on shaping the rhizosphere bacterial community assemblage. The soil physicochemical attributes were analyzed using standard procedures and correlations existing amongst them were also determined. A metagenomic approach was adopted to study the rhizobacterial communities (family level) and were correlated with soil parameters using canonical correspondence analysis (CCA). Compared to other acid sulphate regions, Thakazhi and Kallara soils indicated higher electrical conductivity, available nitrogen, potassium, organic carbon, aluminium as well as iron and lowest pH and available phosphorus. Intense significant relationships were exhibited amongst the acid sulphate properties and soil nutrient contents. The taxa summary after the Illumina MiSeq sequencing revealed the abundant rhizobacterial families in the soil samples as Anaerolineaceae, Ktedonobacteriaceae, Acidothermaceae, Acidimicrobiaceae, Clostridiaceae, Nocardioidaceae, Xanthobacteraceae, Methanobacteriaceae, Sphingomonadaceae and Peptostreptococcaceae. Acidothermaceae (14%) and Acidimicrobiaceae (12%) were found abundant exclusively in highly acid sulphate soil samples. Moreover, only a few shared taxa were observed between the soil samples, which denoted the uniqueness of each sample in terms of rhizobacterial communities. The shared taxa between highly acidic sampling areas include members of Acidothermaceae, Ktedonobacteraceae, Acidimicrobiaceae, Micrococcaceae, Stellaceae and Anaerolineaceae. CCA showed that pH, EC and Al content were the soil properties governing the bacterial assembly in the rhizosphere of actively tillering rice grown in acid sulphate soil followed by P and K. The data generated in the present study are considered to be of use in developing consortia of kari soil specific rice rhizosphere microbial agents which could be used as inoculants in future.

Long-term intercropping shaped soil bacterial microbiome composition and structure of maize fields in a semiarid region

Intercropping has gained attention for its potential to enhance soil health and increase crop yields in agroecosystems, in which soil microbial community play a key regulatory role. Bacteria is critical for a variety of soil biological processes, so promoting the understanding of soil microbiome within bacteria can improve the agricultural management practices. Here, the responses of soil bacterial community composition, functions, and assembly to long-term intercropping were assessed using 16S rRNA gene sequencing in the mountainous area of Southern Ningxia, spanning approximately 10 years until summer 2022. The experiment comprised three field treatments: maize monoculture (MM), intercropping of maize and potato (MP) and intercropping of maize and soybean (MS). The results showed that intercropping altered the relative abundance of major phyla and genera, and life-history strategies, mainly influenced by microbial biomass carbon and enzyme activities. The ratio of K- to r-strategy bacteria showed a trend of MP (0.77) > MM (0.76)> MS (0.56). Soil bacterial community structure of MP and MS was significantly different and similar to that of MM, respectively. Bugbase and PICRUSt2 analysis predicted the phenotype and metabolic pathways of soil bacterial community in maize fields, revealing that maize-legume intercropping increased the oxygen tolerance of soil bacteria. Moreover, intercropping enhanced the co-occurrence network complexity and the roles of homogeneous selection and drift, while bacterial community assembly was mainly driven by stochastic processes in MM (62.32 %), MP (60.68 %), and MS (59.17 %) soils. A variety of complex factors strongly governed bacterial community and assembly processes, such as soil nutrient elements and moisture. In brief, the study revealed the effect of intercropping on soil bacterial community, contributing to the further understanding of agricultural management practices.

Bioremediation Potential of Rhodococcus qingshengii PM1 in Sodium Selenite-Contaminated Soil and Its Impact on Microbial Community Assembly.

Soil microbial communities are particularly sensitive to selenium contamination, which has seriously affected the stability of soil ecological environment and function. In this study, we applied high-throughput 16S rRNA gene sequencing to examine the effects of low and high doses of sodium selenite and the selenite-degrading bacterium, Rhodococcus qingshengii PM1, on soil bacterial community composition, diversity, and assembly processes under controlled laboratory conditions. Our results indicated that sodium selenite and strain PM1 were key predictors of bacterial community structure in selenium-contaminated soils. Exposure to sodium selenite initially led to reductions in microbial diversity and a shift in dominant bacterial groups, particularly an increase in Actinobacteria and a decrease in Acidobacteria. Sodium selenite significantly reduced microbial diversity and simplified co-occurrence networks, whereas inoculation with strain PM1 partially reversed these effects by enhancing community complexity. Ecological modeling, including the normalized stochasticity ratio (NST) and Sloan's neutral community model (NCM), suggested that stochastic processes predominated in the assembly of bacterial communities under selenium stress. Null model analysis further revealed that heterogeneous selection and drift were primary drivers of community turnover, with PM1 inoculation promoting species dispersal and buffering against the negative impacts of selenium. These findings shed light on microbial community assembly mechanisms under selenium contamination and highlight the potential of strain PM1 for the bioremediation of selenium-affected soils.

Biotic Interaction Underpins the Assembly Processes of the Bacterial Community Across the Sediment-Water Interface in a Subalpine Lake.

The sediment-water interface is the most active region for biogeochemical processes and biological communities in aquatic ecosystems. As the main drivers of biogeochemical cycles, the assembly mechanisms and the distribution characteristics of microbial communities at this boundary remain unclear. This study investigated the microbial communities across the sediment-water interface in a natural subalpine lake in China. The results indicated that the diversity of bacterial communities in middle sediment was significantly higher than that in overlying water and other sediments (p < 0.001). Pearson's correlation analysis indicated that the diversity was significantly influenced by biotic factors (e.g., diversity of fungus, protozoan and alga) and physicochemical parameters (e.g., total carbon, total organic carbon, nitrate, ammonium and pH) (p < 0.01). Null model analysis revealed that the homogeneous selection dominated the assembly of the bacteria community in sediment, whereas the heterogeneous selection dominated that in overlying water. The least squares path analysis showed that interactions between protozoa and bacteria had a greater impact on bacterial community assembly (p < 0.001). Important taxa influence the assembly by regulating biotic interactions. These findings provided a basis for understanding the importance of biotic interactions in maintaining subalpine lakes' ecosystems across the sediment-water interface.

Interpretation of bacterial composition patterns and community assembly processes in the rhizosphere soil of tea trees in karst areas

Research background and purposeSoil microorganisms that are closely related to plants are important factors affecting plant health. Therefore, elucidating the abundant and rare bacterial species in soil associated with plant diseases is crucial for understanding ecological processes, maintaining the stability of microecological environments, and formulating microbial strategies that are consistent with modern agricultural development.ResultsTea leaf blight leads to an increase in bacterial diversity in the rhizosphere. Random processes dominate the assembly of abundant and rare taxa, while abundant taxa are also influenced by deterministic processes. In the co-occurrence network, the increase in bacterial community diversity mediated by tea cloud leaf blight enhances the stability of the network. Meanwhile, the proportion of positive correlation between rare taxa is relatively high, and the relationship between rare taxa and intermediate taxa is closer. This highly diverse bacteria community maintained the structure and stability of the community to a certain extent.ConclusionThe rare taxa in the rhizosphere and the rhizosphere bacterial community mediated by tea leaf blight have high diversity, which is of great significance for maintaining the stability of the rhizosphere bacterial ecological network. In the future, we will further explore the dynamic changes and interaction patterns of the species in the rhizosphere soil affected by tea tree diseases, and their ecological functions and importance in areas of habitat fragmentation. Overall, there are many microbial resources in the rhizosphere microbiota under the influence of plant diseases that can be used for agricultural practice. The results of this study will enrich the insights into ecodynamics of bacteria in karst areas, especially in karst tea gardens.

Influences of Community Coalescence on the Assembly of Bacterial Communities of the Small-Scale Complex Aquatic System from the Perspective of Bacterial Transmission, Core Taxa, and Co-occurrence Patterns

Recirculating aquaculture and aquaponics are considered sustainable aquaculture models playing important roles in animal-derived protein supply. In these aquaculture systems, microorganisms are crucial for the system stability. The community coalescence by mixing substances and microorganisms from various microhabitats under hydraulic forces is important for shaping the bacterial communities in these small-scale complex systems. However, the influences of community coalescence on bacterial communities remain rarely revealed in these systems. In this study, aquaponics (APS) and recirculating aquaculture (RAS) systems were set up to explore the bacterial community coalescence across different microhabitats, including water, fish feces, biofilter biofilms, and plant rhizosphere environment. Our results showed that diversity and compositions varied across different microhabitats in both systems. However, bacterial transmissions across these microhabitats differed between systems. The core microbiome of the RAS and APS were formed under community coalescence with the highest contribution of bacterial taxa derived from the fish feces. Nevertheless, the plant rhizosphere bacterial community also contributed to the core microbiome of the APS. Furthermore, the core taxa showed a higher average degree than the other nodes in the bacterial community networks in all microhabitats except for the plant rhizosphere environment, implying the important roles of core taxa in maintaining these bacterial community networks. Our results provide new insights into the assembly of bacterial communities under community coalescence in the artificial aquatic ecosystems comprising complex microhabitats, which is vital for developing microbial solutions for regulating the microbial communities to improve system performance in the future.