Search Results (845)

The diversity and complexity of symbiotic microbiota in fish may significantly influence the host’s physiological, metabolic and immunological functions. In order to understand the microbial assembly in Sichuan taimen (Hucho bleekeri), an endangered fish species in the upper reaches of the Yangtze River, the microbiota of the skin, oral cavity and feces of artificially reared individuals and the microbiota of the rearing water were characterized through metagenomic sequencing. The results demonstrated that Pseudomonadota were shared across the skin, oral cavity, feces and rearing water, suggesting that they may constitute a shared microbial group connecting the aquatic environment and host mucosal surfaces. Based on functional prediction analyses, these taxa were potentially associated with organic matter degradation, nutrient cycling, and microbial and immune homeostasis. Likewise, Actinomycetota and Bacillota were consistently detected across multiple mucosal tissues and were predicted to be associated with nutrient transformation, antimicrobial defense, and the maintenance of mucosal microbial stability. Fusobacteriota were detected solely in feces, suggesting a strong tissue-specific colonization capacity. The alpha diversity of the microbiota did not differ significantly among tissues, and the beta diversity revealed strong clustering of host-associated samples and clear separation from water samples. Functional annotation further revealed that the water microbiota exhibited broader yet more dispersed functional potential, whereas host-associated microbiota showed stronger functional specialization closely aligned with host physiological demands. Collectively, the findings are better presented as baseline information for future comparative and hypothesis-driven studies in Sichuan taimen. Full article

Optimizing nitrogen (N) management is essential for sustaining rice productivity and improving soil N retention in paddy ecosystems, yet whether long-term fertilizer postponing (FP) regulates bacterial community assembly and microbial N-cycling potential in a compartment-dependent manner remains unclear. Using soils from an 11-year field experiment, we investigated bacterial communities and eight N-cycling genes in bulk and rhizosphere soils across three rice growth stages. Compared with conventional fertilization (CF), FP significantly increased grain yield, plant N accumulation, soil NH₄⁺-N (8.1%), microbial biomass N (MBN, 4.3%), and urease activity (30.3%). N-cycling genes showed pronounced temporal variation, generally peaking at the heading stage. FP increased the abundance of genes involved in N fixation, nitrification, and denitrification in bulk soil but reduced most N-cycling genes in the rhizosphere. Although bacterial α-diversity was unchanged, FP significantly altered bacterial community composition. Network and redundancy analysis further showed that bacterial community assembly and N-cycling potential were closely associated with soil C and N status. These findings indicate that long-term FP improves rice productivity by enhancing soil N availability and reshaping bacterial community assembly and microbial N-cycling potential in a compartment-dependent manner, providing new insights into the microbial mechanisms underlying sustainable N management in paddy soils. Full article

Water-soluble blue microbial pigments with antioxidant activity remain rare, and their host-level protective mechanisms are poorly understood. Here, we identified the genetic basis of blue pigment biosynthesis in the glacier-derived strain Arthrobacter antioxidans QL17. Heavy-ion mutagenesis yielded a hyperpigmented mutant (M157) and a pigment-deficient mutant (M186), and pigment yield was positively associated with hydrogen peroxide (H₂O₂) tolerance. Genome mining identified MWM45_RS16760 as the sole core biosynthetic gene in a candidate nonribosomal peptide synthetase (NRPS)-like cluster. The encoded protein displayed an adenylation–peptidyl carrier protein–thioesterase (A-PCP-TE) architecture with a predicted L-glutamine-specific A domain, and its transcript abundance paralleled pigment production across the three strains. Phylogenetic analysis placed MWM45_RS16760 in a distinct actinomycete-associated indigoidine-like lineage separated from the characterized BpsA and IndC branches. Heterologous expression in Escherichia coli reconstructed a blue-pigment-producing phenotype, increased H₂O₂ tolerance, and was accompanied by enhanced extracellular DPPH and ABTS radical-scavenging activities in the culture supernatant. Comparative transcriptomics further revealed coordinated activation of oxidative-stress and proteostasis responses alongside repression of tryptophan biosynthesis and flagellar assembly. These findings identify MWM45_RS16760 as a candidate indigoidine-like NRPS associated with blue pigment biosynthesis and oxidative-stress resistance, with heterologous expression linked to enhanced radical scavenging and coordinated transcriptional reprogramming, expanding the phylogenetic and functional diversity of indigoidine-like systems. Full article

Continuous cropping obstacles (CCOs) severely disrupt the soil physical structure, nutrient cycling, and microbial community balance, leading to decreased crop productivity. However, the effects of soil amendment interventions on bacterial, fungal, and archaeal communities in foxtail millet (Setaria italica (L.) P. Beauvois.) systems are not well comprehended. Selected physical, chemical, biological soil amendment and crop rotations were evaluated for their effects on rhizosphere soil microbial diversity, composition, network characteristics, community assembly processes, niche breadth, and multi-functionality. High-throughput sequencing of 16S rRNA and ITS regions demonstrated that earthworm castings significantly enhanced archaeal Chao1, Shannon diversity, and multi-functionality. Meanwhile, Bacillus mucilaginosus enhanced fungal diversity, and B. subtilis promoted bacterial network complexity. In continuous cropping soil alone, microbial communities exhibited low diversity and were predominantly governed by ecological drift. In contrast, soil amendment treatments shifted assembly toward deterministic processes, including homogeneous and heterogeneous selection. However, the analysis demonstrated greater complexity and niche width in bacterial communities than in fungal or archaeal communities, with keystone modules driven by Actinomycetota, Ascomycota, and Halobacteriota. Structural equation modeling indicated that soil physicochemical properties directly mediated rhizosphere soil microbial alpha diversity, which in turn positively influenced multi-functionality. Overall, organic amendments and microbial inoculants were associated with increases in microbial diversity, network stability, and functionality in this pot experiment, suggesting that such practices may help mitigate CCOs and sustainably improve foxtail millet productivity in dryland agricultural systems. Full article

The gut microbiome of rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) is increasingly recognized as a functional interface linking dietary inputs, epithelial barrier integrity, mucosal immunity, environmental stress, disease susceptibility, and antimicrobial-resistance risk in intensive aquaculture. Based on available salmonid studies and relevant evidence from broader fish and aquaculture systems, this review synthesizes current knowledge on salmonid gut microbial composition, nutritional modulation, microbiome–mucosal immune interactions, aquaculture stressors, antibiotic exposure, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), metagenomics, multi-omics, and emerging microbiome-informed decision-support tools. Current evidence does not support a universally stable single-core microbiota in these species. Instead, community structure is shaped by developmental stage, freshwater–seawater transition, intestinal segment, digesta versus mucosa sampling, diet, temperature, stress, health status, and methodological workflow. Feed substitution and functional additives can remodel the gut microbiota, but these shifts should be interpreted alongside histology, barrier function, metabolic profiles, immune indicators, and disease-resistance phenotypes. Antibiotic exposure may reduce acute bacterial disease pressure while disturbing community structure and potentially enriching ARGs or ARG–MGE associations. Risk assessment should therefore move beyond ARG abundance toward host–ARG–MGE linkage using shotgun metagenomics, metagenome-assembled genomes, long-read sequencing, Hi-C, and externally validated multi-omics models. Machine learning and artificial intelligence approaches may support feature screening, risk stratification, and decision support, but their application in salmonid gut-health management remains at an early stage and requires external validation across sites, production stages, diets, and seasons. Full article

Unraveling rhizosphere microbial assembly and plant–microbe co-adaptation is essential for understanding how fragile mountain ecosystems respond to environmental stress. This study investigated the rhizosphere bacterial communities of Carex enervis C. A. Mey, a dominant species in arid and semi-arid alpine meadows, along an altitudinal gradient from 1160 to 1860 m. By integrating high-throughput sequencing, iCAMP-based community assembly analysis, niche differentiation assessment, and partial least squares path modeling, we examined associations among macro-environmental gradients, rhizosphere soil conditions, bacterial community assembly, and ammonium nitrogen availability. The results revealed a dual-track assembly pattern. Macro-environmental heterogeneity, particularly in elevation and precipitation, was associated with rare microbial diversity primarily through heterogeneous selection. In contrast, abundance-weighted patterns suggested homogeneous selection of core dominant microbial groups in the rhizosphere. Within several dominant genera, closely related taxa showed divergent covariation patterns rather than uniform responses along the environmental gradient, suggesting potential fine-scale differentiation in environmental responses. Path analysis further indicated that enzyme-based rhizosphere activity proxies were associated with the relative abundance of microbial response groups and with the availability of ammonium nitrogen. These findings suggest that the rhizosphere conditions of Carex enervis are associated with bacterial assembly patterns, fine-scale taxon differentiation, and nutrient-related soil variables along the elevational gradient. This study provides new insight into plant–microbe co-adaptation in arid and semi-arid mountain ecosystems. Full article

Toxoptera aurantii is a globally distributed piercing-sucking pest that severely threatens tea production. While the direct damage caused by aphid feeding is well documented, the systemic effects of infestation on plant-associated and soil microbial communities remain poorly understood. Here, we employed full-length 16S rRNA gene sequencing and untargeted metabolomics to investigate the influence of T. aurantii infestation on the microbiota of tea plants (Camellia sinensis) and rhizosphere soil across four sample compartments: aphid bodies, healthy leaves, aphid-infested leaves, and root-zone soil. Our results revealed pronounced niche-specific microbial assembly patterns. The aphid microbiome exhibited the lowest diversity and was dominated by obligate endosymbionts, including Buchnera aphidicola and the secondary symbiont Serratia symbiotica. Soil harbored the highest microbial diversity with a balanced phylum-level structure. Aphid infestation significantly reduced phyllosphere microbial diversity (Shannon index) and shifted community composition, with a decline in a sequence putatively assigned to Methylobacterium brachiatum and a modest increase in a taxon assigned to the opportunistic plant pathogen OTU assigned to Dickeya chrysanthemi. This pattern suggests a hypothesis that aphid infestation may create conditions permissive for such opportunistic pathogens, although experimental validation is required. Concurrently, infestation was associated with profound metabolic reprograming in tea leaves, including upregulation of defense-related flavonoids and terpenoids and downregulation of several primary metabolites. Notably, the phyllosphere of infested leaves showed reduced microbial diversity and an increased relative abundance of a 16S rRNA sequence assigned to Dickeya chrysanthemi, while certain plant-derived antimicrobial metabolites were decreased. These patterns suggest a possible association between aphid infestation, altered antimicrobial metabolite profiles and increased relative abundance of Dickeya-assigned sequences. These findings demonstrate that T. aurantii infestation triggers a systemic response in the aboveground compartments (aphid and leaf), while the soil compartment maintains a distinct and highly diverse microbial community that serves as a potential reservoir. The study characterizes microbial communities across these three compartments without inferring infestation-driven soil remodeling. This study advances our understanding of tripartite interactions in tea ecosystems and provides a basis for developing microbiome-based strategies for sustainable pest management. Full article

Perennially ice-covered lakes in the McMurdo Dry Valleys, Antarctica, are shaped by permanent stratification, extreme oligotrophy, and salinity gradients, yet these features are vulnerable to climate-driven hydrologic change. Because phytoplankton and associated bacteria regulate carbon flow and nutrient cycling, understanding how algal–bacterial consortia respond to disturbance is key to predicting ecosystem change. We used enrichment cultures from Lakes Bonney and Fryxell to test responses to nutrient deprivation and salinity alteration, two perturbations relevant to climate-driven changes in hydrologic connectivity and expansion of open water moats. Autotrophic enrichments lacking added organic carbon were used to enrich algal–bacterial consortia dependent on photosynthetically derived substrates. Community responses were assessed with 16S rRNA amplicon sequencing of size-fractionated samples, allowing comparison of particle-associated and planktonic communities. Short-term nutrient limitation produced only limited shifts in community composition, indicating resistance to transient nutrient stress. However, bacterial communities were strongly structured by size fraction: particle-associated assemblages separated clearly from planktonic communities and were enriched in taxa linked to algal surfaces and polysaccharide-rich microhabitats, including Flavobacteriales, Sphingobacteriales, Rhizobiales, and Rhodobacterales. Salinity perturbation drove stronger restructuring of bacterial communities, with shallow Lake Bonney enrichments showing greater sensitivity than deeper communities. These findings suggest that algae-associated bacterial communities help structure Antarctic algal enrichment cultures and may influence microbial responses to climate-linked disturbance. Full article

Packing density regulates the microenvironment of tobacco (Nicotiana tabacum L.) fermentation and may thereby influence microbial activity and product quality. However, its effects on microbial community assembly and quality formation remain poorly understood. This study aimed to clarify how packing density affects flue-cured tobacco quality by shaping microbial communities, functional potential, and ecological interactions. Here, we investigated the effects of three packing densities (60%, 70%, and 80%) on chemical components, aroma compounds, microbial community structure, functional potential, co-occurrence networks, and assembly mechanisms of flue-cured tobacco (cv. Piaohe No. 2) after 10 days of fermentation. Moderate density (70%) achieved the most balanced chemical profile, with appropriate nicotine retention, potassium/chlorine ratio, and sugar/nicotine balance. T70 also exhibited the highest levels of total esters, total ketones, and β-ionone, key contributors to fruity, floral, and woody aromas. Microbial analysis revealed that T70 supported the highest diversity and was characterized by the enrichment of aroma-related bacterial taxa, including Bacillus and lactic acid bacteria, as well as the fungal genus Pichia. In contrast, T60 favored aerobic nicotine degraders, whereas T80 selected for obligate anaerobes associated with off-odor production. Functional predictions and network analysis showed that T70 upregulated fatty acid and carotenoid biosynthesis pathways and exhibited the highest modularity, indicating a compartmentalized, functionally complementary community. Neutral model fitting revealed increasing stochasticity with density, with T70 displaying a mixed assembly regime. Collectively, our findings show that packing density influences tobacco quality by regulating microbial community composition, functional potential, network interactions, and assembly processes. These results provide a scientific basis for optimizing packing density in tobacco processing. Full article

Beneficial fungal–bacterial interactions are important drivers of rhizosphere microecology and plant–soil functional coupling in conifer seedling systems, but their strain-combination-specific effects remain insufficiently understood. In this study, Pinus sylvestris var. mongolica seedlings were inoculated with three plant growth-promoting rhizobacteria (PGPR) strains, Serratia plymuthica A13, Acinetobacter lwoffii A07, and Pseudomonas koreensis A20, the ectomycorrhizal fungal strain Suillus luteus N94, and their corresponding co-inoculation combinations. Seedling growth, root architecture, plant nutrients, soil nutrients, soil enzyme activities, bacterial and fungal communities, differential taxa, network key taxa, and plant–soil functional indices were analyzed. Different inoculation treatments produced treatment- and trait-specific responses, with several N94–PGPR combinations showing advantages in particular growth, root, and soil functional traits, while some single-inoculation treatments also showed distinct positive effects. N94_A20 showed the greatest increases in seedling height, total dry weight, soil available phosphorus, and soil multifunctionality, whereas N94_A07 showed the strongest root architecture response and relative interaction index. Co-inoculation also reshaped rhizosphere bacterial and fungal communities and generated treatment-specific microbial enrichment patterns. Massilia, Ramlibacter, Holtermanniella, and Naganishia were positively associated with plant–soil functional indices. These results indicate that PGPR–N94 co-inoculation promotes conifer seedling growth through coordinated changes in root architecture, nutrient acquisition, soil biochemical function, and rhizosphere microbial community assembly. Full article

Biofumigation is increasingly recognized as an effective strategy for managing soilborne diseases. However, the understanding of the mechanisms of biofumigation has mostly focused on its direct inhibitory effects on plant pathogens, while the rhizosphere microbe-mediated effects induced by biofumigation remain unclear. Here, we investigated the effects of broccoli (Brassica oleracea var. italica) biofumigation on potato Fusarium wilt caused by Fusarium oxysporum and elucidated the changes in rhizosphere bacterial assemblage under biofumigation. Results showed that biofumigation significantly reduced disease incidence and increased tuber yield. In vitro assays revealed a strong direct inhibition of F. oxysporum by broccoli biofumigation, but the inhibition rate decreased from 99.78% on the first day to 76.27% on the seventh day. High-throughput sequencing and culture-based analyses demonstrated that biofumigation significantly shifted bacterial community assemblage in potato rhizosphere, enriching antagonistic taxa against F. oxysporum. Functional prediction suggested that biofumigation enriched bacteria associated with nitrogen consumption and methylotrophy. The changes in the rhizosphere bacterial community showed significant correlations with the incidence and severity of Fusarium wilt, indicating that biofumigation indirectly enhanced crop resistance to plant pathogens by altering the rhizosphere microbial community. These findings extend the current understanding of biofumigation beyond direct chemical toxicity and classical antibiosis and highlight its potential as an ecological strategy that harnesses the plant-associated microbiome for disease management. Full article

Beneficial and pathogenic fungal inoculation can substantially influence plant growth by reshaping rhizosphere microbial communities. However, how different fungal inoculants differentially affect microbial community assembly processes, co-occurrence network stability, keystone taxa distribution, and their potential associations with plant growth remains poorly understood. Cucumber was used as the model plant, and Fusarium oxysporum (pathogenic, Foc) and Trichoderma guizhouense (beneficial, Tri) were selected as inoculants. 16S rRNA and ITS2 amplicon sequencing were used to investigate the diversity, composition, assembly processes, and co-occurrence network structure of rhizosphere bacterial and fungal communities, respectively. In addition, we used Zi–Pi topological role analysis, functional prediction, Mantel tests and random forest to characterize keystone taxa and link microbial assembly, network stability to plant nutrient and biomass traits. Foc decreased bacterial diversity while Tri increased it. Tri was associated with greater microbial network connectivity and complexity, as well as network characteristics consistent with higher inferred stability, with more connector keystone taxa enriched in glycan and terpenoid metabolic functions; by contrast, Foc simplified network structure and enriched saprotrophic fungal keystones. Bacterial assembly shifted toward deterministic processes under Foc, whereas stochastic processes remained predominant in Tri and control treatments. Random forest further confirmed divergent drivers: bacterial assembly depended mostly on community composition, while fungal assembly was regulated by plant nutrients and fungal diversity. All microbial properties were tightly linked to plant biomass and nutrient accumulation. Collectively, beneficial and pathogenic fungi exert opposing influences on rhizosphere microbial organization: Tri was associated with more connected microbial communities and a greater diversity of predicted functional traits, whereas Foc strengthened environmental filtering and simplified community structure, with plant–microbe–nutrient feedbacks likely contributing to rhizosphere assembly and ecosystem functionality. Full article

Seasonal freeze–thaw transitions reorganize lake microbiomes, yet the coupling of environmental filters, biotic interactions, and assembly mechanisms across habitats remains unclear. We profiled bacteria and fungi in the water and sediment of Lianhuan Lake during winter (frozen) and spring (thawed) using amplicon sequencing, co-occurrence networks, and assembly models. Despite sharp physicochemical differences, α-diversity remained stable, while β-diversity was mainly driven by habitat (water vs. sediment), with seasonal turnover detectable, particularly for bacteria. Network analysis revealed a clear winter-to-spring shift: the frozen-water (FW) network was complex with high connectivity and 15% cross-domain edges, while frozen sediment (FS) was less connected but more modular. After thaw, both habitats showed reduced connectivity, with thawed sediment (TS) displaying the strongest modularity and an increase in cross-domain links (~16%). Keystone taxa shifted seasonally and by habitat: FW was dominated by peripheral taxa like Polaromonas, Pseudomonas, and Candidatus Limnoluna; FS had connectors such as the families Comamonadaceae and Ilumatobacteraceae. In spring, Luteolibacter and Rhodoferax dominated water, while Flavobacterium and Sutcliffiella took over sediment. Environmental drivers varied by season and habitat: in winter water, pH was the dominant organising factor, with permanganate index (COD_Mn) and ammonia nitrogen (NH₃-N) as secondary hubs, while NH₃-N became central after thaw. In sediments, sediment total nitrogen (STN) and sediment organic matter (SOM) promoted bacterial links in winter, but SOM had a negative effect after thaw. Assembly analyses suggested selection-driven processes, with dispersal-assisted selection for water bacteria (neutral community model (NCM) R² ≈ 0.76), stronger determinism for sediment bacteria (R² ≈ 0.30), and for fungi, assembly governed jointly by heterogeneous selection and dispersal limitation rather than by a single dominant process. These results highlight how freeze–thaw cycles reshape cross-kingdom networks and microbial assembly, providing insights for monitoring seasonally frozen lakes. Full article

Cardiometabolic diseases are increasingly understood as disorders involving compartment-specific redox disruption rather than a uniform excess of reactive oxygen species. This narrative review synthesizes evidence for a proposed gut microbiota–mitochondria ferroptosis framework in which dysbiosis-derived lipopolysaccharide, trimethylamine N-oxide, short-chain fatty acids, bile acids, and tryptophan metabolites may modulate mitochondrial reactive species production, antioxidant defenses, iron handling, lipid peroxide detoxification, and inflammatory signaling. The reference set was assembled through searches of PubMed and Web of Science Core Collection, supplemented by targeted Google Scholar searches and citation chaining during manuscript preparation and revision through June 2026 and was organized around microbial metabolites, mitochondrial redox biology, ferroptosis pathways, disease-specific evidence, and redox-targeted interventions. Because this is a narrative synthesis rather than a systematic review, the framework should be interpreted as hypothesis-generating rather than as a systematically validated pathological model. Across atherosclerosis, diabetic cardiomyopathy, metabolic dysfunction-associated steatotic liver disease, obesity-associated insulin resistance, chronic kidney disease, and cardiorenal metabolic injury, the most consistent mechanistic links involve mtROS, impaired mitophagy, glutathione/GPX4 and SLC7A11 dysfunction, ACSL4-dependent lipid peroxidation, Nrf2 signaling, NLRP3 activation, and cGAS-STING-associated inflammation, although human causal evidence remains uneven. Importantly, much of the current literature supports local links within this sequence rather than a fully verified dysbiosis–metabolite–mitochondria ferroptosis–organ dysfunction chain in the same study. We therefore emphasize evidence tiers, terminology discipline, and biomarker requirements when interpreting ferroptosis-sensitive injury. Polyphenols, flavonoids, probiotics, postbiotics, melatonin, CoQ10-related strategies, mitochondria-targeted antioxidants, and ferroptosis-sensitive approaches may be most translatable when paired with microbiome, metabolomic, lipidomic, pharmacokinetic, and redox biomarkers. Full article

Direct sea discharge outlets served as critical conduits for urban sewage and industrial wastewater disposal, playing dual roles as pollutant dilution channels and hotspots for pathogens and antibiotic resistance genes. Traditional monitoring approaches relying on physicochemical parameters and fecal indicator bacteria failed to capture the latent and cumulative risks posed by complex microbial communities. In this review, a holistic microbiome perspective was adopted to systematically synthesize current knowledge on the bacterial community dynamics, assembly mechanisms, resistome–virulome coupling patterns, mobilome-associated risk characteristics, and emerging biomonitoring strategies in direct sea discharge outlets. By integrating high-throughput multi-omics technologies with ecological network analysis and machine learning, we delineated a paradigm shift from cataloging microbial presence to deciphering functional interactions, risk propagation dynamics, and proactive surveillance strategies. Furthermore, under the “One Health” framework, we discussed emerging research frontiers and future challenges in managing pollution at discharge outlets, aiming to provide a scientific basis for environmental risk management in coastal zones. Full article