Search Results (1,421)

Biochar can improve soil physicochemical properties and microbial habitats; however, its application rate-dependent effects in maize fields of the black soil region remain insufficiently understood under field conditions. A three-year field experiment was conducted in Jiamusi, Heilongjiang Province, China, from 2023 to 2025, with four biochar application rates: 0 (W0), 10 (W1), 20 (W2), and 40 t ha⁻¹ (W3). Soil physicochemical properties, bacterial communities based on 16S rRNA gene sequencing, and fungal communities based on internal transcribed spacer (ITS) sequencing were analyzed to assess changes in soil fertility and microbial community composition and their relationships with environmental factors. Biochar application significantly increased soil organic matter, alkali-hydrolyzable nitrogen, available potassium, and pH. Although W3 produced the greatest nutrient enhancement, W2 exhibited a more balanced overall response across the measured soil fertility and microbial community indicators. Sequencing depth was adequate for all samples, and bacterial alpha diversity was comparatively well maintained under W2 and W3. Fungal alpha diversity exhibited pronounced interannual variation and increased under W3 in 2025. Year accounted for a greater proportion of variation in microbial community structure than did biochar treatment; however, both treatment and the year × treatment interaction also had significant effects. Among the measured soil fertility and microbial community indicators, W2 produced a comparatively balanced overall response, whereas W3 exerted stronger selective effects on microbial communities. Because crop yield, economic feasibility, labile carbon fractions, and long-term ecological outcomes were not assessed, an agronomically optimal biochar application rate cannot yet be determined. Full article

Background: Public fitness facilities are high-contact environments that facilitate microbial transfer via shared surfaces; however, temporal dynamics and device-specific contamination patterns remain insufficiently characterized. Methods: A repeated-measures observational study was conducted in a fitness facility over five consecutive weekdays (Monday to Friday). A total of 180 surface samples were collected from 12 gym devices, each sampled three times daily (morning, noon, and evening). Surface-associated cultivable bacteria were recovered using culture-based methods followed by MALDI-TOF MS identification. Ecological metrics, including species richness and Shannon diversity, were calculated, and taxa were classified by origin (skin-associated versus environmental). Device-specific contamination profiles were developed using a composite index incorporating pathogen presence, contamination frequency, and persistence. Temporal trends and predictors of contamination were analyzed using mixed-effects regression models. All statistical analyses were performed in R. Results: A total of 248 bacterial isolates were identified, representing 61 species across 32 families, with a predominance of skin-associated taxa (72.2%). Sampling time point was a strong independent predictor of contamination (adjusted OR for noon vs. morning: 7.19; p < 0.001). While overall microbial diversity remained stable across devices (Shannon index, p = 0.44), substantial heterogeneity was observed in pathogen prevalence, multispecies burden, and persistence. The functional trainer and leg extension showed the highest composite risk scores (42.3%), while the ab crunch machine and upper body ergometer demonstrated significantly increasing contamination trends over the sampling period (p < 0.05). Co-occurrence analysis showed nonrandom microbial associations, with the strongest positive links between Micrococcus luteus and Staphylococcus saprophyticus (Φ = 0.76) and Staphylococcus aureus (Φ = 0.61). Conclusions: Gym equipment surfaces harbor predominantly human-associated microbial communities exhibiting dynamic temporal contamination patterns, and on selected devices, increasing the baseline contamination across consecutive cleaning cycles. The findings indicate that contamination patterns on shared fitness equipment are dominated by taxa commonly associated with human skin and support targeted hygiene interventions focused on frequently contacted devices and periods of elevated contamination. Full article

Rural greywater management is a critical global challenge due to the lack of centralized treatment in dispersed communities. This study aimed to characterize the pollution characteristics and bacterial community structure of samples from four greywater collection tanks in eastern China using high-throughput sequencing and absolute quantification of the 16S rRNA gene. Pollution characteristics showed spatial heterogeneity: chemical oxygen demand ranged from 19.8 to 272.5 mg/L, total nitrogen from 8.6 to 16.4 mg/L, and dissolved oxygen from 1.3 to 5.3 mg/L. Dissolved greenhouse gases also varied, with N₂O reaching 103.6 ppmv and CH₄ up to 50.4 ppmv. Based on the estimated absolute abundance of 16S rRNA gene copies, we found that the bacterial communities were dominated by Pseudomonadota, Actinomycetota, Bacteroidota, and Bacillota. Key genera such as Acinetobacter, Pseudomonas, and unclassified Enterobacteriaceae were positively correlated with nitrate, suggesting their potential association with denitrification and potential N₂O production. The methanotrophic genus Methyloparacoccus was enriched in a tank with high dissolved organic carbon. Co-occurrence network analysis revealed that core taxa like unclassified Paracoccaceae and Limnohabitans function as module hubs, maintaining community stability. These findings reveal associations between bacterial taxa, pollutant transformation, and greenhouse gas emissions in rural greywater and provide fundamental insights to support the development of low-carbon, resource-oriented treatment technologies. Full article

How do microorganisms in litter and soil affect litter decomposition in a temperate forest? Here, we conducted an 18-month laboratory experiment to assess the decomposition of pure Robinia pseudoacacia, pure Platycladus orientalis, and mixed R. pseudoacacia–P. orientalis litters under four treatments, namely “no microbe” (NM), “litter microbes” (LM), “soil microbes” (SM), and “litter and soil microbes” (LM + SM). Results demonstrated that, compared with SM, LM significantly enhanced the litter weight-loss rate and elevated the potential activities of lignocellulolytic enzymes at 180 days, and this was accompanied by lower cellulose and hemicellulose contents. Structural equation modeling indicated that microorganisms may directly or indirectly influence weight mass loss, partly by regulating these potential enzyme activities that are associated with changes in the litter organic matter composition. Across three forest stands, microbial treatments significantly affected litter decomposition. The standardized direct path coefficients linking microorganisms to the litter-mass-loss rate from highest to lowest were LM + SM, LM, and SM, indicating a synergistic effect between LM and SM that promotes decomposition through coordination. Taxonomically, most bacterial genera differed significantly among microbial treatments, whereas most fungal genera did not. Notably, the standardized direct path coefficient linking bacteria to litter mass loss was larger than that for fungi in both the SM and LM + SM groups. Additionally, field decomposition was faster than in the laboratory, with distinct microbial communities, verifying the environmental modulation of decomposers and the home-field advantage. This study clarifies microbial mechanisms underlying litter decomposition and provides a theoretical basis for forest ecosystem stability and sustainable management. 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

The black sea cucumber, Holothuria forskali, is an emerging target species for aquaculture; however, knowledge of its biology remains limited. Investigating its associated microbiota is a crucial step toward developing a controlled and sustainable aquaculture. In this study, the microbiota of three different body compartments of the host H. forskali—namely, the dorsal epidermis, the posterior intestinal content, and the coelomic fluid—were analysed using targeted metagenomics (V3-V4 rRNA 16S Metabarcoding). We compared host-associated communities with bacterial environmental communities across three periods in 2020 at two sites in south Brittany, totalling 309 analyses (36 environmental samples and 273 sea cucumber samples). The objective was to explore the diversity of the sea cucumber microbiota from the external to the internal regions of the animal. Thus, a total of 8695 OTUs were identified and classified into 52 bacterial phyla, 119 classes, and 45,596 orders. The results highlighted (1) anatomical compartmentalisation—with significantly different bacterial assemblages in terms of diversity, composition, and abundance across the three body regions—(2) host versus environment differences, and (3) temporal variations, as microbial community structures shifted significantly in winter compared to summer and autumn. This analysis identified specific taxa and families associated with each compartment with a potential role in host health. Results also showed relationships between the sea cucumber microbiota and their ambient environment. In fact, the presence of common bacterial taxa observed in the sediment and in the gastrointestinal microbiota supported the feeding behaviour of H. forskali. The sea cucumber microbiome thus appears to be compartmentalised “anatomically”, exhibiting a relatively low abundance of bacteria in the coelomic cavity, distinct from that of the microbial communities of seawater and sediments. This study highlighted the importance of the microbiota for the host and confirmed the existence of a core microbiota within H. forskali. Full article

This study investigates earthworm cocoons as key vectors for the vertical transmission of symbiotic bacteria, a process that profoundly shapes the gut microbiota of offspring and influences their environmental adaptability. However, systematic knowledge of the internal microbiome communities within earthworm cocoons remains limited. Here, we characterized the composition and functional potential of bacterial communities within cocoons of earthworms collected from three composting systems (fermented coffee grounds, cow manure, and residual sludge) using high-throughput sequencing, together with diversity analyses, dominant taxa identification, and FAPROTAX-based functional prediction. Our results indicated that the composting system significantly affects bacterial diversity and community structure. The fermented coffee grounds system supported the highest species richness, whereas the cow manure system exhibited the greatest diversity and evenness. At the phylum level, Pseudomonadota, Actinomycetota, and Bacteroidota predominated across all systems, with Pseudomonadota being particularly abundant (62.01–81.41%). At the genus level, Verminephrobacter and Agromyces were consistently dominant, with Verminephrobacter showing particularly high relative abundance, ranging from 22.42% to 51.51%. Although the composition and abundance of dominant phyla and genera varied among systems, the shared OTUs accounted for a substantial proportion of the relative abundance in each sample (54.65–91.84%). Functional predictions revealed chemoorganoheterotrophy as the predominant metabolic function, with relative abundances ranging from 23.87% to 45.42%. Collectively, these findings provide insights into how composting environments shape the bacterial communities within earthworm cocoons, offering a theoretical foundation for understanding the ecological functions of earthworms and their potential applications in ecological restoration and sustainable agriculture. Full article

Bovine-associated microbial communities play important roles in animal physiology, immune regulation, and mammary health. However, knowledge regarding bacterial populations associated with blood and milk remains limited in healthy dairy cattle exposed to different environmental conditions. In this study, we characterized and compared blood- and milk-associated bacterial communities from clinically healthy Holstein cows during summer and winter in an intensive commercial dairy production system located in northern Mexico using 16S rRNA metabarcoding. Significant differences in alpha and beta diversity metrics were observed according to sample type and season. Milk samples exhibited higher microbial richness and diversity than blood samples, and comparative analyses revealed significant differences in bacterial community composition between sample types and seasonal sampling periods. Bacterial communities were mainly dominated by Proteobacteria, Firmicutes, Actinobacteriota, and Bacteroidota. Differential abundance analyses identified genera associated with environmental exposure or opportunistic infections, including Staphylococcus, Streptococcus, Corynebacterium, Pseudomonas, and Acinetobacter. Overall, the observed bacterial community patterns varied according to sample type and seasonal environmental conditions, highlighting the complexity of host-associated microbial ecosystems in dairy cattle. 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

The Qinghai–Tibet Plateau, a globally significant ecological barrier and a core pastoral region, is persistently constrained by cold and arid climatic conditions, nutrient poor soils, and progressive grassland degradation. These challenges necessitate maintaining forage productivity while enhancing ecological stability. Medicago sativa L., valued for its high nutritional quality and capacity for biological nitrogen fixation, has been widely incorporated into regional grassland systems. Rhizobial inoculation, as an environmentally sustainable agronomic practice, is regarded as an effective approach to improving nutrient use efficiency and promoting ecological restoration; however, its underlying mechanisms in cold and arid environments remain insufficiently understood. This study established a field experiment in Delingha, Qaidam Basin, using the cultivar ‘Beilin 201’. Treatments included an uninoculated control (CK) and four rhizobial seed coating rates: E1 (0.75 g·m⁻²), E2 (1.50 g·m⁻²), E3 (2.24 g·m⁻²), and E4 (3.00 g·m⁻²). The effects on yield, rhizosphere soil physicochemical properties, bacterial community structure, and molecular ecological networks were systematically evaluated. The composite microbial inoculant maintained Medicago sativa L. yield, with only modest and non-significant increases in some treatments. In contrast, soil organic matter increased significantly with application rate (p < 0.001), suggesting a stronger short-term effect on soil properties than on yield. Although network vulnerability was lowest in E4, the differences among treatments were not statistically significant. Mixed effects modeling showed that soil factors (74.79%) and microbial factors (25.12%) jointly influenced yield variation. Structural equation modeling further revealed that microbial factors exerted a positive direct effect on yield (0.3), whereas soil factors exhibited a stronger direct effect (0.57), with inoculation rate primarily influencing yield indirectly through soil mediated pathways. This study elucidates the ecological functions and regulatory mechanisms of rhizobial formulations in high elevation dryland ecosystems and provides both theoretical support and practical guidance for the rational application of microbial fertilizers and the sustainable management of forage systems on the Qinghai–Tibet Plateau. 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

Nitrous oxide (N₂O) is a greenhouse gas that has a global warming potential approximately 300 times that of carbon dioxide (CO₂). It is largely produced in agricultural soils through nitrification and denitrification processes driven by specific microbial functional genes (e.g., amoA, nirS, and nirK), which represent the main source of its emissions. The intensive use of nitrogen fertilizers increases nitrogen surplus in the ecosystem. This in turn accelerates the risk of nitrogen loss through leaching and volatilization, while also accelerating microbial pathways that drive N₂O emissions in the soil. This issue raises severe environmental concerns within the context of global climate change, particularly through the climate-driven escalation of soil salinity, which further alters the microbial community and increases these emissions. Microbial inoculants, including bacteria and arbuscular mycorrhizal fungi, provide eco-friendly biological solutions to mitigate N₂O emissions from agricultural soils. These inoculants could restore nitrogen balance in the soil by several strategies, such as improving nitrogen use efficiency, competing with native nitrifiers, and upregulating nosZ gene expression. This review highlights the current developments in the utilization of microbial inoculants for N₂O mitigation, focusing on key bacterial genera (e.g., Bradyrhizobium, Dyadobacter, Stutzerimonas, Paenibacillus, and Bacillus) and arbuscular mycorrhizal fungi (AMF, e.g., Rhizophagus and Funneliformis), as well as the mechanisms used by these microorganisms. It also discusses the potential of using microbial inoculants in saline-affected soils, as well as the link between salinity and N₂O emissions. Based on these insights, this review presents a thorough framework for the prospective use of microbial inoculants as an effective solution to sustainable agriculture while reducing the environmental hazards associated with N₂O emissions, which endanger global food and climate systems. Full article

Wildlife rehabilitation can alter host-associated microbial communities, yet the effects of temporary managed care on the gut microbiome of insectivorous bats remain poorly understood. We used shotgun metagenomic sequencing to investigate gut microbiome composition in wild and rehabilitated bats from Yorkshire, United Kingdom. A total of 25 faecal metagenomes were analysed from four bat species (Myotis daubentonii, Pipistrellus pipistrellus, Nyctalus noctula, and Nyctalus leisleri), including wild baseline individuals and bats undergoing temporary managed care for 1–49 days. Microbial community structure clustered primarily according to host species and roost location, with no significant separation associated with rehabilitation status. Among bats in managed care, bacterial alpha diversity did not differ significantly with time in care (H = 2.30, p = 0.32). Archaeal communities displayed markedly lower interindividual variation than bacterial communities (coefficient of variation: 12.2% vs. 41.8%), indicating a highly conserved archaeal microbiome across hosts. Rehabilitated bats exhibited modest compositional shifts in bacterial communities, including increased relative abundances of Yersiniaceae and Lactobacillaceae and reduced abundances of environmentally associated taxa such as Pseudomonadaceae and Erwiniaceae. These changes may reflect controlled dietary provision and reduced environmental exposure during care. Overall, no marked rehabilitation-associated differences in gut microbiome diversity or community structure were detected under the current sampling design. These findings are consistent with microbiome stability during temporary managed care, although longitudinal studies are required to confirm microbiome dynamics within individual bats. Nonetheless, this study provides an initial baseline for future microbiome-informed wildlife rehabilitation studies. 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