Search Results (3,736)

Soil microbial carbon use efficiency (CUE) is a pivotal determinant of soil carbon sequestration, yet how forest quality gradients regulate CUE through the interplay of mineral-microbial interactions in subtropical conifer ecosystems remains poorly understood. To address this, we examined the CUE response and its drivers across a forest quality gradient (high-quality to poor-quality stands) in subtropical coniferous forests in China. Soil mineral composition (including soil texture and the contents of Fe₂O₃, CaO, and MgO), physicochemical properties, microbial community diversity, and CUE were quantified. The results showed that CUE decreased by 2.7%, from 0.533 in high-quality stands to 0.519 in low-quality stands. Concurrently, soil organic carbon (SOC), nutrient availability, and microbial diversity exhibited consistent declining trends along the forest quality gradient. The CUE showed a significant positive correlation with SOC (r > 0.90, p < 0.001). Structural equation modeling and random forest revealed that microbial diversity was the most dominant correlated factor of CUE (the total effects on CUE = 0.932), followed by SOC. However, soil minerals indirectly influenced CUE via SOC. These findings highlight microbial diversity as the dominant observed correlate of CUE across forest quality gradients. This study not only deepens the understanding of the microbial mechanisms underlying soil carbon dynamics in subtropical forests but also provides key scientific basis for ecological restoration of poor-quality forests and nature-based climate solutions. Full article

Biochar can enhance microbial-mediated organic phosphorus mineralization, but the underlying mechanisms remain unknown in forest soils with varying pH values. An incubation experiment was conducted using karst (alkaline) and non-karst (acidic) forest soils. Four amounts of bagasse biochar were applied (0, 5, 10, and 15 t·hm⁻²) to assess their effects on soil phosphorus availability and microbial community structure. Olsen-P content of alkaline and acidic forest soils increased with increasing bagasse biochar addition and incubation time, especially in non-karst forest soil. The structure and diversity of phoD-harboring bacterial community of acidic forest soil were significantly altered by the amount of bagasse biochar added and the incubation time, whereas those in alkaline karst forest soil were not significantly affected. The relative abundance of the dominant order Burkholderiales reached (43%) in acidic forest soil, significantly exceeding the (9%) recorded in alkaline karst forest soil. The phoD bacteria in acidic forest soil had more complex microbial networks and were more closely related to phosphorus fractions than those in alkaline forest soil. Structural equation modeling indicated that soil phosphorus availability was directly controlled by bagasse biochar input in acidic forest soil, with an indirect pathway linked to phoD bacterial community structure. The contribution of phoD bacteria to the variation in phosphorus availability was higher in acidic forest soil than in alkaline forest soil based on variance partitioning, indicating that enhancing soil phosphorus availability with bagasse biochar depends on the amount added, soil type, and its regulation of phoD bacterial communities. Full article

This study evaluates the ecological impacts of seawater desalination discharge on coastal marine ecosystems through a sequential analytical framework linking systematic literature synthesis, field-monitoring evidence, spatial analysis, and predictive ecological modeling. The novelty of the study lies in combining multi-regional evidence from Mediterranean coastal zones, Persian Gulf waters, and Pacific coastal environments with threshold-based ecological risk assessment, thereby linking discharge-related environmental stressors with biological responses and ecosystem-function alterations. The systematic review first retained 750 studies published between 2004 and 2024 for qualitative synthesis. On this basis, 59 high-quality references with sufficient numerical information were selected for the main quantitative meta-analysis, while field-monitoring data were used to support the interpretation of distance-based discharge gradients. Spatial interpolation and hierarchical modeling were then applied to evaluate exposure–response patterns and ecological threshold behavior. The results showed that desalination facilities generated measurable ecological impacts mainly within 50–200 m of discharge points, with a critical transition distance of approximately 127 m where hypersaline conditions, typically 1.5–2.0 times ambient seawater levels, were associated with marked changes in marine community structure. Benthic assemblages showed taxon-specific responses, with mollusks and echinoderms exhibiting greater sensitivity than polychaetes and small crustaceans. Marine vegetation declined strongly under combined salinity, thermal, and chemical stress, while phosphonate-based antiscalants accumulated in filter-feeding organisms and produced bioaccumulation factors up to 42.1 times ambient levels. Ecosystem-function indicators, including microbial community composition and sediment organic matter processing, remained altered up to 300 m from discharge points, indicating that functional impacts may extend beyond the primary hypersaline plume. The predictive modeling framework further demonstrated that ecological risk decreased nonlinearly with distance and varied according to discharge intensity, local hydrodynamics, and biological sensitivity. These findings indicate that conventional uniform buffer-based assessment may underestimate the ecological footprint of desalination discharge. Sustainable desalination management should therefore adopt site-specific monitoring, species-sensitive protection thresholds, improved brine-management technologies, and adaptive mitigation strategies based on real-time environmental feedback. Full article

Microorganisms in sediments participate actively in biogeochemical cycling and are essential for maintaining the stability of marine ecosystems. To investigate the spatial impact of seaweed mariculture on sediment bacterial communities, three distinct zones were selected along the Zhanjiang coast, China: the Gracilaria salicornia aquaculture zone, a transition zone (adjacent to the aquaculture area), and a control zone (with no direct mariculture influence). In this study, 16S rRNA gene amplicon sequencing was employed to examine the composition, diversity, and potential functions of sediment bacterial communities across these three zones. The dominant microbial communities identified included Pseudomonadota, Thermodesulfobacteriota, Chloroflexota, and Acidobacteriota. Analyses of α-diversity, β-diversity, and molecular ecological network revealed that the bacterial community in the G. salicornia aquaculture zone exhibited significant differences in species composition, community structure, and interspecies interaction compared with those in the transition and control zones. Environmental factors such as pH, dissolved oxygen (DO) and nitrate (NO₃⁻) exerted significant influence on the bacterial community composition and structure. Predicted functional potential analyses indicated high abundances of pathways related to carbohydrate metabolism and amino acid metabolism. Overall, this study characterizes the spatial distribution patterns of microbial communities in a coastal seaweed mariculture ecosystem and provides important data to support further research on biogeochemical processes mediated by sediment bacteria and their response mechanisms to mariculture activities. Full article

Plateau waters in Northern Sichuan, China, act as critical headwaters of the Yellow River. Microbial communities in water bodies and soil matrices within this region are increasingly pressured by intensive animal rearing; yet few studies have characterized microbial shifts across entire riverine niches. In this study, we employed next-generation sequencing based metagenomics to investigate microbial features, community structure and diversity, metabolic potentials, and antibiotic resistance genes (ARGs) in the Baihe River, a tributary in the source region of the Yellow River. Sampling locations covered the main stem and three tributaries of the Baihe River, spanning from its source, through upstream and downstream segments, to the convergence site with the main stem of the Yellow River. Results revealed that Pseudomonadota and Bacteroidota were the most abundant phyla. The relative abundance of most taxa at multiple taxonomic levels exhibited an increasing trend along the river continuum driven by rising total nitrogen (TN) and total phosphorus (TP) concentrations; however, a notable exception occurred at BH1 (the Baihe source), where the abundance of numerous taxa was markedly higher than in downstream samples. We detected abundant ARGs predominantly associated with antibiotic resistance. Furthermore, prevalent viruses affiliated with the phyla Uroviricota and Nucleocytoviricota, together with pathogenic bacteria, were identified as etiological agents of diverse infectious diseases. This study provides novel perspectives for managing aquatic contamination in plateau river ecosystems by linking environmental variables, microbial succession, and resistome distribution. Full article

Dryland soils of the Caspian region of western Kazakhstan are exposed to environmental stress, including drought, alkalinity, low soil organic matter content, and anthropogenic pressure. In this preliminary study, bacterial communities were investigated in 18 soil samples collected from six sampling groups across Makat (M1, M2), Isatay (I1, I2), and Beyneu (B1, B2) districts. Soil physicochemical properties were measured, and bacterial diversity was analyzed using 16S rRNA gene sequencing of the V3–V4 region. Community composition analysis indicated spatial heterogeneity among the sampled groups. M1 and I1 showed the highest taxon richness, whereas B2 contained the highest number of unique taxa. Genus-level profiles showed that B1 and M2 were mainly associated with Rubrobacter and related actinobacterial taxa; B2 contained higher proportions of Marinobacter, Tychonema, Qipengyuania, and Halomonas; and I2 was enriched with Antarcticibacterium, Salinimicrobium, Rhodococcus, Gillisia, Marinobacter, Dietzia, and Pontibacter. Correlation analysis showed that several bacterial taxa were associated with soil organic matter content, total nitrogen, total phosphorus, exchangeable cations, and pH, although the overall Mantel relationship between soil properties and community structure was not significant. FAPROTAX-based prediction indicated differences in putative heterotrophic, nitrogen-related, sulfur-related, and hydrocarbon-associated functional categories among sites. Because FAPROTAX predictions are based on taxonomic composition, these results should be interpreted only as putative functional potential and not as evidence of actual microbial metabolic activity. These findings suggest that the sampled Caspian dryland soils contain distinct bacterial assemblages and taxa with potential ecological relevance; however, their role in dryland soil resilience or bioremediation should be verified through future culture-based, metagenomic, and functional validation studies. Full article

The Yellow River floodplain relies on plantations for ecological restoration, yet the key factors influencing soil microbial communities remain poorly elucidated. In this study, we investigated soil microbial communities under four representative stand types (Populus tomentosa monoculture (PP), Salix matsudana monoculture (PS), Populus tomentosa-Robinia pseudoacacia mixed plantation (MPR), and Salix matsudana-Populus tomentosa mixed plantation (MSP)) in this region. Using high-throughput sequencing, we compared the soil microbial community composition and diversity across stands, and combined soil physicochemical measurements to evaluate the relationships between community variation and soil factors. The results indicated that soil physicochemical properties differed significantly among stand types, except for available phosphorus. Bacterial α-diversity was highest in MPR, whereas fungal α-diversity was highest in MSP. Variation in microbial community structure (β-diversity) was primarily explained by soil organic carbon, total nitrogen, pH, water content, and electrical conductivity, as indicated by redundancy analysis and Mantel tests. The dominant bacterial phyla were Acidobacteriota, Pseudomonadota (formerly Proteobacteria), and Actinomycetota, while the dominant fungal phyla were Ascomycota, Basidiomycota, and Mortierellomycota. These findings demonstrate significant variation in soil microbial communities among plantation types and highlight the important role of soil physicochemical properties in shaping microbial community composition. Full article

At the archeological site of Pompeii, the deterioration of exposed structures is frequently associated with the combined action of microbial colonization and soluble salts, both recognized as major agents of decay affecting ancient surfaces. Although biocides are commonly applied during cleaning procedures to reduce microbial biomass, their incorporation into restoration-oriented formulations for the protection of porous stone substrates requires careful assessment of efficacy, microbiological risks, and sustainability. This study evaluated the performance of 2,4,5,6-tetrachloroisophthalonitrile (chlorothalonil) and iodopropynyl butylcarbamate (IPBC) as candidate active ingredients for conservation applications in activated new mortars. Yellow tuff, gray tuff, and brick samples collected from different sectors of Pompeii were investigated through culture-based analyses, ATP quantification, and metabolic profiling. Biocidal treatments were subsequently tested under laboratory conditions. The investigated substrates exhibited variable microbial counts and metabolic activity, generally reflecting different degrees of deterioration. Chlorothalonil showed negligible inhibitory effects, whereas IPBC reduced fungal growth in a dose-dependent manner. However, the highest IPBC concentration induced a red chromatic alteration associated with the selection of a bacterial strain preliminarily identified as Micrococcus roseus. Phenotype microarray analyses revealed broad chemical tolerance. Overall, biocidal treatments may alter microbial communities, favor tolerant microorganisms, and produce undesirable aesthetic effects. Finally, the study also assessed the environmental impact associated with laboratory and field activities, highlighting potential mitigation strategies to support more sustainable conservation research practices. Full article

As a precious indigenous goose resource in China, the Zhedong white goose occupies an essential position in the domestic goose industry. However, this breed spontaneously enters a prolonged non-laying period of over two months per year, which greatly limits egg production capacity and restricts the economic development of the goose industry. Herein, this study systematically compared serum physiological indices and serum and fecal metabolome, as well as fecal microbial communities, between laying and non-laying Zhedong white geese, aiming to reveal the key regulatory mechanisms underlying reproductive stage transition. Physiological analyses indicated that non-laying geese had higher serum levels of GnRH, PRL, APOA, and T-AOC, whereas the concentrations of LH, E₂, TNF-α, IL-1, and calcium were significantly reduced; FSH, PROG, and BA levels showed no significant differences between the two groups. Metabolomic analysis identified 277 upregulated and 403 downregulated DAMs in feces, and 386 DAMs in serum. The shared enriched pathways across serum and fecal samples encompassed arginine biosynthesis, histidine metabolism, and pantothenate and CoA biosynthesis, as well as steroid hormone biosynthesis. A total of 120 DAMs overlapped in two specimens, and the non-laying geese presented pronounced depletion of tryptophan-derived metabolites and steroid hormone-related metabolites. Metagenomic results showed no significant difference in gut microbial alpha diversity between groups, while their microbial community structures were clearly differentiated. A total of 774 upregulated and 854 downregulated microbial species were screened in non-laying geese, and these differential microbes were primarily enriched in pathways associated with reproductive hormone signaling, steroid biosynthesis and energy metabolism. Multi-omics correlation analysis verified close associations between differential microbes and reproductive-related metabolites. Certain probiotic strains, including Pediococcus pentosaceus and Lactococcus raffinolactis, were positively correlated with steroid hormones and tryptophan metabolites, and their abundances declined obviously in the non-laying stage. Collectively, this study elaborates the holistic changes in serum biochemistry, gut metabolome and microbiome in geese at different reproductive stages. The dysregulation of amino acid and steroid hormone metabolism, combined with the loss of beneficial intestinal microbes, jointly induces the non-laying phenotype. This study provides new perspectives for understanding the gut–reproductive axis and supplies promising biomarkers to improve the laying performance of geese. Full article

Grain for Green, as an important ecological restoration method, profoundly affects soil nitrogen (N) cycling by altering the soil physicochemical properties and microbial community. Soil nitrogen mineralization is a key process in the terrestrial N cycle. However, the dynamics and underlying driving mechanisms of soil N mineralization rate (Rmin) that respond to afforestation remain unclear. In this study, we selected a typical afforestation sequence in Northeast China, including farmland (F), 21-year-old larch plantation (L21), 42-year-old larch plantation (L42), and natural larch forest (NL). The soil Rmin, associated soil physicochemical properties, and microbial community characteristics were determined to explore the effects of afforestation on soil Rmin and its potential mechanisms of action. The results suggested that soil Rmin was ranked in the order of L42 (0.41 mg kg⁻¹ d⁻¹) > F (0.39 mg kg⁻¹ d⁻¹) > L21 (0.23 mg kg⁻¹ d⁻¹) (p < 0.05) along the afforestation sequence, with no significant difference between L42 and F. Compared to the L42, the NL exhibited significantly lower soil Rmin (0.23 mg kg⁻¹ d⁻¹) (p < 0.05). The changes in soil Rmin during the afforestation were significantly positively related to soil total N (TN) and organic carbon (SOC) concentrations, but significantly negatively related to pH (p < 0.05). Furthermore, the abundances of Proteobacteria and Acidobacteria (bacteria) and Ascomycota (fungi) were also closely correlated with soil Rmin. Structural equation modeling (SEM) analysis further indicated that the afforestation mainly regulated soil Rmin by altering soil temperature (ST) and NH₄⁺-N content. Meanwhile, soil NH₄⁺-N content could also exert a significantly positive effect on soil Rmin by influencing the microbial community. In conclusion, afforestation effectively altered soil Rmin, which was even higher in the plantation than in natural forests. This finding further enhances our understanding of forest restoration and land management practices on soil N cycling in temperate regions. Full article

The intricate interaction of a host’s microbiome, the microbiomes of other hosts, and environmental microbial populations significantly impacts host health, given the essential physiological functions the microbiome performs within the organism. The oral microbiome of domesticated animals is also influenced by a variety of host and environmental factors. This study investigated the characteristics of the oral microbiome of dogs and cats under comparable and disparate living conditions, emphasizing the description of diversity patterns, taxonomic composition, and predicted functional profiles. Oral buccal swabs were collected from four groups of companion animals (n = 5 per group): dogs housed alone in single-pet households (Group A), dogs cohabiting with cats in multi-pet households (Group B), cats cohabiting with dogs from the same households (Group C), and cats housed alone in single-pet households (Group D). The cohabiting groups were derived from five multi-pet households, with one dog and one cat sampled from each household. Amplicon sequence variations (ASVs) were used for downstream analysis after 16S rRNA gene sequencing. Rarefaction curve behavior indicated proper sequencing depth. Alpha diversity varied by group (Shannon index, p = 0.045), with Groups C and D having larger diversity. A Beta diversity study revealed community composition differences (Bray–Curtis dissimilarity, R² = 0.257, p = 0.001), with some overlap between groupings. In all samples, Proteobacteria, Firmicutes, Bacteroidota, and Fusobacteriota dominated the microbiome. The relative abundance of Fusobacterium, Porphyromonas, and Pasteurella varied across groups. Core microbiome analysis identified limited overlap of core ASVs between groups, with most taxa being group-specific. Functional prediction using PICRUSt2 suggested differences in predicted metabolic and cellular pathways. Overall, these exploratory findings suggest that the oral microbiome of companion animals may be influenced by host species and cohabitation conditions. Although limited by the small sample size, the study provides preliminary insights into microbial diversity, community structure, and predicted functional profiles that may inform future One Health-oriented investigations. Full article

The gut microbiota is increasingly examined as a therapeutic target because it contributes to epithelial barrier integrity, microbial metabolite production, bile acid transformation, immune regulation, and communication between the gut and distant organs. This structured narrative review synthesizes evidence on microbiota involvement in metabolic, gastrointestinal, hepatic, cancer, and neuroimmune conditions, including MASLD/MASH, inflammatory bowel disease, irritable bowel syndrome, obesity, type 2 diabetes, hypertension, colorectal cancer, Parkinson’s disease, and autism spectrum disorder. Across these conditions, microbiome findings are biologically plausible but heterogeneous. Many associations are shaped by diet, geography, medication exposure, host genetics, disease stage, sampling methods, and analytical pipelines. Microbial alterations should therefore be interpreted as context-dependent signals and candidate modifiers rather than universal causal markers. Conventional microbiota targeted strategies include diet, physical activity, prebiotics, probiotics, synbiotics, postbiotics, and fecal microbiota transplantation. These approaches are clinically familiar, but their effects are often broad, host specific, strain dependent, and difficult to assign to one mechanism. Fecal microbiota transplantation has the clearest clinical role in recurrent Clostridioides difficile infection, while evidence for most other indications remains inconsistent. Engineered microbial therapeutics offer greater experimental precision through signal sensing, payload delivery, metabolic modulation, and genetic circuit design. However, most evidence remains preclinical or early translational. Progress requires stronger human trials, standardized methods, mechanistic validation, safety monitoring, ecological containment, transparent reporting, and proportionate regulation. Full article

The Loess Hilly Region of northern Shaanxi is one of the most erosion-prone areas in the world due to its porous, erodible loess, steep slopes, and seasonal rainfall. To address this, conversion of sloping farmland to terraces has been extensively conducted across China’s loess regions, as terracing can reduce soil and water loss and enhance soil fertility. However, disturbance of soil layers during terracing can also lead to short-term decline in farmland productivity. This study investigates the effects of terracing operations at two sites of different ground substrate configurations in the Loess Hilly Region. Utilizing geochemical and molecular biological analysis methods, we examined the changes in the physicochemical and microbial properties of the ground substrate after terracing, using adjacent sloping farmlands as control sites. The results show that when the ground substrate configuration remained intact, terracing increased the average water content (from 8.44% to 14.34%) and soil organic carbon (from 2.74 g/kg to 5.76 g/kg) by 70% and 110%, respectively, and increased soil microbial α-diversity by 90%. The microbial community structure was also enhanced with an increase in relative abundance of soil- and plant-benefiting genera such as Streptomyces and Nocardioides, thereby promoting plant growth. Conversely, when the ground substrate configuration was altered, terracing led to a decrease in soil nutrient and moisture content, which was detrimental to crop growth. Therefore, maintaining the integrity of the ground substrate configuration is crucial during the terracing process to achieve optimal soil and water conservation outcomes. Full article

Bacterial communities play vital roles in coastal biogeochemical cycling and ecological stability. Despite their importance, a significant knowledge gap exists regarding their spatiotemporal dynamics and assembly mechanisms in the tropical coastal waters of the Leizhou Peninsula, China. To investigate the bacterial community structure, co-occurrence networks, and assembly processes, we conducted 16S rRNA gene amplicon sequencing on water samples collected seasonally from August 2022 to June 2023. The bacterial communities were dominated by Proteobacteria and Cyanobacteria, and were characterized by a distinct warm-season peak in the relative of Cyanobium. Alpha diversity indices exhibited significant seasonal fluctuations, reaching a minimum in August (autumn) and a maximum in December (winter). These variations were strongly regulated by water temperature and phosphate availability. Redundancy analysis (RDA) identified salinity as the primary deterministic factor shaping community composition. Seasonal environmental heterogeneity, rather than spatial variation, primarily governed bacterial community dynamics. We also observed a seasonal succession in community assembly mechanisms with deterministic filtering dominated in autumn, whereas stochastic processes prevailed in other seasons. Predicted functional profiles indicated a stable core metabolism, although local anthropogenic inputs stimulated specific metabolic adaptations in industrial and aquaculture zones. Our findings reveal that seasonal environmental filtering (especially temperature and salinity) and a shifting balance between stochastic and deterministic assembly processes govern bacterial dynamics in this tropical coastal ecosystem, with anthropogenic inputs modulating local metabolic functions. This study provides fundamental insights into the mechanisms maintaining microbial diversity and stability in tropical coastal waters facing seasonal and human pressures. Full article

Background: The upper gastrointestinal (GI) tract is a complex environment characterized by sharp physicochemical gradients. While the oral microbiome is a major source of microbial seeding for downstream organs, it remains unclear how these communities correlate and diverge across different anatomical sites. This study provides a high-resolution re-analysis of a comprehensive multi-site dataset to delineate the microbial architecture and ecological signatures along the oral–upper GI axis. Method: Human oral, esophageal, gastric mucosal, and gastric juice microbiome sequencing data were retrieved from the publicly available National Center for Biotechnology Information (NCBI) BioProject PRJNA1049979 database. Using these publicly available 16S rRNA sequencing data, we performed an integrated ecological analysis. Microbial diversity, taxonomic composition, and niche-specific community structures were evaluated using Quantitative Insights Into Microbial Ecology 2 (QIIME2) and R-based tools, including linear discriminant analysis effect size (LEfSe) and phylogenetic mapping. Results: The esophageal microbiome showed significantly greater richness and evenness than the oral cavity and stomach. Beta diversity analysis demonstrated clear compositional separation between oral and downstream upper GI communities, whereas gastric samples, particularly gastric juice, showed greater heterogeneity. Although major phyla were shared across sites, their relative abundances differed markedly. Oral samples were enriched with periodontal-associated taxa, including Porphyromonas, Prevotella, Alloprevotella, and Fusobacterium. In contrast, gastric mucosal samples were enriched with Akkermansia muciniphila and Helicobacter pylori, whereas gastric juice was characterized by Sarcina ventriculi, Fusobacterium periodonticum, and Clostridium perfringens. These findings indicate both taxonomic continuity and pronounced site-specific ecological divergence along the oral–upper GI axis. Conclusion: The oral cavity, esophagus, stomach, and gastric juice share a common microbial framework but exhibit distinct community restructuring driven by local environmental selection. This study provides a detailed ecological view of the oral–upper GI microbiome and highlights the importance of site-specific microbial organization in upper GI health and disease. Full article