Search Results (584)

Microbial carbon use efficiency (CUE) is an important indicator of soil organic carbon accumulation and loss and a key parameter in biogeochemical cycling models. Its regulatory mechanism is highly dependent on microbial communities and their dynamic mediation of abiotic factors. Land-use change (e.g., agricultural expansion, deforestation, urbanization) profoundly alter carbon input patterns and soil physicochemical properties, further exacerbating the complexity and uncertainty of CUE. Existing carbon cycle models often neglect microbial ecological processes, resulting in an incomplete understanding of how microbial traits interact with environmental factors to regulate CUE. This paper provides a comprehensive review of the microbial regulation mechanisms of CUE under land-use change and systematically explores how microorganisms drive organic carbon allocation through community compositions, interspecies interactions, and environmental adaptability, with particular emphasis on the synergistic response between microbial communities and abiotic factors. We found that the buffering effect of microbial communities on abiotic factors during land-use change is a key factor determining CUE change patterns. This review not only provides a theoretical framework for clarifying the microbial-dominated carbon turnover mechanism but also lays a scientific foundation for the precise implementation of sustainable land management and carbon neutrality goals. Full article

True slime molds (Eumycetozoa) remain under-explored globally, particularly in water-logged forest habitats. Despite evidence suggesting a high biodiversity potential in the Knyszyn Forest of north-eastern Poland, no systematic effort had previously been undertaken there. In the present survey, plant substrates from eight swampy sub-compartments were incubated for over four months, resulting in the detection of fifteen slime mold species. Four of these taxa are newly reported for northern and north-eastern Poland, while several have been recorded only a handful of times in the global literature. These findings underscore how damp, nutrient-rich conditions foster Eumycetozoa and demonstrate the effectiveness of moist-chamber culturing in revealing rare or overlooked taxa. Current evidence shows that, although slime molds may occasionally colonize living plant or fungal tissues, their influence on crop productivity and tree vitality is negligible; they are therefore better regarded as biodiversity indicators than as pathogens or pests. By establishing a replicable framework for studying water-logged environments worldwide, this work highlights the ecological importance of swamp forests in sustaining microbial and slime mold diversity. Full article

In chili cultivation, obstacles to continuous cropping significantly compromise crop yield and soil health, whereas crop rotation can enhance the microbial environment of the soil and reduce disease incidence. However, its effects on the diversity of rhizosphere soil microbial communities are not clear. In this study, we analyzed the composition and characteristics of rhizosphere soil microbial communities under chili continuous cropping (CC) and chili–cotton crop rotation (CR) using high-throughput sequencing technology. CR treatment reduced the alpha diversity indices (including Chao1, Observed_species, and Shannon index) of bacterial communities and had less of an effect on fungal community diversity. Principal component analysis (PCA) revealed distinct compositional differences in bacterial and fungal communities between the treatments. Compared with CC, CR treatment has altered the structure of the soil microbial community. In terms of bacterial communities, the relative abundance of Firmicutes increased from 12.89% to 17.97%, while the Proteobacteria increased by 6.8%. At the genus level, CR treatment significantly enriched beneficial genera such as RB41 (8.19%), Lactobacillus (4.56%), and Bacillus (1.50%) (p < 0.05). In contrast, the relative abundances of Alternaria and Fusarium in the fungal community decreased by 6.62% and 5.34%, respectively (p < 0.05). Venn diagrams and linear discriminant effect size analysis (LEfSe) further indicated that CR facilitated the enrichment of beneficial bacteria, such as Bacillus, whereas CC favored enrichment of pathogens, such as Firmicutes. Fusarium solani MG6 and F. oxysporum LG2 are the primary chili root-rot pathogens. Optimal growth occurs at 25 °C, pH 6: after 5 days, MG6 colonies reach 6.42 ± 0.04 cm, and LG2 5.33 ± 0.02 cm, peaking in sporulation (p < 0.05). In addition, there are significant differences in the utilization spectra of carbon and nitrogen sources between the two strains of fungi, suggesting their different ecological adaptability. Integrated analyses revealed that CR enhanced soil health and reduced the root rot incidence by optimizing the structure of soil microbial communities, increasing the proportion of beneficial bacteria, and suppressing pathogens, providing a scientific basis for microbial-based soil management strategies in chili cultivation. Full article

In response to the challenges posed by soil degradation in the arid regions of Xinjiang, China, green and organic management practices have emerged as effective alternatives to conventional agricultural management methods, helping to mitigate soil degradation by promoting natural soil recovery and ecological balance. However, most of the existing studies focus on a single management practice or indicator and lack a systematic assessment of the effects of integrated orchard management in arid zones. This study aims to investigate how different agricultural management practices influence soil physicochemical properties and inter-root microbial communities in apple orchards in Xinjiang and to identify the main physicochemical factors affecting the composition of inter-root microbial communities. Inter-root soil samples were collected from apple orchards under green management (GM), organic management (OM), and conventional management (CM) in major apple-producing regions of Xinjiang. Microbial diversity and community composition of the samples were analyzed using high-throughput amplicon sequencing. The results revealed significant differences (p < 0.05) in soil physicochemical properties across different management practices. Specifically, GM significantly reduced soil pH and C:N compared with OM. Both OM and GM significantly decreased soil available nutrient content compared with CM. Moreover, GM and OM significantly increased bacterial diversity and changed the community composition of bacteria and fungi. Proteobacteria and Ascomycota were identified as the dominant bacteria and fungi, respectively, in all management practices. Linear discriminant analysis (LEfSe) showed that biomarkers were more abundant under OM, suggesting that OM may contribute to ecological functions through specific microbial taxa. Co-occurrence network analysis (building a network of microbial interactions) demonstrated that the topologies of bacteria and fungi varied across different management practices and that OM increased the complexity of microbial co-occurrence networks. Mantel test analysis (analyzing soil factors and microbial community correlations) showed that C:N and available potassium (AK) were significantly and positively correlated with the community composition of bacteria and fungi, and that C:N, soil organic carbon (SOC), and alkaline hydrolyzable nitrogen (AN) were significantly and positively correlated with the diversity of fungi. Redundancy analysis (RDA) further indicated that SOC, C:N, and AK were the primary soil physicochemical factors influencing the composition of microbial communities. This study provides theoretical guidance for the sustainable management of orchards in arid zones. Full article

Coastal ecosystems are increasingly threatened by climate change and anthropogenic pressures, which can disrupt microbial communities and favor the emergence of pathogenic organisms. In this study, we applied metagenomic analysis to characterize fungal communities in sediment samples from an urban mangrove subjected to environmental stress. The results revealed a fungal community with reduced richness—28% lower than expected for similar ecosystems—likely linked to physicochemical changes such as heavy metal accumulation, acidic pH, and eutrophication, all typical of urbanized coastal areas. Notably, we detected an increase in potentially pathogenic genera, including Candida, Aspergillus, and Pseudoascochyta, alongside a decrease in key saprotrophic genera such as Fusarium and Thelebolus, indicating a shift in ecological function. The fungal assemblage was dominated by the phyla Ascomycota and Basidiomycota, and despite adverse conditions, symbiotic mycorrhizal fungi remained present, suggesting partial resilience. A considerable fraction of unclassified fungal taxa also points to underexplored microbial diversity with potential ecological or health significance. Importantly, this study does not aim to compare pristine and contaminated environments, but rather to provide a sanitary alert by identifying the presence and potential proliferation of pathogenic fungi in a degraded mangrove system. These findings highlight the sensitivity of mangrove fungal communities to environmental disturbance and reinforce the value of metagenomic approaches for monitoring ecosystem health. Incorporating fungal metagenomic surveillance into environmental management strategies is essential to better understand biodiversity loss, ecological resilience, and potential public health risks in degraded coastal environments. Full article

Landslides are a common geological hazard in mountainous areas, causing significant damage to ecosystems and production activities. Near-natural ecological restoration is considered an effective strategy for post-landslide recovery. To investigate the impact of near-natural restoration strategies on the recovery of plant communities and soil in landslide-affected areas, we selected landslide plots in Lantian County at 1, 6, and 11 years post-landslide as study sites, surveyed plots undergoing near-natural restoration and adjacent undisturbed control plots (CK), and collected and analyzed data on plant communities and soil properties. The results indicate that vegetation succession followed a path from “human intervention to natural competition”: species richness peaked at 1 year post-landslide (D_m = 4.2). By 11 years, dominant species prevailed, with tree species decreasing to 4.1 ± 0.3, while herbaceous diversity increased by 200% (from 4 to 12 species). Soil recovery showed significant temporal effects: total nitrogen (TN) and dehydrogenase activity (DHA) exhibited the greatest increases after 1 year post-landslide (132% and 232%, respectively), and by 11 years, the available nitrogen (AN) in restored plots recovered to 98% of the CK levels. Correlations between plant and soil characteristics strengthened over time: at 1 year, only 6–9 pairs showed significant correlations (p < 0.05), increasing to 21–23 pairs at 11 years. Near-natural restoration drives system recovery through the “selection of native species via competition and activation of microbial functional groups”. The 6–11-year period post-landslide is a critical window for structural optimization, and we recommend phased dynamic regulation to balance biodiversity and ecological functions. Full article

Organic farming is widely recognized as a promising practice for sustainable agriculture, yet its long-term ecological impacts remain insufficiently investigated. In this study, we evaluated these impacts by comparing heavy metal concentrations, soil invertebrate communities, and microbial profiles between long-term organic and conventional farming systems. A comparative analysis was conducted on 24 plot soils from two paired organic and conventional farm systems in Beijing, each managed continuously for over 20 years. Our results revealed that soils under organic management consistently contained 10.8% to 73.7% lower heavy metals, along with reduced geo-accumulation indices (I_geo, a standardized metric for soil contamination assessment), indicating decreased contamination risks. In terms of soil fauna, while conventional soils showed higher Collembola abundance, organic farming significantly enhanced Collembola richness and diversity by 20.6% to 55.0%. Microbial sequencing likewise revealed enhanced richness and diversity of bacteria and fungi in organic soils. These microbial communities also displayed shifts in dominant taxa and more stable co-occurrence networks under organic management. Principal component analysis and Mantel tests identified soil pH and nutrients as key drivers of soil biodiversity, while heavy metals also imposed negative influences. Collectively, these findings demonstrate that long-term organic farming not only mitigates environmental risks associated with soil contaminants but also promotes belowground ecological integrity by supporting biodiversity of soil fauna and microbiota. This study highlights the ecological significance of sustained organic practices and provides critical insights for advancing sustainable agricultural developments. Full article

To investigate the characteristics of rhizosphere soil microbial communities associated with Schisandra sphenanthera across different altitudinal gradients and to reveal the driving factors of microbial community dynamics, this study collected rhizosphere soil samples at four elevations: 900 m (HB1), 1100 m (HB2), 1300 m (HB3), and 1500 m (HB4). High-throughput sequencing and molecular ecological network analysis were employed to analyze the microbial community composition and species interactions. A null model was applied to elucidate community assembly mechanisms. The results demonstrated that bacterial communities were dominated by Proteobacteria, Acidobacteriota, Actinobacteriota, and Chloroflexi. The relative abundance of Proteobacteria increased with elevation, while that of Acidobacteriota and Actinobacteriota declined. Fungal communities were primarily composed of Ascomycota and Basidiomycota, with both showing elevated relative abundances at higher altitudes. Diversity indices revealed that HB2 exhibited the highest bacterial Chao, Ace, and Shannon indices but the lowest Simpson index. For fungi, HB3 displayed the highest Chao and Ace indices, whereas HB4 showed the highest Shannon index and the lowest Simpson index. Ecological network analysis indicated stronger bacterial competition at lower elevations and enhanced cooperation at higher elevations, contrasting with fungal communities that exhibited increased competition at higher altitudes. Altitude and soil nutrients were negatively correlated with soil carbon content, while plant nutrients and fungal diversity positively correlated with soil carbon. Null model analysis suggested that deterministic processes dominated bacterial community assembly, whereas stochastic processes governed fungal assembly. These findings highlight significant altitudinal shifts in the microbial community structure and assembly mechanisms in S. sphenanthera rhizosphere soils, driven by the synergistic effects of soil nutrients, plant growth, and fungal diversity. This study provides critical insights into microbial ecology and carbon cycling in alpine ecosystems, offering a scientific basis for ecosystem management and conservation. Full article

Integrated rice–crayfish (Oryza sativa–Procambarus clarkii) co-culture (RC) systems have gained prominence due to their economic benefits and ecological sustainability; however, the interactions between soil properties and microbial communities in such systems remain poorly understood. This study evaluated the effects of the RC systems on soil physicochemical characteristics and microbial dynamics in paddy fields of southern Henan Province, China, over the 2023 growing season and subsequent fallow period. Using a randomized complete design, rice monoculture (RM, as the control) and RC treatments were compared across replicated plots. Soil and water samples were collected post-harvest and pre-transplanting to assess soil properties, extracellular enzyme activity, and microbial community structure. Results showed that RC significantly enhanced soil moisture by up to 30.2%, increased soil porosity by 9.6%, and nearly tripled soil organic carbon compared to RM. The RC system consistently elevated nitrogen (N), phosphorus (P), and potassium (K) throughout both the rice growth and fallow stages, indicating improved nutrient availability and retention. Elevated extracellular enzyme activities linked to carbon, N, and P cycling were observed under RC, with enzymatic stoichiometry revealing increased microbial nutrient limitation intensity and a shift toward P limitation. Microbial community composition was significantly altered under RC, showing increased biomass, a higher fungi-to-bacteria ratio, and greater relative abundance of Gram-positive bacteria, reflecting enhanced soil biodiversity and ecosystem resilience. Further analyses using the Mantel test and Random Forest identified extracellular enzyme activities, PLFAs, soil moisture, and bulk density as major factors shaping microbial communities. Redundancy analysis (RDA) confirmed that total potassium (TK), vector length (VL), soil pH, and total nitrogen (TN) were the strongest environmental predictors of microbial variation, jointly explaining 74.57% of the total variation. Our findings indicated that RC improves soil physicochemical conditions and microbial function, thereby supporting sustainable nutrient cycling and offering a promising, environmentally sound strategy for enhancing productivity and soil health in rice-based agro-ecosystems. Full article

Microbial communities are crucial to maintaining the ecological health of lakes, but their response to water quality and eutrophication is poorly understood. This study analyzed seasonal variation in the effect of water quality parameters on microbial community structure and function at southern Lake Taihu. We observed poor water quality in autumn (low dissolved oxygen concentration and water transparency) with severe eutrophication (high in nitrogen, phosphorus, and microcystins). Microcystins were a major indicator of water quality that affected total phosphorus and dissolved oxygen concentrations. Redundancy analysis revealed that total nitrogen, total phosphorus, nitrate, ammonium, and microcystins, temperature, and dissolved oxygen all significantly influenced the microbial community. Microbial co-occurrence networks revealed significant seasonal variations, with autumn and winter exhibiting a more complex structure than other seasons. Additionally, we identified microcystin-sensitive microbial species as eutrophication indicators; they are involved in bacterial community components and metabolic function and fluctuate under seasonal changes to water quality. In conclusion, our findings provide insight into the relationship between water quality and microbial communities, offering an empirical basis for improving the sustainable management of Lake Taihu. Full article

Roux-en-Y gastric bypass (RYGB) surgery induces profound gut microbiota alterations that may impact metabolic outcomes. This study investigated site-specific effects of a multicomponent bovine colostrum-honey-serviceberry (CHJ) complex on post-RYGB microbiome changes in obese rats. Twenty-nine Wistar rats underwent RYGB surgery with CHJ supplementation, followed by mucosal-associated microbiota analysis from five gastrointestinal segments using 16S rRNA sequencing and serum metabolite profiling. RYGB caused regional-specific changes: decreased alpha diversity, systematic Proteobacteria increases (31.2 ± 5.1% in duodenum), and reductions in SCFA-producing bacteria (Romboutsia, Roseburia). CHJ supplementation exhibited dual effects on the microbiome: restoration of beneficial bacteria (Lactobacillus, Bifidobacterium) in distal segments while concurrently promoting Enterobacteriaceae growth in proximal regions. CHJ also maintained alpha diversity levels of the mucosa-associated microbiota comparable to those observed in the control group. Disconnects emerged between predicted microbial functions and systemic metabolites: thiamine pathway activation accompanied 78.5% serum vitamin B1 reduction, indicating severe absorption deficits. Three distinct patterns emerged: pro-inflammatory (proximal), decolonization (widespread Helicobacteraceae loss), and restorative (selective CHJ-mediated recovery). Results demonstrate that post-RYGB dysbiosis exhibits profound regional heterogeneity requiring segment-specific interventions and highlight complex interactions between nutritional supplementation and surgically altered gut ecology in determining metabolic outcomes. Full article

Projections indicate that the global urban population is anticipated to reach 67.2% by 2050, accompanied by a threefold increase in urban built-up areas worldwide. Urbanization has profoundly transformed Earth’s natural environment, notably characterized by the drastic reduction and fragmentation of wildlife habitats. These changes contribute to local species extinction, leading to biodiversity loss and profoundly impacting ecological processes and regional sustainable development. However, within urban settings, certain ‘generalist’ species demonstrate survival capabilities contingent upon phenotypic plasticity. The co-evolution of gut microbiota with their hosts emerges as a key driver of this phenotypic plasticity. The presence of diverse gut microbiota constitutes a crucial adaptive mechanism essential for enabling hosts to adjust to rapid environmental shifts. This review comprehensively explores amniote gut microbial changes in the context of urbanization, examining potential drivers of these changes (including diet and environmental pollutants) and their potential consequences for host health (such as physiology, metabolism, immune function, and susceptibility to infectious and non-infectious diseases). Ultimately, the implications of the gut microbiome are highlighted for elucidating key issues in ecology and evolution. This understanding is expected to enhance our comprehension of species adaptation in the Anthropocene. Full article

Climate change has intensified over recent decades, prompting shifts in forest management strategies, particularly in the Sudetes region of Poland, where native species like Norway spruce (Picea abies), European beech (Fagus sylvatica), and silver fir (Abies alba) have historically dominated. To address these changes, non-native species such as Douglas fir (Pseudotsuga menziesii) have been introduced as potential alternatives. This study, conducted in the Jugów and Świerki forest districts, compared the soil properties and water retention capacities of Douglas fir (Dg) and Norway spruce (Sw) stands (age classes from 8–127 years) in the Fresh Mountain Mixed Forest Site habitat. Field measurements included temperature, humidity, organic matter content, water capacity, and granulometric composition. Results indicate that, in comparison to Sw stands, Dg stands were consistently linked to soils that were naturally finer textured. The observed hydrological changes were mostly supported by these textural differences: In all investigated circumstances, Dg soils demonstrated greater water retention, displaying a water capacity that was around 5% higher. In addition to texture, Dg stands showed reduced soil water repellency and a substantially greater organic matter content (59.74% compared to 27.91% in Sw), which further enhanced soil structure and moisture retention. Conversely, with increasing climatic stress, Sw soils, with coarser textures and less organic matter, showed decreased water retention. The study highlights the importance of species selection in sustainable forest management, especially under climate change. Future research should explore long-term ecological impacts, including effects on microbial communities, nutrient cycling, and biodiversity, to optimize forest resilience and sustainability. Full article

Reductive soil disinfestation (RSD) significantly alters soil characteristics, yet its combined effects with bacterial inoculation on subsequent rhizospheric microbial community composition remains poorly understood. To address this knowledge gap, we investigated the effects of RSD and endophytic Brevibacillus laterosporus inoculation on the composition, network, and predicted function of peanut rhizospheric bacteria and fungi. Our results demonstrated that RSD and B. laterosporus inoculation substantially increased rhizospheric bacterial diversity while reducing fungal diversity. Specifically, B. laterosporus-enhanced RSD significantly reshaped the bacterial community, resulting in increased relative abundances of Chloroflexi, Desulfobacterota, and Myxococcota while decreasing those of Firmicutes, Gemmatimonadota, and Acidobacteriota. The fungal community exhibited a more consistent response to RSD and B. laterosporus amendment, with reduced proportions of Ascomycota and Gemmatimonadota but an increase in Chytridiomycota. Network analysis revealed that B. laterosporus inoculation and RSD enhanced the bacterial species complexity and keystone taxa. Furthermore, canonical correspondence analysis indicated strong associations between the soil bacterial community and soil properties, including Eh, EC, NO₃⁻-N, and SOC. Our findings highlight that the shifts in bacterial taxa induced by B. laterosporus inoculation and RSD, particularly the keystone taxa identified in the network, may contribute to the suppression of soil-borne pathogens. Overall, this study provides a novel insight into the shifts in rhizospheric bacterial and fungal communities and their ecological functions after bacteria inoculation and RSD treatment. Full article

Assessing microbial community stability and soil quality requires understanding the role of keystone microbial taxa in maintaining diversity and functionality. This study collected soil samples from four major habitats in the urban and peri-urban areas of 20 highly urbanized provinces in China using both the five-point method and the S-shape method and explored their microbiota through high-throughput sequencing techniques. The data was used to investigate changes in the structural diversity and co-occurrence patterns of keystone microbial communities from peri-urban (agricultural land) to urban environments (hospitals, wastewater treatment plants, and zoos) across different regions. Using network analysis, we examined the structure and symbiosis of soil keystone taxa and their association with environmental factors during urbanization. Results revealed that some urban soils exhibited higher microbial diversity, network complexity, and community stability compared to peri-urban soil. Significant differences were observed in the composition, structure, and potential function of keystone microbial taxa between these environments. Correlation analysis showed a significant negative relationship between keystone taxa and mean annual precipitation (p < 0.05), and a strong positive correlation with soil nutrients, microbial diversity, and community stability (p < 0.05). These findings suggest that diverse keystone taxa are vital for sustaining microbial community stability and that urbanization-induced environmental changes modulate their composition. Shifts in keystone taxa composition reflect alterations in soil health and ecosystem functioning, emphasizing their role as indicators of soil quality during urban development. This study highlights the ecological importance of keystone taxa in shaping microbial resilience under urbanization pressure. Full article