Search Results (1,171)

The saline–alkali soil environment profoundly influences the diversity and composition of soil microbial communities, reshaping their ecological network structures. As a vital staple crop, rice (Oryza sativa L.) plays a crucial role in global food security, highlighting the urgent need to improve its cultivation efficiency in saline–alkali soils. However, the mechanisms by which rice roots recruit beneficial microorganisms from native soils under prolonged saline–alkali stress remain largely unclear, and limited research has been conducted on the effectiveness of microbial inoculants in enhancing rice salt tolerance. This study investigated microbial communities in a saline field subjected to over a decade of continuous rice cultivation. Plant growth-promoting microorganisms were isolated and screened from the rhizosphere. The findings revealed long-term salt stress significantly altered microbial diversity and community composition, although the overall microbial network structure remained resilient. A total of 21 plant growth-promoting strains were identified, indicating that rice roots under sustained salt stress selectively recruit beneficial microbes that contribute to plant growth and stress adaptation. Further experimental validation demonstrated that synthetic microbial communities outperformed individual strains in promoting rice seedling growth under high-salinity conditions, likely due to synergistic microbe and microbe–plant interactions. In conclusion, while saline–alkali conditions disrupt native microbial communities, rice exhibits adaptive capacity by selectively enriching growth-promoting microorganisms. The application of synthetic microbial consortia presents a promising strategy to enhance rice resilience and productivity in saline–alkali environments. Full article

Arid and semi-arid regions show distinctive bacterial groups important for the sustainability of ecosystems and soil health. This study aims to investigate how environmental factors across five Qatari soils influence the taxonomic composition of bacterial communities and their predicted functional roles using 16S rRNA amplicon sequencing and soil chemical analysis. Soil samples from five different locations in Qatar (three coastal and two inland) identified 26 bacterial phyla, which were dominated by Actinomycetota (35–43%), Pseudomonadota (12–16%), and Acidobacteriota (4–13%). Species-level analysis discovered taxa such as Rubrobacter tropicus, Longimicrobium terrae, Gaiella occulta, Kallotenue papyrolyticum, and Sphingomonas jaspsi, suggesting the presence of possible novel microbial families. The functional predictions showed development in pathways related to amino acid metabolism, carbohydrate metabolism, and stress tolerance. In addition, heavy-metal-related taxa, which are known to harbor genes for metal resistance mechanisms including efflux pumps, metal chelation, and oxidative stress tolerance. The presence of Streptomyces, Pseudomonas, and Bacillus highlights their roles in stress tolerance, biodegradation, and metabolite production. These findings improve the understanding of microbial roles in dry soils, especially in nutrient cycling and ecosystem resilience. They highlight the importance of local bacteria for sustaining desert soil functions. Further research is needed to validate these relationships, using metabolomic approaches while monitoring microbial-community-changing aspects under fluctuating environmental conditions. Full article

Accurate genome binning is essential for resolving microbial community structure and functional potential from metagenomic data. However, existing approaches—primarily reliant on tetranucleotide frequency (TNF) and abundance profiles—often perform sub-optimally in the face of complex community compositions, low-abundance taxa, and long-read sequencing datasets. To address these limitations, we present MBGCCA, a novel metagenomic binning framework that synergistically integrates graph neural networks (GNNs), contrastive learning, and information-theoretic regularization to enhance binning accuracy, robustness, and biological coherence. MBGCCA operates in two stages: (1) multimodal information integration, where TNF and abundance profiles are fused via a deep neural network trained using a multi-view contrastive loss, and (2) self-supervised graph representation learning, which leverages assembly graph topology to refine contig embeddings. The contrastive learning objective follows the InfoMax principle by maximizing mutual information across augmented views and modalities, encouraging the model to extract globally consistent and high-information representations. By aligning perturbed graph views while preserving topological structure, MBGCCA effectively captures both global genomic characteristics and local contig relationships. Comprehensive evaluations using both synthetic and real-world datasets—including wastewater and soil microbiomes—demonstrate that MBGCCA consistently outperforms state-of-the-art binning methods, particularly in challenging scenarios marked by sparse data and high community complexity. These results highlight the value of entropy-aware, topology-preserving learning for advancing metagenomic genome reconstruction. Full article

Marsh wetland degradation and shrub expansion, driven by human activities and climate change, can impact carbon, nitrogen, and sulfur cycles by soil microorganisms. There is a paucity of systematic and in-depth research on the impact of shrub expansion in temperate wetlands on soil element cycles, which is a pressing scientific issue that demands resolution. This study used metagenomic sequencing and soil analysis methods to investigate the impact of shrub expansion in the Sanjiang Plain wetlands on carbon, nitrogen, and sulfur cycles in temperate wetland soils, as well as on functional microbial communities. Shrub expansion significantly altered soil carbon, nitrogen, and sulfur cycle processes and the composition (β diversity) of associated functional microbial communities, despite minimal changes in overall α diversity. Significant shifts occurred in the abundance of cycle pathways and related functional genes. Ammonia nitrogen, moisture, and total phosphorus were identified as the primary factors influencing these cycles and the functional microbial communities. Changes in the abundance of specific cycling pathways following shrub expansion are key drivers of functional community structure transformation. These changes may significantly reduce the long-term carbon sequestration potential of wetlands and affect regional climate feedback by altering greenhouse gas fluxes. The findings provide a theoretical basis for managing shrub expansion and assessing wetland function. Full article

The karst region is highly ecologically fragile due to its unique geology and poor water and nutrient retention. Despite long-term restoration, vegetation often remains in the secondary shrubland stage. Soil microorganisms play a vital role in maintaining ecosystem functions, but how microbial communities respond to combined water and nitrogen-phosphorus nutrient changes in karst shrubland remains poorly understood. This knowledge gap hinders effective restoration strategies in karst shrublands. Here, the effects of water, nitrogen, and phosphorous additions and their interactions on soil physico-chemical properties, soil microbial abundance, diversity, community composition, and the co-occurrence network were explored. A full factorial experiment (water × nitrogen × phosphorous, each at two levels) was conducted in a karst shrubland with over 20 years of vegetation restoration, with treatments including control, water (+120 mm yr⁻¹), nitrogen (+20 g N m⁻² yr⁻¹), phosphorus (+16 g P m⁻² yr⁻¹), and their four combinations. Our results suggested that water addition significantly increased soil water content and soil microbial abundance but reduced fungal diversity. Nitrogen addition significantly increased soil nitrate nitrogen content and fungal diversity, and fungal diversity showed an increasing trend under phosphorous addition. The addition of nitrogen and phosphorous did not significantly alter the soil microbial community composition, while water addition showed a tendency to change the soil fungal community composition. Network topological properties, robustness, and vulnerability analyses indicated that individual nitrogen or phosphorous additions, as well as their interactions, reduced network complexity and stability. In contrast, water addition alone or in combination with nitrogen and/or phosphorous alleviated these negative effects, and the water and phosphorous interaction exhibited the highest levels of network complexity and stability. Further analysis showed that the soil pH, available phosphorous, ratio of carbon to phosphorous, and ammonium nitrogen were explanatory variables contributing significantly to soil microbial abundance, diversity, community composition, and network complexity. Overall, these findings highlighted the pivotal role of water availability in enhancing soil microbial stability under nutrient enrichment, offering valuable insights into ecological restoration in karst ecosystems. Full article

To investigate the effects of the endophytic fungus Setophoma terrestris (isolated from Panax notoginseng roots) on the growth and rhizosphere microbiota of understory-cultivated P. notoginseng, we prepared liquid and solid fermentates of the fungus and applied them separately via irrigation. Rhizosphere soil of P. notoginseng was subjected to non-targeted metabolomics and microbiome sequencing for detection and analysis. Relative to the control, P. notoginseng treated with liquid and solid fermentates exhibited increases in plant height (3.5% and 0.7%), chlorophyll content (23.4% and 20.4%), and total saponin content (14.6% and 17.0%), respectively. Non-targeted metabolomics identified 3855 metabolites across 23 classes, with amino acids and their derivatives (21.54%) and benzene derivatives (14.21%) as the primary components. The significantly altered metabolic pathways shared by the two treatment groups included ABC transporters, purine metabolism, and the biosynthesis of various other secondary metabolites. Exogenous addition of S. terrestris significantly affected the composition of the rhizosphere soil microbial community of P. notoginseng and increased the relative abundance of genera such as Bradyrhizobium. In conclusion, the endophytic fungus S. terrestris enhances P. notoginseng growth and modulates both rhizosphere soil metabolites and microbial abundance. This study can provide certain data support for research on endophytic fungi of P. notoginseng. Full article

To investigate the effects of intercropping green manure on the tea plantation ecosystem, this study was conducted using 40-year-old Camellia sinensis cv. “Fuding Dabai” tea plants at the Tea Experimental Base of the Jiangxi Institute of Cash Crops. Four treatments were established: clean tillage (CK), tea intercropped with ryegrass (Lolium perenne, TRG), tea intercropped with rapeseed (Brassica napus, TRP), and tea intercropped with alfalfa (Medicago sativa, TAL). The study systematically evaluated the effects of green manure on tea yield, soil nutrient content, enzyme activity, and microbial community structure. The results showed that intercropping with green manure significantly increased the bud density, hundred-bud weight, and yield of tea in spring, summer, and autumn, with the TAL treatment showing the best overall performance. In terms of soil physicochemical properties, green manure treatments significantly improved soil organic matter, total nitrogen, available nitrogen, available phosphorus, and available potassium contents, with TRP and TAL showing the most pronounced improvements. Enzyme activity analysis indicated that the TRP treatment significantly enhanced the activities of amylase, urease, and invertase. High-throughput sequencing results revealed that green manure treatments significantly increased both the number of bacterial and fungal OTUs (Operational Taxonomic Units) and alpha diversity indices. The TAL and TRP treatments showed superior performance in terms of Shannon, Chao, and ACE indices compared to CK. Principal coordinate analysis (PCoA) indicated that green manure had a greater influence on fungal community structure than on bacterial structure. Correlation analysis demonstrated that dominant microbial taxa were significantly associated with soil nitrogen, phosphorus, and potassium levels, suggesting that green manure modulates microbial community composition by improving soil nutrient status. Intercropping green manure significantly increased tea yield and soil quality compared with clean tillage. Alfalfa intercropping (TAL) increased tea yield by 49.61%, 40.88%, and 43.79% in spring, summer, and autumn, respectively, compared with the control. Soil organic matter and total nitrogen under TAL were 29.02% and 15.67% higher than the control, while rapeseed intercropping (TRP) increased available phosphorus by 186%. TAL and TRP also enhanced microbial diversity, with bacterial Shannon index values 14.11% and 11.25% higher than the control. These results indicate that alfalfa intercropping is the most effective green manure practice for improving tea plantation productivity and soil ecology. Full article

The ecological interface between grasslands and farmlands forms a critical landscape component, significantly contributing to the stability and functioning of ecosystems within the agro-pastoral transition zone of northern China. Nevertheless, the variation patterns and interactions between soil physicochemical attributes and microbial community diversity at this interface remain poorly understood. In this study, we investigated nine sites located within 50 m of the grassland–farmland boundary in the Songnen Plain, northeastern China. We assessed the soil’s physicochemical properties and the composition of bacterial and fungal communities across these sites. Results indicated a declining gradient in soil physicochemical characteristics from grassland to farmland, except for pH and total phosphorus (TP). The composition of bacterial and fungal communities differed notably in response to contrasting land-use types across the ecological interface. Soil environmental variables were closely aligned with shifts observed in bacterial and fungal assemblages. Concentrations of total nitrogen (TN), available phosphorus (AP), alkali-hydrolyzable nitrogen (AN), and available potassium (AK) exhibited inverse correlations with both bacterial and fungal populations. Alterations in microbial community composition were significantly linked to TN, TP, total potassium (TK), AN, AP, AK, and soil pH levels. Variability in soil properties, as well as microbial biomass and diversity, was evident across the grassland–cropland boundary. Long-term utilization and conversion of grassland into cultivated land altered the soil’s physicochemical environment, thereby indirectly shaping the structure of microbial communities, including both bacteria and fungi. These findings provide a valuable basis for understanding the ecological implications of land-use transitions and inform microbial-based indicators for assessing soil health in agro-pastoral ecotones. Full article

Although significant progress has been made in the conservation of Père David’s deer (Elaphurus davidianus) populations, rapid population growth in coastal wetlands has caused severe habitat degradation. This highlights the urgent challenge of balancing ungulate population dynamics with wetland restoration efforts, particularly considering the limited data available on post-disturbance ecosystem recovery in these environments. In this study, we evaluated soil quality and bacterial community dynamics at an abandoned feeding site and a nearby control site within the Dafeng Milu National Nature Reserve during 2020–2021. The goal was to provide a theoretical basis for the ecological restoration of Père David’s deer habitat in coastal wetlands. The main findings are as follows: among the measured indicators, bulk density (BD), soil water content (SWC), sodium (Na⁺), total carbon (TC), total nitrogen (TN), total phosphorus (TP), available potassium (AK), microbial biomass nitrogen (MBN), and the Chao index were selected to form the minimum data set (MDS) for calculating the soil quality index (SQI), effectively reflecting the actual condition of soil quality. Overall, the SQI at the feeding site was lower than that of the control site. Based on the composition of bacterial communities and the functional prediction analysis of bacterial communities in the FAPROTAX database, it is shown that feeding sites are experiencing sustained soil carbon loss, which is clearly caused by the gathering of Père David’s deer. Co-occurring network analyses demonstrated the structure of the bacterial community at the feeding site was decomplexed, and with a lower intensity than the control. In RDA, Na⁺ is the main soil property that affects bacterial communities. These findings suggest that the control of soil salinity is a primary consideration in the development of Père David’s deer habitat restoration programmes, followed by addressing nitrogen supplementation and carbon sequestration. Full article

Afforestation substantially promotes vegetation restoration and modifies soil physical, chemical, and biological properties. The integrated effects of soil properties on soil quality, expressed via a composite soil quality index (SQI), remain unclear despite variations among individual properties. Here, five vegetation restoration treatments were selected as follows: (1) barren land (BL, control), (2) disturbed short-rotation Eucalyptus plantation (REP); (3) undisturbed long-term Eucalyptus plantation (UEP); (4) mixed native-species plantation (MF); and (5) natural forest (NF) following >50 years of restoration. Soil physicochemical properties and microbial community compositions were investigated, and soil quality was evaluated by an integrated SQI. Our results showed that vegetation restoration had strong effects on soil physicochemical properties, soil quality, and microbial communities. Most of the soil physicochemical properties exhibited significant differences among treatments. Soil dissolved organic carbon, total nitrogen, and ammonium nitrogen were the three key soil quality indicators. The SQI increased significantly with vegetation recovery intensity. In both UEP and MF, it reached levels comparable to NF, and was higher in UEP than in REP, implying that short-rotation practices impede soil restoration. In addition, microbial biomass (bacteria, fungi, arbuscular mycorrhizal fungi, actinomycetes, and total microbe PLFAs) increased from BL to NF. All plantations exhibited lower microbial biomass than NF, revealing incomplete recovery and a greater sensitivity to soil physicochemical properties. Conversely, the fungi-to-bacteria biomass ratio decreased sequentially (REP > BL > UEP > MF > NF). Strong positive correlations between microbial biomass and the SQI were observed. These results collectively indicate that afforestation with mixed tree species is optimal for rapid soil restoration, and undisturbed long-term monocultures can achieve similar outcomes. These findings highlight that tree species mixtures and reducing disturbance should be taken into consideration when restoring degraded ecosystems in the tropics. Full article

Tree plantations can help reverse the negative impacts of deforestation and land degradation worldwide, and soil microbial communities play key roles in tree growth and productivity. We studied microbial communities in the bulk soil of five native species monoculture plantations in the Republic of Panamá to assess how bacteria and fungi were affected by soil chemistry and plant identity after seven years of tree growth. Relative to the other species, Terminalia amazonia accumulated over three times the aboveground biomass and had lower mortality. Soil nutrients, especially phosphorus, were low, and we found no differences in soil chemistry across the five plantation types. Similarly, there was no difference in alpha diversity of the soil microbial communities across plantation types, and the bacterial communities showed no compositional variation or enrichment of any individual taxa. However, soil fungal communities differed in T. amazonia plantations as compared to the others, exhibiting enrichment or absence of specific taxa of arbuscular mycorrhizal fungi and putative phytopathogens. Our results suggest that T. amazonia may associate with certain microbial taxa that help it overcome low nutrient availability in these habitats. Consideration of plant–soil–microbe interactions in restoration efforts may facilitate tree growth and help to promote climate resilient forested areas. Full article

Verticillium wilt, a prevalent soil-borne disease, poses a significant challenge to cotton production in Xinjiang, China. Continuous cotton monoculture has increased disease incidence and affected soil microbial diversity in Xinjiang, while crop rotation is recognized as an effective strategy for soil pathogen control. This study investigates how a one-year maize rotation affects Verticillium wilt incidence and soil microbiome composition in cotton fields across northern and southern Xinjiang. The results demonstrated that short-term rotation significantly reduced Verticillium wilt occurrence in both northern and southern Xinjiang. Using high-throughput sequencing of fungal ITS and bacterial 16S rRNA regions, microbial community analysis revealed minimal changes in alpha-diversity but significant structural reorganization between continuous cropping (CC) and rotation (CR) systems, particularly in fungal and bacterial genera composition, with distinct spatial patterns between northern and southern fields. Crop rotation promoted beneficial taxa such as Sphingomonas and Pseudogymnoascus, while reducing the abundance of pathogens such as Verticillium dahliae. LEfSe study suggested Tepidisphaerales and Lasiosphaeriaceae as biomarkers for CR systems, whereas Hypocreales and Blastocatellia dominated in CC soils. Co-occurrence network analysis revealed more bacterial connectivity and modularity under CR, suggesting better microbial interactions and ecological resilience. The increased structural complexity of bacterial networks under CR indicates their greater contribution to soil health maintenance and ecosystem resilience. Our findings demonstrate that short-term crop rotation not only effectively reduces Verticillium wilt incidence but also restructures soil microbial communities, providing an actionable strategy for sustainable cotton cultivation in Xinjiang. Full article

In this study, we assessed soil pollutants and surveyed the bacterial communities using 16S rRNA sequencing to better understand how to improve rehabilitation strategies for nickel-laterite mines in the Philippines. Representative soil samples and rhizospheres from Saccharum spontaneum L. in three post-mining sites rehabilitated in 2015, 2017, and 2019 were collected and analyzed. X-ray diffraction (XRD) identified iron oxyhydroxides, silicates, and clays as major soil components. Based on the pollution load index and contamination degree, the 2015A and 2015B sites were classified as “pristine” and had a “low degree of pollution”, while the remaining sites (2017A, 2017B, 2019A, and 2019B) were considered “moderately contaminated” with nickel, chromium, cobalt, lead, zinc, and copper. An analysis of the bacterial community composition revealed that the phyla Proteobacteria and Actinobacteria, along with the genus Ralstonia, were the most abundant groups across both control and rehabilitated sites. Our results showed that the soil pH and organic matter contents were strongly linked to specific bacterial community composition. These taxa have potential for inoculation in nickel-laterite soils to promote the growth of hyperaccumulator plants. Our results also showed a significant correlation between the structure of the bacterial communities and nickel, chromium, and manganese soil contents, but not with rehabilitation time. Furthermore, we identified the genera Diaphorobacter as potential bioindicators because they are sensitive to nickel and chromium. This study provides valuable baseline data on heavy metal pollution and microbial diversity in a rehabilitated Ni-laterite mine site. Full article

Continuous cropping poses a significant threat to sustainable pepper production by triggering soil degradation and growth inhibition, yet the role of root exudates in this process remains unclear. This study aimed to elucidate how continuous cropping duration (0, 1, 2, and 6 years) alters root exudate composition and drives rhizosphere feedback in green pepper. Pot experiments revealed that long-term continuous cropping (6 years) severely inhibited pepper growth, reducing photosynthetic rate (32.02%), chlorophyll content (12.26%), plant height (23.89%), and yield (42.37%). Critically, the relative abundance of 3,4-dimethylbenzaldehyde in root exudates increased progressively with cropping duration. Exogenous application of this compound or long-term monoculture extracts reduced soil pH and increased electrical conductivity, altered the rhizosphere microbial community (notably decreasing Proteobacteria abundance and fungal diversity while increasing Bacteroidota and Firmicutes), and significantly inhibited root development and vitality. Correlation analysis indicated that fungal communities were more responsive to soil property changes, while bacterial communities correlated more closely with root traits. This study demonstrates that the accumulation of specific root exudates, particularly 3,4-dimethylbenzaldehyde, is a key driver of continuous cropping obstacles in green pepper by disrupting rhizosphere microbial community structure and soil properties. This highlights the importance of managing root exudate dynamics, potentially through crop rotation or soil amendments, to mitigate these obstacles. Full article

The impact of long-term organic (ECO) versus conventional (CON) agricultural management on subsurface soil microbiota diversity and soil physicochemical properties remains unclear in Mediterranean vineyards. This study evaluated long-term ECO and CON effects in the Alt Penedès terroir (Spain), focusing on subsurface soil microbial diversity and soil characteristics. ECO increased the fungal-to-bacterial ratio and ammonium-oxidizing bacteria but reduced total subsurface soil bacterial populations and soil organic carbon. While ECO did not enhance annual yield production in the vineyard, fungal abundance, and ammonium-oxidizing archaea, it slightly increased the overall alpha diversity (Shannon and Inverse Simpson indexes) and significantly altered taxa composition in subsurface soil with a more robust and modular community. Crop management, soil texture, training system, and rootstock, but not vine variety, significantly influenced beta diversity in subsurface soil. The Mantel test revealed subsurface soil texture, Ca²⁺/Mg²⁺ ratio, and salinity as the main key soil drivers shifting the microbial community (beta diversity), while C/N and topsoil organic matter significantly correlated with bacterial abundance; NH₄⁺ correlated with fungal abundance; and N-Kjeldahl, pH, and Mg²⁺/K⁺ correlated with alpha diversity. Integrating soil microbiota and physicochemical monitoring allowed us to confirm the positive effect of long-term agroecological practices on subsurface soil health and to identify the critical factors shaping their microbial communities in Mediterranean vineyards. Full article