Search Results (950)

Driven by increasing demand in the health and wellness industry, Traditional Chinese Medicine (TCM) agriculture currently faces significant challenges related to supply–demand imbalances and continuous cropping obstacles (CCOs). Intercropping and crop rotation can mitigate yield decline and environmental stress by improving microclimates and rhizosphere ecology. However, there is still a lack of bibliometric synthesis within this research area. To analyze research hotspots and evolutionary trends, 192 articles on the intercropping and crop rotation of medicinal plants were collected from the Web of Science Core Collection (1998–2025), including databases such as the Science Citation Index Expanded (SCIE), the Social Science Citation Index (SSCI) and the Conference Proceedings Citation Index (CPCI). The results revealed a steady increase in publication volume over time. China emerged as the most prolific contributor (93 articles), while the United States occupied a pivotal position in the global collaborative network, achieving a high centrality of 0.90. Research hotspots in this field have evolved from an early emphasis on plant yield and quality toward the mechanisms for alleviating CCOs, interspecific interactions within the rhizosphere microbiome, and the ecological management of soil health. Keyword bursts indicate that “microbial community” and “carbon” have emerged as the current research frontiers. To clarify the micro-mechanisms by which intercropping and crop rotation patterns mitigate or prevent CCOs, future research should prioritize the integration of multi-omics approaches to resolve molecular interactions within the “microbe–plant–soil” nexus. Key priorities include the development of functional Synthetic Microbial Communities (SynComs) and the establishment of comprehensive evaluation systems for ecological cultivation. Furthermore, aligning these models with global climate neutrality strategies would facilitate the balance between high-quality medicinal production and ecosystem stability. Full article

Global climate change has altered temperature regimes, hydrological stability, and redox dynamics in inland waters, yet the continental-scale impact of these alterations on sediment microbiomes remains poorly understood. Here, we compiled 562 publicly available 16S rRNA gene datasets from lake sediments across five major climatic zones in China to examine how climatic gradients influence microbial diversity, community assembly, and interaction networks, as well as their associated taxonomic composition and environmental responses. Sediment microbiomes showed clear spatial differentiation in both α- and β-diversity, accompanied by climatic zone-specific taxonomic signatures and biomarker taxa. Community assembly also varied markedly across climatic zones, with stochasticity and dispersal limitation dominating in colder regions, transitional assembly in the south temperate zone, and stronger selective or high-turnover dynamics in the warm subtropics. Importantly, random forest models revealed a clear transition from climate-dominated to anthropogenic-dominated control in sediment microbiome organization: microbial variation in the plateau and temperate regions was primarily associated with climatic and geographic constraints, whereas anthropogenic factors played a more important role in shaping community differentiation in the central subtropical zone. By integrating diversity patterns, taxonomic composition, assembly processes, and network topology, we further propose a three-stage conceptual pattern of sediment microbial community organization along climatic gradients, shifting from a persistence-dominated regime in the cold plateau regions, to an efficiency-dominated regime in the temperate zones, and finally to a plasticity-dominated regime in the warm subtropical regions. These findings would provide a continental-scale framework for understanding sediment microbiome responses to coupled climatic and anthropogenic forcing in inland waters, with implications for future water quality management and ecosystem conservation. Full article

Microplastics (MPs) are emerging pollutants that affect soil–microbe interactions in paddy ecosystems. Periphytic biofilms (PBs) are complex microbial consortia that ubiquitously distribute at the soil–water interface of paddy ecosystems, playing essential roles in nutrient cycling and pollutant migration. However, whether MPs affect the community composition of PBs remains largely unknown. This microcosm study investigated the effects of three types of MPs (polyacrylonitrile, PAN; polyethylene, PE; and polyethylene terephthalate, PET) on the community characteristics of PBs via high-throughput sequencing (16S/18S rRNA) technology. Results showed that the addition of all MPs significantly increased the biomass and chlorophyll-a content of PBs, with PAN inducing the maximum increase (by 331.9% and 128.6%). However, all MPs had no significant effect on the PB α-diversity of bacterial and eukaryotic communities (p > 0.05). As for PB composition, PAN and PET increased the relative abundance of Cyanobacteria, Proteobacteria and Holozoa, PE increased that of Cyanobacteria, Bacteroidota and Blastocladiomycota, and all MPs decreased the relative abundance of Chloroflexi, Actinobacteriota and Basidiomycota. Furthermore, PET decreased the predicted functional potential of natural polymer degradation (cellulolysis, ligninolysis, xylanolysis, ureolysis), nitrogen fixation and nitrate ammonification, while PE increased predicted potential for plastic degradation, nitrate reduction and denitrification. Co-occurrence network analysis suggested that the PE network showed higher connectivity and lower modularity, while the PAN network showed higher modularity. This study advances our understanding of soil MPs–microbe interactions under high-concentration conditions. It also suggests that PB community characteristics may serve as potential bioindicators for soil MP pollution. Full article

The global demand for Salvia miltiorrhiza Bunge in the botanical medicine market is steadily increasing. However, its production has long relied on asexual root propagation, making it highly susceptible to germplasm degradation. Transitioning to seed reproduction offers the advantage of genetic renewal, yet it is constrained by unstable seed vigor and slow seedling growth. In the present study, comprehensive physiological and microbiome analyses of S. miltiorrhiza seeds from 14 regions across 7 provinces in China were conducted to elucidate the association between the seed microbiome and vigor, and to identify plant growth-promoting (PGP) strains. The results demonstrated: (1) Seed physical traits and germination characteristics varied significantly across geographic origins. Seed vigor, exhibiting the highest coefficient of variation, served as a key parameter reflecting germination quality. (2) High-vigor seeds harbored distinct microbial communities characterized by higher diversity indices, greater network complexity, and the significant enrichment of potentially beneficial bacteria (e.g., Pseudomonas). (3) Through correlation-directed screening of isolated pure cultures, Pseudomonas mendocina P-6 and Enterobacter ludwigii BM-12 were identified as exhibiting robust, multi-trait PGP capacity. In planta validation showed that these two strains significantly promoted the growth of 1-month-old S. miltiorrhiza seedlings, increasing total fresh weight by 33.9–71.3%. This study reveals the microecological drivers of seed vigor and provides candidate strains for inoculant development, thereby supporting the sustainable, seed-based propagation of S. miltiorrhiza. Full article

To investigate how steam-explosion pretreatment affects humification during sawdust composting, an aerobic composting experiment was conducted using sawdust, chicken manure, and spent mushroom substrate as feedstocks. Two treatments were established—a steam-explosion-pretreated sawdust group (SEW) and an untreated sawdust control (CK)—each with three replicate reactors. Samples were collected dynamically at five key composting stages (initial, heating, thermophilic, cooling, and maturation) for physicochemical, enzymatic, and microbial community analyses. Linear mixed-effects model analysis revealed that enzyme activities were significantly affected by treatment, composting time, and their interaction. SEW significantly enhanced cellulase and polyphenol oxidase activities, and increased laccase and peroxidase activities at specific stages. Compared with CK (humic substances, 75.30 g/kg), SEW promoted higher humic substance accumulation (120.80 g/kg) and altered the dynamics of dissolved organic carbon. Microbial co-occurrence networks in SEW (50 nodes, 602 edges) were more complex than CK (49 nodes, 464 edges), indicating tighter microbial interactions. Path analysis revealed that HS in CK was mainly influenced by DOC and temperature, while HS in SEW was associated with enzyme activities, microbial diversity, and Pseudogracilibacillus. These results suggest that steam-explosion pretreatment enhances substrate transformation and humic substance formation during composting. Full article

Triplophysa yarkandensis (Cypriniformes: Nemacheilidae), a rare endemic fish in the Tarim River Basin, Xinjiang, China, plays a pivotal role in maintaining the stability of plateau saline–alkaline aquatic ecosystems, yet its survival is increasingly threatened by habitat salinization. However, the multi-dimensional synergistic adaptation mechanisms linking its phenotypic variation, intestinal structure, and associated microbial communities to extreme saline–alkaline stress remain poorly understood. In this study, we innovatively integrated morphological/intestinal histological characterization, 16S rRNA gene sequencing, and microbial ecological analyses (co-occurrence networks and assembly processes) to systematically decode its adaptive strategies. Results revealed that T. yarkandensis exhibits a streamlined body shape, morphological variability, and elongated intestinal villi that may support locomotion and nutrient/ion uptake under osmotic stress. Its gut exerts a stringent selective filter, driving distinct differentiation between water and gut microbial communities—with gut-enriched core taxa (Aurantimicrobium and Aestuariivirga) and functional pathways (unsaturated fatty acid biosynthesis and ABC transporters) specialized for osmoregulation. Notably, the water microbial assembly is dominated by stochastic processes, while the gut assembly relies on host-driven deterministic selection, forming a habitat-specific adaptive pattern. These findings uncover the synergistic adaptation system of host phenotype and gut microbiota for survival in extreme saline–alkaline habitats, advancing our understanding of fish–microbe co-evolution in extreme ecosystems and providing critical theoretical support for the conservation of rare plateau fish, as well as guidance for the utilization of saline–alkaline water resources in aquaculture. Full article

Viruses are key regulators of marine microbial communities, yet their temporal dynamics in tropical intertidal sediments remain poorly characterized. We conducted a year-long metagenomic survey of sandy intertidal sediments in Sanya Bay (60 monthly samples from five sites) to examine viral taxonomy, community structure, lytic proteins, and auxiliary metabolic genes (AMGs). Within the classifiable fraction, the assemblages were consistently dominated by Assiduviridae. However, NMDS analysis revealed a significant overall seasonal shift, with October–December samples separating from the rest of the year. Co-occurrence network analysis identified five co-occurrence modules with distinct temporal patterns, alongside a concurrent decline in module abundance and lytic proteins in October. Functional annotation showed that cysteine and methionine metabolism, primarily driven by DNA methyltransferases, was identified as a highly represented AMG category among the annotated functions, while other pathways displayed seasonal variability. Collectively, these findings suggest that although characterized by a classifiable fraction dominated by Assiduviridae, the highly complex tropical intertidal viral communities undergo substantial seasonal reorganization in structure and functional potential. Full article

Prophylactic antibiotic use in intensive aquaculture promotes antimicrobial resistance, necessitating the development of microbial-based interventions. This study evaluated the individual, complementary, and synergistic effects of Bacillus subtilis natto (BSN) and Lactobacillus plantarum (LP) on the physiological performance and intestinal microecology of juvenile Japanese flounder (Paralichthys olivaceus). Over a 60-day trial, juveniles (initial weight: 5.81 ± 0.03 g) received a basal diet (CON) or a diet supplemented with 10⁷ CFU/g of BSN, LP, or both (BSN+LP). The BSN+LP consortium elicited complementary improvements in final body weight (21.39 ± 0.75 g vs. 18.66 ± 0.44 g in CON) and feed conversion efficiency (p < 0.05). Transcriptomic analysis revealed synergistic upregulation of digestive proteases (trypsin, chymotrypsin). Notably, an in pro-inflammatory markers (IL-1β, TNF-α) was counterbalanced by substantial upregulation of anti-inflammatory cytokines (IL-10, 5.65-fold; TGF-β1, 4.48-fold), suggesting the induction of mucosal tolerance rather than pathological enteritis. High-throughput 16S rRNA sequencing showed that the control cohort had a potential baseline microbial, characterized by a high relative abundance of Proteobacteria. BSN+LP administration significantly altered this microbial community into a fermentative eubiosis enriched in Firmicutes and Bacteroidota. Correlation network analyses confirmed negative interaction dynamics: increased abundance of Lactobacillus, Bacteroides, and Muribaculaceae was negatively correlated with baseline pathobiont abundance. These findings indicate that co-administration of BSN and LP hypothetically enhances metabolic energy harvest via short-chain fatty acid-producing taxa, strengthens the gut–immune axis, and competitively mitigates opportunistic pathogens. Full article

Phosphorus (P) limitation is prevalent in terrestrial ecosystems. Plants can improve soil P availability through the exudation of organic acids and symbiotic interactions with microorganisms. However, associations between different plant functional groups and phosphorus cycling in P limited karst ecosystems remain poorly understood. To investigate this, the exudation rates of oxalic, citric and acetic acids from fine roots, the contents of carbon, nitrogen, and P in leaves and fine roots, and the contents of oxalic, citric and acetic acids, total P, available P (AP), and microbial biomass P in rhizosphere soils were measured across different plant functional groups in a karst ecosystem in southwestern China. Additionally, the activities of acid and alkaline phosphatases were also analyzed, as well as the relative abundance, community structure, diversity, and co-occurrence network patterns of arbuscular mycorrhizal fungi (AMF) and alkaline phosphatase-encoding (phoD) gene-harboring bacteria. The results showed that both the exudation rates and the contents of organic acids and AP were highest in the tree group, followed by the shrub and grass groups. The AP content of the legume group was significantly higher than that of the non-legume group. The exudation rates of oxalic acid were significantly greater than those of citric and acetic acids. AMF diversities were highest in the shrub and legume groups. The diversities of phoD-harboring bacteria decreased from the tree group to the shrub group and then to the grass group, yet there were no significant differences between the legume and non-legume groups. The communities of both AMF and phoD-harboring bacteria exhibited significant differences among these plant functional groups. The prevalent genera of phoD-harboring bacteria across all groups were Pseudomonas and Halomonas, with Halomonas being particularly prevalent in the legume group. The AMF community was dominated by Glomus, which attained its highest relative abundance in the tree and legume groups. Furthermore, the increased exudation rate and content of oxalic acid were associated with higher relative abundances of Glomus in AMF and Pseudomonas and Bacillus among phoD-harboring bacteria. Structural Equation Model (SEM) analysis demonstrated that plant-exuded organic acids, especially oxalic acid, were positively associated with P availability indirectly through their linkages with the diversity and abundance of AMF and phoD-harboring bacteria. The crucial role of oxalic acid was particularly prominent in the tree and legume groups. Our findings suggest that screening AMF and phoD-harboring bacteria with highly efficient P transformation activity and inoculating them into the rhizosphere of plants with high oxalic acid exudation could help improve plant resilience to P limitation and support sustainable restoration in karst ecosystems. Full article

Root exudates are key drivers of rhizosphere microbial assembly, yet their effects across coexisting plant species with different functional roles remain unclear. We examined the effects of root exudates from five desert steppe species in Inner Mongolia: one constructive species, two dominant species, and two accompanying species. Exudates were collected hydroponically and applied to bulk soil in a three-week incubation experiment. Microbial communities were analyzed using high-throughput sequencing, functional prediction, and co-occurrence network analysis. Exudate addition significantly altered bacterial community composition, reducing bacterial richness, while fungal communities showed weaker responses. Exudates from constructive and dominant species enriched Actinobacteria, including Rubrobacter, Arthrobacter, and Solirubrobacter, and increased functional groups linked to chemoheterotrophy and nitrogen transformation. In contrast, exudates from accompanying species induced distinct microbial assemblages without promoting Actinobacteria dominance. Exudate addition also increased bacterial network complexity, suggesting enhanced microbial interactions. Soil pH decreased and available nitrogen and phosphorus increased, strongly correlating with bacterial community shifts. Overall, root exudates mediate species-specific microbial assembly and functional reorganization in desert steppe soils, driven mainly by plant functional roles rather than taxonomic relatedness. This study provides new insights into how plant-derived substrates regulate microbial communities and nutrient cycling in arid ecosystems. Full article

The prized wild mushroom Tricholoma matsutake maintains distinctive microbiota within its dominant zone; however, the spatial and seasonal reorganization of microbiota from taxonomic and functional perspectives remain poorly understood. High-throughput amplicon sequencing was performed in warming (March–June) and cooling (September–December) seasons to compare microbial communities among T. matsutake-dominant (present, visible mycelium) and -nondominant soils (transition, adjacent with present; control, distant from fairy ring). Fungal and bacterial community structures in T. matsutake-dominant soils were obviously distinct (ANOSIM, R > 0.6, p = 0.001), and bacterial communities exhibited clear seasonal separation. The relative abundances of Ascomycota and Mortierellomycota significantly reduced, whereas mycorrhiza-helper bacteria, including Paenibacillus, Bacillus, and Cohnella, were enriched. Functional predictions suggested that the potential expression of cofactor and vitamin biosynthesis, nutrient degradation, and inorganic nutrient metabolism pathways may be enriched in T. matsutake-dominant soil. During the fruiting period, the expression of the predicted amino acid biosynthesis pathway may be reduced, whereas that of the cofactor/carrier/vitamin biosynthesis pathway may be enriched. Our findings suggest that T. matsutake dominance could be associated with the spatial and seasonal restructuring of soil microbial communities, potentially leading to the formation of functionally interconnected microbial networks. Therefore, this study predicts hidden ecological insights that, once biochemically validated, may be used to develop important strategies for the sustainable conservation and artificial cultivation of T. matsutake. Full article

Background: Root-knot nematodes (RKNs) are destructive parasites affecting both agricultural and natural plants. Fagopyrum tataricum, a phenolic-rich edible and medicinal plant, has antidiabetic, anti-inflammatory, and anticancer properties, yet the impact of RKN infection on its rhizosphere microbiome remains unclear. Methods: We employed full-length 16S rRNA gene sequencing (FL16S) to profile bacterial communities in the rhizosphere of healthy and RKN-infected F. tataricum plants. Results: FL16S classified 78.41% of operational taxonomic units (OTUs) at the genus level and 69.18% at the species level. Healthy plants showed higher richness, diversity, and evenness, while principal co-ordinate analysis (PCoA) and PERMANOVA indicated significant RKN-associated shifts in community composition. Dominant phyla included Bacteroidota, Proteobacteria, Patescibacteria, Verrucomicrobiota, Actinobacteriota, Acidobacteriota, and Chloroflexi, with Abditibacteriota enriched in healthy and Acidobacteriota in diseased rhizospheres. At the OTU level, 66 differentially abundant taxa were identified, including nine hub OTUs in healthy plants, suggesting keystone roles in network stability. Network analyses revealed reduced diversity, interactions, and altered intra- and inter-phylum dynamics under RKN infection. Conclusions: These findings provide insight into rhizosphere microbial responses to RKN parasitism in F. tataricum and identify potential microbial biomarkers and biocontrol targets, supporting microbiome-based management strategies. Full article

Alpine treeline and shrubline ecotones are climatically sensitive transition zones where vegetation shifts strongly influence belowground microbial processes. Soil bacteria and fungi, as core component of the soil microbiome, play vital roles in nutrient cycling and plant–soil interactions within these fragile ecosystems. However, the structure and diversity of soil microbial communities across the treeline–shrubline transition remain poorly understood. Here, we investigated soil bacterial and fungal communities across treeline and shrubline ecotones in two mountain on the eastern Tibetan Plateau. We further examined how soil physicochemical properties shaped microbial community assembly. Our results demonstrated that the community composition of both bacteria and fungi differed significantly between the treeline and shrubline ecotones, while the Shannon index showed no significant variation. At the phylum level, Proteobacteria, Actinobacteriota, and Acidobacteriota dominated bacterial communities, while Ascomycota and Basidiomycota were the predominant fungal phyla. Both the network complexity of soil bacterial and fungal communities changed significantly across ecotones. Specifically, bacterial network complexity increased significantly toward the shrubline, whereas fungal network complexity declined. Bacterial community compositions were co-regulated by both environmental and vegetation factors, while fungal community compositions were only regulated by soil pH. Redundancy analysis revealed that soil organic carbon, pH, and moisture were the primary drivers of bacterial community (38.17%), whereas vegetation cover, soil organic carbon, and moisture explained the largest proportion of fungal community (44.79%). Our findings reveal the distribution patterns and underlying shift mechanisms of microbial communities between the treeline and shrubline ecotone. These insights are crucial for mountain biodiversity conservation and for improving predictions of forest responses to climate change. Full article

Schizopygopsis younghusbandi is an endemic and economically important fish in the Qinghai-Xizang Plateau, but its aquaculture is limited by harsh environmental conditions and incomplete understanding of host–microbiome–environment interactions. This study applied metagenomic sequencing to examine how different culture environments affect growth, water microbial communities, and gut microbiome network stability. Three-year-old juveniles (initial body weight 50.57 ± 1.88 g) were reared for 90 days in five systems: conventional pond (P), wetland (WL), concrete tank (G), river (R), and recirculating aquaculture system (RC). No significant differences in initial body weight or length were observed among groups (p > 0.05). Fish in the RC system achieved the highest final body weight, weight gain rate, and specific growth rate (p < 0.05), while survival rates were highest in the river and RC groups and lowest in ponds (p < 0.05). Microbial diversity and community composition differed significantly among culture modes, with bacterial and protozoan communities showing the strongest environmental responsiveness. Co-occurrence network analyses revealed that RC and G systems exhibited higher network complexity, density, and proportion of positive correlations, reflecting enhanced microbial interaction and ecological stability, whereas the WL system showed reduced network connectivity. Correlation analysis indicated that bacterial abundance was positively associated with total nitrogen, total phosphorus, and dissolved oxygen (p < 0.05), highlighting environmental regulation of microbial assemblages. Overall, the aquaculture environment shapes gut microbial networks, which closely relate to growth performance. Recirculating aquaculture systems can mitigate growth limitations in plateau fish by stabilizing the environment and reinforcing gut microbial communities, providing a sustainable strategy for high-altitude aquaculture development. Full article

Aquatic–terrestrial ecotones are highly dynamic biogeochemical hotspots where hydrological fluctuations profoundly influence microbial community structure and ecosystem functioning. However, the mechanisms underlying microbial community responses across hydrological gradients remain insufficiently understood. In this study, 16S rRNA gene sequencing was used to comparatively analyze bacterial communities in the waterward and landward zones of the drawdown area of the Danjiangkou Reservoir. The results showed that bacterial community composition differed significantly between the two zones, and waterlogging markedly increased bacterial α-diversity. Community variation was primarily associated with key environmental factors, including total phosphorus (TP), soil moisture content (SMC), and nitrate nitrogen (NO₃⁻-N). Compared with the landward zone, stochastic processes contributed more to community assembly in the waterward zone, which also exhibited higher network complexity and topological stability. In addition, several keystone taxa were identified, suggesting their potential roles in maintaining network structure and ecological stability. Functional prediction further revealed distinct metabolic potentials between zones, with enhanced anaerobic and redox-related functions in the waterward zone and predominantly aerobic metabolism in the landward zone. These findings suggest that hydrological fluctuations reshape bacterial community structure and potential ecological functions by jointly regulating water availability and nutrient dynamics. This study provides new insights into microbial ecological processes in reservoir riparian zones and offers a scientific basis for the management of aquatic–terrestrial ecotone ecosystems. Full article