Search Results (424)

Carbon (C) is crucial for nutrient cycling and the assembly of microbial populations in the soil. However, it is still unclear how the C-source utilization characteristics of microbes in distinct types of soils respond to changes in soil phosphorus (P) activity. This study investigated how the addition of different C sources with different decomposition rates (glucose, hemicellulose, and lignin) affects P transformation in two distinct agricultural soils (i.e., Mollisols and Fluvo-aquic soil). Results revealed that the short-term glucose addition to soil induced rapid acidification and microbial biomass accumulation, thereby significantly increasing labile P (NaHCO₃-P_i, NaOH-P_o) content in Fluvo-aquic soil. Lignin amendment promoted gradual HCl-P release in Mollisols, reflecting differential microbial utilization strategies. Glucose stimulated phosphatase activity (2.5–3.0× control) and phoD gene abundance (4.8×) in Fluvo-aquic soil in the early stage, favoring the growth of Pseudomonas and Burkholderia, whereas lignin sustained the mineralization of fungal-associated P in Mollisols (1.8–2.3× phosphatase activity) by enhancing the abundance of Streptomyces and Bradyrhizobium. Soil type dictated P mobilization efficiency. The Fluvo-aquic soil exhibited rapid but transient P release via bacterial dominance, while Mollisols retained slower yet persistent P availability through specialized microbial consortia. Notably, glucose enhanced organic P mineralization by stimulating C decomposition by microbes, particularly in C-rich Mollisols. Lignin increased P availability in Mollisols via Fe/Al-P desorption. However, in Fluvo-aquic soil, lignin reduced the availability of P through microbial immobilization. These findings highlight that C source degradability and soil properties interactively govern microbial-mediated P cycling in soil. Therefore, organic amendments in contrasting agroecosystems need to be optimized. Full article

Vegetation restoration is an effective strategy to improve the ecosystem function of the Loess Plateau. Soil microbiomes play a critical role in maintaining soil multifunctionality (SMF). However, the role of aggregate-scale microbial communities and interactions in regulating SMF during vegetation restoration remains poorly understood. Here, we selected six types of vegetation restoration measures in the Loess Plateau, including natural grassland (NL), Medicago sativa (MS), Hippophae rhamnoides (HR), Caragana korshinskii (CK), Armeniaca vulgaris (AV), and Populus alba (PA), and used abandoned land (AL) as a control to identify key microbial mechanisms driving SMF at the aggregate scale. The results show that vegetation restoration increased bacterial diversity, fungal network complexity, and SMF, especially in AV. In contrast, fungal diversity and bacterial network complexity exhibited asynchronous dynamics across different-sized aggregates. Soil microbial diversity peaked at micro-aggregates (0.053–0.25 mm), while fungal network complexity increased with decreasing aggregate size. The structural equation model confirmed that fungal community composition in large macro-aggregates (>2 mm) and fungal network complexity in <2 mm aggregates were the key drivers of SMF. Our results emphasize the divergent mechanisms by which microbial properties influence SMF across aggregate sizes, highlighting the importance of fungal communities in maintaining soil ecosystem functions. Full article

Grasslands, as dominant terrestrial ecosystems, significantly influence soil microbial communities through alterations in soil properties. However, their effects on spatial patterns of soil microbial communities are still under-investigated. To address this, we quantified taxa–area (TAR) and node–area (NAR) relationships for prokaryotic and fungal communities across temperate steppe (TS), alpine steppe (AS), and alpine meadow (AM). Our findings indicated that the spatial turnover of both prokaryotic and fungal communities were higher in alpine steppe and alpine meadow than in temperate steppe, mirroring the gradient of soil environmental heterogeneity. Notably, overall species richness increased logarithmically with sampling area in all grasslands; in striking contrast, co-occurring richness exhibited an increasing and then decreasing trend in AS and AM, but declined monotonically in TS, indicating that microbial interaction networks collapse once a critical spatial threshold is exceeded regulated by ecosystem type and environmental heterogeneity. In growing season, the stochastic dominance in prokaryotic assembly (Normalized stochasticity ratio = 0.71–0.89) and deterministic dominance in fungal assembly (Normalized stochasticity ratio = 0.23–0.37) can be explained by their differences in niche breadth and migration rate. These scale-dependent biogeographic patterns demonstrate that grassland type impacts distinct interactions and spatial patterns of microbial communities. These findings provide novel insights into a comprehensive understanding of how grassland type mediates soil microbial community. Full article

The mechanism by which litter–soil interface properties interact to shape the composition and diversity of litter decomposition-driving microorganisms remains unclear. Here, litter and surface soil samples were collected from three typical forest types on the Loess Plateau: Pinus tabulaeformis forest (PF), Quercus acutissima forest (QF), and their mixed forest (MF). Litter and soil chemical properties, along with litter microbial community structure, were analyzed to clarify microbial diversity differences across stands. Across the three forests, litter microbes showed no significant differences in multiple diversity indices, but dominant genera differed significantly. At all taxonomic levels, litter bacterial and fungal diversity followed the order MF < PF < QF. QF had the highest litter total nitrogen (LTN) and phosphorus (LTP) and significantly higher soil ammonia nitrogen (NH₄⁺-N) than PF and MF. Correlation analysis indicated that LTN, LTP, soil organic carbon (SOC), and soil NH₄⁺-N primarily influenced bacterial and fungal community composition and diversity. Redundancy analysis revealed litter organic carbon (LOC) as the dominant environmental driver shaping both communities, with soil NH₄⁺-N exerting a stronger effect on bacteria and nitrate nitrogen (NO₃⁻-N) on fungi. These findings deepen understanding of soil–litter–microbe interactions in forest ecosystems, laying a scientific foundation for forest management and protection. Full article

Calonectria ilicicola (anamorph: Cylindrocladium parasiticum) is a globally important soil-borne fungal pathogen, causing Cylindrocladium black rot (CBR) in peanuts (Arachis hypogaea) and red crown rot (RCR) in soybeans (Glycine max), two legume crops central to global food security. Under favorable conditions, these diseases can cause yield losses of 15–50%, with severe epidemics causing substantial economic damage. A defining feature of C. ilicicola is its production of melanized microsclerotia that persist in soil for up to seven years, complicating long-term disease management across major production regions worldwide. The recent spread of RCR into the U.S. Midwest highlights the adaptive potential of the pathogen and underscores the urgency of updated, integrated control strategies. This review synthesizes current knowledge on disease symptoms, pathogen biology, the life cycle, isolation techniques, and molecular diagnostics, with particular emphasis on recent genomic and multiomics advances. These approaches have identified key virulence-associated genes and core pathogenicity factors, providing new insights into host–pathogen interactions and enabling more targeted resistance breeding through marker-assisted selection and the use of wild germplasm. We critically evaluate integrated disease management strategies, including host resistance, chemical and biological control, cultural practices, and physical interventions, highlighting their complementarities and limitations. By integrating classical pathology with emerging molecular and ecological innovations, this review provides a comprehensive background for developing more effective and sustainable management approaches for CBR and RCR. Full article

The plant microbiome plays important roles in plant growth and resistance, but its assembly and affecting factors have not been fully studied for most of the agricultural plants. In this study, the endophytic mycobiota of the leaves and roots and the rhizosphere soils of five pummelo varieties were profiled based on the amplicon sequencing of the fungal internal transcribed spacer (ITS). The fungal richness and diversity were significantly different among the compartments, but not among the pummelo varieties. The composition and structure of the endophytic mycobiota of the compartments were significantly different across all five pummelo varieties. These suggest that the variety effect is weaker than the compartment effect, but still significant in shaping the pummelo mycobiota. Specifically, the dominant leaf endophytic fungal taxa (e.g., Fusarium and Zasmidium), and the root selection of fungal genera from the rhizosphere soils, were significantly different among the varieties. And also, the variety effect is more significant in shaping the leaf endophytic mycobiota than those of the roots. Finally, the pummelo varieties also showed some consistent alterations on the endophytic mycobiota, such as the root enrichment of Exophiala species. Our study indicates that the endophytic mycobiota of pummelos is significantly and interactively affected by plant variety and compartment effects, and suggests some fungi of interest for further tests. Full article

Urban parks are key to urban ecosystems, where soil microbe-plant-soil interactions sustain ecosystem services. Using high-throughput sequencing and multivariate statistics, this study explored how plant species diversity affects soil microbial community structure, functional diversity, and environmental drivers. Results showed that fungal and bacterial OTUs differed across plant diversity gradients, with Ascomycota (fungi) and Actinobacteriota/Proteobacteria (bacteria) dominant. Soil organic carbon (SOC) was positively correlated with Verrucomicrobia, while Acidobacteriota increased with lower SOC. Fungi were more sensitive to pH than bacteria. Partial Least Squares Path Modeling (PLS-PM) indicated that plant diversity was significantly positively associated with fungal community structure and was indirectly associated with bacterial diversity via soil factors (e.g., SOC, pH), with fungal community variation more explained than bacterial. Higher plant diversity was associated with elevated SOC and a higher relative abundance of putative nutrient-cycling taxa (e.g., Rhizobium), suggesting a potential enhancement of soil nutrient cycling capacity. This study demonstrates that plant diversity shapes microbial communities directly and via soil properties, highlighting synergistic effects. We propose arbor-shrub-herb composite vegetation in urban forest management to optimize microbial habitats and ecological services. Full article

Soil microbial communities are fundamental to ecosystem function and soil health, yet how differing land-use intensities shape these communities and their interaction networks remains unclear. We investigated soils from greenhouse cultivation (GH), arched shed systems (ASs), and open farmlands (FLs) to compare microbial composition, diversity, and network stability under contrasting management intensities. GH soils had the highest electrical conductivity, ca. ~3.9 times higher than FL soil and ~1.9 times higher than AS soil, alongside elevated soil organic matter, total N, and available nutrients. AS soil maintained intermediate nutrient levels. Bacterial α-diversity was higher in AS and GH soils than in FL soil, whereas fungal α-diversity was comparable among systems despite differences in community composition. Microbial co-occurrence network analysis revealed the most complex and robust network in ASs, followed by FLs, while GH soil had the simplest and least stable network. Structural equation modeling showed that soil chemical properties had the largest direct influence on network complexity and stability, followed by soil enzyme activities; microbial diversity and key taxa also contributed to network complexity and stability. Overall, the moderately managed AS was superior to GH and FLs in sustaining a diverse and resilient soil microbiome and network. These findings provided actionable knowledge for optimizing land management to maintain soil ecological function. Full article

Chinese fir (Cunninghamia lanceolata) is a cornerstone timber species in southern China. However, yet its plantation productivity frequently declines under successive rotations, threatening long-term sustainability. While belowground processes are suspected drivers, the mechanisms—particularly plant–soil–microbe interactions—remain poorly resolved. To address this, we examined a chronosequence of C. lanceolata plantations (5, 15, 20, and 30 years) in Jingdezhen, Jiangxi Province, integrating soil physicochemical assays, high-throughput sequencing, and extracellular enzyme activity profiling. We found that near-mature stands (20 years) exhibited a 60.7% decline in mean annual volume increment relative to mid-aged stands (15 years), despite continued increases in individual tree volume—suggesting a strategic shift from resource-acquisitive to nutrient-conservative growth. Peak values of soil organic carbon (32.87 g·kg⁻¹), total nitrogen (2.51 g·kg⁻¹), microbial biomass carbon (487.33 mg·kg⁻¹), and phosphorus (25.65 mg·kg⁻¹) coincided with this stage, reflecting accelerated nutrient turnover and intensified plant–microbe competition. Microbial communities shifted markedly over time: Basidiomycota and Acidobacteria became dominant in mature stands, replacing earlier Ascomycota and Proteobacteria. Random Forest and Partial Least Squares Path Modeling (PLS-SEM) identified total nitrogen, ammonium nitrogen, and total phosphorus as key predictors of productivity. PLS-SEM further revealed that stand age directly enhanced productivity (β = 0.869) via improved soil properties, but also indirectly suppressed it by stimulating microbial biomass (β = 0.845)—a “dual-effect” that intensified nutrient competition. Fungal and bacterial functional profiles were complementary: under phosphorus limitation, fungi upregulated acid phosphatase to enhance P acquisition, while bacteria predominately mediated nitrogen mineralization. Our results demonstrate a coordinated “soil–microbe–enzyme” feedback mechanism regulating productivity dynamics in C. lanceolata plantations. These insights advance a mechanistic understanding of rotation-associated decline and underscore the potential for targeted nutrient and microbial management to sustain long-term plantation yields. Full article

Soil fungi play an indispensable role in maintaining soil ecosystem functions. However, how forest succession and soil depth interactively shape fungal community composition and diversity remains poorly understood. To address this, we investigated fungal communities across four successional stages and two soil depths (0–10 cm and 40–60 cm) in a subalpine forest on the eastern Qinghai–Tibetan Plateau using Illumina high-throughput sequencing. Results showed that the soil fungal community composition of different trophic modes varied significantly with both succession and soil depth. The α-diversity of symbiotic and saprotrophic fungi responded to succession in a depth-dependent manner, while β-diversity across all trophic modes was primarily driven by species turnover. Soil properties and vegetation factors collectively explained 69.85–82.91% of the variation in soil fungal community composition, with their effects being dependent on both soil depth and trophic mode. Specifically, in topsoil, the β-diversity of symbiotic fungi was influenced only by soil property heterogeneity, whereas that of saprotrophic and pathogenic fungi was shaped by both vegetation and soil property heterogeneity. In subsoil, symbiotic fungal β-diversity was co-regulated by vegetation and soil properties heterogeneity, while saprotrophic fungal β-diversity was driven solely by soil properties heterogeneity. This study demonstrates that soil depth modulates the successional dynamics of soil fungal communities and highlights the trophic-dependent drivers of fungal assembly in forest soils. Full article

Background: Gastrodiae Rhizoma, the dried tuber of Gastrodia elata Bl. (Orchidaceae), is a traditional Chinese medicinal (TCM) and edible plant. Its quality formation is closely associated with rhizosphere microorganisms; however, the specific underlying mechanisms remain unclear. Methods: Tubers and rhizosphere soils were collected from seven major production regions of G. elata. Soil physicochemical properties were analyzed, and integrative analyses combining soil microbiome and untargeted metabolome profiling were conducted. The anti-inflammatory activity of G. elata extracts was evaluated using a RAW264.7 macrophage model. Multivariate statistical approaches, including OPLS-DA and correlation network analysis, were used to decipher relationships among environmental factors, microbial communities, metabolic profiles, and bioactivities. Results: A total of 39,250 bacterial ASVs and 10,544 fungal ASVs were identified. The bacterial community, dominated by Proteobacteria and Acidobacteria, was strongly influenced by soil chemical factors, including pH and total nitrogen. The fungal community, primarily composed of Ascomycota and Basidiomycota, exhibited marked sensitivity to altitudinal gradients. Correlation analysis revealed that key secondary metabolites, including flavonoids and phenolic acids, along with their anti-inflammatory activities, were significantly associated with rhizosphere microorganisms such as Edaphobaculum, Hypocrea, and Pseudomonas. Conclusions: Our findings outline the pathways connecting environmental factors, the microbiome, and functional metabolites in G. elata, highlighting the importance of environmental–microbial interactions in determining metabolic outcomes. This work provides new insights into the ecological and molecular mechanisms behind the quality formation of this medicinal plant. Full article

Phosphate fertilizer is essential for crop production but poses environmental risks in agriculture. The agronomic and environmental thresholds for phosphorus application in Southwest China’s purple soils (Luvic Xerosols) remain poorly defined. We combined soil phosphorus fractionation, root phenotyping, and microbial community analysis (16S rRNA and ITS amplicon sequencing) to explore soil–microbe–plant interactions in a 12-year field experiment with five P application rates (0, 37.5, 75, 112.5 and 150 kg P₂O₅ ha⁻¹ yr⁻¹). Results showed that beyond 75 kg ha⁻¹, the medium-soluble phosphorus pool increased significantly while stable phosphorus decreased. Fungal diversity was more sensitive to high phosphorus than bacterial diversity. Maize yield plateaued at 75–150 kg ha⁻¹, mainly due to increased grain weight and optimized root architecture. An environmental risk threshold was identified at 83.54 kg ha⁻¹ and an optimal yield threshold at 84.65 kg ha⁻¹, enabling high yield with low environmental risk via microbially mediated phosphorus activation. Therefore, this research reveals that the phosphorus input threshold can provide a basis for reducing phosphorus application, regulating phosphorus components, and maintaining microbial diversity and network complexity in purple soil dryland farming systems, thereby ensuring maize yield. Full article

Nematode-trapping fungi act as predators of nematodes in soil ecosystems, forming a typical predator–prey relationship. However, this interaction is frequently influenced by environmental factors such as nutrient state. In this study, we demonstrate that starved nematodes had better chances of escaping A. oligospora predation by inhibiting A. oligospora trap formation. Starved nematodes showed downregulated acyl-CoA oxidase genes (acox-1.2/1.3/1.4) and reduced ascaroside pheromone production (ascr#1/#3/#5/#9), thus diminishing A. oligospora trap induction. In soils with uneven nutrient content, nutrient deficiencies can activate this mechanism locally, thereby reducing predation. When avoidance fails, nematodes rely on canonical innate immune pathways (FSHR-1, ATFS-1, and PMK-1) to improve survival during capture. In response to this predation, nematodes have evolved multiple strategies to defend against these pressures, closely linked to their nutritional status. Together, these findings link local nutrient availability to both fungal predation efficiency and the robustness of nematode defenses in soil ecosystems. Full article

The rhizosheath plays a critical but poorly understood role in plant–microbe interactions. However, it still remains unclear how host selection versus geographical isolation contributes to microbial community assembly within the rhizosheath. This study characterized the bacterial and fungal communities in the rhizosheath and surrounding bulk soil of Leymus racemosus using 16S rRNA and ITS high-throughput sequencing. Results showed that the bacterial community was strongly shaped by host selection within the rhizosheath, based on significantly reduced α-diversity and distinct β-diversity (Permutation tests, p < 0.001) compared to bulk soil. Furthermore, the core bacterial community structure was highly similar between the two geographically separated sites (PERMANOVA, p = 0.089). In contrast, the fungal community exhibited weaker habitat specificity but showed significant, though weak, geographical divergence (β-diversity, Permutation tests, p = 0.028). The explanatory power of geographical distance for fungal community variation was low (R² = 0.095) and less than that of the rhizosheath microhabitat (R² = 0.142). In conclusion, the rhizosheath imposes a strong filtering effect on bacterial communities. The weaker habitat specificity and stronger geographical signal observed for fungi suggest potential regulation by local dispersal limitation or historical colonization processes. This study provides insights into the assembly mechanisms of the plant rhizosphere microbial community. Full article

Conventional chemical-based control methods for soil-borne diseases often degrade soil quality. The recycling of organic wastes offers a promising solution to simultaneously alleviate environmental pollution and restore soil health. As a beneficial fungus, Trichoderma plays a crucial role in enhancing plant performance. However, knowledge of the mechanisms through which organic wastes and Trichoderma interact to influence plant performance remains limited. We investigated how the combined application of organic wastes (chitin and straw) and a biocontrol fungus (Trichoderma) influenced the rhizosphere microbiome to improve plant performance. Compared with the control, organic waste alone, and Trichoderma alone treatments, the combined application of organic wastes and Trichoderma significantly (p < 0.05) increased cucumber yield and reduced pathogen density. Increased yield and reduced pathogen density were associated with changes in bacterial and fungal communities induced by this combined application treatment. Indeed, this combined application treatment enabled plants to recruit certain potentially beneficial core bacterial (e.g., Streptomyces and Flavisolibacter) and fungal taxa (e.g., Trichoderma), increasing their positive interactions in the rhizosphere. We demonstrate that the combined application of organic wastes and Trichoderma can shape distinct rhizosphere bacterial and fungal communities, promoting an increase in beneficial microorganisms and their positive interactions, which contribute to enhanced plant performance. Full article