Search Results (2,516)

Extracellular enzyme stoichiometry is a key indicator for assessing nutrient limitation experienced by soil microorganisms. Yet, the characteristics of enzyme-inferred microbial nutrient limitation in rhizosphere soil under the combined agricultural practices of intercropping and straw retention remain unclear. Here, we conducted a field experiment in the black soil region of Northeast China to quantify the effects of intercropping and straw retention on soil nutrients, microbial biomass, extracellular enzyme activities, and their C:N:P stoichiometry in the rhizosphere of maize and peanut. Our results showed that compared with sole cropping, intercropping increased soil organic carbon (SOC) by 6.21–13.57%, total nitrogen (TN) by 8.57–12.49%, and total phosphorus (TP) by 12.01–40.29% in the rhizosphere. The vector analysis revealed an average vector length (VL) of 1.68 and 1.57 for extracellular enzymes in the rhizosphere soil of maize and peanut, with a vector angle (VA) of 37.80° and 34.67°, respectively. These values suggest that soil microorganisms in the rhizosphere of both crops experienced C limitation, and that the degree of enzyme-inferred N limitation was modulated by microbial C acquisition strategies, with a dynamic trade-off between the two. This N limitation was more pronounced in the peanut rhizosphere. Notably, the combined treatment of intercropping and full straw retention increased the VA of peanut by 5.38%, corresponding to a partial alleviation of enzyme-inferred N limitation in the rhizosphere soil. The extracellular enzyme C:N:P stoichiometry in the rhizosphere soil of maize and peanut was 1.33:1.29:1.00 and 0.89:1.29:1.00, respectively. Microbial biomass nitrogen (MBN) was the primary factor affecting enzyme-inferred microbial nutrient limitation (explaining 54.6% of variation). The extracellular enzyme stoichiometric characteristics of rhizosphere soil differed significantly between the two crops. Intercropping had a stronger impact on rhizosphere microbial nutrient limitation than straw retention, and their synergistic effect was associated with a partial alleviation of rhizosphere enzyme-inferred N limitation by enhancing extracellular enzyme activity. These findings demonstrate that integrated intercropping and straw retention can support sustainable soil management in black soil agroecosystems. Full article

Forest understorey herbs are an under-studied component of subtropical mountain forest biodiversity, yet they include several genera of high medicinal and economic value. The rhizomes of Polygonatum (Liliaceae) are a prominent example, but the forest-ecological controls on their bioactive composition in wild populations—particularly for co-occurring congeners—remain poorly resolved. We sampled 92 wild plants of Polygonatum cyrtonema and P. filipes along four altitudinal transects (330–1730 m) in a subtropical mountain forest reserve in southeastern China, quantifying total polysaccharide, three flavonoid monomers (rutin, quercetin, and methylophiopogonanone B), and two LC–MS class signals (ΣFlavonoid, ΣSaponin), together with 13 topographic, edaphic, and biotic predictors. The two species displayed the following distinct rhizome chemical phenotypes: P. cyrtonema tended toward higher ΣSaponin; P. filipes toward higher ΣFlavonoid. The clearest pattern was a robust species × altitude interaction for total polysaccharide (p = 0.002), with the two species following opposite altitudinal trajectories. In multivariate forward-selected redundancy analysis, canopy closure and species identity emerged as the only retained environmental predictors, identifying forest light environment as the strongest single environmental correlate of rhizome chemical variation. Species-specific bivariate analyses further revealed contrasting driver hierarchies as follows: P. cyrtonema chemistry tracked topography, whereas P. filipes chemistry tracked rhizosphere soil enzymes and chemistry; only soil temperature and urease activity were shared across species. These results argue that altitude is not a uniform predictor of rhizome chemistry in wild Polygonatum, and support species-specific, canopy-aware management of medicinal forest understorey herbs in subtropical mountain forests. Full article

Charcoal rot, caused by the pathogen Macrophomina, is becoming an increasing challenge in Australia’s northern cropping systems, with few effective management options available. The use of non-indigenous biocontrol agents raises ecological and regulatory concerns, which highlights the need to identify locally adapted microbial antagonists. In this study, indigenous Trichoderma isolates were collected from rhizosphere soils across Queensland and northern New South Wales and characterised using multilocus sequencing (ITS, tef-1α, rpb2) coupled with phylogenetic analysis. Twenty-six isolates were resolved into six species, dominated by T. azevedoi and T. afroharzianum. Dual-culture assays revealed substantial variation in antagonistic capacity, with several isolates achieving >70% inhibition of Macrophomina growth and maintaining consistent performance across pathogen genotypes. Functional screening indicated that enzyme-associated antibiosis was widespread, whereas volatile-mediated inhibition was restricted to a small subset of isolates. These findings demonstrate that biocontrol potential in indigenous Trichoderma populations is highly strain-dependent rather than species-driven. By integrating multilocus identification with functional screening, this study provides a practical framework for selecting locally adapted biocontrol candidates. This work establishes a foundation for developing region-specific biological control strategies and supports a shift toward targeted, strain-level selection for effective management of charcoal rot. Full article

Biological control is one of the most effective strategies for managing crop fungal diseases such as rice blast, which severely threatens global food security. However, the limited availability of microbial biocontrol resources and incomplete understanding of their mechanisms hinder the development of practical biocontrol technologies for rice blast. In this study, a Bacillus stercoris strain, JK-6, isolated from the rhizosphere soil of rice, was identified as a promising biocontrol agent with strong antagonistic activity against multiple fungal pathogens. The fermentation broth of JK-6 yielded inhibition rates of 94.96% against Magnaporthe oryzae (rice blast), 75.83% against Bipolaris maydis (maize southern leaf blight), and 70.46% against Fusarium graminearum (wheat head blight). Whole-genome sequencing of JK-6 revealed 12 biosynthetic gene clusters, one of which was responsible for the biosynthesis of the lipopeptide surfactin. Further assays showed that 200 μM surfactin exhibited broad-spectrum antifungal activity, with inhibition rates of 82.90%, 66.76%, and 52.54% against M. oryzae, B. maydis, and F. graminearum, respectively. Mechanistically, surfactin suppresses fungal growth by downregulating genes involved in integral and intrinsic membrane components and oxygen transport, as validated by transcriptomic analysis. Our discoveries not only advance the conceptual understanding of the surfactin-mediated JK-6 antagonistic activity against fungal diseases but also offer an effective new approach for the practical control of crop fungal diseases. Full article

Driven by increasingly severe drought stress associated with global warming, this study investigated a synthetic microbial community, SynCom-SASW01, with strong stress tolerance and plant growth-promoting potential, and systematically elucidated its mechanisms for enhancing drought resistance in wheat (Triticum aestivum L.). Dual-site field trials demonstrated that SynCom-SASW01 significantly alleviated drought-induced growth suppression, increasing grain yields by 10.42% and 8.52% at the Hohhot and Hulunbuir sites, respectively. This improvement was primarily associated with increased effective tiller number and enhanced root vigor. Physiologically, inoculation promoted root proline and glutathione accumulation and enhanced antioxidant enzyme activities, including superoxide dismutase, thereby reducing malondialdehyde levels. Environmental analyses showed that the consortium established rhizosphere “micro-reservoirs” through exopolysaccharide secretion, improving soil relative water content and the availability of alkali-hydrolyzable nitrogen and phosphorus. High-throughput sequencing revealed that SynCom-SASW01 reshaped the endosphere microbiome through early colonization priority effects, selectively enriching beneficial taxa such as Pseudomonas. Functional prediction indicated upregulated branched-chain amino acid biosynthesis, promoting osmotic adjustment and redox homeostasis. These findings provide a microbiome-based strategy for stabilizing wheat productivity in arid regions. Full article

Soil fungi are key drivers of terrestrial ecosystem functioning, contributing to organic matter decomposition, nutrient cycling, and plant–microorganism interactions. Despite their importance, the global distribution and structural biases of public sequence records for soil fungi remain incompletely characterized. In this study, we analyzed soil-associated fungal DNA sequences retrieved from the NCBI GenBank database using a custom R-based bioinformatics pipeline. Following filtering and metadata standardization, 544,554 filtered sequence records were obtained. The taxonomic composition of the dataset consisted primarily of Ascomycota (69.62%), followed by Basidiomycota, Glomeromycota, and Mucoromycota, with Trichoderma, Penicillium, and Aspergillus representing the most frequent genera. The geographic distribution revealed strong sampling bias, with China and the United States accounting for over one-third of all records. Ecological metadata indicated that rhizospheric and forest soils were the most common sources of the deposited sequences. At the same time, gene marker analyses confirmed the widespread use of the ITS region as the primary fungal barcode. Sequence diversity analyses revealed continental variation, with Europe and Asia showing higher medians, while the ordination highlighted clustering of sequence profiles, particularly among records from extreme environments. This study demonstrates the potential of public sequence databases for large-scale biodiversity assessments while highlighting the influence of sampling bias and the limitations of metadata. Full article

Medicinal plants are rich sources of bioactive secondary metabolites, yet their long-term effects on the rhizosphere (RS) microbial communities remain poorly understood, particularly with respect to microbial selection and functional potential. This study evaluated the number of selected groups of microorganisms culturable in vitro in the RS and bulk soil (BS) within 10-year monocultures of 11 medicinal plant species, and as a targeted case study, we performed shotgun metagenomic profiling for Allium ursinum. The abundance of microorganisms differed markedly among plant species, indicating species-specific RS selection. Azotobacter spp. showed the strongest variation: they were not detected in the RS of Allium ursinum, Thymus vulgaris, and Carum carvi, whereas higher counts were observed under Artemisia dracunculus (135.1 × 10² CFU g⁻¹ DM), Melissa officinalis (67.1 × 10² CFU g⁻¹ DM) and Calendula officinalis (38.8× 10² CFU g⁻¹ DM). Azotobacter spp. may serve as a sensitive candidate indicator of RS imbalance. Metagenomic analysis of the A. ursinum-associated soil revealed fine-scale taxonomic restructuring, while major functional categories remained broadly similar between the RS and BS. The novelty of this study lies in the development of the Integrated Microbiological Health Soil Index (IMHSI) and the proposal of a Nitrogen Enrichment Index (NEI) as exploratory composite metrics that integrate selected functional microbial groups. Full article

Climate change and soil degradation pose a challenge to grape quality, motivating the development of integrated monitoring approaches combining soil analysis with remote sensing techniques. However, harmonized information addressing this multidisciplinary challenge remains scarce. Therefore, this systematic review synthesizes the scientific literature published since 2020 with the aim of (i) identifying key soil properties and techniques applied, (ii) evaluating remote sensing approaches and their integration with soil data, and (iii) highlighting knowledge gaps and challenges for sustainable precision viticulture. A search in Scopus yielded 197 full-text articles classified into three thematic groups and analyzed using a standardized extraction protocol. Our synthesis reveals that pH, electrical conductivity, soil organic matter, and cation exchange capacity are the most consistently reported physicochemical parameters across the reviewed studies, while next-generation sequencing and multi-omics approaches are increasingly adopted in microbiological research to characterize rhizosphere communities and their links to terroir expression. In remote sensing, multispectral UAV platforms and satellite missions (Sentinel-2, Landsat) combined with vegetation indices, principally NDVI, dominate the toolset for monitoring vine vigor and water status. Nevertheless, genuine integration of remote-sensing outputs with root-zone soil measurements remains uncommon, with most studies treating both data streams independently. The principal knowledge gaps identified concern the absence of standardized sustainability assessment frameworks, limited cross-terroir transferability of predictive models, and insufficient long-term multi-site datasets to underpin climate change adaptation in vineyard management. Full article

Continuous cropping obstacles (CCOs) severely restrict the sustainable development of the ginger industry, yet the response mechanisms of rhizosphere microbiome and metabolome to microbial fertilizer under different continuous cropping durations remain unclear. Here, a field experiment was conducted in ginger fields with 5-year (short-term) and 20-year (long-term) continuous cropping history under conventional chemical fertilization, with or without additional microbial fertilizer application. Rhizosphere soil samples were analyzed via metagenomic sequencing and UPLC–MS/MS. Long-term continuous cropping caused severe soil acidification (pH 5.18–5.26 vs. 6.82–6.98 in short-term) and pathogen enrichment. Microbial fertilizer reduced the disease index by 43.47% under long-term cropping and by 31.48% under short-term cropping. It also improved soil properties and enzyme activities (e.g., urease activity increased nearly 12-fold), enriched beneficial genera (Pedobacter, Flavobacterium, Pseudomonas), activated arginine and proline metabolism, and promoted 4-guanidinobutanoic acid accumulation, forming a positive feedback loop with beneficial microbes. In conclusion, microbial fertilizer alleviates ginger CCOs by reshaping the rhizosphere microbiome and metabolome in a continuous cropping duration-dependent manner. Full article

Intensive agricultural practices based on continuous monocropping and prolonged bare-soil fallows have contributed to soil degradation and loss of biological functioning. Replacing fallows with cover crops (CCs) is a promising strategy to restore soil quality, yet their legacy effects on rhizosphere fungal communities remain poorly understood. This study evaluated the legacy effects of Urochloa (syn. Brachiaria) brizantha cover cropping on rhizosphere fungal communities, as well as soil physicochemical and biological properties, in a degraded common bean system. A field experiment with a randomized complete block design included: bare fallow (BM), one (B1) or two (B2) CC cycles before bean, a perennial pasture (PB), and a pristine soil reference (PS). High-throughput sequencing showed that Urochloa-based treatments significantly shifted fungal community composition compared to BM, increasing saprotrophic and beneficial taxa (e.g., Mortierella, Penicillium, Coprinellus) and reducing potential pathogens such as Fusarium. These changes were associated with higher soil organic carbon, aggregate stability, microbial biomass, and enzyme activities, especially in B2 and PB. Indicator taxa identified by LEfSe were linked to organic matter decomposition and nutrient cycling. Multivariate analyses revealed strong associations between fungal community structure and soil properties. Overall, U. brizantha cover cropping induced measurable legacy effects, promoting soil biological recovery even after short-term implementation. Full article

Cacti thrive in arid and coastal environments partly through associations with beneficial endophytic and rhizosphere bacteria; however, current knowledge remains limited. This study aimed to assess the diversity of cultivable bacteria associated with Opuntia dillenii and evaluate their potential as Plant Growth-Promoting (PGP) agents. Endophytic bacteria were isolated from cladodes and roots, while rhizobacteria were recovered from rhizosphere soil. Bacterial isolates were identified using morphological characteristics and 16S rRNA/gyrB sequencing, followed by screening for PGP traits, pH and temperature tolerance. A total of 31 isolates were obtained, including 23 endophytes and 8 rhizobacteria, mainly affiliated with Firmicutes, Actinobacteria, and Proteobacteria. Bacillus (35.48%) and Priestia (32.25%) predominated, with Priestia flexa as the most prevalent species. The most frequent PGP traits were phosphate solubilization (80.65%), proteolytic activity (70.97%), siderophore production (67.74%), and nitrogenase activity (64.52%). The highest phosphate solubilization indices were observed for strain R3 (3.41), R6 (3.39) and S6 (3.21), whilst the highest indole-3-acetic acid yields were recorded for C9 (172.88 µg/mL), R11 (96.22 µg/mL) and C3 (90.94 µg/mL), and the strongest siderophore production for C3 (30.37 mm), C7 (27.96 mm) and S7 (27.88 mm). These findings highlight O. dillenii-associated coastal bacteria as promising resources for plant growth and plant stress resilience. Full article

This study characterizes AP-20-A, a lytic podovirus infecting Sinorhizobium meliloti, isolated from agricultural chernozem. Its 49.4 kbp genome shows negligible intergenomic similarity with known rhizobiophages (<2%). Core structural proteins—the major capsid protein (MCP) and terminase large subunit (TerL)—show closest homology to podoviruses infecting Paenibacillus, rather than to alphaproteobacterial viruses, suggesting cross-phylum horizontal gene transfer. This exchange is ecologically plausible, as Paenibacillus and Sinorhizobium co-exist in the rhizosphere. Over 63% of predicted proteins are functionally uncharacterized, with structural homologs detected in bacteria, archaea, and eukaryotes. We report the first identification in a rhizobiophage of a Tad2-like domain, predicted to block the bacterial Thoeris type II anti-phage defense. AP-20-A infected 56% of native S. meliloti strains; agrocenose isolates showed higher resistance than phytocenose isolates, evidence of local co-evolution. Among susceptible strains, 60% entered putative pseudolysogeny (with one strain exhibiting growth stimulation), whereas a symbiotically elite inoculant strain was completely lysed within hours. Some host strains carry additional AbiE systems; whether these independent defense–counterdefense layers interact during infection remains unknown. We conclude that resident phages represent a selective force that can disrupt inoculant establishment, underscoring the need to integrate soil virome assessment into agricultural microbiome management. Full article

Organic vegetable cultivation requires soil management strategies that improve carbon balance and suppress soilborne diseases. This study evaluated the efficacy of acidified microbial biochar pellets (ABPM) in enhancing net ecosystem carbon balance (NECB) and suppressing clubroot disease (Plasmodiophora brassicae) during organic Chinese cabbage (Brassica rapa ssp. pekinensis) cultivation. In a field-scale evaluation, three treatments were compared: guano fertilizer (control), ABPM 27 (inoculated with Pseudomonas fluorescens 22BCO027), and ABPM 86 (inoculated with Bacillus megaterium 22BCO086). Soil incorporation of ABPM 27 and ABPM 86 significantly increased soil carbon sequestration by 29.1% and 22.4%, respectively, while simultaneously reducing cumulative greenhouse gas emissions under the experimental conditions. This resulted in positive NECB values of 2.63 and 2.94 t CO₂-eq ha⁻¹, suggesting enhanced carbon retention potential within the studied cultivation system. Beyond its impact on carbon dynamics, ABPM 27 increased marketable yield by 8.6% (77.4 t ha⁻¹) and reduced clubroot incidence by 46.2%. Rhizosphere microbial analysis revealed that ABPM 27 promoted late-season microbial diversity and the persistence of beneficial Bacillus spp. and Pseudomonas spp. populations. These findings suggest the potential multifunctional role of microbially engineered biochar pellets in improving crop production, carbon retention, and pathogen suppression under organic cultivation conditions. However, these findings are based on a single-season field experiment and NECB-based carbon balance estimates, and therefore require validation across multiple growing seasons and cultivation environments. Full article

Rice–fish co-culture is widely promoted for mitigating nitrous oxide (N₂O) emissions from paddy soils, yet how the duration of co-culture reshapes the underlying nitrogen-cycling microbial community under low-nitrogen input remains poorly understood. This study aimed to (i) characterize how co-culture duration alters the rhizosphere microbial functional potential for N₂O production and consumption, and (ii) identify the water and soil variables linking fish activity to that response. The experiment was conducted during the 2024 rice growing season in the Qingtian rice–fish system (Zhejiang Province, China), a traditional agricultural heritage system managed without chemical fertilizer or supplementary feed. Three treatments (i.e., rice monoculture, first-year co-culture, and long-established (~10-year) co-culture) were compared using six independently bunded replicate plots each. Rhizosphere soils were collected at the tillering, heading and maturity stages for shotgun metagenomic profiling of nitrogen-cycling functional genes, with concurrent measurement of N₂O flux and water and soil physicochemical properties. Fluxes were uniformly low and did not differ among treatments (p > 0.05), defining a substrate-limited baseline. Against this baseline, first-year co-culture induced a coordinated shift toward complete denitrification (nosZ increased by 25–33% across all stages; nosZ/(nirK + nirS) rose to 0.99 at heading), associated with a transient water organic carbon pulse and dissolved-oxygen availability. The long-established system resembled monoculture, indicating a non-monotonic, duration-dependent response. Full article

Alfalfa (Medicago sativa L.) is widely recognized as a major forage crop, yet its role as a multifunctional biological input in sustainable horticultural production remains underexplored. This review evaluates alfalfa as a biological nitrogen source, organic fertilization resource, and biofertilizer-supporting crop within vegetable, medicinal, and perennial horticultural systems. Due to its high capacity for biological nitrogen fixation, alfalfa can supply substantial amounts of plant-available nitrogen, reducing dependency on synthetic fertilizers and supporting environmentally sound nutrient management. When used as green manure, cover crop, intercrop, mulch source, compost feedstock, or processed organic fertilizer, alfalfa enhances the soil organic carbon (SOC), improves soil structure, and increases the water-holding capacity properties particularly critical in intensive horticultural production. Higher SOC levels also contribute to the improved tolerance of horticultural crops to drought and heat stress through enhanced soil moisture retention and rhizosphere buffering. Alfalfa-based organic inputs stimulate rhizosphere microbial biomass, enzymatic activity, and functional genes associated with nitrogen cycling, strengthening plant–microbe interactions that underpin biofertilizer effectiveness. Evidence from vegetable and perennial systems indicates that alfalfa-derived amendments and rotations increase soil nitrogen availability, support yield stability, and improve soil health over the long-term. In orchards and vineyards, alfalfa cover cropping contributes to carbon sequestration, erosion control, and enhanced soil biological functioning. Overall, alfalfa emerges as a strategic species for integrating organic fertilization and biofertilizer-based approaches into modern horticultural systems, supporting reduced mineral fertilizer inputs while sustaining productivity, soil health, and environmental quality. Full article