Search Results (1,106)

Under-forest cultivation of morels is increasingly constrained by soil ecological deterioration, which has become a major obstacle to its sustainable development. This study characterized hyphosphere soil microbiomes of Morchella sextelata M. Kuo under pine canopy at four distances from the fruiting body: 0 cm (R), 20 cm (R₂₀), 40 cm (R₄₀), and uncultivated control (CK). Bacterial and fungal community composition and diversity were analyzed using Illumina NovaSeq high-throughput sequencing. Results showed that the dominant bacterial phyla were Proteobacteria and Acidobacteriota, with RB41, Sphingomonas, and Dongia as the dominant genera. Relative to CK, the abundances of Acidobacteriota and RB41 in R increased by 4.45% and 6.16%, respectively, whereas R₂₀ was enriched in Proteobacteria (+7.77%), Sphingomonas (+0.95%), Dongia, and Bradyrhizobium. For fungi, Ascomycota and Basidiomycota were the dominant phyla, with the principal genera being Sebacina, Microbotryales_gen_Incertae_sedis, and Oidiodendron. Compared with CK, morel cultivation decreased the abundances of Ascomycota and Oidiodendron, with the greatest reductions in R₂₀ (by 8.73% and 3.67%, respectively), while increasing the abundances of Basidiomycota, Sebacina, and Microbotryales_gen_Incertae_sedis, again most markedly in R₂₀, by 17.56%, 14.82%, and 5.74%, respectively. Morel cultivation significantly reduced microbial diversity and evenness (Shannon, Simpson, and Pielou), with the lowest diversity and highest dominance in Zone R. Partial least squares structural equation modeling (PLS-SEM) revealed that soil chemical properties and enzyme activities negatively drove dominant bacterial genera but positively drove dominant fungal genera. Overall, under-forest cultivation of M. sextelata significantly reduced hyphosphere microbial diversity and reshaped microbial community structure in a distance-dependent manner: Zone R was dominated by Acidobacteriota; Zone R₂₀ was enriched with nitrogen-cycling beneficial bacteria (Dongia, Sphingomonas, and Bradyrhizobium) and beneficial fungi (Sebacina and Microbotryales_gen_Incertae_sedis); Zone R₄₀ exhibited relatively optimal fungal diversity. Full article

Returning spent mushroom substrate (SMS) to the field is an effective way to dispose of it. However, given the substantial nutrient consumption associated with Volvariella volvacea SMS, their effects on soil properties and crop performance warrant further investigation. By analyzing the effects of three different application rates of SMS on soil nutrients and lettuce (Lactuca sativa L.) quality, the results showed that the group with 1.5 kg m⁻² SMS addition improved the total nitrogen (+21.2%), and organic content (+27.9%) in soil, and it demonstrated particularly outstanding performance in enhancing the survival rate (+21.9%), average weight (+71.7%), chlorophyll content (+45.6%), and total phenolic content (+25.2%) of lettuce. By comparing the soil microbial communities in the control group, the SMS (1.5 kg m⁻²) treatment group, and the organic fertilizer treatment group, it was found that they were mainly composed of Group S1, S2, and S3 microorganisms, respectively. The microbial community evenness in the treatment groups was greater than that in the control group. Furthermore, the results also revealed that the microbial conversion efficiency of nitrogen and phosphorus in the SMS treatment group was higher than the control group, which promoted nutrient cycling and improved the quality of lettuce. Our analysis provides an environmentally friendly way for Volvariella volvacea SMS disposal. Full article

Native soils host diverse symbiotic microflora that contribute to sustainable agricultural practices and plant establishment. This study aims to investigate the benefits of rhizosphere soil microbiota associated with four Mediterranean native plants, Rhus pentaphylla (NS1), Drimia maritima (NS2), Pistacia lentiscus (NS3), and Withania frutescens (NS4), growing in proximity to the local Moroccan almond variety Prunus dulcis (Mill.) (NS5). Native soils were applied directly as living substrates to evaluate their effects on the germination and early development of almond, with particular emphasis on the potential of arbuscular mycorrhizal fungi (AMFs). Root analysis revealed high mycorrhizal colonization intensity (M% = 87.5–95%) and infectivity (F% = 100%). Under the tested soil conditions, three native soils (NS1, NS3, and NS5) achieved germination rates exceeding 70% after 28 days. Moreover, NS5 and NS1 soils showed the strongest effects on almond germination and seedling growth, respectively. Overall, the use of native soils enhanced almond germination and early development, highlighting the role of AMFs as natural biofertilizers. The associated native plant species may also function as nurse plants that facilitate almond establishment. These findings support the use of the rhizosphere microbiome as a bio-based strategy to promote sustainable almond cultivation in local and Mediterranean agroecosystems. Full article

Intensive horticultural management modifies soil physicochemical conditions, yet its effects on microbial community assembly and functional organization remain poorly resolved. This study examined bulk soil (BS) and rhizosphere soil (Rh) bacterial communities associated with tomato plants grown in two contrasting commercial horticultural establishments: a long-term intensive monoculture (>10 years; MC) and a recently established system (FC). Total bacterial abundance and community structure were characterized using qPCR and 16S rRNA gene amplicon sequencing, respectively; the abundance and diversity of functional plant-growth-promoting (PGP) genes—nifH, phoD, and acdS—were assessed by qPCR and DGGE profiling. The MC system, associated with increased salinity, nutrient accumulation, and organic matter content, supported higher bacterial abundance, whereas the FC system showed a higher relative abundance of PGP genes. Amplicon sequencing revealed significant differentiation between BS and Rh, identifying microhabitat in tomato-associated soil as the primary driver of taxonomic structure, while site effects were weaker. In contrast, DGGE profiling supported differences in functional gene composition between management systems, whereas predicted pathway profiles inferred from 16S data were comparatively similar across samples. Overall, these results indicate that horticultural intensification is associated with shifts in predicted functional potential that are not paralleled by major changes in taxonomic structure. Full article

Silicon is increasingly applied in agriculture to improve plant productivity under both abiotic and biotic stress constraints. Nevertheless, its mechanisms of action are often studied separately at the soil, plant, or microbiome levels, limiting a comprehensive understanding of its overall impact on agroecosystem functioning. This review proposes an integrated perspective of the soil–plant–microbiome continuum, linking silicon chemistry in soil solutions with the effects of silicon amendments on soil properties and the processes of uptake, transport, and deposition in the plants. We show that silicon bioavailability depends on maintaining a pool of dissolved silicon dominated by orthosilicic acid, regulated by mineral weathering, adsorption–desorption dynamics, polymerization, pH, iron and aluminum oxides, and organic matter. In soils, silicon inputs can improve structure, modulate acidity and cation exchange balances, influence nutrient availability, and reduce the mobility of certain metals. They may also affect enzymatic activities and microbial community composition. In plants, silicon uptake and transport, mediated by specific transporters, contribute to tissue silicification, the maintenance of leaf architecture, and the regulation of water, ionic, and redox homeostasis. These processes provide a basis for enhanced tolerance to drought, salinity, and metal toxicity, as well as biotic stress caused by pathogens and pests. Finally, we discuss key limitations to the agronomic application of silicon, including the diagnosis of the silicic status of soils, the choice of source and mode of application, and the genotypic variability of acquisition, as well as the need for multi-site tests and more robust mechanistic validations. This synthesis provides a coherent mechanistic framework to better define the conditions under which silicon can serve as a reliable tool for sustainable crop management under climate change. Full article

Subterranean termites, particularly Odontotermes obesus, cause severe damage to forest nurseries and plantations in arid and semi-arid ecosystems. This study demonstrates the dual functional role of endophytic entomopathogenic fungi, Metarhizium anisopliae and Beauveria bassiana, in termite suppression and induction of plant defense responses. Laboratory bioassays revealed significantly higher virulence of M. anisopliae, with a lower LT₅₀ (lethal time required to cause 50% mortality) of 33.1 h compared to B. bassiana (46.7 h), a steeper probit slope (5.4 ± 0.3), and strong model fit (R² = 0.95), indicating rapid and synchronized mortality. Endophytic colonization varied across host species and application methods, with soil incorporation consistently outperforming foliar inoculation. Maximum colonization (82.5%) was recorded in Tecomella undulata and exceeded 80% in Azadirachta indica under M. anisopliae. Biochemical analyses revealed significant increases in protein (up to 3.5 mg g⁻¹), phenols (3.7 mg g⁻¹), and tannins (2.7 mg g⁻¹). Activity of defense enzymes was significantly enhanced, with catalase reaching 263.5 U mL⁻¹, while Phenylalanine ammonia-lyase and Tyrosine ammonia-lyase exceeded 170 and 198 U mL⁻¹, respectively, indicating activation of antioxidant and phenylpropanoid pathways. Molecular docking analysis further revealed strong interactions between fungal metabolites and termite cellulase, with Bassianin (−8.4 kcal mol⁻¹) and Tenellin (−8.1 kcal mol⁻¹) showing the highest binding affinities. These findings highlight the combined biochemical and molecular mechanisms underlying fungal-mediated termite suppression and plant defense induction, and future research should prioritize transcriptomic validation, rhizosphere microbiome interactions, formulation optimization, and long-term multi-location field evaluation to support sustainable termite management strategies. Full article

Thismia species are non-photosynthetic plants entirely dependent on fungal partners for carbon and nutrients. While their arbuscular mycorrhizal associations are well-documented, bacterial symbiont roles remain unexplored. Using 16S rRNA gene amplicon sequencing, we investigated endophytic bacterial communities in T. gardneriana, T. javanica, and T. mirabilis from geographically distinct locations in Thailand. Despite geographic separation, Thismia spp. consistently harbored bacterial compositions taxonomically and functionally distinct from surrounding soil microbiomes. Root endospheres were significantly enriched in Pseudomonadota and Bacteroidota, particularly Puia, while showing reduced compositional dynamics of Acidobacteriota and Planctomycetota. Bacterial communities in Thismia roots were markedly distinct from surrounding soil, while root endosphere communities from geographically distinct habitats clustered together regardless of spatial separation. Mantel and partial Mantel tests confirmed that host species identity, not geographical location, was the primary predictor of root bacterial community structure. Functional prediction analyses suggested root-associated communities were enriched for nitrogen cycling pathways, particularly nitrogen fixation and nitrate reduction. The selective enrichment of Bacteroidota, known for nitrogen fixation and phosphate mobilization, suggests these bacteria provide critical nutritional support in nutrient-poor forest floor environments. Isolated root strains belonged exclusively to Bacillota, including Neobacillus with plant growth-promoting traits. Our findings highlight the importance of tripartite plant–fungal–bacterial interactions in Thismia nutritional ecology. Full article

Microbial communities associated with the rhizosphere and phyllosphere are recognized as fundamental components influencing essential plant processes, including nutrient acquisition, growth promotion, and tolerance to stress. Biological control agents (BCAs), such as Trichoderma spp. and Bacillus spp., are widely applied in citrus crops. However, while BCAs effectiveness against plant pathogens is widely established, their resulting impact on indigenous, non-target bacterial and fungal communities remains poorly understood. The aim of this study was to evaluate the non-target effects of two commercial microbial formulations—one containing Trichoderma asperellum ICC 012 and T. gamsii ICC 080, and the other Bacillus amyloliquefaciens QST 713—on the resident microbiomes of Citrus volkameriana seedlings by using the amplicon-based metagenomic analysis, targeting the 16S rRNA and ITS1 regions. The application of the Trichoderma formulation as a soil drench in the rhizosphere resulted in minimal changes to the overall composition and diversity (α- and β-diversity) of the bacterial communities. This stability is considered a desirable trait for overall soil health. However, specific taxonomic changes were observed, such as a notable decrease in the genus Rhodococcus (0.4% vs. 1.5% in controls) among bacteria. In the fungal communities, the treatment led to a significant shift in phylum relative abundance, characterized by an increase in Basidiomycota (38% vs. 28% in controls) and a corresponding decrease in Ascomycota (51% vs. 56% in controls). Successful colonization was confirmed by a substantially higher relative abundance of the inoculated Trichoderma genus compared to control plants (1.4% vs. 0.1% in controls). Conversely, the foliar application of the Bacillus product induced a substantial restructuring of the phyllosphere bacterial community. This treatment caused a statistically significant reduction in bacterial α-diversity and a clear differentiation in community composition (β-diversity) relative to untreated controls. The successful colonization by the BCA resulted in the dominance of the Bacillus genus in the treated samples (27% vs. 2% in controls). Importantly, this ecological shift was accompanied by the enrichment of other beneficial bacterial taxa, including Sphingomonas (15% vs. 4% in controls) and the Burkholderia-Caballeronia-Paraburkholderia group (4% vs. 2% in controls). While fungal phyla abundances remained generally stable in the phyllosphere, specific genera such as Cladosporium (15% vs. 23% in controls) and Symmetrospora (21% vs. 13% in controls) prevailed post-treatment. In conclusion, these findings highlight the importance of considering non-target microbiome shift when implementing microbial biocontrol strategies in citrus production systems, since in this study was demonstrated that commercial BCAs exert a markedly differential influence based on the compartment of application: Trichoderma promoted ecological stability in the rhizosphere, whereas Bacillus induced a directional community shift in the phyllosphere. Full article

Negative plant–soil feedback (NPSF) drives yield decline in monocropping systems, yet how intraspecific competition modulates NPSF across planting densities remains unclear. We conducted a two-stage plant–soil feedback experiment using five crops (Triticum aestivum L., Zea mays L., Solanum lycopersicum L., Cucumis sativus L., and Panax notoginseng (Burkill) F.H. Chen) with contrasting NPSF intensities under four planting densities (30 × 30 to 8 × 8 cm). Crops with stronger NPSF (P. notoginseng) showed pronounced density-dependent biomass reductions, whereas those with moderate (S. lycopersicum, C. sativus) or low (Z. mays, T. aestivum) NPSF were largely density-insensitive. Given its sensitivity, P. notoginseng was used to explore mechanisms. High-density planting (8 × 8 cm) intensified NPSF, reducing seedling survival by 88.54% and biomass by 56.08% compared with low-density controls (30 × 30 cm). Microbiome profiling showed enrichment of pathogenic Fusarium spp. and depletion of beneficial Humicola spp. under high density. Metabolomic analysis identified linoleic acid and oleamide as key root exudates upregulated under high-density stress, which selectively stimulated Fusarium growth as preferred carbon sources. Collectively, these results reveal a density-dependent feedback in which intensified competition reshapes root exudation, promotes pathogen proliferation, and suppresses beneficial taxa, thereby amplifying NPSF. This provides mechanistic insights into microbially mediated NPSF under density stress and highlights the importance of optimizing planting density to sustain crop productivity. Full article

Background/Objectives: Glyphosate-based formulations are globally pervasive pollutants increasingly recognized as potential contributors to antimicrobial resistance (AMR) in environmental microbiomes. Although glyphosate is designed to inhibit plant 5-enolpyruvylshikimate-3-phosphate synthase, it also affects microbial metabolism, stress response, and genetic exchange. This review synthesizes the pathways through which glyphosate, its metabolite aminomethylphosphonic acid (AMPA), and commercial mixtures influence resistance-associated phenotypes and the dissemination of antibiotic resistance (ABR). Methods: A critical synthesis of the literature was conducted to evaluate the mechanistic and ecological interactions between glyphosate exposure and bacterial resistance in soil, aquatic, and host-associated microbiomes. Results: Experimental evidence showed that sublethal glyphosate exposure induced oxidative stress, altered membrane permeability, activated multidrug efflux pumps, and promoted tolerance phenotypes that could modify antibiotic susceptibility. It also enhances mutation rates and horizontal gene transfer processes associated with the emergence of resistance under controlled conditions. At the community level, glyphosate exposure is associated with microbiome restructuring and enrichment of resistance determinants, often without major shifts in overall diversity of the microbiome. These effects have been reported at environmentally relevant concentrations, although the evidence remains largely derived from laboratory and mesocosm studies. Conclusions: Glyphosate acts as both a biochemical modulator of resistance-related phenotypes and an environmental selective pressure that shapes microbial communities. Its widespread use and environmental persistence position it as a context-dependent contributor to the emergence and dissemination of AMR through interacting mechanistic and ecological pathways. Integrating AMR endpoints into pesticide risk assessments and surveillance frameworks is warranted, in addition to expanded field-based validation. 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

With the continuing intensification of modern agriculture, pesticides and antibiotics are extensively used to control pests and diseases, but their improper use and indirect inputs have resulted in widespread contamination of agricultural environments and food products. This review synthesizes how these contaminants enter agroecosystems, their occurrence across soils, waters and agricultural products, and the processes that redistribute residues across air–water–soil interfaces and into the soil–plant continuum. We summarize cross-media transport pathways (e.g., runoff/leaching, volatilization–deposition and irrigation-driven redistribution) and relate environmental exposure to plant uptake using a harmonized indicator set, including the bioconcentration factor (BCF), translocation factor (TF), octanol–water partition coefficient (log Kow) and soil organic carbon–water partition coefficient (Koc). We further discuss key determinants of crop accumulation, including compound-specific properties, soil characteristics and plant physiological traits, and highlight how these factors jointly shape residue profiles in edible tissues. Finally, we outline research priorities for source reduction, standardized multi-matrix surveillance, fate-to-uptake modeling, and microbiome-enabled remediation strategies to support pollution control, food safety and public health. Full article

Climate variability is a major driver of belowground microbial assembly, yet its effects on rhizosphere microbiomes in perennial crops remain insufficiently resolved. We investigated how macroclimatic oscillations associated with the El Niño–Southern Oscillation (ENSO) influence bacterial communities in the rhizosphere of Coffea arabica. Using 16S rRNA amplicon sequencing across five sampling campaigns covering El Niño, La Niña, and Neutral phases in the Colombian Andes, together with multivariate and variance-partitioning analyses, we quantified the relative contributions of climatic and edaphic factors to rhizosphere community structure. PERMANOVA across three dissimilarity metrics showed that the ENSO explained 11–17% of β-diversity, exceeding the contribution of intra-annual seasonality (6–12%). Ordination analyses indicated moderate compositional differentiation with considerable overlap among ENSO groups, consistent with gradual community turnover under contrasting hydroclimatic conditions. Rainfall and soil pH emerged as the main edaphic correlates of community composition, although their independent effects were no longer significant after accounting for the ENSO phase and season. Despite these shifts, the rhizosphere remained dominated by Acidobacteriota, Actinobacteriota, and Proteobacteria, and a prevalence-defined core microbiome (genera detected in ≥85% of samples) was maintained across climatic phases and seasons. These results indicate that, within the explained fraction of variation, macroclimatic variability contributed more to rhizosphere bacterial turnover than local edaphic heterogeneity, while a conserved prevalence-defined bacterial core may contribute to taxonomic stability in climate-sensitive coffee systems. Full article

The synergistic effects of soil acidification and heavy metal pollution present major challenges for global agroecosystems. To systematically trace the evolution of research and identify key topics in this field, this study employed CiteSpace to visualize and analyze 691 records from the China National Knowledge Infrastructure (CNKI) and 6747 highly relevant articles or reviews from the Web of Science (WOS) Core Collection database from 2005 to 2025. The results indicate a steady to rapid rise in global publications, with China contributing the largest share, at 2468 publications. This has produced a research cluster centered around the Chinese Academy of Sciences (CAS); however, the centrality of its international cooperation remains limited. Studies in the CNKI database are driven by agricultural needs, focusing on national food security, rice yield stability, improvement of arable land, and heavy metal passivation and remediation, with a concentration on basic agricultural science. By contrast, research in the WOS database emphasizes fundamental mechanisms and interdisciplinary integration, addressing aluminum toxicity, microbial communities, the nitrogen cycle, and global climate change, intersecting fields such as environmental science, soil science, ecology, and microbiology. The evolution of research hotspots shows a clear trajectory: from acidity regulation and chemical speciation analysis of heavy metals (2005–2013), to heavy metal passivation, remediation, and phytoremediation (2014–2018), and then to biochar materials, microbiome analysis, and the synergistic role of carbon sequestration (2019–2025). This study argues that future research should move beyond single remediation measures and adopt integrated strategic management to jointly improve bioremediation efficiency, promote soil carbon sequestration and soil health, and enhance microbial adaptation to global climate change. Full article

Astragalus membranaceus is an important perennial medicinal plant whose roots constitute its primary medicinal organ; however, its cultivation is severely constrained by root rot caused by Fusarium oxysporum. This study aimed to characterize differences in the rhizosphere microbiome between healthy and diseased plants, identify antagonistic microorganisms from healthy rhizosphere soils, and investigate their suppressive effects on F. oxysporum and the associated host metabolic responses. High-throughput sequencing was used to compare bacterial and fungal communities in the rhizospheres of healthy and diseased plants. Microorganisms were isolated from healthy rhizosphere soils and screened for antagonistic activity against F. oxysporum, followed by validation in pot experiments. Metabolomic analysis was further conducted to assess host metabolic responses to microbial treatment. Root rot disease significantly altered the dominant composition of rhizosphere microbial communities and was associated with reduced fungal diversity and lower bacterial richness in diseased soils. Co-occurrence network analysis revealed increased complexity in bacterial networks and strengthened positive correlations among fungal taxa under diseased conditions. A total of 81 microbial strains were isolated from healthy rhizosphere soils, among which Penicillium halotolerans exhibited the strongest inhibitory activity against the mycelial growth of F. oxysporum. Pot experiments further supported its suppressive effect on Astragalus root rot. Metabolomic analysis indicated that P. halotolerans treatment was associated with changes in host metabolic profiles related to energy metabolism, defense-associated protein synthesis, and nutrient uptake. Overall, this study identified P. halotolerans as a fungal strain with antagonistic activity against F. oxysporum and provided initial evidence for its association with the suppression of Astragalus root rot. These findings offer candidate microbial resources and mechanistic insights for understanding rhizosphere-associated disease suppression in Astragalus membranaceus. Full article