Search Results (238)

Desertification strongly alters soil microbial communities in dryland ecosystems, yet the reassembly of fungal functional groups and their interactions under increasing aridity remain unclear. This study aimed to determine how desertification reshapes arbuscular mycorrhizal fungi (AMF) and endophytic fungal groups in the rhizosphere of Stipa breviflora and Artemisia frigida, as well as how these shifts are associated with fungal network fragmentation. Rhizosphere soil internal transcribed spacer (ITS) sequencing and AMF-specific amplicon sequencing, combined with root colonization assessment, functional annotation, co-occurrence network analysis, and partial least squares path modeling (PLS-PM), were used to assess shifts in fungal communities along the desertification gradient. Desertification significantly reduced soil multifunctionality and fungal diversity, accompanied by a shift in community composition from environmentally sensitive taxa to stress-tolerant groups. Along the desertification gradient, AMF diversity and colonization decreased, whereas FUNGuild-inferred endophytic fungal abundance and microscopically observed dark septate endophytes (DSEs) colonization increased. FUNGuild-inferred endophytic fungal abundance was negatively correlated with AMF diversity. Co-occurrence networks showed reduced connectivity and increased fragmentation under desertification, especially at the desert steppe and steppe desert stages. PLS-PM analysis revealed that desertification directly increased fungal network fragmentation and indirectly promoted fragmentation through increased FUNGuild-inferred endophytic fungi and reduced AMF diversity, whereas soil multifunctionality mainly reflected environmental deterioration along the gradient. These findings demonstrate the functional reassembly of rhizosphere fungi under desertification and suggest that compensatory shifts among fungal guilds may contribute to ecosystem stability in dryland grasslands. Full article

Nowadays, approximately 50% of chemical surfactants come from petrochemical sources and pose environmental risks due to poor biodegradability, affecting microbial communities, aquatic organisms, and terrestrial ecosystems. Biosurfactants are eco-friendly alternatives, thanks to their strong surface tension-reducing activity, stability, low toxicity, and biodegradability, but their large-scale production is still limited by high costs and low yields. In this study, rice husk was evaluated as a renewable substrate from the agro-industrial field for lipopeptide production by the endophytic Bacillus subtilis AC7. Medium optimization through Plackett–Burman designs identified nitrogen sources and pH 6.5 as key factors enhancing biosurfactant production. Under optimized conditions, surfactin production increased from 4.2 mg/L in untreated rice husk to 266–276 mg/L with NaNO₃ and NH₄NO₃ supplementation, respectively. Combined laccase–amylolytic pretreatment further improved substrate utilization, enhancing sugar availability and supporting higher biomass and metabolic activity. In bench-scale fermentation, this condition yielded the highest surfactin concentration (237.5 mg/L). LC-MS/MS analysis confirmed surfactin as the main product, with C15 as the dominant homologue, in both shake-flask and bench-scale fermentations. These findings highlight a novel, sustainable process for surfactin production, offering a renewable alternative to synthetic surfactants while addressing both environmental and economic concerns. Full article

Fusarium root rot (caused by Fusarium verticillioides) is a destructive soilborne disease in maize, significantly reducing crop yields. The root symbiotic fungi Trichoderma species have been confirmed as effective biocontrol microbes for Fusarium root rot; however, the mechanistic role of Trichoderma-induced endophytes in suppressing Fusarium root rot in maize remains unclear. This study found that Trichoderma harzianum T30 significantly reduced the abundance of pathogens by 48.9% and increased the abundance of potentially antagonistic Bacillus strains (33%) in the root endophytic bacterial community. In addition, the hyd1 gene in T. harzianum T30 induced a 7.5-fold upregulation of ZmOPR7 in maize roots compared to the Δhyd1 mutant treatment, a gene related to the jasmonic acid (JA) pathway. Further, several endophytic Bacillus strains were specifically induced by a hyd1-overexpressing strain, including B. amyloliquefaciens MX66, B. velezensis C9, and B. velezensis GAGAN3. Three endophytes significantly (p < 0.05) reduced Fusarium root rot incidence in maize by 46.6–55.0% and upregulated the expression of jasmonic acid/ethylene (JA/ET) pathway-related genes (ZmOPR7, ZmOPR8 and ZmEIL1) by 5.4-, 1.5-, and 4.6-fold, respectively, compared to untreated controls. Meanwhile, the Bacillus strain also improved maize plant growth. This study examined how overexpression of the T. harzianum elicitor gene hyd1 (in the OE-hyd1 strain) affects the colonization dynamics of beneficial endophytic bacteria in maize roots. Additionally, it further suggested the contribution of selected endophytic Bacillus strains in suppressing Fusarium root rot in maize. Full article

Cannabis sativa L. is a multipurpose crop of increasing agricultural and medical relevance, whose productivity and phytocannabinoid profile are influenced not only by genotype and environmental factors but also by the composition of its microbiota. This review synthesizes current knowledge (2020–2026) on the rhizosphere and endophytic microbiota of hemp, with particular emphasis on plant growth-promoting bacteria (PGPB) and their mechanisms of action. Molecular studies indicate that hemp-associated bacterial communities are dominated by Proteobacteria, Actinobacteriota, Firmicutes and Bacteroidota, with genotype-, tissue- and developmental-stage-dependent variation. PGPB influence plant performance through direct mechanisms, including biological nitrogen fixation, phosphate solubilization, siderophore production and phytohormone synthesis (indole-3-acetic acid (IAA), gibberellins, cytokinins, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase), as well as indirect mechanisms such as antibiosis, enzyme-mediated pathogen inhibition and induction of systemic tolerance to abiotic stress. Experimental studies demonstrate that inoculation with selected strains or consortia can enhance biomass accumulation, improve germination and root architecture, increase resistance to Fusarium oxysporum and modulate cannabinoid and terpene profiles. Importantly, plant responses are cultivar-specific, highlighting the need for genotype-tailored microbial formulations. Full article

The microbial community plays a crucial role in plant health and sustainable agricultural development by influencing plant physiology and development. This study aimed to explore the biocontrol potential of Bacillus subtilis A9, an endophytic bacterium isolated from Morchella sextelata, against rot disease caused by Lecanicillium aphanocladii. Metagenomic and metabolomic analyses were conducted on Morchella sextelata samples sprayed with B. subtilis A9 and a control group sprayed with LB medium. Metagenomic sequencing revealed that B. subtilis A9 significantly altered the microbial community structure and functional composition of Morchella sextelata, enriching genes related to biofilm formation, arginine and proline metabolism, and sulfur metabolism. Metabolomic analysis indicated significant upregulation of stress-resistant metabolites such as L-proline, ketoleucine, and pelargonic acid. Integrated multi-omics analysis demonstrated a strong correlation between the microbial community structure and the metabolomic profile, suggesting that B. subtilis A9 may be related to the disease-resistance response in the Morchella sextelata microecosystem. These findings provide a theoretical basis for the biological control of Morchella sextelata rot disease and support the development of green biocontrol strategies. Full article

As microplastic pollution intensifies, its impact on soil microbial communities has drawn widespread attention. This study treated soil samples with five microplastics, including polystyrene (PS), polyethylene (PE), polypropylene (PP), polyvinyl chloride (PVC), and polyethylene terephthalate (PET), to assess effects on soil properties. High-throughput sequencing was used to analyze soil fungal community structure and functional diversity. Results showed that microplastic treatments significantly altered pH, total carbon (TC), ammonium nitrogen (NH₄⁺-N), nitrate nitrogen (NO₃⁻-N), and available phosphorus (AP). Notably, all treatments reduced NO₃⁻-N levels. Fungal community composition was affected, particularly Mortierellomycota and the genera Mortierella, Plectosphaerella, Pseudogymnoascus, Penicillium, Tuber, and Stachybotrys. Functional analysis revealed decreases in certain groups, especially Endophyte–Plant Saprotroph–Undefined Saprotroph and Endophyte–Plant Pathogen–Plant Saprotroph, in PE, PS, and PVC treatments. Mantel analysis further indicated that soil pH, NH₄⁺-N, and NO₃⁻-N significantly influenced fungal communities. These results highlight that microplastic pollution alters soil properties, thereby affecting fungal communities in a microplastic-type dependent manner, providing a theoretical basis for soil health management and pollution mitigation. Full article

Pinus cembroides is among the pine species best adapted to arid and semi-arid ecosystems in the Americas, and its potential distribution is projected to expand under climate change. However, the success of this expansion will depend on belowground processes, particularly the role of soil fungal communities, which in subtropical forests are key for nutrient cycling and plant resilience to environmental stress. Yet their vertical stratification and responses to forest management remain poorly understood, especially in semi-arid systems. Here, we characterized fungal communities from mineral soil and litter associated with P. cembroides across a forest management gradient (mature forests, disturbed stands, and pine plantations) at the southern limit of the species’ distribution. We evaluated the influence of climatic, edaphic, vegetation structure, and microbial activity variables (soil moisture, precipitation, pH, tree density, vegetation cover, temperature and extracellular enzyme activity) on fungal community composition. We found strong vertical stratification between litter and mineral soil. When both substrates were analyzed together as an integrated soil profile, forest condition had no significant effect on alpha diversity; however, substrate-specific analyses revealed higher richness in mineral soil of mature forests compared to disturbed and plantation sites, while litter communities showed no significant differences among conditions. Litter communities were characterized by saprotrophic and endophytic fungi, whereas mineral soil communities were enriched in ectomycorrhizal and other root-associated taxa. Distance-based redundancy analysis indicated that fungal community composition was primarily associated with moisture content, precipitation, pH, tree density, and carbon-degrading enzyme activity. These results highlight the importance of substrate differentiation and environmental gradients in shaping fungal communities in semi-arid pine forests, and provide a baseline for understanding how management and climate change influence soil fungal diversity and ecosystem functioning. Full article

Nymphaea candida Presl is a rare and endangered waterlily species, and cultivating robust seedlings suitable for artificial propagation has become a critical issue for the conservation of this species. In this study, Aspergillus sp., an endophytic fungus isolated from the roots of N. candida, showed the capability of solubilizing phosphate and potassium and producing siderophores. The application of Aspergillus sp. significantly increased leaf length, leaf width, leaf number, and root length of N. candida seedlings by 97.83%, 131.37%, 94.12%, and 171.25%, respectively. Meanwhile, Aspergillus sp. application significantly enhanced soil organic matter content, alkali-hydrolyzable nitrogen content, sucrase activity, and peroxidase activity by 6.57%, 31.62%, 23.26%, and 7.53%, respectively. Moreover, Aspergillus sp. enriched beneficial microorganisms including Cyanobium, Aquicella, and Cryptomycota to form a more stable rhizosphere soil microenvironment. Additionally, Aspergillus sp. upregulated genes involved in photosynthesis and photosynthesis–antenna protein pathways in N. candida leaves, with the expression levels of psbA, petG, and psbH significantly increasing by 2.17, 4.48, and 0.28-fold, respectively. Therefore, the endophytic fungus Aspergillus sp. might be a reliable tool for the propagation of N. candida seedlings, which would be helpful for the conservation of this rare and endangered aquatic plant species. Full article

Mango (Mangifera indica L.), a major tropical fruit crop, suffers severe anthracnose damage caused by Colletotrichum spp., and traditional chemical control has environmental and food safety risks, with plant-microbe interaction-based biological control as a sustainable alternative. However, the regulatory role of phyllosphere microbiota in the tripartite interactions among mango, beneficial microbes and Colletotrichum remains unclear. This study explored phyllosphere microbiota’s function in mango resistance to Colletotrichum and clarified the biocontrol mechanism of key beneficial isolates. We found Colletotrichum infection significantly reshaped mango leaf endophytic and epiphytic microbial communities, enriching Burkholderia, Acinetobacter, Bacillus and other dominant genera. We isolated a B. subtilis strain L-1 from the epiphytic microbiota that was 18-fold enriched in Colletotrichum-infected mango leaves. This strain exhibited potent antagonistic activity against Colletotrichum siamense with a relative inhibition rate of 82.10%, and delivered 79.77% biocontrol efficacy on mango leaves via two synergistic pathways: inhibiting pathogen spore germination and penetration by producing antimicrobial secreted metabolites and volatile organic compounds, and enhancing host disease resistance. Our findings advance the understanding of plant-phyllosphere microbiota-pathogen tripartite interactions and provide elite microbial resources for sustainable anthracnose management. Full article

The desert ecosystem harbors a resilient microbial community that sustains plant life under extreme stress. Understanding the endophytic microbiota of desert flora provides key insights into how these microorganisms enable plant survival and maintain ecological balance in arid landscapes. To date, the endophytic bacterial communities of dominant desert plants in the Arabian Peninsula have not been comprehensively characterized. Here, we investigated the endophytic microbiota of five co-adapted desert species, namely, Schweinfurthia papilionacea, Sesuvium verrucosum, Ochtocloa compressa, Helianthemum nummularium, and Convolvulus arvensis. These plants coexist in hyper-arid habitats and exhibit exceptional tolerance to drought, salinity, and nutrient scarcity. We hypothesized that, despite their phylogenetic divergence, these plants host functionally convergent microbial communities shaped by desert selection pressures. Using 16S rRNA gene amplicon sequencing, we obtained 3.4 million high-quality reads from 25 samples. Clustering at 97% similarity revealed 35 phyla and 17 dominant genera, highlighting notable microbial richness and ecological complexity. Alpha-diversity indices showed comparable species richness across hosts, while beta-diversity indicated community differentiation driven by environmental filtering. The dominant phyla included Pseudomonadota, Actinomycetota, Cyanobacteriota, and Bacillota, reflecting microbial adaptation to extreme desert conditions. Functional pathway prediction revealed enrichment of genes associated with DNA repair and protein turnover, suggesting metabolic flexibility and enhanced survival under stress. Overall, this study provides a comparative metagenomic insight into the endophytic bacterial communities of five desert plant species, uncovering a consistent pattern of functional convergence across diverse hosts. The findings suggest the presence of shared functional traits among the endophytic microbiota examined here, offering preliminary evidence for microbial contributions to plant resilience in arid environments. Full article

Soil cadmium (Cd) contamination is a persistent threat to global food security, requiring sustainable in situ remediation strategies. While hyperaccumulating plants possess specialized traits for metal extraction, their low biomass limits large-scale application. This study investigates the potential of a core endophytic synthetic community (SynCom-NS)—characterized by heavy metal tolerance and growth-promoting traits, originally derived from the hyperaccumulator Sedum alfredii—by assessing its ability to modulate the remediation phenotype of a high-biomass non-host crop, Brassica juncea. Pot experiments revealed that SynCom-NS root-zone application significantly alleviated Cd toxicity, increasing total fresh weight by 82% and chlorophyll content by 33%. Crucially, the consortium bypassed the “growth-dilution” trade-off, facilitating a 4.07-fold increase in shoot Cd accumulation. Multi-omics analysis demonstrated a systemic modulation of the host’s defense machinery, marked by a >3-fold surge in glutathione (GSH) levels and the induction of phenylpropanoid biosynthesis for cell wall reinforcement. SynCom-NS application also mediated tissue-specific regulation of the key metal transporter HMA4, upregulating its expression in roots to accelerate long-distance translocation while downregulating it in shoots. These findings demonstrate that specialized core microbiomes function as potent bio-inoculants, offering a promising biological strategy for engineering high-efficiency phytoremediation systems. Full article

Controlled environment agriculture (CEA) relies on hydroponic systems to achieve high yields, yet optimizing plant performance remains a challenge. Beneficial endophytic bacteria offer a sustainable solution by promoting growth and nutrient uptake. Here, we investigated the mechanistic basis of growth enhancement in lettuce (Lactuca sativa) inoculated with Pseudomonas psychrotolerans IALR632 in a nutrient film technique (NFT) system. Growth measurements showed significant increases in shoot and root biomass and leaf greenness. RNA-seq profiling at 4, 10, and 15 days after transplanting revealed dynamic transcriptional reprogramming, with 38, 796, and 7642 differentially expressed genes, respectively. MapMan and GO analyses indicated up-regulation of pathways related to cell wall remodeling, lipid metabolism, nitrogen assimilation, and stress adaptation, alongside modulation of ethylene signaling. Root bacterial microbiome through 16S metabarcoding sequencing demonstrated distinct community shifts, confirmed by analysis of similarity (ANOSIM) (R = 1, p = 0.028), with enrichment of genera linked to nutrient cycling and plant growth promotion. These findings provide integrated molecular and ecological evidence that IALR632 enhances lettuce growth by coordinating host gene expression and rhizobiome restructuring, offering a mechanistic framework for microbial inoculant strategies in hydroponic horticulture. Full article

Hypersaline waters contaminated with crude oil represent a major obstacle for phytoremediation, as few plant species tolerate both high salinity and hydrocarbon toxicity. In this study, the halophyte Halocnemum strobilaceum (Pallas) M. Bieb. was grown hydroponically in hypersaline solutions (50 and 80 g L⁻¹ NaCl) containing crude oil (600 mg L⁻¹). The plant was inoculated with endophytic bacteria isolated in a previous step from its root and selected for salt tolerance and hydrocarbon-degrading potential. The plant behaviour was assessed through growth and photosynthetic performance, while the degradation of hydrocarbons (C < 12 and C > 12) was monitored over time. At 50 g L⁻¹ NaCl, crude oil reduced the plant growth by 60%, but inoculation with endophytic bacteria mitigated this decline, demonstrating their positive influence under combined salt and hydrocarbon stress. At 80 g L⁻¹ NaCl, neither plant biomass nor chlorophyll fluorescence was significantly affected by crude oil, with or without bacterial inoculation, consistent with the strong intrinsic salt tolerance of H. strobilaceum, which likely buffered additional stress inputs. Metagenomic analyses revealed distinct root-associated microbial communities under different treatments, suggesting synergistic plant–microbe interactions that enhanced photosynthetic efficiency and metabolic stability. The presence of endophytes accelerated the degradation of aliphatic hydrocarbons (C10–C40) at both salinity levels. These findings highlight the potential of endophytic bacteria to enhance resilience in H. strobilaceum and its phytoremediation capacity, offering a promising nature-based approach for the sustainable treatment of highly saline, crude oil-contaminated industrial waters. Full article

Lycium ruthenicum is a typical desert halophyte with strong stress resistance and high medicinal value in the Tarim Basin. Root endophytic microbes play critical roles in host adaptation, nutrient cycling, and secondary metabolite accumulation. To clarify the diversity patterns of root endophytic bacteria and fungi and their relationships with environmental factors and fruit quality, high-throughput sequencing was used to analyze microbial community characteristics of Lycium ruthenicum collected from different habitats in the Tarim Basin. The results showed that rarefaction curves of alpha diversity indices (Chao1, Shannon, Pielou_e) tended to be saturated, indicating sufficient sequencing depth. Principal coordinate analysis (PCoA) revealed significant habitat-driven differentiation in both bacterial and fungal community structures. Community composition analysis showed that the relative abundance of dominant taxa at the phylum and genus levels differed significantly among sampling sites. Co-occurrence network analysis indicated that bacterial and fungal networks exhibited high modularity and were dominated by positive synergistic interactions, with Pseudomonas, Bacillus, Sphingomonas, Alternaria, and Fusarium as key hub genera. Moreover, root endophytic communities were significantly correlated with climatic variables, soil physicochemical properties, and fruit quality traits, including anthocyanin (AC), proanthocyanidin (PA), total flavonoids (TF), and total polyphenols (TP). Several keystone microbial genera were closely associated with the accumulation of functional metabolites in fruits. This study reveals the biogeographic distribution and co-occurrence characteristics of root endophytes in Lycium ruthenicum and provides a theoretical basis for understanding microbe–host–environment interactions and the quality improvement of desert medicinal plants. Full article

Fungal endophytes are microorganisms that inhabit plant tissues without causing disease and emerge as critical mediators of plant stress tolerance, nutrient acquisition, and ecosystem resilience under diverse climate change scenarios. Their unique position within the host allows them to modulate physiological responses more closely than external microbiota. This review explores how endophytic fungi contribute to plant adaptation under climate-induced stresses such as heat, salinity, drought, pollution, and nutrient limitation, with a focus on molecular crosstalk, functional trait modules, and metabolic trade-offs. Key findings emphasize multilayered signaling systems, including MAMP/DAMP recognition, phytohormone regulation, immune tuning, ROS dynamics, and effector deployment, while emerging mechanisms such as cross-kingdom RNA and extracellular vesicle (EV)-mediated exchange are discussed as promising but currently limited in empirical validation within many endophytic systems. Endophytes also enhance nutrient exchange through conditional carbon-for-benefit trade and may shape rhizosphere microbiota and soil activities through plant-mediated inputs. Integrative multi-omics approaches provide predominantly correlational insights into the mechanistic basis of these effects, linking molecular function to ecosystem and community outcomes. These insights have potential applications in climate-resilient agriculture, phytoremediation, and ecosystem restoration; however, their large-scale implementation requires further field-based validation and context-specific assessment. Future priorities should focus on trait-based selection, ecological modeling, and biosafety evaluation to translate microbial functions into reliable field-level strategies that support sustainable crop performance under accelerating environmental stress. Full article