Search Results (64)

Microbiomes play a pivotal role in sustaining plant function and broader ecosystem processes. Leguminous plants host vast populations of intracellular bacteria within specialized root organs known as nodules. The intricate mutualism between legumes and rhizobia ensures a stable supply of biologically fixed nitrogen (N) essential for plant growth. While rhizobia remain the central actors in this symbiosis, recent discoveries reveal the presence of non-rhizobial endophytes within nodules, suggesting a complex interplay shaped by host selection and compatibility with rhizobial partners. Understanding the structure and dynamics of crop nodule-associated microbial communities is thus critical for optimizing host responses to rhizobia and for leveraging beneficial plant–microbe interactions. This review explores the dualistic nature—both facilitative and inhibitory—of the nodule microbiome in relation to nodulation. We examine the diversity of soil bacteria that stimulate nodulation and those that ultimately colonize nodule tissues, questioning whether these functional groups overlap. Furthermore, we discuss the molecular dialogs and counter-signaling mechanisms that regulate endophyte ingress into nodules, and evaluate how nodule endophytes contribute to plant performance and soil fertility. Full article

To elucidate the potential of integrated multi-omics approaches for studying systemic mechanisms of mycorrhizal fungi in mediating plant-microbe interactions, this study employed the Tuber-inoculated Corylus system as a model to demonstrate how high-throughput profiling can investigate how fungal inoculation reshapes the rhizosphere microbial community and correlates with host metabolism. A pot experiment was conducted comparing inoculated (CTG) and non-inoculated (CK) plants, followed by integrated multi-omics analysis involving high-throughput sequencing (16S/ITS), functional prediction (PICRUSt2/FUNGuild), and metabolomics (UPLC-MS/MS). The results demonstrated that inoculation significantly restructured the fungal community, establishing Tuber as a dominant symbiotic guild and effectively suppressing pathogenic fungi. Although bacterial alpha diversity remained stable, the functional profile shifted markedly toward symbiotic support, including antibiotic biosynthesis and environmental adaptation. Concurrently, root metabolic reprogramming occurred, characterized by upregulation of strigolactones and downregulation of gibberellin A5, suggesting a potential “symbiosis-priority” strategy wherein carbon allocation shifted from structural growth to energy storage, and plant defense transitioned from broad-spectrum resistance to targeted regulation. Multi-omics correlation analysis further revealed notable associations between microbial communities and root metabolites, proposing a model in which Tuber acts as a core regulator that collaborates with the host to assemble a complementary micro-ecosystem. In summary, the integrated approach successfully captured multi-level changes, suggesting that Tuber-Corylus symbiosis constitutes a fungus-driven process that transforms the rhizosphere from a competitive state into a mutualistic state, thereby illustrating the role of mycorrhizal fungi as “ecosystem engineers” and providing a methodological framework for green agriculture research. Full article

Drought stress severely impacts agricultural productivity, yet mechanisms underlying microbial enhancement of plant drought tolerance remain poorly understood. This study investigated whether Sphingobacterium nripensae DR205 exhibits drought-specific plant growth promotion through conditional metabolic activation. We combined plant cultivation experiments, genome sequencing, and comparative transcriptomics to evaluate DR205 responses under normal and drought conditions with or without root exudates. DR205 showed minimal growth promotion under normal conditions but enhanced plant biomass by 74–344% specifically under drought stress. Genome analysis revealed complete pathways for both stress tolerance (osmolyte biosynthesis and antioxidant systems) and plant interaction (IAA production and nutrient mobilization). Transcriptomics uncovered dramatic metabolic reprogramming under drought, with branched-chain amino acid (BCAA) biosynthesis genes shifting from 27-fold suppression under root exudates to 17-fold upregulation under drought. Lysine biosynthesis showed similar drought-specific activation patterns. Critically, drought signals overrode plant signals maintaining BCAA activation regardless of root exudate presence and ensuring metabolic investment in plant support occurred specifically during water deficit. This conditional mutualism represents a novel bacterial strategy where plant support is selectively activated during environmental stress. These findings challenge conventional PGPR paradigms and offer new approaches for developing climate-resilient agricultural systems through targeted application of stress-responsive beneficial microbes. Full article

Plant–microbe interactions exert a significant influence on host stress responses; however, the molecular mechanisms underlying these effects remain inadequately understood. In this study, we characterize FaMAN8, an α-mannosidase from Fragaria × ananassa, to explore its role in adaptation to heat waves and water deficit, as well as its modulation by fungal endophytes. Transcriptomic analysis identified FaMAN8 as the sole α-mannosidase isoform highly conserved across reported sequences, with root-specific induction under conditions of heat stress, deficient irrigation, and endophytic colonization. Structural modeling revealed that FaMAN8 exhibits the canonical domain organization of glycoside hydrolase family 38 (GH38) enzymes, featuring a conserved catalytic architecture and metal-binding site. Molecular docking and dynamics simulations with the Man₃GlcNAc₂ ligand indicated a stable binding pocket involving key catalytic residues and strong electrostatic complementarity. MM-GBSA and free energy landscape analyses further supported the thermodynamic stability of the protein–ligand complex. Cavity analysis revealed a larger active site in FaMAN8 compared to its homolog JbMAN, suggesting broader substrate accommodation. Collectively, these findings identify FaMAN8 as a stress-responsive glycosidase potentially involved in glycan remodeling during beneficial root–fungus interactions. This work provides molecular insights into plant–microbe symbiosis and lays the groundwork for microbiome-informed strategies to enhance crop stress resilience. Full article

The excessive use of chemical fertilizers results in environmental issues, including loss of soil fertility, eutrophication, increased soil acidity, alterations in soil characteristics, and disrupted plant–microbe symbiosis. Here, we synthesize recent studies available from up to 2025, focusing on engineered biochar and its application in addressing issues of soil nutrient imbalance, soil pollution from inorganic and organic pollutants, soil acidification, salinity, and greenhouse gas emissions from fields. Application of engineered biochar enhanced the removal of Cr (VI), Cd²⁺, Ni²⁺, Zn²⁺, Hg²⁺, and Eu³⁺ by 85%, 73%, 57.2%, 12.7%, 99.3%, and 99.2%, respectively, while Cu²⁺ and V⁵⁺ removal increased by 4 and 39.9 times. Adsorption capacities for Sb⁵⁺, Tl⁺, and F⁻ were 237.53, 1123, and 83.05 mg g⁻¹, respectively, and the optimal proportion of polycyclic aromatic hydrocarbon (PAH) removal was 57%. Herbicides such as imazapyr were reduced by 23% and 78%. Low-temperature pyrolyzed biochar showed high cation exchange capacity (CEC) resulting from improved surface functional groups. Although biochar application led to a yield increase of 43.3%, the biochar–compost mix enhanced it by 155%. The analysis demonstrates the need for future studies on the cost-effectiveness of biochar post-processing, large-scale biochar aging studies, re-application impact, and studies on biochar–compost or biochar–fertilizer mix productivity. Full article

Tropical peatlands in Indonesia are increasingly degraded by conventional oil palm practices involving drainage and chemical fertilizers. This study evaluates AeroHydro Culture (AHC), a method applying microbe-enriched organic media aboveground, as a sustainable alternative that maintains high groundwater levels while supporting plant productivity. Field trials were conducted at two sites: a managed plantation in Siak and a degraded, abandoned plantation in Pulang Pisau. Ten months after treatment, AHC plots showed development of aerial-like lateral roots, improved chlorophyll levels, and increased arbuscular mycorrhizae colonization (from 0–46% to 22–73% in Siak, and 1.7–20% to 16–60% in Pulang Pisau). In Siak, AHC significantly increased IAA-producing and proteolytic bacteria in the 0–25 cm soil layer and raised oil palm yield by 36% over controls. This yield benefit was sustained in 2025, five years after the initial application. In Pulang Pisau, AHC also enhanced microbial abundance and promoted growth in the native species Shorea balangeran, suggesting its potential for reforestation. Drone imagery confirmed visible long-term differences in canopy color, supporting lasting physiological improvement. These results demonstrate that AHC promotes plant–microbe symbiosis, enhances nutrient acquisition, and sustains oil palm yield under saturated conditions. AHC offers a promising strategy for peatland rehabilitation where ecological recovery and agricultural productivity must be achieved in parallel. Full article

The mycoheterotrophic orchid Gastrodia elata relies entirely on symbiosis with Armillaria for nutrient acquisition during tuber development. The signaling mechanisms underlying this interaction have long been a research focus, and several pathways, such as phytohormone-mediated signaling, have been reported. However, the role of plant-derived extracellular vesicles (PDEVs) in G. elata–Armillaria communication remains unexplored. In this study, we conducted a comprehensive lipidomic analysis of G. elata-derived extracellular vesicles (GDEVs) isolated from juvenile, immature (active symbiosis), and mature tubers. By employing high-resolution mass spectrometry and advanced statistical methods, we established a detailed EV lipidome profile for G. elata, identifying 996 lipid species spanning eight major classes. Distinct lipidomic remodeling was observed throughout tuber maturation. Notably, as the immature stage corresponds to the period of peak symbiotic activity, targeted lipidome comparisons enabled the identification of core lipid markers, particularly Glc-sitosterols and the polyketide 7,8-dehydroastaxanthin, which are highly enriched during active symbiosis and potentially associated with inter-kingdom communication. These findings suggest that developmentally regulated lipid transport via EVs plays a critical role in mediating G. elata–Armillaria interaction. Our work not only illuminates the contribution of vesicle lipids to plant–fungal interaction but also provides a methodological foundation for investigating EV-mediated signaling in non-model plant–microbe systems. Full article

Climate change has intensified extreme weather events and accelerated soil salinization, posing serious threats to crop yield and quality. Salinity stress, now affecting about 20% of irrigated lands, is expected to worsen due to rising temperatures and sea levels. At the same time, the global population is projected to exceed 9 billion by 2050, demanding a 70% increase in food production (UN, 2019; FAO). Agriculture, responsible for 34% of global greenhouse gas emissions, urgently needs sustainable solutions. Microbial inoculants, known as “plant probiotics,” offer a promising eco-friendly alternative by enhancing crop resilience and reducing environmental impact. In this study, we evaluated the plant growth-promoting (PGP) traits and melatonin-producing capacity of Bacillus aerius EH2-5. To assess its efficacy under salt stress, soybean seedlings at the VC stage were inoculated with EH2-5 and subsequently subjected to salinity stress using 150 mM and 100 mM NaCl treatments. Plant growth parameters, the expression levels of salinity-related genes, and the activities of antioxidant enzymes were measured to determine the microbe’s role in promoting plant growth and mitigating salt-induced oxidative stress. Here, our study shows that the melatonin-synthesizing Bacillus aerius EH2-5 (7.48 ng/mL at 24 h after inoculation in Trp spiked LB media) significantly improved host plant (Glycine max L.) growth, biomass, and photosynthesis and reduced oxidative stress during salinity stress conditions than the non-inculcated control. Whole genome sequencing of Bacillus aerius EH2-5 identified key plant growth-promoting and salinity stress-related genes, including znuA, znuB, znuC, and zur (zinc uptake); ptsN, aspA, and nrgB (nitrogen metabolism); and phoH and pstS (phosphate transport). Genes involved in tryptophan biosynthesis and transport, such as trpA, trpB, trpP, and tspO, along with siderophore-related genes yusV, yfhA, and yfiY, were also detected. The presence of multiple stress-responsive genes, including dnaK, dps, treA, cspB, srkA, and copZ, suggests EH2-5′s genomic potential to enhance plant tolerance to salinity and other abiotic stresses. Inoculation with Bacillus aerius EH2-5 significantly enhanced soybean growth and reduced salt-induced damage, as evidenced by increased shoot biomass (29%, 41%), leaf numbers (12% and 13%), and chlorophyll content (40%, 21%) under 100 mM and 150 mM NaCl compared to non-inoculated plants. These results indicate EH2-5′s strong potential as a plant growth-promoting and salinity stress-alleviating rhizobacterium. The EH2-5 symbiosis significantly enhanced a key ABA biosynthesis enzyme-related gene NCED3, dehydration responsive transcription factors DREB2A and NAC29 salinity stresses (100 mM and 150 mM). Moreover, the reduced expression of peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT) by 16%, 29%, and 24%, respectively, and decreased levels of malondialdehyde (MDA) and hydroxy peroxidase (H₂O₂) by 12% and 23% were observed under 100 mM NaCl compared to non-inoculated plants. This study demonstrated that Bacillus aerius EH2-5, a melatonin-producing strain, not only functions effectively as a biofertilizer but also alleviates plant stress in a manner comparable to the application of exogenous melatonin. These findings highlight the potential of utilizing melatonin-producing microbes as a viable alternative to chemical treatments. Therefore, further research should focus on enhancing the melatonin biosynthetic capacity of EH2-5, improving its colonization efficiency in plants, and developing synergistic microbial consortia (SynComs) with melatonin-producing capabilities. Such efforts will contribute to the development and field application of EH2-5 as a promising plant biostimulant for sustainable agriculture. Full article

Monoculture plantation systems face increasing challenges in sustaining ecosystem multifunctionality (EMF) under intensive management and climate change, with long-term functional trajectories remaining poorly understood. Although biodiversity–EMF relationships are well-documented in natural forests, the drivers of multifunctionality in managed plantations, particularly age-dependent dynamics, require further investigation. This study examines how stand development influences EMF in Castanopsis hystrix L. plantations, a dominant subtropical timber species in China, by assessing six ecosystem functions (carbon stocks, wood production, nutrient cycling, decomposition, symbiosis, and water regulation) of six forest ages (6, 10, 15, 25, 30, and 34 years). The results demonstrate substantial age-dependent functional enhancement, with carbon stocks and wood production increasing by 467% and 2016% in mature stand (34 year) relative to younger stand (6 year). Nutrient cycling and water regulation showed intermediate gains (6% and 23%). Structural equation modeling identified plant diversity and microbial community composition as direct primary drivers. Tree biomass profiles emerged as the strongest biological predictors of EMF (p < 0.01), exceeding abiotic factors. These findings highlight that C. hystrix plantations can achieve high multifunctionality through stand maturation facilitated by synergistic interactions between plants and microbes. Conservation of understory vegetation and soil biodiversity represents a critical strategy for sustaining EMF, providing a science-based framework for climate-resilient plantation management in subtropical regions. Full article

Despite chemical exchange often serving as the first step in plant–microbe interactions, the specialized chemical metabolites produced by grass–Epichloë endophyte symbiosis as mediators of host growth, nutrient acquisition, and modulators of the rhizosphere community under low-nitrogen conditions are areas lacking in knowledge. In this study, we investigated the plant growth-promoting effects of the Epichloë endophyte strain and identified the growth of the Epichloë strain under different types of nitrogen source treatments. In addition to the in vitro test, we evaluated growth performance for Epichloë endophyte–infected plants (E+) and Epichloë endophyte–free plants (E−) in a pot trial under 0.01 mol/L urea treatment. Seedlings from E+ and E− groups were collected to analyze the plant bacterial microbiome and root metabolites. The E. gansuensis endophyte strain was found not to produce indoleacetic acid (IAA), pectinase, or contain ferritin. The nitrogenase gene, essential for nitrogen fixation, was also absent. These results suggest that E. gansuensis endophyte strains themselves do not contain attributes to promote plant growth. Concerning N fertilization, it was observed an increase in the colony diameter of E. gansuensis strain was observed only in the NO₃⁻-N (NN) treatment, while inhibition was observed in the urea-N (UN) treatment. E. gansuensis endophyte symbiosis significantly increased tiller number and plant dry weight. Overall, our results suggest that the E+ plants had more root forks and greater average root diameter compared to E− plants under the UN treatment. In a pot experiment using UN, data from 16S rRNA amplicon sequencing revealed that E. gansuensis endophyte infection significantly altered the bacterial community composition in shoot and root, and significantly increased Shannon (p < 0.001) and Chao 1 (p < 0.01) indexes. The relative abundance of Acidobacteriota, Actinomycetota, Cyanobacteriota, Fibrobacterota, Myxococcota, and Patescibacteria in the shoot, and Cyanobacteriota, Pseudomonadota, and Verrucomicrobiota in the root were significantly increased by E. gansuensis endophyte infection. Similarly, E. gansuensis endophyte symbiosis shifted the metabolite composition of the host plants, with the E+ plants showing a higher number of metabolites than the E− plants. In addition, co-metabolism network analysis revealed that the positive relevance between exudates and microorganisms in the root of the E+ plants is higher than that of the E− plants. These findings provide valuable insights into the knowledge of the effects of the symbiotic relationship between host plants and Epichloë endophyte on interspecific interactions of plant microbiome, beneficial for harnessing endophytic symbiosis, promoting plant growth. Full article

Salt accumulation in arable lands causes significant abiotic stress, resulting in a 10% loss in global arable land area and jeopardizing food production and agricultural sustainability. In order to attain high and sustainable food production, it is imperative to enhance traditional agricultural practices with modern technology to enable the restoration of arable lands afflicted by salinity. This review consolidates recent rice-specific advancements aimed at enhancing salt stress resilience through integrated strategies. We explore the functions of primary and secondary metabolic pathways, organic amendments, microbial symbiosis, and plant growth regulators in reducing the negative impacts of salt. Furthermore, we highlight the significance of emerging genetic and epigenetic technologies, including gene editing and transcriptional regulation, in developing salt-tolerant rice cultivars. Physiological studies reveal salt stress responses in rice plants, biochemical analyses identify stress-related metabolites, microbial investigations uncover beneficial plant–microbe interactions, and molecular approaches enable the identification of key genes—together providing essential insights for developing salt-tolerant rice varieties. We present a comprehensive overview of the multilayered strategies—ranging from agronomic management and physiological adaptations to molecular breeding and microbial applications—that have been developed and refined over recent decades. These approaches have significantly contributed to understanding and improving salinity tolerance mechanisms in rice. This review provides a foundational framework for future research and practical implementation in stress-resilient rice farming systems. Full article

Cerium dioxide nanoparticles (CeO₂-NPs) are increasingly used in various industrial applications, leading to their inevitable release into the environment including the soil ecosystem. In soil, CeO₂-NPs are taken up by plants, translocated, and accumulated in plant tissues. Within plant tissues, CeO₂-NPs have been shown to interfere with critical metabolic pathways, which may affect plant health and productivity. Moreover, their presence in soil can influence soil physico-chemical and biological properties, including microbial communities within the rhizosphere, where they can alter microbial physiology, diversity, and enzymatic activities. These interactions raise concerns about the potential disruption of plant–microbe symbiosis essential for plant nutrition and soil health. Despite these challenges, CeO₂-NPs hold potential as tools for enhancing crop productivity and resilience to stress, such as drought or heavy metal contamination. However, understanding the balance between their beneficial and harmful effects is crucial for their safe application in agriculture. To date, the overall impact of CeO₂-NPs on soil -plant system and the underlying mechanism remains unclear. Therefore, this review analyses the recent research findings to provide a comprehensive understanding of the fate of CeO₂-NPs in soil–plant systems and the implications for soil health, plant growth, and agricultural productivity. As the current research is limited by inconsistent findings, often due to variations in experimental conditions, it is essential to study CeO₂-NPs under more ecologically relevant settings. This review further emphasizes the need for future research to assess the long-term environmental impacts of CeO₂-NPs in soil–plant systems and to develop guidelines for their responsible use in sustainable agriculture. Full article

The phyllosphere microbiome of aquatic macrophytes constitutes an integral component of freshwater ecosystems, serving crucial functions in global biogeochemical cycling and anthropogenic pollutant remediation. In this study, we examined the assembly mechanisms of epiphytic bacterial communities across four phylogenetically diverse macrophyte species (Scirpus validus, Hippuris vulgaris, Nymphoides peltatum, and Myriophyllum spicatum) inhabiting Ningwu Mayinghai Lake (38.87° N, 112.20° E), a vulnerable subalpine freshwater system in Shanxi Province, China. Through 16S rRNA amplicon sequencing, we demonstrate marked phyllospheric microbiome divergence, as follows: Gammaproteobacteria dominated S. validus, H. vulgaris and N. peltatum, while Alphaproteobacteria dominated in M. spicatum. The nitrate, nitrite, and pH value of water bodies and the chlorophyll, leaf nitrogen, and carbon contents of plant leaves are the main driving forces affecting the changes in the β-diversity of epiphytic bacterial communities of four plant species. The partitioning of assembly processes revealed that deterministic dominance governed S. validus and M. spicatum, where niche-based selection contributed 67.5% and 100% to community assembly, respectively. Conversely, stochastic processes explained 100% of the variability in H. vulgaris and N. peltatum microbiomes, predominantly mediated by dispersal limitation and ecological drift. This investigation advances the understanding of microbial community structural dynamics and diversity stabilization strategies in aquatic macrophyte-associated microbiomes, while establishing conceptual frameworks between plant–microbe symbiosis and the ecological homeostasis mechanisms within vulnerable subalpine freshwater ecosystems. The empirical references derived from these findings offer novel perspectives for developing conservation strategies aimed at sustaining biodiversity equilibrium in high-altitude lake habitats, particularly in the climatically sensitive regions of north-central China. Full article

Salt accumulation can degrade soil properties, decrease its productivity, and harm its ecological functions. Introducing salt-tolerant plant species associated with arbuscular mycorrhizal fungi (AMF) can act as an effective biological method for restoring salinized soils. AMF colonize plant roots and improve their nutrient acquisition capacity. However, there is limited knowledge on how AMF affects the production of signaling molecules, e.g., abscisic acid (ABA), salicylic acid (SA), and jasmonic acid (JA), related to plant–microbe interactions under salinity. Here, we assess the potential benefits of the AMF Rhizophagus intraradices in enhancing plant growth and nutrient uptake in addition to modulating stress hormone signaling levels (ABA, SA, and JA) of the facultative halophyte Sulla carnosa under saline conditions. Plants were grown in pots filled with soil and irrigated with 200 mM NaCl for 1 month. AMF symbiosis substantially increased the shoot dry weight (+107%), root dry weight (+67%), photosynthetic pigment content (chlorophyll a, chlorophyll b, and carotenoids), and nutrient uptake (C, N, P, K, Cu, and Zn) while significantly limiting the increase in the shoot Na⁺ concentration and H₂O₂ content caused by salinity stress. Mycorrhizal symbiosis significantly enhanced the root and shoot SA levels by 450% and 32%, respectively, compared to the stressed non-inoculated plants, potentially contributing to enhanced systemic resistance and osmotic adjustment under saline conditions. Salt stress increased the shoot ABA content, especially in R. intraradices-inoculated plants (113% higher than in stressed non-mycorrhizal plants). These findings confirm that AMF mitigated the adverse effects of salinity on S. carnosa by increasing the SA and ABA levels and reducing oxidative damage. Full article

The establishment of artificial grassland is a good pathway for resolving serious social and economic problems in the Qinghai–Tibet Plateau. Some beneficial indigenous microbes may be used to improve productivity in artificial grassland. The genome of the indigenous dark septate fungus, Exophiala tremulae CICC2537, was sequenced and assembled at the chromosome level using the PacBio sequencing platform, with the assistance of the Hi-C technique for scaffolding, and its 3D genome structures were investigated. The genome size of E. tremulae is 51.903848 Mb, and it contains eight chromosomes. A total of 12,277 protein-coding genes were predicted, and 11,932 genes (97.19%) were annotated. As for the distribution of exon and intron number and the distribution of gene GC and CDS GC, E. tremulae showed similar distribution patterns to the other investigated members of the genus Exophiala. The analysis of carbohydrate-active enzymes showed that E. tremulae possesses the greatest number of enzymes with auxiliary activities and the lowest number of enzymes with carbohydrate-binding modules among the investigated fungi. The total number of candidate effector proteins was 3337, out of which cytoplasmic and apoplastic effector proteins made up 3100 and 163, respectively. The whole genome of E. tremulae contained 40 compartment As and 76 compartment Bs, and there was no significant difference in GC content in its compartment As and Bs. The whole genome of E. tremulae was predicted to contain 155 topologically associating domains (TADs), and their average length was 250,000 bp, but there were no significant differences in the numbers of genes and the GC content per bin localized within the boundaries and interiors of TADs. Comparative genome analysis showed that E. tremulae diverged from Exophiala mesophila about 34.1 (30.0–39.1) Myr ago, and from Exophiala calicioides about 85.6 (76.1–90.6) Myr ago. Compared with all the investigated fungi, the numbers of contraction and expansion gene families in the E. tremulae genome were 13 and 89, respectively, and the numbers of contraction and expansion genes were 14 and 670, respectively. Our work provides a basis for the use of the dark septate fungus in alpine artificial grassland and further research into its symbiosis mechanisms, which may improve the growth of plant species used in the Qinghai–Tibet Plateau. Full article