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Microbes perform diverse and vital functions in animals, plants, and humans, and among them, plant-associated microbiomes, especially endophytes, have attracted growing scientific interest in recent years. Numerous plant species thriving in diverse environments have been shown to host endophytic microbes. While endophytic bacteria commonly colonize plant tissues such as stems, roots, and leaves, seed-associated endophytes generally exhibit lower diversity compared to those in other plant compartments. Nevertheless, seed-borne microbes are of particular importance, as they represent the initial microbial inoculum that influences a plant’s critical early developmental stages. The seed endophytic microbiome is of particular interest due to its potential for vertical transmission and its capacity to produce a broad array of phytohormones, enzymes, antimicrobial compounds, and other secondary metabolites. Collectively, these functions contribute to enhanced plant biomass and yield, especially under abiotic and biotic stress conditions. Despite their multifaceted roles, seed microbiomes remain underexplored in plant ecology, and their potential benefits are not yet fully understood. This review highlights recent advances in our understanding of the diversity, community composition, mechanisms of action, and agricultural significance of seed endophytic microbes. Furthermore, it synthesizes current insights into how seed endophytes promote plant health and productivity and proposes future research directions to fully harness their potential in sustainable agriculture. Full article

Heavy metal pollution represents a pervasive environmental challenge that significantly exacerbates the ever-increasing crisis of antimicrobial resistance and the capacity of microorganisms to endure and proliferate despite antibiotic interventions. This review examines the intricate relationship between heavy metals and AMR, with an emphasis on the underlying molecular mechanisms and ecological ramifications. Common environmental metals, including arsenic, mercury, cadmium, and lead, exert substantial selective pressures on microbial communities. These induce oxidative stress and DNA damage, potentially leading to mutations that enhance antibiotic resistance. Key microbial responses include the overexpression of efflux pumps that expel both metals and antibiotics, production of detoxifying enzymes, and formation of protective biofilms, all of which contribute to the emergence of multidrug-resistant strains. In the soil environment, particularly the rhizosphere, heavy metals disrupt plant–microbe interactions by inhibiting beneficial organisms, such as rhizobacteria, mycorrhizal fungi, and actinomycetes, thereby impairing nutrient cycling and plant health. Nonetheless, certain microbial consortia can tolerate and detoxify heavy metals through sequestration and biotransformation, rendering them valuable for bioremediation. Advances in biotechnology, including gene editing and the development of engineered metal-resistant microbes, offer promising solutions for mitigating the spread of metal-driven AMR and restoring ecological balance. By understanding the interplay between metal pollution and microbial resistance, we can more effectively devise strategies for environmental protection and public health. Full article

In plateau wetlands, the interactions of herbaceous roots with ectorhizosphere soil microorganisms represent an important way to realize their ecological functions. Global change-induced aridification of plateau wetlands has altered long-established functional synergistic relationships between plant roots and ectorhizosphere soil microbes, but we still know little about this phenomenon. In this context, nine typical wetlands with three different moisture statuses were selected from the eastern Tibetan Plateau in this study to analyze the relationships among herbaceous plant root traits and microbial communities and functions. The results revealed that drought significantly inhibited the accumulation of root biomass and surface area as well as the development of root volumes and diameters. Similarly, drought significantly reduced the diversity of ectorhizosphere soil microbial communities and the relative abundances of key phyla of archaea and bacteria. Redundancy analysis revealed that plant root traits and ectorhizosphere soil microbes were equally regulated by soil physicochemical properties. Functional genes related to carbohydrate metabolism were significantly associated with functional traits related to plant root elongation and nutrient uptake. Functional genes related to carbon and energy metabolism were significantly associated with traits related to plant root support and storage. Key genes such as CS,gltA, and G6PD,zwf help to improve the drought resistance and barrenness resistance of plant roots. This study helps to elucidate the synergistic mechanism of plant and soil microbial functions in plateau wetlands under drought stress, and provides a basis for evolutionary research and conservation of wetland ecosystems in the context of global change. Full article

Glycyrrhiza uralensis (G. uralensis), a leguminous plant, is an important medicinal and economic plant in saline–alkaline soils of arid regions in China. Its main bioactive components include liquiritin, glycyrrhizic acid, and flavonoids, which play significant roles in maintaining human health and preventing and adjuvantly treating related diseases. However, the cultivation of G. uralensis is easily restricted by adverse soil conditions in these regions, characterized by high salinity, high alkalinity, and nutrient deficiency. This study investigated the impacts of four multistrain microbial inoculants (Pa, Pb, Pc, Pd) on the growth performance and bioactive compound accumulation of G. uralensis in moderately saline–sodic soil. The aim was to screen the most beneficial inoculant from these strains, which were isolated from the rhizosphere of plants in moderately saline–alkaline soils of the Hexi Corridor and possess native advantages with excellent adaptability to arid environments. The results showed that inoculant Pc, comprising Pseudomonas silesiensis, Arthrobacter sp. GCG3, and Rhizobium sp. DG1, exhibited superior performance: it induced a 0.86-unit reduction in lateral root number relative to the control, while promoting significant increases in single-plant dry weight (101.70%), single-plant liquiritin (177.93%), single-plant glycyrrhizic acid (106.10%), and single-plant total flavonoids (107.64%). Application of the composite microbial inoculant Pc induced no significant changes in the pH and soluble salt content of G. uralensis rhizospheric soils. However, it promoted root utilization of soil organic matter and nitrate, while significantly increasing the contents of available potassium and available phosphorus in the rhizosphere. High-throughput sequencing revealed that Pc reorganized the rhizospheric microbial communities of G. uralensis, inducing pronounced shifts in the relative abundances of rhizospheric bacteria and fungi, leading to significant enrichment of target bacterial genera (Arthrobacter, Pseudomonas, Rhizobium), concomitant suppression of pathogenic fungi, and proliferation of beneficial fungi (Mortierella, Cladosporium). Correlation analyses showed that these microbial shifts were linked to improved plant nutrition and secondary metabolite biosynthesis. This study highlights Pc as a sustainable strategy to enhance G. uralensis yield and medicinal quality in saline–alkali ecosystems by mediating microbe–plant–nutrient interactions. Full article

Microbe–microbe interactions have been explored at the molecular level to a lesser degree than plant–pathogen interactions, primarily due to the economic impact of crop losses caused by pathogenic microorganisms. Effector proteins are well known for their role in disease development in many plant–pathogen pleinteractions, but there is increasing evidence showing their involvement in other types of interaction, including microbe–microbe interactions. Through the use of LC-MS/MS sequencing, effector candidates were identified in the in vitro interaction between a banana pathogen, Pseudocercospora fijiensis and a biological control agent, Trichoderma harzianum. The diverse interaction secretome revealed various glycoside hydrolase families, proteases and oxidoreductases. T. harzianum secreted more proteins in the microbial interaction compared to P. fijiensis, but its presence induced the secretion of more P. fijiensis proteins that were exclusive to the interaction secretome. The interaction secretome, containing 256 proteins, was screened for effector candidates using the algorithms EffHunter and WideEffHunter. Candidates with common fungal effector motifs and domains such as LysM, Cerato-platanin, NPP1 and CFEM, among others, were identified. Homologs of true effectors and virulence factors were found in the interaction secretome of T. harzianum and P. fijiensis. Further characterization revealed a potential novel effector of T. harzianum. Full article

The current proceedings summarize the presentations delivered during the third International Electronic Conference on Microbiology (ECM 2025), which was held online from 1 to 3 April 2025, via the SciForum platform. This virtual event brought together researchers from around the world to share recent advances in microbiological sciences. The ECM 2025 highlighted recent developments across a broad spectrum of microbiological research, including antimicrobial resistance, gut microbiota, infectious diseases, and environmental microbiomes. Participants shared their work through online presentations and abstracts, with selected submissions invited for full publication. The event fostered global collaboration, promoted open-access science, and showcased innovative tools for studying and managing microbial systems in health, agriculture, and industry. The multidisciplinary program was organized into several thematic sessions: S1. Gut Microbiota and Health Disease. S2. Foodborne Pathogens and Food Safety. S3. Antimicrobial Agents and Resistance. S4. Emerging Infectious Diseases. S5. Microbiome and Soil Science. S6. Microbial Characterization and Bioprocess. S7. Microbe–Plant Interactions. This conference report presents summaries of the contributions made by participating authors over the three-day event. Full article

The role of rhizosphere bacteria in facilitating plant invasion is increasingly acknowledged, yet the influence of specific microbial functional traits remains insufficiently understood. This study addresses this gap by isolating two bacterial strains, Bacillus sp. ScRB44 and Pseudomonas sp. ScRB22, from the rhizosphere of the invasive weed Solidago canadensis. We assessed their nitrogen utilization capacity and indoleacetic acid (IAA) production capabilities to evaluate their ecological functions. Our three-stage experimental design encompassed strain promotion, nutrient stress, and competition phases. Bacillus sp. ScRB44 demonstrated robust IAA production and significantly improved the nitrogen utilization efficiency, significantly enhancing S. canadensis growth, especially under nutrient-poor conditions, and promoting a shift in biomass allocation toward the roots, thereby conferring a competitive advantage over native species. Conversely, Pseudomonas sp. ScRB22 exhibited limited functional activity and a negligible impact on plant performance. These findings underscore that the ecological impact of rhizosphere bacteria on invasive weeds is closely linked to their specific growth-promoting functions. By enhancing stress adaptation and optimizing resource allocation, certain microorganisms may facilitate the establishment of invasive weeds in adverse environments. This study highlights the significance of microbial functional traits in invasion ecology and suggests novel approaches for microbiome-based invasive weed management, with potential applications in agricultural soil health improvement and ecological restoration. Full article

Stipagrostis pennata is an important plant in desert ecosystems. Its seed-endophytic bacteria may play a critical role in plant growth and environmental adaptation processes. This study systematically analyzed the community composition and potential plant growth-promoting (PGP) functions of seed-endophytic bacteria associated with S. pennata. The results showed that while the overall diversity of bacterial communities from different sampling sites was similar, significant differences were observed in specific functional genes and species abundances. Nine endophytic bacterial strains were isolated from the seeds, among which Bacillus altitudinis strain L7 exhibited phosphorus solubilizing capabilities, nitrogen fixing, IAA production, siderophore generation, and multi-hydrolytic enzyme activities. Additionally, the genomic sequencing of L7 revealed the key genes involved in plant growth promotion and environmental adaptation, including Na⁺ efflux systems, K⁺ transport systems, compatible solute synthesis genes, and the gene clusters associated with nitrogen metabolism, IAA synthesis, phosphate solubilization, and siderophore synthesis. Strain L7 exhibits salt and osmotic stress tolerance while promoting plant growth, providing a promising candidate for desert microbial resource utilization and plant biostimulant development. Full article

Recent advances in microbiome studies have deepened our understanding of endosymbionts and gut-associated microbiota in host biology. Of those, lepidopteran systems in particular harbor a complex and diverse microbiome with various microbial taxa that are stable and transmitted between larval and adult stages, and others that are transient and context-dependent. We highlight key microorganisms—including Bacillus, Lactobacillus, Escherichia coli, Pseudomonas, Rhizobium, Fusarium, Aspergillus, Saccharomyces, Bifidobacterium, and Wolbachia—that play critical roles in microbial ecology, biotechnology, and microbiome studies. The fitness implications of these microbial communities can be variable; some microbes improve host performance, while others neither positively nor negatively impact host fitness, or their impact is undetectable. This review examines the central position played by the gut microbiota in interactions of insects with plants, highlighting the functions of the microbiota in the manipulation of the behavior of herbivorous pests, modulating plant physiology, and regulating higher trophic levels in natural food webs. It also bridges microbiome ecology and applied pest management, emphasizing S. frugiperda as a model for symbiont-based intervention. As gut microbiota are central to the life history of herbivorous pests, we consider how these interactions can be exploited to drive the development of new, environmentally sound biocontrol strategies. Novel biotechnological strategies, including symbiont-based RNA interference (RNAi) and paratransgenesis, represent promising but still immature technologies with major obstacles to overcome in their practical application. However, microbiota-mediated pest control is an attractive strategy to move towards sustainable agriculture. Significantly, the gut microbiota of S. frugiperda is essential for S. frugiperda to adapt to a wide spectrum of host plants and different ecological niches. Studies have revealed that the microbiome of S. frugiperda has a close positive relationship with the fitness and susceptibility to entomopathogenic fungi; therefore, targeting the S. frugiperda microbiome may have good potential for innovative biocontrol strategies in the future. Full article

Plant-essential phosphorus (P) is a sparingly available mineral in soils. Phosphorus fertilizers—produced by the transformation of insoluble to soluble phosphates—are thus applied to agroecosystems. With advancements in commercial agriculture, crops have been increasingly adapted to grow in fertile environments. Wild crop relatives, however, are adapted to grow in unfertilized soils. In response to these two conditions of P bioavailability (fertilized agroecosystems and unfertilized natural soils), domesticated crops and wild species employ different strategies to grow and develop. It is essential to understand strategies related to P acquisition that may have been lost to domestication, and here we present, for the first time, that across species, modern cultivars engage in physical (i.e., root morphological) mechanisms while their wild relatives promote ecological (i.e., root-microbial) mechanisms. Domesticated crops showcase shallower root system architecture and engage in topsoil foraging to acquire P from the nutrient-stratified environments common to fertilized agroecosystems. Wild species associate with P-cycling bacteria and AM fungi. This divergence in P recovery strategies is a novel delineation of current research that has implications for enhancing agricultural sustainability. By identifying the traits related to P recovery that have been lost to domestication, we can strengthen the P recovery responses by modern crops and reduce P fertilization. Full article

Azospirillum is a well-studied genus of plant growth-promoting rhizobacteria (PGPR) and one of the most extensively researched diazotrophs. This genus can colonize rhizosphere soil and enhance plant growth and productivity by supplying essential nutrients to the host. Azospirillum–plant interactions involve multiple mechanisms, including nitrogen fixation, the production of phytohormones (auxins, cytokinins, indole acetic acid (IAA), and gibberellins), plant growth regulators, siderophore production, phosphate solubilization, and the synthesis of various bioactive molecules, such as flavonoids, hydrogen cyanide (HCN), and catalase. Thus, Azospirillum is involved in plant growth and development. The genus Azospirillum also enhances membrane activity by modifying the composition of membrane phospholipids and fatty acids, thereby ensuring membrane fluidity under water deficiency. It promotes the development of adventitious root systems, increases mineral and water uptake, mitigates environmental stressors (both biotic and abiotic), and exhibits antipathogenic activity. Biological nitrogen fixation (BNF) is the primary mechanism of Azospirillum, which is governed by structural nif genes present in all diazotrophic species. Globally, Azospirillum spp. are widely used as inoculants for commercial crop production. It is considered a non-pathogenic bacterium that can be utilized as a biofertilizer for a variety of crops, particularly cereals and grasses such as rice and wheat, which are economically significant for agriculture. Furthermore, Azospirillum spp. influence gene expression pathways in plants, enhancing their resistance to biotic and abiotic stressors. Advances in genomics and transcriptomics have provided new insights into plant-microbe interactions. This review explored the molecular mechanisms underlying the role of Azospirillum spp. in plant growth. Additionally, BNF phytohormone synthesis, root architecture modification for nutrient uptake and stress tolerance, and immobilization for enhanced crop production are also important. A deeper understanding of the molecular basis of Azospirillum in biofertilizer and biostimulant development, as well as genetically engineered and immobilized strains for improved phosphate solubilization and nitrogen fixation, will contribute to sustainable agricultural practices and help to meet global food security demands. Full article

Soil salinization poses a critical threat to global agriculture, necessitating innovative strategies for sustainable remediation. This review synthesizes advances in leveraging plant–microbe interactions to remediate saline–alkali soils, focusing on oilseed crops—Brassica napus, Glycine max, Arachis hypogaea, Helianthus annuus, and Sesamum indicum—as keystone species for ecosystem restoration. These crops exhibit unique adaptive strategies, including root architectural plasticity and exudate-mediated recruitment of stress-resilient microbiomes (Proteobacteria, Actinobacteria, and Ascomycota), which collectively stabilize soil structure and enhance nutrient cycling, ion homeostasis, and soil aggregation to mitigate soil salinity and alkalinity. Emerging technologies further amplify these natural synergies: nanomaterials optimize nutrient delivery and microbial colonization, while artificial intelligence (AI) models predict optimal plant growth-promoting rhizobacteria (PGPR) combinations and simulate remediation outcomes. This integration establishes a roadmap for precision microbiome engineering, offering scalable strategies to restore soil health and ensure food security in saline–alkali ecosystems. Full article

Nanomaterials have emerged as a transformative technology in agricultural science, offering innovative solutions to improve plant–microbe interactions and crop productivity. The unique properties, such as high surface area, tunability, and reactivity, of nanomaterials, including nanoparticles, carbon-based materials, and electrospun fibers, render them ideal for applications such as nutrient delivery systems, microbial inoculants, and environmental monitoring. This review explores various types of nanomaterials employed in agriculture, focusing on their role in enhancing microbial colonization and soil health and optimizing plant growth. Key nanofabrication techniques, including top-down and bottom-up manufacturing, electrospinning, and nanoparticle synthesis, are discussed in relation to controlled release systems and microbial inoculants. Additionally, the influence of surface properties such as charge, porosity, and hydrophobicity on microbial adhesion and colonization is examined. Moreover, the potential of nanocoatings and electrospun fibers to enhance seed protection and promote beneficial microbial interactions is investigated. Furthermore, the integration of nanosensors for detecting pH, reactive oxygen species, and metabolites offers real-time insights into the biochemical dynamics of plant–microbe systems, applicable to precision farming. Finally, the environmental and safety considerations regarding the use of nanomaterials, including biodegradability, nanotoxicity, and regulatory concerns, are addressed. This review emphasizes the potential of nanomaterials to revolutionize sustainable agricultural practices by improving crop health, nutrient efficiency, and environmental resilience. Full article

Exploring the mechanisms by which green agricultural production reduces emissions and enhances carbon sequestration in soil can provide a scientific basis for greenhouse gas reduction and sustainable development in farmland. This study uses a combination of meta-analysis and field experiments to evaluate the impact of different agricultural management practices and climatic conditions on soil organic carbon (SOC) and the emissions of CO₂ and CH₄, as well as the role of microorganisms. The results indicate the following: (1) Meta-analysis reveals that the long-term application of organic fertilizers in green agriculture increases SOC at a rate four times higher than that of chemical fertilizers. No-till and straw return practices significantly reduce CO₂ emissions from alkaline soils by 30.7% (p < 0.05). Warm and humid climates in low-altitude regions are more conducive to soil carbon sequestration. (2) Structural equation modeling of plant–microbe–soil carbon interactions shows that plant species diversity (PSD) indirectly affects microbial biomass by influencing organic matter indicators, mineral properties, and physicochemical characteristics, thereby regulating soil carbon sequestration and greenhouse gas emissions. (3) Field experiments conducted in the typical green farming research area of Chenzhuang reveal that soils managed under natural farming absorb CH₄ at a rate three times higher than those under conventional farming, and the stoichiometric ratios of soil enzymes in the former are close to 1. The peak SOC (19.90 g/kg) in the surface soil of Chenzhuang is found near fields cultivated with natural farming measures. This study provides theoretical support and practical guidance for the sustainable development of green agriculture. Full article

Microplastic pollution threatens coastal wetland ecosystems, yet its impacts on the dominant plant species and soil properties remain poorly understood. We investigated the effects of four microplastic types (PP, PE, PS, PET) at three concentrations (0.1%, 0.5%, 1% w/w) on Scirpus mariqueter, a keystone species in the coastal wetlands of China, and the associated soil physicochemical properties. In a controlled pot experiment, microplastics significantly altered the plant biomass, vegetative traits, and reproductive strategies, with type-specific and concentration-dependent responses. PET and PE strongly suppressed the belowground and total biomass (p < 0.05), with reductions in the belowground biomass of 42.87% and 44.13%, respectively, at a 0.1% concentration. PP promoted seed production, particularly increasing the seed number by 25.23% at a 0.1% concentration (p < 0.05). The soil NH₄⁺-N, moisture, and EC were key mediators, with NH₄⁺-N declines linked to biomass reductions via nitrogen limitation. The Spearman correlations confirmed strong associations between the plant traits and soil properties, particularly nitrogen forms. These findings reveal that microplastics disrupt wetland plant performance and soil environments, potentially impairing carbon sequestration and ecosystem stability. Our study underscores the urgent need for microplastic risk assessments in coastal wetlands and highlights soil–microbe–plant interactions as critical mechanisms for future investigation. Full article