Search Results (1,269)

Soil salinization severely threatens global crop production. Understanding the relationship between crop saline–alkaline tolerance physiology and the rhizosphere microbiome, and leveraging beneficial microorganisms to enhance crop stress resistance, holds importance for sustainable agricultural development. This study investigated the physiological and rhizosphere microbial responses of two soybean cultivars with different saline–alkaline tolerance to stress. Under saline–alkaline conditions, the tolerant cultivar exhibited superior physiological performance, including higher chlorophyll content, photosynthetic efficiency, and elevated activities of antioxidant enzymes (SOD, POD, and CAT), alongside reduced oxidative damage (MDA) and greater biomass accumulation. Combined metagenomic and physiological analyses revealed significant correlations of Bradyrhizobium and Solirubrobacter with key physiological indicators, including dry weight, PI_ABS, φₚₒ, and MDA. The tolerant cultivar selectively enriched distinct marker microbes, such as Bradyrhizobium sp. and Bradyrhizobium liaoningense, in its rhizosphere. We conclude that the tolerant cultivar exhibits strong intrinsic physiological resistance. This resistance is further enhanced by a beneficially assembled rhizosphere microbiome, while the host plant’s physiology remains the dominant factor. Full article

The introduction of living mulches into an orchard can be considered an agroecological practice that can provide several ecosystem services related to integrated crop protection, also in relation to the impact on soil microbiome. In this study, the introduction in an organic apple orchard of two plant mixtures designed as multifunctional living mulches to reduce weed competition and increase shelter for beneficial arthropods was evaluated in relation to their impact on soil nutrient content and bacterial activity indices. One mixture was composed of Trifolium repens (20%) and Festuca ovina (80%), the second made of 40 different plant species including legumes, flowering species and grasses. Both living mulches increased N-nitrate levels in spring, and the two-component plant mixture was also able to improve P and K levels in soil at the same time, in comparison to the natural cover (control). The two mixtures induced an increase in bacterial activity in the beginning (40 plant species mix) or middle of the growing season (two-component plant mix), without major effects on bacterial biodiversity at the phyla level, showing a high share of Proteobacteria and Actinobacteriota among treatments. Nevertheless, both plant mixtures modified the phenotypic profile of the bacterial population, measured with the Biolog method, of different classes of C sources including carbohydrates, amino acids and carboxylic acid. The results are pointing to possible benefits of the practice on soil microbial activity, which will have to be confirmed by longer studies. Full article

The increasing biogeochemical imbalance of nitrogen (N) heightens the importance of studying rhizosphere bacteria, which aid crop nutrient uptake, and their responses to N deficiency. The aim of the study was to assess variety-specific responses of the tomatoes and their associated rhizobacteriome to low N availability. Three determinant varieties of Solanum lycopersicum L. were cultivated in pot-scale experiment during 10 weeks on low-fertility substrate (sod-podzolic soil:peat:clay:sand, 1:1:1:2, v/v), half of which were supplemented with ammonium nitrate (60 mg N kg⁻¹ in total). A comprehensive methodology was employed, including 16S rRNA metagenomic Nanopore sequencing, quantitative assessment of N-cycling bacteria, and analysis of plant growth, photosynthetic pigments, total N in biomass, and fine root architecture. Results demonstrated that N deficiency significantly reduced plant biomass and photosynthetic pigments. The rhizosphere contained a diverse community of N-transforming bacteria (38 identified genera), whose composition and relative abundance were strongly influenced by both tomato variety and N fertilization. Nitrogen application increased the abundance of N-fixers and altered alpha-diversity in a variety-dependent manner. Significant correlations were found between the abundance of key bacterial genera (e.g., Stenotrophomonas, Rhizobium) and N parameters in plants and substrates. The study concludes that the response of the tomato rhizobacteriome to N availability is variety-specific, which is important for the development of microbiome management strategies for enhancing N use efficiency. Full article

Maintaining the balance between the host and commensal microorganisms is essential for skin health. The disruption of this equilibrium (dysbiosis) can contribute to inflammatory and infectious diseases and accelerate skin aging. Dysbiosis also accompanies skin cancers and may influence their progression. Causes of dysbiosis include exogenous factors such as cosmetics, UV radiation, pollution, and diet, as well as endogenous factors like stress, hormonal imbalances, and aging. Standard antibacterial treatments often eliminate beneficial microbes and may exacerbate conditions. Consequently, there is growing interest in alternative strategies—notably natural plant- and animal-derived products—that can modulate the skin microbiome more selectively and gently. This review presents current knowledge on skin microbiome physiology and dysbiosis and discusses natural compounds and microbiome-based therapies (probiotics, prebiotics, postbiotics) that modulate the skin microbiota. Unlike prior reviews, we provide a comparative perspective on emerging compound classes (e.g., peptides, lipids) and integrate the skin–gut axis concept into the framework, highlighting mechanistic insights at molecular and clinical levels. Our synthesis emphasizes distinct modes of action and evidence levels—from in vitro mechanisms to clinical outcomes—and offers guidance for formulation of microbiome-compatible products. Full article

Plant growth-promoting bacteria (PGPB) associated with Coffea arabica L. and Coffea canephora Pierre ex Froehner offer a viable strategy to reduce synthetic inputs and enhance resilience in coffee agroecosystems. This review synthesizes evidence from the past decade on rhizosphere-associated and endophytic taxa, their plant growth-promotion and biocontrol mechanisms and the resulting agronomic outcomes. A compartment-specific core microbiome is reported, in the rhizosphere of both hosts, in which Bacillus and Pseudomonas consistently dominate. Within endophytic communities, Bacillus predominates across tissues (roots, leaves and seeds), whereas accompanying genera are host- and tissue-specific. In C. arabica, endophytes frequently include Pseudomonas in roots and leaves. In C. canephora, root endophytes recurrently include Burkholderia, Kitasatospora and Rahnella, while seed endophytes are enriched for Curtobacterium. Functionally, coffee-associated PGPB solubilize phosphate; fix atmospheric nitrogen via biological nitrogen fixation; produce auxins; synthesize siderophores; and express 1-aminocyclopropane-1-carboxylate deaminase. Indirect benefits include the production of antifungal and nematicidal metabolites, secretion of hydrolytic enzymes and elicitation of induced systemic resistance. Under greenhouse conditions, inoculation with PGPB commonly improves germination, shoot and root biomass, nutrient uptake and tolerance to drought or nutrient limitation. Notable biocontrol activity against fungal phytopathogens and plant-parasitic nematodes has also been documented. Key priorities for translation to practice should include (i) multi-site, multi-season field trials to quantify performance, persistence and economic returns; (ii) strain-resolved omics to link taxa to functions expressed within the plant host; (iii) improved bioformulations compatible with farm management and (iv) rationally designed consortia aligned with production goals and biosafety frameworks. Full article

The soil microbiome is an essential component of agroecosystems. However, managing it remains a challenge due to our limited knowledge of how various environmental factors interact and shape its spatial distribution. This study presents a hierarchical ecological model to explain the assembly of the microbiome in sloping agricultural landscapes. Through a comprehensive analysis of bacterial and fungal communities, as well as the examination of metabolic and phytopathogenic profiles across a topographic gradient, we have demonstrated that topography acts as the main filter, structuring bacterial communities. Land use, on the other hand, serves as a secondary filter, refining fungal functional guilds. Our results suggest that hydrological conditions in floodplains favor the growth of stress-tolerant bacterial communities with low diversity, dominated by Actinomycetota. Fungal communities, on the other hand, are directly influenced by land use. Long-term fallow periods lead to an enrichment of arbuscular mycorrhiza, while agroecosystems shift towards pathogenic and saprotrophic niches. Furthermore, we identify specific topographic positions that may be hotspots for phytopathogenic pressure. These hotspots are linked to certain taxa, such as Ustilaginaceae and Didymellaceae, which may pose a threat to plant health. The derived hierarchical model provides a scientific foundation for topography-aware precision agriculture. It promotes stratified management, prioritizing erosion control and soil restoration on slopes, customizing nutrient inputs in fertile floodplains, and implementing targeted phytosanitary monitoring in identified risk areas. Our research thus offers a practical framework for harnessing soil spatial variability to improve soil health and proactively manage disease risks in agricultural systems. Full article

Sugarcane smut, caused by the fungal pathogen Sporisorium scitamineum, leads to significant economic losses in the global sugarcane industry. Bio-organic fertilizers (BF) offer a promising and sustainable strategy to mitigate smut incidence and enhance sugarcane growth. While the application of BF is known to modulate root exudates and rhizosphere microbial community structure, thereby promoting disease resistance, the precise mechanisms underpinning BF-mediated suppression of sugarcane smut remain largely unclear. This study investigated the microbiological mechanisms of smut suppression using a pot experiment, comparing a novel BF treatment (composted substrate enriched with Bacillus subtilis, Bacillus altitudinis, Bacillus cereus, Trichoderma harzianum, and Trichoderma longibrachiatum, biochar, and calcium carbonate) with a control receiving only conventional organic fertilizer. BF application significantly increased plant height (by 95.2%), dry weight (137.5%), fresh weight (253.3%), and sugar content (43.1%) relative to the control. Furthermore, the BF treatment enhanced catalase activity by 167.8% and peroxidase activity by 102.3% in sugarcane leaves, while the control effectiveness against the incidence of smut disease reached 88.0%. Analysis of the rhizosphere microbiome revealed that BF application significantly altered microbial alpha- and beta-diversity. Specifically, the BF treatment notably enriched beneficial genera such as Pseudomonas and Meyerozyma. Beta-diversity analysis revealed distinct microbial community structures in BF-treated rhizosphere soil compared to the control. Correlation and random forest analyses identified Pseudomonas and Meyerozyma as key taxa that were positively associated with sugarcane growth parameters and negatively correlated with smut incidence. These findings elucidate the dual role of this novel BF in enhancing sugarcane growth and suppressing smut incidence through the strategic reshaping of the rhizosphere microbiome. Full article

The secondary metabolite 2,4-diacetylphloroglucinol (2,4-DAPG), which is produced by Pseudomonas bacteria, is a potent antimicrobial agent with well-documented properties that suppress phytopathogens. However, its broader ecological impact on soil microbial communities is not understood. Through a combination of controlled microcosm and field trials, we have demonstrated that the effects of 2,4-DAPG are highly context-dependent. Laboratory exposure (10 mg kg⁻¹) altered the abundance of 8.53% of bacterial and 6.91% of fungal amplicon sequence variants, and simplified the bacterial co-occurrence networks (reduced number of nodes and links). In contrast, field conditions amplified bacterial sensitivity (the Shannon index decreased from 4.77 to 4.17, p < 0.05) but maintained fungal stability (Shannon index varied from 3.93 to 3.97, p > 0.05); these conditions affected a smaller proportion of fungal ASVs (4.23%). Taxonomic analysis revealed consistent suppression of fungi of the Mucoromycota (e.g., Mortierella) and context-dependent shifts in bacteria, with an enrichment of Bacillota (e.g., Bacillus, Paenibacillus) in the laboratory but not in the field. Enzymatic responses revealed a dose-dependent activation of the C-cycle, with up to 7.4-fold increases in the laboratory and up to a 10.5-fold increase in the field. P- and N- cycles showed more complex dynamics, with acid phosphatase activity increasing 3.8-fold in laboratory conditions and recovering from initial suppression to an increase of 144% in field conditions, while N-acetylglucosaminidase activity increased and L-leucine aminopeptidase decreased under laboratory conditions. Our results suggest that the response of microorganisms to 2,4-DAPG in natural soils is reduced, probably due to functional redundancy and pre-adaptation to abiotic stresses. This difference between laboratory and field studies warns against extrapolating data from controlled experiments to predict outcomes in agricultural ecosystems, and emphasizes the need for a context-specific evaluation of biocontrol agents. Full article

Plant-derived extracellular vesicles (PDEVs) are rapidly gaining popularity in cosmetics and regenerative medicine due to their biocompatibility, natural origin and promising bioactive properties. Nevertheless, the absence of standardized guidelines for their characterization has resulted in an inconsistent, unregulated landscape. This compromises product reproducibility, consumer safety, and scientific credibility. Here, a comprehensive set of minimal characterization guidelines for PDEVs is proposed to include physical and chemical profiling, molecular marker identification, cargo analysis, and stability assessment under storage and formulation conditions. Functional validation through cellular uptake assays, activity tests, and advanced in vitro or ex vivo models that replicate realistic skin exposure scenarios is pivotal. Requirements for transparent labelling, reproducible sourcing, batch-to-batch consistency, and biological activity substantiation to support claims related to skin regeneration, anti-aging, and microbiome modulation are also required. By establishing a harmonized baseline for quality and efficacy evaluation, these guidelines aim to elevate the scientific standards and promote the safe, ethical, and effective use of PDEV-based ingredients in cosmetic and biomedical applications. Full article

The human gut microbiome is a complex ecosystem of microorganisms fundamental to human health, influencing metabolism, immunity, and neurological function. Dysbiosis, or an imbalance in this microbial community, is increasingly linked to a range of chronic diseases, from inflammatory bowel disease to metabolic syndrome. This article explores the therapeutic potential of several common botanicals in modulating the gut microbiota and promoting intestinal health. We delve into the phytochemical composition and pharmacological properties of nine medicinal plants: globe artichoke, aloe vera, German chamomile, pot marigold, Ceylon cinnamon, dandelion, fennel, garlic, ginger, and green tea. We focus on their anti-inflammatory, antioxidant, antimicrobial, and prebiotic effects. The article also discusses the scientific evidence supporting their use, acknowledges the limitations of current research, and highlights considerations for safe and effective application. We conclude by summarising the significant role of these herbal remedies in modern complementary medicine and proposing future research directions to further elucidate their mechanisms of action and optimise their use for gut health. Full article

The Nearctic leafhopper Scaphoideus titanus is the primary vector of Flavescence Dorée, a severe grapevine disease in Europe. This insect can complete its life cycle on both cultivated Vitis vinifera and American Vitis species, including rootstock-derived plants that have gone wild. While the movement of S. titanus between wild and cultivated vines is well documented, its biological implications remain unclear, particularly regarding the role of the insect-associated microbiome. In this study, we investigated how rearing S. titanus nymphs on different host plants, including American Vitis and several V. vinifera cultivars, affects its bacterial community. 16S rRNA metabarcoding revealed that the bacterial microbiome was dominated by two obligate symbionts, namely ‘Candidatus Karelsulcia’ and ‘Candidatus Cardinium’, with moderate but significant differences in microbial diversity among host plants and developmental stages. When these dominant symbionts were excluded, variability in the remaining bacterial community increased, indicating a modulation of minor taxa according to the plant offered. These findings suggest that host plant species influence the microbiome structure, potentially affecting the insect performance and the microbial exchange between wild and cultivated vines in the field, contributing to disease dynamics. Full article

The plant microbiome is pivotal to sustainable agriculture and global food security, yet some challenges hinder fully harnessing it for field-scale impact. These challenges span measurement and integration, ecological predictability and translation across environments and seasons. Key obstacles include technical challenges, notably overcoming the limits of current sequencing for low-abundance taxa and whole-community coverage, integrating multi-omics data to uncover functional traits, addressing spatiotemporal variability in microbial dynamics, deciphering the interplay between plant genotypes and microbial communities, and enforcing standardized controls, metadata, depth targets and reproducible workflows. The rise of synthetic biology, omics tools, and artificial intelligence offers promising avenues for engineering plant–microbe interactions, yet their adoption requires regulatory, ethical, and scalability issues alongside clear economic viability for end-users and explicit accounting for evolutionary dynamics, including microbial adaptation and horizontal gene transfer to ensure durability. Furthermore, there is a need to translate research findings into field-ready applications that are validated across various soils, genotypes, and climates, while ensuring that advances benefit diverse regions through global, interdisciplinary collaboration, fair access, and benefit-sharing. Therefore, this review synthesizes current barriers and promising experimental and computational strategies to advance plant microbiome research. Consequently, a roadmap for fostering resilient, climate-smart, and resource-efficient agricultural systems focused on benchmarked, field-validated workflows is proposed. Full article

Sugarcane is highly sensitive to the variations in soil moisture content capacity, and upregulated water stress efficiency restricts its development and crop output. Rhizospheric microbes and metabolites play key roles to mitigate the adverse effects of abiotic stresses, i.e., drought stress. The drought-tolerant wild sugarcane relative, Saccharum arundinaceum Retz., remains poorly characterized with respect to its rhizosphere microbial community dynamics under water limitation. To address this, we analyzed drought-associated shifts in the rhizosphere microbiome and metabolome by comparing native plants from a long-term arid habitat in Guangxi, China, with plants from an irrigated cultivation environment. We analyzed the effects of agronomic traits, soil properties, enzyme activities, and 16S rRNA sequencing and untargeted metabolomics to characterize microbial communities and metabolites, with correlation analyses. Results demonstrated that wild plants possessed thicker stems, higher proline levels, and increased antioxidant enzyme activity. Their rhizospheres were enriched with Actinobacteria, Proteobacteria, and Chloroflexi, which exhibited upregulated urease and acid phosphatase activities. Metabolites linked to phosphotransferase systems and sugar metabolisms were also more abundant. Positive correlations between these microbes, metabolites, and drought traits reveal site-specific microbial–metabolic modules that confer drought resilience, providing valuable insights for sugarcane breeding programs. Full article

Background: Commercial oral care products commonly incorporate synthetic antimicrobials such as cetylpyridinium chloride (Cetyl Cl.), L-Arginine (L-arg.), and stannous fluoride (SnF₂). Although effective against oral pathogens, these agents are often associated with adverse effects including mucosal irritation, taste alteration, and disruption of the oral microbiome. These limitations have spurred growing interest in safer, plant-based alternatives. In this study, we present a two-pronged in vitro oral care testing model that integrates cell assays with machine-guided quantitative microscopy analyses to assess both antibacterial efficacy and host biocompatibility of botanical extracts. Methods: Using Miswak (Salvadora persica) and Neem (Azadirachta indica) as representative natural products, we conducted antibacterial and antibiofilm testing including the evaluation of the minimum inhibitory concentration (MIC), minimum biofilm inhibitory concentration (MBIC), and minimum biofilm eradication concentration (MBEC), alongside biocompatibility assessments via MTT cell viability assays on probiotic bacteria and mammalian oral cells. To evaluate biofilm structure and disruption, we employed scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM), augmented with machine-guided Weka segmentation and automated image analysis. Results: Our findings show that Miswak and Neem extracts exhibited 75–100% antibacterial and antibiofilm efficacy against all tested bacteria, as demonstrated by cell assays and microscopy analyses, comparable to synthetic oral care agents. They also maintained ~100% viability toward commensal microbes and mammalian oral cells, whereas Cetyl Cl. and SnF₂ showed dose-dependent cytotoxicity. Conclusions: This dual-assessment oral care testing model provides a comprehensive and biologically relevant framework for the discovery and screening of safe and effective natural herbal extracts in oral care applications. Full article