Search Results (129)

In resource-poor sandy habitats, alien plant co-invasion often triggers intense belowground competition mediated by rhizosphere microorganisms. However, the mechanisms by which these plants overcome nutrient limitations remain unclear. Here, we conducted an eight-month in situ monitoring of single- and co-invasion plots of Solanum rostratum and Cenchrus pauciflorus Benth. in the Horqin Sandy Land. By integrating soil enzyme assays with 16S rRNA and internal transcribed spacer (ITS) amplicon sequencing, we characterized their rhizosphere microbial community assembly. Co-invasion exposed both species to convergent biotic stress, characterized by the significant enrichment of the pathogenic fungi Didymella and Pseudogymnoascus (linear discriminant analysis (LDA) > 4.0). To mitigate these pressures, the dominant competitor, S. rostratum, specifically recruited a cross-kingdom phosphate-solubilizing consortium comprising Bacillus and Penicillium (LDA > 4.0). This targeted recruitment significantly enhanced rhizosphere activities, increasing phosphatase and sucrase to 86.10 U/g and 2.17 U/g, respectively, thereby maintaining available phosphorus at a high level (35.55 mg/kg). Conversely, the subordinate competitor, C. pauciflorus, lost key native stress-resistant bacteria such as Rubrobacter (relative abundance dropping from 5.39% to 3.27%) and failed to recruit effective microbes, leading to the rapid depletion of available phosphorus (dropping to 21.38 mg/kg). Ultimately, under dual nutrient and pathogenic stress, the precise recruitment and functional integration of cross-kingdom phosphate-solubilizing microbes are strongly linked to the divergent belowground competitive outcomes between these co-invading plants. Full article

Saline ecosystems, including saline lakes, are indeed major hotbeds of microbial novelty, harboring diverse and largely unexplored microbes. The sebkha of Lake Naïla (Morocco), an ecologically protected area registered under the Ramsar Convention in 1998, remains largely unexplored. Isolation using three different selective media enabled seven phenotypically distinct actinobacterial isolates to be obtained. Molecular characterization, based on 16S RNA gene sequencing, was used to identify strains as members of the genera Streptomyces, Nocardiopsis, and Prauserella. Three strains showed antimicrobial potential against pathogenic microorganisms, with Streptomyces sp. strain 43 exhibiting the most potent effects. Additionally, all isolates displayed plant-growth-promoting (PGP) traits, including phosphate solubilization, auxin (IAA) synthesis, siderophore secretion, and ammonia production. Notably, Nocardiopsis sp. strain 42 produced the highest IAA levels (282 μg/mL), while Streptomyces sp. strain 39, Streptomyces sp. strain 43, and Streptomyces sp. strain 48 excelled in phosphate solubilization. GC-MS profiling of Streptomyces sp. strain 43 revealed a complex metabolite repertoire, including 1,2-propanediol and nonanal, highlighting the strain’s versatile secondary metabolism. These findings highlight that the sebkha of Lake Naïla represents a rich source of halophilic actinobacteria with promising dual potential for antimicrobial and biofertilizer applications. The findings provide a solid basis for new perspectives on biotechnology applications and sustainable agriculture. Full article

As food demand increases, agricultural practices have evolved, prompting increased exploration of sustainable ecological techniques and utilization of plant-associated microorganisms. In this context, plant fitness has been enhanced by plant growth-promoting microorganisms (PGPM), which stimulate growth through direct mechanisms, such as improved nutrient availability and phytohormone production, as well as indirect mechanisms, including protection against phytopathogens and suppression of soil-borne diseases. However, these innate capabilities of PGPM can be further improved through genomic modification or editing. This article reviews advances in the genomic engineering of plant-beneficial microorganisms as tools to enhance their positive effects on crop performance and environmental remediation. The genetic modification strategies analyzed here include random mutagenesis, targeted genome editing (such as CRISPR-Cas), gene over-expression, genome shuffling, RNA interference, metabolic pathway engineering, and synthetic biology approaches. These tools have enabled the optimization of functions, such as nitrogen fixation, phosphate solubilization, secondary metabolite production, biocontrol, stress tolerance, and bioremediation. However, we propose expanding the discussion of their regulation and use in various countries. Additionally, these modifications must be efficient and safe for the beneficial microbiota associated with the target crop, as well as for humans, animals, and the environment, all of which depend on sustainable agricultural practices. Full article

Tomato (Solanum lycopersicum) is a globally important high-value cash crop. However, long-term continuous cropping causes frequent soil-borne diseases and soil microecological imbalance, while overreliance on chemical pesticides leads to pesticide residues and water eutrophication. Plant growth-promoting rhizobacteria (PGPR) are key resources for addressing tomato cultivation challenges, with their functions partly depending on the rhizosphere microenvironment inherently shaped by seedling tray materials. Using rhizosphere soil and substrates of tomato at different growth stages under biomass (BM) and plastic (PM) seedling tray treatments, this study combined culture-independent and culture-dependent techniques to analyze microbial community characteristics and screen high-efficiency PGPR. Results showed that pH and available nitrogen drove microbial community assembly. BM significantly enriched beneficial taxa (e.g., Trichoderma and Bacillus) and enhanced culturable microbial abundance and genetic diversity, while PM enriched potential pathogens (e.g., Fusarium and Pyrenochaeta). The multifunctional strain S25095 from BM, with phosphate-solubilizing, potassium-solubilizing, and indole-3-acetic acid (IAA)-producing abilities, significantly promoted tomato shoot and root growth, outperforming single-functional strains and synthetic consortia. This study reveals the effects of growth stages and seedling tray treatments on tomato rhizosphere microorganisms, providing valuable PGPR resources for tomato cultivation. Full article

Abiotic stress factors, including drought and salinity, severely limit crop productivity worldwide. Furthermore, the extensive use of herbicides, such as glyphosate, disrupts beneficial soil microbiota, further impairing crop growth. Plant growth-promoting bacteria (PGPB) represent a sustainable and efficient strategy to enhance crop yields, particularly under unfavorable environmental and soil conditions. In this study, we characterized Paenibacillus sp. JSM-10, newly isolated from glyphosate-exposed agricultural soil, for its stress tolerance and plant growth-promoting potential, including its morphology examined using complementary microscopy techniques. The strain tolerated up to 0.5 g/L glyphosate, 15 g/L NaCl, and 100 g/L polyethylene glycol (PEG-6000) without significant growth inhibition (p > 0.05), demonstrating robust resilience to such multiple abiotic stresses. Beyond its tolerance, the strain exhibited several beneficial characteristics, including indole-3-acetic acid (IAA) synthesis, siderophore production, and inorganic phosphate solubilization. Furthermore, both living cells and culture filtrates of JSM-10 exhibited a positive trend toward enhancing buckwheat growth under normal and saline conditions, with effect sizes ranging from Hedges’ g = 0.56−0.92. In addition, JSM-10 exhibited antagonistic activity against a range of pathogenic microorganisms, including Nigrospora oryzae, Bipolaris sorokiniana, Alternaria spp., and Escherichia coli. Altogether, these characteristics highlight the Paenibacillus sp. JSM-10 strain and its culture filtrates as promising candidates for application in organic farming aimed at promoting plant growth and improving stress tolerance via plant–microbe interactions. 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

The Sanjiang Plain is a key black soil agricultural zone in Northeast China. The conversion of dry-lands (DL) to paddy fields (PF) alters soil aggregate phosphorus (P) fractions and microbial diversity, yet the underlying mechanisms are unclear. This study compared DL and PF (converted from DL) soils. The results showed that electrical conductivity (EC) and soil organic carbon (SOC) increased significantly after the dryland-to-paddy conversion (p < 0.05). The proportions of macroaggregates and microaggregates increased, while the silt+clay fraction declined (p < 0.05), indicating enhanced aggregate stability. Soil total P increased by 16.04%, of which 83.81%, was attributed to macroaggregate-associated P. The dominant P fractions shifted from NaOH-Po to NaOH-Pi and HCl-Pi. The land-use change also markedly altered the soil microbial community structure, leading to increased abundances of Bradyrhizobium and Pseudomonas and decreased abundances of Streptomyces and Mesorhizobium, collectively driving the transformation of P fractions. The key functional genes identified were gcd, phoD, and phnA. However, this study did not capture the temporal dynamics of P forms and microbial community structure across different stages of land-use conversion. Future research should track these dynamics throughout the conversion process to clarify the mechanisms of P evolution. Full article

Cool-season (C3) forage grasses are a cornerstone of temperate grassland systems, where improving productivity, nutritive value, and stress resilience is essential for sustainable forage production. In this context, plant growth-promoting microorganisms (PGPMs) have gained increasing attention as potential alternatives or complements to mineral and organic fertilization in grassland management. This review synthesizes current knowledge on the role of bacterial and fungal PGPM in enhancing the growth, nutrient use efficiency, and stress tolerance of C3 forage grasses, with particular emphasis on species of the genus Lolium. Available evidence indicates that PGPMs can substantially improve biomass production and plant performance under both optimal and stress conditions through a range of direct and indirect mechanisms. These include phytohormone production, nitrogen fixation, phosphate solubilization, as well as the activation of antioxidant defense systems and stabilization of plant water relations under stress. While Lolium perenne L. and Lolium multiflorum Lam. remain the most extensively studied model species, comparable growth-promoting responses have also been reported for Dactylis glomerata L., Festuca species, and Festulolium hybrids. Increasing attention is being directed toward bacterial and fungal endophytes, which may provide more persistent physiological benefits due to their close association with plant tissues. However, PGPM effects are often strongly species-, genotype-, and environment-dependent, particularly in complex grassland systems. Overall, PGPMs represent a promising tool for sustainable grassland management, although their effective application will require long-term field studies conducted under realistic meadow and pasture conditions. Full article

The overreliance on non-renewable phosphate fertilizers necessitates sustainable alternatives for phosphorus recycling in agriculture. This study aimed to characterize and enhance the metabolic activity of phosphate-solubilizing microorganisms isolated from compost by eliciting them with two distinct mesoporous silica nanoparticles: standard SBA-15-S and short-pore SBA-15-C. Bacterial strains with broad-spectrum P solubilization and mineralization capacities were isolated from the mesophilic phases of tomato greenhouse and cow manure composts. These isolates received treatment with nanoparticle concentrations of 0.1, 10, and 100 ppm. The results demonstrated that nanoparticle elicitation significantly altered microbial growth, solubilization halos on tricalcium phosphate, and the specific activity of acid, neutral, and alkaline phosphatases in a strain- and nanoparticle-dependent manner. Notably, SBA-15-C at 100 ppm consistently enhanced multiple P-recycling properties across several strains, including Proteus and Myroides species. Principal component analysis revealed distinct behavioral clusters between composting phases and isolation methods. The findings indicate that tailored silicon oxide nanostructures can serve as eustressors to modulate and enhance the P-solubilizing and mineralizing functions of compost-derived microbiota, offering a promising nanobiostimulation strategy for developing enhanced biofertilizers. Full article

Phosphate-solubilizing microorganisms (PSMs) show promise for sustainable agriculture, yet inconsistent field performance limits their application. We investigated phosphate solubilization mechanisms in Enterobacter ludwigii strains GMG278, GMG291, GMG378 and Enterobacter soli GMG1156 through greenhouse wheat experiments, high-performance liquid chromatography (HPLC) organic acid analysis, and comparative genomics. Greenhouse trials demonstrated that bacterial inoculation compensated for phosphorus deficiency, with GMG291, GMG1156, and GMG278 showing superior performance. HPLC identified malic acid as the predominant secreted organic acid, with E. soli producing threefold higher concentrations than E. ludwigii strains. Phosphate solubilization efficiency followed the order FePO₄ > AlPO₄ > Ca₃(PO₄)₂, with maximal release (95.9–97.7 μg/mL) from iron phosphate despite lower malic acid secretion, suggesting siderophore involvement. An inverse correlation between malic acid levels and soluble phosphate concentrations likely reflects competitive bacterial phosphate uptake and secondary precipitation processes. Comparative genomics revealed missense mutations in the LuxR transcriptional regulator of strain GMG378 (Asp86Asn and Arg97Leu) near predicted DNA-binding domains, correlating with reduced solubilization capacity. Phosphate solubilization in Enterobacter proceeds primarily through metal–malic acid complex formation, with strain-specific efficiency linked to LuxR-regulated biofilm formation genes. These findings suggest PSM screening should incorporate biofilm-related genetic markers alongside acid production measurements. Full article

In mycorrhizal symbiotic relationships, non-photosynthetic myco-heterotrophic plants are unable to supply photosynthates to their associated fungi. On the contrary, they rely on fungal carbon to sustain their own growth. Mycorrhizal fungi can mediate plant interactions with the rhizosphere microbiome, which contributes to the promotion of plant growth and nutrient uptake. However, the microbial community and key microbial species that function during the growth of the myco-heterotrophic plant Cheilotheca humilis remain unclear. In this study, we evaluated the microbial community associated with Cheilotheca humilis, which was confirmed via morphological characteristics typical of this plant species. Metagenomic analysis showed that the Afipia carboxidovorans was dominant at species level. Based on the LDA score, Bradyrhizobium ottawaense exhibited the higher abundance in the CH-B group (related to bud) while Afipia carboxidovorans was identified from the CH-F group (related to flower). Microbial co-occurrence networks showed that the Rhizobium genus, Herbaspirillum genus, and Cyanobacteriota were defined as core functional microbial species. To explore the potential microorganisms, metagenome-assembled genomes (MAGs) of the rhizosphere microbiome identified 14 medium- and high-quality MAGs, mainly involved in carbon fixation, nitrogen transformation, and phosphorus metabolism, possibly providing nutrients for the plant. Furthermore, a total of 67 rhizospheric and 66 endophytic microorganisms were isolated and obtained. In vitro experiments showed that the mycorrhizal helper bacteria (MHBs) Rhizobium genus and Pseudomonas genus possessed the ability of nitrogen fixation, phosphate solubilization, and siderophores production. Most importantly, the mycorrhizal fungus Humicolopsis cephalosporioides was obtained, which could potentially produce cellulase to supply carbohydrates for host. The findings suggest the mycorrhizal fungus Humicolopsis cephalosporioides and helper bacteria have great potential in the growth of the myco-heterotrophic plant Cheilotheca humilis. Full article

The undefined microbial ecology of Aconitum carmichaelii root rot in western Yunnan constrains the advancement of eco-friendly control strategies. The identification of potential pathogenic determinants affecting A. carmichaelii growth is imperative for sustainable cultivation and ecosystem integrity. High-throughput sequencing was employed to profile microbial communities across four critical niches, namely rhizosphere soil, tuberous root epidermis, root endosphere, and fibrous roots of healthy and diseased A. carmichaelii. The physicochemical properties of corresponding rhizosphere soils were concurrently analyzed. Putative pathogens were isolated from diseased rhizospheres and tubers through culturing with Koch’s postulates validation, while beneficial microorganisms exhibiting antagonism against pathogens and plant growth-promoting (PGP) traits were isolated from healthy rhizospheres. Highly virulent strains (2F14, FZ1, L23) and their consortia were targeted for suppression. Strain DX3, demonstrating optimal PGP and antagonistic capacity in vitro, was selected for pot trials evaluating growth enhancement and disease control efficacy. Significant disparities in rhizosphere soil properties and bacterial/fungal community structures were evident between healthy and diseased cohorts. Fifteen putative pathogens spanning eight species across four genera were isolated: Fusarium solani, F. avenaceum, Clonostachys rosea, Mucor racemosus, M. irregularis, M. hiemalis, Serratia liquefaciens, and S. marcescens. Concurrently, eight PGP biocontrol strains were identified: Bacillus amyloliquefaciens, B. velezensis, B. subtilis, B. pumilus, and Paenibacillus polymyxa. Pot trials revealed that Bacillus spp. enhanced soil physiochemical properties through nitrogen fixation, phosphate solubilization, potassium mobilization, siderophore production, and cellulose degradation, significantly promoting plant growth. Critically, DX3 inoculation elevated defense-related enzyme activities in A. carmichaelii, enhanced host resistance to root rot, and achieved >50% disease suppression efficacy. This work delineates key pathogenic determinants of Yunnan A. carmichaelii root rot and identifies promising multifunctional microbial resources with dual PGP and biocontrol attributes. Our findings provide novel insights into rhizosphere microbiome-mediated plant health and establish a paradigm for sustainable disease management. Full article

The phyllosphere, the aerial part of plants, serves as a crucial habitat for diverse microorganisms. Phyllosphere bacteria can activate protective mechanisms that help plants resist disease. This study focuses on isolating and characterizing phyllosphere bacteria from cucurbits to evaluate their potential in controlling Colletotrichum orbiculare, a pathogen causing anthracnose in cucumbers. Among the 76 bacterial isolates collected, 11 exhibited strong antagonistic effects against C. orbiculare in vitro. Morphological and 16S rRNA analyses identified these isolates as different Bacillus species, including B. vallismortis, B. velezensis, B. amyloliquefaciens, and B. subtilis. These bacteria demonstrated essential plant-growth-promoting and biocontrol traits, such as motility, biofilm formation, phosphate solubilization, nitrogen fixation, and the production of indole acetic acid. Most of the bacterial strains also produced biocontrol compounds such as ammonia, acetoin, siderophores, hydrogen cyanide, chitinase, protease, lipase, and cellulase. The application of these bacteria significantly enhanced cucumber growth in both non-manured and organically manured soils, showing improvements in root and shoot length, chlorophyll content, and biomass accumulation. Additionally, bacterial treatments effectively reduced anthracnose severity, with isolates GL-10 and L-1 showing the highest disease suppression in both soil types. Colonization studies showed that phyllobacteria preferentially colonized healthy leaves over roots and diseased tissues, and they were more effective in manure-amended soils. These results suggest that Bacillus phyllobacteria have strong potential as sustainable bio-stimulants and biocontrol agents, offering an effective approach for enhancing cucumber growth and disease control under both fertilized and unfertilized soil conditions. Full article

The bacterial diversity of soils cultivated with avocado (Persea americana M.) is influenced by different factors, perhaps the most decisive being the type of agronomic management used by farmers. In conventional agronomic management (CM), high doses of agrochemicals are applied, in contrast to organic agronomic management (OM), where organic fertilizers are used. This alters the diversity and abundance of soil microorganism populations, which in turn affects crop health. This study aimed to isolate and morphologically characterize rhizospheric bacteria from avocado trees under different agronomic management systems (CM and OM). For the bacterial isolates, their ability to promote plant growth in vitro was determined through biochemical tests for phosphorus and calcium solubilization and nitrogen fixation. In addition, their in vivo effect on tomato (S. lycopersicum) growth was evaluated, and their antagonistic capacity against Fusarium sp. was assessed. The results showed differences in the quantity, diversity, and morphologies of bacterial isolates depending on the type of agronomic management. A higher Shannon diversity index was found in OM (2.44) compared to CM (1.75). A total of 35 bacterial isolates were obtained from both management types. A greater number of isolates from OM soils exhibited in vitro PGP activity; notably, eight isolates from OM plots showed phosphate-solubilizing activity, compared to only one from CM plots. Furthermore, although all isolates demonstrated nitrogen fixing capacity, those from OM orchards produced significantly higher nitrate levels than the control (Azospirillum vinelandii). On the other hand, inoculation of tomato plants with bacterial isolates from OM soils increased plant height, root length, and total fresh and dry biomass compared to isolates from CM soils. Likewise, OM isolates exhibited greater antagonistic activity against Fusarium sp. These findings demonstrate the impact of agronomic management on soil bacterial populations and its effect on plant growth and protection against pathogens. Full article

With the increasing severity of global climate change and soil salinization, the development of microorganisms that enhance crop salt tolerance has become a critical focus of agricultural research. In this study, we explored the potential of a novel Streptomyces species Qhu-G9 as a plant growth-promoting rhizobacterium (PGPR) under salt stress conditions, employing whole-genome sequencing and functional annotation. The genomic analysis revealed that Qhu-G9 harbors various genes related to plant growth promotion, including those involved in phosphate solubilization, indole-3-acetic acid (IAA) biosynthesis, antioxidant activity, and nitrogen fixation. A total of 8528 coding genes were annotated in Qhu-G9, with a significant proportion related to cell metabolism, catalytic activity, and membrane transport, suggesting its broad growth-promoting potential. In vitro experiments demonstrated that Qhu-G9 exhibited strong iron siderophore production, IAA synthesis, phosphate solubilization, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, all of which correlate with its plant growth-promoting capacity. Further plant growth trials revealed that Qhu-G9 significantly enhances the growth of Avena sativa and Onobrychis viciifolia seedlings under salt stress conditions, improving key physiological parameters, such as chlorophyll content, relative water content, and photosynthetic efficiency. Under salt stress conditions, inoculation with Qhu-G9 resulted in notable increases in total biomass, root length, and plant height. Biochemical analyses further confirmed that Qhu-G9 alleviates the oxidative damage induced by salt stress by boosting antioxidant enzyme activities, reducing peroxide levels, and promoting the accumulation of osmotic regulators. These findings suggest that Qhu-G9 holds great promise as a PGPR that not only promotes plant growth, but also enhances plant tolerance to salt stress; thus, it has significant agricultural potential. Full article