Search Results (691)

The rhizosphere microbiome plays an important role in carbon- and nitrogen-cycling in soil and in the stress response of plants. It also affects the function of the ammonium transporter (AmtB) that senses nitrogen levels inside and outside the cells of the associative nitrogen-fixing bacterium GXGL-4A. However, the potential mechanism of the interaction between the AmtB deletion mutant of GXGL-4A (∆amtB) and microorganisms in the rhizosphere of plants under low-nitrogen stress is still unclear. As revealed by transcriptome analyses, mutation of the amtB gene in GXGL-4A resulted in a significant up-regulation of many functional genes associated with nitrogen fixation and transportation at transcription level. The application of ∆amtB changed the nitrogen level in the rhizosphere of cucumber seedlings and reshaped the microbial community structure in the rhizosphere, enriching the relative abundance of Actinobacteriota and Gemmatimonadota. Based on bacterial functional prediction analyses, the metabolic capacities of rhizobacteria were improved after inoculation of cucumber seedlings with the original strain GXGL-4A or the ∆amtB mutant, resulting in the enhancement of amino acids, lipids, and carbohydrates in the cucumber rhizosphere, which promoted the growth of cucumber plants under a low-nitrogen stress condition. The results contribute to understanding the biological function of gene amtB, revealing the regulatory role of the strain GXGL-4A on cucumber rhizosphere nitrogen metabolism and laying a theoretical foundation for the development of efficient nitrogen-fixing bacterial agents for sustainable agricultural production. Full article

Background: Developments in biology, genetics, soil science, plant breeding, engineering, and agricultural microbiology are driving advances in soil microbiology and microbial biotechnology. Material and methods: The literature for this review was collected by searching leading scientific databases such as Embase, Medline/PubMed, Scopus, and Web of Science. Results: Recent advances in soil microbiology and biotechnology are discussed, emphasizing the role of microorganisms in sustainable agriculture. It has been shown that soil and plant microbiomes significantly contribute to improving soil fertility and plant and soil health. Microbes promote plant growth through various mechanisms, including potassium, phosphorus, and zinc solubilization, biological nitrogen fixation, production of ammonia, HCN, siderophores, and other secondary metabolites with antagonistic effects. The diversity of microbiomes related to crops, plant protection, and the environment is analyzed, as well as their role in improving food quality, especially under stress conditions. Particular attention was paid to the diversity of microbiomes and their mechanisms supporting plant growth and soil fertility. Conclusions: The key role of soil microorganisms in sustainable agriculture was highlighted. They can support the production of natural substances used as plant protection products, as well as biopesticides, bioregulators, or biofertilizers. Microbial biotechnology also offers potential in the production of sustainable chemicals, such as biofuels or biodegradable plastics (PHA) from plant sugars, and in the production of pharmaceuticals, including antibiotics, hormones, or enzymes. Full article

Climate change negatively affects agriculture, causing desertification, salinisation, and drought. The biochar hydroinfiltrator (ES Patent No.: ES2793448 B2) is a device that increases the capture of rainwater or irrigation water for crops by increasing infiltration rates. Biochar, produced via biomass pyrolysis, has emerged as a promising agricultural amendment, as it helps to optimise moisture retention and improve soil structure, key aspects for boosting crop yields. There is growing interest in microorganisms’ plant-growth-promoting activity (PGP) by carrying out different activities considered growth promoters. The aim of the present study is to evaluate the use of a biochar hydroinfiltrator as a promoter of microbial activity when it is used in soil. Metagenomic analysis of soils with and without the device reveals that genera Bacillus and Sphingomonas became particularly enriched in soils with hydroinfiltrators. Also, in order to understand the interaction between the uses of biochar together with bacteria PGP, an in vitro test was carried out. Two microorganisms, previously selected for their characteristics as plant growth promoters, were inoculated in soils with and without biochar and they grew better after 15 to 30 days of inoculation, showing major CFU counts. This combined strategy—biochar hydroinfiltrator and PGP bacteria—offers an innovative, eco-friendly approach to sustainable agriculture, particularly under drought stress. Full article

Soil salinization poses a significant constraint to agricultural productivity. However, certain plant growth-promoting bacteria (PGPB) can mitigate salinity stress and enhance crop performance. In this study, a bacterial isolate, R-18, isolated from saline-alkali soil in Ningxia, China, was identified as Enterobacter bugandensis based on 16S rRNA gene sequencing. The isolate was characterized for its morphological, biochemical, and plant growth-promoting traits and was evaluated for its potential to alleviate NaCl-induced stress in maize (Zea mays L.) under hydroponic conditions. Isolate R-18 exhibited halotolerance, surviving at NaCl concentrations ranging from 2.0% to 10.0%, and alkaliphilic adaptation, growing at pH 8.0–11.0. Biochemical assays confirmed it as a Gram-negative bacterium, displaying positive reactions in the Voges–Proskauer (V–P) tests, catalase activity, citrate utilization, fluorescent pigment production, starch hydrolysis, gelatin liquefaction, and ammonia production, while testing negative for the methyl red and cellulose hydrolysis. Notably, isolate R-18 demonstrated multiple plant growth-promoting attributes, including nitrogen fixation, phosphate and potassium solubilization, ACC deaminase activity, and indole-3-acetic acid (IAA) biosynthesis. Under 100 mM NaCl stress, inoculation with isolate R-18 significantly enhanced maize growth, increasing plant height, stem dry weight, root fresh weight, and root dry weight by 20.64%, 47.06%, 34.52%, and 31.25%, respectively. Furthermore, isolate R-18 improved ion homeostasis by elevating the K⁺/Na⁺ ratio in maize tissues. Physiological analyses revealed increased chlorophyll and proline content, alongside reduced malondialdehyde (MDA) levels, indicating mitigated oxidative damage. Antioxidant enzyme activity was modulated, with decreased superoxide dismutase (SOD) and peroxidase (POD) activities but increased catalase (CAT) activity. These findings demonstrated that Enterobacter bugandensis R-18 effectively alleviated NaCl-induced growth inhibition in maize by enhancing osmotic adjustment, reducing oxidative stress, and improving ion balance. Full article

Soil salinity adversely affects crop growth and development, leading to reduced soil fertility and agricultural productivity. The indigenous salt-tolerant plant growth-promoting rhizobacteria (PGPR), as a sustainable microbial resource, do not only promote growth and alleviate salt stress, but also improve the soil microecology of crops. The strain H5 isolated from saline-alkali soil in Bachu of Xinjiang was studied through whole-genome analysis, functional annotation, and plant growth-promoting, salt-tolerant trait gene analysis. Phylogenetic tree analysis and 16S rDNA sequencing confirmed its classification within the genus Halomonas. Functional annotation revealed that the H5 genome harbored multiple functional gene clusters associated with plant growth promotion and salt tolerance, which were critically involved in key biological processes such as bacterial survival, nutrient acquisition, environmental adaptation, and plant growth promotion. The pot experiment under moderate salt stress demonstrated that seed inoculation with Halomonas sp. H5 not only significantly improved the agronomic traits of tomato seedlings, but also increased plant antioxidant enzyme activities under salt stress. Additionally, soil analysis revealed H5 treatment significantly decreased the total salt (9.33%) and electrical conductivity (8.09%), while significantly improving organic matter content (11.19%) and total nitrogen content (10.81%), respectively (p < 0.05). Inoculation of strain H5 induced taxonomic and functional shifts in the rhizosphere microbial community, increasing the relative abundance of microorganisms associated with plant growth-promoting and carbon and nitrogen cycles, and reduced the relative abundance of the genera Alternaria (15.14%) and Fusarium (9.76%), which are closely related to tomato diseases (p < 0.05). Overall, this strain exhibits significant potential in alleviating abiotic stress, enhancing growth, improving disease resistance, and optimizing soil microecological conditions in tomato plants. These results provide a valuable microbial resource for saline soil remediation and utilization. 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

Microorganisms (bacteria and algae) are important components of biological soil crusts, which exhibit crucial functions in promoting plant growth, maintaining soil structure, and improving soil nutrient content. To determine the effects of combined inoculation on the growth of Poa annua and sandy soils, four species of bacteria and algae were isolated and identified from biological soil crusts (during different developmental stages in a karst rocky desertification area). The soil quality was evaluated based on a soil quality index (SQI), growth indicators of Poa annua, soil physicochemical properties, and a stability analysis of aggregates. With the application of nutrient-poor sandy soils as the substrate, different treatment inoculation solutions were inoculated onto Poa annua. The results revealed that bacteria–algal co-inoculation reduces soil acidity, enhances soil nutrient content and aggregate stability, improves soil quality, and protects plant growth. Notably, compared with the single application of bacterial solution and algal solution, the combined application of bacteria–algal solution significantly improves the sandy soil quality. Full article

Ecological restoration in the cold and high-altitude mining areas of the Qinghai–Tibet Plateau is faced with dual challenges of extreme environments and insufficient microbial adaptability. This study aimed to screen local microbial resources with both extreme environmental adaptability and plant-growth-promoting functions. Local fungi (DK; F18-3) and commercially available bacteria (B0) were used as materials to explore their regulatory mechanisms for plant growth, soil physicochemical factors, microbial communities, and metabolic profiles in the field. Compared to bacterial treatments, local fungi treatments exhibited stronger ecological restoration efficacy. In addition, the DK and F18-3 strains, respectively, increased shoot and root biomass by 23.43% and 195.58% and significantly enhanced soil nutrient content and enzyme activity. Microbiome analysis further implied that, compared with the CK, DK treatment could significantly improve the α-diversity of fungi in the rhizosphere soil (the Shannon index increased by 14.27%) and increased the amount of unique bacterial genera in the rhizosphere soil of plants, totaling fourteen genera. Meanwhile, this aggregated the most biomarkers and beneficial microorganisms and strengthened the interactions among beneficial microorganisms. After DK treatment, twenty of the positively accumulated differential metabolites (DMs) in the plant rhizosphere were highly positively associated with six plant traits such as shoot length and root length, as well as beneficial microorganisms (e.g., Apodus and Pseudogymnoascus), but two DMs were highly negatively related to plant pathogenic fungi (including Cistella and Alternaria). Specifically, DK mainly inhibited the growth of pathogenic fungi through regulating the accumulation of D-(+)-Malic acid and Gamma-Aminobutyric acid (Cistella and Alternaria decreased by 84.20% and 58.53%, respectively). In contrast, the F18-3 strain mainly exerted its antibacterial effect by enriching Acidovorax genus microorganisms. This study verified the core role of local fungi in the restoration of mining areas in the Qinghai–Tibet Plateau and provided a new direction for the development of microbial agents for ecological restoration in the Qinghai–Tibet Plateau. Full article

Plant growth-promoting rhizobacteria (PGPR) are beneficial rhizosphere microorganisms for plants. They can promote plant absorption of nutrients, inhibit pathogenic microorganisms, enhance plant tolerance to abiotic and biotic stresses, and improve plant growth. Isolating new beneficial microbes and elucidating their promoting mechanisms can facilitate the development of microbial fertilizers. This study combined transcriptome sequencing and related experiments to analyze the mechanism by which the endophytic fungus ‘BF-F’ promotes the growth of Sesuvium portulacastrum. We inoculated the ‘BF-F’ fungus beside S. portulacastrum seedlings as the experimental group. Meanwhile, S. portulacastrum seedlings not inoculated with ‘BF-F’ were set as the control group. After inoculation for 0 d, 7 d, 14 d, 21 d, and 28 d, the plant height and the number of roots were measured. Furthermore, transcriptome sequencing on the roots and leaves of the S. portulacastrum was conducted. Differentially expressed genes were screened, and KEGG enrichment analysis was performed. Nitrogen metabolism-related genes were selected, and qRT-PCR was conducted on these genes. Furthermore, we analyzed the metabolomics of ‘BF-F’ and its hormone products. The results showed that inoculation of ‘BF-F’ significantly promoted the growth of S. portulacastrum. After ‘BF-F’ inoculation, a large number of genes in S. portulacastrum were differentially expressed. The KEGG pathway enrichment results indicated that the ‘BF-F’ treatment affected multiple metabolic pathways in S. portulacastrum, including hormone signal transduction and nitrogen metabolism. The auxin signaling pathway was enhanced because of a decrease in AUX expression and an increase in ARF expression. Contrary to the auxin signal transduction pathway, the zeatin (ZT) signaling pathway was suppressed after the ‘BF-F’ treatment. ‘BF-F’ increased the expression of genes related to nitrogen metabolism (NRT, AMT, NR, and GAGOT), thereby promoting the nitrogen content in S. portulacastrum. The metabolites of ‘BF-F’ were analyzed, and we found that ‘BF-F’ can synthesize IAA and ZT, which are important for plant growth. Overall, ‘BF-F’ can produce IAA and enhance the nitrogen use efficiency of plants, which could have the potential to be used for developing a microbial fertilizer. 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

Drought, an increasingly prevalent climate stressor due to global warming, profoundly impacts agricultural systems, particularly the soil microbiome. Soil microorganisms are crucial for nutrient cycling, plant health, and ecosystem stability; however, drought-induced changes disrupt microbial community structure, function, and interactions with plants. This review synthesizes current knowledge on the effects of drought on soil microbiomes, with a focus on microbial diversity, resilience, and functional shifts in agricultural contexts. It highlights key microbial mechanisms underpinning plant drought tolerance, including symbioses with plant growth-promoting bacteria and fungi. Furthermore, it addresses knowledge gaps in the long-term effects of repeated drought events, microbial adaptations, and plant–soil feedback mechanisms. By advancing our understanding of drought–microbiome dynamics, this review aims to inform sustainable agricultural practices and resilience strategies to mitigate the adverse impacts of drought on crop productivity and ecosystem health. Full article

Plant growth-promoting rhizobacteria (PGPR) are beneficial soil microorganisms that enhance plant growth and stress tolerance through various mechanisms, including phytohormone production, EPS production, phosphate solubilization, and extracellular enzyme production. These bacteria establish endosymbiotic relationships with plants, improving nutrient availability and overall crop productivity. Despite extensive research on PGPR isolation, their practical application in agricultural fields has faced challenges due to environmental stresses and limited survival during storage. To address these limitations, the present study aimed to isolate salt-tolerant bacterial strains and formulate them with organic carriers to enhance their stability and effectiveness under saline conditions. The isolated bacterial strains exhibited high salt tolerance, surviving NaCl concentrations of up to 850 millimolar. These strains demonstrated basic key plant growth-promoting traits, including phosphate solubilization, auxin production, and nitrogen fixation. The application of carrier-based formulations with both strains, Bacillus wiedmannii (RR2) and Bacillus paramobilis (RR3), improved physiological and biochemical parameters in wheat plants subjected to salinity stress. The treated plants, when subjected to salinity stress, showed notable increases in chlorophyll a (73.3% by Peat + RR3), chlorophyll b (41.1% by Compost + RR3), carotenoids (51.1% by Peat + RR3), relative water content (77.7% by Compost + RR2), proline (75.8% by compost + RR3), and total sugar content (12.4% by peat + RR2), as compared to the stressed control. Plant yield parameters such as stem length (35.1% by Peat + RR3), spike length (22.5% by Peat + RR2), number of spikes (67.6% by Peat + RR3), and grain weight (39.8% by Peat + RR3) were also enhanced and compared to the stressed control. These results demonstrate the potential of the selected salt-tolerant PGPR strains (ST-strains) to mitigate salinity stress and improve wheat yield under natural field conditions. The study highlights the significance of carrier-based PGPR applications as an effective and sustainable approach for enhancing crop productivity in saline-affected soils. Full article

Plant species harbor diverse rhizospheric bacteria within their resilient root zones, serving as a valuable reservoir of bioactive microorganisms with strong potential for natural antifungal and plant growth-promoting applications. This study aimed to investigate the antagonistic potential of Bacillus zhangzhouensis, isolated from Zygophyllum oxianum in the Aral Sea region, Uzbekistan, against the fungal pathogen Cytospora mali. Due to its strong antifungal activity, B. zhangzhouensis was selected for bioactive compound profiling. Methanolic extracts were fractionated via silica and Sephadex gel chromatography, followed by antifungal screening using the agar diffusion method. A highly active fraction (dichloromethane/methanol, 9:1) underwent further purification, yielding twelve antifungal sub-fractions. Mass spectrometry analysis across positive and negative ion modes identified 2475 metabolites, with polar solvents—particularly methanol—enhancing compound recovery. Refinement using Bacillus-specific references identified six known antibiotics. Four pure compounds were isolated and structurally characterized using NMR: oleanolic acid, ursolic acid, cyclo-(Pro-Ser), and uracil. Their growth regulatory activity was assessed on Amaranthus retroflexus, Nicotiana benthamiana, triticale, and Triticum aestivum at concentrations of 5, 20, 100, and 500 mg L−1. All compounds negatively affected root growth in a concentration-dependent manner, especially in monocots. Interestingly, some treatments enhanced stem growth, particularly in N. benthamiana. These findings indicate that B. zhangzhouensis produces diverse bioactive compounds with dual antifungal and plant growth-modulatory effects, highlighting its potential as a biocontrol agent and a source of natural bioactive compounds. Full article

Sweet cherry (Prunus avium L.), as a high-economic-value fruit with both nutritional and health functions, faces severely constrained plant growth due to underdeveloped root systems and suboptimal orchard site conditions. Plant growth-promoting rhizobacteria (PGPR) demonstrate application potential in regulating plant development and improving soil structure through the release of volatile organic compounds (VOCs). This study systematically evaluated the effects of VOCs from three PGPR strains—Pantoea ananatis D1-28, Burkholderia sp. D4-24, and Burkholderia territorii D4-36—on cherry root development and rhizosphere microbial communities. The results indicate that when D1-28 and D4-24 strains were at 10³ cfu·mL⁻¹ and D4-36 was at 10⁵ CFU·mL⁻¹, their VOCs exhibited optimal growth-promoting effects. Compared with the control group, significant improvements were observed in cherry seedling parameters, including plant height, total biomass, root length, root surface area, and root volume. The VOCs from these strains synergistically promoted plant growth by regulating auxin synthesis pathways in cherry roots while enhancing the relative abundance of beneficial rhizosphere microorganisms. This study establishes the strain-concentration–effect relationship, providing a theoretical foundation to optimize soil microbial environments and promote cherry root development using PGPR. Full article

Plant-growth-promoting fungi (PGPF) play a central role in promoting sustainable agriculture by improving plant growth and resilience. The aim of this literature review is to survey the impacts of Trichoderma spp. and Penicillium spp. on various agricultural and horticultural plants. The information provided in this manuscript was obtained from randomized control experiments, review articles, and analytical studies and observations gathered from numerous literature sources such as Scopus, Google Scholar, PubMed, and Science Direct. The keywords used were the common and Latin names of various agricultural and horticultural species, fungal endophytes, plant-growth-promoting fungi, Trichoderma, Penicillium, microbial biostimulants, and biotic and abiotic stresses. Endophytic fungi refer to fungi that live in plant tissues throughout part of or the entire life cycle by starting a mutually beneficial symbiotic relationship with its host without any negative effects. They are also capable of producing compounds and a variety of bioactive components such as terpenoids, steroids, flavonoids, alkaloids, and phenolic components. Penicillium is extensively known for its production of secondary metabolites, its impact as a bioinoculant to help with crop productivity, and its effectiveness in sustainable crop production. The plant-growth-promotion effects of Trichoderma spp. are related to better absorption of mineral nutrients, enhanced morphological growth, better reproductive potential and yield, and better induction of disease resistance. Both Penicillium spp. and Trichoderma spp. are effective, affordable, safe, and eco-friendly biocontrol agents for various plant species, and they can be considered economically important microorganisms for both agricultural and horticultural sciences. The present review article aims to present the most up-to-date results and findings regarding the practical applications of two important types of PGPF, namely Penicillium spp., and Trichoderma spp., in agricultural and horticultural species, considering the mechanisms of actions of these species of fungi. Full article