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PubMedDate not supplied

[Use of ultrasound in the quantitative estimation of soil and rhizospheric microorganisms].

Ultrasonic treatment of soil, though being very effective for desorption of cells and deaggregation of microcolonies, may damage and kill microorganisms. Possible application and effectiveness of ultrasonic treatment was studied in this work with chernozem (dry and wet samples), rhizosphere and rhizoplane of pea. An ultrasonic disintegrator of low frequency is recommended for dry soils. Ultrasound cannot be recommended for treating rhizosphere and rhizoplane of plants without checking its effectiveness in each case.

Bacteriological Techniques↗
PubMed2026

Rhizosphere Dialogue: Microorganisms Mediated by Root Exudates Alleviate Drought Stress in Grasses.

Drought stress threatens the ecological functions and economic value of grasses, posing a major challenge to their sustainable production. Plants co-evolve with rhizosphere microbial communities, sometimes described as the plant's second genome, that can contribute to drought adaptation. Drought alters root architecture, hormonal and redox regulation and belowground carbon allocation, thereby modifying the quantity and composition of root exudation and reshaping the rhizosphere environment. This review uses the rhizosphere dialogue as an integrative framework to link these plant responses with microbial recruitment and subsequent feedback to the host. We summarise three linked stages of this dialogue: drought-induced changes in root exudation; microbial recruitment and colonisation through chemotaxis, attachment, biofilm formation, and root colonisation; and microbiome-mediated feedback that improves plant water relations, hormonal and redox homoeostasis, nutrient acquisition, and root function. We highlight microbial extracellular polymeric substances, 1-aminocyclopropane-1-carboxylate deaminase, and microbial volatile organic compounds as key mediators of drought alleviation. We then discuss how this framework may inform rational synthetic microbial community (SynCom) design, microbiome-informed breeding, artificial intelligence and machine-learning assisted strain prioritisation, rhizosphere legacy effects, and real-time monitoring. Future work should distinguish active exudate-mediated recruitment from drought-driven environmental filtering and integrate multi-omics, plant genetics, functional validation, and multi-location field trials to determine whether rhizosphere dialogue can become a predictive framework for climate-resilient grass production.

drought stress↗
PubMed1979

Microorganisms in the rhizosphere of wheat colonized by the fungus Gaeumannomyces graminis var. tritici.

The population of microorganisms in wheat rhizosphere changed in the presence of the fungus Gaeumannomyces graminis var. tritici causing the take-all of wheat. In the majority of cases when the soil was artificially contaminated by the fungus, both the number of bacteria in the rhizosphere and the bacteria/fungi ratio temporarily increased. At the beginning bacteria growing in the presence of NH4+ predominated, later bacteria utilizing organic N-substances prevailed. Pseudomonas fluorescens and the related species colonized the rhizosphere and the soil to a greater extent in the presence of G. graminis. The wheat rhizosphere with G. graminis was found to contain a higher level of the slime-producing bacterium Agrobacterium spp.; this microorganism occurred on hyphal surfaces (in hyphosphere) of both G. graminis growing in soil and Mucor spp. Changes in microbial populations in the wheat rhizosphere during the first stage of colonization by G. graminis can be partly explained by a simultaneous rhizosphere colonization by microorganisms which accompany this fungus in soil. In the period of increase in the number of bacteria in rhizosphere a temporary stimulation of wheat growth was observed.

Actinomycetales↗
PubMed1979

Accelerated mineralization of two organophosphate insecticides in the rhizosphere.

Numerous xenobiotic compounds, including the organophosphate insecticides O, O-diethyl-O-(2-isopropyl-6-methyl-4-pyrimidinyl) phosphorothioate (diazinon) and O, O-diethyl-O-p-nitrophenyl phosphorothioate (parathion), appear to be degraded in the soil environment by an initial cometabolic attack. Comparing the mineralization rates of radiolabeled diazinon and parathion in root-free and in rhizosphere soil, we tested our hypothesis that, because of the presence of root exudates, the rhizosphere is an especially favorable environment for such co-metabolic transformations. The insecticides were added individually at 5 mug/g to sealed flasks containing either soil permeated by the root system of a bush bean plant or identical soil without roots. Periodically, the flask atmospheres were flushed through traps and the evolved (14)CO(2) was quantitated. Bush bean plant roots without associated rhizosphere microorganisms failed to produce a significant amount of (14)CO(2). During 1 month of incubation, rhizosphere flasks mineralized 12.9 and 17.9% of the added diazinon and parathion radiocarbon, respectively, compared to 5.0 and 7.8% by the soil without roots. The mineralization of parathion but not of diazinon was stimulated in a similar manner when soil without roots was repeatedly irrigated with a root exudate produced in aseptic solution culture. Viable counts of microorganisms on soil extract agar were not significantly altered by root permeation or by root exudate treatment of the soil, leaving population selection and/or enhanced cometabolic activity as the most plausible interpretations for the observed stimulatory effects. Rhizosphere interactions may substantially shorten the predicted half-lives of some xenobiotic compounds in soil.

Bacteria↗
PubMed2026

PGPR inoculation and growth enhancement of crops cultivated in hydroponic systems.

Plant growth-promoting rhizobacteria (PGPR) are ubiquitous rhizosphere microorganisms that promote plant health through various mechanisms. Although the study of PGPR inoculants in soil has been done for ages, their application in hydroponic systems has received relatively limited attention. This review identifies PGPR inoculants that are commonly used in hydroponics, methods of application, and their effects on plant growth and nutrient use efficiency. Literature shows that PGPR inoculants improve plant performance in controlled hydroponic systems through the production of growth-stimulating substances, nitrogen fixation, and improved nutrient acquisition. However, the plant growth responses are highly variable depending on the composition of nutrient solutions, environmental factors, crop and microbe species, and the type of hydroponic system. The review identifies various challenges of PGPR inoculation in hydroponic systems and future research directions to address the current gaps. Generally, the productivity of hydroponic systems can be enhanced through advanced inoculation strategies and the development of suitable carrier materials to improve inoculant survival, viability, and functions. Emphasis should also be placed on designing system-specific microbial consortia and Synthetic communities that are tailored to the unique ecological conditions of hydroponic systems.

Hydroponics↗
PubMed2026

Plant-derived and microbial biostimulants in sustainable agriculture: mechanisms, applications, and challenges.

Plant biostimulants have emerged as transformative and sustainable tools for improving crop productivity, resource-use efficiency, and resilience under rapidly intensifying environmental stresses. Unlike conventional agrochemicals, biostimulants function by activating physiological, biochemical, and molecular processes that optimize plant performance without directly supplying nutrients or exerting pesticidal effects. This review comprehensively examines the integrated roles of plant-derived and microbial biostimulants in sustainable agriculture, with particular emphasis on microbial-mediated mechanisms underlying plant stress adaptation and rhizosphere functioning. Plant-derived biostimulants, including seaweed extracts, humic substances, protein hydrolysates, amino acids, and chitosan, enhance nutrient acquisition, root architecture, hormonal regulation, and antioxidant defense systems. More importantly, microbial biostimulants, such as plant growth-promoting rhizobacteria (PGPR), endophytic microorganisms, mycorrhizal fungi, actinomycetes, yeasts, and cyanobacteria, exert multifunctional effects through biological nitrogen fixation, mineral solubilization, phytohormone biosynthesis, volatile signaling, osmolyte accumulation, pathogen suppression, and modulation of stress-responsive genes. These beneficial microorganisms reshape rhizosphere microbial communities, improve nutrient cycling, and enhance plant tolerance to drought, salinity, heat, and heavy metal toxicity. Emerging evidence from genomics, transcriptomics, metabolomics, and microbiome-based investigations has further revealed the molecular networks and signaling pathways governing biostimulant-induced resilience and plant-microbe interactions. Despite their substantial promise, inconsistent field performance, formulation instability, regulatory limitations, and inadequate mechanistic understanding continue to restrict their large-scale adoption. This review highlights recent advances in microbial and plant-derived biostimulants while identifying critical knowledge gaps and future opportunities for precision biostimulant engineering, microbiome manipulation, and climate-resilient crop management. The integration of next generation biostimulant technologies into sustainable agricultural systems may significantly reduce dependence on agrochemicals while improving crop productivity, environmental sustainability, and global food security.

Agriculture↗
PubMed1975

Soil microflora of the rhizosphere of plants from several habitats in the botanical garden in Poznań.

The abundance and activity of certain groups of soil microorganisms were estimated in the rhizosphere of 13 plants from four different habitats at several dates. An additional study was made of the rhizosphere microflora of Ledum palustre from a peat-bog. Numbers of proteolytic, nitrate assimilating, denitrifying, and cellulolytic bacteria were estimated. The intensity of ammonification, nitrification and Clostridium growth was estimated. The studies have revealed that the abundance and the activity of all the groups of bacteria studied depended on the habitat. Within one habitat, however, the influence of the plant was sometimes more pronounced than that of the habitat itself, particularly on the abundance of proteolytic bacteria (Fig. 1). The date of sampling had very little effect on the abundance of all the bacterial groups studied except the cellulolytic bacteria.

Bacteria↗
PubMed1979

Investigations into rhizosphere microflora of some plants in Libya.

The present investigation deals with the effect of raising Hordeum vulgare and Arachis hypogaea at two different stages on the microbial rhizosphere population. The studies were extended to reveal the microbiological occurrence in different horizons of a soil profile corresponding in length to root regions. Bacteria were most abundant, followed by actinomycetes while fungi were less abundant and more restricted in their distribution. The three groups of microorganisms varied markedly in the rhizosphere of the two plants under investigation. The plant age had a great influence on the frequency of occurrence of the different microorganisms. One strain of bacteria, six fungi and the members of the grey series of Streptomyces were dominant. Actinomycetes and fungi diminished with the depth of soil, while the bacterial counts increased.

Actinomycetaceae↗
PubMed2026

Metabolome-driven rhizosphere microbiome assembly determining the health of medicinal herb (Angelica sinensis) against root rot.

BACKGROUND: The rhizosphere-associated microbiota plays a crucial role in plant responses to disease stress. Plant secondary metabolites are recognized as crucial mediators in the assembly of rhizosphere microbial communities, particularly by enhancing the colonization of beneficial microorganisms. Despite this recognized importance, a deeper understanding of how such metabolome-driven microbiome assembly specifically determines plant resistance against soil-borne diseases is still lacking. RESULTS: Here, we focused on the widely planted medicinal plant Angelica sinensis and demonstrated that root rot-diseased rhizosphere soils (DRS) exhibited a higher relative abundance of Fusarium and a lower relative abundance of Streptomyces compared to healthy rhizosphere soils (HRS). Shotgun metagenomic sequencing revealed that metabolism-associated genes, particularly those related to steroid degradation, are significantly enriched in HRS samples. Subsequent genome and functional gene analysis of Streptomyces revealed that the steroid degradation-related genes are associated with rhizosphere colonization in hosts. Rhizosphere Streptomyces S15 directly antagonized Fusarium and enhanced the root resistance of A. sinensis. Comparative metabolomics showed that A. sinensis plants from HRS secreted more lipid and lipid-like molecules than those from DRS, especially sterol lipids and long-chain fatty acids, which promoted the growth of Streptomyces S15 isolates. Transcriptome analysis validated that the lipid hormones are essential for sporulation, biofilm formation, and streptomycin biosynthesis of S15 strain. Finally, exogenous application of synbiotics (lipid prebiotics and S15) to A. sinensis resulted in the enrichment of S15-homologous Streptomyces amplicon sequence variant (ASV), further establishing beneficial bacterial communities in Fusarium-stressed rhizospheres. CONCLUSIONS: Our study proposes that A. sinensis recruits steroid-metabolizing Streptomyces species by exuding key lipid compounds (i.e., methyl jasmonate and brassinolide) to combat Fusarium root rot. This study provides novel insights into using functional synbiotics as a promising strategy for manipulating plant-microbiome interactions to promote sustainable agriculture. Video Abstract.

Rhizosphere↗
PubMed2026

Gluconacetobacter diazotrophicus as a plant growth-promoting endophyte: mechanistic insights and translational prospects for sustainable agriculture.

With the growing interest in sustainable agriculture, there has been a surge in exploration of multitrophic interactions between plants and microbes that can help plants adapt to changing environments and enhance their resilience to climate changes. One such beneficial microbe is Gluconacetobacter diazotrophicus, an aerobic, nitrogen-fixing endophyte currently being studied because of its ability to fix atmospheric nitrogen within plant tissues under aerobic conditions. This endophyte also promotes plant growth through processes like phytohormone production, nutrient solubilization, and improved stress tolerance of the plant. Recent advances in genomics and systems biology have provided valuable insights into the metabolism, interactions, and functions of this microorganism inside the host plants and its contribution to rhizosphere and endosphere dynamics. Despite considerable advances in understanding this organism, there are still limitations to its application due to its poor field performance, environmental variations, and difficulties in formulation production. This review consolidates the current knowledge on the ecology, physiology, and molecular mechanisms of Gluconacetobacter diazotrophicus, critically assesses its limitations, and identifies future research priorities to enhance its translational potential.

Gluconacetobacter↗
PubMed2026

A novel biocontrol Pseudomonas species with broad-spectrum antagonistic activity against phytopathogens.

Bacterial and fungal diseases cause significant losses in horticultural crops, and biocontrol using beneficial microorganisms offers a sustainable alternative to chemical pesticides. In this study, a novel Pseudomonas strain D3 was isolated from Actinidiae rhizosphere. D3 exhibited strong antibacterial activity in LB medium but showed no activity against fungi or oomycetes. However, when cultured in KIDO medium, it demonstrated potent antifungal activity. Phylogenetic analysis based on 16S rRNA gene showed that D3 was most closely related to Pseudomonas mosselii CIP_105259T, while whole-genome sequencing revealed ANI values below 95% with eight known P. mosselii strains. Digital DNA-DNA hybridization (dDDH) further confirmed its genomic distinctiveness, with the highest dDDH value (58.2%) against the type strain P. mosselii DSM 17497T, well below the 70% species delineation threshold, supporting D3 as a novel Pseudomonas species. Functional validation via targeted gene knockout revealed a dichotomy in the antagonistic mechanisms of D3. Knockout of individual biosynthetic gene clusters (BGCs) only partially reduced antibacterial activity against Pseudomonas syringae pv. actinidiae, indicating that multiple BGCs contribute to this activity in a partially redundant manner. In contrast, disruption of a specific lipopeptide synthase cluster completely abolished antifungal activity against Valsa mali. LC-MS/MS analysis confirmed that this lipopeptide was produced exclusively in KIDO medium, consistent with the observed medium-dependent antifungal activity. Detached leaf and twig assays showed that D3 provides strong preventive biocontrol against both pathogens. Collectively, strain D3 employs a dual biocontrol mechanism, combining antibacterial activity mediated by multiple BGCs with lipopeptide-dependent antifungal activity, positioning it as a promising agent for sustainable disease management in horticultural crops.

Pseudomonas↗
PubMed2026

Desert-derived Ensifer sp. SA403 enhances potato salt tolerance by reshaping rhizosphere microbiome functions and host responses.

Soil salinization increasingly threatens global food security, and potato (Solanum tuberosum L.), a moderately salt-sensitive crop, is particularly vulnerable to saline soils. Plant growth-promoting rhizobacteria (PGPR) offer a promising strategy to improve crop performance, yet how PGPR interact with native microorganisms to enhance potato salt tolerance remains poorly understood. In this study, we identified a desert-derived PGPR strain, Ensifer sp. SA403, which substantially enhanced potato performance under high salinity across sterile, non-sterile and field conditions. Physiologically, inoculation with SA403 reduced shoot Na⁺ accumulation and increased the K⁺/Na⁺ ratio; notably, these effects were markedly stronger in non-sterile substrates than under sterile conditions, indicating that SA403-mediated ion homeostasis relies on cooperation with the resident microbiota rather than on the strain acting alone. Metagenomic profiling indicated that SA403 strain reshaped rhizosphere communities, significantly enriching beneficial taxa such as Priestia and Bradyrhizobium, and upregulated functional pathways involved in glutathione and sulfur metabolism. Furthermore, host transcriptomic analyses showed that SA403 modulated plant responses to salt stress, with differentially expressed genes enriched in jasmonic acid signaling, ethanolamine metabolism and amino-acid biosynthesis pathways. Field trials on saline soils confirmed that SA403 significantly increased seedling emergence and tuber weight. Together, our results demonstrate that SA403 functions as a biological mediator that optimizes rhizosphere microecology and coordinates ion balance and host signaling to enhance potato salt tolerance. These findings support the potential of SA403 as a robust PGPR-based tool for sustainable potato production on saline soils.

Rhizosphere↗
PubMedDate not supplied

Influence of organic matter on the effectiveness of mineral fertilizers.

The influence of composted peat on the effectiveness of different doses of mineral fertilizers was studied in model greenhouse experiments with barley of the Pirkka variety cultivated in sand and poorly cultivated sandy-loam soil. It was shown that the use of a large amount of composted peat (10% of the weight of the substrate) contributed under the experimental conditions to a pronounced increase in plant productivity only when increased doses of mineral fertilizers were used (NPK at 0.2 g/kg of substrate). A direct correlation between yields and number of microflora in the rhizosphere was not revealed. Conditions were modeled under which increased yield occurred when development of microflora was poor, while the lowest yields were noted when there was an increase in the number of microorganisms. At the same time, the variants with maximal numbers of microorganisms and size of yields did coincide.

Agriculture↗
PubMed2025

Genome insights into the Bacillus paramycoides RZ3MS14: a multitrait plant growth-promoting rhizobacterium from Amazonian rainforest able to improve the sugarcane growth.

The genus Bacillus features species with remarkable plant growth-promoting traits (PGPTs) and is widely recognized for its biotechnological potential in sustainable agriculture. Among them, Bacillus paramycoides has recently attracted attention for its versatility in green synthesis of biopolymers, metal-based nanoparticles, and inhibition fungal phytopathogens; however, its PGPTs remain poorly underexplored. In this study, an integrated genomic and physiological approach was applied to B. paramycoides RZ3MS14, isolated from the guarana rhizosphere in Amazonian rainforest, to explore and correlate its potential PGPTs through in vitro and in vivo assays. The genome of B. paramycoides RZ3MS14 harbors genes related to N/P/Fe mobilization, bacillibactin synthesis, exopolysaccharides and biofilm formation, plant signaling, stress tolerance, biocontrol, and antibiotic resistance. Functional validation through in vitro assays, confirmed the strain's ability to solubilize phosphate, mineralize phytate, and produce siderophores, auxins, exopolysaccharides, and biofilm. These findings point diverse plant-growth promoting (PGP) traits that contributed to significant improvements in sugarcane growth and root architecture in the greenhouse. Specifically, root dry mass, shoot dry mass, root length, root surface area, and root volume increased by 225.92%, 520.89%, 231.47%, 242.25%, and 252.92%, respectively. Bacillus paramycoides RZ3MS14 exhibited a low antagonistic effect against the phytopathogenic fungi Fusarium verticillioides and Ceratocystis paradoxa. In contrast, microbial volatiles defined synergistic interactions with beneficial fungi Trichoderma afroharzianum and Purpureocillium lilacinum. This is the first study to unveil the PGP attributes of B. paramycoides, underscoring RZ3MS14's potential as a sugarcane bioinput and providing insights into its combined application with other microorganisms.

Saccharum↗
PubMed2025

Whole-Genome Analysis and Growth-Promoting Mechanism of Klebsiella pneumoniae YMK25 from Maize Rhizobacteria.

Plant growth-promoting rhizobacteria (PGPR) are microorganisms that enhance plant growth through various mechanisms. In the context of global agriculture, which faces fertilizer dependency and environmental pollution, developing eco-friendly microbial fertilizers has become crucial for enhancing agricultural sustainability. To identify highly effective PGPR, we isolated 102 bacterial strains from maize rhizosphere soil using the dilution plating method. The strains were screened for growth-promoting abilities using functional media, resulting in the selection of strain YMK25 for its exceptional capabilities in nitrogen fixation, solubilization of inorganic and organic phosphorus, indole-3-acetic acid (IAA) production, and siderophore production. Strain YMK25 produced IAA at a concentration of 80.49 ± 0.68 μg/mL and exhibited a relative siderophore expression level of 43.68%. Morphological analysis, 16S rDNA gene sequence analysis, and whole-genome sequencing confirmed that strain YMK25 is Klebsiella pneumoniae. Whole-genome analysis revealed a total genome length of 5,115,280 bp, a GC content of 57.61%, and it contained 4746 coding genes. Gene annotation results indicated genes involved in siderophore synthesis, phosphatase activity, and other plant growth-promoting functions, which align with the verified characteristics of strain YMK25. Furthermore, this strain exhibited significant metabolic capabilities. The pot experiment demonstrated that strain YMK25 promotes maize plant growth and assists in nutrient fixation in these plants. In conclusion, strain YMK25 is a high-quality PGPR with substantial potential for application in agricultural production, presenting promise for widespread use in sustainable agriculture.

Klebsiella pneumoniae↗
PubMed2024

Predictions of rhizosphere microbiome dynamics with a genome-informed and trait-based energy budget model.

Soil microbiomes are highly diverse, and to improve their representation in biogeochemical models, microbial genome data can be leveraged to infer key functional traits. By integrating genome-inferred traits into a theory-based hierarchical framework, emergent behaviour arising from interactions of individual traits can be predicted. Here we combine theory-driven predictions of substrate uptake kinetics with a genome-informed trait-based dynamic energy budget model to predict emergent life-history traits and trade-offs in soil bacteria. When applied to a plant microbiome system, the model accurately predicted distinct substrate-acquisition strategies that aligned with observations, uncovering resource-dependent trade-offs between microbial growth rate and efficiency. For instance, inherently slower-growing microorganisms, favoured by organic acid exudation at later plant growth stages, exhibited enhanced carbon use efficiency (yield) without sacrificing growth rate (power). This insight has implications for retaining plant root-derived carbon in soils and highlights the power of data-driven, trait-based approaches for improving microbial representation in biogeochemical models.

Rhizosphere↗