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PubMed1977

Studies on phosphate-solubilizing bacteria in soil and rhizosphere of different plants. II. Selection of the most efficient phosphate-dissolvers and their morphological grouping.

Two hundred colonies which showed positive reaction on the plates prepared for the phosphate-dissolving bacteria from control soil rhizosphere soils and rhizoplane samples of maize, peas, or cotton were isolated at random. Fifty isolates were selected as the most efficient isolates according to their capability for increasing the amounts of available phosphorus in the media with corresponding decreases in pH values. The percentage of the most efficient isolates differed according to type of plant and location of isolation. Not only the morphological types of the phosphate-dissolving bacteria differed in soil and in rhizosphere, but they also differed in the rhizosphere soil of each special plant. Morphological differences in the isolates from rhizosphere soil and from rhizoplane samples of the same plant were also occurring. The abundance of mycelial-forming bacteria and of aerobic sporeformers in Egyptian soil is important as they are well known to resist adverse conditions, such as high temperature and dryness to which our soils are subjected most time of the year.

Bacteria↗

PubMed1977

[A contribution to the study of respiration in soil and in the rhizosphere of winter wheat (author's transl)].

In a complete respiration test, involving also other analyses, soil respiration (CO2 evolved) was measured in a fertilization experiment in the rhizosphere of the plants in untreated soil. The highest and most effective CO2 production was obtained by the variants "rhizosphere, fertilized with nitrogen". The decreasing order of the influence on CO2 production is as follows: rhizosphere, nitrogen fertilization, organogenetic state of the plant. With glucose addition, nitrogen fertilization predominated over the effect of the rhizosphere.

Carbon Dioxide↗

PubMed2026

Characterization of culturable endophytes and microbial communities in the rhizosphere and pitcher fluid of the carnivorous plant Nepenthes khasiana.

Endophytes colonize plant tissues through roots and shoots without causing harm and can move throughout the plant via its vascular system. However, little is known about culturable endophytes, particularly bacteria, in pitcher plants, and their possible entry through pitcher fluid remains unexplored. To address this gap, we isolated endophytes from the pitcher plant Nepenthes khasiana, and performed metagenomic analysis of its rhizospheric soil and pitcher fluid, from which bacteria and fungi were also isolated, to investigate the possible origin of these endophytes. We found that culturable endophytic bacteria were predominantly associated with roots and seeds, whereas endophytic fungi were more abundant across the N. khasiana pitcher. Although most endophytes were restricted to specific tissues, some exhibited a broader distribution across nearly the entire plant. Several OTUs from the rhizospheric soil matched endophytes at the genus level, including some that were also detected in the pitcher fluid. Specifically, three bacterial genera - Enterobacter, Staphylococcus and Bacillus - and one fungal genus, Cladosporium, detected in the pitcher fluid, matched the isolated endophytes. These findings suggest that endophytes in N. khasiana most likely originate from the rhizosphere, with possible migration into the pitcher fluid.

Rhizosphere↗

PubMed2025

Contrasting rhizosphere nitrogen dynamics in Andropogoneae grasses.

Nitrogen (N) fertilization in crop production significantly impacts ecosystems, often disrupting natural plant-microbe-soil interactions and causing environmental pollution. This study tested the hypothesis that diverse species adapting independently to various environments might exhibit a wide range of rhizosphere nutrient management strategies, and some of them may be conducive to an efficient N economy for crops. We analyzed the N cycle in the rhizospheres of 36 Andropogoneae grass species related to maize and sorghum and observed significant phylogenetic variation among their impacts on N availability and losses. All three annual species examined, including sorghum and maize, function as N 'Conservationists', reducing soil nitrification potential and conserving NH4 +. In contrast, seven of the assayed perennial species enhance nitrification and leaching ('Leachers'). Four other species exhibit similar nitrification stimulation effects but limited NO3 - losses ('Nitrate Keepers'). We complemented the controlled phenotypic evaluation with an evolutionary-ecological analysis of the same species. We identified several soil characteristics associated with the phylogenetic variation in rhizosphere N dynamics across grasses and highlighted the crucial roles of a few transporter genes in soil N management and utilization. In addition to the ecological and genetic insights, these findings offer valuable guidelines for future maize breeding efforts to enhance agricultural N efficiency and sustainability.

Rhizosphere↗

PubMed2026

Mikania micrantha invasion restructures rhizosphere nitrogen cycling through enzyme activation, microbial recruitment, and allelopathic regulation.

BACKGROUND: Plant invasions profoundly influence terrestrial ecosystems by reshaping nutrient cycling processes. However, the mechanisms through which invasive plants such as Mikania micrantha modulate soil nitrogen (N) cycling and microbial communities remain insufficiently explored. Moreover, comparative studies with indigenous congener are scarce, limiting insights into whether such effects reflect species-specific strategies or genus-wide traits. This study investigates how M. micrantha modulates nitrogen metabolic pathways and rhizosphere microecology using combined metagenomic and metabolomic analyses. RESULTS: Integrated analyses revealed that M. micrantha established a distinctive "high total nitrogen-low mineral nitrogen" profile in the rhizosphere soil. Metagenomic profiling showed consistent enrichment of key ammonium assimilation enzymes, including glutamine synthetase and glutamate dehydrogenase, promoting enhanced incorporation of NH₄⁺ into organic nitrogen pools. In contrast, genes encoding nitrate reductase and nitrate transporters were significantly lower in relative abundance, limiting nitrate assimilation. Mikania micrantha also selectively enriched nitrogen-fixing microbes (notably rhizobia genera) and plant growth-promoting rhizobacteria (PGPR), thereby enhancing biological nitrogen fixation capacity. Metabolomic analysis further identified several allelopathic compounds in invaded soils at higher relative abundance, particularly epicatechin, which exhibited inhibitory effects on nitrifying bacteria. Compared with the congener Mikania cordata, which exerted weaker impacts on soil nitrogen cycling and microbial assembly, M. micrantha deployed a more comprehensive strategy integrating biochemical, microbial, and metabolic regulation. CONCLUSIONS: These findings demonstrate that under greenhouse-controlled conditions, M. micrantha reconfigures rhizosphere nitrogen cycling through a multi-dimensional strategy that couples biochemical regulation, microbial recruitment, and metabolite-mediated interference, thereby suggesting a potential mechanism that may contribute to its ecological advantage in natural settings. Video Abstract.

Rhizosphere↗

PubMed2026

Two Bacillus PGPB Strains in Wheat and Soybean: Wheat Growth Promotion Without Detectable Rhizosphere Microbiome Restructuring.

Plant growth-promoting bacteria (PGPB) are increasingly deployed as biofertilizers, yet the link between an inoculant's genomic potential and its realized effect on the plant is rarely assessed within an integrative framework that jointly captures the rhizosphere microbiome, plant phenotype, and strain genome. Two Bacillus strains-B. halotolerans 1453 and B. pumilus 630-were applied to wheat and soybean in a factorial pot experiment (2 strains × 2 application methods × 3 frequencies + control, 3-4 replicates). Rhizosphere samples (n = 67 after filtering) were profiled by 16S rRNA sequencing with PICRUSt2 functional prediction and compositional validation (Aitchison PERMANOVA, ALDEx2, ANCOM-BC2). The PGPB gene repertoire was characterized by genome mining (481 marker genes, 14 categories). Wheat phenotype (six traits) and soybean height were analyzed with models appropriate for count data (Negative Binomial and binomial GLMs) for treatment-vs.-control comparisons, and with factorial ANOVA for decomposition into main effects and interactions. Crop identity was the dominant factor shaping both microbiome structure and function (PERMANOVA R2 = 14.7% taxonomically and R2 = 7.8% functionally, both p < 0.001), with biologically meaningful taxonomic differences between wheat and soybean; strain, application count and method had no significant effect on community composition (R2 < 4% each), and co-occurrence networks showed no reliable differences between crops once read depth and sample size were controlled for. Despite this neutrality at the microbiome level, inoculation significantly increased wheat spike count (NB-GLM, all 12 treatments vs. control, padj 0.0002-0.031), ear weight, and stem count, with application count the strongest source of variability and a pronounced strain × application count. Strain 1453 outperformed 630 in spike count (+23.1%, p = 0.012) and ear weight (+20.4%, p = 0.023); we hypothesize that this may be related to its more complete DNRA pathway (narGHI + nirB-nirD) and biocontrol genes (bacE, srfAA). Strain 630 produced a less pronounced effect than strain 1453 but was subject to smaller fluctuations across replicates (CV ≈ 16-21% vs. ≈24-26% for 1453), which may reflect better resilience to environmental fluctuations, possibly due to its confirmed rsbV/rsbW stress-tolerance regulon. Rhizosphere microbiome composition differed clearly by crop (wheat vs. soybean) but showed no detectable response to strain, application method, or application count. Despite this lack of a microbiome signal, inoculation significantly increased wheat spike count and ear weight, with the magnitude and stability of this effect differing by strain. We hypothesize that this strain-dependent difference relates to underlying genomic differences-particularly in nitrogen metabolism (DNRA pathway) and stress-tolerance genes-though this link has not been tested directly and remains a hypothesis for future work.

Triticum↗

PubMed1978

Effect of volatile substances released from Origanum majorana and Ocimum basilicum on the rhizosphere and phyllosphere fungi of Phaseolus vulgaris.

Differences were found in the counts and occurrence of fungi in the phyllosphere and thizosphere of two representatives of the Lamiacea family, Origanum majorana and Ocimum basilicum, and in the phyllosphere and rhizosphere of Phaseolus vulgaris growing separately or in coenosis with O. majorana or O. basilicum. Both the volatile substances released from ground leaves of the two latter plant species and the root exudates affected considerably spore germination of isolated phylospheric and rhizospheric fungi. The results indicated a possible role of root exudates and volatile substances released from leaves in colonization of rhizosphere and/or phyllosphere by fungi, especially in associations of various plants.

Air Microbiology↗

PubMed1976

Rhizosphere mycoflora of wheat after foliar application of chlorocholine chloride, urea and 4-chloro-2-methylphenoxyacetic acid.

A single-step spraying of wheat during shooting under field conditions with solutions of CCC (chlorocholine chloride), CCC and urea, CCC and Aminex (ammonium salt of 4-chloro-2-methylphenoxyacetic acid), or CCC, urea and Aminex caused changes both in numbers and composition of the rhizosphere mycoflora. The numbers both in the rhizosphere of differently treated plants and in the free soil decreased during vegetation. A more pronounced effect in the number of fungi was demonstrated in plants treated only with CCC. The difference was more considerable during first 10 days after the spray. As far as the relative occurrence of individual genera in the rhizosphere soil is concerned, fungi of the genera Penicillium Link ex Fr., Fusarium Link ex Fr., Verticillium Nees and Trichoderma Pers were most influenced after the treatment with the used agents.

Choline↗

PubMed1977

Studies on the rhizosphere and rhizoplane microflora of common-bean and barley.

Both broad bean and barley plants stimulated bacteria (total), N-fixing clostridia, Azotobacter ammonifiers, and aerobic cellulose-decomposers in their rhizosphere zone. The rhizosphere effects were generally positive until the 8th week of either plant growth. However, the rhizosphere effect differed according to type of plant, growth phase of each single plant, and type of micro-organism under study. The presence of high numbers of micro-organisms in the rhizoplane samples (washed ruptured roots) of each plant supports the evidence that roots of these plants are colonized with soil micro-organisms.

Azotobacter↗

PubMed1978

Studies of the mycoparasitism in rhizosphere of emerging sugar-beet.

Pythium oligandrum Drechsler was found as a very weak pathogen of emerging sugar-beet by means of the inoculation of the sterilized soil. The hyperparasitic ability of Pythium oligandrum Drechsler to relative species, viz. Pythium ultimum Trow and Pythium debaryanum (Hesse) were proved in rhizosphere of emerging sugar-beet. The rhizosphere soil inoculation by P. ultimum resulted in the sugar-beet emergence about 3% while the sugar-beet emergence achieved 110% if P. ultimum and P. oligandrum were inoculated simultaneously. The sugar-beet emergence due to the dual inoculation of rhizosphere soil by P. ultimum and P. debaryanum was about 3%, whereas due to P. ultimum, P. debaryanum, and P. oligandrum 77%.

Antibiosis↗

PubMed2026

Bacterial motility in rhizosphere colonization: mechanisms, constraints, and implications for microbial inoculants.

Although the potential of microbial inoculants for sustainable agriculture and environmental restoration has been widely recognized, their field performance remains highly variable and often unpredictable. Current research and development frameworks for microbial inoculants primarily focus on their plant growth-promoting functions and metabolic traits, often overlooking the ecological processes that determine whether introduced strains can successfully disperse, access, and establish within the rhizosphere. Increasing evidence suggests that successful dispersal and establishment cannot be assumed in the highly heterogeneous conditions of soil systems. Here, we summarize the key mechanisms underlying bacterial motility and discuss its role within the broader framework of microbial dispersal, highlighting how motility-mediated processes contribute to rhizosphere colonization. We propose that bacterial motility represents a key mechanistic determinant of biofertilizer efficacy. Its role extends beyond the ability of inoculant strains to physically reach the rhizosphere, encompassing competitive colonization on the root surface, long-term persistence, and the ability to respond to dynamic root-derived chemical gradients associated with newly developing root tissues. We argue that inoculant motility should be elevated from a passive descriptive trait to a core design parameter that can be systematically incorporated and regulated during the development and optimization of microbial inoculants. We outline a multi-tiered strategic framework for next-generation biofertilizer engineering that integrates strain selection, community design, motility regulation, and deployment strategies, thereby unlocking the full potential of synthetic microbial consortia for sustainable agriculture, ecosystem restoration, and climate change mitigation.

Biofertilizer↗

PubMed1979

Populations of the spinach wilt pathogen, Fusarium oxysporum f. sp. spinaciae, in the root tissues, rhizosphere, and soil in the field.

Populations of Fusarium oxysporum f. sp. spinaciae in root tissues and rhizosphere soil of diseased spinach plants were higher than in the root tissues and rhizosphere soil of healthy plants. Populations in soil rhizosphere were higher than in nonrhizosphere soil. The fungus populations were very low in the root tissues of the nonsusceptible strawberry, broccoli, chinese cabbage, and mustard grown in the infested field. The populations were low at the beginning of the season, increased, and remained high during the summer, then dropped in the fall. The fungus populations ranged from 1600 to 2600 propagules/g in the top 10 cm of soil, declined sharply between 11 and 20 cm, and were nondetectable between 41 and 60 cm.

Fusarium↗

PubMed2026

Streptomyces songxianensis sp. nov. SX92T: biocontrol of tobacco black shank and modulation of the rhizosphere microbiome.

Streptomyces species are well-known for their potential in biocontrol and plant growth promotion, with the rhizosphere serving a rich reservoir for novel isolates. In this study, a Streptomyces strain (SX92T) was isolated from the rhizosphere of healthy tobacco plants. In dual-culture assays, SX92T displayed broad-spectrum antagonistic activity against six major fungal pathogens of tobacco, with the highest inhibition (59.22%) against Phytophthora nicotianae, the causal agent of tobacco black shank. Polyphasic taxonomic characterization, combining 16S rRNA gene phylogeny, distinctive physiological traits, chemotaxonomic markers (LL-diaminopimelic acid, major menaquinones MK-10(H₄) and MK-9(H₈), and predominant fatty acids anteiso-C₁₅:₀ and C₁₆:₀), and genome-based metrics (ANI and dDDH), clearly distinguished SX92T from its closest relatives. Accordingly, strain SX92T is proposed as the type strain of a novel species, Streptomyces songxianensis sp. nov. The genome of SX92T is 9.69 Mb in size with a G + C content of 71% and contains 26 biosynthetic gene clusters, including one showing 100% similarity to the albaflavenone cluster. In field trials, application of SX92T fermentation broth significantly improved tobacco agronomic traits and reduced black shank incidence by 44.97%. Furthermore, SX92T treatment reshaped the rhizosphere microbiome by enriching beneficial bacteria such as Flavobacterium and altering the relative abundance of specific fungi, including a reduction in the arbuscular mycorrhizal fungus Rhizophagus irregularis. It also shifted soil enzyme activities, with increased cellulase and decreased catalase levels. These findings establish Streptomyces songxianensis SX92T as a promising multifunctional biocontrol agent for sustainable tobacco production.

Streptomyces↗

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↗

PubMed2026

Discovery of specific rhizosphere bacteria Rhodanobacter involved in KAI2-mediated drought tolerance in Arabidopsis.

The KARRIKIN INSENSITIVE 2 (KAI2) receptor has been reported to contribute to drought tolerance in Arabidopsis. However, the extent to which KAI2's function in drought tolerance depends on soil microbiota remains unclear. This study demonstrates that the rhizosphere microbiome is indispensable for KAI2-mediated drought tolerance. We isolated specific Rhodanobacter sp. and confirmed its role in enhancing drought tolerance in Arabidopsis. Notably, Rhodanobacter sp. was found to specifically secrete the key isoflavone daidzin. We found that daidzin had a similar function with KAI2 agonist, desmethyl-type germinone, and induced interaction between KAI2 and SUPRESSOR OF MORE AXILLARY GROWTH 2 1. Moreover, the exogenous application of daidzin enhanced drought tolerance by modulating the expression of karrikin response and drought-related genes, in a KAI2-dependent manner. Our findings suggest that the rhizosphere microbiome plays a crucial role in facilitating KAI2-mediated drought tolerance in Arabidopsis, with Rhodanobacter sp. contributing through the secretion of daidzin.

Arabidopsis↗

PubMed1977

Population dynamics of Fusarium spp. in pea rhizosphere as affected by soil amendments.

In nonamended soil, vegetative growth and sporulation of Fusarium spp. were higher in the rhizosphere than in the soil. Sporulation was favoured by young plants and decreased with increasing plant age. Amendments with low C/N oil-cakes enhanced vegetative growth and sporulation in root-free soil. The extent of stimulation varied with the nature of organic matter used and the stage of its decomposition. Sporulation was suppressed by castor cake and sawdust with urea amendments. Rhizosphere cf pea altered the effect of different amendments.

Fabaceae↗

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↗

PubMed1975

Interactions between Azotobacter and "phosphobacteria" and their establishment in the rhizosphere as affected by soil fertility.

The effects on plant growth of "bacterial fertilizers" prepared from Azotobacter spp. and phosphate-solubilizing bacteria ("phosphobacteria") have been the subject of much controversy. Cases where no plant-growth stimulation occurred may often be accounted for by the failure to establish the bacterial inocula in the rhizosphere. Three factors that may influence inocula establishment, i.e. soil fertility, manuring, and interactions between Azotobacter and "phosphobacteria," were examined in pot experiments, designed for statistical analysis, in two neutral-alkaline soils, using lavender plants (Lavandula spica L.). During the experiments the numbers of Azotobacter and "phosphobacteria" were counted. Dry weights of roots and shoots were recorded after 16 weeks of growth. At the end of the experiments there were always more Azotobacter and "phosphobacteria" in the rhizospheres when plants were inoculated with both groups of organisms together than when they were inoculated singly. Addition of 2% farmyard manure to the richer soil enhanced this effect. Plant growth was greatest when seedlings were inoculated with both Azotobacter and the "phosphobacteria".

Azotobacter↗