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PubMed2026

Climate and soil shape Daqu wheat quality and seed microbiome via rhizosphere taxa and microbial assembly.

The grain quality and seed microbiome of Daqu wheat are fundamental determinants of Daqu fermentation performance; however, the mechanisms by which cultivation environments influence these traits via rhizosphere microbial communities remain unclear. Bacterial and fungal communities across the bulk soil-rhizosphere-seed continuum of three wheat cultivars grown in four ecoregions were characterized using absolute quantitative amplicon sequencing. The rhizosphere microbiome was treated as a central intermediary, while the response variables were seed microbial diversity and grain-quality traits, including starch content, protein content, and grain hardness. Twelve physicochemical properties of soil and 11 climatic factors were integrated into a multidimensional association framework. Environmental conditions exerted stronger influences on both seed quality traits and microbial diversity than cultivar identity. Distinct regional signatures were also evident in rhizosphere microbiomes, with environmental gradients explaining community variation more effectively than geographic distance. Bacterial communities exhibited greater sensitivity to environmental fluctuations than fungi. Mantel analyses identified available nitrogen, precipitation, and atmospheric pressure as significant drivers of core rhizosphere taxa (P < 0.05). iCAMP revealed that stochastic processes predominantly governed rhizosphere bacterial assembly, whereas stochastic and deterministic mechanisms jointly shaped fungal assembly. Partial least squares path modeling further uncovered a rhizosphere-mediated environment-seed cascade, wherein sunlight intensity and duration, atmospheric pressure, and soil nitrogen directly or indirectly affected seed wet gluten content, grain hardness, and seed microbial diversity through their influences on rhizosphere microbiota. Rhizosphere bacterial diversity was negatively associated with seed bacterial diversity (path coefficient = -0.118, P < 0.05), indicating that rhizosphere communities may shape seed endophytic bacterial assemblages via environmental filtering and competitive interactions. Collectively, these findings elucidate how environments shape the quality and seed microbiomes of Daqu wheat, providing scientific guidance for optimal site selection and the standardized production of high-quality brewing wheat for industrial Baijiu.

Triticum↗

PubMed1979

Nitrogen fixers in the rhizosphere of certain desert plants.

Six species of common desert range plants; Achillea sp., Aristida plumosa, Artemisia herba-alba, Haloxylon articulatum, and Heliotropium ramosissimum were colleted from Western Desert in Iraq. Counts of Azotobacter spp. and total bacteria were estimated in both rhizosphere and non-rhizosphere soils. Biomass and total nitrogen content of the plants were determined. The R/N ratio (ratio between rhizosphere to non-rhizosphere) for Azotobacter sp. ranged between 1 to 19.5 with an average of 4.96. The number of Azotobacter in the rhizosphere ranged between 6.8 X 10(3) to 47 X 10(3) cells/g, while in the non-rhizosphere it ranged from 2 X 10(3) to 21 X 10(3). Aristida plumosa harboured the highest number, i.e., 47 X 10(3) cells/g, while Artemisia herba-alba showed the least, i.e., 6.8 X 10(3) cells/g. Total counts of bacteria in the rhizosphere ranged between 17.2 X 10(6) and 97 X 10(6) cells/g, that of the non-rhizosphere between 1.5 X 10(6) and 18 X 10(6) cells/g. The R/N ratio ranged between 2.03 X 22.5 with an average of 7.28. An appreciable gain of dry weight and total nitrogen was observed. Between 13 and 152 g with an average of 78.9 g dry weight and between 347 and 6684.0 mg with an average of 2452.0 mg nitrogen per plant were found. The possible contribution of Azotobacter to the nitrogen economy of the plants is discussed and further suggested.

Azotobacter↗

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↗

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

Rhizosphere mycoflora of healthy and yellow vein mosaic virus infected okra (Abelmoschus esculentus) plants.

Investigations on the rhizosphere mycoflora of healthy and virus (YVMV) infected okra plants showed a higher fungal population in the rhizosphere of healthy plants at preflowering and post-flowering stages than in that of diseased ones. Maximum population was observed during flowering both in healthy and diseased plant rhizosphere as well as in non-rhizosphere soil. However, virus infected plants showed a higher population at the flowering stage than healthy ones. The quantitative differences in the rhizosphere of healthy and diseased plants during flowering seem to be due to a change in C/N ratio and amino acids. The drastic reduction in diseased plant rhizospheres during the post-flowering stage may be due to either change in C/N ratio unfavourable to mycoflora or production of some toxic substances inhibiting multiplication of the mycoflora.

Mosaic Viruses↗

PubMed2026

Metagenomic Insights Into Microbial Diversity of Tea Rhizosphere of the Kangra Valley.

This study provides the first metagenomic assessment of microbial diversity from the tea rhizosphere of the Kangra valley. Tea rhizosphere soil samples were collected from 4 locations (Dharamshala, Baijnath, Palampur, and Joginder Nagar) of the Kangra valley. DNA extracts of rhizosphere samples were analysed for bacterial and Archaeal diversity using amplicon sequencing (V3-V4) region of the 16S rRNA gene and Fungal diversity using ITS1 and ITS2 regions. Baijnath and Palampur samples showed the highest bacterial richness, while Dharamshala and Palampur had the highest fungal richness. Proteobacteria was a dominant phylum in all the rhizosphere samples, followed by Firmicutes, Actinobacteria, Acidobacteria, and Bacteroidetes. A total of 11 fungal phyla were identified among all the locations, with abundance of Ascomycota and Basidiomycota. For the Archaea domain, uncultured archaeon and Aeropyrum camini were the most common found among all the locations. A small fraction (< 0.5%) of Bacillus and Pseudomonas species were observed among all the locations. Alpha and beta diversity indices displayed notable differences within and between microbial diversities. Soil factors were variably associated with microbial diversity, with nitrogen positively aligned with fungal diversity, while EC and K were associated with Archaeal diversity. Soil pH and OM% showed moderate associations with bacterial diversity. These findings provided valuable and comprehensive insights into tea rhizosphere microbial ecology and could be used to better understand microbial functions and their role in plant health.

Rhizosphere↗

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↗

PubMed2026

Manipulation of rhizosphere microbiome by Microbacterium sp. GB16_1_BI to promote plant growth.

AIM: The bioinoculant properties of a newly identified ammonium-releasing novel strain of Actinomycetota-Microbacterium bengalense sp. nov. GB16_1_BI (Accession number: SRX9280401) on the microbiome structure of rice rhizosphere were assessed. METHODS AND RESULT: GB16_1_BI may inhibit most bacteria present in the rice rhizosphere as well as encouraged the growth of rare bacteria specific to the waterlogged rice rhizosphere. The genome sequence as well as untargeted metabolome analyses of GB16_1_BI showed abundance of secondary metabolites with probable antimicrobial activity. Amplicon sequencing of the 16S rRNA V3-V4 region from the rhizosphere of the black rice showed inhibition of most bacteria by GB16_1_BI. Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) analysis showed increased abundance in the marker genes for nitrogen cycling (nifH, nrfA, and nrt) but not for nifD or nifK, which was also reflected in the ANOSIM analysis in the OTUs of the N-fixing bacteria. Higher abundance of the nitrogen-fixing methanotrophs, Methylosinus and Methylocystis in inoculated plants also led to study of the marker genes for methane metabolism. CONCLUSION: Microbes present in the rhizosphere contribute to the biogeochemical cycle by transforming unavailable minerals and by retaining nutrients for their growth, which get released after death for plant adsorption. However, not all microbes contribute positively to plant growth. Microbes compete with plants for nutrients, cause disease, or produce harmful greenhouse gases. Hence, GB16_1_BI could influence plant growth predominantly by suppressing microbes and encouraged niche-specific microbes specifically involved in nitrogen cycling.

Rhizosphere↗

PubMed1979

Occurrence of certain physiological groups of soil micro-organisms in the rhizosphere and rhizoplane of watermelon, cucumber, and cowpea.

A field experiment was run for studying the occurrence of ammonifiers, Azotobacter, aerobic cellulose-decomposers, and nitrifiers in rhizosphere soils as well as in rhizoplane samples of watermelon, cucumber, or cowpea at different stages of growth. In unamended soil, all the heterotrophs were generally stimulated in the rhizosphere of each plant, especially the leguminous one, resulting in positive rhizosphere effects. In amended soil, on the other hand, both negative and positive (but lower than in unamended soil) rhizosphere effects were recorded for the heterotrophs. The rhizosphere effects differed according to the type of plant, to the growth phase of each single plant, and to physiological properties of micro-organisms under study. A modified method for removing and treating the rhizoplane samples is suggested. The presence of high number of the heterotrophs and the absence of the autotrophs may support the evidence that roots of the studied plants are colonized with ammonifiers, Azotobacter, and cellulose-decomposers, but not with nitrifiers.

Aerobiosis↗

PubMed2025

Metagenomic analysis of microbial community dynamics in konjac rhizosphere during soft rot disease progression.

Amorphophallus konjac, the sole glucomannan-rich species in the Araceae family, faces significant yield and quality losses due to soft rot disease. Understanding the relationship between soil microbial communities and soft rot incidence is critical for sustainable konjac production. Metagenomic profiling was employed to systematically characterize the spatiotemporal dynamics of rhizosphere microbiomes during disease progression. Microbial alpha diversity (Chao1 index) exhibited a significant peak in the rhizosphere of diseased plants at the mature stage, contrasting with stable diversity patterns in healthy and latently infected groups, indicating dysbiosis-associated richness inflation during disease progression. Principal coordinate analysis (PCoA) revealed significant divergence in rhizosphere microbial structures between diseased and healthy/latently infected groups, with higher compositional variability observed in diseased samples. At the phylum level, Chloroflexi and Acidobacteria abundances in healthy mature plants exceeded those in diseased plants by 11.54% and 4.6%, respectively, while pathogenic Rhizopus arrhizus and Rhizopus microsporus were significantly enriched in diseased mature plants. Correlation analyses demonstrated predominantly negative associations between bacterial species and soil factors, contrasting with positive fungal correlations. KEGG pathway annotation identified carbohydrate metabolism and amino acid synthesis as core microbial functions in the konjac rhizosphere. Collectively, Chloroflexi and Acidobacteria were validated as putative biocontrol agents, while Rhizopus spp. emerged as key drivers of soft rot development. These findings provide mechanistic insights for designing microbiome-based biocontrol strategies to mitigate konjac soft rot, offering a sustainable alternative to conventional agrochemical reliance. KEY POINTS: • Diseased konjac microbial richness peaks; healthy plants enrich Chloroflexi/Acidobacteria. • Rhizopus pathogens drive soft rot; bacteria and fungi show opposing soil factor links. • Lays groundwork for microbiome approaches to cut agrochemicals in konjac rot control.

Rhizosphere↗

PubMed2025

Impacts of non-spherical polyethylene nanoplastics on microbial communities and antibiotic resistance genes in the rhizosphere of pea (Pisum sativum L.): An integrated metagenomic and metabolomic analysis.

The ecological effects of nanoplastics (NPs) has become a growing concern; however, the influence of non-spherical NPs-which better represent real-world morphologies-remains poorly understood. This study investigated the impact of non-spherical polyethylene (PE) NPs on the growth of pea (Pisum sativum L.) and its rhizosphere microenvironment across different concentration levels (0, 20, and 200 mg/kg) using integrated metagenomics and metabolomics. Results showed that high-dose (200 mg/kg) exposure significantly inhibited plant growth. Although soil physicochemical properties remained unchanged, the rhizosphere microbial communities experienced significant restructuring, characterized by a marked enrichment of Pseudomonas and a reduction in beneficial Rhizobium populations. Metagenomic analysis revealed a concurrent increase in the abundance and diversity of antibiotic resistance genes (ARGs) under non-spherical PE-NP stress. This was accompanied by a shift in bacterial host composition, with a trend toward a higher prevalence of potentially pathogenic taxa such as Pseudomonas aeruginosa. Metabolomics analysis further revealed that non-spherical PE-NPs altered the rhizosphere metabolite profile, thereby significantly driving the succession of ARG hosts. Our integrated analysis enhances the understanding of how non-spherical PE-NPs disrupt microbial communities and elevate the risks of ARGs in rhizosphere soil, highlighting the significance of incorporating environmentally relevant NPs into environmental risk assessments.

Pisum sativum↗

PubMed2026

Amplicon and metagenomic sequencing reveal thifluzamide drive rhizosphere microbial structural shifts and functional adaption.

Thifluzamide (TF) is a widely used phenyl urea fungicide in rice production; however, its impacts on the structural composition and functional dynamics of the rhizosphere microbiome remain poorly understood. Here, we systematically investigated the effects of TF on the structure, interactions, and functional potential of the rice (Oryza sativa L.) rhizosphere microbiome using integrated amplicon sequencing and metagenomic approaches. TF application significantly altered both bacterial and fungal community composition, bacterial diversity was markedly reduced, whereas fungal diversity increased. With bacterial diversity markedly reduced while fungal diversity increased. Beta-diversity analyses revealed strong treatment-driven community separation, indicating pronounced TF-induced microbial restructuring. Co-occurrence network analysis demonstrated reduced complexity and connectivity in bacterial networks but increased negative co-occurrence patterns within fungal communities, suggesting contrasting stability responses between microbial kingdoms. Metagenomic profiling further revealed substantial functional shifts, including the differential enrichment of KEGG and COG pathways associated with xenobiotic metabolism. Notably, while total ARG abundance remained stable, TF exposure altered the resistome profile by selectively enriching specific classes of antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), and mobile genetic elements (MGEs). Strong positive correlations between MGEs and ARGs highlighted an elevated potential for horizontal gene transfer. Metagenome-assembled genome (MAG) analysis identified specific TF-enriched bacterial taxa, including Methylophilus, Sulfurospirillum, and Azospirillum, which harbored genes involved in pesticide degradation and xenobiotic transformation. Collectively, these findings demonstrate that TF profoundly reshapes the rice rhizosphere microbiome by altering microbial diversity, interaction networks, resistance gene profiles, and functional capacities. This study provides genomic insights into fungicide-microbiome interactions, underscoring the potential ecological implications associated with TF application, while identifying candidate microbial taxa that may contribute to pesticide degradation and rhizosphere microecology resilience.

Rhizosphere↗

PubMed2026

The Rhizosphere Microbiome: A Key Mediator of Crop Responses to Fertilization Strategies.

The rhizosphere microbiome, the plant's "second genome" is pivotal for crop nutrient acquisition, health, and stress responses. While fertilization ensures high agricultural yields, a key challenge is reshaping this microbiome to boost crop performance. This review synthesizes how mineral, organic, and bio-organic/microbial inoculant fertilizers affect rhizosphere microbial structure, diversity, and function. Long-term excessive mineral fertilizers (especially nitrogen) reduce microbial diversity, diminish beneficial groups (e.g., diazotrophs, PGPR), and disrupt microbial networks via soil acidification and altered root exudates, causing continuous cropping obstacles. In contrast, organic fertilizers improve soil microenvironments, maintaining high microbial diversity, enriching beneficial taxa (e.g., Proteobacteria, Actinobacteria), and enhancing community complexity. Bio-organic fertilizers/microbial inoculants "engineer" the microbiome by introducing exogenous beneficial microbes (e.g., Bacillus, Pseudomonas, AMF), directly promoting growth, suppressing diseases, and "reconditioning" indigenous beneficial communities. We also clarify how fertilization regulates plant-microbe dialog via root exudates and rhizosphere chemistry (e.g., pH, ion balance), discuss current challenges (causality, lab-to-field translation, genotype-microbiome-fertilization interactions), and outline future directions. Integrating rhizosphere microbiome management into fertilization is crucial for reducing chemical fertilizer reliance and advancing agricultural green transformation.

fertilization strategies microbial community assem↗

PubMed1977

Studies on phosphate-solubilizing bacteria in soil and rhizosphere of different plants. I. Occurrence of bacteria, acid producers, and phosphate dissolvers.

Occurrence of bacteria (total), acid producing and phosphate dissolving micro-organisms in soil, rhizosphere, and rizoplane of Egyptian cotton, peas, or maize during their different growth phases was studied. The rhizosphere effects were generally positive and differed according to type of plant, growth phase of each special plant, and type of micro-organism under study. The high densities of bacteria, acid-producers, and phosphate-dissolvers in the rhizoplane samples suggest the conclusion that roots of the studied plants are colonized with these soil micro-organisms. The role of the micro-organism and the mechanism of the noted colonization is not fully understood yet. However, the presence of high numbers of bacteria in the rhizosphere zones of all plants is undoubtedly important, since they may convert organic and inorganic substances into available plant nutrients. The acidproducing organisms were greatly stimulated in the rhizosphere of all plants. Consequently, the production of acid, especially in alkaline soils such as in Egypt, may directly or indirectly react with insoluble inorganic compounds, converting their nutrient elements into available forms for the growing plants. But not all acid-producers are considered as phosphate-dissolvers. Therefore, the presence of high numbers of phosphate-dissolving bacteria in the rhizophere zones may explain how the growing plants can obtain their requirements in such alkaline soils.

Bacteria↗

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↗

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↗