Jan 2026· International Journal of Microbiology· Vol 2026· 0 citations· 70 references
Medicine
TL;DR
This study clarifies the compartment‐specific distribution patterns of bacterial microbiomes and polyphyllins in P. polyphylla and their correlative relationships, deepens the understanding of plant‐microbiome interactions in medicinal plants, and provides a theoretical basis for optimizing P. polyphylla cultivation strategies and developing microbial inoculants for sustainable agricultural production.
Abstract
Paris polyphylla (P. polyphylla) is a valuable traditional Chinese medicinal plant, yet the spatial distribution of its compartment‐specific bacterial microbiomes and their correlative relationships with bioactive polyphyllins remain poorly characterized. Here, we combined 16S rRNA amplicon sequencing, metabolite analysis, and bioinformatics to investigate the distribution patterns of bacterial communities and polyphyllins across bulk soil (BS), rhizosphere soil (RS), root endospheres (REs), stem endospheres (SEs), and leaf endospheres (LEs) of P. polyphylla. A spot inoculation assay was further used to verify the interactions between the dominant genus Pseudomonas (strain Pseudomonas palleroniana P6) and key polyphyllin I and VII. The results showed that polyphyllin I and II were highly accumulated in aerial SEs and leaves, whereas polyphyllin VI, VII, and diosgenin were predominantly concentrated in REs. Bacterial diversity and richness showed a gradual decline from BS to LE, with ecological niche differentiation identified as the primary driver of bacterial community divergence across compartments, which was further modulated by polyphyllin content. Pseudomonas, the dominant genus in all compartments, displayed a decreasing relative abundance with ascending compartmental niches, and its abundance was significantly negatively correlated with polyphyllin I levels but positively correlated with polyphyllin VII levels—a trend experimentally validated by gradient polyphyllin concentration‐based microbial growth assays. Redundancy analysis (RDA) indicated that polyphyllin content (especially VI, VII, and diosgenin) significantly influenced bacterial community composition. Additionally, P. polyphylla exhibited selective enrichment of beneficial microbes, with selection pressure intensifying progressively across compartments. This study clarifies the compartment‐specific distribution patterns of bacterial microbiomes and polyphyllins in P. polyphylla and their correlative relationships, deepens the understanding of plant‐microbiome interactions in medicinal plants, and provides a theoretical basis for optimizing P. polyphylla cultivation strategies and developing microbial inoculants for sustainable agricultural production.
Summary Ecological niche partitioning shapes microbial communities in terrestrial mosses, yet its underlying mechanisms and associated viral diversity remain poorly understood. Here, we characterized prokaryotic and viral communities in the rhizosphere soil (Rs) and endophytic niche (Pc) of Pogonatum cirratum using amplicon and metagenomic sequencing. Rs exhibited higher species richness, co-dominated by Pseudomonadota, Acidobacteriota, and Actinomycetota, whereas Pc was dominated by Pseudomonadota (81.13%) but showed greater functional diversity. Source tracking revealed that 10.57% of Pc taxa originated from Rs, suggesting host-mediated filtration of beneficial microbes. Deterministic processes predominantly governed prokaryotic assembly, with iron cycling accounting for ∼14% of total metabolic potential in both niches. Rs contained more biosynthetic gene clusters, while viral communities diverged in taxonomy and auxiliary metabolic genes profiles. These findings demonstrate that P. cirratum maintains compartmentalized prokaryotic and viral communities through niche-specific abiotic filtering and biotic selection, promoting nutrient acquisition and stress resilience in bryophyte-dominated ecosystems.
Chao-Jian Hu, Muhammad Asif, Jinhui Liu et al.· iScience· 0 citations
Cowpea (
Vigna unguiculata
[L.] Walp.) is an important grain legume in semiarid Africa, where it contributes to food security and livelihood resilience in smallholder farming systems. However, information on the soil bacterial microbiome associated with cowpea production in semiarid eastern Kenya remains limited.
This study investigated heterogeneity of soil physicochemical properties and bacterial community structure in cowpea farms from Machakos and Kitui Counties via 16S rRNA amplicon next-generation sequencing (NGS), with the aim of improving the understanding of belowground microbial patterns in these production systems.
Most measured soil physicochemical properties varied significantly among farms, indicating substantial field-level heterogeneity, whereas county-level differences were less pronounced. Across all the samples, the bacterial communities were dominated by Actinomycetota, followed by Pseudomonadota, Bacillota, Chloroflexota, and Acidobacteriota. Rhizobial genera of agronomic relevance, including
Bradyrhizobium
,
Rhizobium
,
Ensifer
, and
Mesorhizobium
, were detected across farms, with
Bradyrhizobium
showing the highest relative abundance. The alpha-diversity indices varied among the samples, while the beta-diversity analysis revealed significant differences in the bacterial community composition between the counties. Preliminary correlation analysis revealed associations between selected soil variables and the distributions of dominant bacterial taxa and rhizobial genera, however none of these pairwise correlations remained significant after Benjamini-Hochberg FDR correction.
Cowpea farm soils in semiarid eastern Kenya harbor compositionally distinct bacterial communities that vary with farm-level edaphic heterogeneity, with native rhizobial genera detected across all sites indicating ecologically relevant symbiotic bacterial resources; a direct test (Mantel test, constrained ordination) did not establish the measured soil variables as significant drivers of this compositional variation at the present sample size. These findings establish a baseline for soil bacterial ecology in Kenyan cowpea systems and demonstrate that site-specific, microbiome-informed strategies are needed for sustainable soil fertility management and effective deployment of native rhizobial inoculants in semiarid smallholder agriculture.
A. Khater, E. Njeru, S. Githiri· Frontiers in Soil Science· 0 citations
Soil microbiomes are critical for sustaining ecosystem functioning and soil health. Monocropping often disrupts soil microbial communities, leading to yield penalties and soil degradation. Although bio-organic fertilizers are widely used to alleviate the negative effects of monocropping, their long-term associations with microbial community structure and ecosystem functioning across monocropping durations remain insufficiently understood. Here, we collected 72 soil samples from Hami melon (Cucumis melo) fields at three sites in Turpan, northwestern China. All sampled fields received Bacillus subtilis–based bio-organic fertilizer and consisted of independently managed 1-year (M1), 3-year (M3), and 5-year (M5) monocropping systems sampled within the same year. Across fields with longer monocropping durations, key putative fungal pathogens, including Fusarium, Monosporascus, and Alternaria, showed lower relative abundances, whereas potentially beneficial bacterial taxa such as Bacillus, Paenibacillus, Sphingomonas, and Lysobacter were enriched. However, both bacterial and fungal communities exhibited reduced Bray–Curtis dissimilarity and β-dispersion, consistent with increasing microbial homogenization. Although the overall phylogenetic diversity of bacterial and fungal communities remained comparatively stable, the relative abundance and richness of rare taxa declined across monocropping durations. In addition, bacterial co-occurrence networks exhibited reduced complexity in fields with longer monocropping durations, while fungal subnetworks remained comparatively stable. Among the evaluated soil ecosystem functions, carbon degradation exhibited a non-linear response pattern and reached its highest value in M3, whereas nutrient cycling, carbon storage, and physical structure remained relatively stable across monocropping durations. Overall, our findings suggest that prolonged monocropping combined with long-term Bacillus subtilis–based bio-organic fertilization is associated with microbial community homogenization and simplified bacterial network structures, while most soil ecosystem functions remain comparatively stable.
Guozhi Hu, Muxi Xie, Guangzhou Wang et al.· Frontiers in Microbiology· 0 citations
These distinct functional profiles demonstrates that the protected root endomicrobiome specializes in plant signalling and nutrient assimilation, while the rhizosphere microbiome, facing higher competition, specializes in nutrient acquisition and stress resilience.
Vrishali Rajendra Bankar, S. Chapadgaonkar, Kausik Bhattacharyya et al.· Frontiers in Bioinformatics· 0 citations
Tissue-associated microbial communities contribute to plant adaptation in extreme environments, yet the compartment-specific organization of tissue-associated bacterial communities in desert halophytes remains insufficiently understood. This study investigated how plant tissue type may influence the tissue-associated bacterial phytobiome of
Salvadora persica
growing under saline desert conditions along the western coast of Saudi Arabia. Leaf and root tissues were collected and analyzed using high throughput
16S rRNA
gene amplicon sequencing. After quality filtering, non-chimeric reads were processed using DADA2 for amplicon sequence variant (ASV) inference, and microbial diversity and community structure were assessed using alpha diversity indices, rarefaction analysis, beta diversity metrics, principal coordinates analysis (PCoA), and UniFrac-based clustering. Sequencing produced 68,817–108,461 high-quality non-chimeric reads per sample. Leaf tissue-associated bacterial communities were highly conserved and taxonomically simplified (10–22 ASVs; Shannon index 0.89–1.01; Faith’s PD 1.92–4.02), dominated mainly by Cyanobacteriota and Pseudomonadota. Root tissue-associated bacterial communities exhibited substantially higher richness and phylogenetic complexity (286–508 ASVs; Faith’s PD 31.03–51.05), with one root sample showing dominance of Bacillota and Bacteroidota and enrichment of anaerobic genera, while other root samples were enriched in Cyanobacteriota and Pseudomonadota alongside diverse low-abundance soil-associated phyla. Beta diversity analyses revealed compartment-associated patterns, where ordination and phylogenetic clustering suggested separation between leaf- and root-associated communities; however, permutational multivariate analysis of variance (PERMANOVA) did not detect statistically significant differences between compartments based on Bray–Curtis and unweighted UniFrac distances. Overall, the data indicates trends consistent with compartment differentiation in diversity and composition between leaf- and root-associated bacterial communities in
S. persica
, supporting compartment-associated structuring of tissue-associated bacterial assemblages under saline desert conditions and providing a foundation for future functional and metagenomic investigations.
R. Jalal· Journal of King Saud Univers...· 0 citations
Rhizospheric microbial communities are critical to the health and productivity of coffee plantations. This study investigated the microbiome of robusta coffee (Coffea canephora) across three major cultivation areas in Vietnam (Dak-Nong, Dak-Lak, and Gia-Lai) to assess its role in Fusarium suppression. Using ITS amplicon-based metagenomics and culture-dependent approaches, we analyzed fungal community structure in relation to location, plant age, and health status. Metagenomic analysis revealed no significant differences in bacterial communities between healthy and diseased rhizospheres, whereas fungal communities showed clear distinctions, particularly in young plants (<2 years). These differences diminished in mature plants (≥2 years) but continued to vary with age (2–10 years). Healthy rhizospheres were enriched with beneficial fungi, while diseased soils contained more phytopathogenic genera. Fusarium was prevalent in all regions, with higher abundance in diseased soils, whereas Trichoderma, a known biocontrol agent, was more abundant in healthy soils but declined with plant age. Of 343 fungal isolates, 46 strains exhibited strong antagonistic activity against Fusarium, representing 10 genera, including Aspergillus, Penicillium, Gongronella, and Talaromyces. Although Trichoderma isolates were less frequent, they showed promising biocontrol potential. These findings underscore the role of rhizospheric fungi in managing Fusarium wilt and identify candidate biocontrol agents for sustainable robusta coffee cultivation.
Ha Thu Nguyen, C. Bez, Minh Quang Tran et al.· Plant Pathology Journal· 0 citations