From diversity to function: microbiome-mediated plant growth promotion, secondary metabolism, and antimicrobial resistance in Rauwolfia serpentina

Whole-genome sequencing and characterization of Pseudomonas stutzeri P1 endophyte isolated from potato unveils plant growth-promoting and other traits

The potential of P1 as a promising bioinoculant candidate for sustainable agriculture in the potato sector is demonstrated and the genome lacked major virulence factors and antimicrobial traits, supporting the non-pathogenic nature of the P1 strain.

The functional structure of foxtail millet rhizoplane microbiome and its association with yield

ABSTRACT Root-associated microbial communities profoundly influence plant growth and productivity. Although the rhizosphere microbiome has been extensively studied, the functional distinctiveness and host-specific role of the closely adhering rhizoplane microbiota remain unclear. In this study, we performed deep metagenomic sequencing of both the rhizosphere and rhizoplane microbiomes in foxtail millet (Setaria italica). We constructed a comprehensive non-redundant gene catalog, reconstructed 595 metagenome-assembled genomes (MAGs), and analyzed the co-occurrence networks. Our results revealed that the rhizoplane sustains a core microbial network with greater complexity and connectivity than rhizospheres. Metabolically, the rhizoplane microbiome is enriched in the functions underlying host adaptation, including ammonium production and polysaccharide decomposition. Our results showed that the associations between microbial features (taxonomic and functional) and yield were significantly stronger in the rhizoplane than in the rhizosphere. We identified 22 yield-positive MAGs, primarily from Bacillales, harboring genes for plant growth-promoting traits, such as nutrient solubilization and phytohormone synthesis. Collectively, our findings illustrate that the rhizoplane is not only a subset of the rhizosphere but also a critical host-microbe interface and functional hotspot where specialized microbial processes are directly coordinated to enhance plant performance and yield. IMPORTANCE Plant roots selectively recruit diverse and beneficial microorganisms from the surrounding soil, assembling a distinctive rhizosphere microbiome. Substantial research, primarily utilizing amplicon sequencing, has elucidated the taxonomic composition of these rhizosphere communities across a wide range of plant species. The functional architecture, assembly processes, and coexistence mechanisms of the rhizoplane microbiome remain poorly understood, and their link to host plant traits is unclear. We elucidate the taxonomic and functional structural disparities between the rhizosphere and rhizoplane microbiomes, thereby clarifying the composition and functional roles of the rhizoplane microbiome, and further examine the association between the rhizoplane microbiome and millet yield. A deeper understanding of root-associated microbial communities may inform the development of effective agricultural probiotics, thereby enhancing sustainable farming practices. Additionally, the candidate biomarkers identified in this work offer potential targets for improving cultivation practices and supporting the long-term agricultural sustainability of foxtail millet. Plant roots selectively recruit diverse and beneficial microorganisms from the surrounding soil, assembling a distinctive rhizosphere microbiome. Substantial research, primarily utilizing amplicon sequencing, has elucidated the taxonomic composition of these rhizosphere communities across a wide range of plant species. The functional architecture, assembly processes, and coexistence mechanisms of the rhizoplane microbiome remain poorly understood, and their link to host plant traits is unclear. We elucidate the taxonomic and functional structural disparities between the rhizosphere and rhizoplane microbiomes, thereby clarifying the composition and functional roles of the rhizoplane microbiome, and further examine the association between the rhizoplane microbiome and millet yield. A deeper understanding of root-associated microbial communities may inform the development of effective agricultural probiotics, thereby enhancing sustainable farming practices. Additionally, the candidate biomarkers identified in this work offer potential targets for improving cultivation practices and supporting the long-term agricultural sustainability of foxtail millet.

Effects of single and synthetic microbial community inoculants on the rhizosphere soil and root microbiomes of rice (Oryza sativa).

This study compared the effects of a single-strain microbial inoculant, Brevundimonas diminuta NH1, and a synthetic microbial community (FSQN) composed of Bacillus amyloliquefaciens FH1, Ochrobactrum tritici S112, Gluconacetobacter liquefaciens QZR14, and B. diminuta NH1 on the rhizosphere soil and root microbiomes of rice (Oryza sativa) to investigate how these inoculation strategies differ in microbiome regulation and growth promotion. High-throughput sequencing was used to assess microbial α- and β-diversity, community composition, predicted bacterial and fungal functions, and correlations between microbiome shifts and rice growth traits. We found that neither inoculant significantly affected microbial α-diversity, but both significantly altered β-diversity in rhizosphere soil and roots. Compared with the control, the single-strain treatment mainly enriched Mortierella, Glaciozyma, and Bovista in rhizosphere soil, and Clostridium sensu stricto, Cronobacter, Exiguobacterium, Kosakonia, and Pseudomonas in roots. The synthetic community mainly enriched Mortierella, Tausonia, Fusarium, and Glomerella in rhizosphere soil, and Exiguobacterium, Pseudomonas, and Rhodotorula in roots. Functional prediction indicated that the single-strain inoculant enhanced sulfur respiration, ureolysis, xylanolysis, and denitrification-related functions, whereas the synthetic community enhanced ectomycorrhizal, endomycorrhizal, and plant-saprotrophic functions. Shoot height and dry weight were may positively associated with enriched taxa and functions, particularly Mortierella, Exiguobacterium, and endophytic functions.

Beneficial microbes isolated from the strawberry rhizosphere: development of growth-promoting and anthracnose-suppressive SynComs

Diversity and functional traits of indigenous microbiome in Hilla agricultural soils: implications for biocontrol and bioremediation

Indigenous bacterial and archaeal communities in agricultural soils were analyzed to provide a basis for biocontrol and bioremediation solutions to be reintroduced in affected areas and showed in vitro the most promising combination of PGP traits, metal tolerance, and antifungal activity against most phytopathogenic fungi.

Metagenomic profiling of tobacco root endophytes reveals a disease-suppressive Enterobacter strain against Fusarium solani

Tobacco root rot, caused by Fusarium species, is a persistent soil-borne disease that threatens tobacco production. To identify endophytic contributors to disease suppression, this study compared the root endophytic microbiomes of healthy and diseased tobacco plants using metagenomic sequencing and isolated functional bacteria from healthy roots. Metagenomic analysis of 30 root samples (223 Gb) generated 2.9 million non-redundant genes and identified 1,953 core genera. Healthy plants contained distinct endophytic microbial communities enriched in bacterial taxa and pathways associated with secondary metabolite biosynthesis, siderophore production, chemotaxis, biofilm formation, and carbohydrate metabolism. This microbiome-guided approach identified TM-1, an endophytic Enterobacter strain that significantly inhibited Fusarium solani by 62.29% in a dual-culture assay. Transcriptome profiling revealed that TM-1 treatment broadly altered F. solani gene expression, with prominent effects on ribosome function, amino acid biosynthesis, carbon metabolism, and glycolysis. TM-1 disrupted sugar transporter-related gene expression, and deletion of five representative genes significantly restricted fungal mycelial growth, with the strongest inhibition (66.47%) observed for the hexose transporter homolog MRS44_010803. These results indicate that healthy tobacco roots harbor disease-suppressive endophytic microorganisms and suggest that TM-1 may suppress F. solani by interfering with sugar transport and carbon acquisition. These findings provide a potential biocontrol resource for the sustainable management of tobacco root rot.