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

Integrative functional profiling of rhizospheric and endophytic bacteria reveals Lelliottia aquatilis as a multifunctional PGPR in Himalayan ecosystems

This study introduces L. aquatilis strain MC3 as an emerging candidate for bioinoculant development and one of the first reports for identification of L. aquatilis as multifunctional PGPR from Himalayan ecosystems.

Functional Characterization of Wheat Seed Endophytic Bacteria Reveals Plant Growth-Promoting Traits and Potential Biocontrol Activity Against Fusarium Pathogens.

Seed-associated microbiota are emerging as key determinants of early plant establishment and resilience, yet their functional potential in wheat remains underexplored. Here, we isolated and functionally characterized culturable bacterial endophytes from seeds of Triticum aestivum cvs. Saekeumkang, Baeggang, and Ariheuk to assess plant growth promotion and pathogen suppression. Sixteen bacterial strains, belonging to Pseudomonadota, Actinomycetota, and Bacillota, were identified using 16S rRNA gene sequencing. Functional assays revealed the high prevalence of plant growth-promoting traits, with all isolates producing indole-3-acetic acid and 56.25% exhibiting phosphate-solubilizing activity, whereas siderophore production was restricted to Pseudomonas poae WSSR12. Despite this apparent functional redundancy, in planta assays demonstrated strong strain-specific effects on seedling biomass. Neobacillus cucumis WSSR17 consistently induced the highest increase in fresh weight. In parallel, dual culture assays against multiple Fusarium pathogens revealed that only one isolate, Calidifontibacillus erzurumensis WSSR11, showed consistent antifungal activity across all tested Fusarium strains. Notably, isolates combining multiple functional traits did not always correspond to the strongest growth promotion, underscoring the importance of host-microbe compatibility and trait expression in planta. Collectively, these findings reveal a functionally diverse seed endophytic community with complementary roles in plant growth and disease suppression. We propose that rational selection and combination of complementary strains, particularly N. cucumis WSSR17 (growth promotion), C. erzurumensis WSSR11 (biocontrol), and P. poae WSSR12 (multifunctional nutrient mobilization) could enable the development of targeted, multi-strain bioinoculant strategies for wheat. This study advances our understanding of seed microbiome functionality and provides a foundation for microbiome-informed crop improvement.

Integrated genomic and metabolomic insights into sesame rhizosphere-derived multi-trait Pseudomonas aeruginosa SIRJ8 with salinity stress alleviation and biocontrol potential

Plant growth-promoting rhizobacteria (PGPR) offer microbe-based models for understanding crop resilience under environmental stress; however, environmental bacteria exhibiting both plant-beneficial functions and opportunistic pathogenic traits remain poorly understood, complicating their safe translation into agricultural applications. To address this gap, the present study undertakes an integrated genomic-metabolomic analysis of Pseudomonas aeruginosa SIRJ8, a strain isolated from the sesame ( Sesamum indicum L.) rhizosphere. Functionally, P. aeruginosa SIRJ8 displayed robust plant growth promoting attributes and tolerance to salinity levels up to 7.5% NaCl under in vitro conditions. It also showed pronounced antagonistic activity, achieving up to 82.7% inhibition of Fusarium spp. mycelial growth and 54.9% reduction of post-harvest tomato rot specifically against F. fujikuroi . Furthermore, in planta experiments showed that SIRJ8 significantly improved rice (BRRI Dhan 28) growth relative to the corresponding uninoculated plants exposed to the same salinity level, increasing shoot length by 49.6% and dry biomass by 50.3% under 150 mM NaCl. Genomic analysis revealed a 6.59 Mb genome with an open pan-genome architecture (α = 0.11). Among 169 strain-specific genes, we identified determinates for nutrient acquisition ( pqqF , tonB2 ), salinity resilience ( kshB , cfa ), and biocontrol ( hcp , chitinase class I). Genome mining via antiSMASH identified 21 biosynthetic gene clusters, including 100% homologous pathways for hydrogen cyanide and pseudopaline alongside several uncharacterized NRPS-like and RiPP-like clusters, suggesting a diverse specialized metabolome for competition and iron acquisition. GC-MS profiling and molecular docking identified key metabolites, including diketopiperazines and phenolic compounds, as potent candidates for fungal growth inhibition. While SIRJ8 harbors several canonical virulence-associated determinants (type III and type VI secretion systems, toxA , exoS , exoT , exoY genes), phenotypic biosafety assays demonstrated non-hemolytic behaviour and antibiotic susceptibility profile characteristic of non-clinical, environmental isolates. Collectively, this work delivers high-resolution mechanistic insights into the genomic and metabolomic features of P. aeruginosa SIRJ8, highlighting the functional and ecological intricacy of rhizosphere-associated bacteria. Although SIRJ8 exhibited multiple plant-beneficial traits, its virulence-associated genomic repertoire precludes its consideration as an agricultural bioinoculant at present and underscores the necessity of comprehensive biosafety evaluation before any practical application.

Characterization of a Salt-Tolerant Plant Growth-Promoting Streptomyces levis Strain H from the Rhizosphere Soil of Oryza sativa

Preliminary evidence is provided of the potential of a Streptomyces levis strain as a PGP bacterium under saline conditions and Seed germination efficiency revealed that the 24 hrs culture of isolate H had a significantly greater effect on rice seed germination than the 48 hrs culture.

Integrating biocontrol efficacy and genomic potential of Bacillus velezensis BJ-1141: from broad-spectrum antagonism to tomato Fusarium wilt suppression.

B. velezensis BJ-1141 is a multifunctional bacterial strain with strong biocontrol efficacy and plant growth-promoting traits, supported by genomic evidence, and represents a promising candidate for sustainable crop disease management.

Genomic and functional characterization of Rhizobium metallidurans NS41, a heavy-metal-resistant, non-legume-associated endophyte that reduces oxidative stress in metal-exposed maize