Exploring the Genomic, Plant Growth Promoting, and Biocontrol Potential of a novum species 'Candidatus Pseudomonas auctus' JDE115 with its description

Abstract

'Candidatus Pseudomonas auctus' sp. nov. JDE115 is a Gram-negative, facultative anaerobic, motile, rod-shaped, and fluorescent bacterium isolated from soybean (Glycine max) root nodules in Virginia. Growth occurred at 0–5.0% NaCl (optimum 1%), pH 6.0–10.0 (optimum 7.0), and 10–40°C (optimum 28°C). Phylogenetic analysis based on the 16S rRNA gene and whole-genome sequencing placed JDE115 within the genus Pseudomonas, with the highest similarity to Pseudomonas glycinae MS586, but below species delineation thresholds for ANI (94.59%) and GGDC (57.10%). Chemotaxonomic analysis identified ubiquinone-9 (Q-9) as the dominant quinone and C16:0, C17:0 cyclo, and summed features 3 and 8 as major fatty acids. The DNA G+C content was 60.68 mol%. These features support the designation of JDE115 as a novel species. Genome sequencing revealed a 6.18 Mb genome with 5,648 genes, including 5,509 protein-coding genes. Functional annotation identified traits linked to phosphate, potassium, and zinc solubilization, siderophore production, systemic resistance induction, and antimicrobial compound biosynthesis, positioning JDE115 as a strong candidate for sustainable agriculture as both a biofertilizer and biocontrol agent. Functional assays demonstrated that JDE115 promotes plant growth under nutrient-deficient conditions. Inoculation of soybean plants with JDE115 enhanced shoot biomass, root development, nodule numbers, and total nitrogen uptake. Auxin production, phosphate solubilization, and biofilm formation traits contribute to its beneficial plant interactions, highlighting its potential as a multifunctional bioinoculant for sustainable agriculture and food security. JDE115 also exhibited potent biocontrol activity against the soil-borne fungal pathogen Agroathelia rolfsii, the causal agent of southern blight. Dual-culture and broth assays showed complete fungal inhibition, and scanning electron microscopy confirmed structural damage to fungal sclerotia. JDE115 produces a range of antifungal compounds, including chitinase, glucanase, protease, cellulase, siderophores, hydrogen cyanide, and volatile organic compounds (VOCs) such as dimethyl disulfide (DMDS) and 1-undecene. Greenhouse experiments confirmed that JDE115-treated soybean plants remained disease-free, while untreated controls succumbed to infection. Further evaluations demonstrated that JDE115 effectively suppresses soybean cyst nematode (Heterodera glycines) and root-knot nematodes (Meloidogyne spp.). Greenhouse assays revealed over 90% local and 85% systemic suppression of SCN reproduction. VOC profiling confirmed the production of DMDS and 1-undecene, with bioassays showing that 1-undecene induces nematode avoidance and mortality without direct contact. High hydrogen cyanide production and enzymatic inhibition of egg hatching and juvenile survival contribute to its nematicidal activity. Overall, 'Candidatus Pseudomonas auctus' JDE115 demonstrates broad-spectrum plant growth-promotion and biocontrol capabilities. Its multimodal mechanisms—including nutrient mobilization, systemic resistance induction, and pathogen and pest antagonism—position it as a promising microbial tool for integrated pest management and sustainable crop production.