Integrated genomic and metabolomic insights into sesame rhizosphere-derived multi-trait Pseudomonas aeruginosa SIRJ8 with salinity stress alleviation and biocontrol potential
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.
Abstract
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.
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.
Poonam Patel, K. Raval, Satyamitra Shekh et al.· Frontiers in Microbiology· 0 citations
Salinity is a major abiotic stress that severely restricts crop productivity. Despite considerable potential, the role of Trichoderma afroharzianum T22 in the molecular responses and root microbiome dynamics associated with salinity tolerance remains poorly understood in sorghum. In this study, T. afroharzianum inoculation alleviated salinity-induced stress by improving chlorophyll content, growth parameters, and nutrient balance, while restricting root-to-shoot Na+ translocation. Split-root experiments showed that T. afroharzianum application to a single root compartment was insufficient to improve whole-plant performance under salinity, whereas inoculation of both compartments restored growth and chlorophyll-related traits. RNA-seq analysis showed the upregulation of genes involved in symbiosis, hormone signaling, antioxidant defense, and ion homeostasis, accompanied by repression of genes involved in ethylene biosynthesis and senescence in the roots. KEGG enrichment analysis further revealed activation of secondary metabolic pathways involved in stress adaptation. Furthermore, 16S rRNA sequencing showed that T. afroharzianum inoculation was associated with shifts in the root bacterial community without significantly altering alpha diversity, while selectively enriching putatively beneficial taxa, including Dyella mobilis, Luteibacter rhizovicinus, and Luteibacter yeojuensis under salinity. In addition, a conserved core microbiome was retained across treatments and was dominated by Streptomyces, Rhizobium, Dyella, and Labrys. Further, Janibacter was identified as a characteristic indicator taxon of T. afroharzianum inoculation, while Streptomyces showed the highest overall indicator value. Multi-omics integration analysis revealed that T. afroharzianum-associated microbial taxa were strongly associated with hormone signaling, redox homeostasis, mineral transport, and secondary metabolism under salinity stress. Particularly, Streptomyces and Luteibacter were the two genera most strongly associated with plant growth traits, whereas Rhizobium and Mucilaginibacter showed stronger positive correlations with tissue Na+ accumulation. Collectively, these findings provide new insights into T. afroharzianum-mediated salinity tolerance in sorghum and highlight its potential as a microbial biostimulant, warranting further validation across diverse sorghum genotypes in field conditions.
Ruby Bagchi, Bishrant Pant, Hong-Liang Wang et al.· Microbiology Research· 0 citations
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.
S. Devi, Riya Chandel, D. Thakur et al.· Frontiers in Systems Biology· 0 citations
Soil nutrient transformation capacity is a critical determinant of sustainable productivity in perennial cropping systems; however, the extent to which high-yielding crops actively regulate rhizosphere microbial assembly to maintain nutrient availability remains poorly understood. We investigated whether root exudates from high-yielding alfalfa (Medicago sativa L.) selectively recruit plant growth-promoting rhizobacteria (PGPR) to enhance nutrient transformation. In an 8-year continuous alfalfa system (2018-2025), high-yielding cultivars increased soil organic carbon by 8.64%, total nitrogen by 6.01%, and moderately labile phosphorus fractions by 1.62%. Rhizobox experiments demonstrated that root exudates enhanced growth only with an active microbiome. High-yielding alfalfa enriched PGPR communities, specifically Ensifer, Pseudomonas, and Bacillus. Isolated strains exhibited N fixation, P solubilisation, and IAA production. Metabolomic profiling revealed that exudates were enriched in specific sugars and amino acids. Maltopentaose, maltotetraose, taurine, N-acetyl-L-leucine, and asparagine functioned as chemoattractants, stimulating PGPR proliferation and biofilm formation. These findings demonstrate that root exudate-mediated, targeted recruitment of functional PGPR enhances N fixation and P transformation, thereby supporting sustained high alfalfa productivity. This study demonstrates a key rhizosphere mechanism underlying the long-term sustainability of high-yielding perennial legume systems and provides a mechanistic basis for microbiome-informed sustainable alfalfa production and management.
Yanliang Sun, Kongqin Wei, Kaixin Yang et al.· Plant, Cell and Environment· 0 citations
Global climate change and the escalating drought cycles have severely compromised agricultural productivity in marginalized agroecosystems worldwide. This has necessitated a deeper understanding of the role of the phytobiome in the host plant's resilience. Although seed biopriming with plant growth-promoting bacteria (PGPB) is widely acknowledged for alleviating abiotic stress, the role of PGPB biofilms in enhancing the efficiency of biopriming remains a critical knowledge gap. In this study, the biofilm-forming capacity of nine thermohalotolerant, ACC-deaminase-producing PGPB strains previously isolated from the rhizosphere of Cyamopsis tetragonoloba grown in arid regions of India was evaluated. Strains were classified into biofilm-forming and biofilm-deficient groups based on pellicle formation, wrinkle formation by macrocolony, safranin staining quantification (OD492 > 2.5 v/s OD492 < 0.5), FTIR spectroscopy, and FESEM analyses. Selected representatives of both groups, Bacillus altitudinis C-17 and Bacillus subtilis J-35 (biofilm-forming), and Enterobacter cloacae C-35 (biofilm-deficient), were subjected to comparative seed biopriming assays, carried out on a drought-susceptible variety of C. tetragonoloba under simulated drought (-1.5 MPa). Results revealed that simulated drought completely arrested seed germination in the unprimed control group, whereas biopriming with the biofilm-forming strain J-35 restored germination by >70% (p < 0.005). The biofilm-deficient strain, C-35, showed a non-significant recovery (p = 0.476). In pot assay conducted under water deficit, biopriming with biofilm-forming PGPBs significantly improved seedling vigor, as evidenced by improved root length, shoot length, leaf area, and wilting index. Statistical analyses revealed that biofilm formation strongly correlated with enhanced seed colonization efficiency (R2 = 0.953, p < 0.005). Furthermore, biofilm-forming strains induced robust modulation of host oxidative homeostasis, as evident from ∼15.8-fold increase in proline content, a 3- to 5-fold increase in superoxide dismutase activity, and a negative correlation with harmful H2O2 accumulation (R = -0.816). These observations clearly demonstrate that enhanced biopriming by biofilm-forming PGPBs stems from the underlying mechanism in which biofilms act as biological anchors, enhancing seed colonization and triggering robust modulation of the host plant's antioxidant machinery. These findings provide a fundamental understanding necessary to exploit the social microbial behavior in developing next-generation bioinoculants for crops grown in climate-vulnerable agroecosystems, including drought-prone arid and semi-arid regions. The core hypothesis tested in this study is that biofilm formation by PGPB serves as more than a microbial survival strategy; it is a critical functional determinant of phytobiome resilience that enhances host physiological plasticity and abiotic stress resilience through persistent host-microbe interaction and the systemic modulation of oxidative stress.
Ragini Dolhey, Kamalpreet Kaur, Mamta Bajiya et al.· Plant physiology and biochem...· 0 citations
The potential of SZ01 as a microbial inoculant to promote plant growth and productivity in saline–alkaline environments, with implications for both medicinal and agricultural crop production, is highlighted.
