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<p>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 <i>Pseudomonas aeruginosa</i> SIRJ8, a strain isolated from the sesame (<i>Sesamum indicum</i> L.) rhizosphere. Functionally, <i>P. aeruginosa</i> 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 <i>Fusarium</i> spp. mycelial growth and 54.9% reduction of post-harvest tomato rot specifically against <i>F. fujikuroi</i>. 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&#xa0;Mb genome with an open pan-genome architecture (α = 0.11). Among 169 strain-specific genes, we identified determinates for nutrient acquisition (<i>pqqF</i>,<i> tonB2</i>), salinity resilience (<i>kshB</i>,<i> cfa</i>), and biocontrol (<i>hcp</i>, 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, <i>toxA</i>,<i> exoS</i>,<i> exoT</i>,<i> exoY</i> 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 <i>P. aeruginosa</i> 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.</p>

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

  • 期刊论文

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  • 发表日期：

    2026年8月3日

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  • Sanjoy Kumar Mukharjee,
  • Md. Faruk Hasan,
  • Biswanath Sikdar

摘要

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.