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Background <p>The growing need for sustainable farming methods has led to increased efforts to understand plant-beneficial microbes that can serve as alternatives to chemical fertilizers and pesticides. Among these, bacteria from the <i>Pseudomonas chlororaphis</i> group have emerged as particularly promising candidates due to their metabolic versatility and ability to produce a diverse arsenal of bioactive compounds.</p> Results <p>In this study, we conducted an extensive comparative genomic analysis of two <i>Pseudomonas chlororaphis</i> strains, FS-2 (endophytic) and RP-4 (rhizoplane-associated), to explore their plant growth-promoting and biocidal capacities. Whole-genome analysis using antiSMASH and functional annotation tools identified several biosynthetic gene clusters (BGCs) involved in the production of secondary metabolites, such as phenazines, pyoverdine, pyrrolnitrin, hydrogen cyanide, and the cyclic lipopeptide white line-inducing principle (WLIP). Some additional clusters with low similarity to known references, including arylpolyenes, butyrolactones, and resorcinol derivatives, were also observed within these genomes, indicating the ability to produce uncharacterized bioactive compounds. Genes for the biosynthesis of plant growth-promoting features including indole-3-acetic acid, siderophore, biofilm formation, solubilization of organic compounds, and stress adaption were also present in both genomes. Additionally, bacteriocin-like operons pyocins and colicins were also present in the genomes of FS-2 and RP-4. Average nucleotide identity analysis indicated a high level of conservation (99.58% ANI) between FS-2 and RP-4, however, differences in the genome and the presence of strain-specific biosynthetic gene clusters (BGCs) indicate adaptive evolution.</p> Conclusions <p>The overall comparative genomic insights into <i>P. chlororaphis</i> strains FS-2 and RP-4 indicate their metabolic and plant-beneficial characteristics for rhizosphere competence and their use as biological control agents.</p>

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Comparative genome analysis of Pseudomonas chlororaphis strains reveals biosynthetic diversity underlying plant growth promotion and soil health improvement

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年3月6日

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  • Izzah Shahid,
  • Lucas Gabriel Castellani,
  • Abdul Aziz Eida,
  • Emrah Nikerel,
  • Deeba Noreen Baig,
  • Qurat ul Ain Hanif,
  • Maged M. Saad,
  • Kauser Abdulla Malik,
  • Samina Mehnaz

摘要

Background

The growing need for sustainable farming methods has led to increased efforts to understand plant-beneficial microbes that can serve as alternatives to chemical fertilizers and pesticides. Among these, bacteria from the Pseudomonas chlororaphis group have emerged as particularly promising candidates due to their metabolic versatility and ability to produce a diverse arsenal of bioactive compounds.

Results

In this study, we conducted an extensive comparative genomic analysis of two Pseudomonas chlororaphis strains, FS-2 (endophytic) and RP-4 (rhizoplane-associated), to explore their plant growth-promoting and biocidal capacities. Whole-genome analysis using antiSMASH and functional annotation tools identified several biosynthetic gene clusters (BGCs) involved in the production of secondary metabolites, such as phenazines, pyoverdine, pyrrolnitrin, hydrogen cyanide, and the cyclic lipopeptide white line-inducing principle (WLIP). Some additional clusters with low similarity to known references, including arylpolyenes, butyrolactones, and resorcinol derivatives, were also observed within these genomes, indicating the ability to produce uncharacterized bioactive compounds. Genes for the biosynthesis of plant growth-promoting features including indole-3-acetic acid, siderophore, biofilm formation, solubilization of organic compounds, and stress adaption were also present in both genomes. Additionally, bacteriocin-like operons pyocins and colicins were also present in the genomes of FS-2 and RP-4. Average nucleotide identity analysis indicated a high level of conservation (99.58% ANI) between FS-2 and RP-4, however, differences in the genome and the presence of strain-specific biosynthetic gene clusters (BGCs) indicate adaptive evolution.

Conclusions

The overall comparative genomic insights into P. chlororaphis strains FS-2 and RP-4 indicate their metabolic and plant-beneficial characteristics for rhizosphere competence and their use as biological control agents.