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Background and aims <p>Although the SEMIA Rhizobia Culture Collection has been instrumental to Brazil’s successful rhizobial inoculant program, most strains remain classified based solely on 16S rRNA gene analyses or phenotypic tests. Here we provide genome‑level taxonomic resolution for the collection’s common‑bean (<i>Phaseolus&#xa0;vulgaris</i> L.) nodule subset and evaluate the distribution of host-association genes.</p> Methods <p>Genomes from 94 strains were sequenced, taxonomically classified using genome‑based metrics, and screened for nodulation (<i>nod, nol</i> and <i>noe</i>), nitrogen‑fixation (<i>nif</i>), and tryptophan‑biosynthesis genes (<i>trp</i>).</p> Results <p>Phylogenomic analysis resolved the collection into 26 species. <i>Rhizobium</i> was predominant, with 66 strains spanning 18 species. The remaining accessions comprised 14 strains of <i>Agrobacterium tumefaciens</i>, three of <i>Agrobacterium leguminum</i>, three of <i>Paraburkholderia fungorum</i>, three of <i>Neorhizobium cellulosilyticum</i>, two of <i>Bradyrhizobium centrosematis</i>, and single representatives of <i>Pararhizobium giardinii</i>, <i>Stenotrophomonas maltophilia</i> and <i>Mycobacterium monacense</i>. The canonical symbiosis loci <i>nodABC</i> together with <i>nifHDK</i> co‑occurred in 29 strains (31% of the collection), predominantly within the recognized common bean symbiont species (e.g. <i>R. tropici</i>, <i>R. phaseoli</i>, <i>R. leguminosarum</i>, and <i>R. gallicum</i>) but also in <i>B. centrosematis</i>, <i>R. mongolense</i>, and <i>R. sp001657485</i>. In contrast, most of the strains retained <i>trpABCDE</i>(<i>G</i>) operon associated with indole‑3‑acetic‑acid biosynthesis.</p> Conclusion <p>Our genomic characterization of the SEMIA common‑bean collection revealed not only canonical rhizobia but also diverse associated bacteria possessing potential plant growth promoting traits. This work significantly boosts the SEMIA collection's utility as a genetic resource for both fundamental research and the development of plant inoculants.</p>

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Genomic analysis of 94 SEMIA strains isolated from common bean nodules: species diversity and genes related to nodulation, nitrogen fixation, and tryptophan metabolism

  • 期刊论文

  • 发表日期：

    2025年12月12日

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  • Alvina Fernanda de Vargas,
  • Bruno Britto Lisboa,
  • Adriana Ambrosini,
  • Fernando Hayashi Sant’Anna,
  • Camille Eichelberger Granada,
  • Anelise Beneduzi da Silveira,
  • Jackson Freitas Brilhante de São José,
  • Emanuel Maltempi de Souza,
  • Luciane Maria Pereira Passaglia,
  • Luciano Kayser Vargas,
  • Camila Gazolla Volpiano

摘要

Background and aims

Although the SEMIA Rhizobia Culture Collection has been instrumental to Brazil’s successful rhizobial inoculant program, most strains remain classified based solely on 16S rRNA gene analyses or phenotypic tests. Here we provide genome‑level taxonomic resolution for the collection’s common‑bean (Phaseolus vulgaris L.) nodule subset and evaluate the distribution of host-association genes.

Methods

Genomes from 94 strains were sequenced, taxonomically classified using genome‑based metrics, and screened for nodulation (nod, nol and noe), nitrogen‑fixation (nif), and tryptophan‑biosynthesis genes (trp).

Results

Phylogenomic analysis resolved the collection into 26 species. Rhizobium was predominant, with 66 strains spanning 18 species. The remaining accessions comprised 14 strains of Agrobacterium tumefaciens, three of Agrobacterium leguminum, three of Paraburkholderia fungorum, three of Neorhizobium cellulosilyticum, two of Bradyrhizobium centrosematis, and single representatives of Pararhizobium giardinii, Stenotrophomonas maltophilia and Mycobacterium monacense. The canonical symbiosis loci nodABC together with nifHDK co‑occurred in 29 strains (31% of the collection), predominantly within the recognized common bean symbiont species (e.g. R. tropici, R. phaseoli, R. leguminosarum, and R. gallicum) but also in B. centrosematis, R. mongolense, and R. sp001657485. In contrast, most of the strains retained trpABCDE(G) operon associated with indole‑3‑acetic‑acid biosynthesis.

Conclusion

Our genomic characterization of the SEMIA common‑bean collection revealed not only canonical rhizobia but also diverse associated bacteria possessing potential plant growth promoting traits. This work significantly boosts the SEMIA collection's utility as a genetic resource for both fundamental research and the development of plant inoculants.