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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 75, Issue 1

sp. nov., a novel endophytic bacterium with plant growth-promoting potential, isolated from root nodules of in Northwestern Algeria No Access

Abstract

A thorough polyphasic taxonomic study, integrating genome-based taxonomic approaches, was carried out to characterize the RB5 strain isolated from root nodules of growing on the coastal dunes of Bousfer Beach (Oran, Algeria). The 16S rRNA gene sequence analysis revealed that strain RB5 had the highest similarity to LMG27940 (98.94%) and IzPS32d (98.73%). Phylogenetic studies, including both 16S rRNA gene sequence and multilocus sequence analysis using 16S , and housekeeping genes, positioned RB5 in a distinct branch alongside its closest relative, LMG27940. Phylogenomic analysis using the Bac120 marker set and Type (Strain) Genome Server confirmed the unique position of RB5 and its close relationship with LMG27940. Similarly, genomic comparisons using average nucleotide identity based on (ANIb) and digital DNA–DNA hybridization (dDDH) revealed values of 92.85 and 59.3%, respectively, when compared with its closest relative, LMG27940. Both values fall below the established species delimitation thresholds of 95–96% for ANIb and 70% for dDDH, providing strong genomic evidence that strain RB5 represents a novel species. Further average nucleotide identity comparisons with unclassified spp. (384 genomes) and metagenomic-derived genomes from the Genome Taxonomy Database (GTDB) showed values between 84.27 and 89.2%, indicating that strain RB5 belongs to a unique evolutionary line. The genome of RB5, with a size of 6 311 310 bp and a G+C content of 60%, harbours several key genes associated with plant growth-promoting traits, making it a promising candidate for sustainable agriculture. Phenotypically, RB5 strain is an aerobic, rod-shaped, Gram-negative, non-spore-forming bacterium that is motile with a single polar flagellum. It grows under a wide range of temperature (4–42 °C) and pH (5–10) conditions and tolerates up to 6% (w/v) NaCl. The main cellular fatty acid composition of RB5 includes C, C cyclo and the summed features 3 consisting of C ω7c/ ω6c. Based on the phylogenetic, phenotypic, chemotaxonomic and genome comparison analyses, strain RB5 was identified as a novel species of the genus , for which the name sp. nov. is proposed. The type strain is RB5 (=DSM 117471=LMG 33633=CIP 112482).

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Keyword(s): Pseudomonas retamae sp. nov. , endophyte , nodule , phylogenomic , polyphasic taxonomy and Retama monosperma
Funding
This study was supported by the:
  • Ministry of Higher Education and Scientific Research (MESRS)
    • Principal Award Recipient: SELAMINawel
  • General Directorate of Scientific Research and Technological Development (DGRSDT)
    • Principal Award Recipient: SELAMINawel
© 2025 The Authors
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2025-01-15
2026-03-13

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Pseudomonas retamae sp. nov., a novel endophytic bacterium with plant growth-promoting potential, isolated from root nodules of Retama monosperma in Northwestern Algeria
Int J Syst Evol Microbiol 75, 006646 (2025); https://doi.org/10.1099/ijsem.0.006646
/content/journal/ijsem/10.1099/ijsem.0.006646
/content/journal/ijsem/10.1099/ijsem.0.006646
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