Strain NR3T, an endophytic bacterium, was isolated from the root nodules of Retama monosperma collected in the coastal dunes of Cap-Falcon beach, northwestern Algeria. Its taxonomic position was determined using a polyphasic approach. Analysis of the 16S rRNA gene sequence revealed that strain NR3T shared the highest pairwise sequence similarity with Pseudomonas canavaninivorans HB002T (99.6%), Pseudomonas alvandae SWRI17T (99.5%), Pseudomonas bijieensis L22-9T (99.5%), and Pseudomonas tehranensis SWRI196T (99.4%). Further 16S rRNA phylogenetic analysis confirmed these species as its closest relatives. Multi-locus sequence analysis (MLSA) based on four housekeeping genes (16S rRNA, gyrB, rpoB and rpoD) positioned strain NR3T in a distinct, well-separated clade, differentiating it from all other Pseudomonas species. A comprehensive phylogenomic analysis, conducted using the Type (Strain) Genome Server and genome-scale phylogenetic reconstruction, based on a concatenated alignment of 72 housekeeping genes reinforced the unique phylogenetic placement of strain NR3T, highlighting its divergence from its closest relatives, including P. canavaninivorans HB002T, P. alvandae SWRI17T, while identifying “Pseudomonas agronomica” SAICEU22T as its nearest phylogenetic neighbor. Whole-genome sequence comparisons using digital DNA-DNA hybridization (dDDH) and pairwise orthologous average nucleotide identity (OrthoANIu) yielded values well below the species delineation thresholds (39.0 and 38.6% for dDDH, 89.5 and 89.2% for OrthoANIu), further confirming that strain NR3T represents a distinct Pseudomonas species. The genome of strain NR3T consists of 5,694,417 bp with a G + C content of 60.7% and is predicted to encode 5102 coding sequences (CDSs). Notably, several genes associated with plant growth-promoting traits, particularly those involved in phosphate solubilization, were identified, suggesting its potential for enhancing sustainable agricultural practices. The phenotypic characterization revealed that strain NR3T is a Gram-negative, rod-shaped, motile bacterium. It grows at temperatures ranging from 4 to 47 °C, with an optimum at 28 °C, within a pH range of 5.0 to 10.0 (optimum at pH 7), and tolerates NaCl concentrations up to 4% (w/v), with optimal growth at 0.5%. The predominant cellular fatty acids of strain NR3T are C16:0, summed feature 2 (C14:0 3–OH/C16:1 iso I), and summed feature 8 (C18:1 ω7c/C18:1 ω6c). Based on phylogenetic, genomic, and phenotypic analyses, strain NR3T (= DSM 117380T = CIP 112483T = LMG 33617T) is designated as the type strain of a novel Pseudomonas species, for which the name Pseudomonas algeriensis sp. nov. is proposed.

Pseudomonas algeriensis sp. nov.: A Promising Phosphate-Solubilizing Endophytic Bacterium Isolated from Legume Root Nodules in the Coastal Dunes of Northwest Algeria

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发表日期：

2025年10月6日

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Chahrazed Aibeche,
Nawel Selami,
Fatima El-Haouaria Zitouni-Haouar,
Omar Khelil,
Slimane Choubane,
Kheira Errouane,
Abderrezak Djabeur

摘要

Strain NR3^T, an endophytic bacterium, was isolated from the root nodules of Retama monosperma collected in the coastal dunes of Cap-Falcon beach, northwestern Algeria. Its taxonomic position was determined using a polyphasic approach. Analysis of the 16S rRNA gene sequence revealed that strain NR3^T shared the highest pairwise sequence similarity with Pseudomonas canavaninivorans HB002^T (99.6%), Pseudomonas alvandae SWRI17^T (99.5%), Pseudomonas bijieensis L22-9^T (99.5%), and Pseudomonas tehranensis SWRI196^T (99.4%). Further 16S rRNA phylogenetic analysis confirmed these species as its closest relatives. Multi-locus sequence analysis (MLSA) based on four housekeeping genes (16S rRNA, gyrB, rpoB and rpoD) positioned strain NR3^T in a distinct, well-separated clade, differentiating it from all other Pseudomonas species. A comprehensive phylogenomic analysis, conducted using the Type (Strain) Genome Server and genome-scale phylogenetic reconstruction, based on a concatenated alignment of 72 housekeeping genes reinforced the unique phylogenetic placement of strain NR3^T, highlighting its divergence from its closest relatives, including P. canavaninivorans HB002^T, P. alvandae SWRI17^T, while identifying “Pseudomonas agronomica” SAICEU22^T as its nearest phylogenetic neighbor. Whole-genome sequence comparisons using digital DNA-DNA hybridization (dDDH) and pairwise orthologous average nucleotide identity (OrthoANIu) yielded values well below the species delineation thresholds (39.0 and 38.6% for dDDH, 89.5 and 89.2% for OrthoANIu), further confirming that strain NR3^T represents a distinct Pseudomonas species. The genome of strain NR3^T consists of 5,694,417 bp with a G + C content of 60.7% and is predicted to encode 5102 coding sequences (CDSs). Notably, several genes associated with plant growth-promoting traits, particularly those involved in phosphate solubilization, were identified, suggesting its potential for enhancing sustainable agricultural practices. The phenotypic characterization revealed that strain NR3^T is a Gram-negative, rod-shaped, motile bacterium. It grows at temperatures ranging from 4 to 47 °C, with an optimum at 28 °C, within a pH range of 5.0 to 10.0 (optimum at pH 7), and tolerates NaCl concentrations up to 4% (w/v), with optimal growth at 0.5%. The predominant cellular fatty acids of strain NR3^T are C_16:0, summed feature 2 (C_14:0 3–OH/C_16:1 iso I), and summed feature 8 (C_18:1 ω7c/C_18:1 ω6c). Based on phylogenetic, genomic, and phenotypic analyses, strain NR3^T (= DSM 117380^T = CIP 112483^T = LMG 33617^T) is designated as the type strain of a novel Pseudomonas species, for which the name Pseudomonas algeriensis sp. nov. is proposed.