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<p>Soil microbes play a crucial role in biogeochemical cycling and are a valuable resource for discovering novel taxa with environmental applications. This study aimed to explore rhizospheric microbial diversity for potential biotechnological and ecological relevance. The taxonomic placement of strain NCCP-28<sup>T</sup> was determined through polyphasic characterization. Isolated from the rhizospheric soil of a legume, strain NCCP-28<sup>T</sup> exhibited Gram-positive, motile, aerobic, and rod-shaped cells that produced endospores. Additionally, it tested negative for oxidase but positive for catalase. The cells were grown at a pH range of 6‒10 (optimum of 7.0) or over a 20‒45&#xa0;°C range (optimum of 30&#xa0;°C) and could thrive in 0‒10% NaCl (optimum of 1% w/v). Strain NCCP-28<sup>T</sup> also tolerated heavy metals, including chromium (450&#xa0;ppm), copper (300&#xa0;ppm), and zinc (550&#xa0;ppm). Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain NCCP-28<sup>T</sup> is closely related to Niallia nealsonii DSM 15077<sup>T</sup>, exhibiting 97.79% sequence similarity. However, strain NCCP-28<sup>T</sup> formed a distinct and well-supported clade in the phylogenomic tree, clearly separating it from its nearest relatives. This distinction was further substantiated by whole-genome comparisons, including digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values, which collectively support the classification of strain NCCP-28<sup>T</sup> as a novel species within the genus Niallia. Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and unknown amino phospholipids were included in the polar lipid profile of the strain. The predominant fatty acids (&gt; 10%) included anteiso-C<sub>15:0</sub>, iso-C<sub>15:0</sub>, and C<sub>16:0</sub>. However, MK-7 and MK-8 are respiratory quinones. Strain NCCP-28<sup>T</sup> classified as a distinct species within the genus <i>Niallia</i> based on its phylogenetic, phenotypic, chemotaxonomic and genotypic traits and was designated the type strain NCCP-28<sup>T</sup> (CGMCC1.62018<sup>T</sup> = GDMCC1.4390<sup>T</sup>), which was named <i>Niallia pakistanensis</i> sp. nov. These findings emphasize microbial systematics, environmental microbiology, and functional genomics. The ecological origin, genomic insights, and adaptive traits of strain NCCP-28<sup>T</sup> support its potential application in environmental sustainability and microbial biotechnology.</p>

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Genomic and taxonomic characterization of Niallia pakistanensis sp. nov. NCCP-28T: a novel antibiotic-resistant and heavy-metal-tolerant bacterium isolated from the legume rhizosphere in Pakistan

  • 期刊论文

  • 发表日期：

    2025年7月23日

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  • Sadia Manzoor,
  • Saira Abbas,
  • Sobia Zulfiqar,
  • Dildar Wu,
  • Hong-Chuan Wang,
  • Wen-Jun Li,
  • Muhammad Arshad,
  • Iftikhar Ahmed

摘要

Soil microbes play a crucial role in biogeochemical cycling and are a valuable resource for discovering novel taxa with environmental applications. This study aimed to explore rhizospheric microbial diversity for potential biotechnological and ecological relevance. The taxonomic placement of strain NCCP-28T was determined through polyphasic characterization. Isolated from the rhizospheric soil of a legume, strain NCCP-28T exhibited Gram-positive, motile, aerobic, and rod-shaped cells that produced endospores. Additionally, it tested negative for oxidase but positive for catalase. The cells were grown at a pH range of 6‒10 (optimum of 7.0) or over a 20‒45 °C range (optimum of 30 °C) and could thrive in 0‒10% NaCl (optimum of 1% w/v). Strain NCCP-28T also tolerated heavy metals, including chromium (450 ppm), copper (300 ppm), and zinc (550 ppm). Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain NCCP-28T is closely related to Niallia nealsonii DSM 15077T, exhibiting 97.79% sequence similarity. However, strain NCCP-28T formed a distinct and well-supported clade in the phylogenomic tree, clearly separating it from its nearest relatives. This distinction was further substantiated by whole-genome comparisons, including digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values, which collectively support the classification of strain NCCP-28T as a novel species within the genus Niallia. Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and unknown amino phospholipids were included in the polar lipid profile of the strain. The predominant fatty acids (> 10%) included anteiso-C15:0, iso-C15:0, and C16:0. However, MK-7 and MK-8 are respiratory quinones. Strain NCCP-28T classified as a distinct species within the genus Niallia based on its phylogenetic, phenotypic, chemotaxonomic and genotypic traits and was designated the type strain NCCP-28T (CGMCC1.62018T = GDMCC1.4390T), which was named Niallia pakistanensis sp. nov. These findings emphasize microbial systematics, environmental microbiology, and functional genomics. The ecological origin, genomic insights, and adaptive traits of strain NCCP-28T support its potential application in environmental sustainability and microbial biotechnology.