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.

Abstract

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^T was determined through polyphasic characterization. Isolated from the rhizospheric soil of a legume, strain NCCP-28^T 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-28^T 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-28^T is closely related to Niallia nealsonii DSM 15077^T, exhibiting 97.79% sequence similarity. However, strain NCCP-28^T 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^T 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-C_15:0, iso-C_15:0, and C_16:0. However, MK-7 and MK-8 are respiratory quinones. Strain NCCP-28^T 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-28^T (CGMCC1.62018^T = GDMCC1.4390^T), 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-28^T support its potential application in environmental sustainability and microbial biotechnology.