Nocardioides lacus sp. nov., a novel member of the Actinomycetota isolated from a freshwater pond.

Abstract

A Gram-positive, aerobic, short rod-shaped, white-coloured bacterium, designated strain BP30^T, was isolated from a freshwater pond. Growth occurred at 15-35 °C (optimum, 30 °C) and pH 5.5-8.5 (optimum, pH 7) in the presence of 0-0.5 % NaCl (optimum, 0 %). 16S rRNA gene phylogenetic analysis showed that this strain was most closely related to Nocardioides marinus CL-DD14ᵀ (97.07%), Nocardioides terrae VA15ᵀ (97.03%), Nocardioides opuntiae OS1-21ᵀ (96.96%), Nocardioides panacihumi Gsoil 616ᵀ (96.94%) and Nocardioides nematodiphilus R-N-C8ᵀ (96.87%) but formed a distinct lineage within the genus Nocardioides. Phylogenetic and phylogenomic analyses further revealed that this strain clustered with N. nematodiphilus R-N-C8ᵀ and Nocardioides baekrokdamisoli B2-12ᵀ (96.04%) in the tree. The predominant respiratory quinone was menaquinone-8 (H₄), and the major fatty acids were iso-C_16 : 0, C_18 : 0 and 10-methyl C_18 : 0 (tuberculostearic acid). The polar lipids in strain BP30^T consisted primarily of phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G+C content was 70.9 mol%. Phylogenetic, average nt identity, digital DNA-DNA hybridization, phylogenomic, physiological and biochemical data indicated that the novel strain was distinct from other members of the genus Nocardioides. Notably, genome annotation of strain BP30^T revealed broad metabolic versatility, including complete pathways for central carbohydrate and aa metabolism and the biosynthesis of key cofactors and vitamins. The presence of genes for the degradation of aromatic hydrocarbons suggests a potential role in the bioremediation of polluted environments. Based on the genotypic, phenotypic and chemotaxonomic features, strain BP30^T (=KACC 22205^T=JCM 34558^T) is proposed as a novel species of the genus Nocardioides, named Nocardioides lacus sp. nov.