Nocardioides agri sp. nov., isolated from garden soil

A novel bacterial strain, designated as MAH-18^T, was isolated from soil sampled in a flower garden. Cells of strain MAH-18^T were Gram-stain-positive, aerobic, motile, and rod-shaped. The colonies were beige in colour, smooth, and spherical when grown on Reasoner's 2A agar medium. Strain MAH-18^T grew at 20-40 °C, pH 6.0-8.0, and 0-1.0 % NaCl. Cells were able to hydrolyse aesculin, gelatin, and Tween 20. According to the 16S rRNA gene sequence comparisons, the isolate was determined to be a member of the genus Nocardioides and most closely related to Nocardioides pyridinolyticus OS4^T (97.9 %), Nocardioides hankookensis DS-30^T (97.9 %), Nocardioides aquiterrae GW-9^T (97.6 %), Nocardioides soli mbc-2^T (97.5 %), Nocardioides conyzicola HWE 2-02^T (97.4 %), and Nocardioides mangrovi GBK3QG-3^T (96.3 %). Strain MAH-18^T has a draft genome size of 4 788 325 bp (eight contigs), 4572 protein-coding genes, 46 tRNA, and three rRNA genes. The average nucleotide identity and digital DNA-DNA hybridization values between strain MAH-18^T and the closest type strains were 81.5-83.4 % and 24.4-25.8 %, respectively. In silico genome mining revealed several biosynthetic gene clusters in the genome of the novel strain MAH-18^T. The G+C content of the genomic DNA of strain was 72.2 mol% and the predominant isoprenoid quinone was MK-8 (H₄). The main polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, and unknown phospholipids. The major cellular fatty acids were determined to be C_16:0 iso and C_17 : 1  ω6c. The DNA-DNA hybridization results and phenotypic, genotypic, and chemotaxonomic data demonstrated that strain MAH-18^T represents a novel species, for which the name Nocardioides agri sp. nov. is proposed, with MAH-18^T as the type strain (=KACC 19744^T=CGMCC 1.13656^T).