Genomic insights into Neopusillimonas aestuarii sp. nov., a novel estuarine bacterium with adaptations for ectoine biosynthesis and stress tolerance

Abstract

A novel Gram-stain-negative, aerobic rod-shaped bacterial strain, which was catalase- and oxidase-positive, designated as DMV24BSW_D^T, was isolated from the estuarine waters of the Bhavnagar (India) coast of the Arabian Sea. Its 16S rRNA gene exhibited 99.52% similarity with Neopusillimonas maritima 17-4A^T, followed by 97.95% similarity with the Pusillimonas caeni strain EBR-8–1 and 97.4% similarity with the P. noertemannii strain BN9^T. Phylogenomic analysis using BPGA (14,332 aa) and UBCG (90,261 bp) tools revealed a unique phylogenetic position within the genus Neopusillimonas. The genome exhibited a G + C content of 53.25%. In comparison with N. maritima 17-4A^T, the strain demonstrated an average nucleotide identity (ANIb) of 94.47% and a digital DNA-DNA hybridization (dDDH) value of 60.1%, indicating distinct genomic divergence. The genome of DMV24BSW_D^T contains several unique metabolic genes that facilitate efficient electron transfer during aerobic respiration. Additionally, it harbours one intact prophage and four defective prophages, indicating ongoing viral interactions. The genome encodes a complete pathway for ectoine biosynthesis and transportation. Strain DMV24BSW_D^T tested positive for gelatin hydrolysis and demonstrated the ability to utilize a wide range of carbohydrates, including α-D-glucose, D-melibiose, D-fructose, L-rhamnose, and various organic acids, such as methyl pyruvate and propionic acid, along with tolerance to fluctuating pH (5 to 10) and salinity (0–4% NaCl). The major polar lipids included phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylethanolamine, while fatty acid analysis revealed C_12:0, C_16:0, C_17:0 cyclo, and summed feature 2 (C_12:0 aldehyde/unknown) as major components. The respiratory quinones identified were MK-7 and MK-8. These comprehensive phenotypic, chemotaxonomic, and genomic characteristics support the unique taxonomic position of DMV24BSW_D^T within the genus Neopusillimonas and the proposal of a novel species of the genus Neopusillimonas, for which the name Neopusillimonas aestuarii sp. nov. (Type strain DMV24BSW_D^T = MCC 2506 ^T = KCTC 72453 ^T = JCM 34508 ^T) is proposed.