Taxogenomic and Physiological Characterization of Halomonas shizuishanensis sp. nov. Reveals Osmotic-Adaptation Traits and an Ammonium-Utilization Phenotype

Abstract

Extreme saline–alkaline environments impose simultaneous osmotic and nitrogen stresses, yet the traits that enable microbial persistence and nitrogen utilization under these conditions remain incompletely understood. Here, we isolated and characterized a novel bacterium, Halomonas shizuishanensis DWK9T, from a saline–alkaline soil (salinity 5.75 g/kg, pH 8.35) in Shizuishan City, Ningxia, China, using a polyphasic taxonomic and genomic approach. Strain DWK9T grew at 0–20% (w/v) NaCl and pH 7.0–10.0. Although its 16S ribosomal RNA gene shared 98.4% similarity with H. lutescens Q1UTT, phylogenomic analysis and genome-based indices, including average nucleotide identity (88.12%) and digital DNA-DNA hybridization (32.5%), supported its classification as a distinct species. Genome analysis identified a complete ectABC cluster and genes annotated for ammonium assimilation and nitrate/nitrite metabolism, including glnA, gdhA, nasA, narGK, and nirBD. Physiological experiments showed that extracellular ammonium nitrogen concentrations decreased in inoculated cultures relative to the corresponding sterile control, concomitantly with bacterial growth, while nitrite nitrogen accumulated only to a limited extent. These findings provide genomic and physiological observations relevant to osmotic adaptation and inorganic-nitrogen dynamics in a halotolerant bacterium from a saline–alkaline ecosystem.