Alkalihalobacterium elongatum gen. nov. sp. nov.: An Antibiotic-Producing Bacterium Isolated From Lonar Lake and Reclassification of the Genus Alkalihalobacillus Into Seven Novel Genera

A Gram-stain positive, long, rod-shaped, motile, and spore-forming bacterium (MEB199(T)) was isolated from a sediment sample collected from Lonar Lake, India. The strain was oxidase and catalase positive. The strain grew optimally at pH 10, NaCl concentration of 3.5% at 37°C. The major fatty acids were iso-C(15:0), iso-C(16:0), anteiso-C(15:0), and iso-C(17:0). The peptidoglycan contained meso-diaminopimelic acid (meso-DAP). Phosphatidylethanolamine, diphosphatidylglycerol, and phosphatidylglycerol were the major polar lipids of MEB199(T). Phylogenetic analysis based on 16S rRNA gene sequence showed that strain MEB199(T) belonged to the family Bacillaceae and exhibited a distinctive position among the members of the genus Alkalihalobacillus (Ahb.). Strain MEB199(T) shared the highest 16S rRNA gene sequence similarity with Alkalihalobacillus alkalinitrilicus ANL-iso4(T) (98.36%), whereas with type species Ahb. alcalophilus DSM 485(T), it is 94.91%, indicating that strain MEB199(T) is distinctly related to the genus Alkalihalobacillus. The G + C content of genomic DNA was 36.47 mol%. The digital DNA–DNA hybridization (dDDH) (23.6%) and average nucleotide identity (ANI) (81%) values between strain MEB199(T) and Ahb. alkalinitrilicus ANL-iso4(T) confirmed the novelty of this new species. The pairwise identity based on the 16S rRNA gene sequence between the species of genus Alkalihalobacillus ranges from 87.4 to 99.81% indicating the heterogeneity in the genus. The different phylogenetic analysis based on the genome showed that the members of the genus Alkalihalobacillus separated into eight distinct clades. The intra-clade average amino acid identity (AAI) and percentage of conserved proteins (POCP) range from 52 to 68% and 37 to 59%, respectively, which are interspersed on the intra-genera cutoff values; therefore, we reassess the taxonomy of genus Alkalihalobacillus. The phenotypic analysis also corroborated the differentiation between these clades. Based on the phylogenetic analysis, genomic indices, and phenotypic traits, we propose the reclassification of the genus Alkalihalobacillus into seven new genera for which the names Alkalihalobacterium gen. nov., Halalkalibacterium gen. nov., Halalkalibacter gen. nov., Shouchella gen. nov., Pseudalkalibacillus gen. nov., Alkalicoccobacillus gen. nov., and Alkalihalophilus gen. nov. are proposed and provide an emended description of Alkalihalobacillus sensu stricto. Also, we propose the Ahb. okuhidensis as a heterotypic synonym of Alkalihalobacillus halodurans. Based on the polyphasic taxonomic analysis, strain MEB199(T) represents a novel species of newly proposed genus for which the name Alkalihalobacterium elongatum gen. nov. sp. nov. is proposed. The type strain is MEB199(T) (= MCC 2982(T), = JCM 33704(T), = NBRC 114256(T), = CGMCC 1.17254(T)).