Natronorarus salvus gen. nov., sp. nov., Halalkalicoccus ordinarius sp. nov., and Halalkalicoccus salilacus sp. nov., halophilic archaea from a soda lake and two saline lakes, and proposal to classify the genera Halalkalicoccus and Natronorarus into Halalkalicoccaceae fam. nov. in the order Halobacteriales within the class Halobacteria.

Four novel halophilic archaeal strains CGA53, CG83, FCH27, and SEDH24 were isolated from a soda lake and two saline lakes in China, respectively. Strain CGA53 showed the highest 16S rRNA gene similarity (92.6%) to Salinilacihabitans rarus AD-4, and the other three strains were found to be related to Halalkalicoccus species with similarities of 97.6-98.3%. Metagenomic studies indicated that these four strains are low abundant inhabitants detected in these hypersaline environments, and only one MAG of Chagannuoer Soda Lake (CG) could be assigned to the genus Halalkalicoccus. Their growth occurred at 20-60 °C (optima, 42, 37, 37-42, and 35 °C), 0.9-5.1 M NaCl (optima, 3.9, 2.6, 3.5, and 3 M), and 0-1.0 M MgCl (optima, 0.5, 0.7, and 0.1) and pH 5.5-10.5 (optima, 9.0, 7.5, 7.0, and 7.0), respectively. Phylogenetic and phylogenomic analyses revealed that strains CG83, FCH27, and SEDH24 cluster with the current species of the genus Halalkalicoccus, and strain CGA53 forms an independent branch separated from this genus. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values among strains CGA53, CG83, FCH27, SEDH24, and the type species of the current genera within the class Halobacteria were 67.4-81.6%, 16.5-28.6% and 49.7-74.1%, respectively, clearly lower than the cutoff values for species demarcation. Strain CGA53 may represent a novel species of a new genus according to the cutoff value for genus demarcation of 65% AAI. Diverse differential phenotypic characteristics, such as nutrition, biochemical activities, antibiotic sensitivity, and HS formation, were found among these four strains and Halalkalicoccus species. Genome-based classification supported that strains CGA53, CG83, FCH27, SEDH24, and the current species of Halalkalicoccus represent a novel family of the order Halobacteriales within the class Halobacteria.