Genome-based classification of the class Halobacteria and description of Haladaptataceae fam. nov. and Halorubellaceae fam. nov

Abstract

Currently, there are four mainstream taxonomic opinions on the classification of the class Halobacteria at the family and order levels. The International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Halobacteria (ICSP), List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Centre for Biotechnology Information (NCBI) adopted taxonomies have three to four orders and up to eight families, while the Genome Taxonomy Database (GTDB) taxonomy proposes only one order with nine families. To resolve the taxonomic inconsistency, phylogenomic analyses based on concatenated single-copy orthologous proteins and 122 concatenated conserved single-copy marker proteins were conducted to infer the taxonomic status of the current representatives of the class Halobacteria at the family and order levels. The current 76 genera with validly published names of the class Halobacteria were able to be assigned into eight families in one order. On the basis of these results, it is proposed that the current species with validly published names of the class Halobacteria should be remerged into the order Halobacteriales , then assigned to eight families, Haladaptataceae, Haloarculaceae , Halobacteriaceae , Halococcaceae , Haloferacaceae , Natronoarchaeaceae, Natrialbaceae and Halorubellaceae. Thus, Haladaptataceae fam. nov. is described based on Haladaptatus , Halomicrococcus and Halorussus and Halorubellaceae fam. nov. is proposed incorporating Haloarchaeobius and Halorubellus , respectively.

Halospeciosus flavus gen. nov., sp. nov. and Haladaptatus caseinilyticus sp. nov., halophilic archaea isolated from saline soil of an inland solar saltern and offshore sediment

“…The average nucleotide identity (ANI), digital DNA–DNA hybridisation (dDDH) and average amino acid identity (AAI) values were calculated using the JSpeciesWS online ANI calculator, the Genome-to-Genome Distance Calculator and the AAI calculator [20–22], respectively. The phylogenomic tree was reconstructed using GTDB-Tk [23] and iq-tree 1.6.1 software [24] as described previously [1].…”

“…At present, the class Halobacteria includes two orders and nine families [1]. The family Halobacteriaceae was first established in 1974 by Gibbons [2], and currently consists of six genera, Halanaeroarchaeum , Halarchaeum , Halobacterium , Halocalculus , Halodesulfurarchaeum and Salarchaeum [1]. These genera were assigned to the family Halobacteriaceae based on the results of phylogenomic analyses.…”

“…Halophilic archaea of the class Halobacteria are a specific group within the domain Archaea distributed in diverse salt environments. At present, the class Halobacteria includes two orders and nine families [1]. The family Halobacteriaceae was first established in 1974 by Gibbons [2], and currently consists of six genera, Halanaeroarchaeum , Halarchaeum , Halobacterium , Halocalculus , Halodesulfurarchaeum and Salarchaeum [1].…”

Halomicrococcus gelatinilyticus sp. nov. and Halosimplex aquaticum sp. nov., halophilic archaea isolated from saline soil and an inland solar saltern

“…The overall genome-related indexes, including average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA–DNA hybridization (dDDH), were calculated using the JSpeciesWS online ANI calculator [24], an AAI calculator [25] and the Genome-to-Genome Distance Calculator 3.0 [26], respectively. The genome-based phylogenetic tree was reconstructed according to the Genome Taxonomy Database (GTDB) [27] as described previously [9]. The Kyoto Encyclopedia of Genes and Genomes (KEGG) [28] database was searched to identify and confirm the general metabolic pathways.…”

“…The genera Halomicrococcus and Halosimplex are currently classified within the families Haladaptataceae and Haloarculaceae , respectively, in the order Halobacteriales , class Halobacteria [9]. The genus Halomicrococcus was created in 2020 to describe the type species Halomicrococcus hydrotolerans based on a strain isolated from a subterranean salt deposit sampled at Yunnan salt mine [10].…”