Description of Halosolutus amylolyticus gen. nov., sp. nov., Halosolutus halophilus sp. nov. and Halosolutus gelatinilyticus sp. nov., and genome-based taxonomy of genera Natribaculum and Halovarius

Sun, Yaping; Wang, Beibei; Zheng, Xi-Wen; Wu, Zhang-Ping; Hou, Jing; Cui, Heng‐Lin

doi:10.1099/ijsem.0.005598

“…In the phylogenomic tree, most representatives of the 76 genera clustered with each other forming a genus clade, except for three species, Halopiger djelfimassiliensis , Halopiger goleimassiliensis and Natrialba swarupiae , which did not cluster with the other species of their respective genera. The topology of this tree indicated that Halopiger djelfimassiliensis is related to the species of the genus Halosolutus [20]; Halopiger goleimassiliensis is a species of the genus Natrarchaeobaculum ; and Natrialba swarupiae should be assigned to the genus Natrarchaeobius . Putting aside these three problematic species, the current 76 genera with validly published names gathered into eight, tightly clustered, monophyletic groups which were supported by high bootstrap values and separated from the ‘ Halorutilaceae ’ of the ‘ Halorutilales ’ recently described by Durán-Viseras et al [8].…”

Section: Resultsmentioning

confidence: 99%

“…In this study, the genera Halomicrococcus [28] and Halorussus [29] were found to be two relatives of the genus Haladaptatus and should be assigned to the family ‘ Haladaptataceae ’. The Natrialbaceae cluster contains 19 genera, Halobiforma [30], Halopiger [31], Halosolutus [20], Halostagnicola [32], Haloterrigena [33], Halovivax [34], Natrarchaeobaculum [35], Natrarchaeobius [36], Natrialba [37], Natribaculum [38], Natrinema [39], Natronobacterium [40], Natronobiforma [41], Natronococcus [40], Natronolimnohabitans [35], Natronorubrum [42], Natronolimnobius [43], Salinadaptatus [44] and Saliphagus [45]. The family Natronoarchaeaceae has been described recently within the order Halobacteriales , composed of the genera Halostella [46] , Natranaeroarchaeum [7], Natronoarchaeum [47] and Salinarchaeum …”

Section: Resultsmentioning

confidence: 99%

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

Cui

¹

,

Han

²

,

Hou

³

et al. 2023

International Journal of Systematic and Evolutionary Microbiology

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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.

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“…The PHA biosynthesis genes of strains ZS-10 T and GSL13 T were explored based on the genome sequences [29]. Both strains contained the gene cluster encoding for PhaB, PhaC, PhaE, PhaP and PhaR in their genomes (Fig.…”

Section: Resultsmentioning

confidence: 99%

Salinigranum marinum sp. nov. and Halohasta salina sp. nov., halophilic archaea isolated from sediment of a marine saltern and inland saline soil

Cheng,

Li,

Tan

et al. 2023

International Journal of Systematic and Evolutionary Microbiology

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Two halophilic archaeal strains, ZS-10T and GSL13T, were isolated from the Zhoushan marine saltern in Zhejiang, and an inland saline soil from the Tarim Basin, Xinjiang, PR China, respectively. The cells of strain ZS-10T were pleomorphic while those of strain GSL13T were rod-shaped. Both of them stained Gram-negative and formed red-pigmented colonies on agar plates and their cells lysed in distilled water. The optimum growth of strain ZS-10T was observed at 40 °C, 3.4 M NaCl, 0.03 M MgCl2 and pH 7.5, while that of strain GSL13T was at 37 °C, 3.1 M NaCl, 0.5 M MgCl2 and pH 7.5. Phylogenetic and phylogenomic analyses indicated that these two strains were related to Salinigranum and Halohasta , respectively. Strains ZS-10T and GSL13T could be differentiated from the current members of Salinigranum and Halohasta based on the comparison of diverse phenotypic characteristics. The average amino acid identity, average nucleotide identity and digital DNA–DNA hybridization values among strain ZS-10T and current species of Salinigranum were 75.8–78.6 %, 80.6–81.9 % and 24.3–26.1 %, respectively. These values between strain GSL13T and current species of Halohasta were 78.4–80.8 %, 79.8–82.8% and 22.7–25.7 %, respectively, clearly below the threshold values for species demarcation. The polar lipids of strain ZS-10T were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me) and sulphated mannosyl glucosyl diether (S-DGD-1), while those of strain GSL13T were phosphatidic acid, PG, PGP-Me, phosphatidylglycerol sulphate and S-DGD-1. The polar lipid profile of strain GSL13T was identical to those of Halohasta , whereas strain ZS-10T did not contain the minor glycolipids detected in the current Salinigranum species. The phenotypic, phylogenetic and genome-based results suggested that strains ZS-10T (=CGMCC 1.12868T=JCM 30241T) and GSL13T (=CGMCC 1.15214T=JCM 30841T) represent two novel species, for which the names Salinigranum marinum sp. nov. and Halohasta salina sp. nov. are proposed.

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“…The biotechnological potential of functional genes was referenced to the approach described by Sun et al . [33]. OrthoVenn2 [34] was used to compare the orthologous gene clusters (OCs) among strains Gai3-17 T , XZYJT26 T , Halobacterium salinarum DSM 3754 T , Halobacterium jilantaiense CGMCC 1.5337 T and Halobacterium litoreum ZS-54-S2 T .…”

Section: Methodsmentioning

confidence: 99%

“…The genomes of strains Gai3-17 T and XZYJT26 T were annotated utilizing Rapid Annotation using Subsystems Technology (rast) to explore the potential physiological functions of the strains. The biotechnological potential of functional genes was referenced to the approach described by Sun et al [33]. OrthoVenn2 [34] was used to compare the orthologous gene clusters (OCs) among strains Gai3-17 T , XZYJT26 T , Halobacterium salinarum DSM 3754 T , Halobacterium jilantaiense CGMCC 1.5337 T and Halobacterium litoreum ZS-54-S2 T .…”

Section: Genome Analysismentioning

confidence: 99%

Halobacterium wangiae sp. nov. and Halobacterium zhouii sp. nov., two extremely halophilic archaea isolated from sediment of a salt lake and saline soil of an inland saltern

Wang,

Bao,

Sun

et al. 2023

International Journal of Systematic and Evolutionary Microbiology

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Two novel halophilic archaeal strains, Gai3-17T and XZYJT26T, were isolated from the sediment of Gaize salt lake and the saline soil of Mangkang ancient solar saltern in Tibet, PR China, respectively. Strains Gai3-17T and XZYJT26T were related to each other (96.5 and 89.7% similarity, respectively) and showed 97.5–95.4 and 91.5–87.7% similarities to the current members of Halobacterium based on 16S rRNA and rpoB′ genes. The phylogenomic analysis indicated that strains Gai3-17T and XZYJT26T formed two distinct clades and clustered with the Halobacterium species. The two strains can be differentiated from the type strains of the six species with validly published names based on several phenotypic characteristics. The phospholipids of the two strains were phosphatidic acid, phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. One major glycolipid, sulphated galactosyl mannosyl glucosyl diether, was detected in strain Gai3-17T, while four glycolipids, mannosyl glucosyl diether, sulphated mannosyl glucosyl diether, disulphated mannosyl glucosyl diether and sulphated galactosyl mannosyl glucosyl diether were observed in strain XZYJT26T. The average nucleotide identity, digital DNA–DNA hybridization and amino acid identity values among the two strains and the members of Halobacterium were no more than 81, 25 and 77 %, respectively. These overall genome-related indices were below the threshold values for species boundary, indicating that strains Gai3-17T and XZYJT26T represent two novel species of Halobacterium . Thus, two novel species, Halobacterium wangiae sp. nov. and Halobacterium zhouii sp. nov., are proposed to accommodate strains Gai3-17T (=CGMCC 1.16101T=JCM 33551T) and XZYJT26T (=CGMCC 1.16682T=JCM 33556T), respectively.

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Description of Halosolutus amylolyticus gen. nov., sp. nov., Halosolutus halophilus sp. nov. and Halosolutus gelatinilyticus sp. nov., and genome-based taxonomy of genera Natribaculum and Halovarius

Cited by 16 publications

References 41 publications

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

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

Salinigranum marinum sp. nov. and Halohasta salina sp. nov., halophilic archaea isolated from sediment of a marine saltern and inland saline soil

Halobacterium wangiae sp. nov. and Halobacterium zhouii sp. nov., two extremely halophilic archaea isolated from sediment of a salt lake and saline soil of an inland saltern

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