A novel extremely halophilic strain, designated ZY19T, was isolated from a rock salt sample from Yunnan salt mine, PR China. Strain ZY19T is neutrophilic, non-motile and requires at least 10% (w/v) NaCl for growth. Optimal growth is observed at 20–25% (w/v) NaCl, pH 7.5–8.0 and 42 °C. Mg2+ is not required for growth. The cells do not lyse in distilled water. On the basis of 16S rRNA gene sequence analysis, strain ZY19T belongs to the genus Haloterrigena (Htg.) and is closely related to Haloterrigena salina XH-65T (98.5% sequence similarity) and Haloterrigena turkmenica DSM 5511T (97.9%). Phylogenetic and phylogenomic analysis showed that strain ZY19T clusters with the species Htg. salina and Htg. turkmenica forming an independent clade separated from other members of the genus. The value of genomic average nucleotide identity (ANI) between strains ZY19T and its close relative, Htg. salina XH-65T was 94.2%. DNA–DNA relatedness between strains ZY19T and Htg. salina XH-65T revealed by in silico DNA–DNA hybridization (DDH) was 56.3%. Both the ANI value and the degree of in silico DDH are below the accepted threshold for members of the same species. The major polar lipids were found to consist of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, sulfated diglycosyl-diether-1 and mannose-2, 6-disulfate (1 → 2)-glucose glycerol diether. The genomic DNA G+C content was determined to be 64.5 mol%. Based on the results of the phenotypic, chemotaxonomic, genetic similarity and inferred phylogeny, strain ZY19T is distinct from other validly named species and thus represents a novel species within the genus Haloterrigena, for which the name Haloterrigena salifodinae sp. nov. is proposed. The type strain is ZY19T (=CGMCC 1.16114T=NBRC 112981T).
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Basic local alignment search tool
Average nucleotide identity
China General Microbiological Culture Collection Center
- DSM, DSMZ:
Deutsche Sammlung von Mikroorganismen und Zellkulturen
Dimethyl sulphoxide HPLC, high performance liquid chromatography
Amoozegar MA, Siroosi M, Atashgahi S, Smidt H, Ventosa A (2017) Systematics of haloarchaea and biotechnological potential of their hydrolytic enzymes. Microbiology 163:623–645
Auch AF, von Jan M, Klenk HP, Göker M (2010) Digital DNA–DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2:117–134
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477
Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu XW, De Meyer S, Trujillo ME (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466
Corcelli A, Lobasso S (2006) Characterization of lipids of halophilic archaea. In: Rainey FA, Oren A (eds) Methods in microbiology, extremophiles. Elsevier/Academic, Amsterdam, pp 585–613
Cui HL, Tohty D, Zhou PJ, Liu SJ (2006) Haloterrigena longa sp. nov. and Haloterrigena limicola sp. nov., extremely halophilic archaea isolated from a salt lake. Int J Syst Evol Microbiol 56:1837–1840
Ding JY, Chen SC, Lai MC, Liao TL (2017) Haloterrigena mahii sp. nov., an extremely halophilic archaeon from a solar saltern. Int J Syst Evol Microbiol 67:1333–1338
Dussault HP (1955) An improved technique for staining red halophilic bacteria. J Bacteriol 70:484–485
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
Gonzalez C, Gutierrez C, Ramirez C (1978) Halobacterium vallismortis sp. nov. An amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 24:710–715
Gutiérrez MC, Castillo AM, Kamekura M, Ventosa A (2008) Haloterrigena salina sp. nov., an extremely halophilic archaeon isolated from a salt lake. Int J Syst Evol Microbiol 58:2880–2884
Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95–98
Kamekura M (1993) Lipids of extreme halophiles. In: Vreeland RH, Hochstein LI (eds) The biology of halophilic bacteria. CRC Press, Boca Raton, pp 135–161
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874
Marmur J (1961) A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 3:208–218
Medlar AJ, Toronen P, Holm L (2018) AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination. Nucleic Acids Res 46:W479–W485
Meier-Kolthoff JP, Göker M, Spröer C, Klenk HP (2013) When should a DDH experiment be mandatory in microbial taxonomy? Arch Microbiol 195:413–418
Minegishi H, Kamekura M, Itoh T, Echigo A, Usami R, Hashimoto T (2010) Further refinement of the phylogeny of the Halobacteriaceae based on the full-length RNA polymerase subunit B’ (rpoB′) gene. Int J Syst Evol Microbiol 60:2398–2408
Montalvo-Rodríguez R, López-Garriga J, Vreeland RH, Oren A, Ventosa A, Kamekura M (2000) Haloterrigena thermotolerans sp. nov., a halophilic archaeon from Puerto Rico. Int J Syst Evol Microbiol 3:1065–1071
Oren A, Ventosa A, Grant WD (1997) Proposed minimal standards for description of new taxa in the order Halobacteriales. Int J Syst Bacteriol 47:233–238
Oren A, Arahal DR, Ventosa A (2009) Emended descriptions of genera of the family Halobacteriaceae. Int J Syst Evol Microbiol 59:637–642
Papke RT, White E, Reddy P, Weigel G, Kamekura M, Minegishi H, Usami R, Ventosa A (2011) A multilocus sequence analysis approach to the phylogeny and taxonomy of the Halobacteriales. Int J Syst Evol Microbiol 61:2984–2995
Roh SW, Nam YD, Chang HW, Kim KH, Sung Y, Kim MS, Oh HM, Bae JW (2009) Haloterrigena jeotgali sp. nov., an extremely halophilic archaeon from salt-fermented food. Int J Syst Evol Microbiol 59:2359–2363
Romano I, Poli A, Finore I, Huertas FJ, Gambacorta A, Pelliccione S, Nicolaus G, Lama L, Nicolaus B (2007) Haloterrigena hispanica sp. nov., an extremely halophilic archaeon from Fuente de Piedra, southern Spain. Int J Syst Evol Microbiol 57:1499–1503
Segata N, Börnigen D, Morgan XC, Huttenhower C (2013) PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun 4:2304
Selim S, Hagagy N (2015) Genome sequence of carboxylesterase, carboxylase and xylose isomerase producing alkaliphilic haloarchaeon Haloterrigena turkmenica WANU15. Genomics Data 7:70–72
Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC, pp 607–654
Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680
Ventosa A, Gutiérrez MC, Kamekura M, Dyall-Smith ML (1999) Proposal to transfer Halococcus turkmenicus, Halobacterium trapanicum JCM 9743 and strain GSL-11 to Haloterrigena turkmenica gen. nov., comb. nov. Int J Syst Bacteriol 1:131–136
Wang S, Yang Q, Liu ZH, Sun L, Wei D, Zhang JZ, Song JZ, Yuan HF (2010) Haloterrigena daqingensis sp. nov., an extremely haloalkaliphilic archaeon isolated from a saline–alkaline soil. Int J Syst Evol Microbiol 60:2267–2271
Xu XW, Liu SJ, Tohty D, Oren A, Wu M, Zhou PJ (2005) Haloterrigena saccharevitans sp. nov., an extremely halophilic archaeon from Xin-Jiang, China. Int J Syst Evol Microbiol 55:2539–2542
Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 67:1613–1617
Zvyagintseva IS, Tarasov AL (1987) Extreme halophilic bacteria from alkaline soils. Mikrobiologiya 56:839–844 (in Russian)
We thank Professor Zhu L. Yang and Dr. Bang Feng from the Kunming Institute of Botany, Chinese Academy of Sciences for their helps in sample collection and data analysis, and we also thank Dr. Hao Yan from the College of Life Sciences, Anhui Normal University, for his technical assistance.
This work was supported by grants from the National Natural Science Foundation of China (31460003), the Anhui Provincial Key Lab. of the Conservation and Exploitation of Biological Resources (591601), the China Scholarship Council (201808340054) and the Department of Education Anhui Province, China.
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The cell morphology, thin-layer chromatogram of polar lipids and Neighbor-Joining phylogenetic trees of 16S rRNA and rpoB′ are available with the online supplementary material.
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Chen, S., Xu, Y., Sun, S. et al. Haloterrigena salifodinae sp. nov., an extremely halophilic archaeon isolated from a subterranean rock salt. Antonie van Leeuwenhoek 112, 1317–1329 (2019). https://doi.org/10.1007/s10482-019-01264-w
- Salt mine
- Rock salt
- Polyphasic taxonomy
- Multilocus sequence analysis