1887

Abstract

Four halophilic archaeal strains, YPL8, SLN56, LT61 and KZCA68, were isolated from a salt mine, saline soil and a salt lake located in different regions of China. Sequence similarities of 16S rRNA and genes among strains YPL8, SLN56, LT61 and the current members of were 94.1–98.2 % and 89.3–95.1 %, respectively, while these values among strain KZCA68 and the current members of were 97.2–97.4 % and 91.7–91.9 %, respectively. The average nucleotide identity, DNA–DNA hybridization and average amino acid identity values among these four strains and their closely related species were all lower than the threshold values for species boundary. All four strains were unable to hydrolyse casein, gelatin, or Tween 80. Strain YPL8 contained phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1), disulfated mannosyl glucosyl diether (S-DGD) and sulfated mannosyl glucosyl diether-phosphatidic acid (S-DGD-PA). Strain SLN56 contained PA, PG, phosphatidylglycerol sulphate (PGS), PGP-Me, S-DGD-1, S-DGD and S-DGD-PA. Strain LT61 contained PA, PG, PGS, PGP-Me, S-DGD-1 and S-DGD. The phospholipids of strain KZCA68 were PA, PG and PGP-Me. These results showed that strains YPL8 (=CGMCC 1.13883=JCM 31181), SLN56 (=CGMCC 1.14945=JCM 30832) and LT61 (=CGMCC 1.14942=JCM 30668) represent novel species of the genus , for which the names, sp. nov., sp. nov. and sp. nov. are proposed. Strain KZCA68 (=CGMCC 1.17211=JCM 34158) represents a novel species of , for which the name sp. nov. is proposed.

Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 32070003)
    • Principle Award Recipient: Heng-LinCui
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005385
2022-05-26
2024-04-18
Loading full text...

Full text loading...

References

  1. Cui HL, Dyall-Smith ML. Cultivation of halophilic archaea (class Halobacteria) from thalassohaline and athalassohaline environments. Mar Life Sci Technol 2021; 3:243–251 [View Article]
    [Google Scholar]
  2. Enache M, Itoh T, Fukushima T, Usami R, Dumitru L et al. Phylogenetic relationships within the family Halobacteriaceae inferred from rpoBʹ gene and protein sequences. Int J Syst Evol Microbiol 2007; 57:2289–2295 [View Article] [PubMed]
    [Google Scholar]
  3. Minegishi H, Kamekura M, Itoh T, Echigo A, Usami R et al. Further refinement of the phylogeny of the Halobacteriaceae based on the full-length RNA polymerase subunit Bʹ (rpoBʹ) gene. Int J Syst Evol Microbiol 2010; 60:2398–2408 [View Article] [PubMed]
    [Google Scholar]
  4. Papke RT, White E, Reddy P, Weigel G, Kamekura M et al. A multilocus sequence analysis approach to the phylogeny and taxonomy of the Halobacteriales. Int J Syst Evol Microbiol 2011; 61:2984–2995 [View Article] [PubMed]
    [Google Scholar]
  5. Tindall BJ. Taxonomic problems arising in the genera Haloterrigena and Natrinema. Int J Syst Evol Microbiol 2003; 53:1697–1698 [View Article] [PubMed]
    [Google Scholar]
  6. Wright A-DG. Phylogenetic relationships within the order Halobacteriales inferred from 16S rRNA gene sequences. Int J Syst Evol Microbiol 2006; 56:1223–1227 [View Article] [PubMed]
    [Google Scholar]
  7. de la Haba RR, Minegishi H, Kamekura M, Shimane Y, Ventosa A. Phylogenomics of Haloarchaea: the controversy of the genera Natrinema-Haloterrigena. Front Microbiol 2021; 12:740909 [View Article] [PubMed]
    [Google Scholar]
  8. McGenity TJ, Gemmell RT, Grant WD. Proposal of a new halobacterial genus Natrinema gen. nov., with two species Natrinema pellirubrum nom. nov. and Natrinema pallidum nom. nov. Int J Syst Bacteriol 1998; 48:1187–1196 [View Article] [PubMed]
    [Google Scholar]
  9. Oren A, Garrity GM. Valid publication of new names and new combinations effectively published outside the IJSEM. Validation List no. 203. Int J Syst Evol Microbiol 2022; 72:1–11 [View Article]
    [Google Scholar]
  10. Xin H, Itoh T, Zhou P, Suzuki K, Kamekura M et al. Natrinema versiforme sp. nov., an extremely halophilic archaeon from Aibi salt lake, Xinjiang, China. Int J Syst Evol Microbiol 2000; 50 Pt 3:1297–1303 [View Article] [PubMed]
    [Google Scholar]
  11. Montalvo-Rodríguez R, López-Garriga J, Vreeland RH, Oren A, Ventosa A et al. Haloterrigena thermotolerans sp. nov., a halophilic archaeon from Puerto Rico. Int J Syst Evol Microbiol 2000; 50:1065–1071 [View Article] [PubMed]
    [Google Scholar]
  12. Roh SW, Nam Y-D, Chang H-W, Kim K-H, Sung Y et al. Haloterrigena jeotgali sp. nov., an extremely halophilic archaeon from salt-fermented food. Int J Syst Evol Microbiol 2009; 59:2359–2363 [View Article] [PubMed]
    [Google Scholar]
  13. Xu X-W, Ren P-G, Liu S-J, Wu M, Zhou P-J. Natrinema altunense sp. nov., an extremely halophilic archaeon isolated from a salt lake in Altun Mountain in Xinjiang, China. Int J Syst Evol Microbiol 2005; 55:1311–1314 [View Article] [PubMed]
    [Google Scholar]
  14. Xu X-W, Liu S-J, Tohty D, Oren A, Wu M et al. Haloterrigena saccharevitans sp. nov., an extremely halophilic archaeon from Xin-Jiang, China. Int J Syst Evol Microbiol 2005; 55:2539–2542 [View Article] [PubMed]
    [Google Scholar]
  15. Castillo AM, Gutiérrez MC, Kamekura M, Xue Y, Ma Y et al. Natrinema ejinorense sp. nov., isolated from a saline lake in Inner Mongolia, China. Int J Syst Evol Microbiol 2006; 56:2683–2687 [View Article] [PubMed]
    [Google Scholar]
  16. Cui HL, Tohty D, Zhou PJ, Liu SJ. Haloterrigena longa sp. nov. and Haloterrigena limicola sp. nov., extremely halophilic archaea isolated from a salt lake. Int J Syst Evol Microbiol 2006; 56:1837–1840 [View Article] [PubMed]
    [Google Scholar]
  17. Romano I, Poli A, Finore I, Huertas FJ, Gambacorta A et al. Haloterrigena hispanica sp. nov., an extremely halophilic archaeon from Fuente de Piedra, southern Spain. Int J Syst Evol Microbiol 2007; 57:1499–1503 [View Article] [PubMed]
    [Google Scholar]
  18. Tapingkae W, Tanasupawat S, Itoh T, Parkin KL, Benjakul S et al. Natrinema gari sp. nov., a halophilic archaeon isolated from fish sauce in Thailand. Int J Syst Evol Microbiol 2008; 58:2378–2383 [View Article] [PubMed]
    [Google Scholar]
  19. Albuquerque L, Taborda M, La Cono V, Yakimov M, da Costa MS. Natrinema salaciae sp. nov., a halophilic archaeon isolated from the deep, hypersaline anoxic Lake Medee in the Eastern Mediterranean Sea. Syst Appl Microbiol 2012; 35:368–373 [View Article] [PubMed]
    [Google Scholar]
  20. Zhang WY, Meng Y, Zhu XF, Wu M. Halopiger salifodinae sp. nov., an extremely halophilic archaeon isolated from a salt mine. Int J Syst Evol Microbiol 2013; 63:3563–3567 [View Article] [PubMed]
    [Google Scholar]
  21. Ding JY, Chen SC, Lai MC, Liao TL. Haloterrigena mahii sp. nov., an extremely halophilic archaeon from a solar saltern. Int J Syst Evol Microbiol 2017; 67:1333–1338 [View Article]
    [Google Scholar]
  22. Rasooli M, Naghoni A, Amoozegar MA, Mirfeizi L, Moshtaghi Nikou M et al. Natrinema soli sp. nov., a novel halophilic archaeon isolated from a hypersaline wetland. Int J Syst Evol Microbiol 2017; 67:2142–2147 [View Article]
    [Google Scholar]
  23. Ventosa A, Gutiérrez MC, Kamekura M, Dyall-Smith ML. Proposal to transfer halococcus turkmenicus, halobacterium trapanicum JCM 9743 and strain GSL-11 to haloterrigena turkmenica gen. nov., comb. nov. Int J Syst Bacteriol 1999; 49:131–136 [View Article]
    [Google Scholar]
  24. Gutiérrez MC, Castillo AM, Kamekura M, Ventosa A. Haloterrigena salina sp. nov., an extremely halophilic archaeon isolated from a salt lake. Int J Syst Evol Microbiol 2008; 58:2880–2884 [View Article]
    [Google Scholar]
  25. Chen S, Xu Y, Sun S, Chen F. Haloterrigena salifodinae sp. nov., an extremely halophilic archaeon isolated from a subterranean rock salt. Antonie van Leeuwenhoek 2019; 112:1317–1329 [View Article]
    [Google Scholar]
  26. Han D, Cui HL. Halostella pelagica sp. nov. and Halostella litorea sp. nov., isolated from salted brown alga Laminaria. Int J Syst Evol Microbiol 2020; 70:1969–1976 [View Article]
    [Google Scholar]
  27. Cui HL, Yang X, Mou YZ. Salinarchaeum laminariae gen. nov., sp. nov.: a new member of the family Halobacteriaceae isolated from salted brown alga Laminaria. Extremophiles 2011; 15:625–631 [View Article] [PubMed]
    [Google Scholar]
  28. Cui HL, Zhou PJ, Oren A, Liu SJ. Intraspecific polymorphism of 16S rRNA genes in two halophilic archaeal genera, Haloarcula and Halomicrobium. Extremophiles 2009; 13:31–37 [View Article] [PubMed]
    [Google Scholar]
  29. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article]
    [Google Scholar]
  30. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  31. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
    [Google Scholar]
  32. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 1971; 20:406 [View Article]
    [Google Scholar]
  33. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
    [Google Scholar]
  34. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
    [Google Scholar]
  35. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
    [Google Scholar]
  36. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:e73 [View Article] [PubMed]
    [Google Scholar]
  37. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res 2004; 32:D277–80 [View Article] [PubMed]
    [Google Scholar]
  38. Li L, Stoeckert CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 2003; 13:2178–2189 [View Article] [PubMed]
    [Google Scholar]
  39. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
    [Google Scholar]
  40. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009; 25:1972–1973 [View Article] [PubMed]
    [Google Scholar]
  41. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article] [PubMed]
    [Google Scholar]
  42. Oren A, Ventosa A, Grant WD. Proposed minimal standards for description of new taxa in the order Halobacteriales. Int J Syst Bacteriol 1997; 47:233–238 [View Article]
    [Google Scholar]
  43. Cui HL, Gao X, Yang X, Xu XW. Halorussus rarus gen. nov., sp. nov., a new member of the family Halobacteriaceae isolated from a marine solar saltern. Extremophiles 2010; 14:493–499 [View Article] [PubMed]
    [Google Scholar]
  44. Wainø M, Tindall BJ, Ingvorsen K. Halorhabdus utahensis gen. nov., sp. nov., an aerobic, extremely halophilic member of the Archaea from Great Salt Lake, Utah. Int J Syst Evol Microbiol 2000; 50:183–190 [View Article] [PubMed]
    [Google Scholar]
  45. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article] [PubMed]
    [Google Scholar]
  46. Corral P, de la Haba RR, Infante-Domínguez C, Sánchez-Porro C, Amoozegar MA et al. Halorubrum chaoviator Mancinelli et al. 2009 is a later, heterotypic synonym of Halorubrum ezzemoulense Kharroub et al. 2006. Emended description of Halorubrum ezzemoulense Kharroub et al. 2006. Int J Syst Evol Microbiol 2018; 68:3657–3665 [View Article]
    [Google Scholar]
  47. de la Haba RR, Corral P, Sánchez-Porro C, Infante-Domínguez C, Makkay AM et al. Genotypic and lipid analyses of strains from the archaeal genus Halorubrum reveal insights into their taxonomy, divergence, and population structure. Front Microbiol 2018; 9:512 [View Article]
    [Google Scholar]
  48. Infante-Domínguez C, Haba RR, Corral P, Sanchez-Porro C, Arahal DR. Genome-based analyses reveal a synonymy among Halorubrum distributum Zvyagintseva and Tarasov 1989; Oren and Ventosa 1996, Halorubrum terrestre Ventosa et al. 2004, Halorubrum arcis Xu et al. 2007 and Halorubrum litoreum Cui et al. 2007. emended description of Halorubrum distributum Zvyagintseva and Tarasov 1989; Oren and Ventosa 1996. Int J Syst Evol Microbiol 2020; 70:1698–1705 [View Article]
    [Google Scholar]
  49. Thane Papke R. A critique of prokaryotic species concepts. Methods Mol Biol 2009; 532:379–395 [View Article]
    [Google Scholar]
  50. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article]
    [Google Scholar]
  51. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
    [Google Scholar]
  52. Lobasso S, Pérez-Davó A, Vitale R, Sánchez MM, Corcelli A. Deciphering archaeal glycolipids of an extremely halophilic archaeon of the genus Halobellus by MALDI-TOF/MS. Chem Phys Lipids 2015; 186:1–8 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005385
Loading
/content/journal/ijsem/10.1099/ijsem.0.005385
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error