1887

Abstract

A filamentous cell-shaped halophilic archaeon (strain AD-1) was isolated from Aiding Salt Lake, PR China. Its colonies on HCM7 agar plates were pinkish white, 1–4 mm (diameter), elevated and round. The optimum conditions for growth were observed at 42 °C, 4.3 M NaCl, 0.01 M MgCl and pH 7. Strain AD-1 could hydrolyse Tween 60, Tween 80, starch and gelatin. Phylogenetic analysis based on 16S rRNA gene, rpoB′ and the concatenated 484 single-copy orthologous proteins revealed that strain AD-1 formed a clade with SPP-AMP-1. The average nucleotide identity and DNA–DNA hybridization values between strain AD-1 and SPP-AMP-1 were both below the species delineation thresholds (95~96 and 70 %, respectively). The major phospholipids of strain AD-1 were phosphatidic acid, phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, while the major glycolipids were sulphated galactosyl mannosyl glucosyl diether, galactosyl mannosyl glucosyl diether and glucosyl mannosyl glucosyl diether. The phenotypic, phylogenetic and genome-based analyses suggested that strain AD-1 (=CGMCC 1.13724=JCM 32960) represents a novel species, 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.0.005637
2022-12-16
2024-05-09
Loading full text...

Full text loading...

References

  1. Cui H-L, 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. Oren A. Microbial life at high salt concentrations: phylogenetic and metabolic diversity. Saline Syst 2008; 4:1–13 [View Article] [PubMed]
    [Google Scholar]
  3. Xin Y-J, Bao C-X, Li S-Y, Hu X-Y, Zhu L et al. Genome-based taxonomy of genera Halomicrobium and Halosiccatus, and description of Halomicrobium salinisoli sp. nov. Syst Appl Microbiol 2022; 45:126308 [View Article]
    [Google Scholar]
  4. Sorokin DY, Kublanov IV, Yakimov MM, Rijpstra WIC, Sinninghe Damsté JS. Halanaeroarchaeum sulfurireducens gen. nov., sp. nov., the first obligately anaerobic sulfur-respiring haloarchaeon, isolated from a hypersaline lake. Int J Syst Evol Microbiol 2016; 66:2377–2381 [View Article] [PubMed]
    [Google Scholar]
  5. Sorokin DY, Messina E, Smedile F, Roman P, Damsté JSS et al. Discovery of anaerobic lithoheterotrophic haloarchaea, ubiquitous in hypersaline habitats. ISME J 2017; 11:1245–1260 [View Article] [PubMed]
    [Google Scholar]
  6. Verma A, Pal Y, Kumar P, Krishnamurthi S. Halocatena pleomorpha gen. nov. sp. nov., an extremely halophilic archaeon of family Halobacteriaceae isolated from saltpan soil. Int J Syst Evol Microbiol 2020; 70:3693–3700 [View Article]
    [Google Scholar]
  7. Han D, Cui H-L. 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]
  8. Tao C-Q, Ding Y, Zhao Y-J, Cui H-L. Natronorubrum halophilum sp. nov. isolated from two inland salt lakes. J Microbiol 2020; 58:105–112 [View Article] [PubMed]
    [Google Scholar]
  9. Cui H-L, Yang X, Mou Y-Z. 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]
  10. Cui H-L, Zhou P-J, Oren A, Liu S-J. Intraspecific polymorphism of 16S rRNA genes in two halophilic archaeal genera, Haloarcula and Halomicrobium. Extremophiles 2009; 13:31–37 [View Article]
    [Google Scholar]
  11. 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 B’ (rpoB’) gene. Int J Syst Evol Microbiol 2010; 60:2398–2408 [View Article]
    [Google Scholar]
  12. 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]
    [Google Scholar]
  13. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article]
    [Google Scholar]
  14. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  15. 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]
  16. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
    [Google Scholar]
  17. Lagkouvardos I, Joseph D, Kapfhammer M, Giritli S, Horn M et al. IMNGS: a comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies. Sci Rep 2016; 6:1–9 [View Article] [PubMed]
    [Google Scholar]
  18. 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]
  19. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:1–14 [View Article] [PubMed]
    [Google Scholar]
  20. 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]
    [Google Scholar]
  21. Qin Q-L, Xie B-B, Zhang X-Y, Chen X-L, Zhou B-C et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article] [PubMed]
    [Google Scholar]
  22. 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]
  23. Zhao Y, Wu J, Yang J, Sun S, Xiao J et al. PGAP: pan-genomes analysis pipeline. Bioinformatics 2012; 28:416–418 [View Article] [PubMed]
    [Google Scholar]
  24. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M et al. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 2006; 34:D354–7 [View Article]
    [Google Scholar]
  25. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:1–15 [View Article] [PubMed]
    [Google Scholar]
  26. Xu L, Dong Z, Fang L, Luo Y, Wei Z et al. OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res 2019; 47:W52–W58 [View Article]
    [Google Scholar]
  27. 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]
  28. Cui H-L, Gao X, Yang X, Xu X-W. 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]
  29. 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]
  30. 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]
    [Google Scholar]
  31. 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] [PubMed]
    [Google Scholar]
  32. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 2009; 106:19126–19131 [View Article]
    [Google Scholar]
  33. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
    [Google Scholar]
  34. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci 2005; 102:2567–2572 [View Article]
    [Google Scholar]
  35. Grim CJ, Kotewicz ML, Power KA, Gopinath G, Franco AA et al. Pan-genome analysis of the emerging foodborne pathogen Cronobacter spp. suggests a species-level bidirectional divergence driven by niche adaptation. BMC Genomics 2013; 14:1–16 [View Article] [PubMed]
    [Google Scholar]
  36. Chan JZ-M, Halachev MR, Loman NJ, Constantinidou C, Pallen MJ. Defining bacterial species in the genomic era: insights from the genus Acinetobacter. BMC Microbiol 2012; 12:1–11 [View Article] [PubMed]
    [Google Scholar]
  37. Han J, Lu Q, Zhou L, Zhou J, Xiang H. Molecular characterization of the phaECHm genes, required for biosynthesis of poly(3-hydroxybutyrate) in the extremely halophilic archaeon Haloarcula marismortui. Appl Environ Microbiol 2007; 73:6058–6065 [View Article] [PubMed]
    [Google Scholar]
  38. Quillaguamán J, Guzmán H, Van-Thuoc D, Hatti-Kaul R. Synthesis and production of polyhydroxyalkanoates by halophiles: current potential and future prospects. Appl Microbiol Biotechnol 2010; 85:1687–1696 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005637
Loading
/content/journal/ijsem/10.1099/ijsem.0.005637
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