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Volume 69, Issue 5

Halonotius aquaticus sp. nov., a new haloarchaeon isolated from a marine saltern Free

Abstract

A halophilic archaeon, strain F13-13, was isolated from a marine saltern located in Isla Cristina, Huelva, on the south-west coast of Spain. It was a Gram-stain-negative, motile and aerobic haloarchaeon. It grew at 28–50 °C (optimum, 37 °C), pH 6.0–8.5 (pH 7.5) and in 15–30 % (w/v) total salts (25 %). Phylogenetic analyses based on the 16S rRNA gene sequences showed that strain F13-13 is a member of the genus Halonotius , the most closely related species being Halonotius pteroides 1.15.5 (96.7 % sequence similarity). The 16S rRNA gene sequence similarity to species of other genera is lower than 93.4 %. Strain F13-13 was also found to be closely related to Halonotius pteroides 1.15.5 (91.4 %) on the basis of rpoB′ gene sequence analysis. The Genome-to-Genome Distance Calculator relatedness result between strain F13-13 and Halonotius pteroides CECT 7525 was 35 %, a value lower than the 70 % threshold accepted for species delineation. The average nucleotide identity values based on OrthoANI, ANIb and ANIm of strain F13-13 and Halonotius pteroides CECT 7525 were 88.7, 87.8 and 89.4 %, respectively, these values are also lower than the threshold accepted for species delineation. The DNA G+C content of this isolate was 61.2 mol%. The major lipids of strain F13-13 were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and sulphated diglycosyl diether. Based on the phylogenetic, phenotypic, genotypic and chemotaxonomic characterization, we propose the placement of strain F13-13 as a new species within the genus Halonotius , with the name Halonotius aquaticus sp. nov. The type strain is F13-13 (=CECT 9386=IBRC-M 11204).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Haloarchaea , Halobacteria , Halonotius and new species
© 2019 IUMS
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2019-02-21
2024-04-19
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References

  1. Burns DG, Janssen PH, Itoh T, Kamekura M, Echigo A et al. Halonotius pteroides gen. nov., sp. nov., an extremely halophilic archaeon recovered from a saltern crystallizer. Int J Syst Evol Microbiol 2010; 60:1196–1199 [View Article][PubMed]
     [Google Scholar]
  2. Parte AC. LPSN-List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article][PubMed]
     [Google Scholar]
  3. Han R, Zhang X, Liu J, Long Q, Chen L et al. Microbial community structure and diversity within hypersaline Keke Salt Lake environments. Can J Microbiol 2017; 63:895–908 [View Article][PubMed]
     [Google Scholar]
  4. Çınar S, Mutlu MB. Comparative analysis of prokaryotic diversity in solar salterns in eastern Anatolia (Turkey). Extremophiles 2016; 20:589–601 [View Article][PubMed]
     [Google Scholar]
  5. Henriet O, Fourmentin J, Delincé B, Mahillon J. Exploring the diversity of extremely halophilic archaea in food-grade salts. Int J Food Microbiol 2014; 191:36–44 [View Article][PubMed]
     [Google Scholar]
  6. Podell S, Emerson JB, Jones CM, Ugalde JA, Welch S et al. Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community. ISME J 2014; 8:979–990 [View Article][PubMed]
     [Google Scholar]
  7. Subow NN. Oceanographical tables. commissariat of agriculture of usSR. Hydro-Meteorological Committee of USSR Moscow: Oceanographical Institute of USSR; 1931
     [Google Scholar]
  8. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961; 3:208–IN1 [View Article]
     [Google Scholar]
  9. Sambrook J, Russell DW. (editors) Molecular Cloning: A Laboratory Manual Cold Spring Harbor, NY: Laboratory Press; 2001
     [Google Scholar]
  10. Delong EF. Archaea in coastal marine environments. Proc Natl Acad Sci USA 1992; 89:5685–5689 [View Article][PubMed]
     [Google Scholar]
  11. Arahal DR, Dewhirst FE, Paster BJ, Volcani BE, Ventosa A. Phylogenetic analyses of some extremely halophilic archaea isolated from Dead Sea water, determined on the basis of their 16S rRNA sequences. Appl Environ Microbiol 1996; 62:3779–3786[PubMed]
     [Google Scholar]
  12. Fullmer MS, Soucy SM, Swithers KS, Makkay AM, Wheeler R et al. Population and genomic analysis of the genus Halorubrum. Front Microbiol 2014; 5:140 [View Article][PubMed]
     [Google Scholar]
  13. Yoon SH, Ha SM, 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]
  14. Ludwig W, Strunk O, Westram R, Richter L, Meier H et al. ARB: a software environment for sequence data. Nucleic Acids Res 2004; 32:1363–1371 [View Article][PubMed]
     [Google Scholar]
  15. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
     [Google Scholar]
  16. 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]
  17. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  18. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  19. 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][PubMed]
     [Google Scholar]
  20. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article][PubMed]
     [Google Scholar]
  21. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821–829 [View Article][PubMed]
     [Google Scholar]
  22. Nurk S, Bankevich A, Antipov D, Gurevich A, Korobeynikov A et al. Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads. Res Comput Mol Bio 2013158–170
     [Google Scholar]
  23. Haft DH, Dicuccio M, Badretdin A, Brover V, Chetvernin V et al. RefSeq: an update on prokaryotic genome annotation and curation. Nucleic Acids Res 2018; 46:D851–D860 [View Article][PubMed]
     [Google Scholar]
  24. Lee I, Ouk Kim Y, Park SC, 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]
  25. 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]
  26. 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]
  27. Stackebrandt E, Goebel BM. Taxonomic note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994; 44:846–849 [View Article]
     [Google Scholar]
  28. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PA, Kämpfer P et al. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 2002; 52:1043–1047 [View Article][PubMed]
     [Google Scholar]
  29. 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]
  30. 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]
  31. Dussault HP. An improved technique for staining red halophilic bacteria. J Bacteriol 1955; 70:484–485[PubMed]
     [Google Scholar]
  32. Scorpio R. Fundamentals of Acids, Bases, Buffers and Their Application to Biochemical Systems Kendall/Hunt Publishing Company; 2000
     [Google Scholar]
  33. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703 [View Article][PubMed]
     [Google Scholar]
  34. Barrow GI, Feltham RKA. Steel's Manual for the Identification of Medical Bacteria, 3rd ed. Cambridge: Cambridge University Press; 2003
     [Google Scholar]
  35. Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washintong, DC: American Society for Microbiology; 1994
     [Google Scholar]
  36. Smibert RM. Krieg NR General characterization. In Gerhardt P, Murray RGE, Costilow EW, Nester Wood WA, Krieg NR et al. (editors) Manual of Methods for General Bacteriology Washintong, DC: American Society for Microbiology; 1981 pp. 409–443
     [Google Scholar]
  37. Ventosa A, Quesada E, Rodriguez-Valera F, Ruiz-Berraquero F, Ramos-Cormenzana A. Numerical taxonomy of moderately halophilic Gram-negative rods. Microbiology 1982; 128:1959–1968 [View Article]
     [Google Scholar]
  38. Bauer AW, Kirby WM, Sherris JC, Turck M. Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 1966; 45:493–496 [View Article][PubMed]
     [Google Scholar]
  39. Corcelli A, Lobasso S. Characterization of lipids of halophilic archaea. In Rainey FA, Oren A. (editors) Methods in Microbiology, Extremophiles Amsterdam: Elsevier/Academic; 2006 pp. 585–613
     [Google Scholar]
  40. Angelini R, Corral P, Lopalco P, Ventosa A, Corcelli A. Novel ether lipid cardiolipins in archaeal membranes of extreme haloalkaliphiles. Biochim Biophys Acta 2012; 1818:1365–1373 [View Article][PubMed]
     [Google Scholar]
  41. Corral P, Gutiérrez MC, Castillo AM, Domínguez M, Lopalco P et al. Natronococcus roseus sp. nov., a haloalkaliphilic archaeon from a hypersaline lake. Int J Syst Evol Microbiol 2013; 63:104–108 [View Article][PubMed]
     [Google Scholar]
  42. Kates M. Techniques of lipidology, laboratory techniques. In Burdon RH, van Knippenberg PH. (editors) Biochemistry and Molecular Biology Amsterdam: Elsevier; 1986 pp. 100–110
     [Google Scholar]
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Halonotius aquaticus sp. nov., a new haloarchaeon isolated from a marine saltern
Int J Syst Evol Microbiol 69, 1306 (2019); https://doi.org/10.1099/ijsem.0.003309
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