1887

Abstract

The haloarchaeal genera and , belonging to the family , order , class , within the phylum , have previously exhibited significant phylogenetic and taxonomic overlaps. This issue was recently resolved by merging the two genera into a single genus, . However, and were described almost simultaneously with the proposal to unify the genera and . Their names were validly published under the International Code of Nomenclature of Prokaryotes (ICNP) according to Validation List no. 217, alongside six species and the transfer of the existing species into the genus . Therefore a phylogenetic, phylogenomic, and comparative genomic analysis was carried out to clarify the taxonomic status of these two haloarchaeal species, and , with lower priority than the six new species of the genus . Phylogenetic studies of 16S rRNA and gene sequences, along with phylogenomic reconstructions using single-copy core-orthologous proteins, indicated that the two species clustered with the members of the genus . The overall genome relatedness indexes (OGRIs), comparative analyses of phenotypic features, and polar lipid profiles further supported their taxonomic reassignment as two separate species within the genus . Consequently, we propose the reclassification of Straková . 2024 and Straková . 2024 into the genus , as comb. nov. and comb. nov., respectively, in accordance with the ICNP.

Funding
This study was supported by the:
  • Ministerio de Universidades (Award PID2020-118136GB-I00)
    • Principle Award Recipient: AntonioVentosa
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006510
2024-09-16
2024-11-05
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/74/9/ijsem006510.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.006510&mimeType=html&fmt=ahah

References

  1. Torreblanca M, Rodriguez-Valera F, Juez G, Ventosa A, Kamekura M et al. Classification of non-alkaliphilic halobacteria based on numerical taxonomy and polar lipid composition, and description of Haloarcula gen. nov. and Haloferax gen. nov. Syst Appl Microbiol 1986; 8:89–99 [View Article]
    [Google Scholar]
  2. Echigo A, Minegishi H, Shimane Y, Kamekura M, Itoh T et al. Halomicroarcula pellucida gen. nov., sp. nov., a non-pigmented, transparent-colony-forming, halophilic archaeon isolated from solar salt. Int J Syst Evol Microbiol 2013; 63:3556–3562 [View Article] [PubMed]
    [Google Scholar]
  3. Durán-Viseras A, Sánchez-Porro C, Ventosa A. Genomic insights into new species of the genus Halomicroarcula reveals potential for new osmoadaptative strategies in halophilic archaea. Front Microbiol 2021; 12:751746 [View Article] [PubMed]
    [Google Scholar]
  4. Ma X, Hu Y, Li X-X, Tan S, Cheng M et al. Genome-based taxonomy of genera Haloarcula and Halomicroarcula, and description of six novel species of Haloarcula. Extremophiles 2024; 28:10 [View Article]
    [Google Scholar]
  5. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
    [Google Scholar]
  6. Yang Y, Cui HL, Zhou PJ, Liu SJ. Haloarcula amylolytica sp. nov., an extremely halophilic archaeon isolated from Aibi salt lake in Xin-Jiang, China. Int J Syst Evol Microbiol 2007; 57:103–106 [View Article] [PubMed]
    [Google Scholar]
  7. Ihara K, Watanabe S, Tamura T. Haloarcula argentinensis sp. nov. and Haloarcula mukohataei sp. nov., two new extremely halophilic archaea collected in Argentina. Int J Syst Bacteriol 1997; 47:73–77 [View Article] [PubMed]
    [Google Scholar]
  8. Juez G, Rodriguez-Valera F, Ventosa A, Kushner DJ. Haloarcula hispanica spec. nov. and Haloferax gibbonsii spec. nov., two new species of extremely halophilic archaebacteria. Syst Appl Microbiol 1986; 8:75–79 [View Article]
    [Google Scholar]
  9. Takashina T, Hamamoto T, Otozai K, Grant WD, Horikoshi K. Haloarcula japonica sp. nov., a new triangular halophilic archaebacterium. Syst Appl Microbiol 1990; 13:177–181 [View Article]
    [Google Scholar]
  10. Enomoto S, Shimane Y, Ihara K, Kamekura M, Itoh T et al. Haloarcula mannanilytica sp. nov., a galactomannan-degrading haloarchaeon isolated from commercial salt. Int J Syst Evol Microbiol 2020; 70:6331–6337 [View Article] [PubMed]
    [Google Scholar]
  11. Oren A, Ginzburg M, Ginzburg BZ, Hochstein LI, Volcani BE. Haloarcula marismortui (Volcani) sp. nov., nom. rev., an extremely halophilic bacterium from the Dead Sea. Int J Syst Bacteriol 1990; 40:209–210 [View Article] [PubMed]
    [Google Scholar]
  12. Ma X, Hu Y, Li X-X, Tan S, Cheng M et al. Halomicroarcula laminariae sp. nov. and Halomicroarcula marina sp. nov., extremely halophilic archaea isolated from salted brown alga Laminaria and coastal saline-alkali lands. Int J Syst Evol Microbiol 2023; 73:5889 [View Article] [PubMed]
    [Google Scholar]
  13. Barreteau H, Vandervennet M, Guédon L, Point V, Canaan S et al. Haloarcula sebkhae sp. nov., an extremely halophilic archaeon from Algerian hypersaline environment. Int J Syst Evol Microbiol 2019; 69:732–738 [View Article] [PubMed]
    [Google Scholar]
  14. Straková D, Galisteo C, de la Haba RR, Ventosa A. Characterization of Haloarcula terrestris sp. nov. and reclassification of a Haloarcula species based on a taxogenomic approach. Int J Syst Evol Microbiol 2023; 73:006157 [View Article] [PubMed]
    [Google Scholar]
  15. Oren A, Ventosa A, Gutiérrez MC, Kamekura M. Haloarcula quadrata sp. nov., a square, motile archaeon isolated from a brine pool in Sinai (Egypt). Int J Syst Bacteriol 1999; 49:1149–1155 [View Article] [PubMed]
    [Google Scholar]
  16. Namwong S, Tanasupawat S, Kudo T, Itoh T. Haloarcula salaria sp. nov. and Haloarcula tradensis sp. nov., isolated from salt in Thai fish sauce. Int J Syst Evol Microbiol 2011; 61:231–236 [View Article] [PubMed]
    [Google Scholar]
  17. Straková D, Sánchez-Porro C, de la Haba RR, Ventosa A. Decoding the genomic profile of the Halomicroarcula genus: comparative analysis and characterization of two novel species. Microorganisms 2024; 12:334 [View Article] [PubMed]
    [Google Scholar]
  18. Oren A, Göker M. Validation List no. 217. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2024; 74:006275 [View Article] [PubMed]
    [Google Scholar]
  19. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article] [PubMed]
    [Google Scholar]
  20. 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]
  21. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  22. 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]
  23. Felsenstein J. Parsimony in systematics: biological and statistical issues. Annu Rev Ecol Syst 1983; 14:313–333 [View Article]
    [Google Scholar]
  24. Galisteo C. Gitana: phyloGenetic Imaging Tool for Adjusting Nodes and other Arrangements; 2022 https://github.com/cristinagalisteo/gitana accessed 3 June 2022
  25. Riesco R, Trujillo ME. Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2024; 74:006300 [View Article] [PubMed]
    [Google Scholar]
  26. Cui H-L, Hou J, Amoozegar MA, Dyall-Smith ML, de la Haba RR et al. Proposed minimal standards for description of new taxa of the class Halobacteria. Int J Syst Evol Microbiol 2024; 74:006290 [View Article] [PubMed]
    [Google Scholar]
  27. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ 2016; 4:e1900v1 [View Article]
    [Google Scholar]
  28. Edgar RC. Muscle5: high-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny. Nat Commun 2022; 13:6968 [View Article]
    [Google Scholar]
  29. Price MN, Dehal PS, Arkin AP. FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS One 2010; 5:e9490 [View Article] [PubMed]
    [Google Scholar]
  30. 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]
  31. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article]
    [Google Scholar]
  32. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 2013; 14:60 [View Article] [PubMed]
    [Google Scholar]
  33. 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]
  34. 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]
  35. 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]
  36. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article] [PubMed]
    [Google Scholar]
  37. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article] [PubMed]
    [Google Scholar]
  38. Konstantinidis KT, Tiedje JM. Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr Opin Microbiol 2007; 10:504–509 [View Article]
    [Google Scholar]
  39. Gonzalez C, Gutierrez C, Ramirez C. Halobacterium vallismortis sp. nov. an amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 1978; 24:710–715 [View Article] [PubMed]
    [Google Scholar]
  40. Oren A, Arahal DR, Göker M, Moore ERB, Rossello-Mora R et al. International Code of Nomenclature of Prokaryotes. Prokaryotic Code (2022 Revision). Int J Syst Evol Microbiol 2023; 73:005585 [View Article]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006510
Loading
/content/journal/ijsem/10.1099/ijsem.0.006510
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