1887

Abstract

The genus , currently including four species, is a member of the order , class and consists of obligately alkaliphilic and extremely halophilic members found exclusively in highly alkaline hypersaline soda lakes. The species were classified into this genus mostly based on phylogenetic analysis of the 16S rRNA gene. However, a more advanced phylogenomic reconstruction based on 122 conserved single-copy archaeal protein markers clearly indicates a polyphyletic origin of the species included into this genus, thus warranting its reclassification into three separate genera. We therefore propose to transfer (type strain N-1311) to a new genus as comb. nov. and to transfer (type strain JW/NM-HA 15) and (type strain AArc1) to a new genus as comb. nov. and comb. nov. The phylogenomic differentiation of these four species is also supported by the ANI/AAI distances and unique phenotypes. The most important physiological differences includes a previously unreported ability for cellulose and xylan utilization in , thermophily in and anaerobic sulfur respiration in . We further present an emended description of .

Funding
This study was supported by the:
  • Mikhail M. Yakimov , H2020 European Research Council () , (Award H2020-BG-2014-2)
  • Alexander Y. Merkel , Russian Science Foundation , (Award 17-7430025)
  • Dimitry Y Sorokin , Российский Фонд Фундаментальных Исследований (РФФИ) , (Award 19-04-00401)
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2020-05-06
2020-06-04
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References

  1. Itoh T, Yamaguchi T, Zhou P, Takashina T. Natronolimnobius baerhuensis gen. nov., sp. nov. and Natronolimnobius innermongolicus sp. nov., novel haloalkaliphilic archaea isolated from soda lakes in Inner Mongolia, China. Extremophiles 2005; 9:111–116 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  2. Itoh T. Natronolimnobius. Bergey's Manual of Systematic of Bacteria and Archaea Published by John Wiley & Sons, Inc., in association with Bergey’s Manual Trust; 2016
    [Google Scholar]
  3. Gupta RS, Naushad S, Baker S. Phylogenomic analyses and molecular signatures for the class Halobacteria and its two major clades: a proposal for division of the class Halobacteria into an emended order Halobacteriales and two new orders, Haloferacales ord. nov. and Natrialbales ord. nov., containing the novel families Haloferacaceae fam. nov. and Natrialbaceae fam. nov. Int J Syst Evol Microbiol 2015; 65:1050–1069 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  4. Zhao B, Hu Q, Guo X, Liao Z, Sarmiento F et al. Natronolimnobius aegyptiacus sp. nov., an extremely halophilic alkalithermophilic archaeon isolated from the athalassohaline Wadi an Natrun, Egypt. Int J Syst Evol Microbiol 2018; 68:498–506 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  5. Sorokin DY, Messina E, La Cono V, Ferrer M, Ciordia S et al. Sulfur respiration in a group of facultatively anaerobic natronoarchaea ubiquitous in hypersaline soda lakes. Front Microbiol 2018; 9:2359 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  6. Sorokin DY, Yakimov M, Messina E, Merkel AY, Bale NJ et al. Natronolimnobius sulfurireducens sp. nov. and Halalkaliarchaeum desulfuricum gen. nov., sp. nov., the first sulfur-respiring alkaliphilic haloarchaea from hypersaline alkaline lakes. Int J Syst Evol Microbiol 2019; 69:2662–2673 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  7. Sorokin DY, Elcheninov AG, Toshchakov SV, Bale NJ, Sinninghe Damsté JS et al. Natrarchaeobius chitinivorans gen. nov., sp. nov., and Natrarchaeobius halalkaliphilus sp. nov., alkaliphilic, chitin-utilizing haloarchaea from hypersaline alkaline lakes. Syst Appl Microbiol 2019; 42:309–318 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  8. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018; 36:996–1004 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  9. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  10. Nakamura T, Yamada KD, Tomii K, Katoh K. Parallelization of MAFFT for large-scale multiple sequence alignments. Bioinformatics 2018; 34:2490–2492 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  11. 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 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  12. Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010; 59:307–321 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  13. Anisimova M, Gascuel O. Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. Syst Biol 2006; 55:539–552 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  14. Lefort V, Longueville J-E, Gascuel O. Sms: smart model selection in PhyML. Mol Biol Evol 2017; 34:2422–2424 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  15. 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 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  16. Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28:1823–1829 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  17. 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; 14:60 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  18. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe 2014; 9:111–118 [CrossRef]
    [Google Scholar]
  19. Sorokin DY, Toshchakov SV, Kolganova TV, Kublanov IV. Halo(natrono)archaea isolated from hypersaline lakes utilize cellulose and chitin as growth substrates. Front Microbiol 2015; 6:942 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  20. Bale NJ, Sorokin DY, Hopmans EC, Koenen M, Rijpstra WIC et al. New insights into the polar lipid composition of halophilic euryarchaea from hyper saline lakes. Front Microbiol 2019; 10:377 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  21. Grant BD, Jones BE. Bacteria, archaea and viruses of soda lakes. In Schagerl M. editor Soda lakes of East Africa Switzerland: Springer; 2016 pp 97–147
    [Google Scholar]
  22. Sorokin DY, Khijniak TV, Kostrikina NA, Elcheninov AG, Toshchakov SV et al. Natronobiforma cellulositropha gen. nov., sp. nov., a novel haloalkaliphilic member of the family Natrialbaceae (class Halobacteria) from hypersaline alkaline lakes. Syst Appl Microbiol 2018; 41:355–362 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  23. Sorokin DY, Kublanov IV, Elcheninov AG, Oren A. Natronobiforma. Bergey's Manual of Systematic of Bacteria and Archaea Published by John Wiley & Sons, Inc., in association with Bergey’s Manual Trust; 2019
    [Google Scholar]
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