1887

Abstract

A novel Gram-stain-negative, aerobic and rod-shaped halophilic archaeon, designated HD8-45, was isolated from the red brine of salted brown alga produced at Dalian, PR China. According to the results of 16S rRNA gene and gene sequence comparisons, strain HD8-45 showed the highest sequence similarity to the corresponding genes of YGH44 (95.1 and 85.2 % similarities, respectively), EB27 (91.2 and 86.0 % similarities, respectively). The low sequence similarity and the phylogeny implied the novel generic status of strain HD8-45. Genomic relatedness analyses showed that strain HD8-45 were clearly distinguished from other species in the order , with average nucleotide identity, amino acid identity and DNA–DNA hybridization values not more than 75.1, 65.6 and 21.5 %. The polar lipid pattern contained phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, two major glycolipids and two minor glycolipids. The two major glycolipids and a minor glycolipid were chromatographically identical to disulfated mannosyl glucosyl diether, sulfated mannosyl glucosyl diether and mannosyl glucosyl diether, respectively. The major respiratory quinones were menaquinone MK-8 and MK-8(H). The DNA G+C content was 62.0 mol% () and 61.9 mol% (genome). All these results showed that strain HD8-45 represents a novel species of a new genus in the order , for which the name gen. nov., sp. nov. is proposed. The type strain of is HD8-45 (=CGMCC 1.15328=JCM 31107).

Funding
This study was supported by the:
  • National Science & Technology Infrastructure Program of China (Award 2017FY100302)
    • Principle Award Recipient: Heng-Lin Cui
  • National Natural Science Foundation of China (Award 31770005)
    • Principle Award Recipient: Heng-Lin Cui
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004114
2020-03-26
2024-04-27
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/4/2879.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004114&mimeType=html&fmt=ahah

References

  1. Oren A. Microbial life at high salt concentrations: phylogenetic and metabolic diversity. Saline Systems 2008; 4:2 [View Article]
    [Google Scholar]
  2. 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]
    [Google Scholar]
  3. 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]
  4. Zhang W-J, Cui H-L. Halomicroarcula salina sp. nov., isolated from a marine solar saltern. Int J Syst Evol Microbiol 2015; 65:1628–1633 [View Article]
    [Google Scholar]
  5. Makhdoumi-Kakhki A, Amoozegar MA, Bagheri M, Ramezani M, Ventosa A. Haloarchaeobius iranensis gen. nov., sp. nov., an extremely halophilic archaeon isolated from a saline lake. Int J Syst Evol Microbiol 2012; 62:1021–1026 [View Article]
    [Google Scholar]
  6. Chen S, Xu Y, Liu H-C, Yang A-N, Ke L-X. Halobaculum roseum sp. nov., isolated from underground salt deposits. Int J Syst Evol Microbiol 2017; 67:818–823 [View Article]
    [Google Scholar]
  7. Chen S, Xu Y, Sun S, Liu J, Chen F. Halomicrococcus hydrotolerans gen. nov., sp. nov., an extremely halophilic archaeon isolated from a subterranean salt deposit. Int J Syst Evol Microbiol 2020
    [Google Scholar]
  8. Durán-Viseras A, Sánchez-Porro C, Ventosa A. Halorientalis pallida sp. nov., an extremely halophilic archaeon isolated from a marine saltern. Int J Syst Evol Microbiol 2019; 69:3636–3643 [View Article]
    [Google Scholar]
  9. Cui H-L, Mou Y-Z, Yang X, Zhou Y-G, Liu H-C et al. Halorubellus salinus gen. nov., sp. nov. and Halorubellus litoreus sp. nov., novel halophilic archaea isolated from a marine solar saltern. Syst Appl Microbiol 2012; 35:30–34 [View Article]
    [Google Scholar]
  10. Han D, Zhu L, Cui H-L. Halorussus litoreus sp. nov., isolated from the salted brown alga Laminaria . Int J Syst Evol Microbiol 2019; 69:767–772 [View Article]
    [Google Scholar]
  11. Yuan P-P, Xu J-Q, Xu W-M, Wang Z, Yin S et al. Halosimplex litoreum sp. nov., isolated from a marine solar saltern. Antonie van Leeuwenhoek 2015; 108:483–489 [View Article]
    [Google Scholar]
  12. Han D, Hong L-G, Xu Q, Cui H-L. Halostella limicola sp. nov., isolated from saline soil sampled at the Tarim Basin. Int J Syst Evol Microbiol 2019; 69:3299–3304 [View Article]
    [Google Scholar]
  13. Han D, Zhang W-J, Cui H-L, Li Z-R. Halovenus rubra sp. nov., isolated from salted brown alga Laminaria . Curr Microbiol 2015; 70:91–95 [View Article]
    [Google Scholar]
  14. Qiu X-X, Zhao M-L, Cui H-L. Natronoarchaeum rubrum sp. nov., isolated from a marine solar saltern, and emended description of the genus Natronoarchaeum . Int J Syst Evol Microbiol 2014; 64:952–956 [View Article]
    [Google Scholar]
  15. Boucher Y, Douady CJ, Sharma AK, Kamekura M, Doolittle WF. Intragenomic heterogeneity and intergenomic recombination among haloarchaeal rRNA genes. J Bacteriol 2004; 186:3980–3990 [View Article]
    [Google Scholar]
  16. Cui H-L, Z-Z, Li Y, Zhou Y. Salinirussus salinus gen. nov., sp. nov., isolated from a marine solar saltern. Int J Syst Evol Microbiol 2017; 67:3622–3626 [View Article]
    [Google Scholar]
  17. Baati H, Guermazi S, Amdouni R, Gharsallah N, Sghir A et al. Prokaryotic diversity of a Tunisian multipond solar saltern. Extremophiles 2008; 12:505–518 [View Article]
    [Google Scholar]
  18. 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]
  19. 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]
  20. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
    [Google Scholar]
  21. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article]
    [Google Scholar]
  22. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
    [Google Scholar]
  23. 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]
  24. 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]
    [Google Scholar]
  25. Vreeland RH, Straight S, Krammes J, Dougherty K, Rosenzweig WD et al. Halosimplex carlsbadense gen. nov., sp. nov., a unique halophilic archaeon, with three 16S rRNA genes, that grows only in defined medium with glycerol and acetate or pyruvate. Extremophiles 2002; 6:445–452 [View Article]
    [Google Scholar]
  26. Minegishi H, Kamekura M, Kitajima-Ihara T, Nakasone K, Echigo A et al. Gene orders in the upstream of 16S rRNA genes divide genera of the family Halobacteriaceae into two groups. Int J Syst Evol Microbiol 2012; 62:188–195 [View Article]
    [Google Scholar]
  27. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with glimmer. Bioinformatics 2007; 23:673–679 [View Article]
    [Google Scholar]
  28. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res 2004; 32:277D–280 [View Article]
    [Google Scholar]
  29. Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000; 28:33–36 [View Article]
    [Google Scholar]
  30. Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B et al. UniProt: the universal protein knowledgebase. Nucleic Acids Res 2004; 32:115D–119 [View Article]
    [Google Scholar]
  31. Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P et al. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res 2017; 45:D566–D573 [View Article]
    [Google Scholar]
  32. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964 [View Article]
    [Google Scholar]
  33. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article]
    [Google Scholar]
  34. Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 2007; 35:W52–W57 [View Article]
    [Google Scholar]
  35. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article]
    [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]
    [Google Scholar]
  37. 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 [View Article]
    [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]
    [Google Scholar]
  39. Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article]
    [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]
    [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]
    [Google Scholar]
  42. Marmur J, Doty P. Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 1962; 5:109–118 [View Article]
    [Google Scholar]
  43. Infante-Domínguez C, Corral P, Sánchez-Porro C, Ventosa A. Halovenus salina sp. nov., an extremely halophilic archaeon isolated from a saltern. Int J Syst Evol Microbiol 2015; 65:3016–3023 [View Article]
    [Google Scholar]
  44. 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]
  45. 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 [View Article]
    [Google Scholar]
  46. 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]
    [Google Scholar]
  47. 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]
  48. 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]
    [Google Scholar]
  49. 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 Pt 1:183–190 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004114
Loading
/content/journal/ijsem/10.1099/ijsem.0.004114
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