1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 4

sp. nov., sp. nov. and sp. nov., isolated from salted brown alga No Access

Abstract

Four halophilic archaeal strains, designated HD8-83, LYG-36, DLLS-82 and RC-68, were isolated from the salted brown alga of three different origins (Dalian, Lianyungang, Dalian and Rongcheng) in PR China. All strains had pleomorphic rod cells that were motile, lysed in distilled water, stained Gram-negative, and formed red-pigmented colonies on agar plate (except for DLLS-82, which formed white colonies). Based on phylogenetic analyses of the 16S rRNA genes, strain HD8-83 was closely related to HD8-51 (97.9 % similarity), strain LYG-36 and DLLS-82 to TBN4 (94.4 % and 94.7 % similarities, respectively), and strain RC-68 to YJ-37-H (96.9 % similarity). Results of phylogenetic analyses based on genes and 728 concatenated single-copy orthologous clusters also showed that these strains formed three different branches and clustered tightly with the members. The average nucleotide identity, average amino acid identity and DNA–DNA hybridization values between strains LYG-36 and DLLS-82 were 98.9, 98 and 92.4%, showing that they were different strains of the same species. While those values between the isolates and other members were below 84.7, 82.9 and 28.9 %, respectively. Based on the phenotypic, chemotaxonomic and phylogenetic properties, strains HD8-83, LYG-36, DLLS-82 and RC-68 represent three novel species of the genus for which the names sp. nov. (type strain: HD8-83=CGMCC 1.15334=JCM 31110), sp. nov. (type strain: LYG-36=CGMCC 1.13606=JCM 32952; reference strain: DLLS-82=CGMCC 1.13604=JCM 32951) and sp. nov. (type strain: RC-68=CGMCC 1.13609=JCM 32953) are proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): halophilic archaea , Halorussus halobius sp. nov. , Halorussus marinus sp. nov. , Halorussus pelagicus sp. nov. , Laminaria and salted brown alga
Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 31770005)
    • Principle Award Recipient: Heng-LinCui
© 2022 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005313
2022-04-07
2024-04-26
Loading full text...

Full text loading...

References

  1. Taormina PJ. Implications of salt and sodium reduction on microbial food safety. Crit Rev Food Sci Nutr 2010; 50:209–227 [View Article] [PubMed]
     [Google Scholar]
  2. Wei W, Zhang X, Hou Z, Hu X, Wang Y et al. Microbial regulation of deterioration and preservation of salted kelp under different temperature and salinity conditions. Foods 2021; 10:1723 [View Article] [PubMed]
     [Google Scholar]
  3. Yadav AN, Sharma D, Gulati S, Singh S, Dey R et al. Haloarchaea endowed with phosphorus solubilization attribute implicated in phosphorus cycle. Sci Rep 2015; 5:12293 [View Article] [PubMed]
     [Google Scholar]
  4. 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]
  5. 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]
  6. Yuan P-P, Ye W-T, Pan J-X, Han D, Zhang W-J et al. Halorussus amylolyticus sp. nov., isolated from an inland salt lake. Int J Syst Evol Microbiol 2015; 65:3734–3738 [View Article] [PubMed]
     [Google Scholar]
  7. Yuan P-P, Yin S, Han D, Zhang W-J, Cui H-L. Halorussus ruber sp. nov., isolated from an inland salt lake of cchina. Arch Microbiol 2015; 197:91–95
     [Google Scholar]
  8. Xu J-Q, Xu W-M, Li Y, Zhou Y, Lü Z-Z et al. Halorussus salinus sp. nov., isolated from a marine solar saltern. Arch Microbiol 2016; 198:957–961 [View Article]
     [Google Scholar]
  9. 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] [PubMed]
     [Google Scholar]
  10. Ding Y, Han D, Cui H-L. Halorussus halophilus sp. nov., A Novel Halophilic Archaeon Isolated from A Marine Solar Saltern. Curr Microbiol 2020; 77:1321–1327 [View Article] [PubMed]
     [Google Scholar]
  11. 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]
  12. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012; 1:18 [View Article] [PubMed]
     [Google Scholar]
  13. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
     [Google Scholar]
  14. 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] [PubMed]
     [Google Scholar]
  15. 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] [PubMed]
     [Google Scholar]
  16. 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 Bʹ (rpoBʹ) gene. Int J Syst Evol Microbiol 2010; 60:2398–2408 [View Article] [PubMed]
     [Google Scholar]
  17. Tamura K, Stecher G, Peterson DS, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article]
     [Google Scholar]
  18. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  19. 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]
  20. 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]
  21. 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] [PubMed]
     [Google Scholar]
  22. Li L, Stoeckert CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 2003; 13:2178–2189 [View Article] [PubMed]
     [Google Scholar]
  23. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
     [Google Scholar]
  24. 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] [PubMed]
     [Google Scholar]
  25. 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]
  26. 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]
  27. Luo CW, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:e73 [View Article] [PubMed]
     [Google Scholar]
  28. 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] [PubMed]
     [Google Scholar]
  29. Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 2016; 428:726–731 [View Article] [PubMed]
     [Google Scholar]
  30. 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] [PubMed]
     [Google Scholar]
  31. Kim M, Oh HS, Park SC, 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]
  32. 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]
  33. 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]
  34. 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]
  35. 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; 50:183–190 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005313
Loading
Halorussus halobius sp. nov., Halorussus marinus sp. nov. and Halorussus pelagicus sp. nov., isolated from salted brown alga Laminaria
Int J Syst Evol Microbiol 72, 005313 (2022); https://doi.org/10.1099/ijsem.0.005313
/content/journal/ijsem/10.1099/ijsem.0.005313
/content/journal/ijsem/10.1099/ijsem.0.005313
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

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