1887

Abstract

A novel bacterium, strain Seoho-28, was isolated from a shallow eutrophic lake during the end of cyanobacterial harmful algal blooms and was characterized taxonomically and phylogenetically. Strain Seoho-28 was a Gram-stain-negative, aerobic, rod-shaped and non-motile bacterium. The strain grew optimally with 0 % NaCl and at 25–30 °C on Reasoner's 2A medium. The phylogenetic analysis based on 16S rRNA gene sequences positioned the novel strain among the order , but sequence similarities to known species were less than 94.7 %. The genomic DNA G+C content of the strain Seoho-28 was 74.2 mol%. Genomic comparisons of strain Seoho-28 with families in the order were made using the Genome-to-Genome Distance Calculator, average nucleotide identity and average amino acid identity analyses (values indicated ≤14.9, ≤73.5 and ≤57.8 %, respectively). Strain Seoho-28 contained C-iso, C 9 and C as major fatty acids and MK-7 (H) as the major quinone. Strain Seoho-28 contained diphosphatidylglycerol, phosphatidylinositol and an unidentified phospholipid as major polar lipids. - and -diaminopimelic acids were the diagnostic diamino acids in the cell-wall peptidoglycan. Based on the genotypic, chemotaxonomic and phenotypic results, strain Seoho-28 represents a novel genus and species, gen. nov., sp. nov., which belongs to a new family in the order and the class . The type strain is Seoho-28 (=KCTC 39791=JCM 31881).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003846
2019-11-07
2019-11-17
Loading full text...

Full text loading...

References

  1. Srivastava A, Singh S, Ahn C-Y, Oh H-M, Asthana RK. Monitoring approaches for a toxic cyanobacterial bloom. Environ Sci Technol 2013;47: 8999– 9013 [CrossRef]
    [Google Scholar]
  2. Woodhouse JN, Kinsela AS, Collins RN, Bowling LC, Honeyman GL et al. Microbial communities reflect temporal changes in cyanobacterial composition in a shallow ephemeral freshwater lake. ISME J 2016;10: 1337– 1351 [CrossRef]
    [Google Scholar]
  3. Cui Y, Jin L, Ko S-R, Chun S-J, Oh H-S et al. Periphyton effects on bacterial assemblages and harmful cyanobacterial blooms in a eutrophic freshwater lake: a mesocosm study. Sci Rep 2017;7: 7827 [CrossRef]
    [Google Scholar]
  4. Reddy GSN, Garcia-Pichel F. Description of Patulibacter americanus sp. nov., isolated from biological soil crusts, emended description of the genus Patulibacter Takahashi et al. 2006 and proposal of Solirubrobacterales ord. nov. and Thermoleophilales ord. nov. Int J Syst Evol Microbiol 2009;59: 87– 94 [CrossRef]
    [Google Scholar]
  5. Takahashi Y, Matsumoto A, Morisaki K, Omura S. Patulibacter minatonensis gen. nov., sp. nov., a novel actinobacterium isolated using an agar medium supplemented with superoxide dismutase, and proposal of Patulibacteraceae fam. nov. Int J Syst Evol Microbiol 2006;56: 401– 406 [CrossRef]
    [Google Scholar]
  6. Foesel BU, Geppert A, Rohde M, Overmann J. Parviterribacter kavangonensis gen. nov., sp. nov. and Parviterribacter multiflagellatus sp. nov., novel members of Parviterribacteraceae fam. nov. within the order Solirubrobacterales, and emended descriptions of the classes Thermoleophilia and Rubrobacteria and their orders and families. Int J Syst Evol Microbiol 2016;66: 652– 665 [CrossRef]
    [Google Scholar]
  7. Zhi X-Y, Li W-J, Stackebrandt E. An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. Int J Syst Evol Microbiol 2009;59: 589– 608 [CrossRef]
    [Google Scholar]
  8. Seki T, Matsumoto A, Ōmura S, Takahashi Y. Distribution and isolation of strains belonging to the order Solirubrobacterales. J Antibiot 2015;68: 763– 766 [CrossRef]
    [Google Scholar]
  9. Dastager SG, Mawlankar R, Mual P, Verma A, Krishnamurthi S et al. Bacillus encimensis sp. nov. isolated from marine sediment. Int J Syst Evol Microbiol 2015;65: 1421– 1425 [CrossRef]
    [Google Scholar]
  10. Tarrand JJ, Groschel DH. Rapid, modified oxidase test for oxidase-variable bacterial isolates. J Clin Microbiol 1982;16: 772– 774
    [Google Scholar]
  11. Bates RG, Bower VE. Alkaline solutions for pH control. Anal Chem 1956;28: 1322– 1324 [CrossRef]
    [Google Scholar]
  12. Gomori G. Preparation of buffers for use in enzyme studies. Methods Enzymol 1955;1: 138– 146
    [Google Scholar]
  13. Sasser M 2001; Identification of bacteria by gas chromatography of cellular fatty acids [database on the Internet]. Available from www.microbialid.com/PDF/TechNote_101.pdf
    [Google Scholar]
  14. Cui Y, Baek S-H, Wang L, Lee H-G, Cui C et al. Streptomyces panacagri sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2012;62: 780– 785 [CrossRef]
    [Google Scholar]
  15. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990;66: 199– 202 [CrossRef]
    [Google Scholar]
  16. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959;37: 911– 917 [CrossRef]
    [Google Scholar]
  17. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl microbiol 1974;28: 226– 231
    [Google Scholar]
  18. Yang N, Ren B, Dai H, Liu Z, Zhou Y et al. Gracilibacillus xinjiangensis sp. nov., a new member of the genus Gracilibacillus isolated from Xinjiang region, China. Antonie van Leeuwenhoek 2013;104: 809– 816 [CrossRef]
    [Google Scholar]
  19. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014;30: 2068– 2069 [CrossRef]
    [Google Scholar]
  20. Thompson J, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997;25: 4876– 4882 [CrossRef]
    [Google Scholar]
  21. Hall TA. Editor BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp Ser 1999;41: 95– 98
    [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
    [Google Scholar]
  23. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17: 368– 376 [CrossRef]
    [Google Scholar]
  24. 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 [CrossRef]
    [Google Scholar]
  25. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39: 783– 791 [CrossRef]
    [Google Scholar]
  26. 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]
    [Google Scholar]
  27. Yoon S-H, Ha S-min, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017;110: 1281– 1286 [CrossRef]
    [Google Scholar]
  28. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008;9: 9– 75 [CrossRef]
    [Google Scholar]
  29. Pulschen AA, Bendia AG, Fricker AD, Pellizari VH, Galante D et al. Isolation of uncultured bacteria from Antarctica using long incubation periods and low nutritional media. Front Microbiol 2017;8: 1346 [CrossRef]
    [Google Scholar]
  30. Gao Q, Garcia-Pichel F. Microbial ultraviolet sunscreens. Nat Rev Microbiol 2011;9: 791– 802 [CrossRef]
    [Google Scholar]
  31. Goris J, Klappenbach JA, Vandamme P, Coenye T, Konstantinidis KT et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007;57: 81– 91 [CrossRef]
    [Google Scholar]
  32. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014;42: e73 [CrossRef]
    [Google Scholar]
  33. Zuo G, Hao B. CVTree3 web server for whole-genome-based and alignment-free prokaryotic phylogeny and taxonomy. Genomics Proteomics Bioinformatics 2015;13: 321– 331 [CrossRef]
    [Google Scholar]
  34. Takahashi Y. Genus Kitasatospora, taxonomic features and diversity of secondary metabolites. J Antibiot 2017;70: 506– 513 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003846
Loading
/content/journal/ijsem/10.1099/ijsem.0.003846
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