1887

Abstract

A Gram-stain positive, pleomorphic, oxidase-negative, non-motile isolate from the ulcer of a farmed Atlantic salmon (), designated strain T11b, was subjected to a comprehensive taxonomic investigation. A comparative analysis of the 16S rRNA gene sequence showed highest similarities to the type strains of (98.1 %) and and (both 98.0 %). The highest ANI value observed between the assembled genome of T11b and the publicly available and type strain genomes were 81.15 and 80.99 %, respectively. The major respiratory quinone was menaquinone MK-9(H). The polyamine pattern contained predominantly spermidine. The polar lipid profile consisted of the major lipids diphosphatidylglycerol, phosphatidylglycerol, monogalactosyl-diacylglycerol and dimannosylglyceride. Minor amouts of trimannosyldiacylglycerol and phosphatidylinositol were also detected. The peptidoglycan was of the type A3α -Lys–-Ser-Thr–-Ala (A11.23). In the fatty acid profile, anteiso and iso branched fatty acids predominated (anteiso C, iso C, anteiso C). Moderate to low DNA–DNA similarities, physiological traits as well as unique traits in the fatty acid pattern distinguished strain T11b from the next related species. All these data point to the fact that strain T11b represents a novel species of the genus for which we propose the name sp. nov. The type strain is T11b (=CIP 111621=CCM 8854=LMG 30632=DSM 107127).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004002
2020-01-27
2020-02-28
Loading full text...

Full text loading...

References

  1. Jones D, Keddie RM. The genus Arthrobacter. Prokaryotes 2006;3:945–960
    [Google Scholar]
  2. Busse H-J. Review of the taxonomy of the genus Arthrobacter, emendation of the genus Arthrobacter sensu lato, proposal to reclassify selected species of the genus Arthrobacter in the novel genera Glutamicibacter gen. nov., Paeniglutamicibacter gen. nov., Pseudoglutamicibacter gen. nov., Paenarthrobacter gen. nov. and Pseudarthrobacter gen. nov., and emended description of Arthrobacter roseus. Int J Syst Evol Microbiol 2016;66:9–37 [CrossRef]
    [Google Scholar]
  3. Avendaño-Herrera R. Enfermedades Infecciosas Del Cultivo De Salmónidos En Chile Y El Mundo NIVA Chile S.A; 2011; p508
    [Google Scholar]
  4. Valdebenito S, Avendaño-Herrera R. Phenotypic, serological and genetic characterization of Flavobacterium psychrophilum strains isolated from salmonids in Chile. J Fish Dis 2009;32:321–333 [CrossRef]
    [Google Scholar]
  5. Zhang X-Y, Zhang Y-J, Chen X-L, Qin Q-L, Zhao D-L et al. Myroides profundi sp. nov., isolated from deep-sea sediment of the southern Okinawa Trough. FEMS Microbiol Lett 2008;287:108–112 [CrossRef]
    [Google Scholar]
  6. Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
    [Google Scholar]
  7. Kämpfer P, Steiof M, Dott W. Microbiological characterization of a fuel-oil contaminated site including numerical identification of heterotrophic water and soil bacteria. Microb Ecol 1991;21:227–251 [CrossRef]
    [Google Scholar]
  8. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012;19:455–477 [CrossRef]
    [Google Scholar]
  9. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014;30:2068–2069 [CrossRef]
    [Google Scholar]
  10. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991;173:697–703 [CrossRef]
    [Google Scholar]
  11. 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 [CrossRef]
    [Google Scholar]
  12. Ludwig W et al. ARB: a software environment for sequence data. Nucleic Acids Res 2004;32:1363–1371 [CrossRef]
    [Google Scholar]
  13. Yarza P, Richter M, Peplies J, Euzeby J, Amann R et al. The all-species living tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 2008;31:241–250 [CrossRef]
    [Google Scholar]
  14. Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012;28:1823–1829 [CrossRef]
    [Google Scholar]
  15. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef]
    [Google Scholar]
  16. Jukes TH, Cantor CR.Evolution of the protein molecules In Munro HN. editor Mammalian Protein Metabolism New York: Academic Press; 1969; p132
    [Google Scholar]
  17. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006;22:2688–2690 [CrossRef]
    [Google Scholar]
  18. Felsenstein J. Phylip (Phylogeny Inference Package) Version 3.6. Distributed by the Author Seattle: Department of Genome Sciences, University of Washington; 2005
    [Google Scholar]
  19. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef]
    [Google Scholar]
  20. Brosius J, Palmer ML, Kennedy PJ, Noller HF. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci U S A 1978;75:4801–4805 [CrossRef]
    [Google Scholar]
  21. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018;9:5114 [CrossRef]
    [Google Scholar]
  22. 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]
  23. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009;106:19126–19131 [CrossRef]
    [Google Scholar]
  24. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990;66:199–202 [CrossRef]
    [Google Scholar]
  25. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990;13:128–130 [CrossRef]
    [Google Scholar]
  26. Altenburgera P, Kämpferb P, Makristathisc A, Lubitza W, Bussea H-J. Classification of bacteria isolated from a medieval wall painting. J Biotechnol 1996;47:39–52 [CrossRef]
    [Google Scholar]
  27. Busse J, Auling G. Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 1988;11:1–8 [CrossRef]
    [Google Scholar]
  28. Altenburger P, Kämpfer P, Akimov VN, Lubitz W, Busse H-J. Polyamine distribution in actinomycetes with group B peptidoglycan and species of the genera Brevibacterium, Corynebacterium, and Tsukamurella. Int J Syst Bacteriol 1997;47:270–277 [CrossRef]
    [Google Scholar]
  29. Stolz A, Busse H-J, Kämpfer P. Pseudomonas knackmussii sp. nov. Int J Syst Evol Microbiol 2007;57:572–576 [CrossRef]
    [Google Scholar]
  30. Schumann P. Peptidoglycan structure. Methods Microbiol 2011;38:101–129
    [Google Scholar]
  31. Ding L, Hirose T, Yokota A. Four novel Arthrobacter species isolated from filtration substrate. Int J Syst Evol Microbiol 2009;59:856–862 [CrossRef]
    [Google Scholar]
  32. Borodina E, Kelly DP, Schumann P, Rainey FA, Ward-Rainey NL et al. Enzymes of dimethylsulfone metabolism and the phylogenetic characterization of the facultative methylotrophs Arthrobacter sulfonivorans sp. nov., Arthrobacter methylotrophus sp. nov., and Hyphomicrobium sulfonivorans sp. nov. Arch Microbiol 2002;177:173–183 [CrossRef]
    [Google Scholar]
  33. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996;42:989–1005 [CrossRef]
    [Google Scholar]
  34. Ziemke F, Höfle MG, Lalucat J, Rosselló-Mora R. Reclassification of Shewanella putrefaciens Owen's genomic group II as Shewanella baltica sp. nov. Int J Syst Bacteriol 1998;48:179–186 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004002
Loading
/content/journal/ijsem/10.1099/ijsem.0.004002
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