1887

Abstract

A novel Gram-positive, non-motile, non-spore-forming and aerobic bacterium, designated strain VA37-3, was isolated from a marine sediment sample collected at 19.2 m water depth from Valparaíso bay, Chile. Strain VA37-3 exhibits 97.6 % 16S rRNA gene sequence similarity to Corynebacterium marinum D7015, 96.4 % to Corynebacterium humireducens MFC-5 and 96 % to Corynebacterium testudinoris M935/96/4; and a rpoB gene sequence similarity of 85.1 % to Corynebacterium pollutisoli VMS11, both analyses suggesting that strain VA37-3 represents a novel species of Corynebacterium . Physiological testing indicated that strain VA37-3 requires artificial sea water or sodium-supplemented media for growth, representing the first obligate marine actinomycete of the genus Corynebacterium . The genome of the proposed new species, along with the type strains of its most closely related species were sequenced and characterized. In silico genome-based similarity analyses revealed an ANIb of 72.8 % ( C. marinum D7015), ANIm of 85.0 % ( Corynebacterium mustelae DSM 45274), tetra of 0.90 ( Corynebacterium callunae DSM 20147) and ggdc of 24.7 % ( Corynebacterium kutscheri DSM 20755) when compared with the closest related strains. The genomic DNA G+C content of strain VA37-3 was 57.0 %. Chemotaxonomic assessment of strain VN6-2 showed the major fatty acids were C18 : 1ω9c and C16 : 0. Menaquinones predominantly consisted of MK-8(II-H2). Polar lipids consisted of diphosphatidylglycerol, glycolipids, phosphatidylglycerol, phosphoglycolipid and phosphatidylinositol. Mycolic acids also were present. Overall, the results from phylogenetic, phenotypic and genomic analyses confirmed that strain VA37-3 represents a novel species of the genus Corynebacterium , for which the name Corynebacterium alimapuense sp. nov. is proposed, with VA37-3 as the type strain (=CCUG 69366=NCIMB 15118).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003237
2019-01-28
2019-10-20
Loading full text...

Full text loading...

References

  1. Macleod RA. The question of the existence of specific marine bacteria. Bacteriol Rev 1965;29:9–23[PubMed]
    [Google Scholar]
  2. Bruns A, Philipp H, Cypionka H, Brinkhoff T. Aeromicrobium marinum sp. nov., an abundant pelagic bacterium isolated from the German Wadden Sea. Int J Syst Evol Microbiol 2003;53:1917–1923 [CrossRef][PubMed]
    [Google Scholar]
  3. Maldonado LA, Fenical W, Jensen PR, Kauffman CA, Mincer TJ et al. Salinispora arenicola gen. nov., sp. nov. and Salinispora tropica sp. nov., obligate marine actinomycetes belonging to the family Micromonosporaceae. Int J Syst Evol Microbiol 2005;55:1759–1766 [CrossRef][PubMed]
    [Google Scholar]
  4. Tian XP, Xu Y, Zhang J, Li J, Chen Z et al. Streptomyces oceani sp. nov., a new obligate marine actinomycete isolated from a deep-sea sample of seep authigenic carbonate nodule in South China Sea. Antonie van Leeuwenhoek 2012;102:335–343 [CrossRef][PubMed]
    [Google Scholar]
  5. Yousif G, Busarakam K, Kim BY, Goodfellow M. Streptomyces mangrovi sp. nov., isolated from mangrove forest sediment. Antonie van Leeuwenhoek 2015;108:783–791 [CrossRef][PubMed]
    [Google Scholar]
  6. Pimentel-Elardo SM, Tiro LP, Grozdanov L, Hentschel U. Saccharopolyspora cebuensis sp. nov., a novel actinomycete isolated from a Philippine sponge (Porifera). Int J Syst Evol Microbiol 2008;58:628–632 [CrossRef][PubMed]
    [Google Scholar]
  7. Lehmann KB, Neumann R. Atlas und Grundriss der Bakteriologie und Lehrbuch der speziellen bakteriologischen Diagnostik. JF Lehmann, München 1896
    [Google Scholar]
  8. Pascual C, Foster G, Alvarez N, Collins MD. Corynebacterium phocae sp. nov., isolated from the common seal (Phoca vitulina). Int J Syst Bacteriol 1998;48 Pt 2:601–604 [CrossRef][PubMed]
    [Google Scholar]
  9. Collins MD, Hoyles L, Foster G, Falsen E. Corynebacterium caspium sp. nov., from a Caspian seal (Phoca caspica). Int J Syst Evol Microbiol 2004;54:925–928 [CrossRef][PubMed]
    [Google Scholar]
  10. Goyache J, Vela AI, Collins MD, Ballesteros C, Briones V et al. Corynebacterium spheniscorum sp. nov., isolated from the cloacae of wild penguins. Int J Syst Evol Microbiol 2003;53:43–46 [CrossRef][PubMed]
    [Google Scholar]
  11. Goyache J, Ballesteros C, Vela AI, Collins MD, Briones V et al. Corynebacterium sphenisci sp. nov., isolated from wild penguins. Int J Syst Evol Microbiol 2003;53:1009–1012 [CrossRef][PubMed]
    [Google Scholar]
  12. Ben-Dov E, Ben Yosef DZ, Pavlov V, Kushmaro A. Corynebacterium maris sp. nov., a marine bacterium isolated from the mucus of the coral Fungia granulosa. Int J Syst Evol Microbiol 2009;59:2458–2463 [CrossRef][PubMed]
    [Google Scholar]
  13. Zj D, Jordan EM, Rooney AP, Chen GJ, Austin B et al. isolated from coastal sediment. Int J Syst Evol Microbiol 2010;60:1944–1947
    [Google Scholar]
  14. Claverías FP, Undabarrena A, González M, Seeger M, Cámara B. Culturable diversity and antimicrobial activity of Actinobacteria from marine sediments in Valparaíso bay, Chile. Front Microbiol 2015;6:737 [CrossRef][PubMed]
    [Google Scholar]
  15. Kester DR, Duedall IW, Connors DN, Pytkowicz RM. Preparation of artificial seawater1. Limnol Oceanogr 1967;12:176–179 [CrossRef]
    [Google Scholar]
  16. Cámara B, Herrera C, González M, Couve E, Hofer B et al. From PCBs to highly toxic metabolites by the biphenyl pathway. Environ Microbiol 2004;6:842–850 [CrossRef][PubMed]
    [Google Scholar]
  17. Undabarrena A, Beltrametti F, Claverías FP, González M, Moore ER et al. Exploring the diversity and antimicrobial potential of Marine Actinobacteria from the Comau Fjord in Northern Patagonia, Chile. Front Microbiol 2016;7:1135 [CrossRef][PubMed]
    [Google Scholar]
  18. Undabarrena A, Ugalde JA, Seeger M, Cámara B. -Genomic data mining of the marine actinobacteria Streptomyces sp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis. PeerJ 2017;5:e2912 [CrossRef][PubMed]
    [Google Scholar]
  19. Rainey FA, Klatte S, Kroppenstedt RM, Stackebrandt E. Dietzia, a new genus including Dietzia maris comb. nov., formerly Rhodococcus maris. Int J Syst Bacteriol 1995;45:32–36 [CrossRef][PubMed]
    [Google Scholar]
  20. 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]
  21. Tindall BJ. Lipid composition of halobacterium lacusprofundi. FEMS Microbiol Lett 1990;66:199–202 [CrossRef]
    [Google Scholar]
  22. Tindall BJ. Respiratory lipoquinones as biomarkers. In Akkermans A, de Bruijn F, van Elsas D. (editors) Molecular Microbial Ecology Manual, section 4.1.5, supplement 1. Dordrecht: Kluwer; 1996
    [Google Scholar]
  23. Upadhyay A, Fontes FL, Gonzalez-Juarrero M, McNeil MR, Crans DC et al. Partial saturation of menaquinone in mycobacterium tuberculosis: function and essentiality of a novel reductase, men. J ACS Cent Sci 2015;1:292–302 [CrossRef][PubMed]
    [Google Scholar]
  24. Frischmann A, Knoll A, Hilbert F, Zasada AA, Kämpfer P et al. Corynebacterium epidermidicanis sp. nov., isolated from skin of a dog. Int J Syst Evol Microbiol 2012;62:2194–2200 [CrossRef][PubMed]
    [Google Scholar]
  25. Hahne J, Kloster T, Rathmann S, Weber M, Lipski A. Isolation and characterization of Corynebacterium spp. from bulk tank raw cow's milk of different dairy farms in Germany. PLoS One 2018;13:e0194365 [CrossRef][PubMed]
    [Google Scholar]
  26. Tatusova T, Ciufo S, Federhen S, Fedorov B, McVeigh R et al. Update on RefSeq microbial genomes resources. Nucleic Acids Res 2015;43:D599–D605 [CrossRef][PubMed]
    [Google Scholar]
  27. Khamis A, Raoult D, La Scola B. rpoB gene sequencing for identification of Corynebacterium species. J Clin Microbiol 2004;42:3925–3931 [CrossRef][PubMed]
    [Google Scholar]
  28. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007;23:2947–2948 [CrossRef][PubMed]
    [Google Scholar]
  29. Posada D. jModelTest: phylogenetic model averaging. Mol Biol Evol 2008;25:1253–1256 [CrossRef][PubMed]
    [Google Scholar]
  30. Posada D, Buckley TR. Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests. Syst Biol 2004;53:793–808 [CrossRef][PubMed]
    [Google Scholar]
  31. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  32. Guindon S. PhyML – manual version 3.0. 2012;40 Available fromhttp://www.atgc-montpellier.fr/phyml
  33. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  34. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  35. 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]
    [Google Scholar]
  36. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  37. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013;14:60 [CrossRef][PubMed]
    [Google Scholar]
  38. Negi V, Singh Y, Schumann P, Lal R. Corynebacteriumpollutisoli sp. nov., isolated from hexachlorocyclohexane-contaminated soil. Int J Syst Evol Microbiol 2016;66:3531–3537 [CrossRef][PubMed]
    [Google Scholar]
  39. Kim PS, Shin NR, Hyun DW, Kim JY, Whon TW et al. Corynebacterium atrinae sp. nov., isolated from the gastrointestinal tract of a pen shell, Atrina pectinata. Int J Syst Evol Microbiol 2015;65:531–536 [CrossRef][PubMed]
    [Google Scholar]
  40. Collins MD, Hoyles L, Hutson RA, Foster G, Falsen E et al. Corynebacterium testudinoris nov., from a tortoise, and Corynebacterium felinum sp. nov., from a Scottish wild cat. Int J Syst Evol Microbiol 2001;51:1349–1352
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003237
Loading
/content/journal/ijsem/10.1099/ijsem.0.003237
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most Cited This Month

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