1887

Abstract

A Gram-stain-negative, pink-pigmented, rod-shaped, non-flagellated, aerobic bacterium, designated strain SM1701, was isolated from a rotten seaweed collected off Fildes Peninsula, King George Island, West Antarctica. The strain grew at 4–30 °C, pH 6.0–8.0 and with 0.5–5 % (w/v) NaCl. It hydrolysed gelatin and Tweens (40, 60 and 80), but did not reduce nitrates to nitrites. The major cellular fatty acids of strain SM1701 were iso-C, iso-CG, iso-CG, C and iso-C 3-OH. Polar lipids included phosphatidylethanolamine, one unidentified aminolipid, two unidentified glycolipids and one unidentified aminoglycolipid. The major respiratory quinone was MK-7. The genomic DNA G+C content of strain SM1701 was 34.1 mol%. It showed high 16S rRNA gene sequence similarities to (93.8 %) and (92.5 %) and less than 91 % sequence similarities to other known members in the family . Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SM1701 constituted a distinct lineage within the family . The phylogenetic trees based on concatenated 261 protein sequences from genome sequences showed that strain SM1701 occupied a branch separated from those of known genera in the family of , indicating it may belong to a new genus. On the basis of the polyphasic characterization of strain SM1701 in this study, it is considered to represent a novel species in a new genus in the family , for which the name gen. nov., sp. nov. is proposed. The type strain is SM1701 (=KCTC 62302=NBRC 113201=CGMCC 1.16510).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003809
2019-10-29
2019-11-15
Loading full text...

Full text loading...

References

  1. Munoz R, Rosselló-Móra R, Amann R. Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov. Syst Appl Microbiol 2016;39: 281– 296 [CrossRef]
    [Google Scholar]
  2. Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2016;66: 2463– 2466 [CrossRef]
    [Google Scholar]
  3. Bowman JP, Nichols CM, Gibson JAE. Algoriphagus ratkowskyi gen. nov., sp. nov., Brumimicrobium glaciale gen. nov., sp. nov., Cryomorpha ignava gen. nov., sp. nov. and Crocinitomix catalasitica gen. nov., sp. nov., novel flavobacteria isolated from various polar habitats. Int J Syst Evol Microbiol 2003;53: 1343– 1355 [CrossRef]
    [Google Scholar]
  4. O'Sullivan LA, Rinna J, Humphreys G, Weightman AJ, Fry JC. Fluviicola taffensis gen. nov., sp. nov., a novel freshwater bacterium of the family Cryomorphaceae in the phylum 'Bacteroidetes'. Int J Syst Evol Microbiol 2005;55: 2189– 2194 [CrossRef]
    [Google Scholar]
  5. Lau KWK, Ren J, Wai NLM, Qian PY, Wong PK et al. Lishizhenia caseinilytica gen. nov., sp. nov., a marine bacterium of the phylum Bacteroidetes. Int J Syst Evol Microbiol 2006;56: 2317– 2322 [CrossRef]
    [Google Scholar]
  6. Muramatsu Y, Takahashi M, Kamakura Y, Suzuki KI, Nakagawa Y. Salinirepens amamiensis gen. nov., sp. nov., a member of the family Cryomorphaceae isolated from seawater, and emended descriptions of the genera Fluviicola and Wandonia. Int J Syst Evol Microbiol 2012;62: 2235– 2240 [CrossRef]
    [Google Scholar]
  7. Lee DH, Choi EK, Moon SR, Ahn S, Lee YS et al. Wandonia haliotis gen. nov., sp. nov., a marine bacterium of the family Cryomorphaceae, phylum Bacteroidetes. Int J Syst Evol Microbiol 2010;60: 510– 514 [CrossRef]
    [Google Scholar]
  8. Lane DJ. 16S/23S rRNA sequencing In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991; pp 115– 175
    [Google Scholar]
  9. Yoon SH, Ha SM, 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]
  10. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980;16: 111– 120 [CrossRef]
    [Google Scholar]
  11. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39: 783– 791 [CrossRef]
    [Google Scholar]
  12. 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]
  13. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17: 368– 376 [CrossRef]
    [Google Scholar]
  14. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971;20: 406– 416 [CrossRef]
    [Google Scholar]
  15. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011;28: 2731– 2739 [CrossRef]
    [Google Scholar]
  16. Chen LP, Xu HY, Fu SZ, Fan HX, Zhou YG et al. Lishizhenia tianjinensis sp. nov., isolated from coastal seawater. Int J Syst Evol Microbiol 2009;59: 2400– 2403 [CrossRef]
    [Google Scholar]
  17. Xu L, Wu YH, Zhou P, Cheng H, Liu Q et al. Investigation of the thermophilic mechanism in the genus Porphyrobacter by comparative genomic analysis. BMC Genomics 2018;19: 385 [CrossRef]
    [Google Scholar]
  18. Lechner M, Findeiß S, Steiner L, Marz M, Stadler PF et al. Proteinortho: Detection of (Co-)orthologs in large-scale analysis. BMC Bioinformatics 2011;12: 124 [CrossRef]
    [Google Scholar]
  19. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013;30: 772– 780 [CrossRef]
    [Google Scholar]
  20. 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 [CrossRef]
    [Google Scholar]
  21. Nguyen LT, 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 [CrossRef]
    [Google Scholar]
  22. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33: 1870– 1874 [CrossRef]
    [Google Scholar]
  23. 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]
    [Google Scholar]
  24. 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]
    [Google Scholar]
  25. 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]
    [Google Scholar]
  26. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the AD hoc Committee on reconciliation of approaches to bacterial Systematics. Int J Syst Evol Microbiol 1987;37: 463– 464 [CrossRef]
    [Google Scholar]
  27. Komagata K, Suzuki K. Lipid and cell wall analysis in bacterial Systematics. Methods Microbiol 1987;19: 161– 207
    [Google Scholar]
  28. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980;48: 459– 470 [CrossRef]
    [Google Scholar]
  29. Murray RGE, Doetsch RN, Robinow CF. Determinative and cytological light microscopy In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp 21– 41
    [Google Scholar]
  30. Bernardet JF, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002;52: 1049– 1070 [CrossRef]
    [Google Scholar]
  31. Smibert RM, Krieg NR. Phenotypic characterization In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp 607– 654
    [Google Scholar]
  32. Bowman JP. Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 2000;50: 1861– 1868 [CrossRef]
    [Google Scholar]
  33. Shi MJ, Han JR, Zhang H, Xie ZH, Du ZJ. Crocinitomix algicola sp. nov., isolated from Gracilaria blodgettii. Int J Syst Evol Microbiol 2017;67: 4020– 4023 [CrossRef]
    [Google Scholar]
  34. Yang SH, Seo HS, Oh HM, Kim SJ, Lee JH et al. Brumimicrobium mesophilum sp. nov., isolated from a tidal flat sediment, and emended descriptions of the genus Brumimicrobium and Brumimicrobium glaciale. Int J Syst Evol Microbiol 2013;63: 1105– 1110 [CrossRef]
    [Google Scholar]
  35. Zhang H, Han JR, Shi MJ, Du ZJ, Chen GJ. Brumimicrobium aurantiacum sp. nov., isolated from coastal sediment. Int J Syst Evol Microbiol 2017;67: 3256– 3260 [CrossRef]
    [Google Scholar]
  36. Dahal RH, Kim J. Fluviicola kyonggii sp. nov., a bacterium isolated from forest soil and emended description of the genus Fluviicola. Int J Syst Evol Microbiol 2018;68: 1885– 1889 [CrossRef]
    [Google Scholar]
  37. Yang HX, Wang X, Liu XW, Zhang J, Yang GQ et al. Fluviicola hefeinensis sp. nov., isolated from the wastewater of a chemical factory. Int J Syst Evol Microbiol 2014;64: 700– 704 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003809
Loading
/content/journal/ijsem/10.1099/ijsem.0.003809
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