1887

Abstract

A marine strain, designated KK4, was isolated from the surface of a starfish, , which was collected from seawater off the coast of Hokkaido, Japan. Strain KK4 is a Gram-stain-negative, non-spore-forming, rod-shaped, aerobic bacterium that forms yellow-pigmented colonies. A phylogenetic relationship analysis, based on 16S rRNA gene sequences, revealed that strain KK4 was closely related to IMCC12008, IMCC3101 and KMM 3912, with similarities of 96.9, 95.8 and 95.6 %, respectively, but low sequence similarities (<94 %) among other genera in the family . Genomic similarities between strain KK4 and the three type strains based on average nucleotide identity and digital DNA–DNA hybridization values were lower than the species delineation thresholds. Moreover, phylogenetic tree based on genome sequences showed that strain KK4 was clustered with IMCC12008 and formed a branch independent from the cluster including type species of the genera , , , and . Amino acid identity values between strain KK4/ IMCC12008 and the neighbour type species/strains were 61.9–68.2% and 61.5–67.4 %, which were lower than the genus delineation threshold, implying the novel genus status of strain KK4. Strain KK4 growth occurred at pH 6.0–9.0, 4–30 °C and in NaCl concentrations of 0.5–5.0 %, and optimally at pH 7.0, 25 °C and 3.0 %, respectively. Unlike strains, strain KK4 could assimilate glucose, mannose, galactose and acetate. The major quinone and fatty acids were menaquinone-6 and iso-C (27.5 %), iso-C G (22.5 %) and iso-C 3-OH (12.8 %), respectively. Based on genetic, phylogenetic and phenotypic properties, strain KK4 represents a novel species of the genus , for which the name gen. nov., sp. nov. is proposed. The type strain is KK4 (=JCM 33344=KCTC 72225). In addition, based on the current data, should be reclassified as comb. nov.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004254
2020-06-15
2020-11-25
Loading full text...

Full text loading...

References

  1. Nedashkovskaya OI, Kim SB, Han SK, Rhee MS, Lysenko AM et al. Ulvibacter litoralis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from the green alga Ulva fenestrata . Int J Syst Evol Microbiol 2004; 54:119–123 [CrossRef]
    [Google Scholar]
  2. Choi T-H, Lee HK, Lee K, Cho J-C. Ulvibacter antarcticus sp. nov., isolated from Antarctic coastal seawater. Int J Syst Evol Microbiol 2007; 57:2922–2925 [CrossRef]
    [Google Scholar]
  3. Baek K, Jo H, Choi A, Kang I, Cho J-C. Ulvibacter marinus sp. nov., isolated from coastal seawater. Int J Syst Evol Microbiol 2014; 64:2041–2046 [CrossRef]
    [Google Scholar]
  4. Barbeyron T, L'Haridon S, Corre E, Kloareg B, Potin P. Zobellia galactanovorans gen. nov., sp. nov., a marine species of Flavobacteriaceae isolated from a red alga, and classification of [Cytophaga] uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Zobellia uliginosa gen. nov., comb. nov . Int J Syst Evol Microbiol 2001; 51:985–997 [CrossRef]
    [Google Scholar]
  5. Macian MC et al. Gelidibacter mesophilus sp. nov., a novel marine bacterium in the family Flavobacteriaceae . Int J Syst Evol Microbiol 2002; 52:1325–1329 [CrossRef]
    [Google Scholar]
  6. Khan ST, Nakagawa Y, Harayama S. Sediminibacter furfurosus gen. nov., sp. nov. and Gilvibacter sediminis gen. nov., sp. nov., novel members of the family Flavobacteriaceae . Int J Syst Evol Microbiol 2007; 57:265–269 [CrossRef]
    [Google Scholar]
  7. Kim J-H, Kim K-Y, Hahm Y-T, Kim B-S, Chun J et al. Actibacter sediminis gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from tidal flat sediment. Int J Syst Evol Microbiol 2008; 58:139–143 [CrossRef]
    [Google Scholar]
  8. Emil Ruff S, Probandt D, Zinkann A-C, Iversen MH, Klaas C et al. Indications for algae-degrading benthic microbial communities in deep-sea sediments along the Antarctic polar front. Deep Sea Research Part II: Topical Studies in Oceanography 2014; 108:6–16 [CrossRef]
    [Google Scholar]
  9. Thiele S, Fuchs BM, Ramaiah N, Amann R. Microbial community response during the iron fertilization experiment LOHAFEX. Appl Environ Microbiol 2012; 78:8803–8812 [CrossRef]
    [Google Scholar]
  10. Teeling H, Fuchs BM, Becher D, Klockow C, Gardebrecht A et al. Substrate-Controlled succession of marine bacterioplankton populations induced by a phytoplankton Bloom. Science 2012; 336:608–611 [CrossRef]
    [Google Scholar]
  11. Hahnke RL, Bennke CM, Fuchs BM, Mann AJ, Rhiel E et al. Dilution cultivation of marine heterotrophic bacteria abundant after a spring phytoplankton Bloom in the North sea. Environ Microbiol 2015; 17:3515–3526 [CrossRef]
    [Google Scholar]
  12. El-Swais H, Dunn KA, Bielawski JP, Li WKW, Walsh DA. Seasonal assemblages and short-lived blooms in coastal north-west Atlantic Ocean bacterioplankton. Environ Microbiol 2015; 17:3642–3661 [CrossRef]
    [Google Scholar]
  13. Das S, Dash HR. Microbial Biotechnology-A Laboratory Manual for Bacterial Systems Springer; 2014
    [Google Scholar]
  14. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [CrossRef]
    [Google Scholar]
  15. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. Isme J 2012; 6:1621–1624 [CrossRef][PubMed]
    [Google Scholar]
  16. Parada AE, Needham DM, Fuhrman JA. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ Microbiol 2016; 18:1403–1414 [CrossRef]
    [Google Scholar]
  17. 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][PubMed]
    [Google Scholar]
  18. Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM et al. Ribosomal database project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 2014; 42:D633–D642 [CrossRef]
    [Google Scholar]
  19. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526
    [Google Scholar]
  20. 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]
  21. Kim M, Oh H-S, Park S-C, 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 [CrossRef]
    [Google Scholar]
  22. Itoh H, Kawano K, Kihara M. Draft Genome Sequence of Agarivorans sp. Strain Toyoura001, Isolated from an Abalone Gut. Microbiol Resour Announc 2019; 8:e00169–00119 [CrossRef]
    [Google Scholar]
  23. 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]
  24. 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]
  25. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: atoolbox for specialized analyses of microbial genomes and meta-genomes. PeerJ Preprints 2016e1900v1
    [Google Scholar]
  26. SI N, Kim YO, Yoon SH, SM H, Baek I et al. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285
    [Google Scholar]
  27. Kanehisa M, Sato Y. KEGG Mapper for inferring cellular functions from protein sequences. Protein Sci 2020; 29:28–35 [CrossRef]
    [Google Scholar]
  28. Skennerton CT, Ward LM, Michel A, Metcalfe K, Valiente C et al. Genomic reconstruction of an uncultured hydrothermal vent gammaproteobacterial methanotroph (family Methylothermaceae) indicates multiple adaptations to oxygen limitation. Front Microbiol 2015; 6:1425 [CrossRef]
    [Google Scholar]
  29. Orata FD, Meier-Kolthoff JP, Sauvageau D, Stein LY. Phylogenomic analysis of the gammaproteobacterial methanotrophs (order Methylococcales) calls for the reclassification of members at the genus and species levels. Front Microbiol 2018; 9:3162 [CrossRef]
    [Google Scholar]
  30. Xu Z, Masuda Y, Itoh H, Ushijima N, Shiratori Y et al. Geomonas oryzae gen. nov., sp. nov., Geomonas edaphica sp. nov., Geomonas ferrireducens sp. nov., Geomonas terrae sp. nov., four ferric-reducing bacteria isolated from paddy soil, and reclassification of three species of the genus Geobacter as members of the genus Geomonas gen. nov. Front Microbiol 2019; 10:2201 [CrossRef]
    [Google Scholar]
  31. Nicholson AC, Gulvik CA, Whitney AM, Humrighouse BW, Bell ME et al. Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens. Int J Syst Evol Microbiol 2020ijsem003935
    [Google Scholar]
  32. Nowak-Thompson B, Hammer PE, Hill DS, Stafford J, Torkewitz N et al. 2,5-Dialkylresorcinol biosynthesis in Pseudomonas aurantiaca: novel head-to-head condensation of two fatty acid-derived precursors. J Bacteriol 2003; 185:860–869 [CrossRef]
    [Google Scholar]
  33. McBride MJ, Xie G, Martens EC, Lapidus A, Henrissat B et al. Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis. Appl Environ Microbiol 2009; 75:6864–6875 [CrossRef]
    [Google Scholar]
  34. 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
    [Google Scholar]
  35. Romanenko LA, Uchino M, Frolova GM, Mikhailov VV. Marixanthomonas ophiurae gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from a deep-sea brittle star. Int J Syst Evol Microbiol 2007; 57:457–462 [CrossRef]
    [Google Scholar]
  36. YH W, Xamxidin M, Meng FX, Zhang XQ, Wang CS et al. Marinirhabdus gelatinilytica gen. nov., sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2016; 66:3095–3101
    [Google Scholar]
  37. Yang S-H, Oh JH, Seo H-S, Lee J-H, Kwon KK. Marinirhabdus citrea sp. nov., a marine bacterium isolated from a seaweed. Int J Syst Evol Microbiol 2018; 68:547–551 [CrossRef]
    [Google Scholar]
  38. Park S, Yoshizawa S, Inomata K, Kogure K, Yokota A. Aureitalea marina gen. nov., sp. nov., a member of the family Flavobacteriaceae, isolated from seawater. Int J Syst Evol Microbiol 2012; 62:912–916 [CrossRef]
    [Google Scholar]
  39. Liu J-J, Zhang X-Q, Pan J, Sun C, Zhang Y et al. Aequorivita viscosa sp. nov., isolated from an intertidal zone, and emended descriptions of Aequorivita antarctica and Aequorivita capsosiphonis . Int J Syst Evol Microbiol 2013; 63:3192–3196 [CrossRef]
    [Google Scholar]
  40. Bowman JP, Nichols DS. Aequorivita gen. nov., a member of the family Flavobacteriaceae isolated from terrestrial and marine Antarctic habitats.. Int J Syst Evol Microbiol 2002; 52:1533–1541 [CrossRef][PubMed]
    [Google Scholar]
  41. Nedashkovskaya OI, Suzuki M, Vysotskii MV, Mikhailov VV. Vitellibacter vladivostokensis gen. nov., sp. nov., a new member of the phylum Cytophaga–Flavobacterium–Bacteroides . Int J Syst Evol Microbiol 2003; 53:1281–1286 [CrossRef]
    [Google Scholar]
  42. Park SC, Baik KS, Kim MS, Kim SS, Kim SR et al. Aequorivita capsosiphonis sp. nov., isolated from the green alga Capsosiphon fulvescens, and emended description of the genus Aequorivita . Int J Syst Evol Microbiol 2009; 59:724–728 [CrossRef]
    [Google Scholar]
  43. Park S, Lee K-C, Bae KS, Yoon J-H. Vitellibacter soesokkakensis sp. nov., isolated from the junction between the ocean and a freshwater spring and emended description of the genus Vitellibacter . Int J Syst Evol Microbiol 2014; 64:588–593 [CrossRef]
    [Google Scholar]
  44. Fautz E, Reichenbach H. A simple test for flexirubin-type pigments. FEMS Microbiol Lett 1980; 8:87–91 [CrossRef]
    [Google Scholar]
  45. 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]
  46. Kim S-G, Pheng S, Lee Y-J, Eom MK, Shin D-H. Agarivorans aestuarii sp. nov., an agar-degrading bacterium isolated from a tidal flat. Int J Syst Evol Microbiol 2016; 66:3119–3124 [CrossRef]
    [Google Scholar]
  47. Barbeyron T, Lerat Y, Sassi J-F, Le Panse S, Helbert W et al. Persicivirga ulvanivorans sp. nov., a marine member of the family Flavobacteriaceae that degrades ulvan from green algae. Int J Syst Evol Microbiol 2011; 61:1899–1905 [CrossRef]
    [Google Scholar]
  48. Nishijima M, Araki-Sakai M, Sano H. Identification of isoprenoid quinones by frit-FAB liquid chromatography–mass spectrometry for the chemotaxonomy of microorganisms. J Microbiol Methods 1997; 28:113–122 [CrossRef]
    [Google Scholar]
  49. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, Technical note 101. Microbial ID: Newark, Del; 1990
    [Google Scholar]
  50. Da Costa MS, Albuquerque L, Nobre MF, Wait R. The identification of polar lipids in prokaryotes. Methods Microbiol 2011; 38:165–181
    [Google Scholar]
  51. Tanizawa Y, Fujisawa T, Nakamura Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 2018; 34:1037–1039 [CrossRef]
    [Google Scholar]
  52. García-López M, Meier-Kolthoff JP, Tindall B, Gronow S, Woyke T et al. Analysis of 1000 type-strain genomes improves taxonomic classification of Bacteroidetes . Front Microbiol 2083; 2019:10
    [Google Scholar]
  53. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [CrossRef]
    [Google Scholar]
  54. Qin Q-L, Xie B-B, Zhang X-Y, Chen X-L, Zhou B-C et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [CrossRef]
    [Google Scholar]
  55. Barco RA, Garrity GM, Scott JJ, Amend JP, Nealson KH et al. A genus definition for bacteria and archaea based on a standard genome relatedness index. mBio 2020; 11: [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004254
Loading
/content/journal/ijsem/10.1099/ijsem.0.004254
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month 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