1887

Abstract

Strain KT0803 was isolated from coastal eutrophic surface waters of Helgoland Roads near the island of Helgoland, North Sea, Germany. The taxonomic position of the strain, previously known as ‘ Gramella forsetii ’ KT0803, was investigated by using a polyphasic approach. The strain was Gram-stain-negative, chemo-organotrophic, heterotrophic, strictly aerobic, oxidase- and catalase-positive, rod-shaped, motile by gliding and had orange–yellow carotenoid pigments, but was negative for flexirubin-type pigments. It grew optimally at 22–25 °C, at pH 7.5 and at a salinity between 2–3 %. Strain KT0803 hydrolysed the polysaccharides laminarin, alginate, pachyman and starch. The respiratory quinone was MK-6. Polar lipids comprised phosphatidylethanolamine, six unidentified lipids and two unidentified aminolipids. The predominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 1ω7c and iso-C17 : 1ω7c, with smaller amounts of iso-C15 : 0 2-OH, C15 : 0, anteiso-C15 : 0 and C17 : 1ω6c. The G+C content of the genomic DNA was 36.6 mol%. The 16S rRNA gene sequence identities were 98.6 % with Gramella echinicola DSM 19838, 98.3 % with Gramella gaetbulicola DSM 23082, 98.1 % with Gramella aestuariivivens BG-MY13 and Gramella aquimixticola HJM-19, 98.0 % with Gramella lutea YJ019, 97.9 % with Gramella portivictoriae DSM 23547 and 96.9 % with Gramella marina KMM 6048. The DNA–DNA relatedness values were <35 % between strain KT0803 and type strains with >98.2 % 16S rRNA gene sequence identity. Based on the chemotaxonomic, phenotypic and genomic characteristics, strain KT0803 has been assigned to the genus Gramella , as Gramella forsetii sp. nov. The type strain is KT0803 (=DSM 17595=CGMCC 1.15422). An emended description of Gramella gaetbulicola Cho et al. 2011 is also proposed.

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2017-04-03
2019-10-22
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References

  1. Nedashkovskaya OI, Kim SB, Lysenko AM, Frolova GM, Mikhailov VV et al. Gramella echinicola gen. nov., sp. nov., a novel halophilic bacterium of the family Flavobacteriaceae isolated from the sea urchin Strongylocentrotus intermedius. Int J Syst Evol Microbiol 2005;55:391–394 [CrossRef][PubMed]
    [Google Scholar]
  2. Liu K, Li S, Jiao N, Tang K. Gramella flava sp. nov., a member of the family Flavobacteriaceae isolated from seawater. Int J Syst Evol Microbiol 2014;64:165–168 [CrossRef][PubMed]
    [Google Scholar]
  3. Shahina M, Hameed A, Lin SY, Lee RJ, Lee MR et al. Gramella planctonica sp. nov., a zeaxanthin-producing bacterium isolated from surface seawater, and emended descriptions of Gramella aestuarii and Gramella echinicola. Antonie van leeuwenhoek 2014;105:771–779 [CrossRef][PubMed]
    [Google Scholar]
  4. Shahina M, Hameed A, Lin SY, Lee RJ, Lee MR et al. Gramella planctonica sp. nov. In List of New Names and New Combinations Previously Effectively, but not Validly, Published, Validation List no. 158. Int J Syst Evol Microbiol 2014;64:2184–2187[CrossRef]
    [Google Scholar]
  5. Lau SC, Tsoi MM, Li X, Plakhotnikova I, Dobretsov S et al. Gramella portivictoriae sp. nov., a novel member of the family Flavobacteriaceae isolated from marine sediment. Int J Syst Evol Microbiol 2005;55:2497–2500 [CrossRef][PubMed]
    [Google Scholar]
  6. Cho SH, Chae SH, Cho M, Kim TU, Choi S et al. Gramella gaetbulicola sp. nov., a member of the family Flavobacteriaceae isolated from foreshore soil. Int J Syst Evol Microbiol 2011;61:2654–2658 [CrossRef][PubMed]
    [Google Scholar]
  7. Jeong SH, Jin HM, Jeon CO. Gramella aestuarii sp. nov., isolated from a tidal flat, and emended description of Gramella echinicola. Int J Syst Evol Microbiol 2013;63:2872–2878 [CrossRef][PubMed]
    [Google Scholar]
  8. Hameed A, Shahina M, Lin SY, Liu YC, Lai WA et al. Gramella oceani sp. nov., a zeaxanthin-producing bacterium of the family Flavobacteriaceae isolated from marine sediment. Int J Syst Evol Microbiol 2014;64:2675–2681 [CrossRef][PubMed]
    [Google Scholar]
  9. Park JM, Park S, Won SM, Jung YT, Shin KS et al. Gramella aestuariivivens sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2015;65:1262–1267 [CrossRef][PubMed]
    [Google Scholar]
  10. Park S, Kim S, Jung YT, Yoon JH. Gramella aquimixticola sp. nov., isolated from water of an estuary environment. Int J Syst Evol Microbiol 2015;65:4244–4249 [CrossRef][PubMed]
    [Google Scholar]
  11. Yoon J, Jo Y, Kim GJ, Choi H. Gramella lutea sp. nov., a novel species of the family Flavobacteriaceae isolated from marine sediment. Curr Microbiol 2015;71:252–258 [CrossRef][PubMed]
    [Google Scholar]
  12. Nedashkovskaya OI, Kim SB, Bae KS. Gramella marina sp. nov., isolated from the sea urchin Strongylocentrotus intermedius. Int J Syst Evol Microbiol 2010;60:2799–2802 [CrossRef][PubMed]
    [Google Scholar]
  13. Eilers H, Pernthaler J, Glöckner FO, Amann R. Culturability and in situ abundance of pelagic bacteria from the North Sea. Appl Environ Microbiol 2000;66:3044–3051 [CrossRef][PubMed]
    [Google Scholar]
  14. Gerdts G, Wichels A, Döpke H, Klings K-W, Gunkel W et al. 40-year long-term study of microbial parameters near Helgoland (German Bight, North Sea): historical view and future perspectives. Helgol Mar Res 2004;58:230–242 [CrossRef]
    [Google Scholar]
  15. Schut F, Prins RA, Gottschal JC. Oligotrophy and pelagic marine bacteria: facts and fiction. Aquatic Microbial Ecology 1997;12:177–202 [CrossRef]
    [Google Scholar]
  16. Bauer M, Kube M, Teeling H, Richter M, Lombardot T et al. Whole genome analysis of the marine Bacteroidetes ‘Gramella forsetii’ reveals adaptations to degradation of polymeric organic matter. Environ Microbiol 2006;8:2201–2213 [CrossRef][PubMed]
    [Google Scholar]
  17. Sonnenburg ED, Zheng H, Joglekar P, Higginbottom SK, Firbank SJ et al. Specificity of polysaccharide use in intestinal bacteroides species determines diet-induced microbiota alterations. Cell 2010;141:1241–1252 [CrossRef][PubMed]
    [Google Scholar]
  18. Kabisch A, Otto A, König S, Becher D, Albrecht D et al. Functional characterization of polysaccharide utilization loci in the marine Bacteroidetes ‘Gramella forsetii’ KT0803. ISME J 2014;8:1492–1502 [CrossRef][PubMed]
    [Google Scholar]
  19. McBride MJ, Zhu Y. Gliding motility and Por secretion system genes are widespread among members of the phylum Bacteroidetes. J Bacteriol 2013;195:270–278 [CrossRef][PubMed]
    [Google Scholar]
  20. Bernardet J-F, Segers P, Vancanneyt M, Berthe F, Kersters K et al. Cutting a gordian knot: emended classification and description of the genus Flavobacterium, emended description of the Family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (Basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Bacteriol 1996;46:128–148 [CrossRef]
    [Google Scholar]
  21. 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][PubMed]
    [Google Scholar]
  22. Hahnke RL, Harder J. Phylogenetic diversity of Flavobacteria isolated from the North Sea on solid media. Syst Appl Microbiol 2013;36:497–504 [CrossRef][PubMed]
    [Google Scholar]
  23. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Chapter 15: phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM. et al. (editors) Methods for General and Molecular Microbiology, 3rd ed. Washington, DC: American Society of Microbiology; 2007; pp.330–393
    [Google Scholar]
  24. De Ley J, Cattoir H, Reynaerts A. The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 1970;12:133–142 [CrossRef][PubMed]
    [Google Scholar]
  25. Huss VA, Festl H, Schleifer KH. Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 1983;4:184–192 [CrossRef][PubMed]
    [Google Scholar]
  26. Auch AF, Klenk HP, Göker M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2010;2:142–148 [CrossRef][PubMed]
    [Google Scholar]
  27. 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]
  28. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V et al. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res 2009;37:D233–D238 [CrossRef][PubMed]
    [Google Scholar]
  29. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 2014;42:D490–D495 [CrossRef][PubMed]
    [Google Scholar]
  30. Rawlings ND, Waller M, Barrett AJ, Bateman A. MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Res 2014;42:D503–D509 [CrossRef][PubMed]
    [Google Scholar]
  31. 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]
  32. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990;20:16
    [Google Scholar]
  33. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990;66:199–202 [CrossRef]
    [Google Scholar]
  34. 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]
  35. Meier-Kolthoff JP, Göker M, Spröer C, Klenk HP. When should a DDH experiment be mandatory in microbial taxonomy?. Arch Microbiol 2013;195:413–418 [CrossRef][PubMed]
    [Google Scholar]
  36. Rosselló-Móra R, Amann R. Past and future species definitions for Bacteria and Archaea. Syst Appl Microbiol 2015;38:209–216 [CrossRef][PubMed]
    [Google Scholar]
  37. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006;33:152–155
    [Google Scholar]
  38. Kim M, Oh HS, Park SC, 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][PubMed]
    [Google Scholar]
  39. Rosselló-Mora R, Amann R. The species concept for prokaryotes. FEMS Microbiol Rev 2001;25:39–67 [CrossRef][PubMed]
    [Google Scholar]
  40. Bernardet JF. Family I. Flavobacteriaceae Reichenbach 1992b, 327VP (Effective publication: Reichenbach 1989b, 2013.) emend. Bernardet, Segers, Van- canneyt, Berthe, Kersters and Vandamme 1996, 145 emend. Bernardet, Nakagawa and Holmes 2002, 1057. In Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ. et al (editors) Bergey’s Manual of Systematic Bacteriology. The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes, 2nd ed.vol. 4 New York, NY: Springer; 2011; pp.106–314
    [Google Scholar]
  41. Panschin I, Huang S, Meier-Kolthoff JP, Tindall BJ, Rohde M et al. Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050T (DSM 19838T) and Gramella portivictoriae UST040801-001T (DSM 23547T), and emended description of Gramella echinicola Nedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictoriae Lau et al. 2005. Stand Genomic Sci 2016;11:1–12 [CrossRef][PubMed]
    [Google Scholar]
  42. Göker M, Cleland D, Saunders E, Lapidus A, Nolan M et al. Complete genome sequence of Isosphaera pallida type strain (IS1BT). Stand Genomic Sci 2011;4:63–71 [CrossRef][PubMed]
    [Google Scholar]
  43. 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][PubMed]
    [Google Scholar]
  44. Yarza P, Ludwig W, Euzéby J, Amann R, Schleifer KH et al. Update of the All-Species Living Tree project based on 16s and 23s rRNA sequence analyses. Syst Appl Microbiol 2010;33:291–299 [CrossRef][PubMed]
    [Google Scholar]
  45. Ludwig W, Strunk O, Westram R, Richter L, Meier H et al. ARB: a software environment for sequence data. Nucleic Acids Res 2004;32:1363–1371 [CrossRef][PubMed]
    [Google Scholar]
  46. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 2007;35:7188–7196 [CrossRef][PubMed]
    [Google Scholar]
  47. Herzog P, Winkler I, Wolking D, Kämpfer P, Lipski A. Chryseobacterium ureilyticum sp. nov., Chryseobacterium gambrini sp. nov., Chryseobacterium pallidum sp. nov. and Chryseobacterium molle sp. nov., isolated from beer-bottling plants. Int J Syst Evol Microbiol 2008;58:26–33 [CrossRef][PubMed]
    [Google Scholar]
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