Phylogenetic diversity of Flavobacteria isolated from the North Sea on solid media

Systematic and Applied Microbiology

Volumn 36, Issue 7, 2013, Pages 497-504

  Hahnke, Richard L ^a   Harder, Jens ^a  

^a MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

Author keywords

Bacteroidetes; Cultivation; Flavobacteria; Flexirubin; Helgoland; Iridescence; Janssand; North Sea; Sylt; Taxonomy

Indexed keywords

AGAR; KANAMYCIN; RNA 16S; SEA WATER;

AQUIMARINA; ARTICLE; BACTERIAL GENE; BACTERIUM ISOLATION; CARBON SOURCE; CELL PHAGOCYTOSIS; DILUTION; FLAVOBACTERIA; FLAVOBACTERIACEAE; FLAVOBACTERIUM; GENE SEQUENCE; GRAMELLA; INCUBATION TIME; KROKINOBACTER; LEEUWENHOEKIELLA; LOW TEMPERATURE; LUTIBACTER; MARIXANTHOMONAS; NONHUMAN; NONLABENS; NORTH SEA; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENY; POLARIBACTER; PRIORITY JOURNAL; SEDIMINICOLA; SEQUENCE HOMOLOGY; TENACIBACULUM; ULVIBACTER; WINOGRADSKYELLA;

ANIMALIA; BACTEROIDETES; FLAMMEOVIRGACEAE; FLAVOBACTERIA; FLAVOBACTERIACEAE;

BACTEROIDETES; CULTIVATION; FLAVOBACTERIA; FLEXIRUBIN; HELGOLAND; IRIDESCENCE; JANSSAND; NORTH SEA; SYLT; TAXONOMY;

ANIMALS; BACTERIOLOGICAL TECHNIQUES; CLUSTER ANALYSIS; CULTURE MEDIA; DNA, BACTERIAL; DNA, RIBOSOMAL; FLAVOBACTERIACEAE; GENETIC VARIATION; GEOLOGIC SEDIMENTS; MOLECULAR SEQUENCE DATA; NORTH SEA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEAWATER; SEQUENCE ANALYSIS, DNA;

EID: 84884209603     PISSN: 07232020     EISSN: 16180984     Source Type: Journal    
DOI: 10.1016/j.syapm.2013.06.006     Document Type: Article

References (58)

1. Abell G.C.J., Bowman J.P. Colonization and community dynamics of class Flavobacteria on diatom detritus in experimental mesocosms based on Southern Ocean seawater. FEMS Microbiol. Ecol. 2005, 53:379-391.
2. Alongi D.M. Coastal Ecosystem Processes 1998, CRC Press, Boca Raton, USA.
3. Alonso C., Warnecke F., Amann R., Pernthaler J. High local and global diversity of Flavobacteria in marine plankton. Environ. Microbiol. 2007, 9:1253-1266.
4. Barbeyron T., Carpentier F., L'Haridon S., Schüler M., Michel G., Amann R. Description of Maribacter forsetii sp. nov., a marine Flavobacteriaceae isolated from North Sea water, and emended description of the genus Maribacter. Int. J. Syst. Evol. Microbiol. 2008, 58:790-797.
5. Bauer M., Kube M., Teeling H., Richter M., Lombardot T., Allers E., Würdemann C.A., Quast C., Kuhl H., Knaust F., Woebken D., Bischof K., Mussmann M., Choudhuri J.V., Meyer F., Reinhardt R., Amann R.I., Glöckner F.O. Whole genome analysis of the marine Bacteroidetes 'Gramella forsetii' reveals adaptations to degradation of polymeric organic matter. Environ. Microbiol. 2006, 8:2201-2213.
6. Bernardet J.-F. Class II. Flavobacteriia class. nov. Bergey's Manual of Systematic Bacteriology. The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes 2010, 106-314. Springer, New York, NY. N.R. Krieg, J.T. Staley, D.R. Brown, B.P. Hedlund, B.J. Paster (Eds.).
7. Bernardet J.F., 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.
8. Brandt P., Gerdts G., Boersma M., Wiltshire K.H., Wichels A. Comparison of different DNA-extraction techniques to investigate the bacterial community of marine copepods. Helgoland Mar. Res. 2010, 64:331-342.
9. Bruns A., Rohde M., Berthe-Corti L. Muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from German North Sea intertidal sediment. Int. J. Syst. Evol. Microbiol. 2001, 51:1997-2006.
10. Cantarel B.L., Coutinho P.M., Rancurel C., Bernard T., Lombard V., Henrissat B. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 2009, 37:D233-D238.
11. Cole J.R., Wang Q., Cardenas E., Fish J., Chai B., Farris R.J., Kulam-Syed-Mohideen A.S., McGarrell D.M., Marsh T., Garrity G.M., Tiedje J.M. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 2009, 37:D141-D145.
12. Colwell R.R., Citarella R.V., Chen P.K. DNA base composition of Cytophaga marinoflava n. sp. determined by buoyant density measurements in cesium chloride. Can. J. Microbiol. 1966, 12:1099-1103.
13. Doucet S.M., Meadows M.G. Iridescence: a functional perspective. J. R. Soc. Interface 2009, 6:S115-S132.
14. Eilers H., Pernthaler J., Glöckner F.O., Amann R. Culturability and in situ abundance of pelagic bacteria from the North Sea. Appl. Environ. Microbiol. 2000, 66:3044-3051.
15. Euzéby J.P. List of bacterial names with standing in nomenclature: a folder available on the Internet. Int. J. Syst. Bacteriol. 1997, 47:590-592. http://www.bacterio.cict.fr/.
16. Fautz E., Reichenbach H. A simple test for flexirubin-type pigments. FEMS Microbiol. Lett. 1980, 8:87-91.
17. Flint K.P. A note on a selective agar medium for the enumeration of Flavobacterium species in water. J. Appl. Bacteriol. 1985, 59:561-566.
18. Frette L., Jørgensen N.O.G., Irming H., Kroer N. Tenacibaculum skagerrakense sp. nov., a marine bacterium isolated from the pelagic zone in Skagerrak, Denmark. Int. J. Syst. Evol. Microbiol. 2004, 54:519-524.
19. Gao H., Matyka M., Liu B., Khalili A., Kostka J.E., Collins G., Jansen S., Holtappels M., Jensen M.M., Badewien T.H., Beck M., Grunwald M., de Beer D., Lavik G., Kuypers M.M.M. Intensive and extensive nitrogen loss from intertidal permeable sediments of the Wadden Sea. Limnol. Oceanogr. 2012, 57:185-198.
20. Gómez-Pereira P.R., Fuchs B.M., Alonso C., Oliver M.J., van Beusekom J.E.E., Amann R. Distinct flavobacterial communities in contrasting water masses of the North Atlantic Ocean. ISME J. 2010, 4:472-487.
21. Grossart H.P., Schlingloff A., Bernhard M., Simon M., Brinkhoff T. Antagonistic activity of bacteria isolated from organic aggregates of the German Wadden Sea. FEMS Microbiol. Ecol. 2004, 47:387-396.
22. Hansen G.H., Bergh Ø., Michaelsen J., Knappskog D. Flexibacter ovolyticus sp. nov., a pathogen of eggs and larvae of Atlantic halibut, Hippoglossus hippoglossus L. Int. J. Syst. Bacteriol. 1992, 42:451-458.
23. Janssen P.H., Yates P.S., Grinton B.E., Taylor P.M., Sait M. Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Appl. Environ. Microbiol. 2002, 68:2391-2396.
24. Johansen J.E., Nielsen P., Sjohølm C. Description of Cellulophaga baltica gen. nov., sp. nov., and Cellulophaga fucicola gen. nov., sp. nov. and reclassification of [Cytophaga] lytica to Cellulophaga lytica gen. nov., comb. nov. Int. J. Syst. Bacteriol. 1999, 49:1231-1240.
25. Jukes T.H., Cantor C.R. Evolution of protein molecules. Mammalian Protein Metabolism 1969, 21-132. Academic Press, New York, USA. H.N. Munro (Ed.).
26. Kientz B., Marie P., Rosenfeld E. Effect of abiotic factors on the unique glitter-like iridescence of Cellulophaga lytica. FEMS Microbiol. Lett. 2012, 333:101-108.
27. Kientz B., Vukusic P., Luke S., Rosenfeld E. Iridescence of a marine bacterium and classification of prokaryotic structural colors. Appl. Environ. Microbiol. 2012, 78:2092-2099.
28. Kirchman D.L. The ecology of Cytophaga-Flavobacteria in aquatic environments. FEMS Microbiol. Ecol. 2002, 39:91-100.
29. Klindworth A., Pruesse E., Schweer T., Peplies J., Quast C., Horn M., Glöckner F.O. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013, 41:e1.
30. Klippel B., Lochner A., Bruce D.C., Davenport K.W., Detter C., Goodwin L.A., Han J., Han S.S., Hauser L., Land M.L., Nolan M., Ovchinnikova G., Pennacchio L., Pitluck S., Tapia R., Woyke T., Wiebusch S., Basner A., Abe F., Horikoshi K., Keller M., Antranikian G. Complete genome sequences of Krokinobacter sp. strain 4H-3-7-5 and Lacinutrix sp. strain 5H-3-7-4, polysaccharide-degrading members of the family Flavobacteriaceae. J. Bacteriol. 2011, 193:4545-4546.
31. Llobet-Brossa E., Rosselló-Móra R., Amann R. Microbial community composition of Wadden Sea sediments as revealed by fluorescence in situ hybridization. Appl. Environ. Microbiol. 1998, 64:2691-2696.
32. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar, Buchner A., Lai T., Steppi S., Jobb G., Förster W., Brettske I., Gerber S., Ginhart A.W., Gross O., Grumann S., Hermann S., Jost R., König A., Liss T., Lüßmann R., May M., Nonhoff B., Reichel B., Strehlow R., Stamatakis A., Stuckmann N., Vilbig A., Lenke M., Ludwig T., Bode A., Schleifer K.H. ARB: a software environment for sequence data. Nucleic Acids Res. 2004, 32:1363-1371.
33. Musat N., Werner U., Knittel K., Kolb S., Dodenhof T., van Beusekom J.E.E., de Beer D., Dubilier N., Amann R. Microbial community structure of sandy intertidal sediments in the North Sea, Sylt-Rømø Basin, Wadden Sea. Syst. Appl. Microbiol. 2006, 29:333-348.
34. Muyzer G., Teske A., Wirsen C., Jannasch H. Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch. Microbiol. 1995, 164:165-172.
35. Nedashkovskaya O.I., Vancanneyt M., Dawyndt P., Engelbeen K., Vandemeulebroecke K., Cleenwerck I., Hoste B., Mergaert J., Tan T.-L., Frolova G.M., Mikhailov V.V., Swings J. Reclassification of [Cytophaga] marinoflava Reichenbach 1989 as Leeuwenhoekiella marinoflava gen. nov., comb. nov. and description of Leeuwenhoekiella aequorea sp. nov. Int. J. Syst. Evol. Microbiol. 2005, 55:1033-1038.
36. O'Sullivan L.A., Rinna J., Humphreys G., Weightman A.J., Fry J.C. Culturable phylogenetic diversity of the phylum 'Bacteroidetes' from river epilithon and coastal water and description of novel members of the family Flavobacteriaceae: Epilithonimonas tenax gen. nov., sp. nov. and Persicivirga xylanidelens gen. nov., sp. nov. Int. J. Syst. Evol. Microbiol. 2006, 56:169-180.
37. Pfennig N., Trüper H.G. Isolation of members of the families Chromatiaceae and Chlorobiaceae. The Prokaryotes 1981, 279-289. Springer-Verlag, Berlin, Germany. M.P. Starr, H. Stolp, H.G. Trüper, A. Balows, H.G. Schlegel (Eds.).
38. Port A., Gurgel K.-W., Staneva J., Schulz-Stellenfleth J., Stanev E.V. Tidal and wind-driven surface currents in the German Bight: HFR observations versus model simulations. Ocean Dyn. 2011, 61:1567-1585.
39. Pruesse E., Quast C., Knittel K., Fuchs B.M., Ludwig W.G., Peplies J., Glöckner F.O. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007, 35:7188-7196.
40. Riedel T., Tomasch J., Buchholz I., Jacobs J., Kollenberg M., Gerdts G., Wichels A., Brinkhoff T., Cypionka H., Wagner-Döbler I. Constitutive expression of the proteorhodopsin gene by a flavobacterium strain representative of the proteorhodopsin-producing microbial community in the North Sea. Appl. Environ. Microbiol. 2010, 76:3187-3197.
41. Rink B., Martens T., Fischer D., Lemke A., Grossart H.P., Simon M., Brinkhoff T. Short-term dynamics of bacterial communities in a tidally affected coastal ecosystem. FEMS Microbiol. Ecol. 2008, 66:306-319.
42. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4:406-425.
43. Salaün S., Kervarec N., Potin P., Haras D., Piotto M., La Barre S. Whole-cell spectroscopy is a convenient tool to assist molecular identification of cultivatable marine bacteria and to investigate their adaptive metabolism. Talanta 2010, 80:1758-1770.
44. Sapp M., Wichels A., Gerdts G. Impacts of cultivation of marine diatoms on the associated bacterial community. Appl. Environ. Microbiol. 2007, 73:3117-3120.
45. Stackebrandt E., Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol. Today 2006, 33:152-155.
46. Stevens H., Simon M., Brinkhoff T. Cultivable bacteria from bulk water, aggregates, and surface sediments of a tidal flat ecosystem. Ocean Dyn. 2009, 59:291-304.
47. Stevens H., Stübner M., Simon M., Brinkhoff T. Phylogeny of Proteobacteria and Bacteroidetes from oxic habitats of a tidal flat ecosystem. FEMS Microbiol. Ecol. 2005, 54:351-365.
48. Suzuki M., Nakagawa Y., Harayama S., Yamamoto S. Phylogenetic analysis and taxonomic study of marine Cytophaga-like bacteria: proposal for Tenacibaculum gen. nov. with Tenacibaculum maritimum comb. nov. and Tenacibaculum ovolyticum comb. nov., and description of Tenacibaculum mesophilum sp. nov. and Tenacibaculum amylolyticum sp. nov. Int. J. Syst. Evol. Microbiol. 2001, 51:1639-1652.
49. Teeling H., Fuchs B.M., Becher D., Klockow C., Gardebrecht A., Bennke C.M., Kassabgy M., Huang S., Mann A.J., Waldmann J., Weber M., Klindworth A., Otto A., Lange J., Bernhardt J., Reinsch C., Hecker M., Peplies J., Bockelmann F.D., Callies U., Gerdts G., Wichels A., Wiltshire K.H., Glöckner F.O., Schweder T., Amann R. Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science 2012, 336:608-611.
50. Teske A., Brinkhoff T., Muyzer G., Moser D.P., Rethmeier J., Jannasch H.W. Diversity of thiosulfate-oxidizing bacteria from marine sediments and hydrothermal vents. Appl. Environ. Microbiol. 2000, 66:3125-3133.
51. Wichels A., Würtz S., Döpke H., Schütt C., Gerdts G. Bacterial diversity in the breadcrumb sponge Halichondria panicea (Pallas). FEMS Microbiol. Ecol. 2006, 56:102-118.
52. Widdel F., Bak F. Gram-negative mesophilic sulfate-reducing bacteria. The Prokaryotes 1992, 3352-3378. Springer Verlag, Berlin, Germany. A. Balows, H.G. Trüper, M. Dworkin, W. Harder (Eds.).
53. Winkelmann N., Harder J. An improved isolation method for attached-living Planctomycetes of the genus Rhodopirellula. J. Microbiol. Methods 2009, 77:276-284.
54. Yarza P., Ludwig W., Euzéby J., Amann R., Schleifer K.-H., Glöckner F.O., Rosselló-Móra R. Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses. Syst. Appl. Microbiol. 2010, 33:291-299.
55. Zinger L., Amaral-Zettler L.A., Fuhrman J.A., Horner-Devine M.C., Huse S.M., Welch D.B.M., Martiny J.B.H., Sogin M., Boetius A., Ramette A. Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems. PLoS ONE 2011, 6:e24570.
56. ZoBell C.E. Studies on marine bacteria. I. The cultural requirements of heterotrophic aerobes. J. Mar. Res. 1941, 4:42-75.
57. ZoBell C.E., Johnson F.H. The influence of hydrostatic pressure on the growth and viability of terrestrial and marine bacteria. J. Bacteriol. 1949, 57:179-189.
58. Zubkov M.V., Fuchs B.M., Archer S.D., Kiene R.P., Amann R., Burkill P.H. Linking the composition of bacterioplankton to rapid turnover of dissolved dimethylsulphoniopropionate in an algal bloom in the North Sea. Environ. Microbiol. 2001, 3:304-311.