Comparison of different DNA-extraction techniques to investigate the bacterial community of marine copepods

Helgoland Marine Research

Volumn 64, Issue 4, 2010, Pages 331-342

  Brandt, Petra ^a   Gerdts, Gunnar ^a   Boersma, Maarten ^a   Wiltshire, Karen H ^a   Wichels, Antje ^a  

^a ALFRED WEGENER INSTITUTE FOR POLAR AND MARINE RESEARCH   (Germany)

Author keywords

Bacteria; Copepod; DGGE; DNA extraction; Helgoland roads

Indexed keywords

CRUSTACEAN; DNA; MICROBIAL COMMUNITY;

ATLANTIC OCEAN; NORTH SEA;

ACARTIA; ACARTIA TONSA; ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); COPEPODA; TEMORA;

EID: 78449238459     PISSN: 1438387X     EISSN: 14383888     Source Type: Journal    
DOI: 10.1007/s10152-010-0188-1     Document Type: Article

References (48)

1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 25: 3389-3402.
2. Azam F, Fenchel T, Field JG, Gray JS, Meyer-Reil LA, Thingstad F (1983) The ecological role of water-column microbes in the sea. Mar Ecol Prog Ser 10: 257-263.
3. Carman KR, Dobbs FC (1997) Epibiotic microorganisms on copepods and other marine crustaceans. Microsc Res Tech 37: 116-135.
4. Casamayor EO, Schäfer H, Bañeras L, Pedrós-Alió C, Muyzer G (2000) Identification of and spatio-temporal differences between microbial assemblages from two neighboring sulfurous lakes: comparison by microscopy and denaturing gradient gel electrophoresis. Appl Environ Microbiol 66: 499-508.
5. Cole JR, Chai B, Marsh TL, Farris RJ, Wang Q, Kulam SA, Chandra S, McGarrell DM, Schmidt TM, Garrity GM, Tiedje JM (2003) The ribosomal database project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucl Acids Res 31: 442-443.
6. Cooksey KE, Wigglesworth-Cooksey B (1995) Adhesion of bacteria and diatoms to surfaces in the sea: a review. Aquat Microb Ecol 9: 87-96.
7. Costerton JW, Geesey GG, Cheng K-J (1978) How bacteria stick. Sci Am 238: 86-95.
8. Cushing DH (1989) A difference in structure between ecosystems in strongly stratified waters and in those that are only weakly stratified. J Plankton Res 11: 1-13.
9. Dang H, Li T, Chen M, Huang G (2008) Cross-ocean distribution of Rhodobacterales bacteria as primary surface colonizers in temperate coastal marine waters. Appl Environ Microbiol 74: 52-60.
10. Dawson MP, Humphrey BA, Marshall KC (1981) Adhesion: a tactic in the survival strategy of a marine Vibrio during starvation. Curr Microbiol 6: 195-199.
11. Eilers H, Pernthaler J, Peplies J, Glöckner FO, Gerdts G, Amann R (2001) Isolation of novel pelagic bacteria from the German Bight and their seasonal contributions to surface picoplankton. Appl Environ Microbiol 67: 5134-5142.
12. Felsenstein J (1993) Phylip (phylogeny inference package), version 3. 5c. Department of Genetics, University of Washington, Seattle.
13. Hansen B, Bech G (1996) Bacteria associated with a marine planktonic copepod in culture. I. Bacterial genera in seawater, body surface, intestines and fecal pellets and succession during fecal pellet degradation. J Plankton Res 18: 257-273.
14. Hasegawa T, Koike I, Mukai H (2001) Fate of food nitrogen in marine copepods. Mar Ecol Prog Ser 210: 167-174.
15. Huq A, Small EB, West PA, Huq MI, Rahman R, Colwell RR (1983) Ecological relationships between Vibrio cholerae and planktonic crustacean copepods. Appl Environ Microbiol 45: 275-283.
16. Huq A, West PA, Small EB, Huq MI, Colwell RR (1984) Influence of water temperature, salinity, and pH on survival and growth of toxigenic Vibrio cholerae serovar 01 associated with live copepods in laboratory microcosms. Appl Environ Microbiol 48: 420-424.
17. Kan J, Wang K, Chen F (2006) Temporal variation and detection limit of an estuarine bacterioplankton community analyzed by denaturing gradient gel electrophoresis (DGGE). Aquat Microb Ecol 42: 7-18.
18. Liao P-C, Huang B-H, Huang S (2007) Microbial community composition of the Danshui river estuary of Northern Taiwan and the practicality of the phylogenetic method in microbial barcoding. Microb Ecol 54: 497-507.
19. 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 AW, 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 (2004) Arb: a software environment for sequence data. Nucl Acids Res 32: 1363-1371.
20. Matz C, McDougald D, Moreno A, Yung P, Yildiz F, Kjelleberg S (2005) Biofilm formation and phenotypic variation enhance predation-driven persistence of Vibrio cholerae. PNAS 102: 16819-16824.
21. Møller EF (2005) Sloppy feeding in marine copepods: prey-size-dependent production of dissolved organic carbon. J Plankton Res 27: 27-35.
22. Møller EF, Nielsen TG (2001) Production of bacterial substrate by marine copepods: effect of phytoplankton biomass and cell size. J Plankton Res 23: 527-536.
23. Møller EF, Thor P, Nielsen TG (2003) Production of DOC by Calanus finmarchicus, C. glacialis and C. hyperboreus through sloppy feeding and leakage from fecal pellets. Mar Ecol Prog Ser 262: 185-191.
24. Møller EF, Riemann L, Søndergaard M (2007) Bacteria associated with copepods: abundance, activity and community composition. Aquat Microb Ecol 47: 99-106.
25. Morris RM, Longnecker K, Giovannoni SJ (2006) Pirellula and OM43 are among the dominant lineages identified in an Oregon coast diatom bloom. Environ Microbiol 8: 1361-1370.
26. Murray AE, Hollibaugh JT, Orrego C (1996) Phylogenetic compositions of bacterioplankton from two California estuaries compared by denaturing gradient gel electrophoresis of 16S rDNA fragments. Appl Environ Microbiol 62: 2676-2680.
27. Muyzer G, Smalla K (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient electrophoresis (TGGE) in microbial ecology. Antonie van Leeuwenhoek 73: 127-141.
28. Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59: 695-700.
29. Nagasawa S (1989) Bacterial epibionts of copepods. Science Prog 73: 169-176.
30. Nagasawa S, Simidu U, Nemoto T (1985) Scanning electron microscopy investigation of bacterial colonization of the marine copepod Acartia clausi. Mar Biol 87: 61-66.
31. Nalin DR, Daya V, Reid A, Levine MM, Cisneros L (1979) Adsorption and growth of Vibrio cholerae on chitin. Infect Immun 25: 768-770.
32. Nübel U, Engelen B, Felske A, Snaidr J, Wieshuber A, Amann RI, Ludwig W, Backhaus H (1996) Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J Bacteriol 178: 5636-5643.
33. Olsen SN, Westh P, Hansen BW (2005) Real-time quantification of microbial degradation of copepod fecal pellets monitored by isothermal microcalorimetry. Aquat Microb Ecol 40: 259-267.
34. Payne MS, Hall MR, Sly L, Bourne DG (2007) Microbial diversity within early-stage cultured Panulirus ornatus phyllosomas. Appl Environ Microbiol 73: 1940-1951.
35. Peter H, Sommaruga R (2008) An evaluation of methods to study the gut bacterial community composition of freshwater zooplankton. J Plankton Res 30: 997-1006.
36. Roose-Amsaleg CL, Garnier-Sillam E, Harry M (2001) Extraction and purification of microbial DNA from soil and sediment samples. Appl Soil Ecol 18: 47-60.
37. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: A laboratory manual, Cold Spring Harbor Laboratory Press.
38. Sapp M, Wichels A, Wiltshire KH, Gerdts G (2007) Bacterial community dynamics during the winter-spring transition in the North Sea. FEMS Microbiol Ecol 59: 622-637.
39. Sieburth JM, Willis P-J, Johnson KM, Burney CM, Lavoie DM, Hinga KR, Caron DA, French FW III, Johnson PW, Davis PG (1976) Dissolved organic matter and heterotrophic microneuston in the surface microlayers of the North Atlantic. Science 194: 1415-1418.
40. Sigler WV, Miniaci C, Zeyer J (2004) Electrophoresis time impacts the denaturing gradient gel electrophoresis-based assessment of bacterial community structure. J Microbiol Methods 57: 17-22.
41. Sochard MR, Wilson DF, Austin B, Colwell RR (1979) Bacteria associated with the surface and gut of marine copepods. Appl Environ Microbiol 37: 750-759.
42. Steinberg DK, Nelson NB, Carlson CA, Prusak AC (2004) Production of chromophoric dissolved organic matter (CDOM) in the open ocean by zooplankton and the colonial cyanobacterium Trichodesmium spp. Mar Ecol Prog Ser 267: 45-56.
43. Tamplin ML, Gauzens AL, Huq A, Sack DA, Colwell RR (1990) Attachment of Vibrio cholerae serogroup 01 to zooplankton and phytoplankton of Bangladesh waters. Appl Environ Microbiol 56: 1977-1980.
44. Tang KW (2005) Copepods as microbial hotspots in the ocean: effects of host feeding activities on attached bacteria. Aquat Microb Ecol 38: 31-40.
45. Tang KW, Freund CS, Schweitzer CL (2006a) Occurrence of copepod carcasses in the lower Chesapeake Bay and their decomposition by ambient microbes. Estuar Coast Shelf Sci 68: 499-508.
46. Tang KW, Hutalle KML, Grossart H-P (2006b) Microbial abundance, composition and enzymatic activity during decomposition of copepod carcasses. Aquat Microb Ecol 45: 219-227.
47. v. Wintzingerode F, Göbel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21: 213-229.
48. Zobell CE (1943) The effect of solid surfaces upon bacterial activity. J Bacteriol 46: 39-56.