Development and validation of a molecular technique for the analysis of archived formalin-preserved phytoplankton samples permits retrospective assessment of Emiliania huxleyi communities

Journal of Microbiological Methods

Volumn 73, Issue 2, 2008, Pages 118-124

  Ripley, Steven J ^a,b   Baker, Andrea C ^b   Miller, Peter I ^c   Walne, Anthony W ^d   Schroeder, Declan C ^b  

^a UNIVERSITY OF PLYMOUTH   (United Kingdom)

^b THE LABORATORY   (United Kingdom)

^c PLYMOUTH MARINE LABORATORY   (United Kingdom)

^d THE LABORATORY   (United Kingdom)

Author keywords

Continuous plankton recorder; Emiliania huxleyi; PCR

Indexed keywords

CALCIUM CARBONATE; FORMALDEHYDE; NUCLEIC ACID;

ALGA; ALLELE; ARTICLE; CONTROLLED STUDY; DNA DEGRADATION; DNA MODIFICATION; EMILIANIA HUXLEYI; MOLECULAR BIOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYTOPLANKTON; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; UNTRANSLATED REGION;

BASE SEQUENCE; DNA, ALGAL; ENVIRONMENTAL MICROBIOLOGY; FIXATIVES; FORMALDEHYDE; MOLECULAR SEQUENCE DATA; PHYTOPLANKTON; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EMILIANIA HUXLEYI; HAPTOPHYCEAE;

EID: 42249094874     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2008.02.001     Document Type: Article

References (31)

1. Batten S.D., Clark R., Flinkman J., Hays G., John E., John A.W.G., Jonas T., Lindley J.A., Stevens D.P., and Walne A. CPR sampling: the technical background, materials and methods, consistency and comparability. Prog. Oceanogr. 57 (2003) 193-215
2. Bhadury P., Austen M.C., Bilton D.T., Lambshead P.J.D., Rogers A.D., and Smerdon G.R. Combined morphological and molecular analysis of individual nematodes through short-term preservation in formalin. Mol. Ecol. Notes 5 (2005) 965-968
3. Brown C.W., and Podestá G.P. Remote sensing of coccolithophore blooms in the Western South Atlantic Ocean. Remote Sens. Environ. 60 (1997) 83-91
4. Bucklin A., and Allen L.D. MtDNA sequencing from zooplankton after long-term preservation in buffered formalin. Mol. Phylogenet. Evol. 30 (2004) 879-882
5. Burkill P.H., Archer S.D., Robinson C., Nightingale P.D., Groom S.B., Tarran G.A., and Zubkov M.V. Dimethyl sulphide biogeochemistry within a coccolithophore bloom (DISCO): an overview. Deep-Sea Res. Oceanogr. B 49 (2002) 2863-2885
6. Corstjens P.L.A.M., Van Der Kooij A., Linschooten C., Brouwers G.J., Westbroek P., and De Vrind-De Jong E.W. GPA, a calcium-binding protein in the coccolithophorid Emiliania huxleyi (Prymnesiophyceae). J. Phycol. 34 (1998) 622-630
7. Coxall H.K., Wilson P.A., Palike H., Lear C.H., and Backman J. Rapid stepwise onset of Antarctic glaciation and deeper calcite compensation in the Pacific Ocean. Nature 433 (2005) 53-57
8. De Giorgi C., Finetti Sialer M., and Lamberti F. Formalin-induced infidelity in PCR-amplified DNA fragments. Mol. Cell. Probes 8 (1994) 459-462
9. Edwards M., and Richardson A.J. Impact of climate change on marine pelagic phenology and trophic mismatch. Nature 430 (2004) 881-884
10. France S.C., and Kocher T.D. DNA sequencing of formalin-fixed crustaceans from archival research collections. Mol. Mar. Biol. Biotechnol. 5 (1996) 304-313
11. Guillard R.R.L. Culture of phytoplankton for feeding marine invertebrates. In: Smith W.L., and Chanley M.H. (Eds). Culture of marine invertebrate animals (1975), Plenum Press 29-60
12. Hamazaki S., Koshiba M., Habuchi T., Takahashi R., and Sugiyama T. The effect of formalin fixation on restriction endonuclease digestion of DNA and PCR amplification. Pathol. Res. Prac. 189 (1993) 553-557
13. Hays G.C., Warner A.J., John A.W.G., Harbour D.S., and Holligan P.M. Coccolithophores and the Continuous Plankton Recorder survey. J. Mar. Biol. Assoc. U.K. 75 (1995) 503-506
14. Hays G.C., Richardson A.J., and Robinson C. Climate change and marine plankton. Trends Ecol. Evol. 20 (2005) 337-344
15. Herfort L., Thake B., and Roberts J. Acquisition and use of bicarbonate by Emiliania huxleyi. New Phytol. 156 (2002) 427-436
16. Holligan P.M., Groom S.B., and Harbour D.S. What controls the distribution of the coccolithophore, Emiliania huxleyi, in the North Sea?. Fisheries Oceanogr. 2 (1993) 175-183
17. Holligan P.M., Viollier M., Harbour D.S., Camus P., and Champagne- Philippe M. Satellite and ship studies of coccolithophore production along a continental shelf edge. Nature 304 (1983) 339-342
18. Kirby R.R., and Lindley J.A. Molecular analysis of Continuous Plankton Recorder samples, an examination of echinoderm larvae in the North Sea. J. Mar. Biol. Assoc. U.K. 85 (2005) 451-459
19. Koshiba M., Ogawa K., Hamazaki S., Sugiyama T., Ogawa O., and Kitajima T. The effect of formalin fixation on DNA and the extraction of high-molecular-weight DNA from fixed and embedded tissues. Pathol. Res. Pract. 189 (1993) 66-72
20. Martinez-Martinez J., Schroeder D.C., Larsen A., Bratbak G., and Wilson W.H. Molecular dynamics of Emiliania huxleyi and co-occurring viruses in two separate mesocosm studies. Appl. Environ. Microbiol. 73 (2007) 554-562
21. Merico A., Tyrrell T., Lessard E.J., Oguz T., Stabeno P.J., Zeeman S.I., and Whitledge T.E. Modelling phytoplankton succession on the Bering Sea shelf: role of climate influences and trophic interactions in generating Emiliania huxleyi blooms 1997-2000. Deep-Sea Res. Oceanogr. A 51 (2004) 1803-1826
22. Paasche E. A review of the coccolithophorid Emiliania huxleyi (Prymnesiophyceae), with particular reference to growth, coccolith formation, and calcification-photosynthesis interactions. Phycologia 40 (2001) 503-529
23. Richardson A.J., and Schoeman D.S. Climate impact on plankton ecosystems in the Northeast Atlantic. Science 305 (2004) 1609-1612
24. Richardson A.J., Walne A.W., John A.W.G., Jonas T.D., Lindley J.A., Sims D.W., Stevens D., and Witt M. Using continuous plankton recorder data. Prog. Oceanogr. 68 (2006) 27-74
25. Robertson J.E., Robinson C., Turner D.R., Holligan P., Watson A.J., Boyd P., Fernandez E., and Finch M. The impact of a coccolithophore bloom on oceanic carbon uptake in the northeast Atlantic during summer 1991. Deep-Sea Res. Oceanogr. A 41 (1994) 297-314
26. Sambrook J., Fritsch E.F., and Maniatis T. Molecular Cloning - A Laboratory Manual (1989), Cold Spring Harbour Laboratory Press
27. Schander C., and Halanych K.M. DNA, PCR and formalinized animal tissue - a short review and protocols. Org. Divers. Evol. 3 (2003) 195-205
28. Schroeder D.C., Biggi G.F., Hall M., Davy J., Martínez Martínez J., Richardson A.J., Malin G., and Wilson W.H. A genetic marker to separate Emiliania huxleyi (Prymnesiophyceae) morphotypes. J. Phycol. 41 (2005) 874-879
29. Vanbleijswijk J.D.L., Kempers R.S., Veldhuis M.J., and Westbroek P. Cell and growth characteristics of type-A and type-B of Emiliania huxleyi (Prymnesiophyceae) as determined by flow cytometry and chemical analyses. J. Phycol. 30 (1994) 230-240
30. Westbroek P. A model system approach to biological climate forcing. The example of Emiliania huxleyi. Glob. Planet. Change 8 (1993) 27-46
31. Widdicombe C.E., Archer S.D., Burkill P.H., and Widdicombe S. Diversity and structure of the microplankton community during a coccolithophore bloom in the stratified northern North Sea. Deep-Sea Res. Oceanogr. B 49 (2002) 2887-2903