A novel cost effective and high-throughput isolation and identification method for marine microalgae

Plant Methods

Volumn 10, Issue 1, 2014, Pages

  Jahn, Martin T ^a,b   Schmidt, Katrin ^a   Mock, Thomas ^a  

^a UNIVERSITY OF EAST ANGLIA   (United Kingdom)

^b UNIVERSITY OF WÜRZBURG   (Germany)

Author keywords

Cultivation; Direct PCR; Isolation; Marine microalgae; Taxonomy

Indexed keywords

EID: 84905857927     PISSN: None     EISSN: 17464811     Source Type: Journal    
DOI: 10.1186/1746-4811-10-26     Document Type: Article

References (44)

1. Platt T, Fuentes-Yaco C, Frank KT. Marine ecology: spring algal bloom and larval fish survival. Nature 2003, 423:398-399.
2. Gosselin M, Levasseur M, Wheeler PA, Horner RA, Booth BC. New measurements of phytoplankton and ice algal production in the Arctic Ocean. Deep Sea Res Part II Top Stud Oceanography 1997, 44:1623-1644.
3. Schwartz RE, Hirsch CF, Sesin DF, Flor JE, Chartrain M, Fromtling RE, Harris GH, Salvatore MJ, Liesch JM, Yudin K. Pharmaceuticals from cultured algae. J Ind Microbiol 1990, 5:113-123.
4. Borowitzka MA. Microalgae as sources of pharmaceuticals and other biologically active compounds. J Appl Phycol 1995, 7:3-15.
5. Kim SK, Ravichandran YD, Khan SB, Kim YT. Prospective of the cosmeceuticals derived from marine organisms. Biotechnol Bioproc E 2008, 13:511-523.
6. Lee RF, Valkirs AO, Seligman PF. Importance of microalgae in the biodegradation of tributyltin in estuarine waters. Environ Sci Technol 1989, 23:1515-1518.
7. Cardinale BJ. Biodiversity improves water quality through niche partitioning. Nature 2011, 472:86-89.
8. EI-Sheekh M, Ghareib M, EL-Souod GA. Biodegradation of phenolic and polycyclic aromatic compounds by some algae and Cyanobacteria. J Bioremediation Biodegradation 2011, 3:133.
9. Waltz E. Biotech's green gold?. Nat Biotech 2009, 27:15-18.
10. Toseland A, Daines SJ, Clark JR, Kirkham A, Strauss J, Uhlig C, Lenton TM, Valentin K, Pearson GA, Moulton V, Mock T. The impact of temperature on marine phytoplankton resource allocation and metabolism. Nat Clim Change 2013, 3:979-984.
11. Cuvelier ML, Allen AE, Monier A, McCrow JP, Messie´ M, Tringe SG, Woyke T, Welsh RM, Ishoey T, Lee J-H, Binder BJ, DuPont CL, Latasa M, Guigand C, Buck KR, Hilton J, Thiagarajan M, Caler E, Read B, Lasken RS, Chavez FP, Worden AZ. Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton. Proc Natl Acad Sci 2010, 107:14679-14684.
12. Worden AZ, Lee J-H, Mock T, Rouze´ P, Simmons MP, Aerts AL, Allen AE, Cuvelier ML, Derelle E, Everett MV, Foulon E, Grimwood J, Gundlach H, Henrissat B, Napoli C, McDonald SM, Parker MS, Rombauts S, Salamov A, Von Dassow P, Badger JH, Coutinho PM, Demir E, Dubchak I, Gentemann C, Eikrem W, Gready JE, John U, Lanier W, Lindquist EA, et al. Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science 2009, 324:268-272.
13. Marchetti A, Schruth DM, Durkin CA, Parker MS, Kodner RB, Berthiaume CT, Morales R, Allen AE, Armbrust EV. Comparative metatranscriptomics identifies molecular bases for the physiological responses of phytoplankton to varying iron availability. Proc Natl Acad Sci 2012, 109:E317-E325.
14. Chen W, Zhang C, Song LR, Sommerfeld M, Hu Q. A high throughput Nile red method for quantitative measurement of neutral lipids in microalgae. J Microbiol Meth 2009, 77:41-47.
15. Slocombe SP, Zhang QY, Black KD, Day JG, Stanley MS. Comparison of screening methods for high-throughput determination of oil yields in micro-algal biofuel strains. J Appl Phycol 2013, 25:961-972.
16. Plaza M, Santoyo S, Jaime L, Garci´a-Blairsy Reina G, Herrero M, Señora´ns FJ, Iba´ñez E. Screening for bioactive compounds from algae. J Pharm Biomed Anal 2010, 51:450-455.
17. Wuyts J, De Rijk P, Van de Peer Y, Pison G, Rousseeuw P, De Wachter R. Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA. Nucleic Acids Res 2000, 28:4698-4708.
18. Davies H, Bignell GR, Cox C, Stephens P, Edkins S, Clegg S, Teague J, Woffendin H, Garnett MJ, Bottomley W, Davis N, Dicks E, Ewing R, Floyd Y, Gray K, Hall S, Hawes R, Hughes J, Kosmidou V, Menzies A, Mould C, Parker A, Stevens C, Watt S, Hooper S, Wilson R, Jayatilake H, Gusterson BA, Cooper C, Shipley J, Hargrave D, et al. Mutations of the BRAF gene in human cancer. Nature 2002, 417:949-954.
19. Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. error probabilities. Genome Res 1998, 8:186-194.
20. Applied Biosystems™ User bulletin- KB™ basecaller software v1.4.1. [http://tools.lifetechnologies.com/content/sfs/manuals/cms_079032.pdf], Applied Biosystems™.
21. Day JG, Fleck RA, Benson EE. Cryopreservation-recalcitrance in microalgae: novel approaches to identify and avoid cryo-injury. J Appl Phycol 2000, 12:369-377.
22. Bui TVL, Ross IL, Jakob G, Hankamer B. Impact of procedural steps and cryopreservation agents in the cryopreservation of Chlorophyte microalgae. PLoS One 2013, 8:e78668.
23. Andersen RA, Kawachi M. Traditional microalgae isolation techniques. Algal culturing techniques 2005, 83-100. Burlington, USA: Elsevier Academic Press, Andersen RA.
24. Booth BC, Horner RA. Microalgae on the arctic ocean section, 1994: species abundance and biomass. Deep Sea Res Part II Top Stud Oceanography 1997, 44:1607-1622.
25. Zhang F, He JF, Xia LH, Cai MH, Lin L, Guang YZ. Applying and comparing two chemometric methods in absorption spectral analysis of photopigments from Arctic microalgae. J Microbiol Meth 2010, 83:120-126.
26. Vaulot D, Le Gall F, Marie D, Guillou L, Partensky F. The Roscoff Culture Collection (RCC): a collection dedicated to marine picoplankton. Nova Hedwigia 2004, 79:49-70.
27. Lizotte MP, Priscu JC. Photosynthesis- irradiance relationships in phytoplankton from the physically stable water column of a perennially ice- covered lake (Lake Bonney, Antarctica). J Phycol 1992, 28:179-185.
28. Pocock T, Lachance M-A, Pro¨schold T, Priscu JC, Kim SS, Huner NPA. Identification of a psychrophilic green alga from Lake Bonney Antarctica: Chlamydomonas raudensis Ettl. (UWO 241) Chlorophyceae. J Phycol 2004, 40:1138-1148.
29. Sa¨wstro¨m C, Mumford P, Marshall W, Hodson A, Laybourn-Parry J. The microbial communities and primary productivity of cryoconite holes in an Arctic glacier (Svalbard 79°N). Polar Biol 2002, 25:591-596.
30. Majaneva M, Rintala J-M, Piisila¨ M, Fewer DP, Blomster J. Comparison of wintertime eukaryotic community from sea ice and open water in the Baltic Sea, based on sequencing of the 18S rRNA gene. Polar Biol 2012, 35:875-889.
31. Doan TTY, Sivaloganathan B, Obbard JP. Screening of marine microalgae for biodiesel feedstock. Biomass Bioenergy 2011, 35:2534-2544.
32. Montero MF, Aristiza´bal M, Garci´a Reina G. Isolation of high-lipid content strains of the marine microalga Tetraselmis suecica for biodiesel production by flow cytometry and single-cell sorting. J Appl Phycol 2011, 23:1053-1057.
33. Wan MX, Rosenberg JN, Faruq J, Betenbaugh MJ, Xia JL. An improved colony PCR procedure for genetic screening of Chlorella and related microalgae. Biotechnol Lett 2011, 33:1615-1619.
34. Radha S, Fathima AA, Iyappan S, Ramya M. Direct colony PCR for rapid identification of varied microalgae from freshwater environment. J Appl Phycol 2013, 25:609-613.
35. Zamora I, Feldman J, Marshall W. PCR-based assay for mating type and diploidy in Chlamydomonas. Biotechniques 2004, 37:534-536.
36. Stoeck T, Bass D, Nebel M, Christen R, Jones MD, Breiner HW, Richards TA. Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Mol Ecol 2010, 19(Suppl 1):21-31.
37. Eurofins MWG Operon Sequencing result guide. 2011, 2014. http://www.eurofinsgenomics.eu, Eurofins MWG Operon.
38. Guillard RRL. Culture of Phytoplankton for feeding marine invertebrates. Culture of Marine Invertebrate Animals 1975, 29-60. New York, USA: Plenum Press, Smith WL, Chanley MH.
39. Applied Biosystems™ System profile applied biosystems 3130 and 3130xl genetic analyzers. [www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_041990.pdf], Applied Biosystems™.
40. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
41. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997, 25:4876-4882.
42. Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 2007, 56:564-577.
43. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 2013, 30:2725-2729.
44. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980, 16:111-120.