Marine Biotechnology

, Volume 14, Issue 2, pp 129–142 | Cite as

Molecular Detection, Quantification, and Diversity Evaluation of Microalgae

  • Vinitha Ebenezer
  • Linda K. Medlin
  • Jang-Seu Ki
Review Article


This study reviews the available molecular methods and new high-throughput technologies for their practical use in the molecular detection, quantification, and diversity assessment of microalgae. Molecular methods applied to other groups of organisms can be adopted for microalgal studies because they generally detect universal biomolecules, such as nucleic acids or proteins. These methods are primarily related to species detection and discrimination among various microalgae. Among current molecular methods, some molecular tools are highly valuable for small-scale detection [e.g., single-cell polymerase chain reaction (PCR), quantitative real-time PCR (qPCR), and biosensors], whereas others are more useful for large-scale, high-throughput detection [e.g., terminal restriction length polymorphism, isothermal nucleic acid sequence-based amplification, loop-mediated isothermal amplification, microarray, and next generation sequencing (NGS) techniques]. Each molecular technique has its own strengths in detecting microalgae, but they may sometimes have limitations in terms of detection of other organisms. Among current technologies, qPCR may be considered the best method for molecular quantification of microalgae. Metagenomic microalgal diversity can easily be achieved by 454 pyrosequencing rather than by the clone library method. Current NGS, third and fourth generation technologies pave the way for the high-throughput detection and quantification of microalgal diversity, and have significant potential for future use in field monitoring.


Microalgae Molecular techniques Detection Quantification Diversity 



This work was supported by both the Marine and Extreme Genome Research Center Program of the Ministry of Land, Transportation and Maritime Affairs, Republic of Korea, and by the National Research Foundation of Korea Grant funded by the Korean Government (MEST) (NRF-C1ABA001-2011-0018573).


  1. Ahn S, Kulis DM, Erdner DL, Anderson DM, Walt DR (2006) Fiber-optic for the simultaneous detection of multiple harmful algal bloom species. Appl Environ Microb 72(9):5742–5749CrossRefGoogle Scholar
  2. Alpermann TJ, Tillmann U, Beszteri B, Cembella AD, John U (2010) Phenotypic variation and genotypic diversity in a planktonic population of the toxigenic marine dinoflagellate Alexandrium tamarense (Dinophyceae). J Phycol 46:18–32CrossRefGoogle Scholar
  3. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59(1):143–169PubMedGoogle Scholar
  4. Amaral-Zettler LA, McCliment EA, Ducklow HW, Huse SM (2009) A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes. PLoS One 4(7):e6372PubMedCrossRefGoogle Scholar
  5. Anderson DM (1995) Identification of harmful algal species using molecular probes: an emerging technology. In: Lassus P, Arzul G, Erard E, Gentien P, Marcaillou C (eds) Harmful marine algal blooms. Lavoiser Science Publishers, Paris, pp 3–13Google Scholar
  6. Anderson DM, Walt DW (2009) A fiber optic microarray for the detection and enumeration of harmful algal bloom (HAB) species. Internal report: The NOAA/UNH cooperative institute for coastal and estuarine environmental technology (CICEET).
  7. Anderson DM, Kulis DM, Erdner D, Ahn S, Walt DR (2006) Fibre optic microarrays for the detection and enumeration of harmful algal bloom. Afr J Mar Sci 28(2):231–235CrossRefGoogle Scholar
  8. Andree KB, Fernández-Tejedor M, Elandaloussi LM, Quijano-Scheggia S, Sampedro N, Garcés E, Camp J, Diogéne J (2011) Quantitative PCR coupled with melt curve analysis for detection of selected Pseudo-nitzschia spp. (Bacillariophyceae) from the North Western Mediterranean sea. Appl Environ Microb 77(5):1651–1659CrossRefGoogle Scholar
  9. Anthony RM, Brown TJ, French GL (2000) Rapid diagnosis of bacteremia by universal amplification of 23S ribosomal DNA followed by hybridization to an oligonucleotide array. J Clin Microbiol 38(2):781–788PubMedGoogle Scholar
  10. Becker EW (2007) Microalgae as a source of protein. Biotenol Adv 25(2):207–210CrossRefGoogle Scholar
  11. Bertozzini E, PennaA PE, Bruce I, Magnani M (2005) Development of new procedures for the isolation of phytoplankton DNA from fixed samples. J Appl Phycol 17:223–229CrossRefGoogle Scholar
  12. Biegala IC, Kennaway G, Alverca E, Lennon JF, Vaulot D, Simon N (2002) Identification of bacteria associated with dinoflagellates (Dinophyceae) Alexandrium spp using tyramide signal amplification-fluorescent in situ hybridisation and confocal microscopy. J Phycol 38(2):404–411CrossRefGoogle Scholar
  13. Bott NJ, Ophel-Kellener KM, Sierp MT, Rowling KP, Mckay AC, Loo MGK, Tanner JE, Deveney MR (2010) Toward routine, DNA-based detection methods for marine pests. Biotechnol Adv 28:706–714PubMedCrossRefGoogle Scholar
  14. Bråte J, Klaveness D, Rygh T, Jakobsen KS, Shalchian-Tabrizi K (2010) Telonemia-specific environmental 18S rDNA PCR reveals unknown diversity and multiple marine-freshwater colonizations. BMC Microbiol 10:168. doi: 10.1186/1471-2180-10-168 PubMedCrossRefGoogle Scholar
  15. Britschgi TB, Giovannoni SJ (1991) Phylogenetic analysis of a natural marine bacterioplankton population by rRNA gene cloning and sequencing. Appl Environ Microbiol 57(6):1707–1713PubMedGoogle Scholar
  16. Brown MR (2002) Nutritional value of microalgae for aquculture. In: Cruz-Suárez LE, Ricque-Marie D, Tapia-Salazar M, Gaxiola-Cortés MG, Simoes N (eds) Avances en Nutrición Acuícola VI. Memorias del VI Simposium Internacional de Nutrición Acuícola. 3 al 6 de Septiembre del 2002. Cancún, Quintana Roo, MéxicoGoogle Scholar
  17. Burki F, Kudryavtsev A, Matz MV, Aglyamova GV, Bulman S, Fiers M, Keeling PJ, Pawlowski J (2010) Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists. BMC Evol Biol 10:377PubMedCrossRefGoogle Scholar
  18. Casper ET, Patterson SS, Bhanushali P, Farmer A, Smith M, Fries DP, Paul JH (2007) A handheld NASBA analyzer for the field detection and quantification of Karenia brevis. Harmful Algae 6(1):112–118CrossRefGoogle Scholar
  19. Casteleyn G, Leliaert F, Backeljau T, Debeer AE, Kotaki Y, Rhodes L, Lundholm N, Sabbe K, Vyverman W (2010) Limits to gene flow in a cosmopolitan marine planktonic diatom. Proc Natl Acad Sci USA 107(29):12952–12957PubMedCrossRefGoogle Scholar
  20. Cembella AD, Sullivan JJ, Boyer GL, Taylor FJR, Anderson RJ (1987) Variations in paralytic shellfish toxin composition within the Protogonyaulax tamarensis/catenella species complex: red tide dinoflagellates. Biochem Syst Ecol 15:171–186CrossRefGoogle Scholar
  21. Cheng KC, Ogden KL (2011) Algal biofuels: the research. American Institute of Chemical Engineers (AICHE).
  22. Cheung MK, Au CH, Chu KH, Kwan HS, Wong CK (2010) Composition and genetic diversity of pico eukaryotes in subtropical coastal waters as revealed by 454 pyrosequencing. ISME J 4:1053–1059PubMedCrossRefGoogle Scholar
  23. Chisti Y (2007) Biodiesel from microalgae. Biotechnol Adv 25(3):294–306PubMedCrossRefGoogle Scholar
  24. Cho SY, Nagai S, Nishitani G, Han MS (2009) Development of compound microsatellite markers in red-tide-causing dinoflagellate Akashiwo sanguinea (Dinophyceae). Mol Ecol Resour 9:915–917PubMedCrossRefGoogle Scholar
  25. Countway P, Gast RJ, Savala P, Caron DA (2005) Protistan diversity estimates based on 18S rDNA from seawater incubations in the Western North Atlantic. J Eukaryot Microbiol 52(2):95–106PubMedCrossRefGoogle Scholar
  26. de Bruin A, Ibelings BW, Donk EV (2003) Molecular techniques in phytoplankton research: from allozyme electrophoresis to genomics. Hydrobiologia 491(1–3):47–63CrossRefGoogle Scholar
  27. Delong EF, Pace NR (1991) Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J Bacteriol 173(14):4371–4378PubMedGoogle Scholar
  28. Diaz MR, Jacobson JW, Goodwin KD, Dubar SA, Fell JW (2010) Molecular detection of harmful algal blooms (HABs) using locked nucleic acids and bead array technology. Limnol Oceanogr Methods 8:269–284PubMedCrossRefGoogle Scholar
  29. Díez B, Pedrós-Alió C, Marsh TL, Massana R (2001) Application of denaturing gradient gel electrophoresis (DGGE) to study the diversity of marine Pico eukaryotic assemblages and comparison of DGGE with other molecular techniques. Appl Environ Microbiol 67(7):2942–2951PubMedCrossRefGoogle Scholar
  30. Dyhrman ST, Erdner D, La Du J, Galac M, Anderson DM (2006) Molecular quantification of toxic Alexandrium fundyense in the Gulf of Maine using real-time PCR. Harmful Algae 5(3):242–250CrossRefGoogle Scholar
  31. Dyhrman ST, Haley ST, Borchert JA, Lona B, Kollars N, Erdner DL (2010) Parallel analyses of Alexandrium catenella cell concentrations and shellfish toxicity in the Puget Sound. Appl Environ Microb 76(14):4647–4654CrossRefGoogle Scholar
  32. Edgcomb V, Orsi W, Bunge J, Jeon S, Christen R, Leslin C, Holder M, Taylor GT, Suarez P, Varela R, Epstein S (2011) Protistan microbial observatory in the Cariaco Basin, Caribbean I. pyrosequencing vs sanger insights in to species richness. ISME J 5:1344–1356. doi: 10.1038/ismej.2011.6 PubMedCrossRefGoogle Scholar
  33. Edvardsen B, Shalchian-Tabrizi K, Jakobsen KS, Medlin LK, Dahl E, Brubak S, Paasche E (2003) Genetic variability and molecular phylogeny of Dinophysis species (Dinophyceae) from Norwegian waters inferred from single cells analysis of rDNA. J Phycol 39(2):395–408CrossRefGoogle Scholar
  34. Edwards RA, Rodriguez-Brito B, Wegley L, Haynes M, Breitbart M, Peterson DM, Saar MO, Alexander S, Alexander EC, Rohwer F (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics 7:57PubMedCrossRefGoogle Scholar
  35. Ellison CK, Burton RS (2005) Application of bead array technology to community dynamics of marine phytoplankton. Mar Ecol Prog Ser 288:75–85CrossRefGoogle Scholar
  36. Elmqvist T, Folke C, Nyström M, Peterson G, Bengtsson J, Walker B, Norberg J (2003) Response diversity, ecosystem change, ecosystem change, and resilience. Fron Ecol Environ 1:488–494CrossRefGoogle Scholar
  37. Erdner DL, Percy L, Keafer B, Lewis J, Anderson DM (2010) A quantitative real-time PCR assay for the identification and enumeration of Alexandrium cysts in marine sediments. Deep Sea Res PT II 57:279–287CrossRefGoogle Scholar
  38. Evans KM, Chepurnov VA, Mann DG (2009) Ten microsatellite markers for the freshwater diatom Sellaphora capitata. Mol Ecol Resour 9:216–218PubMedCrossRefGoogle Scholar
  39. Galluzzi L, Penna A, Bertozzini E, Vila M, Garces E, Magnani M (2004) Development of a real-time PCR assay for rapid detection and quantification of Alexandrium minutum (a dinoflagellate). Appl Environ Microbiol 70(2):1199–1206PubMedCrossRefGoogle Scholar
  40. Galluzzi L, Bertozzini E, Penna A, Perini F, Garcés E, Magnani M (2010) Analysis of rRNA gene content in the Mediterranean dinoflagellate Alexandrium catenella and Alexandrium taylori: implications for the quantitative real-time PCR-based monitoring methods. J Appl Phycol 22(1):1–9CrossRefGoogle Scholar
  41. Galluzzi L, Cegna A, Casabianca S, Penna A, Saunders N, Magnani M (2011) Development of an oligonucleotide microarray for the detection and monitoring of marine dinoflagellates. J Microbiol Meth 84(2):234–242CrossRefGoogle Scholar
  42. Gescher C, Metfies K, Frickenhaus S, Knefelkamp B, Wiltshire KH, Medlin LK (2008) Feasibility of assessing the community composition of Prasinophytes at the Helgoland Roads sampling site with a DNA microarray. Appl Env Microbiol 74:5305–5316CrossRefGoogle Scholar
  43. Godhe A, Asplund ME, Härnström K, Saravanan V, Tyagi A, Karunasagar I (2008) Quantification of diatom and dinoflagellate biomasses in coastal marine seawater samples by real-time PCR. Appl Environ Microbiol 74(23):7174–7182PubMedCrossRefGoogle Scholar
  44. Guo Z, Guilfoyle RA, Thiel AJ, Wang R, Smith LM (1994) Direct fluorescence analysis of genetic polymorphisms by hybridization with oligonucleotides arrays on glass supports. Nucleic Acids Res 22:5456–5465PubMedCrossRefGoogle Scholar
  45. Handy SM, Demir E, Hutchins DA, Portune KJ, Whereat EB, Hare CE, Rose JM, Warner M, Farestad M, Cary S, Coyne KJ (2008) Using quantitative real-time PCR to study competition and community dynamics among Delaware Inland Bays harmful algae in field and laboratory studies. Harmful Algae 7(5):599–613CrossRefGoogle Scholar
  46. Hosoi-Tanabe S, Sako Y (2005) Rapid detection of natural cells of Alexandrium tamarense and A. catenella (Dinophyceae) by fluorescence in situ hybridization. Harmful Algae 4(2):319–328CrossRefGoogle Scholar
  47. Hosoi-Tanabe S, Sako Y (2006) Development and application of fluorescence in situ hybridization (FISH) method for simple and rapid identification of the toxic dinoflagellates Alexandrium tamarense and Alexandrium catenella in cultured and natural seawater. Fish Sci 72(1):77–82CrossRefGoogle Scholar
  48. Hubbard KA, Rocap G, Armbrust EV (2008) Inter- and intraspecific community structure within the diatom genus Pseudo-nitzschia (Bacillariophyceae). J Phycol 44(3):637–649CrossRefGoogle Scholar
  49. Joo S, Lee S-R, Park S (2010) Monitoring of phytoplankton community structure using terminal restriction fragment length polymorphism (T-RFLP). J Microbiol Meth 81(1):61–68CrossRefGoogle Scholar
  50. Ki J-S (2011) Hypervariable regions (V1-V9) of the dinoflagellate 18S rRNA using a large dataset for marker considerations. J Appl Phycol. doi: 10.1007/s10811-011-9730-z
  51. Ki J-S, Han M-S (2005) Sequence-based diagnostics and phylogenetic approach of uncultured freshwater dinoflagellate Peridinium (Dinophyceae) species, based on single-cell sequencing of rDNA. J Appl Phycol 17(2):147–153CrossRefGoogle Scholar
  52. Ki J-S, Han M-S (2006) A low-density oligonucleotide array study for parallel detection of harmful algal species using hybridization of consensus PCR products of LSU rDNA D2 domain. Biosens Bioelectron 21(9):1812–1821PubMedCrossRefGoogle Scholar
  53. Ki J-S, Jang GY, Han M-S (2004) Integrated method for single-cell DNA extraction, PCR amplification, and sequencing of ribosomal DNA from harmful dinoflagellates Cochlodinium polykrikoides and Alexandrium catenella. Mar Biotechnol 6(6):587–593PubMedCrossRefGoogle Scholar
  54. Kudela RM, Howard MDA, Jenkins BD, Miller PE, Smith GJ (2010) Using the molecular toolbox to compare harmful algal blooms in upwelling systems. Prog Oceanogr 85(1–2):108–121CrossRefGoogle Scholar
  55. Kumari N, Srivastava AK, Bhargava P, Rai LK (2009) Molecular approaches towards assessment of cyanobacterial biodiversity. Afr J Biotechnol 8(18):4284–4298Google Scholar
  56. Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR (1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci USA 82(20):6955–6959PubMedCrossRefGoogle Scholar
  57. Lepère C, Vaulot D, Scanlan DJ (2009) Photosynthetic picoeukaryotic community structure in the South East Pacific Ocean encompassing the most oligotrophic waters on Earth. Environ Microbiol 11(12):3105–3117PubMedCrossRefGoogle Scholar
  58. Lindquist HDA (1997) Probes for the specific detection of Cryptosporidium parvum. Water Res 31(10):2668–2671CrossRefGoogle Scholar
  59. Litaker RW, Tester PA (2006) Molecular approaches to the study of phytoplankton life cycles: implications for harmful algal bloom ecology. In: Granéli E, Turner T (eds) Ecology of harmful algae, ecological studies, vol 189. Springer, Heidelberg, pp 299–309CrossRefGoogle Scholar
  60. Liu W, Marsh T, Cheng H, Forney L (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63:4516–4522PubMedGoogle Scholar
  61. Liu H, Wang H, Shi Z, Wang H, Yang C, Silke S, Tan W, Li Z (2006) TaqMan probe array for quantitative detection of DNA targets. Nucleic Acids Res 34(1):1–8CrossRefGoogle Scholar
  62. Man-Aharonovich D, Philosof A, Kirkup BC, Gal FL, Yogev T, Berman-Frank I, Polz MF, Vaulot D, Béjà O (2010) Diversity of active marine picoeukaryotes in the Eastern Mediterranean Sea unveiled using photosystem-II psbA transcripts. ISME J 4:1044–1052PubMedCrossRefGoogle Scholar
  63. Mao F, Leung W-Y, Xin X (2007) Characterization of EvaGreen and the implication of its physicochemical properties for qPCR applications. BMC Biotechnol 7:76PubMedCrossRefGoogle Scholar
  64. McCliment EA, Nelson CE, Carlson CA, Alldredge AL, Witting J, Amaral-Zettler LA (2011) An all-taxon microbial inventory of the Moorea coral reef ecosystem. ISME J. doi: 10.1038/ismej.2011.108
  65. Medinger R, Nolte V, Pandey RV (2010) Diversity in a hidden world: potential and limitation of next generation sequencing for surveys of molecular diversity of eukaryotic microorganisms. Mol Ecol 19(1):32–40PubMedCrossRefGoogle Scholar
  66. Medlin LK, Kooistra WHCF (2010) Methods to estimate the diversity in the marine photosynthetic protist community with illustrations from case studies: a review. Diversity 2:973–1014CrossRefGoogle Scholar
  67. Medlin LK, Lange M, Noethig EV (2000) Genetic diversity in the marine phytoplankton: a review and a consideration of Antarctic phytoplankton. Antarct Sc 12:325–331Google Scholar
  68. Medlin LK, Metfies K, Mehl H, Wiltshire K, Valentin K (2006) Picoplankton diversity at the Helgoland Time Series Site as assessed by three molecular methods. Microb Ecol 167:1432–1451Google Scholar
  69. Medlin LK, Metfies K, John U, Olsen J (2007) Algal molecular systematics: a review of the past and prospects for the future. In: Broadie J, Lewis J (eds) Unravelling the algae: the past, present and future of algal systematics. Sys Assn Special Vol Ser 75. CRC Press, Taylor & Francis Group, London, pp 341–353CrossRefGoogle Scholar
  70. Metfies K, Medlin LK (2008) Feasibility of transferring fluorescent in situ hybridization probes to an 18S rRNA gene phylochip and mapping of signal intensities. Appl Envron Microbiol 74:2814–2821CrossRefGoogle Scholar
  71. Metfies K, Huljic S, Lange M, Medlin LK (2005) Electrochemical detection of the toxic dinoflagellate Alexandrium ostenfeldii with a DNA-biosensor. Biosens Bioelectron 20:1349–1357PubMedCrossRefGoogle Scholar
  72. Metfies K, Töbe K, Scholin CA, Medlin LK (2006) Laboratory and field applications of ribosomal RNA probes to aid the detection and monitoring of Harmful Algae. In: Granéli E, Turner JT (eds) Ecology of harmful algae. Springer Verlag, Berlin, Heidelberg, pp 11–325Google Scholar
  73. Metzker ML (2010) Sequencing technologies—the next generation. Nat Rev 11:31–46CrossRefGoogle Scholar
  74. Mitterer G, Huber M, Leidinger E, Kiristis C, Lubitz W, Mueller MW, Schmidt WM (2004) Microarray-based identification of bacteria in clinical samples by solid-phase PCR amplification of 23S ribosomal DNA sequences. J Clin Microbiol 42(2):1048–1057PubMedCrossRefGoogle Scholar
  75. Moreira D, López-García P (2002) The molecular ecology of microbial eukaryotes unveils a hidden world. Trends Microbiol 10:31–38PubMedCrossRefGoogle Scholar
  76. Mori Y, Nagamine K, Tomita N, Notomi T (2001) Detection of loop-mediated isothermal amplification reaction by turbidity derived from magnesium pyrophosphate formation. Biochem Bioph Res Co 289:150–154CrossRefGoogle Scholar
  77. Nagai SC, Lian S, Yamaguchi M, Hamaguchi Y, Matsuyama S, Itakura H, Shimada S, Kaga H, Yamauchi Y, Sonda T, Kim C, Hogetsu T (2007) Microsatellite markers reveal population genetic structure of the toxic dinoflagellate Alexandrium tamarense (Dinophyceae) in Japanese coastal waters. J Phycol 43:43–54CrossRefGoogle Scholar
  78. Not F, Latasa M, Marie D, Cariou T, Vaulot D, Simon N (2004) A single species, Micromonas pusilla (Prasinophyceae), dominates the eukaryotic picoplankton in the Western English Channel. Appl Environ Microbiol 70(7):4064–4072PubMedCrossRefGoogle Scholar
  79. Not F, Gausling R, Azam F, Heidelberg JF, Worden AZ (2007) Vertical distribution of picoeukaryotic diversity in the open ocean. Environ Microbiol 9:1233–1252PubMedCrossRefGoogle Scholar
  80. Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, Amino N, Hase T (2000) Loop-mediated isothermal amplification of DNA. Nucleic Acids Res 28:E63PubMedCrossRefGoogle Scholar
  81. Nowrousian M (2010) Net-generation sequencing techniques for eukaryotic microorganisms: sequencing based solutions to biological problems. Eukaryot Cell 9(9):1300–1310PubMedCrossRefGoogle Scholar
  82. Oldach DW, Delwiche CF, Jakobsen KS, Tengs T, Brown EG, Kempton JW, Schaefer EF, Bowers HA, Glasgow HB Jr, Burkholder JM, Steidinger KA, Rublee PA (2000) Heteroduplex mobility assay-guided sequence discovery: elucidation of the small subunit (18S) rDNA sequences of Pfiesteria piscicida and related dinoflagellates from complex algal culture and environmental sample DNA pools. Proc Natl Acad Sci USA 97(8):4303–4308PubMedCrossRefGoogle Scholar
  83. Park TG, Salas MF, Bolch CJS, Hallegraeff GM (2007) Development of a realtime PCR probe for quantification of the heterotrophic dinoflagellate Cryptoperidiniopsis brodyi (Dinophyceae) in environmental samples. Appl Environ Microbiol 73:2552–2560PubMedCrossRefGoogle Scholar
  84. Park TG, Park YT, Lee Y (2009) Development of a SYTO9 based real-time PCR probe for detection and quantification of toxic dinoflagellate Karlodinium veneficum (Dinophyceae) in environmental samples. Phycologia 48(1):32–43CrossRefGoogle Scholar
  85. Penna A, Galluzzi L (2008) PCR techniques a diagnostic tool for the identification and enumeration of toxic marine phytoplankton species. In: Evangelista V, Barsanti L, Frassanito AM, Passarelli V, Gualtieri P (eds) Algal toxins: nature, occurrence, effect and detection. Springer Science + Business media BV, pp 261–284Google Scholar
  86. Perini F, Casabianca A, Battocchi C, Accoroni S, Totti C, Penna A (2011) New approaches using the real-time PCR method for estimation of the toxic marine dinoflagellate Ostreopsis cf. ovata in marine environmental. PLoS One 6(3):e17699. doi: 10.1371/journal.pone.0017699 PubMedCrossRefGoogle Scholar
  87. Petrosino JF, Highlander S, Luna RA, Gibbs RA, Versalovic MD (2009) Metagenomic pyrosequencing and microbial identification. Clin Chem 55(5):856–866PubMedCrossRefGoogle Scholar
  88. Potvin M, Lovejoy C (2009) PCR-based diversity estimates of artificial and environmental 18s rRNA gene libraries. J Eukaryot Microbiol 56(2):174–181PubMedCrossRefGoogle Scholar
  89. Richlen ML, Barber PH (2005) A technique for the rapid extraction of microalgal DNA from single live and preserved cells. Mol Ecol Notes 5:688–691CrossRefGoogle Scholar
  90. Ripley SJ, Baker AS, Miller PI, Walne AW, Schroeder DC (2008) Development and validation of a molecular technique for the analysis of archived formalin-preserved phytoplankton samples permits retrospective assessment of Emiliania huxleyi communities. J Microbiol Meth. doi: 10.1016/j.mimet.2008.02.001
  91. Roesch LFW, Fulthorpe RR, Riva A, Casella G, Hadwin AK, Kent AD, Daroub SH, Camargo FA, Farmerie WG, Triplett EW (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1(4):283–290PubMedGoogle Scholar
  92. Roesch LFW, Lorca GL, Casella G, Giongo A, Naranjo A, Pionzio AM (2009) Culture-independent identification of gut bacteria correlated with the onset of diabetes in a rat model. ISME J 3:536–548PubMedCrossRefGoogle Scholar
  93. Rothberg JM, Leamon JH (2008) The development and impact of 454 sequencing. Nat Biotechnol 26:1117–1124PubMedCrossRefGoogle Scholar
  94. Rublee PA, Kempton JW, Schaefer EF, Allen C, Harris J, Oldach DW, Bowers H, Tengs T, Burkholder JM, Glasgow HB (2001) Use of molecular probes to assess geographic distribution of Pfiesteria species. Environ Health Perspect 109(5):765–767PubMedCrossRefGoogle Scholar
  95. Sako Y, Kim CH, Ninomiya H, Adachi M, Ishida Y (1990) Isozyme and cross analysis of mating populations in the Alexandrium catenella/tamarense species complex. In: Granéli E, Sundstrom B, Edler L, Anderson DM (eds) Toxic marine phytoplankton. Elsevier, New York, pp 320–323Google Scholar
  96. Sarno D, Kooistra WHCF, Medlin LK, Percopo I, Zingone A (2005) Diversity in the genus Skeletonema (Bacillariophyceae): Skeletonema costatum (Bacillariophyceae) consists of several genetically and morphologically distinct species with the description of four new species. J Phycol 41:151–176CrossRefGoogle Scholar
  97. Schlötterer C (1998) Ribosomal DNA probes and primers. In: Karp A, Isaac PG, Ingram DS (eds) Molecular tools for screening biodiversity. Chapman & Hall, London, pp 267–276CrossRefGoogle Scholar
  98. Scholin CA, Anderson DA (1993) Population analysis of toxic and non-toxic Alexandrium species using ribosomal RNA signature sequences. In: Smayda TJ, Shimizu Y (eds) Toxic phytoplankton blooms in the sea. Elsevier, Amsterdam, pp 95–102Google Scholar
  99. Scholin CA, Herzog M, Sogin ML, Anderson DM (1994) Identification of group and strain-specific genetic markers for globally distributed Alexandrium (Dinophyceae). II. Sequence analysis of a fragment of the LSU rRNA gene. J Phycol 30:999–1011CrossRefGoogle Scholar
  100. Scorzetti G, Brand LE, Hitchcock GL, Rein KS, Sinigalliano CD, Fell JW (2009) Multiple simultaneous detection of harmful algal blooms (HABs) through a high throughput bead array technology, with potential use in phytoplankton community analysis. Harmful Algae 8:196–211PubMedCrossRefGoogle Scholar
  101. Sellner KG, Gregory E, Doucette J, Kirkpatric GJ (2003) Harmful algal blooms: causes, impacts and detection. J Ind Microbiol Biotechnol 30:383–440PubMedCrossRefGoogle Scholar
  102. Shalchian-Tabrizi K, Reier-Røberg K, Ree DK, Klaveness D, Brate J (2011) Marine-freshwater colonizations of haptophytes inferred from phylogeny of environmental 18S rDNA sequences. J Eukaryot Microbiol 58(11):315–318PubMedCrossRefGoogle Scholar
  103. Shapiro LP, Campbell L, Haugen EM (1989) Immunochemical recognition of phytoplankton species. Mar Ecol Prog Ser 57:219–224CrossRefGoogle Scholar
  104. Shendure J, Ji H (2008) Next generation DNA sequencing. Nat Biotechnol 26:1135–1145PubMedCrossRefGoogle Scholar
  105. Shi Y, Tyson GW, DeLong EF (2009) Metatranscriptomics reveals unique microbial small RNAs in the ocean’s water column. Nature 459(7244):266–269PubMedCrossRefGoogle Scholar
  106. Shi XL, Lepère C, Scanlan DJ, Vaulot D (2011) Plastid 16S rRNA gene diversity among eukaryotic picophytoplankton sorted by flow cytometry from the South Pacific Ocean. PLoS One 6(4):e18979. doi: 10.1371/journal.pone.0018979 PubMedCrossRefGoogle Scholar
  107. Simon N, Campbell L, Örnȯlfsdȯttir E, Groben R, Guillou L, Lange M, Medlin LK (2000) Oligonucleotide probes for the identification of three algal groups by dot blot and Fluorescent Whole-Cell Hybridization. J Eukaryot Microbiol 47(1):76–84PubMedCrossRefGoogle Scholar
  108. Soto K, Collantes G, Zahr M, Kuzhar J (2005) Simultaneous enumeration of Phaeodactylum tricornutum (MCB292) and bacteria growing in mixed communities. Invest Mar Valparaiso 33(2):143–149Google Scholar
  109. Stackebrandt E (2006) Molecular identification, systematics, and population structure of prokaryotes. Springer-Verlag Berlin Heidelberg, Germany, pp 51–80CrossRefGoogle Scholar
  110. Stoeck T, Epstein S (2003) Novel eukaryotic lineages inferred from small-subunit rRNA analyses of oxygen-depleted marine environments. Appl Environ Microbiol 69(5):2657–2663PubMedCrossRefGoogle Scholar
  111. Stoeck T, Bass D, Nebel M, Christen R, Jones MD, Breiner HW, Richard TA (2010) Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Mol Ecol 19(1):21–31PubMedCrossRefGoogle Scholar
  112. Tai V, Poon AF, Paulsen IT, Palenik B (2011) Selection in coastal Synechococcus (cyanobacteria) populations eva;uated from environmental metagenomics. PLoS One 6(9):e24249PubMedCrossRefGoogle Scholar
  113. Takano Y, Horiguchi T (2006) Acquiring scanning electron microscopical. Light microscopical and multiple gene sequence data from a single dinoflagellate cell. J Phycol 42:251–256CrossRefGoogle Scholar
  114. Töbe K, Eller G, Medlin LK (2006) Automated detection and enumeration for toxic algae by solid-phase cytometry and the introduction of a new probe for Prymnesium parvum (Haptophyta:Prymnesiophyceae). J Plank Res 28(7):643–657CrossRefGoogle Scholar
  115. Toyoda K, Nagasaki K, Tomaru Y (2010) Application of real-time PCR assay for detection and quantification of bloom-forming diatom Chaetoceros tenuissimus Meunier. Plankton Benthos Res 5(2):56–61CrossRefGoogle Scholar
  116. Tyrrell JV, Connell LB, Scholin CA (2002) Monitoring for Heterosigma akashiwo using a sandwich hybridization assay. Harmful Algae 1:205–214CrossRefGoogle Scholar
  117. Ulrich RM, Casper ET, Campbell L, Richardson B, Heil CA, Paul JH (2010) Detection and quantification of Karenia mikimotoi using real-time nucleic acid sequence-based amplification with internal control RNA (IC-NASBA). Harmful Algae 9(1):116–122CrossRefGoogle Scholar
  118. Vaulot D, Eikrem W, Viprey M, Moreau H (2008) The diversity of small eukaryotic phytoplankton (3 mm) in marine ecosystems. FEMS Microbiol Rev 32:795–820PubMedCrossRefGoogle Scholar
  119. Wang L, Li MJ, Alam Y, Geng Z, Yamasaki S, Shi L (2008) Loop-mediated isothermal amplification method for rapid detection of the toxic dinoflagellate Alexandrium, which causes algal blooms and poisoning of shellfish. FEMS Microbiol Lett 282:15–21PubMedCrossRefGoogle Scholar
  120. Widmer F, Hartmann M, Frey B, Kölliker B (2006) A novel strategy to extract specific phylogenetics sequence information from community T-RFLP. J Microbiol Meth 66:512–520CrossRefGoogle Scholar
  121. Wu Z, Irizarry RA, Gentleman R, Murillo FM, Spencer F (2003) A model based background adjustment for oligonucleotide expression arrays. Technical report, Johns Hopkins University, dept of biostatistics working papers.
  122. Yershov G, Barsky V, Kirillov E, Kreindlin K, Ivanov I, Parinov S, Guschin D, Drobishev A, Dubiley S (1996) DNA analysis and diagnostics on oligonucleotide microchips. Proc Natl Acad Sci USA 93(10):4913–4918PubMedCrossRefGoogle Scholar
  123. Yoon HS, Price DC, Stepanauskas R, Rajah VD, Sieracki ME, Wilson WH, Yang EC, Duffy S, Bhattacharya D (2011) Single-cell genomics reveals organismal interactions in uncultivated marine protists. Science 332:714–717PubMedCrossRefGoogle Scholar
  124. Zhu F, Massana R, Not F, Marie D, Vaulot D (2005) Mapping of picoeukaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene. FEMS Microbiol Ecol 52:79–92PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Vinitha Ebenezer
    • 1
  • Linda K. Medlin
    • 2
  • Jang-Seu Ki
    • 1
  1. 1.Department of Green Life Science, College of ConvergenceSangmyung UniversitySeoulSouth Korea
  2. 2.Paris 6, CNRS, UMR 7621, LOMIC, Observatoire OcéanologiqueUniversité Pierre et Marie CurieBanyuls-sur-MerFrance

Personalised recommendations