Advertisement

Future Perspectives of DNA Barcoding in Marine Zooplanktons and Invertebrates

  • Farhina PashaEmail author
  • Shalini Saggu
  • Maryam Fahad Albalawi
Chapter

Abstract

The World registry of marine species as of May, 2015 show 229,409 accepted species; of which 220,461 checked (96 %) 421,632 species names including synonyms 527,721 taxon names. Therefore there was a desperate need for developing new molecular method for clarifying obscurities in customary taxonomy. As most of the organisms in marine habitat are microscopic, sample size is large, and most of all the sample preservation is a tricky and expertise requiring job, marine taxonomic identification progress has been very slow. Therefore there was an urgent need of “fast, simple, reliable and inexpensive” method for identification of marine diversity and the answer came as a technique known as “DNA Barcoding”. DNA barcoding has emerged as an ideal technique for taxonomic identification of marine taxa, as morphological characters are less reliable and often lead to cryptic species overlapping. Combining genomic study with DNA barcode can be a very effective solution. With all the advantages and limitations there is a strong implementation of DNA barcode on large scale barcode campaigns that will provide enormous amount of data for proper marine taxonomy especially in marine invertebrates.

Keywords

DNA barcoding Marine invertebrates Biodiversity Cytochrome oxidase gene Species identification 

Notes

Acknowledgments

The authors would like to acknowledge, University of Tabuk, Tabuk, Saudi Arabia. The author would also like to thanks Department of Biology, Faculty of Sciences, Saudi Digital Library and University Library providing the facility for literature survey and collection.

References

  1. Beaugrand G (2009) Decadal changes in climate and ecosystems in the North Atlantic Ocean and adjacent seas. Deep-Sea Res Part II 56(8–10):656–673CrossRefGoogle Scholar
  2. Behnke A, Friedl T, Chepurnov VA, Mann DG (2004) Reproductive compatibility and rDNA sequence analyses in the Sellaphorapupula species complex (Bacillariophyta). J Phycol 40:193–208CrossRefGoogle Scholar
  3. Bhadury P, Austen MC, Bilton DT, Lambshead PJD, Rogers AD, Smerdon GR (2006) Development and evaluation of a DNA-barcoding approach for the rapid identification of nematodes. Mar Ecol Prog Ser 320:1–9CrossRefGoogle Scholar
  4. Blaxter M (2003) Counting angels with DNA. Nature 421:122–124PubMedCrossRefGoogle Scholar
  5. Boltovskoy D, Correa N, Boltovskoy A (2002) Marine zooplanktonic diversity: a view from the South Atlantic. Oceanol Acta 25:271–278CrossRefGoogle Scholar
  6. Bouchet P (2006) The magnitude of marine biodiversity. In: Duarte CM (ed) The exploration of marine biodiversity: scientific and technological challenges. Fundacion BBVA, Bilbao, pp 31–64Google Scholar
  7. Bucklin A, Steinke D, Blanco-Bercial L (2011) DNA barcoding of marine metazoa. Annu Rev Mar Sci 3:471–508CrossRefGoogle Scholar
  8. Busse HJ, Denner EBM, Lubitz W (1996) Classification and identification of bacteria: current approaches to an old problem. Overview of methods used in bacterial systematics. J Biotechnol 47:3–38PubMedCrossRefGoogle Scholar
  9. Clare EL, Lim BK, Engstrom MD, Eger JL, Hebert PDN (2007) DNA barcoding of neotropical bats: species identification and discovery within Guyana. Mol Ecol Notes 7:184–190CrossRefGoogle Scholar
  10. Collins RA, Cruickshank RH (2013) The seven deadly sins of DNA barcoding. Mol Ecol Resour 13:969–975PubMedGoogle Scholar
  11. Costa FO, deWaard JR, Boutillier J, Ratnasingham S, Dooh RT, Hajibabaei M, Hebert PDN (2007) Biological identifications through DNA barcodes: the case of the Crustacea. Can J Fish Aquat Sci 64:272–295CrossRefGoogle Scholar
  12. Erpenbeck D, Hooper JNA, Wörheide G (2006) CO1 phylogenies in diploblasts and the ‘Barcoding of Life’—are we sequencing a suboptimal partition? Mol Ecol Notes 6:550–553CrossRefGoogle Scholar
  13. Evans KM, Wortley AH, Mann DG (2007) An assessment of potential diatom “barcode” genes (cox1, rbcL, 18S and ITS rDNA) and their effectiveness in determining relationships in Sellaphora (Bacillariophyta). Protist 158:349–364PubMedCrossRefGoogle Scholar
  14. Falkowski PG, Barber RT, Smetacek V (1998) Biogeochemical controls and feedbacks on ocean primary production. Science 281:200–207PubMedCrossRefGoogle Scholar
  15. Field CB, Behrenfeld MJ, Randerson JT, Falkowski PG (1998) Primary production of the biosphere: integrating terrestrial and oceanic components. Science 281:237–240PubMedCrossRefGoogle Scholar
  16. Grassle JF, Maciolek NJ (1992) Deep-sea species richness—regional and local diversity estimates from quantitative bottom samples. Am Nat 139:313–341CrossRefGoogle Scholar
  17. Hamsher SE, Evans KM, Mann DG, Poulíčková A, Saunders GW (2011) Barcoding diatoms: exploring alternativesto COI-5P. Protist 162:405–422PubMedCrossRefGoogle Scholar
  18. Harris R, Wiebe P, Lenz J, Skjoldal H, Huntley M (2000) ICES zooplankton methodology manual. Academic Press, San DiegoGoogle Scholar
  19. Hebert PDN, Cywinska A, Ball SL, Ward JR (2003) Biological identifications through DNA barcodes. Proc R Soc Lond B 270:313–321CrossRefGoogle Scholar
  20. Jahn R, Zetzsche H, Reinhardt R, Gemeinholzer B (2007) Diatoms and DNA barcoding: a pilot study on an environmental sample. In: Kusber WH, Jahn R (eds) Proceedings of the 1st central European diatom meeting Berlin, Botanic Garden and Botanical Museum Berlin-Dahlem. Freie Universitat Berlin, pp 63–68Google Scholar
  21. Jennings RM, Bucklin A, Ossenbrügger H, Hopcroft RR (2010) Species diversity of planktonic gastropods (Pteropoda and Heteropoda) from six ocean basins based on DNA barcode analysis. Deep-Sea Res II 57:2199–2210Google Scholar
  22. Kemppainen P, Panova M, Hollander J, Johannesson K (2009) Complete lack of mitochondrial divergence between two species of NE Atlantic marine intertidal gastropods. J Evol Biol 22:2000–2011PubMedCrossRefGoogle Scholar
  23. Kerr KC, Stoeckle MY, Dove CJ, Weigt LA, Francis CM, Hebert PDN (2007) Comprehensive DNA barcode coverage of North American birds. Mol Ecol Notes 7:535–543PubMedPubMedCentralCrossRefGoogle Scholar
  24. Knowlton N (1993) Sibling species in the sea. Annu Rev Ecol Evol Syst 24:189–216CrossRefGoogle Scholar
  25. Kochzius M, Nölte M, Weber H, Silkenbeumer N, Hjörleifsdottir S, Hreggvidsson GO, Marteinsson V, Kappel K, Planes S, Tinti F, Magoulas A, Vazquez EG, Turan C, Hervet C, Falgueras DC, Antoniou A, Land M, Blohm D (2008) DNA microarrays for identifying fishes. Mar Biotechnol 10:207–217PubMedPubMedCentralCrossRefGoogle Scholar
  26. Krabbe K, Leese F, Mayer C, Tollrian R, Held C (2010) Cryptic mitochondrial lineages in the widespread pycnogonid Colossende ismegalonyx Hoek, 1881 from Antarctic and Subantarctic waters. Polar Biol 33:281–292CrossRefGoogle Scholar
  27. Leun TLF, Donald KM, Keeney DB, Koehle AV, Peoples RC, Poulin R (2009) Trematode parasites of Otago Harbour (New Zealand) soft-sediment intertidal ecosystems: life cycles, ecological roles and DNA barcodes. NZ J Mar Freshwater Res 43:857–865CrossRefGoogle Scholar
  28. Luddington IA, Kaczmarska I, Lovejoy C (2012) Distance and character-based evaluation of the V4 region of the 18 S rRNA gene for the identification of diatoms (Bacillariophyceae). PLoS ONE 7:e45664PubMedPubMedCentralCrossRefGoogle Scholar
  29. MacGillivary ML, Kaczmarska I (2011) Survey of the efficacy of a short fragment of the rbcL gene as a supplemental DNA barcode for diatoms. J Eukaryot Microbiol 58:529–536PubMedCrossRefGoogle Scholar
  30. Mann DG, Droop SJM (1996) Biodiversity, biogeography and conservation of diatoms. Hydrobiologia 336:19–32CrossRefGoogle Scholar
  31. Mann DG (1999) The species concept in diatoms. Phycologia 38:437–495CrossRefGoogle Scholar
  32. Meyer CP, Paulay G (2005) DNA barcoding: error rates based on comprehensive sampling. PLoS Biol 3:2229–2238Google Scholar
  33. Monaghan MT, Balke M, Ryan-Gregory T, Vogler AP (2005) DNA-based species delineation in tropical beetles using mitochondrial and nuclear markers. Philos Trans R Soc B 360:1925–1933CrossRefGoogle Scholar
  34. Moniz MBJ, Kaczmarska I (2010) Barcoding of diatoms: nuclear encoded ITS revisited. Protist 161:7–34PubMedCrossRefGoogle Scholar
  35. Moniz MBJ, Kaczmarska I (2009) Barcoding diatoms: is there a good marker? Mol Ecol Resour 9(Suppl. 1):65–74PubMedCrossRefGoogle Scholar
  36. Morrow C, Cárdenas P (2015) Proposal for a revised classification of the Demospongiae (Porifera). Front Zool 12:7PubMedPubMedCentralCrossRefGoogle Scholar
  37. Moura CJ, Harris DJ, Cunha MR, Rogers AD (2008) DNA barcoding reveals cryptic diversity in marine hydroids (Cnidaria, Hydrozoa) from coastal and deep-sea environments. Zool Scr 37:93–108Google Scholar
  38. Nielsen JF, Lavery S, Lorz AN (2009) Synopsis of a new collection of sea spiders (Arthropoda: Pycnogonida) from the Ross Sea, Antarctica. Polar Biol 32:1147–1155CrossRefGoogle Scholar
  39. Plaisance L, Knowlton N, Paulay G, Meyer C (2009) Reef-associated crustacean fauna: biodiversity estimates using semi-quantitative sampling and DNA barcoding. Coral Reefs 28:977–986CrossRefGoogle Scholar
  40. Planque B, Taylor AH (1998) Long-term changes in zooplankton and the climate of the North Atlantic. ICES J Mar Sci 55(4):644–654CrossRefGoogle Scholar
  41. Radulovici AE, Sainte-Marie B, Dufresne F (2009) DNA barcoding of marine crustaceans from the Estuary and Gulf of St Lawrence: a regional-scale approach. Mol Ecol Resour 9:181–187PubMedCrossRefGoogle Scholar
  42. Shearer TL, Coffroth MA (2008) Barcoding corals: limited by interspecific divergence, not intraspecific variation. Mol Ecol Resour 8:247–255PubMedCrossRefGoogle Scholar
  43. Smetacek V (1999) Diatoms and the carbon ocean cycle. Protist 150:25–32PubMedCrossRefGoogle Scholar
  44. Stoermer EP, Smol JP (1999) The diatoms: applications to the environmental and earth sciences. Cambridge University Press, CambridgeCrossRefGoogle Scholar
  45. Trobajo R, Clavero E, Evans KM, Vanormelinge P, McGregor RC, Mann DG (2011) The use of partial cox1 rbcL and LSU rDNA sequences for phylogenetics and species identification within the Nitzschiapaleacomplex (Bacillariophyceae). Eur J Phycol 45:413–425CrossRefGoogle Scholar
  46. Vogler AP, Monaghan MT (2006) Recent advances in DNA taxonomy. J Zool Syst Evol Res 45:1–10CrossRefGoogle Scholar
  47. Ward RD, Holmes BH, O’Hara TD (2008) DNA barcoding discriminates echinoderm species. Mol Ecol Resour 8:1202–1211PubMedCrossRefGoogle Scholar
  48. Waugh J (2007) DNA barcoding in animal species: progress, potential and pitfalls. BioEssays 29:188–197PubMedCrossRefGoogle Scholar
  49. Wong EHK, Hanner RH (2008) DNA barcoding detects market substitution in North American seafood. Food Res Int 41:828–837CrossRefGoogle Scholar
  50. Zimmermann J, Jahn R, Gemeinholzer B (2011) Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene including new primers and protocols. Organ Divers Evol 11:173–192CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Farhina Pasha
    • 1
    Email author
  • Shalini Saggu
    • 1
  • Maryam Fahad Albalawi
    • 1
  1. 1.Faculty of Sciences, Department of BiologyUniversity of TabukTabukSaudi Arabia

Personalised recommendations