Aquatic Plant Biodiversity and DNA Barcoding

  • Sufia Irfan
  • Aishah Alatawi


Life on Earth is abundant, diverse, and intricate in organization with different interconnected strata. This complexity of life system is completely under control of genetic, organismal, and ecological diversity. Biodiversity is collection of all species of animals, plants, fungi, and microbial organisms living on Earth and the variety of habitats inhabited by them. It is the degree of nature’s variety or variation within the natural system, both in terms of number and frequency. Alterations and interference by humans within the ecosystems have resulted in extensive impairment and fragmentations of habitats. Diminishing populations gives rise to inbreeding, genetic drift, and a loss of genetic variation and, therefore, creates vulnerability of species toward environmental changes. Biodiversity in aquatic ecosystem is immense. Since the beginning of time, every cradle of life and civilization has developed in and around aquatic bodies. Whether flowing or static, aquatic bodies are important to our physical chemical and biological world. A significant number of diverse plant species is found in and around aquatic bodies: flowering plant, mosses, liverworts, species of encrusting lichens, stoneworts, and other large algal species; aquatic bodies downstream support a rich diverse species of plants. Identification of rich submerged biota in freshwater and marine aquatic ecosystem is a difficult task to accomplish. In order to understand distributions, patterns, and abundances for populations or species, the collection (detection) and identification of individuals from their physical origins must be undertaken. However, species detection is sometimes extremely difficult especially in marine and aquatic environments where organisms have complex life cycles, and direct observation of early development stages is almost impossible. DNA barcode is used by biologists and ecologist to a standardized short sequence of DNA that can be recovered and featured as a unique identification marker for all species in the biosphere. DNA barcoding has presented the conventional taxonomy in digital format. This review describes a summary of available information on historical background of DNA barcoding, biodiversity in aquatic habitats, and available resources of DNA barcoding in marine and freshwater systems. DNA barcoding has been established as a mature field of biodiversity sciences filing the conceptual gap between traditional taxonomy and different fields of molecular systematics.


Aquatic ecosystem Biodiversity eDNA 


  1. Bell KL et al (2016) Pollen DNA barcoding: current applications and future prospects. Genome 59:629–640CrossRefPubMedGoogle Scholar
  2. Bunn SE, Arthington AH (2002) Basic principles and ecological consequences of altered flow regimes for aquatic biodiversity. Environ Manag 30(4):492–507CrossRefGoogle Scholar
  3. CBOL Plant Working Group (2009) A DNA barcode for land plants. Proc Natl Acad Sci USA 106:12794–12797CrossRefGoogle Scholar
  4. Chase MW, Salamin N, Wilkinson M, Dunwell JM, Kesanakurthi RP, Haidar N, Savolainen V (2005) Land plants and DNA barcodes: short-term and long-term goals. Philos Trans R Soc Lond B Biol Sci 360:1889–1895CrossRefPubMedPubMedCentralGoogle Scholar
  5. Chase MW et al (2007) A proposal for a standardized protocol to barcode all land plants. Taxon 56:295–299Google Scholar
  6. Cho Y, Mower JP, Qiu YL, Palmer JD (2004) Mitochondrial substitution rates are extraordinarily elevated and variable in a genus of flowering plants. Proc Natl Acad Sci U S A 101:17741–17746CrossRefPubMedPubMedCentralGoogle Scholar
  7. Consortium for the Barcode of Life (2009) CBOL approves matK and rbcL as the BARCODE regions for land plants. doi: DNA barcoding 4469. Accessed 15 Dec 2017
  8. Cowen RK, Paris CB, Srinivasan A (2006) Scaling of connectivity in marine populations. Science 311:522–527CrossRefPubMedGoogle Scholar
  9. David AJ, Flecker Alexander S (1993) Biodiversity conservation in running waters. Bioscience 43(1):32CrossRefGoogle Scholar
  10. de Vere N et al (2012) DNA barcoding the native flowering plants and conifers of Wales. PLoS One 7(6):e37945. Scholar
  11. DeSalle R, Egan MG, Siddall M (2005) The unholy trinity: taxonomy, species delimitation and DNA barcoding. Philos Trans R Soc B 360:1905–1916CrossRefGoogle Scholar
  12. Díaz-Ferguson EE, Moyer GR (2014) History, applications, methodological issues and perspectives for the use of environmental DNA (eDNA) in marine and freshwater environments. Rev Biol Trop 62(4):1273–1284CrossRefPubMedGoogle Scholar
  13. Dudgeon D et al (2006) Freshwater biodiversity: importance, threats, status and conservation challenges. Biol Rev 81:163–182CrossRefGoogle Scholar
  14. Erickson DL, Spouge J, Resch A, Weigt LA, Kress JW (2008) DNA barcoding in land plants: developing standards to quantify and maximize success. Taxon 57:1304–1316PubMedPubMedCentralGoogle Scholar
  15. Fazekas AJ et al (2008) Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well. PLoS One 3:e2802CrossRefPubMedPubMedCentralGoogle Scholar
  16. Fazekas AJ, Kesanakurti PR, Burgess KS, Percy DM, Graham SW, Barrett SC, Newmaster SG et al (2009) Are plant species inherently harder to discriminate than animal species using DNA barcoding markers? Mol Ecol Resour 9:130–139CrossRefPubMedGoogle Scholar
  17. Ford CS et al (2009) Selection of candidate coding DNA barcoding regions for use on land plants. Bot Linn Soc 159:1–11CrossRefGoogle Scholar
  18. Ficetola F, Miaud C, Pompanon F, Taberlet P (2008) Species detection using environmental DNA from water samples. Biol Lett 4:423–425CrossRefPubMedPubMedCentralGoogle Scholar
  19. Gibbs JP (2000) Wetland loss and biodiversity conservation. Conserv Biol 14(1):314–317CrossRefGoogle Scholar
  20. Hebert PDN, Cywinska A, Ball SL, de Waard JR (2003) Biological identifications through DNA barcodes. Proc R Soc Lond B 270:313–321CrossRefGoogle Scholar
  21. Hubert N, Hanner R (2015) DNA barcoding, species delineation and taxonomy: a historical perspective. DNA Barcodes 3:44–58Google Scholar
  22. Heywood VH, Baste I (1995) Introduction. In: Heywood VH, Watson RT (eds) Global biodiversity assessment. Cambridge University Press, Cambridge, pp 1–19Google Scholar
  23. Kearns CA (2010) Conservation of biodiversity. Nat Educ Knowl 3(10):7Google Scholar
  24. Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH (2005) Use of DNA barcodes to identify flowering plants. Proc Natl Acad Sci U S A 102:8369–8374CrossRefPubMedPubMedCentralGoogle Scholar
  25. Lahaye R, Savolainen V, Duthoit S, Maurin O, van der Bank M (2008) A test of psbK–psbI and atpF–atpH as potential plant DNA barcodes using the flora of the Kruger National Park as a model system (South Africa). Nat Proc.
  26. Layton A (2006) Development of Bactereroides 16S rRNA gene Taqman-base real time PCR assays for estimation of total, human and bovine fecal pollution in rivers. Appl Environ Microbiol 72(6):4214–4224CrossRefPubMedPubMedCentralGoogle Scholar
  27. Lee HL, Yi DK, Kim JS, Kim KJ (2007) Development of plant DNA barcoding markers from the variable noncoding regions of chloroplast genome. In: Abstract presented at the Second International Barcode of Life Conference, Academia Sinica, Taipei, Taiwan, September 2017, pp 18–20.
  28. Miller SE (2007) DNA barcoding and the renaissance of taxonomy. Proc Nat Acad Sci USA 104:4775–4776CrossRefPubMedGoogle Scholar
  29. Mower JP, Touzet P, Gummow JS, Delph LF, Palmer JD (2007) Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants. BMC Evol Biol 7:135.
  30. Mutia TM (2009) Biodiversity conservation; Presented at short course IV on exploration for geothermal resources, organized by UNU-GTP, KenGen and GDC, at Lake Naivasha, Kenya, November 1–22, 2009Google Scholar
  31. Newmaster SG, Fazekas AJ, Steeves RAD, Janovec J (2008) Testing candidate plant barcode regions in the Myristicaceae. Mol Ecol Notes 8:480–490CrossRefGoogle Scholar
  32. Ogram A, Sayler G, Barkay T (1987) The extraction and purification of microbial DNA from sediments. J Microbiol Methods 7:57–66CrossRefGoogle Scholar
  33. Palmer JD, Adams KL, Cho Y, Parkinson CL, Qiu YL, Song K (2000) Dynamic evolution of plant mitochondrial genomes: mobile genes and introns and highly variable mutation rates. Proc Natl Acad Sci U S A 97:6960–6966CrossRefPubMedPubMedCentralGoogle Scholar
  34. Parikh P, Unadka K, Nagar P (2015) Evolutionary analysis based on DNA barcoding of certain aquatic plants using rbcL gene sequences. Int J Sci Eng Res 6(7):1410–1421Google Scholar
  35. Ramel C (1998) Biodiversity and intraspecific genetic variation. Pure Appl Chem 70(11):2079–2084CrossRefGoogle Scholar
  36. Randall Hughes A et al (2008) Ecological consequences of genetic diversity. Ecol Lett 11:609–623CrossRefPubMedGoogle Scholar
  37. Rieseberg LH, Wood TE, Baack EJ (2006) The nature of plant species. Nature 440:524–527CrossRefPubMedPubMedCentralGoogle Scholar
  38. Rivera-Ocasio E, Aide TM, Mcmillan WO (2002) Patterns of genetic diversity and biogeographical history of the tropical wetland tree, Pterocarpus officinalis (Jacq.), in the Caribbean basin. Mol Ecol 11:675–683CrossRefPubMedGoogle Scholar
  39. Starr JR, Naczi RFC, Chouinard BN (2009) Plant DNA barcodes and species resolution in sedges (Carex, Cyperaceae). Mol Ecol Resour 9(Suppl. 1):151–163CrossRefPubMedGoogle Scholar
  40. Sytsma MD (2008) Introduction: workshop on submersed aquatic plant research priorities. J Aquat Plant Manag 46:1–7Google Scholar
  41. Thomsen P (2012) Monitoring endangered freshwater biodiversity using environmental DNA. Mol Ecol 21:2565–2573CrossRefPubMedGoogle Scholar
  42. Vijayan K, Tsou CH (2010) DNA barcoding in plants: taxonomy in a new perspective. Curr Sci 99(11):1530–1541Google Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Biology Department, College of ScienceFaculty of Science, University of TabukTabukSaudi Arabia

Personalised recommendations