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DNA Barcoding in Marine Nematodes: Successes and Pitfalls

  • Punyasloke BhaduryEmail author
Chapter

Abstract

The phylum Nematoda is one of the most diverse and abundant in every ecological niche including terrestrial and aquatic environments. It has been estimated that the abundance of nematodes can reach up to 108 individuals per square metre. Like any other environment, sedimentary layer of marine environments are rich in benthic fauna and free-living marine nematodes constitute an important component of benthic domain. These organisms are present in all types of marine habitat including from shallow coastal environment to deep-sea. The structural and functional organization of nematode assemblages can provide precious information on the ‘health’ of ecosystem in which they live, and they are widely recognized as excellent bioindicators of natural and anthropogenic disturbances. The long term success of DNA barcoding as a tool for speeding up identification of marine nematodes during biodiversity and ecosystem monitoring studies will also depend on large scale international efforts such as along the line of Census of Marine Life (CoML) programs. To conclude, morpho-taxonomy coupled with DNA taxonomy using DNA barcoding as a technique could be implemented for undertaking studies on marine nematodes.

Keywords

Bioindicators Coastal Census of Marine Life DNA barcodes Nematoda 

References

  1. Appeltans W, Ahyong ST, Anderson G, Angel MV, Artois T, Bailly N, Bamber R, Barber A, Bartsch I, Berta A, Błażewicz-Paszkowycz M, Bock P, Boxshall G, Boyko CB, Brandão SN, Bray RA, Bruce NL, Cairns SD, Chan TY, Cheng L, Collins AG, Cribb T, Curini-Galletti M, Dahdouh-Guebas F, Davie PJ, Dawson MN, De Clerck O, Decock W, De Grave S, de Voogd NJ, Domning DP, Emig CC, Erséus C, Eschmeyer W, Fauchald K, Fautin DG, Feist SW, Fransen CH, Furuya H, Garcia-Alvarez O, Gerken S, Gibson D, Gittenberger A, Gofas S, Gómez-Daglio L, Gordon DP, Guiry MD, Hernandez F, Hoeksema BW, Hopcroft RR, Jaume D, Kirk P, Koedam N, Koenemann S, Kolb JB, Kristensen RM, Kroh A, Lambert G, Lazarus DB, Lemaitre R, Longshaw M, Lowry J, Macpherson E, Madin LP, Mah C, Mapstone G, McLaughlin PA, Mees J, Meland K, Messing CG, Mills CE, Molodtsova TN, Mooi R, Neuhaus B, Ng PK, Nielsen C, Norenburg J, Opresko DM, Osawa M, Paulay G, Perrin W, Pilger JF, Poore GC, Pugh P, Read GB, Reimer JD, Rius M, Rocha RM, Saiz-Salinas JI, Scarabino V, Schierwater B, Schmidt-Rhaesa A, Schnabel KE, Schotte M, Schuchert P, Schwabe E, Segers H, Self-Sullivan C, Shenkar N, Siegel V, Sterrer W, Stöhr S, Swalla B, Tasker ML, Thuesen EV, Timm T, Todaro MA, Turon X, Tyler S, Uetz P, van der Land J, Vanhoorne B, van Ofwegen LP, van Soest RW, Vanaverbeke J, Walker-Smith G, Walter TC, Warren A, Williams GC, Wilson SP, Costello MJ (2012) The magnitude of global marine species diversity. Curr Biol 22:2189–2202CrossRefPubMedGoogle Scholar
  2. Armenteros M, Rojas-Corzo A, Ruiz-Abierno A, Derycke S, Backeljau T, Decraemer W (2014a) Systematics and DNA barcoding of free-living marine nematodes with emphasis on tropical desmodorids using nuclear SSU rDNA and mitochondrial COI sequences. Nematology 16:979–989Google Scholar
  3. Armenteros M, Ruiz-Abierno A, Decraemer W (2014b) Taxonomy of Stilbonematinae (Nematoda: Desmodoridae): description of two new and three known species and phylogenetic relationships within the family. Zool J Linn Soc 171:1–21Google Scholar
  4. Armstrong MR, Blok VC, Phillips MS (2000) A multipartite mitochondrial genome in the potato cyst nematode Globodera pallida. Genetics 154:181–192PubMedPubMedCentralGoogle Scholar
  5. Avise JC, Walker D (1999) Species realities and number in sexual vertebrates: perspectives from an asexually transmitted genome. Proc Natl Acad Sci USA 96:992–995CrossRefPubMedPubMedCentralGoogle Scholar
  6. Balsamo M, Albertelli G, Ceccherelli VU, Coccioni R, Colangelo MA, Curini-Galletti M, Danovaro R, D’Addabbo R, Leonardis C, Fabiano M, Frontalini F, Gallo M, Gambi C, Guidi L, Moreno M, Pusceddu A, Sandulli R, Semprucci F, Todaro MA, Tongiorgi P (2010) Meiofauna of the Adriatic Sea: current state of knowledge and future perspective. Chem Ecol 26:45–63CrossRefGoogle Scholar
  7. Bhadury P, Annapurna C (2011a) Marine barcoding—how will it help Indian marine benthic studies. Ind J Geo-Mar Sci 40:645–647Google Scholar
  8. Bhadury P, Austen MC (2010) Barcoding marine nematodes: an improved set of nematode 18S rRNA primers to overcome eukaryotic co-interference. Hydrobiologia 641:245–251CrossRefGoogle Scholar
  9. 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
  10. Bhadury P, Austen MC, Bilton DT, Lambshead PJD, Rogers AD, Smerdon GR (2008) Evaluation of combined morphological and molecular techniques for marine nematode (Terschellingia spp.) identification. Mar Biol 154:509–518CrossRefGoogle Scholar
  11. Bhadury P, Bik H, Lambshead JD, Austen MC, Smerdon GR, Rogers AD (2011b) Molecular diversity of fungal phylotypes co-amplified alongside nematodes from coastal and deep-sea marine environments. PLoS ONE 6:e26445Google Scholar
  12. Bik HM, Porazinska DL, Creer S, Caporaso JG, Knight R, Thomas WK (2012) Sequencing our way towards understanding global eukaryotic biodiversity. Trends Ecol Evol 27:233–243CrossRefPubMedPubMedCentralGoogle Scholar
  13. Bik HM, Lunt DH, Thomas WKT, Lambshead PJD (2010b) Low endemism, continued deepshallow interchanges, and evidence for cosmopolitan distributions in free-living marine nematodes (order Enoplida). BMC Evol Biol 10:389Google Scholar
  14. Blaxter ML, De Ley P, Garey JR, Liu LX, Scheldeman P, Vierstraete A, Vanfleteren JR, Mackey LY, Dorris M, Frisse LM, Vida JT, Thomas WK (1998) A molecular evolutionary framework for the phylum Nematoda. Nature 392:71–75Google Scholar
  15. Boufahja F, Sellami B, Dellali M, Aïssa P, Mahmoudi E, Beyrem H (2011a) A microcosm experiment on the effects of permethrin on a free-living nematode assemblage. Nematology 13:901–909Google Scholar
  16. Boufahja F, Hedfi A, Amorri J, Aïssa P, Beyrem H, Mahmoudi E (2011b) Examination of the bioindicator potential of Oncholaimus campylocercoides (Nematoda, Oncholaimidae) from Bizerte bay (Tunisia). Ecol Ind 11:1139–1148Google Scholar
  17. Bucklin A, Steinke D, Blanco-Bercial L (2011) DNA barcoding of marine metazoa. Ann Rev Mar Sci 3:471–508CrossRefPubMedGoogle Scholar
  18. Chen XY, Daniell TJ, Neilson R, O’Flaherty V, Griffiths BS (2010) A comparison of molecular methods for monitoring soil nematodes and their use as biological indicators. Eur J Soil Biol 46:319–324CrossRefGoogle Scholar
  19. Cook AA, Bhadury P, Debenham NJ, Meldal BHM, Blaxter ML, Smerdon GR, Austen MC, Lambshead PJD, Rogers AD (2005) Denaturing gradient gel electrophoresis as a tool for the identification of marine nematodes. Mar Ecol Prog Ser 291:103–113CrossRefGoogle Scholar
  20. Creer S, Fonseca VG, Porazinska DL, Giblin-Davis RM, Sung W, Power DM, Packer M, Carvalho GR, Blaxter ML, Lambshead PJD, Thomas WK (2010) Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises. Mol Ecol 19:4–20CrossRefPubMedGoogle Scholar
  21. Cunha BP, Brito S, Fonseca G (2013) Zygonemella: the forgotten genus of the family Xyalidae (Nematoda). Zootaxa 3669:179–183Google Scholar
  22. Darling A, Bik HM, Jospin G, Lowe E, Eisen JA (2014) PhyloSift: a pipeline for phylogenetic taxonomy assignments from environmental metagenome data. Peer J 2:e243CrossRefPubMedPubMedCentralGoogle Scholar
  23. De Ley P, De Ley IM, Morris K, Abebe E, Mundo Ocampo M, Yoder M, Heras J, Waumann D, Rocha Olivares A, Burr AHJ (2005) An integrated approach to fast and informative morphological vouchering of nematodes for applications in molecular barcoding. Phil Trans R Soc Lond B 360:1945–1958CrossRefGoogle Scholar
  24. Derycke S, Remerie T, Vierstraete A, Backeljau T, Vanfleteren J, Vincx M, Moens T (2005) Mitochondrial DNA variation and cryptic speciation within the free-living marine nematode Pellioditis marina. Mar Ecol Prog Ser 300:91–103CrossRefGoogle Scholar
  25. Derycke S, Backeljau T, Vlaeminck C, Vierstraete A, Vanfleteren J, Vincx M, Moens T (2006) Seasonal dynamics of population genetic structure in cryptic taxa of the Pellioditis marina complex (Nematoda: Rhabditida). Genetica 128:307–321CrossRefPubMedGoogle Scholar
  26. Derycke S, Backeljau T, Vlaeminck C, Vierstraete A, Vanfleteren J, Vincx M, Moens T (2007) Spatiotemporal analysis of population genetic structure in Geomonhystera disjuncta (Nematoda, Monhysteridae) reveals high levels of molecular diversity. Mar Biol 15:1799–1812CrossRefGoogle Scholar
  27. Derycke S, Fonseca G, Vierstraete A, Vanfleteren J, Vincx M, Moens T (2008) Disentangling taxonomy within the Rhabditis (Pellioditis) marina (Nematoda, Rhabditidae) species complex using molecular and morphological tools. Zool J Linn Soc 152:1–15CrossRefGoogle Scholar
  28. Derycke S, Vanaverbeke J, Rigaux A, Backeljau T, Moens T (2010a) Exploring the use of Cytochrome Oxidase c subunit 1 (COI) for DNA barcoding of free-living marine nematodes. PLoS ONE 5:e13716Google Scholar
  29. Derycke S, De Ley P, De Ley IT, Holovachov O, Rigaux A, Moens T (2010b) Linking DNA sequences to morphology: cryptic diversity and population genetic structure in the marine nematode Thoracostoma trachygaster (Nematoda, Leptosomatidae). Zool Scripta 39:276–289Google Scholar
  30. Donn S, Griffiths BS, Neilson R, Daniell TJ (2008) DNA extraction from soil nematodes for multi-sample community studies. Appl Soil Ecol 38:20–26CrossRefGoogle Scholar
  31. Erpenbeck D, Hooper JNA, Worheide G (2006) CO1 phylogenies in diploblasts and the ‘Barcoding of Life’—are we sequencing a suboptimal partition? Mol Ecol Notes 6:50–553CrossRefGoogle Scholar
  32. Floyd R, Abebe E, Papert A, Blaxter ML (2002) Molecular barcodes for soil nematode identification. Mol Ecol 11:839–850CrossRefPubMedGoogle Scholar
  33. Floyd R, Rogers AD, Lambshead PJD, Smith CR (2005) Nematode-specific PCR primers for the 18S small subunit rRNA gene. Mol Ecol Notes 5:611–612CrossRefGoogle Scholar
  34. Fonseca G, Derycke S, Moens T (2008) Integrative taxonomy in two free-living nematode species complexes. Biol J Linn 94:737–753CrossRefGoogle Scholar
  35. Fonseca VG, Carvalho GR, Sung W, Johnson HF, Power DM, Neill SP, Packer M, Blaxter ML, Lambshead PJD, Thomas WK, Creer S (2010) Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nat Comm. doi: 10.1038/ncomms1095 Google Scholar
  36. Fonseca VG, Carvalho GR, Nichols B, Quince C, Johnson HF, Neill SP, Lambshead JD, Thomas WK, Power DM, Creer S (2014) Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes. Glob Ecol Biogeogr 23:1293–1302CrossRefGoogle Scholar
  37. Hebert PDN, Gregory TR (2005) The promise of DNA barcoding for taxonomy. Syst Biol 54:852–859CrossRefPubMedGoogle Scholar
  38. Hebert PDN, Cywinska A, Ball SL, Dewaard JR (2003) Biological identifications through DNA barcodes. Proc R Soc Lond B 270:313–321CrossRefGoogle Scholar
  39. Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004) Identification of birds through DNA barcodes. PLoS Biol 2:e312CrossRefPubMedCentralGoogle Scholar
  40. Holterman M, Rybarczyk K, Van Den Elsen S, Van Megen H, Mooyman P, Peña Santiago R, Bongers T, Bakker J, Helder J (2008) A ribosomal DNA-based framework for the detection and quantification of stress-sensitive nematode families in terrestrial habitats. Mol Ecol Res 8:23–34CrossRefGoogle Scholar
  41. Huang DW, Meier R, Todd PA, Chou LM (2008) Slow mitochondrial COI sequence evolution at the base of the metazoan tree and its implications for DNA barcoding. J Mol Evol 66:167–174CrossRefPubMedGoogle Scholar
  42. Hyman BC, Lewis SC, Tang S, Wu Z (2011) Rampant gene rearrangement and haplotype hypervariation among nematode mitochondrial genomes. Genetica 139:611–615CrossRefPubMedGoogle Scholar
  43. Kumar A, Sen D, Bhadury P (2015) Unraveling free-living marine nematode community structure from a biodiversity rich tropical coastal setting based on molecular approaches. Mar Biodiversi 45:537–547Google Scholar
  44. Lallias D, Hiddink JG, Fonseca VG, Gaspar JM, Sung W, Neill SP, Barnes N, Ferrero T, Hall N, Lambshead PJD, Packer M, Kelley Thomas W, Creer S (2015) Environmental metabarcoding reveals heterogeneous drivers of microbial eukaryote diversity in contrasting estuarine ecosystems. ISME J 9:1208–1221CrossRefPubMedGoogle Scholar
  45. Lambshead PJD (2004) Marine nematode biodiversity. In: Chen ZX, Chen SY, Dickson DW (eds) Nematology: advances and perspectives, vol 1. CABI Publishing, Wallingford, pp 439–468Google Scholar
  46. Lecroq B, Lejzerowicz F, Bachar D, Christen R, Esling P, Baerlocher L, Østerås M, Farinelli L, Pawlowski J (2011) Ultra-deep sequencing of foraminiferal microbarcodes unveils hidden richness of early monothalamous lineages in deep-sea sediments. Proc Natl Acad Sci USA 108:13177–13182CrossRefPubMedPubMedCentralGoogle Scholar
  47. Lunt DH, Hyman BC (1997) Animal mitochondrial DNA recombination. Nature 387:247CrossRefPubMedGoogle Scholar
  48. Meldal BHM, Debenham NJ, De Ley P, De Ley IT, Vanfleteren JR, Vierstraete AR, Bert W, Borgonie G, Moens T, Tyler PA, Austen MC, Blaxter ML, Rogers AD, Lambshead PJ (2007) An improved molecular phylogeny of the Nematoda with special emphasis on marine nematode taxa. Mol Phylogenet Evol 42:622–636Google Scholar
  49. Miller SE (2007) DNA barcoding and the renaissance of taxonomy. Proc Natl Acad Sci USA 104:4775–4784CrossRefPubMedPubMedCentralGoogle Scholar
  50. Neres PF, Da Fonseca-Genevois VG, Torres RA, Da Fonseca Cavalcanti M, De Castro FJV, Da Silva NRR, Rieger TT, Decraemer W (2010) Morphological and molecular taxonomy of a new Daptonema (Nematoda, Xyalidae) with comments on the systematics of some related taxa. Zool J Linn Soc 158:1–15CrossRefGoogle Scholar
  51. Pereira TJ, Fonseca G, Mundo-Ocampo M, Guilherme BC, Rocha-Olivares A (2010) Diversity of free-living marine nematodes (Enoplida) from Baja California assessed by integrative taxonomy. Mar Biol 157:1665–1678CrossRefPubMedPubMedCentralGoogle Scholar
  52. Radulovici AE, Archambault P, Dufresne F (2010) DNA barcodes for marine biodiversity: moving fast forward? Diversity 2:450–472CrossRefGoogle Scholar
  53. Rho HS, Decraemer W, Sørensen MV, Min WG, Jung J, Kim W (2011) Megadraconema cornutum, a new genus and species from Korea, with a discussion of its classification and relationships within the family Draconematidae (Nematoda, Desmodorida) based on morphological and molecular characters. Zool Sci 28:68–84Google Scholar
  54. Rodrigues Da Silva NR, Da Silva MC, Fonseca Genevois V, De Esteves AM, De Ley P, Decraemer W, Rieger TT, Dos Santos Correia MT (2010) Marine nematode taxonomy in the age of DNA: the present and future of molecular tools to assess their biodiversity. Nematology 12:661–672CrossRefGoogle Scholar
  55. Savolainen V, Cowan RS, Vogler AP, Roderick GK, Lane R (2005) Towards writing the encyclopedia of life: an introduction to DNA barcoding. Phil Trans R Soc Lond B 360:1805–1811CrossRefGoogle Scholar
  56. Semprucci F, Losi V, Moreno M (2015) A review of Italian research on free-living marine nematodes and the future perspectives in their use as Ecological Indicators (EcoInd). Mediterr Mar Sci 16:352–365CrossRefGoogle Scholar
  57. Song H, Buhay JE, Whiting MF, Crandall KA (2008) Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified. Proc Natl Acad Sci USA 105:13486–13491CrossRefPubMedPubMedCentralGoogle Scholar
  58. Stoltzfus A, Lapp H, Matasci N, Deus H, Sidlauskas B, Zmasek CM, Vaidya G, Pontelli E, Cranston K, Vos R, Webb CO, Harmon LJ, Pirrung M, O’Meara B, Pennell MW, Mirarab S, Rosenberg MS, Balhoff JP, Bik HM, Heath T, Midford P, Brown JW, McTavish EJ, Sukumaran J, Westneat M, Alfaro ME, Steele A (2013) Phylotastic! making tree-of-life knowledge accessible, re-usable and convenient. BMC Bioinform 14:158CrossRefGoogle Scholar
  59. Tchesunov AV, Portnova DA, Campenhout JV (2015) Description of two free-living nematode species of Halomonhystera disjuncta complex (Nematoda: Monhysterida) from two peculiar habitats in the sea. Helgoland Mar Res 69:57–85Google Scholar
  60. Valentini A, Pompanon F, Taberlet P (2008) DNA barcoding for ecologists. Trends Ecol Evol 24:110–117CrossRefPubMedGoogle Scholar
  61. Waite IS, O’Donnell AG, Harrison A, Davies JT, Colvan SR, Ekschmitt K, Dogan H, Wolters V, Bongers T, Bongers M, Bakonyi G, Nagy P, Papatheodorou EM, Stamou GP, Boström S (2003) Design and evaluation of nematode 18S rDNA primers for PCR and denaturing gradient gel electrophoresis (DGGE) of soil community DNA. Soil Biol Biochem 35:1165–1173CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  1. 1.Integrative Taxonomy and Microbial Ecology Research Group, Department of Biological SciencesIndian Institute of Science Education and Research KolkataNadiaIndia

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