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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
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 22:2189–2202
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 16:979–989
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 171:1–21
Armstrong MR, Blok VC, Phillips MS (2000) A multipartite mitochondrial genome in the potato cyst nematode Globodera pallida. Genetics 154:181–192
Avise JC, Walker D (1999) Species realities and number in sexual vertebrates: perspectives from an asexually transmitted genome. Proc Natl Acad Sci USA 96:992–995
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 26:45–63
Bhadury P, Annapurna C (2011a) Marine barcoding—how will it help Indian marine benthic studies. Ind J Geo-Mar Sci 40:645–647
Bhadury P, Austen MC (2010) Barcoding marine nematodes: an improved set of nematode 18S rRNA primers to overcome eukaryotic co-interference. Hydrobiologia 641:245–251
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 320:1–9
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 154:509–518
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:e26445
Bik HM, Porazinska DL, Creer S, Caporaso JG, Knight R, Thomas WK (2012) Sequencing our way towards understanding global eukaryotic biodiversity. Trends Ecol Evol 27:233–243
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 10:389
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 392:71–75
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 13:901–909
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 11:1139–1148
Bucklin A, Steinke D, Blanco-Bercial L (2011) DNA barcoding of marine metazoa. Ann Rev Mar Sci 3:471–508
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 46:319–324
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 291:103–113
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 19:4–20
Cunha BP, Brito S, Fonseca G (2013) Zygonemella: the forgotten genus of the family Xyalidae (Nematoda). Zootaxa 3669:179–183
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:e243
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 360:1945–1958
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 300:91–103
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 128:307–321
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 15:1799–1812
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 152:1–15
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:e13716
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 39:276–289
Donn S, Griffiths BS, Neilson R, Daniell TJ (2008) DNA extraction from soil nematodes for multi-sample community studies. Appl Soil Ecol 38:20–26
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 6:50–553
Floyd R, Abebe E, Papert A, Blaxter ML (2002) Molecular barcodes for soil nematode identification. Mol Ecol 11:839–850
Floyd R, Rogers AD, Lambshead PJD, Smith CR (2005) Nematode-specific PCR primers for the 18S small subunit rRNA gene. Mol Ecol Notes 5:611–612
Fonseca G, Derycke S, Moens T (2008) Integrative taxonomy in two free-living nematode species complexes. Biol J Linn 94:737–753
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
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 23:1293–1302
Hebert PDN, Gregory TR (2005) The promise of DNA barcoding for taxonomy. Syst Biol 54:852–859
Hebert PDN, Cywinska A, Ball SL, Dewaard JR (2003) Biological identifications through DNA barcodes. Proc R Soc Lond B 270:313–321
Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004) Identification of birds through DNA barcodes. PLoS Biol 2:e312
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 8:23–34
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 66:167–174
Hyman BC, Lewis SC, Tang S, Wu Z (2011) Rampant gene rearrangement and haplotype hypervariation among nematode mitochondrial genomes. Genetica 139:611–615
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 45:537–547
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 9:1208–1221
Lambshead PJD (2004) Marine nematode biodiversity. In: Chen ZX, Chen SY, Dickson DW (eds) Nematology: advances and perspectives, vol 1. CABI Publishing, Wallingford, pp 439–468
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 108:13177–13182
Lunt DH, Hyman BC (1997) Animal mitochondrial DNA recombination. Nature 387:247
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 42:622–636
Miller SE (2007) DNA barcoding and the renaissance of taxonomy. Proc Natl Acad Sci USA 104:4775–4784
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 158:1–15
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 157:1665–1678
Radulovici AE, Archambault P, Dufresne F (2010) DNA barcodes for marine biodiversity: moving fast forward? Diversity 2:450–472
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 28:68–84
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 12:661–672
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 360:1805–1811
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 16:352–365
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 105:13486–13491
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 14:158
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 69:57–85
Valentini A, Pompanon F, Taberlet P (2008) DNA barcoding for ecologists. Trends Ecol Evol 24:110–117
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 35:1165–1173
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer International Publishing Switzerland
About this chapter
Cite this chapter
Bhadury, P. (2016). DNA Barcoding in Marine Nematodes: Successes and Pitfalls. In: Trivedi, S., Ansari, A., Ghosh, S., Rehman, H. (eds) DNA Barcoding in Marine Perspectives. Springer, Cham. https://doi.org/10.1007/978-3-319-41840-7_8
Download citation
DOI: https://doi.org/10.1007/978-3-319-41840-7_8
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-41838-4
Online ISBN: 978-3-319-41840-7
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)