Skip to main content
SpringerLink
Log in
Book cover

Biodiversity and Chemotaxonomy pp 43–53Cite as

Molecular Approaches to Explore Coastal Benthic Metazoan Diversity—Success and Constraints

  • Chapter
  • First Online:

  • 526 Accesses

Part of the book series: Sustainable Development and Biodiversity ((SDEB,volume 24))

Abstract

Coastal environments are represented by rich biotopes and harbour diverse organismal groups, many of which are yet to be explored. The metazoan phyla found in the sediment of coastal environments are critical to ecosystem functioning. The abundance and diversity of benthic metazoan phyla such as the free-living marine nematodes in various coastal biotopes are not fully understood from the viewpoint of biodiversity. Molecular tools such as next-generation sequencing (NGS) approach offer a way to develop robust metabarcodes. Generation and processing of NGS data including metabarcode sequences involve computational understanding. Metabarcodes obtained using NGS platforms are providing improved understanding of biodiversity-rich sedimentary metazoan groups such as free-living marine nematodes. Some of these aspects in terms of NGS platforms, data processing and examples of application of NGS to explore benthic metazoan diversity with focus on free-living nematode communities have been discussed.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  • Adams MD, Celniker SE, Holt RA, Evans CA et al (2000) The genome sequence of Drosophila melanogaster. Science 287:2185–2195

    Article  Google Scholar 

  • Bhadury P, Bik H, Lambshead JD, Austen MC, Smerdon GR, Rogers AD (2011) Molecular diversity of fungal phylotypes co-amplified alongside nematodes from coastal and deep-sea marine environments. PLoS ONE 6:e2644

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • Blaxter ML et al (2005) Defining operational taxonomic units using DNA barcode data. Philos Trans R Soc B Biol Sci 360:1935–1943

    Article  CAS  Google Scholar 

  • Bonilla-Rosso G, Souza V, Eguiarte LE (2008) Metagenómica, genómica y ecología molecular: la nueva ecología en el bicentenario de Darwin. TIP Revista Especializada en Ciencias Químico-Biológicas 11:41–51

    Google Scholar 

  • Boufahja F, Semprucci F, Beyrem H, Bhadury P (2015) Marine nematode taxonomy in Africa: promising prospects against scarcity of information. J Nematology 47:198–206

    Google Scholar 

  • Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD et al (2010) QIIME allows analysis of high throughput community sequencing data. Nat Methods 7:335–336

    Article  CAS  Google Scholar 

  • Chariton AA, Court LN, Hartley DM, Colloff MJ, Hardy CM (2010) Ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA. Front Ecol Environ 8:233–238

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • Danovaro R, Fraschetti S (2002) Meiofaunal vertical zonation on hard bottoms: comparison with soft-bottom meiofauna. Mar Ecol Progr Ser 230:159–169

    Article  Google Scholar 

  • del Campo J et al (2014) The others: our biased perspective of eukaryotic genomes. Trends Ecol Evol 29:252–259

    Article  Google Scholar 

  • Eguiarte LE, Aguirre-Liguori JA, Jardón-Barbolla L, Aguirre-Planter E, Souza V (2013) Genómica de poblaciones: nada en Evolución va a tener sentido si no es a la luz de la genómica, y nada en genómica tendrá sentido si no es a la luz de la evolución. TIP Revista Especializada En Ciencias Químico-Biológicas 16:42–56

    Article  CAS  Google Scholar 

  • Epp LS, Boessenkool S, Bellemain EP, Haile J, Esposito A et al (2012) New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems. Mol Ecol 21:1821–1833

    Article  CAS  Google Scholar 

  • 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. https://doi.org/10.1038/ncomms1095

    Article  Google Scholar 

  • Ghosh A, Bhadury P (2019) Methods of assessment of microbial diversity in natural environments. In: Das S, Dash H (eds) Microbial diversity in the genomic era, Academic Press, p 770

    Google Scholar 

  • Giere O (2009) Meiobenthology: the microscopic motile fauna of aquatic sediments. Springer, Heidelberg

    Google Scholar 

  • Hao X, Jiang R, Chen T (2011) Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering. Bioinformatics 27:611–618

    Article  CAS  Google Scholar 

  • Hirai J, Tsuda A (2015) Metagenetic community analysis of epipelagic planktonic copepods in the tropical and subtropical Pacific. Mar Ecol Prog Ser 534:65–78. https://doi.org/10.3354/meps11404

    Article  CAS  Google Scholar 

  • Hirai J, Yasuike M, Fujiwara A, Nakamura Y, Hamaoka S, Katakura S et al (2015) Effects of plankton net characteristics on metagenetic community analysis of metazoan zooplankton in a coastal marine ecosystem. J Exp Mar Biol Ecol 469:36–43

    Article  Google Scholar 

  • Ibarra-Laclette E, Lyons E, Hernández-Guzmán G, Pérez-Torres CA, Carretero-Paulet L et al (2013) Architecture and evolution of a minute plant genome. Nature 498:94–98

    Article  CAS  Google Scholar 

  • Knowlton N (1993) Sibling species in the sea. Ann Rev Ecol Syst 24:189–216

    Article  Google Scholar 

  • Kim H, Kim H, Hwang H, Kim W (2017) Metagenomic analysis of the marine coastal invertebrates of South Korea as assessed by Ilumina MiSeq. Animal Cells Sys 21

    Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  Google Scholar 

  • Lawton JH, Bignell DE, Bolton B et al (1998) Biodiversity inventories, indicator taxa and effects of habitat modification in tropical forest. Nature 391:72–76

    Article  CAS  Google Scholar 

  • Leray M, Knowlton N (2015) DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity. Proc Natl Acad Sci USA 112:2076–2081

    Article  CAS  Google Scholar 

  • Leray M, Knowlton N (2016) Censusing marine eukaryotic diversity in the twenty-first century. Phil Trans R Soc B 371:20150331

    Article  Google Scholar 

  • Liu L, Li Y, Li S, Hu N, He Y, Pong R, Lin D, Lu L, Law M (2012) Comparison of next-generation sequencing systems. J Biomed Biotechnol 2012:251364

    PubMed  PubMed Central  Google Scholar 

  • López-Escardó D, Paps J, de Vargas C, Massana R, Ruiz-Trillo I, del Campo J (2018) Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity. Sci Rep 8:9106

    Article  Google Scholar 

  • Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M (2014) Swarm: robust and fast clustering method for amplicon-based studies. Peer J 2:e593

    Article  Google Scholar 

  • Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387–402

    Article  CAS  Google Scholar 

  • Mathee K, Narasimhan G, Valdes C, Qiu X, Matewish JM et al (2008) Dynamics of Pseudomonas aeruginosa genome evolution. Proc Natl Acad Sci USA 105:3100–3105

    Article  CAS  Google Scholar 

  • Pearman JK, Irigoien X (2015) Assessment of Zooplankton Community Composition along a Depth Profile in the Central Red Sea. PLoS ONE 10(7): e0133487. https://doi.org/10.1371/journal.pone.0133487

    Article  Google Scholar 

  • Ratnasingham S, Hebert PDN (2007) BOLD: The Barcode of Life Data System. Mol Ecol Notes 7:355–364. http://www.barcodinglife.org

  • Reeder J, Knight R (2010) Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat Methods 7:668–669

    Article  CAS  Google Scholar 

  • Riesenfeld CS, Schloss PD, Handelsman J (2004) Metagenomics: genomic analysis of microbial communities. Annu Rev Genet 38:525–552

    Article  CAS  Google Scholar 

  • Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W et al (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475:348–352

    Article  CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • Shokralla S, Spall JL, Gibson JF, Hajibabaei M (2012) Next-generation sequencing technologies for environmental DNA research. Mol Ecol 21:1794–1805

    Article  CAS  Google Scholar 

  • Taberlet P, Coissac E, Pompanon F, Brochmann C, Willerslev E (2012) Towards next generation biodiversity assessment using DNA metabarcoding. Mol Ecol 21:2045–2050

    Article  CAS  Google Scholar 

  • Thompson JF, Milos P (2011) The properties and applications of single-molecule DNA sequencing. Genome Biol 12:217–226

    Article  CAS  Google Scholar 

  • Thomsen PF, Willerslev E (2015) Environmental DNA—an emerging tool in conservation for monitoring past and present biodiversity. Biol Conserv 183:4–18

    Article  Google Scholar 

  • Yi X, Liang Y, Huerta-Sánchez E, Jin X, Xi Z et al (2010) Sequencing of 50 human exomes reveals adaptation to high altitude. Science 329:75–78

    Article  CAS  Google Scholar 

  • Yoccoz NG (2012) The future of environmental DNA in ecology. Mol Ecol 21:2031–2038

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Integrative Taxonomy and Microbial Ecology Research Group, Department of Biological Sciences & Centre for Climate and Environmental Studies, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, 741246, West Bengal, India

    Punyasloke Bhadury

Authors
  1. Punyasloke Bhadury
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Punyasloke Bhadury .

Editor information

Editors and Affiliations

  1. Botany Department, Mohanlal Sukhadia University, Udaipur, India

    Kishan Gopal Ramawat

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Bhadury, P. (2019). Molecular Approaches to Explore Coastal Benthic Metazoan Diversity—Success and Constraints. In: Ramawat, K. (eds) Biodiversity and Chemotaxonomy. Sustainable Development and Biodiversity, vol 24. Springer, Cham. https://doi.org/10.1007/978-3-030-30746-2_3

Download citation

Publish with us

Policies and ethics

Search

Navigation