Jump to ContentJump to Main Navigation
Show Summary Details

Polish Polar Research

The Journal of Committee on Polar Research of Polish Academy of Sciences

4 Issues per year


IMPACT FACTOR 2015: 1.182
5-year IMPACT FACTOR: 1.242

SCImago Journal Rank (SJR) 2015: 0.556
Source Normalized Impact per Paper (SNIP) 2015: 0.645
Impact per Publication (IPP) 2015: 1.183

Open Access
Online
ISSN
2081-8262
See all formats and pricing

Field and Laboratory Methods for DNA Studies on Deep-sea Isopod Crustaceans

Torben Riehl
  • Universität Hamburg, Zoologisches Institut und Zoologisches Museum, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
  • Senckenberg am Meer, Deutsches Zentrum für Marine Biodiversitätsforschung (DZMB), c/o Biozentrum Grindel, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
  • Email:
/ Nils Brenke
  • Senckenberg am Meer, Deutsches Zentrum für Marine Biodiversitätsforschung (DZMB), Südstrand 44, 26382 Wilhelmshaven, Germany
/ Saskia Brix
  • Senckenberg am Meer, Deutsches Zentrum für Marine Biodiversitätsforschung (DZMB), c/o Biozentrum Grindel, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
/ Amy Driskell
  • Smithsonian Institution, Laboratories of Analytical Biology, National Museum of Natural History, P.O. Box 37012 MRC 183, Washington D.C., 20013-7012, USA
/ Stefanie Kaiser
  • Senckenberg am Meer, Deutsches Zentrum für Marine Biodiversitätsforschung (DZMB), Südstrand 44, 26382 Wilhelmshaven, Germany
/ Angelika Brandt
  • Universität Hamburg, Zoologisches Institut und Zoologisches Museum, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
Published Online: 2014-07-29 | DOI: https://doi.org/10.2478/popore-2014-0018

Abstract

Field and laboratory protocols that originally led to the success of published studies have previously been only briefly laid out in the methods sections of scientific publications. For the sake of repeatability, we regard the details of the methodology that allowed broad-range DNA studies on deep-sea isopods too valuable to be neglected. Here, a comprehensive summary of protocols for the retrieval of the samples, fixation on board research vessels, PCR amplification and cycle sequencing of altogether six loci (three mitochondrial and three nuclear) is provided. These were adapted from previous protocols and developed especially for asellote Isopoda from deep-sea samples but have been successfully used in some other peracarids as well. In total, about 2300 specimens of isopods, 100 amphipods and 300 tanaids were sequenced mainly for COI and 16S and partly for the other markers. Although we did not set up an experimental design, we were able to analyze amplification and sequencing success of different methods on 16S and compare success rates for COI and 16S. The primer pair 16S SF/SR was generally reliable and led to better results than universal primers in all studied Janiroidea, except Munnopsidae and Dendrotionidae. The widely applied universal primers for the barcoding region of COI are problematic to use in deep-sea isopods with a success rate of 45–79% varying with family. To improve this, we recommend the development of taxon-specific primers.

Keywords: Icelandic waters; PCR; DNA sequencing; barcoding; Janiroidea; benthos; bathyal; abyssal

References

  • ALLCOCK A.L., BARRATT I., ELÉAUME M., LINSE K., NORMAN M.D., SMITH P.J., STEINKE D., STEVENSD.W. and STRUGNELLJ.M. 2011. Cryptic speciation and the circumpolarity debate: A case study on endemic Southern Ocean octopuses using the COI barcode of life. Deep Sea Research Part II 58: 242–249.

  • ALTSCHULS.F., GISH W., MILLERW., MYERSE.W. Aand LIPMAND.J. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403–410.

  • ASMYHR M.G. and COOPER S.J.B. 2012. Difficulties barcoding in the dark: the case of crustaceanstygofauna from eastern Australia. Invertebrate Systematics 26: 583–591. [Crossref]

  • BARBIER E.B., MORENO-MATEOS D., ROGERS A.D., ARONSON J., PENDLETON L., DANOVARO R., HENRY L.A., MORATO T., ARDRON J. and VAN DOVER C.L. 2014. Protect the deep sea. Nature 505: 475–477.

  • BENSON D.A., KARSCH-MIZRACHI I., LIPMAN D.J., OSTELL J. and WHEELER D.L. 2008. GenBank. Nucleic Acids Research 36: D25–30.

  • BŁAŻEWICZ-PASZKOWYCZ M., JENNINGS R.M., JESKULKE K. and BRIX S. 2014. Discovery of swimming males of Paratanaoidea (Tanaidacea). Polish Polar Research 35 (2): 415–453.

  • BOYLE E.E., ZARDUS J.D., CHASE M.R., ETTER R.J. and REX M.A. 2004. Strategies for molecular genetic studies of preserved deep-sea macrofauna. Deep-Sea Research Part I 51: 1319–1336.

  • BRANDT A., BRIX S., HELD C. and KIHARA T.-C. (in press) Rare in the deep – enigmatic species of the Serolidae Dana, 1853 (Crustacea: Isopoda) revisited. Description of a new species of Glabroserolis and redescription of Atlantoserolis vemae Menzies, 1962. Zoological Journal of the Linnean Society.

  • BRANDT A., ELSNER N., BRENKE N., GOLOVAN O., MALYUTINA M.V., RIEHL T., SCHWABE E. and WÜRZBERG L. 2013. Epifauna of the Sea of Japan collected via a new epibenthic sledge equipped with camera and environmental sensor systems. Deep-Sea Research Part II 86–87: 43–55.

  • BRANDTA., GOODAYA.J., BRANDAO S.N., BRIXS., BRÖKELANDW., CEDHAGENT., CHOUDHURY M., CORNELIUS N., DANIS B., DE MESEL I., DIAZ R.J., GILLAN D. C., EBBE B., HOWE J.A., JANUSSEN D., KAISER S., LINSE K., MALYUTINA M. V., PAWLOWSKI J., RAUPACH M.J. and VANREUSEL A. 2007. First insights into the biodiversity and biogeography of the Southern Ocean deep sea. Nature 447: 307–311.

  • BRENKE N. 2005. An epibenthic sledge for operations on marine soft bottom and bedrock. Marine Technology Society Journal 39: 10–21. [Crossref]

  • BRIX S., BAUERNFEIND W., BRENKE N., BŁAŻEWICZ-PASZKOWYCZ M., BORGES V., BULDT K., CANNON J., DÍAZ AGRAS G., FIEGE D., FIORENTINO D., HARALDSDÓTTIR S., HOFFMANN S., HOLST S., HÜTTMANN F., JESKULKE K., JENNINGS R.M., KOCOT K., KHODAMI S., LUCAS RODRIGUEZY., MARTINEZ ARBIZU P., MEIßNER K., MIKKELSEN N., MILLERM., MURRAYA., NEUMANN H., OSTMAN A., RIEHL T., SCHNURR S., SVAVARSSON J. and YASUHARA M. 2012. IceAGE – Icelandic marine Animals: Genetics and Ecology. Cruise report. Senatskommission für Ozeanographie der Deutschen Forschungsgemeinschaft MARUM. Zentrum für Marine Umweltwissenschaften der Universität Bremen, Leitstelle Deutsche Forschungsschiffe Institut für Meereskunde der Universität Hamburg, Hamburg: 41 pp.

  • BRIX S., LEESE F., RIEHL T. and KIHARA T.C. 2014. A new genus and new species of Desmosomatidae Sars, 1897 (Isopoda) from the eastern South Atlantic abyss described by means of integrative taxonomy. Marine Biodiversity doi:10.1007/s12526-014-0218-3.

  • BRIX S., RIEHL T. and LEESE F. 2011. First genetic data for Haploniscus rostratus and Haploniscus unicornis from neighbouring deep-sea basins in the South Atlantic. Zootaxa 2838: 79-84.

  • BRIX S., SVAVARSSON J., and LEESE F. 2014. A multi-gene analysis reveals multiple highly divergent lineages of the isopod Chelator insignis (Hansen, 1916) south of Iceland. Polish Polar Research 35 (2): 225-242.

  • BRÖKELAND W. 2010. Description of four new species from the Haploniscus unicornis Menzies, 1956 complex (Isopoda: Asellota: Haploniscidae). Zootaxa 2536: 1-35.

  • BRÖKELAND W. and RAUPACH M.J. 2008. A species complex within the isopod genus Haploniscus (Crustacea: Malacostraca: Peracarida) from the Southern Ocean deep sea: a morphological and molecular approach. Zoological Journal of the Linnean Society 152: 655-706.

  • DERYCKE S., VANAVERBEKEJ., RIGAUX A., BACKELJAUT. andMOENS T. 2010. Exploring the Use of Cytochrome Oxidase c Subunit 1 (COI) for DNA Barcoding of Free-Living Marine Nematodes. PLoS ONE 5: e13716.

  • DREYER H. and WÄGELE J.-W. 2001. Parasites of crustaceans (Isopoda: Bopyridae) evolved from fish parasites: Molecular and morphological evidence. Zoology 103: 157-178.

  • DREYER H. and WÄGELE J.-W. 2002. The Scutocoxifera tax. nov. and the information content of nuclear ssu rDNA sequences for reconstruction of isopod phylogeny (Peracarida: Isopoda). Journal of Crustacean Biology 22: 217-234. [Crossref]

  • FOLMER O., BLACK M., HOEH W., LUTZ R. and VRIJENHOEK R. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology 3: 294-299. [PubMed]

  • FRASER C.I., NIKULA R. and WATERS J.M. 2011. Oceanic rafting by a coastal community. Proceedings of the Royal Society B: Biological Sciences 278: 649-655.

  • GAGE J.D. 2004. Diversity in deep-sea benthic macrofauna: the importance of local ecology, the larger scale, history and the Antarctic. Deep Sea Research Part II 51: 1689-1708.

  • GEMEINHOLZER B., REY I., WEISING K., GRUNDMANN M., MUELLNER A. M., ZETZSCHE H., DROEGE G., SEBERG O., PETERSEN G., RAWSON D. and WEIGT L. A. 2010. Organizing specimen and tissue preservation in the field for subsequent molecular analyses. In: J. Eymann, J. Degreeg, C. Häuser, J.C. Monje, Y. Samyn and D. Vanden Spiegel (eds) Manual of field recording techniques and protocols for all taxa biodiversity inventories. ABC Taxa. Belgian Development Cooperation, Meise: 129-157.

  • GIBBS J. 2009. Integrative taxonomy identifies new (and old) species in the Lasioglossum (Dialictus) tegulare (Robertson) species group (Hymenoptera, Halictidae). Zootaxa 2032: 1-38.

  • GLASBY G.P. 2002. Deep seabed mining: past failures and future prospects. Marine Georesources and Geotechnology 20: 161-176.

  • HAUSDORFB. 2011. Progress toward a general species concept. Evolution 65: 923-931. [Crossref]

  • HAVERMANS C, SONET G., D’UDEKEM D’ACOZ C, NAGY Z. T., MARTIN P., BRIX S., RIEHL T., AGRAWAL S. and HELD C. 2013. Genetic and morphological divergences in the cosmopolitan deep-sea amphipod Eurythenes gryllus reveal a diverse abyss and a bipolar species. PLoS ONE 8: e74218.

  • HEBERT P.D.N., CYWINSKA A., BALL S.L. and DEWAARD J.R. 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society of London, Series B: Biological Sciences 270: 313-321.

  • HELD C. 2000. Phylogeny and biogeography of serolid isopods (Crustacea, Isopoda, Serolidae) and the use of ribosomal expansion segments in molecular systematics. Molecular Phylogenetics and Evolution 15: 165-178. [Crossref] [PubMed]

  • HESSLER R.R., WILSON G.D.F. and THISTLE D. 1979. The deep-sea isopods: a biogeographic and phylogenetic overview. Sarsia 64: 67-75.

  • HILLIS D.M. and DIXON M.T. 1991. Ribosomal DNA: molecular evolution and phylogenetic inference. The Quarterly Review of Biology 66: 411-453. [Crossref] [PubMed]

  • HOAGLAND P., BEAULIEU S., TIVEY M.A., EGGERT R. G., GERMAN C, GLOWKA L. and LIN J. 2010. Deep-sea mining of seafloor massive sulfides. Marine Policy 34: 728-732. [Crossref]

  • KAISER S. and BRENKE N. (in press) Epibenthic sledges. In: M.R. Clark, M. Consalvey and A.A. Rowden (eds) Biological Sampling in the Deep Sea. Wiley-Blackwell.

  • KATOH K., MISAWA K., KUMA K. and MIYATA T. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30: 3059-3066. [Crossref] [PubMed]

  • KILPERT F., HELD C. and PODSIADLOWSKI L. 2012. Multiple rearrangements in mitochondrial genomes of Isopoda and phylogenetic implications. Molecular Phylogenetics and Evolution 64: 106-117. [PubMed] [Crossref]

  • LENAERS G, MAROTEAUX L., MICHOT B. and HERZOG M. 1989. Dinoflagellates in evolution. A molecular phylogenetic analysis of large subunit ribosomal RNA. Journal of Molecular Evolution 29: 40-51. [Crossref] [PubMed]

  • LINSE K., JACKSON J.A., MALYUTINA M.V. and BRANDT A. 2014. Shallow-water northern hemisphere Jaera (Crustacea, Isopoda, Janiridae) found on whale bones in the Southern Ocean deep sea: ecology and description of Jaera tyleri sp. nov. PloS ONE 9: e93018.

  • MALLET J.1995. A species definition for the modern synthesis. Trends in Ecology and Evolution 10: 294-299.

  • MAYR E. 1942. Systematics and the origin of species: From the viewpoint of a zoologist. Columbia University Press, New York: 334 pp.

  • MAYR E. 2000. The biological species concept. In: Q.D. Wheeler and N.I. Platnick (eds) Species concepts and phylogenetic theory: a debate. Columbia University Press, New York: 17-29.

  • MEYER C.P., GELLER J. B. and PAULAY G. 2005. Fine scale endemism on coral reefs: archipelagic differentiation in turbidid gastropods. Evolution 59: 113-125. [PubMed] [Crossref]

  • MICHEL-SALZAT A. and BOUCHON D. 2000. Phylogenetic analysis of mitochondrial LSU rRNA in oniscids. Comptes Rendus de l’Academie des Sciences Series III Sciences de la Vie 323: 827-837.

  • MORA C, TITTENSOR D.P., ADL S., SIMPSON A.G.B. and WORM B. 2011. How many species are there on Earth and in the ocean? PLoS Biology 9: e1001127. [Crossref]

  • NAGY Z.T. 2010. A hands-on overview of tissue preservation methods for molecular genetic analyses. Organisms, Diversity and Evolution 10: 91-105.

  • OMILIAN A.R. and TAYLOR D.J. 2001. Rate acceleration and long-branch attraction in a conserved gene of cryptic daphniid (Crustacea) species. Molecular Biology and Evolution 18: 2201-2212. [Crossref]

  • OSBORN K.J. 2009. Relationships within the Munnopsidae (Crustacea, Isopoda, Asellota) based on three genes. Zoologica Scripta 38: 617-635. [Crossref]

  • PALUMBIS.R., MARTIN A., ROMANO S., MCMILLAN W.O., STICEL. and GRABOWSKI G. 1991. The simple fool’s guide to PCR. Version 2. University of Hawaii Press, Honolulu: 45 pp.

  • PONS J., BARRACLOUGH T.G., GOMEZ-ZURITA J., CARDOSO A., DURAN D.P., HAZELL S., KAMOUN S., SUMLIN W.D. and VOGLER A.P. 2006. Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Systematic Biology 55: 595-609. [Crossref] [PubMed]

  • QUICKE D.L.J., LOPEZ-VAAMONDE C. and BELSHAW R. 1999. Preservation of hymenopteran specimens for subsequent molecular and morphological study. Zoologica Scripta 28: 261-267. [Crossref]

  • RADULOVICI A.E., BERNARD S.-M. and DUFRESNE F. 2009. DNA barcoding of marine crustaceans from the Estuary and Gulf of St Lawrence: a regional-scale approach. Molecular Ecology Resources 9: 181-187. [Crossref]

  • RAUPACH M.J., HELD C. and WÄGELE J.-W. 2004. Multiple colonization of the deep sea by the Asellota (Crustacea: Peracarida: Isopoda). Deep Sea Research Part II51: 1787-1795.

  • RAUPACH M.J., MALYUTINA M.V., BRANDT A. and WÄGELE J.-W. 2007. Molecular data reveal a highly diverse species flock within the munnopsoid deep-sea isopod Betamorpha fusiformis (Barnard, 1920) (Crustacea: Isopoda: Asellota) in the Southern Ocean. Deep Sea Research Part II54: 1820-1830.

  • RAUPACH M.J., MAYER C, MALYUTINA M.V. and WÄGELE J.-W. 2009. Multiple origins of deep-sea Asellota (Crustacea: Isopoda) from shallow waters revealed by molecular data. Proceedings of the Royal Society B: Biological Sciences 276: 799-808.

  • RAUPACH M.J. and WÄGELE J.-W. 2006. Distinguishing cryptic species in Antarctic Asellota (Crustacea: Isopoda) - a preliminary study of mitochondrial DNA in Acanthaspidia drygalskii. Antarctic Science 18: 191-198. [Crossref]

  • REX MA. and ETTER R.J. 2010. Deep-sea biodiversity: Pattern and scale. Harvard University Press Cambridge MA, London: 354 pp.

  • RIEHLT. and BRANDT A. 2010. Descriptions of two new species in the genus Macrostylis Sars, 1864 (Isopoda, Asellota, Macrostylidae) from the Weddell Sea (Southern Ocean), with a synonymisation of the genus Desmostylis Brandt, 1992 with Macrostylis. Zookeys 57: 9-49.

  • RIEHL T. and BRANDT A. 2013. Southern Ocean Macrostylidae reviewed with a key to the species and new descriptions from Maud Rise. Zootaxa 3692: 160-203.

  • RIEHLT. and KAISER S. 2012. Conquered from the deep sea? A new deep-sea isopod species from the Antarctic shelf shows pattern of recent colonization. PLoS ONE 7: e49354.

  • RIEHL T., WILSON G.D.F. and HESSLER R.R. 2012. New Macrostylidae Hansen, 1916 (Crustacea: Isopoda) from the Gay Head-Bermuda transect with special consideration of sexual dimorphism. Zootaxa 3277: 1-26.

  • SCHANDER C. and HALANYCH K.M. 2003. DNA, PCR and formalinized animal tissue - a short review and protocols. Organisms Diversity and Evolution 3: 195-205.

  • SCHNURR S. and BRIXS. 2012. Eugerdella huberti sp. nov. - a new species of Desmosomatidae Sars, 1897 (Crustacea, Isopoda) from the deep-sea of the South Atlantic Ocean. Marine Biodiversity 42: 13-24. [Crossref]

  • SCHWENTNER M., TIMMS B.V. and RICHTER S. 2011. An integrative approach to species delineation incorporating different species concepts: a case study of Limnadopsis (Branchiopoda: Spinicaudata). Biological Journal of the Linnean Society 104: 575-599. [Crossref]

  • SITES J.W. and MARSHALL J.C. 2004. Operational criteria for delimiting species. Annual Review of Ecology, Evolution and Systematics 35: 199-227. [Crossref]

  • TESKE P.R., MCQUAID CD., FRONEMAN P.W. and BARKER N.P. 2006. Impacts of marine biogeographic boundaries on phylogeographic patterns of three South African estuarine crustaceans. Marine Ecology Progress Series 314: 283-293. [Crossref]

  • THOMPSON J.D., HIGGINS D.G. and GIBSON T.J. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penaltiandes and weight matrix choice. Nucleic Acids Research 22: 4673-4680. [PubMed] [Crossref]

  • TSANG L.M., CHAN B.K.K., SHIH F.-L., CHU K.H. and ALLEN CHEN C. 2009. Host-associated speciation in the coral barnacle Wanella milleporae (Cirripedia: Pyrgomatidae) inhabiting the Millepora coral. Molecular Ecology 18: 1463-1475. [Crossref]

  • WÄGELE J.-W., HOLLAND B., DREYER H. and HACKETHAL B. 2003. Searching factors causing implausible non-monophyly: ssu rDNA phylogeny of Isopoda Asellota (Crustacea: Peracarida) and faster evolution in marine than in freshwater habitats. Molecular Phylogenetics and Evolution 28: 536-551. [PubMed] [Crossref]

  • WEIGT LA., DRISKELL A.C., ORMOS A., MEYER C. and COLLINS A. 2012. Introduction to Animal DNA Barcoding Protocols. Molecular Biology 858: 11-16.

  • WETZER R. 2001. Hierarchical analysis of mtDNA variation and the use of mtDNA for isopod (Crustacea: Peracarida: Isopoda) systematics. Contributions to Zoology 70: 23-39.

  • WILSON G.D.F. 1982. Systematics of a species complex in the deep-sea genus Eurycope, with a revision of six previously described species (Crustacea, Isopoda, Eurycopidae). University of California Press, Berkley, Los Angeles, London: 64 pp.

  • WILSON G.D.F. 1983. Variation in the deep-sea isopod Eurycope iphthima (Asellota, Eurycopidae): depth related clines in rostral morphology and in population structure. Journal of Crustacean Biology 3: 127-140. [Crossref]

  • WILSON G.D.F. 1986. Evolution of the female cuticular organ in the Asellota (Crustacea, Isopoda). Journal of Morphology 190: 297-305.

  • WILSON G.D.F. 1991. Functional morphology and evolution of isopod genitalia. In: R.T. Bauer and J.W. Martin (eds) Crustacean sexual biology. Columbia University Press, New York: 228-245.

  • WILSON G.D.F. 2008. Local and regional species diversity of benthic Isopoda (Crustacea) in the deep Gulf of Mexico. Deep-Sea Research Part II55: 2634–2649.

  • ZEALE M.R.K., BUTLIN R.K., BARKER G.L.A., LEES D.C. and JONES G. 2011. Taxon-specific PCR for DNA barcoding arthropod prey in bat faeces. Molecular Ecology Resources 11: 236-244. [Crossref] [PubMed]

  • ZHANG Z., SCHWARTZ S., WAGNER L. and MILLER W. 2000. A greedy algorithm for aligning DNA sequences. Journal of Computational biology 7: 203-214. [Crossref]

About the article

Received: 2014-02-20

Accepted: 2014-06-10

Published Online: 2014-07-29


Citation Information: Polish Polar Research, ISSN (Online) 2081-8262, DOI: https://doi.org/10.2478/popore-2014-0018. Export Citation

© 2014 Polish Academy of Sciences. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License. (CC BY-NC-ND 3.0)

Citing Articles

Here you can find all Crossref-listed publications in which this article is cited. If you would like to receive automatic email messages as soon as this article is cited in other publications, simply activate the “Citation Alert” on the top of this page.

[1]
A. Brandt, N.O. Elsner, M.V. Malyutina, N. Brenke, O.A. Golovan, A.V. Lavrenteva, and T. Riehl
Deep Sea Research Part II: Topical Studies in Oceanography, 2015, Volume 111, Page 175

Comments (0)

Please log in or register to comment.
Log in