DNADIVE

Full title

DNADIVE: eDNA Detection for crayfish invasIVE species in streams of Luxembourg: Development of a molecular toolbox


This public-public research project is supported by the
Luxembourg National Research Fund (PUBLIC2-17/SR/11816664)

Abstract

Oronectes_limosusDNADIVE aims at developing a toolbox for the molecular monitoring of invasive crayfish in the streams of Luxembourg. Three exotic species (Orconectes limosus, Pacifastacus leniusculus and Astacus leptodactylus) and a native one (Astacus astacus) will be targeted during this project. This molecular toolbox will encompass several techniques of detection comprising (1) a simple amplification method easily performed in a laboratory with few elements, (2) a digital droplet amplification (ddPCR) which is a more elaborated lab method that can allow for a higher detection sensitivity and a possible quantification of DNA that could be related through the proxy of biomass and abundance to the size of the populations detected and (3) an isotherm amplification method (iPCR) i.e. a simple, cost effective approach which will allow for a field detection usable by non-trained agents. The results will enable the development of a predictive species distribution model for the target species and allow to infer their impact on freshwater communities through the comparison with previous sampling campaigns.

This set of methods has the high potential to efficiently contribute to early detection and routine monitoring of the invasive crayfish species in Luxembourg, thus allowing for a timely and efficient decision-making and appropriate management.

Project status

Project funded by Fonds national de la recherche Luxembourg, Musée national d´histoire naturelle Luxembourg, Ministry of sustainable development and infrastructure. Duration: 3 years (01.05.2018 – 30.04.2021).

Project consortium: Fondation faune-flore, Musée national d´histoire naturelle Luxembourg, Luxembourg Institute of Science and Technology, Ministry of sustainable development and infrastructure.

Host institution: Fondation faune-flore @ Centre de recherche scientifique, Musée national d’histoire naturelle.

Contact

David PORCO
Musée national d’histoire naturelle
Research centre
Life science department
Research units: Invertebrate zoology & Population biology and Evolution
24, rue Münster
L-2160 Luxembourg
phone: (+352) 46 22 33 -264
fax: (+352) 46 38 48
david.porco@mnhn.lu

Publications

Molecular taxonomy (DNA barcoding)

  • PORCO D., Chang C., Dupont L., James S., Richard B., Decaëns T. (2017) A reference library of DNA barcodes for the earthworms from Upper Normandy: biodiversity assessment, new records, potential cases of cryptic diversity and ongoing speciation. Applied Soil Ecology – Sous presse.
  • Potapov M., PORCO D., Deharveng L. (2017) A new member of the genus Isotomurus from Kuril Islands (Collembola: Isotomidae) : returning to the problem of “color pattern species“. Zootaxa – Soumis.
  • Shekhovtsov S.V., Berman D.I., Bazarova N.E., Bulakhova N.A., PORCO D., Peltek S.E. (2016) Cryptic genetic lineages in Eisenia nordenskioldi pallida (Oligochaeta, Lumbricidae) and diversification history of the E. nordenskioldi complex. European Journal of Soil Biology, 75:151-156.
  • Dupont L., PORCO D., Symondson W.O.C., Roy V. (2016) Hybridization relics complicate barcode-based identification of species in earthworms. Molecular Ecology Ressources, 16: 883-894.
  • Cameron E.K., Decaëns T., Lapied E., PORCO D., Eisenhauer N. (2016) Earthworm databases and ecological theory: Synthesis of current initiatives and main research directions. Applied Soil Ecology, 104: 85-90.
  • Paoletti M.G., Blakemore R.J., Csuzdi C., Dorigo L., Dreon A.L., Gavinelli F., Lazzarini F., Manno N., Moretto E., PORCO D., Ruzzier E., Toniello V., Squartini A., Concheri G., Zanardo M., Alba-Tercedor J. (2016) Barcoding Eophila crodabepis sp. nov. (Annelida, Oligochaeta, Lumbricidae), a large stripy earthworm from Alpine foothills of Northeastern Italy similar to Eophila tellinii (Rosa, 1888). PLoS One, 11: e0151799.
  • Schneider C., PORCO D., Deharveng L. (2016) Two new Megalothorax species of the minimus group (Collembola, Neelidae). ZooKeys, 554: 37-68.
  • Decaëns T., PORCO D., James S.W., Brown G.G., Chassany V., Dubs F., Dupont L., Lapied E., Rougerie R., Rossi J.-P., Roy V. (2016) DNA barcoding reveals diversity patterns of earthworm communities in remote tropical forests of French Guiana. Soil Biology and Biochemistry, 92: 171-183.
  • Lukić M., PORCO D., Bedos A., Deharveng L. (2015) The puzzling distribution of Heteromurus (Verhoeffiella) absoloni Kseneman, 1938 (Collembola: Entomobryidae: Heteromurinae) resolved: detailed redescription of the nominal species and description of a new species from Catalonia (Spain). Zootaxa, 4039: 249-275.
  • Deharveng L., Zoughailech A., Hamra-Kroua S., PORCO D. (2015) A new species of Deutonura (Collembola: Neanuridae: Neanurinae) from north-eastern Algeria, and characterisation of two intraspecific lineages by their barcodes. Zootaxa, 3920, 281-290.
  • PORCO D., Skarżyński D., Decaëns T., Hebert P.D.N., Deharveng L. (2014) Barcoding the Collembola of Churchill: a molecular taxonomic reassessment of species diversity in a sub-Arctic area. Molecular Ecology Ressources, 14, 249-261.
  • Greenslade P., Stevens M.I., PORCO D. (2013) Measuring changes in molecular and geographical distribution after forty years of a possible endemic genus of South Australian Collembola (Springtail). The South Australian Naturalist 87, 18-21.
  • PORCO D., Decaëns T., Deharveng L., James S.W., Skarżyński D., Erséus C., Butt K., Richard B., Hebert P. (2013) Biological invasions in soil: DNA barcoding as a monitoring tool in a multiple taxa survey targeting European earthworms and collembolans in North America. Biological Invasions 15: 899-910.
  • Stoev, P., Komerički, A., Akkari, N., Liu, S., Zhou, X., Weigand, A., Hostens. J., Hunter C., Edmunds S., PORCO D., Zapparoli M., Georgiev T., Mietchen D., Roberts D., Faulwetter S., Smith V., Penev, L. (2013) Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data. Biodiversity Data Journal, 1, e1013.
  • Decaëns T., PORCO D., Rougerie R., Brown G.G., James S.W. (2013) Potential of DNA barcoding for earthworm research in taxonomy and ecology. Applied Soil Ecology 65: 35-42.
  • PORCO D., Potapov M., Bedos A., Busmachiu G., Weiner W.M., Hamra-Kroua S., Deharveng L. (2012) Cryptic diversity in the ubiquist species Parisotoma notabilis (Collembola, Isotomidae): a long used chimeric species? PLoS One 7: e46056.
  • PORCO D., Bedos A., Greenslade P., Janion C., Skarżyński D., Stevens M.I., Jansen van Vuuren B., Deharveng L. (2012) Challenging species delimitation in Collembola: cryptic diversity among common springtails unveiled by DNA barcoding. Invertebrates Systematics 26: 470-477.
  • Dózsa-Farkas K., PORCO D. and Boros G. (2012) Are Bryodrilus parvus Nurminen, 1970 and Bryodrilus librus (Nielsen and Christensen, 1959) (Annelida: Enchytraeidae) really different species? A revision based on DNA barcodes and morphological data. Zootaxa 3276: 38-50.
  • Janion C., Bedos A., Bengtsson J., Deharveng L., Jansen van Vuuren B., Leinaas H. P., Liua A., Malmström A., PORCO D. and Chown Steven L. (2011) Springtail diversity in South Africa. South African Journal of Science 107: 75-81.
  • Stevens M.I., PORCO D., D’Haese C.A. and Deharveng L. (2011) Comments on “Taxonomy and the DNA Barcoding Enterprise” by Ebach (2011). Zootaxa 2838: 85-88.
  • Dupont L., Lazrek F., PORCO D., King R.A., Rougerie R., Symondson W.O.C., Livet A., Richard B., Decaëns T., Butt K. R. and Mathieu J. (2011) New insight into the genetic structure of the Allolobophora chlorotica aggregate in Europe using microsatellite and mitochondrial data. Pedobiologia 54: 217-224.
  • James S.W., PORCO D., Decaëns T., Richard B., Rougerie R. and Erséus C. (2010) DNA barcoding reveals cryptic diversity in Lumbricus terrestris L., 1758 (Clitellata): Resurrection of L. herculeus (Savigny, 1826). PLoS One 5: e15629.
    PORCO D., Bedos A. and Deharveng L. (2010) Description and DNA barcoding assessment of the new species Deutonura gibbosa (Collembola: Neanuridae: Neanurinae), a common springtail of Alps and Jura. Zootaxa, 2639: 59-68.
  • PORCO D., Rougerie R., Deharveng L. and Hebert P. (2010) Coupling non-destructive DNA extraction and voucher retrieval for small soft-bodied Arthropods in a highthroughput context: the example of Collembola. Molecular Ecology Resources, 10: 942-945.
  • Stoev P., Akkari N., Zapparoli M., PORCO D., Enghof H., Edgecombe G. D., Georgiev T. and Penev L. (2010) The centipede genus Eupolybothrus Verhoeff, 1907 (Chilopoda: Lithobiomorpha: Lithobiidae) in North Africa, a cybertaxonomic revision, with a key to all species in the genus and the first use of DNA barcoding for the group. ZooKeys, 50: 29-77.
  • Richard B., Decaëns T., Rougerie R., James S., PORCO D., Hebert P. (2010) Re-integrating earthworm juveniles in soil diversity studies: species identification through DNA barcoding. Molecular Ecology Resources, 10: 606–614.
  • Rougerie R., Decaëns T., Deharveng L., PORCO D., James S. W., Chang C., Richard B. and Hebert P. D.N. (2009) DNA barcodes for soil animal taxonomy: transcending the final frontier. Pesquisa Agropecuaria Brasileira, 44: 789-802.

Chemical ecology

  • PORCO D., Bedos A. and Deharveng L. (2010) Cuticular compounds bring new insight in the post-glacial recolonization of a Pyrenean area: Deutonura deficiens Deharveng, 1979 complex, a case study. PLoS One 5: e14405.
  • PORCO D. and Deharveng L. (2009) Phylogeny of Collembola based on cuticular compounds: inherent usefulness and limitation of a character type. Naturwissenschaften, 96: 943-954.
  • PORCO D., Deharveng L. and Skarżyński D. (2009) Sex pheromone in Tetrodontophora bielanesis (Waga, 1842) (Collembola: Onychiuridae): Indirect reproduction mediated by cuticular compounds. Pedobiologia, 53: 59-63.
  • PORCO D. and Deharveng L. (2007) 1,3-dimethoxybenzene, a chemotaxonomic marker for the Neanurinae subfamily (Collembola). Biochemical Systematics and Ecology, 35: 160-161.
  • PORCO D., Deharveng L. and Gers C. (2004) Sexual discrimination with cuticular lipids in Schoetella ununguiculata (Collembola). Pedobiologia, 48: 581-583.

Hybrid zones

  • Rougerie R., Deharveng L., PORCO D. and Bedos A. (2006) Geographical barriers and ecological gradients: geographical distribution of the subspecies and morphotypes of Deutonura deficiens Deharveng 1979 (Collembola: Neanuridae). Pedobiologia, 50: 83-93.