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DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe
Title DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe Author Leese Florian Co-authors Altermatt Florian Bouchez Agnès Ekrem Torbjørn Hering Daniel Meissner Kristian Mergen Patricia Pawlowski Jan Piggott Jeremy Jay Rimet Frédéric Steinke Dirk Taberlet Pierre Weigand Alexander M. Abarenkov Kessy Beja Pedro Bervoets Lieven Björnsdóttir Snaedis Boets Pieter Boggero A. Bones Atle Magnar Borja Ángel Bruce Kat Bursić Vojislava Carlsson Jeans Čiampor Fedor SAVBOTAN - Botanický ústav SAV ORCID Čiamporová-Zaťovičová Zuzana SAVBOTAN - Botanický ústav SAV ORCID Coissac Eric Costa Filipe Costache Marieta Creer Simon Csabai Zoltán Deiner Kristy DelValls Ángel Drakare Stina Duarte Sofia Eleršek Tina Fazi Stefano Fišer Cene Flot Jean-François Fonseca Vera Fontaneto Diego Grabowski Michael Graf Wolfram Guðbrandsson Jóhannes Hellström Micaela Hershkovitz Yaron Hollingsworth Peter Japoshvili Bella Jones John I. Kahlert Maria Stroil Belma Kalamujic Kasapidis Panagiotis Kelly Martyn G. Kelly-Quinn Mary Keskin Emre Kõljalg Urmas Ljubešić Zrinka Maček Irena Mächler Elvira Mahon Andrew Marečková Marketa Mejdandzic Maja Mircheva Georgina Montagna Matteo Moritz Christian Mulk Vallo Naumoski Andreja Navodaru Ion Padisák Judit Pálsson Snæbjörn Panksep Kristel Penev Lyubomir Petrusek Adam Pfannkuchen Martin Andreas Primmer Craig R. Rinkevich Baruch Rotter Ana Schmidt-Kloiber Astrid Segurado Pedro Speksnijder Arjen Stoev Pavel Strand Malin Šulčius Sigitas Sundberg Per Traugott Michael Tsigenopoulos Costas Turon Xavier Valentini Alice Hoorn Berry B. van der Várbíró Gábor Hadjilyra Marlen Ines Vasquez Viguri Javier Vitonytė Irma Voglier Alfried Vrålstad Trude Wägele Wolfgang Wenne Roman Winding Anne Woodward Guy Zegura Bojana Zimmermann Jonas Source document Research Ideas and Outcomes. Vol. 2 (2016), art. no. e11321 Language eng - English Country BG - Bulgaria URL URL link Document kind rozpis článkov z periodík (rbx) Citations STOECKLE, M.Y. - SOBOLEVA, L. - CHARLOP-POWERS, Z. Aquatic environmental DNA detects seasonal fish abundance and habitat preference in an urban estuary. In PLOS ONE. ISSN 1932-6203, APR 12 2017, vol. 12, no. 4. Pinna, M. - Janzen, S. - Franco, A. - Specchia, V. - Marini, G. Role of habitats and sampling techniques on macroinvertebrate descriptors and ecological indicators: An experiment in a protected Mediterranean lagoon, In Ecological Indicators, 2017, vol. 83, p. 495-503. ISSN 1470-160X SALMASO, N. - ANNEVILLE, O. - STRAILE, D. - VIAROLI, P. European large perialpine lakes under anthropogenic pressures and climate change: present status, research gaps and future challenges. In HYDROBIOLOGIA. ISSN 0018-8158, NOV 2018, vol. 824, no. 1, SI, p. 1-32. BUTTIGIEG, P.L. - FADEEV, E. - BIENHOLD, C. - HEHEMANN, L. - OFFRE, P. - BOETIUS, A. Marine microbes in 4D-using time series observation to assess the dynamics of the ocean microbiome and its links to ocean health. In CURRENT OPINION IN MICROBIOLOGY. ISSN 1369-5274, JUN 2018, vol. 43, p. 169-185. HAVEMANN, N. - GOSSNER, M.M. - HENDRICH, L. - MORINIERE, J. - NIEDRINGHAUS, R. - SCHAFER, P. - RAUPACH, M.J. From water striders to water bugs: the molecular diversity of aquatic Heteroptera (Gerromorpha, Nepomorpha) of Germany based on DNA barcodes. In PEERJ. ISSN 2167-8359, MAY 2 2018, vol. 6. LAROCHE, O. - WOOD, S.A. - TREMBLAY, L.A. - ELLIS, J.I. - LEAR, G. - POCHON, X. A cross-taxa study using environmental DNA/RNA metabarcoding to measure biological impacts of offshore oil and gas drilling and production operations. In MARINE POLLUTION BULLETIN. ISSN 0025-326X, FEB 2018, vol. 127, p. 97-107. ECKERT, I.M.K. - LITTLEFAIR, J.E. - ZHANG, G.K. - CHAIN, F.J.J. - CREASE, T.J. - CRISTESCU, M.E. Bioinformatics for Biomonitoring: Species Detection and Diversity Estimates Across Next-Generation Sequencing Platforms. In NEXT GENERATION BIOMONITORING, PT 2. ISSN 0065-2504, 2018, vol. 59, 2, p. 1-32. Brack, W. - Escher, B.I. - Müller, E. et al. Towards a holistic and solution-oriented monitoring of chemical status of European water bodies: how to support the EU strategy for a non-toxic environment?. In Environmental Sciences Europe, 2018, vol. 30, art. no. 33. ISSN: 2190-4707. Leasi, F. - Sevigny, J.L. - Laflamme, E.M. et al. Biodiversity estimates and ecological interpretations of meiofaunal communities are biased by the taxonomic approach. In Communications Biology, 2018, vol. 1, art. no. 112. ISSN 2399-3642. doi:10.1038/s42003-018-0119-2 Pešić, V. - Karaman, G.S. - Kostianoy, A.G. - Vukašinović-Pešić, V. Conclusions: Recent Advances and the Future Prospects of the Lake Skadar/Shkodra Environment. In: Pešić V., Karaman G., Kostianoy A. (eds) The Skadar/Shkodra Lake Environment. The Handbook of Environmental Chemistry, vol 80. Cham: Springer 2018, p. 481-500. ISBN 978-3-319-99249-5. SIEGENTHALER, A. - WANGENSTEEN, O.S. - SOTO, A.Z. - BENVENUTO, C. - CORRIGAN, L. - MARIANI, S. Metabarcoding of shrimp stomach content: Harnessing a natural sampler for fish biodiversity monitoring. In MOLECULAR ECOLOGY RESOURCES. ISSN 1755-098X, JAN 2019, vol. 19, no. 1, p. 206-220. HAJIBABAEI, M. - PORTER, T.M. - WRIGHT, M. - RUDAR, J. COI metabarcoding primer choice affects richness and recovery of indicator taxa in freshwater systems. In PLOS ONE. ISSN 1932-6203, SEP 12 2019, vol. 14, no. 9. RIBEIRO, H. - MARTINS, A. - GONCALVES, M. - GUEDES, M. - TOMASINO, M.P. - DIAS, N. - DIAS, A. - MUCHA, A.P. - CARVALHO, M.F. - ALMEIDA, C.M.R. - RAMOS, S. - ALMEIDA, J.M. - SILVA, E. - MAGALHAES, C. Development of an autonomous biosampler to capture in situ aquatic microbiomes. In PLOS ONE. ISSN 1932-6203, MAY 15 2019, vol. 14, no. 5. FILIPE, A.F. - FEIO, M.J. - GARCIA-RAVENTOS, A. - RAMIAO, J.P. - PACE, G. - MARTINS, F.M.S. - MAGALHAES, M.F. The European Water Framework Directive facing current challenges: recommendations for a more efficient biological assessment of inland surface waters. In INLAND WATERS. ISSN 2044-2041, 2019, vol. 9, no. 1, p. 95-103. BELLE, C.C. - STOECKLE, B.C. - GEIST, J. Taxonomic and geographical representation of freshwater environmental DNA research in aquatic conservation. In AQUATIC CONSERVATION-MARINE AND FRESHWATER ECOSYSTEMS. ISSN 1052-7613, NOV 2019, vol. 29, no. 11, p. 1996-2009. KOWALSKA, Zuzanna - PNIEWSKI, Filip - LATALA, Adam. DNA barcoding A new device in phycologist's toolbox. In ECOHYDROLOGY & HYDROBIOLOGY. ISSN 1642-3593, 2019, vol. 19, no. 3, pp. 417-427. FERNÁNDEZ, S., RODRÍGUEZ‐MARTÍNEZ, S., GARCIA‐VAZQUEZ, E. & ARDURA, A. How can eDNA contribute in riverine macroinvertebrate assessment? A metabarcoding approach in the Nalón River (Asturias, Northern Spain). In Environmental DNA, 2019, vol. 1, p. 385-401. ISSN 2637-4943 (online). https://doi.org/10.1002/edn3.40 XIONG, W. - HUANG, X.N. - CHEN, Y.Y. - FU, R.Y. - DU, X. - CHEN, X.Y. - ZHAN, A.B. Zooplankton biodiversity monitoring in polluted freshwater ecosystems: A technical review. In ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY. ISSN 2666-4984, JAN 2020, vol. 1. MURRIA, C. - VAISANEN, L.O.S. - SOMMA, S. - WANGENSTEEN, O.S. - ARNEDO, M.A. - PRAT, N. Towards an Iberian DNA barcode reference library of freshwater macroinvertebrates and fishes. In LIMNETICA. ISSN 0213-8409, 2020, vol. 39, no. 1, p. 73-92. EDGE, T.A. - BAIRD, D.J. - BILODEAU, G. - GAGNE, N. - GREER, C. - KONKIN, D. - NEWTON, G. - SEGUIN, A. - BEAUDETTE, L. - BILKHU, S. - BUSH, A. - CHEN, W. - COMTE, J. - CONDIE, J. - CREVECOEUR, S. - EL-KAYSSI, N. - EMILSON, E.J.S. - FANCY, D.L. - KANDALAFT, I. - KHAN, I.U.H. - KING, I. - KREUTZWEISER, D. - LAPEN, D. - LAWRENCE, J. - LOWE, C. - LUNG, O. - MARTINEAU, C. - MEIER, M. - OGDEN, N. - PARE, D. - PHILLIPS, L. - PORTER, T.M. - SACHS, J. - STALEY, Z. - STEEVES, R. - VENIER, L. - VERES, T. - WATSON, C. - WATSON, S. - MACKLIN, J. The Ecobiomics project: Advancing metagenomics assessment of soil health and freshwater quality in Canada. In SCIENCE OF THE TOTAL ENVIRONMENT. ISSN 0048-9697, MAR 25 2020, vol. 710. SPECCHIA, V. - TZAFESTA, E. - MARINI, G. - SCARCELLA, S. - D'ATTIS, S. - PINNA, M. Gap Analysis for DNA Barcode Reference Libraries for Aquatic Macroinvertebrate Species in the Apulia Region (Southeast of Italy). In JOURNAL OF MARINE SCIENCE AND ENGINEERING. JUL 2020, vol. 8, no. 7. MIYA, M. - GOTOH, R.O. - SADO, T. MiFish metabarcoding: a high-throughput approach for simultaneous detection of multiple fish species from environmental DNA and other samples. In FISHERIES SCIENCE. ISSN 0919-9268, NOV 2020, vol. 86, no. 6, p. 939-970. GAUTHIER, Mailys - KONECNY-DUPRE, Lara - NGUYEN, Agnes - ELBRECHT, Vasco - DATRY, Thibault - DOUADY, Christophe - LEFEBURE, Tristan. Enhancing DNA metabarcoding performance and applicability with bait capture enrichment and DNA from conservative ethanol. In MOLECULAR ECOLOGY RESOURCES. ISSN 1755-098X, 2020, vol. 20, no. 1, pp. 79-96. Dostupné na: https://doi.org/10.1111/1755-0998.13088. SCHENK, Janina - HOESS, Sebastian - BRINKE, Marvin - KLEINBOELTING, Nils - BRUECHNER-HUETTEMANN, Henrike - TRAUNSPURGER, Walter. Nematodes as bioindicators of polluted sediments using metabarcoding and microscopic taxonomy. In ENVIRONMENT INTERNATIONAL. ISSN 0160-4120, 2020, vol. 143, no., pp. Dostupné na: https://doi.org/10.1016/j.envint.2020.105922. HOSSEINI, H. - SAADAOUI, I. - MOHEIMANI, N. - AL SAIDI, M. - JAMALI, F.A. - AL JABRI, H. - BEN HAMADOU, R. Marine health of the Arabian Gulf: Drivers of pollution and assessment approaches focusing on desalination activities. In MARINE POLLUTION BULLETIN. ISSN 0025-326X, MAR 2021, vol. 164. Available at: https://doi.org/10.1016/j.marpolbul.2021.112085. WANG, S.P. - YAN, Z.G. - HANFLING, B. - ZHENG, X. - WANG, P.Y. - FAN, J.T. - LI, J.L. Methodology of fish eDNA and its applications in ecology and environment. In SCIENCE OF THE TOTAL ENVIRONMENT. ISSN 0048-9697, FEB 10 2021, vol. 755, 2. Available at: https://doi.org/10.1016/j.scitotenv.2020.142622. TZAFESTA, E. - ZANGARO, F. - SPECCHIA, V. - PINNA, M. An Overview of DNA-Based Applications for the Assessment of Benthic Macroinvertebrates Biodiversity in Mediterranean Aquatic Ecosystems. In DIVERSITY-BASEL. MAR 2021, vol. 13, no. 3. Available at: https://doi.org/10.3390/d13030112. LAROCHE, O. - POCHON, X. - WOOD, S.A. - KEELEY, N. Beyond taxonomy: Validating functional inference approaches in the context of fish-farm impact assessments. In MOLECULAR ECOLOGY RESOURCES. ISSN 1755-098X, OCT 2021, vol. 21, no. 7, p. 2264-2277. Available at: https://doi.org/10.1111/1755-0998.13426. DE JONGE, N. - KUNTKE, F. - HESSELSOE, M. - NIELSEN, J.L. Ecological quality in freshwater streams is reflected across all three domains of life. In ECOLOGICAL INDICATORS. ISSN 1470-160X, NOV 2021, vol. 130. Available at: https://doi.org/10.1016/j.ecolind.2021.108059. MORISETTE, J. - BURGIEL, S. - BRANTLEY, K. - DANIEL, W.M. - DARLING, J. - DAVIS, J. - FRANKLIN, T. - GADDIS, K. - HUNTER, M. - LANCE, R. - LESKEY, T. - PASSAMANECK, Y. - PIAGGIO, A. - RECTOR, B. - SEPULVEDA, A. - SMITH, M. - STEPIEN, C.A. - WILCOX, T. Strategic considerations for invasive species managers in the utilization of environmental DNA (eDNA): steps for incorporating this powerful surveillance tool. In MANAGEMENT OF BIOLOGICAL INVASIONS. ISSN 1989-8649, SEP 2021, vol. 12, no. 3, p. 747-775. Available at: https://doi.org/10.3391/mbi.2021.12.3.15. PINNA, M. - SACCOMANNO, B. - MARINI, G. - ZANGARO, F. - KABAYEVA, A. - KHALAJ, M. - SHAIMARDAN, L. - D'ATTIS, S. - TZAFESTA, E. - SPECCHIA, V. Testing the Influence of Incomplete DNA Barcode Libraries on Ecological Status Assessment of Mediterranean Transitional Waters. In BIOLOGY-BASEL. NOV 2021, vol. 10, no. 11. Available at: https://doi.org/10.3390/biology10111092. ZANGARO, F. - SACCOMANNO, B. - TZAFESTA, E. - BOZZEDA, F. - SPECCHIA, V. - PINNA, M. Current limitations and future prospects of detection and biomonitoring of NIS in the Mediterranean Sea through environmental DNA. In NEOBIOTA. ISSN 1619-0033, DEC 14 2021, vol. 70, p. 151-165. Available at: https://doi.org/10.3897/neobiota.70.71862. MILHAU, Tristan - VALENTINI, Alice - POULET, Nicolas - ROSET, Nicolas - JEAN, Pauline - GABORIAUD, Coline - DEJEAN, Tony. Seasonal dynamics of riverine fish communities using eDNA. In JOURNAL OF FISH BIOLOGY, 2021, vol. 98, no. 2, pp. 387-398. ISSN 0022-1112. Dostupné na: https://doi.org/10.1111/jfb.14190. PEARMAN, J.K. - WOOD, S.A. - VANDERGOES, M.J. - ATALAH, J. - WATERS, S. - ADAMSON, J. - THOMSON-LAING, G. - THOMPSON, L. - HOWARTH, J.D. - HAMILTON, D.P. - POCHON, X. - BIESSY, L. - BRASELL, K.A. - DAHL, J. - ELLISON, R. - FITZSIMONS, S.J. - GARD, H. - GERRARD, T. - GREGERSEN, R. - HOLLOWAY, M. - LI, X. - KELLY, D.J. - MARTIN, R. - MCFARLANE, K. - MCKAY, N.P. - MOODY, A. - MOY, C.M. - NAEHER, S. - NEWNHAM, R. - PARAI, R. - PICARD, M. - PUDDICK, J. - REES, A.B.H. - REYES, L. - SCHALLENBERG, M. - SHEPHERD, C. - SHORT, J. - SIMON, K.S. - STEINER, K. - SUNDE, C. - TEREZOW, M. - TIBBY, J. A bacterial index to estimate lake trophic level: National scale validation. In SCIENCE OF THE TOTAL ENVIRONMENT. ISSN 0048-9697, MAR 15 2022, vol. 812. Available at: https://doi.org/10.1016/j.scitotenv.2021.152385. SPECCHIA, V. - SACCOMANNO, B. - ZANGARO, F. - TZAFESTA, E. - PINNA, M. Exploring the Biodiversity of a European NATURA 2000 Mediterranean Lagoon through eDNA Metabarcoding. In DIVERSITY-BASEL. NOV 2022, vol. 14, no. 11. Available at: https://doi.org/10.3390/d14110991. LEASI, F. - CLINE, J.L. DNA metabarcoding reveals impacts of anthropogenic stressors on freshwater meiofauna. In LIMNOLOGICA. ISSN 0075-9511, SEP 2022, vol. 96. Available at: https://doi.org/10.1016/j.limno.2022.126005. SEMENIUK, C.A.D. - JEFFRIES, K.M. - LI, T. - BETTLES, C.M. - COOKE, S.J. - DUFOUR, B.A. - HALFYARD, E.A. - HEATH, J.W. - KEESHIG, K. - MANDRAK, N.E. - MUIR, A.J. - POSTMA, L. - HEATH, D.D. Innovating transcriptomics for practitioners in freshwater fish management and conservation: best practices across diverse resource-sector users. In REVIEWS IN FISH BIOLOGY AND FISHERIES. ISSN 0960-3166, SEP 2022, vol. 32, no. 3, p. 921-939. Available at: https://doi.org/10.1007/s11160-022-09715-w. RAHMAN, M.M. - BURIAN, A. - CREEDY, T.J. - VOGLER, A.P. DNA-based assessment of environmental degradation in an unknown fauna: The freshwater macroinvertebrates of the Indo-Burmese hotspot. In JOURNAL OF APPLIED ECOLOGY. ISSN 0021-8901, JUN 2022, vol. 59, no. 6, p. 1644-1658. Available at: https://doi.org/10.1111/1365-2664.14174. KULAS, A. - UDOVIC, M.G. - TAPOLCZAI, K. - ZUTINIC, P. - ORLIC, S. - LEVKOV, Z. Diatom eDNA metabarcoding and morphological methods for bioassessment of karstic river. In SCIENCE OF THE TOTAL ENVIRONMENT. ISSN 0048-9697, JUL 10 2022, vol. 829. Available at: https://doi.org/10.1016/j.scitotenv.2022.154536. SACCò, M. - GUZIK, M.T. - VAN DER HEYDE, M. - NEVILL, P. - COOPER, S.J.B. - AUSTIN, A.D. - COATES, P.J. - ALLENTOFT, M.E. - WHITE, N.E. eDNA in subterranean ecosystems: Applications, technical aspects, and future prospects. In SCIENCE OF THE TOTAL ENVIRONMENT. ISSN 0048-9697, MAY 10 2022, vol. 820. Available at: https://doi.org/10.1016/j.scitotenv.2022.153223. FAYRAM, A.H. - WOOD, J.S. - SWIGLE, B. A comparison of genetically and morphometrically identified macroinvertebrate community index scores with implications for aquatic life use attainment. In ENVIRONMENTAL MONITORING AND ASSESSMENT. ISSN 0167-6369, JAN 2022, vol. 194, no. 1. Available at: https://doi.org/10.1007/s10661-021-09525-w. Category ADEB - Scientific papers in other foreign journals not registered in Current Contents Connect without IF (non-impacted) Category of document (from 2022) V3 - Vedecký výstup publikačnej činnosti z časopisu Type of document článok Year 2016 
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