Metabarcoding approach for nonindigenous species surveillance in marine coastal waters

Marine Pollution Bulletin

Volumn 100, Issue 1, 2015, Pages 53-59

  Zaiko, Anastasija ^a,b   Samuiloviene, Aurelija ^a   Ardura, Alba ^a,c   Garcia Vazquez, Eva ^c  

^a KLAIPEDA UNIVERSITY   (Lithuania)

^b CAWTHRON INSTITUTE   (New Zealand)

^c UNIVERSITY OF OVIEDO   (Spain)

Author keywords

Baltic sea; COI; High throughput sequencing; Nonindigenous species

Indexed keywords

BIODIVERSITY;

BALTIC SEA; COI; CONVENTIONAL APPROACH; HIGH-THROUGHPUT SEQUENCING; MARINE COASTAL WATER; MORPHOLOGICAL ANALYSIS; NONINDIGENOUS SPECIES; PLANKTON COMMUNITIES;

THROUGHPUT;

BIODIVERSITY; COASTAL WATER; ECOLOGICAL IMPACT; ENVIRONMENTAL MONITORING; INVASIVE SPECIES; PLANKTON;

ARTICLE; BALTIC SEA; BIODIVERSITY; COASTAL WATERS; CYTOCHROME C OXIDASE SUBUNIT I GENE; DNA BARCODING; EXOTIC SPECIES; HIGH THROUGHPUT SEQUENCING; INTRODUCED SPECIES; LITHUANIA; METABARCODING; MONITORING; NONHUMAN; PLANKTON; SPECIES INVASION; ANIMAL; BIOLOGY; CHEMISTRY; CLASSIFICATION; ECOSYSTEM; ENVIRONMENTAL PROTECTION; GENETICS; RUSSIAN FEDERATION; SEA; ZOOPLANKTON;

ATLANTIC OCEAN; BALTIC SEA;

DNA;

ANIMALS; BIODIVERSITY; COMPUTATIONAL BIOLOGY; CONSERVATION OF NATURAL RESOURCES; DNA; ECOSYSTEM; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; INTRODUCED SPECIES; OCEANS AND SEAS; RUSSIA; ZOOPLANKTON;

EID: 84945358711     PISSN: 0025326X     EISSN: 18793363     Source Type: Journal    
DOI: 10.1016/j.marpolbul.2015.09.030     Document Type: Article

References (40)

1. Aleksandrov S.V., Zhigalova N.N., Zezera A.S. Long-term dynamics of zooplankton in the southeastern Baltic sea. Russ. J. Mar. Biol. 2009, 35:296-304.
2. Ardura A., Planes S., Garcia-Vazquez E. Applications of DNA barcoding to fish landings: authentication and diversity assessment. ZooKeys 2013, 49.
3. Aylagas E., Borja A., Rodriguez-Ezpeleta N. Metabarcoding: towards a genetics based marine biotic index (gAMBI). PLoS One 2014, 9.
4. Blank M., Laine A.O., Jurss K., Bastrop R. Molecular identification key based on PCR/RFLP for three polychaete sibling species of the genus Marenzelleria, and the species' current distribution in the Baltic sea. Helgol. Mar. Res. 2008, 62:129-141.
5. Caroppo C., Buttino I., Camatti E., Caruso G., De Angelis R., Facca C., Giovanardi F., Lazzara L., Mangoni O., Magaletti E. State of the art and perspectives on the use of planktonic communities as indicators of environmental status in relation to EU marine strategy framework directive. Biol Mar Mediterr 2013, 20(1):65-73.
6. Creer S., Fonseca V.G., Porazinska D.L., et al. Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promise. Molecular Ecology 2010, 19:4-20.
7. Dippner J.W., Kornilovs G., Sidrevics L. Long-term variability of mesozooplankton in the central Baltic sea. J. Mar. Syst. 2000, 25:23-31.
8. Edgar R.C., Haas B.J., Clemente J.C., Quince C., Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011, 27:2194-2200.
9. Freire M., Genzano G.N., Neumann-Leitao S., Perez C.D. The non-indigenous medusa Blackfordia virginica (hydrozoa, leptothecata) in tropical Brazil: 50years of unnoticed presence. Biol. Invasions 2014, 16:1-5.
10. Frey K.G., Herrera-Galeano J.E., Redden C.L., Luu T.V., Servetas S.L., Mateczun A.J., Mokashi V.P., Bishop-Lilly K.A. Comparison of three next-generation sequencing platforms for metagenomic sequencing and identification of pathogens in blood. BMC Genomics 2014, 15:96.
11. Geller J., Meyer C., Parker M., Hawk H. Redesign of PCR primers for mitochondrial cytochrome c oxidase subunit I for marine invertebrates and application in all-taxa biotic surveys. Mol. Ecol. 2013, 13:851-861.
12. Hajibabaei M., Singer G.A., Hebert P.D.N., Hickey D.A. DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends Genet. 2007, 23:167-171.
13. Hajibabaei M., Shokralla S., Zhou X., Singer G.A., Baird D.J. Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos. PLoS One 2011, 6.
14. Hällfors H., Uusitalo L., Lips U. Report on Gaps in Monitoring Programs. GES-REG WP4 2013, (28pp.).
15. HELCOM Manual for Marine Monitoring in the COMBINE Programme of HELCOM, Part C 2005, (http://sea.helcom.fi/Monas/CombineManual2/PartC/CFrame.htm).
16. Hopkins G.W., Freckleton R.P. Declines in the numbers of amateur and professional taxonomists: implications for conservation. Anim. Conserv. 2002, 5:245-249.
17. Ji Y., Ashton L., Pedley S.M., Edwards D.P., Tang Y., Nakamura A., Kitching R., Dolman P.M., Woodcock P., Edwards F.A., Larsen T.H., Hsu W.W., Benedick S., Hamer K.C., Wilcove D.S., Bruce C., Wang X., Levi T., Lott M., Emerson B.C., Yu D.W. Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding. Ecol. Lett. 2013, 16:1245-1257.
18. Kelly R.P., Port J.A., Yamahara K.M., Martone R.G., Lowell N., Thomsen P.F., Mach M.E., Bennet M., Prahler E., Caldwell M.R., Crowder L.B. Harnessing DNA to improve environmental management. Science 2014, 344:1455-1456.
19. Kim K.C., Byrne L.B. Biodiversity loss and the taxonomic bottleneck: emerging biodiversity science. Ecol. Res. 2006, 21:794-810.
20. Lehtiniemi M., Ojaveer H., David M., Galil B., Gollasch S., McKenzie C., Minchin D., Occhipinti-Ambrogi A., Olenin S., Pederson J. Dose of truth-monitoring marine non-indigenous species to serve legislative requirements. Mar. Policy 2015, 54:26-35.
21. Leppäkoski E., Gollasch S., Gruszka P., Ojaveer H., Olenin S., Panov V. The Baltic a sea of invaders. Can. J. Fish. Aquat. Sci. 2002, 59:1175-1188.
22. Medlin L.K., Kooistra W.H. Methods to estimate the diversity in the marine photosynthetic protist community with illustrations from case studies: a review. Diversity 2010, 2:973-1014.
23. Michalek M., Werner M. Abundance and distribution of Marenzelleria species in the Baltic sea. HELCOM Baltic Sea Environment Fact Sheets 2012, (http://www.helcom.fi/baltic-sea-trends/environment-fact-sheets/).
24. Ojaveer H., Jaanus A., MacKenzie B.R., Martin G., Olenin S., Radziejewska T., Telesh I., Zettler M.L., Zaiko A. Status of biodiversity in the Baltic sea. PLoS ONE Collection: Marine Biodiversity and Biogeography Regional Comparisons of Global Issues 2010, 5:e12467.
25. Oksanen J., Blanchet F.G., Kindt R., Legendre P., Minchin P.R., O'Hara R.B., Simpson G.L., Solymos P., Stevens M.H.H., Wagner H. Vegan: community ecology package version 22-0 Available from:. http://cran.r-project.org/web/packages/vegan/vegan.pdf.
26. Olenin S., Elliott M., Bysveen I., Culverhouse P.F., Daunys D., Dubelaar G.B.J., Gollasch S., Goulletquer P., Jelmert A., Kantor Y., Bringsvor Mezeth K., Minchin D., Occhipinti-Ambrogi A., Olenina I., Vandekerkhove J. Recommendations on methods for the detection and control of biological pollution in marine coastal waters. Mar. Pollut. Bull. 2011, 62:2598-2604.
27. Patrício J., Little S., Mazik K., Thomson S., Zampoukas N., Teixeira H., Solaun O., Uyarria M., Papadopoulou N., Kaboglu G., et al. SWOT analysis of monitoring networks in Europe. DEVOTES Deliverable 1.4 (Public Report) 2014, (100pp.).
28. Pochon X., Bott N.J., Smith K.F., Wood S.A. Evaluating detection limits of Next-Generation Sequencing for the surveillance and monitoring of international marine pests. PLoS One 2013, 8:e73935. 10.71371/journal.pone.0073935.
29. Ratnasingham S., Hebert P.D.N. BOLD: the barcode of life data system (www.Barcodinglife.org). Mol. Ecol. Notes 2007, 7:355-364.
30. Ratnasingham S., Hebert P.D.N. BOLD: The Barcode of Life Data System (www.barcodinglife.org). Molecular Ecology Notes 2010, 7:355-364.
31. Ratnasingham S., Hebert P.D.N. A DNA-based registry for all animal species: the barcode index number (BIN) system. PLoS One 2013, 8(8).
32. Rilov G., Crooks J.A. Biological Invasions in Marine Ecosystems: Ecological, Management, and Geographic Perspectives 2009, 204. Springer, Berlin, Germany.
33. Schloss P.D., Westcott S., Ryabin T., Hall J.R., Hartmann M., Hollister E.B., Lesniewski R.A., Oakley B.B., Parks D.H., Robinson C.J., Sahl J.W., Stres B., Thallinger G.G., Van Horn D.J., Weber C.F. Introducing mother: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 2009, 75(23):7537-7541.
34. Taberlet P., Coissac E., Hajibabaei M., Rieseberg L.H. Environmental DNA. Mol. Ecol. 2012, 21:1789-1793.
35. Tang C.Q., Leasi F., Obertegger U., Kieneke A., Barraclough T.G., Fontaneto D. The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna. Proceedings of the National Academy of Sciences 2012, 109:16208-16212.
36. Telesh I., Postel L., Heerkloss R., Mironova E., Skarlato S. Zooplankton of the Open Baltic Sea: extended Atlas. Marine Science Reports 2009, 76. Leibniz institute for Baltic Sea Research, Warnemunde.
37. Wood S.A., Smith K.F., Banks J.C., Tremblay L.A., Rhodes L., Mountfort D., Cary S.C., Pochon X. Molecular genetic tools for environmental monitoring of New Zealand's aquatic habitats, past, present and the future. N. Z. J. Mar. Freshw. Res. 2013, 47:90-119.
38. Zaiko A., Lehtiniemi M., Narscius A., Olenin S. Assessment of bioinvasion impacts on a regional scale: a comparative approach. Biol. Invasions 2011, 13:1739-1765.
39. Zaiko A., Minchin D., Olenin S. "The day after tomorrow": anatomy of an 'r' strategist aquatic invasion. Aquat. Invasions 2014, 9:145-155.
40. Zaiko A., Martinez J.L., Schmidt-Petersen J., Ribicic D., Samuiloviene A., Garcia-Vazquez E. Metabarcoding approach for the ballast water surveillance - an advantageous solution or an awkward challenge?. Mar. Pollut. Bull. 2015, 92(1--2):25-34.