University of Groningen
Marine benthic metabarcoding Klunder, Lise Margriet
DOI:
10.33612/diss.135301602
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2020
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Klunder, L. M. (2020). Marine benthic metabarcoding: Anthropogenic effects on benthic diversity from shore to deep sea; assessed by metabarcoding and traditional taxonomy. University of Groningen.
https://doi.org/10.33612/diss.135301602
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REFERENCE LIST
REFERENCE LIST
Adams, D.K., Arellano, S.M., Govenar, B., 2012. Larval dispersal: vent life in the water column. Oceanography 25, 256-268. doi:10.2307/24861164
Alawi, M., Schneider, B., Kallmeyer, J., 2014. A procedure for separate recovery of extra- and intracellular DNA from a single marine sediment sample. J. Microbiol. Methods 104, 36–42. doi:10.1016/j.
mimet.2014.06.009.
Alberdi, A., Aizpurua, O., Gilbert, M. T. P., Bohmann, K., 2018. Scrutinizing key steps for reliable metabarcoding of environmental samples. Methods Ecol. Evol. 9, 134–147. doi:10.1111/2041-210X.12849.
Anadón, R., Danovaro, R., Dippner, J.W., Drinkwater, K.F., Hawkins, S.J., O’Sullivan, G., Oguz, T., Reid, P.C., 2007. Impacts of Climate Change on the European Marine and Coastal Environment Ecosystems Approach. Eur. Sci. Found. 84.
Anderson, M.J., Santana-Garcon, J., 2015. Measures of precision for dissimilarity-based multivariate analysis of ecological communities. Ecology Letters 18, 66-73. doi:10.1111/ele.12385
Apothéloz-Perret-Gentil, L., Cordonier, A., Straub, F., Iseli, J., Esling, P., Pawlowski, J., 2017. Taxonomy-free molecular diatom index for high-throughput eDNA biomonitoring. Mol. Ecol. Resour. 17, 1231–1242.
doi:10.1111/1755-0998.12668.
Arntz, W.E., Rumohr, H., 1982. An experimental study of macrobenthic colonization and succession, and the importance of seasonal variation in temperate latitudes. J. Exp. Mar. Bio. Ecol. 64, 17–45.
doi:10.1016/0022-0981(82)90066-1.
Austen, M., Lambshead, P., Hutchings, P., Boucher, G.l., Snelgrove, P., Heip, C., King, G., Koike, I., Smith, C., 2002 Biodiversity links above and below the marine sediment-water interface that may influence community stability. Biodiversity and conservation 11, 113-136. doi:10.1023/A:1014098917535 Aylagas, E., Borja, Á., Muxika, I., Rodríguez-Ezpeleta, N., 2018. Adapting metabarcoding-based benthic
biomonitoring into routine marine ecological status assessment networks. Ecol. Indic. 95, 194–202.
doi:10.1016/j.ecolind.2018.07.044.
Aylagas, E., Mendibil, I., Borja, Á., Rodríguez-Ezpeleta, N., 2016. Marine sediment sample pre-processing for macroinvertebrates metabarcoding: Mechanical enrichment and homogenization. Front. Mar. Sci.
3, 1–8. doi:10.3389/fmars.2016.00203.
Aylagas, E., Rodríguez-Ezpeleta, N., 2016. Analysis of Illumina MiSeq metabarcoding data: Application to benthic indices for environmental monitoring. Humana Press, New York, NY, pp. 237–249.
doi:10.1007/978-1-4939-3774-5_16
Baeye, M., Fettweis, M. 2015. In situ observations of suspended particulate matter plumes at an offshore wind farm, southern North Sea. Geo-Marine Letters, 35: 247–255. doi:10.1007/s00367-015-0404-8 Baird, D.J., Hajibabaei, M., 2012. Biomonitoring 2.0: A new paradigm in ecosystem assessment made possible
by next-generation DNA sequencing. Mol. Ecol. 21, 2039–2044. doi:10.1111/j.1365-294X.2012.05519.x Baker, E.T.E., German, C.C.R., 2004. On the global distribution of hydrothermal vent fields. Geophys. Monogr.
Ser. 148, 245–266. doi:10.1029/148GM10
Bálint, M., Pfenninger, M., Grossart, H.P., Taberlet, P., Vellend, M., Leibold, M. A., Englund, G., Bowler, D., 2018. Environmental DNA Time Series in Ecology. Trends Ecol. Evol. 33, 945–957. doi:10.1016/J.
TREE.2018.09.003.
Balsamo, M., Semprucci, F., Frontalini, F., Coccioni, R., 2012. Meiofauna as a tool for marine ecosystem biomonitoring. Mar. Ecosyst. A. Cruzado (Ed.), InTech, 310pp 77–104. doi:10.5772/34423
Balvočiūtė, M., Huson, D.H., 2017. SILVA, RDP, Greengenes, NCBI and OTT — how do these taxonomies compare? BMC Genomics 18, 114. doi:10.1186/s12864-017-3501-4
Barnes, M. A., and Turner, C. R., 2016. The ecology of environmental DNA and implications for conservation genetics. Conserv. Genet. 17, 1–17. doi:10.1007/s10592-015-0775-4.
Berry, D., Mahfoudh, K. Ben, Wagner, M., Loy, A., 2011. Barcoded primers used in multiplex amplicon pyrosequencing bias amplification. Appl. Environ. Microbiol. 77, 7846–7849. doi:10.1128/AEM.05220-11 Berry, T. E., Osterrieder, S. K., Murray, D. C., Coghlan, M. L., Richardson, A. J., Grealy, A. K., et al., 2017. DNA metabarcoding for diet analysis and biodiversity: A case study using the endangered Australian sea lion (Neophoca cinerea). Ecol. Evol. 7, 5435–5453. doi:10.1002/ece3.3123.
Beaulieu, S.E., Sayre-Mccord, R.T., Mills, S.W., Pradillon, F., Watanabe, H., 2015. Swimming speeds of polychaete larvae collected near deep-sea hydrothermal vents. Mar. Ecol. 36, 133–143. doi:10.1111/
maec.12207
Beukema, J.J., Cadée, G.C., 1997. Local differences in macrozoobenthic response to enhanced food supply caused by mild eutrophication in a Wadden Sea area. Food is only locally a limiting factor. Limnol.
Oceanogr. 42, 1424–1435. doi:10.4319/lo.1997.42.6.1424
Beukema, J. J., 1974. Seasonal changes in the biomass of the macro-benthos of a tidal flat area in the Dutch Wadden Sea. Netherlands J. Sea Res. 8, 94–107. doi:10.1016/0077-7579(74)90028-3.
Beukema, J. J., 1995. Long-term effects of mechanical harvesting of lugworms Arenicola marina on the zoobenthic community of a tidal flat in the Wadden Sea. Netherlands J. Sea Res. 33, 219–227.
doi:10.1016/0077-7579(95)90008-X.
Bienert, F., De Danieli, S., Miquel, C., Coissac, E., Poillot, C., Brun, J.J., Taberlet, P., 2012. Tracking earthworm communities from soil DNA. Mol. Ecol. 21, 2017–2030. doi:10.1111/j.1365-294X.2011.05407.x Bijkerk, R., and Dekker, P. I., 1991. De wadpier Arenicola marina (Polychaeta). Ecologisch profiel. RWS-
rapportage AH005.
Bijleveld, A. I., Compton, T. J., Klunder, L., Holthuijsen, S., Ten Horn, J., Koolhaas, A., Dekinga, A., van der Meer, J., van der Veer, H.W., 2018. Presence-absence of marine macrozoobenthos does not generally predict abundance and biomass. Sci. Rep. 8, 1–12. doi:10.1038/s41598-018-21285-1.
Bijma, J., Portner, H.O., Yesson, C., Rogers, A.D., 2013. Climate change and the oceans – What does the future hold? Marine Pollution Bulletin, 74, 495-505. doi:10.1016/j.marpolbul.2013.07.022
Bik, H. M., Porazinska, D. L., Creer, S., Caporaso, J. G., Knight, R., Thomas, W. K., 2012. Sequencing our way towards understanding global eukaryotic biodiversity. Trends Ecol. Evol. 27, 233–243. doi:10.1016/j.
tree.2011.11.010.
Bik, H.M., Fournier, D., Sung, R., Bergeron, R., Kelly Thomas, W., 2013. Intra-genomic variation in the ribosomal repeats of nematodes. PLoS ONE 8(10). doi:10.1371/journal.pone.0078230
Bista, I., Carvalho, G. R., Walsh, K., Seymour, M., Hajibabaei, M., Lallias, D., Christmas, M., Creer, S., 2017.
Annual time-series analysis of aqueous eDNA reveals ecologically relevant dynamics of lake ecosystem biodiversity. Nat. Commun. 8, 14087. doi:10.1038/ncomms14087.
Blome, D., Schleier, U., Van Bernem, K.H., 1999. Analysis of the small-scale spatial patterns of free-living marine nematodes from tidal flats in the East Frisian Wadden Sea. Mar. Biol. 133, 717–726. doi:10.1007/
s002270050513
Bohan, D.A., Vacher, C., Tamaddoni-Nezhad, A., Raybould, A., Dumbrell, A.J., Woodward, G., 2017. Next- generation global biomonitoring: large-scale, automated reconstruction of ecological networks. Trends Ecol. Evol., 21, 477-487. doi:10.1016/j.tree.2017.03.001
Bomkamp, R.E., Page, H.M., Dugan, J.E. 2004. Role of food subsidies and habitat structure in influencing benthic communities of shell mounds at sites of existing and former offshore oil platforms. Marine Biology, 146: 201–211. doi:10.1007/s00227-004-1413-8
Boschen, R.E., Rowden, A.A., Clark, M.R., Gardner, J.P.A., 2013. Mining of deep-sea seafloor massive sulfides:
A review of the deposits, their benthic communities, impacts from mining, regulatory frameworks and management strategies. Ocean Coast. Manag. 84, 54–67. doi:10.1016/j.ocecoaman.2013.07.005 Boschen, R.E., Rowden, A.A., Clark, M.R., Pallentin, A., Gardner, J.P.A., 2016. Seafloor massive sulfide
deposits support unique megafaunal assemblages: Implications for seabed mining and conservation.
Mar. Environ. Res. 115, 78–88. doi:10.1016/j.marenvres.2016.02.005
Bowden, D.A., Rowden, A.A., Leduc, D., Beaumont, J., Clark, M.R., 2016. Deep-sea seabed habitats: Do they support distinct mega-epifaunal communities that have different vulnerabilities to anthropogenic disturbance? Deep. Res. Part I Oceanogr. Res. Pap. 107, 31–47. doi:10.1016/j.dsr.2015.10.011 Boyd, S.E., Rees, H.L., Richardson, C.A., 2000. Nematodes as Sensitive Indicators of Change at Dredged
Material Disposal Sites. Estuar. Coast. Shelf Sci. 51, 805–819. doi:10.1006/ecss.2000.0722
Brandão, M.C., Freire, A.S., Burton, R.S., 2016. Estimating diversity of crabs (Decapoda: Brachyura) in a no-take marine protected area of the SW Atlantic coast through DNA barcoding of larvae. Systematics and Biodiversity 3, 288-302. doi:10.1080/14772000.2016.1140245
Brannock, P.M., Waits, D.S., Sharma, J., Halanych, K.M., 2014. High-throughput sequencing characterizes intertidal meiofaunal communities in Northern Gulf of Mexico (Dauphin Island and Mobile Bay, Alabama). Biol. Bull. 227, 161–174. doi:10.1086/BBLv227n2p161
Brannock, P.M., Halanych, K.M., 2015. Meiofaunal community analysis by high-throughput sequencing:
Comparison of extraction, quality filtering, and clustering methods. Mar. Genomics 23, 67–75.
doi:10.1016/j.margen.2015.05.007
Brannock, P., Learman, D., Mahon, A., Santos, S., Halanych, K., 2018. Meiobenthic community composition and biodiversity along a 5500 km transect of Western Antarctica: a metabarcoding analysis. Mar. Ecol.
Prog. Ser. 603, 47–60. doi:10.3354/meps12717.
Buchanan, J.B. 1964. A comparative study of some features of the biology of Amphiura Filiformis and Amphiura Chiajei (Ophiuroidea) considered in relation to their distribution. Journal of the Marine Biological Association of the United Kingdom, 44: 565. doi:10.1017/S0025315400027776
Bucklin, A., Steinke, D., Blanco-Bercial, L., 2011. DNA Barcoding of Marine Metazoa. Ann. Rev. Mar. Sci. 3, 471–508. doi:10.1146/annurev-marine-120308-080950
Cahill, A.E., Pearman, J.K., Borja, A., Carugati, L., Carvalho, S., Danovaro, R., Dashfield, S., David, R., Féral, J.-P., Olenin, S., Šiaulys, A., Somerfield, P.J., Trayanova, A., Uyarra, M.C., Chenuil, A., 2018. A comparative analysis of metabarcoding and morphology-based identification of benthic communities across different regional seas. Ecol. Evol. 8, 8908–8920. doi:10.1002/ece3.4283
Callahan, B. J., McMurdie, P. J., Holmes, S. P., 2017. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME J. 11, 2639–2643. doi:10.1038/ismej.2017.119.
Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., Fierer, N., Gonzalez Pena, A., Goodrich, J.K., Gordon, J.I., Huttley, G.A., Kelly, S.T., Knights, D., Koenig, J.E., Ley, R.E., Lozupone, C.A., McDonald, D., Muegge, B.D., Pirrung, M., Reeder, J., Sevinsky, J.R., Turnbaugh, P.J., Walters, W.A., Widmann, J., Yatsunenko, T., Zaneveld, J., Knight, R., 2010. QIIME allows high throughput community sequencing data. Nat. Methods 7, 335–336. doi:10.1038/nmeth0510-335
Cardoso, P., Erwin, T.L., Borges, P.A.V., New, T.R., 2011. The seven impediments in invertebrate conservation and how to overcome them. Biol. Conserv. 144, 2647–2655. doi:10.1016/j.biocon.2011.07.024 Carpenter, J.R., Merckelbach, L., Callies, U., Clark, S., Gaslikova, L., Baschek, B. 2016. Potential impacts of
offshore wind farms on North Sea stratification. PLoS ONE, 11: 1–28. doi:10.1371/journal.pone.0160830 Carugati, L., Corinaldesi, C., Dell’Anno, A., Danovaro, R., 2015. Metagenetic tools for the census of marine meiofaunal biodiversity: An overview. Mar. Genomics 24, 11–20. doi:10.1016/j.margen.2015.04.010 Cave, R.R., German, C.R., Thomson, J., Nesbitt, R.W., 2002. Fluxes to sediments underlying the Rainbow
hydrothermal plume at 36°14’N on the Mid-Atlantic Ridge. Geochim. Cosmochim. Acta 66, 1905–1923.
doi:10.1016/S0016-7037(02)00823-2
Chapin, F.S., Zavaleta, E.S., Eviner, V.T., Naylor, R.L., Vitousek, P.M., Reynolds, H.L., Hooper, D.U., Lavorel, S., Sala, O.E., Hobbie, S.E., Mack, M.C., Díaz, S., 2000. Consequences of changing biodiversity. Nature 405, 234–42. doi:10.1038/35012241
Chariton, A.A., Court, L.N., Hartley, D.M., Colloff, M.J., Hardy, C.M., 2010. Ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA. Front. Ecol. Environ. 8, 233–238.
doi:10.1890/090115
Chariton, A.A., Stephenson, S., Morgan, M.J., Steven, A.D.L., Colloff, M.J., Court, L.N., Hardy, C.M., 2015.
Metabarcoding of benthic eukaryote communities predicts the ecological condition of estuaries.
Environ. Pollut. 203, 165–174. doi:10.1016/j.envpol.2015.03.047
Charlou, J., Donval, J., Fouquet, Y., Jean-Baptiste, P., Holm, N., 2002. Geochemistry of high H2 and CH4 vent fluids issuing from ultramafic rocks at the Rainbow hydrothermal field (36°14′N, MAR). Chem. Geol.
191, 345–359. doi:10.1016/S0009-2541(02)00134-1
Christianen, M.J.A., Middelburg, J.J., Holthuijsen, S.J., Jouta, J., Compton, T.J., van der Heide, T., Piersma, T., Sinninghe Damsté, J.S., van der Veer, H.W., Schouten, S., Olff, H., 2017. Benthic primary producers are key to sustain the Wadden Sea food web: stable carbon isotope analysis at landscape scale. Ecology 98, 1498-1512. doi: 10.1002/ecy.1837
Claisse, J.T., Pondella, D.J., Love, M., Zahn, L.A., Williams, C.M., Bull, A.S., 2015. Impacts from partial removal of decommissioned oil and gas platforms on fish biomass and production on the remaining platform structure and surrounding Shell mounds. PLoS ONE, 10: 1–19. doi:10.1371/journal.pone.0135812 Coates, D.A., Deschutter, Y., Vincx, M., Vanverbeke, J. 2014. Enrichment and shifts in macrobenthic
assemblages in an offshore wind farm area in the Belgian part of the North Sea. Marine Environmental Research, 95: 1–12. doi:10.1016/j/marenvres.2013.12.008
Coissac, E., Riaz, T., Puillandre, N., 2012. Bioinformatic challenges for DNA metabarcoding of plants and animals. Mol. Ecol. 21, 1834–1847. doi:10.1111/j.1365-294X.2012.05550.x
Cole, J.R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R.J., Kulam-Syed-Mohideen, A.S., McGarrell, D.M., Marsh, T., Garrity, G.M., Tiedje, J.M., 2009. The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37. doi:10.1093/nar/gkn879
Collins, R.A., Cruickshank, R.H., 2013. The seven deadly sins of DNA barcoding. Mol. Ecol. Resour. 13, 969–
975. doi:10.1111/1755-0998.12046
Collins, P.C., Croot, P., Carlsson, J., Colaço, A., Grehan, A., Hyeong, K., Kennedy, R., Mohn, C., Smith, S., Yamamoto, H., Rowden, A., 2013. A primer for the Environmental Impact Assessment of mining at seafloor massive sulfide deposits. Mar. Policy 42, 198–209. doi:10.1016/J.MARPOL.2013.01.020 Coma, R., Ribes, M., Gili, J.-M., Zabala, M., 2000. Seasonality in coastal benthic ecosystems. Trends Ecol.
Evol. 15, 448–453. doi:10.1016/S0169-5347(00)01970-4.
Compton, T.J., Holthuijsen, S., Koolhaas, A., Dekinga, A., ten Horn, J., Smith, J., Galama, Y., Brugge, M., van der Wal, D., van der Meer, J., van der Veer, H.W., Piersma, T., 2013. Distinctly variable mudscapes:
Distribution gradients of intertidal macrofauna across the Dutch Wadden Sea. J. Sea Res. 82, 103–116.
doi:10.1016/j.seares.2013.02.002
Coolen, J., 2017. North Sea reefs : benthic biodiversity of artificial and rocky reefs in the southern North Sea (Doctoral dissertation, chapter 4)
Cordier, T., Lanzen, A., Apothelox-Perret-Gentil, L., Stoeck, T., Pawlowski, J., 2019. Embracing environmental genomics and machine learning for routine biomonitoring. Trends in Microbiologi 27, 387-397.
doi:10.1016/j.tim.2018.10.012
Corinaldesi, C., Beolchini, F., Dell’Anno, A., 2008. Damage and degradation rates of extracellular DNA in marine sediments: Implications for the preservation of gene sequences. Mol. Ecol. 17, 3939–3951.
doi:10.1111/j.1365-294X.2008.03880.x
Corinaldesi, C., Barucca, M., Luna, G.M., Dell’Anno, A., 2011. Preservation, origin and genetic imprint of extracellular DNA in permanently anoxic deep-sea sediments. Mol. Ecol. 20, 642–654. doi:10.1111/
j.1365-294X.2010.04958.x
Costello, M.J., 2015. Biodiversity: The known, unknown, and rates of extinction. Curr. Biol. 25, R368–R371.
doi:10.1016/j.cub.2015.03.051
Costello, M.J., Chaudhary, C., 2017. Marine Biodiversity, Biogeography, Deep-Sea Gradients, and Conservation. Curr. Biol. 27, R511–R527. doi:10.1016/j.cub.2017.04.060
Covich, A, Austen, M., Barlocher, F., Chauvet, E., Cardinale, B., Biles, C., Inchausti, P., Dangles, O., Solan, M., Gessner, M., Statzner, B., Moss, B., 2004. The role of biodiversity in the functioning of freshwater and marine benthic ecosystems. Bioscience 54, 767-775.doi:10.1641/0006-3568(2004)054[0767:TRO- BIT]2.0.CO;2
Cowart, D.A., Pinheiro, M., Mouchel, O., Maguer, M., Grall, J., Miné, J., Arnaud-Haond, S., 2015.
Metabarcoding is powerful yet still blind: A comparative analysis of morphological and molecular surveys of seagrass communities. PLoS One 10, 1–26. doi:10.1371/journal.pone.0117562
Cowen, J.P., Massoth, G.J., Feely, R.A., 1990. Scavenging rates of dissolved manganese in a hydrothermal vent plume. Deep Sea Res. Part A. Oceanogr. Res. Pap. 37, 1619–1637. doi:10.1016/0198-0149(90)90065-4 Cowen, R.K., Sponaugle, S., 2009. Larval dispersal and marine population connectivity. Ann. Rev. Mar. Sci.
1, 443–466. doi:10.1146/annurev.marine.010908.163757
Creer, S., Deiner, K., Frey, S., Porazinska, D., Taberlet, P., Thomas, W.K., Potter, C., Bik, H.M., 2016. The ecologist’s field guide to sequence-based identification of biodiversity. Methods Ecol. Evol. 7, 1008–
1018. doi:10.1111/2041-210X.12574
Cristescu, M.E., 2014. From barcoding single individuals to metabarcoding biological communities: Towards an integrative approach to the study of global biodiversity. Trends Ecol. Evol. 29, 566–571. doi:10.1016/j.
tree.2014.08.001
Daan, R., Mulder, M., 2006. Macrobenthic fauna in the Dutch sector of the North Sea in 2005 and a comparison with previous data. NIOZ-report 2006-3.
Daily, G.C., Söderqvist, T., Aniyar, S., Arrow, K., Dasgupta, P., Ehrlich, P.R., Folke, C., Jansson, A., Jansson, B.-O., Kautsky, N., Levin, S., Lubchenco, J., Mäler, K.-G., Simpson, D., Starrett, D., Tilman, D., Soderqvist, T., Maler, K.-G., Walker, B., 2000. The Value of Nature and the Nature of Value. Walk. Source Sci. New Ser. 289, 395–396. doi:10.1890/154-9295-10.4.171
Danovaro, R., Gambi, C., Dell’Anno, A., Corinaldesi, C., Fraschetti, S., Vanreusel, A., Vincx, M., Gooday, A.J., 2008. Exponential Decline of Deep-Sea Ecosystem Functioning Linked to Benthic Biodiversity Loss. Curr.
Biol. 18, 1–8. doi:10.1016/j.cub.2007.11.056
Danovaro, R., Gambi, C., Mazzola, A., Mirto, S. 2002. Influence of artificial reefs on the surrounding infauna:
analysis of meiofauna. ICES Journal of Marine Science, 59: 356–362. doi:10.1006/jmsc.2002.1223 Danovaro, R., Gambi, C., Manini, E., Fabiano, M., 2000. Meiofauna response to a dynamic river plume front.
Mar. Biol. 137, 359–370. doi:10.1007/s002270000353
Danovaro, R., Dell’Anno, A., Corinaldesi, C., Magagnini, M., Noble, R., Tamburini, C., Weinbauer, M., 2008.
Major viral impact on the functioning of benthic deep-sea ecosystems. Nature 454, 1084–1087.
doi:10.1038/nature07268
Danovaro, R., Snelgrove, P.V.R., Tyler, P., 2014. Challenging the paradigms of deep-sea ecology. Trends Ecol.
Evol. 29, 465–475. doi:10.1016/J.TREE.2014.06.002
Davis, N., VanBlaricom, G.R., Dayton, P.K. 1982. Man-made structures on marine sediments: Effects on adjacent benthic communities. Marine Biology, 70: 295–303. doi:10.1007/BF00396848
De Barba, M., Miquel, C., Boyer, F., Mercier, C., Rioux, D., Coissac, E., Taberlet, P., 2014. DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet. Mol.
Ecol. Resour. 14, 306–323. doi:10.1111/1755-0998.12188.
Deagle, B.E., Thomas, A.C., Shaffer, A.K., Trites, A.W., Jarman, S.N. 2013. Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: Which counts count? Molecular Ecology Resources, 13: 620–633. doi:10.1111/1755-0988.12103
Deagle, B.E., Jarman, S.N., Coissac, E., Pompanon, F., Taberlet, P., 2014. DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match. Biol. Lett. 10, 20140562–20140562.
doi:10.1098/rsbl.2014.0562
Deagle, B. E., Thomas, A. C., McInnes, J. C., Clarke, L. J., Vesterinen, E. J., Clare, E. L., Kartzinel, T.R., Evenson, J.P., 2019. Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data? Mol. Ecol. 28, 391–406. doi:10.1111/mec.14734.
Degraer, S. and Brabant, R. 2012. Offshore wind farms in the Belgian part of the North Sea Heading for an understanding of environmental impacts. Royal Belgian Institute for Natural Sciences.
Dell’Anno, A., Bompadre, S., Danovaro, R. 2002. Quantification, base composition, and fate of extracellular DNA in marine sediments. Limnology and Oceanography, 47: 899–905. doi:10.4319/lo.2002.47.3.0899 Dell’Anno, A., and Corinaldesi, C., 2004. Degradation and Turnover of Extracellular DNA in Marine Sediments : Ecological and Methodological Considerations Degradation and Turnover of Extracellular DNA in Marine Sediments : Ecological and Methodological Considerations. Appl. Environ. Microbiol.
70, 4384–4386. doi:10.1128/AEM.70.7.4384.
Dell’Anno, A., Carugati, L., Corinaldesi, C., Riccioni, G., Danovaro, R., 2015. Unveiling the biodiversity of deep-sea nematodes through metabarcoding: Are we ready to bypass the classical taxonomy? PLoS One 10, 1–18. doi:10.1371/journal.pone.0144928.
Delmont, T.O., Robe, P., Clark, I., Simonet, P., Vogel, T.M., 2011. Metagenomic comparison of direct and indirect soil DNA extraction approaches. J. Microbiol. Methods 86, 397–400. doi:10.1016/j.
mimet.2011.06.013
De Mesel, I., Kerckhof, F., Norro, A., Rumes, B., Degraer, S. 2015. Succession and seasonal dynamics of the epifauna community on offshore wind farm foundations and their role as stepping stones for non- indigenous species. Hydrobiologia, 756: 37–50. doi:10.1007/s10750-014-2157-1
Desbruyères, D., Seqonzac, M., 1997. Handbook of deep-sea hydrothermal vent fauna. IFREMER, Brest.
Diaz, R. J., Solan, M., Valente, R. M., 2004. A review of approaches for classifying benthic habitats and evaluating habitat quality. J. Environ. Manage. 73, 165–181. doi:10.1016/j.jenvman.2004.06.004.
Dick, G.J., Clement, B.G., Webb, S.M., Fodrie, F.J., Bargar, J.R., Tebo, B.M., 2009. Enzymatic microbial Mn(II) oxidation and Mn biooxide production in the Guaymas Basin deep-sea hydrothermal plume. Geochim.
Cosmochim. Acta 73, 6517–6530. doi:10.1016/J.GCA.2009.07.039
Drent, J., 2013. Monitoring van effecten op de bodemfauna door wadpierenvisserij op de Vlakte van Kerken in de periode 2008-2011. NIOZ-report.
Douville, E., Charlou, J.., Oelkers, E.., Bienvenu, P., Jove Colon, C.., Donval, J.., Fouquet, Y., Prieur, D., Appriou, P., 2002. The rainbow vent fluids (36°14′N, MAR): the influence of ultramafic rocks and phase separation on trace metal content in Mid-Atlantic Ridge hydrothermal fluids. Chem. Geol. 184, 37–48. doi:10.1016/
S0009-2541(01)00351-5
Duineveld, G.C.A., Bergman, M.J.N., Lavaleye, M.S.S. 2007. Effects of an area closed to fisheries on the composition of the benthic fauna in the southern North Sea. ICES Journal of Marine Science, 64: 1–10.
doi:10.1093/icesjms/fsm029
Duinveld, G., & shipboard scientific party, 2016. Report Pelagia cruise 64pe412 TREASURE (Towards Responsible ExtrAction of SUbmarine Resources). Horta – Horta 25 June – 13 July 2016. NIOZ-report, 41pp.
Edmonds, H.N., German, C.R., 2004. Particle geochemistry in the Rainbow hydrothermal plume, Mid-Atlantic Ridge. Geochim. Cosmochim. Acta 68, 759–772. doi:10.1016/S0016-7037(03)00498-8
Elbrecht, V. and Leese, F., 2015. Can DNA-based ecosystem assessments quantify species abundance? Testing primer bias and biomass-sequence relationships with an innovative metabarcoding protocol. PLoS One 10, 1–16. doi:10.1371/journal.pone.0130324
Elbrecht, V., Peinert, B., Leese, F., 2017. Sorting things out: Assessing effects of unequal specimen biomass on DNA metabarcoding. Ecol. Evol. 7, 6918–6926. doi:10.1002/ece3.3192.
Elbrecht, V., Vamos, E. E., Steinke, D., Leese, F., 2018. Estimating intraspecific genetic diversity from community DNA metabarcoding data. PeerJ 6, e4644. doi:10.7717/peerj.4644.
Engelbrektson, A., Kunin, V., Wrighton, K.C., Zvenigorodsky, N., Chen, F., Ochman, H., Hugenholtz, P., 2010.
Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J. 4, 642–647. doi:10.1038/ismej.2009.153
Ficetola, G. F., Miaud, C., Pompanon, F., Taberlet, P., 2008. Species detection using environmental DNA from water samples. Biol. Lett. 4, 423–425. doi:10.1098/rsbl.2008.0118.
Ficetola, G. F., Pansu, J., Bonin, A., Coissac, E., Giguet-Covex, C., De Barba, M., et al., 2015. Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data. Mol. Ecol.
Resour. 15, 543–556. doi:10.1111/1755-0998.12338. doi:10.1111/1755-0998.12338
Findlay, A.J., Gartman, A., Shaw, T.J., Luther, G.W., 2015. Trace metal concentration and partitioning in the first 1.5 m of hydrothermal vent plumes along the Mid-Atlantic Ridge: TAG, Snakepit, and Rainbow.
Chem. Geol. 412, 117–131. doi:10.1016/J.CHEMGEO.2015.07.021
Flannery, E. and Przeslawski, R., 2015. Comparison of sampling methods to assess benthic marine biodiversity : Are spatial and ecological relationships consistent among sampling gear? Canberra.
doi:10.11636/Record.2015.007
Folmer, E. O., Drent, J., Troost, K., Büttger, H., Dankers, N., Jansen, J., van Stralen, M., Millat, G., Herlyn, M., Philippart, C.J.M., 2014. Large-Scale Spatial Dynamics of Intertidal Mussel (Mytilus edulis L.) Bed Coverage in the German and Dutch Wadden Sea. Ecosystems 17, 550–566. doi:10.1007/s10021-013- 9742-4.
Folmer, O., Black, M., Hoeh, W., Lutz, R., Vrijenhoek, R., 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 3, 294–299. doi:10.1371/journal.pone.0013102
Fonseca, V.G., Carvalho, G.R., Sung, W., Johnson, H.F., Power, D.M., Neill, S.P., Packer, M., Blaxter, M.L., Lambshead, P.J.D., Thomas, W.K., Creer, S., 2010. Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nat. Commun. 1, 98. doi:10.1038/ncomms1095
Fonseca, V.G., Carvalho, G.R., Nichols, B., Quince, C., Johnson, H.F., Neill, S.P., Lambshead, J.D., Thomas, W.K., Power, D.M., Creer, S., 2014. Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes. Glob. Ecol. Biogeogr. 23, 1293–1302. doi:10.1111/geb.12223
Fouquet, Y., Charlou, J.L., Ondreas, H., 1997. Discovery and first submersible investigations on the Rainbow hydrothermal field on the MAR. EOS Trans AGU 78.
Fowler, A.M., Macreadie, P.I., Jones, D.O.B., Booth, D.J. 2014. Ocean & Coastal Management A multi-criteria decision approach to decommissioning of offshore oil and gas infrastructure. Ocean and Coastal Management, 87: 20–29. doi:10.1016/j.ocecoaman.2013.10.019
Fraschetti, S., Guarnieri, G., Gambi, C., Bevilacqua, S., Terlizzi, A., Danovaro, R., 2016. Impact of offshore gas platforms on the structural and functional biodiversity of nematodes. Mar. Environ. Res. 115, 56–64.
doi:10.1016/j.marenvres.2016.02.001
Gage, J.D., Tyler, P.A., 1991. Deep-sea biology. A natural history of organisms at the deep-sea floor.
Cambridge University Press, 504pp.
Galkin, S. V., 1997. Megafauna associated with hydrothermal vents in the Manus Back-Arc Basin (Bismarck Sea). Mar. Geol. 142, 197–206. doi:10.1016/S0025-3227(97)00051-0
Garlapati, D., Charankumar, B., Ramu, K., Madeswaran, P., Ramana Murthy, M. V., 2019. A review on the applications and recent advances in environmental DNA (eDNA) metagenomics. Rev. Environ. Sci. Bio/
Technology 18, 389–411. doi:10.1007/s11157-019-09501-4.
Gaston, K.J., 1996. Biodiversity. Blackwell Science Ltd, Oxford.
Gee, J.M. and Warwick, R.M. 1985. Effects of organic enrichment on meiofaunal abundance and community structure in sublittoral soft sediments. Journal of Experimental Marine Biology and Ecology, 91: 247–262.
German, C.R. and Parson, L.M., 1996. Hydrothermal exploration near the Azores Triple Junction: tectonic control of venting at slow-spreading ridges? Earth Planet. Sci. Lett. 138, 93–104. doi:10.1016/0012- 821X(95)00224-Z
German, C.R., Richards, K.J., Rudnicki, M.D., Lam, M.M., Charlou, J.L., 1998. Topographic control of a dispersing hydrothermal plume. Earth Planet. Sci. Lett. 156, 267–273. doi:10.1016/S0012- 821X(98)00020-X
German, C.R., Thurnherr, A.M., Knoery, J., Charlou, J.L., Jean-Baptiste, P., Edmonds, H.N., 2010. Heat, volume and chemical fluxes from submarine venting: A synthesis of results from the Rainbow hydrothermal field, 36°N MAR. Deep. Res. Part I Oceanogr. Res. Pap. 57, 518–527. doi:10.1016/j.dsr.2009.12.011 Glenn, T. C., 2011. Field guide to next-generation DNA sequencers. Mol. Ecol. Resour. 11, 759–769.
doi:10.1111/j.1755-0998.2011.03024.x.
Gollner, S., Riemer, B., Arbizu, P.M., Le Bris, N., Bright, M., 2010. Diversity of meiofauna from the 9 50’n East Pacific Rise across a gradient of hydrothermal fluid emission. PLoS ONE 5: e12321. doi:10.1371/
journal.pone.0012321
Gollner, S., Govenar, B., Arbizu, P.M., Mills, S., Le Bris, N., Weinbauer, M., Shank, T.M., Bright, M., 2015.
Differences in recovery between deep-sea hydrothermal vent and vent-proximate communities after a volcanic eruption. Deep. Res. Part I Oceanogr. Res. Pap. 106, 167–182. doi:10.1016/j.dsr.2015.10.008 Gollner, S., Stuckas, H., Kihara, T.C., Laurent, S., Kodami, S., Martinez Arbizu, P., 2016. Mitochondrial DNA
analyses indicate high diversity, expansive population growth and high genetic connectivity of vent copepods (Dirivultidae) across different oceans. PLos One 11. doi:10.1371/journal.pone.0163776 Gray, J., 2000. The measurement of marine species diversity, with an application to the benthic fauna of the
Norwegian continental shelf. J. Exp. Mar. Bio. Ecol. 250, 23–49. doi:10.1016/S0022-0981(00)00178-7 Gray, J.S., 1997. Marine biodiversity: patterns, threats and conservation needs. Biodivers. Conserv. 6,
153–175. doi:10.1023/A:1018335901847
Grey, E. K., Bernatchez, L., Cassey, P., Deiner, K., Deveney, M., Howland, K. L., Lacoursiere-Foussel, A., Chee Yew Leong, S., Li, Y., Olds, B., Pfrender, M.E., Prowse, T.A.A., Renshaw, M.A., Lodge, D.M., 2018. Effects of sampling effort on biodiversity patterns estimated from environmental DNA metabarcoding surveys.
Sci. Rep. 8, 8843. doi:10.1038/s41598-018-27048-2.
Guardiola, M., Uriz, M.J., Taberlet, P., Coissac, E., Wangensteen, O.S., Turon, X., 2015. Deep-sea, deep- sequencing: Metabarcoding extracellular DNA from sediments of marine canyons. PLoS One 10.
doi:10.1371/journal.pone.0139633
Guardiola, M., Wangensteen, O.S., Taberlet, P., Coissac, E., Uriz, M.J., Turon, X., 2016. Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA. PeerJ 4, e2807.
doi:10.7717/peerj.2807
Gudmundsson, H., 1985. Life History Patterns of Polychaete Species of the Family Spionidae. J. Mar. Biol.
Assoc. United Kingdom 65, 93–111. doi:10.1017/S0025315400060835
Günther, C.P., 1992. Dispersal of intertidal invertebrates: A strategy to react to disturbance of different scales? Netherlands J. Sea Res. 30, 45–56. doi:10.1016/0077-7579(92)90044-F.
Haalboom, S., Price, D.M., Mienis, F., van Bleijswijk, J.D.L., de Stigter, H.C., Witte, H.J., Reichart, G.J., Duineveld, G.C.A., in review 2019. Successional patterns of (trace) metals and microorganisms in the Rainbow hydrothermal vent plume at the Mid-Atlantic Ridge. Biogeosciences Discuss. doi:10.5194/
bg-2019-189.
Hadziavdic, K., Lekang, K., Lanzen, A., Jonassen, I., Thompson, E.M., Troedsson, C., 2014. Characterization of the 18s rRNA gene for designing universal eukaryote specific primers. PLoS One 9. doi:10.1371/
journal.pone.0087624
Hajibabaei, M., Shokralla, S., Zhou, X., Singer, G.A.C., Baird, D.J., 2011. Environmental barcoding: A next- generation sequencing approach for biomonitoring applications using river benthos. PLoS One 6.
doi:10.1371/journal.pone.0017497
Halpern, B.S., Walbridge, S., Selkoe, K.A., Kappel, C. V., Micheli, F., D’Agrosa, C., Bruno, J.F., Casey, K.S., Ebert, C., Fox, H.E., Fujita, R., Heinemann, D., Lenihan, H.S., Madin, E.M.P., Perry, M.T., Selig, E.R., Spalding, M., Steneck, R., Watson, R., 2008. A Global Map of Human Impact on Marine Ecosystems. Science 80, 948–952. doi:10.1126/science.1149345
Hartmann-Schröder, G., 1996. Annelida, Borstenwürmer, Polychaeta. 2nd revised ed. Die Tierwelt Deutschalands und der angrenzenden Meeresteile nach ihren Merkmalen und nach ihrer Lebensweise, 58. Gustav Fischer, Jena. 648pp.
Hayward, P., Ryland, J. (eds). 1995. Handbook of the marine fauna of north-west Europe. Oxford University Press, Oxford, 800pp.
Hebert, P.D.N., Ratnasingham, S., de Waard, J.R., 2003. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc. R. Soc. B Biol. Sci. 270, S96–S99. doi:10.1098/
rsbl.2003.0025
Hebert, P.D.N., Cywinska, A., Ball, S.L., deWaard, J.R., 2003. Biological identifications through DNA barcodes.
Proc. R. Soc. B Biol. Sci. 270, 313–321. doi:10.1098/rspb.2002.2218
Heery, E.C., Bishop, M.J., Critchley, L.P., Bugnot, A.B., Airoldi, L., Mayer-Pinto, M., Sheehan, E.V., Coleman, R.A., Loke, L.H.L., Johnston, E.L., Komyakova, V., Morris, R.L., Strain, E.M.A., Naylor, L.A., Dafforn, K.A., 2017. Identifying the consequences of ocean sprawl for sedimentary habitats. Journal of Experimental Marine Biology and Ecology, 492: 31–48. doi:10.1016/j.jembe.2017.01.020
Heiligenberg, T. van den, 1987. Effects of mechanincal and manual harvesting of lugworms Arenicola marina L. on the benthic fauna of tidal flats in the Dutch Waddden Sea. Biol. Conserv. 39, 165–177.
Heip, C., Vincx, M., Vranken, G., 1985. The Ecology of Marine Nematodes.pdf. Oceanogr. Mar. Biol. An Annu. Rev. 23, 399–489.
Herbold, C.W., Pelikan, C., Kuzyk, O., Hausmann, B., Angel, R., Berry, D., Loy, A., 2015. A flexible and economical barcoding approach for highly multiplexed amplicon sequencing of diverse target genes.
Front. Microbiol. 6. doi:10.3389/fmicb.2015.00731
Hooper, D.U., Adair, E.C., Cardinale, B.J., Byrnes, J.E.K., Hungate, B.A., Matulich, K.L., Gonzalez, A., Duffy, J.E., Gamfeldt, L., O’Connor, M.I., 2012. A global synthesis reveals biodiversity loss as a major driver of ecosystem change. Nature 1–5. doi:10.1038/nature11118
Hortal, J., de Bello, F., Diniz-Filho, J.A.F., Lewinsohn, T.M., Lobo, J.M., Ladle, R.J., 2015. Seven Shortfalls that Beset Large-Scale Knowledge of Biodiversity. Annu. Rev. Ecol. Evol. Syst. 46, 523–549. doi:10.1146/
annurev-ecolsys-112414-054400
Hugerth, L.W., Muller, E.E.L., Hu, Y.O.O., Lebrun, L.A.M., Roume, H., Lundin, D., Wilmes, P., Andersson, A.F., 2014. Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia. PLoS One 9. doi:10.1371/journal.pone.0095567
Jackson, M.C., Weyl, O.L.F., Altermatt, F., Durance, I., Friberg, N., Dumbrell, A.J., Piggot, J.J., Tiegs, S.D., Tockner, K., Krug, C.B., Leadley, P.W., Woodward, G., 2016. Recommendations for the next generation of global freshwater biological monitoring tools. Advances in ecological research 55, 615-636. doi:10.1016/
bs.aecr.2016.08.008
Jerde, C. L., Mahon, A. R., Chadderton, W. L., and Lodge, D. M., 2011. “Sight-unseen” detection of rare aquatic species using environmental DNA. Conserv. Lett. 4, 150–157. doi:10.1111/j.1755-263X.2010.00158.x.
Jerde, C. L., 2019. Can we manage fisheries with the inherent uncertainty from eDNA? J. Fish Biol., jfb.14218.
doi:10.1111/jfb.14218.
Jeunen, G., Knapp, M., Spencer, H. G., Lamare, M. D., Taylor, H. R., Stat, M., Bunce, M., Gemmel, N.J., 2019.
Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water movement. Mol. Ecol. Resour. 19, 426–438. doi:10.1111/1755-0998.12982.
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., 2013. Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding. Ecol. Lett. 16, 1245–1257. doi:10.1111/ele.12162
Jørgensen, D. 2012. OSPAR’s exclusion of rigs-to-reefs in the North Sea. Ocean and Coastal Management, 58: 57–61. doi:10.1016/j.ocecoaman.2011.12.012
Josefson, A.B., and Jensen, J.N. 1992. Growth patterns of Amphiura filiformis support the hypothesis of organic enrichment in the Skagerrak-Kattegat area. Marine Biology, 112: 615–624. doi:10.1007/
BF00346179
Jumars, P.A., Dorgan, K.M., Lindsay, S.M., 2015. Diet of Worms Emended: An Update of Polychaete Feeding Guilds. Ann. Rev. Mar. Sci. 7, 497–520. doi:10.1146/annurev-marine-010814-020007
Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxton, S., Cooper, A., Markowitz, S., Duran, C., Thierer, T., Ashton, B., Meintjes, P., Drummond, A., 2012. Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data.
Bioinformatics 28, 1647–1649. doi:10.1093/bioinformatics/bts199
Kelly, R. P., O’Donnell, J. L., Lowell, N. C., Shelton, A. O., Samhouri, J. F., Hennessey, S. M., Feist, B.E., William, G.D., 2016. Genetic signatures of ecological diversity along an urbanization gradient. PeerJ 4, e2444.
doi:10.7717/peerj.2444.
Kelly, R. P., Shelton, A. O., and Gallego, R., 2019. Understanding PCR Processes to Draw Meaningful Conclusions from Environmental DNA Studies. Sci. Rep. 9, 1–14. doi:10.1038/s41598-019-48546-x.
Khripounoff, A., Vangriesheim, A., Crassous, P., Segonzac, M., Colaço, A., Desbruyères, D., Barthelemy, R., 2001. Particle flux in the Rainbow hydrothermal vent field (Mid-Atlantic Ridge): Dynamics, mineral and biological composition. J. Mar. Res. 59, 633–656. doi:10.1357/002224001762842217
Klunder, L., Lavaleye, M., Kleine Schaars, L., Dekker, R., Holthuijsen, S., van der Veer, H.W., (2019). Distribution of the dwarf surf clam Mulinia lateralis (Say, 1822) in the Wadden Sea after first introduction.
BioInvasions Rec. 8, 818–827. doi:10.3391/bir.2019.8.4.10.
Krone, R., Gutow, L., Joschko, T.J., and Schröder, A. 2013. Epifauna dynamics at an offshore foundation e Implications of future wind power farming in the North Sea. Marine Environmental Research, 85: 1–12.
doi:10.1016/j.marenvres.2012.12.004
Lacoursière-Roussel, A. and Deiner, K., 2019. Environmental DNA is not the tool by itself. J. Fish Biol., jfb.14177. doi:10.1111/jfb.14177.
Lacoursière-Roussel, A., Howland, K., Normandeau, E., Grey, E. K., Archambault, P., Deiner, K., Lodge, D.M., Hernandez, C., Leduc, N., Bernatchez, L., 2018. eDNA metabarcoding as a new surveillance approach for coastal Arctic biodiversity. Ecol. Evol. 8, 7763–7777. doi:10.1002/ece3.4213.
Lallias, D., Hiddink, J.G., Fonseca, V.G., Gaspar, J.M., Sung, W., Neill, S.P., Barnes, N., Ferrero, T., Hall, N., Lambshead, P.J.D., Packer, M., Kelley Thomas, W., Creer, S., 2014. Environmental metabarcoding reveals heterogeneous drivers of microbial eukaryote diversity in contrasting estuarine ecosystems. The ISME Journal, 9: 1208–1221. doi:10.1038/ismej.2014.213
Lamb, P. D., Hunter, E., Pinnegar, J. K., Creer, S., Davies, R. G., Taylor, M. I., 2019. How quantitative is metabarcoding: A meta-analytical approach. Mol. Ecol. 28, 420–430. doi:10.1111/mec.14920.
Lanzén, A., Lekang, K., Jonassen, I., Thompson, E.M., Troedsson, C., 2016. High-throughput metabarcoding of eukaryotic diversity for environmental monitoring of offshore oil-drilling activities. Mol. Ecol. 25, 4392–4406. doi:10.1111/mec.13761
Lanzén, A., Lekang, K., Jonassen, I., Thompson, E. M., and Troedsson, C., 2017. DNA extraction replicates improve diversity and compositional dissimilarity in metabarcoding of eukaryotes in marine sediments.
PLoS One 12, 1–18. doi:10.1371/journal.pone.0179443.
Laroche, O., Wood, S. A., Tremblay, L. A., Ellis, J. I., Lejzerowicz, F., Pawlowski, J., Lear, G., Atalah, J., Pochon, X., 2016. First evaluation of foraminiferal metabarcoding for monitoring environmental impact from an offshore oil drilling site. Mar. Environ. Res. 120, 225–235. doi:10.1016/j.marenvres.2016.08.009.
Laroche, O., Wood, S. A., Tremblay, L. A., Ellis, J. I., Lear, G., Pochon, X., 2018. A cross-taxa study using environmental DNA/RNA metabarcoding to measure biological impacts of offshore oil and gas drilling and production operations. Mar. Pollut. Bull. 127, 97–107. doi:10.1016/J.MARPOLBUL.2017.11.042.
Legendre, P. and Gallagher, E. D., 2001. Ecologically meaningful transformations for ordination of species data. Oecologia 129, 271–280. doi:10.1007/s004420100716.
Lejzerowicz, F., Esling, P., Pillet, L., Wilding, T.A., Black, K.D., Pawlowski, J., 2015. High-throughput sequencing and morphology perform equally well for benthic monitoring of marine ecosystems. Sci. Rep. 5, 13932.
doi:10.1038/srep13932
Lekang, K., Thompson, E., Troedsson, C., 2015. A comparison of DNA extraction methods for biodiversity studies of eukaryotes in marine sediments. Aquat. Microb. Ecol. 75, 15–25. doi:10.3354/ame01741 Leopold, M. F. and Bos, O. G., 2009. Wwadpierenvisserij in de Waddenzee. IMARES-report C013/09 Leray, M. and Knowlton, N., 2016. Censusing marine eukaryotic diversity in the twenty-first century. Philos.
Trans. R. Soc. Lond. B. Biol. Sci. 371, 20150331. doi:10.1098/rstb.2015.0331
Leray, M. and Knowlton, N., 2015. DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity. Proc. Natl. Acad. Sci. 112, 2076–2081. doi:10.1073/pnas.1424997112 Leray, M., Yang, J.Y., Meyer, C.P., Mills, S.C., Agudelo, N., Ranwez, V., Boehm, J.T., Machida, R.J., 2013. A
new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents. Front. Zool. 10, 34.
doi:10.1186/1742-9994-10-34
Levin, L.A., Boesch, D.F., Covich, A., Dahm, C., Erséus, C., Ewel, K.C., Kneib, R.T., Moldenke, A., Palmer, M.A., Snelgrove, P., Strayer, D., Weslawski, J.M., 2001. The function of marine critical transition zones and the importance of sediment biodiversity. Ecosystems 4, 430–451. doi:10.1007/s10021-001-0021-4 Levin, L.A., Baco, A.R., Bowden, D.A., Colaco, A., Cordes, E.E., Cunha, M.R., Demopoulos, A.W.J., Gobin, J.,
Grupe, B.M., Le, J., Metaxas, A., Netburn, A.N., Rouse, G.W., Thurber, A.R., Tunnicliffe, V., Van Dover, C.L., Vanreusel, A., Watling, L., 2016. Hydrothermal Vents and Methane Seeps: Rethinking the Sphere of Influence. Front. Mar. Sci. 3, 1–23. doi:10.3389/fmars.2016.00072
Lindeboom, H.J., Kouwenhoven, H.J., Bergman, M.J.N., Bouma, S., Brasseur, S., Daan, R., Fijn, R.C., de Haan, D., Dirksen, S., van Hal, R., Hille Ris Lambers, R., ter Hofstede, R., Krijgsveld, K.L., Leopold, M., Scheidat, M., 2011. Short-term ecological effects of an offshore wind farm in the Dutch coastal zone; a compilation. Environmental Research Letters, 6: 035101. doi:10.1088/1748/9326/6/3/035101 Liu, Z., Desantis, T.Z., Andersen, G.L., Knight, R., 2008. Accurate taxonomy assignments from 16S rRNA
sequences produced by highly parallel pyrosequencers. Nucleic Acids Res. 36. doi:10.1093/nar/gkn491
Lobo, J., Costa, P.M., Teixeira, M. AL, Ferreira, M.S., Costa, M.H., Costa, F.O., 2013. Enhanced primers for amplification of DNA barcodes from a broad range of marine metazoans. BMC Ecol. 13, 34.
doi:10.1186/1472-6785-13-34
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.
doi:10.1038/s41598-018-27509-8
López-González, P.J., Rodríguez, E., Gili, J.-M., Segonzac, M., 2003. New records on sea anemones (Anthozoa:
Actiniaria) from hydrothermal vents and cold seeps. Zool. Verh. 345, 215–243.
Luttikhuizen, P.C., Dekker, R., 2010. Pseudo-cryptic species Arenicola defodiens and Arenicola marina (Polychaete: Arenicolidae) in Wadden Sea, North Sea and Skagerrak: Morphological and molecular variation. Journal of Sea Research 63, 17-23. doi:S138511010900080X
Maar, M., Bolding, K., Petersen, J.K., Hansen, J.L.S., and Timmermann, K. 2009. Local effects of blue mussels around turbine foundations in an ecosystem model of Nysted off-shore wind farm, Denmark. Journal of Sea Research, 62: 159–174. doi:10.1016/j.seares.2009.01.008
Makiola, A, Compson, Z.G, Baird, D.J, Barnes, M.A., Boerlijst, S.P., Bouchez, A., Brennan, G., Bush, A., Canard, E., Cordier, T., Creer, S., Curry, R.A., David, P., Dumbrell, A .J, Gravel, D., Hajibabaei, M., Hayden, B., Hoorn, B.Y.V., Jarne, P., Jones, J.I., Karimi, B., Keck, F., Kelly, M., Knot, I.E., Krol, L., Massol, F., Monk, W.A., Murphy, J., Pawlowski, J., Poisot, T., Porter, T.M., Randall, K.C., Ransome, E., Ravigné, V., Raybould, A., Robin, S., Schrama, M., Schatz, B. , Tamaddoni-Nezhad, A., Trimbos, K.B., Vacher, C., Vasselon, V., Wood, S., Woodward, G., Bohan, D.A., 2020. Key questions for next-generations biomonitoring. Frontiers in Environmental Science, 09. doi:10.3389/fenvs.2019.00197
Manoukian, S., Spagnolo, A., Scarcella, G., Punzo, E., Angelini, R., and Fabi, G. 2010. Effects of two offshore gas platforms on soft-bottom benthic communities (northwestern Adriatic Sea, Italy). Marine Environmental Research, 70: 402–410. doi:10.1016/j.marenvres.2010.08.004
Mapstone, G.M., 2014. Global diversity and review of Siphonophorae (Cnidaria: Hydrozoa). PLoS One 9, e87737. doi:10.1371/journal.pone.0087737
May, R.M., 1988. How Many Species Are There on Earth? Science 80, 1441–1449. doi:10.1126/
science.241.4872.1441
McLusky, D., Anderson, F., and Wolfe-Murphy, S., 1983. Distribution and population recovery of Arenicola marina and other benthic fauna after bait digging . Mar. Ecol. Prog. Ser. 11, 173–179. doi:10.3354/
meps011173.
McMurdie, P. J. and Holmes, S., 2014. Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible.
PLoS Comput. Biol. 10, e1003531. doi:10.1371/journal.pcbi.1003531.
Mendoza, M. and Henkel, S.K. 2017. Benthic effects of artificial structures deployed in a tidal estuary.
Plankton and Benthos Research, 12: 179–189. doi:10.3800/pbr.12.179
Merrie, A. and Olsson, P., 2014. An innovation and agency perspective on the emergence and spread of Marine Spatial Planning. Mar. Policy 44, 366–374. doi:10.1016/J.MARPOL.2013.10.006
Metaxas, A., 2004. Spatial and temporal patterns in larval supply at hydrothermal vents in the northeast Pacific Ocean. Limnol. Oceanogr. 49, 1949–1956. doi:10.4319/lo.2004.49.6.1949
Miller, K.A., Thompson, K.F., Johnston, P., Santillo, D., 2018. An overview of seabed mining including the current state of development, environmental impacts, and knowledge gaps. Front. Mar. Sci. 4, 418.
doi:10.3389/fmars.2017.00418
Mullineaux, L.S., Adams, D.K., Mills, S.W., Beaulieu, S.E., 2010. Larvae from afar colonize deep-sea hydrothermal vents after a catastrophic eruption. Proc. Natl. Acad. Sci. U. S. A. 107, 7829–34.
doi:10.1073/pnas.0913187107
Nakajima, R., Yamamoto, H., Kawagucci, S., Takaya, Y., Nozaki, T., Chen, C., Fujikura, K., Miwa, T., Takai, K., 2015. Post-drilling changes in seabed landscape and megabenthos in a deep-sea hydrothermal system, the Iheya North field, Okinawa Trough. PLoS One 10. doi:10.1371/journal.pone.0123095
Nascimento, F., Lallias, D., Bik, H., Creer, S., 2018. Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing. Scientific reports 8, 11737. doi:10.1038/s41598-018-30179-1
Newell, R. C., Seiderer, L. J., Hitchcock, D. R., 1998. The impact of dredging works in coastal waters: A review of the sensitivity to disturbance and subsequent recovery of biological resources on the sea bed. Oceanogr. Mar. Biol. 36, 127–178.
Nichols, R., Vollmers, C., Newsom, L., Wang, Y., Heintzman, P., Leighton, M., Green, R., Shapiro, B., 2018.
Minimizing polymerase biases in metabarcoding. Mol. ecol. resources 18-5. doi:10.1111/1755- 0998.12895
Nickrent, D.L. and Sargent, M.L., 1991. An overview of the secondary structure of the V4 region of eukaryotic small-subunit ribosomal RNA. Nucleic Acids Res. 19, 227–235. doi:10.1093/nar/19.2.227
Patrício, J., Neto, J. M., Teixeira, H., Salas, F., Marques, J. C., 2009. The robustness of ecological indicators to detect long-term changes in the macrobenthos of estuarine systems. Mar. Environ. Res. 68, 25–36.
doi:10.1016/j.marenvres.2009.04.001.
Pawlowski, J., Esling, P., Lejzerowicz, F., Cedhagen, T., Wilding, T. A., 2014. Environmental monitoring through protist next-generation sequencing metabarcoding: Assessing the impact of fish farming on benthic foraminifera communities. Mol. Ecol. Resour. 14, 1129–1140. doi:10.1111/1755-0998.12261.
Pawlowski, J., Kelly-Quinn, M., Altermatt, F., Apothéloz-Perret-Gentil, L., Beja, P., Boggero, A., Borja, A., Bouchez, A., Cordier, T., Domaizon, I., Feio, M.J., Filipe, A.F., Fornaroli, R., Graf, W., Herder, J., van der Hoorn, B., Iwan Jones, J., Sagova-Mareckova, M., Moritz, C., Barquín, J., Piggott, J.J., Pinna, M., Rimet, F., Rinkevich, B., Sousa-Santos, C., Specchia, V., Trobajo, R., Vasselon, V., Vitecek, S., Zimmerman, J., Weigand, A., Leese, F., Kahlert, M., 2018. The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems. Sci. Total Environ. 637–638, 1295–1310. doi:10.1016/j.scitotenv.2018.05.002
Pearman, J.K., Anlauf, H., Irigoien, X., Carvalho, S., 2016. Please mind the gap - Visual census and cryptic biodiversity assessment at central Red Sea coral reefs. Mar. Environ. Res. 118, 20–30. doi:10.1016/j.
marenvres.2016.04.011
Philippart, C. J. M., van Bleijswijk, J. D. L., Kromkamp, J. C., Zuur, A. F., Herman, P. M. J., 2014. Reproductive phenology of coastal marine bivalves in a seasonal environment. J. Plankton Res. 36, 1512–1527.
doi:10.1093/plankt/fbu073.
Picken, G., Baine, M., Heaps, L., Side, J. 2000. Rigs to reefs in the North Sea. In artificial reefs in European seas. Springer Netherlands, Dordrecht , pp. 331–342.
Piersma, T., Koolhaas, A., Dekinga, A., Beukema, J. J., Dekker, R., Essink, K. (2002). Long-term indirect effects of mechanical cockle-dredging on intertidal bivalve stocks in the Wadden Sea. J. Appl. Ecol. 38, 976–990.
doi:10.1046/j.1365-2664.2001.00652.x.
Piñol, J., Mir, G., Gomez-Polo, P., Agustí, N., 2015. Universal and blocking primer mismatches limit the use of high-throughput DNA sequencing for the quantitative metabarcoding of arthropods. Mol. Ecol. Resour.
15, 819–830. doi:10.1111/1755-0998.12355.
Piñol, J., Senar, M. A., Symondson, W. O. C., 2019. The choice of universal primers and the characteristics of the species mixture determine when DNA metabarcoding can be quantitative. Mol. Ecol. 28, 407–419.
doi:10.1111/mec.14776.
Plum, C., Gollner, S., Martinez-Arbizu, P., Bright, M., 2015. Diversity and composition of the copepod communities associated with megafauna around a cold seep in the Gulf of Mexico with remarks on species biogeography. Marine Biodiversity 45-3, 419-432. doi:10.1007/s12526-014-0310-8
Plummer, E. and Twin, J., 2015. A Comparison of Three Bioinformatics Pipelines for the Analysis of Preterm Gut Microbiota using 16S rRNA Gene Sequencing Data. J. Proteomics Bioinform. 8. doi:10.4172/
jpb.1000381.
Pochon, X., Zaiko, A., Fletcher, L. M., Laroche, O., Wood, S. A., 2017. Wanted dead or alive? Using metabarcoding of environmental DNA and RNA to distinguish living assemblages for biosecurity applications. PLoS One 12, e0187636. doi:10.1371/journal.pone.0187636.
Podowski, E., Ma, S., Luther, G., Wardrop, D., Fisher, C., 2010. Biotic and abiotic factors affecting distributions of megafauna in diffuse flow on andesite and basalt along the Eastern Lau Spreading Center, Tonga.
Mar. Ecol. Prog. Ser. 418, 25–45. doi:10.3354/meps08797
Pompanon, F., Deagle, B. E., Symondson, W. O. C., Brown, D. S., Jarman, S. N., Taberlet, P., 2012. Who is eating what: Diet assessment using next generation sequencing. Mol. Ecol. 21, 1931–1950. doi:10.1111/j.1365- 294X.2011.05403.x.
Pompanon, F., Samadi, S., 2015. Next generation sequencing for characterizing biodiversity: promises and challenges. Genetica 143, 133–138. doi:10.1007/s10709-015-9816-7
Porazinska, D. L., Sung, W., Giblin-Davis, R. M., Thomas, W. K., 2010. Reproducibility of read numbers in high-throughput sequencing analysis of nematode community composition and structure. Mol. Ecol.
Resour. 10, 666–676. doi:10.1111/j.1755-0998.2009.02819.x.
Porter, T.M., Gibson, J.F., Shokralla, S., Baird, D.J., Golding, G.B., Hajibabaei, M., 2014. Rapid and accurate taxonomic classification of insect (class Insecta) cytochrome c oxidase subunit 1 (COI) DNA barcode sequences using a naïve Bayesian classifier. Mol. Ecol. Resour. 14, 929–942. doi:10.1111/1755- 0998.12240
Pruesse, E., Quast, C., Knittel, K., Fuchs, B.M., Ludwig, W., Peplies, J., Glöckner, F.O., 2007. SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35, 7188–7196. doi:10.1093/nar/gkm864
Rognes, T., Flouri, T., Nichols, B., Quince, C., Mahé, F., 2016. VSEARCH: a versatile open source tool for metagenomics. PeerJ 4, e2584. doi:10.7717/peerj.2584
Riaz, T., Shehzad, W., Viari, A., Pompanon, F., Taberlet, P., Coissac, E., 2011. EcoPrimers: Inference of new DNA barcode markers from whole genome sequence analysis. Nucleic Acids Res. 39, 1–11. doi:10.1093/
nar/gkr732
Richardson, R.T., Bengtsson-Palme, J., Johnson, R.M., 2017. Evaluating and optimizing the performance of software commonly used for the taxonomic classification of DNA metabarcoding sequence data. Mol.
Ecol. Resour. 17, 760–769. doi:10.1111/1755-0998.12628
Rudolph, D., Bos, K., Luijendijk, A., Rietema, K., and Out, J. 2004. Scour Around Offshore Structures, Analysis of Field Measurements. Proceedings 2nd International Conference Scour Erosion: 400–407.
Ruggiero, M.A., Gordon, D.P., Orrell, T.M., Bailly, N., Bourgoin, T., Brusca, R.C., Cavalier-Smith, T., Guiry, M.D., Kirk, P.M., 2015. A Higher Level Classification of All Living Organisms. PLoS One 10, e0119248.
doi:10.1371/journal.pone.0119248
Rutgers van der Loeff, M.M., Lavaleye, M.S.S., 1986. Sediments, fauna, and the dispersal of radionuclides at the N.E. Atlantic dumpsite for low-level radioactive waste.
Sanger, F., Nicklen, S., Coulson, A.R., 1977. DNA sequencing with chain-terminating inhibitors. Proc. Natl.
Acad. Sci. 74, 5463–5467. doi:10.1073/pnas.74.12.5463
Savidge, W. B. and Taghon, G. L., 1988. Passive and active components of colonization following two types of disturbance on intertidal sandflat. J. Exp. Mar. Bio. Ecol. 115, 137–155. doi:10.1016/0022- 0981(88)90099-8.
Sarrazin, J., Legendre, P., de Busserolles, F., Fabri, M.C., Guilini, K., Ivanenko, V.N., Morineaux, M., Vanreusel, A., Sarradin, P.M., 2015. Biodiversity patterns, environmental drivers and indicator species on a high- temperature hydrothermal edifice, Mid-Atlantic Ridge. Deep. Res. Part II Top. Stud. Oceanogr. 121, 177–192. doi:10.1016/j.dsr2.2015.04.013
Schmid-Araya, J.M. and Schmid, P.E., 2001. Trophic relationships: integrating meiofauna into a realistic benthic food web. Freshwater biology 44, 149-163. doi:10.1046/j.1365-2427.2000.00594.x
Sen, A., Kim, S., Miller, A.J., Hovey, K.J., Hourdez, S., Luther, G.W., Fisher, C.R., 2016. Peripheral communities of the Eastern Lau Spreading Center and Valu Fa Ridge: community composition, temporal change and comparison to near-vent communities. Mar. Ecol. 37, 599–617. doi:10.1111/maec.12313
Sen, A., Podowski, E.L., Becker, E.L., Shearer, E.A., Gartman, A., Yücel, M., Hourdez, S., Luther, G.W.I., Fisher, C.R., 2014. Community succession in hydrothermal vent habitats of the Eastern Lau Spreading Center and Valu Fa Ridge, Tonga. Limnol. Oceanogr. 59, 1510–1528. doi:10.4319/lo.2014.59.5.1510
Severmann, S., Johnson, C.M., Beard, B.L., German, C.R., Edmonds, H.N., Chiba, H., Green, D.R.H., 2004.
The effect of plume processes on the Fe isotope composition of hydrothermally derived Fe in the deep ocean as inferred from the Rainbow vent site, Mid-Atlantic Ridge, 36°14′N. Earth Planet. Sci. Lett. 225, 63–76. doi:10.1016/j.epsl.2004.06.001
Shull, D. H., 1997. Mechanisms of infaunal polychaete dispersal and colonization in an intertidal sandflat.
J. Mar. Res. 55, 153–179. doi:10.1357/0022240973224454.
Sinniger, F., Pawlowski, J., Harii, S., Gooday, A.J., Yamamoto, H., Chevaldonné, P., Cedhagen, T., Carvalho, G., Creer, S., 2016. Worldwide Analysis of Sedimentary DNA Reveals Major Gaps in Taxonomic Knowledge of Deep-Sea Benthos. Front. Mar. Sci. 3, 1–14. doi:10.3389/fmars.2016.00092
Snelgrove, P.V.R., 1997. The Importance of Marine Sediment Biodiversity in Ecosystem Processes. Ambio 26, 578–583.
Solan, M., 2004. Extinction and Ecosystem Function in the Marine Benthos. Science 80, 1177–1180.
doi:10.1126/science.1103960
Spilmont, N., 2013. The Future of Benthic Indicators: Moving up to the Intertidal. Open J. Mar. Sci. 03, 76–86.
doi:10.4236/ojms.2013.32A008
Stap, T. Van Der, Coolen, J.W.P., and Lindeboom, H.J. 2016. Marine Fouling Assemblages on Offshore Gas Platforms in the Southern North Sea : Effects of Depth and Distance from Shore on Biodiversity: PLoS ONE, 19–21. doi:10.1371/journal.pone.0146324
Stewart, K. A., 2019. Understanding the effects of biotic and abiotic factors on sources of aquatic environmental DNA. Biodivers. Conserv. 28, 983–1001. doi:10.1007/s10531-019-01709-8.
