M. J. Attrill, A Rehabilitated Estuarine Ecosystem: The Environment and Ecology of the Thames Estuary, 1998.

M. J. Attrill, A testable linear model for diversity trends in estuaries, J Anim Ecol, vol.71, pp.262-269, 2002.

M. J. Attrill and S. D. Rundle, Ecotone of ecocline: ecological boundaries in estuaries, Estuar Coast Shelf S, vol.55, pp.929-936, 2002.

D. J. Baird and M. Hajibabaei, Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing, Mol Ecol, vol.21, pp.2039-2044, 2012.

A. Basset, E. Barbone, M. Elliott, B. Li, S. E. Jorgensen et al., A unifying approach to understanding transitional waters: fundamental from ecotone ecosystems, Estuar Coast Shelf S, vol.132, pp.5-16, 2012.

H. M. Bik, D. L. Porazinska, S. Creer, J. G. Caporaso, R. Knight et al., Sequencing our way towards understanding global eukaryotic biodiversity, Trends Ecol Evol, vol.27, pp.233-243, 2012.

H. M. Bik, D. Fournier, W. Sung, R. D. Bergeron, and W. K. Thomas, Intra-genomic variation in the ribosomal repeats of nematodes, PLoS One, vol.8, p.78230, 2013.

M. L. Blaxter, D. Ley, P. Garey, J. R. Liu, L. X. Scheldeman et al., A molecular evolutionary framework for the phylum Nematoda, Nature, vol.392, pp.71-75, 1998.

K. Bohmann, A. Evans, M. T. Gilbert, G. R. Carvalho, S. Creer et al., Environmental DNA for wildlife biology and biodiversity monitoring, Trends Ecol Evol, vol.29, pp.358-367, 2014.

G. M. Branch and A. Pringle, The impact of the sand prawn Callianassa kraussi Stebbing on sediment turnover and on bacteria, meiofauna, and benthic microflora, J Exp Mar Biol Ecol, vol.107, pp.219-235, 1987.

J. G. Caporaso, J. Kuczynski, J. Stombaugh, K. Bittinger, F. D. Bushman et al., QIIME allows analysis of high-throughput community sequencing data, Nat Methods, vol.7, pp.335-336, 2010.

L. M. Carrascal, I. Galvan, and O. Gordo, Partial least squares regression as an alternative to current regression methods used in ecology, Oikos, vol.118, pp.681-690, 2009.

A. A. Chariton, L. N. Court, D. M. Hartley, M. J. Colloff, and C. M. Hardy, Ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA, Front Ecol Environ, vol.8, pp.233-238, 2010.

I. Chong and C. Jun, Performance of some variable selection methods when multicollinearity is present, Chemometr Intell Lab Syst, vol.78, pp.103-112, 2005.

J. Christensen, B. Hewitson, A. Busuioc, A. Chen, X. Gao et al., Climate Change 2007: The Physical Science Basis. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change, pp.847-940, 2007.

K. R. Clarke, Non-parametric multivariate analyses of changes in community structure, Aust J Ecol, vol.18, pp.117-143, 1993.

K. R. Clarke and R. N. Gorley, PRIMER v6: User Manual/ Tutorial PRIMER-E, 2006.

S. Creer, V. G. Fonseca, D. L. Porazinska, R. M. Giblin-davis, W. Sung et al., Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises, Mol Ecol, vol.19, pp.4-20, 2010.

R. C. Edgar, Search and clustering orders of magnitude faster than BLAST, Bioinformatics, vol.26, pp.2460-2461, 2010.

R. C. Edgar, B. J. Haas, J. C. Clemente, C. Quince, and R. Knight, UCHIME improves sensitivity and speed of chimera detection, Bioinformatics, vol.27, pp.2194-2200, 2011.

M. Elliott and A. K. Whitfield, Challenging paradigms in estuarine ecology and management, Estuar Coast Shelf S, vol.94, pp.306-314, 2011.

T. J. Ferrero, N. J. Debenham, and P. Lambshead, The nematodes of the Thames estuary: assemblage structure and biodiversity, with a test of Attrill's linear model, Estuar Coast Shelf S, vol.79, pp.409-418, 2008.

V. G. Fonseca, G. R. Carvalho, W. Sung, H. F. Johnson, D. M. Power et al., Second-generation environmental sequencing unmasks marine metazoan biodiversity, Nat Commun, vol.1, p.98, 2010.

V. G. Fonseca, M. Packer, G. R. Carvalho, D. Power, J. Lambshead et al., Isolation of marine meiofauna from sandy sediments: from decanting to DNA extraction, Nat Protoc Exchange, 2011.

V. G. Fonseca, G. R. Carvalho, B. Nichols, C. Quince, H. F. Johnson et al., Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes, Global Ecol Biogeogr, vol.23, pp.1293-1302, 2014.

O. Giere, Meiobenthology: The Microscopic Motile Fauna of Aquatic Sediments, 2009.

T. C. Glenn, Field guide to next generation sequencers, Mol Ecol Resour, vol.11, pp.759-769, 2011.

G. Graf, Benthic-pelagic coupling -a benthic view, Oceanogr Mar Biol, vol.30, pp.149-190, 1992.

C. Heip, M. Vincx, and G. Vranken, The ecology of marine nematodes, Oceanogr Mar Biol, vol.23, pp.399-489, 1985.

Y. Ji, L. Ashton, S. M. Pedley, D. P. Edwards, Y. Tang et al., Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding, Ecol Lett, vol.16, pp.1245-1257, 2013.

A. J. Kenny and I. Sotheran, Characterising the physical properties of seabed habitats, Eleftheriou A (ed) Methods for the Study of Marine Benthos, pp.47-95, 2013.

W. J. Langston, B. S. Chesman, and G. R. Burt, Characterisation of European Marine Sites, Mersey Estuary SPA. Marine Biological Association of the United Kingdom, 2006.

M. Loreau, S. Naeem, P. Inchausti, J. Bengtsson, J. P. Grime et al., Ecology -biodiversity and ecosystem functioning: current knowledge and future challenges, Science, vol.294, pp.804-808, 2001.

J. Martiny, B. Bohannan, J. H. Brown, R. K. Colwell, J. A. Fuhrman et al., Microbial biogeography: putting microorganisms on the map, Nat Rev Microbiol, vol.4, pp.102-112, 2006.

P. Matthiessen and L. Rjcps, Contaminants and their effects on estuarine and coastal organisms in the United Kingdom in the late twentieth century, Environ Pollut, vol.120, pp.739-757, 2002.

B. H. Mevik and R. Wehrens, The pls package: principal component and partial least squares regression in R, J Stat Softw, vol.18, pp.1-24, 2007.

S. P. Neill, E. J. Litt, S. J. Couch, and A. G. Davies, The impact of tidal stream turbines on large-scale sediment dynamics, Renew Energ, vol.34, pp.2803-2812, 2009.

, The Mersey estuary: a report on environmental quality, Water Quality Series, 1995.

J. Oksanen, F. G. Blanchet, R. Kindt, P. Legendre, P. R. Minchin et al., vegan: Community Ecology Package, 2013.

M. Power, M. J. Attrill, and R. M. Thomas, Trends in agricultural pesticide (atrazine, lindane, simazine) concentrations in the Thames Estuary, Environ Pollut, vol.104, pp.31-39, 1999.

E. Pruesse, C. Quast, K. Knittel, B. Fuchs, W. Ludwig et al., SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB, Nucl Acids Res, vol.35, pp.7188-7196, 2007.

, Environmental metabarcoding of microbial diversity D Lallias et al

J. Reeder and R. Knight, Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions, Nat Methods, vol.7, pp.668-669, 2010.

R. Rosenberg, M. Blomqvist, H. C. Nilsson, H. Cederwall, and A. Dimming, Marine quality assessment by use of benthic species-abundance distributions: a proposed new protocol within the European Union Water Framework Directive, Mar Pollut Bull, vol.49, pp.728-739, 2004.

D. Schrö-ter, W. Cramer, R. Leemans, I. C. Prentice, M. B. Araú-jo et al., Ecosystem service supply and vulnerability to global change in Europe, Science, vol.310, pp.1333-1337, 2005.

W. Struthers, From Manchester Docks to Salford Quays: ten years of environmental improvements in the Mersey Basin Campaign, J Chart Inst Water Env Manage, vol.11, pp.1-7, 1997.

P. Taberlet, E. Coissac, M. Hajibabaei, and L. H. Rieseberg, Environmental DNA, Mol Ecol, vol.21, pp.1789-1793, 2012.
URL : https://hal.archives-ouvertes.fr/insu-00845082

P. Taberlet, E. Coissac, F. Pompanon, C. Brochmann, and E. Willerslev, Towards next-generation biodiversity assessment using DNA metabarcoding, Mol Ecol, vol.21, pp.2045-2050, 2012.

D. Tinsley, The Thames Estuary: a history of the impact of humans on the environment and a description of the current approach to environmental management, Attrill MJ, pp.5-25, 1998.

A. Valentini, F. Pompanon, and P. Taberlet, DNA barcoding for ecologists, Trends Ecol Evol, vol.24, pp.110-117, 2009.
URL : https://hal.archives-ouvertes.fr/halsde-00378005

M. Vellend, Conceptual synthesis in community ecology, Quart Rev Biol, vol.85, pp.183-206, 2010.

D. A. Wardle, R. D. Bardgett, J. N. Klironomos, H. Setälä, W. H. Van-der-putten et al., Ecological linkages between aboveground and belowground biota, vol.304, pp.1629-1633, 2004.

A. K. Whitfield, M. Elliott, A. Basset, S. Blaber, and R. J. West, Paradigms in estuarine ecology -a review of the Remane diagram with a suggested revised model for estuaries, Estuar Coast Shelf S, vol.97, pp.78-90, 2012.

M. Yoder, I. Ley, I. W. King, M. Mundo-ocampo, J. Mann et al., DESS: a versatile solution for preserving morphology and extractable DNA of nematodes, Nematology, vol.8, pp.367-376, 2006.