G. Duchemin, F. J. Jorissen, F. Andrieux-loyer, F. Le-loc'h, C. Hily et al., Living benthic foraminifera from "La Grande Vasiere", French Atlantic continental shelf: Faunal composition and microhabitats, Journal of Foraminiferal Research, vol.35, pp.198-218, 2005.

P. P. Eichler, B. B. Eichler, B. S. Gupta, and A. R. Rodrigues, Foraminifera as indicators of marine pollutant contamination on the inner continental shelf of southern Brazil, Marine Pollution Bulletin, vol.64, pp.22-30, 2012.

A. M. Ellis, S. J. Culver, D. J. Mallinson, D. R. Corbett, E. Leorri et al., The influence of aquaculture on modern foraminifera and sediments in the Setiu estuary and lagoon, Journal of Foraminiferal Research, vol.44, pp.390-415, 2014.

S. R. Ernst, J. Morvan, E. Geslin, A. Le-bihan, and F. J. Jorissen, Benthic foraminiferal response to experimentally induced Erika oil pollution, Marine Micropaleontology, vol.61, pp.76-93, 2006.
URL : https://hal.archives-ouvertes.fr/hal-01576708

R. W. Feyling-hanssen, Mikropaleontologiens teknikk, Norges geol. Unders, vol.203, pp.35-48, 1958.

F. Frontalini and R. Coccioni, Benthic foraminifera as bioindicators of pollution: A review of Italian research over the last three decades, vol.54, pp.115-127, 2011.

H. Gebhardt and C. Rupp, Vergleich der Anreicherung von Foraminiferenschalen und anderer Mikrofossilien aus sandigen Sedimenten mit Hilfe von Zinkchlorid-Lösung und Tetrachlorkohlenstoff, Jb. Geol. B.-A, vol.148, pp.177-181, 2008.

T. G. Gibson and W. M. Walker, Flotation methods for obtaining foraminifera from sediment samples, Journal of Paleontology, pp.1294-1297, 1967.

M. R. Gregory and K. A. Johnston, A nontoxic substitute for hazardous heavy liquids-aqueous sodium polytungstate (3Na2WO4 . 9WO3 . H2O) solution (Note), New Zealand Journal of Geology and Geophysics, vol.30, pp.317-320, 1987.

P. Hallock, B. H. Lidz, E. M. Cockey-burkhard, and K. B. Donnelly, Foraminifera as bioindicators in croal reef assessment and monitoring the FORAM index, Coastal Monitoring through Partnerships. Presented at the Fifth Symposium on the Environmental Monitoring and Assessment Program (EMAP), pp.221-238, 2003.

J. R. Haynes, Foraminifera, 1981.

S. H. Hurlbert, The Nonconcept of Species Diversity: A Critique and Alternative Parameters, Ecology, vol.52, pp.577-586, 1971.

A. Jarvis, H. I. Reuter, A. Nelson, and E. Guevara, Hole-filled SRTM for the globe Version 4, available from the CGIAR-CSI SRTM 90m Database, 2008.

F. J. Jorissen, E. Bicchi, G. Duchemin, J. Durrieu, F. Galgani et al., Impact of oil-based drill mud disposal on benthic foraminiferal assemblages on the continental margin off Angola. Deep-Sea Research Part II, Topical Studies in Oceanography, vol.56, pp.2270-2291, 2009.

E. References-alve, S. Korsun, J. Schönfeld, N. Dijkstra, E. Golikova et al., Foram-AMBI: A sensitivity index based on benthic foraminiferal faunas from North-East Atlantic and Arctic fjords, continental shelves and slopes, Marine Micropaleontology, vol.122, pp.1-12, 2016.

E. Alve, S. Hess, V. M. Bouchet, J. K. Dolven, and B. Rygg, Intercalibration of benthic foraminiferal and macrofaunal biotic indices: An example from the Norwegian Skagerrak coast, Ecological Indicators, vol.96, pp.107-115, 2019.

É. Armynot-du-châtelet, V. Bout-roumazeilles, A. Riboulleau, and A. Trentesaux, Sediment (grain size and clay mineralogy) and organic matter quality control on living benthic foraminifera, vol.52, pp.75-84, 2009.

T. S. Arnarson, K. , and R. G. , Organic-mineral interactions in marine sediments studied using density fractionation and X-ray photoelectron spectroscopy, Organic Geochemistry, vol.32, pp.1401-1415, 2001.

Z. Bainbridge, S. Lewis, R. Bartley, K. Fabricius, C. Collier et al., Fine sediment and particulate organic matter: A review and case study on ridge-to-reef transport, transformations, fates, and impacts on marine ecosystems, Marine Pollution Bulletin, vol.135, pp.1205-1220, 2018.

R. Bao, C. Mcintyre, M. Zhao, C. Zhu, S. Kao et al., Widespread dispersal and aging of organic carbon in shallow marginal seas, Geology, vol.44, pp.791-794, 2016.

R. Bao, M. Zhao, A. Mcnichol, V. Galy, C. Mcintyre et al., Temporal constraints on lateral organic matter transport along a coastal mud belt, Organic Geochemistry, vol.128, pp.86-93, 2019.

C. Barras, F. J. Jorissen, C. Labrune, B. Andral, and P. Boissery, Live benthic foraminiferal faunas from the French Mediterranean Coast: Towards a new biotic index of environmental quality, Ecological Indicators, vol.36, pp.719-743, 2014.

C. Barras, F. J. Jorissen, B. Parent, E. Bicchi, L. Charrieau et al., Étude des faunes de foraminifères benthiques de la côte méditerranéenne française : mise en place d'un nouvel indice biotique dans le cadre de Directive Cadre Eau -Campagne DCE 2012. UMR CNRS 6112 LPG-BIAF, 2015.

J. Barusseau, M. B. Diouf, M. De-la-bardonne, and N. Ghandour, Méthodologie pour une simulation des transformations granulométriques de sables de la zone d'avant-côte, Oceanologica Acta, vol.22, pp.179-191, 1999.

J. Barusseau, Influence of Mixtures of Grain-Size Populations on the Parametric and Modal Characteristics of Coastal Sands, Journal of Sedimentary Research, vol.81, pp.611-629, 2011.

F. Baudin, N. Tribovillard, and J. Trichet, Géologie de la matière organique, Géosphères. EDP Sciences, 2017.

T. S. Bianchi, X. Cui, N. E. Blair, D. J. Burdige, T. I. Eglinton et al., Centers of organic carbon burial and oxidation at the land-ocean interface, Organic Geochemistry, vol.115, pp.138-155, 2018.

S. Birk, W. Bonne, A. Borja, S. Brucet, A. Courrat et al., Three hundred ways to assess Europe's surface waters: An almost complete overview of biological methods to implement the Water Framework Directive, Ecological Indicators, vol.18, pp.31-41, 2012.

M. J. Bock and L. M. Mayer, Mesodensity organo-clay associations in a near-shore sediment, Marine Geology, vol.163, pp.65-75, 2000.

Á. Borja, J. Franco, and V. Pérez, A Marine Biotic Index to Establish the Ecological Quality of Soft-Bottom Benthos Within European Estuarine and Coastal Environments, Marine Pollution Bulletin, vol.40, pp.1100-1114, 2000.

Á. Borja, D. M. Dauer, and A. Grémare, The importance of setting targets and reference conditions in assessing marine ecosystem quality, Ecological Indicators, vol.12, pp.1-7, 2012.

I. A. Duijnstee, S. R. Ernst, and G. J. Van-der-zwaan, Effect of anoxia on the vertical migration of benthic foraminifera, Marine Ecology Progress Series, vol.246, pp.85-94, 2003.

M. H. Engel and M. , Organic Geochemistry: Principles and Applications. Topics in geobiology, vol.861, 1993.

J. G. Ferreira, J. H. Andersen, A. Borja, S. B. Bricker, J. Camp et al., Overview of eutrophication indicators to assess environmental status within the European Marine Strategy Framework Directive, Estuarine, Coastal and Shelf Science, vol.93, pp.117-131, 2011.

B. W. Flemming, Process and pattern of sediment mixing in a microtidal coastal lagoon along the west coast of South Africa, Tide-influenced sedimentary environments and facies, pp.275-288, 1988.

B. W. Flemming, The influence of grain-size analysis methods and sediment mixing on curve shapes and textural parameters: Implications for sediment trend analysis, Sedimentary Geology, vol.202, pp.425-435, 2007.

R. L. Folk and W. C. Ward, Brazos River bar: A Study in the Significance of Grain Size Parameters, Journal of Sedimentary Petrology, vol.27, pp.3-26, 1957.

P. R. Gammon, L. A. Neville, R. T. Patterson, M. M. Savard, and G. T. Swindles, A log-normal spectral analysis of inorganic grain-size distributions from a Canadian boreal lake core: Towards refining depositional process proxy data from high latitude lakes, Sedimentology, vol.64, pp.609-630, 2017.

E. G. Gregorich, M. H. Beare, U. F. Mckim, and J. O. Skjemstad, Chemical and Biological Characteristics of Physically Uncomplexed Organic Matter, Soil Science Society of America Journal, vol.70, p.975, 2006.

J. I. Hedges, R. G. Keil, and G. L. Cowie, Sedimentary diagenesis: organic perspectives with inorganic overlays, Chemical Geology, vol.107, pp.487-492, 1993.

J. I. Hedges, K. , and R. G. , Organic geochemical perspectives on estuarine processes: sorption reactions and consequences, Marine Chemistry, vol.65, pp.55-65, 1999.

A. J. Horowitz and K. A. Elrick, The relation of stream sediment surface area, grain size and composition to trace element chemistry, Applied Geochemistry, vol.2, pp.437-451, 1987.

J. Hyland, L. Balthis, I. Karakassis, P. Magni, A. Petrov et al., Organic carbon content of sediments as an indicator of stress in the marine benthos, Marine Ecology Progress Series, vol.295, pp.91-103, 2005.

A. Jarvis, H. I. Reuter, A. Nelson, and E. Guevara, Hole-filled SRTM for the globe Version 4, available from the CGIAR-CSI SRTM 90m Database, 2008.

F. J. Jorissen, The distribution of benthic foraminifera in the Adriatic Sea, Marine Micropaleontology, vol.12, pp.21-48, 1987.

R. V. Tyson, G. J. Van-der-zwaan, and F. J. Jorissen, Biofacial patterns in river-induced shelf anoxia, Models. SEPM (Society for Sedimentary Geology, vol.58, pp.65-82, 1991.

S. G. Wakeham, E. A. Canuel, E. J. Lerberg, P. Mason, T. P. Sampere et al., Partitioning of organic matter in continental margin sediments among density fractions, Marine Chemistry, vol.115, pp.211-225, 2009.

C. E. Weaver, Clays, muds, and shales. Developments in sedimentology, Distributors for the U.S. and Canada, vol.819, 1989.

G. J. Weltje, End-member modeling of compositional data: Numericalstatistical algorithms for solving the explicit mixing problem, Mathematical Geology, vol.29, pp.503-549, 1997.

C. K. Wentworth, A Scale of Grade and Class Terms for Clastic Sediments, The Journal of Geology, vol.30, pp.377-392, 1922.

M. J. Wilson, The origin and formation of clay minerals in soils: past, present and future perspectives, Clay Minerals, vol.34, pp.7-25, 1999.

J. Xiao, Z. Chang, J. Fan, L. Zhou, D. Zhai et al., The link between grain-size components and depositional processes in a modern clastic lake: Grain-size components of Hulun Lake sediments, Sedimentology, vol.59, pp.1050-1062, 2012.

E. Alve, A. Lepland, J. Magnusson, and K. Backer-owe, Monitoring strategies for re-establishment of ecological reference conditions: Possibilities and limitations, Marine Pollution Bulletin, vol.59, pp.297-310, 2009.

E. Alve, S. Korsun, J. Schönfeld, N. Dijkstra, E. Golikova et al., Foram-AMBI: A sensitivity index based on benthic foraminiferal faunas from North-East Atlantic and Arctic fjords, continental shelves and slopes, Marine Micropaleontology, vol.122, pp.1-12, 2016.

C. Barras and F. J. Jorissen, Étude des faunes de foraminifères benthiques de la côte méditerranéenne française : mise en place d'un nouvel indice biotique dans le cadre de Directive Cadre Eau -Campagne DCE, Laboratoire des Bio-Indicateurs Actuels et Fossiles (BIAF) Université d'Angers, 2009.

M. J. Bock and L. M. Mayer, Mesodensity organo-clay associations in a near-shore sediment, Marine Geology, vol.163, pp.65-75, 2000.

A. Borja, I. Muxika, and J. Franco, The application of a Marine Biotic Index to different impact sources affecting soft-bottom benthic communities along European coasts, Marine Pollution Bulletin, vol.46, pp.835-845, 2003.

Á. Borja and I. Muxika, Guidelines for the use of AMBI (AZTI's Marine Biotic Index) in the assessment of the benthic ecological quality, Marine Pollution Bulletin, vol.50, pp.787-789, 2005.

Á. Borja, D. M. Dauer, and A. Grémare, The importance of setting targets and reference conditions in assessing marine ecosystem quality, Ecological Indicators, vol.12, pp.1-7, 2012.

Á. Borja, J. Mader, and I. Muxika, Instructions for the use of the AMBI index software (Version 5.0), Revista de Investigación Marina, vol.19, pp.71-82, 2012.

V. M. Bouchet, E. Alve, B. Rygg, and R. J. Telford, Benthic foraminifera provide a promising tool for ecological quality assessment of marine waters, Ecological Indicators, vol.23, pp.66-75, 2012.

V. M. Bouchet, E. Goberville, and F. Frontalini, Benthic foraminifera to assess Ecological Quality Statuses in Italian transitional waters, Ecological Indicators, vol.84, pp.130-139, 2018.

A. Chao and S. Tsung-jen, Nonparametric estimation of Shannon's index of diversity when there are unseen species in sample, Environmental and Ecological Statistics, vol.10, pp.429-443, 2003.

M. D. Dimiza, M. V. Triantaphyllou, O. Koukousioura, P. Hallock, N. Simboura et al., The Foram Stress Index: A new tool for environmental assessment of soft-bottom environments using benthic foraminifera. A case study from the Saronikos Gulf, Ecological Indicators, vol.60, pp.611-621, 2016.

J. K. Dolven, E. Alve, B. Rygg, and J. Magnusson, Defining past ecological status and in situ reference conditions using benthic foraminifera: A case study from the Oslofjord, Norway. Ecological Indicators, vol.29, pp.219-233, 2013.

L. Ferraro, I. Alberico, F. Lirer, and M. Vallefuoco, Distribution of benthic foraminifera from the southern Tyrrhenian continental shelf, 2012.

R. Lincei, , vol.23, pp.103-119

F. Francescangeli, E. Armynot-du-chatelet, G. Billon, A. Trentesaux, and V. M. Bouchet, Palaeo-ecological quality status based on foraminifera of Boulogne-sur-Mer harbour (Pas-de-Calais, Northeastern France) over the last 200 years, Marine Environmental Research, vol.117, pp.32-43, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01388708

D. J. Gillett, S. B. Weisberg, T. Grayson, A. Hamilton, V. Hansen et al., Effect of ecological group classification schemes on performance of the AMBI benthic index in US coastal waters, Ecological Indicators, vol.50, pp.99-107, 2015.

S. Gobert, S. Sartoretto, V. Rico-raimondino, B. Andral, A. Chery et al., Assessment of the ecological status of Mediterranean French coastal waters as required by the Water Framework Directive using the Posidonia oceanica Rapid Easy Index: PREI, Marine Pollution Bulletin, vol.58, pp.1727-1733, 2009.

A. Grémare, C. Labrune, E. Vanden-berghe, J. Amouroux, G. Bachelet et al., Comparison of the performances of two biotic indices based on the MacroBen database, Marine Ecology Progress Series, vol.382, pp.297-311, 2009.

J. Hausser and K. Strimmer, Estimation of Entropy, Mutual Information and Related Quantities, 2014.

J. I. Hedges, R. G. Keil, and G. L. Cowie, Sedimentary diagenesis: organic perspectives with inorganic overlays, Chemical Geology, vol.107, pp.487-492, 1993.

M. O. Hill, Diversity and Evenness: A Unifying Notation and Its Consequences, Ecology, vol.54, pp.427-432, 1973.

A. Jarvis, H. I. Reuter, A. Nelson, and E. Guevara, Hole-filled SRTM for the globe Version 4, available from the CGIAR-CSI SRTM 90m Database, 2008.

F. J. Jorissen, The distribution of benthic foraminifera in the Adriatic Sea, Marine Micropaleontology, vol.12, pp.21-48, 1987.

F. J. Jorissen, Benthic foraminifera from the Adriatic Sea: principles of phenotypic variation, vol.174, 1988.

F. J. Jorissen, H. De-stigter, and J. G. Widmark, A conceptual model explaining benthic foraminiferal microhabitats, Marine Micropaleontology, vol.26, pp.3-15, 1995.

F. J. Jorissen, Benthic foraminiferal microhabitats below the sediment-water interface, Modern Foraminifera, pp.161-179, 1999.

F. J. Jorissen, M. P. Nardelli, A. Almogi-labin, C. Barras, L. Bergamin et al., Developing Foram-AMBI for biomonitoring in the Mediterranean: Species assignments to ecological categories, Marine Micropaleontology, vol.140, pp.33-45, 2018.

, Marine Information Service, EMODnet Digital Bathymetry (DTM), 2016.

B. Martínez-crego, T. Alcoverro, and J. Romero, Biotic indices for assessing the status of coastal waters: a review of strengths and weaknesses, Journal of Environmental Monitoring, vol.12, p.1013, 2010.

I. Muxika, Á. Borja, and J. Bald, Using historical data, expert judgement and multivariate analysis in assessing reference conditions and benthic ecological status, according to the European Water Framework Directive, Marine Pollution Bulletin, vol.55, pp.16-29, 2007.

H. C. Nilsson and R. Rosenberg, Succession in marine benthic habitats and fauna in response to oxygen deficiency: analysed by sediment profileimaging and by grab samples, Marine Ecology Progress Series, vol.197, pp.139-149, 2000.

B. Parent, C. Barras, J. , and F. , An optimised method to concentrate living (Rose Bengal-stained) benthic foraminifera from sandy sediments by high density liquids, Marine Micropaleontology, vol.144, pp.1-13, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01877332

T. H. Pearson and R. Rosenberg, Macrobenthic succession in relation to organic enrichment and pollution of the marine environment, Oceanography and Marine Biology -An Annual Review, vol.16, pp.229-311, 1978.

A. Puente and R. J. Diaz, Response of benthos to ocean outfall discharges: does a general pattern exist?, Marine Pollution Bulletin, vol.101, pp.174-181, 2015.

B. P. Robertson, C. Savage, J. P. Gardner, B. M. Robertson, and L. M. Stevens, Optimising a widely-used coastal health index through quantitative ecological group classifications and associated thresholds, Ecological Indicators, vol.69, pp.595-605, 2016.

E. Romano, L. Bergamin, A. Ausili, G. Pierfranceschi, C. Maggi et al., ) example from the Norwegian Skagerrak coast, Ecological Indicators, vol.96, pp.107-115, 2009.

A. Oceanologie, DONIA EXPERT : Cartographie détaillée des habitats marins -Données consultées le 03/2019 sur la plateforme de surveillance MEDTRIX, 2019.

S. Avnaim-katav, O. Hyams-kaphzan, Y. Milker, and A. Almogi-labin, Bathymetric zonation of modern shelf benthic foraminifera in the Levantine Basin, eastern Mediterranean Sea, Journal of Sea Research, vol.99, pp.97-106, 2015.

D. Basso and S. Spezzaferri, The distribution of living (stained) benthic foraminifera in Iskendrerum Bay (Eastern Turkey): a statistical approach, vol.39, pp.359-379, 2000.

D. Basso, Carbonate production by calcareous red algae and global change, Geodiversitas, vol.34, pp.13-33, 2012.

D. Basso, L. Babbini, S. Kaleb, V. A. Bracchi, and A. Falace, Monitoring deep Mediterranean rhodolith beds: Monitoring deep Mediterranean rhodolith beds. Aquatic Conservation: Marine and Freshwater Ecosystems, vol.26, pp.549-561, 2016.

V. M. Bouchet, E. Alve, B. Rygg, and R. J. Telford, Benthic foraminifera provide a promising tool for ecological quality assessment of marine waters, Ecological Indicators, vol.23, pp.66-75, 2012.

V. M. Bouchet, E. Goberville, and F. Frontalini, Benthic foraminifera to assess Ecological Quality Statuses in Italian transitional waters, Ecological Indicators, vol.84, pp.130-139, 2018.

J. R. Bray, C. , and J. T. , An Ordination of the Upland Forest Communities of Southern Wisconsin, Ecological Monographs, vol.27, pp.325-349, 1957.

C. Buosi, E. Armynot-du-châtelet, and A. Cherchi, Benthic Foraminifera Assemblages in the Current-Dominated Strait of Bonifacio (Mediterranean Sea), The Journal of Foraminiferal Research, vol.42, pp.39-55, 2012.

F. Cesbron, E. Geslin, F. J. Jorissen, M. L. Delgard, L. Charrieau et al., Vertical distribution and respiration rates of benthic foraminifera: Contribution to aerobic remineralization in intertidal mudflats covered by Zostera noltei meadows, Estuarine, Coastal and Shelf Science, vol.179, pp.23-38, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01453027

C. Chende?, M. A. Kaminski, S. Filipescu, A. E. Aksu, Y. et al., The response of Modern Benthic Foraminiferal assemblages to water-mass properties along the southern shelf of the Marmara Sea, Acta Palaeontologica Romaniae, vol.4, pp.69-80, 2004.

, /60/CE du Parlement Européen et du Conseil du 23 octobre 2000 établissant un cadre pour une politique communautaire dans le domaine de l'eau, Journal officiel des Communautés, pp.1-72, 2000.

H. C. De-stigter, F. J. Jorissen, and G. J. Van-der-zwaan, Bathymetric Distribution and Microhabitat Partitioning of Live, 1998.

, Benthic Foraminifera Along a Shelf to Bathyal Transect in the Southern Adriatic Sea, Journal of Foraminiferal Research, vol.38, pp.40-65

J. Debenay and F. Redois, Distribution of the twenty seven dominant species of shelf benthic foraminifers on the continental shelf, north of Dakar (Senegal), Marine Micropaleontology, vol.29, pp.237-255, 1997.

P. Diz, G. Francés, and G. Rosón, Effects of contrasting upwellingdownwelling on benthic foraminiferal distribution in the Ría de Vigo (NW Spain), Journal of Marine Systems, vol.60, pp.1-18, 2006.

P. Diz and G. Francés, Distribution of live benthic foraminifera in the Ría de Vigo, Marine Micropaleontology, vol.66, pp.165-191, 2008.

S. Donnici and R. Serandrei-barbero, The benthic foraminiferal communities of the northern Adriatic continental shelf, Marine Micropaleontology, vol.44, pp.92-123, 2002.

S. Ernst, Experimental effects of an organic matter pulse and oxygen depletion on a benthic foraminiferal shelf community, The Journal of Foraminiferal Research, vol.35, pp.177-197, 2005.

L. Ferraro, I. Alberico, F. Lirer, and M. Vallefuoco, Distribution of benthic foraminifera from the southern Tyrrhenian continental shelf, 2012.

R. Lincei, , vol.23, pp.103-119

S. P. Ferraro, F. A. Cole, W. A. Deben, and R. C. Swartz, Power-Cost Efficiency of Eight Macrobenthic Sampling Schemes in Puget Sound, Journal canadien des sciences halieutiques et aquatiques, vol.46, pp.2157-2165, 1989.

F. Frontalini, F. Semprucci, R. Coccioni, M. Balsamo, P. Bittoni et al., On the quantitative distribution and community structure of the meio and macrofaunal communities in the coastal area of the Central Adriatic Sea (Italy), Environmental Monitoring and Assessment, vol.180, pp.325-344, 2011.

A. Goineau, C. Fontanier, F. J. Jorissen, B. Lansard, R. Buscail et al., Live (stained) benthic foraminifera from the Rhône prodelta, Journal of Sea Research, vol.65, pp.58-75, 2011.

A. Goineau, C. Fontanier, F. Jorissen, R. Buscail, P. Kerhervé et al., Temporal variability of live (stained) benthic foraminiferal faunas in a river-dominated shelf &ndash, 2012.

, Biogeosciences, vol.9, pp.1367-1388

H. Got, A. , and J. C. , The Holocene sedimentation on the Gulf of Lions margin: a quantitative approach, Continental Shelf Research, vol.10, pp.841-855, 1990.

J. Hohenegger, W. E. Piller, and C. Baal, Horizontal and vertical spatial microdistribution of foraminifers in the shallow subtidal Gulf of Trieste, northern Adriatic Sea, The Journal of Foraminiferal Research, vol.23, pp.79-101, 1993.

F. Holon, N. Mouquet, P. Boissery, M. Bouchoucha, G. Delaruelle et al., Fine-Scale Cartography of Human Impacts along French Mediterranean Coasts: A Relevant Map for the Management of Marine Ecosystems, PLOS ONE, vol.10, p.135473, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01921178

S. H. Hurlbert, The Nonconcept of Species Diversity: A Critique and Alternative Parameters, Ecology, vol.52, pp.577-586, 1971.

O. Hyams-kaphzan, A. Almogi-labin, D. Sivan, and C. Benjamini, Benthic foraminifera assemblage change along the southeastern Mediterranean inner shelf due to fall-off of Nile-derived siliciclastics, Neues Jahrbuch für Geologie und Paläontologie -Abhandlungen, vol.248, pp.315-344, 2008.

O. Hyams-kaphzan, A. Almogi-labin, C. Benjamini, and B. Herut, Natural oligotrophy vs. pollution-induced eutrophy on the SE Mediterranean shallow shelf (Israel): Environmental parameters and benthic foraminifera, Marine Pollution Bulletin, vol.58, pp.1888-1902, 2009.

O. Hyams-kaphzan, H. Lubinevsky, O. Crouvi, Y. Harlavan, B. Herut et al., Live and dead deep-sea benthic foraminiferal macrofauna of the Levantine basin (SE Mediterranean) and their ecological characteristics, Deep Sea Research Part I: Oceanographic Research Papers, vol.136, pp.72-83, 2018.

A. Jarvis, H. I. Reuter, A. Nelson, and E. Guevara, Hole-filled SRTM for the globe Version 4, available from the CGIAR-CSI SRTM 90m Database, 2008.

F. J. Jorissen, The distribution of benthic foraminifera in the Adriatic Sea, Marine Micropaleontology, vol.12, pp.21-48, 1987.

F. J. Jorissen, H. De-stigter, and J. G. Widmark, A conceptual model explaining benthic foraminiferal microhabitats, Marine Micropaleontology, vol.26, pp.3-15, 1995.

F. J. Jorissen, Benthic foraminiferal microhabitats below the sediment-water interface, Modern Foraminifera, pp.161-179, 1999.

K. A. Koho, R. García, H. C. De-stigter, E. Epping, E. Koning et al., Sedimentary labile organic carbon and pore water redox control on species distribution of benthic foraminifera: A case study from Lisbon-Setúbal Canyon (southern Portugal), Progress in Oceanography, vol.79, pp.55-82, 2008.

C. Labrune, J. M. Amouroux, R. Sarda, E. Dutrieux, S. Thorin et al., Characterization of the ecological quality of the coastal Gulf of Lions (NW Mediterranean). A comparative approach based on three biotic indices, Marine Pollution Bulletin, vol.52, pp.34-47, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00089680

C. Labrune, A. Grémare, J. Amouroux, R. Sardá, J. Gil et al., Structure and diversity of shallow soft-bottom benthic macrofauna in the Gulf of Lions, Helgoland Marine Research, vol.62, pp.201-214, 2008.

U. Lie, A Quantitative Study in Puget Sound, Fiskeridirektoratets skrifter, vol.14, pp.229-556, 1963.

A. R. Longhurst, The Sampling Problem in Benthic Ecology, Proceedings of the New Zealand Ecological Society, pp.8-12, 1958.

, Marine Information Service, EMODnet Digital Bathymetry (DTM), 2016.

M. V. Martins, F. Silva, L. L. Laut, F. Frontalini, I. M. Clemente et al., Response of Benthic Foraminifera to Organic Matter Quantity and Quality and Bioavailable Concentrations of Metals in Aveiro Lagoon (Portugal), PLOS ONE, vol.10, p.118077, 2015.

I. Mendes, R. Gonzalez, J. M. Dias, F. Lobo, and V. Martins, Factors influencing recent benthic foraminifera distribution on the Guadiana shelf (Southwestern Iberia), Marine Micropaleontology, vol.51, pp.171-192, 2004.

F. Micheli, B. S. Halpern, S. Walbridge, S. Ciriaco, F. Ferretti et al., Cumulative Human Impacts on Mediterranean and Black Sea Marine Ecosystems: Assessing Current Pressures and Opportunities, PLoS ONE, vol.8, p.79889, 2013.

Y. Milker, G. Schmiedl, C. Betzler, M. Römer, D. Jaramillo-vogel et al., Distribution of recent benthic foraminifera in shelf carbonate environments of the Western Mediterranean Sea, Marine Micropaleontology, vol.73, pp.207-225, 2009.

M. Mojtahid, F. J. Jorissen, B. Lansard, C. Fontanier, B. Bombled et al., Spatial distribution of live benthic foraminifera in the Rhône prodelta: Faunal response to a continental-marine organic matter gradient, Marine Micropaleontology, vol.70, pp.177-200, 2009.

J. W. Murray, On the Foraminiferida of the Plymouth region, Journal of the Marine Biological Association of the United Kingdom, vol.45, p.481, 1965.

J. W. Murray, Foraminifers of the Western Approaches to the English Channel, Micropaleontology, vol.16, p.471, 1970.

J. W. Murray, E. Alve, and A. Cundy, The origin of modern agglutinated foraminiferal assemblages: evidence from a stratified fjord, Estuarine, Coastal and Shelf Science, vol.58, pp.677-697, 2003.

J. W. Murray, A. , and E. , The distribution of agglutinated foraminifera in NW European seas: Baseline data for the interpretation of fossil assemblages, Palaeontologia Electronica, vol.14, p.41, 2011.

J. Oksanen, F. G. Blanchet, M. Friendly, R. Kindt, P. Legendre et al., vegan: Community Ecology Package, 2017.

M. Phipps, F. Jorissen, A. Pusceddu, S. Bianchelli, D. Stigter et al., Live Benthic Foraminiferal Faunas Along a Bathymetrical Transect (282-4987 m) on the Portuguese Margin, vol.42, pp.66-81, 2012.

E. C. Pielou, The measurement of diversity in different types of biological collections, Journal of theoretical biology, vol.13, pp.131-144, 1966.

A. Puente and R. J. Diaz, Response of benthos to ocean outfall discharges: does a general pattern exist?, Marine Pollution Bulletin, vol.101, pp.174-181, 2015.

. R-core-team, R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, 2017.

R. Rosenberg, Marine benthic faunal successinal stages and related sedimentary activity, Scientia Marina, vol.65, pp.107-119, 2001.

V. Roussiez, J. Aloisi, A. Monaco, L. , and W. , Early muddy deposits along the Gulf of Lions shoreline: A key for a better understanding of land-to-sea transfer of sediments and associated pollutant fluxes, Marine Geology, pp.345-358, 2005.

J. Schönfeld, E. Alve, E. Geslin, F. Jorissen, S. Korsun et al., The FOBIMO (FOraminiferal BIo-MOnitoring) initiative-Towards a standardised protocol for soft-bottom benthic foraminiferal monitoring studies, Marine Micropaleontology, pp.94-95, 2012.

C. E. Shannon, A mathematical theory of communication, The Bell System Technical Journal, vol.27, pp.379-423, 1948.

J. H. Ward, Hierarchical Grouping to Optimize an Objective Function, Journal of the American Statistical Association, vol.58, p.236, 1963.

E. Alve, Benthic Foraminiferal responses to estuarine pollution: a review, Journal of Foraminiferal Research, vol.25, pp.190-2003, 1995.

R. N. Arieli, A. Almogi-labin, S. Abramovich, and B. Herut, The effect of thermal pollution on benthic foraminiferal assemblages in the Mediterranean shoreface adjacent to Hadera power plant (Israel), Marine Pollution Bulletin, vol.62, pp.1002-1012, 2011.

Y. Azov, Eastern Mediterranean-a marine desert, Marine Pollution Bulletin, vol.23, pp.225-232, 1991.

D. M. Barmawidjaja, G. J. Van-der-zwaan, F. J. Jorissen, and S. Puskaric, 150 years of eutrophication in the northern Adriatic Sea: Evidence from a benthic foraminiferal record, Marine Geology, vol.122, pp.367-384, 1995.

Á. Borja, D. M. Dauer, and A. Grémare, The importance of setting targets and reference conditions in assessing marine ecosystem quality, Ecological Indicators, vol.12, pp.1-7, 2012.

V. M. Bouchet, E. Alve, B. Rygg, and R. J. Telford, Benthic foraminifera provide a promising tool for ecological quality assessment of marine waters, Ecological Indicators, vol.23, pp.66-75, 2012.

J. Dauvin, G. Bellan, and D. Bellan-santini, Benthic indicators: From subjectivity to objectivity -Where is the line?, Marine Pollution Bulletin, vol.60, pp.947-953, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00664358

P. Diz, G. Francés, and G. Rosón, Effects of contrasting upwellingdownwelling on benthic foraminiferal distribution in the Ría de Vigo (NW Spain), Journal of Marine Systems, vol.60, pp.1-18, 2006.

P. Diz and G. Francés, Distribution of live benthic foraminifera in the Ría de Vigo, Marine Micropaleontology, vol.66, pp.165-191, 2008.

I. Duijnstee, I. De-lugt, H. Vonk-noordegraaf, and B. Van-der-zwaan, Temporal variability of foraminiferal densities in the northern Adriatic Sea, Marine Micropaleontology, vol.50, pp.125-148, 2004.

I. A. Duijnstee, S. R. Ernst, and G. J. Van-der-zwaan, Effect of anoxia on the vertical migration of benthic foraminifera, Marine Ecology Progress Series, vol.246, pp.85-94, 2003.

S. Ernst, I. Duijnstee, and B. Van-der-zwaan, The dynamics of the benthic foraminiferal microhabitat: recovery after experimental disturbance, Marine Micropaleontology, vol.46, pp.343-361, 2002.

S. Ernst, Experimental effects of an organic matter pulse and oxygen depletion on a benthic foraminiferal shelf community, The Journal of Foraminiferal Research, vol.35, pp.177-197, 2005.

F. Frontalini and R. Coccioni, Benthic foraminifera as bioindicators of pollution: A review of Italian research over the last three decades, vol.54, pp.115-127, 2011.

E. Garzanti, S. Andò, M. Padoan, G. Vezzoli, and A. Kammar, The modern Nile sediment system: Processes and products, Quaternary Science Reviews, vol.130, pp.9-56, 2015.

F. Gelman, R. Binstock, and L. Halicz, Application of the Walkley-Black titration for the organic carbon quantification in organic rich sedimentary rocks, Fuel, vol.96, pp.608-610, 2012.

M. Glémarec and C. Hily, Perturbations apportées à la macrofaune benthique de la baie de Concarneau par les effluents urbains et portuaires, 1981.

, Acta Oecologica Oecologia Applicata, vol.2, pp.139-150

A. Goineau, C. Fontanier, F. J. Jorissen, B. Lansard, R. Buscail et al., Live (stained) benthic foraminifera from the Rhône prodelta, Journal of Sea Research, vol.65, pp.58-75, 2011.

J. Grall and M. Glémarec, Using biotic indices to estimate macrobenthic community perturbations in the Bay of Brest, Estuarine, Coastal and Shelf Science, vol.44, pp.43-53, 1997.

J. S. Gray and T. H. Pearson, Objective Selection of Sensitive Species Indicative of Pollution-Induced Change in Benthic Communities. I. Comparative Methodology, Marine Ecology Progress Series, vol.9, pp.111-119, 1982.

P. Springer-netherlands, . Beach, U. S. Fl, O. Hyams-kaphzan, A. Almogi-labin et al., Benthic foraminifera assemblage change along the southeastern Mediterranean inner shelf due to fall-off of Nile-derived siliciclastics, Neues Jahrbuch für Geologie und Paläontologie -Abhandlungen, vol.248, pp.315-344, 2008.

F. J. Jorissen, D. M. Barmawidjaja, S. Puskaric, and G. J. Van-der-zwaan, Vertical distribution of benthic foraminifera in the northern Adriatic Sea: The relation with the organic flux, Marine Micropaleontology, vol.19, pp.131-146, 1992.

F. J. Jorissen, H. De-stigter, and J. G. Widmark, A conceptual model explaining benthic foraminiferal microhabitats, Marine Micropaleontology, vol.26, pp.3-15, 1995.

F. J. Jorissen, Benthic foraminiferal microhabitats below the sediment-water interface, Modern Foraminifera, pp.161-179, 1999.

F. J. Jorissen, E. Bicchi, G. Duchemin, J. Durrieu, F. Galgani et al., Impact of oil-based drill mud disposal on benthic foraminiferal assemblages on the continental margin off Angola, Deep-Sea Research Part II: Topical Studies in Oceanography, vol.56, pp.2270-2291, 2009.

N. Kress, B. Herut, and B. S. Galil, Sewage sludge impact on sediment quality and benthic assemblages off the Mediterranean coast of Israel-a long-term study, Marine Environmental Research, vol.57, pp.213-233, 2004.

N. Kress, E. Shoham-frider, and B. S. Galil, Twenty two years of sewage sludge marine disposal monitoring in the Eastern Mediterranean Sea: Impact on sediment quality and infauna and the response to load reduction, Marine Pollution Bulletin, vol.110, pp.99-111, 2016.

P. Lazzari, C. Solidoro, V. Ibello, S. Salon, A. Teruzzi et al., Seasonal and inter-annual variability of plankton chlorophyll and primary production in the Mediterranean Sea: a modelling approach, Biogeosciences, vol.9, pp.217-233, 2012.

S. Lê, J. Josse, and F. Husson, FactoMineR: A Package for Multivariate Analysis, Journal of Statistical Software, vol.25, pp.1-18, 2008.

K. Leonardsson, M. Blomqvist, M. Magnusson, A. Wikström, and R. Rosenberg, Calculation of species sensitivity values and their precision in marine benthic faunal quality indices, Marine Pollution Bulletin, vol.93, pp.94-102, 2015.

M. Mojtahid, F. J. Jorissen, J. Durrieu, F. Galgani, H. Howa et al., Benthic foraminifera as bio-indicators of drill cutting disposal in tropical east Atlantic outer shelf environments, Marine Micropaleontology, vol.61, pp.58-75, 2006.

M. Mojtahid, F. J. Jorissen, and T. H. Pearson, Comparison of benthic foraminiferal and macrofaunal responses to organic pollution in the Firth of Clyde (Scotland), Marine Pollution Bulletin, vol.56, pp.42-76, 2008.

M. Mojtahid, F. Jorissen, B. Lansard, and C. Fontanier, Microhabitat selection of benthic foraminifera in sediments off the Rhône river mouth (NW Mediterranean), Journal of Foraminiferal Research, vol.40, pp.231-246, 2010.

I. Muxika, Á. Borja, and W. Bonne, The suitability of the marine biotic index (AMBI) to new impact sources along European coasts, Ecological Indicators, vol.5, pp.19-31, 2005.

J. Oksanen, F. G. Blanchet, M. Friendly, R. Kindt, P. Legendre et al., vegan: Community Ecology Package, 2017.

S. Pinedo, E. Jordana, and E. Ballesteros, A critical analysis on the response of macroinvertebrate communities along disturbance gradients: description of MEDOCC (MEDiterranean OCCidental) index, Marine Ecology, vol.36, pp.141-154, 2015.

R. Pinto, J. Patrício, A. Baeta, B. D. Fath, J. M. Neto et al., Review and evaluation of estuarine biotic indices to assess benthic condition, Ecological Indicators, vol.9, pp.1-25, 2009.

A. Puente and R. J. Diaz, Response of benthos to ocean outfall discharges: does a general pattern exist?, Marine Pollution Bulletin, vol.101, pp.174-181, 2015.

. R-core-team, R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, 2017.

R. Rosenberg, Marine benthic faunal successinal stages and related sedimentary activity, Scientia Marina, vol.65, pp.107-119, 2001.

A. Sabbatini, S. Bonatto, S. Bianchelli, A. Pusceddu, R. Danovaro et al., Foraminiferal assemblages and trophic state in coastal sediments of the Adriatic Sea, Journal of Marine Systems, pp.163-174, 2012.

D. B. Scott, R. Tobin, M. Williamson, F. S. Medioli, J. S. Latimer et al., Pollution monitoring in two North American estuaries: historical reconstructions using benthic foraminifera, Journal of Foraminiferal Research, vol.35, pp.65-82, 2005.

C. E. Shannon, A mathematical theory of communication, The Bell System Technical Journal, vol.27, pp.379-423, 1948.

N. Simboura and A. Zenetos, Benthic indicators to use in Ecological Quality classification of Mediterranean soft bottom marine ecosystems, including a new Biotic Index, Mediterranean Marine Science, vol.3, p.77, 2002.

R. Tadir, C. Benjamini, A. Almogi-labin, O. Hyams-kaphzan, G. J. Van-der-zwaan et al., Temporal trends in live foraminiferal assemblages near a pollution outfall on the Levant shelf, Marine Pollution Bulletin, vol.117, pp.65-82, 1991.

V. Yanko, J. Kronfeld, and A. Flexer, Response of benthic Foraminifera to various pollution sources; implications for pollution monitoring, The Journal of Foraminiferal Research, vol.24, pp.1-17, 1994.

, Assignations écologiques d'espèces 7.3.1. Cas litigieux d'assignation d'espèces

. Nous, . Tsi-med, and . Le-foram, AMBI sur deux zones d'études très distinctes. Les côtes méditerranéennes françaises (Chapitre 5), où l'enrichissement en matière organique, qu'il soit d'origine naturelle ou anthropique, est diffus, et un site de rejet ponctuel d'une station d'épuration sur les côtes israéliennes

, Perspectives : apport des traits fonctionnels

. Poff, Ces traits fonctionnels peuvent être le micro-habitat, le régime alimentaire, l'étendue de tolérance au taux d'oxygène, etc. Ces caractères peuvent être liés à une pression ou non. Le gain, la perte ou les modifications de ces fonctions sont indicateurs de la communauté seule, 2006.

, Dans une optique de simplification, l'assignation des espèces aux EG se fait sur un trait fonctionnel particulier, la tolérance aux enrichissements en matière organique

. Cependant-;-jorissen, Leptohalysis scotti et Caronia silvestrii réagissent fortement et positivement aux enrichissements en matière organique, correspondant à un fort opportunisme. Cependant, Caronia silvestrii semble beaucoup plus tolérante à de faibles concentrations en oxygène que Leptohalysis scotti. Si l'on se réfère au modèle TROX, les deux paramètres principaux qui expliquent la micro-distribution des foraminifères dans le sédiment sont la matière organique et l'oxygène, Jorissen, 1995.

. D'autre-part-;-risgaard-petersen, ces dernières années, des études se focalisant sur le métabolisme des foraminifères ont permis de mettre en évidence des capacités spécifiques à certaines espèces de foraminifères. Par exemple, plusieurs espèces sont capables de dénitrifier afin de vivre dans des conditions anoxiques, 2006.

. Piña-ochoa, Resting stage in benthic foraminiferal propagules: a key feature for dispersal? Evidence from two shallow-water species, leur permettant ainsi d'être un acteur majeur dans les cycles biogéochimiques en conditions anoxiques. Néanmoins, d'autres espèces, non-dénitrifiantes, ont également été observées vivantes dans des environnements anoxiques, laissant la porte ouverte à d'autres adaptations métaboliques, comme par Références Alve, vol.21, pp.95-96, 2002.

É. Armynot-du-châtelet and J. Debenay, The anthropogenic impact on the western French coasts as revealed by foraminifera: A review, vol.53, pp.129-137, 2010.

D. Basso and S. Spezzaferri, The distribution of living (stained) benthic foraminifera in Iskendrerum Bay (Eastern Turkey): a statistical approach, vol.39, pp.359-379, 2000.

T. S. Bianchi, X. Cui, N. E. Blair, D. J. Burdige, T. I. Eglinton et al., Centers of organic carbon burial and oxidation at the land-ocean interface, Organic Geochemistry, vol.115, pp.138-155, 2018.

C. Bird, M. Schweizer, A. Roberts, W. E. Austin, K. L. Knudsen et al., The genetic diversity, morphology, biogeography, and taxonomic designations of Ammonia (Foraminifera) in the Northeast Atlantic, Marine Micropaleontology, p.0377839818300860, 2019.

Á. Borja and I. Muxika, Guidelines for the use of AMBI (AZTI's Marine Biotic Index) in the assessment of the benthic ecological quality, Marine Pollution Bulletin, vol.50, pp.787-789, 2005.

Á. Borja, A. Ranasinghe, and S. B. Weisberg, Assessing ecological integrity in marine waters, using multiple indices and ecosystem components: Challenges for the future, Marine Pollution Bulletin, vol.59, pp.1-4, 2009.

Á. Borja, D. M. Dauer, and A. Grémare, The importance of setting targets and reference conditions in assessing marine ecosystem quality, Ecological Indicators, vol.12, pp.1-7, 2012.

Á. Borja, M. Elliott, J. H. Andersen, A. C. Cardoso, J. Carstensen et al., Good Environmental Status of marine ecosystems: What is it and how do we know when we have attained it?, Marine Pollution Bulletin, vol.76, pp.16-27, 2013.

V. M. Bouchet, E. Alve, B. Rygg, and R. J. Telford, Benthic foraminifera provide a promising tool for ecological quality assessment of marine waters, Ecological Indicators, vol.23, pp.66-75, 2012.

V. M. Bouchet, E. Goberville, and F. Frontalini, Benthic foraminifera to assess Ecological Quality Statuses in Italian transitional waters, Ecological Indicators, vol.84, pp.130-139, 2018.

L. Carvalho, E. B. Mackay, A. C. Cardoso, A. Baattrup-pedersen, S. Birk et al., Protecting and restoring Europe's waters: An analysis of the future development needs of the Water Framework Directive, Science of The Total Environment, vol.658, pp.1228-1238, 2019.

L. M. Charrieau, H. L. Filipsson, K. Ljung, M. Chierici, K. L. Knudsen et al., The effects of multiple stressors on the distribution of coastal benthic foraminifera: A case study from the Skagerrak-Baltic Sea region, Marine Micropaleontology, vol.139, pp.42-56, 2018.

, /60/CE du Parlement Européen et du Conseil du 23 octobre 2000 établissant un cadre pour une politique communautaire dans le domaine de l'eau, Journal officiel des Communautés, pp.1-72, 2000.

K. F. Darling, M. Schweizer, K. L. Knudsen, K. M. Evans, C. Bird et al., The genetic diversity, phylogeography and morphology of Elphidiidae (Foraminifera) in the Northeast Atlantic, Marine Micropaleontology, vol.129, pp.1-23, 2016.

J. C. Dauvin and T. Ruellet, Polychaete/amphipod ratio revisited, Marine Pollution Bulletin, vol.55, pp.215-224, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00481551

J. Debenay, E. Tsakiridis, R. Soulard, and H. Grossel, ): the influence of pollution, Factors determining the distribution of foraminiferal assemblages in Port Joinville Harbor, vol.43, pp.75-118, 2001.

K. Deiner, H. M. Bik, E. Mächler, M. Seymour, A. Lacoursière-roussel et al., Environmental DNA metabarcoding: Transforming how we survey animal and plant communities, Molecular Ecology, vol.26, pp.5872-5895, 2017.

M. Denoyelle, E. Geslin, F. J. Jorissen, L. Cazes, and F. Galgani, Innovative use of foraminifera in ecotoxicology: A marine chronic bioassay for testing potential toxicity of drilling muds, Ecological Indicators, vol.12, pp.17-25, 2012.

I. Duijnstee, I. De-lugt, H. Vonk-noordegraaf, and B. Van-der-zwaan, Temporal variability of foraminiferal densities in the northern Adriatic Sea, Marine Micropaleontology, vol.50, pp.125-148, 2004.

S. Ernst, I. Duijnstee, and B. Van-der-zwaan, The dynamics of the benthic foraminiferal microhabitat: recovery after experimental disturbance, Marine Micropaleontology, vol.46, pp.343-361, 2002.

S. Ernst, Experimental effects of an organic matter pulse and oxygen depletion on a benthic foraminiferal shelf community, The Journal of Foraminiferal Research, vol.35, pp.177-197, 2005.

L. Ferraro, M. Sprovieri, I. Alberico, F. Lirer, L. Prevedello et al., Benthic foraminifera and heavy metals distribution: A case study from the Naples Harbour, Environmental Pollution, vol.142, pp.274-287, 2006.

F. Frontalini and R. Coccioni, Benthic foraminifera for heavy metal pollution monitoring: A case study from the central Adriatic Sea coast of Italy, Estuarine, Coastal and Shelf Science, vol.76, pp.404-417, 2008.

F. Frontalini and R. Coccioni, Benthic foraminifera as bioindicators of pollution: A review of Italian research over the last three decades, vol.54, pp.115-127, 2011.

F. Frontalini, M. P. Nardelli, D. Curzi, A. Martín-gonzález, A. Sabbatini et al., Benthic foraminiferal ultrastructural alteration induced by heavy metals, Marine Micropaleontology, vol.138, pp.83-89, 2018.

F. Frontalini, M. Greco, L. Di-bella, F. Lejzerowicz, E. Reo et al., Assessing the effect of mercury pollution on cultured benthic foraminifera community using morphological and eDNA metabarcoding approaches, Marine Pollution Bulletin, vol.129, pp.512-524, 2018.

A. Goineau, C. Fontanier, F. J. Jorissen, B. Lansard, R. Buscail et al., Live (stained) benthic foraminifera from the Rhône prodelta, Journal of Sea Research, vol.65, pp.58-75, 2011.

P. Grosjean, M. Picheral, C. Warembourg, and G. Gorsky, Enumeration, measurement, and identification of net zooplankton samples using the ZOOSCAN digital imaging system, ICES Journal of Marine Science, vol.61, pp.518-525, 2004.

J. I. Hedges, R. G. Keil, and G. L. Cowie, Sedimentary diagenesis: organic perspectives with inorganic overlays, Chemical Geology, vol.107, pp.487-492, 1993.

D. Hering, A. Borja, J. I. Jones, D. Pont, P. Boets et al., Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive, Water Research, vol.138, pp.192-205, 2018.

T. Jauffrais, B. Jesus, V. Méléder, and E. Geslin, Functional xanthophyll cycle and pigment content of a kleptoplastic benthic foraminifer: Haynesina germanica, PLOS ONE, vol.12, p.172678, 2017.

F. J. Jorissen, Benthic foraminifera from the Adriatic Sea: principles of phenotypic variation, vol.174, 1988.

F. J. Jorissen, H. De-stigter, and J. G. Widmark, A conceptual model explaining benthic foraminiferal microhabitats, Marine Micropaleontology, vol.26, pp.3-15, 1995.

F. J. Jorissen, Benthic foraminiferal microhabitats below the sediment-water interface, Modern Foraminifera, pp.161-179, 1999.

F. J. Jorissen, E. Bicchi, G. Duchemin, J. Durrieu, F. Galgani et al., Impact of oil-based drill mud disposal on benthic foraminiferal assemblages on the continental margin off Angola, Deep-Sea Research Part II: Topical Studies in Oceanography, vol.56, pp.2270-2291, 2009.

R. G. Keil, E. Tsamakis, C. B. Fuh, J. C. Giddings, and J. I. Hedges, Mineralogical and textural controls on the organic composition of coastal marine sediments: Hydrodynamic separation using SPLITT-fractionation, Geochimica et Cosmochimica Acta, vol.58, pp.879-893, 1994.

F. Lejzerowicz, P. Esling, W. Majewski, W. Szczucinski, J. Decelle et al., Ancient DNA complements microfossil record in deep-sea subsurface sediments, Biology Letters, vol.9, pp.20130283-20130283, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01258222

F. Lejzerowicz, P. Esling, L. Pillet, T. A. Wilding, K. D. Black et al., High-throughput sequencing and morphology perform equally well for benthic monitoring of marine ecosystems, Scientific Reports, p.20, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01245135

C. Lekieffre, J. E. Spangenberg, G. Mabilleau, S. Escrig, A. Meibom et al., Surviving anoxia in marine sediments: The metabolic response of ubiquitous benthic foraminifera (Ammonia tepida), PLOS ONE, vol.12, p.177604, 2017.

C. Lekieffre, T. Jauffrais, E. Geslin, B. Jesus, J. M. Bernhard et al., Inorganic carbon and nitrogen assimilation in cellular compartments of a benthic kleptoplastic foraminifer, Scientific Reports, vol.8, 2018.

L. M. Mayer, Relationships between mineral surfaces and organic carbon concentrations in soils and sediments, Chemical Geology, vol.114, pp.347-363, 1994.

S. Menezes, D. J. Baird, and A. M. Soares, Beyond taxonomy: a review of macroinvertebrate trait-based community descriptors as tools for freshwater biomonitoring: Trait-based community descriptors, Journal of Applied Ecology, vol.47, pp.711-719, 2010.

R. Mitra, T. M. Marchitto, Q. Ge, B. Zhong, B. Kanakiya et al., Automated species-level identification of planktic foraminifera using convolutional neural networks, with comparison to human performance, Marine Micropaleontology, vol.147, pp.16-24, 2019.

J. Paw?owska, F. Lejzerowicz, P. Esling, W. Szczuci?ski, M. Zaj?czkowski et al., Ancient DNA sheds new light on the Svalbard foraminiferal fossil record of the last millennium, Geobiology, vol.12, pp.277-288, 2014.

J. Paw?owska, M. Zaj?czkowski, M. ??cka, F. Lejzerowicz, P. Esling et al., Palaeoceanographic changes in Hornsund Fjord (Spitsbergen, Svalbard) overthe last millennium: new insights from ancient DNA, Climate of the Past, vol.12, pp.1459-1472, 2016.

J. Pawlowski, F. Lejzerowicz, L. Apotheloz-perret-gentil, J. Visco, and P. Esling, Protist metabarcoding and environmental biomonitoring: Time for change, European Journal of Protistology, vol.55, pp.12-25, 2016.

J. Pawlowski, M. Kelly-quinn, F. Altermatt, L. Apothéloz-perret-gentil, P. Beja et al., The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems, Science of The Total Environment, pp.1295-1310, 2018.

M. Phipps, F. Jorissen, A. Pusceddu, S. Bianchelli, D. Stigter et al., Live Benthic Foraminiferal Faunas Along a Bathymetrical Transect (282-4987 m) on the Portuguese Margin, vol.42, pp.66-81, 2012.

E. Piña-ochoa, S. Høgslund, E. Geslin, T. Cedhagen, N. P. Revsbech et al., Widespread occurrence of nitrate storage and denitrification among Foraminifera and Gromiida, Proceedings of the National Academy of Sciences, vol.107, pp.1148-1153, 2010.

N. L. Poff, J. D. Olden, N. K. Vieira, D. S. Finn, M. P. Simmons et al., Functional trait niches of North American lotic insects: traits-based ecological applications in light of phylogenetic relationships, Journal of the North American Benthological Society, vol.25, pp.730-755, 2006.

E. T. Premuzic, C. M. Benkovitz, J. S. Gaffney, and J. J. Walsh, The nature and distribution of organic matter in the surface sediments of world oceans and seas, Organic Geochemistry, vol.4, pp.63-77, 1982.

P. Regnier, P. Friedlingstein, P. Ciais, F. T. Mackenzie, N. Gruber et al., Anthropogenic perturbation of the carbon fluxes from land to ocean, Nature Geoscience, vol.6, pp.597-607, 2013.

N. Risgaard-petersen, A. M. Langezaal, S. Ingvardsen, M. C. Schmid, M. S. Jetten et al., Evidence for complete denitrification in a benthic foraminifer, Nature, vol.443, pp.93-96, 2006.

R. Rosenberg, Marine benthic faunal successinal stages and related sedimentary activity, Scientia Marina, vol.65, pp.107-119, 2001.

J. Schönfeld, History and development of methods in Recent benthic foraminiferal studies, Journal of Micropalaeontology, vol.31, pp.53-72, 2012.

M. Schweizer, I. Polovodova, A. Nikulina, and J. Schönfeld, Molecular identification of Ammonia and Elphidium species (Foraminifera, Rotaliida) from the Kiel Fjord (SW Baltic Sea) with rDNA sequences, Helgoland Marine Research, vol.65, pp.1-10, 2011.

J. P. Syvitski, C. J. Vörösmarty, A. J. Kettner, and P. Green, Impact of Humans on the Flux of Terrestrial Sediment to the Global Coastal Ocean, Science, vol.308, pp.376-380, 2005.

D. Titelboim, A. Almogi-labin, B. Herut, M. Kucera, C. Schmidt et al., Selective responses of benthic foraminifera to thermal pollution, Marine Pollution Bulletin, vol.105, pp.324-336, 2016.

G. Van-hoey, S. Degraer, and M. Vincx, Macrobenthic community structure of soft-bottom sediments at the Belgian Continental Shelf, Estuarine, Coastal and Shelf Science, vol.59, pp.599-613, 2004.

M. L. Zettler, C. E. Proffitt, A. Darr, S. Degraer, L. Devriese et al., On the Myths of Indicator Species: Issues and Further Consideration in the Use of Static Concepts for Ecological Applications, PLoS ONE, vol.8, p.78219, 2013.

B. Zhong, Q. Ge, B. Kanakiya, R. Mitra, T. Marchitto et al., A Comparative Study of Image Classification Algorithms for Foraminifera Identification, 2017 IEEE Symposium Series on Computational Intelligence (SSCI), p.8, 2017.

, Planche 1 : 1) Ammodiscus planus, 2) Glomospira charoides, 3) Glomospira gordialis, 4) Glomospira sp. 1, 5) Ammoscalaria pseudospiralis, 6) Ammoscalaria sp. 1, 7) Ammoscalaria sp. 2, 8) Bigenerina nodosaria, 9) Clavulina cylindrica, 10) Lagenammina atlantica, 11) Eggerelloides scaber, 12) Lagenammina difflugiformis, échelle = 100 µm Planche 2 : 1) Ammoglobigerina globigeriniformis, 2) Haplophragmoides canariensis, 3) Recurvoides sp. 1, 4) Tritaxis sp., 5) Trochammina sp., 6) Trochamminula sp., 7) Leptohalysis scotti, 8) Nouria cf. polymorphinoides, 9) Nouria polymorphinoides, 10) Deuterammina sp

, Reophax micaceus, 5) Reophax scorpiurus, 6) Reophax sp. 1, 7) Reophax subfusiformis, 8) Siphotextularia concava, 9) Textularia agglutinans, 10) Textularia truncata, 11) Textularia conica, 12) Textularia sagittula, échelle = 100 µm Planche 4 : 1) Ammonia beccarii, 2) Pseudoeponides falsobeccarii, 3) Ammonia perlucida, 4) Ammonia tepida, 5) Asterigerinata mamilla, 6) Buccella granulata, 7) Gavelinopsis praegeri, 8) Neoconorbina terquemi, échelle = 100 µm Planche 5 : 1) Gyroidina umbonata, 2) Gyroidina sp. 1, 3) Planorbulina mediterranensis, 4) Spirillina vivipara, échelle = 100 µm, sauf 2b = 20 µm Planche 6 : 1) Cancris auriculus, 2) Valvulineria bradyana, 3) Cibicides lobatulus, 4) Cibicides refulgens, 5) Hanzawaia boueana, 6) Rosalina vilardebouana, 7) Rosalina bradyi, 8) Rosalina globularis, 9) Stomatorbina concentrica, échelle = 100 µm Planche 7 : 1) Elphidium advenum, 2) Elphidium crispum, 3) Elphidium granosum, 4) Elphidium incertum, 5) Elphidium macellum, 6) Elphidium poeyanum, 7) Nonion depressulum, 8) Nonion scaphum, 9) Astrononion stelligerum, 10) Melonis barleeanus, 11) Cassidulina oblonga, 12) Nonionella turgida, 13) Nonionella stella, échelle = 100 µm Planche 8 : 1) Bolivina dilatata, 2) Bolivina pseudoplicata, 3) Bolivina pygmea, 4) Bolivina spathulata, 5) Bolivina subaenariensis, 6) Bulimina aculeata, 7) Bulimina elongata, 8) Bulimina gibba, 9) Bulimina costata, 10) Reussella spinulosa, 11) Rectuvigerina phlegeri, 12) Robertinoides bradyi

, Lenticulina peregrina, 8) Amphicoryna scalaris, 9) Oolina acuticosta, 10) Astacolus insolitus ; 11) Globobulimina affinis, 12) Lagena hexagona, 13) Lagena striata, 14) Lagena semistriata, 15) Lagena elongata, 16) Hyalinonetrion gracillimum, échelle = 100 µm, sauf 3b, 4b et 6b = 20 µm Planche 10 : 1) Adelosina elegans, 2) Adelosina ferussaci, 3) Adelosina longirostra, 4) Adelosina sp. 1, 5) Cornuspira foliacea, 6) Cornuspira involvens, 7) Lachlanella undulata, 8) Miliolinella subrotunda, 9) Pyrgo elongata, 10) Spiroloculina elevata, 11) Spiroloculina excavata, échelle = 100 µm Planche 11 : 1) Quinqueloculina aspera f. aspera, 2) Quinqueloculina aspera f. quadrata, 3) Quinqueloculina aspera f. rugosa, 4) Quinqueloculina aspera f. berthelotiana, 5) Quinqueloculina bosciana, 6) Quinqueloculina cf. bosciana, 7) Quinqueloculina stelligera, 8) Quinqueloculina laevigata, 9) Quinqueloculina cf. laevigata, échelle = 100 µm Planche 12 : 1) Quinqueloculina costata f. lucida, 2), ) Dentalina bradyensis, 2) Dentalina subsoluta, 3) Dentalina sp., 4) Nodosaria sp., 5) Pyramidulina catesbyi, 6) Glandulina sp., 7), vol.9

, Triloculina oblonga, 7) Triloculina trigonula, 8) Sigmoilina grata, 9) Sigmoilina sp. 2, 10) Sigmoilinita sp. 1, échelle = 100 µm

C. .. Commons,

. .. Remerciements,

. .. Sommaire,

.. .. Directive-cadre-sur-l'eau,

. .. Mer-méditerranée,

. .. Références,

, Chapitre 2 : An optimised method to concentrate living (Rose Bengal-stained) benthic foraminifera from sandy sediments by high density liquids, p.21

. .. Abstract,

, 3.4. Recovery of specific groups of foraminifera

. .. Discussion, Impact of density separation on the composition of the foraminiferal faunas and on biotic indices

. .. Acknowledgements,

. .. References,

. .. Appendices, A: State of the art of density separation methods

, Appendix 2.B: Sediment particle characteristics

, Appendix 2.C: Recovery rates (%) in the floated fraction for specific groups of foraminiferal species and sediment according to the separation solution and its density

, Appendix 2.D: Complete census of foraminifera

, Appendix 2.E: Type of samples and separation solutions used in the literature for density separation on foraminifera

, Appendix 2.F: Literature data: recovery rates (%) in the floated fraction for foraminifera in the total samples according to the separation solution and its density

. .. , New insights in environmental quality assessment by combining benthic foraminiferal community studies and grain size analysis, Chapitre, vol.3, p.61

. .. Abstract, Treatment of the different sediment fractions

D. .. Results, 75 3.3.2.1. Organic matter content: correction for production of ash during the loss on ignition

, Individual grain size distribution of the three sediment components

, 3.4. Utilisation of GSA data in biotic indices: how to correct for the natural trophic status?

. .. References,

, Comparison of four foraminiferal indices assessing the environmental quality of coastal Mediterranean soft bottom environments, Chapitre, vol.4

. .. Abstract, Biotic indices based on group of indicator species

D. .. Results, 3.2.2. Comparing the indices using original species assignments

, Testing the indices with the same list of indicator species for all indices

. .. , 108 4.3.3. Corrections for the natural trophic state

. .. References,

. .. Appendices,

. .. , B: Species assignment for the biotic indices based on groups of indicator species (TSI-Med, Foram-AMBI, and FSI), p.121

, Évaluation de la qualité environnementale des substrats meubles de la côte méditerranéenne française par les faunes de foraminifères benthiques, Chapitre, vol.5

. .. Résumé,

, 3.3. Répartition des espèces sensibles et tolérantes à l'enrichissement en matière organique

. Tsi-med and D. De-mesure, , 2015.

, 154 5.4.1. Communautés des foraminifères benthiques et leurs milieux de vie

, Stations montrant une augmentation des valeurs de TSI-Med au cours du temps

, Stations montrant une diminution des valeurs de TSI-Med au cours du temps

, Variations des valeurs de TSI-Med variables sans tendance temporelle claire

. .. Comparaison-avec-le-foram-ambi,

. .. Références,

. .. Appendices, A : Paramètres environnementaux principaux pour chaque station

, Appendice 5.B : Paramètres faunistiques des stations échantillonnées

, Appendice 5.C : Information complémentaires sur l'évolution de la qualité écologique de certaines stations

, D : Pour chaque station sont indiqué les changements maximums de position géographique et de profondeur entre les années, l'hétérogénéité spatiale, les tendances suivies par le changement d'EQS entre les années et les causes des variations de la qualité écologique pour chaque station

, Appendice 5.E : Abondances relatives d'Eggerelloides scaber et Reophax fusiformis pour chaque station

, Testing two biotic indices based on living (Rose Bengal-stained) benthic foraminiferal communities along a well-defined organic matter gradient in the eastern Mediterranean, Chapitre, vol.6

. .. Abstract, 2.2. Sampling and treatment of the foraminiferal faunas

, Previous studies on foraminifera and on macrofauna in the study area

, Foraminiferal successions along the organic enrichment gradient

C. Scotti and .. .. ,

, Correction for natural eutrophic conditions

. .. References,

. .. Appendix, A: Information on the sampled stations

. .. Synthèse, Chapitre

, 2.2. Indices biotiques basés sur les groupes écologiques : mode de prise en compte de ces groupes écologiques

, Perspectives : définition des limites entre les EQS

. .. Assignations-Écologiques-d'espèces, 4.1. Estimation de l'état trophique naturel par l'analyse de la granulométrie du sédiment

. .. Foram-ambi, 6.2. Perspectives : les conditions naturelles du milieu : l'apport potentiel de l'étude des faunes préservées dans les archives sédimentaires, Perspectives : diffusion des indices : TSI-Med

. .. Références,