@article {9111,
	title = {New species of Pavlovophyceae (Haptophyta) and revision of the genera Exanthemachrysis, Rebecca and Pavlova},
	journal = {European Journal of Taxonomy},
	volume = {861},
	year = {2023},
	month = {08-03-2023},
	pages = {21 - 47},
	abstract = {The justification of the 4 genera that currently compose the class Pavlovophyceae is based on a low number of species and a relative paucity of available, traceable and referenced cultures. Previous integrative phylogeny work revealed strains that can refine and strengthen our knowledge of the genera\&nbsp;in the class. The application of multiple light and electron microscopy techniques allowed us to prioritize\&nbsp;the cytomorphological characters (pyrenoid, thylakoid, stigma, knob-scales, life stage / life cycle) used for\&nbsp;the taxonomy of these algae and to describe two new species:\&nbsp;Exanthemachrysis fresneliae\&nbsp;Véron sp. nov. and\&nbsp;Rebecca billardiae\&nbsp;Véron sp. nov. Consequently, revisions of the two genera\&nbsp;Exanthemachrysis\&nbsp;Lepailleur emend. Véron and\&nbsp;Rebecca\&nbsp;Green emend. Véron were made. In addition, the genus\&nbsp;Pavlova\&nbsp;Butcher emend Véron is revised in the light of these characters. Particular emphasis is placed on the life\&nbsp;stages and habitat of the species.},
	keywords = {habitats, Haptophytes, New species, Phytoplankton, pyrenoid.},
	issn = {2118-9773},
	doi = {10.5852/ejt.2023.861.2063},
	url = {https://europeanjournaloftaxonomy.eu/index.php/ejt/article/view/2063},
	author = {Beno{\^\i}t V{\'e}ron and Rougier, Etienne and Taylor, Anthony and Goux, Didier}
}
@article {6668,
	title = {Modelling the functioning of a coupled microphytobenthic-EPS-bacterial system in intertidal mudflats},
	journal = {Marine Environmental Research},
	volume = {150},
	year = {2019},
	abstract = {A mechanistic and biogeochemical model was developed to analyze the interactions between microphytobenthos (MPB), bacteria and nutrients in a tidal system. Behavioral vertical migration was hypothesized as being controlled by exogenous factors (tide and light) but also by endogenous factors (carbon and nitrogen requirements). The secretion of Extracellular Polymeric Substances (EPS) during photosynthesis (overflow metabolism) and migration of diatoms was also formulated. Similarities in MPB dynamics between observations and simulations support the assumption that carbon and nitrogen ratios are additional key processes behind the vertical migration of diatoms in the sediment. The model satisfactorily reproduced the three growth phases of the MPB development observed in a mesocosm (the lag phase, the logarithmic growth, and the plateau). Besides, nutrient availability, which could be induced by faunal bioturbation, significantly determined the extent of MPB biomass and development. The plateau phase observed in the last days of simulations appeared to be attributed to a nutrient depletion in the system, emphasizing the importance of nutrient availability. The model, although improvable especially on the formulation of the EPS excretion and bacteria development, already updated understanding of several aspects of benthic-system functioning during experimental conditions. {\textcopyright} 2019 Elsevier Ltd},
	keywords = {Bacillariophyta, bacteria, Bacteria (microorganisms), bacterial growth, bacterium, Biogeochemical modeling, biogeochemistry, Biomass, Carbon, Carbon and nitrogen, Carbon and nitrogen ratios, Diatom, diel vertical migration, exopolymer, Experimental conditions, Extracellular polymeric substances, intertidal environment, intertidal zone, light, mesocosm, microbial community, Microphytobenthos, Migration, modeling, mudflat, Nitrogen, nonhuman, Nutrient availability, Nutrients, nutritional requirement, organic carbon, organismal interaction, Photosynthesis, Phytobenthos, Phytoplankton, polymer, Review, simulation, tide, vertical migration},
	issn = {01411136},
	doi = {10.1016/j.marenvres.2019.104754},
	url = {https://www.sciencedirect.com/science/article/abs/pii/S0141113619300704},
	author = {Rakotomalala, C and Katell Guizien and Karine Granger{\'e} and S{\'e}bastien Lefebvre and Christine Dupuy and Francis Orvain}
}
@article {Meddeb201967,
	title = {A new type of plankton food web functioning in coastal waters revealed by coupling Monte Carlo Markov chain linear inverse method and ecological network analysis},
	journal = {Ecological Indicators},
	volume = {104},
	year = {2019},
	note = {cited By 0},
	pages = {67-85},
	publisher = {Elsevier B.V.},
	abstract = {Plankton food webs (PFW) typology is based on different categories of functioning, according to the dominant processes and the role played by heterotrophic bacteria, small vs large phytoplankton, and small vs large zooplankton. Investigating the structure and the function of planktonic food webs in two SW Mediterranean waters (inshore and marine sites) at four seasons, using inverse (LIM-MCMC) and ecological network (ENA) analyses, we identified a new type of food web, called the {\textquotedblleft}bacterial multivorous food web{\textquotedblright}. This food web adds to the conventional trophic continuum as previously reported. The {\textquotedblleft}bacterial multivorous food web{\textquotedblright} present in winter showed the lowest primary production among seasons, but highest bacterial production. Several food web ratios characterized this new typology e.g. picophytoplankton net primary production to total primary production varied from 0.20 to 0.28; bacterial to primary production ratio is higher than values reported in global scale (≅1); bacterial net production to the potential protozoan prey net production was high (\&gt;0.2). In this special food web, carbon was mostly recycled, with a moderate fraction channeled to deep waters, which lead to a higher retention of carbon inside the ecosystem. This winter PFW also seemed to be the most organized, specialized, stable and mature, as related to common interpretations of ENA. The spring was characterized by herbivorous food web, with highest activity coinciding with low stability. Although less usual, the herbivorous pathway was also observed during summer, in inshore waters. The autumn food webs, which functioned as multivorous or microbial food webs, appeared to be stable and mature. Finally, our study demonstrates the usefulness of food web models derived ratios combined with ecological network analysis indices to conduct evaluation of the structure and functioning of ecosystems and potentially to support management decisions in marine environment. {\textcopyright} 2019},
	keywords = {Bacteria (microorganisms), bacterium, Carbon, Chemical contamination, coastal water, Coastal waters, ecological modeling, Ecology, ecosystem function, Ecosystems, Electric network analysis, Food microbiology, food web, Food web model, Food webs, inverse analysis, Inverse problems, Markov chain, Markov processes, Mediterranean sea, Monte Carlo analysis, Monte Carlo methods, net primary production, network analysis, Phytoplankton, picoplankton, Plankton, Protozoa, protozoan, Seasonal variation, trophic status, Trophic structure},
	issn = {1470160X},
	doi = {10.1016/j.ecolind.2019.04.077},
	url = {https://www.sciencedirect.com/science/article/abs/pii/S1470160X19303243},
	author = {Meddeb, M. and Nathalie Niquil and Grami, B. and Mejri, K. and Haraldsson, M. and Chaalali, A. and Pringault, O. and Hlaili, A.S.}
}
@article {Meddeb201866,
	title = {Plankton food-web functioning in anthropogenically impacted coastal waters (SW Mediterranean Sea): An ecological network analysis},
	journal = {Progress in Oceanography},
	volume = {162},
	year = {2018},
	note = {cited By 4},
	pages = {66-82},
	publisher = {Elsevier Ltd},
	abstract = {The study is the first attempt to (i) model spring food webs in three SW Mediterranean ecosystems which are under different anthropogenic pressures and (ii) to project the consequence of this stress on their function. Linear inverse models were built using the Monte Carlo method coupled with Markov Chains to characterize the food-web status of the Lagoon, the Channel (inshore waters under high eutrophication and chemical contamination) and the Bay of Bizerte (offshore waters under less anthropogenic pressure). Ecological network analysis was used for the description of structural and functional properties of each food web and for inter-ecosystem comparisons. Our results showed that more carbon was produced by phytoplankton in the inshore waters (966{\textendash}1234 mg C m-2 d-1) compared to the Bay (727 mg C m-2 d-1). The total ecosystem carbon inputs into the three food webs was supported by high primary production, which was mainly due to \&gt;10 {\textmu}m algae. However, the three carbon pathways were characterized by low detritivory and a high herbivory which was mainly assigned to protozooplankton. This latter was efficient in channelling biogenic carbon. In the Lagoon and the Channel, foods webs acted almost as a multivorous structure with a tendency towards herbivorous one, whereas in the Bay the herbivorous pathway was more dominant. Ecological indices revealed that the Lagoon and the Channel food webs/systems had high total system throughput and thus were more active than the Bay. The Bay food web, which had a high relative ascendency value, was more organized and specialized. This inter{\textendash}ecosystem difference could be due to the varying levels of anthropogenic impact among sites. Indeed, the low value of Finn{\textquoteright}s cycling index indicated that the three systems are disturbed, but the Lagoon and the Channel, with low average path lengths, appeared to be more stressed, as both sites have undergone higher chemical pollution and nutrient loading. This study shows that ecosystem models combined with ecological indices provide a powerful approach to detect change in environmental status and anthropogenic impacts. {\textcopyright} 2018},
	keywords = {Algae, anthropogenic effect, Anthropogenic impacts, Anthropogenic pressures, Bizerte, Bizerte Bay, Chemical analysis, Chemical contamination, coastal water, community structure, Ecological network analysis, Ecology, ecosystem function, ecosystem modeling, Ecosystems, eutrophication, food web, Food webs, Functional properties, Inverse problems, Lakes, Linear inverse models, Markov processes, Mediterranean coastal waters, Mediterranean ecosystem, Mediterranean sea, Monte Carlo methods, network analysis, Phytoplankton, Plankton, primary production, Tunisia, Zooplankton},
	issn = {00796611},
	doi = {10.1016/j.pocean.2018.02.013},
	url = {https://www.sciencedirect.com/science/article/abs/pii/S0079661117300782},
	author = {Meddeb, M. and Grami, B. and Chaalali, A. and Haraldsson, M. and Nathalie Niquil and Pringault, O. and Sakka Hlaili, A.}
}
@article {6667,
	title = {Dynamics of particulate organic matter composition in coastal systems: A spatio-temporal study at multi-systems scale},
	journal = {Progress in Oceanography},
	volume = {156},
	year = {2017},
	pages = {221-239},
	abstract = {In coastal systems, the multiplicity of sources fueling the pool of particulate organic matter (POM) leads to divergent estimations of POM composition. Eleven systems (two littoral systems, eight embayments and semi-enclosed systems and one estuary) distributed along the three maritime fa{\c c}ades of France were studied for two to eight years in order to quantify the relative contribution of organic matter sources to the surface-water POM pool in coastal systems. This study was based on carbon and nitrogen elemental and isotopic ratios, used for running mixing models. The POM of the estuary is dominated by terrestrial material (93\% on average), whereas the POM of the other systems is dominated by phytoplankton (84\% on average). Nevertheless, for the latter systems, the POM composition varies in space, with (1) systems where POM is highly composed of phytoplankton (>=93\%), (2) systems characterized by a non-negligible contribution of benthic (8{\textendash}19\%) and/or river (7{\textendash}19\%) POM sources, and (3) the Mediterranean systems characterized by the contribution of diazotroph organisms (ca. 14\%). A continent-to-ocean gradient of river and/or benthic POM contribution is observed. Finally, time series reveal (1) seasonal variations of POM composition, (2) differences in seasonality between systems, and (3) an inshore-offshore gradient of seasonality within each system that were sampled at several stations. Spatial and seasonal patterns of POM composition are mainly due to local to regional processes such as hydrodynamics and sedimentary hydrodynamic (e.g. resuspension processes, changes in river flows, wind patterns influencing along-shore currents) but also due to the geomorphology of the systems (depth of the water column, distance to the shore). Future studies investigating the link between these forcings and POM composition would help to better understand the dynamics of POM composition in coastal systems. {\textcopyright} 2017 Elsevier Ltd},
	keywords = {bacterium, benthos, biogeochemistry, Biological materials, C and n stable isotopes, C:N ratio, Carbon, carbon isotope, Coastal systems, coastal zone, Fluid dynamics, France, geomorphology, Hydrodynamics, Isotopes, isotopic ratio, Mediterranean sea, Meta analysis, meta-analysis, Mixing, Mixing models, nitrogen isotope, Organic compounds, particulate organic matter, Particulate organic matters, Phytoplankton, prokaryote, Rivers, seasonality, spatiotemporal analysis, stable isotope, Surface water, Surface waters, terrestrial deposit, Time series},
	issn = {00796611},
	doi = {10.1016/j.pocean.2017.03.001},
	url = {https://www.sciencedirect.com/science/article/abs/pii/S0079661116301914},
	author = {Li{\'e}nart, Camilla and Savoye, Nicolas and Bozec, Yann and Elsa Breton and Conan, Pascal and David, Val{\'e}rie and Eric Feunteun and Karine Granger{\'e} and Kerherv{\'e}, P. and Lebreton, B. and S{\'e}bastien Lefebvre and St{\'e}phane L{\textquoteright}Helguen and Mousseau, Laure and Raimbault, P and Richard, P. and Riera, P. and Sauriau, P.-G. and Gauthier Schaal and Aubert, F. and Aubin, S. and Bichon, S. and Boinet, C. and Bourasseau, L. and Br{\'e}ret, M. and Caparros, J. and Cariou, T. and Charlier, K. and Claquin, P. and Vincent Cornille and Corre, A.-M. and Costes, L. and Crispi, O. and Muriel Crouvoisier and Czamanski, M. and Del Amo, Y. and Derriennic, H. and Dindinaud, F. and Durozier, M. and Hanquiez, V. and Antoine Nowaczyk and Devesa, J. and Ferreira, S. and Fornier, M. and Garcia, F. and Garcia, N. and Geslin, S. and Emilie Grossteffan and Gueux, A. and Guillaudeau, J. and Guillou, G. and Joly, O. and Lachauss{\'e}e, N. and Lafont, M. and Lamoureux, J. and Lecuyer, E. and Lehodey, J.-P. and Lemeille, D. and Leroux, C. and Mac{\'e}, E. and Maria, E. and Pineau, P. and Petit, F. and Pujo-Pay, M. and Rimelin-Maury, P. and Sultan, E.}
}
@article {Thorel2017192,
	title = {Nutrient ratios influence variability in Pseudo-nitzschia species diversity and particulate domoic acid production in the Bay of Seine (France)},
	journal = {Harmful Algae},
	volume = {68},
	year = {2017},
	note = {cited By 15},
	pages = {192-205},
	publisher = {Elsevier B.V.},
	abstract = {The population dynamics of different Pseudo-nitzschia species, along with particulate domoic acid (pDA) concentrations, were studied from May 2012 to December 2013 in the Bay of Seine (English Channel, Normandy). While Pseudo-nitzschia spp. blooms occurred during the two years of study, Pseudo-nitzschia species diversity and particulate domoic acid concentrations varied greatly. In 2012, three different species were identified during the spring bloom (P. australis, P. pungens and P. fraudulenta) with high pDA concentrations (\~{}1400 ng l-1) resulting in shellfish harvesting closures. In contrast, the 2013 spring was characterised by a P. delicatissima bloom without any toxic event. Above all, the results show that high pDA concentrations coincided with the presence of P. australis and with potential silicate limitation (Si:N \&lt; 1), while nitrate concentrations were still replete. The contrasting environmental conditions between 2012 and 2013 highlight different environmental controls that might favour the development of either P. delicatissima or P. australis. This study points to the key role of Pseudo-nitzschia diversity and cellular toxicity in the control of particulate domoic acid variations and highlights the fact that diversity and toxicity are influenced by nutrients, especially nutrient ratios. {\textcopyright} 2017 Elsevier B.V.},
	keywords = {analogs and derivatives, analysis, Bay, Bays, Biodiversity, chemistry, Diatom, Diatoms, Domoic acid, France, Geography, kainic acid, Nitrates, nitric acid derivative, particulate matter, phosphate, Phosphates, Physiology, Phytoplankton, Principal Component Analysis, season, Seasons, species difference, Species Specificity, time factor, Time Factors},
	issn = {15689883},
	doi = {10.1016/j.hal.2017.07.005},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85028543709\&doi=10.1016\%2fj.hal.2017.07.005\&partnerID=40\&md5=def23b37b0d16a1ae7ab65a7ef2b940b},
	author = {Thorel, Maxine and Pascal Claquin and Mathilde Schapira and Romain Le Gendre and Riou, Philippe and Didier Goux and Bertrand Le Roy and Raimbault, V and Deton-Cabanillas, A.-F. and Bazin, Pauline and Kientz-Bouchart, Val{\'e}rie and Juliette Fauchot}
}
@article {3278,
	title = {Complex patterns in phytoplankton and microeukaryote diversity along the estuarine continuum},
	journal = {Hydrobiologia},
	volume = {726},
	year = {2014},
	pages = {155-178},
	keywords = {18S rDNA clone libraries, Diversity, Estuarine gradient, Microeukaryotes, Microscopy, Phytoplankton, semiarid area},
	doi = {10.1007/s10750-013- 1761-9},
	author = {Bazin, Pauline and Fabien Jouenne and Deton-Cabanillas, Anne-Flore and Perez-Ruzafa, Angel and Beno{\^\i}t V{\'e}ron}
}
@article {5820,
	title = {{Synchronous response of marine plankton ecosystems to climate in the Northeast Atlantic and the North Sea}},
	journal = {Journal of Marine Systems},
	volume = {129},
	year = {2014},
	pages = {189{\textendash}202},
	abstract = {<p>Over the last few decades, global warming has accelerated both the rate and magnitude of changes observed in many functional units of the Earth System. In this context, plankton are sentinel organisms because they are sensitive to subtle levels of changes in temperature and might help in identifying the current effects of climate change on pelagic ecosystems. In this paper, we performed a comparative approach in two regions of the North Atlantic (i.e. the Northeast Atlantic and the North Sea) to explore the relationships between changes in marine plankton, the regional physico-chemical environment and large-scale hydro-climatic forcing using four key indices: the North Atlantic Oscillation (NAO), the Atlantic Multidecadal Oscillation (AMO), the East Atlantic (EA) pattern and Northern Hemisphere Temperature (NHT) anomalies. Our analyses suggest that long-term changes in the states of the two ecosystems were synchronous and correlated to the same large-scale hydro-climatic variables: NHT anomalies, the AMO and to a lesser extent the EA pattern. No significant correlation was found between long-term ecosystem modifications and the state of the NAO. Our results suggest that the effect of climate on these ecosystems has mainly occurred in both regions through the modulation of the thermal regime. {\textcopyright} 2013 Elsevier B.V.</p>
},
	keywords = {Climate Change, Large-scale hydro-climatic indices, Long-term changes, North Atlantic, Phytoplankton, Zooplankton},
	author = {Goberville, Eric and Gr{\'e}gory Beaugrand and Martin Edwards}
}
