Phytoplankton supports food webs in all aquatic ecosystems. Ecological studies highlighted the links between environmental variables and species successions in situ. However, the role of life cycle characteristics on phytoplankton community dynamics remains poorly characterized. In diatoms, sexual reproduction creates new genetic combinations and prevents excessive cell size miniaturization. It has been extensively studied in vitro but seldom in the natural environment. Here, analyzing metatranscriptomic data in the light of the expression patterns previously characterized in vitro, we identified a synchronized and transient sexual reproduction event during a bloom of the toxic diatom species Pseudo-nitzschia australis. Despite the complexity of environmental conditions encountered in situ, sexual reproduction appeared to be the strongest differential gene expression signal that occurred during the bloom. The potential link between environmental conditions and the initiation of sexual reproduction remain to be determined, but sexual reproduction probably had a major impact on the bloom dynamic.

The pre-eutrophic state of marine waters is generally not well known, complicating target setting for management measures to combat eutrophication. We present results from an OSPAR ICG-EMO model assessment to simulate the pre-eutrophic state of North-East Atlantic marine waters. Using an ecosystem model ensemble combined with an observation-based weighting method we derive sophisticated estimates for key eutrophication indicators. Eight modelling centres applied the same riverine nutrient loads, atmospheric nutrient deposition rates and boundary conditions to their specific model set-up to ensure comparability. The pre-eutrophic state was defined as a historic scenario of estimated nutrient inputs (riverine, atmospheric) at around the year 1900, before the invention and widespread use of industrial fertilizers. The period 2009-2014 was used by all participants to simulate both the current state of eutrophication and the pre-eutrophic scenario, to ensure that differences are solely due to the changes in nutrient inputs between the scenarios. Mean values were reported for winter dissolved inorganic nutrients and total nutrients (nitrogen, phosphorus) and the nitrogen to phosphorus ratio, and for growing season chlorophyll, chlorophyll 90th percentile, near-bed oxygen minimum and net phytoplankton production on the level of the OSPAR assessment areas. Results showed distinctly lower nutrient concentrations and nitrogen to phosphorus ratio’s in coastal areas under pre-eutrophic conditions compared to current conditions (except in the Meuse Plume and Seine Plume areas). Chlorophyll concentrations were estimated to be as much as ~40% lower in some areas, as were dissolved inorganic phosphorus levels. Dissolved inorganic nitrogen levels were found to be up to 60% lower in certain assessment areas. The weighted average approach reduced model disparities, and delivered pre-eutrophic concentrations in each assessment area. Our results open the possibility to establish reference values for indicators of eutrophication across marine regions. The use of the new assessment areas ensures local ecosystem functioning is better represented while political boundaries are largely ignored. As such, the reference values are less associated to member states boundaries than to ecosystem boundaries.

The main objective was to study relationships between the regional biogeography of Dinophysis species and water masses circulation along the European Atlantic coast. Hydrodynamic connectivities were estimated with a Lagrangian approach. Available and validated physical hindcasts from regional hydrodynamical models, with different resolutions were used. The target area is the Bay of Biscay (NE Atlantic) and connectivity was evaluated between a set of spatially distributed stations and during temporally specified periods. Different indexes related to connectivity properties such as mean, median, most frequent transit times were calculated. To illustrate the dispersion pattern, a molecular approach was jointly set-up to describe the species composition of this genus. At the seasonal scale, a high connectivity within the Bay of Biscay was observed with a slight northward connectivity from Galicia coastal waters to the Shelf of the Bay of Biscay. By comparison to the connectivity between shelf waters of French Brittany and English Channel waters, a higher connectivity between shelf waters of French Brittany and the Celtic Sea shelf was observed. The species mixing in the Bay of Biscay from Galicia waters to the Celtic Sea was confirmed by the genetic analyses despite the absence of Dinophysis sacculus in natural samples. The molecular methodology developed for this work, permitting at least the description of the species composition, also highlights, at the European scale, an unexpected low genetic variability which echoes the complex taxonomic classification inside the genus and the difficulties encountered by national monitoring programs to reach a taxonomic resolution at species level. It is now necessary to start some monitoring at the species level before realizing mid- or long-term forecasts.

Decadal time series of chlorophyll a concentrations sampled at high and low frequencies are explored to study climate-induced impacts on the processes inducing interannual variations in the initiation of the phytoplankton growing period (IPGP) in early spring. We specifically detail the IPGP in two contrasting coastal temperate ecosystems under the influence of rivers highly rich in nutrients: the Bay of Brest and the Bay of Vilaine. In both coastal ecosystems, we observed a large interannual variation in the IPGP influenced by sea temperature, river inputs, light availability (modulated by solar radiation and water turbidity), and turbulent mixing generated by tidal currents, wind stress, and river runoff. We show that the IPGP is delayed by around 30 d in 2019 in comparison with 2010. In situ observations and a one-dimensional vertical model coupling hydrodynamics, biogeochemistry, and sediment dynamics show that the IPGP generally does not depend on one specific environmental factor but on the interaction between several environmental factors. In these two bays, we demonstrate that the IPGP is mainly caused by sea surface temperature and available light conditions, mostly controlled by the turbidity of the system before first blooms. While both bays are hydrodynamically contrasted, the processes that modulate the IPGP are similar. In both bays, the IPGP can be delayed by cold spells and flood events at the end of winter, provided that these extreme events last several days.

In a future scenario of increasing temperatures in North-Atlantic waters, the risk associated with the expansion of the harmful, benthic dinoflagellate Ostreopsis cf. siamensis has to be evaluated and monitored. Microscopy observations and spatio-temporal surveys of environmental DNA (eDNA) were associated with Lagrangian particle dispersal simulations to: (i) establish the current colonization of the species in the Bay of Biscay, (ii) assess the spatial connectivity among sampling zones that explain this distribution, and (iii) identify the sentinel zones to monitor future expansion. Throughout a sampling campaign carried out in August to September 2018, microscope analysis showed that the species develops in the south-east of the bay where optimal temperatures foster blooms. Quantitative PCR analyses revealed its presence across almost the whole bay to the western English Channel. An eDNA time-series collected on plastic samplers showed that the species occurs in the bay from April to September. Due to the water circulation, colonization of the whole bay from the southern blooming zones is explained by inter-site connectivity. Key areas in the middle of the bay permit continuous dispersal connectivity towards the north. These key areas are proposed as sentinel zones to monitor O. cf. siamensis invasions towards the presumably warming water of the North-East Atlantic.

Intertidal communities dominated by canopy-forming brown algae (Phaeophyceae) usually prove to be highly productive systems, based on short-term measurements. However, long-term metabolism (primary production and respiration) is sensitive to several factors acting on different time scales (e.g. tidal cycle, seasonality), making its assessment challenging. Here, we used mathematical modelling to investigate the metabolism of aFucus serratus-dominated community on daily and annual time scales. This widespread community, which is usually characteristic of the low mid-intertidal level of temperate rocky shores, is submerged for approximately 83% of the time at our study site (Brittany, France). The model incorporated a large spectrum of physiological (e.g. estimates of primary production versus irradiance parameters) and environmental (e.g. temperature, incident irradiance, depth of the water column) parameters measuredin situ. The model simulation predicted that net community primary production (NCP) peaks at 8.0 gC m-2d-1in late spring, when environmental conditions are most favorable. In contrast, during fall and winter, respiration frequently overcomes primary production, making the system heterotrophic on a daily basis. For the year as a whole, simulation predicted that the community acts as an autotrophic system, with its annual gross primary production amounting to ca. 1301 gC m-2and annual respiration to ca. 899 gC m-2. According to this simulation, the annual NCP of our intertidalF. serratuscommunity therefore reached 402 gC m-2, which is comparable to subtidal communities dominated by canopy-forming brown algae. Although theF. serratuscommunity lives mostly underwater, it was particularly autotrophic during aerial exposures.

Abstract. The evolution of eutrophication (i.e., phytoplankton biomass) during recent decades was examined in the coastal waters of Vilaine Bay (VB, France) in relation to those in their main external nutrient sources, the Loire and Vilaine Rivers. Dynamic Linear Models, corroborated by the Mann-Kendall test, were used to study long-term trends and seasonality of dissolved inorganic nutrient and chlorophyll a concentrations (Chl a) in rivers and coastal waters between 1980 and 2013. The reduction in dissolved riverine inorganic phosphorus concentrations (DIP) from the early 1990s led to the decrease in their Chl a levels. However, dissolved inorganic nitrogen concentrations (DIN) decreased only slightly in the Vilaine and actually increased in the Loire, especially during summer. Simultaneously, phytoplankton in the VB has undergone profound changes with: (1) increase in biomass, (2) change in the position of the annual peak from spring to summer, and (3) increase in diatom:dinoflagellate ratios, especially in summer. The increase in phytoplankton biomass in VB, particularly in summer, was probably due to increased DIN loads from the Loire, sustained by internal regeneration of DIP and dissolved silicate from sediments. This long-term ecosystem-scale analysis reports the consequence of nutrient management scenarios focused solely on P reduction. Freshwater ecosystems upstream reveal successful recoveries through the control of P alone, while eutrophication continues to increase downstream, especially during the period of N limitation. Therefore, nutrient management strategies, paying particular attention to diffuse N-sources, are required to control eutrophication in receiving coastal waters.

The work presented here aims at comparing monitoring of S-metolachlor, the major pesticide in use in the Arcachon Bay (South West of France, transitional coastal area), by chemical analysis (monthly passive sampling) and contaminant dissipation modeling from sources (Mars-2D model). The global strategy consisted in i) identifying the major sources of S-metolachlor to the Bay, ii) monitoring these sources for 12 months, and iii) comparing modeled data in the Bay based on measured inputs, to chemical measurements made inside the Bay along with the 12-month source monitoring. Results first showed that the major S-metolachlor surface inputs to the Arcachon Bay are mainly from one single source. Modeled and measured data were in good agreement at 5 sites in the Bay, both in terms of concentration range and seasonal trends. Modeling thus offers a cost-effective solution for monitoring contaminants in transitional waters, overcoming in addition the technical limitations for measuring pg L-1 or lower levels in coastal waters. However, we highlighted that secondary sources may affect accuracy at local level.

Since the mid-20th century, Mediterranean lagoons have been affected by eutrophication, leading to significant changes in primary producers. In the early 2000s, management actions have been implemented to reduce nutrient inputs with the aim to achieve a good ecological status as requested by the EU water framework directive. As a result of these actions, a sharp decline in nutrient loads has been recorded in several lagoons leading to an oligotrophication of the water column. The analyses of a long-term data set (1998-2015) of 21 polyhaline and euhaline lagoons with contrasting trophic status allowed us to infer a general scheme for the changes in macrophyte assemblages during the oligotrophication process. Placing hypertrophic and oligotrophic conditions end to end, we inferred that the general pattern for the re-oligotrophication trajectory in Mediterranean coastal lagoons is described by the following sequence, with regime shifts between each state: (1) bare non-vegetated sediments, phytoplankton-dominated state; (2) opportunistic macroalgae; (3) seagrass and perennial macroalgae dominated state. However, we did not observe the latter regime shift for the most eutrophicated lagoons, which, so far, remained stuck in the opportunistic macroalgae state. So far, the shift from dominance of opportunistic macroalgae to a system dominated by seagrasses was only observed in a single lagoon where seagrasses had never completely disappeared, which possibly relates to resilience. More generally, the conditions favoring regime shifts from opportunistic macroalgae to seagrasses are still poorly understood. In conclusion, we describe a generic pattern for re-oligotrophication of Mediterranean coastal lagoons, although a full recovery from highly eutrophied to oligotrophic conditions may require more than a decade and may include conditions that remain so far poorly recognized.

A large spectrum of coastal lagoon types with a wide range of environmental conditions is observed along the French Mediterranean coast. These comprise wide trophic and salinity gradients, ranging from oligotrophic to hypertrophic status, and from nearly freshwater to slightly above marine Mediterranean Sea water salinities, respectively. The statistical analysis of a long-term dataset, including water column variables and observations of macrophyte genera, showed that salinity, depth, and then trophic status, were important factors explaining the distribution of benthic macrophytes for the soft-bottom sediments in the 34 studied French Mediterranean lagoons. Based on this, we assumed that the vegetation succession along the eutrophication gradient was different according to the lagoon salinity ranges. Euhaline and polyhaline lagoons follow the well-known Schramm schematic model, where aquatic angiosperm such as seagrasses dominate under oligotrophic conditions, and opportunistic macroalgae and phytoplankton dominate under eutrophic and hypertrophic conditions. In oligohaline and mesohaline lagoons, the succession is probably an intermediate scheme between the successions observed in small temperate lakes and in marine coastal ecosystems due to the presence of both brackish and freshwater species. We thus propose a conceptual scheme for the oligohaline and mesohaline lagoons.

Understanding the phenology of phytoplankton species is still a challenge and despite a lot of theoretical work on competition for ressources this process is under-represented in deterministic models. To study the main driver of the species selection, we thus used a trait-based model that keeps phenotypic variability through physiological trait parameterization. We next validate the results by using a key species, the toxic dinoflagellate Alexandrium minutum. Due to their monitoring, we show that harmful algae are ideal models for studying ecological niches and for contributing to this more global challenge. As a first step, a dimensionless model of an estuary (France) was built with water temperature and water exchanges deduced from a hydro-dynamic model. The biological parametrisation takes into account the size (from pico- to microphytoplankton) and the type of assimilation. The results show that temperature, competition for nutrients and dilution are important factors regulating the community structure and \textit{Alexandrium minutum} dynamics (more especially the bloom initiation and magnitude). These drivers contribute to determine the ecological niche of A. minutum, to influence the shape of its blooms and to provide potential explanations of its interannual variability. This approach mainly introduce more flexibility of the community structure to study how environmental forcing could drive its evolution.

The worldwide decline of seagrass meadows may result in the loss of relevant ecosystem services such as the carbon sequestration within marine ecosystems. In this paper, net primary production (NPP) of Zostera noltei meadows was assessed in the Arcachon Bay (SW France) with the aim of understanding the impact of meadows decline on C sequestration capacity at a basin scale. Net growth rates obtained by means of a year-long leaf-marking experiment (2005-2006) were coupled to interannual biomass measurements (1983-2010) to obtain a direct estimate of NPP. Concurrently, an indirect estimate was obtained through a mathematical model which embedded natural factors variation (temperature, light and nutrients). Z. noltei seasonal growth and leaf morphometry followed a unimodal pattern with a peak in late summer and a minimum in winter; the interannual biomass assessment showed a steadiness at spatial and temporal scales. Net primary production simulated by the mathematical model resulted lower than that obtained by the leaf-marking and biomass method. Moreover, a temporal shift among models was evident, given to the dependence of the simulation mainly on the irradiance. Daily NPP ranged from 0.4 +/- 0.2 to 8.4 +/- 0.4 gm m(-2) d(-1), corresponding to an annual NPP of 1134.2 +/- 100.2 g(Dw) m(-2) y(-1) and to a net C fixation of 362.9 +/- 88.1 g C m(-2) y(-1). By considering the loss of 33% of Z. noltei meadows in the Arcachon Bay in the period 1989-2010, it can be estimated a decline of C sequestration capacity from 24,846 +/- 6030 ton C y(-1) (1989) to 16,564 +/- 4020 ton C y(-1) (2007) at the basin scale. (C) 2016 Elsevier Ltd. All rights reserved.

Within the framework of research aimed at using genetic methods to evaluate harmful species distribution and their impact on coastal ecosystems, a portion of the ITS1rDNA of Alexandrium minutum was amplified by real-time PCR from DNA extracts of superficial (1–3cm) sediments of 30 subtidal and intertidal stations of the Bay of Brest (Brittany, France), during the winters of 2013 and 2015. Cell germinations and rDNA amplifications of A. minutum were obtained for sediments of all sampled stations, demonstrating that the whole bay is currently contaminated by this toxic species. Coherent estimations of ITS1rDNA copy numbers were obtained for the two sampling cruises, supporting the hypothesis of regular accumulation of A. minutum resting stages in the south-eastern, more confined embayments of the study area, where fine-muddy sediments are also more abundant. Higher ITS1rDNA copy numbers were detected in sediments of areas where blooms have been seasonally detected since 2012. This result suggests that specific genetic material estimations in superficial sediments of the bay may be a proxy of the cyst banks of A. minutum. The simulation of particle trajectory analyses by a Lagrangian physical model showed that blooms occurring in the south-eastern part of the bay are disconnected from those of the north-eastern zone. The heterogeneous distribution of A. minutum inferred from both water and sediment suggests the existence of potential barriers for the dispersal of this species in the Bay of Brest and encourages finer analyses at the population level for this species within semi-enclosed coastal ecosystems.

Asari (=Manila) clam, Ruditapes philippinarum, is the second bivalve mollusc in terms of production in the world and, in many coastal areas, can beget important socio-economic issues. In Europe, this species was introduced after 1973. In Arcachon Bay, after a decade of aquaculture attempt, Asari clam rapidly constituted neo-naturalized population which is now fished. However, recent studies emphasized the decline of population and individual performances. In the framework of a national project (REPAMEP), some elements of fitness, stressors and responses in Arcachon Bay were measured and compared to international data (41 publications, 9 countries). The condition index (CI = flesh weight/shell weight) was the lowest among all compared sites. Variation in average Chla concentration explained 30% of variation of CI among different areas. Among potential diseases, perkinsosis was particularly prevalent in Arcachon Bay, with high abundance, and Asari clams underwent Brown Muscle Disease, a pathology strictly restricted to this lagoon. Overall element contamination was relatively low, although arsenic, cobalt, nickel and chromium displayed higher values than in other ecosystems where Asari clam is exploited. Finally, total hemocyte count (THC) of Asari clam in Arcachon Bay, related to the immune system activity, exhibited values that were also under what is generally observed elsewhere. In conclusion, this study, with all reserves due to heterogeneity of available data, suggest that the particularly low fitness of Asari clam in Arcachon Bay is due to poor trophic condition, high prevalence and intensity of a disease (perkinsosis), moderate inorganic contamination, and poor efficiency of the immune system. (C) 2015 Elsevier Ltd. All rights reserved.

This study presents an assessment of the contributions of various primary producers to the global annual production and N/P cycles of a coastal system, namely the Arcachon Bay, by means of a numerical model. This 3D model fully couples hydrodynamic with ecological processes and simulates nitrogen, silicon and phosphorus cycles as well as phytoplankton, macroalgae and seagrasses. Total annual production rates for the different components were calculated for different years (2005, 2007 and 2009) during a time period of drastic reduction in seagrass beds since 2005. The total demand of nitrogen and phosphorus was also calculated and discussed with regards to the riverine inputs. Moreover, this study presents the first estimation of particulate organic carbon export to the adjacent open ocean.The calculated annual net production for the Arcachon Bay (except microphytobenthos, not included in the model) ranges between 22,850 and 35,300 tons of carbon. The main producers are seagrasses in all the years considered with a contribution ranging from 56% to 81% of global production. According to our model, the -30% reduction in seagrass bed surface between 2005 and 2007, led to an approximate 55% reduction in seagrass production, while during the same period of time, macroalgae and phytoplankton enhanced their productions by about +83% and +46% respectively. Nonetheless, the phytoplankton production remains about eightfold higher than the macroalgae production. Our results also highlight the importance of remineralisation inside the Bay, since riverine inputs only fulfill at maximum 73% nitrogen and 13% phosphorus demands during the years 2005, 2007 and 2009. Calculated advection allowed a rough estimate of the organic matter export: about 10% of the total production in the bay was exported, originating mainly from the seagrass compartment, since most of the labile organic matter was remineralised inside the bay. (C) 2015 Elsevier Ltd. All rights reserved.

The aim of the present study was to identify environmental factors that could explain the distribution of different pathologies of commercially exploited intertidal bivalves in an Atlantic lagoon, Arcachon Bay. In particular, the role of the salinity gradient as a driver was explored. The Manila clam Ruditapes philippinarum experienced two severe pathologies, perkinsosis, which is due to a protozoan parasite, and brown muscle disease (BMD), the etiological agent of which remains unknown. Perkinsus olseni infection was very low in a small low-salinity area but, at the scale of the entire lagoon, was more influenced by organic matter content in the sediment and by emersion time. BMD prevalence was also 2.6 times higher in the higher organic content area but was also negatively correlated with salinity. The sympatric cockle (Cerastoderma edule) was affected by eight trematode species. These parasites have a complex life cycle that generally involves three free-living host species. The distribution of the different trematode communities was rather patchy within Arcachon Bay with no clear relationship with measured environmental factors. The dominance of particular trematode species could be due to the presence of other hosts involved in their life cycle, making it more difficult to detect a major environmental driver. This survey demonstrated that salinity is not a major factor explaining disease distribution in this temperate lagoon. This result has consequences for the research of 'refuge areas' (free of diseases) or 'hot spots' (heavy infection) for species of high economic value.