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Microphytobenthos (MPB) are a key primary producer of intertidal mudflats. MPB face strong variability in incident irradiance during low tides. Despite photoprotection and photoacclimation, such variations can translate into photoinhibition of MPB cells. This study explores the effect of photoinhibition on MPB primary production (PP) over a large and productive temperate mudflat (Brouage mudflat, NW France). We used a regional and high-resolution tri-dimensional hydrodynamic model coupled to a MPB model with or without photoinhibition. Photoinhibition leads to a 20% (-0.79 t C) decrease of the simulated MPB PP over the entire mudflat. As the upper shore is exposed to light more frequently and longer than the lower shore, the decrease of MPB PP is higher on the upper shore (-29%) than on the lower shore (-5%). With the highest photosynthetically active radiation cumulated over the mudflat, the decrease of MPB PP due to photoinhibition is the highest during spring and spring tides (-22% and -23%, respectively). The model suggests MPB photoinhibition is sensitive to the photoacclimation status of MPB cells through the light saturation parameter. This first modeling attempt to account for MPB photoinhibition is highly constrained by our current theoretical knowledge and limitations on the MPB growth physiology, but it suggests that this process can have a substantial impact on the MPB PP. As such, assessing the MPB photosynthetic response to the highly variable environmental conditions that prevail in large and productive intertidal mudflats is a real challenge for quantifying MPB PP from a synoptic to inter-annual time scale. Plain Language Summary Benthic micro-algae or microphytobenthos (MPB) inhabiting the surficial sediment sustain the high biological production of intertidal mudflats. MPB achieve photosynthesis by aggregating into a dense biofilm at the mud surface during daytime low tides. As MPB can be exposed to short-term variations and high light levels, they change their short-term physiology and position within the sediment to protect themselves. However, such strategies can be outbalanced by a too long stressful light exposure. In this study, we explore with a numerical model the impact of photoinhibition on MPB primary production (PP) over a large and very productive mudflat (NW France). The model suggests that photoinhibition can strongly impact MPB PP. With photoinhibition, the yearly PP decreases by 20 % over the whole mudflat. The model suggests MPB PP is sensitive to the photoacclimation status of MPB cells, i.e. their light use efficiency at a given light level. This first modeling attempt to account for MPB photoinhibition is highly constrained by our current theoretical knowledge and limitations on the MPB growth physiology, but it suggests that this process can have a substantial impact on the MPB PP.

Seagrass meadows play an important role in “blue carbon” sequestration and storage, but their dynamic metabolism is not fully understood. In a dense Zostera marina meadow, we measured benthic O2 fluxes by aquatic eddy covariance, water column concentrations of O2, and partial pressures of CO2 (pCO2) over 21 full days during peak growing season in April and June. Seagrass metabolism, derived from the O2 flux, varied markedly between the 2 months as biomass accumulated and water temperature increased from 16°C to 28°C, triggering a twofold increase in respiration and a trophic shift of the seagrass meadow from being a carbon sink to a carbon source. Seagrass metabolism was the major driver of diurnal fluctuations in water column O2 concentration and pCO2, ranging from 173 to 377 μmol L−1 and 193 to 859 ppmv, respectively. This 4.5‐fold variation in pCO2 was observed despite buffering by the carbonate system. Hysteresis in diurnal water column pCO2 vs. O2 concentration was attributed to storage of O2 and CO2 in seagrass tissue, air–water exchange of O2 and CO2, and CO2 storage in surface sediment. There was a ~ 1:1 mol‐to‐mol stoichiometric relationship between diurnal fluctuations in concentrations of O2 and dissolved inorganic carbon. Our measurements showed no stimulation of photosynthesis at high CO2 and low O2 concentrations, even though CO2 reached levels used in IPCC ocean acidification scenarios. This field study does not support the notion that seagrass meadows may be “winners” in future oceans with elevated CO2 concentrations and more frequent temperature extremes.

To the best of our knowledge, the understanding of benthic metabolism of coastal sedimentary areas is still limited due to the complexity of determining their true in situ dynamics over large spatial and temporal scales. Multidisciplinary methodological approaches are then necessary to increase our comprehension of factors controlling benthic processes and fluxes. An aquatic Eddy Covariance (EC) system and Benthic Chambers (BC) were simultaneously deployed during the winter of 2013 in the Bay of Brest within a Maerl bed and a bare mudflat to quantify and compare O2 exchange at the sediment–water interface. Environmental abiotic parameters (i.e., light, temperature, salinity, current velocity and water depth) were additionally monitored to better understand the mechanisms driving benthic O2 exchange. At both sites, EC measurements showed short-term variations (i.e. 15 min) in benthic O2 fluxes according to environmental conditions. At the Maerl station, EC fluxes ranged from-21.0 mmol m−2 d−1 to 71.3 mmol m−2 d −1 and averaged 22.0 ± 32.7 mmol m−2 d−1 (mean ± SD), whilst at the bare muddy station, EC fluxes ranged from -43.1mmol m−2 d−1 to 12.1 mmol m−2 d −1 and averaged -15.9 ± 14.0 mmol m−2 d−1 (mean ± SD) during the total deployment. Eddy Covariance and Benthic Chambers measurements showed similar patterns of temporal O2 flux changes at both sites. However, at the Maerl station, BC may have underestimated community respiration. This may be due to the relative large size of the EC footprint (compared to BC), which takes into account the mesoscale spatial heterogeneity (e.g. may have included contributions from bare sediment patches). Also, we hypothesize that the influence of bioturbation induced by large-sized mobile benthic fauna on sediment oxygen consumption was not fully captured by BC compared to EC. Overall, the results of the present study highlight the importance of taking into account specific methodology limitations with respect to sediment spatial macro-heterogeneity and short-term variations of environmental parameters to accurately assess benthic O2 exchange in the various benthic ecosystems of the coastal zone.

Subtropical seagrass meadows play a major role in the coastal carbon cycle, but the nature of air–water CO2 exchanges over these ecosystems is still poorly understood. The complex physical forcing of air–water exchange in coastal waters challenges our ability to quantify bulk exchanges of CO2 and water (evaporation), emphasizing the need for direct measurements. We describe the first direct measurements of evaporation and CO2 flux over a calcifying seagrass meadow near Bob Allen Keys, Florida. Over the 78‐d study, CO2 emissions were 36% greater during the day than at night, and the site was a net CO2 source to the atmosphere of 0.27 ± 0.17 μmol m−2 s−1 (x̅ ± standard deviation). A quarter (23%) of the diurnal variability in CO2 flux was caused by the effect of changing water temperature on gas solubility. Furthermore, evaporation rates were ~ 10 times greater than precipitation, causing a 14% increase in salinity, a potential precursor of seagrass die‐offs. Evaporation rates were not correlated with solar radiation, but instead with air–water temperature gradient and wind shear. We also confirm the role of convective forcing on night‐time enhancement and day‐time suppression of gas transfer. At this site, temperature trends are regulated by solar heating, combined with shallow water depth and relatively consistent air temperature. Our findings indicate that evaporation and air–water CO2 exchange over shallow, tropical, and subtropical seagrass ecosystems may be fundamentally different than in submerged vegetated environments elsewhere, in part due to the complex physical forcing of coastal air–sea gas transfer., Deutscher Akademischer Austauschdienst http://dx.doi.org/10.13039/501100001655, National Science Foundation http://dx.doi.org/10.13039/100000001

Coastal vegetated habitats like seagrass meadows can mitigate anthropogenic carbon emissions by sequestering CO2 as “blue carbon” (BC). Already, some coastal ecosystems are actively managed to enhance BC storage, with associated BC stocks included in national greenhouse gas inventories. However, the extent to which BC burial fluxes are enhanced or counteracted by other carbon fluxes, especially air‐water CO2 flux (FCO2) remains poorly understood. In this study, we synthesized all available direct FCO2 measurements over seagrass meadows made using atmospheric Eddy Covariance, across a globally representative range of ecotypes. Of the four sites with seasonal data coverage, two were net CO2 sources, with average FCO2 equivalent to 44%–115% of the global average BC burial rate. At the remaining sites, net CO2 uptake was 101%–888% of average BC burial. A wavelet coherence analysis demonstrated that FCO2 was most strongly related to physical factors like temperature, wind, and tides. In particular, tidal forcing was a key driver of global‐scale patterns in FCO2, likely due to a combination of lateral carbon exchange, bottom‐driven turbulence, and pore‐water pumping. Lastly, sea‐surface drag coefficients were always greater than the prediction for the open ocean, supporting a universal enhancement of gas‐transfer in shallow coastal waters. Our study points to the need for a more comprehensive approach to BC assessments, considering not only organic carbon storage, but also air‐water CO2 exchange, and its complex biogeochemical and physical drivers., Plain Language Summary: Carbon storage is a valuable ecosystem service of seagrass meadows, serving as a possible pathway to draw down atmospheric carbon dioxide (CO2) levels. However, this approach may be unsuccessful if carbon storage in sediments is exceeded by the release of CO2 from the water. To better understand the scope of this problem, we compiled all available measurements of air‐water CO2 exchange over seagrass meadows. We found that rates of CO2 release or uptake were indeed large, even when compared with potential rates of carbon storage in seagrass soils. However, these large air‐water exchanges of CO2 did not occur for the same reason everywhere. While light availability was sometimes a strong predictor of air‐water CO2 exchange, tidal mixing and temperature were also very important, revealing a much more complex network of drivers than previously thought. Despite these diverse conditions, we found one key similarity across all sites, in that rates of air‐water gas transfer appear to always be greater than would be expected for the open ocean. Taken together, the results of our study show that assessments of carbon storage in coastal seagrass ecosystems will be incomplete if they do not consider exchanges of CO2 between the water and air., Key Points: Direct measurements show that air‐water CO2 exchange over seagrass meadows is of similar magnitude to carbon burial rates. Key drivers are tides, temperature, light, and wind, which off in importance over hourly seasonal time scales. Surface drag coefficients were greater than open water prediction, suggesting a near‐universal gas transfer enhancement across all sites., Bundesministerium für Bildung und Forschung (BMBF) http://dx.doi.org/10.13039/501100002347, Florida Coastal Everglades LTER, Consejo Nacional de Ciencia y Tecnología (CONACYT) http://dx.doi.org/10.13039/501100003141, MEXT, Japan Society for the Promotion of Science (JSPS) http://dx.doi.org/10.13039/501100001691, Ethicon Endo‐Surgery http://dx.doi.org/10.13039/100005566, Deutscher Akademischer Austauschdienst http://dx.doi.org/10.13039/501100001655, National Science Foundation http://dx.doi.org/10.13039/100000001, Vetenskapsrådet http://dx.doi.org/10.13039/501100004359, Uppsala Universitet http://dx.doi.org/10.13039/501100007051, Agence Nationale de la Recherche http://dx.doi.org/10.13039/501100001665, Université de Bordeaux http://dx.doi.org/10.13039/501100006251, Institut National de la Recherche Agronomique http://dx.doi.org/10.13039/501100006488

International audience; Microphytobenthos (MPB) at the sediment surface of intertidal mudflats are known to show a high spatial and temporal variability in response to the biotic and abiotic conditions prevailing at the mud surface. It makes long-term and large-scale monitoring of MPB Gross Primary Production (GPP) difficult to set up. In this study, we developed the first 3D physical-biological coupled model (MARS-3D) that explicitly simulates GPP of intertidal MPB at the mudflat scale, and we compared the outputs with in situ and space remote sensing MPB GPP data. We discuss the sources of discrepancies between the modeling and the remote sensing approach in the light of future developments to be done. For instance, the remote sensing algorithm provides a very synoptic view of the mudflat GPP. It is well-suited to achieve diagnostic estimates of MPB GPP at the synoptic spatial and temporal scale. By contrast, the MARS-3D model provides a more dynamic representation of the MPB activity and prognostic estimates of MPB GPP over the mudflat. It is very relevant to resolve the seasonal and inter-annual dynamics of MPB. Getting comparable GPP estimates derived from the remote sensing algorithm and 3D physical-biological coupled model will further require a better convergence in terms of equations structure, biological constants parameterization, and source data used (i.e., vegetation index vs. chlorophyll a). Setting a common parameterization in both the numerical model and remote sensing algorithm might be challenging in a perspective of mapping MPB PP over large mudflats from a synoptic to inter-annual time scale, but it could open the door to a new way of quantifying MPB GPP over large intertidal mudflats.

Measurements of carbon dioxide fluxes were performed over a temperate intertidal mudflat in southwestern France using the micrometeorological Eddy Covariance (EC) technique. EC measurements were carried out in two contrasting sites of the Arcachon flat during four periods and in three different seasons (autumn 2007, summer 2008, autumn 2008 and spring 2009). In addition, satellite images of the tidal flat at low tide were used to link the net ecosystem CO2 exchange (NEE) with the occupation of the mudflat by primary producers, particularly by Zostera noltii meadows. CO2 fluxes during the four deployments showed important spatial and temporal variations, with the flat rapidly shifting from sink to source with the tide. Absolute CO2 fluxes showed generally small negative (influx) and positive (efflux) values, with larger values up to −13 μmol m−2 s−1 for influxes and 19 μmol m−2 s−1 for effluxes. Low tide during the day was mostly associated with a net uptake of atmospheric CO2. In contrast, during immersion and during low tide at night, CO2 fluxes where positive, negative or close to zero, depending on the season and the site. During the autumn of 2007, at the innermost station with a patchy Zostera noltii bed (cover of 22 ± 14% in the wind direction of measurements), CO2 influx was −1.7 ± 1.7 μmol m−2 s−1 at low tide during the day, and the efflux was 2.7 ± 3.7 μmol m−2 s−1 at low tide during the night. A gross primary production (GPP) of 4.4 ± 4.1 μmol m−2 s−1 during emersion could be attributed to microphytobenthic communities. During the summer and autumn of 2008, at the central station with a dense eelgrass bed (92 ± 10%), CO2 uptakes at low tide during the day were −1.5 ± 1.2 and −0.9 ± 1.7 μmol m−2 s−1, respectively. Night time effluxes of CO2 were 1.0 ± 0.9 and 0.2 ± 1.1 μmol m−2 s−1 in summer and autumn, respectively, resulting in a GPP during emersion of 2.5 ± 1.5 and 1.1 ± 2.0 μmol m−2 s−1, respectively, attributed primarily to the seagrass community. At the same station in April 2009, before Zostera noltii started to grow, the CO2 uptake at low tide during the day was the highest (−2.7 ± 2.0 μmol m−2 s−1). Influxes of CO2 were also observed during immersion at the central station in spring and early autumn and were apparently related to phytoplankton blooms occurring at the mouth of the flat, followed by the advection of CO2-depleted water with the flooding tide. Although winter data as well as water carbon measurements would be necessary to determine a precise CO2 budget for the flat, our results suggest that tidal flat ecosystems are a modest contributor to the CO2 budget of the coastal ocean.

We have studied 15 catchments supplying freshwater to a French Atlantic coastal lagoon, where increase in nitrogen loads due to agriculture is supposed to have destabilized the ecosystem in the last decades. The catchment is a lowland composed of Pleistocene sands with an average slope of 0.25%. To study the nutrient export in relation to land-use surface waters were sampled bi-weekly between October 2006 and January 2009 and land-use was established by plane photographs and Geographic Information System (GIS). Cultivated pine forests represent more than 80% of the total surface and 7% of the catchment area has been deforested recently. Significant areas of some catchments are used for maize crop. Housing is confined to the coastal zone. Maize and forest crop give a robust signature in terms of nitrate export. In view of modeling the nutrient fluxes, we have established the mean export rate for every land-use: forested parcels, deforested parcels, cultivated surfaces, and housing areas export 45, 93, 2850, and 61 kg N-nitrate km(-2) year(-1), respectively. Exports of ammonium, dissolved organic N (DON), and dissolved inorganic P (DIP) could not be related to land use. The mean export is 13, 100, and 0.57 kg km(-2) year(-1) for N-ammonium, DON, and DIP, respectively. The modeling of nitrogen flux is in good agreement with our measures for the largest catchment, which supplies about 90% of the total continental DIN flux. However, small catchments are more dynamic due to hydrological conditions and the model is less accurate. This work has permitted to complete and unify scattered studies about nutrient cycling in this area. Thus we have established and compared the nitrogen budget of cornfields and cultivated pine forest. We have emphasized that (i) fertilizer use should be reduced in cornfields because they stock between 200 and 6400 kg DIN km(-2) year(-1), and (ii) the nitrogen budget in pine forest mostly depends on tree harvesting and symbiotic N-fixation, which is poorly constrained. Export of N by rivers represents a small contribution to the N budget of soils.