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The properties of incident light play a crucial role in the mating process of diatoms, a group of ecologically important microalgae. While species-specific requirements for light intensity and photoperiod have been observed in several diatom species, little is known about the light spectrum that allows sexual reproduction. Here, we study the effects of spectral properties and light intensity on the initiation and progression of sexual reproduction in the model benthic diatom Seminavis robusta. We found that distinct stages of the mating process have different requirements for light. Vigorous mating pair formation occurred under a broad range of light intensities, ranging from 10 to 81 µE m−2 s−1, while gametogenesis and subsequent stages were strongly affected by moderate light intensities of 27 µE m−2 s−1 and up. In addition, light of blue or blue–green wavelengths was required for the formation of mating pairs. Combining flow cytometric analysis with expression profiling of the diatom-specific cyclin dsCyc2 suggests that progression through a blue light-dependent checkpoint in the G1 cell cycle phase is essential for induction of sexual reproduction. Taken together, we expand the current model of mating in benthic pennate diatoms, which relies on the interplay between light, cell cycle and sex pheromone signaling.

Ionic liquids (IL) are regarded as the solution to the modern world’s need to create and use compounds that exhibit a range of desirable properties while having a low environmental impact. However, recent reports are shattering the image of ionic liquids as environmentally friendly substances, especially in relation to the aquatic environment, revealing their potentially toxic effects. To assess the potential environmental impact of ILs, we conducted an experiment involving 1-butyl-3-methylimidazolium chloride ([BMIM]Cl), a substance considered to be the least hazardous among the imidazolium chloride ILs, on Baltic microphytobenthic communities. Microphytobenthos collected from the environment was tested under controlled laboratory conditions, and both the cell counts and the chloroplast condition were used as endpoints. It was shown that [BMIM]Cl at concentrations of 10−3 and 10−2, considered safe based on a cumulative impact assessment, has a negative effect on the condition of the microalgal cells and causes a reduction in population size. Although, under the influence of [BMIM]Cl, only a small proportion of the species was eliminated from the communities, only two species among those important to the communities showed resistance to this compound and eventually began to dominate the communities.

The toxic effect of exposure to arsenic, As(V), at concentrations of 0 to 30 mg L−1, for 49 days, on epipsammic biofilms, was evaluated in a microcosm experiment. The growth and composition of biofilms developed on sediments containing As concentrations of 31 mg kg−1 and 85 mg kg−1 were compared, using photosynthetic parameters and Live/Dead stains as end points. A toxic effect of arsenic could not be demonstrated; however, biofilm growth was higher over the sediment with higher arsenic concentrations, suggesting the development of pollution-induced community induced tolerance (PICT). Nevertheless, PICT was not observed after exposure to high arsenic concentration in the laboratory, as there were no differences in algal growth between the previous 0 and 30 mg L−1 systems exposed to new 30 mg As L−1 dissolution over 29 days. The algal composition was affected by the added arsenic, and brown algae were the most tolerant compared to green algae and cyanophyceae, as their percentage increased from 25 and 33% in the control samples to 57 and 47% in the samples with the highest added As concentration. In turn, the biofilm development influenced arsenic redistribution and speciation. Arsenic concentration in water decreased with time during the incubation experiment, retained by the sediment particles and the biofilm. In the biofilm, extracellular As was significantly higher (up to 11 times) than intracellular arsenic. As(V) was the predominant species in water and in the biofilm, but products of biotic transformation, namely As(III), DMA(V) and MMA(V), were also found in the solution and in the biofilm in some systems, demonstrating reduction and methylation by the organisms. As a conclusion, a toxic effect was not detected for the concentrations evaluated. Biofilms naturally exposed in the river system to high As concentrations acquire pollution-induced tolerance; however, tolerance was not acquired by exposure to 30 mg L−1 for 29 days in the laboratory.

The microphytobenthos (MPB), the communities of benthic microalgae that colonize the intertidal flats of estuaries, form highly productive and dense biofilms in the photic layer during diurnal low tides. MPB assemblages are exposed to extreme conditions such as high and low temperature, high irradiances and UV radiation, or high salinities. This study aimed to test the effect of extreme temperatures on the photoinactivation and repair of photosystem II (PSII) of these natural communities. The study was carried out in two intertidal sites of the Ria de Aveiro with different sediment characteristics and MPB communities, epipelic and epipsammic. Sampling was carried out during one year, from autumn 2020 to summer of 2021. Lincomycin was used to inhibit the repair of photoinactivation PSII. The study was also conducted in two species representatives of eppipelic and epipsammic communities, Seminavis robusta and Staurosirella guenter-grassii, respectively. The results showed an important effect of low temperature on PSII photoinactivation, for all sampling sites and occasions, and for both species. These results contradict a hypothesis recently put forward stating that abiotic stress, particularly low temperature, does not induce photoinactivation of PSII. It is concluded that more research is needed to clarify the true role of abiotic stress in PSII photoinactivation and algal productivity under natural conditions. O microfitobentos (MPB), as comunidades de microalgas bênticas que colonizam as zonas de entremarés dos estuários, formam biofilmes altamente produtivos e densos na camada fótica durante as marés baixas diurnas. As comunidades de MPB são expostas a condições extremas, como alta e baixa temperatura, altas irradiâncias e radiação UV, ou salinidades extremas. Este estudo teve como objetivo testar o efeito de temperaturas extremas na fotoinativação e reparação do fotossistema II (PSII) dessas comunidades naturais. O estudo foi realizado em dois locais intertidais da Ria de Aveiro com características sedimentares e comunidades MPB diferentes, dominadas por comunidades epipélicas e epipsâmicas. A amostragem foi realizada ao longo de um ano, entre outono de 2020 até ao verão de 2021. Foi utilizado lincomicina como inibidor da reparação do PSII. O estudo também foi realizado em duas espécies representativas das comunidades de MPB epipélica e epipsâmica, Seminavis robusta e Staurosirella guenter-grassii, respetivamente. Os resultados mostraram um importante efeito da baixa temperatura na fotoinativação do PSII, para todos os locais e ocasiões de amostragem e para ambas as espécies. Esses resultados contradizem uma hipótese recentemente apresentada de que o stress abiótico, nomeadamente a baixa temperatura, não induz a fotoinativação do PSII. Conclui-se que mais é necessária mais investigação, para esclarecer o verdadeiro papel do stress abiótico na fotoinativação e reparação do PSII e na produtividade de algas em condições naturais. Mestrado em Biologia Marinha Aplicada

63 species of diatoms were found in the microphytobenthos of the Odessa bay hard grounds and the adjacent aquatory. Prevailing pennate forms of diatoms (53 species) were being compared with centrical ones (10 species) as to their systematic composition. The representatives of genera Licmophora, Navicula, Nitzschia, Tabularia made up the basis of microphytobenthos species composition. The found diatoms are mostly poly- (34,9 %) and mesohalobic (30,2 %), alkalyphylic (65,0 %), multizonal (46,0 %) and boreal (30,2 %). by their ecologic indicators. They are mostly a- (11,1 %) and P-Mesosaprobic (20,6 %) in relation to pollution. There has been shown that the quantity of a-Mesosaprobic diatoms is 1,5 times as much as the regions with high technological loading (the Datcha Kovalevskogo and the Oil Terminal of Odessa port). In spring and autumn we observed the greatest abundance of diatoms., Проанализировано разнообразие диатомовых водорослей (63 вида), обнаруженных в обрастаниях твердых субстратов некоторых районов побережья Одесского залива и сопредельной акватории. По видовому составу преобладали пеннатные формы (53 вида); центрических было меньше (10 видов). Представители родов Licmophora, Navicula, Nitzschia, Tabulariaсоставляли основу видового состава обрастаний. По экологическим характеристикам обнаруженные диатомеи в основном являются поли- и мезогалобами (соответственно 34,9 % и 30,2%), алкалифилами (65,0 %), мультизональными (46,0 %) и бореальными (30,2 %). По отношению к загрязнению они в основном являются а- (11,1%) и Р-мезосапробами (20,6%). Показано, что количество а-мезосапробов почти в 1,5 раза выше в районах с высокой техногенной нагрузкой (Дача Ковалевского и Нефтегавань Одесского порта). Наибольшая численность водорослей наблюдалась весной и осенью., Вивчали таксономічний склад діатомових водоростей (63 види), знайдених в обростаннях твердих субстратів деяких районів узбережжя Одеської затоки та суміжної акваторії. За систематичним складом переважали пенатні форми (53 види) порівняно з центричними (10 видів). Представники родів Licmophora, Navicula, Nitzschia, Tabularia складали основу видового складу обростань. За екологічними показниками знайдені діатомеї в основному є полі- та мезогалобами (відповідно 34,9 % та 30,2 %), алкаліфілами (65,0 %), мультизональними (46,0 %) та бореальними (30,2 %). По відношенню до забруднення вони в основному є а-(11,1 %) та Р-мезосапробами (20,6 %). Показано, що кількість а-мезосапробів майже у 1,5 рази вища у районах з високим техногенним навантаженням (райони Дачі Ковалевського та Нафтогавані Одеського порту).

Miсrophytobenthos ofthe Lower Dniesterwas studied. It has been found 185 species of algae, belonging to 76 genera, 49 families, 26 orders, 10 classes and 6 divisions. 34 species ofthem are new for algae florae ofofthe Lower Dniester., Исследован видовой состав водорослей бентоса водоемов нижнего Днестра. На протяжении 2000- 2006 гг. найдено 185 видов, которые относятся к 76 родам, 49 семействам, 26 порядкам, 10 классам и 6 отделам. Из них 34 вида альгофлоры водоемов нижнего Днестра обнаружены впервые., Досліджено видовий склад водоростей бентосу водойм басейну нижнього Дністра. На протязі 2000- 2006 рр. знайдено 185 видів, які належать до 76 родів, 49 родин, 26 порядків, 10 класів і 6 відділів. З них 34 види для альгофлори водойм нижнього Дністра наведені вперше

Dietary specialization is common in animals and has important implications for individual fitness, inter‐ and intraspecific competition, and the adaptive potential of a species. Diet composition can be influenced by age‐ and sex‐related factors including an individual's morphology, social status, and acquired skills; however, specialization may only be necessary when competition is intensified by high population densities or increased energetic demands.To better understand the role of age‐ and sex‐related dietary specialization in facilitating seasonal resource partitioning, we inferred the contribution of biofilm, microphytobenthos, and benthic invertebrates to the diets of western sandpipers (Calidris mauri) from different demographic groups during mid‐winter (January/February) and at the onset of the breeding migration (April) using stable isotope mixing models. Western sandpipers are sexually dimorphic with females having significantly greater body mass and bill length than males.Diet composition differed between seasons and among demographic groups. In winter, prey consumption was similar among demographic groups, but, in spring, diet composition differed with bill length and body mass explaining 31% of the total variation in diet composition. Epifaunal invertebrates made up a greater proportion of the diet in males which had lesser mass and shorter bills than females. Consumption of Polychaeta increased with increasing bill length and was greatest in adult females. In contrast, consumption of microphytobenthos, thought to be an important food source for migrating sandpipers, increased with decreasing bill length and was greatest in juvenile males.Our results provide the first evidence that age‐ and sex‐related dietary specialization in western sandpipers facilitate seasonal resource partitioning that could reduce competition during spring at the onset of the breeding migration.Our study underscores the importance of examining resource partitioning throughout the annual cycle to inform fitness and demographic models and facilitate conservation efforts., Our results provide the first evidence of seasonal differences in diet composition among demographic groups of western sandpipers, supporting the conclusion that age‐ and sex‐related dietary specialization facilitate seasonal resource partitioning in this species. Differences in diet composition among demographic groups were more pronounced at the onset of migration in spring compared to mid‐winter following the expectation that the consumption of biofilm and microphytobenthos provides energy for sandpipers during their breeding migration and reduces competition when high densities of birds occupy foraging sites. In spring, juveniles, particularly juvenile males, consumed more biofilm and microphytobenthos than adults supporting our hypothesis that sandpipers with shorter bills, lesser mass, and less prey handling experience would consume the greatest amount of biofilm and microphytobenthos. Photo credit: William Chan.

The global biodiversity loss has increased the need to understand the effects of decreasing diversity, but our knowledge on how species loss will affect the functioning of communities and ecosystems is still very limited. Here, the levels of taxonomic and functional beta diversity and the effect of species loss on functional beta diversity were investigated in an estuary that provides a naturally steep environmental gradient. The study was conducted using diatoms that are among the most important microorganisms in all aquatic ecosystems and globally account for 40% of marine primary production. Along the estuary, the taxonomic beta diversity of diatom communities was high (Bray-Curtis taxonomic similarity 0.044) and strongly controlled by the environment, particularly wind exposure, salinity, and temperature. In contrast, the functional beta diversity was low (Bray-Curtis functional similarity 0.658) and much less controlled by the environment. Thus, the diatom communities stayed functionally almost similar despite large changes in species composition and environment. This may indicate that, through high taxonomic diversity and redundancy in functions, microorganisms provide an insurance effect against environmental change. However, when studying the effect of decreasing species richness on functional similarity of communities, simulated species loss to 45% of the current species richness decreased functional similarity significantly. This suggests that decreasing species richness may increase variability and reduce the stability and resilience of communities. These results highlight the importance of high taxonomic biodiversity for the stable functioning of benthic communities. Electronic supplementary material The online version of this article (10.1007/s00248-020-01576-9) contains supplementary material, which is available to authorized users.

International audience; Nitrogen loads in natural waters remain elevated in populated and agricultural areas with serious impact on estuarine and coastal ecosystems. Intertidal sediments can play a significant role in attenuating the high nitrogen levels in water via microbial nitrate reduction, in general dominated by denitrification. These heterotrophic processes are heavily mediated by both the quantity and quality of organic matter available. Benthic microalgae were experimentally investigated as organic carbon source for denitrifying microbes in intertidal mudflat sediments from the Seine Estuary (France). Dry microphytobenthos (including algae and their extracellular polymeric substances) were added to sediments and nitrate reduction rates were monitored over a two-week period using anoxic controlled flow-through reactor approach. Our results show that microphytobenthos addition resulted in significantly higher nitrate reduction (67–332% increase), highly related to the added amount of microphytobenthos. Moreover, increase of the low molecular weight carbohydrates consumption (11–39%) highlight the measurable contribution of extracellular polymeric substances to the carbon consumption during nitrate reduction. The addition of microphytobenthos increased the abundance of nitrite reductase genes, especially those encoding the nirS gene (43–152% increase) while nitrous oxide reductase genes (nosZ gene) remained constant. Microphytobenthos appeared to favor complete denitrification as suggested by an increase in nirS and a decrease in clade II nosZ gene copy numbers. This study confirms experimentally the assumption that microbes use microalgae and particularly labile extracellular polymeric substances as a carbon substrate for nitrate reduction. These results reinforce the impact played by microphytobenthos in intertidal mudflats by highlighting their role on denitrifying microbes and nitrate removal from water.

Historic shipwrecks form an anthropogenic landmark in marine environment, yet their influence on the local geochemistry and microbiology remains largely unexplored. In this study, sediment and steel hull samples were taken around the V-1302 John Mahn, a World War II shipwreck, at increasing distance from the wreck, in different directions. Polycyclic aromatic hydrocarbons (PAH’s), explosives, and heavy metal levels were determined and related to the microbial composition. Benz(a)anthracene and fluoranthene remain present at the mg kg-1 level, probably originating from the coal bunker. These PAH’s indicate that the wreck is still influencing the surrounding sediments however the effects are very dependent on which side of the wreck is being studied. Known PAH degrading taxa like Rhodobacteraceae and Chromatiaceae were more abundant in samples with high aromatic pollutant content. Moreover, sulphate reducing bacteria (such as Desulfobulbia), proven to be involved in steel corrosion, were found present in the biofilm. This study shows that even after 80 years, a historic shipwreck can still significantly steer the surrounding sediment chemistry and microbial ecology.

Increasing anthropogenic pressures on marine and coastal ecosystems, particularly in the English Channel, are causing changes in habitats, ecosystems and the various associated ecosystem functions. The construction of marine and coastal structures such as dikes as well as the emergence of several projects to install offshore wind turbines is constantly increasing on the French coasts of the English Channel. With these different projects, the artificialization of certain habitats becomes inevitable, so it is essential to assess their ecosystem impacts, and, if possible, to limit them. The MARINEFF project was born in this context, it aims to reconcile human development and ecological benefit. The development of these many coastal infrastructures can also make it possible to create new habitats. The objective of this PhD is to assess biological colonization processes at different scales as well as certain ecological functions such as the primary production on different types of marine infrastructures under controlled conditions and in situ situations on two site the Rade of Cherbourg and the Bay of Seine. Modulated fluorescence (PAM) measurements carried out on the different compartments of benthic primary producers made it possible to evaluate the primary production function and its evolution according to the forcing’s tested or observed. An important part of this PhD focused on the study of hard substrate microphytobenthos, its growth, its photobiology in relation to the type of colonized substrate, its surface structure and the impact of different forcing’s on these parameters. On a larger scale, the development of benthic communities has also been characterized for both sites and on different infrastructures. In situ primary production measurements combined with biodiversity and PAM assessment have made it possible to describe the colonization processes of artificial infrastructures and to assess their effectiveness. This work brings a new vision to the benthic ecology associated with artificial hard substrates and makes it possible to provide reliable estimates of the impact of these structures on the ecosystem.; L’accroissement des pressions anthropiques sur les écosystèmes marins et côtiers, en particulier en Manche, provoquent des modifications des habitats, des écosystèmes et des différentes fonctions écosystémiques associées. La construction d’ouvrages maritimes et côtiers tels que les digues ou des ouvrages portuaires ainsi que l’émergence de plusieurs projets d’implantation d’éoliennes off-shore est en augmentation constante sur les côtes de la Manche française. Avec ces différents projets, l’artificialisation de certains habitats devient inévitable, il est donc primordial d’évaluer leurs impacts écosystémiques, et, si possible, de les limiter. Le projet MARINEFF est né dans ce contexte, il vise à concilier développement humain et bénéfice écologique. Le développement de ces nombreuses infrastructures côtières crée de nouveaux habitats. L’objectif de ces travaux a été d’évaluer les processus de colonisation biologique à différentes échelles ainsi que certaines fonctions écologiques comme la production primaire sur différents types d’infrastructures marines en conditions contrôlées et en situation in situ dans deux sites la rade de Cherbourg et la baie de Seine. Les mesures de fluorescence modulée (PAM) réalisées sur les différents compartiments de producteurs primaires benthiques ont permis d’évaluer la fonction de production primaire et son évolution en fonction des forçages testés ou observés. Une part importante de ce travail s’est concentrée sur l’étude du microphytobenthos de substrat dur, sa croissance, sa photobiologie en relation avec le type de substrat colonisé, sa structure de surface et l’impact de différents forçages sur ces paramètres. A une plus grande échelle, le développement des communautés benthiques a également été caractérisé sur les deux sites et sur différentes infrastructures. Des mesures de production primaire in situ associées à des mesures de biodiversité et de PAM ont permis de décrire les processus de colonisation d’infrastructures artificielles et d’évaluer leur efficacité. Ces travaux apportent une nouvelle vision à l’écologie benthique associée aux substrats durs artificiels et apportent des estimations fiables de l’impact de ces structures sur l’écosystème.

Increasing anthropogenic pressures on marine and coastal ecosystems, particularly in the English Channel, are causing changes in habitats, ecosystems and the various associated ecosystem functions. The construction of marine and coastal structures such as dikes as well as the emergence of several projects to install offshore wind turbines is constantly increasing on the French coasts of the English Channel. With these different projects, the concretization of certain habitats becomes inevitable, so it is essential to assess their ecosystem impacts, and, if possible, to limit them. The MARINEFF project was born in this context, it aims to reconcile human development and ecological benefit. The development of these many coastal infrastructures can also make it possible to create new habitats. The objective of this PhD is to assess biological colonization processes at different scales as well as certain ecological functions such as the primary production on different types of marine infrastructures under controlled conditions and in situ situations on two site the Rade of Cherbourg and the Bay of Seine. Modulated fluorescence (PAM) measurements carried out on the different compartments of benthic primary producers made it possible to evaluate the primary production function and its evolution according to the forcing’s tested or observed. An important part of this PhD focused on the study of hard substrate microphytobenthos, its growth, its photobiology in relation to the type of colonized substrate, its surface structure and the impact of different forcing’s on these parameters. On a larger scale, the development of benthic communities has also been characterized for both sites and on different infrastructures. In situ primary production measurements combined with biodiversity and PAM assessment have made it possible to describe the colonization processes of artificial infrastructures and to assess their effectiveness. This work brings a new vision to the benthic ecology associated with artificial hard substrates and makes it possible to provide reliable estimates of the impact of these structures on the ecosystem.; L’accroissement des pressions anthropiques sur les écosystèmes marins et côtiers, en particulier en Manche, provoquent des modifications des habitats, des écosystèmes et des différentes fonctions écosystémiques associées. La construction d’ouvrages maritimes et côtiers tels que les digues ou des ouvrages portuaires ainsi que l’émergence de plusieurs projets d’implantation d’éoliennes off-shore est en augmentation constante sur les côtes de la Manche française. Avec ces différents projets, la bétonisation de certains habitats devient inévitable, il est donc primordial d’évaluer leurs impacts écosystémiques, et, si possible, de les limiter. Le projet MARINEFF est né dans ce contexte, il vise à concilier développement humain et bénéfice écologique. Le développement de ces nombreuses infrastructures côtières crée de nouveaux habitats. L’objectif de ces travaux a été d’évaluer les processus de colonisation biologique à différentes échelles ainsi que certaines fonctions écologiques comme la production primaire sur différents types d’infrastructures marines en conditions contrôlées et en situation in situ dans deux sites La Rade de Cherbourg et la baie de Seine. Les mesures de fluorescence modulée (PAM) réalisées sur les différents compartiments de producteurs primaires benthiques ont permis d’évaluer la fonction de production primaire et son évolution en fonction des forçages testés ou observés. Une part importante de ce travail s’est concentrée sur l’étude du microphytobenthos de substrat dur, sa croissance, sa photobiologie en relation avec le type de substrat colonisé, sa structure de surface et l’impact de différents forçages sur ces paramètres. A une plus grande échelle, le développement des communautés benthiques a également été caractérisé sur les deux sites et sur différentes infrastructures. Des mesures de production primaire in situ associées à des mesures de biodiversité et de PAM ont permis de décrire les processus de colonisation d’infrastructures artificielles et d’évaluer leur efficacité. Ces travaux apportent une nouvelle vision à l’écologie benthique associée aux substrats durs artificiels et apportent des estimations fiables de l’impact de ces structures sur l’écosystème.

Funding: The research leading to these results received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 730984, ASSEMBLE Plus project. AJW was funded by the John Templeton Grant 60501, “Putting the Extended Evolutionary Synthesis to the Test”. DMP and AJB were supported by the NERC Blue-coast award (NE/N016009/1). The microphytobenthos that form transient biofilms are important primary producers in intertidal, depositional habitats, yet we have only a limited understanding of how they respond to the cumulative impacts of the growing range of anthropogenic stressors to which they are exposed. We know even less about how the temporal alignment of exposure – such as duration and exposure sequence – may affect the response. Estuarine biofilms were cultured in mesocosms and exposed to the herbicide glyphosate and titanium dioxide (TiO2) nanoparticles in different sequences (glyphosate-first or TiO2-first), as well as in the presence and absence of physical disturbance. We found that at environmentally realistic chemical concentrations, the order of exposure was less important than the total stressor scenario in terms of impacts on key functional attributes and diatom community structure. Physical disturbance did not have an impact on functional attributes, regardless of exposure sequence. Publisher PDF

Remote sensing is a relevant method to map inaccessible areas, such as intertidal mudflats. However, image classification is challenging due to spectral similarity between microphytobenthos and oyster reefs. Because these elements are strongly related to local geomorphic features, including biogenic structures, a new mapping method has been developed to overcome the current obstacles. This method is based on unmanned aerial vehicles (UAV), RGB, and multispectral (four bands: green, red, red-edge, and near-infrared) surveys that combine high spatial resolution (e.g., 5 cm pixel), geomorphic mapping, and machine learning random forest (RF) classification. A mudflat on the Atlantic coast of France (Marennes-Oléron bay) was surveyed based on this method and by using the structure from motion (SfM) photogrammetric approach to produce orthophotographs and digital surface models (DSM). Eight classes of mudflat surface based on indexes, such as NDVI and spectral bands normalised to NIR, were identified either on the whole image (i.e., standard RF classification) or after segmentation into five geomorphic units mapped from DSM (i.e., geomorphic-based RF classification). The classification accuracy was higher with the geomorphic-based RF classification (93.12%) than with the standard RF classification (73.45%), showing the added value of combining topographic and radiometric data to map soft-bottom intertidal areas and the user-friendly potential of this method in applications to other ecosystems, such as wetlands or peatlands.

The fish parasite, Neoergasilus japonicus (Harada, 1930), native to Eastern Siberia and the Amur River catchment area, invaded European water bodies in the middle of the last century, possibly due to the human-mediated distribution of fish in the Amur complex (i.e., the genera Hypophthalmichthys and Ctenopharyngodon). In the deep karst lake, Grand Laoucien (Marseille area, France), this species had an unusually high population density (from 1000 ind./ m3 in zooplankton to 4000 ind./ m3 in the nearshore area) during the free-living period of its life cycle. The annual cycle of N. japonicus includes a 5-month overwintering of fertilized females attached to fish fins and, following this, a five- to six-generation chain from March to November, when the free-living stages in the population alternate with parasite females which attach to their hosts for breeding. The population density of the parasites in zooplankton increased exponentially from spring to autumn, which positively correlated with temperature. We found a strong correlation between N. japonicus density and the community development of microphytobenthos, but not between N. japonicus and phyto- or zooplankton dynamics. The local contributing factors included a seasonal three-fold decrease in water levels and the development of anoxia in profundal waters, which led to a high ambient fish density and thus susceptibility to the parasite. Although the free-living parasite represented only 1% of zooplankton production, it consumed up to 25% of small invertebrate productivity. The maximum intensity of infection reached 140 parasites per fish, or 4.14 per g of weight. The high infection of fish with this parasite, in our opinion, indicated the danger it poses to the local ichthyofauna, which first encountered this new parasite.

Soft‐bottomed intertidal flats are essential foraging areas for shorebirds but are severely impacted by threats such as coastal development and climate change. Notwithstanding the urgency for humanintervention (conservation, restoration and creation) of tidal flats, few ecologically based technical guidelines exist for the artificial (clearly intended human intervention) intertidal flats, and none explicitly consider the unique properties of intertidal biofilm as a critical food source for small‐bodied shorebirds. We propose that effective human intervention in intertidal flat ecosystems can be developed through mirroring the needs of small‐bodied shorebirds. Scientific evidence from intertidal flat recovery projects in Japan is summarized, and foraging requirements of shorebirds are reviewed with a focus on intertidal biofilm as a critical food source. These findings are used to propose the primary goal of intervention, that is maximizing total energy intake for population recovery of small‐bodied shorebirds through biofilm. Three sub‐goals are presented for creating environmental conditions in which (1) a broad spectrum of food sources is available, but particularly intertidal biofilm; (2) maximizing energy intake rate per individual; and (3) maximizing foraging activity. We then describe seven key ecologically based technical attributes for artificial intertidal flats that promote use by small‐bodied shorebirds: depositional environment, complex shoreline, gentle slope, gradient of grain sizes from muddy to sandy, maximum water depth at the lowest tide 5 cm or less, freshwater inflow and unobstructed sight‐lines. Critical questions remain for effective intervention in intertidal flat ecosystems, including food web dynamics, variation in the quality and quantity of food sources, especially biofilm, optimal sedimentary environment systems (interaction between grain size, bed slope and elevation), monitoring involving comparisons with appropriate benchmark (control) habitats, quantifying foraging behaviour and the synergy and trade‐offs among ecosystem services.

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.

Benthic diatom communities dominate sheltered shallow inner coastal waters of the atidal Southern Baltic Sea. However, their photosynthetic oxygen production and respiratory oxygen consumption is rarely evaluated. In the Baltic Sea carbon budget benthic diatom communities are often not included, since phytoplankton is regarded as the main primary producer. Therefore, two wind-protected stations (2–49-cm depths) were investigated between July 2010 and April 2012 using undisturbed sediment cores in combination with planar oxygen optodes. We expected strong fluctuations in the biological activity parameters in the incubated cores over the course of the seasons. The sediment particles at both stations were dominated by fine sand with a median grain size of 131–138 µm exhibiting an angular shape with many edges, which were less mobile compared to exposed coastal sites of the Southern Baltic Sea. These sand grains inhabited dense communities of rather small epipsammic diatoms (&lt, 10 µm). Chlorophyll a as a biomass parameter for benthic diatoms fluctuated from 64.8 to 277.3-mg Chl. a m−2 sediment surface. The net primary production and respiration rates exhibited strong variations across the different months at both stations, ranging from 12.9 to 56.9 mg O2 m−2 h−1 and from −6.4 to −137.6 mg O2 m−2 h−1, respectively. From these data, a gross primary production of 13.4 to 59.5 mg C m−2 h−1 was calculated. The results presented confirmed strong seasonal changes (four-fold amplitude) for the activity parameters and, hence, provided important production biological information for sheltered sediments of the Southern Baltic Sea. These data clearly indicate that benthic diatoms, although often ignored until now, represent a key component in the primary production of these coastal habitats when compared to similar studies at other locations of the Baltic Sea and, hence, should be considered in any carbon budget model of this brackish water ecosystem.

The fish parasite, Neoergasilus japonicus (Harada, 1930), native to Eastern Siberia and the Amur River catchment area, invaded European water bodies in the middle of the last century, possibly due to the human-mediated distribution of fish in the Amur complex (i.e., the genera Hypophthalmichthys and Ctenopharyngodon). In the deep karst lake, Grand Laoucien (Marseille area, France), this species had an unusually high population density (from 1000 ind./ m3 in zooplankton to 4000 ind./ m3 in the nearshore area) during the free-living period of its life cycle. The annual cycle of N. japonicus includes a 5-month overwintering of fertilized females attached to fish fins and, following this, a five- to six-generation chain from March to November, when the free-living stages in the population alternate with parasite females which attach to their hosts for breeding. The population density of the parasites in zooplankton increased exponentially from spring to autumn, which positively correlated with temperature. We found a strong correlation between N. japonicus density and the community development of microphytobenthos, but not between N. japonicus and phyto- or zooplankton dynamics. The local contributing factors included a seasonal three-fold decrease in water levels and the development of anoxia in profundal waters, which led to a high ambient fish density and thus susceptibility to the parasite. Although the free-living parasite represented only 1% of zooplankton production, it consumed up to 25% of small invertebrate productivity. The maximum intensity of infection reached 140 parasites per fish, or 4.14 per g of weight. The high infection of fish with this parasite, in our opinion, indicated the danger it poses to the local ichthyofauna, which first encountered this new parasite.

JAH received funding from The Oceans of Change Project. DMP received funding from the MASTS pooling initiative (The Marine Alliance for Science and Technology for Scotland) and their support is gratefully acknowledged. MASTS is funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions". 1. Sediment dwelling, microscopic primary producers, that occupy sediments in the photic zone, are commonly referred to as microphytobenthos (MPB). The MPB are essential components of soft‐sediment systems, but are often overlooked when assessing coastal ecosystem functionality and service delivery. 2. The MPB are involved in several complex interactions and feedback that underpin the delivery of vital ecosystem services. MPB profoundly influence the flow and cycling of carbon and nutrients, such as nitrogen, directly and indirectly underpinning highly productive shallow water marine food webs. The MPB can also stabilize sediments through the formation of biofilms, and significantly improve water quality by mediating the benthic–pelagic coupling of nutrients, sediment and pollutants. 3.The functional role of the MPB is compromised by increasing anthropogenic pressures such as nutrient enrichment, sedimentation, herbicides and emerging contaminants such as microplastic pollution. However, MPB are extremely good at buffering the effects of these land‐sourced stressors at the interface between land and sea. 4. Synthesis. Society often appreciates the final provisioning of goods and services from our coastal marine environments. However, provisioning services are only possible due to the multitude of supporting and regulating services that underpin them. Microphytobenthos (MPB) are central to benthic ecological networks, and contribute to ecosystem service delivery through various pathways. Understanding the critical role of MPB in complex networks is therefore essential to appreciate their importance in ecosystem function and service delivery into the future. Postprint

Most studies on sediment-inhabiting microphytobenthos are based on the biomass present on the surface layers of intertidal flats. However, large amounts of microalgal biomass are known to exist below the surface. This study tested the role of subsurface microalgal biomass as a potential source of photosynthetically active cells for the biofilm on the surface. The resilience of buried cells was evaluated by exposing samples from various depths to surface conditions and investigating the recovery of photosynthetic activity. Additionally, vertical migration by subsurface epipelic diatoms was followed at sub-millimeter scales to evaluate its role for transporting cells to the vicinity of the sediment surface. Finally the relative importance of subsurface microalgal biomass was assessed by estimating the proportion of subsurface:surface biomass for different types of sediments from the Ria de Aveiro. Vertical profiles of chlorophyll a, 10 cm-deep, were measured on samples from three intertidal sites, representative of the range of sediment characteristics found in this estuary. The ratio of total biomass to surface biomass (‘subsurface biomass fraction’) based on total biomass (0–10 cm depth interval; Csub, total) and on viable biomass (between the surface and the maximum depth with significant photosynthetic recovery; Csub, viable). The experiments showed that buried cells were able to recover photosynthetic activity within 1.5–3 h of light exposure, with the rate of recovery being dependent on depth and type of sediment. Furthermore, subsurface vertical migration was found to enable motile cells to reach the surface from layers deeper than 1 mm within a low tide period. Overall, the results showed that surface biomass (0–0.5 cm) only accounted for one fifth to one third of the total biomass present between the surface and 10 cm, and that the amount of subsurface viable biomass reached 2–3 times the biomass present at the surface. Applying the estimates of Csub, total and Csub, viable to the whole intertidal area of the Ria de Aveiro, spatially-weighted averages for subsurface biomass fractions were found to reach 3.8 and 2.1 respectively.

Nitrification rates are low in permeable intertidal sand flats such that the water column is the primary source of nitrate to the sediment. During tidal inundation, nitrate is supplied to the pore space by advection rather than diffusion, relieving the microorganisms that reside in the sand from nitrate limitation and supporting higher denitrification rates than those observed under diffusive transport. Sand flats are also home to an abundant community of benthic photosynthetic microorganisms, the microphytobenthos (MPB). Diatoms are an important component of the MPB that can take up and store high concentrations of nitrate within their cells, giving them the potential to alter nitrate availability in the surrounding porewater. We tested whether nitrate uptake by the MPB near the sediment surface decreases its availability to denitrifiers along deeper porewater flow paths. In laboratory experiments, we used NOx (nitrate + nitrite) microbiosensors to confirm that, in the spring, net NOx consumption in the zone of MPB photosynthetic activity was stimulated by light. The maximum potential denitrification rate, measured at high spatial resolution using microsensors with acetylene and nitrate added, occurred below 1.4 cm, much deeper than light-induced NOx uptake (0.13 cm). Therefore, the shallower MPB had the potential to decrease NOx supply to the deeper sediments and limit denitrification. However, when applying a realistic downward advective flow to sediment from our study site, NOx always reached the depths of maximum denitrification potential, regardless of light availability or season. We conclude that during tidal inundation porewater advection overwhelms any influence of shallow NOx uptake by the MPB and drives water column NOx to the depths of maximum denitrification potential.

International audience; The effects of herbicide diuron on photosynthesis and vertical migration of intertidal microphytobenthos (MPB) assemblages were investigated using chlorophyll fluorometry. The results shown diuron ≤ 60 μgꞏL-1 had no obvious effect on MPB vertical migration during 24 h indicated by consistent rhythm. Low concentration of 10 μgꞏL-1 diuron had no significant influence on MPB photosynthesis throughout, however, high concentrations of 40, 50, and 60 μgꞏL-1 had significant impacts exhibited by decreased parameters of maximum relative electron transport rate (rETRmax), maximal PS II quantum yield (Fv/Fm) and non-photochemical quenching (NPQ). For middle concentrations of 20 and 30 μgꞏL-1 , above decreased 3 parameters recovered sooner or later after 2 h or 16.5 h. Comparatively, rETRmax, Fv/Fm and NPQ are concentration dependent and more sensitive than other parameters in assessing diuron toxicity. This study revealed the potential of using MPB assemblages and chlorophyll fluorometry for rapid assessing diuron toxicity in coastal sediments.

The contribution of unvegetated tidal flats to global net primary production is comparable to that of some vegetated coastal habitats. However, compared to carbon flux regulating factors in vegetated habitats, those in unvegetated tidal flats are not well understood, particularly in terms of their cause-effect relationships. Maximum gross primary production (GPPm), net primary production (NPP) and total respiration (TR) during emersion at noon when the irradiance level was at the saturation level for photosynthesis in nine unvegetated tidal flats across the Taiwan Strait in tropical and subtropical regions were determined in winter and summer from 2011 to 2016 to examine the direct and indirect relationships between sediment characteristics and carbon fluxes by using structural equation models (SEM). Most of the GPPm and NPP values were higher in winter than in summer. Conversely, the TR values were higher in summer than in winter. The NPP values at some sites shifted to negative values in summer, indicating the sites were carbon sources. The values of GPPm, TR and NPP for the tidal flats all increased significantly with increasing sediment mud content. The SEM results showed that the sediment mud content directly increased GPPm or indirectly increased GPPm via a compositional shift in benthic microalgae. The sediment mud content also directly increased TR or indirectly increased TR via increased organic matter content. The contribution of benthic microalgal and macrofaunal biomass to TR was relatively minor. This result suggests that primary production was stimulated mainly by the organic matter content rather than by increased microalgal biomass. With the integrated SEM framework, our results showed mechanistic evidence of how sediment mud content acted as a critical factor regulating carbon fluxes in unvegetated tidal flats.

Microphytobenthos (MPB) is composed of unicellular photosynthetic organisms that colonize intertidal sediments within the first millimeters of the photic zone and form biofilms at low tide. In estuaries, this benthic group can represent the main primary producer and deliver several ecosystem services. However, it is not currently used as a bioindicator of water quality, contrary to the widespread use of phytobenthos in freshwater settings. This study assesses the potential of developing MBP metrics to assess water quality in transitional waters using Sentinel-2 (S2) satellite imagery. A Random Forest machine learning classification was used to distinguish different types of intertidal vegetation in 26 French estuaries and bays, in particular MPB and green macroalgae (chlorophytes), using multispectral indices. High accuracy was generally achieved for the identification of MPB when compared with field validation data, for both User’s and Producer’s accuracies, which corresponded to 94% and 84% respectively. Two Earth observation variables were retrieved: the Normalized Difference Vegetation Index (NDVI), a proxy of MPB biomass, and MPB percent cover integrated over the entire intertidal area of the water body. From a total of 918 S2 images from over a full year, 28% were exploitable due to the combined requirements of cloud-free pixels collected during low tide. With its 10 m spatial resolution, S2 was able to map all estuaries. MPB percent cover showed a stronger gradient between estuaries than MPB NDVI. MPB percent cover was also significantly correlated with green macroalgae percent cover, and a group of estuaries characterized by the highest MPB and green macroalgae coverage corresponded to eutrophic sites impacted by intensive farming activities. A multivariate analysis confirmed that MPB percent cover was indeed related to nutrients. It was also related to sediment type which was one of the main factors underlying differences between estuaries. This work is a first step toward a water quality metric using MPB, and several recommendations are proposed to refine this approach. Sentinel-2 imagery, which is publicly available, presents an interesting compromise to map estuarine microphytobenthos in order to assess the ecological status of transitional waters.

Ecosystem engineering is a ubiquitous process by which the biological activity of a species shapes habitat diversity and often creates local biodiversity hotspots. The honeycomb-worm Sabellaria alveolata, an intertidal ecosystem engineer, actively builds reefs across Europe by aggregating sand. Here, we used carbon and nitrogen isotopic compositions measured on basal resources and bentho-demersal consumers (fish, mega- and macroinvertebrates) to empirically investigate how non-trophic interactions (ecosystem engineering) modify food web structure and functioning. Three sediment types corresponding to different substrata and species assemblages were sampled: a control soft sediment (medium to muddy sand, before the establishment of S. alveolata), the sediment engineered by S. alveolata (hardened 3D structures), and the soft sediment under the influence of S. alveolata (associated sediment). Using consumer community isotopic biplots (biomass-weighted), niche metrics (standard ellipse area), and mixing models, we found that S. alveolata, through the physical structure it creates, the stimulation of basal resources (microphytobenthos and Ulva), and the diversification of suspension-feeding species, promotes benthic-pelagic coupling and a habitat-wide form of ‘gardening,’ which further leads to trophic pathway diversification and limits trophic competition between the engineer species and associated suspension-feeders. Furthermore, our results help to refine the definition of S. alveolata reefs as the sum of the engineered and associated sediments since they are part of a single reef food web coupled by the stimulated basal resources and consumers. Finally, the non-trophic and trophic interactions mediated by S. alveolata and the associated macrofauna seem to promote the establishment of a temporally stable and probably highly resilient reef habitat.

Estuarine morphology evolves from a combination of various drivers, including hydrodynamics, sediment input, human interference and ecology. The latter has been shown to affect local morphology through eco-engineering, meaning the modification of the physical habitat through the presence or activity of the prevailing species. Despite many studies confirming eco-engineering effects on local morphology, our understanding of how eco-engineers determine the morphology of entire estuaries is still limited. This understanding is however crucial to better describe the past formation of tidal systems, to guarantee their sustainable usage, and to protect our coasts against the future impacts of climate change. In this PhD thesis, a novel eco-morphodynamic model is presented to elucidate the effects of various eco-engineers in estuaries. The modelling framework captures the feedback between environmental processes, eco-engineering and changes in habitat through the adapting morphology. The model revealed that eco-engineering by vegetation is one main determinant for the establishment and expansion of saltmarshes in dynamic estuaries. Hereby, this effect depends on the vegetation age marked by increasing plant sizes and resilience to stress, which defines a distinct density zonation. The expansion of the saltmarsh enhances the accumulation of mud on intertidal bars, depending on vegetation properties: The species-specific establishment strategy controls the abundance and thickness of mud layers in estuaries. At the scale of intertidal flats, species-specific establishment, growth, mortality rules control the formation of tidal channel networks, associated levee formation and drainage density. Climate-induced shifts in dominant species affect the channel network, enhancing the capacity to drain marshes and export sediment, reducing their resilience against sea level rise. Macrozoobenthic bioturbators enhance the system-wide erosion of the estuary by resuspending cohesive mud. Through their activity, these species reduce bed elevations, expose the supratidal area and cause lateral expansion of the estuary. Biofilms stabilize mud and morphology, but their effect reduces when macrobenthos grazes on them. A combination of several bioturbators and biofilms results in a restructured species community, solely as a consequence of the eco-engineering effects: The altered habitat by one species allows for the colonization by another, which outcompetes the first species. These ecological interactions lead to an adapted morphology, showing that the prediction of morphological evolution is not trivial and requires the consideration of ecosystem interactions. Sea level rise reduces mud content of the estuary promoting a species shift, where a sand-prone bioturbator thrives and expands its habitat while a mud-prone species almost disappears. This shift of dominating eco-engineers has implications for the net eco-engineering effect, morphology and estuarine resilience to sea level rise. In ancient estuaries of the Palaeozoic, the evolution of plant traits that include root development, increasing plant densities and dimensions and enhanced resilience against environmental stresses, gradually increased estuarine mud content. Here, the onset of arborescent vegetation led to system-scale mud deposition as opposed to previously observed local mud deposition within plant patches. These results indicate that the earliest small plants had the capacity to eco-engineer their environment and that the greening of the continents affected morphologies, which rendered pre-vegetation sedimentary processes non-uniformitarian.

International audience; Microphytobenthos is most often the primary source of carbon for coastal soft-sediment communities, especially in intertidal and shallow subtidal environments. The influence of benthic macrofaunal organisms on microphytobenthic biomass, spatial distribution and photosynthetic capacities is not only resulting from their feeding intensity but also indirectly from their bioturbation activity, which regulates nutrient fluxes and sediment mixing. This study compares the impact of two species (Hediste diversicolor and Scrobicularia plana) that dominate macrofaunal communities in estuarine intertidal mudflats on microphytobenthic biomass and photosynthetic activity. Imaging-PAM fluorescence was used to non-invasively map the development of microphytobenthic biomass and to assess its spatial extent. Our results showed that, due to intense deposit feeding, Scrobicularia plana quickly limited microphytobenthos growth and photosynthetic activity, even at low density (

Thanks are due to FCT/MCTES for the financial support to CESAM (UIDP/50017/2020 + UIDB/50017/2020), through national funds, to JS, and to the NERC Blue-coast project to DMP (NE/N016009/1).

Whilst the demand for nutritious and sustainable seafood is increasing, fishing yields are declining due to overfishing and climate change. The inshore aquaculture of marine molluscs&mdash, e.g., the suspension-feeding cockle Cerastoderma edule for NW Europe&mdash, might be an alternative practice if cost-effective and nature-based technology enhances growth and survival. Our inshore experiments revealed that increasing the seawater residence time resulted in improved water quality. The reduction in sediment loads and stimulation of pelagic microalgal growth resulted in enhanced shell growth and meat content of the wild cockles seeded into the system. Shorter residence times resulted also in an increase in benthic microalgae, but the concurrent increase in silt content of the sediment appeared to hamper effective filtration by cockles. The growth conditions (with respect to the water and sediment quality) for the inshore cultivation of cockles can indeed be improved by means of ecological engineering, suggesting that the inshore aquaculture of marine shellfish can provide sustainable food and income for coastal communities, in particular when the shellfish farms are located in low-lying salinized coastal areas where common agriculture practices are no longer profitable. The involvement of the shellfishery industry was and will be crucial for studying and understanding the complex practice of cockle cultivation.

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.

The interaction between microbial communities and benthic algae as nitrogen (N) regulators in poorly illuminated sediments is scarcely investigated in the literature. The role of sediments as sources or sinks of N was analyzed in spring and summer in sandy and muddy sediments in a turbid freshwater estuary, the Curonian Lagoon, Lithuania. Seasonality in this ecosystem is strongly marked by phytoplankton community succession with diatoms dominating in spring and cyanobacteria dominating in summer. Fluxes of dissolved gas and inorganic N and rates of denitrification of water column nitrate (Dw) and of nitrate produced by nitrification (Dn) and sedimentary features, including the macromolecular quality of organic matter (OM), were measured. Shallow/sandy sites had benthic diatoms, while at deep/muddy sites, settled pelagic microalgae were found. The OM in surface sediments was always higher at muddy than at sandy sites, and biochemical analyses revealed that at muddy sites the OM nutritional value changed seasonally. In spring, sandy sediments were net autotrophic and retained N, while muddy sediments were net heterotrophic and displayed higher rates of denitrification, mostly sustained by Dw. In summer, benthic oxygen demand increased dramatically, whereas denitrification, mostly sustained by Dn, decreased in muddy and remained unchanged in sandy sediments. The ratio between denitrification and oxygen demand was significantly lower in sandy compared with muddy sediments and in summer compared with spring. Muddy sediments displayed seasonally distinct biochemical composition with a larger fraction of lipids coinciding with cyanobacteria blooms and a seasonal switch from inorganic N sink to source. Sandy sediments had similar composition in both seasons and retained inorganic N also in summer. Nitrogen uptake by microphytobenthos at sandy sites always exceeded the amount loss via denitrification, and benthic diatoms appeared to inhibit denitrification, even in the dark and under conditions of elevated N availability. In spring, denitrification attenuated N delivery from the estuary to the coastal area by nearly 35%. In summer, denitrification was comparable (~100%) with the much lower N export from the watershed, but N loss was probably offset by large rates of N-fixation.

Mud accretion and establishment of biostabilizers, such as microphytobenthos and saltmarsh vegetation, govern the development of estuarine morphology. Mud facilitates saltmarsh survival and microphytobenthos growth, which in turn promotes sedimentation and reduces mud erosion. Consequently, an increasing extent and thickness of mud cover might lead to a stabilization of large‐scale estuarine morphology. To disentangle the interactions between saltmarsh establishment, microphytobenthos colonization, and mud layer formation, we use our novel eco‐morphodynamic model applied to the Western Scheldt estuary. Our model shows that presence of dynamic saltmarsh vegetation and microphytobenthos enhances predictions of mud location in the computations compared to field data. Saltmarsh establishment is partly determined by the antecedent mud content in the bed, resulting in varying emerging vegetation coverage between model experiments of a generic saltmarsh and a saltmarsh species that requires prior mud for establishment. In contrast to microphytobenthos enhancing seasonal mud accretion during their growth period, saltmarshes promote largest accretion when lower biomass and high water levels are present. Interestingly, thick long‐term mud is enhanced despite the biostabilizers seasonal growth. The combination of saltmarsh and microphytobenthos leads to expanding saltmarsh cover and mud area. Generally, mud layer thickness is governed by the ratio of hydroperiod and maximum flow velocity that is mediated by the biostabilizers. On estuary scale, the presence of intertidal vegetation leads to increased mud volumes in the intertidal. Mud layers are enhanced in extent by a mud‐dependent species and in thickness by a generic species. Thus, local biostabilization alters large‐scale morphology controlling long‐term estuarine development.

Publisher: Elsevier B.V.; International audience; Meiofauna are known to have an important role on many ecological processes, although, their role in food web dynamics is often poorly understood, partially as they have been an overlooked and under sampled organism group. Here, we used quantitative food web modeling to evaluate the trophic relationship between meiofauna and their food sources and how meiofauna can mediate the carbon flow to higher trophic levels in five contrasting soft-bottom intertidal habitats (including seagrass beds, mudflats and sandflats). Carbon flow networks were constructed using the linear inverse model-Markov chain Monte Carlo technique, with increased resolution of the meiofauna compartments (i.e. biomass and feeding ecology of the different trophic groups of meiofauna) compared to most previous modeling studies. These models highlighted that the flows between the highly productive microphytobenthos and the meiofauna compartments play an important role in transferring carbon to the higher trophic levels, typically more efficiently so than macrofauna. The pathway from microphytobenthos to meiofauna represented the largest flow in all habitats and resulted in high production of meiofauna independent of habitat. All trophic groups of meiofauna, except for selective deposit feeders, had a very high dependency on microphytobenthos. Selective deposit feeders relied instead on a wider range of food sources, with varying contributions of bacteria, microphytobenthos and sediment organic matter. Ecological network analyses (e.g. cycling, throughput and ascendency) of the modeled systems highlighted the close positive relationship between the food web efficiency and the assimilation of high-quality food sources by primary consumers, e.g. meiofauna and macrofauna. Large proportions of these flows can be attributed to trophic groups of meiofauna. The sensitivity of the network properties to the representation of meiofauna in the models leads to recommending a greater attention in ecological data monitoring and integrating meiofauna into food web models. © 2020 Elsevier B.V.

Carbon fixation by microphytobenthic algae of intertidal flats often dominates the total primary production of turbid, temperate estuaries. Whilst remote sensing can accurately measure the spatial distribution of photosynthetic biofilms at the mesoscale (1–300 m), variability at smaller scales requires in-situ investigation. Here, changes in biomass and photosynthetic activity of microphytobenthos (MPB) at the micro-scale (m′) in-situ with solar irradiance. No evidence was found for photoinhibition, with Fv/Fm values consistently high, indicating an ability of the diatom biofilm to remain productive under periods of high irradiance. The maximum rate of photosynthesis reached with artificial light was rarely achieved in-situ, even with full solar exposure. There was, however, a very good agreement between the predicted rate at ambient irradiance, and that actually measured. Composite photosynthesis-irradiance curves over the whole experimental period were similar, and showed the same initial slopes, but the maximum rate of relative photosynthetic electron transport (rETRm) based on the in-situ measurement was lower. When total depth-averaged primary production during low tide was calculated, the differences between methods varied between 5 and 13%, and were smallest when surface irradiance values were highest. These results show that the protocol used to measure the photosynthetic activity of the MPB had only minor importance on the overall productivity estimate compared to accurate knowledge of photosynthetically active biomass and irradiance.

The gross primary production (GPP) of intertidal mudflat microphytobenthos supports important ecosystem services such as shoreline stabilization and food production, and it contributes to blue carbon. However, monitoring microphytobenthos GPP over a long-term and large spatial scale is rendered difficult by its high temporal and spatial variability. To overcome this issue, we developed an algorithm to map microphytobenthos GPP in which the following are coupled: (i) NDVI maps derived from high spatial resolution satellite images (SPOT6 or Pléiades), estimating the horizontal distribution of the microphytobenthos biomass; (ii) emersion time, photosynthetically active radiation (PAR), and mud surface temperature simulated from the physical model MARS-3D; (iii) photophysiological parameters retrieved from Production–irradiance (P–E) curves, obtained under controlled conditions of PAR and temperature, using benthic chambers, and expressing the production rate into mg C h–1 m–2 ndvi–1. The productivity was directly calibrated to NDVI to be consistent with remote-sensing measurements of microphytobenthos biomass and was spatially upscaled using satellite-derived NDVI maps acquired at different seasons. The remotely sensed microphytobenthos GPP reasonably compared with in situ GPP measurements. It was highest in March with a daily production reaching 50.2 mg C m–2 d–1, and lowest in July with a daily production of 22.3 mg C m–2 d–1. Our remote sensing algorithm is a new step in the perspective of mapping microphytobenthos GPP over large mudflats to estimate its actual contribution to ecosystem functions, including blue carbon, from local and global scales.

The movement of sediment and associated microphytobenthos (MPB) between the upper mudflat and salt marsh in a macrotidal estuary was investigated by comparing the variability of benthic chlorophyll a (Chl. a) and suspended Chl. a during flood and ebb spring tides during the 2015 supermoon event. Sampling was carried out for 4 days in August and September. Flood-tide water carried significantly higher amounts of Chl. a from the mudflat transition zone onto the salt marsh compared to the amount of leaving the salt marsh during ebb tides. Suspended solid loads, suspended Chl. a concentrations, and diatom species composition provided evidence that resuspended mudflat sediments containing biofilm material were transferred onto the salt marsh by flood tide. Significant negative correlations between sediment Chl. a concentrations on the upper mudflat transition zone and Chl. a concentrations in flood-tide water indicated biostabilization of sediments by biofilms reducing sediment resuspension. Mean wind speed had a significant positive effect on resuspending Chl. a from the salt marsh sediment surface into the ebb tide (p < 0.001). The amount of Chl. a being resuspended in flood and ebb tidal waters was significantly correlated with MPB biomass on the sediment surface on the mudflat and salt marsh, respectively. Resuspended diatoms over the mudflat during high tide shared a total of 54.3% similar species with diatoms recorded in flood tidal water over the salt marsh. Diatom taxa characteristic of salt marsh assemblages, and some deposited diatom taxa were resuspended and carried off the salt marsh during ebb tide. Resuspension of Chl. a in both flood and ebb waters was significantly controlled by the tidal range (both significant at p < 0.001). During spring tides, there was a net movement of characteristic MPB mudflat diatom taxa and sediment from the adjacent mudflat to the salt marsh, contributing to the accumulation of material within vegetated marshes during summer months.

Proliferation of urban structures and mangrove forests in estuaries are altering the shading of intertidal sediments. Urbanisation also tends to increase nutrient loads in estuaries, which can have numerous direct and indirect effects on estuarine flora and fauna. Mangrove canopy shades the sediment and provides nutrients to the ecosystem via leaf litter. Microphytobenthos, macrobenthos, sediment erodibility and various biogeochemical properties of sediments have been shown to differ significantly between unshaded intertidal sediment and nearby sediment under a mangrove canopy. This study tested the effects of experimental manipulation of shading and addition of nutrients on the microphytobenthos, macrobenthos, sediment erodibility and selected biogeochemical properties of exposed mudflat next to the seaward edge of a mangrove forest. In the first of two experiments, shading of plots was increased by the addition of black Perspex roofs for comparison with unshaded plots and plots with clear Perspex roofs; the addition of nutrients was done in an orthogonal design. Clear roofs were originally intended as a procedural control, but due to sedimentation on their upper surface caused intermediate levels of shading. Sediment and benthos were sampled after two weeks. Nutrients were omitted in the second experiment, with plots sampled after two weeks or three months. The only effect of nutrients was a small negative effect on chlorophyll a and colloidal carbohydrate. Intermediate shading (clear roofs) consistently increased measures of microphytobenthos biomass (e.g. Fo and chlorophyll a) and biogeochemical properties associated with microphytobenthos such as colloidal carbohydrate. Substantial shading (black roofs) decreased measures of microphytobenthos biomass and microphytobenthos associated biogeochemical properties. Effects on the fauna were much smaller and inconsistent with previous studies, after 3 months assemblages were different under black roofs compared to clear roofs and control plots, with differences primarily driven by changes in the oligochaetes. Natural or anthropogenic changes in shading at larger spatial scales are likely therefore to directly and indirectly change microphytobenthos, sediment properties, macrofauna and hence ecosystem functions; but any flow-on effects to the fauna are difficult to predict without further experiments to understand the indirect and direct responses of fauna to changing microphytobenthos and properties of intertidal sediment.

The physiology of the diel movements of epipelic microphytobenthic diatoms is not fully understood. As well, the evolutionary pressures that led to migratory behavior and the ecological role of vertical migrations remain unknown. The behavioral photoprotection hypothesis, according to which the diatoms move along the vertical light gradient to find their optimal light environment, is the most generally accepted. However, the motion is associated with an energy cost that has not been fully acknowledged before. To throw light on this issue, we looked at the mechanisms of diatom locomotion and reviewed their patterns of movement. Making use of published data, we estimated an energy cost of 0.12 pJ for a typical diatom cell to move upward (or downward) in a 400 μm photic zone. This amounts to 3.93 ×10−18 mol of ATP, which are released by the oxidation of 1.31 ×10−19 mol of glucose. This represents only 0.0001% of the daily net photosynthetic production of a typical microphytobenthic diatom cell, showing that diel vertical migrations have a negligible impact on cell and ecosystem energy budget. Even though the migration energy cost of individual cells may depart almost two orders of magnitude from the central value presented for a typical diatom (depending on cell size, velocity of displacement, and viscosity of the medium), the maximum value calculated is still negligible from the metabolic and ecologic point of view. Results show that behavioral photoprotection might be an energetically cheap mechanism, offering competitive advantages when compared with structural/physiological photoprotection.

In aquatic habitats, diatoms are frequently found in association with Proteobacteria, many members of which employ cell-to-cell communication via N-acyl homoserine lactones (AHLs). It has been suggested that diatoms could distinguish between beneficial and algicidal bacteria in their surroundings by sensing AHLs. Although some microalgae can interfere with AHL signaling, e.g., by releasing AHL mimics or degrading them, molecular responses to AHLs in microalgae are still unclear. Therefore, we tested the effects of short-chained AHLs, i.e., N-hexanoyl homoserine lactone (C6-HSL), N-3-hydroxyhexanoyl homoserine lactone (OH-C6-HSL), and N-3-oxohexanoyl homoserine lactone (oxo-C6-HSL) and long-chained AHLs, i.e., N-tetradecanoyl homoserine lactone (C14-HSL), N-3-hydroxytetradecanoyl homoserine lactone (OH-C14-HSL), and N-3-oxotetradecanoyl homoserine lactone (oxo-C14-HSL), on growth of the benthic diatom Seminavis robusta. All tested short-chained AHLs did not affect diatom growth, while long-chained AHLs promoted (C14-HSL) or inhibited (OH-C14-HSL and oxo-C14-HSL) growth. To investigate the physiological effects of these long-chained AHLs in more detail, an RNA-seq experiment was performed during which S. robusta was treated with the growth-promoting C14-HSL and the growth-inhibiting oxo-C14-HSL. One tetramic acid was also tested (TA14), a structural rearrangement product of oxo-C14-HSL, which also induced growth inhibition in S. robusta. After 3 days of treatment, analysis revealed that 3,410 genes were differentially expressed in response to at least one of the compounds. In the treatment with the growth-promoting C14-HSL many genes involved in intracellular signaling were upregulated. On the other hand, exposure to growth-inhibiting oxo-C14-HSL and TA14 triggered a switch in lipid metabolism towards increased fatty acid degradation. In addition, oxo-C14-HSL led to downregulation of cell cycle genes, which is in agreement with the stagnation of cell growth in this treatment. Combined, our results indicate that bacterial signaling molecules with high structural similarity induce contrasting physiological responses in S. robusta.

Artificial light at night (ALAN) has been recently recognized as a globally widespread anthropogenic disturbance, characterized by different intensities and spectra, as well as spatial and temporal variability. Among marine organisms, those living on coastal areas are particularly exposed to artificial light. Some recent studies anticipated a potential for influences of ALAN on microphytobenthos (MPB) on rocky shores, either direct or indirectly mediated by trophic relationships. Here we emphasize the need for further investigations in different habitats, as well as on synergistic interferences with other stressors already impinging on coastal areas. The study of effects of ALAN poses new challenges in MPB research, including those related to the use of instruments for measuring both the light environment and the functioning of microbial photoautotrophs at night, and to the development of common monitoring approaches and manipulative experiments.

International audience; Intertidal benthic diatoms experience a highly variable light regime, which especially challenges these organisms to cope with excess light energy during low tide. Non-photochemical quenching of chlorophyll fluorescence (NPQ) is one of the most rapid mechanisms diatoms possess to dissipate excess energy. Its capacity is mainly defined by the xanthophyll cycle (XC) and Light-Harvesting Complex X (LHCX) proteins. Whereas the XC and its relation to NPQ have been relatively well-studied in both planktonic and benthic diatoms, our current knowledge about LHCX proteins and their potential involvement in NPQ regulation is largely restricted to planktonic diatoms. While recent studies using immuno-blotting have revealed the presence of light regulated LHCX proteins in benthic diatom communities and isolates, nothing is as yet known about the diversity, identity and transcriptional regulation or function of these proteins. We identified LHCX genes in the draft genome of the model benthic diatom Seminavis robusta and followed their transcriptional regulation during a day/night cycle and during exposure to high light conditions. The S. robusta genome contains 17 LHCX sequences, which is much more than in the sequenced planktonic model diatoms (4-5), but similar to the number of LHCX genes in the sea ice associated diatom Fragilariopsis cylindrus. LHCX diversification in both species, however, appears to have occurred independently. Interestingly, the S. robusta genome contains LHCX genes that are related to the LHCX6 of the model centric diatom Thalassiosira pseudonana, which are lacking in the well-studied pennate model diatom Phaeodactylum tricornutum. All investigated LHCX genes, with exception of SrLHCX6, were upregulated during the daily dark-light transition. Exposure to 2,000 µmol photons m −2 s −1 , furthermore, increased transcription of all investigated LHCX genes. Our data suggest that the diversification and involvement of several light regulated LHCX genes in the photophysiology of S. robusta may represent an adaptation to the complex and highly variable light environment this benthic diatom species can be exposed to.

Excessive primary productivity due to nutrient inputs is a potential problem in coastal areas when resulting in high organic matter sedimentation rates. Microphytobenthos and heterotrophic bacteria are two components of the benthic ecosystem that contribute to nutrient cycling and decomposition of organic matter. In this context, the effects of nutrient addition and the associated in situ produced organic matter on microphytobenthos community composition and benthic bacterial viability were assessed in a mesocosm experiment for 58 days. The experimental setup included triplicate mesocosms filled with sediment and water under three levels of nutrient addition (‘control’, ‘low’ and ‘high’). Benthic algal community composition was assessed using chemotaxonomy and bacterial viability was estimated using flow cytometry and a double-staining protocol. Multivariate analysis detected a significant effect of treatment and time on microphytobenthic community composition indicating a difference between control and low mesocosms and also between low and high treatments at Day 12 and Day 24 of the experiment. Nonetheless, microphytobenthos implied high resistance and redundancy of benthic algae to disturbance as all three treatments showed no significant difference in community structure between Day 0 and Day 58. Bacterial viability responded quickly to the high nutrient addition and was significantly lower than in the ‘control’ and ‘low’ treatments at Days 6 and 12. Both pelagic and benthic environmental variables were correlated to these changes in benthic community.

Tidal estuaries are regarded as highly important ecosystems, mostly due to their high primary productivity and associated role as carbon sinks. In these ecosystems, primary productivity is mainly due to the photosynthetic carbon fixation by phytoplankton and microphytobenthos. The productivity of the two communities has been mostly studied separately, and directly comparable estimates of their carbon fixation rates in the same estuary are relatively scarce. The present study aimed to characterize the spatio-temporal variability of the productivity of phytoplankton and microphytobenthos in a tidal estuary, the Ria de Aveiro (Portugal). The productivity of the two communities was determined using a common methodological approach, based on measurements of in vivo chlorophyll fluorescence, allowing the estimation of the annual ecosystem-level budget for carbon fixation by the two groups. Productivity rates were determined based on synoptic in situ measurements of absolute rates of electron transport rate of photosystem II, using Pulse Amplitude Modulation fluorometry. Chlorophyll fluorescence indices were accompanied by measurements of salinity, temperature, water turbidity, solar irradiance, and planktonic and benthic microalgal biomass. Measurements were carried out hourly, along four spring-neap tidal cycles distributed along 1 year, on three sites of the estuary. The most pronounced trends in the spatio-temporal variability of the photophysiology and productivity of the two communities were the following: (i) maximum biomass and productivity were reached later for microphytobenthos (summer-autumn) than for phytoplankton (spring-summer); (ii) the absorption cross-section of PSII was generally higher for phytoplankton; (iii) the two groups showed a similar photoacclimation state, but microphytobenthos appeared as high light-acclimated when compared to phytoplankton. Biomass-specific productivity was on average higher for phytoplankton than for microphytobenthos, averaging 68.0 and 19.1 mg C mg Chl a–1 d–1, respectively. However, areal depth-integrated production rates were generally higher for the microphytobenthos than for the phytoplankton, averaging 264.5 and 140.0 mg C m–2 d–1, respectively. On an annual basis, phytoplankton productivity averaged 49.9 g C m–2 yr–1 while the productivity of microphytobenthos averaged 105.2 g C m–2 yr–1. When upscaling to the whole estuary, annual primary production rates of phytoplankton and microphytobenthos reached 4894.3 and 7534.0 t C yr–1, respectively, representing 39.4 and 60.6% of the combined total of 12428.3 t C yr–1 determined for the two communities in the Ria de Aveiro.

The global biodiversity loss has raised interest in the different facets of diversity, and the importance of diversity for ecosystem functions has been recognized. However, our knowledge on seasonal and inter-annual variation in the composition and diversity of communities is still poor. Here, we investigated the seasonal and inter-annual changes in taxonomic and functional community composition and diversity of benthic diatoms in a coastal habitat of the northern Baltic Sea, where seasonal and inter-annual variation of climate is pronounced. We found that the taxonomic and functional alpha diversity remained stable at seasonal and inter-annual level despite strong changes in community composition. However, alpha diversity decreased during an exceptionally warm winter possibly due to disturbances induced by the lack of ice. This may suggest that climate warming and consequently limited ice cover will affect the diversity of benthic communities.

Microphytobenthos (MPB), the photosynthetic primary producing component of microbenthos, shows variable patterns in its biomass distribution along the intertidal gradient as a result of the interactions of factors such as light, tides, temperature, and grazing pressure. These patterns have been studied more extensively in northern European estuaries than southern European coastal systems. Even less information is available regarding temporal changes in MPB primary production rates in these systems. For this reason, we followed the seasonal changes in net production in light and dark respiration rates (determined by oxygen microelectrodes) and MPB biomass (estimated by sediment chlorophyll a) along the intertidal gradient of the inner Cadiz Bay during a year. Sediment cores were collected along two transects (five sampling stations per transect) with distinct sediment granulometry: one muddy [Puerto Real (PR)] and one muddy-sandy transect [San Fernando (SF)]. Our results show that MPB biomass and net production increased seawards reaching their maxima in winter. In contrast to what is observed in northern European systems, the higher solar irradiance and temperatures occurring in summer in southern Spain likely inhibit MPB production. In Cadiz Bay, spatial patterns of MPB biomass and net production depended on season and location due to the environmental heterogeneity observed. Environmental variables, analyzed by principal component analysis (PCA), were used to explain the variability of MPB metabolism by multiple regression. Selected principal component (PC) axes explained 60% of the net production in light and 41% of the dark respiration rates variability in PR, while they only accounted for 25% of the same rates in SF. The differences observed between transects and the variability in the environmental variables explaining them highlight the importance of considering the spatial heterogeneity of our system to estimate the contribution of MPB to the inner Cadiz Bay productivity. In our case, this contribution is significant accounting for up to 49% of the total benthic production of the inner Cadiz Bay intertidal sediments, confirming previous global estimates.

Diatoms usually dominate microphytobenthic biofilms in coastal and estuarine intertidal environments. Yet, functional studies on biofilms often skip species analysis because benthic diatoms are notoriously difficult to extract from sediments and challenging to identify at that taxonomic level. Valid, less time-consuming alternatives would surely be welcomed and increase the inclusion of community structure information in microphytobenthos (MPB) ecophysiological studies. Starting with an original 181-species abundances matrix (OSM), obtained during a 2-year spatial–temporal survey in a Tagus Estuary intertidal flat with contrasting sediment textures, the current study assessed the effectiveness of several approaches to species abundances analysis. The effect of excluding abundance data or rare species, the influence of taxonomic resolution, or the use of size-based metrics on biotic multivariate patterns was examined by an objective comparison that replicated these different approaches on three different levels: (1) inter-matrix correlations, (2) performance in several non-parametric multivariate analyses (ANOSIM, MDS), and (3) correlations with the environmental dataset. When compared with the OSM, all matrices had strong or very strong positive correlations. All discriminated successfully spatial patterns, separating well assemblages from sandy and muddy sediments, and all had significant correlations with the environmental dataset. Apart from the relative biovolume species matrix (BSM), only the species matrices were able to discriminate significantly temporal patterns. The exclusion of the rarest species (48% of total) had a negligible effect, with the common and original species abundances matrices having a ρ > 0.99 correlation. Of the alternative approaches to species abundances, species presence/absence and the genera abundances matrices yielded the best results overall. Genera presence/absence and the size-class matrices had intermediate performances, with the former performing comparatively poorly with regard to seasonal patterns. BSM had the lowest correlation with the environmental variable dataset (ρ = 0.598) and the worst overall performance in the other multivariate routines. This means that either a high-taxonomic resolution qualitative analysis (i.e. species presence/absence) or, in alternatively, a genus-level analysis retaining abundance data may be sufficient to describe basic spatial differences in estuarine intertidal flats. However, if seasonal variations in mudflat diatom assemblage structure are to be detected, species-level abundance data are still necessary.

Diatoms usually dominate microphytobenthic biofilms in coastal and estuarine intertidal environments. Yet, functional studies on biofilms often skip species analysis because benthic diatoms are notoriously difficult to extract from sediments and challenging to identify at that taxonomic level. Valid, less time-consuming alternatives would surely be welcomed and increase the inclusion of community structure information in microphytobenthos (MPB) ecophysiological studies. Starting with an original 181-species abundances matrix (OSM), obtained during a 2-year spatial–temporal survey in a Tagus Estuary intertidal flat with contrasting sediment textures, the current study assessed the effectiveness of several approaches to species abundances analysis. The effect of excluding abundance data or rare species, the influence of taxonomic resolution, or the use of size-based metrics on biotic multivariate patterns was examined by an objective comparison that replicated these different approaches on three different levels: (1) inter-matrix correlations, (2) performance in several non-parametric multivariate analyses (ANOSIM, MDS), and (3) correlations with the environmental dataset. When compared with the OSM, all matrices had strong or very strong positive correlations. All discriminated successfully spatial patterns, separating well assemblages from sandy and muddy sediments, and all had significant correlations with the environmental dataset. Apart from the relative biovolume species matrix (BSM), only the species matrices were able to discriminate significantly temporal patterns. The exclusion of the rarest species (48% of total) had a negligible effect, with the common and original species abundances matrices having a ρ > 0.99 correlation. Of the alternative approaches to species abundances, species presence/absence and the genera abundances matrices yielded the best results overall. Genera presence/absence and the size-class matrices had intermediate performances, with the former performing comparatively poorly with regard to seasonal patterns. BSM had the lowest correlation with the environmental variable dataset (ρ = 0.598) and the worst overall performance in the other multivariate routines. This means that either a high-taxonomic resolution qualitative analysis (i.e. species presence/absence) or, in alternatively, a genus-level analysis retaining abundance data may be sufficient to describe basic spatial differences in estuarine intertidal flats. However, if seasonal variations in mudflat diatom assemblage structure are to be detected, species-level abundance data are still necessary.

International audience; Mangrove forests are highly productive coastal ecosystems that significantly influence global carbon cycling. This study characterized the sources of dissolved organic carbon (DOC), particulate organic carbon (POC) and dissolved inorganic carbon (DIC) and the processes affecting their distributions in a mangrove-influenced estuary located in French Guiana (FG), a region representative of these dynamic systems down drift of the Amazon River. Four sampling cruises were carried out between 2013 and 2015 in surface waters of the estuary during dry and wet seasons. Stable isotopes (δ13DOC, δ13POC, δ13DIC), elemental ratios and optical properties (absorption) were used as proxies to identify different C sources. Property–salinity relationships revealed regions of approximately linear mixing (e.g., alkalinity) or net sources or sinks (e.g., DOC). DIC speciation and isotopic distributions demonstrated dynamic source–sink reaction processes within the estuary. DOC was the major form of organic carbon representing mixtures of terrestrial sources (e.g., pore water, litter leaching) and very high concentration (400–800 µM) compared to other mangrove settings (e.g. Brazilian, Sundarbans, African). Highly negative δ13POC (− 40‰) in the riverine part presumably suggests the role of freshwater phytoplankton in the dry season and methanotrophic sources derived from senescent mangrove deposits or upstream hydrothermal dam during the wet season. Microphytobenthos and marine phytoplankton were the primary sources of POC inshore and DOC offshore, respectively. Mangrove products and benthic microalgae dominated estuarine sources of C in FG coastal waters (~ 10 km, inner shelf region), and there was extensive exchange of C between forest and tidal flat and the estuarine reservoirs.