A prey–predator experimental setup was conducted in a shallow coastal ecosystem characterized by a bare intertidal mudflat to test if benthic biofilm resuspension causing microalgae inputs and carbon export toward nanoflagellates would favour the highest planktonic trophic level (i.e. mesozooplankton) when nutrient concentrations are high in the water column. Mesozooplankton predation and somatic production were studied by comparing the evolution of the prey assemblage (diversity and abundances) in the presence and absence of these predators during 24 h experiments. The results were then statistically analysed according to the cross-calculation method. Biofilm resuspension caused (i) a direct input of benthic microorganisms that had changed prey structure in term of diversity and/or size and (ii) a differential growth ability between prey taxa. Both reasons implied a bottom-up control on both micro- and mesozooplankton. The carbon export toward heterotrophic nanoflagellates favoured pelagic ciliate growth while mesozooplankton benefited from largest diatoms with high growth rates, both benthic and R-strategist pelagic species. Even if these microbial and herbivorous pathways are controlled by benthic inputs, they seemed to be totally disconnected since ciliates represented only a small part of mesozooplankton diet. The sensitivity of mesozooplankton production appeared species-dependent with the most tolerant taxa dominating the zooplankton assemblages. This suggests a role of the intensities and the frequencies of biofilm resuspension on the spatio-temporal structuring of mesozooplankton in macrotidal coastal ecosystems.

Benthic dinoflagellates collected in spring–summer 2010 and 2011 from intertidal sandy sediments of the shore of Wimereux (north-east English Channel, France) were examined by light microscopy, and some of them by scanning electron microscopy. High dinoflagellate species richness, 70 species, was evidenced when compared to the plankton observed in the coastal waters of the north-east English Channel. The greatest difficulty in performing accurate species identification mainly concerned the heterotrophic species of Amphidinium sensu lato, the laterally flattened species of Amphidiniopsis, as well as some heterotrophic species of Thecadinium. Several undescribed species are here illustrated, mainly within these genera. The differences in size between species of Herdmania and Sabulodinium suggest the occurrence of at least a second species for these monotypic genera. The species Amphidiniopsis hexagona, A. rotundata, A. uroensis and Sinophysis minima are reported for the first time in the Atlantic Ocean and on European coasts. Although these species were only previously known from the Pacific Ocean, they should not necessarily be considered as newcomers or invasive species due to the scarce coverage of the previous studies on sand-dwelling dinoflagellates.

Microphytobenthos (MPB) contributes up to half the primary production of estuaries. These microorganisms are sensitive to changes in sediment temperatures, particularly the extreme temperatures during exposure periods. This study investigates the physiological responses of MPB to freezing temperatures at two locations near Hobart, Tasmania during winter. Photosynthetic parameters were measured at 2 mm intervals to a depth of 10 mm. FV/FM values at three different distances from the shoreline at Kings Beach and Browns River in winter were between 0.584 and 0.617. rETRmax values were between 24.696 and 20.773. Maximum α values peaked in the subsurface rather than at the sediment surface. In vitro laboratory experiments (down to −5°C) showed little difference in response between the control and treatment groups, indicating no apparent effects of short term freezing on the MPB. Little change in photosynthetic parameters in response to freezing was probably associated with the resistance of light-harvesting reactions to freezing temperatures, recovery of the plasmalemma integrity or cryoprotection. Sediment composition and species composition were similar at both sampling sites. Therefore, responses of MPB were not due to species and grain size composition.

Microphytobenthos need photoadaptive strategies to survive the highly dynamic light environment in which they reside. Xanthophyll pigments can provide photoprotection by cycling electrons between epoxide and de-epoxide forms, dissipating excess light energy as heat. This study examined the xanthophyll cycle in microphytobenthos on a tidally exposed substrate at Browns River, Tasmania. Fv/Fm decreased from 0.52±0.01 to 0.47±0.01 at noon in surface samples and a decrease in the diadinoxanthin:chlorophyll-a ratio from 0.022±0.003 to 0.015±0.005 also suggests that the microphytobenthos was under physiological stress at noon. The results indicate that the cells exposed to light at the surface migrated deeper into the sediments and replenished the epoxide form of their xanthophylls. The results suggest that micrphytobenthos utilizes both behavioural and physiological strategies to survive in the dynamic intertidal environment.

A single trophic interaction between two major biotic components within similar ecosystems can reveal high variability. In fact, in situ measurements of the trophic interactions, as provided by the field application of stable isotopes, are likely to reveal strong differences in patterns. An illustration of such a geographical plasticity is provided when regarding the trophic interaction between two major components of intertidal habitats namely, the oyster Crassostrea gigas and the microphytobenthos. The contribution of benthic diatoms to oysters' diets ranged from 4.4±3.5% in the Mont St Michel bay to 69.6±1.1% in the Marennes-Oléron bay, as estimated from δ13C and δ15N analyses. Concerning food web investigations, these results point out serious limits for extrapolating qualitative and quantitative observations related to the major trophic links between identical food sources and consumers inhabiting similar ecosystems.

This investigation was motivated by the lack of ultraviolet radiation (UVR, 280–400 nm) studies on Antarctic benthic marine microalgae. The objective was to estimate the impact of UV-B (280–315 nm) and UV-A (315–400 nm), on photosynthetic efficiency, species composition, cell density and specific growth rate in a semi-natural soft-bottom diatom community. In both experiments, cell density increased over time. The most frequently observed species were Navicula cancellata, Cylindrotheca closterium, Nitzschia spp., and Petroneis plagiostoma. For both experiments, a shift in species composition and a decreased photosystem II (PSII) maximum efficiency (Fv/Fm) over time was observed, irrespective of treatment. UVR significantly reduced Fv/Fm on days 3 and 10 (Expt 1), disappearing on the last sampling date. A similar trend was found in Expt 2. A significant UV effect on cell density was observed in Expt 1 (day 10) but not in Expt 2. No treatment effects on species composition or specific growth rate were found. Thus, the UV effects were transient (photosynthetic efficiency and cell density) and the growth of the benthic diatoms was generally unaffected. Overall, according to our results, UVR does not seem to be a threat to benthic marine Antarctic diatoms.

Microphytobenthos are the major intertidal primary producers in many estuarine systems and assessment of their biomass is essential in ecological studies. Algal biomass can be assessed by the use of proxy measurements, e.g. chlorophyll a (Chl a), using a lengthy and destructive extraction procedure. Fluorescence is a non-destructive and in situ alternative, recently applied to microphytobenthos, using the minimum fluorescence signal (Fo) as a measurement of Chl a. In this study, Fo after 15 min of dark adaptation (Fo15) showed a significant positive correlation with Chl a (r = 0.84, p<0.001, n = 24). The relationship between Fo15 and Chl a extracted from sediment samples of increasing sample depth (0.2–2 mm) became less significant as sediment depth increased. The strongest relationship between Fo15 and Chl a, expressed as concentration (mg m−2) and content (mg kg−1), was found when all data were combined, but nearly comparable levels of association were found for in situ measurements using sediment cores up to 2.0 mm deep. Results suggested that full dark adaptation was not always achieved because a significant negative correlation was observed between Fv/Fm and ambient irradiance for seasonal data. In addition, Fo15 showed a more significant correlation with Chl a than with Fm15, suggesting some residual level of non-photochemical quenching after 15 min in the dark. Despite the incomplete dark adaptation, the highly significant relationships between Fo15 and both Chl a concentration and content suggest that the use of Fo15 is a suitable in situ proxy method of estimating algal biomass.

How are microphytobenthic biofilms adapted to the high incident irradiances and temperatures, low inorganic nutrient concentrations and high desiccation stresses on intertidal flats present in tropical environments? This study investigated biofilms subject to different environmental conditions in a range of tropical sites in Suva lagoon, Fiji. PAM fluorescence was used to measure photophysiological responses to the light climate. Biofilm colloidal carbohydrate, extracellular polymeric substances (EPS) and low molecular weight (MW) carbohydrate concentrations and diel carbohydrate production patterns were measured. Average biomass (Chl a) ranged from 15 to 36 mg m−2, and was highest in seagrass bed sediments, but biomass was not correlated with water column or sediment porewater nutrient concentrations. Biofilm photophysiology differed significantly along a combined gradient of light and nutrient availability, with Fv/Fm, relative ETRmax and Ek of biofilms highest in mangrove and intertidal main island sites and lowest in subtidal coral reef flats. Subtidal biofilms showed photoinhibition at irradiances >1000 μmol m−2 s−1. Significant correlations between Chl a and colloidal carbohydrate concentrations were present (except on intertidal sandflats), and tropical biofilms had higher ratios of colloidal carbohydrate and EPS to Chl a than temperate estuarine biofilms, probably due to a combination of high irradiance and low nutrient availability leading to the production of excess photoassimilates. The percentage of EPS present in the colloidal fraction was highest in coral sand biofilms (42%), which had the lowest nutrient concentrations, compared with other sites (25–32%). Intertidal biofilms predominantly consisted of large motile taxa and showed strong rhythms of vertical migration. During tidal emersion, high sediment temperatures (41 °C), irradiance (>2300 μmol m−2 s−1) and salinity (49‰) stimulated downward migration. In silty sediments, migration resulted in a reduction in photosynthetic activity during the midday period but, in sands with high light penetration (to a depth of >1700 μm), high production rates of EPS (18.2 μg carbo. μg Chl a−1 h−1) and low MW carbohydrate exudates (40.2 μg carbo. μg Chl a−1 h−1) occurred. Vertical migration, high Ek and high rates of photoassimilate dumping are all adaptations to living in the tropical intertidal zone. Seagrass and reef flat biofilms consisted of a diverse non-migratory flora of motile and non-motile taxa that were not subject to such extreme temperature and irradiance conditions. Low values of photosynthetic parameters and high colloidal and EPS content indicated that these biofilms were nutrient-limited.

The excretion of extracellular polymeric substances (EPS) by an axenic culture of the benthic diatom Cylindrotheca closterium was investigated. Two sequential extraction steps proved to be sufficient to remove the bulk of the EPS present. Soluble EPS was recovered by a simple centrifugation step and represented a fraction that was not or was only loosely associated with diatom cells. For the extraction of bound EPS, different procedures were compared. The best results were obtained using distilled water as extraction solvent (1 h, 30 °C). The sugars that were recovered using this procedure were typically associated with aggregates of diatoms. In addition to the distinct differences in localization of the different types of EPS, their temporal dynamics differed in relation to the light–dark cycle. Soluble EPS were continuously released into the medium at a rate of 1·6 pg cell−1 day−1. In contrast, the production of bound EPS was highly light-dependent. In the dark, this bound EPS rapidly disappeared, probably as the result of its utilization by the diatoms.

The composition (% relative abundance) of the benthic diatom community was studied in the littoral zone (0–5 m) of the NW and E coasts of the brackish, non-tidal Gulf of Riga, in the Baltic Sea. The samples were collected concomitantly with measurements of sediment primary productivity and chlorophyll a during three cruises, representing three seasons (autumn, spring, summer). At all depths, the living diatom community was dominated by epipsammic species, the most abundant taxa being Martyana atomus, a species of Fragilariaceae and Achnanthes delicatula. The community was characterized by a stable composition and a high species diversity throughout the study period (Shannon–Weaver, mean H′ = 4·4). Principal Component Analyses (PCA), together with Redundancy Analysis (RDA) based on 129 taxa, revealed both spatial (site and depth) and seasonal differences in the diatom communities. However, these differences were mainly caused by the varying proportions of taxa common in both sampling areas in all three seasons, rather than by actual major taxonomic changes in the species present in communities. The distribution of the typical epipsammic species along the depth gradient was not uni-directional. The dominance of attached life forms, and the absence of a well-developed epipelic community, reflects the physically dynamic substratum, particularly in the eastern part of the Gulf. As a result, primary productivity is kept rather low, decreasing rapidly with depth due to frequent turbidity of the water column.

Intertidal cohesive estuarine sediments frequently support extensive microphytobenthic biofilms, which are usually dominated by epipelic (motile) diatoms. The distribution of different diatom taxa varies along estuarine gradients, but it is not clear what the causative factors are in determining these patterns. In many estuaries, salinity covaries with other environmental gradients, particularly with nutrient concentrations when the river is the main nutrient source. Autecological information is required to aid interpretation of these field distributions. In this study the maximum specific growth rate (μ) and stationary phase biomass of four common taxa of estuarine epipelic diatoms (Navicula phyllepta, N. perminuta, N. salinarum and Cylindrotheca closterium) were measured in axenic unialgal cultures grown under a range of nitrogen and salinity regimes. All three Navicula species and two different clones of C. closterium showed significant differences in their response to a range of ammonium (10–4000 μM) and nitrate (10–2000 μM) concentrations across a salinity range of 10–35‰. Growth rates of N. phyllepta were significantly lower at ammonium concentrations > 400 μM, but the other three taxa showed little evidence of ammonium toxicity, even at concentrations > 1 mM. On the basis of the response of each species, the following putative ranking of preferences for inorganic nitrogen concentrations (lowest to highest, with salinity optima in parentheses) was constructed: N. phyllepta (10–20‰) – N. perminuta (10–30‰) – N. salinarum (20–35‰)/C. closterium (clone 1, 10–25‰, clone 2, 25–35‰). Such a ranking should be interpreted cautiously, as interclonal differences and adaptation to local environmental conditions can alter the preferences of taxa. These autecological data are partially supported by previously published data on field distribution, and suggest that certain taxa may have value as trophic indicator species.

The production and composition of extracellular polymeric substances (EPS) in axenic batch cultures of the benthic marine epipelic diatoms Navicula salinarum and Cylindrotheca closterium were investigated. EPS was secreted into the medium and the bulk was loosely associated with the cells. Neither N. salinarum nor C. closterium formed a well-defined polysaccharide capsule. EPS of both N. salinarum and C. closterium consisted predominantly of polysaccharide but small quantities of protein were present as well. EPS also contained uronic acids and SO42− groups. Analysis of monosaccharides using gas chromatography showed that for both species glucose and xylose were the main constituents, but several other monosaccharides were present in smaller quantities. Two fractions of EPS were distinguished: a small amount was secreted into the medium and a second fraction was extracted in water at 30°C. For both species the two fractions differed somewhat in composition, indicating that they represented two different types of EPS. The EPS produced by N. salinarum and by C. closterium differed in their composition. The rate of EPS production in batch culture was highest during the transition from exponential growth to stationary growth. Negatively charged groups such as uronic acids and sulphated sugars determine the adhesion capacity of EPS and probably play an important role in the stabilization of intertidal sediments on which these diatoms grow and produce biofilms.

Fluxes of nutrients (NH4+, NO3-, PO43- and Si(OH)4) were studied on an intertidal mudflat in Marennes-Oléron Bay, France, at two different seasons and at different times of the emersion period. Fluxes through the sediment-water interface were both calculated from vertical profiles of nutrient concentration in pore-water (diffusive fluxes, JD) and measured in light and dark benthic mini-chambers (measured fluxes, J0). Results indicate that ammonia was mainly released in summer while nitrate was mainly taken up in late winter. This uptake from the overlying water was probably due to the coupling of nitrification-denitrification within the sediment. The J0/JD ratio further indicates that bioturbation likely enhanced ammonia release in summer. Concerning phosphate, the comparison of diffusive and measured fluxes suggests that PO43- could be assimilated by the biofilm in winter while it was released in summer at a high rate due to both bioturbation and desorption because of the relative anoxic conditions in summer. Silica was always released by the sediment, but at a higher rate in summer. Statistically significant differences in measured fluxes were detected in dark chambers at different times of low tide, thus suggesting a short-term variability of fluxes. Microphytobenthos preferred ammonia to nitrate, but assimilated nitrate when ammonia was not available. It also turned out that benthic cells could be limited in nitrogen during low tide in late winter. In summer, ammonia was not limiting and microphytobenthic activity significantly decreased the measured flux of NH4+ in the middle of low tide when its photosynthetic capacity was highest.