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Phytoplankton play a central role in the planetary cycling of important elements and compounds. Understanding how phytoplankton are responding to climate change is consequently a major question in Earth Sciences. Monitoring phytoplankton is key to answering this question. Satellite remote sensing of ocean colour is our only means of monitoring phytoplankton in the entire surface ocean at high temporal and large spatial scales, and the continuous ocean-colour data record is now approaching a length suitable for addressing questions around climate change, at least in some regions. Yet, developing ocean-colour algorithms for climate change studies requires addressing issues of ambiguity in the ocean-colour signal. For example, for the same chlorophyll-a concentration (Chl-a) of phytoplankton, the colour of the ocean can be different depending on the type of phytoplankton present. One route to tackle the issue of ambiguity is by enriching the ocean-colour data with information on sea surface temperature (SST), a good proxy of changes in three phytoplankton size classes (PSCs) independent of changes in total Chl-a, a measure of phytoplankton biomass. Using a global surface in-situ dataset of HPLC (high performance liquid chromatography) pigments, size-fractionated filtration data, and concurrent satellite SST spanning from 1991 to 2021, we re-tuned, validated and advanced an SST-dependent three-component model that quantifies the relationship between total Chl-a and Chl-a associated with the three PSCs (pico-, nano- and microplankton). Similar to previous studies, striking dependencies between model parameters and SST were captured, which were found to improve model performance significantly. These relationships were applied to 40 years of monthly composites of satellite SST, and significant trends in model parameters were observed globally, in response to climate warming. Changes in these parameters highlight issues in estimating long-term trends in phytoplankton biomass (Chl-a) from ocean colour using standard empirical algorithms, which implicitly assume a fixed relationship between total Chl-a and Chl-a of the three size classes. The proposed ecological model will be at the centre of a new ocean-colour modelling framework, designed for investigating the response of phytoplankton to climate change, described in subsequent parts of this series of papers., This work is supported primarily by a UKRI Future Leader Fellowship (MR/V022792/1). Additional supports from the UK National Centre for Earth Observation (NCEO), the Simons Foundation Project Collaboration on Computational Biogeochemical Modeling of Marine Ecosystems (CBIOMES, 549947, Shubha Sathyendranath), and Royal Society International Exchanges 2021 Cost Share (NSFC) grant (IEC NSFC 211058) are acknowledged. Astrid Bracher and Vanda Brotas are funded by the European Union’s Horizon 2020 Research and Innovation Programme (N810139): Project Portugal Twinning for Innovation and Excellence in Marine Science and Earth Observation (PORTWIMS). Astrid Bracher is also funded by the ESA 656 S5P+Innovation Theme 7 Ocean Colour (S5POC) project (No. 4000127533/19/I-NS). The AWI in-situ data are supported by the Helmholtz Infrastructure Initiative FRAM. Tarron Lamont and Ray Barlow acknowledge funding, logistical, and administrative support from the South African National Department of Forestry, Fisheries and the Environment (DFFE), Bayworld Centre for Research and Education (BCRE), and the South African National Research Foundation (NRF grants: 129229 and 132073). Fang Shen is funded by National Natural Science Foundation of China (No. 42076187 and No. 41771378) for the sampling of in-situ data in eastern China seas. The Atlantic Meridional Transect (AMT) is funded by the UK Natural Environment Research Council (NERC) through its National Capability Long-term Single Centre Science Programme, Climate Linked Atlantic Sector Science (grant number NE/R015953/1) to Plymouth Marine Laboratory. This work contributes to the international IMBeR project and is contribution number 386 of the AMT programme. The authors would like to acknowledge all the contributors who have shared in-situ data to the public domains, including the Western Channel Observatory, TARA Ocean, Rothera Research Station, NASA SeaBASS, ADON, Government of Canada, DATAONE, BCODMO, EDI Data Portal, PANGAEA, and BODC, and all the scientists and crew who were involved in the collection of in-situ data are sincerely appreciated. We thank NOAA for providing daily and monthly OISST (version 2) SST data; ESA for providing monthly SST-CCI (version 2.1) SST data; ESA for providing monthly OC-CCI (version 5.0) Chl-a climatology data; GEBCO for providing bathymetric data (GEBCO2021 Grid). The authors also thank Hongyan Xi for providing comments and suggestions on the early version of the manuscript.

A global in-situ data set for validation of ocean-colour products from the ESA Ocean Colour Climate Change Initiative (OC-CCI) is presented. This version of the compilation, starting in 1997, now extends to 2021, which is important for the validation of the most recent satellite optical sensors such as Sentinel 3B OLCI and NOAA-20 VIIRS. The data set comprises in-situ observations of the following variables: spectral remote-sensing reflectance, concentration of chlorophyll-a, spectral inherent optical properties, spectral diffuse attenuation coefficient and total suspended matter. Data were obtained from multi-project archives acquired via open internet services, or from individual projects, acquired directly from data providers. Methodologies were implemented for homogenisation, quality control and merging of all data. Minimal changes were made on the original data, other than conversion to a standard format, elimination of some points after quality control and averaging of observations that were close in time and space. The result is a merged table available in text format. Overall, the size of the data set grew with 151,673 rows, with each row representing a unique station in space and time (cf 136,250 rows in previous version; Valente et al., 2019). Observations of remote-sensing reflectance increased to 68,641 (cf 59,781 in previous version; Valente et al., 2019). There was also a near tenfold increase in chlorophyll data since 2016. Metadata of each in situ measurement (original source, cruise or experiment, principal investigator) are included in the final table. By making the metadata available, provenance is better documented, and it is also possible to analyse each set of data separately. The compiled data are available at https://doi.pangaea.de/10.1594/PANGAEA.941318 (Valente et al., 2022)., SI

While primary productivity is more stable in oceanic regions, it may vary to a great extent with the proximity to coasts, where mesoscale processes may intertwine and shape phytoplankton community composition and biomass. Sometimes, this may lead to the development of anomalous phytoplankton blooms (i.e., episodic blooms that exceed several times the average phytoplankton biomass). A massive bloom observed off the Western Iberian Coast (SW Europe) during March 2009 prompted a full investigation on its spatial and temporal extent, its causes, and its potential impact on the ecosystem. Results revealed that the March 2009 bloom was both novel in terms of biomass in a regional context and one of the largest anomalous blooms until now described in terms of relative magnitude. Its causes were due to a concurrence of long-term (deep winter MLD) and short-term factors (coastal upwelling, sudden changes in the water column, consistent offshore water transport). Its impact on the regional ecosystem is difficult to gauge, although the high concentrations of particulate organic carbon at surface during the bloom period suggests that it may have had a significant local impact. Since climate change is expected to increase the frequency and intensity of extreme weather events, it is possible that anomalous blooms will also become more frequent, expanding their role in shaping carbon export and food webs. These results are crucial for the monitoring of the Western Iberian Coast and are applicable to other complex coastal upwelling regions where phytoplankton biomass and variability have a crucial link to fisheries.

Phytoplankton biomass, through its proxy, Chlorophyll a, has been assessed at synoptic temporal and spatial scales with satellite remote sensing (RS) for over two decades. Also, RS algorithms to monitor relative size classes abundance are widely used; however, differentiating functional types from RS, as well as the assessment of phytoplankton structure, in terms of carbon remains a challenge. Hence, the main motivation of this work it to discuss the links between size classes and phytoplankton groups, in order to foster the capability of assessing phytoplankton community structure and phytoplankton size fractionated carbon budgets. To accomplish our goal, we used data (on nutrients, photosynthetic pigments concentration and cell numbers per taxa) collected in surface samples along a transect on the Atlantic Ocean, during the 25th Atlantic Meridional Transect cruise (AMT25) between 50° N and 50° S, from nutrient-rich high latitudes to the oligotrophic gyres. We compared phytoplankton size classes from two methodological approaches: (i) using the concentration of diagnostic photosynthetic pigments, and assessing the abundance of the three size classes, micro-, nano-, and picoplankton, and (ii) identifying and enumerating phytoplankton taxa by microscopy or by flow cytometry, converting into carbon, and dividing the community into five size classes, according to their cell carbon content. The distribution of phytoplankton community in the different oceanographic regions is presented in terms of size classes, taxonomic groups and functional types, and discussed in relation to the environmental oceanographic conditions. The distribution of seven functional types along the transect showed the dominance of picoautotrophs in the Atlantic gyres and high biomass of diatoms and autotrophic dinoflagellates (ADinos) in higher northern and southern latitudes, where larger cells constituted the major component of the biomass. Total carbon ranged from 65 to 4 mg carbon m–3, at latitudes 45° S and 27° N, respectively. The pigment and cell carbon approaches gave good consistency for picoplankton and microplankton size classes, but nanoplankton size class was overestimated by the pigment-based approach. The limitation of enumerating methods to accurately resolve cells between 5 and 10 μm might be cause of this mismatch, and is highlighted as a knowledge gap. Finally, the three-component model of Brewin et al. was fitted to the Chlorophyll a (Chla) data and, for the first time, to the carbon data, to extract the biomass of three size classes of phytoplankton. The general pattern of the model fitted to the carbon data was in accordance with the fits to Chla data. The ratio of the parameter representing the asymptotic maximum biomass gave reasonable values for Carbon:Chla ratios, with an overall median of 112, but with higher values for picoplankton (170) than for combined pico-nanoplankton (36). The approach may be useful for inferring size-fractionated carbon from Earth Observation.

To establish effective water quality monitoring strategies in estuaries, it is imperative to identify and understand the main drivers for the variation of water quality parameters. The tidal effect is an important factor of the daily and fortnightly variability in several estuaries. However, the extent of that influence on the different physicochemical and biological parameters is still overlooked in some estuarine systems, such as the Sado Estuary, a mesotidal estuary located on the west coast of Portugal. The main objective of this study was to determine how the water quality parameters of the Sado Estuary varied with the fortnightly and the semidiurnal tidal variation. To achieve this goal, sampling campaigns were conducted in May/18, Nov/18 and Jun/19, under neap and spring tidal conditions, with data collection over the tidal cycle. Results were observed to be significantly influenced by the tidal variation, in a large area of the estuary. Flood seemed to mitigate possible effects of nutrient enrichment in the water column. Additionally, significant differences were also observed when considering the different sampling stations. Temperature, Suspended Particulate Matter (SPM) and nutrients showed the highest values at low water. Lastly, the implications of the tidal variability in the evaluation of the water quality according to Water Framework Directive were also discussed, highlighting the importance of studying short-time scale variations and the worst-case scenario to ensure water quality is maintained. These findings are relevant for the implementation of regional management plans and to promote sustainable development.

Coccolithophores are among the most important calcifying pelagic organisms. To assess how coccolithophore species with different coccolith-carbonate mass and distinct ecological resilience to ocean warming will influence the “rain ratio” and the “biological carbon pump”, 1 yr of species-specific coccolith-carbonate export fluxes were quantified using sediment traps moored at four sites between NW Africa and the Caribbean (i.e., CB-20°N/21°W, at 1214 m; M1-12°N/23°W, at 1150 m; M2-14°N/37°W, at 1235 m; M4-12°N/49°W, at 1130 m). Highest coccolith-CaCO3 fluxes at the westernmost site M4, where the nutricline is deepest along the tropical North Atlantic, were dominated by deep-dwelling small-sized coccolithspecies Florisphaera profunda and Gladiolithus flabellatus. Total coccolith-CaCO3 fluxesof 371 mg m−2 yr−1 at M4 were followed by 165 mg m−2 yr−1 at the north-easternmost CB, 130 mg m−2 yr−1 at M1, and 114 mg m−2 yr −1 at M2 in between. Coccoliths accounted for nearly half of the total carbonate flux at M4 (45%), much higher compared to 23% at M2 and 15% at M1 and CB. At site M4, highest ratios of coccolith-CaCO3 to particulate organic carbon fluxes and weak correlations between the carbonate of deep-dwelling species and particulate organic carbon suggest that increasing productivity in the lower photic zone in response to ocean warming might enhance the rain ratio and reduce the coccolith-ballasting efficiency. The resulting weakened biological carbon pump could, however, be counterbalanced by increasing frequency of Saharan dust outbreaks across the tropical Atlantic, providing mineral ballast as well as nutrients to fuel fast-blooming and ballast-efficient coccolithophore species.

Hyperspectral satellite data are a source of the top of the atmosphere radiance signal which can be used for novel algorithms aimed for observations of marine ecosystems and the light-lit ocean. Atmospheric sensors such as SCIAMACHY, GOME-2 and OMI have proven in the past to yield valuable information on phytoplankton diversity, sun-induced marine fluorescence, and the underwater light field, however at low coverage and spatial resolution. Within the ESA Sentinel-5p+ Innovation themes, we explore TROPOMI's potential for deriving the diffuse attenuation coefficient and the quantification of different phytoplankton groups. As commonly used for the retrieval of atmospheric trace gases, we apply the differential optical absorption spectroscopy combined with radiative transfer modeling (RTM) to infer these oceanic parameters. We present results on a measure describing the diminishing of incoming radiation in the ocean with depth, the diffuse attenuation coefficient KD. KD is derived by the retrieval of the vibrational Raman scattering signal in backscattered radiances measured by TROPOMI in the UV and spectral range which then is further converted to the associated KD using RTM. The final TROMPOMI KD data sets resolved for three spectral regions (UV-B+short wave UV-A, UV-A and short blue) agree well with in situ data sampled during an expedition with RV Polarstern in 2018 in the Atlantic Ocean. Further, KD-blue compared to wavelength-converted KD(490nm) products (OLCI-A and the merged OC-CCI) from common, multispectral, ocean color sensors, show that differences between the three data sets are within uncertainties given for the OC-CCI product. Our study shows for the first time KD products for the UV spectral range retrieved from space based data. TROPOMI KD-blue results have higher quality and much higher spatial coverage and resolution than previous ones from SCIAMACHY, GOME-2 and OMI. Additionally, first results on TROPOMI’s potential for retrieving three phytoplankton groups will be shown and compared to similar multispectral phytoplankton group data for the same time period and ocean region as shown for TROPOMI KD.

Monitoring water quality parameters and their ecological effects in transitional waters is usually performed through in situ sampling programs. These are expensive and time-consuming, and often do not represent the total area of interest. Remote sensing techniques offer enormous advantages by providing cost-effective systematic observations of a large water system. This study evaluates the potential of water quality monitoring using Sentinel-2 observations for the period 2018-2020 for the Sado estuary (Portugal), through an algorithm intercomparison exercise and time-series analysis of different water quality parameters (i.e., colored dissolved organic matter (CDOM), chlorophyll-a (Chl-a), suspended particulate matter (SPM), and turbidity). Results suggest that Sentinel-2 is useful for monitoring these parameters in a highly dynamic system, however, with challenges in retrieving accurate data for some of the variables, such as Chl-a. Spatio-temporal variability results were consistent with historical data, presenting the highest values of CDOM, Chl-a, SPM and turbidity during Spring and Summer. This work is the first study providing annual and seasonal coverage with high spatial resolution (10 m) for the Sado estuary, being a key contribution for the definition of effective monitoring programs. Moreover, the potential of remote sensing methodologies for continuous water quality monitoring in transitional systems under the scope of the European Water Framework Directive is briefly discussed.

Two ocean colour features in the western Iberian margin (western Europe) were described in present work. They were identified in 10 years (2002–2012) of MODIS-AQUA normalized water-leaving radiance (nLw) at 555 nm and their causes were investigated using complementary satellite, in-situ and model data. One feature was a band of high nLw555 (>0.8 mW cm−2 μm−1 sr−1) with exceptionally large widths (>20 km) along the coast. Over the 10-year period, this wide coastal band of high nLw555 only occurred during winter, following better the increases in wave height, than the increases in precipitation and river discharge. The band seemed particularly associated with episodes of large wave heights (>6 m), under weak thermal stratification and northerly winds. Findings suggest that the band is the signature of exceptional offshore extensions of the more reflective turbid coastal waters, as a result of wave-induced sediment resuspension along the coast. The other feature consisted in areas of equally high nLw555, but separated from the coast by more than 40 km. These offshore areas of high nLw555 shared spectral signatures of phytoplankton, namely coccolithophores, typically formed during spring following water column re-stratification and reached larger areas after winters with deeper oceanic mixed layers. Less commonly, they also occurred from summer to autumn. Results indicate they are mainly the signature of enhanced coccolithophore abundances that also create turbid reflective waters due to their calcite plates. The used methodology separated the two features in time and therefore seems to allow for satellite monitoring of sediment resuspension and coccolithophore blooms off west Iberia and similar coastal environments, which is particularly relevant for detecting events of sediment transport, potentially linked to water quality problems, and long-term changes in phytoplankton composition.

Changes in temperature and CO2 are typically associated with climate change, but they also act on shorter time scales, leading to alterations in phytoplankton physiology and community structure. Interactions among stressors may cause synergistic or antagonistic effects on phytoplankton dynamics. Therefore, the main goal of this work is to understand the short-term isolated and interactive effects of warming and high CO2 on phytoplankton nutrient consumption, growth, production, and community structure in the Ria Formosa coastal lagoon (southern Portugal). We performed microcosm experiments with temperature and CO2 manipulation, and dilution experiments under temperature increase, using winter phytoplankton assemblages. Phytoplankton responses were evaluated using inverted and epifluorescence microscopy. Overall, phytoplankton growth and microzooplankton grazing on phytoplankton decreased with warming. Negative antagonist interactions with CO2 alleviated the negative effect of temperature on phytoplankton and cryptophytes. In contrast, higher temperature benefited smaller-sized phytoplankton, namely cyanobacteria and eukaryotic picophytoplankton. Diatom growth was not affected by temperature, probably due to nutrient limitation, but high CO2 had a positive effect on diatoms, alleviating the effect of nutrient limitation. Results suggest that this winter phytoplankton assemblage is well acclimated to ambient conditions, and short-term increases in temperature are detrimental, but can be alleviated by high CO2. DL57/2016/CP1361/CT0017 info:eu-repo/semantics/publishedVersion

Early detection of dense harmful algal blooms (HABs) is possible using ocean colour remote sensing. Some algorithms require a training dataset, usually constructed from satellite images with a priori knowledge of the existence of the bloom. This approach can be limited if there is a lack of in situ observations, coincident with satellite images. A laboratory experiment collected biological and bio-optical data from a culture of Karenia mikimotoi, a harmful phytoplankton dinoflagellate. These data showed characteristic signals in chlorophyll-specific absorption and backscattering coefficients. The bio-optical data from the culture and a bio-optical model were used to construct a training dataset for an existing statistical classifier. MERIS imagery over the European continental shelf were processed with the classifier using different training datasets. The differences in positive rates of detection of K. mikimotoi between using an algorithm trained with purely manually selected areas on satellite images and using laboratory data as training was overall in situ observations of non-harmful high chlorophyll blooms in the area would improve testing of the ability to distinguish harmful from non-harmful high chlorophyll blooms. This approach can be expanded to use additional wavelengths, different satellite sensors and different phytoplankton genera.

The Northern Antarctic Peninsula (NAP), located in West Antarctica, is amongst the most impacted regions worldwide by recent warming events. Its vulnerability to climate change has already led to an accumulation of severe changes along its ecosystems. This work reviews the current findings on impacts observed in phytoplankton communities occurring in the NAP, with a focus on its causes, consequences, and the potential research priorities for an integrated comprehension of the physical-biological coupling and climate perspective. Evident changes in phytoplankton biomass, community composition and size structure, as well as potential bottom-up impacts to the ecosystem are discussed. Surface wind, sea ice and meltwater dynamics, as the main drivers of the upper layer structure, are identified as the leading factors shaping phytoplankton. Short- and long-term scenarios are suggested for phytoplankton communities in the NAP, both indicating a future increase of the importance of small flagellates at the expense of diatoms, with potential devastating impacts for the ecosystem. Five main research gaps in the current understanding of the phytoplankton response to climate change in the region are identified: i) anthropogenic signal has yet to be disentangled from natural climate variability; ii) the influence of small-scale ocean circulation processes on phytoplankton is poorly understood; iii) the potential consequences to regional food webs must be clarified; iv) the magnitude and risk of potential changes in phytoplankton composition is relatively unknown; and v) a better understanding of phytoplankton physiological responses to changes in the environmental conditions is required. Future research directions, along with specific suggestions on how to follow them, are equally suggested. Overall, while the current knowledge has shed light on the response of phytoplankton to climate change, in order to truly comprehend and predict changes in phytoplankton communities there must be a robust collaboration effort integrating both Antarctic research programs and the whole scientific community under a common research framework.

Aquaculture has become the fastest-growing sector of the food industry worldwide. The increase of intensive aquaculture practices, however, has been raising global concern about economic and social impacts, but mostly due to the associated potential environmental impacts. The aim of this report is to make a preliminary assessment of the impact of an intensive sea bass aquaculture (Dicentrarchus labrax, L. 1758) on surrounding coastal waters. The aquaculture site is located at the SW Iberian coast (Sines, Portugal), having 16 cages, each holding approximately 150,000 specimens at different stages of growth. We present a spatial and temporal description of environmental physical, chemical, and biological parameters taken in the course of four monitoring campaigns conducted between June 2018 and April 2019. All monitored parameters, except phosphate concentration in October only at one sampling station, showed values within the desirable ranges for marine finfish production and the natural range of Portuguese coastal waters. So far, results do not reveal any detrimental impact of the production units on local water quality, although more research is needed. The preliminary findings suggest that the lack of stress on the receiving waters may be attributed to the hydrodynamic regime in the production area, the feeding strategy, and the dimension of the production.

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.

This deliverable aims at defining the details of the products and service to be developed in close cooperation with large user groups, including the DANUBIUS European research infrastructure, GEO AquaWatch/Blue Planet, Lagoons for Life and end-users in regional case studies. The deliverable also includes a detailed description of the case studies that will be considered as exemplars in the project

Spectrally resolved water-leaving radiances (ocean colour) and inferred chlorophyll concentration are key to studying phytoplankton dynamics at seasonal and inter-annual scales, for a better understanding of the role of phytoplankton in marine biogeochemistry; the global carbon cycle; and the response of marine ecosystems to climate variability, change and feedback processes. Ocean colour data also have a critical role in operational observation systems monitoring coastal eutrophication, harmful algal blooms, and sediment plumes. The contiguous ocean-colour record reached 21 years in 2018; however, it is comprised of a number of one-off missions such that creating a consistent time-series of ocean-colour data requires merging of the individual sensors (including MERIS, Aqua-MODIS, SeaWiFS, VIIRS, and OLCI) with differing sensor characteristics, without introducing artefacts. By contrast, the next decade will see consistent observations from operational ocean colour series with sensors of similar design and with a replacement strategy. Also, by 2029 the record will start to be of sufficient duration to discriminate climate change impacts from natural variability, at least in some regions. This paper describes the current status and future prospects in the field of ocean colour focusing on large to medium resolution observations of oceans and coastal seas. It reviews the user requirements in terms of products and uncertainty characteristics and then describes features of current and future satellite ocean-colour sensors, both operational and innovative. The key role of in situ validation and calibration is highlighted as are ground segments that process the data received from the ocean-colour sensors and deliver analysis-ready products to end-users. Example applications of the ocean-colour data are presented, focusing on the climate data record and operational applications including water quality and assimilation into numerical models. Current capacity building and training activities pertinent to ocean colour are described and finally a summary of future perspectives is provided.

Understanding the natural variability of coastal ecosystems, and in particular distinguishing between the natural fluctuations and the ones that are caused by anthropogenic interventions and long-term climatic variability, is a major concern for establishing adequate management and adaptation strategies. The Aveiro lagoon, a shallow coastal lagoon (Portugal), holds one of the largest saltmarshes and saltpans in Europe and is a very important ecosystem from both economic and ecological viewpoints, making the protection of its water masses a requirement. To better understand the variability of its ecosystem, the factors controlling seasonal, inter-annual and long-term variability of the water quality in the Aveiro lagoon were thus analyzed. The statistical analysis was based on a set of climatic, hydrological and water quality observations undertaken between 1985 and 2010. Seasonal variations were mostly related with the seasonal variation of the main climatic and hydrological drivers, while long-term shifts were typically driven by the anthropogenic interventions in the lagoon. After the adoption of secondary treatment for industrial effluents on 1992, a recovery from hypoxia conditions occurred in the upstream area of the lagoon. After 2000 lower concentrations of silicates occurred downstream, and may also derive from some anthropogenic modifications (e.g., shunting of river water to the sewage system, deepening of the inlet) that may have affected the physical dynamics. In the downstream area of the lagoon, chlorophyll a presented a downward trend between 1985 and 2010 and lower concentrations after 2000, which were probably associated with the lower concentrations of silicates. Results from the data analysis showed that the seasonal, inter-annual and long-term trends observed in the Aveiro lagoon depend on the influence of both anthropogenic and climate drivers, putting in evidence the need to combine these different drivers when evaluating and developing management strategies for estuarine ecosystems.

Monitoring temporal changes in phytoplankton dynamics in high latitude lakes is particularly timely for understanding the impacts of warming on aquatic ecosystems. In this study, we analyzed 33-years of high resolution (30 m) Landsat (LT) data for reconstructing seasonal patterns of chlorophyll a (chl a) concentration in four lakes across Finland, between 60°N and 64°N. Chl a models based on LT spectral bands were calibrated using 17-years (2000–2016) of field measurements collected across the four lakes. These models were then applied for estimating chl a using the entire LT-5 and 7 archives. Approximately 630 images, from 1984 to 2017, were analyzed for each lake. The chl a seasonal patterns were characterized using phenology metrics, and the time-series of LT-based chl a estimates were used for identifying temporal shifts in the seasonal patterns of chl a concentration. Our results showed an increase in the length of phytoplankton growth season in three of the lakes. The highest increase was observed in Lake Köyliönjärvi, where the length of growth season has increased by 28 days from the baseline period of 1984–1994 to 2007–2017. The increase in the length of season was mainly attributed to an earlier start of phytoplankton blooms. We further analyzed surface temperature (Ts) and precipitation data to verify if climatic factors could explain the shifts in the seasonal patterns of chl a. We found no direct relationship between Ts and chl a seasonal patterns. Similarly, the phenological metrics of Ts, in particular length of season, did not show significant temporal trends. On the other hand, we identify potential links between changes in precipitation patterns and the increase in the phytoplankton season length. We verified a significant increase in the rainfall contribution to the total precipitation during the autumn and winter, accompanied by a decline in snowfall volumes. This could indicate an increasing runoff volume during the beginning of spring, contributing to an earlier onset of the phytoplankton blooms, although further assessments are needed to analyze historical streamflow values and nearby land cover data. Likewise, additional studies are needed to better understand why chl a patterns in some lakes seem to be more resilient than in others. peerReviewed

Surface sediments were sampled at 18 stations from 7 to 64 m depth off the SE coast of Algarve to characterize the organic matter contents in the inner and middle shelf. For each sediment sample, grain size, mineralogy and total organic carbon analyses were carried out, as well as pigment analyses (19’ but-fucoxanthin, fucoxanthin, 19’ hex-fucoxanthin, chlorophyll-a, chlorophyll-b, pheophytin-a, pheophorbide-a, alpha-carotene, beta-carotene, anteraxanthin, diadinoxanthin, diatoxanthin, lutein and zeoxanthin). In addition, the ratios between each pigment and the total organic carbon (TOC) percentage, and between the chlorophyll-a concentration and the pheophytin-a and the pheophorbide-a concentrations were calculated to establish pigment indices. A Multidimensional scaling (MDS) analysis highlights three regions in the SE coast of Algarve according to depth, percentages of TOC, sediment grain size and mineralogy, concentration of pigments highly susceptible to degradation, concentration of refractory pigments (pigments not susceptible to degradation) and different preservation conditions (based on the pigment index values). The results highlight a correlation between pigments concentration and environmental variables, showing the eastern limit of West coastal upwelling plumes influence along the Algarve continental shelf.

The accuracy of three satellite models of primary production (PP) of varying complexity was assessed against 95 in situ 14C uptake measurements from the North East Atlantic Ocean (NEA). The models were run using the European Space Agency (ESA), Ocean Colour Climate Change Initiative (OC-CCI) version 3.0 data. The objectives of the study were to determine which is the most accurate PP model for the region in different provinces and seasons, what is the accuracy of the models using both high (daily) and low (weekly) temporal resolution OC-CCI data, and whether the performance of the models is improved by implementing a photoinhibition function? The Platt-Sathyendranath primary production model (PPPSM) was the most accurate over all NEA provinces and, specifically, in the Atlantic Arctic province (ARCT) and North Atlantic Drift (NADR) provinces. The implementation of a photoinhibition function in the PPPSM reduced its accuracy, especially at lower range PP. The Vertical Generalized Production Model-VGPM (PPVGPM) tended to over-estimate PP, especially in summer and in the NADR. The accuracy of PPVGPM improved with the implementation of a photoinhibition function in summer. The absorption model of primary production (PPAph), with and without photoinhibition, was the least accurate model for the NEA. Mapped images of each model showed that the PPVGPM was 150% higher in the NADR compared to PPPSM. In the North Atlantic Subtropical Gyre (NAST) province, PPAph was 355% higher than PPPSM, whereas PPVGPM was 215% higher. A sensitivity analysis indicated that chlorophyll-a (Chl a), or the absorption of phytoplankton, at 443 nm (aph (443)) caused the largest error in the estimation of PP, followed by the photosynthetic rate terms and then the irradiance functions used for each model.

Phytoplankton size structure is an important indicator of the state of the pelagic ecosystem. Stimulated by the paucity of in situ observations on size structure, and by the sampling advantages of autonomous remote platforms, new efforts are being made to infer the size-structure of the phytoplankton from oceanographic variables that may be measured at high temporal and spatial resolution, such as total chlorophyll concentration. Large-scale analysis of in situ data has revealed coherent relationships between size-fractionated chlorophyll and total chlorophyll that can be quantified using the three-component model of Brewin et al. (2010). However, there are variations surrounding these general relationships. In this paper, we first revise the three-component model using a global dataset of surface phytoplankton pigment measurements. Then, using estimates of the average irradiance in the mixed-layer, we investigate the influence of ambient light on the parameters of the three-component model. We observe significant relationships between model parameters and the average irradiance in the mixed-layer, consistent with ecological knowledge. These relationships are incorporated explicitly into the three-component model to illustrate variations in the relationship between size-structure and total chlorophyll, ensuing from variations in light availability. The new model may be used as a tool to investigate modifications in size-structure in the context of a changing climate.

Dietary inclusion of IMTA-cultivated Gracilaria vermiculophylla was evaluated in rainbow trout. Growth and feed efficiency were determined in fish fed 0 % (CTRL), 5 % (G5), and 10 % (G10) of the red seaweed for 91 days. Carotenoid concentration (skin and muscle), immunological parameters, and intestinal morphology were also evaluated. G10 group showed the lowest final body weight, with feed and protein efficiency ratios being significantly lower than the CTRL. Although protein intake was similar among groups, G10 diet induced the lowest protein retention and gain probably due to its smallest intestine diameter and lowest villi height. Fish fed G10 diet displayed higher carotenoid content in the skin (16.7 μg g−1) when compared with the CTRL group, but a lower concentration was registered in the flesh (0.23 μg g−1). Instrumental color showed that fillets were more luminous (L*), less yellowish (b*), and more reddish (a*) with seaweed inclusion and the lowest chrome intensity (C*) in the G10 group confirmed the lowest muscle carotenoid content in these fish. G5 diet enhanced the innate immune response of rainbow trout inducing the highest peroxidase, alternative complement (ACH50), and lysozyme activities. The inclusion of Gracilaria meal in diets for rainbow trout is possible up to 5 %, but a higher inclusion level impairs growth.

Chlorophyll-a satellite products are routinely used in oceanography, providing a synoptic and global view of phytoplankton abundance. However, these products lack information on the community structure of the phytoplankton, which is crucial for ecological modelling and ecosystem studies. To assess the usefulness of existing methods to differentiate phytoplankton functional types (PFT) or phytoplankton size classes from satellite data, in-situ phytoplankton samples collected in the Western Iberian coast, on the North-East Atlantic, were analysed for pigments and absorption spectra. Water samples were collected in five different locations, four of which were located near the shore and another in an open-ocean, seamount region. Three different modelling approaches for deriving phytoplankton size classes were applied to the in situ data. Approaches tested provide phytoplankton size class information based on the input of pigments data (Brewin et al., 2010), absorption spectra data (Ciotti et al., 2002) or both (Uitz et al., 2008). Following Uitz et al. (2008), results revealed high variability in microphytoplankton chlorophyll-specific absorption coefficients, ranging from 0.01 to 0.09 m2 (mg chl)− 1 between 400 and 500 nm. This spectral analysis suggested, in one of the regions, the existence of small cells (< 20 μm) in the fraction of phytoplankton presumed to be microphytoplankton (based on diagnostic pigments). Ciotti et al. (2002) approach yielded the highest differences between modelled and measured absorption spectra for the locations where samples had high variability in community structure and cell size. The Brewin et al. (2010) pigment-based model was adjusted and a set of model coefficients are presented and recommended for future studies in offshore water of the Western Iberian coast.

This document concerns the collection, analysis and on-line experimentation of ocean color data off the Western Iberian Peninsula. Field measurements have been acquired during the BIOMETORE field campaign in summer 2016 to evaluate and enhance Earth observation capabilities of the Copernicus program. Deliverables of the Ocean and Land Colour Instrument on board of the Sentinel-3 satellite of the European Space Agency are of specific interest. Preliminary evaluations confirm the quality of the in situ measurements to address the match-up future analysis of radiometric values and derived data products. On-line experimentation undertaken with the WebEnhanced Service To Ocean Color demonstrates the feasibility of enabling in a transparent way the user's access to complex functionalities such as neural network applications. FCT [IF/00541/2013/CP1181] info:eu-repo/semantics/publishedVersion

A multi-sensor satellite approach based on ocean colour, sunglint and Synthetic Aperture Radar imagery is used to study the impact of interacting internal tidal (IT) waves on near-surface chlorophyll-a distribution, in the central Bay of Biscay. Satellite imagery was initially used to characterize the internal solitary wave (ISW) field in the study area, where the “local generation mechanism” was found to be associated with two distinct regions of enhanced barotropic tidal forcing. IT beams formed at the French shelf-break, and generated from critical bathymetry in the vicinities of one of these regions, were found to be consistent with “locally generated” ISWs. Representative case studies illustrate the existence of two different axes of IT propagation originating from the French shelf-break, which intersect close to 46°N, − 7°E, where strong IT interaction has been previously identified. Evidence of constructive interference between large IT waves is then presented and shown to be consistent with enhanced levels of chlorophyll-a concentration detected by means of ocean colour satellite sensors. Finally, the results obtained from satellite climatological mean chlorophyll-a concentration from late summer (i.e. September, when ITs and ISWs can meet ideal propagation conditions) suggest that elevated IT activity plays a significant role in phytoplankton vertical distribution, and therefore influences the late summer ecology in the central Bay of Biscay.

Ocean colour is recognised as an Essential Climate Variable (ECV) by the Global Climate Observing System (GCOS), and spectrally-resolved water-leaving radiances (or remote-sensing reflectances) in the visible domain, and chlorophyll-a concentration are identified as required ECV products. Time series of the products at the global scale and at high spatial resolution, derived from ocean-colour data, are key to studying the dynamics of phytoplankton at seasonal and inter-annual scales, their role in marine biogeochemistry, the global carbon cycle, the modulation of how phytoplankton distribute solar-induced heat in the upper layers of the ocean, and the response of the marine ecosystem to climate variability and change. However, generating a long time series of these products from ocean-colour data is not a trivial task: algorithms that are best suited for climate studies have to be selected from a number that are available for atmospheric correction of the satellite signal and for retrieval of chlorophyll-a concentration, since satellites have a finite life span, data from multiple sensors have to be merged to create a single time series, and any uncorrected inter-sensor biases could introduce artefacts in the series, e.g., different sensors monitor radiances at different wavebands such that producing a consistent time series of reflectances is not straightforward. Another requirement is that the products have to be validated against in situ observations. Furthermore, the uncertainties in the products have to be quantified, ideally on a pixel-by-pixel basis, to facilitate applications and interpretations that are consistent with the quality of the data. This paper outlines an approach that was adopted for generating an ocean-colour time series for climate studies, using data from the MERIS (MEdium spectral Resolution Imaging Spectrometer) sensor of the European Space Agency, the SeaWiFS (Sea-viewing Wide-Field-of-view Sensor) and MODIS-Aqua (Moderate-resolution Imaging Spectroradiometer-Aqua) sensors from the National Aeronautics and Space Administration (USA), and VIIRS (Visible and Infrared Imaging Radiometer Suite) from the National Oceanic and Atmospheric Administration (USA). The time series now covers the period from late 1997 to end of 2018. To ensure that the products meet, as well as possible, the requirements of the user community, marine-ecosystem modellers, and remote-sensing scientists were consulted at the outset on their immediate and longer-term requirements as well as on their expectations of ocean-colour data for use in climate research. Taking the user requirements into account, a series of objective criteria were established, against which available algorithms for processing ocean-colour data were evaluated and ranked. The algorithms that performed best with respect to the climate user requirements were selected to process data from the satellite sensors. Remote-sensing reflectance data from MODIS-Aqua, MERIS, and VIIRS were band-shifted to match the wavebands of SeaWiFS. Overlapping data were used to correct for mean biases between sensors at every pixel. The remote-sensing reflectance data derived from the sensors were merged, and the selected in-water algorithm was applied to the merged data to generate maps of chlorophyll concentration, inherent optical properties at SeaWiFS wavelengths, and the diffuse attenuation coefficient at 490 nm. The merged products were validated against in situ observations. The uncertainties established on the basis of comparisons with in situ data were combined with an optical classification of the remote-sensing reflectance data using a fuzzy-logic approach, and were used to generate uncertainties (root mean square difference and bias) for each product at each pixel.

Internal tidal wave propagation introduces vertical motions within the water column, especially near the pycnocline, forcing water particles to undergo upward and downward motions. Since neutrally buoyant phytoplankton cells are usually passive, these cells can be significantly displaced in the vertical (tens of metres). In this paper we investigate the effects of large-amplitude internal tidal waves on chlorophyll vertical distribution in the region of the Nazare Canyon west of Portugal, using in-situ and multi-sensor satellite data. The results confirm the occurrence of enhanced levels of chlorophyll detected by a satellite ocean colour sensor that are spatially correlated with internal tides. It is shown that internal tidal waves expose phytoplankton to larger light intensities. Maximum exposure is localised where the internal tide crests occur at noon, but an average increase occurs along the wavelength of a progressive semi-diurnal internal tide during a full day, due to the exponential attenuation of light in the water column. Hence, internal waves can increase the amount of carbon uptake in comparison with an unperturbed water column. The results suggest that internal tidal waves can make a significant impact on biological processes such as primary production, with the generation of local-scale (35 km×10 km) patchiness of enhanced production on 3–4 day timescales.

The spatio-temporal variation of microphytobenthos (MPB) at the scale of a large estuary (Tagus estuary, Portugal) was studied using a combination of field and satellite remote sensing data during 2003. This is the first attempt to use remote sensing to study MPB in an ecosystem with a Mediterranean-like climate. Satellite pour l'Observation de la Terre (SPOT) and Medium Resolution Imaging Spectrometer (MERIS) images were used to map benthic microalgae through the application of a Normalized Difference Vegetation index (NDVI). A significant relationship between in-situ benthic chlorophyll a measurements and SPOT NDVI values was used to derive a map for biomass spatial distribution. At the scale of the whole intertidal area, NDVI time-series from 2003 revealed that MPB showed clear temporal variations, with lower values observed in summer compared to winter. This seasonal trend was found both in the SPOT and MERIS images and may be the result of extreme high temperatures that inhibit MPB growth. The main MPB biofilms were spatially stable through time at a large scale. Maximum NDVI values during the winter were found in the high shore with decreasing NDVI values towards the low shore. MPB light limitation at the lowest bathymetries is likely to occur in winter due to the high turbidity of Tagus estuary. The biomass spatial distribution map, obtained for January 2003, indicated low values ranging from 0 to 20 mg Chl a m

During summer 2008 and spring 2009, surface oceanographic surveys were carried out around three islands of the Azores archipelago (Terceira, Sao Miguel and Santa Maria) to assess the phytoplankton distribution and associated physico-chemical processes. The Azores archipelago is a major feature in the biogeochemical North Atlantic Subtropical Gyre (NAST) province although its influence on the productivity of the surrounding ocean is poorly known. Surface phytoplankton was studied by microscopy and HPLC (High Precision Liquid Chromatography). The mean values for biomass proxy Chlorophyll a (Chl a ) ranged from 0.04 to 0.55 μg L −1 (Chl a maximum = 0.86 μg L −1 ) and coccolithophores were the most abundant group, followed by small flagellates, Cyanobacteria, diatoms and dinoflagellates being the least abundant group. The distribution of phytoplankton and coccolithophore species in particular presented seasonal differences and was consistent with the nearshore influence of warm subtropical waters from the south Azores current and colder subpolar waters from the north. The satellite-derived circulation patterns showed southward cold water intrusions off Terceira and northward warm water intrusions off Santa Maria. The warmer waters signal was confirmed by the subtropical coccolithophore assemblage, being Discosphaera tubifera a constant presence under these conditions. The regions of enhanced biomass, either resulting from northern cooler waters or from island induced processes, were characterized by the presence of Emiliania huxleyi . Diatoms and dinoflagellates indicated coastal and regional processes of nutrient enrichment and areas of physical stability, respectively.

Over the past decade, techniques have been presented to derive the community structure of phytoplankton at synoptic scales using satellite ocean-color data. There is a growing demand from the ecosystem modeling community to use these products for model evaluation and data assimilation. Yet, from the perspective of an ecosystem modeler these products are of limited use unless: (i) the phytoplankton products provided by the remote-sensing community match those required by the ecosystem modelers; and (ii) information on per-pixel uncertainty is provided to evaluate data quality. Using a large dataset collected in the North Atlantic, we re-tune a method to estimate the chlorophyll concentration of three phytoplankton groups, partitioned according to size [pico- (< R m), nano- (2-20 mu m) and micro-phytoplankton (>20 mu m)]. The method is modified to account for the influence of sea surface temperature, also available from satellite data, on model parameters and on the partitioning of microphytoplankton into diatoms and dinoflagellates, such that the phytoplankton groups provided match those simulated in a state of the art marine ecosystem model (the European Regional Seas Ecosystem Model, ERSEM). The method is validated using another dataset, independent of the data used to parameterize the method, of more than 800 satellite and in situ match-ups. Using fuzzy-logic techniques for deriving per-pixel uncertainty, developed within the ESA Ocean Colour Climate Change Initiative (OC-CCI), the match-up dataset is used to derive the root mean square error and the bias between in situ and satellite estimates of the chlorophyll for each phytoplankton group, for 14 different optical water types (OWT). These values are then used with satellite estimates of OWTs to map uncertainty in chlorophyll on a per pixel basis for each phytoplankton group. It is envisaged these satellite products will be useful for those working on the validation of, and assimilation of data into, marine ecosystem models that simulate different phytoplankton groups.

International audience; To improve our understanding of the role of phytoplankton for marine ecosystems and global biogeochemical cycles, information on the global distribution of major phytoplankton groups is essential. Although algorithms have been developed to assess phytoplankton diversity from space for over two decades, so far the application of these data sets has been limited. This scientific roadmap identifies user needs, summarizes the current state of the art, and pinpoints major gaps in long-term objectives to deliver space-derived phytoplankton diversity data that meets the user requirements. These major gaps in using ocean color to estimate phytoplankton community structure were identified as: (a) the mismatch between satellite, in situ and model data on phytoplankton composition, (b) the lack of quantitative uncertainty estimates provided with satellite data, (c) the spectral limitation of current sensors to enable the full exploitation of backscattered sunlight, and (d) the very limited applicability of satellite algorithms determining phytoplankton composition for regional, especially coastal or inland, waters. Recommendation for actions include but are not limited to: (i) an increased communication and round-robin exercises among and within the related expert groups, (ii) the launching of higher spectrally and spatially resolved sensors, (iii) the development of algorithms that exploit hyperspectral information, and of (iv) techniques to merge and synergistically use the various streams of continuous information on phytoplankton diversity from various satellite sensors' and in situ data to ensure long-term monitoring of phytoplankton composition.

The main goal of this study was to evaluate short-term interactions between increased CO2, UVR and inorganic macronutrients (N, P and Si) on summer phytoplankton assemblages in the Ria Formosa coastal lagoon (SW Iberia), subjected to intense anthropogenic pressures and highly vulnerable to climate change. A multifactorial experiment using 20 different nutrient-enriched microcosms exposed to different spectral and CO2 conditions was designed. Before and after a 24-h in situ incubation, phytoplankton abundance and composition were analysed. Impacts and interactive effects of high CO2, UVR and nutrients varied among different functional groups. Increased UVR had negative effects on diatoms and cyanobacteria and positive effects on cryptophytes, whereas increased CO2 inhibited cyanobacteria but increased cryptophyte growth. A positive synergistic interaction between CO2 and UVR was observed for diatoms; high CO2 counteracted the negative effects of UVR under ambient nutrient concentrations. Nutrient enrichments suppressed the negative effects of high CO2 and UVR on cyanobacteria and diatoms, respectively. Beneficial effects of CO2 were observed for diatoms and cryptophytes under combined additions of nitrate and ammonium, suggesting that growth may be limited by DIC availability when the primary limitation by nitrogen is alleviated. Beneficial effects of high CO2 and UVR in diatoms were also induced or intensified by ammonium additions. info:eu-repo/semantics/publishedVersion

Domoic acid (DA) is a neurotoxin produced by Pseudo-nitzschia diatoms that is accumulated in the highest concentrations in filter-feeding organisms, such as bivalve molluscs. Although DA is a water-soluble molecule that is rapidly cleared from most marine organisms, it appears that octopus may consistently contain DA in the digestive gland. To test this hypothesis, specimens of Octopus vulgaris were caught for DA analysis when Pseudo-nitzschia cells were not observed in seawater and DA was not detected in octopus food items, i.e. mussels. DA was consistently detected in each octopus specimen (n=32) analysed and its concentrations varied from 1.0 to 26.6 µg g−1. DA sub-cellular distribution was evaluated in the digestive gland of six specimens in order to prove whether DA preferably accumulates in some cell compartment. DA was predominantly found (>90%) in the soluble fraction (cytosol) and to a lesser extent in the insoluble fractions (nucleic, mitochondrial, lysosomal, microsomal). This disposit...

The microphytobenthos (MPB) – Hydrobia ulvae trophic interaction is one of the main channels of material transfer to higher trophic levels in intertidal mudflats. A new non-invasive approach to evaluate the grazing activity of H. ulvae on microphytobenthos is proposed. The effects of season and period (combination of tide and day/night) on ingestion rates of H. ulvae (using 14Clabeled MPB) and egested pheopigments a (using HPLC pigment analysis) were also investigated. H. ulvae ingestion rate was found to vary significantly over season and period, being higher in summer and during diurnal low tide periods. This is possibly related to higher growth rates of H. ulvaein summer, as well as to an increase in surface MPB biomass during diurnal low tides. A highly significant relationship was found between ingested chl a and egested pheophorbide a, allowing the estimation of ingestion rate from the amount of egested pheophorbide a on H. ulvae faecal pellets. This new non-invasive methodology may allow the improvement of long-term studies of consumption rates and the evaluation of grazing of H. ulvae on MPB. We thank I. Macário, P. Pochelon and T. Salvaterra for assistance in field work; M. Ruivo for assistance in HPLC and A. Luísa Santos for assistance in the Radioisotope Laboratory; A. Almeida for hosting the radioisotope work in the Radioisotope Laboratory at the Department of Biology, University of Aveiro; and 3 anonymous reviewers for critical comments on the manuscript. H.C. was supported by FCT – Fundação para a Ciência e Tecnologia (SFRH/BD/23720/ 2005). This work is part of the research project Benthic link – trophic links regulated by tidal and daily rhythms: benthic microflora and fauna in estuaries’, funded by FCT (POCI/BIABDE/61977/2004). Both grants were allocated by FCT under the Support Community Framework III, Operational Programme Science, Technology and Innovation. The methods used in this study comply with Portuguese legislation on animal experimentation. published

The distribution and composition of phytoplankton assemblages were studied in the Nazare submarine canyon, during an upwelling event, using high-performance liquid chromatography (HPLC) pigment analysis, complemented by microscopic qualitative observations. High chlorophyll a (Chl a) concentrations were recorded in the canyon head, near the coast, where values greater than 4 μg L− 1 were observed. In contrast, Chl a was relatively low in offshore regions, with values below 0.5 μg L− 1. The most abundant accessory pigments were fucoxanthin, peridinin, diadinoxanthin and 19′-hexanoyloxyfucoxanthin. Pigment data information was analyzed using the CHEMTAX software to estimate the contribution of different taxonomic groups to total Chl a. North of the canyon head, an area with high concentration of peridinin-containing dinoflagellates was identified (with presence of chain-forming toxic dinoflagellates). The presence of these organisms was associated with mixed water columns and phosphate values lower than the ones south of the canyon head, where a dominance of diatoms was recorded. The rest of the study region showed a dominance of prymnesiophytes and a significant contribution of cyanobacteria at oceanic stations. This study demonstrates the usefulness of using pigment analysis to study spatial distribution of phytoplankton groups in relation to a complex physical environment.

Tagus estuary is one of the largest estuaries of Western Europe. With the aim of unravelling the drivers of primary production in this shallow and turbid nutrient replete estuary, we tested the hypothesis that light availability is a major factor controlling phytoplankton production. Environmental parameters, phytoplankton biomass, community composition, and photosynthetic parameters were monitored at two sites in the estuary during a complete annual cycle. Despite the fact that nutrient concentrations were always above growth-limiting values, Chl a concentrations were relatively low throughout the study period. High water column turbidity, due to riverine inputs, promoted a rapid attenuation of light and created a compressed profile with optimal photosynthetic conditions. Therefore, the phytoplankton community, dominated by small cells, such as diatoms and cryptophycean flagellates, displayed highly photosynthetic efficiency and low light-saturated photosynthetic rates as a photo-acclimation response to low light conditions year-round. Primary production rate was unimodal, peaking in the summer months. In such estuarine system, gross primary production could thus be predicted by an existing robust empirical model based on pigment standing crop (Chl a), surface irradiance (E 0) and optical depth (Z eup). Compared to other shallow estuaries, the Tagus can be classified as a low- to moderately productive estuary, being the turbidity-induced low light conditions the principal factor limiting phytoplankton growth.

International audience; Intertidal soft sediment microphytobenthic biofilms are often dominated by diatoms, which are able to regulate their photosynthesis by physiological processes (e.g. down-regulation through the xanthophyll cycle, referred to as non-photochemical quenching, NPQ) and behavioural processes (e.g. vertical cell movement in the sediment–biofilm matrix). This study investigated these 2 processes over a 6 h emersion period using chemical inhibitors under 2 light treatments (ambient and constant light at 300 µmol m–2 s–1). Latrunculin A (Lat A) was used to inhibit cell movement and dithiothreitol (DTT) to inhibit NPQ. HPLC analysis for chlorophyll a and spectral analysis (Normalised Difference Vegetation Index) indicated that Lat A significantly inhibited cell movement. Photosynthetic activity was measured using variable chlorophyll fluorescence and radiolabelled carbon uptake and showed that the non-migratory, Lat A-treated biofilms were severely inhibited as a result of the high accumulated light dose (significantly reduced maximum relative electron transport rate, rETRmax, and light utilisation coefficient, α, compared to the migratory DTT and control-treated biofilms). No significant patterns were observed for 14C data, although a decrease in uptake rate was observed over the measurement period. NPQ was investigated using HPLC analysis of xanthophyll pigments (diatoxanthin and the percentage de-epoxidation of diadinoxanthin), chlorophyll fluorescence (change in maximum fluorescence yield) and the 2nd order spectral derivative index (diatoxanthin index). Patterns between methods varied, but overall data indicated greater NPQ induction in the non-migratory Lat A treatment and little or no NPQ induction in the DTT and control treatments. Overall, the data resulted in 2 main conclusions: (1) the primary response to accumulated light dose was vertical movement, which when inhibited resulted in severe down-regulation/photoinhibition; (2) diatoms down-regulated their photosynthetic activity in response to accumulated light dose (e.g. over an emersion period) using a combination of vertical migration and physiological mechanisms that may contribute to diel and/or tidal patterns in productivity.

Time series of satellite-derived surface chlorophyll-a concentration (Chl) in 1997-2009 were used to examine for trends in the timing of the annual phytoplankton bloom maximum. Significant trends towards earlier phytoplankton blooms were detected in about 11 % of the area of the Arctic Ocean with valid Chl data, e.g. in the Hudson Bay, Foxe Basin, Baffin Sea, off the coasts of Greenland, in the Kara Sea and around Novaya Zemlya. These areas roughly coincide with areas where ice concentration has decreased in early summer (June), thus making the earlier blooms possible. In the selected areas, the annual phytoplankton bloom maximum has advanced by up to 50 days which may have consequences for the Arctic food chain and carbon cycling. Outside the Arctic, the annual Chl maximum has become earlier in boreal North Pacific but later in the North Atlantic.

Coastal ecosystem processes are largely influenced by the interaction of different factors operating at various temporal and spatial scales, specifically those responsible for primary production patterns that modulate zooplankton and subsequent trophic levels. Hydrological processes, such as tidal cycles and coastal currents, nutrients availability, phytoplankton groups (studied through algal pigment signatures analysed by HPLC), and zooplankton abundance and distribution were investigated at the Sofala Bank (Mozambique), with special emphasis on their horizontal distribution and vertical dynamics (48 h). Horizontal distribution has shown inshore–offshore gradients in all analysed parameters, as well as inshore waters intrusion probably related to Zambezi River delta runoff. Tidal currents were responsible for major hydrological vertical variations and for horizontal and vertical advection of phytoplankton biomass in the surface and deepest layers, respectively. Nutrient concentrations were typical from oligotrophic regions, and nutrient ratios were strongly influenced by depleted nitrate + nitrite concentrations, indicating low estuarine discharges typical from the dry season. The very low N:P ratio obtained suggests strong nitrogen limitation to phytoplankton communities, supporting the low phytoplankton abundance observed. Both phytoplankton pigments and zooplankton were found mainly near the bottom (40 m depth), despite the latter displayed vertical migrations triggered by light variations. Phytoplankton community was dominated by microflagellates, specifically prymnesiophyceans, and behaved as a whole, except Cyanobacteria that displayed vertical distribution movements different from other phytoplankton groups, being mainly concentrated at mid-water column depths (10–20 m). This investigation enhances physico-chemical phenomena and their importance determining the planktonic communities vertical dynamics at Sofala Bank, a tropical coastal ecosystem of the Western Indian Ocean where planktonic dynamics are still poorly described and understood.

Phytoplankton biomass and composition were monitored for four coastal lagoons of the Algarve, Portugal, from February to November 2006. The phytoplankton community in the freshwater lagoons - Dunas Douradas (FW1) and Garrao (FW2) - as determined by biomarker pigment concentration using high-performance liquid chromatography and the pro- gram CHEMTAX, was dominated by diatoms and chlorophytes. For the brackish lagoons - Salgados (BW1) and Almargem (BW2) - cyanophytes and diatoms were the most important groups respectively. The trophic state indices, based on algal biomass, classify FW1, FW2 and BW1 lagoons as hypertrophic, whereas BW2 is classified as mesotrophic. Signs of eutro- phication in the former lagoons include large phytoplankton biomass (chlorophyll-a) fluctuations, the presence of phyto- plankton taxa that usually thrive under nutrient-enriched conditions and high concentrations of chlorophyll-a-degradation products. Chemotaxonomic analyses derived from high-performance liquid chromatography data might constitute a valu- able tool for achieving Water Framework Directive requirements for an evaluation system based on phytoplankton taxo- nomic composition.

Data were collected in the Tagus estuary from 1999–2007 on a monthly basis and combined with published results and for several previous years between 1980 and 1995, so that a comprehensive analysis could be performed over a non-continuous 27-year period. Sampling conditions and methods were similar for all datasets. Extreme wet and dry years were observed. River flow was strongly linked to phytoplankton abundance, with the highest biomass attained in dry years. The observed range of annual median Chl a was 1.8–7.6 µg L−1 and the overall median was 3.5 µg L−1. Dissolved inorganic nitrogen (DIN) and silicate showed a clear seasonal pattern, with a maximum in winter−spring, indicating a freshwater origin. Although wastewater treatment started in 1990, no difference was detected from 1980 to the present in terms of DIN and phosphorus. The recorded seasonal pattern for biomass with highest values in late spring–summer period is comparable to other temperate tidally influenced ecosystems. In spite of interannual differences in terms of Chl a concentration or the time of the maximum Chl a occurrence, a repeatable pattern could be identified. The mean growth development time for phytoplankton was 163 days (June 12) ranging 129–206 days (May 9–July 26) during the sampling period. No obvious changes in phytoplankton community structure were observed over time: diatoms were always the dominant group, and cryptophytes were relatively abundant throughout autumn–winter. The dominant species have remained essentially the same since 1969. River inflow, light availability, and temperature were the major factors shaping phytoplankton variability patterns. The strong influence of tidal mixing on the estuarine waters appears to lower the risk of potential eutrophication in the Tagus estuary. The lack of change in nutrients and phytoplankton biomass and composition observed in this study is an important contribution towards the assessment of natural variability versus responses to man-induced inputs in this severely anthropogenically disturbed estuary.

Tagus intertidal microphytobenthos (MPB) assemblages were characterized over a wide range of sediment type and tidal height and the possible effects of these variables on MPB spatial distribution and photo-adaptation mechanisms were investigated. Two transects with six different sediment type and different tidal height sites were sampled once every two months from 2002 to 2004. Upper shore and sandy sites showed higher chlorophyll a (chl a) content, with sandy sediments showing a biomass peak in late winter–early spring, and muddy sites showing no obvious seasonal pattern. Stepwise multiple linear regressions showed that only SiO2, tidal height and sediment particle size 60 μm. Epipelic biofilms showed evidence of being low light-acclimated (high fucoxanthin/chl a) and of photo-regulating by vertical migration movements (presence of endogenous vertical rhythms and lower diatoxanthin/diadinoxanthin). Epipsammic biofilms showed higher diatoxanthin/diadinoxanthin ratios and no vertical migration rhythms. Thus, the two diatom biofilm types had distinct strategies to photo-regulate: epipelic diatoms using vertical migration to position themselves at the sediment depth of optimum light conditions, and epipsammic diatoms using the xanthophyll cycle to photo-regulate. Further studies comparing epipsammic and epipelic assemblages are necessary to better understand MPB photo-regulation mechanisms.

The phytoplankton distribution and composition in Lisbon bay was studied, at a short time scale based on a weekly sampling, during one year (April 2004 – May 2005), using microscopic examination and pigment analysis with high-performance liquid chromatography (HPLC). This work is a contribution to the knowledge on species succession and ecology of coastal communities. The frequency of the sampling permitted monitoring peak blooming and decaying, a process which frequently occurred within 1 –2 weeks. Cell counts determined that the classes Dinophyceae, Bacillariophyceae and Prymnesiophyceae dominated the assemblages. Maxima abundances and diversity of phytoplankton were observed from spring to autumn. HPLC analysis reflected the major seasonal variations observed by the cell counts and in addition detected the presence of four small sized phytoplankton classes that were not identified by microscopy. Phytoplankton counts were essential to identify the main contributing species to total chlorophyll a. Fucoxantin, peridinin and 19′-hexanoyloxyfucoxanthin appeared as good indicators for diatoms, dinoflagellates and coccolithophores, respectively, with synchronized seasonal variations and significant positive correlations.

The effects of the motility inhibitors 2,3-butanedione monoxime (BDM) and latranculin A (Lat A) on the motility, photosynthetic activity and pigment composition of the benthic diatoms Cylindrotheca closterium and Pleurosigma angulatum were studied. BDM inhibited diatom gliding, preventing motility at concentrations of 12.5 mM and 50 mM for C. closterium and P. angulatum, respectively. For both species, the quantum yield of PSII (ΔF/Fm′) decreased with increasing concentrations of BDM. Reduced excitation at PSII reaction centres were caused by BDM-induced conversion of the pigment diadinoxanthin to diatoxanthin, through the activation of the xanthophyll cycle. Lat A inhibited diatom gliding, preventing motility at concentrations of 0.1 μM and 0.25 μM for C. closterium and P. angulatum, respectively. Concentrations of Lat A as high as 1 μM showed no significant effects on the PSII quantum yield, on the light-response curves of relative electron transport rate (initial slope of light curve, a, and maximum re...