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Dissolved Organic Carbon (DOC) is the largest organic carbon pool in the ocean. Considering the biotic and abiotic factors controlling DOC processes, indirect satellite methods for open ocean DOC estimation can be developed, using conceptual, empirical or statistical models, driven by multiple satellite products. In this study, we infer a time series of global DOC from data of the European Space Agency’s (ESA) Ocean Colour Climate Change Initiative (OC-CCI) in combination with a global database of in situ DOC observations. We tested empirical machine learning modelling approaches in which the available in situ data are used to train the models and to find empirical relationships between DOC and variables available from remote sensing. Of the tested methods, a random forest regression showed the best results, and the details of this model are further reported here. We present a time series of global open ocean DOC concentrations between 2010–2018 that is made freely available through the archive of the UK Centre for Environmental Data Analysis (CEDA).

In the oceanic surface layer, particulate organic carbon (POC) constitutes the biggest pool of particulate material of biological origin, encompassing phytoplankton, zooplankton, bacteria, and organic detritus. POC is of general interest in studies of biologically-mediated fluxes of carbon in the ocean, and over the years, several empirical algorithms have been proposed to retrieve POC concentrations from satellite products. These algorithms can be categorised into those that make use of remote-sensing-reflectance data directly, and those that are dependent on chlorophyll concentration and particle backscattering coefficient derived from reflectance values. In this study, a global database of in situ measurements of POC is assembled, against which these different types of algorithms are tested using daily matchup data extracted from the Ocean Colour Climate Change Initiative (OC-CCI; version 5). Through analyses of residuals, pixel-by-pixel uncertainties, and validation based on optical water types, areas for POC algorithm improvement are identified, particularly in regions underrepresented in the in situ POC data sets, such as coastal and high-latitude waters. We conclude that POC algorithms have reached a state of maturity and further improvements can be sought in blending algorithms for different optical water types when the required in situ data becomes available. The best performing band ratio algorithm was tuned to the OC-CCI version 5 product and used to produce a global time series of POC between 1997–2020 that is freely available.

This paper analyses a time series of chlorophyll-a profiles in the Adriatic from 1997 to 2019, and compares the data with satellite products with the view of analysing and reducing uncertainties in the corresponding satellite products. Three sources of uncertainties in satellite chlorophyll-a concentration are examined: (a) the algorithm itself; (b) the vertical structure of the water column; and (c) the phytoplankton community structure. Global and regional algorithms were examined, along with a local algorithm tuned using the time series data. The global algorithm produced the largest uncertainties when compared with the in situ data, followed by the regional and local algorithms. Correlation coefficient for the local algorithm was 0.690 - a significant increase from regional’s 0.420 and global’s 0.042. Both the global and the regional algorithms exhibited systemic errors that inversely were related to chlorophyll-a concentration, while the local algorithm displayed some reduction in the systematic errors, highlighting the value of local in situ observations, for improving sub-regional and local algorithms for retrieval of chlorophyll-a concentration from satellite ocean colour data. While the mixed layer has not shown any direct correlation with the uncertainties, it may facilitate exceptionally strong vertical gradients in chlorophyll-a profiles after summer blooms that take role as the main source of high differences between satellite observations and surface chlorophyll-a concentration. As such, it is important to supplement satellite measurements with vertical profiles to ensure valid readings and exercise caution when dealing with data post-blooms. These instances occurred in less than 3% of all cases. Differences in the phytoplankton community structures have shown direct correlation to estimation error - Miozoa is associated with low error, Bacillariophyta with high error, while Phytoflagellates abundance tips the error between underestimation and overestimation.

Visible spectral radiometry of seawater, often referred to as ocean colour, from space, provides a synoptic view of surface phytoplankton, and other optically-active constituents, at high temporal resolution, that is unsurpassed by any other technology. Yet, in-situ observations of ocean colour are critical to the success of the satellite, tracking the calibration of the radiometers and validating atmospheric correction algorithms. Owing to the high cost of commercial field radiometers, as well as the high costs associated with ocean-based field work, ocean colour scientists are plagued by a sparsity of high quality in-situ radiometric observations, particularly in remote regions. In this perspective article, we highlight potential to increase the number of in-situ observations of ocean colour by harnessing superyachts. Using openly-available data processing software, we show that automated ocean colour data collected using a superyacht can be used for the validation of an ocean colour satellite, with comparable results to traditional validation studies. Reaching out to wealthy citizen scientists may help fill gaps in our ability to monitor the colour of the ocean.

Whereas the vertical transport of biomass from productive surface waters to the deep ocean (the biological pump) is a critical component of the global carbon cycle, its magnitude and variability is poorly understood. Global-scale estimates of ocean carbon export vary widely, ranging from ∼5 to ∼20 Gt C y – 1 due to uncertainties in methods and unclear definitions. Satellite-derived properties such as phytoplankton biomass, sea surface temperature, and light attenuation at depth provide information about the oceanic ecosystem with unprecedented coverage and resolution in time and space. These products have been the basis of an intense effort over several decades to constrain different biogeochemical production rates and fluxes in the ocean. One critical challenge in this effort has been to estimate the magnitude of the biological pump from satellite-derived properties by establishing how much of the primary production is exported out of the euphotic zone, a flux that is called export production. Here we present a review of existing algorithms for estimating export production from satellite-derived properties, available in-situ datasets that can be used for testing the algorithms, and earlier evaluations of the proposed algorithms. The satellite-derived products used in the algorithm evaluation are all based largely on the Ocean Colour Climate Change Initiative (OC-CCI) products, and carbon products derived from them. The different resources are combined in a meta-analysis.

We demonstrate the ability of flow cytometry to determine species specific cellular carbon and chlorophyll content in vivo by using laboratory cultures of phytoplankton encompassing a wide range of cell sizes. When applied to the large Atlantic Meridional Transect flow cytometry dataset, we reveal patterns in the species-specific phytoplankton carbon (C), chlorophyll (Chl) and C:Chl ratio. For Prochlorococcus the range of C:Chl is between 2 – 604; for Synechococcus 0.5 – 558. Using a Random Forest machine learning approach, we show that predictability of phytoplankton C:Chl, dominated by the prevalence of Prochlorococcus, is largely driven by silicate and nitrite concentration in the Atlantic Ocean.

Water is an essential natural resource, but increasingly water also forms a threat to the human population, with floods being the most common natural disaster worldwide. Earth Observation has the potential for developing cost-effective methods to monitor risk, with free and open data available at the global scale. In this study, we present the application of remote sensing observations to map flooded areas, using the Vembanad-Kol-Wetland system in the southwest of India as a case study. In August 2018, this region experienced an extremely heavy monsoon season, which caused once-in-a-century floods that led to nearly 500 deaths and the displacement of over a million people. We review the use of existing algorithms to map flooded areas in the Lake Vembanad region using the spectral reflectances of the green, red and near-infrared bands from the MSI sensor on board Sentinel-2. Although the MSI sensor has no cloud-penetrating capability, we show that the Modified Normalised Difference Water Index and the Automated Water Extraction Index can be used to generate flood maps from multi-spectral visible remote sensing observations to complement commonly used SAR-based techniques to enhance temporal coverage (from 12 to 5 days). We also show that local knowledge of paddy cultivation practices can be used to map the manoeuvring of water levels and exclude inundated paddy fields to improve the accuracy of flood maps in the study region. The flood mapping addressed here has the potential to become part of a solution package based on multi-spectral visible remote sensing with capabilities to simultaneously monitor water quality and risk of human pathogens in the environment, providing additional important services during natural disasters.

This work represents a modification of the Context Conditional Generative Adversarial Network as a novel implementation of a non-linear gap reconstruction approach of missing satellite-derived chlorophyll a concentration data. By adjusting the loss functions of the network to focus on the structural credibility of the reconstruction, high numerical and structural reconstruction accuracies have been achieved in comparison to the original network architecture. The network also draws information from proxy data, sea surface temperature, and bathymetry, in this case, to improve the reconstruction quality. The implementation of this novel concept has been tested on the Adriatic Sea. The most accurate model reports an average error of 0.06mgm−3 and a relative error of 3.87%. A non-deterministic method for the gap-free training dataset creation is also devised, further expanding the possibility of combining other various oceanographic data to possibly improve the reconstruction efforts. This method, the first of its kind, has satisfied the accuracy requirements set by scientific communities and standards, thus proving its validity in the initial stages of conceptual utilisation.

Abstract In the absence of an effective vaccine or drug therapy, non-pharmaceutical interventions are the only option for control of the outbreak of the coronavirus disease 2019, a pandemic with global implications. Each of the over 200 countries affected has followed its own path in dealing with the crisis, making it difficult to evaluate the effectiveness of measures implemented, either individually, or collectively. In this paper we analyse the case of the south Indian state of Kerala, which received much attention in the international media for its actions in containing the spread of the disease in the early months of the pandemic, but later succumbed to a second wave. We use a model to study the trajectory of the disease in the state during the first four months of the outbreak. We then use the model for a retrospective analysis of measures taken to combat the spread of the disease, to evaluate their impact. Because of the differences in the trajectory of the outbreak in Kerala, we argue that it is a model worthy of a place in the discussion on how the world might best handle this and other, future, pandemics.

Information on the intracellular content and functional diversity of phytoplankton pigments can provide valuable insight on the ecophysiological state of primary producers and the flow of energy within aquatic ecosystems. Combined global datasets of analytical flow cytometry (AFC) cell counts and High-Performance Liquid Chromatography (HPLC) pigment concentrations were used to examine vertical and seasonal variability in the ratios of phytoplankton pigments in relation to indices of cellular photoacclimation. Across all open ocean datasets, the weight-to-weight ratio of photoprotective to photosynthetic pigments showed a strong depth dependence that tracked the vertical decline in the relative availability of light. The Bermuda Atlantic Time-series Study (BATS) dataset revealed a general increase in surface values of the relative concentrations of photoprotective carotenoids from the winter-spring phytoplankton communities dominated by low-light acclimated eukaryotic microalgae to the summer and early autumn communities dominated by high-light acclimated picocyanobacteria. In Prochlorococcus-dominated waters, the vertical decline in the relative contribution of photoprotective pigments to total pigment concentration could be attributed in large part to changes in the cellular content of photosynthetic pigments (PSP) rather than photoprotective pigments (PPP), as evidenced by a depth-dependent increase of the intracellular concentration of the divinyl chlorophyll-a (DVChl-a) whilst the intracellular concentration of the PPP zeaxanthin remained relatively uniform with depth. The ability of Prochlorococcus cells to adjust their DVChl-a cell-1 over a large gradient in light intensity was reflected in more highly variable estimates of carbon-to-Chl-a ratio compared to those reported for other phytoplankton groups. This cellular property is likely the combined result of photoacclimatory changes at the cellular level and a shift in dominant ecotypes. Developing a mechanistic understanding of sources of variability in pigmentation of picocyanobacteria is critical if the pigment markers and bio-optical properties of these cells are to be used to map their biogeography and serve as indicators of photoacclimatory state of subtropical phytoplankton communities more broadly. It would also allow better assessment of effects on, and adaptability of phytoplankton communities in the tropical/subtropical ocean due to climate change.

Despite the critical role phytoplankton play in marine biogeochemical cycles, direct methods for determining the content of two key elements in natural phytoplankton samples, nitrogen (N) and carbon (C), remain difficult, and such observations are sparse. Here, we extend an existing approach to derive phytoplankton N and C indirectly from a large dataset of in-situ particulate N and C, and Turner fluorometric chlorophyll-a (Chl-a), gathered in the off-shore waters of the Northwest Atlantic and the Arabian Sea. This method uses quantile regression (QR) to partition particulate C and N into autotrophic and non-autotrophic fractions. Both the phytoplankton C and N estimates were combined to compute the C:N ratio. The algal contributions to total N and C increased with increasing Chl-a, whilst the C:N ratio decreased with increasing Chl-a. However, the C:N ratio remained close to the Redfield ratio over the entire Chl-a range. Five different phytoplankton taxa within the samples were identified using data from high-performance liquid chromatography pigment analysis. All algal groups had a C:N ratio higher than Redfield, but for diatoms, the ratio was closer to the Redfield ratio, whereas for Prochlorococcus, other cyanobacteria and green algae, the ratio was significantly higher. The model was applied to remotely-sensed estimates of Chl-a to map the geographical distribution of phytoplankton C, N, and C:N in the two regions from where the data were acquired. Estimates of phytoplankton C and N were found to be consistent with literature values, indirectly validating the approach. The work illustrates how a simple model can be used to derive information on the phytoplankton elemental composition, and be applied to remote sensing data, to map pools of elements like nitrogen, not currently provided by satellite services.

Space-based Earth observation (EO), in the form of long-term climate data records, has been crucial in the monitoring and quantification of slow changes in the climate system—from accumulating greenhouse gases (GHGs) in the atmosphere, increasing surface temperatures, and melting sea-ice, glaciers and ice sheets, to rising sea-level. In addition to documenting a changing climate, EO is needed for effective policy making, implementation and monitoring, and ultimately to measure progress and achievements towards the overarching goals of the United Nations Framework Convention on Climate Change (UNFCCC) Paris Agreement to combat climate change. The best approach for translating EO into actionable information for policymakers and other stakeholders is, however, far from clear. For example, climate change is now self-evident through increasingly intense and frequent extreme events—heatwaves, droughts, wildfires, and flooding—costing human lives and significant economic damage, even though single events do not constitute “climate”. EO can capture and visualize the impacts of such events in single images, and thus help quantify and ultimately manage them within the framework of the UNFCCC Paris Agreement, both at the national level (via the Enhanced Transparency Framework) and global level (via the Global Stocktake). We present a transdisciplinary perspective, across policy and science, and also theory and practice, that sheds light on the potential of EO to inform mitigation, including sinks and reservoirs of greenhouse gases, and adaptation, including loss and damage. Yet to be successful with this new mandate, EO science must undergo a radical overhaul: it must become more user-oriented, collaborative, and transdisciplinary; span the range from fiducial to contextual data; and embrace new technologies for data analysis (e.g., artificial intelligence). Only this will allow the creation of the knowledge base and actionable climate information needed to guide the UNFCCC Paris Agreement to a just and equitable success.

Ecosystem fragility is an often used term in oceanography yet to this day it lacks a precise and widely accepted definition. Defining and subsequently quantifying fragility would be of great value, for such measures could be used to objectively ascertain the level of risk marine ecosystems face. Risk assessments could further be used to define the level of protection a given ocean region requires from economic activity, such as fisheries. With this aim we introduce to the oceanographic literature the concepts of marginal production and fragility, which we define for marine photosynthesis, the base of the oceanic food web. We demonstrate that marine photosynthesis is always fragile with respect to light, implying variability in surface irradiance acts unfavourably on biomass. We also demonstrate that marine photosynthesis can be both fragile and antifragile with respect to the mixed-layer depth, implying variability in mixed-layer depth can act both favourably and unfavourably on biomass. Quantification of marginal production and fragility is presented on data from two open ocean stations: Hawaii Ocean Time Series and Bermuda Atlantic Time-Series Study. Seasonal cycle of biomass is modelled and the effects of primary production fragility are analysed. A new tipping point for marine phytoplankton is identified in the form of a depth horizon. Using the new definitions presented here a rich archive of data can be used straightforwardly to quantify primary production fragility. The definitions can also be used to predict when primary production enters the fragile state during the seasonal cycle.

A growing coastal population is leading to increased anthropogenic pollution that greatly affects coastal and inland water bodies, especially in the tropics. The Sustainable Development Goal-14, ‘Life below water’ emphasises the importance of conservation and sustainable use of the ocean and its resources. Pollution management practices often include monitoring of water quality using in situ observations of chlorophyll-a (chl-a) and total suspended matter (TSM). Satellite technology, including the MultiSpectral Instrument (MSI) sensor onboard Sentinel-2, enables the continuous monitoring of these variables in inland waters at high spatial and temporal resolutions. To improve the monitoring of water quality in the tropical Vembanad-Kol-Wetland (VKW) system, situated on the southwest coast of India, we present two regionally tuned satellite algorithms developed to estimate chl-a and TSM concentrations. The new algorithms estimate the chl-a and TSM concentrations from the simulated reflectance values as a function of the inherent optical properties using a forward modelling approach. The model was parameterised using the National Aeronautics and Space Administration (NASA) bio-Optical Marine Algorithm Dataset (NOMAD) and in situ measurements collected in the VKW system. To assess model performance, results were compared with in situ measurements of chl-a and TSM and other existing satellite-based models of chl-a and TSM. For satellite application, two different atmospheric correction methods (ACOLITE and POLYMER) were tested and satellite matchups were used to validate the new chl-a and TSM algorithms following standard validation procedures. The results demonstrated that the new algorithms were in good agreement with in situ observations and outperform existing chl-a and TSM algorithms. The new regional satellite algorithms can be used to monitor water quality within the VKW system to support the sustainable management under natural (cyclones, floods, rainfall, and tsunami) and anthropogenic pressures (industrial effluents, agricultural practices, recreational activities, construction, and demolishing concrete structures) and help achieve Sustainable Development Goal 14.

Citizen science aims to mobilise the general public, motivated by curiosity, to collect scientific data and contribute to the advancement of scientific knowledge. In this article, we describe a citizen science network that has been developed to assess the water quality in a 100 km long tropical lake-estuarine system (Vembanad Lake), which directly or indirectly influences the livelihood of around 1.6 million people. Deterioration of water quality in the lake has resulted in frequent outbreaks of water-associated diseases, leading to morbidity and occasionally, to mortality. Water colour and clarity are easily measurable and can be used to study water quality. Continuous observations on relevant spatial and temporal scales can be used to generate maps of water colour and clarity for identifying areas that are turbid or eutrophic. A network of citizen scientists was established with the support of students from 16 colleges affiliated with three universities of Kerala (India) and research institutions, and stakeholders such as houseboat owners, non-government organisations (NGOs), regular commuters, inland fishermen, and others residing in the vicinity of Vembanad Lake and keen to contribute. Mini Secchi disks, with Forel-Ule colour scale stickers, were used to measure the colour and clarity of the water. A mobile application, named “TurbAqua,” was developed for easy transmission of data in near-real time. In-situ data from scientists were used to check the quality of a subset of the citizen observations. We highlight the major economic benefits from the citizen network, with stakeholders voluntarily monitoring water quality in the lake at low cost, and the increased potential for sustainable monitoring in the long term. The data can be used to validate satellite products of water quality and can provide scientific information on natural or anthropogenic events impacting the lake. Citizens provided with scientific tools can make their own judgement on the quality of water that they use, helping toward Sustainable Development Goal 6 of clean water. The study highlights potential for world-wide application of similar citizen-science initiatives, using simple tools for generating long-term time series data sets, which may also help monitor climate change.

Algal pigment composition is an indicator of phytoplankton community structure that can be estimated from optical observations. Assessing the potential capability to retrieve different types of pigments from phytoplankton absorption is critical for further applications. This study investigated the performance of three models and the utility of hyperspectral in vivo phytoplankton absorption spectra for retrieving pigment composition using a large database (n = 1392). Models based on chlorophyll-a (Chl-a model), Gaussian decomposition (Gaussian model), and partial least squares (PLS) regression (PLS model) were compared. Both the Gaussian model and the PLS model were applied to hyperspectral phytoplankton absorption data. Statistical analysis revealed the advantages and limitations of each model. The Chl-a model performed well for chlorophyll-c (Chl-c), diadinoxanthin, fucoxanthin, photosynthetic carotenoids (PSC), and photoprotective carotenoids (PPC), with a median absolute percent difference for cross-validation (MAPDCV) < 58%. The Gaussian model yielded good results for predicting Chl-a, Chl-c, PSC, and PPC (MAPDCV < 43%). The performance of the PLS model was comparable to that of the Chl-a model, and it exhibited improved retrievals of chlorophyll-b, alloxanthin, peridinin, and zeaxanthin. Additional work undertaken with the PLS model revealed the prospects of hyperspectral-resolution data and spectral derivative analyses for retrieving marker pigment concentrations. This study demonstrated the applicability of in situ hyperspectral phytoplankton absorption data for retrieving pigment composition and provided useful insights regarding the development of bio-optical algorithms from hyperspectral and satellite-based ocean-colour observations.

Since the article “Primary Production, an Index of Climate Change in the Ocean: Satellite-Based Estimates over Two Decades” by Kulk et al [...]

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.

Turbidity and water colour are two easily measurable properties used to monitor pollution. Here, we highlight the utility of a low-cost device—3D printed, hand-held Mini Secchi disk (3DMSD) with Forel-Ule (FU) colour scale sticker on its outer casing—in combination with a mobile phone application (‘TurbAqua’) that was provided to laymen for assessing the water quality of a shallow lake region after demolition of four high-rise buildings on the shores of the lake. The demolition of the buildings in January 2020 on the banks of a tropical estuary—Vembanad Lake (a Ramsar site) in southern India—for violation of Indian Coastal Regulation Zone norms created public uproar, owing to the consequences of subsequent air and water pollution. Measurements of Secchi depth and water colour using the 3DMSD along with measurements of other important water quality variables such as temperature, salinity, pH, and dissolved oxygen (DO) using portable instruments were taken for a duration of five weeks after the demolition to assess the changes in water quality. Paired t-test analyses of variations in water quality variables between the second week of demolition and consecutive weeks up to the fifth week showed that there were significant increases in pH, dissolved oxygen, and Secchi depth over time, i.e., the impact of demolition waste on the Vembanad Lake water quality was found to be relatively short-lived, with water clarity, colour, and DO returning to levels typical of that period of year within 4–5 weeks. With increasing duration after demolition, there was a general decrease in the FU colour index to 17 at most stations, but it did not drop to 15 or below, i.e., towards green or blue colour indicating clearer waters, during the sampling period. There was no significant change in salinity from the second week to the fifth week after demolition, suggesting little influence of other factors (e.g., precipitation or changes in tidal currents) on the inferred impact of demolition waste. Comparison with pre-demolition conditions in the previous year (2019) showed that the relative changes in DO, Secchi depth, and pH were very high in 2020, clearly depicting the impact of demolition waste on the water quality of the lake. Match-ups of the turbidity of the water column immediately before and after the demolition using Sentinel 2 data were in good agreement with the in situ data collected. Our study highlights the power of citizen science tools in monitoring lakes and managing water resources and articulates how these activities provide support to Sustainable Development Goal (SDG) targets on Health (Goal 3), Water quality (Goal 6), and Life under the water (Goal 14).

The United Nation’s Sustainable Development Goal Life Below Water (SDG-14) aims to “conserve and sustainably use the oceans, seas, and marine resources for sustainable development”. Within SDG-14, targets 14.1 and 14.2 deal with marine pollution and the adverse impacts of human activities on aquatic systems. Here, we present a remote-sensing-based analysis of short-term changes in the Vembanad-Kol wetland system in the southwest of India. The region has experienced high levels of anthropogenic pressures, including from agriculture, industry, and tourism, leading to adverse ecological and socioeconomic impacts with consequences not only for achieving the targets set out in SDG-14, but also those related to water quality (SDG-6) and health (SDG-3). To move towards the sustainable management of coastal and aquatic ecosystems such as Lake Vembanad, it is important to understand how both natural and anthropogenic processes affect water quality. In 2020, a unique opportunity arose to study water quality in Lake Vembanad during a period when anthropogenic pressures were reduced due to a nationwide lockdown in response to the global pandemic caused by SARS-CoV-2 (25 March–31 May 2020). Using Sentinel-2 and Landsat-8 multi-spectral remote sensing and in situ observations to analyse changes in five different water quality indicators, we show that water quality improved in large areas of Lake Vembanad during the lockdown in 2020, especially in the more central and southern regions, as evidenced by a decrease in total suspended matter, turbidity, and the absorption by coloured dissolved organic matter, all leading to clearer waters as indicated by the Forel-Ule classification of water colour. Further analysis of longer term trends (2013–2020) showed that water quality has been improving over time in the more northern regions of Lake Vembanad independent of the lockdown. The improvement in water quality during the lockdown in April–May 2020 illustrates the importance of addressing anthropogenic activities for the sustainable management of coastal ecosystems and water resources.

Vibrio cholerae, the bacterium responsible for the disease cholera, is a naturally-occurring bacterium, commonly found in many natural tropical water bodies. In the context of the U.N. Sustainable Development Goals (SDG) targets on health (Goal 3), water quality (Goal 6), life under water (Goal 14), and clean water and sanitation (Goal 6), which aim to “ensure availability and sustainable management of water and sanitation for all”, we investigated the environmental reservoirs of V. cholerae in Vembanad Lake, the largest lake in Kerala (India), where cholera is endemic. The response of environmental reservoirs of V. cholerae to variability in essential climate variables may play a pivotal role in determining the quality of natural water resources, and whether they might be safe for human consumption or not. The hydrodynamics of Vembanad Lake, and the man-made barrier that divides the lake, resulted in spatial and temporal variability in salinity (1–32 psu) and temperature (23 to 36 °C). The higher ends of this salinity and temperature ranges fall outside the preferred growth conditions for V. cholerae reported in the literature. The bacteria were associated with filtered water as well as with phyto- and zooplankton in the lake. Their association with benthic organisms and sediments was poor to nil. The prevalence of high laminarinase and chitinase enzyme expression (more than 50 µgmL−1 min−1) among V. cholerae could underlie their high association with phyto- and zooplankton. Furthermore, the diversity in the phytoplankton community in the lake, with dominance of genera such as Skeletonema sp., Microcystis sp., Aulacoseira sp., and Anabaena sp., which changed with location and season, and associated changes in the zooplankton community, could also have affected the dynamics of the bacteria in the lake. The probability of presence or absence of V. cholerae could be expressed as a function of chlorophyll concentration in the water, which suggests that risk maps for the entire lake can be generated using satellite-derived chlorophyll data. In situ observations and satellite-based extrapolations suggest that the risks from environmental V. cholerae in the lake can be quite high (with probability in the range of 0.5 to 1) everywhere in the lake, but higher values are encountered more frequently in the southern part of the lake. Remote sensing has an important role to play in meeting SDG goals related to health, water quality and life under water, as demonstrated in this example related to cholera.

The editorial team are delighted to present this Special Issue of Sensors focused on Remote Sensing of Ocean Color: Theory and Applications. We believe that this is a timely opportunity to showcase current developments across a broad range of topics in ocean color remote sensing (OCRS). Although the field is well-established, in this Special Issue we are able to highlight advances in the applications of the technology, our understanding of the underpinning science, and its relevance in the context of monitoring climate change and engaging public participation.

Primary production by marine phytoplankton is one of the largest fluxes of carbon on our planet. In the past few decades, considerable progress has been made in estimating global primary production at high spatial and temporal scales by combining in situ measurements of primary production with remote-sensing observations of phytoplankton biomass. One of the major challenges in this approach lies in the assignment of the appropriate model parameters that define the photosynthetic response of phytoplankton to the light field. In the present study, a global database of in situ measurements of photosynthesis versus irradiance (P-I) parameters and a 20-year record of climate quality satellite observations were used to assess global primary production and its variability with seasons and locations as well as between years. In addition, the sensitivity of the computed primary production to potential changes in the photosynthetic response of phytoplankton cells under changing environmental conditions was investigated. Global annual primary production varied from 38.8 to 42.1 Gt C yr − 1 over the period of 1998−2018. Inter-annual changes in global primary production did not follow a linear trend, and regional differences in the magnitude and direction of change in primary production were observed. Trends in primary production followed directly from changes in chlorophyll-a and were related to changes in the physico-chemical conditions of the water column due to inter-annual and multidecadal climate oscillations. Moreover, the sensitivity analysis in which P-I parameters were adjusted by ±1 standard deviation showed the importance of accurately assigning photosynthetic parameters in global and regional calculations of primary production. The assimilation number of the P-I curve showed strong relationships with environmental variables such as temperature and had a practically one-to-one relationship with the magnitude of change in primary production. In the future, such empirical relationships could potentially be used for a more dynamic assignment of photosynthetic rates in the estimation of global primary production. Relationships between the initial slope of the P-I curve and environmental variables were more elusive.

Coastal waters are optically diverse; studying their optical characteristics is an important application of satellite oceanography. In coastal ecosystems of the northern Indian Ocean, optical diversity has been little studied, except for the global analysis by Mélin and Vantrepotte (2015). This paper is a contribution toward identification and characterization of optical classes in the coastal regions of the northern Indian Ocean. The study identified eight optical classes using the monthly climatological datasets of remote sensing reflectance for the 1998–2013 period from the Ocean Color Climate Change Initiative (OC-CCI, www.oceancolour.org). The optical classification we adopted uses the fuzzy logic method, based on Moore et al. (2009). The seasonal variations of the eight resultant optical classes of the coastal waters of the northern Indian Ocean were explored. From the mean reflectance spectral signals obtained, it appears that classes 1–6 belong to Case-1 waters and classes 7 and 8 correspond to Case-2 waters. Classes 1 to 2 appear in deeper oligotrophic waters; classes 3–6 are present in intermediate depths; classes 7 and 8 are mostly found within inshore eutrophic regions with high chlorophyll concentrations, sediments from river plumes and land runoffs. The optical variability between seasons (the summer and winter monsoon and the intermonsoon seasons) are influenced by variations in physical forcing, such as surface winds, ocean currents, precipitation, and sediment influx from rivers and land runoff. Optical diversity index ranged from around 0.3 to 1.36. High diversity indices ranging between 1 and 1.36 were found in areas dominated by classes 1–4, whereas low diversity indices 0.3 occurred in areas where classes 7 and 8 dominated. The variations in the dominant optical classes are shown to be related to changes in chlorophyll concentration and suspended sediment load, as indicated by remote sensing reflectance at 670 nm. On the other hand, optical diversity appears to be high in zones of transition between dominant optical classes.

Knowing the spatial and temporal distribution of the underwater light field, i.e., the spectral and angular structure of the radiant intensity at any point in the water column, is essential to understanding the biogeochemical processes that control the composition and evolution of aquatic ecosystems and their impact on climate and reaction to climate change. At present, only a few properties are reliably retrieved from space, either directly or via water-leaving radiance. Existing satellite products are limited to planar photosynthetically available radiation (PAR) and ultraviolet (UV) irradiance above the surface and diffuse attenuation coefficient. Examples of operational products are provided, and their advantages and drawbacks are examined. The usefulness and convenience of these products notwithstanding, there is a need, as expressed by the user community, for other products, i.e., sub-surface planar and scalar fluxes, average cosine, spectral fluxes (UV to visible), diurnal fluxes, absorbed fraction of PAR by live algae (APAR), surface albedo, vertical attenuation, and heating rate, and for associating uncertainties to any product on a pixel-by-pixel basis. Methodologies to obtain the new products are qualitatively discussed in view of most recent scientific knowledge and current and future satellite missions, and specific algorithms are presented for some new products, namely sub-surface fluxes and average cosine. A strategy and roadmap (short, medium, and long term) for usage and development priorities is provided, taking into account needs and readiness level. Combining observations from satellites overpassing at different times and geostationary satellites should be pursued to improve the quality of daily-integrated radiation fields, and products should be generated without gaps to provide boundary conditions for general circulation and biogeochemical models. Examples of new products, i.e., daily scalar PAR below the surface, daily average cosine for PAR, and sub-surface spectral scalar fluxes are presented. A procedure to estimate algorithm uncertainties in the total uncertainty budget for above-surface daily PAR, based on radiative simulations for expected situations, is described. In the future, space-borne lidars with ocean profiling capability offer the best hope for improving our knowledge of sub-surface fields. To maximize temporal coverage, space agencies should consider placing ocean-color instruments in L1 orbit, where the sunlit part of the Earth can be frequently observed.

Over the past decade, a number of methods have been developed to estimate size-class primary production from either in situ phytoplankton pigment data or remotely-sensed data. In this context, the first objective of this study was to compare two methods of estimating size class specific (micro-, nano-, and pico-phytoplankton) photosynthesis-irradiance (PE) parameters from pigment data. The second objective was to analyse the relationship between environmental variables (temperature, nitrate and PAR) and PE parameters in the different size-classes. A large dataset was used of simultaneous measurements of the PE parameters (n = 1,260) and phytoplankton pigment markers (n = 2,326), from 3 different institutes. There were no significant differences in mean PE parameters of the different size classes between the chemotaxonomic method of Uitz et al. (2008) and the pigment markers and carbon-to-Chl a ratios method of Sathyendranath et al. (2009). For both methods, mean maximum photosynthetic rates (PmB) for micro-phytoplankton were significantly lower than those for pico-phytoplankton and nano-phytoplankton. The mean light limited slope (αB) for nano-phytoplankton were significantly higher than for the other size taxa. For micro-phytoplankton dominated samples identified using the Sathyendranath et al. (2009) method, both PmB and αB exhibited a significant, positive linear relationship with temperature, whereas for pico-phytoplankton the correlation with temperature was negative. Nano-phytoplankton dominated samples showed a positive correlation between PmB and temperature, whereas for αB and the light saturation parameter (Ek) the correlations were not significant. For the Uitz et al. (2008) method, only micro-phytoplankton PmB, pico-phytoplankton αB, nano- and pico-phytoplankton Ek exhibited significant relationships with temperature. The temperature ranges occupied by the size classes derived using these methods differed. The Uitz et al. (2008) method exhibited a wider temperature range compared to those derived from the Sathyendranath et al. (2009) method. The differences arise from the classification of mixed populations. Based on these patterns, we therefore recommend using the Sathyendranath et al. (2009) method to derive micro-phytoplankton PE parameters at sea water temperatures up to 8°C during monospecific blooms and the Uitz et al. (2008) method to derive PE parameters of mixed populations over the temperature range from 8 to 18°C. Both methods exhibited similar relationships between pico-phytoplankton PE parameters and temperatures >18°C.

In climate research, an important task is to characterize the relationships between Essential Climate Variables (ECVs). Here, satellite-derived data sets have been used to examine the seasonal cycle of phytoplankton (chlorophyll concentration) in the waters off Somalia, and its relationship to aerosols, winds and Sea Surface Temperature (SST). Chlorophyll-a (Chl-a) concentration, Aerosol Optical Thickness (AOT), Ångström Exponent (AE), Dust Optical Thickness (DOT), SST and sea-surface wind data for a 16-year period were assembled from various sources. The data were used to explore whether there is evidence to show that dust aerosols enhance Chl-a concentration in the study area. The Cross Correlation Function (CCF) showed highest positive correlation (r2 = 0.3) in the western Arabian Sea when AOT led Chl-a by 1–2 time steps (here, 1 time step is 8 days). A 2 × 2° box off Somalia was selected for further investigations. The correlations of alongshore wind speed, Ekman Mass Transport (EMT) and SST with Chl-a were higher than that of AOT, for a lag of 8 days. When all four variables were considered together in a multiple linear regression, the increase in r2 associated with the AOT is only about 0.02, a consequence of covariance among AOT, SST, EMT and alongshore wind speed. The AOT data show presence of dust aerosols most frequently during the summer monsoon season (June–September). When the analyses were repeated for the dust aerosol events, the correlations were generally lower, but still significant. Again, the inclusion of DOT in the multiple linear regression increased the correlation coefficient by only 2%, indicating minor enhancement in Chl-a concentration. Interestingly, during summer monsoon season, there is a higher probability of finding more instances of positive changes in Chl-a after one time step, regardless of whether there is dust aerosol or not. On the other hand, during the winter monsoon season (November–December) and rest of the year, the probability of Chl-a enhancement is higher when dust aerosol is present than when it is absent. The phase relationship in the 8-day climatologies of Chl-a and AOT (derived from NASA's SeaWiFS and MODIS-A ocean colour processing chain) showed that AOT led Chl-a for most of the summer monsoon season, except when Chl-a was very high, during which time, Chl-a led AOT. The phase shift in the Chl-a and AOT climatological relationship at the Chl-a peak was not observed when AOT from Aerosol Climate Change Initiative (Aerosol-CCI) was used.

The differences among phytoplankton carbon (Cphy) predictions from six ocean color algorithms are investigated by comparison with in situ estimates of phytoplankton carbon. The common satellite data used as input for the algorithms is the Ocean Color Climate Change Initiative merged product. The matching in situ data are derived from flow cytometric cell counts and per-cell carbon estimates for different types of pico-phytoplankton. This combination of satellite and in situ data provides a relatively large matching dataset (N > 500), which is independent from most of the algorithms tested and spans almost two orders of magnitude in Cphy. Results show that not a single algorithm outperforms any of the other when using all matching data. Concentrating on the oligotrophic regions (Chlorophyll-a concentration, B, less than 0.15 mg Chl m−3), where flow cytometric analysis captures most of the phytoplankton biomass, reveals significant differences in algorithm performance. The bias ranges from −35 to +150% and unbiased root mean squared difference from 5 to 10 mg C m−3 among algorithms, with chlorophyll-based algorithms performing better than the rest. The backscattering-based algorithms produce different results at the clearest waters and these differences are discussed in terms of the different algorithms used for optical particle backscattering coefficient (bbp) retrieval.

An equation is derived to express the sensitivity of daily, watercolumn production by phytoplankton in the ocean to variations in irradiance at the sea surface. Assuming no spectral effects, and a vertically uniform chlorophyll profile, the sensitivity is a function only of the dimensionless irradiance. Spectral effects can be accounted for as a function of the chlorophyll concentration. At the global scale, the relative reduction in daily production consequent on halving the surface irradiance (representing the expected scope for variation in surface irradiance under natural conditions) is found to be from 30 to 40%. Choice of data source for irradiance may incur a further systematic error of up to 15%. Given that local irradiance (the principal forcing for primary production) may vary from day to day, the issue of how to archive production data for the most generality is discussed and recommendations made in this regard.

A widely-used theory of the photoacclimatory response in phytoplankton has, until now, been solved using a mathematical approximation that puts strong limitations on its applicability in natural conditions. We report an exact, analytic solution for the chlorophyll-to-carbon ratio as a function of the dimensionless irradiance (mixed layer irradiance normalized to the photoadaptation parameter for phytoplankton) that is applicable over the full range of irradiance occurring in natural conditions. Application of the exact solution for remote-sensing of phytoplankton carbon at large scales is illustrated using satellite-derived chlorophyll, surface irradiance data and mean photosynthesis-irradiance parameters for the season assigned to every pixel on the basis of ecological provinces. When the exact solution was compared with the approximate one at the global scale, for a particular month (May 2010), the results differed by at least 15% for about 70% of Northern Hemisphere pixels (analysis was performed during the northern hemisphere Spring bloom period) and by more than 50% for 24% of Northern Hemisphere pixels (approximate solution overestimates the carbon-to-chlorophyll ratio compared with the exact solution). Generally, the divergence between the two solutions increases with increasing available light, raising the question of the appropriate timescale for specifying the forcing irradiance in ecosystem models.

Particulate Organic Carbon (POC) plays a vital role in the ocean carbon cycle. Though relatively small compared with other carbon pools, the POC pool is responsible for large fluxes and is linked to many important ocean biogeochemical processes. The satellite ocean-color signal is influenced by particle composition, size, and concentration and provides a way to observe variability in the POC pool at a range of temporal and spatial scales. To provide accurate estimates of POC concentration from satellite ocean color data requires algorithms that are well validated, with uncertainties characterized. Here, a number of algorithms to derive POC using different optical variables are applied to merged satellite ocean color data provided by the Ocean Color Climate Change Initiative (OC-CCI) and validated against the largest database of in situ POC measurements currently available. The results of this validation exercise indicate satisfactory levels of performance from several algorithms (highest performance was observed from the algorithms of Loisel et al., 2002; Stramski et al., 2008) and uncertainties that are within the requirements of the user community. Estimates of the standing stock of the POC can be made by applying these algorithms, and yield an estimated mixed-layer integrated global stock of POC between 0.77 and 1.3 Pg C of carbon. Performance of the algorithms vary regionally, suggesting that blending of region-specific algorithms may provide the best way forward for generating global POC products.

Oceanic phytoplankton respond rapidly to a complex spectrum of climate-driven perturbations, confounding attempts to isolate the principal causes of observed changes. A dominant mode of variability in the Earth-climate system is that generated by the El Niño phenomenon. Marked variations are observed in the centroid of anomalous warming in the Equatorial Pacific under El Niño, associated with quite different alterations in environmental and biological properties. Here, using observational and reanalysis datasets, we differentiate the regional physical forcing mechanisms, and compile a global atlas of associated impacts on oceanic phytoplankton caused by two extreme types of El Niño. We find robust evidence that during Eastern Pacific (EP) and Central Pacific (CP) types of El Niño, impacts on phytoplankton can be felt everywhere, but tend to be greatest in the tropics and subtropics, encompassing up to 67% of the total affected areas, with the remaining 33% being areas located in high-latitudes. Our analysis also highlights considerable and sometimes opposing regional effects. During EP El Niño, we estimate decreases of −56 TgC/y in the tropical eastern Pacific Ocean, and −82 TgC/y in the western Indian Ocean, and increase of +13 TgC/y in eastern Indian Ocean, whereas during CP El Niño, we estimate decreases −68 TgC/y in the tropical western Pacific Ocean and −10 TgC/y in the central Atlantic Ocean. We advocate that analysis of the dominant mechanisms forcing the biophysical under El Niño variability may provide a useful guide to improve our understanding of projected changes in the marine ecosystem in a warming climate and support development of adaptation and mitigation plans.

The effect of biomass dynamics on the estimation of watercolumn primary production is analyzed, by coupling a primary production model to a simple growth equation for phytoplankton. The production model is formulated with depth- and time-resolved biomass, and placed in the context of earlier models, with emphasis on the canonical solution for watercolumn production. A relation between the canonical solution and the general solution for the case of an arbitrary depth-dependent biomass profile was derived, together with an analytical solution for watercolumn production in case of a depth dependent biomass profile described with the shifted Gaussian function. The analysis was further extended to the case of a time-dependent, mixed-layer biomass, and two additional analytical solutions to this problem were derived, the first in case of increasing mixed-layer biomass and the second in case of declining biomass. The solutions were tested with Hawaii Ocean Time-series data. The canonical solution for mixed-layer production has proven to be a good model for this data set. The shifted Gaussian function was demonstrated to be an accurate model for the measured biomass profiles and the shifted Gaussian parameters extracted from the measured profiles were further used in the analytical solution for watercolumn production and results compared with data. The influence of time-dependent biomass on mixed-layer production was studied through analytical solutions. Re-examining the Critical Depth Hypothesis we derived an expression for the daily increase in mixed-layer biomass. Finally, the work was placed in a remote sensing context and the time-dependent model for biomass related to the remotely sensed-biomass.

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.

We present a model that estimates the spectral phytoplankton absorption coefficient ( a p h ( λ ) ) of four phytoplankton groups (picophytoplankton, nanophytoplankton, dinoflagellates, and diatoms) as a function of the total chlorophyll-a concentration (C) and sea surface temperature (SST). Concurrent data on a p h ( λ ) (at 12 visible wavelengths), C and SST, from the surface layer ( a p h ( λ ) with a similar performance to two earlier models, using either in situ or satellite data as input. Although more complex, the new model has the advantage of being able to determine a p h ( λ ) for four phytoplankton groups and of incorporating the influence of SST on the composition of the four groups. We integrate the new four-population absorption model into a simple model of ocean colour, to illustrate the influence of changes in SST on phytoplankton community structure, and consequently, the blue-to-green ratio of remote-sensing reflectance. We also present a method of propagating error through the model and illustrate the technique by mapping errors in group-specific a p h ( λ ) using a satellite image. We envisage the model will be useful for ecosystem model validation and assimilation exercises and for investigating the influence of temperature change on ocean colour.

Two expanding areas of science and technology are citizen science and three-dimensional (3D) printing. Citizen science has a proven capability to generate reliable data and contribute to unexpected scientific discovery. It can put science into the hands of the citizens, increasing understanding, promoting environmental stewardship, and leading to the production of large databases for use in environmental monitoring. 3D printing has the potential to create cheap, bespoke scientific instruments that have formerly required dedicated facilities to assemble. It can put instrument manufacturing into the hands of any citizen who has access to a 3D printer. In this paper, we present a simple hand-held device designed to measure the Secchi depth and water colour (Forel Ule scale) of lake, estuarine and nearshore regions. The device is manufactured with marine resistant materials (mostly biodegradable) using a 3D printer and basic workshop tools. It is inexpensive to manufacture, lightweight, easy to use, and accessible to a wide range of users. It builds on a long tradition in optical limnology and oceanography, but is modified for ease of operation in smaller water bodies, and from small watercraft and platforms. We provide detailed instructions on how to build the device and highlight examples of its use for scientific education, citizen science, satellite validation of ocean colour data, and low-cost monitoring of water clarity, colour and temperature.

In 1962, a series of in situ primary production measurements began in the Adriatic Sea, at a station near the island of Vis. To this day, over 55 years of monthly measurements through the photic zone have been accumulated, including close to 3000 production measurements at different depths. The measurements are conducted over a six-hour period around noon, and the average production rate extrapolated linearly over day length to calculate daily production. Here, a non-linear primary production model is used to correct these estimates for potential overestimation of daily production due to linear extrapolation. The assimilation numbers are recovered from the measured production profiles and subsequently used to model production at depth. Using the recovered parameters, the model explained 87% of variability in measured normalized production at depth. The model is then used to calculate daily production at depth, and it is observed to give on average 20% lower daily production at depth than the estimates based on linear extrapolation. Subsequently, water column production is calculated, and here, the model predicted on average 26% lower water column production. With the recovered parameters and the known magnitude of the overestimation, the time-series of water column production is then re-established with the non-linearly-corrected data. During this 55-year period, distinct regimes were observed, which were classified with a regime shift detection method. It is then demonstrated how the recovered parameters can be used in a remote sensing application. A seasonal cycle of the recovered assimilation number is constructed along with the seasonal cycle of remotely-sensed chlorophyll. The two are then used to model the seasonal cycle of water column production. An upper and a lower bound on the seasonal cycle of water column production based on remotely-sensed chlorophyll data are then presented. Measured water column production was found to be well within the range of remotely-sensed estimates. With this work, the utility of in situ measurements as a means of providing information on the assimilation number is presented and its application as a reference for remote sensing models highlighted.

Computing the vertical structure of primary production in ocean ecosystem models requires information about the vertical distribution of available light, chlorophyll concentration and photosynthesis response parameters. Conversely, given information on vertical structure of chlorophyll and light, we can extract photosynthesis parameters from vertical profiles of primary production measured at sea, as we illustrate here for the Bermuda Atlantic Time-Series Study. The procedure is based on a model of the production profile, which itself depends on the underwater light field. To model the light field, attenuation coefficients were estimated from measured optical profiles using a simple model of exponential decay of photosynthetically-available irradiance with depth, which accounted for 97% of the variance in the measured optical data. With the underwater light climate known, an analytical solution for the production profile was employed to recover photosynthesis parameters by minimizing the residual model error. The recovered parameters were used to model normalized production profiles and normalized watercolumn production. The model explained 95% of the variance in the measured normalized production at depth and 97% of the variance in measured normalized watercolumn production. A shifted Gaussian function was used to model biomass profiles and accounted for 93% of the variance in measured biomass at depth. An analytical solution for watercolumn production with the shifted Gaussian biomass was also tested. With the recovered photosynthesis parameters, maximum instantaneous growth rates were estimated by using a literature value for the carbon-to-chlorophyll ratio in this region of the Atlantic. An exact relationship between the maximum instantaneous growth rate and the daily growth rate in the ocean was derived. It was shown that calculating the growth rate by dividing the production by the carbon-to-chlorophyll ratio is equivalent to calculating it from the ratio of the final to the initial biomass, even when production is time dependent. Finally, the seasonal cycle of the recovered assimilation number at the Bermuda Station was constructed and analysed. The presented approach enables the estimation of photosynthesis parameters and growth rates from measured production profiles with only a few model assumptions, and increases the utility of in situ primary production measurements. The retrieved parameters have direct applications in satellite-based estimates of primary production from ocean-colour data, of which we give an example.

The unicellular cyanobacterium Prochlorococcus is the most dominant resident of the subtropical gyres, which are considered to be the largest biomes on earth. In this study, the spatial and temporal variability in the global distribution of Prochlorococcus was estimated in the Atlantic Ocean using an empirical model based on data from 13 Atlantic Meridional Transect cruises. Our model uses satellite-derived sea surface temperature (SST), remote-sensing reflectance at 443 and 488 nm, and the water temperature at a depth of 200 m from Argo data. The model divides the population of Prochlorococcus into two groups: ProI, which dominates under high-light conditions associated with the surface, and ProII, which favors low light found near the deep chlorophyll maximum. ProI and ProII are then summed to provide vertical profiles of the concentration of Prochlorococcus cells. This model predicts that Prochlorococcus cells contribute 32 Mt of carbon biomass (7.4 × 1026 cells) to the Atlantic Ocean, concentrated mainly within the subtropical gyres (35%) and areas near the Equatorial Convergence Zone (30%). When projected globally, 3.4 × 1027 Prochlorococcus cells represent 171 Mt of carbon biomass, with 43% of this global biomass allocated to the upper ocean (0–45 m depth). Annual cell standing stocks were relatively stable between the years 2003 and 2014, and the contribution of the gyres varies seasonally as gyres expand and contract, tracking changes in light and temperature, with lowest cell abundances during the boreal and austral winter (1.4 × 1013 cells m−2), when surface cell concentrations were highest (9.8 × 104 cells mL−1), whereas the opposite scenario was observed in spring–summer (2 × 1013 cells m−2). This model provides a three-dimensional view of the abundance of Prochlorococcus cells, revealing that Prochlorococcus contributes significantly to total phytoplankton biomass in the Atlantic Ocean, and can be applied using either in situ measurements at the sea surface (r2 = 0.83) or remote-sensing observables (r2 = 0.58).

Uncertainty estimation is crucial to establishing confidence in any data analysis, and this is especially true for Essential Climate Variables, including ocean colour. Methods for deriving uncertainty vary greatly across data types, so a generic statistics-based approach applicable to multiple data types is an advantage to simplify the use and understanding of uncertainty data. Progress towards rigorous uncertainty analysis of ocean colour has been slow, in part because of the complexity of ocean colour processing. Here, we present a general approach to uncertainty characterisation, using a database of satellite-in situ matchups to generate a statistical model of satellite uncertainty as a function of its contributing variables. With an example NASA MODIS-Aqua chlorophyll-a matchups database mostly covering the north Atlantic, we demonstrate a model that explains 67% of the squared error in log(chlorophyll-a) as a potentially correctable bias, with the remaining uncertainty being characterised as standard deviation and standard error at each pixel. The method is quite general, depending only on the existence of a suitable database of matchups or reference values, and can be applied to other sensors and data types such as other satellite observed Essential Climate Variables, empirical algorithms derived from in situ data, or even model data.

Optical remote sensing of aquatic vegetation in shallow water is an essential aid to ecosystem protection, but it is difficult because the spectral characteristics of the vegetation are sensitive to external features such as water background effects, atmospheric effects, and the structural properties of the canopy. A global sensitivity analysis of an aquatic vegetation radiative transfer model provides invaluable background for algorithm development for use in optical remote sensing. Here, we use the extended Fourier Amplitude Sensitivity Test (EFAST) method for the modelling. Four different cases were identified by subdividing the ranges of water depth and leaf area index (LAI) involved. The results indicate that the reflectance of emergent vegetation is affected mainly by the concentrations of chlorophyll a + b in leaves (Cab), leaf inclination distribution function parameter (LIDFa) and LAI. The parameter LAI is influential in sparse vegetation cases whereas Cab and LIDFa are influential in dense vegetation cases. Canopy reflectance for submerged vegetation is dominated by water parameters. Relatively, LAI and Cab are highly sensitive vegetation parameters. The analysis is extended to vegetation index as well, which takes the Sentinel-2A as the reference sensor. It shows that NDAVI (Normalized Difference Aquatic Vegetation Index) is suitable for retrieving LAI in all cases except deep-sparse for emergent vegetation, whereas NDVI (Normalized Difference Vegetation Index) would be better in the deep-sparse case. NDVI, NDAVI and WAVI (Water Adjusted Vegetation Index), respectively, are suitable for retrieving Cab, Car and LIDFa in dense cases. For submerged vegetation, the sensitivity of LAI to NDAVI is relatively high only in the shallow-sparse case. The adjustment factor L in SAVI and WAVI fails to suppress the sensitivity to water constituent parameters. The sensitivity of LAI and Cab to NDVI in deep cases is relatively higher than that to the other indices, which may provide clues for the construction of inversion algorithms in macrophyte remote sensing in the aquatic environment using spectral signatures in the visible and near infrared regions.

The influence of phytoplankton on the spectral structure of the submarine irradiance field is reviewed. The implications for the ocean system of the spectral response by phytoplankton to the ambient light field are discussed. For example, it provides the basis for retrieval of phytoplankton biomass by visible spectral radiometry (ocean-colour remote sensing). In the computation of primary production, the results of spectral models differ in a known and systematic manner from those of non-spectral ones. The bias can be corrected without risk of incurring additional random errors. The models in use for phytoplankton growth, whether based on available light or absorbed light, whether expressed in terms of chlorophyll or carbon, are shown all to conform to the same basic formalism with the same parameters. Residual uncertainty lies less with the models than with the parameters required for their implementation. The submarine light field and the spectral characteristics of phytoplankton carry latent information on phytoplankton community structure. Differences in spectral response by different functional types of phytoplankton are small but significant. Optical considerations limit the maximum phytoplankton biomass that can be sustained in a given surface mixed layer. Moreover, the upper bound on the biomass depends on the spectral response of the dominant phytoplankton taxa. As a result, an optical control exists in the mixed layer that tends to resist extreme excursions of the biomass and also to maintain biodiversity in the phytoplankton.

At the global and regional scales, the distribution and abundance of marine phytoplankton are under the control of physical forcing. Moreover, the community structure and the size structure of phytoplankton assemblages also appear to be under physical control. Areas of the ocean with common physical forcing (ecological provinces) may be expected to have phytoplankton communities that respond in a similar fashion to changes in local forcing, and with ecophysiological rate parameters that are predictable from local environmental conditions. In modelling the marine ecosystem, relevant parameters may be assigned according to a partition into ecological provinces. To the extent that physical forcing of the ocean is not constant within or between years, the boundaries of the provinces should be considered as dynamic. The dynamics and the associated changes in taxa can be revealed by remote sensing.

Phytoplankton samples collected from two cruises off the coast of Chile were analysed for pigment composition and absorption characteristics. High pigment concentrations (up to 20 mg chl-a m-3) were found in the upwelled waters over the shelf break off the coast of Concepción during spring (October 1998), but relatively oligotrophic conditions were found further offshore. Similarly, stations further north (between Coquimbo and Iquique), sampled during the austral summer (February 1999), also showed low pigment concentrations, characterised by the presence of prymnesiophytes, and cyanobacteria including Prochlorococcus sp. The specific absorption coefficient of phytoplankton at 443 nm (a*ph(443)) was much higher for the offshore population than the inshore population, which was dominated by large diatoms. These differences are attributed to changes in pigment packaging and pigment composition. The relative proportion of non-photosynthetic carotenoids to chl-a, together with the ratio of the peak height of the Gaussian bands in the blue and red regions of the spectrum, p(435)/p(676), (an indicator of the importance of the packaging effect) could account for up to 92 % of the total variation in a*ph(443). Blue/green absorption ratios were strongly related to the relative concentration of 19'-hexanoyloxyfucoxanthin and fucoxanthin. A reasonable agreement was found between in situ and satellite estimates of chl-a (SeaWiFS data) despite the large variability in phytoplankton specific absorption coefficients, suggesting that the `global' absorption-to-chlorophyll relationships encompass the regional variations observed off the coast of Chile. Satellite chl-a was overestimated in oligotrophic water when compared to HPLC chl-a measurements, apparently because of the high specific absorption coefficients of phytoplankton in the offshore waters. On the other hand, ship and satellite data were in closer agreement when in situ fluorometric chl-a data was used. It is likely that the correlation between in situ and satellite chl-a could be improved by using regional algorithmsLa composición de pigmentos y las características de absorción fueron analizadas en muestras de fitoplancton recolectadas en dos cruceros frente a las costas Chile. Se encontraron altas concentraciones de pigmentos (hasta 20 mg chl-a m-3) en aguas de surgencia sobre el quiebre de la plataforma frente a Concepción durante la primavera, octubre de 1998; sin embargo, se encontraron condiciones relativamente oligotróficas costa afuera. De manera similar, estaciones más al norte (entre Coquimbo e Iquique), muestreadas durante el verano austral (febrero de 1999), también mostraron bajas concentraciones de pigmentos, caracterizados por la presencia de primnesioficeas y cianobacterias (Synechococccus sp. y Prochlorococcus sp.). El coeficiente de absorción específico del fitoplancton a 443 nm (a*ph(443)) fue mucho mayor para las poblaciones costa afuera que para las poblaciones costeras, las cuales estaban dominadas por diatomeas. Esta diferencia fue atribuida a cambios en el empaquetamiento y composición de pigmentos. La proporción relativa entre carotenoides no-fotosintéticos y chl-a, junto con la razón de la altura del pico de las bandas Gausianas en las regiones azul y roja del espectro p(435)/p(676) (un índice del efecto de empaquetamiento), representa hasta el 92 % de la variación total en a*ph(443). Las razones de absorción azul/verde estuvieron relacionadas fuertemente a la concentración relativa de 19'-hexanoiloxifucoxantina y fucoxantina. Se encontró una relación aceptable entre las estimaciones de chl-a (datos de SeaWiFS) medidas in situ y las obtenidas con el satélite, a pesar de la gran variabilidad en los coeficientes de absorción específica del fitoplancton, sugiriendo que las relaciones de absorción de clorofila "global" abarcan las variaciones regionales observadas a la altura de las costas de Chile. Las mediciones de chl-a satelitales fueron sobreestimadas en aguas oligotróficas cuando se compararon con determinaciones HPLC de chl- a, aparentemente por los coeficientes específicos de absorción altos del fitoplancton en mar abierto. Además, los datos obtenidos por barco y de satélite estuvieron estrechamente relacionados cuando se utilizaron datos de chl- a in situ y fluorométricos. Probablemente la correlación entre la chl- a in situ y satelital podría ser mejorada utilizando algoritmos regionales

The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3 billion bp). Though a few major microbial clades dominate the planktonic marine niche, the dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled data being unique at a 98% sequence identity cutoff. Using the metadata associated with each sample and sequencing library, we developed new comparative genomic and assembly methods. One comparative genomic method, termed "fragment recruitment," addressed questions of genome structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical diversity of genes and gene families. A second method, termed "extreme assembly," made possible the assembly and reconstruction of large segments of abundant but clearly nonclonal organisms. Within all abundant populations analyzed, we found extensive intra-ribotype diversity in several forms: (1) extensive sequence variation within orthologous regions throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most individual sequencing reads are unique; (2) numerous changes in gene content some with direct adaptive implications; and (3) hypervariable genomic islands that are too variable to assemble. The intra-ribotype diversity is organized into genetically isolated populations that have overlapping but independent distributions, implying distinct environmental preference. We present novel methods for measuring the genomic similarity between metagenomic samples and show how they may be grouped into several community types. Specific functional adaptations can be identified both within individual ribotypes and across the entire community, including proteorhodopsin spectral tuning and the presence or absence of the phosphate-binding gene PstS.