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Valente, A, Sathyendranath S, Brotas V, Groom S, Grant M, Taberner M, Antoine D, Arnone R, Balch WM, Barker K, Barlow R, Belanger S, Berthon JF, Besiktepe S, Borsheim Y, Bracher A, Brando V, Canuti E, Chavez F, Cianca A, Claustre H, Clementson L, Crout R, Frouin R, Garcia-Soto C, Gibb SW, Gould R, Hooker SB, Kahru M, Kampel M, Klein H, Kratzer S, Kudela R, Ledesma J, Loisel H, Matrai P, McKee D, Mitchell BG, Moisan T, Muller-Karger F, O'Dowd L, Ondrusek M, Platt T, Poulton AJ, Repecaud M, Schroeder T, Smythe T, Smythe-Wright D, Sosik HM, Twardowski M, Vellucci V, Voss K, Werdell J, Wernand M, Wright S, Zibordi G.  2019.  A compilation of global bio-optical in situ data for ocean-colour satellite applications - version two. Earth System Science Data. 11:1037-1068.   10.5194/essd-11-1037-2019   AbstractWebsite

A global compilation of in situ data is useful to evaluate the quality of ocean-colour satellite data records. Here we describe the data compiled for the validation of the ocean-colour products from the ESA Ocean Colour Climate Change Initiative (OC-CCI). The data were acquired from several sources (including, inter alia, MOBY, BOUSSOLE, AERONET-OC, SeaBASS, NOMAD, MERMAID, AMT, ICES, HOT and GeP&CO) and span the period from 1997 to 2018. Observations of the following variables were compiled: spectral remote-sensing reflectances, concentrations of chlorophyll a, spectral inherent optical properties, spectral diffuse attenuation coefficients and total suspended matter. The data were from multi-project archives acquired via open internet services or from individual projects, acquired directly from data providers. Methodologies were implemented for homogenization, quality control and merging of all data. No changes were made to the original data, other than averaging of observations that were close in time and space, elimination of some points after quality control and conversion to a standard format. The final result is a merged table designed for validation of satellite-derived ocean-colour products and available in text format. Metadata of each in situ measurement (original source, cruise or experiment, principal investigator) was propagated throughout the work and made available 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. This paper also describes the changes that were made to the compilation in relation to the previous version (Valente et al., 2016). The compiled data are available at (Valente et al., 2019).

Jamet, C, Ibrahim A, Ahmad Z, Angelini F, Babin M, Behrenfeld MJ, Boss E, Cairns B, Churnside J, Chowdhary J, Davis AB, Dionisi D, Duforet-Gaurier L, Franz B, Frouin R, Gao M, Gray D, Hasekamp O, He XQ, Hostetler C, Kalashnikova OV, Knobelspiesse K, Lacour L, Loisel H, Martins V, Rehm E, Remer L, Sanhaj I, Stamnes K, Stamnes S, Victori S, Werdell J, Zhai PW.  2019.  Going beyond standard ocean color observations: Lidar and polarimetry. Frontiers in Marine Science. 6   10.3389/fmars.2019.00251   AbstractWebsite

Passive ocean color images have provided a sustained synoptic view of the distribution of ocean optical properties and color and biogeochemical parameters for the past 20-plus years. These images have revolutionized our view of the ocean. Remote sensing of ocean color has relied on measurements of the radiance emerging at the top of the atmosphere, thus neglecting the polarization and the vertical components. Ocean color remote sensing utilizes the intensity and spectral variation of visible light scattered upward from beneath the ocean surface to derive concentrations of biogeochemical constituents and inherent optical properties within the ocean surface layer. However, these measurements have some limitations. Specifically, the measured property is a weighted-integrated value over a relatively shallow depth, it provides no information during the night and retrieval are compromised by clouds, absorbing aerosols, and low Sun zenithal angles. In addition, ocean color data provide limited information on the morphology and size distribution of marine particles. Major advances in our understanding of global ocean ecosystems will require measurements from new technologies, specifically lidar and polarimetry. These new techniques have been widely used for atmospheric applications but have not had as much as interest from the ocean color community. This is due to many factors including limited access to in-situ instruments and/or space-borne sensors and lack of attention in university courses and ocean science summer schools curricula. However, lidar and polarimetry technology will complement standard ocean color products by providing depth-resolved values of attenuation and scattering parameters and additional information about particles morphology and chemical composition. This review aims at presenting the basics of these techniques, examples of applications and at advocating for the development of in-situ and space-borne sensors. Recommendations are provided on actions that would foster the embrace of lidar and polarimetry as powerful remote sensing tools by the ocean science community.

Ramon, D, Steinmetz F, Jolivet D, Compiegne M, Frouin R.  2019.  Modeling polarized radiative transfer in the ocean-atmosphere system with the GPU-accelerated SMART-G Monte Carlo code. Journal of Quantitative Spectroscopy & Radiative Transfer. 222:89-107.   10.1016/j.jqsrt.2018.10.017   AbstractWebsite

SMART-G (Speed-Up Monte-Carlo Advanced Radiative Transfer code with GPU) is a radiative transfer solver for the coupled ocean-atmosphere system with a wavy interface. It is based on the Monte-Carlo technique, works in either plane-parallel or spherical-shell geometry, and accounts for polarization. The vector code is written in CUDA (Compute Unified Device Architecture) and runs on GPUs (Graphic Processing Units). For typical simulations, the GPU-based code running on the Nvidia GTX 1070 card is shown to be 100 time faster than a state of the art CPU-based code running on an AMD Phenomllx4 965 at 3.4GHz. This makes SMART-G competitive, in terms of computational efficiency, with codes based on other techniques (e.g., discrete ordinate, doubling-adding, matrix-operator, and successive-orders-ofscattering), while allowing maximum flexibility regarding the scope of the simulations. The monochromatic version of the code without trans-spectral processes (Raman scattering, fluorescence) is described, including the treatment of photon propagation and interactive processes (elastic scattering, absorption, reflection, refraction, but not thermal emission) and variance reduction (local estimate). Benchmark values are accurately reproduced for clear and cloudy atmospheres over a wavy reflecting surface and a black ocean. Results obtained for a diffusely reflecting ocean agree with those from a discrete ordinate code. SMART-G may be used, not only as a reference code, but also to simulate the signal/imagery observed/produced by optical sensors, create accurate look-up tables, and investigate new remote sensing techniques. (C) 2018 Elsevier Ltd. All rights reserved.

Frouin, R, Ramon D, Boss E, Jolivet D, Compiegne M, Tan J, Bouman H, Jackson T, Franz B, Plett T, Sathyendranath S.  2018.  Satellite radiation products for ocean biology and biogeochemistry: Needs, state-of-the-art, gaps, development priorities, and opportunities. Frontiers in Marine Science. 5   10.3389/fmars.2018.00003   AbstractWebsite

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.

Betancur-Turizo, SP, Gonzalez-Silvera A, Santamaria-del-Angel E, Tan J, Frouin R.  2018.  Evaluation of semi-analytical algorithms to retrieve particulate and dissolved absorption coefficients in Gulf of California optically complex waters. Remote Sensing. 10   10.3390/rs10091443   AbstractWebsite

Two semi-analytical algorithms, Generalized Inherent Optical Property (GIOP) and Garver-Siegel-Maritorena (GSM), were evaluated in terms of how well they reproduced the absorption coefficient of phytoplankton (a(ph)(lambda)) and dissolved and detrital organic matter (a(dg)(lambda)) at three wavelengths (lambda of 412, 443, and 488 nm) in a zone with optically complex waters, the Upper Gulf of California (UGC) and the Northern Gulf of California (NGC). In the UGC, detritus determines most of the total light absorption, whereas, in the NGC, chromophoric dissolved organic material (CDOM) and phytoplankton dominate. Upon comparing the results of each model with a database assembled from four cruises done from spring to summer (March through September) between 2011 and 2013, it was found that GIOP is a better estimator for a(ph)(lambda) than GSM, independently of the region. However, both algorithms underestimate in situ values in the NGC, whereas they overestimate them in the UGC. Errors are associated with the following: (a) the constant a*(ph)(lambda) value used by GSM and GIOP (0.055 m(2) mgChla(-1)) is higher than the most frequent value observed in this study's data (0.03 m(2) mgChla(-1)), and (b) satellite-derived chlorophyll a concentration (Chla) is biased high compared with in situ Chla. GIOP gave also better results for the a(dg)(lambda) estimation than GSM, especially in the NGC. The spectral slope S-dg was identified as an important parameter for estimating a(dg)(lambda), and this study's results indicated that the use of a fixed input value in models was not adequate. The evaluation confirms the lack of generality of algorithms like GIOP and GSM, whose reflectance model is too simplified to capture expected variability. Finally, a greater monitoring effort is suggested in the study area regarding the collection of in situ reflectance data, which would allow explaining the effects that detritus and CDOM may have on the semi-analytical reflectance inversions, as well as isolating the possible influence of the atmosphere on the satellite-derived water reflectance and Chla.

Dupouy, C, Frouin R, Tedetti M, Maillard M, Rodier M, Lombard F, Guidi L, Picheral M, Neveux J, Duhamel S, Charriere B, Sempere R.  2018.  Diazotrophic Trichodesmium impact on UV-Vis radiance and pigment composition in the western tropical South Pacific. Biogeosciences. 15:5249-5269.   10.5194/bg-15-5249-2018   AbstractWebsite

We assessed the influence of the marine diazotrophic cyanobacterium Trichodesmium on the bio-optical properties of western tropical South Pacific (WTSP) waters (18-22 degrees S, 160 degrees E-160 degrees W) during the February-March 2015 OUTPACE cruise. We performed measurements of backscattering and absorption coefficients, irradiance, and radiance in the euphotic zone with a Satlantic MicroPro free-fall profiler and took Underwater Vision Profiler 5 (UPV5) pictures for counting the largest Trichodesmium spp. colonies. Pigment concentrations were determined by fluorimetry and high-performance liquid chromatography and picoplankton abundance by flow cytometry. Trichome concentration was estimated from pigment algorithms and validated by surface visual counts. The abundance of large colonies counted by the UVP5 (maximum 7093 colonies m(-3)) was well correlated to the trichome concentrations (maximum 2093 trichomes L-1) with an aggregation factor of 600. In the Melanesian archipelago, a maximum of 4715 trichomes L-1 was enumerated in pump samples (3.2 m) at 20 degrees S, 167 30 degrees E. High Trichodesmium abundance was always associated with absorption peaks of mycosporine-like amino acids (330, 360 nm) and high particulate backscattering, but not with high Chl a fluorescence or blue particulate absorption (440 nm). Along the west-to-east transect, Trichodesmium together with Prochlorococcus represented the major part of total chlorophyll concentration; the contribution of other groups were relatively small or negligible. The Trichodesmium contribution to total chlorophyll concentration was the highest in the Melanesian archipelago around New Caledonia and Vanuatu (60 %), progressively decreased to the vicinity of the islands of Fiji (30 %), and reached a minimum in the South Pacific Gyre where Prochlorococcus dominated chlorophyll concentration. The contribution of Trichodesmium to zeaxanthin was respectively 50, 40 and 20% for these regions. During the OUTPACE cruise, the relationship between normalized water-leaving radiance (nL(w)) in the ultraviolet and visible and chlorophyll concentration was similar to that found during the BIOSOPE cruise in the eastern tropical Pacific. Principal component analysis (PCA) of OUTPACE data showed that nL(w) at 305, 325, 340, 380, 412 and 440 nm was strongly correlated to chlorophyll and zeaxanthin, while nL(w) at 490 and 565 nm exhibited lower correlations. These results, as well as differences in the PCA of BIOSOPE data, indicated that nL(w) variability in the greenish blue and yellowish green during OUTPACE was influenced by other variables associated with Trichodesmium presence, such as backscattering coefficient, phycoerythrin fluorescence and/or zeaxanthin absorption, suggesting that Trichodesmium detection should involve examination of nLw in this spectral domain.

Rousset, G, De Boissieu F, Menkes CE, Lefevre J, Frouin R, Rodier M, Ridoux V, Laran S, Bonnet S, Dupouy C.  2018.  Remote sensing of Trichodesmium spp. mats in the western tropical South Pacific. Biogeosciences. 15:5203-5219.   10.5194/bg-15-5203-2018   AbstractWebsite

Trichodesmium is the major nitrogen-fixing species in the western tropical South Pacific (WTSP) region, a hot spot of diazotrophy. Due to the paucity of in situ observations, remote-sensing methods for detecting Trichodesmium presence on a large scale have been investigated to assess the regional-to-global impact of this organism on primary production and carbon cycling. A number of algorithms have been developed to identify Trichodesmium surface blooms from space, but determining with confidence their accuracy has been difficult, chiefly because of the scarcity of sea-truth information at the time of satellite overpass. Here, we use a series of new cruises as well as airborne surveys over the WTSP to evaluate their ability to detect Trichodesmium surface blooms in the satellite imagery. The evaluation, performed on MODIS data at 250 m and 1 km resolution acquired over the region, shows limitations due to spatial resolution, clouds, and atmospheric correction. A new satellite-based algorithm is designed to alleviate some of these limitations, by exploiting optimally spectral features in the atmospherically corrected reflectance at 531, 645, 678, 748, and 869 nm. This algorithm outperforms former ones near clouds, limiting false positive detection and allowing regional-scale automation. Compared with observations, 80 % of the detected mats are within a 2 km range, demonstrating the good statistical skill of the new algorithm. Application to MODIS imagery acquired during the February-March 2015 OUTPACE campaign reveals the presence of surface blooms northwest and east of New Caledonia and near 20 degrees S-172 degrees W in qualitative agreement with measured nitrogen fixation rates. Improving Trichodesmium detection requires measuring ocean color at higher spectral and spatial (< 250 m) resolution than MODIS, taking into account environment properties (e.g., wind, sea surface temperature), fluorescence, and spatial structure of filaments, and a better understanding of Trichodesmium dynamics, including aggregation processes to generate surface mats. Such sub-mesoscale aggregation processes for Trichodesmium are yet to be understood.

Favareto, LR, Rudorff N, Kampel M, Frouin R, Rottgers R, Doxaran D, Murakami H, Dupouy C.  2018.  Bio-optical characterization and ocean colour inversion in the eastern lagoon of New Caledonia, South Tropical Pacific. Remote Sensing. 10   10.3390/rs10071043   AbstractWebsite

The Eastern Lagoon of New Caledonia (ELNC) is a semi-enclosed system surrounded by an extensive coral reef barrier. The system has been suffering impacts from climate variability and anthropogenic activities, including mining exploitation. Satellite monitoring is thus an essential tool to detect such changes. The present study aimed to assess the bio-optical variability of the ELNC and examine the applicability of ocean colour algorithms, using in situ bio-optical and radiometric data, collected during the March 2014 CALIOPE 2 cruise. The chlorophyll a concentration (Chla) varied from 0.13-0.72 mg.m(-3), and the coastal stations were spectrally dominated by non-algal particles (NAP) and coloured dissolved organic matter (CDOM) (>80% of the total non-water absorption at 443 nm), due to the contribution of allochthonous sources. The phytoplankton specific absorption was generally lower (mean, 0.049 m(2).mg Chla(-1)) than typical values observed for the corresponding Chla range, as well as the spectral slopes of the absorption of CDOM plus NAP (a(dg)) (mean, 0.016 nm(-1)) and of the particle backscattering coefficient (b(bp)) (mean, 0.07 nm(-1)). The remote sensing reflectance obtained using two in-water approaches and modelled from Inherent Optical Properties (IOPs) showed less than 20% relative percent differences (RPD). Chla estimates were highly biased for the empirical (OC4 and OC3) and semi-analytical (GSM, QAA, GIOP, LMI) algorithms, especially at the coastal stations. Excluding these stations, the GSM01 yielded the best retrievals with 35-40% RPD. a(dg)(443) was well retrieved by all algorithms with similar to 18% RPD, and b(bp)(443) with similar to 40% RPD. Turbidity algorithms also performed reasonably well (30% RPD), showing the capacity and usefulness of the derived products to monitor the water quality of the ELNC, provided accurate atmospheric correction of the satellite data. Regionally tuned algorithms may potentially improve the Chla retrievals, but better parameterization schemes that consider the spatiotemporal variability of the specific IOPs are still needed.

Muller-Karger, FE, Hestir E, Ade C, Turpie K, Roberts DA, Siegel D, Miller RJ, Humm D, Izenberg N, Keller M, Morgan F, Frouin R, Dekker AG, Gardner R, Goodman J, Schaeffer B, Franz BA, Pahlevan N, Mannino AG, Concha JA, Ackleson SG, Cavanaugh KC, Romanou A, Tzortziou M, Boss ES, Pavlick R, Freeman A, Rousseaux CS, Dunne J, Long MC, Klein E, McKinley GA, Goes J, Letelier R, Kavanaugh M, Roffer M, Bracher A, Arrigo KR, Dierssen H, Zhang XD, Davis FW, Best B, Guralnick R, Moisan J, Sosik HM, Kudela R, Mouw CB, Barnard AH, Palacios S, Roesler C, Drakou EG, Appeltans W, Jetz W.  2018.  Satellite sensor requirements for monitoring essential biodiversity variables of coastal ecosystems. Ecological Applications. 28:749-760.   10.1002/eap.1682   AbstractWebsite

The biodiversity and high productivity of coastal terrestrial and aquatic habitats are the foundation for important benefits to human societies around the world. These globally distributed habitats need frequent and broad systematic assessments, but field surveys only cover a small fraction of these areas. Satellite-based sensors can repeatedly record the visible and near-infrared reflectance spectra that contain the absorption, scattering, and fluorescence signatures of functional phytoplankton groups, colored dissolved matter, and particulate matter near the surface ocean, and of biologically structured habitats (floating and emergent vegetation, benthic habitats like coral, seagrass, and algae). These measures can be incorporated into Essential Biodiversity Variables (EBVs), including the distribution, abundance, and traits of groups of species populations, and used to evaluate habitat fragmentation. However, current and planned satellites are not designed to observe the EBVs that change rapidly with extreme tides, salinity, temperatures, storms, pollution, or physical habitat destruction over scales relevant to human activity. Making these observations requires a new generation of satellite sensors able to sample with these combined characteristics: (1) spatial resolution on the order of 30 to 100-m pixels or smaller; (2) spectral resolution on the order of 5nm in the visible and 10nm in the short-wave infrared spectrum (or at least two or more bands at 1,030, 1,240, 1,630, 2,125, and/or 2,260nm) for atmospheric correction and aquatic and vegetation assessments; (3) radiometric quality with signal to noise ratios (SNR) above 800 (relative to signal levels typical of the open ocean), 14-bit digitization, absolute radiometric calibration <2%, relative calibration of 0.2%, polarization sensitivity <1%, high radiometric stability and linearity, and operations designed to minimize sunglint; and (4) temporal resolution of hours to days. We refer to these combined specifications as H4 imaging. Enabling H4 imaging is vital for the conservation and management of global biodiversity and ecosystem services, including food provisioning and water security. An agile satellite in a 3-d repeat low-Earth orbit could sample 30-km swath images of several hundred coastal habitats daily. Nine H4 satellites would provide weekly coverage of global coastal zones. Such satellite constellations are now feasible and are used in various applications.

Ruiz, MG, Lutz V, Frouin R.  2017.  Spectral absorption by marine chromophoric dissolved organic matter: Laboratory determination and piecewise regression modeling. Marine Chemistry. 194:10-21.   10.1016/j.marchem.2017.03.012   AbstractWebsite

Chromophoric dissolved organic matter (CDOM) is an important light-absorbing component of seawater. Yet spectrophotometric determinations of CDOM absorption from existing laboratory methods differ substantially. Since CDOM absorption in the visible usually remains below the detection limit of traditional spectrophotometers, its spectral shape has been modeled from the ultra-violet, by applying a single exponential model (SEM) from which a unique parameter, the spectral slope S, is derived. The usefulness of SEM and S is controversial, due to the lack of agreement on the fitting procedures and the poor ability of the SEM to fit equally well all CDOM absorption spectra. In view of this, empirical factors affecting the measurement of CDOM absorption coefficient by spectrophotometry were tested. No differences in CDOM spectra obtained by filtration through 0.2 mu m membrane or 0.7 mu m GFF filters were found for either high (Case II) or low (Case I) CDOM content situations. Two spectral shape groups were distinguished after applying a multivariate approach to 145 spectra from the.South Atlantic, Strait of Magallanes, and South Pacific. The two groups were associated mainly with coastal and oceanic waters. A segmented regression model (SRM) with two free breakpoints better represented the CDOM absorption spectra than a SEM. The SRM fitted both CDOM spectral shape groups with accuracy. This concatenated exponential model is useful for understanding CDOM dynamics and developing improved satellite ocean-color algorithms.

Zhai, PW, Knobelspiesse K, Ibrahim A, Franz BA, Hu YX, Gao M, Frouin R.  2017.  Water-leaving contribution to polarized radiation field over ocean. Optics Express. 25:A689-A708.   10.1364/oe.25.00a689   AbstractWebsite

The top-of-atmosphere (TOA) radiation field from a coupled atmosphere-ocean system (CAOS) includes contributions from the atmosphere, surface, and water body. Atmospheric correction of ocean color imagery is to retrieve water-leaving radiance from the TOA measurement, from which ocean bio-optical properties can be obtained. Knowledge of the absolute and relative magnitudes of water-leaving signal in the TOA radiation field is important for designing new atmospheric correction algorithms and developing retrieval algorithms for new ocean biogeochemical parameters. In this paper we present a systematic sensitivity study of water-leaving contribution to the TOA radiation field, from 340 nm to 865 nm, with polarization included. Ocean water inherent optical properties are derived from bio-optical models for two kinds of waters, one dominated by phytoplankton (PDW) and the other by non-algae particles (NDW). In addition to elastic scattering, Raman scattering and fluorescence from dissolved organic matter in ocean waters are included. Our sensitivity study shows that the polarized reflectance is minimized for both CAOS and ocean signals in the backscattering half plane, which leads to numerical instability when calculating water leaving relative contribution, the ratio between polarized water leaving and CAOS signals. If the backscattering plane is excluded, the water-leaving polarized signal contributes less than 9% to the TOA polarized reflectance for PDW in the whole spectra. For NDW, the polarized water leaving contribution can be as much as 20% in the wavelength range from 470 to 670 nm. For wavelengths shorter than 452 nm or longer than 865 nm, the water leaving contribution to the TOA polarized reflectance is in general smaller than 5% for NDW. For the TOA total reflectance, the water-leaving contribution has maximum values ranging from 7% to 16% at variable wavelengths from 400 nm to 550 nm from PDW. The water leaving contribution to the TOA total reflectance can be as large as 35% for NDW, which is in general peaked at 550 nm. Both the total and polarized reflectances from water-leaving contributions approach zero in the ultraviolet and near infrared bands. These facts can be used as constraints or guidelines when estimating the water leaving contribution to the TOA reflectance for new atmospheric correction algorithms for ocean color imagery. (C) 2017 Optical Society of America

Lee, YJ, Matrai PA, Friedrichs MAM, Saba VS, Aumont O, Babin M, Buitenhuis ET, Chevallier M, de Mora L, Dessert M, Dunne JP, Ellingsen IH, Feldman D, Frouin R, Gehlen M, Gorgues T, Ilyina T, Jin MB, John JG, Lawrence J, Manizza M, Menkes CE, Perruche C, Le Fouest V, Popova EE, Romanou A, Samuelsen A, Schwinger J, Seferian R, Stock CA, Tjiputra J, Tremblay B, Ueyoshi K, Vichi M, Yool A, Zhang JL.  2016.  Net primary productivity estimates and environmental variables in the Arctic Ocean: An assessment of coupled physical-biogeochemical models. Journal of Geophysical Research-Oceans. 121:8635-8669.   10.1002/2016jc011993   AbstractWebsite

The relative skill of 21 regional and global biogeochemical models was assessed in terms of how well the models reproduced observed net primary productivity (NPP) and environmental variables such as nitrate concentration (NO3), mixed layer depth (MLD), euphotic layer depth (Z(eu)), and sea ice concentration, by comparing results against a newly updated, quality-controlled in situ NPP database for the Arctic Ocean (1959-2011). The models broadly captured the spatial features of integrated NPP (iNPP) on a pan-Arctic scale. Most models underestimated iNPP by varying degrees in spite of overestimating surface NO3, MLD, and Z(eu) throughout the regions. Among the models, iNPP exhibited little difference over sea ice condition (ice-free versus ice-influenced) and bottom depth (shelf versus deep ocean). The models performed relatively well for the most recent decade and toward the end of Arctic summer. In the Barents and Greenland Seas, regional model skill of surface NO3 was best associated with how well MLD was reproduced. Regionally, iNPP was relatively well simulated in the Beaufort Sea and the central Arctic Basin, where in situ NPP is low and nutrients are mostly depleted. Models performed less well at simulating iNPP in the Greenland and Chukchi Seas, despite the higher model skill in MLD and sea ice concentration, respectively. iNPP model skill was constrained by different factors in different Arctic Ocean regions. Our study suggests that better parameterization of biological and ecological microbial rates (phytoplankton growth and zooplankton grazing) are needed for improved Arctic Ocean biogeochemical modeling.

Laliberte, J, Belanger S, Frouin R.  2016.  Evaluation of satellite-based algorithms to estimate photosynthetically available radiation (PAR) reaching the ocean surface at high northern latitudes. Remote Sensing of Environment. 184:199-211.   10.1016/j.rse.2016.06.014   AbstractWebsite

Two satellite-based methods to estimate daily averaged photosynthetically available radiation (PAR) at the ocean surface are evaluated at high northern latitudes. The first method employs a precomputed Look-Up-Table (LUT) generated from radiative transfer simulations. The LUT associates spectral irradiance reaching the surface to a given set of input parameters, namely solar zenith angle, cloud optical thickness, cloud fraction, ozone concentration, and surface albedo. The second method, as implemented by NASA's Ocean Biology Processing Group (OBPG) in the standard Ocean Color data processing chain, expresses the energy budget of the atmosphere-surface-ocean system via a simple radiative transfer model. The performance of these methods is evaluated using an extensive in situ PAR dataset collected in the Arctic Ocean between 1998 and 2014, with daily values ranging from 0.08 to 61.07 Em(-2) d(-1). A methodology is developed to compare in situ measurements and satellite products of different spatial and temporal resolution. Agreement is generally good between satellite-derived estimates and ship-based data and between methods. Specifically, both methods yield a small positive bias of 6% and 2% and a relative uncertainty larger than that observed at low latitude, with a root mean squared error (RMSE) of 33% and 20% for the LUT and OPBG methods, respectively. This is attributed to the peculiar environmental conditions encountered in the Arctic, namely low solar elevation, changing surface albedo due to sea ice, and persistent cloudiness. The RMSE difference among methods is due to the high temporal resolution (3 h) of the International Satellite Cloud Climatology Project (ISCCP) LUT input not fully compensating for its low spatial resolution (280 km grid cells). The LUT method has the major advantage of providing PAR estimates in all conditions, including ice-covered regions, while the OBPG method is currently limited to open waters and a solar zenith angle lower than 83 degrees. Consequently, the OBPG method may not account for as much as 38% of PAR reaching the Arctic ocean surface annually. Both methods have the potential to provide useful PAR estimates just below the ice, by including information about ice transmittance. (C) 2016 Elsevier Inc. All rights reserved.

Lefevre, J, Menkes C, Bani P, Marchesiello P, Curci G, Grell GA, Frouin R.  2016.  Distribution of sulfur aerosol precursors in the SPCZ released by continuous volcanic degassing at Ambrym, Vanuatu. Journal of Volcanology and Geothermal Research. 322:76-104.   10.1016/j.jvolgeores.2015.07.018   AbstractWebsite

The Melanesian Volcanic Arc (MVA) emits about 12 kT d(-1) of sulfur dioxide (SO2) to the atmosphere from continuous passive (non-explosive) volcanic degassing, which contributes 20% of the global SO2 emission from volcanoes. Here we assess, from up-to-date and long-term observations, the SO2 emission of the Ambrym volcano, one of the dominant volcanoes in the MVA, and we investigate its role as sulfate precursor on the regional distribution of aerosols, using both satellite observations and model results at 1 x 1 spatial resolution from WRF-Chem/GOCART. Without considering aerosol forcing on clouds, our model parameterizations for convection, vertical mixing and cloud properties provide a reliable chemical weather representation, making possible a cross-examination of model solution and observations. This preliminary work enables the identification of biases and limitations affecting both the model (missing sources) and satellite sensors and algorithms (for aerosol detection and classification) and leads to the implementation of improved transport and aerosol processes in the modeling system. On the one hand, the model confirms a 50% underestimation of SO2 emissions due to satellite swath sampling of the Ozone Monitoring Instrument (OMI), consistent with field studies. The OMI irregular sampling also produces a level of noise that impairs its monitoring capacity during short-term volcanic events. On the other hand, the model reveals a large sensitivity on aerosol composition and Aerosol Optical Depth (AOD) due to choices of both the source function in WRF-Chem and size parameters for sea-salt in FIexAOD, the post-processor used to compute offline the simulated AOD. We then proceed to diagnosing the role of SO2 volcanic emission in the regional aerosol composition. The model shows that both dynamics and cloud properties associated with the South Pacific Convergence Zone (SPCZ) have a large influence on the oxidation of SO2 and on the transport pathways of volcanic species across the South Pacific atmosphere. For example, in the tropical cloudy air, the sulfate production in the aqueous phase is very efficient, resulting in the formation of a large cloud of highly scattering sulfate aerosols advected horizontally to Eastern Indonesia, in agreement with the AOD feature captured by MODIS/Aqua, but missed in CALIOP/CALIPSO (lidar) products. Model sensitivity experiments indicate that aerosol re-suspension due to evaporating droplets is a significant pathway for the supply of volcanic sulfur species in the remote marine boundary layer. By strongly modulating the irreversible loss due to wet scavenging, this aerosol process has a similar influence on the sulfur burden as natural emission from volcanoes or biogenic sources like dimethyl sulfate (DMS). The results emphasize the importance of MVA passive degassing and SPCZ dynamics on the aerosol background, and raise questions about potential impacts on the local climate and marine ecosystems. (C) 2015 Elsevier B.V. All rights reserved.

Valente, A, Sathyendranath S, Brotas V, Groom S, Grant M, Taberner M, Antoine D, Arnone R, Balch WM, Barker K, Barlow R, Belanger S, Berthon JF, Besiktepe S, Brando V, Canuti E, Chavez F, Claustre H, Crout R, Frouin R, Garcia-Soto C, Gibb S, Gould R, Hooker S, Kahru M, Klein H, Kratzer S, Loisel H, McKee D, Mitchell BG, Moisan T, Muller-Karger F, O'Dowd L, Ondrusek M, Poulton AJ, Repecaud M, Smyth T, Sosik HM, Twardowski M, Voss K, Werdell J, Wernand M, Zibordi G.  2016.  A compilation of global bio-optical in situ data for ocean-colour satellite applications. Earth System Science Data. 8:235-252.   10.5194/essd-8-235-2016   AbstractWebsite

A compiled set of in situ data is important to evaluate the quality of ocean-colour satellite-data records. Here we describe the data compiled for the validation of the ocean-colour products from the ESA Ocean Colour Climate Change Initiative (OC-CCI). The data were acquired from several sources (MOBY, BOUSSOLE, AERONET-OC, SeaBASS, NOMAD, MERMAID, AMT, ICES, HOT, GeP&CO), span between 1997 and 2012, and have a global distribution. Observations of the following variables were compiled: spectral remote-sensing reflectances, concentrations of chlorophyll a, spectral inherent optical properties and spectral diffuse attenuation coefficients. The data were from multi-project archives acquired via the open internet services or from individual projects, acquired directly from data providers. Methodologies were implemented for homogenisation, quality control and merging of all data. No changes were made to the original data, other than averaging of observations that were close in time and space, elimination of some points after quality control and conversion to a standard format. The final result is a merged table designed for validation of satellite-derived ocean-colour products and available in text format. Metadata of each in situ measurement (original source, cruise or experiment, principal investigator) were preserved throughout the work and made available in the final table. Using all the data in a validation exercise increases the number of matchups and enhances the representativeness of different marine regimes. By making available the metadata, it is also possible to analyse each set of data separately. The compiled data are available at doi: 10.1594/PANGAEA.854832 (Valente et al., 2015).

Lutz, V, Frouin R, Negri R, Silva R, Pompeu M, Rudorff N, Cabral A, Dogliotti A, Martinez G.  2016.  Bio-optical characteristics along the Straits of Magallanes. Continental Shelf Research. 119:56-67.   10.1016/j.csr.2016.03.008   AbstractWebsite

The Straits of Magallanes at the tip of South America connects the Atlantic and Pacific Oceans. The variability in the absorption characteristics by phytoplankton (a(ph)(440)), non-pigmented particles, NPP (a(NPP)(440)), and chromophoric dissolved organic matter, CDOM (a(y)(440)), measured along the Straits in late summer 2011 (RN Melville MV1102 cruise), was analyzed. Satellite-derived monthly PAR data showed that at the time of the cruise the western sector was exposed to a low-light environment (similar to 16 mol quanta m(-2)d(-1)) while the eastern sector received higher irradiance (similar to 28 mol quanta m(-2)d(-1)). In the Patagonian Shelf total absorption was dominated by phytoplankton (up to 76%; aph (440)=0.265 m(-1)), while in the Atlantic Sector of the Straits, the major contributor was NPP (up to 42%; a(NPP)(440)=0.138 m(-1)), and in the Pacific Sector of the Straits CDOM contributed up to 80% of the total absorption (a(y)(440)=0.232 m(-1)). These changes could be related in part to the input of fresh water from glacier melting and rain in the Pacific Sector (a(y)(440) vs salinity r(s)=-0.98). The carbon biomass (C) was composed in its majority by pico-phytoplanlcton and secondly by nano-phytoplankton, with exception of the Atlantic Sector where the micro-phytoplankton dominated. Carbon to chlorophyll-a ratios (C:Chla) were very low throughout the Straits (average of similar to 6) because of photoacclimation to the extremely low light Complementary pigments data obtained in spring 2003 by the BEAGLE expedition indicated the predominance of diatoms all along the Straits, but the bio-optical trend resembled the one found in late summer 2011, i.e., NPP dominated the absorption in the well mixed Atlantic Sector, phytoplankton in the Middle Sector, and CDOM in the Pacific Sector. These results emphasize that underwater light is the major factor affecting phytoplankton growth and physiology, and that prevalent physical and geochemical conditions play an important role regulating the bio-optical properties in this heterogeneous area. These effects should be considered to adjust parameters (such as C:Chla) when running biogeochemical models for this region. (C) 2016 Elsevier Ltd. All rights reserved.

Wattelez, G, Dupouy C, Mangeas M, Lefevre J, Touraivane, Frouin R.  2016.  A statistical algorithm for estimating chlorophyll concentration in the New Caledonian lagoon. Remote Sensing. 8   10.3390/rs8010045   AbstractWebsite

Spatial and temporal dynamics of phytoplankton biomass and water turbidity can provide crucial information about the function, health and vulnerability of lagoon ecosystems (coral reefs, sea grasses, etc.). A statistical algorithm is proposed to estimate chlorophyll-a concentration ([chl-a]) in optically complex waters of the New Caledonian lagoon from MODIS-derived remote-sensing reflectance (R-rs). The algorithm is developed via supervised learning on match-ups gathered from 2002 to 2010. The best performance is obtained by combining two models, selected according to the ratio of R-rs in spectral bands centered on 488 and 555 nm: a log-linear model for low [chl-a] (AFLC) and a support vector machine (SVM) model or a classic model (OC3) for high [chl-a]. The log-linear model is developed based on SVM regression analysis. This approach outperforms the classical OC3 approach, especially in shallow waters, with a root mean squared error 30% lower. The proposed algorithm enables more accurate assessments of [chl-a] and its variability in this typical oligo- to meso-trophic tropical lagoon, from shallow coastal waters and nearby reefs to deeper waters and in the open ocean.

Frouin, R, Pelletier B.  2015.  Bayesian methodology for inverting satellite ocean-color data. Remote Sensing of Environment. 159:332-360.   10.1016/j.rse.2014.12.001   AbstractWebsite

The inverse ocean color problem, i.e., the retrieval of marine reflectance from top-of-atmosphere (TOA) reflectance, is examined in a Bayesian context. The solution is expressed as a probability distribution that measures the likelihood of encountering specific values of the marine reflectance given the observed TOA reflectance. This conditional distribution, the posterior distribution, allows the construction of reliable multi-dimensional confidence domains of the retrieved marine reflectance. The expectation and covariance of the posterior distribution are computed, which gives for each pixel an estimate of the marine reflectance and a measure of its uncertainty. Situations for which forward model and observation are incompatible are also identified. Prior distributions of the forward model parameters that are suitable for use at the global scale, as well as a noise model, are determined. Partition-based models are defined and implemented for SeaWiFS, to approximate numerically the expectation and covariance. The ill-posed nature of the inverse problem is illustrated, indicating that a large set of ocean and atmospheric states, or pre-images, may correspond to very close values of the satellite signal. Theoretical performance is good globally, i.e., on average over all the geometric and geophysical situations considered, with negligible biases and standard deviation decreasing from 0.004 at 412 nm to 0.001 at 670 nm. Errors are smaller for geometries that avoid Sun glint and minimize air mass and aerosol influence, and for small aerosol optical thickness and maritime aerosols. The estimated uncertainty is consistent with the inversion error. The theoretical concepts and inverse models are applied to actual SeaWiFS imagery, and comparisons are made with estimates from the SeaDAS standard atmospheric correction algorithm and in situ measurements. The Bayesian and SeaDAS marine reflectance fields exhibit resemblance in patterns of variability, but the Bayesian imagery is less noisy and characterized by different spatial de-correlation scales. Experimental errors obtained from match-up data are similar to the theoretical errors determined from simulated data. Regionalization of the inverse models is a natural development to improve retrieval accuracy, for example by including explicit knowledge of the space and time variability of atmospheric variables. (C) 2014 Elsevier Inc. All rights reserved.

Belanger, S, Frouin R, Wang M, Goyens C, Stamnes K.  2015.  From surface to top-of-atmosphere. Ocean Colour Remote Sensing in Polar Seas. 16( Babin M, Arrigo K, Belanger S, Forget MH, Eds.).:27-59. Abstract
Zoffoli, ML, Frouin R, Kampel M.  2014.  Water column correction for coral reef studies by remote sensing. Sensors. 14:16881-16931.   10.3390/s140916881   AbstractWebsite

Human activity and natural climate trends constitute a major threat to coral reefs worldwide. Models predict a significant reduction in reef spatial extension together with a decline in biodiversity in the relatively near future. In this context, monitoring programs to detect changes in reef ecosystems are essential. In recent years, coral reef mapping using remote sensing data has benefited from instruments with better resolution and computational advances in storage and processing capabilities. However, the water column represents an additional complexity when extracting information from submerged substrates by remote sensing that demands a correction of its effect. In this article, the basic concepts of bottom substrate remote sensing and water column interference are presented. A compendium of methodologies developed to reduce water column effects in coral ecosystems studied by remote sensing that include their salient features, advantages and drawbacks is provided. Finally, algorithms to retrieve the bottom reflectance are applied to simulated data and actual remote sensing imagery and their performance is compared. The available methods are not able to completely eliminate the water column effect, but they can minimize its influence. Choosing the best method depends on the marine environment, available input data and desired outcome or scientific application.

Rudorff, ND, Frouin R, Kampel M, Goyens C, Meriaux X, Schieber B, Mitchell BG.  2014.  Ocean-color radiometry across the Southern Atlantic and Southeastern Pacific: Accuracy and remote sensing implications. Remote Sensing of Environment. 149:13-32.   10.1016/j.rse.2014.03.029   AbstractWebsite

Ocean color radiometry (OCR) provides valuable data for biogeochemical oceanography. In situ OCR measurements are used in the development and validation of bio-optical models and vicarious calibration of satellite ocean-color sensors. It is thus crucial to obtain accurate in situ OCR measurements, which is a challenge, especially in regions subjected to adverse environmental conditions and where waters are optically complex. In the present work, the accuracy of in situ OCR is analyzed with data acquired in a wide range of bio-geographic provinces across the Southern Atlantic and Southeastern Pacific during the R/V Melville MV1102 cruise. Varied techniques employed to measure above-water remote sensing reflectance (R-rs) are inter-compared. Measured R is also compared with modeled R-rs in a closure experiment. The impact of R-rs uncertainties on the retrieval of chlorophyll a concentration (Chla) and inherent optical properties (IOPs) is evaluated using operational bio-optical algorithms. The relative percent difference (RPD) between R-rs measured by the various techniques ranged from 12 to 26% for the ocean-color bands (412-555 nm), and 3-12% for the ratios (412-510/555). A merged R-rs obtained by averaging the different types of measurements, INS, is recommended to reduce uncertainties. The coefficient of variation of INS and reflectance ratios was 11-13% and 3-5%, respectively. The RPD between INS and modeled R-rs and the corresponding ratios ranged from 18 to 34% and from 13 to 17%, respectively. Complete closure could not be obtained due to both measurement and modeling uncertainties. The impact of INS uncertainties on retrieved Chla and IOPs was generally smaller than the intrinsic errors of the inversion schemes. The results suggest that even though more accurate ocean-color radiometry is desirable, improving retrieval algorithms is essential to properly describing and furthering our understanding of bio-optical variability in the world's oceans. (C) 2014 Elsevier Inc All rights reserved.

Bastidas-Salamanca, M, Gonzalez-Silvera A, Millan-Nunez R, Santamaria-del-Angel E, Frouin R.  2014.  Bio-optical characteristics of the northern Gulf of California during June 2008. International Journal of Oceanography. :384618(13pp.)-384618(13pp.).   10.1155/2014/384618   AbstractWebsite

Bio-optical variables in the Northern Gulf of California were analyzed using in situ and satellite data obtained during a cruise in June 2008. The study area was divided into three bio-optical regions: Upper Gulf (UG), Northern Gulf (NG), and Great Isles (GI). Each region was characterized according to phytoplankton pigment concentration, phytoplankton and nonpigmented material spectral absorption coefficients, and spectral reflectance. Observed patterns were an indication of the shift in bio-optical conditions from north to south going from turbid and eutrophic waters to mesotrophic ones. Although there was a good agreement between satellite and in situ Chl a (RMSE +or-33%), an overestimation of in situ Chl a was observed. This was partly explained by the presence of nonalgal particles, as well as the influence of desert and continental aerosols, which is generally overcorrected in the standard processing. The UG and NG could be considered as Case 2 waters, but they did exhibit different bio-optical characteristics. This implies that both biological and optical properties should be invoked to better understand water reflectance variability in the study region and its implications for the remote sensing of Chl a and biogeochemical processes.

Frouin, R.  2013.  In-flight Calibration of Satellite Ocean-Colour Sensors. IOCCG Report. ( Frouin R, Ed.).:126., Dartmouth, Canada: IOCCG Abstract
Frouin, R, McPherson J.  2012.  Estimating photosynthetically available radiation at the ocean surface from GOCI data. Ocean Science Journal. 47:313-321.   10.1007/s12601-012-0030-6   AbstractWebsite

A technique is presented to estimate photosynthetically available radiation (PAR) at the ocean surface from Geostationary Ocean Color Imager (GOCI) data. The sensor is adapted to the problem, since it measures at visible wavelengths and does not saturate over clouds, and the hourly data provides adequate temporal sampling to describe diurnal variability of clouds. Instantaneous surface PAR is computed as the difference between the solar irradiance incident at the top of the atmosphere (known) and the solar irradiance reflected back to space (derived from GOCI radiance), taking into account absorption and scattering by the clear atmosphere (modeled). Knowledge of pixel composition is not required. Apart from planetary albedo and sun zenith angle, the model parameters are fixed at their climatological values. The instantaneous PAR estimates at hourly intervals are integrated over time to provide daily values. The technique is applied to GOCI imagery acquired on 5 April 2011, and the GOCI daily PAR estimates are compared with those obtained from MODerate Resolution Imaging Spectrometer (MODIS) data. Agreement is good between the two types of estimates, with a coefficient of determination (r(2)) of 0.778, a bias of 0.23 Em(-2)d(-1) (0.5% with higher GOCI values), and a root-mean-squared difference of 5.00 Em(-2)d(-1) (11.2%). Differences in cloudy conditions are attributed to daily cloudiness changes not captured by the MODIS observations. The comparison statistics indicate that GOCI PAR estimates have acceptable accuracy for regional studies of aquatic photosynthesis.

Montes-Hugo, M, Sweeney C, Doney SC, Ducklow H, Frouin R, Martinson DG, Stammerjohn S, Schofield O.  2010.  Seasonal forcing of summer dissolved inorganic carbon and chlorophyll a on the western shelf of the Antarctic Peninsula. Journal of Geophysical Research-Oceans. 115   10.1029/2009jc005267   AbstractWebsite

The Southern Ocean is a climatically sensitive region that plays an important role in the regional and global modulation of atmospheric CO(2). Based on satellite-derived sea ice data, wind and cloudiness estimates from numerical models (National Centers for Environmental Prediction-National Center for Atmospheric Research reanalysis), and in situ measurements of surface (0-20 m depth) chlorophyll a (Chl(Surf)) and dissolved inorganic carbon (DIC(Surf)) concentration, we show sea ice concentration from June to November and spring wind patterns between 1979 and 2006 had a significant influence on midsummer (January) primary productivity and carbonate chemistry for the Western Shelf of the Antarctic Peninsula (WAP, 64 degrees-68 degrees S, 63.4 degrees-73.3 degrees W). In general, strong (>3.5 m s(-1)) and persistent (> 2 months) northerly winds during the previous spring were associated with relatively high (monthly mean > 2 mg m(-3)) Chl(Surf) and low (monthly mean <2 mmol kg(-1)) salinity-corrected DIC (DIC(Surf)*) during midsummer. The greater Chl(Surf) accumulation and DIC(Surf)* depletion was attributed to an earlier growing season characterized by decreased spring sea ice cover or nearshore accumulation of phytoplankton in association with sea ice. The impact of these wind-driven mechanisms on Chl(Surf) and DIC(Surf)* depended on the extent of sea ice area (SIA) during winter. Winter SIA affected phytoplankton blooms by changing the upper mixed layer depth (UMLD) during the subsequent spring and summer (December-January-February). Midsummer DIC(Surf)* was not related to DIC(Surf)* concentration during the previous summer, suggesting an annual replenishment of surface DIC during fall/winter and a relatively stable pool of deep (> 200 m depth) "winter-like" DIC on the WAP.