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We introduced a sediment-induced light attenuation algorithm into a biogeochemical model of the Coupled Ocean–Atmosphere–Wave–Sediment Transport (COAWST) modeling system. A fully coupled ocean–atmospheric–sediment–biogeochemical simulation was carried out to assess the impact of sediment-induced light attenuation on primary production in the northern Gulf of Mexico during the passage of Hurricane Gustav in 2008. When compared with model results without sediment-induced light attenuation, our new model showed a better agreement with satellite data on both the magnitude of nearshore chlorophyll concentration and the spatial distribution of offshore bloom. When Hurricane Gustav approached, resuspended sediment shifted the inner shelf ecosystem from a nutrient-limited one to a light-limited one. Only 1 week after Hurricane Gustav's landfall, accumulated nutrients and a favorable optical environment induced a posthurricane algal bloom in the top 20 m of the water column, while the productivity in the lower water column was still light-limited due to slow-settling sediment. Corresponding with the elevated offshore NO3 flux (38.71 mmol N m -1 s -1) and decreased chlorophyll flux (43.10 mg m -1 s -1), the outer shelf posthurricane bloom should have resulted from the cross-shelf nutrient supply instead of the lateral dispersed chlorophyll. Sensitivity tests indicated that sediment light attenuation efficiency affected primary production when sediment concentration was moderately high. Model uncertainties due to colored dissolved organic matter and parameterization of sediment-induced light attenuation are also discussed. [ABSTRACT FROM AUTHOR]

We introduce a sediment-induced light attenuation algorithm into the biogeochemical model of the Regional Ocean Modeling System (ROMS). A fully coupled ocean-atmospheric-sediment-biogeochemical simulation is carried out to assess the impact of sediment-induced light attenuation on primary production in the northern Gulf of Mexico during Hurricane Gustav in 2008. The new model shows a better agreement with satellite data on both the magnitude of nearshore chlorophyll concentration and the distribution of offshore bloom. When Gustav approaches, resuspended sediments shift the inner shelf ecosystem from a nutrient-limited one to light-limited. One week after Gustav's landfall, accumulated nutrient and favorable optical environment induces a post-hurricane algal bloom in the top 20 m of water column, while the productivity in the lower column is still light-limited due to unsettled sediment. Corresponding with the elevated offshore NO3 flux (38.71 mmol N/m/s) and decreased chlorophyll flux (43.10 mg/m/s), the post-hurricane bloom in the outer shelf is resulted from the cross-shelf nutrient supply instead of the lateral dispersed chlorophyll. Sensitivity tests indicate sediment light attenuation efficiency affects primary production when sediment concentration is moderately high. [ABSTRACT FROM AUTHOR]

Phytoplankton taxonomy, pigment composition and photo-physiological state were studied in Galveston Bay (GB), Texas (USA) following the extreme flooding associated with Hurricane Harvey (August 25-29, 2017) using field and satellite ocean color observations. Percentage of chlorophyll a (Chl a) in different phytoplankton groups were determined from a semi-analytical IOP (inherent optical property) inversion algorithm. The IOP inversion algorithm revealed the dominance of freshwater species (cyanobacteria and green algae) in the bay following the hurricane passage (September 29, 2017) under low salinity conditions associated with the discharge of floodwaters into GB; 2 months after the hurricane (October 29-30, 2017), under more seasonal salinity conditions, the phytoplankton community transitioned to an increase in small sized groups such as haptophyte and prochlorophyte. Sentinel-3A OLCI-derived Chl a obtained using a red/NIR band ratio algorithm for the turbid estuarine waters was highly correlated (R² > 0.90) to HPLC-derived Chl a concentrations. A Non-Negative Least Square (NNLS) inversion model was then applied to OLCI-derived Chl a maps of GB to obtain spatiotemporal distributions of phytoplankton diagnostic pigments; results appeared consistent with extracted phytoplankton taxonomic composition derived from the IOP inversion algorithm. OLCI-derived diagnostic pigment distributions also exhibited good agreement with HPLC measurements, with mean R² ranging from 0.39 for violaxanthin to 0.98 for Chl a. Environmental factors (e.g. floodwaters) combined with phytoplankton taxonomy also strongly modulated phytoplankton physiology in the bay as indicated by measurements of photosynthetic parameters with a Fluorescence Induction and Relaxation (FIRe) system. Phytoplankton in well-mixed waters (mid-bay area) exhibited maximum PSII photochemical efficiency (FV/FM) and low effective absorption cross section (δPSII), while the areas adjacent to the shelf (likely nutrient-limited) showed low FV/FM and elevated values. Overall, the approach using field and ocean color data combined with inversion models allowed, for the first time, an assessment of phytoplankton response to a large hurricane-related floodwater perturbation in a turbid estuarine environment based on its taxonomy, pigment composition and physiological state. [ABSTRACT FROM AUTHOR]

Abstract: The absorption coefficients of phytoplankton (aPHY(λ)), non-algal particles (NAP) (aNAP(λ)) and colored dissolved organic matter (CDOM) (aCDOM(λ)) were investigated and parameterized in the southeastern Bering Sea during July 2008. The absorption coefficients were well structured with respect to hydrographic and biogeochemical characteristics of the shelf. The highest values of aPHY(443) were observed offshore and the lowest values of aPHY(443) were found in the coastal domain, a low productivity region associated with limited macronutrients. Values of aDG(λ) (aCDOM(λ)+aNAP(λ)) revealed an east–west gradient pattern with higher values in the coastal domain, and lower values in the outer domain. Lower chlorophyll specific aPHY(λ) (a*PHY(λ)) observed relative to middle and lower latitude waters indicated a change in pigment composition and/or package effect, which was consistent with phytoplankton community structure. aCDOM(λ) was the dominant light absorbing coefficient at all wavelengths examined except at 676nm. Modeling of remote-sensing reflectance (Rrs(λ)) and the diffuse attenuation coefficient (Kd(λ)) from inherent optical properties revealed the strong influence of aCDOM(λ) on Rrs(λ) and Kd(λ). Good optical closure was achieved between modeled and radiometer measured Rrs(λ) and Kd(λ) with average percent difference of less than 25% and 19% respectively, except at red wavelengths. The aCDOM(λ) accounted for >50% of Kd(λ) which was vertically variable. Chlorophyll-a calculated by the NASA standard chlorophyll-a algorithm (OC4.v6) was overestimated due to higher aCDOM(λ) and underestimated due to lower a*PHY(λ) at low and high concentrations of chlorophyll-a, respectively. [Copyright &y& Elsevier]

Abstract: Chromophoric dissolved organic matter (CDOM) variability in Barataria Basin, Louisiana, USA,was examined by excitation emission matrix (EEM) fluorescence combined with parallel factor analysis (PARAFAC). CDOM optical properties of absorption and fluorescence at 355nm along an axial transect (36 stations) during March, April, and May 2008 showed an increasing trend from the marine end member to the upper basin with mean CDOM absorption of 11.06±5.01, 10.05±4.23, 11.67±6.03 (m− 1) and fluorescence 0.80±0.37, 0.78±0.39, 0.75±0.51 (RU), respectively. PARAFAC analysis identified two terrestrial humic-like (component 1 and 2), one non-humic like (component 3), and one soil derived humic acid like (component 4) components. The spatial variation of the components showed an increasing trend from station 1 (near the mouth of basin) to station 36 (end member of bay; upper basin). Deviations from this increasing trend were observed at a bayou channel with very high chlorophyll-a concentrations especially for component 3 in May 2008 that suggested autochthonous production of CDOM. The variability of components with salinity indicated conservative mixing along the middle part of the transect. Component 1 and 4 were found to be relatively constant, while components 2 and 3 revealed an inverse relationship for the sampling period. Total organic carbon showed increasing trend for each of the components. An increase in humification and a decrease in fluorescence indices along the transect indicated an increase in terrestrial derived organic matter and reduced microbial activity from lower to upper basin. The use of these indices along with PARAFAC results improved dissolved organic matter characterization in the Barataria Basin. [Copyright &y& Elsevier]

Spatial and temporal patterns of bio-optical properties were studied in the Northern Gulf of Mexico during cruises in April and October of 2000, a year during which the discharge volume from the Mississippi River was unusually low. Highly variable surface Chl a concentrations (0.1 to 17 mg m−3) and colored dissolved organic matter (CDOM) absorption (0.07 to 1.1 m−1 at 412 nm) were observed in the study region that generally decreased with increasing salinity waters, being highest nearshore and decreasing at offshore stations. The optical properties of absorption, scattering, and diffuse attenuation coefficients reflected these distributions with phytoplankton particles and CDOM contributing to most of the spatial, vertical, and seasonal variability. The diffuse attenuation coefficient Kd(λ) and spectral remote sensing reflectance Rrs(λ) were linear functions of absorption and backscattering coefficients a(λ) and bb(λ) through the downward average cosine μd and the ratio of variables f/Q at the SeaWiFS wavebands for waters with widely varying bio-optical conditions. Although various Rrs(λ) ratio combinations showed high correlation with surface Chl a concentrations and CDOM absorption at 412 nm, power law equations derived using the Rrs(490)/Rrs(555) and Rrs(510)/Rrs(555) ratios provided the best retrievals of Chl a concentrations and CDOM absorption from SeaWiFS reflectance data. [Copyright &y& Elsevier]

The active hydrodynamics and complex circulation patterns in the northern Gulf of Mexico (nGoM) provide a dynamic scenario to investigate mesoscale responses of the size structure of phytoplankton communities to environmental variability. In this study, a large in-situ dataset acquired in inland, estuarine and coastal waters of the nGoM and U.S. East Coast were utilized to achieve a regional parameterization of the red-NIR ratio-based chlorophyll a (Chl a) algorithm for the high-spatial and spectral resolution Sentinel 3-OLCI ocean color sensor. Using an adaptive scheme, the algorithm was used in combination with other standard Chl a algorithms such as the Neural Network (C2RCC) and OC4ME to optimally extract Chl a in water types ranging from turbid estuarine to clear oceanic waters in the nGoM. This adaptive methodology (Chl a_AD) showed better performance in estimating OLCI-Chl a (R2=0.84, N = 178) compared to any single algorithm in the estuarine-coastal-ocean waters of the nGoM. Next, OLCI-derived phytoplankton spectral absorption coefficients (OLCI-a phy) were obtained for comparison, using a regionally-tuned 3rd order function of OLCI-Chl a based on Multi-regression (MR), and an estuarine-to-ocean adaptive Quasi-Analytical Algorithm (QAA-AD). Finally, an Empirical Orthogonal Function (EOF) algorithm was applied to OLCI-a phy to retrieve phytoplankton size fractions (PSFs) for the river-dominated nGoM region. Results indicate relatively better performance of MR-EOF in estimating f micro (R2=0.87), f nano (R2=0.76) and f pico (R2=0.64) compared to QAA-AD-EOF. Chl a time-series (Oct 2016 – Jan 2020) obtained in the estuaries and shelf waters of the nGoM revealed seasonality (peak/lows in spring/fall) linked to river discharge, where hydrodynamics and wind driven variability due to storms further influenced the phytoplankton biomass spatiotemporal distribution. Microphytoplankton dominated in estuaries and the nGOM inner shelf waters, including the midshelf region during the spring peak river discharge period. PSF dynamics in the outer shelf is strongly influenced by Loop Current eddies where warm offshore waters contribute to the dominance of the picophytoplankton fraction. Floodwater discharge and strong winds due to Hurricane Barry (2019) transported estuarine microphytoplankton into the outer shelf and also increased nanophytoplankton fraction. Such fluctuations in phytoplankton size structure after hurricanes or storms can modify the pelagic food web dynamics in coastal systems. • An adaptive Chlorophyll a algorithm is developed for Sentinel 3A/B-OLCI • Phytoplankton size fraction algorithm based on empirical orthogonal function (EOF) • Spatiotemporal responses of micro-, nano- and pico-phytoplankton were assessed in the nGoM [ABSTRACT FROM AUTHOR]

The Bering Sea is characterized by unique bio-optical properties, which cause unsatisfactory performance of global ocean color algorithms for retrieval of chlorophyll-a (Chl-a). This study evaluates the normalized water-leaving radiance nL w ( λ ) and Chl-a in the eastern Bering Sea that are derived from the Moderate Resolution Imaging Spectroradiometer (MODIS) on the satellite Aqua by comparing them to in situ data. MODIS-Aqua ocean color products were derived using the NOAA Multi-Sensor Level-1 to Level-2 (MSL12) ocean color data processing system. The MODIS-derived nL w ( λ ) showed good agreement with in situ-measured nL w ( λ ). The mean ratios between them for wavelengths 412, 443, 488, and 551 nm ranged from 1.097 to 1.280, with reasonably accurate blue-green radiance ratios in nL w ( λ ) that were used as input for deriving Chl-a. However, compared to in situ data, existing global and regional Chl-a algorithms either overestimate or underestimate Chl-a in the eastern Bering Sea. Therefore, we propose a new algorithm for estimating Chl-a using a blended approach that was tested and applied to MODIS-Aqua images. The histogram distributions of MODIS-Aqua-derived and in situ-measured Chl-a data show that Chl-a data derived using the new algorithm agree reasonably well to in situ measurements. Annual, seasonal, and monthly composite nL w ( λ ) and Chl-a images are produced for the period of 2003 to 2013 in order to interpret the long-term spatial and temporal patterns of nL w ( λ ) and Chl-a. The nL w ( λ ) spectra show strong spectral dependence on seasonal variability with distinct spatial patterns. Although strong seasonal and interannual variability has been observed in Chl-a, there is no apparent trend of either increase or decrease in phytoplankton biomass associated with variability in the physical environment for the 11 years of the study period. [ABSTRACT FROM AUTHOR]

Spectral fluorescence measurements of phytoplankton chlorophyll a (Chl a ), phytoplankton phycobilipigments and variable fluorescence (Fv/Fm), are utilized with High Performance Liquid Chromatography (HPLC) estimates of phytoplankton pigments and microscopic cells counts to construct a comprehensive picture of summer-time phytoplankton communities and their photosynthetic competency in the eastern Bering Sea shelf. Although the Bering Sea was ice-free during our study, the exceptionally cold winter that preceded the summer of 2008 when our cruise took place, facilitated the formation of a “Cold Pool” (<2 °C) and its entrapment at depth in the northern middle shelf. The presence of a strong pycnocline over the entire middle and outer shelves restricted inorganic nutrient fluxes into the surface waters resulting in phytoplankton populations that were photo-physiologically stressed due to nutrient limitation. Elevated Chl a concentr a tions recorded in the Green Belt along the shelf edge of the Bering Sea, were due to Phaeocystis pouchetii and nano-sized cryptophytes. Although inorganic nutrients were not limiting in the Green Belt, Fv/Fm values were low in all probability due to iron limitation. Phytoplankton communities in the low biomass surface waters of the middle shelf were comprised of prasinophytes, haptophytes, cryptophytes and diatoms. In the northern part of the middle shelf, a sinking bloom made up of the centric diatoms Chaeotoceros socialis , Thalassiosira nordenskioeldii and Porosira glacialis was located above the Cold Pool. The high biomass associated with this senescent bloom and its accretion above the pycnocline, suggests that the Cold Pool acts as a barrier, preventing sinking phytoplankton from reaching the bottom where they can become available to benthic organisms. We further posit that if summer-time storms are not energetic enough and the Cold Pool is not eroded, its presence facilitates the transfer of the large spring phytoplankton bloom to the pelagic ecosystem. [ABSTRACT FROM AUTHOR]

Abstract: Cyanobacteria represent a major harmful algal group in fresh to brackish water environments. Lac des Allemands, a freshwater lake of 49km2 southwest of New Orleans, Louisiana on the upper end of the Barataria Estuary, provides a natural laboratory for remote characterization of cyanobacterial blooms because of their seasonal occurrence. The Oceansat-1 satellite Ocean Colour Monitor (OCM) provides measurements similar to SeaWiFS but with higher spatial resolution, and this work is the first attempt to use OCM measurements to quantify cyanobacterial pigments. The satellite signal was first vicariously calibrated using SeaWiFS as a reference, and then corrected to remove the atmospheric effects using a customized atmospheric correction procedure. Then, empirical inversion algorithms were developed to convert the OCM remote sensing reflectance (R rs ) at bands 4 and 5 (centered at 510.6 and 556.4nm, respectively) to concentrations of phycocyanin (PC), the primary cyanobacterial pigment. A holistic approach was used to minimize the influence of other optically active constituents on the PC algorithm. Similarly, empirical algorithms to estimate chlorophyll a (Chl a) concentrations were developed using OCM bands 5 and 6 (centered at 556.4 and 669nm, respectively). The best PC algorithm (R2 =0.7450, p<0.0001, n=72) yielded a root mean square error (RMSE) of 36.92μg/L with a relative RMSE of 10.27% (PC from 2.75 to 363.50μg/L, n=48). The best algorithm for Chl a (R2 =0.7510, p<0.0001, n=72) produced an RMSE of 31.19μg/L with a relative RMSE of 16.56% (Chl a from 9.46 to 212.76μg/L, n=48). While more field data are required to further validate the long-term performance of these algorithms, currently they represent the best protocol for establishing a long time-series of cyanobacterial blooms in the Lac des Allemands using OCM data. [Copyright &y& Elsevier]