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

Phytoplankton functional diversity plays a key role in structuring the ocean carbon cycle and can be estimated using measurements of phytoplankton functional type (PFT) groupings. Concentrations of 18 phytoplankton pigments were calculated using a linear matrix inversion algorithm, with an average r2 value of 0.70 for all pigments with p-values below the statistical threshold of 0.05. The inversion algorithm was then used with a chlorophyll-based absorption spectra model and Moderate Resolution Imaging Spectroradiometer (MODIS-Aqua) chlorophyll observations to calculate phytoplankton pigment concentrations in an area of the Atlantic Ocean off the United States east coast. Pigment distributions were analyzed to assess the distribution of PFTs. Five unique PFTs were found and delineated into three distinct offshore, transition, and open ocean groups. Group 1 (Diatoms) had highest abundance along the coast. Group 2 (prymnesiophytes, prokaryotes, and green algae) was a year-round stable offshore community that extended at reduced levels into the coast. Group 3 (dinoflagellates) dominated offshore between the Groups 1 and 2. Phytoplankton communities were delineated into coastal and offshore populations, with Group 2 having a dampened seasonal cycle, relative to the coastal populations. Shannon Diversity Indices (H) for the PFTs showed both spatial and temporal variability and had a clear non-linear relationship with chlorophyll. Diversity levels varied seasonally with changes in chlorophyll a levels. Peak PFT H was observed on the shelf where frontal features dominate, with diversity levels declining nearshore and offshore. This region marks an ecotone for phytoplankton in the study domain, and is associated with the coastal-side boundary of dinoflagellate dominance. Highest levels of diversity were observed in the tidally well-mixed regions of the Gulf of Maine and along a band that ran along the shelf region of the study area that was narrowest in the summer periods and broadened during the winter. These peak diversity zones were associated with moderate levels (~0.8 mg m−3) of chlorophyll a. While the sign in the linear trends in chlorophyll between 2002 and 2016 varied depending on the region, the trends in the PFT H values were nearly all negative due to the non-linear relationship between chlorophyll levels and H.

Ocean color remote sensing has provided the scientific community with unprecedented global coverage of chlorophyll a, an indicator of phytoplankton biomass. Together, satellite-derived chlorophyll a and knowledge of Phytoplankton Functional Types (PFTs) will improve our limited understanding of marine ecosystem responses to physiochemical climate drivers involved in carbon cycle dynamics and linkages. Using cruise data from the Gulf of Maine and the Middle Atlantic Bight (N=269 pairs of HPLC and phytoplankton absorption samples), two modeling approaches were utilized to predict phytoplankton absorption and pigments. Algorithm I predicts the chlorophyll-specific absorption coefficient ( a p h ⁎ (m2 mg chl a−1)) using inputs of temperature, light, and chlorophyll a. Modeled r2 values (400–700 nm) ranged from 0.79 to 0.99 when compared to in situ observations with ∼25% lower r2 values in the UV region. Algorithm II-a utilizes matrix inversion analysis to predict a p h (m−1, 400–700 nm) and r2 values ranged from 0.89 to 0.99. The prediction of phytoplankton pigments with Algorithm II-b produced r2 values that ranged from 0.40 to 0.93. When used in combination, Algorithm I, and Algorithm II-a are able to use satellite products of SST, PAR, and chlorophyll a (Algorithm I) to predict pigment concentrations and ratios to describe the phytoplankton community. The results of this study demonstrate that the spatial variation in modeled pigment ratios differ significantly from the 10-year SeaWiFS average chlorophyll a data set. Contiguous observations of chlorophyll a and phytoplankton biodiversity will elucidate ecosystem responses with unprecedented complexity.

Recently there have been newly launched ocean color satellites which target the coastlines at unprecedented scales. Science education curricula can benefit from the provision of small low-cost spectroradiometers and curriculum supplemental materials that can be incorporated in a “hands on” teaching approach to explain and demonstrate remote sensing reflectance principles. A lesson in which a progressive set of spectral measurements of familiar and unfamiliar objects and natural waters acquired by students using a small fiberoptic probe and spectroradiometer is presented. This lesson has a dual purpose. The first is to serve as a teaching supplement to high school science curricula while paralleling the National Science Education Standards (NSES) for NASA ocean color products, as well as other satellite ocean products such as GLI and MERIS. The second is to focus on the scientific goals of the graduate-school bound undergraduate student by providing a fundamental understanding of the principles of passive ocean color remote sensing that will perhaps nurture the interest of some students toward research involving utilization of NASA’s Earth science data products. We intend to have these spectroradiometers readily available for use by teachers in the Earth sciences through a publicly available technology library.

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).

Phaeocystis antarctica Karsten exhibits optical changes in pigment packaging during acclimation to drastically different light levels. Here, the three-dimensional morphological rearrangements are shown for two light conditions mimicking limiting and saturating conditions for photosynthesis. Cultures of P. antarctica were grown semi-continuously under light-limiting conditions for growth (14 μmol quanta m−2 s−1) and a light-saturating condition (259 μmol quanta m−2 s−1) for growth. Increased numbers of thylakoids were observed under the low light treatment. In contrast, there were less amounts of thylakoid stacking in each chloroplast under the high light treatment. Electron microscopic tomographic reconstructions illustrate the complexity of the chloroplast organelle where the thylakoids ‘interact’ with the pyrenoid and the chloroplast membrane. Highly complex characteristics, such as bi- and tri-furcations in the thylakoid stacks, were continuous throughout the chloroplast. Other organelles, such as the Golgi apparatus and dense vesicles that may potentially affect cellular scattering and absorption were also observed in both high and low light. These three dimensional thylakoid arrangements have profound implications for cellular photophysiology. They represent a new view of algal chloroplast structure, and provide a starting point for more accurate optical modeling studies.

Mycosporine-like amino acids (MAAs), which occur in diverse taxonomic groups, exhibit in vivo absorption maxima between 310 nm and 360 nm and may play a photoprotective role against ultraviolet (UV) exposure. Using cultures of colonial Phaeocystis antarctica, we examined the relationship between MAA concentration, in vivo UV absorption, photoprotective (carotenoid) and photosynthetic pigments, and photosynthetically available radiation (PAR, 350–700 nm). UV absorption was high; chlorophyll-specific absorption, a * ph, at 330 nm ranged from 0.06 to 0.41 m2/mg chlorophyll a. Values of a * ph (330) were 4–13 times greater than a * ph (676). Mycosporine-glycine, shinorine, and mycosporine-glycine valine are responsible for the strong in vivo UV absorption. The sum of all MAAs increased with irradiance when normalized to chlorophyll a or carbon concentrations, whereas individual MAAs varied independently from each other. Mycosporine-glycine concentrations showed no statistically significant change over the range of light intensities, whereas mycosporine-glycine and shinorine concentrations increased at higher irradiances. The relative fluorescence yield for chlorophyll a was low in the UV region compared to the visible region, implying that absorbed UV radiation (

Primary production models and pigment algorithms for remote optical systems including satellites, moorings, or drifters depend on an improved understanding of the relationship between spectral light absorption, pigments, and photosynthesis for species of phytoplankton that are widespread and numerically abundant. Cultures of colonial Phaeocystis antarctica, a prymnesiophyte that can dominate the phytoplankton community in the Southern Ocean, were grown under blue light at seven different levels ranging from 14 to 542 mmol quanta m 22 s 21 at 48C under nutrient-replete conditions. Chlorophyll-specific absorption ( ) at 436 nm increased linearly from 0.03 to 0.11 m 2 a* ph mg chlorophyll a 21 with increasing light intensities. This variability is attributed to pigment packaging effects and pigmentation. The 2.5-fold range in the values of (676 nm) demonstrates significant pigment packaging effects a* ph due to the intracellular pigment content, single cell diameter within the colony, and thylakoid stacking. Quantum yield for growth (fm) varied 30-fold, ranging from 0.003 to 0.09 mol carbon fixed (mol quanta absorbed) 21 . Under low light conditions, the relatively high fm and high (l) may enable Phaeocystis to accumulate a seed population a* ph to initiate blooms at the beginning of spring when light levels are low, mixed layers are deep, and sea ice is still significant. These aspects of its photophysiology may contribute to the ecological success of Phaeocystis in polar regions.

The absorbance and fluorescence emission spectra for three species of Dinophysis, D. caudata Saville-Kent, D. fortii Pavillard, and D. acuminata Claparede et Lach- mann, were obtained through an in vivo microanalytical technique using a new type of transparent filter. The pig- ment signatures of these Dinophysis species were compared to those of Synechococcus Nageli, a cryptophyte, and two wild rhodophytes, as well as those of another dinoflagellate, a diatom, and a chlorophyte. Phycobilins are not consid- ered a native protein group for dinoflagellates, yet the ab- sorption and fluorescence properties of the three Dino- physis species were demonstrated to closely resemble phy- cobilins and chlorophylls of Rhodomonas Karsten (Cryp- tophyceae). Analyses of Dinophysis species using epifluorescence microscopy found no additional nucleus or nuclear remnant as would be contributed by an endosym- biont.

The seasonal development of the microbial food web in eastern McMurdo Sound, Antarctica, was investigated during and immediately after the 1990–1991 bloom of Phaeocystis sp. (Prymnesiophyceae: Prymnesiales). From 23 November to 7 December, which was before the appearance of macroscopic colonies of Phaeocystis, both phytoplankton and Protozoa were low in abundance. During the Phaeocystis bloom (~10 December to 7 January), phytoplankton biomass was high and was dominated by colonial and singlecelled Phaeocystis, but other phytoplankton taxa, including diatoms and photosynthetic dinoflagellates, co-occurred. Heterotrophic nanoplankton and protozoan microzooplankton increased dramatically in biomass during the bloom. Non-thecate heterotrophic dinoflagellates were the most abundant microzooplankters. There was no evidence for inhibition of the microbial food web by Phaeocystis. By the post-bloom period, macroscopic colonies were rare and phytoplankton biomass had declined markedly. Microzooplankton biomass continued to rise until the end of the sampling period (23 January). Microfaecal pellets (median size range, 10–30 μm) were abundant during the bloom and post-bloom periods. In the post-bloom period, the heterotrophic protistan assemblage became very diverse, with numerous trophic linkages within the microbial food web. The abundance and diversity of the heterotrophic protist assemblage suggests that there was little control of protists by metazoans and that the microbial food web, consisting of bacteria, algae and Protozoa, was poorly coupled to metazoan zooplankton.

Interest in phytoplankton diversity has increased in recent years due to its possible role in regulating climate by production and consumption of greenhouse gases. For example, gases can diffuse across the air-sea interface, many of which are synthesized and emitted by certain phytoplankton species or groups. It has been suggested that these variations play an important role in moderating our climate through backscattering of solar radiation and within cloud formation. Climate will ultimately control fundamental environmental conditions that regulate algal growth, including water temperature, nutrients, and light and thus can be expected to result in changes in the species composition, trophic structure and function of marine ecosystems. In the past several decades, the scientific community has witnessed changes in phytoplankton distribution. The marine phytoplankton community is diverse and includes on the order of tens of thousands of phytoplankton species (Jeffrey & Vesk 1997). On regional scales, phytoplankton biogeography is controlled by the physical, chemical, and meteorological characteristics that force ecosystem dynamics. There is a renewed impetus for new technologies to provide information about the phytoplankton community composition over global scales. Real-time, large-scale taxonomic information, if available, could open up new possibilities and approaches geared toward monitoring highly-dynamic oceanic processes and phenomena such as algal blooms (including harmful algal blooms), frontal structures, eddies, and episodic events (storms, river outflow, and wind mixing). Phytoplankton diversity information provides a valuable quantitative database for structuring sophisticated predictive models that includes taxonomic phytoplankton community information such as size spectra, probability distribution of taxa, and upper trophic level estimations including fisheries productivity (Cheson & Case 1986, De Angelis & Waterhouse 1987). There have been several reviews and books written on phytoplankton community structure, dynamics, and biogeochemistry as measured by ocean color (Mitchell 1994, Martin 2004, Mueller et al. 2004, Miller et al. 2005, Richardson and LeDrew 2006, Longhurst 2007, Robinson 2010).

Phytoplankton absorption spectra and High-Performance Liquid Chromatography (HPLC) pigment observations from the Eastern U.S. and global observations from NASA's SeaBASS archive are used in a linear inverse calculation to extract pigment-specific absorption spectra. Using these pigment-specific absorption spectra to reconstruct the phytoplankton absorption spectra results in high correlations at all visible wavelengths (r(sup 2) from 0.83 to 0.98), and linear regressions (slopes ranging from 0.8 to 1.1). Higher correlations (r(sup 2) from 0.75 to 1.00) are obtained in the visible portion of the spectra when the total phytoplankton absorption spectra are unpackaged by multiplying the entire spectra by a factor that sets the total absorption at 675 nm to that expected from absorption spectra reconstruction using measured pigment concentrations and laboratory-derived pigment-specific absorption spectra. The derived pigment-specific absorption spectra were further used with the total phytoplankton absorption spectra in a second linear inverse calculation to estimate the various phytoplankton HPLC pigments. A comparison between the estimated and measured pigment concentrations for the 18 pigment fields showed good correlations (r(sup 2) greater than 0.5) for 7 pigments and very good correlations (r(sup 2) greater than 0.7) for chlorophyll a and fucoxanthin. Higher correlations result when the analysis is carried out at more local geographic scales. The ability to estimate phytoplankton pigments using pigment-specific absorption spectra is critical for using hyperspectral inverse models to retrieve phytoplankton pigment concentrations and other Inherent Optical Properties (IOPs) from passive remote sensing observations.

Coastal regions within the Mid-Atlantic Bight (MAB) are significantly influenced by regional freshwater fluxes emanating from several large bay systems, most notably the Hudson-Raritan river systems, the Delaware and Chesapeake Bays. The outflows from these bays have high sediment loads and high levels of nutrients, particulate and dissolved organic matter (POM and DOM) associated with them which strongly influence the adjacent coastal margin ecosystems. Our research and observational effort includes the development and deployment of an observing system aimed at characterizing and monitoring the influence of the Chesapeake Bay on the adjacent coastal ocean margin ecosystem. A primary focus of this effort is to develop and apply state-of-the-art technologies and methodologies to support research, observation, monitoring, and management applications in the coastal ocean. We have developed a program that addresses coastal spatial and temporal scales. Our observing system consists of four components including 1) High Frequency (HF) Radar: 3 long-range HF Radar systems for mapping coastal ocean surface currents along Delmarva and 2 standard-range systems for the Chesapeake Bay mouth region, 2) a Coastal Ocean Bio-optical buoY (COBY), which will be deployed southeast of the Maryland-Virginia border at about 40m water depth, and will be instrumented with an above-water spectroradiometer (19 channel UV-VIS-NIR, 10nm BW, sea- and sky-viewing radiometers plus solar reference) on a robotic arm to measure water-leaving radiances, meteorological package, in-water mooring instruments with ADCP, CTD, nitrate sensor, ac-9, ac-s, and fluorometers for chlorophyll, colored dissolved organic matter (CDOM) and phycoerythrin detection; 3) seasonal cruises in the Mid-Atlantic Bight collecting optical, biological, and chemical data; and 4) the Ocean-Atmosphere Sensor Integration System (OASIS), which is comprised of a fleet (6-12) of solar-powered surface autonomous vehicles deployed offshore to measure surface ocean currents, meteorological measurements, surface ocean salinity and temperature, air-sea CO2 fluxes, water-leaving radiances, chlorophyll and CDOM fluorescence, HAB detection, etc. The HF radars, COBY and OASIS are being deployed this summer, with plans for a fully deployed observing system by the end of 2005 or early 2006.

The genus Phaeocystis plays an important role in polar ecosystems and biogeochemical cycles. It blooms frequently and when abundant often contributes more than 50% of the total phytoplankton biomass (1). When blooms of this organism do occur, they are often monospecific in nature or either codominate with very few other species. By nature of the size difference between the single cells (3–8 μm) and millimeter-sized colonies of its lifecycle, it may preferentially offer a food source to the microbial food web while in its single cell stage or alternatively to the traditional food web while in its colonial life stage. It may serve as a significant dissolved organic matter source through exudation or colonial lysis to the microbial food web.

Understanding the light-harvesting properties of algae and higher plants are a fundamental topic in photosynthesis research. Much oceanographic research has focused on characterizing the in vivo chlorophyll-specific absorption coefficient, a*ph (λ) in phytoplankton because it serves as an input variable for bio-optical modeling of photosynthesis using remote sensing instrumentation such as moorings, drifters, and satellites. Values of a*ph (λ) vary spectrally and the magnitude depends on accessory pigments, photo-protective pigments, and pigment packaging effects. Several studies have shown that the contribution of cellular characteristics to a*ph(λ) varies with growth conditions including temperature, light, and nutrients. It has been shown that a*ph (λ) values in Phaeocystis vary predictably at 4°C over light intensities under light limitation. Phaeocystis demonstrated significant pigment package effects that depended on single cell diameter and thylakoid membrane stacking. Using thick sections obtained from fixed and embedded cultures of colonial P. antarctica, we calculated tomographic reconstructions of individual chloroplasts under light-limiting conditions for net photosynthesis in order to gain an understanding of the continuity of thylakoid membranes and understand the spatial relationship between the pyrenoid, the starch containing organelle, and thylakoid membranes.