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The Arctic ice scape is composed by a mosaic of ridges, hummocks, melt ponds, leads, and snow. Under such heterogeneous surfaces, drifting phytoplankton communities are experiencing a wide range of irradiance conditions and intensities that cannot be sampled representatively using single-location measurements. Combining experimentally derived photosynthetic parameters with transmittance measurements acquired at spatial scales ranging from hundreds of meters (using a remotely operated vehicle, ROV) to thousands of meters (using a surface and underice trawl, SUIT), we assessed the sensitivity of water column primary production estimates to multiscale underice light measurements. Daily primary production calculated from transmittance from both the ROV and the SUIT ranged between 0.004 and 939 mgC.m(-2).day(-1). Upscaling these estimates at larger spatial scales using satellite-derived sea ice concentration reduced the variability by 22% (0.004-731 mgC.m(-2).day(-1)). The relative error in primary production estimates was two times lower when combining remote sensing and in situ data compared to ROV-based estimates alone. These results suggest that spatially extensive in situ measurements must be combined with large-footprint sea ice coverage sampling (e.g., remote sensing, aerial imagery) to accurately estimate primary production in ice-covered waters. Also, the results indicated a decreasing error of primary production estimates with increasing sample size and the spatial scale at which in situ measurements are performed. Conversely, existing estimates of spatially integrated phytoplankton primary production in ice-covered waters derived from single-location light measurements may be associated with large statistical errors. Considering these implications is important for modeling scenarios and interpretation of existing measurements in a changing Arctic ecosystem.

The widespread and persistent contamination of freshwater environments by low concentrations of pesticides is a growing concern worldwide. In aquatic environments, herbicide pollution is of greatest concern for phytoplankton, due to their similarities to terrestrial plants. Through the use of Fast Repetition Rate Fluorometry (FRRF) during weeklong experiments on 10 phytoplankton cultures from 4 classes and 4 natural communities, we demonstrate that PSII-inhibiting herbicides, notably atrazine that is extensively used in North America, consistently have effects on freshwater phytoplankton photophysiology at concentrations far below concentrations affecting the most sensitive species in previous studies. The parameters specific to FRRF (Ρ, σ, τ1, τ2, τ3) were those most sensitive to PSII inhibitors, compared to the standard fluorescence parameters derived from other fluorescence protocols such as Pulse Amplitude Modulation (PAM) fluorometry (F0, Fm, Fv/Fm) and extracted chlorophyll a concentrations. Based on these findings, existing national environmental guidelines and standards are insufficient to adequately prevent adverse effects of atrazine and other PSII inhibiting herbicides on algal physiology in aquatic ecosystems.

Studying the biogeochemistry of the Southern Ocean using remote sensing relies on accurate interpretation of ocean colour through bio-optical and biogeochemical relationships between quantities and properties of interest. During the Antarctic Circumnavigation Expedition of the 2016/2017 Austral Summer, we collected a spatially comprehensive dataset of phytoplankton pigment concentrations, particulate absorption and particle size distribution and compared simple bio-optical and particle property relationships as a function of chlorophyll a. Similar to previous studies we find that the chlorophyll-specific phytoplankton absorption coefficient is significantly lower than in other oceans at comparable chlorophyll concentrations. This appears to be driven in part by lower concentrations of accessory pigments per unit chlorophyll a as well as increased pigment packaging due to relatively larger sized phytoplankton at low chlorophyll a than is typically observed in other oceans. We find that the contribution of microphytoplankton (>20 µm size) to chlorophyll a estimates of phytoplankton biomass is significantly higher than expected for the given chlorophyll a concentration, especially in higher latitudes south of the Southern Antarctic Circumpolar Current Front. Phytoplankton pigments are more packaged in larger cells, which resulted in a flattening of phytoplankton spectra as measured in these samples when compared to other ocean regions with similar chlorophyll a concentration. Additionally, we find that at high latitude locations in the Southern Ocean, pheopigment concentrations can exceed mono-vinyl chlorophyll a concentrations. Finally, we observed very different relationships between particle volume and chlorophyll a concentrations in high and low latitude Southern Ocean waters, driven by differences in phytoplankton community composition and acclimation to environmental conditions and varying contribution of non-algal particles to the particulate matter. Our data confirm that, as previously suggested, the relationships between bio-optical properties and chlorophyll a in the Southern Ocean are different to other oceans. In addition, distinct bio-optical properties were evident between high and low latitude regions of the Southern Ocean basin. Here we provide a region-specific set of power law functions describing the phytoplankton absorption spectrum as a function of chlorophyll a.

SummaryNorthern lakes are ice-covered for a large part of the year, yet our understanding of microbial diversity and activity during winter lags behind that of the ice-free period. In this study, we investigated under-ice diversity and metabolism of Verrucomicrobia in seasonally ice-covered lakes in temperate and boreal regions of Quebec, Canada using 16S rRNA sequencing, metagenomics and metatranscriptomics. Verrucomicrobia, particularly the V1, V3 and V4 subdivisions, were abundant during ice-covered periods. A diversity of Verrucomicrobia genomes were reconstructed from Quebec lake metagenomes. Several genomes were associated with the ice-covered period and were represented in winter metatranscriptomes, supporting the notion that Verrucomicrobia are metabolically active under ice. Verrucomicrobia transcriptome analysis revealed a range of metabolisms potentially occurring under ice, including carbohydrate degradation, glycolate utilization, scavenging of chlorophyll degradation products, and urea use. Genes for aerobic sulfur and hydrogen oxidation were expressed, suggesting chemolithotrophy may be an adaptation to conditions where labile carbon may be limited. The expression of genes for flagella biosynthesis and chemotaxis was detected, suggesting Verrucomicrobia may be actively sensing and responding to winter nutrient pulses, such as phytoplankton blooms. These results increase our understanding on the diversity and metabolic processes occurring under ice in northern lakes ecosystems.

When growth irradiance changes, phytoplank- ton acclimates by changing allocations to cellular compo- nents to re-balance their capacity to absorb photons versus their capacity to use the electrons from the oxidation of water at photosystem II. Published changes in the cellular allocations resulting from photoacclimation across algal groups highlight that algae adopt different strategies. We examined the photoacclimation of the photosynthetic ap- paratus of six marine phytoplankters under near-natural diel irradiance patterns. For most of the phytoplankters, Chl a per structural photosystem II unit decreased with increasing growth irradiance, but a parallel decline in op- tical packaging effect allowed cells to maintain their functional absorption cross section serving active photo- system II units (rPSII). Furthermore, no significant changes were observed in the ratio of Chl a per photosystem I. The diatom Skeletonema marinoi proved an exception to this pattern as Chl a per photosystem II is stable and Chl a per photosystem I slightly decreased with light intensity. A clear decrease in the photosystem content per cell was observed for all species except for Thalassiosira oceanica and S. marinoi. Rubisco content per cell showed little variation with irradiance for most algae, except for a 3-fold increase in S. marinoi .A *700 % increase in the Rubis- co:photosystem ratio across species with increasing growth irradiance indicates this is a key cellular stoichiometric adjustment to balance photon absorption capacity and the carbon reduction capacity. Increasing the Rubisco:photo- system ratio occurs through a decrease in the photosystems per cell for most of the phytoplankters in this study, except in the case of S. marinoi where Rubisco per cell increased.

Diurnal variations of phytoplankton size distributions, chlorophyll, carbon and nitrogen content, in vivo fluorescence and associated optical absorption and scattering properties were observed in the laboratory to help understand in situ and spatial observations. We grew triplicate semi-continuous cultures of T. pseudonana, D. tertiolecta, P. tricornutum and E. huxleyi under a sinusoidal light regime. We observed diurnal variations in the particulate absorption (ap), scattering (bp), attenuation (cp), and backscattering coefficients (bbp), which correlate with carbon and Chl concentrations. Relative variations from sunrise of bbp are slightly lower than those of cp, suggesting that bbp diurnal increases observed in nature are partly caused by phytoplankton. Non-concurrent changes of carbon and Chl-specific backscattering and scattering coefficients and optical cross-sections however indicates that using backscattering to infer scattering or biomass must be done with care.

Northern lakes are ice-covered for a large part of the year, yet our understanding of microbial diversity and activity during winter lags behind that of the ice-free period. In this study, we investigated under-ice diversity and metabolism of Verrucomicrobia in seasonally ice-covered lakes in temperate and boreal regions of Quebec, Canada using 16S rRNA sequencing, metagenomics and metatranscriptomics. Verrucomicrobia, particularly the V1, V3 and V4 subdivisions, were abundant during ice-covered periods. A diversity of Verrucomicrobia genomes were reconstructed from Quebec lake metagenomes. Several genomes were associated with the ice-covered period and were represented in winter metatranscriptomes, supporting the notion that Verrucomicrobia are metabolically active under ice. Verrucomicrobia transcriptome analysis revealed a range of metabolisms potentially occurring under ice, including carbohydrate degradation, glycolate utilization, scavenging of chlorophyll degradation products, and urea use. Genes for aerobic sulfur and hydrogen oxidation were expressed, suggesting chemolithotrophy may be an adaptation to conditions where labile carbon may be limited. The expression of genes for flagella biosynthesis and chemotaxis was detected, suggesting Verrucomicrobia may be actively sensing and responding to winter nutrient pulses, such as phytoplankton blooms. These results increase our understanding on the diversity and metabolic processes occurring under ice in northern lakes ecosystems.© 2018 Society for Applied Microbiology and John WileySons Ltd.

In the aquatic environment, particles can be broadly separated into phytoplankton (PHY), non-algal particle (NAP) and dissolved (or very small particle, VSP) fractions. Typically, absorption spectra are inverted to quantify these fractions, but volume scattering functions (VSFs) can also be used. Both absorption spectra and VSFs were used to estimate particle fractions for an experiment in the Chesapeake Bay. A complete set of water inherent optical properties was measured using a suite of commercial instruments and a prototype Multispectral Volume Scattering Meter (MVSM); the chlorophyll concentration, [Chl] was determined using the HPLC method. The total scattering coefficient measured by an ac-s and the VSF at a few backward angles measured by a HydroScat-6 and an ECO-VSF agreed with the LISST and MVSM data within 5%, thus indicating inter-instrument consistency. The size distribution and scattering parameters for PHY, NAP and VSP were inverted from measured VSFs. For the absorption inversion, the "dissolved" absorption spectra were measured for filtrate passing through a 0.2 μm filter, whereas [Chl] and NAP absorption spectra were inverted from the particulate fraction. Even though the total scattering coefficient showed no correlation with [Chl], estimates of [Chl] from the VSF-inversion agreed well with the HPLC measurements (r = 0.68, mean relative errors = −20%). The scattering associated with NAP and VSP both correlated well with the NAP and "dissolved" absorption coefficients, respectively. While NAP dominated forward, and hence total, scattering, our results also suggest that the scattering by VSP was far from negligible and dominated backscattering. Since the sizes of VSP range from 0.02 to 0.2 μm, covering (a portion of) the operationally defined "dissolved" matter, the typical assumption that colored dissolved organic matter (i.e., CDOM) does not scatter may not hold, particularly in a coastal or estuarine environment.

While empirical and semi-analytical algorithms that retrieve phytoplankton biomass from satellite ocean color have matured over the last few decades, the use of Sun-induced chlorophyll fluorescence data measured by spaceborne sensors remains in its infancy. Sun-induced fluorescence has the potential to provide a synoptic global view of aspects of phytoplankton biology that go beyond biomass by observing the quantum yield of fluorescence. While several algorithms have been developed to retrieve the quantum yield, they are prone to biases from different sources. In this study, we assessed the accuracy of several ocean color algorithms to estimate phytoplankton chlorophyll or absorption when they are used together with Sun-induced fluorescence algorithms. Our analysis led us to develop a new type of algorithm for retrieving variability in the quantum yield of fluorescence. Based on a three dimensional lookup table, this algorithm avoided many of the biases present in older algorithms and provided distributions of the quantum yield that showed significant differences compared to previous methods. This algorithmic approach also has the advantage of being robust with respect to sensor characteristics and to the set of underlying proxies that are used, namely phytoplankton biomass, the absorption by chromophoric dissolved organic matter, and the incident irradiance. As such, it would be suitable for merging data from multiple satellite ocean color sensors.

Sun-induced chlorophyll- a fluorescence (SICF) is the emission of red light by chlorophyll- a in the presence of sunlight. In surface waters, chlorophyll- a is present in phytoplankton and SICF is observable in the light leaving the water surface. This allows, in principle, the estimation of phytoplankton absorption from measurements of light leaving water. However, while the concentration of phytoplankton in surface waters is the dominant source of optical variability, phytoplankton physiology and the optical characteristics of water also play a significant role in altering the observed emission. The latter have a particularly strong impact in inland and coastal waters. To examine these interactions and their impact on the observed light field, a four-component bio-optical model was developed to create synthetic datasets of reflectance spectra. These synthetic spectra are used together with field measurements of reflectance to understand the relationships between SICF, phytoplankton abundance, colored dissolved organic matter absorption, and suspended inorganic matter concentration in inland and coastal waters. The retrieval of SICF using hyperspectral data and fluorescence line height algorithms is analyzed by considering the wavebands of past, current, and future ocean color sensors. The use of fluorescence signatures in polarimetric observations and applications to algal bloom detection are also discussed.

International audience; Excitation-emission fluorescence matrices of phytoplankton communities were simulated from laboratory-grown algae and cyanobacteria cultures, to define the optical configurations of theoretical fluorometers that either minimize or maximize the representation of these phytoplankton groups in community variable fluorescence measurements. Excitation sources that match the photosystem II (PSII) action spectrum of cyanobacteria do not necessarily lead to equal representation of cyanobacteria in community fluorescence. In communities with an equal share of algae and cyanobacteria, inducible PSII fluorescence in algae can be retrieved from community fluorescence under blue excitation (450-470 nm) with high accuracy (R (2) = 1.00). The highest correlation between community and cyanobacterial variable fluorescence is obtained under orange-red excitation in the 590-650 nm range (R (2) = 0.54). Gaussian band decomposition reveals that in the presence of cyanobacteria, the emission detection slit must be narrow (up to 10 nm) and centred on PSII chlorophyll-a emission (similar to 683 nm) to avoid severe dampening of the signal by weakly variable phycobilisomal fluorescence and non-variable photosystem I fluorescence. When these optimizations of the optical configuration of the fluorometer are followed, both cyanobacterial and algal cultures in nutrient replete exponential growth exhibit values of the maximum quantum yield of charge separation in PSII in the range of 0.65-0.7.

The use of high-frequency sensors on profiling buoys to investigate physical, chemical, and biological processes in lakes is increasing rapidly. Profiling buoys with automated winches and sensors that collect high-frequency chlorophyll fluorescence (ChlF) profiles in 11 lakes in the Global Lake Ecological Observatory Network (GLEON) allowed the study of the vertical and temporal distribution of ChlF, including the formation of subsurface chlorophyll maxima (SSCM). The effectiveness of 3 methods for sampling phytoplankton distributions in lakes, including (1) manual profiles, (2) single-depth buoys, and (3) profiling buoys were assessed. High-frequency ChlF surface data and profiles were compared to predictions from the Plankton Ecology Group (PEG) model. The depth-integrated ChlF dynamics measured by the profiling buoy data revealed a greater complexity that neither conventional sampling nor the generalized PEG model captured. Conventional sampling techniques would have missed SSCM in 7 of 11 study lakes. Although surface-only ChlF data underestimated average water column ChlF, at times by nearly 2-fold in 4 of the lakes, overall there was a remarkable similarity between surface and mean water column data. Contrary to the PEG model’s proposed negligible role for physical control of phytoplankton during the growing season, thermal structure and light availability were closely associated with ChlF seasonal depth distribution. Thus, an extension of the PEG model is proposed, with a new conceptual framework that explicitly includes physical metrics to better predict SSCM formation in lakes and highlight when profiling buoys are especially informative.

Global ocean color algorithms designed to estimate chlorophyll a concentration (chla) are not accurate at high latitudes. Although a regional Arctic OC4L algorithm was designed to be applicable to high northern latitudes, its applicability remains uncertain. To examine these issues, we investigated the light absorption coefficients of phytoplankton, non-algal particles (NAP), and colored dissolved organic matter (CDOM) and remote sensing reflectance, R-rs(lambda), covering most of the western Arctic Ocean. A higher pigment packaging effect was identified relative to that at lower latitudes. The CDOM absorption dominated and accounted for 76% of the total non-water absorption at 443 nm and did not covary with variations in chla. This absorption is significantly higher than those in other marine environments. We also examined the backscattering coefficient of particles obtained from the inversion of R-rs(lambda) and found that it covaried well with variation in NAP absorption. Our evaluation shows that when turbid waters (R-rs(670) > 0.00042 sr(-1)) are excluded, the performance of the OC4L is good and much better than that of the sea-viewing wide field-of-view sensor (SeaWiFS) OC4V4 and the moderate-resolution imaging spectroradiometer (MODIS) OC3M (root mean square error (RMSE) of 0.13, 0.21, and 0.22, respectively). The reason why the OC4L performs well despite strong CDOM absorption is discussed.

We discuss important sources of variability in sun-induced chlorophyll fluorescence and examine difficulties in deriving fluorescence data products from satellite imagery, with a focus on the MODerate-resolution Imaging Spectroradiometer (MODIS) sensor. Our results indicate that there are limitations in the present MODIS algorithms that could lead to biases in the interpretation of the fluorescence products across gradients of chlorophyll concentration. To avoid some of these limitations, we suggest replacing the calculation of absorbed radiation by phytoplankton (ARP) over a finite depth with integration over the entire water column, and including a term accounting for cellular reabsorption of fluoresced light. These suggestions are incorporated into two new algorithms, based on established bio-optical models for case 1 waters (most open ocean waters), to retrieve chlorophyll concentration and the quantum yield of fluorescence. We compare our results to the results using MODIS algorithms for two regions: one located off the coast of Central America, including the Costa Rica Dome, and the other in the Arabian Sea. The new algorithms provide a similar field for the quantum yield of fluorescence in the first region, while they provide a different and more uniform field in the second region. We suggest that this discrepancy originates from the use of the water leaving radiance at 412 nm in the MODIS standard algorithm, which is not used in our algorithm and can be problematic under certain environmental conditions (e.g., absorbing aerosols or highly scattering waters).

Measured spectral absorption coefficients were inverted to infer phytoplankton concentration in three size classes (picoplankton, nanoplankton, and microplankton), chlorophyll concentration[Chl], and both magnitude and spectral shape of absorption by colored detrital matter (CDM). Our algorithm allowed us to solve for the nonlinear factor of CDM absorption slope separately from the other linear factors, thus fully utilizing the additive characteristic inherent in absorption coefficients. We validated the inversion with three datasets: two spatially distributed global datasets, the Laboratoire d'Oceanographie de Villefranche dataset and the NASA bio-Optical Marine Algorithm Dataset, and a time series coastal dataset, the Martha's Vineyard Coastal Observatory dataset. Comparison with high performance liquid chromatography analyses showed that the phytoplankton size classes can be retrieved with correlation coefficients (r)> 0.7, root mean square errors of 0.2, and median relative errors of 20% in oceanic waters and with similar performance in coastal waters. Much improved agreement was found for the entire phytoplankton population, with r > 0.90 for[Chl] and absorption coefficients (a(ph)) for all three datasets. The inferred a(CDM) (400) and CDM spectral slope agree within +/- 4% of measurements in both oceanic and coastal waters. The results indicate that the chlorophyll-a specific absorption spectra used as an inversion kernel represent well the global mean states for each of the three phytoplankton size classes. The method can be applied to either bulk or particulate absorption data and is spectrally flexible. (C) 2015 Optical Society of America

The objective of the present study was to evaluate the influence of UV radiation on photosynthesis rate, in situ and in laboratory incubations, on size fractionated natural algal assemblages (picoplankton: 0.2-2 μm, nanoplankton: >2 μm) and whole water (total organic carbon TOC). Near surface samples from a mesotrophic high mountain lake (LCD: L. Cadagno, Swiss Alps, Switzerland, 1923 m a.s.l.) and from the oligotrophic pre-alpine L. Lucerne (LLU: Swiss Alps, Switzerland, 434 m a.s.l.) were both incubated at a depth of 30 cm (50 % of surface UV at 323 nm ) in L. Cadagno. At the same time, biological weighting functions for UV inhibition of photosynthesis (BWFs) were determined for the autotrophic picoplankton and whole fraction in a spectral incubator. Photosynthetic assimilation of the pico- and nanoplanktonic algal communities as well as the assimilated total organic carbon (TOC) was estimated separately by 14C uptake under three irradiance conditions: PAR (photosynthetically active radiation), PAR + UVA and PAR + UVA + UVB. UV radiation reduced significantly photosynthesis rate in samples from both lakes (LLU: P = 0.0012; LCD: P = 0.0001). It appears that UVA plus UVB significantly affect the algal assemblage in both lakes; however most of the effect is due to UVA (Mann Whitney U test, two tailed: P = 0.0022). The natural assemblages from LLU transplanted to LCD were more inhibited by UV than the autochthonous assemblages of LCD. Photosynthetic rates of picoplankton from LLU and LCD under full UV exposure was reduced by 73 % and 55 % respectively relative to PAR only. A higher sensitivity of autotrophic picoplankton to the UV radiation, with respect to the nanoplankton, was observed in the biological weighting functions. However this difference was not statistically significant for the in situ incubations.

[1] Depth-integrated models of primary production (DIMs) are used to estimate water column photosynthesis as a function of chlorophyll concentration, irradiance at the surface, the penetration of photosynthetically available radiation (PAR), and parameters of the relationship between photosynthesis and PAR. These models are inherently unable to account for variability in the ratio of photosynthetically utilizable radiation (PUR) to PAR with depth and water type, and they cannot account for the inhibition of photosynthesis by ultraviolet radiation, UVR. These important spectral effects — all sensitive to climate change — are readily described with numerical models that require many computations and are unsuitable for some important applications, including the estimation of aquatic productivity from remote sensing. We present a simple DIM that accounts for the spectral effects of irradiance on photosynthesis, including inhibition by UVR. Water column photosynthesis, normalized to surface chlorophyll and scaled to the maximum rate per unit chlorophyll, is described as a function of four dimensionless derived variables:E*PUR, PUR at the surface scaled to the saturation irradiance for photosynthesis; T*PUR, water transparency, normalized to a depth scale and weighted spectrally for photosynthetic absorption; E*PIR, surface irradiance weighted spectrally for inhibition of photosynthesis; and T*PIR, scaled transparency weighted for photosynthesis-inhibiting radiation. Simple functions of these variables closely approximate (within 6%) the results of a full-spectral numerical model of instantaneous and daily integrated water column photosynthesis with and without UVR for a broad range of water types, solar angles, stratospheric ozone concentrations and biological properties of phytoplankton. The spectral DIM is suitable for examining patterns in global ocean productivity and can be used to assess the biological effects of variations in solar radiation (e.g., ozone depletion) and water clarity in climate-change scenarios for lakes and oceans.

International audience; The light absorption properties of particulate and dissolved materials strongly influence the propagation of visible light in oceanic waters and therefore the accuracy of ocean color algorithms. While the general absorption properties of these materials have been reported for Arctic waters, their seasonal variability remains unknown. We investigated the light absorption coefficients of phytoplankton [a(phi)(lambda)], nonalgal particles [a(NAP)(lambda)], and colored dissolved organic matter [a(CDOM)(lambda)] in both coastal and oceanic waters of the western Arctic Ocean from spring to autumn. Values for the chlorophyll a-specific absorption coefficient of phytoplankton [a(phi)*(440)] declined significantly from the ice melt period in the early spring to the summer. Using high-performance liquid chromatography, we show that the decrease in a(phi)*(440) was due to a strong package effect that overwhelmed the influence of the pigment composition. A decrease in the a(NAP)(lambda) values from spring and summer to autumn likely originated from a decrease in the concentration of phytoplanktonic detritus. The a(CDOM)(lambda) near the surface decreased by 34% from spring to summer as a result of photobleaching by solar radiation. The colored dissolved organic matter (CDOM) absorption values then increased significantly during autumn, resulting from the cumulative injection of Alaskan Coastal Waters into the Arctic as well as CDOM generated in situ. Our results suggest that all of the absorption components are tightly linked to biogeochemical processes, and thus the seasonal variability in a 8 (lambda), a(NAP)(lambda), and a(CDOM)(lambda) should be taken into account in bio-optical models.

International audience; We analyzed a large dataset of simultaneous measurements of phytoplankton pigments, spectral specific absorption coefficient for phytoplankton [a*(lambda)], and photosynthesis versus irradiance (P versus E) curve parameters to examine the possible relationships between phytoplankton community structure and photophysiological properties at large spatial scales. Data were collected in various regions, mostly covering the trophic gradient encountered in the world's open ocean. The community composition is described in terms of biomass of three phytoplankton classes, determined using specific biomarker pigments. We present a general empirical model that describes the dependence of algal photophysiology on both the community composition and the relative irradiance within the water column (essentially reflecting photoacclimation). The application of the model to the in situ dataset enables the identification of vertical profiles of photophysiological properties for each phytoplankton class. The class-specific a*(lambda) obtained are consistent with results from the literature and with previous models developed for small and large cells, both in terms of the absolute values and the vertical patterns. Similarly, for the class-specific P versus E curve parameters, the magnitude and vertical distribution obtained with this method are coherent with previous observations. Large cells (mainly diatoms) may be more efficient in carbon storage than smaller cells, whereas their yield of light absorption is lower. We anticipate that such photophysiological parameterizations can improve primary production models by providing estimates of primary production that are specific to different phytoplankton classes on large scale.

Prochlorococcus, Synechococcus, picophytoeukaryotes and bacterioplankton abundances and contributions to the total particulate organic carbon concentration, derived from the total particle beam attenuation coefficient (cp), were determined across the eastern South Pacific between the Marquesas Islands and the coast of Chile. All flow cytometrically derived abundances decreased towards the hyper-oligotrophic centre of the gyre and were highest at the coast, except for Prochlorococcus, which was not detected under eutrophic conditions. Temperature and nutrient availability appeared important in modulating picophytoplankton abundance, according to the prevailing trophic conditions. Although the non-vegetal particles tended to dominate the cp signal everywhere along the transect (50 to 83%), this dominance seemed to weaken from oligo- to eutrophic conditions, the contributions by vegetal and non-vegetal particles being about equal under mature upwelling conditions. Spatial variability in the vegetal compartment was more important than the non-vegetal one in shaping the water column particle beam attenuation coefficient. Spatial variability in picophytoplankton biomass could be traced by changes in both total chlorophyll a (i.e. mono + divinyl chlorophyll a) concentration and cp. Finally, picophytoeukaryotes contributed ~38% on average to the total integrated phytoplankton carbon biomass or vegetal attenuation signal along the transect, as determined by size measurements (i.e. equivalent spherical diameter) on cells sorted by flow cytometry and optical theory. Although there are some uncertainties associated with these estimates, the new approach used in this work further supports the idea that picophytoeukaryotes play a dominant role in carbon cycling in the upper open ocean, even under hyper-oligotrophic conditions.

[1] A model has been developed to retrieve phytoplankton absorption, a proxy for phytoplankton biomass, from observations of reflectance (R) and the diffuse attenuation coefficient (Kd) collected by moored radiometers in coastal waters, where high concentrations of chromophoric dissolved organic matter (CDOM) confound conventional ocean color algorithms. The inversion uses simultaneously two forward models: (1) a look-up table (LUT) that accounts for instrument geometry and the effect of the solar angle on both R and Kd and (2) an analytical function describing the effects of Sun-induced fluorescence (SIF) of chlorophyll on R. Estimates of phytoplankton biomass (mostly from SIF), the absorption by colored matter, and the particulate backscattering coefficients (mostly from the LUT) are obtained by optimizing the amplitude and shape of the absorption and backscattering coefficients in the forward model to best match the observations. An equation describing the quantum yield of fluorescence (photons fluoresced/photons absorbed) as a function of incident irradiance constrains the model and allows estimates of phytoplankton absorption. Innovations include: the utilization of both R and Kd, providing good separation of the effects of backscattering from absorption; avoidance of reflectance bands between 400 and 600 nm, thereby avoiding interference from bottom reflection and CDOM fluorescence; utilization of the full emission band of SIF; and accounting for the irradiance-dependence of its quantum yield. The model effectively retrieved chlorophyll concentration from an independent data set — r = 0.76, n = 93, with a mean absolute percent error (MAPE) of 24%; this is better than a modern ocean color algorithm (OC4V4) on its validation data set, when restricted to the same range of chlorophyll (r = 0.67, n = 384, MAPE = 51%).

The sensitivity of photosynthesis to ultraviolet radiation (UV) was assessed for phytoplankton assemblages in two Swiss lakes, pre-alpine Lake Lucerne (Vierwaldstattersee) and alpine Lake Cadagno, using both in situ and laboratory incubations. Biological weighting functions for UV inhibition of photosynthesis (BWFs) were determined in the laboratory using polychromatic exposures in a Xe-lamp based incubator. Samples were concurrently incubated in situ under UV exposed and protected bottles (profiles 0‐5 m), while additional spectral treatments were carried out at the 50% UV-B penetration depth: full spectrum, UV-A only (Mylar protected) and UV protected quartz tubes. Both particulate (> 0.2 mm) and total organic carbon incorporation were measured. Measured attenuation coefficients and incident UV spectral irradiance data was used to evaluate a BWF/photosynthesis-irradiance model (BWF/P-I) for in situ exposure conditions and compared with measurements. The BWFs showed sensitivity across the UV spectrum at similar, though somewhat lower, levels than an average BWF for marine assemblages. Relative photosynthesis in situ (UV exposed/UV excluded) was about 40% at the surface and about 60% at the 50% UV-B penetration depth. Similar inhibition was predicted by the BWF/P-I model. Generally, full spectrum (UV-B and UV-A) exposure had little additional effect compared to UV-A only exposure. Reciprocal transfer of samples between lakes showed enhancement of UV effects in L. Cadagno compared to incubation of the same sample in L. Lucerne, consistent with increased UV sensitivity due to the 5°C cooler water temperature in L. Cadagno. Similarly, BWF prediction of in situ response in L. Cadagno was improved by increasing UV sensitivity according to a Q10 of 2.