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This is the accepted manuscript of the paper "Phyto-VFP: a new bio-optical model of pelagic primary production based onvariable fluorescence measures", published as final paper in "Journal of Marine Systems" Volume 204,April 2020, 103304 https://doi.org/10.1016/j.jmarsys.2019.103304 Marine primary production (PP) is a key factor in the regulation of the global carbon cycle, with important potential feedback on climate. Seventy percent of marine PP is generated by phytoplankton photosynthesis. However, the phytoplankton productivity rate is dependent on the photo-physiological state of phytoplankton cells, as well as other environmental conditions. To consider these variables appropriately, refine the current estimates of PP, and reduce the laboursome and lengthy methodologies of radiocarbon estimates, we have created “Phyto-VFP” (Variable Fluorescence Phytoplankton Production), a new bio-optical model classified as a Wavelength and Depth-resolved (WDR) model. The model integrates the effect of the photo-acclimation processes on the “active” fraction of the phytoplankton population with the dynamic of the water column, parametrised through a series of laboratory experiments based on in vivo variable fluorescence measures on the marine diatom Skeletonema costatum (Greville) Cleve. The performance of Phyto-VFP was compared with concurrent estimates of radiocarbon (14C) uptakes, under different dynamic and optical conditions, during two oceanographic cruises (SAMCA3 and SAMCA4) in the Mediterranean Sea. The low Root Mean Square Differences (RMSDs) show that Phyto-VFP performs well when estimating phytoplankton PP. When compared to other biooptical models, Phyto-VFP estimates of PP in coastal waters were closer to radiocarbon measurements than other models could predict [e.g., the Morel model (MM)]. The application of Phyto-VFP to the SAMCA dataset and its comparison to MM allowed the assessment of model performance under three different physical and biological conditions, in which it was possible to analyse how photo-physiological responses of phytoplankton influence PP.

Attempts to merge marine food webs and marine biogeochemical research have recently been developed in response to the need to understand how global change will impact marine ecosystems and resources (Salihoglu et al., 2013; Painting, et al., 2013). Among the multiple drivers that influence ecosystem dynamics, Link et al. (2012) focused on three main processes that affect marine fish productivity: biophysical (environmental), exploitative (fisheries), and trophodynamic (species interactions) factors. Previous paper underlined the relationships among microbial parameters and physical and chemical conditions of waters (Zaccone et al., 2012). With the aim of providing an ecosystem approach to fisheries management, the monitoring of biological and environmental variables was carried out in the frame of the Bansic12 cruise performed in the Sicily Channel (Ibleo-Maltese platform) during July 2012. The Sicily Channel is a spawning area of Engraulis encrasicolus (Linnaeus, 1758), a pelagic species of commercial interest (Basilone et al., 2013). As a consequence, fish eggs and larvae together with microbial assemblages (virio-, autotrophic and heterotrophic pico-, nano- and microplankton) were quantified in terms of abundance and biomass (Andrade et al., 2003; Caroppo et al., 2010; Fonda Umani et al., 2010; La Ferla et al., 2012). To give a more comprehensive picture of microbial role in supporting the flux of biogeochemical elements in the study area, rates of microbial metabolic processes (primary and secondary production, enzymatic hydrolysis of dissolved and particulate matter, and community respiration) were also quantified (La Ferla et al., 2005; La Ferla et al., 2010; Caruso et al., 2014). In addition, the hydrology, the trophic parameters and correlated indices were analyzed to contribute to the understanding of plankton communities dynamism (Leonardi et al., 2009). The euphotic layer was characterized by the presence of the typically oligotrophic MAW (Modified Atlantic Water), flowing eastward along the Sicilian coast. Low nutrient concentrations were recorded, particularly regarding the phosphorus, whose values were close to the detection limit. The diffuse oligotrophy of the area was confirmed by high N/P ratios as well as by low Chl-a values. Particulate Organic Carbon (POC) concentrations were low, as well as those of Particulate Nitrogen (PN). Peaks of POC and PN were recorded at the Deep Chlorophyll Maximum (DCM) or below the thermocline (Leonardi et al., 2014). As regards biological parameters, virus counts were low with a mean value of 1.68E+05 ± 7.0E+04 VPL ml-1 and prokaryotic biomass ranged between 24.9 and 113.0 µg C L-1, mainly composed by curved rods and coccobacilli (range size: 0.160 – 0.459 µm3). Low nucleic acid cells (LNA) prevails over high nucleic acid cells (HNA) with a HNA/LNA mean ratio of 0.56, similar to that occurring in surface layer of several pelagic Mediterranean areas (La Ferla et al., 2012). The picophytoplanktonic biomass (range 0.29–26 µg C L-1), was mostly due to the presence of coccoid cyanobacteria, belonging to the genus Synechococcus. Total nanoplankton biomass (range 0.11-1.71 µg C L-1) showed the highest values at the DCM or below the thermocline. Nanoplankton was represented, among the others, by the dinoflagellates Amphidinium carterae and Heterocapsa niei. The coccolithophorid Emiliania huxleyi and flagellates of uncertain taxonomic identification were also abundant. Microphytoplankton abundance ranged between 6.1 and 40.5 E+03 cells L-1, while biomass between 0.28 and 2.43 µg C L-1. Diatoms and dinoflagellates were the main components of the community, composed by 24 and 30 species, respectively. Concerning microzooplankton, eggs, nauplia and metazoan larval stages prevailed in terms of biomass in almost all samples. Heterotrophic dinoflagellates were the second more relevant group while aloricate Ciliates and Tintinnids did not significantly contribute to the total biomass. Biomass maxima were generally observed at the surface or at the DCM, but never exceeded 16.0 µg C L-1. Finally, anchovy eggs and larvae mainly occurred in the 0-10/0-25 m depth intervals, with highest densities of 4.2 eggs m-3 and 2.6 larvae m-3. The rates of production, hydrolysis and degradation activities were quite low, in agreement with the general oligotrophy of the area and in agreement with this findings, picophytoplankton contribution to total production amounted to over than 65%. In terms of metabolic activities, different spatial distributions were observed between the autotrophic and heterotrophic components. In particular, heterotrophic metabolism showed high values in the layer located below the thermocline and above the DCM. Concerning the enzymatic activities, total leucine aminopeptidase activity showed the highest rates, followed by alkaline phosphatase and beta-Glucosidase (Caruso et al., 2014). Distribution of the dissolved enzymatic activities acting on proteins varied widely along the column, accounting for 5 to 90% of the total enzymatic activity and always prevailed on dissolved b-GLU. Total enzymatic activity rates were comparable to those obtained in the oligotrophic zones of Ionian and Mediterranean Sea (Zaccone et al., 2012), while the analysis of the dissolved fraction was the first report for the Mediterranean. In conclusion, the multidisciplinary scientific approach used in this study depicted a complex picture of the study area evidencing a high heterogeneity and dynamism of plankton communities, probably associated to peculiar hydrology of this ecosystem. On the whole, the study area appeared to be characterized by a relatively efficient microbial food web. However, low trophic conditions were stressed by all the biological and biochemical patterns, suggesting an important role of heterotrophic processes in this area in the examined summer period. Consequently, how and how much the microbial web sustains fish reproduction and larval survival need a more comprehensive analysis and will be focused in further research.

Prokaryotic and phytoplankton interaction plays a key role in relevant processes such as carbon fluxes and nutrient regeneration (Zaccone et al., 2004). Sinking biogenic particles drive respiration in the ocean and related studies are important to determine the flow of organic matter along the water column (Martin et al., 1987; Karl et al., 1987). However, organic matter collected by sediment traps (Langone et al., 2000) or the studies of the disequilibrium 234Th/238U (Aliani et al., 2004) does not take into account the entire pool of oxidable organic matter, which includes the dissolved organic matter present in the seawater. The study of microbial respiration rates instead fills this gap, since respiration includes oxidation of both dissolved and particulate organic mater, providing an integrated estimate of the carbon utilization in the sea (Azzaro et al., 2006). In this context, a study on an Arctic fjord (Kongsfyorden, Svalbard) was done in late summer 2013, with the purpose of knowing the variability of prokaryotic and phytoplanktonic biomass and of microbial remineralization rates over short time scales in a coastal station (water depth ~105 m), where a mooring (Mooring Dirigibile Italia, MDI: 78° 54 .859'N; 12° 15. 411' E) is positioned. The Kongsfjorden was affected by inflow of Atlantic water as well as glacier melt water runoff (Cottier et al., 2005). The experiment comprised 5 samplings performed during a 7 day period in MDI station. For each sampling, photosynthetically active radiation (PAR), temperature and conductivity (salinity) were recorded along the water column with a PNF-300 profiler and a SeaBird Electronics SBE-911 plus profiler, respectively . Water samples were taken at five different depths (surface, 5, 25, 50 and 100 m) to determine nutrients, particulate organic carbon, prokaryotes and phytoplankton biomass, and community respiration. In addition, prokaryotes sunk with the particulate matter were studied into the sediment trap positioned in the MDI during the period between June and September 2013. The latter assessment allowed us to determine the flow of prokaryotes, conveyed from organic matter sinking, throughout the summer. Due to melting of the glaciers in the surface water of the study site, there were sediment loads which strongly limited light penetration and low irradiance (~0.7% E0+) at 5 meters below the surface. Along the water column the intrusion of the salty and warm Atlantic water was visible in the study site and the warm core was at about 25 m depth. PO4 concentrations ranged between 0.43 (surface) and 1 µM (100 m) and in general the values increased from surface to bottom. NH4, NO2 and NO3 significantly changed along the vertical and with time and varied between 0.39 and 5.05µM, 0.01 and 0.67µM, 0.001 and 4.18µM, respectively. Prokaryotic abundances and cell volumes ranged between 5.6 and 15.9 E+05 cells ml-1 and 0.033 and 0.093 µm3, respectively. These latter parameters showed a peak at 25 m depth in the core of incoming Atlantic water. This evidence was not determined in chlorophyll a (range 0.034-1.102 mg m-3), where the highest values were determined at the surface and 5 m depth. Speculations will be made on the variability of the fluxes of carbon remineralization in the short time scale and the different role played by autotrophic and heterotrophic communities along the water column.

The EU Marine Strategy Framework Directive 2008/56/EC (MSFD) defines a framework for Community actions in the field of marine environmental policy in order to achieve and/or maintain the Good Environmental Status (GES) of the European seas by 2020. Microbial assemblages (from viruses to microbial-sized metazoa) provide a major contribution to global biodiversity and play a crucial role in the functioning of marine ecosystems, but are largely ignored by the MSFD. Prokaryotes are only seen as "microbial pathogens", without defining their role in GES indicators. However, structural or functional prokaryotic variables (abundance, biodiversity and metabolism) can be easily incorporated into several MSFD Descriptors (i.e. D1. Biodiversity, D4. Food webs, D5. Eutrophication, D8. Contaminants and D9. Contaminants in seafood) with beneficial effects. The present review provides a critical analysis of the current MSFD descriptors and illustrates the reliability and advantages of the potential incorporation of some prokaryotic variables within the set of indicators of marine environmental quality. Following a cost/benefit analysis against scientific and economic criteria, we conclude that marine microbial components, and particularly prokaryotes, are highly effective for detecting the effects of anthropogenic pressures on marine environments and for assessing changes in the environmental health status. We thus recommend the inclusion of these components in future implementations of the MSFD.