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This chapter gives an overview of the general biogeochemistry in the Mediterranean Sea explaining the particularities of the main biogeochemical variables and the physical, biological, and geochemical processes driving their distribution in the main basins of this marginal sea. Each subsection focuses on one essential variable, starting from dissolved oxygen and following inorganic nutrients, dissolved organic carbon and the CO2 system. A brief overview on the utility of those biogeochemical variables to identify water masses is also given. The chapter concludes with a summary of the projections and threats on biogeochemistry in the Mediterranean Sea under different future climate change scenarios.

Acidic polysaccharides released by phytoplankton and prokaryotic heterotrophs promote the formation of gel-like transparent exopolymer particles (TEPs). TEPs can have a relevant contribution to the biological carbon pump due to their carbon-rich composition and their ability to coagulate and sink towards the deep ocean. However, little is known about TEPs distribution, carbon export, and residence times below the export (200 m) and sequestration (1000 m) depths. We provide the first comprehensive inventory of TEP from the ocean surface to a depth of 4000 meters in the tropical and subtropical Atlantic, Indian, and Pacific Oceans, evaluating its contribution to carbon export and sequestration into the deep ocean. Results indicate that TEP concentration is primarily determined by primary production, with higher concentrations located above the deep chlorophyll maxima. In the deep ocean, TEP concentrations are lower yet mirror the concentrations in the surface, demonstrating the significance of TEP sinking below both the export compartment (2.8 Pg C yr-1; 27% of total POC flux at 200 m) and the sequestration compartment (0.8 Pg C yr-1; 36% of total POC flux at 1000 m). In situ incubation experiments conducted across ocean basins indicate short TEP residence times, averaging 27 and 333 days in the export and sequestration compartments, respectively. These findings reveal that the export and subsequent sequestration of carbon by TEP sinking into the deep ocean diverts it from the long times observed for the dissolved carbon fraction (i.e. centuries) in the global carbon cycle

Biomass is defined as organic matter from living organisms represented in all kingdoms. It is recognized to be an excellent source of proteins, polysaccharides and lipids and, as such, embodies a tailored feedstock for new products and processes to apply in green industries. The industrial processes focused on the valorization of terrestrial biomass are well established, but marine sources still represent an untapped resource. Oceans and seas occupy over 70% of the Earth’s surface and are used intensively in worldwide economies through the fishery industry, as logistical routes, for mining ores and exploitation of fossil fuels, among others. All these activities produce waste. The other source of unused biomass derives from the beach wrack or washed-ashore organic material, especially in highly eutrophicated marine ecosystems. The development of high-added-value products from these side streams has been given priority in recent years due to the detection of a broad range of biopolymers, multiple nutrients and functional compounds that could find applications for human consumption or use in livestock/pet food, pharmaceutical and other industries. This review comprises a broad thematic approach in marine waste valorization, addressing the main achievements in marine biotechnology for advancing the circular economy, ranging from bioremediation applications for pollution treatment to energy and valorization for biomedical applications. It also includes a broad overview of the valorization of side streams in three selected case study areas: Norway, Scotland, and the Baltic Sea.

Biomass is defined as organic matter from living organisms represented in all kingdoms. It is recognized to be an excellent source of proteins, polysaccharides and lipids and, as such, embodies a tailored feedstock for new products and processes to apply in green industries. The industrial processes focused on the valorization of terrestrial biomass are well established, but marine sources still represent an untapped resource. Oceans and seas occupy over 70% of the Earth’s surface and are used intensively in worldwide economies through the fishery industry, as logistical routes, for mining ores and exploitation of fossil fuels, among others. All these activities produce waste. The other source of unused biomass derives from the beach wrack or washed-ashore organic material, especially in highly eutrophicated marine ecosystems. The development of high-added-value products from these side streams has been given priority in recent years due to the detection of a broad range of biopolymers, multiple nutrients and functional compounds that could find applications for human consumption or use in livestock/pet food, pharmaceutical and other industries. This review comprises a broad thematic approach in marine waste valorization, addressing the main achievements in marine biotechnology for advancing the circular economy, ranging from bioremediation applications for pollution treatment to energy and valorization for biomedical applications. It also includes a broad overview of the valorization of side streams in three selected case study areas: Norway, Scotland, and the Baltic Sea.

The vast majority of freshly produced oceanic dissolved organic carbon (DOC) is derived from marine phytoplankton, then rapidly recycled by heterotrophic microbes. A small fraction of this DOC survives long enough to be routed to the interior ocean, which houses the largest and oldest DOC reservoir. DOC reactivity depends upon its intrinsic chemical composition and extrinsic environmental conditions. Therefore, recalcitrance is an emergent property of DOC that is analytically difficult to constrain. New isotopic techniques that track the flow of carbon through individual organic molecules show promise in unveiling specific biosynthetic or degradation pathways that control the metabolic turnover of DOC and its accumulation in the deep ocean. However, a multivariate approach is required to constrain current carbon fluxes so that we may better predict how the cycling of oceanic DOC will be altered with continued climate change. Ocean warming, acidification, and oxygen depletion may upset the balance between the primary production and heterotrophic reworking of DOC, thus modifying the amount and/or composition of recalcitrant DOC. Climate change and anthropogenic activities may enhance mobilization of terrestrial DOC and/or stimulate DOC production in coastal waters, but it is unclear how this would affect the flux of DOC to the open ocean. Here, we assess current knowledge on the oceanic DOC cycle and identify research gaps that must be addressed to successfully implement its use in global scale carbon models.

The global distribution of chromophoric dissolved organic matter (CDOM) in the euphotic layer of the Atlantic, Indian, and Pacific oceans (between 35° N and 40° S) was analyzed by absorption spectroscopy during the Malaspina 2010 circumnavigation. Absorption coefficients at 254 nm (a) and 325 nm (a), indices (a/a) and spectral slopes (between 275 and 295 nm, S) were calculated from the dissolved fraction of the UV absorption spectra to describe the amount and quality of CDOM. Generalized Additive Models (GAMs) were applied to evaluate the relevance of physical and biogeochemical drivers for the variability of CDOM. Besides the low CDOM values, a first division of our data following the Longhurst's biogeographic classification showed significant differences in CDOM levels among provinces. The lowest values of a and a were found in the oligotrophic gyres, particularly in the Indian Ocean, and the highest in the upwelling areas, particularly in the Equatorial Pacific. Opposite distributions were obtained for S and a/a, indicative of higher photobleaching in the gyres. Within each province, whereas a was constant through the photic layer, a increased significantly with depth as a result of the dominance of photobleaching over biological production in the surface layer and the opposite at depth. The Pacific provinces, including the subtropical gyres, showed, however, significantly higher a values, indicative of lower photobleaching/higher biological production. The GAM analysis indicates that a and a were primarily related to chlorophyll a (Chl a), exhibiting a significant positive linear response. Interestingly, Prochlorococcus and Synechococcus abundances were related to these absorption coefficients. Apparent oxygen utilization also contributed to explain the distributions of these absorption coefficients, being inversely related to a and directly related to a. These results are consistent with the premise that a could be a proxy for the concentration of dissolved org

Fluorescent dissolved organic matter (FDOM) in the Mediterranean Sea was analysed by excitation–emission matrix (EEM) spectroscopy and parallel factor (PARAFAC) analysis during the cruise HOTMIX 2014. A 4–component model, including 3 humic–like and 1 protein–like compounds, was obtained. To decipher the environmental factors that dictate the distributions of these components, we run generalized additive models (GAMs) in the epipelagic layer and an optimum multiparametric (OMP) water masses analysis in the meso– and bathypelagic layers. In the epipelagic layer, apparent oxygen utilization (AOU) and temperature presented the most significant effects on the variability of the marine humic-like peak M fluorescence, suggesting that its distribution was controlled by the net community respiration of organic matter and photobleaching. On the contrary, the variability of the soil humic-like peak E and the protein–like peak T fluorescence was explained mainly by the prokaryotic heterotrophic abundance, which decreased eastwards. In the meso– and bathypelagic layers, water mass mixing and basin–scale mineralization processes explained >72% and 63% of the humic–like and protein–like fluorescence variability, respectively. When analysing the two basins separately, the OMP model offered a better explanation of the distribution of fluorescence in the eastern Mediterranean Sea, as expected from the reduced biological activity in this ultra–oligotrophic basin. Furthermore, while western Mediterranean deep waters display the usual trend in the global ocean (increase of humic–like fluorescence and decrease of protein–like fluorescence with higher AOU values), the eastern Mediterranean deep waters presented an opposite trend. Different initial fluorescence intensities of the water masses that mix in the eastern basin, with Adriatic and Aegean origins, seem to be behind this contrasting pattern. The analysis of the transect–scale mineralization processes corroborate this hypothesis, su

We present here the results of a UNESCO/IOC baseline study of the megafaunal assemblages of the polymetallic nodule ecosystem of 5 areas within the Clarion Clipperton Zone (CCZ) of the eastern Pacific Ocean. The work was undertaken with a view to investigating the structure of the epifaunal populations associated with the benthic biotopes being targeted for nodule mining and developing an appropriate set of management tools and options. The general characteristics of nodule ecosystem and assemblages and their sensitivity to deep-sea mining are discussed in relation to water masses, surface to seabed water circulation, the nepheloid layer and processes taking place at the sediment interface. Management tools considered include species diversity and vulnerability indexes, GIS systems, zoning, and 3D rapid environmental assessment (REA). These strategies are proposed for trial during pilot mining operations within the CCZ.

Dissolved organic matter (DOM) plays a key role in global biogeochemical cycles and experiences changes in molecular composition as it undergoes processing. In the semi-closed basins of the oligotrophic Mediterranean Sea, these gradual molecular modifications can be observed in close proximity. In order to extend the spatial resolution of information on DOM molecular composition available from ultrahigh resolution mass spectrometry in this area, we relate this data to optical (fluorescence and absorption spectroscopy) measurements. Covariance between molecular formulae signal intensities and carbon-specific fluorescence intensities was examined by means of Spearman’s rank correlations. Fifty two per cent of the assigned molecular formulae were associated with at least one optical parameter, accounting for 70% of the total mass spectrum signal intensity. Furthermore, we obtained significant multiple linear regressions between optical and intensity-weighted molecular indices. The resulting regression equations were used to estimate molecular parameters such as the double bond equivalent, degradation state and occurrence of unsaturated aliphatic compounds from optical measurements. The statistical linkages between DOM molecular and optical properties illustrate that the simple, rapid and cost-efficient optical spectroscopic measurements provide valuable proxy information on the molecular composition of open ocean marine DOM.

Viruses are a key component of marine ecosystems, but the assessment of their global role in regulating microbial communities and the flux of carbon is precluded by a paucity of data, particularly in the deep ocean. We assessed patterns in viral abundance and production and the role of viral lysis as a driver of prokaryote mortality, from surface to bathypelagic layers, across the tropical and subtropical oceans. Viral abundance showed significant differences between oceans in the epipelagic and mesopelagic, but not in the bathypelagic, and decreased with depth, with an average power-law scaling exponent of −1.03 km−1 from an average of 7.76 × 106 viruses ml−1 in the epipelagic to 0.62 × 106 viruses ml−1 in the bathypelagic layer with an average integrated (0 to 4000 m) viral stock of about 0.004 to 0.044 g C m−2, half of which is found below 775 m. Lysogenic viral production was higher than lytic viral production in surface waters, whereas the opposite was found in the bathypelagic, where prokaryotic mortality due to viruses was estimated to be 60 times higher than grazing. Free viruses had turnover times of 0.1 days in the bathypelagic, revealing that viruses in the bathypelagic are highly dynamic. On the basis of the rates of lysed prokaryotic cells, we estimated that viruses release 145 Gt C year−1 in the global tropical and subtropical oceans. The active viral processes reported here demonstrate the importance of viruses in the production of dissolved organic carbon in the dark ocean, a major pathway in carbon cycling

Detailed examination of the absorption spectra from dark ocean samples allowed us to identify and deconvolve two distinct chromophores centered to 302 nm (UV) and 415 nm (visible) from the exponential decay curve characteristics of humic substances. The UV chromophore was ubiquitous in intermediate and deep waters, and it has been proposed as the secondary absorption peak of nitrate. The visible chromophore was prominent at the central and intermediate water masses of the North Pacific, and it has been proposed as cytochrome c. Subtraction of the modeled absorption spectra of the two chromophores from the measured absorption spectrum of the samples leads to a spectral slope overestimation by 13.3+-6.0% for S 275-295 and 14.8+-10.6% for S 350-400. To only consider the chromophoric fraction of DOM, the absorption spectra of nitrate should be substracted in samples with a [NO3-]:a 302 ration > 70 micromoles

Fluorescent dissolved organic matter (FDOM) in open surface waters (< 200 m) of the Atlantic, Pacific, and Indian oceans was analysed by excitation-emission matrix (EEM) spectroscopy and parallel factor analysis (PARAFAC). A four-component PARAFAC model was fit to the EEMs, which included two humic- (C1 and C2) and two amino acid-like (C3 and C4) components previously identified in ocean waters. Generalized-additive models (GAMs) were used to explore the environmental factors that drive the global distribution of these PARAFAC components. The explained variance for the humic-like components was substantially larger (> 70%) than for the amino acid-like components (< 35%). The environmental variables exhibiting the largest effect on the global distribution of C1 and C2 were apparent oxygen utilisation followed by chlorophyll a. Positive non-linear relationships between both predictor variables and the two humic-like PARAFAC components suggest that their distribution are biologically controlled. Compared with the dark ocean (> 200 m), the relationships of C1 and C2 with AOU indicate a higher C1/AOU and C2/AOU ratios of the humic-like substances in the dark ocean than in the surface ocean where a net effect of photobleaching is also detected. C3 (tryptophan-like) and C4 (tyrosine-like) variability was mostly dictated by salinity (S), by means of positive non-linear relationships, suggesting a primary physical control of their distributions at the global surface ocean scale that could be related to the changing evaporation-precipitation regime. Remarkably, bacterial biomass (BB) only contributed to explain a minor part of the variability of C1 and C4

[EN] The transformation of biologically labile organic matter into refractory compounds by prokaryotic activity has been termed the 'microbial carbon pump' (MCP) and may constitute an effective mechanism to store reduced carbon in the dark ocean. Understanding its generation and its role in carbon sequestration is crucial to assess its relevante in the context of the global carbon cycle. The main aim of this PhD thesis is to test the significance of the chromophoric (CDOM) and fluorescent (FDOM) fractions of dissolved organic matter (DOM) as tracers for the microbial production of recalcitrant DOM in the global ocean. All its content is framed in Malaspina 2010 circumnavigation, which allowed us to produce the first global inventory of the optical properties of DOM in both the surface ocean (<200 m), gathered by Longhurst´s biogegraphic provinces, and the dark ocean (>200 m) by the main water masses., [ES] La transformación de materia orgánica lábil en recalcitrante a consecuencia del metabolismo de los procariotas se ha denominado "bomba microbiana de carbono" y puede constituir un mecanismo efectivo de almacenamiento de carbono reducido en el interior del océano. Comprender la generación de materia orgánica disuelta (MOD) recalcitrante el papel que esta juega en el almacenamiento de carbono en los océanos es crucial para cuantificar su relevancia en el contexto del ciclo global del carbono. En este contexto, el principal objetivo de esta Tesis Doctoral es comprobar la validez de las fracciones cromófora (CMOD) y florescente (FMOD) de la MOD como trazadores de la producción microbiana de MOD recalcitrante en el océnao global. El trabajo se enmarca en la expedición de circunnavegación Malaspina 2010, que ha hecho posible producir el primer inventario global de propiedades ópticas de la MOD tanto en la capa superficial (<200 m), organizado por masas de agua.

Bacterial biomass production is a key parameter for evaluating the role of bacterioplankton in ocean carbon cycling. However, bacterial production cannot be directly measured and is typically estimated from the incorporation rates of radiolabelled leucine. The conversion of leucine uptake rates into bacterial carbon production rates requires the use of conversion factors (CFs) which must be empirically determined. Despite the empirical leucine-to-carbon CFs vary widely across environments very little is known about its potential controlling factors. We conducted a set of 10 surface seawater cultures experiments where the growth of the natural bacterial assemblage was promoted by filtration (removal of grazers) or by both filtration and dilution. Sampling stations were located between 30 ºN and 30 ºS, including the Atlantic, Pacific and Indian oceans. CFs varied from 0.13 to 1.47 Kg C mol Leu-1, being higher in the filtrated than in the filtrated and diluted treatment. The abundance of picocyanobacteria explained 60% of the observed variability. Our results further suggest that the composition of bacterioplankton, as assessed by ARISA fingerprinting, may partially explain the observed variation in CFs.

Marine dissolved organic matter (DOM) is one of the largest reservoirs of reduced carbon on Earth. In the dark ocean (>200 m), most of this carbon is refractory DOM. This refractory DOM, largely produced during microbial mineralization of organic matter, includes humic-like substances generated in situ and detectable by fluorescence spectroscopy. Here we show two ubiquitous humic-like fluorophores with turnover times of 435±41 and 610±55 years, which persist significantly longer than the ∼350 years that the dark global ocean takes to renew. In parallel, decay of a tyrosine-like fluorophore with a turnover time of 379±103 years is also detected. We propose the use of DOM fluorescence to study the cycling of resistant DOM that is preserved at centennial timescales and could represent a mechanism of carbon sequestration (humic-like fraction) and the decaying DOM injected into the dark global ocean, where it decreases at centennial timescales (tyrosine-like fraction). © 2015 Macmillan Publishers Limited. All rights reserved