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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.

Abstract Marine dissolved organic matter (DOM) comprises a vast and unexplored molecular space. Most of it resided in the oceans for thousands of years. It is among the most diverse molecular mixtures known, consisting of millions of individual compounds. More than 1 Eg of this material exists on the planet. As such, it comprises a formidable source of natural products promising significant potential for new biotechnological purposes. Great emphasis has been placed on understanding the role of DOM in biogeochemical cycles and climate attenuation, its lifespan, interaction with microorganisms, as well as its molecular composition. Yet, probing DOM bioactivities is in its infancy, largely because it is technically challenging due to the chemical complexity of the material. It is of considerable interest to develop technologies capable to better discern DOM bioactivities. Modern screening technologies are opening new avenues allowing accelerated identification of bioactivities for small molecules from natural products. These methods diminish a priori the need for laborious chemical fractionation. We examine here the application of untargeted metabolomics and multiplexed high-throughput molecular-phenotypic screening techniques that are providing first insights on previously undetectable DOM bioactivities. Key points • Marine DOM is a vast, unexplored biotechnological resource. • Untargeted bioscreening approaches are emerging for natural product screening. • Perspectives for developing bioscreening platforms for marine DOM are discussed.

Research article, 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, suggesting a production of humic–like and a consumption of protein–like fluorescence in parallel with water mass ageing. Remarkably, the transect–scale variability of the chromophoric dissolved organic matter (CDOM) absorbing at the excitation wavelength of the humic–like peak M indicates an unexpected loss with increasing AOU, which suggests that the consumption of the non–fluorescent fraction of CDOM absorbing at that wavelength exceeded the production of the fluorescent fraction observed here, Project HOTMIX (reference CTM2011–30010–C02 01–MAR and 02–MAR), co–financed with FEDER funds (re ference BES–2012–056175) ; the project MODMED from CSIC (PIE, 201730E020) and the project FERMIO (MINECO, CTM2014–57334–JIN), co–financed with FEDER funds, 3,269

10 pages, 3 figures, 1 table, supporting information https://dx.doi.org/10.1002/2016GL069878.-- The data used are listed in Table 1, and the “Chromophores Toolbox” to estimate the UV and Visible chromophores is available at the Web page “http://ecologia.ugr.es/pages/herramientas/toolbox-matlab?lang=en”

Teira, Eva ... et. al.-- 9 pages, 6 figures, 2 tables, The transformation of leucine incorporation rates to prokaryotic carbon production rates requires the use of either theoretical or empirically determined conversion factors. Empirical leucine-to-carbon conversion factors (eCFs) vary widely across environments, and little is known about their potential controlling factors. We conducted 10 surface seawater manipulation experiments across the world's oceans, where the growth of the natural prokaryotic assemblages was promoted by filtration (i.e., removal of grazers [F treatment]) or filtration combined with dilution (i.e., also relieving resource competition [FD treatment]). The impact of sunlight exposure was also evaluated in the FD treatments, and we did not find a significant effect on the eCFs. The eCFs varied from 0.09 to 1.47 kg C mol Leu and were significantly lower in the FD than in the F samples. Also, changes in bacterial community composition during the incubations, as assessed by automated ribosomal intergenic spacer analysis (ARISA), were more pronounced in the FD than in the F treatments, compared to unmanipulated controls. Thus, we discourage the common procedure of diluting samples (in addition to filtration) for eCF determination. The eCFs in the filtered treatment were negatively correlated with the initial chlorophyll a concentration, picocyanobacterial abundance (mostly Prochlorococcus), and the percentage of heterotrophic prokaryotes with high nucleic acid content (%HNA). The latter two variables explained 80% of the eCF variability in the F treatment, supporting the view that both Prochlorococcus and HNA prokaryotes incorporate leucine in substantial amounts, although this results in relatively low carbon production rates in the oligotrophic ocean, This study was supported by the by the Spanish Ministry of Science and Innovation through project Consolider-Ingenio Malaspina 2010 (CSD2008-00077) and project DIFUNCAR (CTM2008-03790/MAR)

Original research article, Chromophoric dissolved organic matter (CDOM) in the open Mediterranean Sea (MedSea) is barely documented, remaining the basin–wide patterns in intermediate and deep waters still enigmatic. Here, full–depth distributions of CDOM absorption coefficients and spectral slopes recorded during the HOTMIX 2014 cruise are presented and their respective environmental drivers resolved. General Additive Models (GAMs) in surface waters and Optimum MultiParameter (OMP) water mass analysis in deep waters were applied. In the surface, apparent oxygen utilisation (AOU), a proxy to cumulative net community respiration, explained most of the variability of dissolved organic carbon (DOC) and the absorption coefficient at 254 nm (a254), whereas the absorption coefficient at 325 nm (a325), and the spectral slopes were mostly explained by potential temperature, a proxy to stratification and solar radiation, indicating that both water column stability and photobleaching may drive the variability of the UV–A absorbing CDOM components. In deep waters, the effect of water mass mixing and basin–scale mineralization were discerned from local mineralization processes. Water mass mixing and basin–scale mineralization contributed more substantially to explain the variability of DOC, a254 and a325 (82–91%) than the variability of the spectral slopes (35–64%). Local mineralization processes indicate that DOC and CDOM play a more relevant role in the carbon cycle in the Eastern (EastMed) than in the Western (WestMed) Mediterranean: whereas DOC contributed to 66 ± 10% of the oxygen demand in the EastMed, it represented only 24 ± 4% in the WestMed. Independently of basins and layers, a254 revealed as an excellent proxy to the concentration of DOC in the MedSea. Also, the unexpected inverse relationship of a325 with AOU indicates that the consumption of the UV–A absorbing CDOM fraction prevails over their production, Spanish Ministry of Education and Culture, Spanish Ministry of Economy and Competitiviness, FEDER, CSIC, University of Granada, 3,269

The omnipresence of chromophoric dissolved organic matter (CDOM) in the open ocean enables its use as a tracer for biochemical processes throughout the global overturning circulation. We made an inventory of CDOM optical properties, ideal water age (τ), and apparent oxygen utilization (AOU) along the Atlantic, Indian, and Pacific Ocean waters sampled during the Malaspina 2010 expedition. A water mass analysis was applied to obtain intrinsic, hereinafter archetypal, values of τ, AOU, oxygen utilization rate (OUR), and CDOM absorption coefficients, spectral slopes and quantum yield for each one of the 22 water types intercepted during this circumnavigation. Archetypal values of AOU and OUR have been used to trace the differential influence of water mass aging and aging rates, respectively, on CDOM variables. Whereas the absorption coefficient at 325 nm (a325) and the fluorescence quantum yield at 340 nm (Φ340) increased, the spectral slope over the wavelength range 275–295 nm (S275–295) and the ratio of spectral slopes over the ranges 275–295 nm and 350–400 nm (SR) decreased significantly with water mass aging (AOU). Combination of the slope of the linear regression between archetypal AOU and a325 with the estimated global OUR allowed us to obtain a CDOM turnover time of 634 ± 120 years, which exceeds the flushing time of the dark ocean (>200 m) by 46%. This positive relationship supports the assumption of in situ production and accumulation of CDOM as a by-product of microbial metabolism as water masses turn older. Furthermore, our data evidence that global-scale CDOM quantity (a325) is more dependent on aging (AOU), whereas CDOM quality (S275–295, SR, Φ340) is more dependent on aging rate (OUR).

Lara, Elena ... et al.-- 12 pages, 4 figures, 3 tables, supplementary material http://advances.sciencemag.org/content/suppl/2017/09/01/3.9.e1602565.DC1, 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, This work was supported by the Spanish Ministry of Science and Innovation through project Consolider-Ingenio Malaspina 2010 (CSD2008-00077) and funding received through grant FCS/1/2449-01-01 of the Office of Sponsored Research of the King Abdullah University of Science and Technology., We acknowledge support by the CSIC Open Access Publication Initiative through its Unit of Information Resources for Research (URICI).

Original research paper, 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., y the project HOTMIX (grant number CTM2011-30010-C02-MAR) and the project FERMIO (MINECO, CTM2014-57334-JIN), both co-financed with FEDER funds, 2,927

Background. The effluents of the mono-specific aquaculture contain high concentrations of dissolved nutrients and organic matter, which affect negatively water quality of the recipient aquatic ecosystems. A key feature of water quality is its transparency. Chromophoric dissolved organic matter (CDOM) determines most of the light transmission in the ultraviolet and blue bands in the aquatic ecosystems. A sustainable alternative to mono-specific aquaculture is the integrated multitrophic aquaculture that includes species trophically complementary named “extractive” species. Sea cucumbers are recognized as efficient extractive species, with a high potential to improve water quality, due to the consumption of particulate organic matter (POM). However, the effects of sea cucumbers on CDOM are still unknown. Methods. During one year, we biweekly monitored CDOM in two aquaculture tanks with different trophic structure. One of the tanks (-holothurian tank) only contained the primary species, Anemonia sulcata, whereas the other tank (+ holothurian tank) also contained individuals of Holothuria tubulosa and H. forskali. We routinely performed CDOM absorption spectra from 200 nm to 750 nm and determined quantitative (absorption coefficients at 325 nm) and qualitative (spectral slopes and molar absorption coefficients at 325 nm) optical parameters in the inlet waters, in the tanks, and in their corresponding effluents. Results. Absorption coefficients at 325 nm (a325) and spectral slopes from 275 to 295 nm (S275-295) were significantly lower in the effluents of the +holothurian tank (average: 0.33 and 16 μm-1, respectively) than in the effluents of the −holothurian tank (average: 0.69 m-1 and 34 μm-1, respectively), being the former similar to those found in the inlet waters (average: 0.32 m-1 and 22 μm-1, respectively). This reduction in CDOM absorption appears to be mediated by the POM consumption by the holothurians. The reduction of POM concentration in the +holothurian tank may weaken the process of POM disaggregation into dissolved organic matter, which ultimately might have generated CDOM in the –holothurian tank. Discussion. Extractive species such as holothurians improve water transparency through POM consumption, likely because reduces POM disaggregation into CDOM. We suggest that CDOM monitoring in aquaculture facilities, using automatic probes or even remote sensing, could be a useful tool to trace the effectiveness of extractive species at large scales of time and space.

Estuaries present high content of chromophoric and fluorescent dissolved organic matter (CDOM, FDOM) affecting the attenuation of ultraviolet and blue radiation. In temperate and tropical estuaries, the main CDOM source is riverine input that generally mixes conservatively with the oceanic waters leading to negative relationships between CDOM and salinity. In Mediterranean estuaries, riverine inputs are more limited or absent during the dry season producing a negative hydrological budget and, consequently, hypersalinity and an inverse circulation pattern. Much remains to be understood about CDOM and FDOM dynamics during rainy and dry periods in these last estuaries. In this study, we determined DOM absorbance and fluorescence in the Bay of Cadiz, Spain during a rainy (high riverine inputs) and dry (hypersaline conditions) period. We determined the absorption coefficients at 355 nm (a355) and acquired excitationeemission matrices (EEMs). The EEMs showed two fluorescence peaks associated with terrestrial humic-like components (peaks A and C), one peak considered to be a marine humic-like component (peak M), and two peaks considered to be amino acid-like components (peaks T and B). The a355 values ranged from 0.30 to 1.99 m � 1 with the highest values during the dry season. From the rainy season to the dry season, the overall fluorescence intensity increased and fluorescent peaks M, B, and T increased by greater than two orders of magnitude, whereas the fluorescence intensities of peaks A and C changed less than one order of magnitude. Unlike temperate and tropical estuaries, the a355 values and fluorescence of the five peaks were positive and significantly related to salinity, but with different slopes. The inverse nature of the Bay of Cadiz during the dry season could be responsible for these positive trends between CDOM/FDOM and salinity. The slopes of the humic-like peaks A and C were lower than the a355 slope suggesting their preferential losses, likely due to photobleaching. By contrast, the slopes of the amino acid-like peaks B and T were higher than the a355 slope suggesting an in situ production of these fluorophores, likely due to diffusion from salt marsh and coastal sediments.

Corrigendum: Turnover time of fluorescent dissolved organic matter in the dark global ocean

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).

Background Mono-specific aquaculture effluents contain high concentrations of nutrients and organic matter, which affect negatively the water quality of the recipient ecosystems. A fundamental feature of water quality is its transparency. The fraction of dissolved organic matter that absorbs light is named chromophoric dissolved organic matter (CDOM). A sustainable alternative to mono-specific aquaculture is the multitrophic aquaculture that includes species trophically complementary named “extractive” species that uptake the waste byproducts. Sea cucumbers are recognized as efficient extractive species due to the consumption of particulate organic matter (POM). However, the effects of sea cucumbers on CDOM are still unknown. Methods During more than one year, we monitored CDOM in two big-volume tanks with different trophic structure. One of the tanks (−holothurian) only contained around 810 individuals of Anemonia sulcata, whereas the other tank (+holothurian) also included 90 individuals of Holothuria tubulosa and Holothuria forskali. We routinely analyzed CDOM absorption spectra and determined quantitative (absorption coefficients at 325 nm) and qualitative (spectral slopes) optical parameters in the inlet waters, within the tanks, and in their corresponding effluents. To confirm the time-series results, we also performed three experiments. Each experiment consisted of two treatments: +holothurians (+H) and –holothurians (−H). We set up three +H tanks with 80 individuals of A. sulcata and 10 individuals of H. tubulosa in each tank and four –H tanks that contained only 80 individuals of A. sulcata. Results In the time-series, absorption coefficients at 325 nm (a325) and spectral slopes from 275 to 295 nm (S275−295) were significantly lower in the effluent of the +holothurian tank (average: 0.33 m−1 and 16 µm−1, respectively) than in the effluent of the −holothurian tank (average: 0.69 m−1 and 34 µm−1, respectively), the former being similar to those found in the inlet waters (average: 0.32 m−1 and 22 µm−1, respectively). This reduction in the absorption of the dissolved organic matter appears to be mediated by the POM consumption by holothurians. The experiments confirmed the results observed in the time-series. The a325 and S275−295 values were significantly lower in the treatment with holothurians than in the treatment without holothurians indicating a reduction in the concentration of chromophoric organic compounds, particularly of low molecular weight. Discussion Consequently, sea cucumbers appear to improve water transparency in aquaculture tanks. The underlying mechanism of this improvement might be related to the POM consumption by holothurians, which reduces the concentration of CDOM derived from POM disaggregation or to the direct assimilation of dissolved compounds of low molecular weight as chromophoric amino acids.

Catalá, Teresa S. ... et. al.-- 8 pages, 4 figures, 1 table, supplementary information http://www.nature.com/ncomms/2015/150129/ncomms6986/full/ncomms6986.html#/supplementary-information, 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, This study was financed by the Malaspina 2010 circumnavigation expedition (grant number CSD2008–00077). C.R.-C. acknowledges funding through a Beatriu de Pinos postdoctoral fellowship from the Generalitat de Catalunya. M.N.-C. was funded by the CSIC Program ‘Junta para la Ampliación de Estudios’ cofinanced by the ESF