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Mesoscale eddies are frequently observed in the Eastern Tropical North Atlantic (ETNA), yet their effects on the transport and distribution of biogeochemical solutes, and specifically on the production and remineralization of dissolved organic matter (DOM) remain difficult to elucidate. Here, we investigated the submesoscale variability of chromophoric DOM (CDOM) and fluorescent DOM (FDOM) together with microbial production and remineralization processes in two cyclonic eddies (CEs) in the ETNA during summer and winter 2019. One CE, formed near the coast off Mauritania during the post-upwelling season, was sampled along a ∼900 km zonal corridor between Mauritania and the Cape Verde Islands. The other CE, formed nearby Brava Island, was out of coastal influence. Four fluorescent components were identified with parallel factor analysis, two humic-like, and two protein-like components. Humic-like FDOM components correlated to optode-based community respiration and were also good indicators of upwelling associated with the Brava Island CE as they correlated to physical parameters (e.g., temperature) and to dissolved inorganic nitrogen. The tryptophan-like FDOM components correlated with the carbon and nitrogen content of semi-labile DOM, phytoplankton biomass, community respiration, and bacterial production. Overall, our study revealed that DOM optical properties are suitable for tracing freshly produced organic matter and the transport of remineralized DOM within offshore eddies. Key Points: - Four fluorescent dissolved organic matter (FDOM) components were studied in two cyclonic eddies (CEs) in the Eastern Tropical North Atlantic - Tryptophan-like FDOM was an indicator of the CEs' productivity as it correlated with semi-labile dissolved organic matter and microbial metabolic activities - Humic-like FDOM was a by-product of microbial respiration; its distribution within an offshore CE covaried with nutrient upwelling

The Mediterranean Sea is a miniature ocean divided by the Sicily Strait into two basins with a marked west to east trophic gradient and separated of the nearby eastern Atlantic Ocean by the Strait of Gibraltar. Here, we test the hypothesis that these physical and environmental barriers favor the development of specific prokaryotic assemblages, leading to changes in community structure both in the vertical and horizontal spatial scales. By analyzing taxonomic and phylogenetic diversity using amplicon sequence variants (ASVs) of the 16S rRNA gene, we show that there is indeed marked vertical segregation of prokaryotic groups, similar to that found in other areas of the ocean, but also a clear horizontal structuring among the two Mediterranean basins and the adjacent Atlantic waters. Prokaryotic diversity increased with depth and toward the Atlantic, whereas the easternmost stations displayed more phylogenetically diverse phylotypes, despite harboring globally less diverse communities. Basin-indicator taxa (ASVs) accounted for a large fraction of the community (between 50% and 80%) in each of the basins at the surface and bathypelagic layers, being associated with different environmental variables. The existence of biogeographic and environmental barriers in the Mediterranean Sea is likely related to the trophic gradient at the surface and the isolation of water bodies in depth due to the Gibraltar and Sicily straits. Our work highlights the importance of studying microbial regional biogeography and provides the basis for future studies on the impact of this regionalization in the function of Mediterranean Sea prokaryotic communities.

Transparent exopolymer particles (TEP) and Coomassie stainable particles (CSP) are gel-like particles, ubiquitous in the ocean, that affect important biogeochemical processes including organic carbon cycling by planktonic food webs. Despite much research on both groups of particles (especially TEP) over many years, whether they exist as distinctly stainable fractions of the same particles or as independent particles, each with different driving factors, remains unclear. To address this question, we examined the temporal dynamics of TEP and CSP over 2 complete seasonal cycles at 2 coastal sites in the Northwestern Mediterranean Sea, the Blanes Bay Microbial Observatory (BBMO) and the L’Estartit Oceanographic Station (EOS), as well as their spatial distribution along a coast-to-offshore transect. Biological, chemical, and physical variables were measured in parallel. Surface concentrations (mean + standard deviation [SD]) of TEP were 36.7 + 21.5 µg Xanthan Gum (XG) eq L–1 at BBMO and 36.6 + 28.3 µg XG eq L–1 at EOS; for CSP, they were 11.9 + 6.1 µg BSA eq L–1 at BBMO and 13.0 + 5.9 µg BSA eq L–1 at EOS. Seasonal variability was more evident at EOS, where surface TEP and CSP concentrations peaked in summer and spring, respectively, and less predictable at the shore-most station, BBMO. Vertical distributions between surface and 80 m, monitored at EOS, showed highest TEP concentrations within the surface mixed layer during the stratification period, whereas CSP concentrations were highest before the onset of summer stratification. Phytoplankton were the main drivers of TEP and CSP distributions, although nutrient limitation and saturating irradiance also appeared to play important roles. The dynamics and distribution of TEP and CSP were uncoupled both in the coastal sites and along the transect, suggesting that they are different types of particles produced and consumed differently in response to environmental variability.

Transparent exopolymer particles (TEP) and Coomassie stainable particles (CSP) are gel-like particles, ubiquitous in the ocean, that affect important biogeochemical processes including organic carbon cycling by planktonic food webs. Despite much research on both groups of particles (especially TEP) over many years, whether they exist as distinctly stainable fractions of the same particles or as independent particles, each with different driving factors, remains unclear. To address this question, we examined the temporal dynamics of TEP and CSP over 2 complete seasonal cycles at 2 coastal sites in the Northwestern Mediterranean Sea, the Blanes Bay Microbial Observatory (BBMO) and the L’Estartit Oceanographic Station (EOS), as well as their spatial distribution along a coast-to-offshore transect. Biological, chemical, and physical variables were measured in parallel. Surface concentrations (mean ± standard deviation [SD]) of TEP were 36.7 ± 21.5 µg Xanthan Gum (XG) eq L–1 at BBMO and 36.6 ± 28.3 µg XG eq L–1 at EOS; for CSP, they were 11.9 ± 6.1 µg BSA eq L–1 at BBMO and 13.0 ± 5.9 µg BSA eq L–1 at EOS. Seasonal variability was more evident at EOS, where surface TEP and CSP concentrations peaked in summer and spring, respectively, and less predictable at the shore-most station, BBMO. Vertical distributions between surface and 80 m, monitored at EOS, showed highest TEP concentrations within the surface mixed layer during the stratification period, whereas CSP concentrations were highest before the onset of summer stratification. Phytoplankton were the main drivers of TEP and CSP distributions, although nutrient limitation and saturating irradiance also appeared to play important roles. The dynamics and distribution of TEP and CSP were uncoupled both in the coastal sites and along the transect, suggesting that they are different types of particles produced and consumed differently in response to environmental variability.

Marine heterotrophic prokaryotes (HP) play a key role in organic matter processing in the ocean; however, the view of HP as dissolved organic matter (DOM) sources remains underexplored. In this study, we quantified and optically characterized the DOM produced by two single marine bacterial strains. We then tested the availability of these DOM sources to in situ Mediterranean Sea HP communities. Two bacterial strains were used: Photobacterium angustum (a copiotrophic gammaproteobacterium) and Sphingopyxis alaskensis (an oligotrophic alphaproteobacterium). When cultivated on glucose as the sole carbon source, the two strains released from 7% to 23% of initial glucose as bacterial derived DOM (B-DOM), the quality of which (as enrichment in humic or protein-like substances) differed between strains. B-DOM induced significant growth and carbon consumption of natural HP communities, suggesting that it was partly labile. However, B-DOM consistently promoted lower prokaryotic growth efficiencies than in situ DOM. In addition, B-DOM changed HP exoenzymatic activities, enhancing aminopeptidase activity when degrading P. angustum DOM, and alkaline phosphatase activity when using S. alaskensis DOM, and promoted differences in HP diversity and composition. DOM produced by HP affects in situ prokaryotic metabolism and diversity, thus changing the pathways for DOM cycling (e.g. respiration over biomass production) in the ocean.

The Mediterranean Sea is a miniature ocean divided by the Sicily Strait into two basins with a marked west to east trophic gradient and separated of the nearby eastern Atlantic Ocean by the Strait of Gibraltar. Here, we test the hypothesis that these physical and environmental barriers favor the development of specific prokaryotic assemblages, leading to changes in community structure both in the vertical and horizontal spatial scales. By analyzing taxonomic and phylogenetic diversity using amplicon sequence variants (ASVs) of the 16S rRNA gene, we show that there is indeed marked vertical segregation of prokaryotic groups, similar to that found in other areas of the ocean, but also a clear horizontal structuring among the two Mediterranean basins and the adjacent Atlantic waters. Prokaryotic diversity increased with depth and toward the Atlantic, whereas the easternmost stations displayed more phylogenetically diverse phylotypes, despite harboring globally less diverse communities. Basin-indicator taxa (ASVs) accounted for a large fraction of the community (between 50% and 80%) in each of the basins at the surface and bathypelagic layers, being associated with different environmental variables. The existence of biogeographic and environmental barriers in the Mediterranean Sea is likely related to the trophic gradient at the surface and the isolation of water bodies in depth due to the Gibraltar and Sicily straits. Our work highlights the importance of studying microbial regional biogeography and provides the basis for future studies on the impact of this regionalization in the function of Mediterranean Sea prokaryotic communities

We explored how changes of viral abundance and community composition among four contrasting regions in the Southern Ocean relied on physicochemical and microbiological traits. During January–February 2015, we visited areas north and south of the South Orkney Islands (NSO and SSO) characterized by low temperature and salinity and high inorganic nutrient concentration, north of South Georgia Island (NSG) and west of Anvers Island (WA), which have relatively higher temperatures and lower inorganic nutrient concentrations. Surface viral abundance (VA) was highest in NSG (21.50 ± 10.70 × 106 viruses mL−1) and lowest in SSO (2.96 ± 1.48 × 106 viruses mL−1). VA was positively correlated with temperature, prokaryote abundance and prokaryotic heterotrophic production, chlorophyll a, diatoms, haptophytes, fluorescent organic matter, and isoprene concentration, and was negatively correlated with inorganic nutrients (NO3−, SiO42−, PO43−), and dimethyl sulfide (DMS) concentrations. Viral communities determined by randomly amplified polymorphic DNA–polymerase chain reaction (RAPD-PCR) were grouped according to the sampling location, being more similar within them than among regions. The first two axes of a canonical correspondence analysis, including physicochemical (temperature, salinity, inorganic nutrients—NO3−, SiO42−, and dimethyl sulfoniopropionate -DMSP- and isoprene concentrations) and microbiological (chlorophyll a, haptophytes and diatom, and prokaryote abundance and prokaryotic heterotrophic production) factors accounted for 62.9% of the variance. The first axis, temperature-related, accounted for 33.8%; the second one, salinity-related, accounted for 29.1%. Thus, different environmental situations likely select different hosts for viruses, leading to distinct viral communities.

Tesi per compendi de publicacions, Transparent exopolymer particles (TEP) and Coomassie stainable particles (CSP) are operationally defined as organic particles > 0.4 µm that are stainable with the dyes Alcian Blue (specific for acidic polysaccharides) and Coomassie Brilliant Blue (specific for proteins), respectively. They are ubiquitous in the ocean, where they play important roles in biogeochemical processes such as the carbon cycle and sea-air gas and particle exchanges. However, there is a lack of large-scale studies of TEP and CSP distributions in the ocean, particularly in the open ocean, as well as temporal studies following their dynamics over more than one complete seasonal cycle. In addition, it is not clear yet whether these particles represent independent particle fractions or not and which are their main drivers, with a particular lack of information on CSP. In this thesis, TEP and CSP distributions were characterized, combining the horizontal and vertical scales whenever possible, in distinct regions of the ocean: Atlantic Ocean (October-November 2014), Southern Ocean (January 2015 and January-March 2017) and the NW Mediterranean Sea (October 2015). Besides, a time series study was conducted in two coastal stations in the NW Mediterranean Sea for two complete seasonal cycles (2015-2017). In all cases, a number of physical, chemical and biological variables were determined in parallel in order to explore the main drivers of TEP and CSP distributions. TEP concentrations ranged from below detection limit to 446 µg XG eq L-1, whereas CSP concentrations ranged between 0.3 and 52.2 µg BSA eq L-1. The highest TEP concentrations were found in the edge of the Canary Coastal Upwelling, the Southwestern Atlantic Shelf and some regions of the Southern Ocean, whereas the highest CSP concentrations were found in the Southern Ocean. Phytoplankton biomass, and not heterotrophic prokaryotic biomass or activity, is the best predictor of the concentration of both particle types, yet no single taxonomic g, Las partículas exopoliméricas transparentes (TEP) y las partículas teñibles con Coomassie (CSP) se definen operacionalmente como aquellas partículas > 0.4 µm que se tiñen con las tinciones azul alcián (específico para polisacáridos ácidos) y azul de Coomassie (específico para proteínas), respectivamente. Ambos tipos de partículas están presentes en todo el océano y juegan un papel fundamental en varios procesos biogeoquímicos como el ciclo del carbono y el intercambio de gases y partículas entre el océano y la atmósfera. Sin embargo, existen pocos estudios que describan sus distribuciones en el océano a gran escala, o sus dinámicas temporales a lo largo de más de un ciclo estacional completo. En esta tesis, hemos caracterizado la distribución de TEP y CSP, combinando las escalas horizontal y vertical cuando ha sido posible, en diferentes regiones del océano: El océano Atlántico (octubre-noviembre 2014), el océano Antártico (enero 2015 y enero-marzo 2017), y el Mar Mediterráneo noroccidental (octubre 2015). Además, se llevó a cabo un estudio temporal en dos estaciones costeras del Mar Mediterráneo noroccidental, tomando muestras mensuales durante dos ciclos estacionales completos (2015-2017). En todos los casos se analizaron variables físicas, químicas y biológicas en paralelo a las medidas de TEP y CSP, con el fin de explorar los principales factores de regulación de sus distribuciones. Las concentraciones de TEP oscilaron entre valores bajo del límite de detección y 446 µg XG eq L-1, mientras que las concentraciones de CSP oscilaron entre 0.3 y 52.2 µg BSA eq L-1. Las concentraciones más altas de TEP se encontraron en un extremo del afloramiento de la costa canaria, la plataforma continental al suroeste del océano Atlántico y en algunas regiones del océano Antártico, mientras que las concentraciones más elevadas de CSP se observaron en el océano Antártico. La biomasa del fitoplancton, y no la biomasa ni la actividad de los procariotas heterótrofos, es el mejor pred, Les partícules exopolimèriques transparents (TEP) i les partícules tenyibles amb Coomassie (CSP) es defineixen operacionalment com aquelles partícules > 0.4 μm que es tenyeixen amb les tincions blau alcian (específic per polisacàrids àcids) i blau de Coomassie (específic per proteïnes), respectivament. Aquestes partícules son ubiqües a l’oceà i juguen un paper important en processos biogeoquímics com el cicle del carboni i l’intercanvi de gasos i partícules entre el mar i l’atmosfera. No obstant això, hi ha pocs estudis que descriguin les distribucions a gran escala de TEP i CSP a l’oceà, particularment a l’oceà obert, o la seva variació temporal al llarg de més d’un cicle estacional complet. En aquesta tesis hem caracteritzat les distribucions de TEP i CSP, tot combinant les escales horitzontal i vertical quan ha estat possible, en diferents regions de l’oceà: l’oceà Atlàntic (octubre-novembre 2014), l’oceà Antàrtic (gener 2015 i gener-març 2017), i el Mar Mediterrani nord-occidental (octubre 2015). A més, hem dut a terme un estudi temporal en dos estacions costaneres del Mar Mediterrani nordoccidental durant dos cicles estacionals complets (2015-2017). En tots els casos es van mesurar variables físiques, químiques i biològiques en paral·lel, amb la finalitat d’explorar els principals factors de regulació de les distribucions de TEP i CSP. Les concentracions de TEP varen oscil·lar entre per sota del límit de detecció i 446 μg XG eq L-1, mentre que les concentracions de CSP oscil·laren entre 0.3 i 52.2 μg BSA eq L-1. Les concentracions més altes de TEP es van trobar a la vora del aflorament de la costa canària, a la plataforma continental del suroest atlàntic i en algunes regions de l’oceà Antàrtic. La biomassa del fitoplàncton, i no la biomassa ni la activitat dels procariotes heteròtrofs, és el millor predictor de la concentració d’ambdós tipus de partícules. Tanmateix, cap dels grups taxonòmics de fitoplàncton ha resultat ser el productor universalment dominant., Postprint (published version)

The relationships between the structure of the phytoplankton community and the bio-optical properties of surface waters were studied during the TransPEGASO cruise along a transect across the Atlantic Ocean that covered seven biogeographical provinces, from the Alborán Sea (SW Mediterranean) to the Patagonian Shelf. We characterized the composition of the phytoplankton community by means of high-performance liquid chromatography and CHEMTAX pigment analyses applied to whole water and two filtration size classes (<3 and ≥3 µm), flow cytometric determinations and microscopic observations. Additionally, the study was complemented by measurements of the absorption of particulate matter and coloured dissolved organic matter (CDOM). The size class distribution of the chlorophyll a (Chl a) obtained from the size-fractionated filtration (SFF) was compared with that resulting from the diagnostic pigment algorithms (VU) developed by Vidussi et al. (2001) and Uitz et al. (2006), and the total Chl a–based expressions (HI) of Hirata et al. (2011). The seven provinces crossed by the transect could be divided into an oligotrophic group with Chl a<0.25 mg m–3 comprising the tropical and subtropical Atlantic (including the Canary Current Coastal Province), and a eutrophic group (Chl a >0.5 mg m–3) with a single Mediterranean (MEDI) sample and those from the southwestern Atlantic Shelf (SWAS). According to CHEMTAX, the most important taxa in the tropical and subtropical Atlantic were Prochlorococcus, haptophytes and Synechoccoccus, while the MEDI and SWAS were dominated by diatoms and haptophytes. Both the VU and HI algorithms, which are based on pigment composition or Chl a concentration, predicted for SWAS a high proportion of nano- and microphytoplankton, while the SFF indicated dominance of the <3 µm size class. In addition, the CHEMTAX results indicated a high average diatom contribution in this province. However, at several SWAS stations with relatively high values of diatom Chl

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)