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The Ocean microbiome has a crucial role on Earth’s biogeochemical cycles, but also represents a tremendous potential for biological applications as part of the bluebiotechnology. During the last decade, global cruises such asTaraOceans or the Malaspina Expedition have expanded our knowledge on the diversity and genetic repertoire of marine microbes. Nevertheless, there is still a gap of knowledge on broad scale patterns between photic and bathypelagic dark ocean microbes derived from the lack of detailed vertical profiles covering contrasting oceans depth regions. Here we present a dataset of 76 microbial metagenomes of the picoplankton size fraction (0.2-3.0 μm) collected in 11 stations along the Malaspina Expedition circumnavigation that cover vertical profiles sampling at 7 depths, from the surface to the 4000 m deep (or the sea floor in shallower waters). This Malaspina Microbial Vertical Profiles metagenomes (MProfile) dataset produced 1.66 Tbp of raw DNA sequences that assembled into a total 25.3 Gbp. After gene prediction and annotation, we built a 46.3 million non-redundant gene compendium with their corresponding annotations (M-GeneDB-VP), clustered at 95% sequence similarity. This dataset will be a valuable resource for exploring the functional and taxonomic connectivity between the photic and bathypelagic tropical and subtropical ocean at a global scale, while increasing our general knowledge on the Ocean microbiome.

This study is part of the POLARCSIC platform activities.-- 14 pages, 8 figures, 2 tables, supplementary data https://doi.org/10.1016/j.scitotenv.2022.156921, Phytoplankton-derived organic matter sustains heterotrophic marine life in regions away from terrestrial inputs such as the Southern Ocean. Fluorescence spectroscopy has long been used to characterize the fluorescent organic matter (FOM) pool. However, most studies focus only in the dissolved FOM fraction (FDOM) disregarding the contribution of particles. In order to assess the dynamics and drivers of the dissolved and particulate fractions of FOM, we used a Lagrangian approach to follow the time evolution of phytoplankton proliferations at four different sites in the Southern Ocean and compared the FOM in filtered and unfiltered seawater aliquots. We found that filtration had little effects on FOM visible spectrum fluorescence intensities, implying that most of this signal was due to dissolved fluorophores. On the other hand, protein-like fluorescence was strongly supressed by filtration, with fluorescence of particles accounting for up to 90 % of the total protein-like FOM. Photobleaching was identified as the main driver of visible FDOM composition, which was better described by indices of phytoplankton photoacclimation than by measurements of the incident solar radiation dose. In contrast, protein-like FOM intensity and fractionation were primarily related to abundance, composition and physiological state of phytoplankton proliferations. The chlorophyll a concentration from non-diatom phytoplankton explained 91 % of the particulate protein-like FOM variability. The proportion of protein-like fluorescence found in the dissolved phase was predicted by the combination of potential viral and grazing pressures, which accounted for 51 and 29 % of its variability, respectively. Our results show that comparing FOM measurements from filtered and unfiltered seawater provides relevant information on the taxonomic composition and cell integrity of phytoplankton communities. A better understanding of the commonly overlooked FOM fractionation process is essential for the implementation of in situ fluorescence sensors and will also help us better understand the processes that govern OM cycling in marine systems, The study was funded by the Spanish Government through projects PEGASO (CTM2012-37615), BIOGAPS (CTM2016-81008-R) and DOGMA (PID2020-112653GB-I00). MC-B was supported by a predoctoral fellowship from the Spanish Government (FPU16/01925). [...] We also acknowledge the institutional support of the “Severo Ochoa Centre of Excellence” accreditation (CEX2019-000928-S) from the Spanish government

13 pages, 7 figures, 2 tables, supplementary data https://doi.org/10.1016/j.scitotenv.2019.06.524, Transparent exopolymer particles (TEP) are an abundant class of suspended organic particles, mainly formed by polysaccharides, which play important roles in biogeochemical and ecological processes in the ocean. In this study we investigated horizontal and vertical TEP distributions (within the euphotic layer, including the upper surface) and their short-term variability along with a suite of environmental and biological variables in four distinct regions of the Southern Ocean. TEP concentrations in the surface (4 m) averaged 102.3 ± 40.4 μg XG eq. L and typically decreased with depth. Chlorophyll a (Chl a) concentration was a better predictor of TEP variability across the horizontal (R = 0.66, p < 0.001) and vertical (R = 0.74, p < 0.001) scales than prokaryotic heterotrophic abundance and production. Incubation experiments further confirmed the main role of phytoplankton as TEP producers. The highest surface TEP concentrations were found north of the South Orkney Islands (144.4 ± 21.7 μg XG eq. L), where the phytoplankton was dominated by cryptophytes and haptophytes; however, the highest TEP:Chl a ratios were found south of these islands (153.4 ± 29.8 μg XG eq (μg Chl a), compared to a mean of 79.3 ± 54.9 μg XG eq (μg Chl a) in the whole cruise, in association with haptophyte dominance, proximity of sea ice and high exposure to solar radiation. TEP were generally enriched in the upper surface (10 cm) respect to 4 m, despite a lack of biomass enrichment, suggesting either upward transport by positive buoyancy or bubble scavenging, or higher production at the upper surface by light stress or aggregation. TEP concentrations did not present any significant cyclic diel pattern. Altogether, our results suggest that photobiological stress, sea ice melt and turbulence add to phytoplankton productivity in driving TEP distribution across the Antarctic Peninsula area and Atlantic sector of the Southern Ocean, This research was supported by the Spanish Ministry of Economy and Competitiveness through projects PEGASO (CTM2012-37615) and BIOGAPS (CTM2016-81008-R) to RS. MZ was supported by a FPU predoctoral fellowship (FPU13/04630) from the Spanish Ministry of Education and Culture

The bathypelagic ocean (1000-4000 m depth) is the largest aquatic biome on Earth but it is still largely unexplored. Due to its prevalent low dissolved organic carbon concentrations, most of the prokaryotic metabolic activity is assumed to be associated to particles. The role of free-living prokaryotes has thus been mostly ignored, except that of some chemolithoautotrophic lineages. Here we used a global bathypelagic survey of size-fractionated metagenomic and 16S (genes and transcripts) data and performed a differential abundance analysis to explore the functional traits of the different prokaryotic life-strategies, their contribution to the active microbiome, and the role that the quality of the dissolved organic matter (DOM) plays in driving this contribution. We found that free-living prokaryotes have limited capacity to uplift their metabolism in response to environmental changes and display comparatively lower growth rates than particle associated prokaryotes, but are responsible for the synthesis of vitamins in the bathypelagic. Furthermore, their contribution to the active prokaryotic microbiome increased towards waters depleted of labile DOM, which represented a large fraction of the tropical and subtropical ocean sampled stations. This points to a relevant yet overlooked role of free-living prokaryotes in DOM cycling in the vast bathypelagic desert.

19 pages, 4 figures, 4 tables, supplementary material https://doi.org/10.3389/fmicb.2021.635821.-- The original contributions presented in the study are included in the article/Supplementary Materials, further inquiries can be directed to the corresponding authors, Anthropogenic carbon emissions are causing changes in seawater carbonate chemistry including a decline in the pH of the oceans. While its aftermath for calcifying microbes has been widely studied, the effect of ocean acidification (OA) on marine viruses and their microbial hosts is controversial, and even more in combination with another anthropogenic stressor, i.e., human-induced nutrient loads. In this study, two mesocosm acidification experiments with Mediterranean waters from different seasons revealed distinct effects of OA on viruses and viral-mediated prokaryotic mortality depending on the trophic state and the successional stage of the plankton community. In the winter bloom situation, low fluorescence viruses, the most abundant virus-like particle (VLP) subpopulation comprising mostly bacteriophages, were negatively affected by lowered pH with nutrient addition, while the bacterial host abundance was stimulated. High fluorescence viruses, containing cyanophages, were stimulated by OA regardless of the nutrient conditions, while cyanobacteria of the genus Synechococcus were negatively affected by OA. Moreover, the abundance of very high fluorescence viruses infecting small haptophytes tended to be lower under acidification while their putative hosts' abundance was enhanced, suggesting a direct and negative effect of OA on viral–host interactions. In the oligotrophic summer situation, we found a stimulating effect of OA on total viral abundance and the viral populations, suggesting a cascading effect of the elevated pCO2 stimulating autotrophic and heterotrophic production. In winter, viral lysis accounted for 30 ± 16% of the loss of bacterial standing stock per day (VMMBSS) under increased pCO2 compared to 53 ± 35% in the control treatments, without effects of nutrient additions while in summer, OA had no significant effects on VMMBSS (35 ± 20% and 38 ± 5% per day in the OA and control treatments, respectively). We found that phage production and resulting organic carbon release rates significantly reduced under OA in the nutrient replete winter situation, but it was also observed that high nutrient loads lowered the negative effect of OA on viral lysis, suggesting an antagonistic interplay between these two major global ocean stressors in the Anthropocene. In summer, however, viral-mediated carbon release rates were lower and not affected by lowered pH. Eutrophication consistently stimulated viral production regardless of the season or initial conditions. Given the relevant role of viruses for marine carbon cycling and the biological carbon pump, these two anthropogenic stressors may modulate carbon fluxes through their effect on viruses at the base of the pelagic food web in a future global change scenario, The financial support was provided by the Spanish Ministry of Economy and Competitiveness in the framework of the projects STORM (CTM2009–09352), DOREMI (CTM2012-34294), MANIFEST (CTM2012-32017), and PROTOS (CTM2009-08783). We are also grateful for the funding from the Generalitat de Catalunya through the Grup de Diversitat Microbiana en Ecosistemes Acuàtics (2014SGR/1591), Grup de Biogeoquímica Marina i Canvi Global (2017SGR1011) and the Grup d'Estructura i Funció de Xarxes Tròfiques Microbianes Planctòniques (2014SGR/1179) and a grant from the Spanish Ministry of Education (SB2010-0079) to AM. With the institutional support of the Severo Ochoa Center of Excellence accreditation (CEX2019-000928-S).

17 pages, 9 figures, 2 tables, supplementary material https://www.frontiersin.org/articles/10.3389/fmars.2021.683354/full#supplementary-material.-- Data Availability Statement: The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation, Particulate organic matter (POM) lability is one of the key factors determining the residence time of organic carbon (OC) in the marine system. Phytoplankton community composition can influence the rate at which heterotrophic microorganisms decompose phytoplankton detrital particles and thus, it controls the fraction of OC that reaches the ocean depths, where it can be sequestered for climate-relevant spans of time. Here, we compared the degradation dynamics of POM from phytoplankton assemblages of contrasting diatom dominance in the presence of mesopelagic prokaryotic communities during a 19-day degradation experiment. We found that diatom-derived POM exhibited an exponential decay rate approximately three times lower than that derived from a community dominated by flagellated phytoplankton (mainly coccolithophores and nanoflagellates). Additionally, dissolved organic matter (DOM) released during the degradation of diatom particles accumulated over the experiment, whereas only residual increases in DOM were detected during the degradation of non-diatom materials. These results suggest that diatom-dominance enhances the efficiencies of the biological carbon pump and microbial carbon pump through the relatively reduced labilities of diatom particles and of the dissolved materials that arise from their microbial processing, This research was funded by projects SUAVE (CTM2014-54926-R), ANIMA (CTM2015-65720-R), and BIOGAPS (CTM2016-81008-R) and the institutional support of the “Severo Ochoa Centre of Excellence” accreditation (CEX2019-000928-S) from the Spanish government. MC-B was supported by a FPU pre-doctoral contract (FPU16/01925) from the Spanish government. We acknowledge support for the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI)

14 pages, 6 figures, 1 table, supplementary material https://www.frontiersin.org/articles/10.3389/fmicb.2020.01590/full#supplementary-material.-- Data Availability Statement. The raw sequence data have been deposited at the National Center for Biotechnology Information (NCBI). The data can be accessed online (https://www.ncbi.nlm) with the code PRJNA345534, Seasonal dynamics of ocean prokaryotic communities in the free-living fraction have been widely described, but less is known about the seasonality of prokaryotes inhabiting marine particles. We describe the seasonality of bacterial communities in the particulate matter continuum by sampling monthly over two years in a temperate oligotrophic coastal ecosystem and using a serial filtration (including six size-fractions spanning from 0.2 to 200 μm). We observed that bacterial communities in the particulate matter continuum had annual changes following harmonic seasonal oscillations, where alpha, beta, and gamma diversity increased during the warm period and decreased during the cold period. Communities in each size-fraction changed gradually over time, being the communities in larger size-fractions the ones with stronger annual changes. Annual community changes were driven mainly by day length and sea surface temperature, and each size-fraction was additionally affected by other variables (e.g., smaller size-fractions by dissolved PO4 and larger size-fractions by turbidity). While some taxonomic groups mantained their preference for a given size fraction during most of the year, others varied their distribution into different size fractions over time, as e.g., SAR11, which increased its presence in particles during the cold period. Our results indicate that the size-fractionation scheme provides novel seasonal patterns that are not possible to unveil by analyzing only free-living bacteria, and that help to better understand the temporal dynamics of prokaryotes, This research was funded by projects STORM (CTM2009-09352), ADEPT (CTM2011-23458), REMEI (CTM2015-70340-R), ANIMA (CTM2015-65720-R), and MIAU (RTI2018-101025-B-I00) funded by the former Spanish Ministries of Science and Innovation, Ministry of Economy and Competitiveness, and now Science, Innovation and Universities. JH was partially supported by the Chilean National Agency for Research and Development (ANID) (FONDECYT-POSTDOCTORADO 3180152). MM was supported by a CSIC JAEPredoc Grant, by the Ministry of Labor, Employment and Social Security of Spain and by the Chilean National Agency for Research and Development (ANID) (FONDAP-IDEAL 15150003 and FONDECYT-POSTDOCTORADO 3190369). The publication fee was supported by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI), Spain, With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI)

Special issue Microbial Community Structure and Metabolic Networks in Polar Areas.-- 20 pages, 5 figures, 2 tables, supplementary material, 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, The study was supported by the Spanish Ministry of Economy through projects PEGASO (CTM2012-37615) to R. Simó, and BIO-NUC (CGL2013-49020-R) to M. Dall’Osto, With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI)

17 pages, 5 figures, 2 tables, supporting information https://doi.org/10.1111/1462-2920.15292.-- This is the pre-peer reviewed version of the following article: Marta Sebastián, Irene Forn, Adrià Auladell, Markel Gómez‐Letona, M. Montserrat Sala, Josep M. Gasol, Cèlia Marrasé Environmental Microbiology 23(1): 190-206 (2021), which has been published in final form at 10.1111/1462-2920.15292. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions, Different factors affect the way dissolved organic matter (DOM) is processed in the ocean water column, including environmental conditions and the functional capabilities of the communities. Recent studies have shown that bathypelagic prokaryotes are metabolically flexible, but whether this versatility translates into a higher ability to process DOM has been barely explored. Here we performed a multifactorial transplant experiment to compare the growth, activity and changes in DOM quality in surface and bathypelagic waters inoculated with either surface or bathypelagic prokaryotic communities. The effect of nutrient additions to surface waters was also explored. Despite no differences in the cell abundance of surface and deep ocean prokaryotes were observed in any of the treatments, in surface waters with nutrients the heterotrophic production of surface prokaryotes rapidly decreased. Conversely, bathypelagic communities displayed a sustained production throughout the experiment. Incubations with surface prokaryotes always led to a significant accumulation of recalcitrant compounds, which did not occur with bathypelagic prokaryotes, suggesting they have a higher ability to process DOM. These contrasting abilities could be explained by the recruitment of a comparatively larger number of opportunistic taxa within the bathypelagic assemblages, which likely resulted in a broader community capability of substrate utilization, This work was partially supported by grants DOREMI (CTM2012-34294), HOTMIX (CTM2011-30010/MAR), EcoRARE (CTM2014-60467-JIN), ANIMA (CTM2015-65720-R) and MIAU (RTI2018-101025-B-I00), funded by the Spanish Ministry of Science and also by Grup Generalitat 2017SGR/1568. M.S. was supported by a Vieray Clavijo contract funded by the ACIISI and the ULPGC, With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI)

Deep ocean microbial communities rely on the organic carbon produced in the sunlit ocean, yet it remains unknown whether surface processes determine the assembly and function of bathypelagic prokaryotes to a larger extent than deep-sea physicochemical conditions. Here, we explored whether variations in surface phytoplankton assemblages across Atlantic, Pacific and Indian ocean stations can explain structural changes in bathypelagic (ca. 4,000 m) free-living and particle-attached prokaryotic communities (characterized through 16S rRNA gene sequencing), as well as changes in prokaryotic activity and dissolved organic matter (DOM) quality. We show that the spatial structuring of prokaryotic communities in the bathypelagic strongly followed variations in the abundances of surface dinoflagellates and ciliates, as well as gradients in surface primary productivity, but were less influenced by bathypelagic physicochemical conditions. Amino acid-like DOM components in the bathypelagic reflected variations of those components in surface waters, and seemed to control bathypelagic prokaryotic activity. The imprint of surface conditions was more evident in bathypelagic than in shallower mesopelagic (200–1,000 m) communities, suggesting a direct connectivity through fast-sinking particles that escape mesopelagic transformations. Finally, we identified a pool of endemic deep-sea prokaryotic taxa (including potentially chemoautotrophic groups) that appear less connected to surface processes than those bathypelagic taxa with a widespread vertical distribution. Our results suggest that surface planktonic communities shape the spatial structure of the bathypelagic microbiome to a larger extent than the local physicochemical environment, likely through determining the nature of the sinking particles and the associated prokaryotes reaching bathypelagic waters., Spanish Ministry of Economy and Competitiveness (MINECO) through the Consolider-Ingenio program (Malaspina 2010 Expedition) (FEDER funds) CSD2008-00077 CTM2015-70340R CTM2015-65720-R CTM2015-69936-P RTI2018-101025-B-I00 UCE.PP2017.03 CTM2015-69392-C3-2-R, King Abdullah University of Science & Technology, Juan de la Cierva fellowship, GRAMMI project IJCI-2015-23505 RTI2018-099740-J-I00, Viera y Clavijo contract - ACIISI, ULPGC, Comision Nacional de Investigacion Cientifica y Tecnologica (CONICYT) FONDAP-IDEAL15150003 FONDECYT-POSTDOCTORADO 3190369

15 pages, 8 figures, supplementary material https://www.frontiersin.org/articles/10.3389/fmicb.2020.00918/full#supplementary-material, Prokaryotes play a fundamental role in decomposing organic matter in the ocean, but little is known about how microbial metabolic capabilities vary at the global ocean scale and what are the drivers causing this variation. We aimed at obtaining the first global exploration of the functional capabilities of prokaryotes in the ocean, with emphasis on the under-sampled meso- and bathypelagic layers. We explored the potential utilization of 95 carbon sources with Biolog GN2 platesR in 441 prokaryotic communities sampled from surface to bathypelagic waters (down to 4,000 m) at 111 stations distributed across the tropical and subtropical Atlantic, Indian, and Pacific oceans. The resulting metabolic profiles were compared with biological and physico-chemical properties such as fluorescent dissolved organic matter (DOM) or temperature. The relative use of the individual substrates was remarkably consistent across oceanic regions and layers, and only the Equatorial Pacific Ocean showed a different metabolic structure. When grouping substrates by categories, we observed some vertical variations, such as an increased relative utilization of polymers in bathypelagic layers or a higher relative use of P-compounds or amino acids in the surface ocean. The increased relative use of polymers with depth, together with the increases in humic DOM, suggest that deep ocean communities have the capability to process complex DOM. Overall, the main identified driver of the metabolic structure of ocean prokaryotic communities was temperature. Our results represent the first global depiction of the potential use of a variety of carbon sources by prokaryotic communities across the tropical and the subtropical ocean and show that acetic acid clearly emerges as one of the most widely potentially used carbon sources in the ocean, This research was funded by the Spanish Ministry of Economy and Competitiveness under projects Malaspina-2010 Circumnavigation Expedition (grant number CSD2008-00077) and partly by projects ANIMA (CTM2015-65720-R), and MIAU (RTI2018-101025-B-I00). CR-G was supported by a Juan de la Cierva fellowship and the GRAMMI project (IJCI-2015-23505 and RTI2018-099740-J-I00, MICINN, Spain), With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI)

Special issue The Interrelationships between Near-Surface Ecological Processes and Air–Sea Exchange of Gases and Particles.-- 19 figures, 5 figures, 2 tables, 2 appendices.-- Data of this work can be found at the Zenodo repository (https://doi.org/10.5281/zenodo.3773972).-- This research is part of POLARCSIC (https://polarcsic.es/) activities, soprene is a biogenic trace gas produced by terrestrial vegetation and marine phytoplankton. In the remote oceans, where secondary aerosols are mostly biogenic, marine isoprene emissions affect atmospheric chemistry and influence cloud formation and brightness. Here, we present the first compilation of new and published measurements of isoprene concentrations in the Southern Ocean and explore their distribution patterns. Surface ocean isoprene concentrations in November through April span 1 to 94 pM. A band of higher concentrations is observed around a latitude of ≈40 ∘ S and a surface sea temperature of 15 ∘ C. High isoprene also occurs in high productivity waters near islands and continental coasts. We use concurrent measurements of physical, chemical, and biological variables to explore the main potential drivers of isoprene concentration by means of paired regressions and multivariate analysis. Isoprene is best explained by phytoplankton-related variables like the concentrations of chlorophyll-a, photoprotective pigments and particulate organic matter, photosynthetic efficiency (influenced by iron availability), and the chlorophyll-a shares of most phytoplankton groups, and not by macronutrients or bacterial abundance. A simple statistical model based on chlorophyll-a concentration and a sea surface temperature discontinuity accounts for half of the variance of isoprene concentrations in surface waters of the Southern Ocean, This research was supported by the Spanish Ministry of Economy and Competitiveness through project PEGASO (CTM2012–37615) to RS, and by the Swiss Polar Institute and Ferring Pharmaceuticals through project SORPASSO–ACE#8 to RS and project ACE#1 to David Antoine (Remote Sensing and Satellite Research Group, Curtin University) and Sandy Thomalla (Southern Ocean Carbon and Climate Observatory, Council for Scientific and Industrial Research (CSIR) and Marine Research Institute, University of Cape Town). It was also partially funded by the Australian Government through the Australian Research Council’s Discovery Projects funding scheme (project DP160103387) and South African CSIR Parliamentary Grant (SNA2011112600001). Project ACE#1 was also supported by CSIR Southern Ocean Carbon and Climate Observatory (SOCCO) programme. PRR was supported by a “la Caixa” Foundation PhD Fellowship (2015–2019), With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI)

8 pages, 4 figures, 2 figures, supplementary figures https://doi.org/10.1016/j.scitotenv.2021.151443., COVID-19 has led to global population lockdowns that have had indirect effects on terrestrial and marine fauna, yet little is known on their effects on marine planktonic communities. We analysed the effect of the spring 2020 lockdown in a marine coastal area in Blanes Bay, NW Mediterranean. We compared a set of 23 oceanographic, microbial and biogeochemical variables sampled right after the strict lockdown in Spain, with data from the previous 15 years after correcting for long-term trends. Our analysis shows a series of changes in the microbial communities which may have been induced by the combination of the decreased nitrogen atmospheric load, the lower wastewater flux and the reduced fishing activity in the area, among other factors. In particular, we detected a slight decrease beyond the long-term trend in chlorophyll a, in the abundance of several microbial groups (phototrophic nanoflagellates and total prokaryotes) and in prokaryotic activity (heterotrophic prokaryotic production and β-glucosidase activity) which, as a whole, resulted in a moderate increase of oligotrophy in Blanes Bay after the lockdown., Data from the specific sampling in 2020 were supported by the MIAU project of the Spanish Ministerio de Ciencia e Innovación, MICINN (RTI2018-101025-B-I00), while previous years were supported by many Spanish and EU projects. Other projects of the MICINN also supported this research: DOGMA (PID2020-112653GB-I00), DIVAS (PID2019-108457RB-I00), and HICCUP (RTI2018-095083-B-I00). We thank Amanda Con and Juan Rodríguez for providing data of the Blanes WWTP. We sincerely thank Irene Forn, Carolina Antequera, Arturo Lucas, Elisabet Laia Sà and Vanessa Balagué for their invaluable laboratory work. The work of the authors was supported by Generalitat de Catalunya Grups de Recerca Consolidats 2017SGR1568 and 2017SGR1011. This study acknowledges institutional support from the “Severo Ochoa Centre of Excellence” accreditation (CEX2019-000928-S).

11 pages, 6 figures, 2 tables, Transparent Exopolymer Particles (TEPs) are a subclass of organic particles with high impact in biogeochemical and ecological processes, such as the biological carbon pump, air-sea interactions, or the microbial loop. However, the complexity in production and consumption makes TEP dynamics hardly predictable, calling for the need of descriptive studies about the in situ dynamics of these particles. We followed monthly TEP dynamics and combined them with a dataset of environmental variables during three years in a coastal site of the oligotrophic North Western Mediterranean (Blanes Bay). TEP concentration, ranging from 11.3 to 289.1 μg XG eq L (average 81.7 ± 11.7 μg XG eq L), showed recurrent peaks in early summer (June–July). TEP were temporally disconnected from chlorophyll a maxima, that occurred in late winter and early spring (maxima 1.21 μg L), but they were significantly related to the abundance of specific phytoplankton groups (diatoms and dinoflagellates) and also coincided with periods of low nutrient concentrations. The fraction of particulate organic carbon in the form of TEP (the TEP:POC and TEP:PM ratios) were also highest in early summer, indicating that TEP-enriched particles of low density accumulate in surface waters during stratified periods. We hypothesize that the accumulation of these particles affects the microbial food web by enhancing the activity of specific prokaryotic extracellular enzymes (esterase, β-glucosidase and alkaline phosphatase) and promoting the abundance of heterotrophic nanoflagellates, This work was funded by projects STORM (CTM2009-09352/MAR), PEGASO (CTM2012-37615), ANIMA (CTM2015-65720-R) and REMEI (CTM2015-70340-R) of the Spanish Ministry of Science or Economy. [...] EOR was supported by a Juan de la Cierva Fellowship

The bathypelagic ocean is one of the largest ecosystems on Earth and sustains half of the ocean's microbial activity. This microbial activity strongly relies on surface-derived particles, but there is growing evidence that the carbon released through solubilization of these particles may not be sufficient to meet the energy demands of deep ocean prokaryotes. To explore how bathypelagic prokaryotes respond to the absence of external inputs of carbon, we followed the long-term (1 year) dynamics of an enclosed community. Despite the lack of external energy supply, we observed a continuous succession of active prokaryotic phylotypes, which was driven by recruitment of taxa from the seed bank (i.e., initially rare operational taxonomic units [OTUs]). A single OTU belonging to Marine Group I of Thaumarchaeota, which was originally rare, dominated the microbial community for similar to 4 months and played a fundamental role in this succession likely by introducing new organic carbon through chemolithoautotrophy. This carbon presumably produced a priming effect, because after the decline of Thaumarchaeota, the diversity and metabolic potential of the community increased back to the levels present at the start of the experiment. Our study demonstrates the profound versatility of deep microbial communities when facing organic carbon deprivation.

12 pages, 6 figures, supplemental material https://www.frontiersin.org/articles/10.3389/fmicb.2019.00760/full#supplementary-material, Experiments with bacteria in culture have shown that they often display “feast and famine” strategies that allow them to respond with fast growth upon pulses in resource availability, and enter a growth-arrest state when resources are limiting. Although feast responses have been observed in natural communities upon enrichment, it is unknown whether this blooming ability is maintained after long periods of starvation, particularly in systems that are energy limited like the bathypelagic ocean. Here we combined bulk and single-cell activity measurements with 16S rRNA gene amplicon sequencing to explore the response of a bathypelagic community, that had been starved for 1.6 years, to a sudden organic carbon supply. We observed a dramatic change in activity within 30 h, with leucine incorporation rates increasing over two orders of magnitude and the number of translationally active cells (mostly Gammaproteobacteria) increasing 4-fold. The feast response was driven by a single operational taxonomic unit (OTU) affiliated with the Marinobacter genus, which had remained rare during 7 months of starvation. Our work suggests that bathypelagic communities harbor a seed bank of highly persistent and resourceful “feast and famine” strategists that might disproportionally contribute to carbon fluxes through fast responses to occasional pulses of organic matter, This work was supported by grants DIFUMIC (2017SGR/1568, Generalitat de Catalunya), DOREMI (CTM2012-34294), HOTMIX (CTM2011-30010/MAR), REMEI (CTM2015-70340-R), and ANIMA (CTM2015-65720-R) funded by the Spanish Government, and EcoRARE (CTM2014-60467-JIN), funded by the Spanish Government and the European Regional Development Fund (ERDF). CRG was supported by a Juan de la Cierva contract (IJCI-2015-23505) and MS by a Viera y Clavijo contract funded by the ACIISI and the ULPGC

13 pages, 5 figures, 2 tables, supplementary material https://doi.org/10.1016/j.scitotenv.2019.04.361, Organic pollutants are continuously being introduced in seawater with uncharacterized impacts on the engines of the marine biogeochemical cycles, the microorganisms. The effects on marine microbial communities were assessed for perfluoroalkyl substances, organophosphate esters flame retardants and plasticizers, polycyclic aromatic hydrocarbons, and n-alkanes. Dose-response experiments were performed at three stations and at three depths in the NW Mediterranean with contrasted nutrient and pollutant concentrations. In these experiments, the microbial growth rates, the abundances of the main bacterial groups, measured by Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH), and extracellular enzymatic activities, were quantified. Increasing concentrations of organic pollutants (OPs)promoted different responses in the communities that were compound, organism and nutrient availability (trophic status). The largest differences between OP treatments and controls in the growth rates of both heterotrophic and phototrophic microbial groups were observed in seawater from the deep chlorophyll maxima. Furthermore, there was a compound specific stimulation of different extracellular enzymatic activities after the exposure to OPs. Our results revealed that marine microbial communities reacted not only to hydrocarbons, known to be used as a carbon source, but also to low concentrations of organic pollutants of emerging concern in a complex manner, reflecting the variability of various environmental variables. Multiple linear regressions suggested that organic pollutants modulated the bacterial growth and extracellular enzymatic activities, but this modulation was of lower magnitude than the observed pronounced response of the microbial community to nutrient availability, This work has been financed by the Spanish Ministry of Economy and Competitiveness through projects ISOMICS (CTM2015-65691-R), DO-RE-MI (CTM2012-34294), ANIMA (CTM2015-65720-R) and REMEI (CTM2015-70340-R) and by Fundación BBVA award to MVC. ECG acknowledges a FI fellowship from the Generalitat de Catalunya (AGAUR)

17 pages, 5 figures, 4 tables, Transparent exopolymer particles (TEPs) are a class of gel particles, produced mainly by microorganisms, which play important roles in biogeochemical processes such as carbon cycling and export. TEPs (a) are colonized by carbon-consuming microbes; (b) mediate aggregation and sinking of organic matter and organisms, thereby contributing to the biological carbon pump; and (c) accumulate in the surface microlayer (SML) and affect air–sea gas exchange. The first step to evaluate the global influence of TEPs in these processes is the prediction of TEP occurrence in the ocean. Yet, little is known about the physical and biological variables that drive their abundance, particularly in the open ocean. Here we describe the horizontal TEP distribution, along with physical and biological variables, in surface waters along a north–south transect in the Atlantic Ocean during October–November 2014. Two main regions were separated due to remarkable differences: the open Atlantic Ocean (OAO, n=30), and the Southwestern Atlantic Shelf (SWAS, n=10). TEP concentration in the entire transect ranged 18.3–446.8 µg XG eq L−1 and averaged 117.1±119.8 µg XG eq L−1, with the maximum concentrations in the SWAS and in a station located at the edge of the Canary Coastal Upwelling (CU), and the highest TEP to chlorophyll a (TEP:Chl a) ratios in the OAO (183±56) and CU (1760). TEPs were significantly and positively related to Chl a and phytoplankton biomass, expressed in terms of C, along the entire transect. In the OAO, TEPs were positively related to some phytoplankton groups, mainly Synechococcus. They were negatively related to the previous 24 h averaged solar irradiance, suggesting that sunlight, particularly UV radiation, is more a sink than a source for TEP. Multiple regression analyses showed the combined positive effect of phytoplankton and heterotrophic prokaryotes (HPs) on TEP distribution in the OAO. In the SWAS, TEPs were positively related to high nucleic acid-containing prokaryotic cells and total phytoplankton biomass, but not to any particular phytoplankton group. Estimated TEP–carbon constituted an important portion of the particulate organic carbon pool in the entire transect (28 %–110 %), generally higher than the phytoplankton and HP carbon shares, which highlights the importance of TEPs in the cycling of organic matter in the ocean, This research was funded by the Spanish Ministry of Economy and Competitiveness through projects PEGASO (CTM2012–37615) and BIOGAPS (CTM2016-81008-R) to Rafel Simó. Marina Zamanillo was supported by a FPU predoctoralfellowship from the Spanish Ministry of Education and Culture. Eva Ortega-Retuerta was supported by a Marie Curie Actions Intra-European Fellowship (H2020-MSCA-IF-2015-703991)

16 pages, 6 figures, 1 table, supporting information https://dx.doi.org/10.1111/mec.15026, Microbial taxa range from being ubiquitous and abundant across space to extremely rare and endemic, depending on their ecophysiology and on different processes acting locally or regionally. However, little is known about how cosmopolitan or rare taxa combine to constitute communities and whether environmental variations promote changes in their relative abundances. Here we identified the Spatial Abundance Distribution (SpAD) of individual prokaryotic taxa (16S rDNA-defined Operational Taxonomic Units, OTUs) across 108 globally-distributed surface ocean stations. We grouped taxa based on their SpAD shape (“normal-like”- abundant and ubiquitous; “logistic”- globally rare, present in few sites; and “bimodal”- abundant only in certain oceanic regions), and investigated how the abundance of these three categories relates to environmental gradients. Most surface assemblages were numerically dominated by a few cosmopolitan “normal-like” OTUs, yet there was a gradual shift towards assemblages dominated by “logistic” taxa in specific areas with productivity and temperature differing the most from the average conditions in the sampled stations. When we performed the SpAD categorization including additional habitats (deeper layers and particles of varying sizes), the SpAD of many OTUs changed towards fewer “normal-like” shapes, and OTUs categorized as globally rare in the surface ocean became abundant. This suggests that understanding the mechanisms behind microbial rarity and dominance requires expanding the context of study beyond local communities and single habitats. We show that marine bacterial communities comprise taxa displaying a continuum of SpADs, and that variations in their abundances can be linked to habitat transitions or barriers that delimit the distribution of community members, This work was funded by the Spanish Ministry of Economy and Competitiveness (MINECO) through the Consolider‐Ingenio program (Malaspina 2010 Expedition, ref. CSD2008‐00077), with contributions from grant CTM2015‐70340R, CTM2015‐65720‐R, CTM2015‐69936‐P and King Abdullah University of Science and Technology (KAUST). [...]. This is a contribution of Grup Consolidat de Recerca of the Catalan Government 2014SGR/1179. CRG was supported by a Juan de la Cierva (IJCI‐2015‐23505, MINECO, Spain) fellowship and RL by a Ramón y Cajal fellowship (RYC‐2013‐12554, MINECO, Spain). MS was supported by grant EcoRARE (CTM2014‐60467‐JIN), funded by the Spanish Government and the European Regional Development Fund (ERDF), REMEI (CTM2015‐70340‐Rf) funded by the Spanish Government, and a Viera y Clavijo contract funded by the ACIISI and the ULPGC. MM was supported by CONICYT (FONDAP‐IDEAL 15150003). SGA was funded by BIOSENSOMICS through the ‘Convocatoria 2015 de ayudas Fundación BBVA a investigadores y creadores culturales'. RRM is supported by CONICYT FONDECYT 11170748

Vibrio s include several pathogenic bacteria that occur in aquatic environments. The presence of Vibrio has been assessed in many ecosystems by culture-based techniques. However, little is known on the contribution of Vibrio s in the sea, especially in areas subject to harmful algal blooms. A preliminary study in Sant Andreu de Llavaneres beach (NW Mediterranean) showed the presence of some Vibrio species during a recurrent bloom of the harmful benthic dinoflagellate Ostreopsis cf. ovata . In order to establish the importance of Vibrio s in a coastal area of the NW Mediterranean and to study the association with the dinoflagellate, we conducted a sampling monitoring for one year to quantify the concentration of Vibrio s both in the water (free-living and attached to particles) and in the epiphytic community of macroalgae. The aims were 1) to evaluate the relative abundance of Vibrio in the epiphytic and in the planktonic bacterial community, 2) to assess the percentage of free-living and attached Vibrio s in the planktonic community, and 3) to determine whether the presence of Vibrio s is associated with the blooms of the toxic dinoflagellate Ostreopsis or with other environmental parameters. For this purpose, a CARD-FISH molecular probe was applied for the specific detection of bacteria belonging to the genus Vibrio . Cells were quantified and the abundance of both particles and bacteria attached to particles were assessed. The maximum Vibrio concentration (1.3x104 cells ml –1 and 1.4x10 6 cells g –1 FW, for planktonic and epiphytic samples, respectively) was detected in September. Free-living Vibrio s contributed 0.38±0.24% to the total free-living planktonic community and 1.12±0.28% to the epiphytic bacterial community. However, their contribution was particularly high in the planktonic community attached to particles (17.37±20.49%). Although in the planktonic community Vibrio was found preferentially free-living (82.63±20.01%), particles are a niche for Vibrio s, since in particles Vibrio s may represent up to 72% of the total attached bacterial community. Abundance of planktonic Vibrio was correlated with Ostreopsis concentration and it is likely that they play a role in the wound infections suffered by beach users during the bloom.

Special volume: Planet Ocean. Scientia Marina 80(Suppl.1) 2016.-- 10 pages, 7 figures, 1 table, [EN] Vibrios include several pathogenic bacteria that occur in aquatic environments. The presence of Vibrio has been assessed in many ecosystems by culture-based techniques. However, little is known on the contribution of vibrios in the sea, especially in areas subject to harmful algal blooms. A preliminary study in Sant Andreu de Llavaneres beach (NW Mediterranean) showed the presence of some Vibrio species during a recurrent bloom of the harmful benthic dinoflagellate Ostreopsis cf. ovata. In order to establish the importance of vibrios in a coastal area of the NW Mediterranean and to study the association with the dinoflagellate, we conducted a sampling monitoring for one year to quantify the concentration of vibrios both in the water (free-living and attached to particles) and in the epiphytic community of macroalgae. The aims were 1) to evaluate the relative abundance of Vibrio in the epiphytic and in the planktonic bacterial community, 2) to assess the percentage of free-living and attached vibrios in the planktonic community, and 3) to determine whether the presence of vibrios is associated with the blooms of the toxic dinoflagellate Ostreopsis or with other environmental parameters. For this purpose, a CARD-FISH molecular probe was applied for the specific detection of bacteria belonging to the genus Vibrio. Cells were quantified and the abundance of both particles and bacteria attached to particles were assessed. The maximum Vibrio concentration (1.3x104 cells ml–1 and 1.4x106 cells g–1 FW, for planktonic and epiphytic samples, respectively) was detected in September. Free-living vibrios contributed 0.38±0.24% to the total free-living planktonic community and 1.12±0.28% to the epiphytic bacterial community. However, their contribution was particularly high in the planktonic community attached to particles (17.37±20.49%). Although in the planktonic community Vibrio was found preferentially free-living (82.63±20.01%), particles are a niche for vibrios, since in particles vibrios may represent up to 72% of the total attached bacterial community. Abundance of planktonic Vibrio was correlated with Ostreopsis concentration and it is likely that they play a role in the wound infections suffered by beach users during the bloom, [ES] El género Vibrio incluye a varias bacterias patogénicas que se encuentran en ecosistemas acuáticos. La presencia de Vibrio se ha estimado en muchos ecosistemas mediante técnicas basadas en cultivos. Sin embargo, se conoce poco sobre la contribución de vibrios en el mar, especialmente en áreas afectadas por proliferaciones algales nocivas. Un estudio preliminar en la playa de Sant Andreu de Llavaneres (Mediterráneo NO) mostró la presencia de algunas especies de Vibrio durante una proliferación recurrente del dinoflagelado béntico nocivo Ostreopsis cf. ovata. Para poder establecer la relevancia de los vibrios en un área costera del Mediterráneo NO y estudiar su asociación con el dinoflagelado, realizamos un muestreo de monitoreo durante un año para cuantificar la concentración de vibrios tanto en el agua (de vida libre y adheridos a partículas) y en la comunidad epifítica de macroalgas con los objetivos de 1) evaluar la abundancia relativa de Vibrio en la comunidad bacteriana tanto planctónica como epifítica, 2) estimar el porcentaje de vibrios de vida libre y adheridos a partículas en la comunidad bacteriana planctónica y 3) determinar si la presencia de vibrios está relacionada con las proliferaciones del dinoflagelado Ostreopsis o con otros parámetros ambientales. Para este propósito, se aplicó una sonda molecular de CARD-FISH para la detección específica de bacterias pertenecientes al género Vibrio. Se cuantificaron las células y también la abundancia de partículas y de las bacterias adheridas a estas partículas. La máxima concentración de Vibrio (1.3x104 cels ml–1 y 1.4x106 cels g–1 PF, para muestras planctónicas y epifíticas, respectivamente) fue detectada en Septiembre. Los vibrios de vida libre contribuyeron un 0.38±0.24% al total de la comunidad bacteriana de vida libre y un 1.12±0.28% a la comunidad bacteriana epifítica. Sin embargo, su contribución fue especialmente elevada en la comunidad bacteriana adherida a partículas (17.37±20.49%). Aunque en la comunidad planctónica Vibrio se encontraba preferentemente no adheridos a partículas (82.63±20.01%), las partículas constituyen un nicho para vibrios, ya que pueden llegar a representar hasta un 72% de la comunidad bacteriana adherida a partículas. La abundancia de Vibrio en el plancton se correlacionó con la concentración de Ostreopsis, y es posible que éstos jueguen un papel en las infecciones de heridas que sufren los bañistas durante las proliferaciones algales, This work was supported by the Spanish projects ICARO (200830I120), STORM (CTM2009-09352), DOREMI (CTM2012-34294), EBITOX (CTQ2008-06754-C04-04), OSTREORISK (CTM2014-53818-R) and ANIMA (CTM2015-65720), and through an FPI grant to E.B. of the Spanish Ministry of Economy and Competitiveness

Transparent exopolymer particles (TEP) are a class of gel particles produced mainly by microorganisms. TEP play an important role in the ocean carbon cycle, affect sea–air gas exchange and contribute to organic aerosols. The first step to evaluate the TEP influence in these processes is the prediction of TEP occurrence in the ocean. Yet, little is known about the physical and biological variables that control their abundance, particularly in the open ocean. Here we describe horizontal TEP distribution in the surface waters along a North–South transect in the Atlantic Ocean during October–November 2014. Physical and biological variables were run in parallel. Two main regions were separated due to remarkable differences; the open Atlantic Ocean (OAO, n = 30), and the Southwestern Atlantic Shelf (SWAS, n = 10). TEP concentration in the entire transect ranged from 18.3 to 446.8 µg XG eq L−1 and averaged 117.1 ± 119.8 µg XG eq L−1, with the maximum concentrations in the edge of the Canary Coastal Upwelling (CU, n = 1) and the SWAS, but with the highest TEP to chlorophyll a (TEP : Chl a) ratios at the OAO (CU excluded, average 183 ± 56) and CU (1760.4). TEP were significantly and positively related to Chl a and phytoplankton biomass, expressed in terms of C, along the entire transect. In the OAO, TEP were positively related to some phytoplankton groups, mainly to Synechococcus, and negatively related to the previous 24–hours averaged solar radiation, suggesting the predominance of TEP breaking above the induction of TEP production by UV radiation. Multiple regression analyses showed the combined positive effect of phytoplankton and heterotrophic prokaryotes (HP) on TEP distribution in this region. In the SWAS, TEP were positively related to high nucleic acid prokaryotic cells (HNA) and total phytoplankton biomass, but not with any particular phytoplankton group. TEP constituted an important portion of the particulate organic carbon (POC) pool in the entire transect (28.1–109.8 %), and was generally higher than the phytoplankton and HP fraction, highlighting the importance of TEP in the cycle of organic matter in the ocean.

9 pages, 5 figures, 1 table, supporting information www.pnas.org/lookup/suppl/doi:10.1073/pnas.1802470115/-/DCSupplemental., The sinking of organic particles formed in the photic layer is a main vector of carbon export into the deep ocean. Although sinking particles are heavily colonized by microbes, so far it has not been explored whether this process plays a role in transferring prokaryotic diversity from surface to deep oceanic layers. Using Illumina sequencing of the 16S rRNA gene, we explore here the vertical connectivity of the ocean microbiome by characterizing marine prokaryotic communities associated with five different size fractions and examining their compositional variability from surface down to 4,000 m across eight stations sampled in the Atlantic, Pacific, and Indian Oceans during the Malaspina 2010 Expedition. Our results show that the most abundant prokaryotes in the deep ocean are also present in surface waters. This vertical community connectivity seems to occur predominantly through the largest particles because communities in the largest size fractions showed the highest taxonomic similarity throughout the water column, whereas free-living communities were more isolated vertically. Our results further suggest that particle colonization processes occurring in surface waters determine to some extent the composition and biogeography of bathypelagic communities. Overall, we postulate that sinking particles function as vectors that inoculate viable particle-attached surface microbes into the deep-sea realm, determining to a considerable extent the structure, functioning, and biogeography of deep ocean communities, M.M. was supported by a Consejo Superior de Investigaciones Científicas-Junta para la Ampliación de Estudios Grant (CSIC-JAE-Predoc Grant) and by the Ministry of Labor, Employment and Social Security. R.L. was supported by a Ramón y Cajal fellowship (RYC-2013-12554, Ministerio de Economía y Competitividad (MINECO), Spain), and C.R.-G. was supported by a Juan de la Cierva fellowship (IJCI-2015-23505). This is a contribution to the Malaspina 2010 Expedition, funded by the Spanish Ministry of Economy and Competitiveness through the Consolider-Ingenio program (Reference CSD2008-00077)

International audience; The bathypelagic ocean is one of the largest ecosystems on Earth and sustains half of the ocean's microbial activity. This microbial activity strongly relies on surface-derived particles, but there is growing evidence that the carbon released through solubilization of these particles may not be sufficient to meet the energy demands of deep ocean prokaryotes. To explore how bathypelagic prokaryotes respond to the absence of external inputs of carbon, we followed the long-term (1 year) dynamics of an enclosed community. Despite the lack of external energy supply, we observed a continuous succession of active prokaryotic phylotypes, which was driven by recruitment of taxa from the seed bank (i.e., initially rare operational taxonomic units [OTUs]). A single OTU belonging to Marine Group I of Thaumarchaeota, which was originally rare, dominated the microbial community for similar to 4 months and played a fundamental role in this succession likely by introducing new organic carbon through chemolithoautotrophy. This carbon presumably produced a priming effect, because after the decline of Thaumarchaeota, the diversity and metabolic potential of the community increased back to the levels present at the start of the experiment. Our study demonstrates the profound versatility of deep microbial communities when facing organic carbon deprivation.

14 pages, 5 figures, 2 tables, supporting information https://dx.doi.org/10.1111/mec.14421, Biotic and abiotic particles shape the microspatial architecture that defines the microbial aquatic habitat, being particles highly variable in size and quality along oceanic horizontal and vertical gradients. We analysed the prokaryotic (bacterial and archaeal) diversity and community composition present in six distinct particle size classes ranging from the pico- to the microscale (0.2 to 200 μm). Further, we studied their variations along oceanographic horizontal (from the coast to open oceanic waters) and vertical (from the ocean surface into the meso- and bathypelagic ocean) gradients. In general, prokaryotic community composition was more variable with depth than in the transition from the coast to the open ocean. Comparing the six size-fractions, distinct prokaryotic communities were detected in each size-fraction, and whereas bacteria were more diverse in the larger size-fractions, archaea were more diverse in the smaller size-fractions. Comparison of prokaryotic community composition among particle size-fractions showed that most, but not all, taxonomic groups have a preference for a certain size-fraction sustained with depth. Species sorting, or the presence of diverse ecotypes with distinct size-fraction preferences, may explain why this trend is not conserved in all taxa, The present work was possible thanks to the Generalitat de Catalunya Quality Research Group 2014SGR/1179 and projects STORM (CTM2009-09352), ADEPT (CTM2011-23458), NEMO (CTM2011-13137-E), ANIMA (CTM2015-65720-R) and REMEI (CTM2015-70340-R) funded by the former Ministry of Science and Innovation and the Ministry of Economy and Competitiveness. M. Mestre was supported by a JAE-Predoc grant, a Deutscher Akademischer Austausch Dienst (DAAD) grant, and by the Ministry of Labour, Employment and Social Security. The Leibniz society and the MIBI group at IGB are thanked for funding and technical as well as scientific support, respectively. I. Ferrera was funded by a postdoctoral fellowship from the Leibniz society and the IGB. E. Borrull benefited from a FPI predoctoral fellowship from the Spanish Ministry of Economy and Competitiveness. HPG was funded by DFG (German Science Foundation) projects Aquameth (GR1540-21/1), MicroPrime (GR1540-23/1) and Aggregates (GR1540-28/1)

The bathypelagic ocean is one of the largest ecosystems on Earth and sustains half of the ocean's microbial activity. This microbial activity strongly relies on surface-derived particles, but there is growing evidence that the carbon released through solubilization of these particles may not be sufficient to meet the energy demands of deep ocean prokaryotes. To explore how bathypelagic prokaryotes respond to the absence of external inputs of carbon, we followed the long-term (1 year) dynamics of an enclosed community. Despite the lack of external energy supply, we observed a continuous succession of active prokaryotic phylotypes, which was driven by recruitment of taxa from the seed bank (i.e., initially rare operational taxonomic units [OTUs]). A single OTU belonging to Marine Group I of Thaumarchaeota, which was originally rare, dominated the microbial community for ∼ 4 months and played a fundamental role in this succession likely by introducing new organic carbon through chemolithoautotrophy. This carbon presumably produced a priming effect, because after the decline of Thaumarchaeota, the diversity and metabolic potential of the community increased back to the levels present at the start of the experiment. Our study demonstrates the profound versatility of deep microbial communities when facing organic carbon deprivation.

12 pages, 4 figures, 3 tables, supplementary material http://journal.frontiersin.org/article/10.3389/fmicb.2017.00241/full#supplementary-material, During the Austral summer 2009 we studied three areas surrounding the Antarctic Peninsula: the Bellingshausen Sea, the Bransfield Strait and the Weddell Sea. We aimed to investigate, whether viruses or protists were the main agents inducing prokaryotic mortality rates, and the sensitivity to temperature of prokaryotic heterotrophic production and mortality based on the activation energy (Ea) for each process. Seawater samples were taken at seven depths (0.1–100 m) to quantify viruses, prokaryotes and protists abundances, and heterotrophic prokaryotic production (PHP). Viral lytic production, lysogeny, and mortality rates of prokaryotes due to viruses and protists were estimated at surface (0.1–1 m) and at the Deep Fluorescence Maximum (DFM, 12–55 m) at eight representative stations of the three areas. The average viral lytic production ranged from 1.0 ± 0.3 × 107 viruses ml−1 d−1 in the Bellingshausen Sea to1.3 ± 0.7 × 107 viruses ml−1 d−1 in the Bransfield Strait, while lysogeny, when detectable, recorded the lowest value in the Bellingshausen Sea (0.05 ± 0.05 × 107 viruses ml−1 d−1) and the highest in the Weddell Sea (4.3 ± 3.5 × 107 viruses ml−1 d−1). Average mortality rates due to viruses ranged from 9.7 ± 6.1 × 104 cells ml−1 d−1 in the Weddell Sea to 14.3 ± 4.0 × 104 cells ml−1 d−1 in the Bellingshausen Sea, and were higher than averaged grazing rates in the Weddell Sea (5.9 ± 1.1 × 104 cells ml−1 d−1) and in the Bellingshausen Sea (6.8 ± 0.9 × 104 cells ml−1 d−1). The highest impact on prokaryotes by viruses and main differences between viral and protists activities were observed in surface samples: 17.8 ± 6.8 × 104 cells ml−1 d−1 and 6.5 ± 3.9 × 104 cells ml−1 d−1 in the Weddell Sea; 22.1 ± 9.6 × 104 cells ml−1 d−1 and 11.6 ± 1.4 × 104 cells ml−1 d−1 in the Bransfield Strait; and 16.1 ± 5.7 × 104 cells ml−1 d−1 and 7.9 ± 2.6 × 104 cells ml−1 d−1 in the Bellingshausen Sea, respectively. Furthermore, the rate of lysed cells and PHP showed higher sensitivity to temperature than grazing rates by protists. We conclude that viruses were more important mortality agents than protists mainly in surface waters and that viral activity has a higher sensitivity to temperature than grazing rates. This suggests a reduction of the carbon transferred through the microbial food-web that could have implications in the biogeochemical cycles in a future warmer ocean scenario, This study was supported by the following projects: ATOS (POL2006-00550/CTM, P.I.: CD.) funded by the Spanish Ministerio de Ciencia e Innovación, YC work was supported by a Ph.D. fellowship from the MINECO (FPI grant)

12 pages, 6 figures, 3 tables, supplementary material http://journal.frontiersin.org/article/10.3389/fmicb.2016.02159/full#supplementary-material, Transparent Exopolymer Particles (TEP) are relevant in particle and carbon fluxes in the ocean, and have economic impact in the desalination industry affecting reverse osmosis membrane fouling. However, general models of their occurrence and dynamics are not yet possible because of the poorly known co-variations with other physical and biological variables. Here, we describe TEP distributions in the NW Mediterranean Sea during late spring 2012, along perpendicular and parallel transects to the Catalan coast. The stations in the parallel transect were sampled at the surface, while the stations in the perpendicular transect were sampled from the surface to the bathypelagic, including the bottom nepheloid layers. We also followed the short-term TEP dynamics along a 2-day cycle in offshore waters. TEP concentrations in the area ranged from 4.9 to 122.8 and averaged 31.4 ± 12.0 μg XG eq L−1. The distribution of TEP measured in transects parallel to the Catalan Coast correlated those of chlorophyll a (Chla) in May but not in June, when higher TEP-values with respect to Chla were observed. TEP horizontal variability in epipelagic waters from the coast to the open sea also correlated to that of Chla, O2 (that we interpret as a proxy of primary production) and bacterial production (BP). In contrast, the TEP vertical distributions in epipelagic waters were uncoupled from those of Chla, as TEP maxima were located above the deep chlorophyll maxima. The vertical distribution of TEP in the epipelagic zone was correlated with O2 and BP, suggesting combined phytoplankton (through primary production) and bacterial (through carbon reprocessing) TEP sources. However, no clear temporal patterns arose during the 2-day cycle. In meso- and bathypelagic waters, where phytoplanktonic sources are minor, TEP concentrations (10.1 ± 4.3 μg XG eq l−1) were half those in the epipelagic, but we observed relative TEP increments coinciding with the presence of nepheloid layers. These TEP increases were not paralleled by increases in particulate organic carbon, indicating that TEP are likely to act as aggregating agents of the mostly inorganic particles present in these bottom nepheloid layers, This work was funded by projects funded by the Spanish Ministry of Science STORM (CTM2009-09352/MAR), SUMMER (CTM2008-03309/MAR), DOREMI (CTM2012-34294), REMEI (CTM2015-70340-R), ANIMA (CTM2015-65720-R), PEGASO (CTM2012-37615), and Grup consolidat de Recerca de la Generalitat de Catalunya (2014SGR/1179)

17 pages, 9 figures, 3 tables, supplemental material https://www.frontiersin.org/articles/10.3389/fmicb.2017.02215/full#supplementary-material, In oligotrophic regions, such as the Mediterranean Sea, atmospheric deposition has the potential to stimulate heterotrophic prokaryote growth and production in surface waters, especially during the summer stratification period. Previous studies focused on the role of leaching nutrients from mineral particles of Saharan (S) origin, and were restricted to single locations at given times of the year. In this study, we evaluate the effect of atmospheric particles from diverse sources and with a markedly different chemical composition [S dust and anthropogenic (A) aerosols] on marine planktonic communities from three locations of the northwestern Mediterranean with contrasted anthropogenic footprint. Experiments were also carried out at different times of the year, considering diverse initial conditions. We followed the dynamics of the heterotrophic community and a range of biogeochemical and physiological parameters in six experiments. While the effect of aerosols on bacterial abundance was overall low, bacterial heterotrophic production was up to 3.3 and 2.1 times higher in the samples amended with A and S aerosols, respectively, than in the controls. Extracellular enzymatic activities [leu-aminopeptidase (AMA) and β-glucosidase (β-Gl)] were also enhanced with aerosols, especially from A origin. AMA and β-Gl increased up to 7.1 in the samples amended with A aerosols, and up to 1.7 and 2.1 times, respectively, with S dust. The larger stimulation observed with A aerosols might be attributed to their higher content in nitrate. However, the response was variable depending the initial status of the seawater. In addition, we found that both A and S aerosols stimulated bacterial abundance and metabolism significantly more in the absence of competitors and predators, This study was supported by the Spanish Ministerio de Economía y Competitividad through the projects ADEPT (CTM2011-23458), DOREMI (CTM2012-342949), and ANIMA (CTM2015-65720-R, MINECO/FEDER, EU). IM acknowledges the FPI Spanish scholarship program for a pre-doctoral grant (BES 2012-052976). SN received financial support from the National Counsel of Technological and Scientific Development (CNPq) of Brazil. EDS-P was economically supported by the Consejo Nacional de Ciencia y Tecnologia (CONACyT) of Mexico