Tara Oceans CoordinatorsInternational audienceOcean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions, and analyse the resulting ‘global ocean virome’ dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups. This roughly triples the number of known ocean viral populations and doubles the number of candidate bacterial and archaeal virus genera, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks

Abstract. We present an overview of the plankton studies conducted during the last 25 years in the epipelagic offshore waters of the Mediterranean Sea. This quasi-enclosed sea is characterized by a rich and complex physical dynamics with distinctive traits, especially in regard to the thermohaline circulation. Recent investigations have basically confirmed the long-recognised oligotrophic nature of this sea, which increases along both the west-east and the north-south directions. Nutrient availability is low, especially for phosphorous (N:P up to 60), though this limitation may be buffered by inputs from highly populated coasts and from the atmosphere. Phytoplankton biomass, as chl a, generally displays low values (less than 0.2 µg chl a l −1 ) over large areas, with a modest late winter increase. A large bloom (up to 3 µg l −1 ) is observed throughout the late winter and spring exclusively in the NW area. Relatively high biomass values are recorded in fronts and cyclonic gyres. A deep chlorophyll maximum is a permanent feature for the whole basin, except during the late winter mixing. It is found at increasingly greater depths ranging from 30 m in the Alboran Sea to 120 m in the easternmost Levantine basin. Primary production reveals a west-east decreasing trend and ranges between 59 and 150 g C m −2 y −1 (in situ measurements). Overall, the basin is largely dominated by small autotrophs, microheterotrophs and egg-carrying copepod species. The microorganisms (phytoplankton, viruses, bacteria, flagellates and ciliates) and zooplankton components reveal a considerable diversity and

A series of dialysis experiments was performed to study the relative importance of substrate limitation and grazing in controlling the proportion of active cells of coastal marine bacterioplankton. The grazer community was manipulated by filling dialysis bags with unfiltered water and water serially passed through 150-, 40-, and O.&pm pore-size filters. The total number of bacteria, the number of metabolically active cells, bacterial loss rates, and the abundances of heterotrophic nanoflagellates were measured immediately and at 3 and 6 d. Gross growth rates were similar in all treatments, suggesting that ambient nutrient concentrations set an upper limit to the maximum growth rates, whereas grazing determined the net growth rates and the final number of bacteria. Bacterial loss rates, measured as the disappearance of fluorescently labeled minicells, correlated well with the initial density of heterotrophic nanoflagellates in the different treatments. The number of active cells at the end of the experiments varied widely among treatments and reached 2.0 x lo6 ml-l, or over 55% of the total final density in dialysis bags, with little or no grazing by nanoflagellates. The final proportion of active cells was negatively correlated to both the loss rates and the initial nanoflagellate density, and it was estimated that grazing rates on metabolically active bacteria were four or more times higher than those on inactive bacteria. Heterotrophic nanoflagellates thus seemed to control bacterial density by skimming newly growing cells rather than by cropping the standing stock of bacteria.

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Primary producers must respond to the diel changes in light availability. Therefore, detection of diel cycles in bacterial activity would imply tight coupling between the production of photosynthetic dissolved organic carbon (DOC) and its consumption by bacteria. Absence of diel cycles, on the contrary, would indicate that bacteria depend largely upon allochthonous organic carbon and that bacteria are not tightly dependent on photosynthetically produced autochthonous carbon. In 1993 and 1994 we sampled 3 sites in the NW Mediterranean Sea several times a day, and measured several microbial parameters as well as the vertical profiles of DOC along the diel cycle. The sites were selected so that one was on the continental shelf and, thus, was more Influenced by coastal runoff; a second one was over the shelf slope and a third, oceanlc one was located further offshore over a depth of 2000 m. LVe found clear die1 cycles in bacterial total and specific activity always in the oceanic stations and sometimes in the shelf slope stations. Diel changes were detected as changes in both DNA and protein synthesis rates. These diel cycles were accompanied by diel changes in the distribution of total DOC, and by diel changes in the proportion of bacteria containing visible nucleoids. Noon estimates of bactenal activity were more than twice the daily average in the oceanic site, but they were less different in the other 2 sites. DOC chanyed daily by 15 pM (5 to 15% of the total stock) For bacterial activity to explain the diel changes In DOC concentration, bacteria should have growth efficiencies lower than 10 O/o in general, and lower than 2 "h in the oceanic station.

The deep sea, the largest ocean’s compartment, drives planetary-scale biogeochemical cycling. Yet, the functional exploration of its microbial communities lags far behind other environments. Here we analyze 58 metagenomes from tropical and subtropical deep oceans to generate the Malaspina Gene Database. Free-living or particle-attached lifestyles drive functional differences in bathypelagic prokaryotic communities, regardless of their biogeography. Ammonia and CO oxidation pathways are enriched in the free-living microbial communities and dissimilatory nitrate reduction to ammonium and H2 oxidation pathways in the particle-attached, while the Calvin Benson-Bassham cycle is the most prevalent inorganic carbon fixation pathway in both size fractions. Reconstruction of the Malaspina Deep Metagenome-Assembled Genomes reveals unique non-cyanobacterial diazotrophic bacteria and chemolithoautotrophic prokaryotes. The widespread potential to grow both autotrophically and heterotrophically suggests that mixotrophy is an ecologically relevant trait in the deep ocean. These results expand our understanding of the functional microbial structure and metabolic capabilities of the largest Earth aquatic ecosystem.

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The role of the ocean as a sink for CO2 is partially dependent on the downward transport of phytoplankton cells packaged within fast-sinking particles. However, whether such fast-sinking mechanisms deliver fresh organic carbon down to the deep bathypelagic sea and whether this mechanism is prevalent across the ocean requires confirmation. Here we report the ubiquitous presence of healthy photosynthetic cells, dominated by diatoms, down to 4,000 m in the deep dark ocean. Decay experiments with surface phytoplankton suggested that the large proportion (18%) of healthy photosynthetic cells observed, on average, in the dark ocean, requires transport times from a few days to a few weeks, corresponding to sinking rates (124–732 m d−1) comparable to those of fast-sinking aggregates and faecal pellets. These results confirm the expectation that fast-sinking mechanisms inject fresh organic carbon into the deep sea and that this is a prevalent process operating across the global oligotrophic ocean.