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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.

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.

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.

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.

Microplastics are ubiquitous in marine ecosystems and are suitable matrices for bacterial attachment and growth. Studies on the microbes growing on plastics are mainly done using flow cytometry and massive sequencing, which do not allow for the quantification of specific groups and their activity. Here we present the results from a mesocosm experiment, designed to compare the effects of biodegradable and conventional microplastics on planktonic communities of the Baltic Sea. Our specific aim was to study the effects on bacterial activity and abundance using epifluorescence microscopy techniques. Specifically, we applied BONCAT-FISH which simultaneously allows for phylogenetic identification and the detection of the activity of individual bacterial cells. In our experiment, mesocosms were filled with Baltic brackish seawater and amended with 20 microplastic beads·ml -1 in triplicates for several treatments: (i) None (control), (ii) PS, (iii) PLGA and (iv) PS + PLGA. Our results show a low impact of the presence and quality of microplastics on marine bacterial communities during the first 11 days of exposure, with only weak differences in the activity of bacterial communities growing with biodegradable or conventional microplastics additions.

The phylogenetic and functional diversity of the bacterioplankton assemblage associated with blooms of toxic Alexandrium spp. was studied in three harbours of the NW Mediterranean. Denaturing gradient gel electrophoresis and DNA sequence analysis revealed the presence of a bacterium within the Roseobacter clade related to the presence of Alexandrium cells. Phylogenetic diversity was affected by the presence of Alexandrium spp., geographic situation and seasonality. In contrast, functional diversity, assessed with Biolog plates, was clearly affected by seasonality, but not by the presence of Alexandrium, indicating that the presence of the bacterium associated with the blooms was not enough to modify the metabolic pattern of the bacterioplankton assemblage.

The Ocean microbiome has a crucial role in Earth’s biogeochemical cycles. During the last decade, global cruises such as Tara Oceans and the Malaspina Expedition have expanded our understanding of the diversity and genetic repertoire of marine microbes. Nevertheless, there are still knowledge gaps regarding their diversity patterns throughout depth gradients ranging from the surface to the deep ocean. Here we present a dataset of 76 microbial metagenomes (MProfile) of the picoplankton size fraction (0.2–3.0 µm) collected in 11 vertical profiles covering contrasting ocean regions sampled during the Malaspina Expedition circumnavigation (7 depths, from surface to 4,000 m deep). The MProfile dataset produced 1.66 Tbp of raw DNA sequences from which we derived: 17.4 million genes clustered at 95% sequence similarity (M-GeneDB-VP), 2,672 metagenome-assembled genomes (MAGs) of Archaea and Bacteria (Malaspina-VP-MAGs), and over 100,000 viral genomic sequences. This dataset will be a valuable resource for exploring the functional and taxonomic connectivity between the photic and bathypelagic tropical and sub-tropical ocean, while increasing our general knowledge of the Ocean microbiome.

Global warming and the associated ice melt are leading to an increase in the organic carbon in the Arctic Ocean. We evaluated the effects of ice melt on bacterioplankton at 21 stations in the Greenland Sea and Arctic Ocean in the summer of 2007, when a historical minimum of Arctic ice coverage was measured. Polar Surface Waters, which have a low temperature and low salinity and originate mainly from melted ice, contained a very low abundance of bacteria (7.01 × 10⁵ ± 2.20 × 10⁵ cells ml⁻¹); however, these bacteria had high specific bacterial production (2.40 ± 1.61 fmol C bac⁻¹ d⁻¹) compared to those in Atlantic Waters. Specifically, bacterioplankton in Polar Surface Waters showed a preference for utilizing carbohydrates and had significantly higher specific activities of the glycosidases assayed, i.e. β-glucosidase, xylosidase, arabinosidase and cellobiosidase. Furthermore, bacterioplankton in Polar Sea Waters showed preferential growth on some of the carbohydrates in the Biolog Ecoplate, such as d-cellobiose and N-acetyl-d-glucosamine. Our results suggest that climate change and the associated melting of Arctic ice might induce changes in bacterioplankton functional diversity by enhancing the turnover of carbohydrates. Since organic aggregates are largely composed of polysaccharides, higher solubilization of aggregates might modify the carbon cycle, weaken the biological pump and have biogeochemical and ecological implications for the future Arctic Ocean.

The ocean surface microlayer (SML), with physicochemical characteristics different from those of subsurface waters (SSW), results in dense and active viral and microbial communities that may favor virus–host interactions. Conversely, wind speed and/or UV radiation could adversely affect virus infection. Furthermore, in polar regions, organic and inorganic nutrient inputs from melting ice may increase microbial activity in the SML. Since the role of viruses in the microbial food web of the SML is poorly understood in polar oceans, we aimed to study the impact of viruses on prokaryotic communities in the SML and in the SSW in Arctic and Antarctic waters. We hypothesized that a higher viral activity in the SML than in the SSW in both polar systems would be observed. We measured viral and prokaryote abundances, virus-mediated mortality on prokaryotes, heterotrophic and phototrophic nanoflagellate abundance, and environmental factors. In both polar zones, we found small differences in environmental factors between the SML and the SSW. In contrast, despite the adverse effect of wind, viral and prokaryote abundances and virus-mediated mortality on prokaryotes were higher in the SML than in the SSW. As a consequence, the higher carbon flux released by lysed cells in the SML than in the SSW would increase the pool of dissolved organic carbon (DOC) and be rapidly used by other prokaryotes to grow (the viral shunt). Thus, our results suggest that viral activity greatly contributes to the functioning of the microbial food web in the SML, which could influence the biogeochemical cycles of the water column.

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.