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Summary: Grazing controls bacterial abundances and composition in many ecosystems. In marine systems, heterotrophic flagellates (HFs) are important predators. Assemblages of HFs are primarily formed by species still uncultured; therefore, many aspects of their trophic behaviour are poorly known. Here, we assessed the functional response of the whole assemblage and of four taxa grown in an unamended seawater incubation. We used fluorescently labelled bacteria to create a prey gradient of two orders of magnitude in abundance and estimated ingestion rates. Natural HFs had a half‐saturation constant of 6.7 × 105 prey ml−1, a value lower than that of cultured flagellates and within the range of marine planktonic bacterial abundances. Minorisa minuta was well adapted to low prey abundances and very efficient in ingesting bacteria. MAST‐4 and MAST‐7 were also well adapted to the typical marine abundances but less voracious. In contrast, Paraphysomonas imperforata, a typical cultured species, did not achieve ingestion rate saturation even at the highest prey concentration assayed. Our study, beside to set the basis for the fundamental differences between cultured and uncultured bacterial grazers, indicate that the examined predator taxa have different functional responses, suggesting that they occupy distinct ecological niches according to their grazing strategies and prey preferences. [ABSTRACT FROM AUTHOR]

The article active reports on viral processes reported that demonstrate the importance of viruses in the production of dissolved organic carbon in the dark ocean which is a major pathway in carbon cycling. Topics discussed include assessment of patterns in viral abundance and production and the role of viral lysis as a driver of prokaryote mortality and differences between oceans in the epipelagic and mesopelagic, but not in the bathypelagic, and decreased with depth.

The Arctic Ocean is rapidly changing where increasing water temperatures and rapid loss of summer sea-ice will likely influence the structure and functioning of the entire ecosystem. The aim of this study was to synthesize the current state of knowledge on microbial abundances and processes from a regional Pan-Arctic perspective, characterize regulating factors and attempt to predict how patterns may change under a warming scenario. Here we identify some generalized patterns of different microbial variables between the Pacific-fed and the Atlantic-fed sectors of the Arctic Ocean. Bacterial production (BP), abundance and grazing rates by protists (GT) were all higher in the Atlantic-fed region. Bacterial loss by viral lyses (VL) was proportionally more important in the Pacific-fed sector, suggesting a reduced C transfer efficiency within the microbial loop of that region. Using a cross-comparative approach and all available data to build Arrhenius plots, we found a differential response to warming temperatures among various microbial processes. BP and GT responded similarly and more strongly to increases in temperature than VL did, suggesting a shift in the overall influence of viral mortality under a warming scenario. However, together with temperature, resource-related factors also exerted an influence in regulating these rates. We identified large information gaps for more classically studied microbial variable from several Arctic seas. Furthermore, there is limited information on less conventional pathways such as grazing by mixotrophic species, which may be playing a significant role in Arctic microbial trophodynamics. Although generalized patterns could be elucidated, more information is needed to predict and understand how a changing Arctic will alter microbial C pathways and major biogeochemical cycles on regional and seasonal scales. [ABSTRACT FROM AUTHOR]

To evaluate the main factors shaping bacterioplankton phylogenetic and functional diversity in marine coastal waters, we carried out a two-year study based on a monthly sampling in Blanes Bay (NW Mediterranean). We expected the key factors driving bacterial diversity to be (1) temperature and nutrient concentration, together with chlorophyll a concentration as an indicator of phytoplankton biomass and, hence, a carbon source for bacteria (here called bottom-up factors), and (2) top-down pressure (virus- and protist-mediated mortality of bacteria). Phylogenetic diversity was analyzed by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA. Functional diversity was assessed by using monomeric carbon sources in Biolog EcoPlates and by determining the activity of six extracellular enzymes. Our results indicate that the bacterial phylogenetic and functional diversity in this coastal system is shaped mainly by bottom-up factors. A dendrogram analysis of the DGGE banding patterns revealed three main sample clusters. Two clusters differed significantly in temperature, nitrate and chlorophyll a concentration, and the third was characterized by the highest losses of bacterial production due to viral lysis detected over the whole study period. Protistan grazing had no effect on bacterial functional diversity, since there were no correlations between protist-mediated mortality (PMM) and extracellular enzyme activities, and utilization of only two out of the 31 carbon sources (N-acetyl- d -glucosamine and α-cyclodextrin) was correlated with PMM. In contrast, virus-mediated mortality correlated with changes in the percentage of use of four carbon sources, and also with specific leu-aminopeptidase and β-glucosidase activity. This suggests that viral lysate provides a pool of labile carbon sources, presumably including amino acids and glucose, which may inhibit proteolytic and glucosidic activity. Our results indicate that bottom-up factors play a more important role than top-down factors (i.e. viral lysis and protistan grazing) in shaping bacterial community structure and activity. Furthermore, they suggest that viruses play a more important role than protists in modifying community structure and functional diversity of bacteria in oligotrophic marine coastal waters. [ABSTRACT FROM AUTHOR]

We estimated the bacterial production and losses to predators along an open ocean trophic gradient from coastal upwelling waters to oligotrophic waters in the Subtropical Northern Atlantic Ocean. Two zonal sections (21 and 26°N) extending from the NW African shelf to the Open Atlantic Ocean at 26°W were sampled during September–October 2002 (autumn), and May–June 2003 (spring). The main goal was to elucidate whether the impacts of bacterial losses were more important in upwelling rather than in offshore waters. Whereas temperature and salinity decreased and nutrient concentrations increased from offshore to the coastal upwelling regions, phytoplankton, ciliate and bacterial biomass followed a similar trend increasing towards the upwelling zone. In addition, heterotrophic nanoflagellate biomass, bacterial production and grazing rates on bacteria did not follow this pattern, although the highest activities were recorded at upwelling stations. However, at the stations not affected by upwelling the average impact on bacteria expressed as a percentage of bacterial production consumed by predators in autumn and spring (values that varied between 70% ± 6% and 129% ± 15%, respectively) was significantly higher than at the upwelling stations (where it ranged between 49% ± 7% and 68% ± 5%, respectively). Our results suggest that in the upwelling areas bacteria escape from predators and growth cannot be balanced by grazing, while it is at the oligotrophic open ocean stations when, on occasions, grazing can overcome bacterial production. [ABSTRACT FROM PUBLISHER]

Bacterivory was determined in surface waters of Franklin Bay, western Arctic, over a seasonal ice-covered period (winter-spring, 2003-2004). The objectives were to obtain information on the functioning of the microbial food web under the ice, during winter (from 21 December 2003 to 21 March 2004) and during spring (from 22 March 2004 to 29 May 2004), and to test whether bacterial losses would increase after the increase in bacterial production following the spring phytoplankton bloom. Chl a concentrations ranged from 0.04 to 0.36 µg L-1, increasing in March and reaching a peak in April. Bacterial biomass showed no consistent trend for the whole period, and protist biomass followed a pattern similar to that of Chl a. Bacterial production increased 1 week after Chl a concentrations started to increase, while bacterivory rates increased very slightly. Average bacterivory rates in winter (0.16 ± 0.07 µg C L-1 d-1) were not significantly different from those in spring (0.29 ± 0.24 µg C L-1 d-1). Average bacterial production, on the other hand, was similar to bacterivory rates in winter (0.19 ± 0.38 µg C L-1 d-1), but higher than bacterivory in spring (0.93 ± 0.28 µg C L-1 d-1). Therefore, bacterial production was controlled by grazers during winter and by substrate concentration in spring. [ABSTRACT FROM AUTHOR]

Abstract: Mesopelagic prokaryotic communities have often been assumed to be relatively inactive in comparison to those from epipelagic waters, and therefore unresponsive to the presence of nearby upwelled waters. We have studied the zonal (shelf-ocean), latitudinal, and depth (epipelagic–mesopelagic) variability of microbial assemblages in the NW Africa–Canary Islands coastal-transition zone (CTZ). Vertical profiles of bacterial bulk and single-cell activity through the epi- and mesopelagic waters were combined with point measurements of bacterial respiration, leucine-to-carbon conversion factors and leucine-to-thymidine incorporation ratios. The overall picture that emerges from our study is that prokaryotes in the mesopelagic zone of this area are less abundant than in the epipelagic but have comparable levels of activity. The relationship between prokaryotes and heterotrophic nanoflagellates, their main predators, remains constant throughout the water column, further contradicting the assumption that deep ocean bacterial communities are mostly inactive. Both bulk and single-cell activity showed clear differences between stations, with higher mesopelagic activities closer to the shelf or affected by upwelling features. We also tested whether differences in microbial function between stations could be related to differences in bacterial community structure, and conclude that bacterial communities are very similar at similar depths in the deep ocean, even if the stations present order-of-magnitude differences in bacterial function. [Copyright &y& Elsevier]

A set of eight large (20 m³) mesocosms were moored in Johnson's Dock (62°39.576'S, 60°22.408'W, Livingston Island, Antarctica) to experimentally generate a gradient of phytoplankton biomass and production in order to test the extent of coupling between bacteria (heterotrophic Bacteria and Archaea) and phytoplankton, as well as the role of bacterial losses to protist grazers. This was achieved by imposing four light levels (100%, 50%, 25%, and 10%) in the presence or absence of nutrient additions (0.1 mol NH4Cl, 0.1 mol F6Na2Si, and 0.01 mol KH2PO4 per day per mesocosm). The experimental treatments resulted in a broad range of chlorophyll a (Chl a) (0.31-93.5 µg Chl a L-1) and average primary production rates, while bacteria responded in a much narrower range of biomass (3-447 µg C L-1) and production (0.21-15.71 µg C L-1d-1). Results confirm that bacteria--chlorophyll and bacterial production--primary production relationships in the Southern Ocean differ from the typical relationships applicable to aquatic ecosystems elsewhere. Bacteria respond to phytoplankton blooms, but they respond so weakly that bacterial production represents a small percentage of primary production (1-10%). Although other mechanisms might also contribute to the weak bacterial response to phytoplankton blooms, we demonstrate that the reason for it is likely the tight control of bacterial populations by their predators. Protist grazers are able to sustain faster growth rates in the cold waters of the Southern Ocean than are bacteria, thereby preventing bacteria from responding to phytoplankton blooms more forcibly. [ABSTRACT FROM AUTHOR]

Long-term and experimental approaches were used to examine the metabolic balance of the planktonic community in the Bay of Blanes (Spanish Mediterranean). Incubation measurements at weekly intervals for 6 yr revealed that community respiration, R, was consistently larger than gross primary production (GPP) by a factor of 2. The plankton community was net heterotrophic for 2/3 of the study period, with a median P/R ratio of 0.65. The biomass of autotrophs comprised, on average, 41% ± 3% of the planktonic biomass, and the total microplankton biomass was about 2.5-fold greater than that of the primary producers. The monthly average GPP and R were positively correlated with day length, and the planktonic respiration and gross production per unit microplankton biomass increased with increasing water temperature. Experimental nutrient additions had a greater effect on GPP than respiration rates; the increase in R along the nutrient gradient was 7.8% (± 0.4%) of the increase in GPP. As a result, net community production increased in parallel with GPP, shifting from net heterotrophic at low GPP to net autotrophic when GPP increased because of nutrient additions. Our results show that Be R that would be supported by allocthonous inputs was 3.83 ± 0.67 µmol O2 L-1 d-1, and the average GPP required to shift the community from net heterotrophic to net autotrophic was about 4 µmol O2 L-1 d-1. This is well above the average GPP recorded in the Bay of Blanes along this study (2.56 ± 0.13 µmol O2 L-1 d-1), explaining the net heterotrophic nature of the community. [ABSTRACT FROM AUTHOR]

Summary: Ostreococcus is a cosmopolitan marine genus of phytoplankton found in mesotrophic and oligotrophic waters, and the smallest free‐living eukaryotes known to date, with a cell diameter close to 1 μm. Ostreococcus has been extensively studied as a model system to investigate viral–host dynamics in culture, yet the impact of viruses in naturally occurring populations is largely unknown. Here, we used Virus Fluorescence in situ Hybridization (VirusFISH) to visualize and quantify viral‐host dynamics in natural populations of Ostreococcus during a seasonal cycle in the central Cantabrian Sea (Southern Bay of Biscay). Ostreococcus were predominantly found during summer and autumn at surface and 50 m depth, in coastal, mid‐shelf and shelf waters, representing up to 21% of the picoeukaryotic communities. Viral infection was only detected in surface waters, and its impact was variable but highest from May to July and November to December, when up to half of the population was infected. Metatranscriptomic data available from the mid‐shelf station unveiled that the Ostreococcus population was dominated by the species O. lucimarinus. This work represents a proof of concept that the VirusFISH technique can be used to quantify the impact of viruses on targeted populations of key microbes from complex natural communities. [ABSTRACT FROM AUTHOR]

Ciliates are globally distributed eukaryotic organisms inhabiting virtually all environments on Earth. Although ciliates range from 10 µm to a few millimetres in cell size, they are repeatedly reported in the pico‐sized fraction (<2–3 µm) of molecular surveys. Here, we used existing data sets (BioMarKs and Tara Oceans) with different size fractions to demonstrate that the ciliate pico‐sized signal, probably derived from cell breakage during filtration, is informative and reliable to study marine ciliate biodiversity and biogeography. We then used sequences from the pico‐eukaryotic fraction of two circumnavigation expeditions, Malaspina‐2010 and Tara Oceans, to give insights into the taxonomic composition and horizontal and vertical distribution of ciliates in the global ocean. The results suggested a high homogeneity of ciliate communities along the ocean surface from temperate to tropical waters, with ciliate assemblages dominated by a few abundant and widely distributed taxa. Very few taxa were found in a single oceanic region, therefore suggesting a high level of ciliate cosmopolitanism in the global ocean. In vertical profiles, ciliates were detected up to 4,000 m depth, and a clear vertical community structuring was observed. Our results provided evidence supporting ciliates as deeply integrated organisms in the deep‐sea trophic web, where they may play a relevant role as symbionts of metazoans and grazers of prokaryotes and small eukaryotes in the water column and in aggregates. [ABSTRACT FROM AUTHOR]

Background: Isolation of marine microorganisms is fundamental to gather information about their physiology, ecology and genomic content. To date, most of the bacterial isolation efforts have focused on the photic ocean leaving the deep ocean less explored. We have created a marine culture collection of heterotrophic bacteria (MARINHET) using a standard marine medium comprising a total of 1561 bacterial strains, and covering a variety of oceanographic regions from different seasons and years, from 2009 to 2015. Specifically, our marine collection contains isolates from both photic (817) and aphotic layers (744), including the mesopelagic (362) and the bathypelagic (382), from the North Western Mediterranean Sea, the North and South Atlantic Ocean, the Indian, the Pacific, and the Arctic Oceans. We described the taxonomy, the phylogenetic diversity and the biogeography of a fraction of the marine culturable microorganisms to enhance our knowledge about which heterotrophic marine isolates are recurrently retrieved across oceans and along different depths. Results: The partial sequencing of the 16S rRNA gene of all isolates revealed that they mainly affiliate with the classes Alphaproteobacteria (35.9%), Gammaproteobacteria (38.6%), and phylum Bacteroidetes (16.5%). In addition, Alteromonas and Erythrobacter genera were found the most common heterotrophic bacteria in the ocean growing in solid agar medium. When comparing all photic, mesopelagic, and bathypelagic isolates sequences retrieved from different stations, 37% of them were 100% identical. This percentage increased up to 59% when mesopelagic and bathypelagic strains were grouped as the aphotic dataset and compared to the photic dataset of isolates, indicating the ubiquity of some bacterial isolates along different ocean depths. Finally, we isolated three strains that represent a new species, and the genome comparison and phenotypic characterization of two of these strains (ISS653 and ISS1889) concluded that they belong to a new species within the genus Mesonia. Conclusions: Overall, this study highlights the relevance of culture-dependent studies, with focus on marine isolated bacteria from different oceanographic regions and depths, to provide a more comprehensive view of the culturable marine bacteria as part of the total marine microbial diversity. [ABSTRACT FROM AUTHOR]

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−1 and typically decreased with depth. Chlorophyll a (Chl a) concentration was a better predictor of TEP variability across the horizontal (R2 = 0.66, p < 0.001) and vertical (R2 = 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−1), 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)−1, compared to a mean of 79.3 ± 54.9 μg XG eq (μg Chl a)−1 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. Unlabelled Image • Transparent exopolymer particles (TEP) were measured in the Southern Ocean during summer. • Phytoplankton were the main drivers of both horizontal and vertical TEP distribution. • Light stress and sea ice melt and retreat further tuned TEP distribution. • TEP enrichment generally occurred near the upper surface (0.1 vs 4 m). • Upper-surface enrichment was likely enhanced by wind-provoked turbulence and bubbles. [ABSTRACT FROM AUTHOR]

Viruses are the most abundant biological entities on Earth and have fundamental ecological roles in controlling microbial communities. Yet, although their diversity is being increasingly explored, little is known about the extent of viral interactions with their protist hosts as most studies are limited to a few cultivated species. Here, we exploit the potential of single‐cell genomics to unveil viral associations in 65 individual cells of 11 essentially uncultured stramenopiles lineages sampled during the Tara Oceans expedition. We identified viral signals in 57% of the cells, covering nearly every lineage and with narrow host specificity signal. Only seven out of the 64 detected viruses displayed homologies to known viral sequences. A search for our viral sequences in global ocean metagenomes showed that they were preferentially found at the DCM and within the 0.2–3 µm size fraction. Some of the viral signals were widely distributed, while others geographically constrained. Among the viral signals we detected an endogenous mavirus virophage potentially integrated within the nuclear genome of two distant uncultured stramenopiles. Virophages have been previously reported as a cell's defence mechanism against other viruses, and may therefore play an important ecological role in regulating protist populations. Our results point to single‐cell genomics as a powerful tool to investigate viral associations in uncultured protists, suggesting a wide distribution of these relationships, and providing new insights into the global viral diversity. [ABSTRACT FROM AUTHOR]

Planktonic heterotrophic prokaryotes make up the largest living biomass and process most organic matter in the ocean. Determining when and where the biomass and activity of heterotrophic prokaryotes are controlled by resource availability (bottom-up), predation and viral lysis (top-down) or temperature will help in future carbon cycling predictions. We conducted an extensive survey across subtropical and tropical waters of the Atlantic, Indian and Pacific Oceans during the Malaspina 2010 Global Circumnavigation Expedition and assessed indices for these three types of controls at 109 stations (mostly from the surface to 4,000 m depth). Temperature control was approached by the apparent activation energy in eV (ranging from 0.46 to 3.41), bottom-up control by the slope of the log-log relationship between biomass and production rate (ranging from −0.12 to 1.09) and top-down control by an index that considers the relative abundances of heterotrophic nanoflagellates and viruses (ranging from 0.82 to 4.83). We conclude that temperature becomes dominant (i.e. activation energy >1.5 eV) within a narrow window of intermediate values of bottom-up (0.3-0.6) and top-down 0.8-1.2) controls. A pervasive latitudinal pattern of decreasing temperature regulation towards the Equator, regardless of the oceanic basin, suggests that the impact of global warming on marine microbes and their biogeochemical function will be more intense at higher latitudes. Our analysis predicts that 1°C ocean warming will result in increased biomass of heterotrophic prokaryoplankton only in waters with <26°C of mean annual surface temperature. [ABSTRACT FROM AUTHOR]

The free-living (FL) and particle-attached (PA) marine microbial communities have repeatedly been proved to differ in their diversity and composition in the photic ocean and also recently in the bathypelagic ocean at a global scale. However, although high taxonomic ranks exhibit preferences for a PA or FL mode of life, it remains poorly understood whether two clear lifestyles do exist and how these are distributed across the prokaryotic phylogeny. We studied the FL (<0.8 lm) and PA (0.8-20 µm) prokaryotes at 30 stations distributed worldwide within the bathypelagic oceanic realm (2150-4000 m depth) using high-throughput sequencing of the small subunit ribosomal RNA gene (16S rRNA). A high proportion of the bathypelagic prokaryotes were mostly found either attached to particles or freely in the surrounding water but rarely in both types of environments. In particular, this trait was deeply conserved through their phylogeny, suggesting that the deep-ocean particles and the surrounding water constitute two highly distinct niches and that transitions from one to the other have been rare at an evolutionary timescale. As a consequence, PA and FL communities had clear alpha-and beta-diversity differences that exceeded the global-scale geographical variation. Our study organizes the bathypelagic prokaryotic diversity into a reasonable number of ecologically coherent taxa regarding their association with particles, a first step for understanding which are the microbes responsible for the processing of the dissolved and particulate pools of organic matter that have a very different biogeochemical role in the deep ocean. [ABSTRACT FROM AUTHOR]

The dark ocean is one of the largest biomes on Earth, with critical roles in organic matter remineralization and global carbon sequestration. Despite its recognized importance, little is known about some key microbial players, such as the community of heterotrophic protists (HP), which are likely the main consumers of prokaryotic biomass. To investigate this microbial component at a global scale, we determined their abundance and biomass in deepwater column samples from the Malaspina 2010 circumnavigation using a combination of epifluorescence microscopy and flow cytometry. HP were ubiquitously found at all depths investigated down to 4000 m. HP abundances decreased with depth, from an average of 72±19 cells ml−1 in mesopelagic waters down to 11±1 cells ml−1 in bathypelagic waters, whereas their total biomass decreased from 280±46 to 50±14 pg C ml−1. The parameters that better explained the variance of HP abundance were depth and prokaryote abundance, and to lesser extent oxygen concentration. The generally good correlation with prokaryotic abundance suggested active grazing of HP on prokaryotes. On a finer scale, the prokaryote:HP abundance ratio varied at a regional scale, and sites with the highest ratios exhibited a larger contribution of fungi molecular signal. Our study is a step forward towards determining the relationship between HP and their environment, unveiling their importance as players in the dark ocean's microbial food web. [ABSTRACT FROM AUTHOR]

Marine viruses (phages) alter bacterial diversity and evolution with impacts on marine biogeochemical cycles, and yet few well-developed model systems limit opportunities for hypothesis testing. Here we isolate phage B8b from the Mediterranean Sea using Pseudoalteromonas sp. QC-44 as a host and characterize it using myriad techniques. Morphologically, phage B8b was classified as a member of the Siphoviridae family. One-step growth analyses showed that this siphovirus had a latent period of 70 min and released 172 new viral particles per cell. Host range analysis against 89 bacterial host strains revealed that phage B8b infected 3 Pseudoalteromonas strains (52 tested, >99.9% 16S rRNA gene nucleotide identity) and 1 non-Pseudoaltermonas strain belonging to Alteromonas sp. (37 strains from 6 genera tested), which helps bound the phylogenetic distance possible in a phage-mediated horizontal gene transfer event. The Pseudoalteromonas phage B8b genome size was 42.7 kb, with clear structural and replication modules where the former were delineated leveraging identification of 16 structural genes by virion structural proteomics, only 4 of which had any similarity to known structural proteins. In nature, this phage was common in coastal marine environments in both photic and aphotic layers (found in 26.5% of available viral metagenomes), but not abundant in any sample (average per sample abundance was 0.65% of the reads). Together these data improve our understanding of siphoviruses in nature, and provide foundational information for a new ‘rare virosphere’ phage–host model system. [ABSTRACT FROM AUTHOR]

Abstract: Major pathways of biogenic carbon (C) flow are resolved for the planktonic food web of the flaw lead polynya system of the Amundsen Gulf (southeast Beaufort Sea, Arctic Ocean) in spring-summer 2008. This period was relevant to study the effect of climate change on Arctic marine ecosystems as it was characterized by unusually low ice cover and warm sea surface temperature. Our synthesis relied on a mass balance estimate of gross primary production (GPP) of 52.5±12.5gCm−2 calculated using the drawdown of nitrate and dissolved inorganic C, and a seasonal f-ratio of 0.64. Based on chlorophyll a biomass, we estimated that GPP was dominated by phytoplankton (93.6%) over ice algae (6.4%) and by large cells (>5μm, 67.6%) over small cells (<5μm, 32.4%). Ancillary in situ data on bacterial production, zooplankton biomass and respiration, herbivory, bacterivory, vertical particle fluxes, pools of particulate and dissolved organic carbon (POC, DOC), net community production (NCP), as well as selected variables from the literature were used to evaluate the fate of size-fractionated GPP in the ecosystem. The structure and functioning of the planktonic food web was elucidated through inverse analysis using the mean GPP and the 95% confidence limits of every other field measurement as lower and upper constraints. The model computed a net primary production of 49.2gCm−2, which was directly channeled toward dominant calanoid copepods (i.e. Calanus hyperboreus 20%, Calanus glacialis 10%, and Metridia longa 10%), other mesozooplankton (12%), microzooplankton (14%), detrital POC (18%), and DOC (16%). Bacteria required 29.9gCm−2, a demand met entirely by the DOC derived from local biological activities. The ultimate C outflow comprised respiration fluxes (82% of the initial GPP), a small sedimentation (3%), and a modest residual C flow (15%) resulting from NCP, dilution and accumulation. The sinking C flux at the model limit depth (395m) supplied 60% of the estimated benthic C demand (2.8gCm−2), suggesting that the benthos relied partly on other C sources within the bottom boundary layer to fuel its activity. In summary, our results illustrate that the ongoing decline in Arctic sea ice promotes the growth of pelagic communities in the Amundsen Gulf, which benefited from a ∼80% increase in GPP in spring-summer 2008 when compared to 2004 – a year of average ice conditions and relatively low GPP. However, 53% of the secondary production was generated within the microbial food web, the net ecological efficiency of zooplankton populations was not particularly high (13.4%), and the quantity of biogenic C available for trophic export remained low (6.6gCm−2). Hence it is unlikely that the increase in lower food web productivity, such as the one observed in our study, could support new harvestable fishery resources in the offshore Beaufort Sea domain. [Copyright &y& Elsevier]

Viruses are the most abundant biological entities in aquatic systems, infecting from bacteria to mammals. However, there has been little study so far on their impact on marine heterotrophic flagellates (HFs). For this reason, four experiments were carried out between April 2006 and February 2007 in the Blanes Bay Microbial Observatory (NW Mediterranean coast). We investigated whether viruses could affect HF communities, and specifically two uncultured marine stramenopile groups (MAST-4 and MAST-1C). For each experiment, four microcosms containing 12 L of 5-µm filtered seawater were prepared, two received active viruses and the other two received heat-inactivated viruses. Microcosms were then incubated for 48 h in order to measure changes in the abundance of the target groups. In three of the four experiments, both the growth rates of HF and MAST-4 cells and the percentage of MAST-4 cells with respect to HF after 48 h were higher in the heat-inactivated treatment compared with the active viruses treatment. These results indicate that viruses can negatively affect the HF community either directly via lysis of protists or indirectly via lysis of bacteria, and highlight the interactions between, virus, bacteria and protists. [ABSTRACT FROM AUTHOR]

Abstract: The surface microalgal community, including harmful species, dissolved organic matter (DOM), and bacterial and viral populations were studied during an annual cycle (November 2007–October 2008) in a Near-shore (NS) and a Harbour (H) station located in an upwelling area (Sagres, SW Iberian Peninsula). The higher water residence time, water stability and shallowness of harbours in comparison with open waters likely contributed to the differences found between stations regarding chemical variables, statistical correlations and harmful algal proliferations. Also, several differences were noticed from a previous assessment () including higher SST, lower nitrate and chlorophyll a concentrations, along with a shift in the microplankton community structure from diatom to nanoflagellate predominance. These variations feasibly reflect the response of this dynamic system to regional environmental modifications contributing to the understanding of common patterns in environmental change trends. The division of the sampling period into (1) non-upwelling (Non-Uw), (2) “spin-up” of upwelling (SU-Uw), and (3) “spin-down” and relaxation-downwelling (SD-Rel) stages allowed the identification of natural groupings of microplankton samples by Multi Dimensional Scaling (MDS) analysis. Dissolved organic nitrogen (DON) and viruses were the most significant abiotic and biotic variables, respectively, contributing to the dissimilarities between these stages (SIMPER analysis) and, therefore, potentially affecting the microplankton community structure. Harmful algal species and a stable viral community appeared to be favoured by SD-Rel conditions. Data seem to indicate that both Gymnodinium catenatum and Heterosigma akashiwo, the most abundant potentially harmful species, have been imported into the sampling area. Also, the H location, together with potential retention sites developing around the Cabo de São Vicente upwelling centre, may contribute to the local accumulation of harmful species. The associations found between harmful algal species and bacterioplankton and virioplankton call for detailed studies in order to evaluate species-specific interactions. [Copyright &y& Elsevier]

Alexandrium catenella was grown in semi-continuous cultures in L1 growth-medium enriched with concentrated dissolved organic matter (DOM) from a diatom bloom. In medium with full nitrate (880 μM), the average growth rate was 0.32 ± 0.01 day−1 (L1, control without added DOM). Adding natural marine dissolved organic nitrogen (DON) at levels of 20–30 μM above background (10 μM) led to a higher growth rate (L1+DOM, 0.40 ± 0.00 day−1). In medium with lower nitrate level (175 μM) and higher DON (L1/5+DOM treatment), both dissolved inorganic nitrogen and DON were used, leading to the highest growth rates (0.43 ± 0.03 day−1). In medium without nitrate [(L1-N)+DOM treatment], the low ammonium concentrations observed throughout the experiment (<1 μM) as well as the uptake kinetics of A. catenella could not have supported the observed growth rates, leading us to conclude that DON was directly used by this organism, rather than using N remineralized by bacteria (from DON). The decrease of bacteria in DOM enriched bioassays could point to a nutrient limitation and competition with A. catenella for organic matter. Viruses likely contributed as an additional factor to keep the bacterial population from becoming dominant. [ABSTRACT FROM PUBLISHER]

Abstract: Samples were collected during one annual cycle (April 2007–March 2008) at Alfacs Bay (NW Mediterranean Sea) central station in order to assess the influence of organic nutrients in the growth of the microalgae assemblage, with special reference to Pseudo-nitzschia spp. This potentially toxic diatom forms natural and recurrent blooms in the study area. To assess further the relationship between Pseudo-nitzschia spp. and nutrients an enrichment experiment with high molecular weight dissolved organic matter (HMWDOM) was performed with field samples obtained during a Pseudo-nitzschia spp. bloom. HMWDOM was extracted from water collected at Alfacs Bay. Five bioassays were prepared: N+P (seawater with addition of nitrate and phosphate), DOM (addition of HMWDOM), (−N+P)+DOM (nitrogen deficient, with addition of phosphate and HMWDOM), (N+P)+DOM (addition of nitrate, phosphate and HMWDOM), seawater control (without added nutrients), and B+DOM (control of bacteria, without microalgae). The experiment was run in batch mode over 4 days. Results from the field study revealed that the concentrations of organic nutrients mostly surpassed the inorganic pool. Pseudo-nitzschia spp. was the most frequent and abundant taxa of the microalgae community. The micro-planktonic assemblage was arranged according to a seasonal factor (ANOSIM and cluster analysis). DON, nitrate and silicate were the most important abiotic parameters contributing to the dissimilarities between seasons (SIMPER analysis) and thereby potentially influencing the seasonal distribution of microalgae in the representative station. In the experimental investigation, Pseudo-nitzschia cells increased by the end of the experiment in the DOM bioassay but no respective increase was observed for chlorophyll a. This could point to an acquisition of nutrients through the DOM fraction that would conjointly reduce the need of chlorophyll a. The data obtained suggest that organic nutrients may exert an important role in the development of microalgae, including Pseudo-nitzschia spp., in the selected location. [Copyright &y& Elsevier]

The impact of viruses and protists on bacterioplankton mortality was examined monthly during 2 years (May 2005–April 2007) in an oligotrophic coastal environment (NW Mediterranean Sea). We expected that in such type of system, (i) bacterial losses would be caused mainly by protists, and (ii) lysogeny would be an important type of virus–host interaction. During the study period, viruses and grazers together were responsible for 50.6 ± 40.1% day−1 of bacterial standing stock losses (BSS) and 59.7 ± 44.0% day−1 of bacterial production losses (BP). Over the first year (May 2005–April 2006), protists were the principal cause of bacterial mortality, removing 29.9 ± 20.4% day−1 of BSS and 33.9 ± 24.3% day−1 of BP, whereas viral lysis removed 13.5 ± 17.0% day−1 of BSS and 12.3 ± 12.3% day−1 of BP. During the second year (May 2006–April 2007), viruses caused comparable bacterial losses (29.2 ± 14.8% day−1 of BSS and 40.9 ± 20.7% day−1 of BP) to protists (28.6 ± 25.5% day−1 of BSS and 32.4 ± 20.0% day−1 of BP). In 37% of cases higher losses of BP due to viruses than due to protists were found. Lysogenic infection was detected in 11 of 24 samplings. Contrary to our expectations, lytic infections dominated over the two years, and viruses resulted to be a significant source of bacterial mortality in this oligotrophic site. [ABSTRACT FROM AUTHOR]

Abstract: The role of microorganisms in the transfer of carbon of marine systems is very important in open oligotrophic oceans. Here, we analyze the picoplankton structure, the heterotrophic bacterioplankton activity, and the predator–prey relationships between heterotrophic bacteria and nanoflagellates during two large scale cruises in the Central Atlantic Ocean (∼29°N to ∼40°S). Latitud cruises were performed in 1995 between March–April and October–November. During both cruises we crossed the regions of different trophic statuses; where we measured different biological variables both at the surface and at the deep chlorophyll maximum (DCM). The concentration of chlorophyll a varied between 0.1 and 0.8mgm−3, the abundance of heterotrophic bacteria varied between <1.0×105 and >1.0×106 cellsml−1, and that of heterotrophic nanoflagellates between <100 and >1.0×104 cellsml−1. The production of heterotrophic bacteria varied more than three orders of magnitude between <0.01 and 24μgCL−1 d−1; and the growth rates were in the range <0.01–2.1d−1. In the Latitud-II cruise, Prochlorococcus ranged between <103 and >3×105 cellsml−1, Synechococcus between <100 and >1.0×104 cellsml−1, and picoeukaryotes between <100 and >104 cellsml−1. Two empirical models were used to learn more about the relationship between heterotrophic bacteria and nanoflagellates. Most bacterial production was ingested when this production was low, the heterotrophic nanoflagellates could be controlled by preys during Latitud-I cruise at the DCM, and by predators in the surface and in the Latitud-II cruise. Our results were placed in context with others about the structure and function of auto- and heterotrophic picoplankton and heterotrophic nanoplankton in the Central Atlantic Ocean. [Copyright &y& Elsevier]

The article focuses on the role marine viruses on global-scale processes with a nanoscale drive. The authors elaborates that viruses, the smallest and most numerous of all biotic agents, represent the planet's largest pool of genetic diversity. Authors expresses that how and to what extent virus-mediated nanoscale processes are linked to global-scale biodiversity and biogeochemistry is poorly defined.

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. [ABSTRACT FROM AUTHOR]

The effect of oceanic eddies on microbial processes, with emphasis on bacterial losses due to protists and phages, was examined in the Canary Current region (subtropical northeast Atlantic) through the water column (down to 1000 m) during August 2006. Sampling stations were located in cyclonic and anticyclonic eddies, as well as in regions situated outside the influence of the eddy field (far-field stations). In the euphotic zone, in cyclonic eddies losses of bacteria due to viruses and protists were from 25.6% to 69.8%, and from not detected to 46.8% of bacterial production (BP) d-1, respectively. In anticyclonic eddies, these values ranged from 20.6% to 90.2% of BP d-1 for viruses, and from 8.0% to 79.4% of BP d-1 for protists. At far-field stations, losses of bacteria ranged from 48.7% to 66.9% for viruses, and from not detected to 44.8% for protists. In addition, covering all stations and depths (from the epipelagic to the bathypelagic layer), bacterial losses due to viruses were significantly higher than losses by protists, and did not differ significantly among depths except for the stations situated in anticyclonic eddies, where they were significantly higher in the epipelagic layer. Lysogenic infection was more frequent at anticyclonic stations, where the highest pressure of protists on bacteria was observed. Because of the importance of viral activity, we suggest that lysis products from bacteria may be a source of regenerated nutrients in the surface of the oligotrophic ocean, in addition to the input of nutrients upwelled by eddies. [ABSTRACT FROM AUTHOR]