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L’océan est le réservoir le plus important de virus sur la planète avec des abondances allant jusqu’à plusieurs milliards par litre. Ces virus sont une force directrice majeure pour l’évolution et la structuration du monde microbien, mais aussi pour le fonctionnement des grands cycles biogéochimiques dans les écosystèmes marins. Grâce aux techniques de séquençage à haut débit, nous commençons à entrevoir la diversité et la complexité de cette virosphère marine. Cette synthèse décrit les découvertes importantes dans le domaine de l’écologie virale marine et aborde la diversité de ces micro-organismes fascinants, leur impact sur la mortalité microbienne et les cycles de nutriments et d’énergie dans l’océan.

The sea surface microlayer (SSML) is critical to air-sea exchanges of gases and primary aerosols. However, despite the extent of this boundary layer, little is known about its specific bacterial community (bacterioneuston) and how it may affect ocean-atmosphere exchanges. Here, we studied the bacterial community composition in the surface waters of three different basins of the Western Mediterranean Sea and assessed the selective air-sea transfer of marine bacteria through experimental nascent sea spray aerosol production in a 10 L tank with plunging jets. In situ, the bacterioneuston harbored basin-specific enriched taxa and followed a similar spatial pattern as the underlying bacterioplankton community. Aerosolization potential showed that sea spray taxa might be recruited from both the underlying water and the SSML, and that taxa enriched in the bacterioneuston were not always aerosolized. Our results suggest that the Mediterranean nutrient gradient, as well as pulse events such as dust deposition, affect the distribution of the bacterial community at the ocean-atmosphere interface, which may impact biogeochemical processes, climate regulation and bacterial dispersal through aerosolization.

Viruses are key players in marine ecosystems where they infect abundant marine microbes. RNA viruses are emerging as key members of the marine virosphere. They have recently been identified as a potential source of mortality in diatoms, a group of microalgae that accounts for roughly 40% of the primary production in the ocean. Despite their likely importance, their impacts on host populations and ecosystems remain difficult to assess.In this study, we introduce an innovative tool approach that combines automated 3D confocal microscopy with quantitative image analysis and physiological measurements to expand our understanding of viral infection. We followed different stages of infection of the bloom-forming diatomGuinardia delicatulaby the RNA virus GdelRNAV-04 until the complete lysis of the host. From 20h after infection, we observed quantifiable changes in subcellular host morphology and biomass. Our microscopy monitoring also showed that viral infection ofG. delicatulainduced the formation of auxospores as a probable defense strategy against viruses. Our method enables the detection of discriminative morphological features on the subcellular scale and at high throughput for comparing populations, making it a promising approach for the detection quantification of viral infections in the field in the future.

Diatoms are among the most successful marine eukaryotic phytoplankton groups. Their diversity has been investigated in the world’s oceans through expeditions and observations carried out from the equator to the poles. Traditionally, diatom species have been distinguished based on morphological characters of their frustules, but high-throughput sequencing offers new, high-resolution data that can be used to re-examine spatial and/or temporal patterns of diversity. Here we investigated diatoms’ genetic diversity using metabarcoding (18S V4 rRNA gene) obtained along the years 2011 to 2013 at two coastal time series stations (SOMLIT-Astan and LTER-MareChiara) installed respectively off Roscoff in the Western English Channel and in the Gulf of Naples in the Mediterranean Sea. Diatom species pools detected were different, which fitted with previous observations and with our expectations, since these stations are installed in two contrasted pelagic habitats (permanently-mixed versus stratified in summer). However, this analysis also shows a pool of common ASVs among which some are persistent and dominant in both sites. The observed synchronous variations in relative read abundances of shared ASVs assigned to Chaetoceros socialis, C. tenuissimus, Cyclotella, Mediolabrus comicus and Leptocylindrus aporus at the two geographically distant sites could indicate that internal controls of growth rate and sexual reproduction, rather that external environmental parameters are at work.

International audience; Major seasonal community reorganizations and associated biomass variations are landmarks of plankton ecology. However, the processes of plankton community turnover rates have not been fully elucidated so far. Here, we analyse patterns of planktonic protist community succession in temperate latitudes, based on quantitative taxonomic data from both microscopy counts (cells >10 mu m) and ribosomal DNA metabarcoding (size fraction >3 mu m, 18S rRNA gene) from plankton samples collected bimonthly over 8 years (2009-2016) at the SOMLIT-Astan station (Roscoff, Western English Channel). Based on morphology, diatoms were clearly the dominating group all year round and over the study period. Metabarcoding uncovered a wider diversity spectrum and revealed the prevalence of Dinophyceae and diatoms but also of Cryptophyta, Chlorophyta, Cercozoa, Syndiniales and Ciliophora in terms of read counts and or richness. The use of morphological and molecular analyses in combination allowed improving the taxonomic resolution and to identify the sequence of the dominant species and OTUs (18S V4 rDNA-derived taxa) that drive annual plankton successions. We detected that some of these dominant OTUs were benthic as a result of the intense tidal mixing typical of the French coasts in the English Channel. Our analysis of the temporal structure of community changes point to a strong seasonality and resilience. The temporal structure of environmental variables (especially Photosynthetic Active Radiation, temperature and macronutrients) and temporal structures generated by species life cycles and or species interactions, are key drivers of the observed cyclic annual plankton turnover.

Major seasonal community reorganizations and associated biomass variations are landmarks of plankton ecology. However, the processes determining marine species and community turnover rates have not been fully elucidated so far. Here, we analyse patterns of planktonic protist community succession in temperate latitudes, based on quantitative taxonomic data from both microscopy counts and ribosomal DNA metabarcoding from plankton samples collected biweekly over 8 years (2009-2016) at the SOMLIT-Astan station (Roscoff, Western English Channel). Considering the temporal structure of community dynamics (creating temporal correlation), we elucidated the recurrent seasonal pattern of the dominant species and OTUs (rDNA-derived taxa) that drive annual plankton successions. The use of morphological and molecular analyses in combination allowed us to assess absolute species abundance while improving taxonomic resolution, and revealed a greater diversity. Overall, our results underpinned a protist community characterised by a seasonal structure, which is supported by the dominant OTUs. We detected that some were partly benthic as a result of the intense tidal mixing typical of the French coasts in the English Channel. While the occurrence of these microorganisms is driven by the physical and biogeochemical conditions of the environment, internal community processes, such as the complex network of biotic interactions, also play a key role in shaping protist communities.

N2 fixation rates were measured in the 0–1000 m layer at 13 stations located in the open western and central Mediterranean Sea (MS) during the PEACETIME cruise (late spring 2017). While the spatial variability in N2 fixation was not related to Fe, P nor N stocks, the surface composition of the diazotrophic community indicated a strong longitudinal gradient increasing eastward for the relative abundance of non-cyanobacterial diazotrophs (NCDs) (mainly γ-Proteobacteria) and conversely decreasing eastward for photo-heterotrophic group A (UCYN-A) (mainly UCYN-A1 and UCYN-A3), as did N2 fixation rates. UCYN-A4 and UCYN-A3 were identified for the first time in the MS. The westernmost station influenced by Atlantic waters and characterized by highest stocks of N and P displayed a patchy distribution of diazotrophic activity with an exceptionally high rate in the euphotic layer of 72.1 nmolNL-1d-1, which could support up to 19 % of primary production. At this station at 1 % PAR (photosynthetically available radiation) depth, UCYN-A4 represented up to 94 % of the diazotrophic community. These in situ observations of greater relative abundance of UCYN-A at stations with higher nutrient concentrations and dominance of NCDs at more oligotrophic stations suggest that nutrient conditions – even in the nanomolar range – may determine the composition of diazotrophic communities and in turn N2 fixation rates. The impact of Saharan dust deposition on N2 fixation and diazotrophic communities was also investigated, under present and future projected conditions of temperature and pH during short-term (3–4 d) experiments at three stations. New nutrients from simulated dust deposition triggered a significant stimulation of N2 fixation (from 41 % to 565 %). The strongest increase in N2 fixation was observed at the stations dominated by NCDs and did not lead on this short timescale to changes in the diazotrophic community composition. Under projected future conditions, N2 fixation was either increased or unchanged; in that later case this was probably due to a too-low nutrient bioavailability or an increased grazing pressure. The future warming and acidification likely benefited NCDs (Pseudomonas) and UCYN-A2, while disadvantaged UCYN-A3 without knowing which effect (alone or in combination) is the driver, especially since we do not know the temperature optima of these species not yet cultivated as well as the effect of acidification.

Marine viruses interact with microbial hosts in dynamic environments shaped by variation in abiotic factors, including temperature. However, the impacts of temperature on viral infection of phytoplankton are not well understood. Here we coupled mathematical modelling with experiments to explore the effect of temperature on virus-phytoplankton interactions. Our model shows the negative consequences of high temperatures on infection and suggests a temperature-dependent threshold between viral production and degradation. Modelling long-term dynamics in environments with different average temperatures revealed the potential for long-term host-virus coexistence, epidemic free or habitat loss states. We generalised our model to variation in global sea surface temperatures corresponding to present and future seas and show that climate change may differentially influence virus-host dynamics depending on the virus-host pair. Temperature-dependent changes in the infectivity of virus particles may lead to shifts in virus-host habitats in warmer oceans, analogous to projected changes in the habitats of macro-, microorganisms and pathogens.

Marine viruses interact with their microbial hosts in dynamic environments shaped by variations in abiotic factors, including temperature. However, the impacts of temperature on viral infection of phytoplankton are not well understood. Here we coupled mathematical modeling with experimental datasets to explore the effect of temperature on threeMicromonas-prasinovirus pairs. Our model shows the negative consequences of high temperatures on infection and suggests a temperature-dependent threshold between viral production and degradation. Modeling long-term dynamics in environments with different average temperatures revealed the potential for long-term host-virus coexistence, epidemic free, or habitat loss states. Hence, we generalized our model to global sea surface temperature of present and future seas and show that climate change may influence virus-host dynamics differently depending on the virus-host pair. Our study suggests that temperature-dependent changes in the infectivity of virus particles may lead to shifts in virus-host habitats in warmer oceans, analogous to projected changes in the habitats of macro- and micro-organisms.

In less than 50 years, marine viruses shifted from meaningless entities to major players of the oceanic ecosystems. These parasites numerically dominate marine microbial communities and mostly infect micro-organisms (bacteria, microalgae and other protists) that constitute the basis of trophic levels in the ocean. Viruses that replicate though a lysogenic cycle affect genetic expression of the host and promote horizontal gene transfer within the marine microbial communities. Viruses that replicate through a lytic cycle contribute to the control of host population and the release of a large amount of organic matter in the ocean. From the genetic manipulation of their hosts to the modification of the biogeochemical cycles, the marine viruses play a pivotal role for the structure and the functioning of their environment and cannot be excluded from ecological models anymore. This review presents the impact of viruses on the marine environment by focusing on three integration scales: the cell, the community and the ecosystem.

International audience; In the ocean, Bacillariophyta are one of the most successful protistan groups. Due to their considerable biogeochemical implications, diatom diversity, development, and seasonality have been at the center of research, specifically large-sized species. In comparison, nanoplanktonic diatoms are mostly disregarded from routine monitoring and are often underrepresented in genetic reference databases. Here, we identified and investigated the temporal dynamics of relevant nanodiatoms occurring in the Western English Channel (SOMLIT-Astan station). Coupling in situ and laboratory approaches, we revealed that nano-species from the genera Minidiscus and Thalassiosira are key components of the phytoplankton community that thrive in these coastal waters, but they display different seasonal patterns. Some species formed recurrent blooms whilst others were persistent year round. These results raise questions about their regulation in the natural environment. Over a full seasonal cycle at the monitoring station, we succeeded in isolating viruses which infect these minute diatoms, suggesting that these mortality agents may contribute to their control. Overall, our study points out the importance of considering nanodiatom communities within time-series surveys to further understand their role and fate in marine systems.

Viruses represent a driving force in the evolution of microorganisms including those thriving in extreme environments. However, our knowledge of the viral diversity associated to microorganisms inhabiting the deep-sea hydrothermal vents remains limited. The phylum of Thermotogae, including thermophilic bacteria, is well represented in this environment. Only one virus was described in this phylum, MPV1 carried by Marinitoga piezophila. In this study, we report on the functional and genomic characterization of two new bacterioviruses that infect bacteria from the Marinitoga genus. Marinitoga camini virus 1 and 2 (MCV1 and MCV2) are temperate siphoviruses with a linear dsDNA genome of 53.4 kb and 50.5 kb respectively. Here, we present a comparative genomic analysis of the MCV1 and MCV2 viral genomes with that of MPV1. The results indicate that even if the host strains come from geographically distant sites, their genomes share numerous similarities. Interestingly, heavy metals did not induce viral production, instead the host of MCV1 produced membrane vesicles. This study highlights interaction of mobile genetic elements (MGE) with their hosts and the importance of including hosts-MGEs' relationships in ecological studies.

Viruses have recurrently been hypothesized as instrumental in driving microbial population diversity. Nonetheless, viral mediated co-existence of r/k-strategists, predicted in the Killing-the-Winner (KtW) hypothesis, remains controversial and demands empirical evidence. Therefore, we measured the life strategy parameters that characterize the relevant system Micromonas-Micromonas Virus (MicV). A large number of host and viral strains (37 and 17, respectively) were used in a total of 629 cross-infectivity tests. Algal and viral abundances were monitored by flow cytometry and used to calculate values of growth rate, resistance capacity, and viral production. Two main assumptions of the KtW model, namely (1) a resistance-associated cost on growth and (2) a negative correlation between resistance and viral production capacity, were mildly observed and lacked statistical significance. Micromonas strains infected by more MicV strains presented higher lysis and viral production rates as the number of infectious virus strains increased, suggesting a 'one-gate' regulation of infection in this system. MicV strains demonstrated a vast range of virion production capacity, which unexpectedly grew with increasing host-range. Overall, the significant trends observed in here demonstrate strong co-interactions at different levels between Micromonas and MicV populations, however, the role of viruses as major driving force in phytoplankton fitness wasn't explicitly observed.

Viruses influence microbial community structure and biogeochemical cycles in marine environments. Viral attachment to nonhost surfaces could influence host viral infection rates; however, the prevalence of such viral attachment is not investigated quantitatively. We used coastal seawater viral assemblages and, as models, marine vibriophage (SIO-2) and enterobacteriophages (T2 and T4) to investigate their attachment to probable nonhost marine bacteria. We also studied viral attachment to colloids and other abiotic surfaces in seawater. Centrifugation experiments with bacterium-virus mixtures showed substantial viral loss in the supernatant presumably due to the viral attachment to bacteria. This attachment (0.04 to 24 viruses μm−2 [bacterial surface area]) varied with bacterium-virus combinations. Surprisingly, filtering seawater on 0.2-μm Anodisc or polycarbonate filters retained ∼12 to 84% of viruses presumably attached to ≥0.2-μm-sized particles and/or the filter surface. Enzymatic digestion followed by epifluorescence and atomic force microscopy suggested that 7 to 25% of the total viruses were attached via β-glycosidic linkages. Furthermore, a substantial proportion (7 to 48%) of viruses became attached to model abiotic surfaces (polycarbonate, polypropylene, and glass), and this has significance for laboratory protocols as well as studies of virus ecology in particle-rich marine environments. Substantial attachment of viruses to nonhost surfaces could influence virus-driven biogeochemical cycles and microbial community structure. IMPORTANCE Viruses play important roles in altering microbial community structure and biogeochemical cycles in marine environments. Viral attachment to nonhost surfaces can influence host viral infection rates; however, the prevalence of viral attachment to nonhost surfaces and the ratio of attached viruses to total viruses are little known. We used coastal seawater viral assemblages and used marine vibriophage (SIO-2) and enterobacteriophages (T2 and T4) as models to investigate their attachment to abiotic and biotic surfaces in seawater. Viral attachment was observed on several surfaces, such as nonhost bacteria, polymers, filters, cover glasses, and tube surfaces. This study cautions against commonly used protocols that require viral incubation and seawater fractionation. More importantly, these results could influence virus-driven biogeochemical cycles and microbial community structure in the ocean.

International audience; Photosynthetic picoeukaryotes in the genus Micromonas show among the widest latitudinal distributions on Earth, experiencing large thermal gradients from poles to tropics. Micromonas comprises at least four different species often found in sympatry. While such ubiquity might suggest a wide thermal niche, the temperature response of the different strains is still unexplored, leaving many questions as for their ecological success over such diverse ecosystems. Using combined experiments and theory, we characterize the thermal response of eleven Micromonas strains belonging to four 1 species. We demonstrate that the variety of specific responses to temperature in the Micromonas genus makes this environmental factor an ideal marker to describe its global distribution and diversity. We then propose a diversity model for the genus Micromonas, which proves to be representative of the whole phytoplankton diversity. This prominent primary producer is therefore a sentinel organism of phytoplankton diversity at the global scale. We use the diversity within Micromonas to anticipate the potential impact of global warming on oceanic phytoplankton. We develop a dynamic, adaptive model and ran forecast simulations, exploring a range of adaptation time scales, to probe the likely responses to climate change. Results stress how biodiversity erosion depends on the ability of organisms to adapt rapidly to temperature increase.

The genus Micromonas comprises distinct genetic clades that commonly dominate eukaryotic phytoplankton community from polar to tropical waters. This phytoplankter is also recurrently infected by abundant and genetically diverse prasinoviruses. Here we report on the interplay between prasinoviruses and Micromonas with regard to the genetic diversity of this host. For 1 year, we monitored the abundance of three clades of Micromonas and their viruses in the Western English Channel, both in the environment using clade-specific probes and flow cytometry, and in the laboratory using clonal strains of Micromonas clades to assay for their viruses by plaque-forming units. We showed that the seasonal fluctuations of Micromonas clades were closely mirrored by the abundance of their corresponding viruses, indicating that the members of Micromonas genus are susceptible to viral infection, regardless of their genetic affiliation. The characterization of 45 viral isolates revealed that Micromonas clades are attacked by specific virus populations, which exhibit distinctive clade specificity, life strategies and genetic diversity. However, some viruses can also cross-infect different host clades, suggesting a mechanism of horizontal gene transfer within the Micromonas genus. This study provides novel insights into the impact of viral infection for the ecology and evolution of the prominent phytoplankter Micromonas.

Prokaryotic viruses play a major role in the microbial ecology and evolution. However, the virosphere associated with deep-sea hydrothermal ecosystems remains largely unexplored. Numerous instances of lateral gene transfer have contributed to the complex and incongruent evolutionary history of Thermotogales, an order well represented in deep-sea hydrothermal vents. The presence of clustered regularly interspaced short palindromic repeats (CRISPR) loci has been reported in all Thermotogales genomes, suggesting that these bacteria have been exposed to viral infections that could have mediated gene exchange. In this study, we isolated and characterized the first virus infecting bacteria from the order Thermotogales, Marinitoga piezophila virus 1 (MPV1). The host, Marinitoga piezophila is a thermophilic, anaerobic and piezophilic bacterium isolated from a deep-sea hydrothermal chimney. MPV1 is a temperate Siphoviridae-like virus with a 43.7 kb genome. Surprisingly, we found that MPV1 virions carry not only the viral DNA but preferentially package a plasmid of 13.3 kb (pMP1) also carried by M. piezophila. This ‘menage a trois’ highlights potential relevance of selfish genetic elements in facilitating lateral gene transfer in the deep-sea biosphere.

International audience; The genus Micromonas comprises phytoplankton that show among the widest latitudinal distributions on Earth, and members of this genus are recurrently infected by prasinoviruses in contrasted thermal ecosystems. In this study, we assessed how temperature influences the interplay between the main genetic clades of this prominent microalga and their viruses. The growth of three Micromonas strains (Mic-A, Mic-B, Mic-C) and the stability of their respective lytic viruses (MicV-A, MicV-B, MicV-C) were measured over a thermal range of 4-32.5°C. Similar growth temperature optima (T opt) were predicted for all three hosts but Mic-B exhibited a broader thermal tolerance than Mic-A and Mic-C, suggesting distinct thermoacclimation strategies. Similarly, the MicV-C virus displayed a remarkable thermal stability compared with MicV-A and MicV-B. Despite these divergences, infection dynamics showed that temperatures below T opt lengthened lytic cycle kinetics and reduced viral yield and, notably, that infection at temperatures above T opt did not usually result in cell lysis. Two mechanisms operated depending on the temperature and the biological system. Hosts either prevented the production of viral progeny or maintained their ability to produce virions with no apparent cell lysis, pointing to a possible switch in the viral life strategy. Hence, temperature changes critically affect the outcome of Micromonas infection and have implications for ocean biogeochem-istry and evolution.

Summary Viruses attract increasing interest from environmental microbiologists seeking to understand their function and role in coral health. However, little is known about their main ecological traits within the coral holobiont. In this study, a quantitative and qualitative characterization of viral and bacterial communities was conducted on the mucus of seven different coral species of the Van Phong Bay (Vietnam). On average, the concentrations of viruses and bacteria were, respectively, 17- and twofold higher in the mucus than in the surrounding water. The examination of bacterial community composition also showed remarkable differences between mucus and water samples. The percentage of active respiring cells was nearly threefold higher in mucus (m = 24.8%) than in water (m = 8.6%). Interestingly, a positive and highly significant correlation was observed between the proportion of active cells and viral abundance in the mucus, suggesting that the metabolism of the bacterial associates is probably a strong determinant of the distribution of viruses within the coral holobiont. Overall, coral mucus, given its unique physicochemical characteristics and sticking properties, can be regarded as a highly selective biotope for abundant, diversified and specialized symbiotic microbial and viral organisms.

Recent studies showed changes in phytoplankton lipid composition during viral infection and have indicated roles for specific lipids in the mechanisms of algal virus-host interaction. To investigate the generality of these findings and obtain a better understanding of the allocation of specific lipids to viruses, we studied the intact polar lipid (IPL) composition of virally infected and non-infected cultures of the prymnesiophyte Phaeocystis globosa G(A) and its lytic virus PgV-07T. The P. globosa IPL composition was relatively stable over a diel cycle and not strongly affected by viral infection. Glycolipids, phospholipids and betaine lipids were present in both the host and virus, although specific groups such as the diacylglyceryl-hydroxymethyltrimethyl-β-alanines and the sulfoquinovosyldiacylglycerols, were present in a lower proportion or were not detected in the virus. Viral glycosphingolipids (vGSLs), which have been shown to play a role in the infection strategy of the virus EhV-86, infecting the prymnesiophyte Emiliania huxleyi CCMP374, were not encountered. Our results show that the involvement of lipids in virus–algal host interactions can be very different amongst virus–algal host systems.

We report on a genomic and functional analysis of a novel marine siphovirus, the Vibrio phage SIO-2. This phage is lytic for related Vibrio species of great ecological interest including the broadly antagonistic bacterium Vibrio sp. SWAT3 as well as notable members of the Harveyi clade (V.harveyi ATTC BAA-1116 and V.campbellii ATCC 25920). Vibrio phage SIO-2 has a circularly permuted genome of 80598 bp, which displays unusual features. This genome is larger than that of most known siphoviruses and only 38 of the 116 predicted proteins had homologues in databases. Another divergence is manifest by the origin of core genes, most of which share robust similarities with unrelated viruses and bacteria spanning a wide range of phyla. These core genes are arranged in the same order as in most bacteriophages but they are unusually interspaced at two places with insertions of DNA comprising a high density of uncharacterized genes. The acquisition of these DNA inserts is associated with morphological variation of SIO-2 capsid, which assembles as a large (80 nm) shell with a novel T=12 symmetry. These atypical structural features confer on SIO-2 a remarkable stability to a variety of physical, chemical and environmental factors. Given this high level of functional and genomic novelty, SIO-2 emerges as a model of considerable interest in ecological and evolutionary studies.

A laboratory experiment was conducted to examine the temporal dynamics of the particle size distribution (PSD) and associated optical variability caused by viral infection of marine heterotrophic bacteria. The PSD covering a broad range of particle size from < 50 nm to 200 mm was measured in parallel with the spectral particulate absorption and beam attenuation coefficients, from which the particulate scattering coefficient, bp(l), was determined. Within 12 h following infection, the host bacterial population collapsed, viral abundance increased, and submicron particles were produced as bacteria were disrupted and cell debris released, resulting in a large decrease in bp(l) seen as an almost complete clearing of the particle suspension. Throughout the remainder of the experiment, significant changes in the PSD occurred primarily within the size range of relatively large particles (. 4 mm), likely as a result of the aggregation of smaller-sized particles originating from the host lysis. The PSD data were used as input for Mie scattering calculations to evaluate the effects of these particle dynamics in terms of relative contributions of different particle size classes to the scattering and backscattering coefficients. This analysis showed a significant increase in the effect of particle aggregation on light scattering during the second and third days after infection. Viral lysis of bacteria and subsequent particle dynamics produce large variations in the PSD over a broad size range on timescales from hours to a few days, and such processes lead to correspondingly large changes in the suspension optical properties.

The effect of different irradiance levels on the interactions between the algal host and its virus was investigated for two marine phytoplankton, Phaeocystis globosa Scherff. and Micromonas pusilla (Butcher) Manton et Parke. The algal cultures were acclimated at 25, 100, and 250 μmol photons · m(-2) · s(-1) (LL, ML, and HL, respectively), after which they were infected with a lytic virus (PgV-07T and MpV-02T) and monitored under the appropriate irradiance and in darkness. The effect of irradiance levels on the host-virus interactions differed for the two algal host-virus systems examined. For P. globosa, the LL-acclimated cultures showed a 4 h prolonged latent period (11-16 h), which may be related to the subsaturated growth observed at this irradiance. The burst size was reduced by 50% at LL and HL compared to ML (525 PgV · cell(-1) ). The fraction of infectious viruses, however, remained unchanged. Viral replication was prevented when the LL P. globosa cultures were kept in darkness (up to 48 h) but recovered when placed back into the light. PgV-07T still replicated in the dark for the ML- and HL-acclimated cultures, but viral yield was reduced by 50%-85%. For M. pusilla, the burst size (285-360 MpV · cell(-1) ), the infectivity, and the latent period of MpV-02T (7-11 h) remained unaffected by the incident light. Conversely, darkness not only inhibited MpV replication but also resulted in substantial cell lysis of the noninfected cultures. Our study implies that irradiance level is an important factor controlling algal host-virus interactions and hence the dynamics of phytoplankton populations.

': Microzooplankton grazing and vitally mediated mortality of the eukaryotic (3 size classes) and prokaryotic (Synechococcus) picophytoplankton was investigated across the North Sea during summer 2003. The fate of picophytoplankton differed among algal groups and their area of occurrence. Highest viral lysis rates (0.16 to 0.23 d -1 ) were recorded for specific picoeukaryotic groups in the coastal region and at a station at the deep chlorophyll a maximum (DCM). Viral lysis was insignificant at the other stations, despite a considerable percentage of dead algal cells (up to 38%), as determined by staining with the live/dead dye SYTOX Green. Microzooplankton actively grazed on picoeukaryotes (average per group 0.2 to 0.4 d -1 ), independent of the region studied. Grazing on Synechococcus was restricted to the coastal waters (0.7 d -1 ). Grazing by microzooplankton consumed 40 ± 27 % (mean ± SD) of the carbon produced by picophytoplankton, constituting in general the main loss factor. Viral lysis released 8 ± 13% of the total picophytoplankton carbon production, and locally up to 32%.

We report viral-induced mortality rates of the picoeukaryotic (two size classes) and prokaryotic (cyanobacteria Prochlorococcus and Synechococcus) phytoplankton during a cruise in the oligotrophic subtropical northeastern Atlantic (October 2002). A dilution assay, simultaneously estimating viral lysis and microzooplankton grazing, was applied around the deep chlorophyll maximum (DCM) at six stations. For the smallest picoeukaryotes (group I), viral lysis was responsible for 50–100% of the total cell losses, with rates ranging from 0.1 to 0.8 d21. Viral lysis rates were positively linked to the abundance and contribution of large genome-sized (180–225 kb) putative algal viruses. In contrast, the prokaryotic picophytoplankton did not seem to be controlled by viral lysis. For Synechococcus, microzooplankton grazing dominated, with rates between 0.1 and 0.25 d21 (comparable to those for the eukaryotic algae). For Prochlorococcus, both viral lysis and microzooplankton grazing rates were very low (0–0.1 d21). Overall, the total carbon production by the picophytoplankton community was balanced by the combined losses due to viral lysis and microzooplankton grazing. Viral lysis released 0.1–0.3 m go f picophytoplanktonic C L21 d21, which comprised 21% of the total carbon production by picophytoplankton.

We have studied the temporal variation in viral abundances and community assemblage in the eutrophic Lake Loosdrecht through epifluorescence microscopy and pulsed field gel electrophoresis (PFGE). The virioplankton community was a dynamic component of the aquatic community, with abundances ranging between 5.5 x 10(7) and 1.3 x 10(8) virus-like particles ml(-1) and viral genome sizes ranging between 30 and 200 kb. Both viral abundances and community composition followed a distinct seasonal cycle, with high viral abundances observed during spring and summer. Due to the selective and parasitic nature of viral infection, it was expected that viral and host community dynamics would covary both in abundances and community composition. The temporal dynamics of the bacterial and cyanobacterial communities, as potential viral hosts, were studied in addition to a range of environmental parameters to relate these to viral community dynamics. Cyanobacterial and bacterial communities were studied applying epifluorescence microscopy, flow cytometry, and denaturing gradient gel electrophoresis (DGGE). Both bacterial and cyanobacterial communities followed a clear seasonal cycle. Contrary to expectations, viral abundances were neither correlated to abundances of the most dominant plankton groups in Lake Loosdrecht, the bacteria and the filamentous cyanobacteria, nor could we detect a correlation between the assemblage of viral and bacterial or cyanobacterial communities during the overall period. Only during short periods of strong fluctuations in microbial communities could we detect viral community assemblages to covary with cyanobacterial and bacterial communities. Methods with a higher specificity and resolution are probably needed to detect the more subtle virus-host interactions. Viral abundances did however relate to cyanobacterial community assemblage and showed a significant positive correlation to Chl-a as well as prochlorophytes, suggesting that a significant proportion of the viruses in Lake Loosdrecht may be phytoplankton and more specific cyanobacterial viruses. Temporal changes in bacterial abundances were significantly related to viral community assemblage, and vice versa, suggesting an interaction between viral and bacterial communities in Lake Loosdrecht.

An alternate version to the protocol "Simultaneous measurement of grazing and viral lysis of phytoplankton v1"

Viruses attract increasing interest from environmental microbiologists seeking to understand their function and role in coral health. However, little is known about their main ecological traits within the coral holobiont. In this study, a quantitative and qualitative characterization of viral and bacterial communities was conducted on the mucus of seven different coral species of the Van Phong Bay (Vietnam). On average, the concentrations of viruses and bacteria were, respectively, 17- and twofold higher in the mucus than in the surrounding water. The examination of bacterial community composition also showed remarkable differences between mucus and water samples. The percentage of active respiring cells was nearly threefold higher in mucus (m = 24.8%) than in water (m = 8.6%). Interestingly, a positive and highly significant correlation was observed between the proportion of active cells and viral abundance in the mucus, suggesting that the metabolism of the bacterial associates is probably a strong determinant of the distribution of viruses within the coral holobiont. Overall, coral mucus, given its unique physicochemical characteristics and sticking properties, can be regarded as a highly selective biotope for abundant, diversified and specialized symbiotic microbial and viral organisms.

International audience; We have studied the exopolysaccharide produced by Cobetia marina DSMZ 4741, a marine bacterium isolated from coastal seawater. This strain is able to produce a polysaccharide in presence of carbon sources as glucose, mannitol and alginate. The maximum production occurs in aerobic condition, during the end of the exponential phase. The polymer is a non-viscous, acidic heteropolysaccharide of 270 kDa constituted of a repeating unit of: -> 2)-beta-D-Ribf-(1 -> 4)-[7,8-O-(Pyr)]-alpha-D-KDOp-(2 -> This kind of chemical structure is generally related to K-antigen polysaccharide of pathogenic Escherichla coli strains. This is the first time this type of EPS is described from a marine bacterium. Moreover the polysaccharide exhibits a pyruvate substitution on its 3-deoxy-D-manno-oct-2-ulosonic acid (KDO) residue never encountered before. The discovery of such an unexpected EPS with high biotechnological potential is a new incentive for a better exploration of bioactive marine resources. (c) 2015 Elsevier Ltd. All rights reserved.

International audience; Alteromonas macleodii subsp. fijiensis biovar deepsane is a deep-sea ecotype exopolysaccharide-producing bacteria isolated from the polychaete annelid Alvinella pompejana. The high molecular weight biopolymer HYD657 produced by this strain, is the first marine exopolysaccharide (EPS) to be commercialized for cosmetic use. Depolymerization methods are necessary to elucidate the complete structure of this EPS and to generate potentially bioactive oligosaccharides. Enzymatic methods are useful for elucidating polysaccharide structure because they specifically cleave glycosidic bonds and do not require harsh chemical conditions. The HYD657 EPS is structurally complex and no commercially available enzymes are able to effectively degrade it. Here, we present the first results on the endogenous enzymatic depolymerization of a marine EPS of biotechnological interest by the producing strain. Enzymatic activity was detected in the bacterial lysate and was able to decrease the apparent molecular size of the EPS, releasing mainly oligosaccharides. The reduced form of the native polysaccharide showed a slightly modified osidic composition, particularly in terms of molar ratio. Several exoglycosidase activities were measured in the bacterial lysate using paranitrophenyl-osides.

This study reports virally mediated mortality rates of Phaeocystis globosa single cells in the southern North Sea during 2 consecutive spring blooms (2003 and 2004). An adapted dilution method was used to estimate viral lysis and microzooplankton grazing simultaneously. Parallel dilution experiments were performed with 30 kDa ultrafiltrate (virus and grazer-free diluent) and 0.2 μm filtered seawater (grazer-free, but virus-containing diluent). Specific viral lysis rates were calculated from the difference in P. globosa growth rates between the 2 dilution series after 24 h incubation under natural conditions. The validity of this method was tested using a culture of P. globosa infected with a known P. globosa virus (PgV). The field data show that virally induced mortality can be a substantial loss factor for P. globosa single cells (up to 0.35 d -1 ), comparable to that due to microzooplankton grazing (up to 0.4 d -1 ). Viral lysis was the major cause of total P. globosa cell lysis. Assuming no loss due to sinking, viral lysis accounted for 5 to 66 % of the total mortality of P. globosa single cells. Viral lysis and total putative PgV abundance increased concomitantly with abundance of P. globosa single cells whilst the increase in infective PgV was delayed. This delay may be caused by the formation of transparent exopolymeric particles that are generated when P. globosa colonies disrupt and are known to passively adsorb viruses. Viruses and microzooplankton were shown to be major controlling agents of P. globosa single cells, although their relative significance varied over the course of the bloom and between years.

In most aquatic bacterial communities, it is possible to discriminate bacterial cells with a high nucleic acid content (HNA) from those with a low nucleic acid content (LNA) by flow cytometry. The distribution of leucine incorporation rate per cell (specific activity) within the fraction of bacteria with a high apparent nucleic acid content was investigated in coastal seawater using flow cytometry and cell sorting techniques. Bacterial cells from a natural seawater sample were first labeled with tritiated leucine, stained with a fluorescent nucleic acid stain and then sorted based on their fluorescence and scatter signals, assuming that fluorescence was proportional to the cellular nucleic acid content and scatter signals to biovolume. Our results clearly demonstrated that specific activity was heterogeneously distributed within the group of HNA cells and increased with both scatter and fluorescence signals. This shows that important differences in terms of cell-specific rates of activity exist within the HNA group and that specific activity is positively correlated with both the nucleic acid content of cells and their biovolume. We hypothesized that this heterogeneity may be partly due to the structure of bacterial communities. Therefore, further investigations were made by analyzing the nucleic acid content and scatter properties of a set of 10 species isolated from the same coastal area. Our results confirm that both fluorescence and scatter values vary greatly between species at a given growth stage and between growth stages for a given species. Variations reported at different growth stages suggest that both parameters are sensitive to the metabolic activity of individual cells and confirm the positive relationship reported in this study between scatter and fluorescence parameters and specific activity within the HNA cellular fraction of natural communities. Interestingly, it was shown that HNA and LNA cells were present in late stationary phase cultures. This suggests that LNA cells found in natural communities may be dead or dying cells.

Prokaryotic viruses play a major role in the microbial ecology and evolution. However, the virosphere associated with deep-sea hydrothermal ecosystems remains largely unexplored. Numerous instances of lateral gene transfer have contributed to the complex and incongruent evolutionary history of Thermotogales, an order well represented in deep-sea hydrothermal vents. The presence of clustered regularly interspaced short palindromic repeats (CRISPR) loci has been reported in all Thermotogales genomes, suggesting that these bacteria have been exposed to viral infections that could have mediated gene exchange. In this study, we isolated and characterized the first virus infecting bacteria from the order Thermotogales, Marinitoga piezophila virus 1 (MPV1). The host, Marinitoga piezophila is a thermophilic, anaerobic and piezophilic bacterium isolated from a deep-sea hydrothermal chimney. MPV1 is a temperate Siphoviridae-like virus with a 43.7 kb genome. Surprisingly, we found that MPV1 virions carry not only the viral DNA but preferentially package a plasmid of 13.3 kb (pMP1) also carried by M. piezophila. This 'ménage à trois' highlights potential relevance of selfish genetic elements in facilitating lateral gene transfer in the deep-sea biosphere.

The significant impact of dust deposition on heterotrophic bacterial dynamics in the surface oligotrophic ocean has recently been evidenced. Considering the central role of bacteria in the microbial loop, it is likely that dust deposition also affects the structure and the functioning of the whole microbial food web. In the frame of the DUNE project, aiming to estimate the impact of dust deposition on the oligotrophic Mediterranean Sea through mesocosm experiments, the main goal of the present paper was to assess how two successive dust deposition events affect the dynamics of the microbial food web. The first dust seeding delivered new P and N to the amended mesocosms and resulted in a pronounced stimulation of bacterial respiration. It also induced pronounced, but transient, changes in the bacterial community composition. No significant effects were observed on the abundances of viruses and heterotrophic nanoflagellates. The second dust seeding also delivered new P and N to the amended mesocosms but the effect on the microbial food web was very different. Bacterial respiration remained constant and bacterial abundance decreased. Compositional changes following the second seeding were minor compared to the first one. The decrease in bacterial abundance coincided with an increase in virus abundance, resulting in higher virus: bacteria ratios throughout the second seeding period. Our study shows that dust deposition to the surface oligotrophic ocean may involve important modifications of the trophic links among the components of the microbial food web with presumed consequences on C and nutrient cycling.

In the paper "Microbial food web dynamics in response to a Saharan dust event: results from a mesocosm study in the oligotrophic Mediterranean Sea" by E. Pulido-Villena et al. (2014), the following error occurred: Figs. 7 and 8 were incorrectly switched; that is, Fig. 8 appears with the Fig. 7 caption and vice versa. The figures with the correct captions are presented on the next page.

International audience; We report the subnanometer cryo-electron microscopy (cryoEM) reconstruction of a marine siphovirus, the Vibrio phage SIO-2. This phage is lytic for related Vibrio species with significant ecological importance, including the broadly antagonistic bacterium Vibrio sp. SWAT3. The three-dimensional structure of the 800 Å SIO-2, icosahedrally averaged head of the tailed particle revealed a T = 12 quasi-symmetry not previously described in a bacteriophage. Two morphologically distinct types of auxiliary proteins were also identified; one species bound to the surface of hexamers, and the other bound to pentamers. The secondary structure, evident in the electron density, shows that the major capsid protein has the HK97-like fold. The three-dimensional structure of the procapsid form, also presented here, has no "decoration" proteins and reveals a capsomer organization due to the constraints of the T = 12 symmetry.

A sensitive method using Competitive Ligand Exchange-Adsorptive Cathodic Stripping Voltammetry (CLE-ACSV) has been developed to determine for the first time iron (Fe) organic speciation in rainwater over the typical natural range of pH. We have adapted techniques previously developed in other natural waters to rainwater samples, using the competing ligand 1-nitroso-2-naphthol (NN). The blank was equal to 0.17 +/- 0.05 nM (n = 14) and the detection limit (DL) for labile Fe was 0.15 nM which is 10-70 times lower than that of previously published methods. The conditional stability constant for NN under rainwater conditions was calibrated over the pH range 5.52-6.20 through competition with ethylenediaminetetraacetic acid (EDTA). The calculated value of the logarithm of beta'(FE3+(NN)3) increased linearly with increasing pH according to log beta'(FE3+(NN)3) = 2.4 +/- 0.6 x pH + 11.9 +/- 3.5 (salinity =2.9, T= 20 degrees C). The validation of the method was carried out using desferrioxamine mesylate B (DFOB) as a natural model ligand for Fe. Adequate detection windows were defined to detect this class of ligands in rainwater with 40 mu M of NN from pH 5.52 to 6.20. The concentration of Fe-complexing natural ligands was determined for the first time in three unfiltered and one filtered rainwater samples. Organic Fe-complexing ligand concentrations varied from 104.2 +/- 4.1 nM equivalent of Fe(III) to 336.2 +/- 19.0 nM equivalent of Fe(III) and the logarithm of the conditional stability constants, with respect to Fe3+, varied from 21.1 +/- 0.2 to 22.8 +/- 0.3. This method will provide important data for improving our understanding of the role of wet deposition in the biogeochemical cycling of iron.

International audience; High-frequency pCO2 and ancillary data were recorded for seven years during the first deployment of a CARbon Interface OCean Atmosphere (CARIOCA) sensor in the surface waters of a temperate coastal ecosystem, the Bay of Brest, which is impacted by both coastal (via estuaries) and oceanic (North Atlantic via the Iroise Sea) water inputs. The CARIOCA sensor proved to be an excellent tool to constrain the high pCO2 variability in such dynamic coastal ecosystem. Biological processes (e.g. pelagic photosynthesis/respiration) were the main drivers of the seasonal and diurnal pCO2 dynamics throughout seven years of observations. Autotrophic processes were responsible for abrupt pCO2 drawdown of 100 to 200 μatm in spring. During the spring bloom, diurnal variations were driven by diel biological cycle. The average daily drawdown due to autotrophy (observed during highest daily PAR) was equivalent to 10 to 60% of the total pCO2 drawdown observed every year during the spring season. From late summer to fall, heterotrophic processes increased pCO2 in the surface water of the Bay back to the pre-bloom level. The average daily increase due to heterotrophy (observed during lowest daily PAR) corresponded to 10 to 70% of the total pCO2 increase observed every year during the late summer to fall period. Air-sea CO2 fluxes estimates based on hourly, daily and monthly calculations showed that careful consideration of the diurnal variability was needed to accurately estimate air-sea CO2 fluxes in the Bay of Brest. Sampling only during daytime or night-time would induce 8 to 36% error on monthly air-sea CO2 fluxes. This would in turn reverse the direction of the fluxes at annual level for the Bay. The annual emissions of CO2 from the surface waters of the Bay to the atmosphere showed relatively low inter-annual variations with an average of + 0.7 ± 0.4 mol C m-2 yr-1 computed for the study period. Further, air-sea CO2 fluxes computed for the adjacent inner-estuaries and Iroise Sea for an annual cycle were + 17 ± 3 mol C m-2 yr-1 and − 0.2 ± 0.2 mol C m-2 yr-1 , respectively. The spatial gradient showed a clear pattern from strong source to sink of CO2, from the inner-estuaries to the open oceanic waters of the North Atlantic. We suggest that semi-enclosed Bays act as buffers for sea to air emissions of CO2 from inner estuaries to adjacent costal seas.