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It is commonly recognized that viruses control the composition, metabolism, and evolutionary trajectories of prokaryotic communities, with resulting vital feedback on ecosystem functioning and nutrient cycling in a wide range of ecosystems. Although the deep biosphere has been estimated to be the largest reservoir for viruses and their prokaryotic hosts, the biology and ecology of viruses therein remain poorly understood. The deep virosphere is an enigmatic field of study in which many critical questions are still to be answered. Is the deep virosphere simply a repository for deeply preserved, non-functioning virus particles? Or are deep viruses infectious agents that can readily infect suitable hosts and subsequently shape microbial populations and nutrient cycling? Can the cellular content released by viral lysis, and even the organic structures of virions themselves, serve as the source of bioavailable nutrients for microbial activity in the deep biosphere as in other ecosystems? In this review, we synthesize our current knowledge of viruses in the deep biosphere and seek to identify topics with the potential for substantial discoveries in the future.

International audience

Particle sinking is an important process in the ocean, influencing the biogeochemical cycle and driving the long-term preservation of carbon into the deep sea via the biological pump. However, as an important component of marine ecosystems, the role of viruses during sinking is still poorly understood. Therefore, we performed a series of transplantation experiments in the South China Sea to simulate environmental changes during sinking and investigate their effects on viral eco-dynamics and life strategy. Our study demonstrated increased viral production but decreased virus-mediated bacterial mortality after transplantation. A larger burst size and switch from the lysogenic to lytic strategy were shown to contribute to enhanced viral productivity. We provide experimental evidence that surface viral ecological characteristics changed dramatically after transplantation into deep-sea waters, indicating a potential importance of viruses during vertical sinking in the ocean. This effect probably provides positive feedback on the efficiency of the biological pump.

The basic bacterial ecology and diversity was investigated in five running water systems of Southern New Caledonia. These running waters were characterized by potential P-limitation and high concentrations of Ni, Fe, Mn, Cr and Co. The low concentrations of dissolved organic carbon, bacterial and viral abundance, bacterial production and growth efficiency support the characterization of the running waters as oligotroph to ultraoligotroph. Despite these similarities, there were strong differences (Betaproteobacteria is typical for freshwater systems, however, we found also a strong representation of Gammaproteobacteria. Indeed the three bands found at all stations were related to Limnohabitans (Comamonadaceae) and Alteromonadaceae. Strong differences were also found between the free-living and the attached bacterial fraction with Gammaproteobacteria dominating in two systems. A higher representation of Gammaproteobacteria seems typical for metal-rich freshwater habitats. Consistent with fresh water habitats, majority of phylotypes detected in the sediment was affiliated to proteobacteria. Also, none of the sequences showed a 100% identity with data bases, and 10 of the 22 and 2 of the 23 sequences had similarities higher than 97% in the freshwater and sediment. This could indicate specific adaptations of the community composition either due to the high metal concentrations or due to the geographical isolation of the New Caledonia.

Microbial communities on marine aggregates could be influenced by ambient water conditions; however, empirical data are scarce. In this study, we used fingerprint analysis of PCR-amplified 16S rRNA gene fragment to examine how microbial communities on aggregates change in response to different conditions of ambient water. We conducted two experiments using seawater cultures from surface waters of the lagoon and the anthropogenically influenced bay of Nouméa, New Caledonia: a transplant experiment in which the artificially produced aggregates from one station was added to ultra-filtered seawater culture of another station, and a water-flow experiment in which the artificially produced aggregates placed in the ultra-filtered seawater culture with or without water-flow. In a transplant experiment, bacterial community composition (BCC) on the bay and lagoon water aggregates were significantly different (p < 0.05, ANOSIM) at the beginning of experiment. After 11 days of incubation, BCC on the lagoon water aggregates were significantly different (p < 0.05) from transplanted communities. Transplantation effect was also observed in the bay water treatments. In a water-flow experiment, BCC on the bay and lagoon water aggregates were significantly different (p < 0.05) at the beginning of the experiment. BCC on the lagoon and bay water aggregates with and without water-flow treatments were significantly different (p < 0.05) at the end of incubation, and effect of water-flow on BCC were observed in the bay and lagoon water treatments. Our experimental studies suggest that changes in ambient water conditions potentially influence microbial communities on aggregates in the Bay of Nouméa.

Phytoplankton contribute almost half of the world's total primary production. The exudates and viral lysates of phytoplankton are two important forms of dissolved organic matter (DOM) in aquatic environments and fuel heterotrophic prokaryotic metabolism. However, the effect of viral infection on the composition and biological availability of phytoplankton-released DOM is poorly understood. Here, we investigated the optical characteristics and microbial utilization of the exudates and viral lysates of the ecologically important unicellular picophytoplankton Prochlorococcus. Our results showed that Prochlorococcus DOM produced by viral lysis (Pro-vDOM) with phages of three different morphotypes (myovirus P-HM2, siphovirus P-HS2, and podovirus P-SSP7) had higher humic-like fluorescence intensities, lower absorption coefficients, and higher spectral slopes than DOM exuded by Prochlorococcus (Pro-exudate). The results indicate that viral infection altered the composition of Prochlorococcus-derived DOM and might contribute to the pool of oceanic humic-like DOM. Incubation with Pro-vDOM resulted in a greater dissolved organic carbon (DOC) degradation rate and lower absorption spectral slope and heterotrophic bacterial growth rate than incubation with Pro-exudate, suggesting that Pro-vDOM was more bioavailable than Pro-exudate. In addition, the stimulated microbial community succession trajectories were significantly different between the Pro-exudate and Pro-vDOM treatments, indicating that viral lysates play an important role in shaping the heterotrophic bacterial community. Our study demonstrated that viral lysis altered the chemical composition and biological availability of DOM derived from Prochlorococcus, which is the numerically dominant phytoplankton in the oligotrophic ocean. IMPORTANCE The unicellular picocyanobacterium Prochlorococcus is the numerically dominant phytoplankton in the oligotrophic ocean, contributing to the vast majority of marine primary production. Prochlorococcus releases a significant fraction of fixed organic matter into the surrounding environment and supports a vital portion of heterotrophic bacterial activity. Viral lysis is an important biomass loss process of Prochlorococcus. However, little is known about whether and how viral lysis affects Prochlorococcus-released dissolved organic matter (DOM). Our paper shows that viral infection alters the optical properties (such as the absorption coefficients, spectral slopes, and fluorescence intensities) of released DOM and might contribute to a humic-like DOM pool and carbon sequestration in the ocean. Meanwhile, viral lysis also releases various intracellular labile DOM, including amino acids, protein-like DOM, and lower-molecular-weight DOM, increases the bioavailability of DOM, and shapes the successive trajectory of the heterotrophic bacterial community. Our study highlights the importance of viruses in impacting the DOM quality in the ocean.

International audience; The viral component in aquatic systems clearly needs to be incorporated into future ocean and inland water climate models. Viruses have the potential to influence carbon and nutrient cycling in aquatic ecosystems significantly. Changing climate likely has both direct and indirect influence on virus-mediated processes, among them an impact on food webs, biogeochemical cycles and on the overall metabolic performance of whole ecosystems. Here we synthesise current knowledge on potential climate-related consequences for viral assemblages, virus-host interactions and virus functions, and in turn, viral processes contributing to climate change. There is a need to increase the accuracy of predictions of climate change impacts on virus- driven processes, particularly of those linked to biological production and biogeochemical cycles. Comprehension of the relationships between microbial/viral processes and global phenomena is essential to predict the influence on as well as the response of the biosphere to global change.

In 2005/2006, a major volcanic eruption buried faunal communities over a large area of the 9°N East Pacific Rise (EPR) vent field. In late 2006, we initiated colonization studies at several types of post eruption vent communities including those that either survived the eruption, re-established after the eruption, or arisen at new sites. Some of these vents were active whereas others appeared senescent. Although the spatial scale of non-paved (surviving) vent communities was small (several m2 compared to several km2 of total paved area), the remnant individuals at surviving active and senescent vent sites may be important for recolonization. A total of 46 meio- and macrofauna species were encountered at non-paved areas with 33 of those species detected were also present at new sites in 2006. The animals living at non-paved areas represent refuge populations that could act as source populations for new vent sites directly after disturbance. Remnants may be especially important for the meiofauna, where many taxa have limited or no larval dispersal. Meiofauna may reach new vent sites predominantly via migration from local refuge areas, where a reproductive and abundant meiofauna is thriving. These findings are important to consider in any potential future deep-sea mining scenario at deep-sea hydrothermal vents. Within our 4-year study period, we regularly observed vent habitats with tubeworm assemblages that became senescent and died, as vent fluid emissions locally stopped at patches within active vent sites. Senescent vents harbored a species rich mix of typical vent species as well as rare yet undescribed species. The senescent vents contributed significantly to diversity at the 9°N EPR with 55 macrofaunal species (11 singletons) and 74 meiofaunal species (19 singletons). Of these 129 species associated with senescent vents, 60 have not been reported from active vents. Tubeworms and other vent megafauna not only act as foundation species when alive but provide habitat also when dead, sustaining abundant and diverse small sized fauna.

Viral abundance in deep-sea environments is high. However, the biological, ecological and biogeochemical roles of viruses in the deep sea are under debate. In the present study, microcosm incubations of deep-sea bacterioplankton (2,000 m deep) with normal and reduced pressure of viral lysis were conducted in the western Pacific Ocean. We observed a negative effect of viruses on prokaryotic abundance, indicating the top-down control of bacterioplankton by virioplankton in the deep-sea. The decreased bacterial diversity and a different bacterial community structure with diluted viruses indicate that viruses are sustaining a diverse microbial community in deep-sea environments. Network analysis showed that relieving viral pressure decreased the complexity and clustering coefficients but increased the proportion of positive correlations for the potentially active bacterial community, which suggests that viruses impact deep-sea bacterioplankton interactions. Our study provides experimental evidences of the crucial role of viruses in microbial ecology and biogeochemistry in deep-sea ecosystems., Rui Zhang et al. demonstrate that reduced viral pressure decreases the diversity of deep-sea bacterioplankton in the western Pacific Ocean. This study suggests that viruses sustain a diverse microbial community in deep-sea environments.

Lophelia pertusa and Madrepora oculata are the two main species building cold-water coral reefs. Habitats within cold-water coral reefs ecosystems such as the water column, sediments, coral rubble, sponges and other corals host a diverse archaeal community. However, L. pertusa and M. oculata host, if at all, a different archaeal community. The question arises why (some) Archaea are excluded from the holobiont and whether this is potentially contributing to the success of L. pertusa and M. oculata as cold-water coral reef builders.

This chapter addresses the question as to how Mediterranean cold-water corals might fare in the future under anthropogenically-induced global climate change. The focus on three most prominent scleractinian cold-water corals species, the two branching and habitat-forming forms Madrepora oculata, Lophelia pertusa and the solitary cup coral Desmophyllum dianthus. We provide an introduction to climate change principals, highlight the current status of the marine environment with regard to global climate change, and describe how climate change impacts such as ocean acidification are predicted to affect key calcifiers such as scleractinian cold-water corals in the Mediterranean region. A synthesis of the experimental cold-water coral studies conducted to date on climate change impacts: The present state of knowledge reviewed in this chapter takes into account the number of experiments that have been carried out in the Mediterranean as well as for comparative purposes in other parts of the world, to examine the effects of climate change on the corals. We assess the statistical robustness of these experiments and what challenges the presented experiments. A comprehensive multi-study comparison is provided in order to inform on the present state of knowledge, and knowledge gaps, in understanding the effects of global climate change on cold-water corals. Finally we describe what the fate could be for the important scleractinian coral group in the Mediterranean region.

Recent research suggests that corals including cold-water corals harbor a diverse community of bacteria that are not only pathogens but also potential mutualists. Here we review data on bacterial community composition and diversity on the main cold-water corals framework builder species: Lophelia pertusa and Madrepora oculata. Sampling strategies such as box core, video grabs and remotely operated vehicle did not reveal strong differences between bacterial community composition as long as samples were used that looked ‘not contaminated’. However, there were strong differences of bacterial diversity between the two coral species. An analysis of bacterial community composition by pyrosequencing of L. pertusa and M. oculata revealed for the Mediterranean Sea the presence of the potential mutualists already found in the Atlantic indicating a species-specific core microbiome. The data also suggest some biogeographical differences between the Mediterranean Sea and the North Atlantic for both coral species, however, this depends on the phylogenetic levels applied. In addition, there was also indication for a shared microbiome between the Mediterranean Sea and the Atlantic. Therefore species-specific bacterial associations seem to exist, whereas the biogeographical variability can be seen as adaptation to specific environmental conditions.

A 18 month study was performed in the Bay of Villefranche to assess the episodic and seasonal variation of autotrophic and heterotrophic ecosystem processes. A typical spring bloom was encountered, where maximum of gross primary production (GPP) was followed by maxima of bacterial respiration (BR) and production (BP). The trophic balance (heterotrophy vs. autotrophy) of the system did not exhibit any seasonal trend although a strong intra-annual variability was observed. On average, the community tended to be net heterotrophic with a GPP threshold for a balanced metabolism of 1.1 μmol O2 l−1 d−1. Extended forest fires in summer 2003 and a local episodic upwelling in July 2003 likely supplied orthophosphate and nitrate into the system. These events were associated with an enhanced bacterioplankton production (up to 2.4-fold), respiration (up to 4.5-fold) and growth efficiency (up to 2.9-fold) but had no effect on GPP. A Sahara dust wet deposition event in February 2004 stimulated bacterial abundance, production and growth efficiency but not GPP. Our study suggests that short-term disturbances such as wind-driven upwelling, forest fires and Sahara dust depositions can have a significant but previously not sufficiently considered influence on phytoplankton- and bacterioplankton-mediated ecosystem functions and can modify or even mask the seasonal dynamics. The study also indicates that atmospheric deposition of nutrients and particles not only impacts phytoplankton but also bacterioplankton and could, at times, also shift systems stronger towards net heterotrophy.

International audience; During the past 30 years, a vast number of articles have been published on the importance-in terms of abundance, diversity and functional roles-of viruses inhabiting the aquatic world (either marine or freshwater), which include several excellent reviews. Our knowledge, e.g. of the interactions of viruses with the living (organisms) and non-living compartments (i.e. dissolved organic matter/ particles/nutrients/physical factors) in aquatic environments, has considerably increased. Furthermore , recent new ideas, concepts and technologies have shed light on host-virus interactions and the diversity of viral species and functions as discussed in this book. This chapter highlights some of these current advances in the field of aquatic viral ecology. Recently developed models and concepts will also be discussed, further emphasizing the role of defence mechanisms against viruses which appear to be important drivers in strain diversification of host species. Additionally, new environments such as anoxic and benthic sediments have received more attention and novel information has been gathered, e.g. on archaeal and RNA viruses. Interactions within entire food webs, such as with heterotrophic dinoflagellates, oysters and even cascading effects up to cyanobacteria-consuming flamingo populations represent another aspect oflooking at viruses and their role in the global biosphere. The chapter also discusses knowledge gaps and proposes future research avenues.

International audience; In this chapter, we summarize and discuss methods used to study viral interactions in aquatic environments. These methods to assess interactions between viruses, hosts and the environment (including other viruses) are operationally separated into interactions at the molecular, single-cell, and community levels. Many of these methods benefit from the methodological advancements in the field of molecular biology including the 'Omics area'. There are, however, numerous methods from other fields. We also present examples of unanswered questions along with problems solved by these questions. Finally, we conclude that viral interactions with the abiotic environment have received surprisingly little attention, so far, from a methodological perspective.

Mineral dust, volcano ash and soot (black carbon) are among the major solid aerosol inputs to the world ocean. They deliver elements such as C, N, P, S and bioactive trace metals in significant amounts. However, in contrast to mineral dust, the impact of volcano ash and soot on microbial plankton is poorly studied, although total deposition rates are not much lower for volcano ash than for mineral dust in certain basins and soot delivers overall more P into the ocean than mineral dust. Aging processes in the atmosphere during horizontal transport, e.g. due to exposure to UV light and acidic conditions in clouds, increase the solubility and hence bioavailability of volcano ash and soot aerosols. Current findings suggest that volcano ash and soot are a source of nutrients and/or organic carbon, and influence aggregation processes. Volcano ash seems to stimulate phytoplankton, and soot bacterioplankton; both aerosols influence microbial diversity. We argue that volcano ash and soot have a significant, but comparatively less well-studied effects on microbial plankton that should, along with mineral dust, be better implemented into concepts and studies of microbial food webs to improve the mechanistic understanding of the role and performance of autotrophic and heterotrophic microorganisms in the ocean.

International audience; Large amounts of soot are continuously deposited on the global ocean. Even though significant concentrations of soot particles are found in marine waters, the effects of these aerosols on ocean ecosystems are currently unknown. Using a combination of in situ and experimental data, and results from an atmospheric transport model, we show that the deposition of soot particles from an oil-fired power plant impacted biogeochemical properties and the functioning of the pelagic ecosystem in tropical oligotrophic oceanic waters off New Caledonia. Deposition was followed by a major increase in the volume concentration of suspended particles, a change in the particle size spectra that resulted from a stimulation of aggregation processes, a 5% decrease in the concentration of dissolved organic carbon (DOC), a decreases of 33 and 23% in viral and free bacterial abundances, respectively, and a factor~2 increase in the activity of particle-attached bacteria suggesting that soot introduced in the system favored bacterial growth. These patterns were confirmed by experiments with natural seawater conducted with both soot aerosols collected in the study area and standard diesel soot. The data suggest a strong impact of soot deposition on ocean surface particles, DOC, and microbial processes, at least near emission hot spots.

The mesopelagic ('twilight') zone of the ocean is the sandwich layer between euphotic surface waters and the deep ocean. The physical, chemical, and biological processes in this layer strongly influ- ence the marine carbon cycle, although some surpris- ing knowledge gaps remain, e.g. with respect to micro- bial communities. We therefore determined biological parameters such as microbial abundances, community respiration, and bacterial and archaeal community composition (as assessed by 16S rRNA gene PCR dena- turing gradient gel electrophoresis, DGGE) over a sea- sonal time scale (at ca. 46 d intervals for 433 d) at a coastal mesopelagic site in the NW Mediterranean Sea (Point C, 300 m depth) and related them to physico- chemical parameters. Some chemical and most biolog- ical parameters showed strong variability, thus con- firming the emerging view that this water layer is more dynamic than previously thought. Community respira- tion was likely influenced by seasonal changes as indi- cated by its indirect relationship with water density. The high detected community respiration rates (0.23� 1.65 µmol O2 l �1 d �1 ) confirm that the twilight zone plays a critical role as a hub between surface and deep water. Statistical analyses indicate that water stratifica- tion, dissolved organic carbon, and transparent exo - polymeric particles were controlling factors of bacterial community composition, whereas the archaeal com- munity was likely controlled by other mechanisms. A sequence analysis of DGGE bands and a literature comparison suggests some specificity of the mesopela- gic zone regarding bacterial and archaeal community composition, thus further confirming the peculiarity of this water layer.

In order to test the influences of ocean acidification on the ocean pelagic ecosystem, so far the largest CO2 manipulation mesocosm study (European Project on Ocean Acidification, EPOCA) was performed in Kings Bay (Kongsfjorden), Spitsbergen. During a 30 day incubation, bacterial diversity was investigated using DNA fingerprinting and clone library analysis of bacterioplankton samples. Terminal restriction fragment length polymorphism (T-RFLP) analysis of the PCR amplicons of the 16S rRNA genes revealed that general bacterial diversity, taxonomic richness and community structure were influenced by the variation of productivity during the time of incubation, but not the degree of ocean acidification. A BIOENV analysis suggested a complex control of bacterial community structure by various biological and chemical environmental parameters. The maximum apparent diversity of bacterioplankton (i.e., the number of T-RFs) in high and low pCO2 treatments differed significantly. A negative relationship between the relative abundance of Bacteroidetes and pCO2 levels was observed for samples at the end of the experiment by the combination of T-RFLP and clone library analysis. Our study suggests that ocean acidification affects the development of bacterial assemblages and potentially impacts the ecological function of the bacterioplankton in the marine ecosystem.

The anthropogenic increase of carbon dioxide (CO2) alters the seawater carbonate chemistry, with a decline of pH and an increase in the partial pressure of CO2 (pCO2). Although bacteria play a major role in carbon cycling, little is known about the impact of rising pCO2 on bacterial carbon metabolism, especially for natural bacterial communities. In this study, we investigated the effect of rising pCO2 on bacterial production (BP), bacterial respiration (BR) and bacterial carbon metabolism during a mesocosm experiment performed in Kongsfjorden (Svalbard) in 2010. Nine mesocosms with pCO2 levels ranging from ca. 180 to 1400 μatm were deployed in the fjord and monitored for 30 days. Generally BP gradually decreased in all mesocosms in an initial phase, showed a large (3.6-fold average) but temporary increase on day 10, and increased slightly after inorganic nutrient addition. Over the wide range of pCO2 investigated, the patterns in BP and growth rate of bulk and free-living communities were generally similar over time. However, BP of the bulk community significantly decreased with increasing pCO2 after nutrient addition (day 14). In addition, increasing pCO2 enhanced the leucine to thymidine (Leu : TdR) ratio at the end of experiment, suggesting that pCO2 may alter the growth balance of bacteria. Stepwise multiple regression analysis suggests that multiple factors, including pCO2, explained the changes of BP, growth rate and Leu : TdR ratio at the end of the experiment. In contrast to BP, no clear trend and effect of changes of pCO2 was observed for BR, bacterial carbon demand and bacterial growth efficiency. Overall, the results suggest that changes in pCO2 potentially influence bacterial production, growth rate and growth balance rather than the conversion of dissolved organic matter into CO2.

Ocean acidification is a major threat to calcifying marine organisms such as deep-sea cold-water corals (CWCs), but related knowledge is scarce. The aragonite saturation threshold (Ω a ) for calcification, respiration and organic matter fluxes were investigated experimentally in the Mediterranean Madrepora oculata . Over 10 weeks, colonies were maintained under two feeding regimes (uptake of 36.75 and 7.46 µmol C polyp −1 week −1 ) and exposed in 2 week intervals to a consecutively changing air–CO 2 mix ( p CO 2 ) of 400, 1600, 800, 2000 and 400 ppm. There was a significant effect of feeding on calcification at initial ambient p CO 2 , while with consecutive p CO 2 treatments, feeding had no effect on calcification. Respiration was not significantly affected by feeding or p CO 2 levels. Coral skeletons started to dissolve at an average Ω a threshold of 0.92, but recovered and started to calcify again at Ω a ≥1. The surplus energy required to counteract dissolution at elevated p CO 2 (≥1600 µatm) was twice that at ambient p CO 2 . Yet, feeding had no mitigating effect at increasing p CO 2 levels. This could be due to the fact that the energy required for calcification is a small fraction (1–3%) of the total metabolic energy demand and corals even under low food conditions might therefore still be able to allocate this small portion of energy to calcification. The response and resistance to ocean acidification are consequently not controlled by feeding in this species, but more likely by chemical reactions at the site of calcification and exchange processes between the calicoblastic layer and ambient seawater.

We describe a new method to produce marine aggregates from natural organic material based on the sticking properties of transparent exopolymeric particles. Seawater samples were prescreened and ultrafiltered to concentrate the 30 kDa to 10 µm size fraction. First, we produced small magnetizable aggregates by combining glass microfibers and paramagnetic 1-µm beads with the organic matter present in the concentrated solution. The second step involved clustering the small aggregates into a single macro-aggregate, using a small ringshaped magnet as an aggregation nucleus. Viral and bacterial densities, determined after dissolution of the newly formed aggregates with methanol, averaged 13.8 × 106 ± 3.6 × 106 vir. agg.−1 and 4.1 × 106 ± 1.1 × 106 bact. agg.−1. Bacterial respiration and production measurements of single aggregates averaged 8.47 ± 1.72 nmol O2 agg.−1 h−1 and 1.54 ± 0.45 ng C agg.−1 h−1, respectively. Particulate organic carbon and nitrogen content of the newly formed macro-aggregates averaged 31.92 ± 2.67 µg C agg.−1 and 3.44 ± 0.43 µg N agg.−1, respectively. This approach allows the concentration and isolation of the organic matter precursors that compose natural aggregates and provides a simple protocol for recombining those precursors into single newly formed macro-aggregates, which can then be easily manipulated for further investigation. This method is a new tool for investigations into the interactions between microorganisms and marine aggregates and their implications at the ecosystem level, but also into the interactions between aggregates and dissolved organic or inorganic substances.

International audience; In experiments designed primarily to investigate viral lysis, we found that the presence of viruses had a positive effect on the growth of Synechococcus. A Landry-Hassett-type stepwise dilution experiment conducted during a Synechococcus bloom in the Gulf of Mexico used both (i) 0.2-mu m filtered seawater in which the abundance of bacteria and grazers were reduced but the majority of viruses were retained, and (ii) ultrafiltered (30 000 MW cutoff) virus-free seawater in which the abundance of viruses, bacteria and grazers were reduced. High growth rates and frequency of dividing cells (FDCs) were recorded in 0.2-mm filtered treatments while growth was inhibited in incubations with a high proportion of virus-free ultrafiltered water. In two subsequent experiments using Mediterranean Sea populations, a two-point dilution approach in which viral abundance was reduced by 80-90% yielded similar results, and showed that Synechococcus only grew well in the presence of viruses, bacteria and grazers. In four further Mediterranean experiments viruses removed via ultrafiltration were added back, either untreated, or inactivated by a heat treatment. Growth rates and FDCs were higher in the presence of untreated viruses than with viruses inactivated by heat, suggesting that it was not organic matter in the virus-size fraction but rather the presence of infectious viruses which sustained growth. While Synechococcus was also infected by viruses during these experiments, our data imply that growth of Synechococcus may depend upon viral lysis of heterotrophic bacteria. This finding is consistent with the view that nutrient cycling by viral lysis of heterotrophic bacteria may control phytoplankton growth and ecosystem scale carbon production.

Black carbon (BC), the product of incomplete combustion of fossil fuels and biomass, constitutes a significant fraction of the marine organic carbon pool. However, little is known about the possible interactions of BC and marine microorganisms. Here, we report the results of experiments using a standard reference BC material in high concentrations to investigate basic principles of the dynamics of natural bacterial and viral communities with BC particles. We assessed the attachment of viral and bacterial communities using scanning electron, epifluorescence and confocal laser scanning microscopy and shifts in bacterial community composition using 16S rRNA gene denaturing gradient gel electrophoresis (DGGE). In 24-h time-course experiments, BC particles showed a strong potential for absorbing viruses and bacteria. Total viral abundance was reduced, whereas total bacterial abundance was stimulated in the BC treatments. Viral and bacterial abundance on BC particles increased with particle size, whereas the abundances of BC-associated viruses and bacteria per square micrometer surface area decreased significantly with BC particle size. DGGE results suggested that BC has the potential to change bacterial community structure and favour phylotypes related to Glaciecola sp. Our study indicates that BC could influence processes mediated by bacteria and viruses in marine ecosystems.

The biological pump is a process whereby CO(2) in the upper ocean is fixed by primary producers and transported to the deep ocean as sinking biogenic particles or as dissolved organic matter. The fate of most of this exported material is remineralization to CO(2), which accumulates in deep waters until it is eventually ventilated again at the sea surface. However, a proportion of the fixed carbon is not mineralized but is instead stored for millennia as recalcitrant dissolved organic matter. The processes and mechanisms involved in the generation of this large carbon reservoir are poorly understood. Here, we propose the microbial carbon pump as a conceptual framework to address this important, multifaceted biogeochemical problem.

SUMMARY A trade-off between strategies maximizing growth and minimizing losses appears to be a fundamental property of evolving biological entities existing in environments with limited resources. In the special case of unicellular planktonic organisms, the theoretical framework describing the trade-offs between competition and defense specialists is known as the “killing the winner” hypothesis (KtW). KtW describes how the availability of resources and the actions of predators (e.g., heterotrophic flagellates) and parasites (e.g., viruses) determine the composition and biogeochemical impact of such organisms. We extend KtW conceptually by introducing size- or shape-selective grazing of protozoans on prokaryotes into an idealized food web composed of prokaryotes, lytic viruses infecting prokaryotes, and protozoans. This results in a hierarchy analogous to a Russian doll, where KtW principles are at work on a lower level due to selective viral infection and on an upper level due to size- or shape-selective grazing by protozoans. Additionally, we critically discuss predictions and limitations of KtW in light of the recent literature, with particular focus on typically neglected aspects of KtW. Many aspects of KtW have been corroborated by in situ and experimental studies of isolates and natural communities. However, a thorough test of KtW is still hampered by current methodological limitations. In particular, the quantification of nutrient uptake rates of the competing prokaryotic populations and virus population-specific adsorption and decay rates appears to be the most daunting challenge for the years to come.

16 pages, 4 figures, 3 tables, The Mediterranean coast receives large inputs of dust with a potential fertilization effect. We evaluated the effect of a wet dust deposition event on microbial abundance and activity, community structure and metabolic balance. Dust collected during a dust storm event was added to a series of microcosms. We added a realistic concentration (0.05 g L–1) based on the phosphorus concentration contained in the dust and, in addition, we included a P amended tank to distinguish the effect of dust from that of the phosphorus in the dust. We also included a higher dust concentration tank (0.5 g L–1). Dust increased the initial water–phosphorus concentration by 0.3 µM and the dissolved organic carbon (DOC) concentration by 14 µM, and increased bacterial abundance (1.8-fold) and bacterial production (5-fold). At the end of the experiment, primary production and community respiration were stimulated by dust and by P, but the net result of the addition of low amounts of dust was an initial switch towards heterotrophy, whereas the net result of the high-dust (DH) additions and the P addition was a shift towards autotrophy. Bacterial community structure changed little between P and low dust, but these were very different from the control and the DH communities, This work was supported by Spanish projects MODIVUS (CTM2005-04795/MAR), VARITEC (CTM2004-0442-C02) and STORM (CTM2009-09352/MAR), and is a contribution to the European Network of Excellence EUROCEANS and MARBEF

International audience; Cold-water coral ecosystems are more widespread, diverse and productive than previously thought. However, little is known about the interaction of deep-water corals with microorganisms. To understand whether coral species have specific prokaryotic communities, it is necessary to assess the within and between colony variability. This was studied based on 16S rRNA gene and denaturing gradient gel electrophoresis (DGGE) for one of the main cold-water corals Madrepora oculata at Rockall Bank off the coast of Ireland. We successfully applied a rapid, non-toxic and inexpensive method for extracting DNA for 16S rRNA gene fingerprinting of marine prokaryotic communities based on a heat and salt lysis with simultaneous salt extraction (HEATSALT). The within and between colony variability of the community composition of bacteria associated to the mucus and ectodermal tissue of M. oculata was then evaluated using a 16S rRNA gene PCR and DGGE approach. Bacterial community composition (BCC) clearly differed between living coral and reference samples (dead coral and surrounding water; 80% dissimilarity). A large within (35-40% dissimilarity between polyps) and between colony variability (ca. 50% dissimilarity) of BCC was detected. We also found preliminary evidence that BCC differed between M. oculata and Lophelia pertusa. The high intraspecific variability found has consequences for selecting sampling strategies when assessing bacterial diversity and refines the question of controlling mechanisms of bacterial diversity on corals. Sequencing of DGGE bands showed that Spongiobacter type phylotypes (STP) dominated the DGGE bands. STP of M, oculata were grouped together and were different from those detected in other corals and sponges. In addition, the high sequence diversity of STP Suggests specific ecological roles and adaptations of this group in M oculata.

The study site located in the northwestern Mediterranean Sea was visited nine times in 2005–2006 to collect water samples from the epi- (5 m), meso- (200, 600 m), and bathypelagic (1000, 2000 m) zone. Total abundance of prokaryotes and viruses was determined by flow cytometry (FCM). Prokaryotic abundance in the epi-, meso-, and bathypelagic varied between 0.9 and 15.9×10 5 , 0.6 and 2.1×10 5 , and 0.3 and 1.3×10 5 ml −1 , respectively. Variation of viral abundance in the epi-, meso-, and bathypelagic was between 1.2 and 57.5×10 6 , 0.5 and 3.5×10 6 , and 0.4 and 1.3×10 6 ml −1 , respectively. The fraction of low (LNA) and high (HNA) nucleic acid prokaryotes averaged 42.9% and 57.1% throughout the water column and did not differ between depth layers. Throughout the water column the fraction of low, medium, and high fluorescent viruses (Vir-LF, Vir-MF, Vir-HF) averaged 66.3%, 30.2%, and 3.5%. Vir-LF and Vir-MF did not differ between depth layers; however, Vir-HF showed a preference for surface waters. The fraction of LNA cells decreased in the epi- and increased in the bathypelagic with decreasing stratification. The fraction of Vir-LF viruses increased in the epipelagic and decreased in the bathypelagic with increasing prokaryotic abundance. Also, the relationship between viral abundance and the bacterial community was different in surface and deep waters. The data suggest that different mechanisms of interaction between viruses and their prokaryotic hosts prevail at the surface and in deep waters.

We followed the viral response to Fe-enrichment over 3 weeks during the second iron-enrichment experiment (EisenEx) in the Southern Ocean. Although viral abundance increased in a rather constant way during the course of the experiment inside the patch, the production of bacterial viruses and the fraction of infected cells in bacterioplankton exhibited pronounced maxima on days 7 and 21. In contrast, these parameters remained fairly constant outside the Fe-fertilized patch. Viral production was also stimulated directly after the Fe-enrichment. Within the Fe-replete patch, viral abundance and production was on average 2- and 3-fold, respectively, higher than outside the patch. On average 40% of the bacteria contained viruses in a lytic stage inside the Fe-replete patch compared to 21% outside the patch. About 11-12% of the bacteria contained a viral genome inducible with mitomycin C in both inside and outside the patch. Randomly amplified polymorphic desoxyribonucleic acid polymerase chain reaction analysis suggested the development of a specific viral community in the patch. Although short-term stimulation of viral production was likely due to increased bacterial activity, the long-term stimulation was likely also influenced by an increased encounter rate between bacterial viruses and hosts. Viral lysis was responsible for most of the bacterioplankton mortality in the patch. Overall, most of the bacterial carbon production entered the detrital or dissolved organic matter pool via the viral shunt in the patch. © 2009, by the American Society of Limnology and Oceanography, Inc.

International audience; A factorial design was used to assess the roles of turbulence and viral infection in prokaryotic production and diversity in a spring phytoplankton bloom experiment in the Bay of Ville-franche, France, Several consistent trends were observed in 2 experiments: (1) turbulence stimulated prokaryotic production, (2) prokaryotic cell length increased in experimental turbulence and virus treatments, and (3) organic micro-aggregates with attached prokaryotes formed only in the turbulence treatments and seemed to be reduced in the presence of viruses. We conclude that turbulence likely influenced prokaryotes indirectly by affecting micro-aggregate formation and nutrient availability, Turbulence and viruses had only small influences on the number of bacterial and archaeal bands detected by 16S rRNA gene denaturing gradient gel electrophoresis. However, taking into account presence versus absence of specific bands and their intensities, we detected strong effects in the experiments. We not only detected a negative effect of viruses, but also found that some bands increased in intensity in the presence of active viruses, e.g. one of 3 phylotypes affiliated with the Rhodobacteriaceae. In both experiments, several consistent patterns were found: (1) a phylotype affiliated with Roseobacter was negatively affected (in terms of band intensity) by viruses and turbulence, (2) the relative band intensity of a Rhodobacter increased in the turbulence treatments, and (3) a phylotype related to Oceanospirillum was detected only in the turbulence treatment. We suggest that turbulence and viruses play a significant and previously neglected role in shaping prokaryotic diversity, aggregation and production.

Viruses on organic aggregates such as transparent exopolymeric particles (TEP) are not well investigated. The number of TEP-attached viruses was assessed along trophic gradients in the southwestern lagoon of New Caledonia by determining the fraction of viruses removed after magnetic isolation of TEP. In order to isolate TEP magnetically, TEP were formed in the presence of magnetic beads from submicrometer precursors collected along the trophic gradients. The mixed aggregates of TEP-beads-viruses were removed from solution with a magnetic field. The percentage of viruses associated with newly formed TEP averaged 8% (range, 3 to 13%) for most of the stations but was higher (ca. 30%) in one bay characterized by the low renewal rate of its water mass. The number of viruses ( N ) attached to TEP varied as a function of TEP size ( d [in micrometers]) according to the formulas N = 100 d 1.60 and N = 230 d 1.75 , respectively, for TEP occurring in water masses with short (i.e., 40 days) residence times. These two relationships imply that viral abundance decreases with TEP size, and they indicate that water residence time influences viral density and virus-bacterium interactions within aggregates. Our data suggest that the fraction of viruses attached to TEP is highest in areas characterized by a low renewal rate of the water mass and can constitute at times a significant fraction of total virus abundance. Due to the small distance between viruses and hosts on TEP, these particles may be hot spots for viral infection.

To elucidate the potential importance of deep-water viruses in controlling the meso- and bathypelagic picoplankton community, the abundance, decay rate, and diversity of the virioplankton community were determined in the meso- and bathypelagic water masses of the eastern part of the subtropical North Atlantic. Viral abundance averaged 1.4 × 10 6 ml −1 at around 100 m of depth and decreased only by a factor of 2 at 3,000 to 4,000 m of depth. In contrast, picoplankton abundance decreased by 1 order of magnitude to the Lower Deep Water (LDW; 3,500- to 5,000-m depth). The virus-to-picoplankton ratio increased from 9 at about 100 m of depth to 110 in the LDW. Mean viral decay rates were 3.5 × 10 −3 h −1 between 900 m and 2,750 m and 1.1 × 10 −3 h −1 at 4,000 m of depth, corresponding to viral turnover times of 11 and 39 days, respectively. Pulsed-field gel electrophoresis fingerprints obtained from the viral community between 2,400 m and 4,000 m of depth revealed a maximum of only four bands from 4,000 m of depth. Based on the high viral abundance and the low picoplankton production determined via leucine incorporation, we conclude that the viral production calculated from the viral decay is insufficient to maintain the high viral abundance in the deep North Atlantic. Rather, we propose that substantial allochthonous viral input or lysogenic or pseudolysogenic production is required to maintain the high viral abundance detected in the meso- and bathypelagic North Atlantic. Consequently, deep-water prokaryotes are apparently far less controlled in their abundance and taxon richness by lytic prokaryotic phages than the high viral abundance and the virus-to-picoplankton ratio would suggest.

Microbes, i.e. viruses, prokaryotes, protists and fungi are main players in biogeochemical cycles in aquatic and soil systems. As predators, pathogens, commensals and symbionts they are associated with multicellular life forms. Microbes show a dazzling array of biodiversity and it has been argued that due to their small size and huge numbers, microbes are distributed worldwide (‘everything is everywhere’). However, we summarize evidence that even free-living microbes have biogeographies and thus might be subject to at least local extinctions. Furthermore, some microbes do seem to be restricted to very particular environments and are endangered in as much as these environments are threatened. Finally, microbes intimately associated with other organisms share (partially) the biogeographies of their hosts. As far as they are species-specific, they could potentially become extinct along with their hosts. Overall, extinction rates typically reported are underestimates, since they do not take into account associated microorganisms which likely become extinct with the host organism, plant or animal. As multicellular species can have specific viral, prokaryotic, protistan and fungal species associated with them, extinction rates could be several times higher than assumed previously.

The reduction approach to assess virus production and the prokaryotic mortality by viral lysis stops new infection by reducing total virus abundance (and thus virus–host contacts). This allows for easy enumeration of viruses that originate from lysis of already infected cells due to the decreased abundance of free virus particles. This reoccurrence can be quantified and used to assess production and cell lysis rates. Several modifications of the method are presented and compared. The approaches have great potential for elucidating trends in virus production rates as well as for making generalized estimates of the quantitative effects of viruses on marine microbial communities.

For many laboratories, flow cytometry is becoming the routine method for quantifying viruses in aquatic sys-tems because of its high reproducibility, high sample throughput, and ability to distinguish several subpopula-tions of viruses. Comparison of viral counts between flow cytometry and epifluorescence microscopy typicallyshows slopes that are statistically not distinguishable from 1, thus confirming the usefulness of flow cytometry.Here we describe in detail all steps in the procedure, discuss potential problems, and offer solutions. *Corresponding author: E-mail: *corina.brussaard@nioz.nl Acknowledgments Publication costs for the Manual of Aquatic Viral Ecology were pro-vided by the Gordon and Betty Moore Foundation. This document isbased on work partially supported by the U.S. National ScienceFoundation (NSF) to the Scientific Committee for OceanographicResearch under Grant OCE-0608600. Any opinions, findings, and con-clusions or recommendations expressed in this material are those of theauthors and do not necessarily reflect the views of the NSF.We gratefully thank A. Culley, A. Comeau, C. Pedros-Alio, C. Lovejoy,and C. Martineau for their efforts in field sampling; and A. Ortmann, A.Chan, and officers and crew of the CCGS

16 pages, 6 figures, 4 tables, Black carbon (BC) is the carbonaceous residue of the incomplete combustion of fossil fuels and biomass and encompasses a range of chemically heterogeneous substances from partly charred plant material to highly condensed soot aerosols. We addressed the potential role of BC aerosol deposition on marine microbial processes in the ocean by investigating the effects of BC reference material (and its exposure to simulated solar radiation) on viral and bacterial activity in batch cultures with aged seawater. Viruses and bacteria were rapidly adsorbed to BC. No difference between the effect of irradiated and non-irradiated BC on free viral parameters was observed. Bacterial leucine incorporation was higher in the BC treatments than in the BC-free controls. The stimulated bacterial production in the dark BC treatments might be caused by the reduction of viral infection due to adsorption of organic material or by direct use of BC material. Viral production was significantly lower in BC-amended treatments than in BC-free controls, and the estimated fraction of infected cells decreased with increasing BC concentration. Moreover, bacterial activity in the solar-radiation-exposed BC treatments was higher than in the dark BC treatments, indicating that radiation made BC more accessible to bacteria. Our data reveal that BC has the potential to stimulate bacterial activity in the water column, particularly after exposure to solar radiation. Rising BC levels in the atmosphere due to increasing anthropogenic emissions could have far-reaching effects, including potential stimulation of seawater heterotrophy and CO2 production, through its effects on bacteria and viruses. © Inter-Research 2015, Financial support was provided by the European Union in the framework of the BASICS project (EVK3-CT-2002-00078), by the Eur-Oceans Network of Excellence (Project Number WP4-SYSMS-1021), and a Spanish grant from the ministry of education (SB2010-0079) to A.M. J.M.G. is supported by grant STORM from the Spanish MICINN

International audience; Three vertical ocean carbon pumps have been known for almost three decades to sequester atmospheric carbon in the deep-water and sediment reservoirs, i.e. the solubility pump, the carbonate pump, and the soft-tissue (also known as organic, or biological) carbon pump (BCP). These three pumps maintain the vertical gradient in total dissolved inorganic carbon between the surface and deep waters. The more recently proposed microbial carbon pump (MCP) would maintain a gradient between short- and long-lived dissolved organic carbon (DOC; average lifetimes of 100 years, respectively). Long-lived DOC is an additional proposed reservoir of sequestered carbon in the ocean. This review: examines critically aspects of the vertical ocean carbon pumps and the MCP, in particular their physical dimensions and their potential roles in carbon sequestration; normalises the dimensions of the MCP to allow direct comparisons with the three vertical ocean carbon pumps; compares the MCP and vertical ocean carbon pumps; organises in a coherent framework the information available in the literature on refractory DOC; explores the potential effects of the globally changing ocean on the MCP; and identifies the assumptions that generally underlie the MCP studies, as bases for future research. The study: proposes definitions of terms, expressions and concepts related to the four ocean carbon pumps (i.e. three vertical pumps and MCP); defines the magnitude for the MCP as the rate of production of DOC with an average lifetime of >100 years and provides its first estimate for the World Ocean, i.e. 0.2 Pg C year−1; and introduces an operational “first-time-sequestration” criterion that prevents organic carbon fluxes from being assigned to both the BCP and the MCP. In our review of the potential effects of predicted climate-related changes in the ocean environment on the MCP, we found that three of the seven predicted changes could potentially enhance carbon sequestration by the MCP, and three could diminish it.

The effect of P-limitation and viral infection on prokaryotic production (PP) and respiration was determined during the early winter in the Northwestern Mediterranean Sea. Addition of P enhanced prokaryotic growth and viral production. The concentrations of total dissolved nitrogen increased linearly with decreasing viral abundance, PP and growth efficiency across treatments. Our data suggest that microbial growth can also be P-limited in winter and that viral lysis products can be readily used by prokaryotes depending on nutrient availability.

International audience; Deep-sea hydrothermal vents and the surrounding basalt seafloor are subject to major natural disturbance events such as volcanic eruptions. In the near future, anthropogenic disturbance in the form of deep-sea mining could also significantly affect the faunal communities of hydrothermal vents. In this study, we monitor and compare the recovery of insular, highly productive vent communities and vent-proximate basalt communities following a volcanic eruption that destroyed almost all existing communities at the East Pacific Rise, 9 degrees 50'N in 2006. To study the recovery patterns of the benthic communities, we placed settlement substrates at vent sites and their proximate basalt areas and measured the prokaryotic abundance and compared the meio- and macrofaunal species richness and composition at one, two and four years after the eruption. In addition, we collected samples from the overlying water column with a pelagic pump, at one and two years after the volcanic eruption, to determine the abundance of potential meiofauna colonisers. One year after eruption, mean meio- and macrofaunal abundances were not significantly different from pre-eruption values in vent habitats (meio: 8-1838 ind. 64 cm(-2) in 2006; 3-6246 ind. 64 cm(-2) in 2001/02; macro: 95-1600 ind. 64 cm(-2) in 2006; 205-4577 ind. 64 cm(-2) in 2001/02) and on non-vent basalt habitats (meio: 10-1922 ind. 64 cm(-2) in 2006; 8328 ind. 64 cm(-2) in 2003/04; macro: 14-3351 ind. 64 cm(-2) in 2006; 2-63 ind. 64 cm(-2) in 2003/04), but species recovery patterns differed between the two habitat types. In the vent habitat, the initial community recovery was relatively quick but incomplete four years after eruption, which may be due to the good dispersal capabilities of vent endemic macrofauna and vent endemic dirivultid copepods. At vents, 42% of the pre-eruption meio- and 39% of macrofaunal species had returned. In addition, some new species not evident prior to the eruption were found. At the tubeworm site Tica, a total of 26 meio- and 19 macrofaunal species were found in 2009, which contrasts with the 24 meio- and 29 macrofauna species detected at the site in 2001/01 In the basalt habitat, community recovery of meiofauna was slower with only 28% of the original 64 species present four years after eruption. The more limited dispersal capabilities of meiofauna basalt specialists such as nematodes or harpacticoid copepods probably caused this pattern. In contrast, 67% of the original 27 macrofaunal species had recolonized the basalt by 2009. Our results suggest that not only vent communities, but also species-rich communities of vent-proximate habitats require attention in conservation efforts. (C) 2015 Elsevier Ltd. All rights reserved.

Using transmission electron microscopy (TEM), a population of giant virus-like par- ticles (VLPs) with a head diameter of ca. 405 nm and a flexible ca. 1100 nm long tail was detected in a lake-type reservoir. These giant VLPs were abundant in situ at the start of a survey period (3.3 × 10 4 particles ml �1 ) and increased by 7-fold within 96 h. This VLP population vanished in dialysis bag incubations of 0.8 µm-filtered reservoir water (free of bacterivorous flagellates) but increased markedly in the enhanced bacterivory treatment, i.e. 5 µm filtered water. In the latter, incubation, heterotrophic nanoflagellate (HNF) abundance increased approximately 15-fold dur- ing the study. A multiple regression analysis using microbial abundances and grazing rates as parameters indicated that 78% of the variability in the abundance of giant VLPs was explained by HNF abundance and grazing rates. Our data support the hypothesis that this virus population infects flagellates. Observation of a presumptive lysing flagellate cell suggests a viral burst size of 15. Estimations of decay and net production rates from dialysis bag incubations indicate that lysis due to giant viruses could cause between 10 to 60% of the mortality of the total flagellate commu- nity and, thus, viruses are potentially a significant factor shaping the population dynamics of fl a gellates in freshwater.

9 pages, 2 figures, 4 tables, 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. © 2015 Elsevier Ltd., Funding for this research was provided by projects funded by the Spanish Ministry of Science and Innovation (MICINN): MICROVIS, FLAME and MEFISTO (CTM2007-62140 and CGL2010-16304, CTM2013-43767) to D. Vaqué; and STORM, ÍCARO and DOREMI (CTM2009-09352, CTM2008-30I120, CTM2012-34294) to M.M. Sala. The work of J.A. Boras was supported by a PhD fellowship from the Spanish Ministry of Education and Science (an FPU grant)