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Like other seafood products, tuna is highly perishable and sensitive to microbial spoilage. Its consumption, whether fresh or canned, can lead to severe food poisoning due to the activity of specific microorganisms, including histamine-producing bacteria. Yet, many grey areas persist regarding their ecology, conditions of emergence, and proliferation in fish. In this study, we used 16S rRNA barcoding to investigate postmortem changes in the bacteriome of fresh and brine-frozen yellowfin tuna (Thunnus albacares), until late stages of decomposition (i.e. 120 h). The results revealed that despite standard refrigeration storage conditions (i.e. 4°C), a diverse and complex spoilage bacteriome developed in the gut and liver. The relative abundance of spoilage bacterial taxa increased rapidly in both organs, representing 82% of the bacterial communities in fresh yellowfin tuna, and less than 30% in brine-frozen tuna. Photobacterium was identified as one of the dominant bacterial genera, and its temporal dynamics were positively correlated with histamine concentration in both gut and liver samples, which ultimately exceeded the recommended sanitary threshold of 50 ppm in edible parts of tuna. The results from this study show that the sanitary risks associated with the consumption of this widely eaten fish are strongly influenced by postcapture storage conditions.

Although tunas represent a significant part of the global fish economy and a major nutritional resource worldwide, their microbiome still remains poorly documented. Here, we conducted an analysis of the taxonomic composition of the bacterial communities inhabiting the gut, skin, and liver of two most consumed tropical tuna species (skipjack and yellowfin), from individuals caught in the Atlantic and Indian oceans. We hypothesized that each organ harbors a specific microbial assemblage whose composition might vary according to different biotic (sex, species) and/or abiotic (environmental) factors. Our results revealed that the composition of the tuna microbiome was totally independent of fish sex, regardless of the species and ocean considered. Instead, the main determinants of observed diversity were (i) tuna species for the gut and (ii) sampling site for the skin mucus layer and (iii) a combination of both parameters for the liver. Interestingly, 4.5% of all amplicon sequence variants (ASV) were shared by the three organs, highlighting the presence of a core-microbiota whose most abundant representatives belonged to the genera Mycoplasma, Cutibacterium, and Photobacterium. Our study also revealed the presence of a unique and diversified bacterial assemblage within the tuna liver, comprising a substantial proportion of potential histamine-producing bacteria, well known for their pathogenicity and their contribution to fish poisoning cases. These results indicate that this organ is an unexplored microbial niche whose role in the health of both the host and consumers remains to be elucidated.

Off the coast of Vietnam, two recent events seem to have contributed to the death of coral reefs: the rapid invasion of a small marine snail called Drupella, and the emergence of a disease that spreads over corals. We decided to investigate whether there is a link between the corals, the snails, and the disease. We analyzed the mucus covering the surface of corals, both in healthy corals and those infested by Drupella snails. Mucus produced by corals is usually full of helpful microbes, protecting the corals from harmful microbes that can make them ill or kill them. Our analyses showed that, when Drupella eats corals, the snail also removes one of the corals’ primary defenses by eliminating most of the tiny protectors in their mucus. This allows harmful microbes to cause additional damage to the corals.

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.

International audience; Coral reefs host hundreds of thousands of animal species that are increasingly threatened by anthropogenic disturbances. These animals host microbial communities at their surface, playing crucial roles for their fitness. However, the diversity of such microbiomes is mostly described in a few coral species and still poorly defined in other invertebrates and vertebrates. Given the diversity of animal microbiomes, and the diversity of host species inhabiting coral reefs, the contribution of such microbiomes to the total microbial diversity of coral reefs could be important, yet potentially vulnerable to the loss of animal species. Analysis of the surface microbiome from 74 taxa, including teleost fishes, hard and soft corals, crustaceans, echinoderms, bivalves and sponges, revealed that more than 90% of their prokaryotic phylogenetic richness was specific and not recovered in surrounding plankton. Estimate of the total richness associated with coral reef animal surface microbiomes reached up to 2.5% of current estimates of Earth prokaryotic diversity. Therefore, coral reef animal surfaces should be recognized as a hotspot of marine microbial diversity. Loss of the most vulnerable reef animals expected under present-day scenarios of reef degradation would induce an erosion of 28% of the prokaryotic richness, with unknown consequences on coral reef ecosystem functioning.

Microbial communities from hypersaline ponds, dominated by halophilic archaea, are considered specific of such extreme conditions. The associated viral communities have accordingly been shown to display specific features, such as similar morphologies among different sites. However, little is known about the genetic diversity of these halophilic viral communities across the Earth. Here, we studied viral communities in hypersaline ponds sampled on the coast of Senegal (8-36% of salinity) using metagenomics approach, and compared them with hypersaline viromes from Australia and Spain. The specificity of hyperhalophilic viruses could first be demonstrated at a community scale, salinity being a strong discriminating factor between communities. For the major viral group detected in all samples (Caudovirales), only a limited number of halophilic Caudovirales clades were highlighted. These clades gather viruses from different continents and display consistent genetic composition, indicating that they represent related lineages with a worldwide distribution. Non-tailed hyperhalophilic viruses display a greater rate of gene transfer and recombination, with uncharacterized genes conserved across different kind of viruses and plasmids. Thus, hypersaline viral communities around the world appear to form a genetically consistent community that are likely to harbour new genes coding for enzymes specifically adapted to these environments.

The factors controlling estuarine phytoplankton diversity and production are relatively well known in temperate systems. Less however is known about the factors affecting phytoplankton community distribution in tropical estuaries. This is surprising given the economic and ecological importance of these large, deltaic ecosystems, such as are found in South East Asia. Here we present the results from an investigation into the factors controlling phytoplankton distribution and phytoplankton-bacterial coupling in the Bach Dang Estuary, a sub-estuary of the Red River system, in Northern Vietnam. Phytoplankton diversity and primary and bacterial production, nutrients and metallic contaminants (mercury and organotin) were measured during two seasons: wet (July 2008) and dry (March 2009). Phytoplankton community composition differed between the two seasons with only a 2% similarity between July and March. The large spatial extent and complexity of defining the freshwater sources meant that simple mixing diagrams could not be used in this system. We therefore employed multivariate analyses to determine the factors influencing phytoplankton community structure. Salinity and suspended particulate matter were important factors in determining phytoplankton distribution, particularly during the wet season. We also show that phytoplankton community structure is probably influenced by the concentrations of mercury species (inorganic mercury and methyl mercury in both the particulate and dissolved phases) and of tri-, di, and mono-butyl tin species found in this system. Freshwater phytoplankton community composition was associated with dissolved methyl mercury and particulate inorganic mercury concentrations during the wet season, whereas, during the dry season, dissolved methyl mercury and particulate butyl tin species were important factors for the discrimination of the phytoplankton community structure. Phytoplankton-bacterioplankton coupling was also investigated during both seasons. In the inshore, riverine stations the ratio between bacterial production and dissolved primary production was high supporting the hypothesis that bacterial carbon demand is supported by allochthonous riverine carbon sources. The inverse was true in the offshore stations, where BP:DPP values were less than 1, potentially reflecting differences in primary production due to shifting phytoplankton community diversity.

A recent hypothesis considers that many coral pathologies are the result of a sudden structural alteration of the epibiotic bacterial communities in response to environmental disturbances. However, the ecological mechanisms that lead to shifts in their composition are still unclear. In the ocean, viruses represent a major bactericidal agent but little is known on their occurrence within the coral holobiont. Recent reports have revealed that viruses are abundant and diversified within the coral mucus and therefore could be decisive for coral health. However, their mode of action is still unknown, and there is now an urgent need to shed light on the nature of the relationships they might have with the other prokaryotic and eukaryotic members of the holobiont. In this opinion letter, we are putting forward the hypothesis that coral-associated viruses (mostly bacterial and algal viruses), depending on the environmental conditions might either reinforce coral stability or conversely fasten their decline. We propose that these processes are presumably based on an environmentally driven shift in infection strategies allowing viruses to regulate, circumstantially, both coral symbionts (bacteria or Symbiodinium) and surrounding pathogens.

Since the discovery, 2–3 decades ago, that viruses of microbes are abundant in marine ecosystems, aquatic viral ecology has grown increasingly to reach the status of a full scientific discipline in environmental sciences. A dedicated society, the International Society for Viruses of Microorganisms (ISVM) (http://www.isvm.org/), was recently launched. Increasing studies in aquatic viral ecology are a source of novel knowledge related to the biodiversity, the functioning of ecosystems and the evolution of the cellular world. This is because viruses are perhaps the most diverse, abundant, and ubiquitous biological entities in the world’s aquatic ecosystems. They exhibit various lifestyles that intimately depend on living cell metabolism, and are ultimately replicated by members of all three domains of life (Bacteria, Eukarya, Archaea). This establishes viruses as microbial killers and manipulators in the hydrosphere. Lake Pavin is one of the pioneer sites where original ecological data were first provided on the qualitative, quantitative and functional significance of both lytic and temperate viruses of prokaryotes in temperate freshwater lakes, taking into account both seasonal and depth-related variability in the water column and in the sediments. These data were acquired by means of original protocols we developed. In addition to these protocols, we herein provide a synthesis of Lake Pavin studies on viral ecology, focusing on: (i) spatio-temporal dynamics of the diversity of viral communities, (ii) the significance of seasonal and depth-related variations of viral abundance and lytic and lysogenic activities, and (iii) the relative importance of lytic viruses and grazers for bacterial mortality and the biogeochemical implications for the food web dynamics. Unexpected and novel putative viruses were discovered in the deep-aged, dark, and permanently anoxic monimolimnic waters and sediments of Lake Pavin, highlighting the possible endemicity of these habitats. Some of these original viruses resembled dsDNA viruses of hyperthermophilic and hyperhalophilic Archaea. Unusual types of spherical and cubic virus-like particles (VLPs) were also observed for the first time. Infected prokaryotic cells were detected in deep sediment cores, and their vertical distribution correlated with both viral and prokaryotic abundances. Pleomorphic ellipsoid VLPs were visible in filamentous cells tentatively identified as representatives of the archaeal genus Methanosaeta, a major group of methane producers on Earth.

International audience; Size fractionation was performed using water from the Great Reef of Toliara (Madagascar) taken from two different habitats (ocean and lagoon) during the dry and wet seasons, to study the growth and mortality rates of bacterioplankton. Experiments were conducted with 1 and 100% of heterotrophic nanoflagellate (HNF) concentrations and virus-free water was obtained by tangential filtration (10 kDa). During the dry season, in both environments, bacterial abundance and production were significantly lower than values recorded during the wet season. Bacterial growth rates without grazers were 0.88 day–1 in the lagoon and 0.58 day–1 in the ocean. However, growth rates were statistically higher without grazers and viruses (1.58 day–1 and 1.27 day–1). An estimate of virus-induced bacterial mortality revealed the important role played by viruses in the lagoon (0.70 day–1) and the ocean (0.69 day–1). During the wet season, bacterial growth rates without grazers were significantly higher in both environments than were values obtained in the dry season. However, the bacterial growth rates were paradoxally lower in the absence of viruses than with viruses in both environments. Our results suggest that changes in nutrient concentrations can play an important role in the balance between viral lysis and HNF grazing in the bacterial mortality. However, virus-mediated bacterial mortality is likely to act simultaneously with nanoflagellates pressure in their effects on bacterial communities.

Population dynamics in the microbial food web are influenced by resource availability and predator/parasitism activities. Climatic changes, such as an increase in temperature and/or UV radiation, can also modify ecological systems in many ways. A series of enclosure experiments was conducted using natural microbial communities from a Mediterranean lagoon to assess the response of microbial communities to top-down control [grazing by heterotrophic nanoflagellates (HNF), viral lysis] and bottom-up control (nutrients) under various simulated climatic conditions (temperature and UV-B radiations). Different biological assemblages were obtained by separating bacteria and viruses from HNF by size fractionation which were then incubated in whirl-Pak bags exposed to an increase of 3°C and 20% UV-B above the control conditions for 96 h. The assemblages were also provided with an inorganic and organic nutrient supply. The data show (i) a clear nutrient limitation of bacterial growth under all simulated climatic conditions in the absence of HNF, (ii) a great impact of HNF grazing on bacteria irrespective of the nutrient conditions and the simulated climatic conditions, (iii) a significant decrease in burst size (BS) (number of intracellular lytic viruses per bacterium) and a significant increase of VBR (virus to bacterium ratio) in the presence of HNF, and (iv) a much larger temperature effect than UV-B radiation effect on the bacterial dynamics. These results show that top-down factors, essentially HNF grazing, control the dynamics of the lagoon bacterioplankton assemblage and that short-term simulated climate changes are only a secondary effect controlling microbial processes.

Virus-prokaryote interactions were investigated in four natural sites in Senegal (West Africa) covering a salinity gradient ranging from brackish (10‰) to near salt saturation (360‰). Both the viral and the prokaryote communities exhibited remarkable differences in their physiological, ecological and morphological traits along the gradient. Above 240‰ salinity, viral and prokaryotic abundance increased considerably with the emergence of (1) highly active square haloarchaea and of (2) viral particles with pleiomorphic morphologies (predominantly spindle, spherical and linear shaped). Viral life strategies also showed some salinity-driven dependence, switching from a prevalence of lytic to lysogenic modes of infection at the highest salinities. Interestingly, the fraction of lysogenized cells was positively correlated with the proportion of square cells. Overall, the extraordinary abundance of viruses in hypersaline systems (up to 6.8 × 10(8) virus-like particles per milliliter) appears to be partly explained by their high stability and specific ability to persist and proliferate in these apparently restrictive habitats.

12 pages, 4 figures, 3 tables, Previous studies indicate that lysogeny is preponderant when environmental conditions are challenging for the bacterial communities and when their metabolism is reduced. Furthermore, it appears that lysogeny is more frequent within certain bacterial phylogenetic groups. In this comparative study from 10 freshwater reservoirs and 10 coastal lagoons, we aim to disentangle the influence of these different factors. In eight reservoirs and four lagoons, lysogeny was detected by induction assays with mitomycin C, and induction significantly modified the bacterial community composition (BCC), whereas community composition remained constant in ecosystems in which lysogeny was not observed. Among the phylogenetic groups studied, the most abundant ones were Bacteroidetes and α-proteobacteria in lagoons, and β-proteobacteria and Bacteroidetes in reservoirs. These dominant groups comprised the highest proportions of inducible lysogens. In order to unravel the effects of bacterial metabolism from phylogeny on lysogeny, we measured bacterial community physiology and the specific activities of selected phylogenetic groups. The proportion of inducible lysogens within the α- and the β-proteobacteria decreased with increasing group-specific metabolism in lagoons and reservoirs, respectively. In contrast, this relationship was not observed for the other lysogen-containing groups. Hence, both host physiology and phylogeny are critical for the establishment of lysogeny. This study illustrates the importance of lysogeny among the most abundant phylogenetic groups, and further suggests its strong structuring impact on BCC, This work was supported by the French ANR Aquaphage 07 BDIV 015–02 (to TB and YB). Work of HS was supported by the Spanish MEC (SB2006–0060), MCyI (Juan de la Cierva Fellowship JCI-2008–2727) and Portuguese FCT do Ministério da Ciência, Tecnologia e Ensino Superior’ (Grant SFRH/BPD/34041/2006)

Little is known about the ability of phages to successfully colonize contrasting aquatic niches. We conducted experimental cross-infections between viruses and prokaryotes from three tropical sites of West Africa, with distinct salinities: a freshwater reservoir, a marine coastal station and a hypersaline lake. A cellular poison-based method (potassium cyanide) revealed that the addition of native viruses (regardless of the water type) consistently stimulated viral production. Conversely, in all incubations conducted with allochtonous (non-native) viruses, their overall production was not promoted, which suggests a lytic failure. Prokaryotic heterotrophic production increased in fresh and marine water supplemented with native viruses, but not in the hypersaline water. These results point to the role of the viral shunt in low-salinity environments, where the release of bioavailable lysis products might be of high nutritional value for the noninfected prokaryotes. In contrast, in hypersaline water where glycerol is a major carbon and energy source for the heterotrophic community, dissolved organic matter (DOM) of lytic origin may represent a less important DOM source for prokaryotes. Finally, our results suggest that cosmopolitan phages capable of moving between biomes are probably rare in aquatic habitats, supporting the common idea that most wild phages are relatively limited in their host range.

International audience; Viral abundance and processes in the water column and sediments are well studied for some systems; however, we know relatively little about virus–host interactions on particles and how particles influence these interactions. Here we review virus–prokaryote interactions on inorganic and organic particles in the water column. Profiting from recent methodological progress, we show that confocal laser scanning microscopy in combination with lectin and nucleic acid staining is one of the most powerful methods to visualize the distribution of viruses and their hosts on particles such as organic aggregates. Viral abundance on suspended matter ranges from 105 to 1011 ml–1. The main factors controlling viral abundance are the quality, size and age of aggregates and the exposure time of viruses to aggregates. Other factors such as water residence time likely act indirectly. Overall, aggregates appear to play a role of viral scavengers or reservoirs rather than viral factories. Adsorption of viruses to organic aggregates or inorganic particles can stimulate growth of the free-living prokaryotic community, e.g. by reducing viral lysis. Such mechanisms can affect microbial diversity, food web structure and biogeochemical cycles. Viral lysis of bacterio- and phytoplankton influences the formation and fate of aggregates and can, for example, result in a higher stability of algal flocs. Thus, viruses also influence carbon export; however, it is still not clear whether they short-circuit or prime the biological pump. Throughout this review, emphasis has been placed on defining general problems and knowledge gaps in virus–particle interactions and on providing avenues for further research, particularly those linked to global change.

Virucidal properties of sunlight and temperature have been identified for a long time. However, it is less well established if virioplankton communities are evenly susceptible or geographically adapted to these environmental factors. Transplant experiments were conducted between a tropical (Senegal) and temperate (France) site to examine the effect of natural daylight conditions and temperature on the persistence of free viruses in water. Fresh- and seawater viruses from both countries were simultaneously subjected to 12 h of full sunlight and dark exposure under their native and "transplanted" latitudes. Consistently, viruses decayed much faster when incubated abroad, regardless of origin (latitude and/or water type). However, viral losses, in most cases, were not significantly different between sunlight exposed and dark samples, implying that ambient radiation does not exert strong negative effects on virioplankton particles. Rather, temperature clearly emerged as the principal determinant Of viral survival in all samples. This suggests that viruses, under local temperature, can adapt through an evolutionary process to survive for longer periods of time thus increasing their chances to encounter their hosts.

There is increasing suspicion that viral communities play a pivotal role in maintaining coral health, yet their main ecological traits still remain poorly characterized. In this study, we examined the seasonal distribution and reproduction pathways of viruses inhabiting the mucus of the scleractinians Fungia repanda and Acropora formosa collected in Nha Trang Bay (Vietnam) during an 11-month survey. The strong coupling between epibiotic viral and bacterial abundance suggested that phages are dominant among coral-associated viral communities. Mucosal viruses also exhibited significant differences in their main features between the two coral species and were also remarkably contrasted with their planktonic counterparts. For example, their abundance (inferred from epifluorescence counts), lytic production rates (KCN incubations), and the proportion of lysogenic cells (mitomycin C inductions) were, respectively, 2.6-, 9.5-, and 2.2-fold higher in mucus than in the surrounding water. Both lytic and lysogenic indicators were tightly coupled with temperature and salinity, suggesting that the life strategy of viral epibionts is strongly dependent upon environmental circumstances. Finally, our results suggest that coral mucus may represent a highly favorable habitat for viral proliferation, promoting the development of both temperate and virulent phages. Here, we discuss how such an optimized viral arsenal could be crucial for coral viability by presumably forging complex links with both symbiotic and adjacent nonsymbiotic microorganisms.

International audience; Animal-associated microbiota of animals form complex communities, which are suspected to play crucial functions for their host fitness. However, the biodiversity of these communities, including their differences between host species and individuals, have been scarcely studied, especially in case of skin-associated communities. In addition, the intra-individual variability (i.e. between body parts) has never been assessed to date. The objective of this study was to characterize skin bacterial communities of two teleostean fish species, namely the European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata), using a high-throughput DNA sequencing method. In order to focus on intrinsic factors of host-associated bacterial community variability, individuals of the two species were raised in controlled conditions. Bacterial diversity was assessed using a set of four complementary indices, describing the taxonomic and phylogenetic facets of biodiversity and their respective composition (based on presence/absence data) and structure (based on species relative abundances) components. Variability of bacterial diversity was quantified at the interspecific, inter- and intra-individual scales. We demonstrated that fish surfaces host highly diverse bacterial communities, whose composition was very different from that of surrounding bacterioplankton. This high total biodiversity of skin-associated communities was supported by the important variability, between host species, individuals and the different body parts (dorsal, anal, pectoral and caudal fins).

Phytoplankton diversity and abundance in estuarine systems are controlled by many factors. Salinity, turbidity, and inorganic nutrient concentrations and their respective ratios have all been proposed as principal factors that structure phytoplankton diversity and influence the emergence of potentially toxic species. Although much work has been conducted on temperate estuaries, less is known about how phytoplankton diversity is controlled in tropical, monsoonal systems that are subject to large, seasonal shifts in hydrology and to rapidly changing land use. Here, we present the results of an investigation into the factors controlling phytoplankton species composition and distribution in a tropical, monsoonal estuary (Bach Dang estuary, North Vietnam). A total of 245 taxa, 89 genera from six algal divisions were observed. Bacillariophyceae were the most diverse group contributing to 51.4 % of the microalgal assemblage, followed by Dinophyceae (29.8 %), Chlorophyceae (10.2 %), Cyanophyceae (3.7 %), Euglenophyceae (3.7 %) and Dictyochophyceae (1.2 %). The phytoplankton community was structured by inorganic nutrient ratios (DSi:DIP and DIN:DIP) as well as by salinity and turbidity. Evidence of a decrease in phytoplankton diversity concomitant with an increase in abundance and dominance of certain species (e.g., Skeletonema costatum) and the appearance of some potentially toxic species over the last two decades was also found. These changes in phytoplankton diversity are probably due to a combination of land use change resulting in changes in nutrient ratios and concentrations and global change as both rainfall and temperature have increased over the last two decades. It is therefore probable in the future that phytoplankton diversity will continue to change, potentially favoring the emergence of toxic species in this system.

1. The seasonal and vertical distribution of the abundance of virus-like particles (VLPs), together with the abundances of other microbial organisms (bacteria, unpigmented and pigmented nanoflagellates and ciliates), were determined in an oligomesotrophic lake (Pavin, France) and in a eutrophic lake (Aydat, France) between March and December 2000. 2. The abundance of the viral plankton and those of other microbial taxa were significantly higher in the more productive system. The same was for the virus-to-bacteria quotient (VBQ), which averaged seven in Lake Pavin and nine in Lake Aydat. 3. The abundance of viruses increased during the period of thermal stratification in both lakes, with the highest values being recorded at the end of summer/early autumn in the epi- and the metalimnion. The seasonal pattern of abundance of viruses in both lakes in the surface layer was similar, indicating that the dynamics of viruses may be controlled by environmental factors such as light conditions. 4. There was no correlation between the abundance of viruses and protists. We found correlations between viruses and heterotrophic bacteria in the whole water column in Lake Pavin, but only in the dark bottom waters in Lake Aydat. 5. Overall, the empirical findings in this study lead us to speculate that the weaker correlation between bacteria and viruses in Lake Aydat than in Lake Pavin, as well as the higher VBQ in the former, is a consequence of the increasing relative abundance of non-bacteriophage VLPs along the trophic gradient of aquatic systems.

Planktonic microbial communities often appear stable over periods of days and thus tight links are assumed to exist between different functional groups (i.e. producers and consumers). We examined these links by characterizing short-term temporal correspondences in the concentrations and activities of microbial groups sampled from 1 m depth, at a coastal site of the N.W. Mediterranean Sea, in September 2001 every 3 h for 3 days. We estimated the abundance and activity rates of the autotrophic prokaryote Synechococcus, heterotrophic bacteria, viruses, heterotrophic nanoflagellates, as well as dissolved organic carbon concentrations. We found that Synechococcus, heterotrophic bacteria, and viruses displayed distinct patterns. Synechococcus abundance was greatest at midnight and lowest at 21:00 and showed the common pattern of an early evening maximum in dividing cells. In contrast, viral concentrations were minimal at midnight and maximal at 18:00. Viral infection of heterotrophic bacteria was rare (0.5-2.5%) and appeared to peak at 03:00. Heterotrophic bacteria, as % eubacteria-positive cells, peaked at midday, appearing loosely related to relative changes in dissolved organic carbon concentration. Bacterial production as assessed by leucine incorporation showed no consistent temporal pattern but could be related to shifts in the grazing rates of heterotrophic nanoflagellates and viral infection rates. Estimates of virus-induced mortality of heterotrophic bacteria, based on infection frequencies, were only about 10% of cell production. Overall, the dynamics of viruses appeared more closely related to Synechococcus than to heterotrophic bacteria. Thus, we found weak links between dissolved organic carbon concentration, or grazing, and bacterial activity, a possibly strong link between Synechococcus and viruses, and a missing link between light and viruses. (C) 2002 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.

International audience; While considered as sustainable and low-cost agricultural amendments, the impacts of organic fertilizers on downstream aquatic microbial communities remain poorly documented. We investigated the quantity and quality of the dissolved organic matter leaching from agricultural soil amended with compost, vermicompost or biochar and assessed their effects on lake microbial communities, in terms of viral and bacterial abundances, community structure and metabolic potential. The addition of compost and vermicompost significantly increased the amount of dissolved organic carbon in the leachate compared to soil alone. Leachates from these additions, either with or without biochar were highly bioavailable to aquatic microbial communities, though reducing the metabolic potential of the community and harboring more specific communities. Although not affecting bacterial richness or taxonomic distributions, the specific addition of biochar affected the original lake bacterial communities resulting in a strongly different community. This could be partly explained by viral burst and converging bacterial abundances throughout the samples. These results underline the necessity to include off-site impacts of agricultural amendments when considering their cascading effect on downstream aquatic ecosystems. This article is protected by copyright. All rights reserved.

Vermicompost and biochar amendments are management practices which may contribute to sustainable agroecosystems by reducing dependence on inorganic fertilizers. However, little is known about their impacts on soil microorganisms and their transfer and evolution in connected aquatic systems. The aim of this study was to determine the influence of organic manure (buffalo manure, compost or vermicompost) and biochar amendments on bacterial and viral properties in soil and water. A three year experiment was carried out with terrestrial mesocosms which were used to test the effect of organic matter amendment on maize growth. In the last year of the experiment, runoff and infiltration waters from the terrestrial mesocosms were transferred to aquatic mesocosms. Organic fertilization improved soil properties (higher C, N content and pH H 2 O ) and as a consequence increased soil bacterial and viral abundance. Bacterial diversity (Shannon ‘H’ and richness ‘S’ indices calculated from DGGE fingerprint) was also enhanced after the continuous application of organic amendments. Compared with compost, vermicompost reduced viral abundance and S but similar H and bacterial abundance were observed. The pH H 2 O , C content and bacterial and viral abundance increased in the aquatic mesocosms following organic fertilization. As a consequence, bacterial and viral diversity also increased in the water, although no differences were found between compost and vermicompost. Biochar increased soil bacterial abundance for the mineral fertilizer treatment but did not influence bacterial and viral abundance in water. However, the combination of biochar and vermicompost led to an increase of viruses in soil and a reduction of bacteria in water. Similarity dendrograms from the DGGE banding patterns showed that the structure of bacterial communities was mainly influenced by the fertilizer treatments in soil but by the presence of biochar in water. In conclusion, this study demonstrated that the nature of the organic amendment has important consequences on both soil and water microbial abundance and diversity.

The amendment of vermicompost is a management practice that may contribute to sustainable agroecosystems by making them less dependent on inorganic fertilizers. However, little is known about the impact of this practice on soil biota and the flow of microbes to the water system. Using a 30-days laboratory experiment, we investigated the development of the peregrine earthworm species, Dichogaster bolaui , in presence of compost or vermicompost, and assessed its impact on the flow of bacteria and viruses to the water system. The dynamics of soil bacterial diversity (assessed by DGGE) and concentration in water together with their viral parasites were also assessed through an incubation of solution during 5 days (comparison between T 0 and T 5 ). This study highlights the rapid development of D. bolaui after compost amendment. However, the low quality of vermicompost and the absence of organic amendment in the control treatment allowed the survival but not the development of D. bolaui . Higher bacterial and viral abundances in compost and vermicompost substrates led to more important transfer of these communities from the soil to the water system in comparison with the untreated soil, but no difference was observed between compost and vermicompost treatments. In terms of abundance, the bacterial to virus ratio was rather stable in the soil solution but no such a relation was observed in the soil. A reduction of bacterial diversity (OTU) was measured at the end of the incubation period for all the treatments. However, higher number of OTU at T 5 for the compost treatment suggested a better adaptation and/or resistance of soil bacteria to the aquatic system, in comparison with the control treatment. Vermicompost treatment led to intermediate conclusions. The presence of D. bolaui significantly reduced bacterial abundance in the soil organic layer (both compost and vermicompost treatments) but it did not influence bacterial and viral abundance in water, suggesting independent processes. Earthworms buffered bacterial DGGE patterns after five days of incubation, probably through a facilitation of soil bacterial groups more able to resist in solution.

Virus-like particles were observed in thin sections of partially bleaching colonies of the scleractinian Acropora cytherea, collected in the Hon Mun Marine Protected Area (Vietnam). The most common particles were found in the cytoplasm of epidermal cells, exhibiting icosahedral symmetry and measuring 90–140 nm in diameter. Some had a tail-like structure resembling that of certain Hepadnaviridae such as the hepatitis B virus. Some others were tailless with a virion size. Overall, less than 10% of the cells showed obvious signs of infection. Images of virally-parasitized tissues of A. cytherea provide further evidence that corals are a target for viral infection. However, more research is required into their pathogenicity and involvement in bleaching events.

The distribution of viruses inhabiting the coral mucus remains undetermined, as there is no suitable standardized procedure for their separation from this organic matrix, principally owing to its viscosity and autofluorescence. Seven protocols were tested, and the most efficient separations were obtained from a chemical treatment requiring potassium citrate.

Background Small size eukaryotes play a fundamental role in the functioning of coastal ecosystems, however, the way in which these micro-organisms respond to combined effects of water temperature, UVB radiations (UVBR) and nutrient availability is still poorly investigated. Results We coupled molecular tools (18S rRNA gene sequencing and fingerprinting) with microscope-based identification and counting to experimentally investigate the short-term responses of small eukaryotes ( Conclusions This multifactorial experiment highlights the potential impacts, over short time scales, of changing environmental factors on the structure of various functional groups like small primary producers, parasites and saprotrophs which, in response, can modify energy flow in the planktonic food webs.

International audience; Although the structure and dynamics of planktonic viruses in freshwater and seawater environments are relatively well documented, little is known about the occurrence and activity of these viruses in estuaries, especially in the tropics. Viral abundance, life strategies, and morphotype distribution were examined in the Bach Dang Estuary (Vietnam) during the dry season in 2009. The abundance of both viruses and their prokaryotic hosts decreased significantly from upstream to downstream, probably as the result of nutrient dilution and osmotic stress faced by the freshwater communities. The antibiotic mitomycin-C revealed that the fraction of lysogenic cells was substantially higher in the lower seawater part of the estuary (max 27.1%) than in the upper freshwater area where no inducible lysogens were observed. The question of whether there is a massive, continuous induction of marine lysogens caused by the mixing with freshwater is considered. Conversely, the production of lytic viruses declined as salinity increased, indicating a spatial succession of viral life strategies in this tropical estuary. Icosahedral tailless viruses with capsids smaller than 60 nm dominated the viral assemblage throughout the estuary (63.0% to 72.1% of the total viral counts), and their distribution was positively correlated with that of viral lytic production. Interestingly, the gamma-proteobacteria explained a significant portion of the variance in the 90 nm) was explained by the beta-proteobacteria. Overall, these results support the view that the environment, through selection mechanisms, probably shapes the structure of the prokaryotic community. This might be in turn a source of selection for the virioplankton community via specific affiliation favoring particular morphotypes and life strategies.

International audience; 1. Estuaries are interesting sites to examine virus-bacteria interactions since they may vary gradually or abruptly in salinity, which presumably requires physiological, genetic and ecological adaptations. To explore such adjustments in tropical areas, freshwater and seawater samples were collected in the estuarine system of the River Senegal and experimentally subjected to abrupt mixing of seawater with freshwater and vice versa. 2. Production rates of freshwater bacteria (measured by the tritiated thymidine incorporation method) and of viruses (measured by the dilution method) sharply declined immediately after seawater addition, which was followed by a spectacular recovery of the surviving bacterial and viral populations within 24 and 48 h, respectively. 3. Conversely, neither marine bacteria nor viruses were significantly affected by mixing with freshwater. This suggests that the turbulent front between ascending tidal sea water and outwelling fluvial freshwater is a more favourable environment for marine bacterioplankton, which may take advantage of massive bursts of freshwater cells resulting from osmotic shock. 4. In both mixing experiments, the dynamics of virioplankton production followed that of the bacteria within 24 h, suggesting that viruses can rapidly respond to dramatic shifts in the abundance and community composition of bacterial hosts.

International audience; The study of lysogeny in aquatic systems is an often overlooked aspect of microbial ecology, especially in tropical environments. Herein, the fraction of lysogenized cells (FLC) was detected in the surface waters of 20 coastal stations distributed from the eutrophicated shoreline to seaward waters of Hann Bay (Senegal). Concurrently, viral lytic infection rates were extrapolated from the frequency of visibly infected bacterial cells (FVIC), as determined from transmission electron microscopy observations. The experimental induction of prophage was observed in less than 3% of indigenous marine bacteria, suggesting that lysogenic stages of infection are rare in Hann Bay. Similarly, only 0.5-4.7% of bacteria showed visible signs of lytic infection. However, the positive correlation between the fraction of lysogenic and lytic cells (r = 0.67, p < 0.05, n = 20) may actually indicate that the coexistence of both lifestyles may be due to the massive and rapid induction of lysogens, potentially from the high levels of local UV radiation. Overall, we suggest that the determination of FVIC and FLC to examine the predominance of one type of cycle versus the other may be a source of misinterpretation in some particular aquatic environments.

The ecology of virioplankton in tropical aquatic ecosystems is poorly documented, and in particular, there are no references concerning African continental waters in the literature. In this study, we examined virus-bacterium interactions in the pelagic and benthic zones of seven contrasting shallow inland waters in Senegal, including one hypersaline lake. SYBR Gold-stained samples revealed that in the surface layers of the sites, the numbers of viruses were in the same range as the numbers of viruses reported previously for productive temperate systems. Despite high bacterial production rates, the percentages of visibly infected cells (as determined by transmission electron microscopy) were similar to the lowest percentages (range, 0.3 to 1.1%; mean, 0.5%) found previously at pelagic freshwater or marine sites, presumably because of the local environmental and climatic conditions. Since the percentages of lysogenic bacteria were consistently less than 8% for pelagic and benthic samples, lysogeny did not appear to be a dominant strategy for virus propagation at these sites. In the benthic samples, viruses were highly concentrated, but paradoxically, no bacteria were visibly infected. This suggests that sediment provides good conditions for virus preservation but ironically is an unfavorable environment for proliferation. In addition, given the comparable size distributions of viruses in the water and sediment samples, our results support the paradigm that aquatic viruses are ubiquitous and may have moved between the two compartments of the shallow systems examined. Overall, this study provides additional information about the relevance of viruses in tropical areas and indicates that the intensity of virus-bacterium interactions in benthic habitats may lower than the intensity in the adjacent bodies of water.

The discovery of an abundant and diverse virus community in oceans and lakes has profoundly reshaped ideas about global carbon and nutrient fluxes, food web dynamics, and maintenance of microbial biodiversity. These roles are exerted through massive viral impact on the population dynamics of heterotrophic bacterioplankton and primary producers. We took advantage of a shallow wetland system with contrasting microhabitats in close proximity to demonstrate that in marked contrast to pelagic systems, viral infection, determined directly by transmission electron microscopy, and consequently mortality of prokaryotes were surprisingly low in benthic habitats in all seasons. This was true even though free viruses were abundant throughout the year and bacterial infection and mortality rates were high in surrounding water. The habitats in which we found this pattern include sediment, decomposing plant litter, and biofilms on aquatic vegetation. Overall, we detected viruses in only 4 of a total of ∼15,000 bacterial cells inspected in these three habitats; for comparison, nearly 300 of ∼5,000 cells suspended in the water column were infected. The strikingly low incidence of impact of phages in the benthos may have important implications, since a major portion of microbial biodiversity and global carbon and nutrient turnover are associated with surfaces. Therefore, if failure to infect benthic bacteria is a widespread phenomenon, then the global role of viruses in controlling microbial diversity, food web dynamics, and biogeochemical cycles would be greatly diminished compared to predictions based on data from planktonic environments.

International audience; Dialysis bags were used to examine the impact of predation and viral lysis on prokaryotic community composition (PCC) over a 5-day experiment in the oligomesotrophic Lake Pavin (France). The impact of the different predator communities (protists and metazoans) of prokaryotes was estimated by water fractionation (

International audience; Seasonal and depth-related variability in the grazing activity of heterotrophic nanoflagellates (HNF) on viruses was examined in the oligo-mesotrophic Lake Pavin and in the eutrophic Lake Aydat, French Massif Central, between May and November 2000. Ingestion rates (IR) were determined using 50 nm diameter fluorescent microspheres, as virus analogues. In both lakes, highest grazing activities on virus-sized particles were recorded in the metalimnion, at the beginning and the end of the thermal stratification period. Estimated IRs in Lake Pavin (mean = 0.4 viruses HNF-1 h-1, CV = 38.0%) and in Lake Aydat (mean = 0.3 viruses HNF-1 h-1, CV = 35.6%) were not significantly different, in contrast to clearance rates (CR), which were significantly higher in the oligomesotrophic (2.3 x 10-2 nl HNF-1 h-1) than in the eutrophic lake (0.7 × 10-2 nl HNF-1 h-1). CRs for viruses were correlated with CRs for bacteria in Lake Aydat but not in Lake Pavin, suggesting a greater abundance within the HNF assemblages of virus-sized particle feeders in the less productive lake. We estimated that 4.1 and 0.8% of viral production were grazed by HNF in Lake Pavin and Lake Aydat, respectively. Finally, although viruses seem to represent a minor food source for HNF (i.e. compared to bacteria), they may not be inconsequential in their diet, especially in oligotrophic lakes.

We conducted a transplant experiment to elucidate the effects of different levels of grazing pressure, nutrient availability, especially phosphorus, and the impact of viruses on the changes in the structure of bacterioplankton assemblage in a meso-eutrophic reservoir. A sample taken from the nutrient-rich inflow part of the reservoir was size-fractionated and incubated in dialysis bags in both inflow and dam area. The structure of bacterial assemblage was examined by fluorescence in situ hybridization using oligonucleotide probes with different levels of specificity. In terms of the relative proportions of different bacterial groups, we found very few significant changes in the bacterioplankton composition after transplanting the treatments to the nutrient-poor dam area. However, we observed marked shifts in morphology and biomass towards the development of filaments, flocs and “vibrio-like” morphotypes of selected probe-defined groups of bacteria induced by increased grazing pressure. Despite the very high abundances of viruses in all the treatments, their effects on bacterioplankton were rather negligible.

For aquatic systems, especially freshwaters, there is little data on the long-term (i.e., >6-month period) and depth-related variability of viruses. In this study, we examined virus-induced mortality of heterotrophic bacteria over a 10-month period and throughout the water column in two lakes of the French Massif Central, the oligomesotrophic Lake Pavin and the eutrophic Lake Aydat. Concurrently, we estimated nonviral mortality through heterotrophic nanoflagellate and ciliate bacterivory. Overall, viral infection parameters were much less variable than bacterial production. We found that the frequency of visibly infected cells (FVIC), estimated using transmission electron microscopy, peaked in both lakes at the end of spring (May to June) and in early autumn (September to October). FVIC values were significantly higher in Lake Pavin (mean [M] = 1.6%) than in Lake Aydat (M = 1.1%), whereas the opposite trend was observed for burst sizes, which averaged 25.7 and 30.2 virus particles bacterium −1 , respectively. We detected no significant depth-related differences in FVIC or burst size. We found that in both lakes the removal of bacterial production by flagellate grazing (M Pavin = 37.7%, M Aydat = 18.5%) was nearly always more than the production removed by viral lysis (M Pavin = 16.2%, M Aydat = 19%) or ciliate grazing (M Pavin = 2.7%, M Aydat = 8.8%). However, at specific times and locations, viral lysis prevailed over protistan grazing, for example, in the anoxic hypolimnion of Lake Aydat. In addition, viral mortality represented a relatively constant mortality source in a bacterial community showing large variations in growth rate and subject to large variations in loss rates from grazers. Finally, although viruses did not represent the main agent of bacterial mortality, our data seem to show that their relative importance was higher in the less productive system.

International audience; L'abondance des communautés de la boucle microbienne (virus, bactéries hétérotrophes, nanoflagellés non pigmentés et nanoflagellés pigmentés), la production primaire phytoplanctonique totale (TPP) et excrétée (EPP), la production bactérienne (BP), ainsi que l'activité lytique virale (LA) et l'activité bactérivore des nanoflagellés hétérotrophes (FG) ont été estimées, les 15 et 16 juin 1998, dans un lac oligomésotrophe de moyenne montagne (Lac Pavin), à 5 et 10 m de profondeur. Au cours de cette étude, quelle que soit la profondeur, les pertes bactériennes moyennes liées à la lyse virale (LA5 m = 1,7 x 106 cellules.l-1.h-1, LA10 m = 2,0 x 106 cellules.l-1.h-1) étaient, en moyenne, inférieures à celles dues au broutage des flagellés phagotrophes (FG5 m = 10,3 x 106 cellules.l-1.h-1, FG10m = 8,4 x 106 cellules.l-1.h-1). Le bilan estimé des flux de carbone indique qu'en moyenne 17,8 % du carbone issu de la TPP (soit 38,1 % de la EPP) a été utilisé par les bactéries. Par ailleurs, en moyenne 52,7 % de la BP (soit 2,15 % de la TPP) a été consommé par le biais de la prédation des nanoflagellés, alors que 11,0 % de la BP (soit 0,45% de la TPP) a été détruit par la lyse virale.

International audience; Abundances of different compartments of the microbial loop (i.e., viruses, heterotrophic bacteria, nonpigmented nanoflagellates, and pigmented nanoflagellates), bacterial heterotrophic production (BHP), viral lysis, and potential flagellate grazing impacts on the bacterial assemblages were estimated during a short-term study (24 h) conducted in June 1998 in the epilimnion (5 m) and metalimnion (10 m) of a moderate-altitude oligomesotrophic lake (Lake Pavin, France). Viral and bacterial abundances were higher in the metalimnion than in the epilimnion, whereas pigmented and nonpigmented nanoflagellates were more numerous in the epilimnion. The control of the BHP due to viral lysis (determined by examination of viral-containing bacteria using a transmission electron microscope) was significantly higher in the meta- (range = 6.0-33.7%, mean = 15.6%) than in the epilimnion (3.5-10.3%, 6.4%). The same was for the losses of BHP from the potential predation by nanoflagellates which ranged from 0.5 to 115.4% (mean = 38.7%) in the epilimnion, and from 0.7 to 97.5% (mean = 66.7%) in the metalimnion. Finally, estimated viral mediated mortality rates from the percentage of visibly infected cells and potential nanoflagellate grazing rates based on assumed clearance rates suggest that flagellates consumed a larger proportion of bacterial production than was lost to viral lysis.

In this study, we compared different methods—including transmission electron microscopy—and various nucleic acid labeling methods in which we used the fluorochromes 4′,6′-diamidino-2-phenylindole (DAPI), 4-[3-methyl-2,3-dihydro-(benzo-1,3-oxazole)-2-methylmethyledene]-1-(3′-trimethyl ammoniumpropyl)-quinilinium diioide (YOPRO-1), and SYBR Green I, which can be detected by epifluorescence microscopy (EM), for counting viruses in samples obtained from freshwater ecosystems whose trophic status varied and from a culture of T7 phages. From a quantitative and qualitative viewpoint, our results showed that the greatest efficiency for all ecosystems was obtained when we used the EM counting protocol in which YOPRO-1 was the label, as this fluorochrome exhibited strong and very stable fluorescence. A modification of the original protocol in which YOPRO-1 was used is recommended, because this modification makes the protocol faster and allows it to be used for routine analysis of fixed samples. Because SYBR Green I fades very quickly, the use of this fluorochrome is not recommended for systems in which the viral content is very high (>10 8 particles/ml), such as treated domestic sewage effluents. Experiments in which we used DNase and RNase revealed that the number of viruses determined by EM was slightly overestimated (by approximately 15%) because of interference caused by the presence of free nucleic acids.

Coastal ecosystems are frequently submitted to anthropogenic pressure but little is known about how the dynamics of aquatic communities can be altered. The impact of urban and industrial discharges on microbial plankton was studied in Hann Bay near Dakar (Senegal) on the Atlantic Ocean. Spatial patterns were studied using three transects, with a total of 20 stations, during two periods in May and November (before and after the seasonal upwelling), revealing a clear contrast between near shore stations and the intermediate and seaward stations. In November, phytoplankton were associated with dissolved nutrient availability (e.g. with nitrate, r = 0.76) whereas in May, phytoplankton were more correlated with microbial variables (e.g. with heterotrophic nanoflagellates, r = 0.63). Most samples (40) failed to meet the quality levels for the faecal indicator bacteria (FIB) defined by the European Union bathing water quality directive. The topography plays a major role in water circulation explaining the presence of FIB at the seaward stations. The high prevalence of FIB during the two periods suggests chronic pollution and a potential risk to recreational swimmers and fish consumers in Hann Bay. Thus, as demonstrated in various temperate systems, the decline of water quality constitutes a serious problem in many West African countries.

Coastal ecosystems are frequently submitted to anthropogenic pressure but little is known about how the dynamics of aquatic communities can be altered. The impact of urban and industrial discharges on microbial plankton was studied in Hann Bay near Dakar (Senegal) on the Atlantic Ocean. Spatial patterns were studied using three transects, with a total of 20 stations, during two periods in May and November (before and after the seasonal upwelling), revealing a clear contrast between near shore stations and the intermediate and seaward stations. In November, phytoplankton were associated with dissolved nutrient availability (e.g. with nitrate, r = 0.76) whereas in May, phytoplankton were more correlated with microbial variables (e.g. with heterotrophic nanoflagellates, r = 0.63). Most samples (40) failed to meet the quality levels for the faecal indicator bacteria (FIB) defined by the European Union bathing water quality directive. The topography plays a major role in water circulation explaining the presence of FIB at the seaward stations. The high prevalence of FIB during the two periods suggests chronic pollution and a potential risk to recreational swimmers and fish consumers in Hann Bay. Thus, as demonstrated in various temperate systems, the decline of water quality constitutes a serious problem in many West African countries.