2020 |
Chiarello, M., et al. "Exceptional but vulnerable microbial diversity in coral reef animal surface microbiomes." Proc. R. Soc. B-Biol. Sci.. 287.1927 (2020): 20200642.
Résumé: 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.
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2019 |
Villeger, S., et al. "Interspecific differences in the effect of fish on marine microbial plankton." Aquatic Microbial Ecology. 82.3 (2019): 289–298.
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2018 |
Bettarel, Y., et al. "Hordes of Phages in the Gut of the Tilapia Sarotherodon melanotheron." Sci Rep. 8 (2018): 11311.
Résumé: Preliminary studies conducted on the human gastro-intestinal tract have revealed that enteric viral communities play a preponderant role in microbial homeostatis. However to date, such communities have never been investigated in the fish gut. Herein, we examined the main ecological traits of viruses in the digestive tract of a euryhaline fish, the tilapia Sarotherodon melanotheron. Individuals were collected at 8 different sites in Senegal covering a salinity gradient from 3 to 104 parts per thousand, and showing large disparities in their organic pollutant concentrations. Results showed that the gut of S. melanotheron is home to a highly abundant viral community (0.2-10.7 x 10(9) viruses ml(-1)), distinct from the surrounding water, and essentially composed of phages of which a substantial proportion is temperate (the fraction of lysogenized cells-FLC ranging from 8.1 to 33.0%). Also, a positive and significant correlation was detected between FLC and the concentrations of polycyclic aromatic hydrocarbon in sediment, while no clear relationships were found between salinity and any of the microbial parameters considered. Finally, our data suggest that virus-bacteria interactions within the fish intestine are likely sensitive to the presence of particular xenobiotics, which may compromise the balance in the gut microbiota, and subsequently affect the health of their host.
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Bettarel, Y., et al. "Corallivory and the microbial debacle in two branching scleractinians." Isme J.. 12.4 (2018): 1109–1126.
Résumé: The grazing activity by specific marine organisms represents a growing threat to the survival of many scleractinian species. For example, the recent proliferation of the corallivorous gastropod Drupella now constitutes a critical case in all South-East Asian waters. If the damaging effects caused by this marine snail on coral polyps are relatively well known, the indirect incidence of predation on coral microbial associates is still obscure and might also potentially impair coral health. In this study, we compared the main ecological traits of coral-associated bacterial and viral communities living in the mucus layer of Acropora formosa and Acropora millepora, of healthy and predated individuals (i.e., colonized by Drupella rugosa), in the Bay of Van Phong (Vietnam). Our results show a substantial impact of the gastropod on a variety of microbiological markers. Colonized corals harbored much more abundant and active epibiotic bacteria whose community composition shifted toward more pathogenic taxa (belonging to the Vibrionales, Clostridiales, Campylobacterales, and Alteromonadales orders), together with their specific phages. Viral epibionts were also greatly influenced by Drupella corallivory with spectacular modifications in their concentrations, life strategies, genotype richness, and diversity. Novel and abundant circular Rep-encoding ssDNA viruses (CRESS-DNA viruses) were detected and characterized in grazed corals and we propose that their occurrence may serve as indicator of the coral health status. Finally, our results reveal that corallivory can cause severe dysbiosis by altering virus-bacteria interactions in the mucus layer, and ultimately favoring the development of local opportunistic infections.
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Chiarello, M., et al. "Skin microbiome of coral reef fish is highly variable and driven by host phylogeny and diet." Microbiome. 6 (2018): 147.
Résumé: Background: The surface of marine animals is covered by abundant and diversified microbial communities, which have major roles for the health of their host While such microbiomes have been deeply examined in marine invertebrates such as corals and sponges, the microbiomes living on marine vertebrates have received less attention. Specifically, the diversity of these microbiomes, their variability among species, and their drivers are still mostly unknown, especially among the fish species living on coral reefs that contribute to key ecosystem services while they are increasingly affected by human activities. Here, we investigated these knowledge gaps analyzing the skin microbiome of 138 fish individuals belonging to 44 coral reef fish species living in the same area. Results: Prokaryotic communities living on the skin of coral reef fishes are highly diverse, with on average more than 600 OTUs per fish, and differ from planktonic microbes. Skin microbiomes varied between fish individual and species, and interspecific differences were slightly coupled to the phylogenetic affiliation of the host and its ecological traits. Conclusions: These results highlight that coral reef biodiversity is greater than previously appreciated, since the high diversity of macro-organisms supports a highly diversified microbial community. This suggest that beyond the loss of coral reefs-associated macroscopic species, anthropic activities on coral reefs could also lead to a loss of still unexplored host-associated microbial diversity, which urgently needs to be assessed.
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Jacquemot, L., et al. "Therapeutic potential of a new jumbo phage that infects Vibrio coralliilyticus, a widespread coral pathogen." Front. Microbiol.. 9 (2018): 2501.
Résumé: Biological control using bacteriophages is a promising approach for mitigating the devastating effects of coral diseases. Several phages that infect Vibrio coralliilyticus, a widespread coral pathogen, have been isolated, suggesting that this bacterium is permissive to viral infection and is, therefore, a suitable candidate for treatment by phage therapy. In this study, we combined functional and genomic approaches to evaluate the therapeutic potential of BONAISHI, a novel V. coralliilyticus phage, which was isolated from the coral reef in Van Phong Bay (Vietnam). BONAISHI appears to be strictly lytic for several pathogenic strains of V. coralliilyticus and remains infectious over a broad range of environmental conditions. This candidate has an unusually large dsDNA genome (303 kb), with no genes that encode known toxins or implicated in lysogeny control. We identified several proteins involved in host lysis, which may offer an interesting alternative to the use of whole bacteriophages for controlling V. coralliilyticus. A preliminary therapy test showed that adding BONAISHI to an infected culture of Symbiodinium sp. cells reduced the impact of V. coralliilyticus on Symbiodinium sp. photosynthetic activity. This study showed that BONAISHI is able to mitigate V. coralliilyticus infections, making it a good candidate for phage therapy for coral disease.
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2017 |
Chiarello, M., et al. "Captive bottlenose dolphins and killer whales harbor a species-specific skin microbiota that varies among individuals." Scientific Reports. 7.1 (2017): 15269.
Résumé: Marine animals surfaces host diverse microbial communities, which play major roles for host’s health. Most inventories of marine animal surface microbiota have focused on corals and fishes, while cetaceans remain overlooked. The few studies focused on wild cetaceans, making difficult to distinguish intrinsic inter- and/or intraspecific variability in skin microbiota from environmental effects. We used high-throughput sequencing to assess the skin microbiota from 4 body zones of 8 bottlenose dolphins (Tursiops truncatus) and killer whales (Orcinus orca), housed in captivity (Marineland park, France). Overall, cetacean skin microbiota is more diverse than planktonic communities and is dominated by different phylogenetic lineages and functions. In addition, the two cetacean species host different skin microbiotas. Within each species, variability was higher between individuals than between body parts, suggesting a high individuality of cetacean skin microbiota. Overall, the skin microbiota of the assessed cetaceans related more to the humpback whale and fishes’ than to microbiotas of terrestrial mammals.
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Escalas, A., et al. "Functional diversity and redundancy across fish gut, sediment and water bacterial communities." Environ. Microbiol.. 19.8 (2017): 3268–3282.
Résumé: This article explores the functional diversity and redundancy in a bacterial metacommunity constituted of three habitats (sediment, water column and fish gut) in a coastal lagoon under anthropogenic pressure. Comprehensive functional gene arrays covering a wide range of ecological processes and stress resistance genes to estimate the functional potential of bacterial communities were used. Then, diversity partitioning was used to characterize functional diversity and redundancy within (), between () and across () habitats. It was showed that all local communities exhibit a highly diversified potential for the realization of key ecological processes and resistance to various environmental conditions, supporting the growing evidence that macro-organisms microbiomes harbour a high functional potential and are integral components of functional gene dynamics in aquatic bacterial metacommunities. Several levels of functional redundancy at different scales of the bacterial metacommunity were observed (within local communities, within habitats and at the metacommunity level). The results suggested a high potential for the realization of spatial ecological insurance within this ecosystem, that is, the functional compensation among microorganisms for the realization and maintenance of key ecological processes, within and across habitats. Finally, the role of macro-organisms as dispersal vectors of microbes and their potential influence on marine metacommunity dynamics were discussed.
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Fouilland, E., et al. "Significant Change in Marine Plankton Structure and Carbon Production After the Addition of River Water in a Mesocosm Experiment." Microbial Ecology. 74.2 (2017): 289–301.
Résumé: Rivers are known to be major contributors to eutrophication in marine coastal waters, but little is known on the short-term impact of freshwater surges on the structure and functioning of the marine plankton community. The effect of adding river water, reducing the salinity by 15 and 30%, on an autumn plankton community in a Mediterranean coastal lagoon (Thau Lagoon, France) was determined during a 6-day mesocosm experiment. Adding river water brought not only nutrients but also chlorophyceans that did not survive in the brackish mesocosm waters. The addition of water led to initial increases (days 1-2) in bacterial production as well as increases in the abundances of bacterioplankton and picoeukaryotes. After day 3, the increases were more significant for diatoms and dinoflagellates that were already present in the Thau Lagoon water (mainly Pseudo-nitzschia spp. group delicatissima and Prorocentrum triestinum) and other larger organisms (tintinnids, rotifers). At the same time, the abundances of bacterioplankton, cyanobacteria, and picoeukaryote fell, some nutrients (NH4 (+), SiO4 (3-)) returned to pre-input levels, and the plankton structure moved from a trophic food web based on secondary production to the accumulation of primary producers in the mesocosms with added river water. Our results also show that, after freshwater inputs, there is rapid emergence of plankton species that are potentially harmful to living organisms. This suggests that flash flood events may lead to sanitary issues, other than pathogens, in exploited marine areas.
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Troussellier, M., et al. "Sustaining Rare Marine Microorganisms: Macroorganisms As Repositories and Dispersal Agents of Microbial Diversity." Frontiers in Microbiology. 8 (2017): 947.
Résumé: Recent analyses revealed that most of the biodiversity observed in marine microbial communities is represented by organisms with low abundance but, nonetheless essential for ecosystem dynamics and processes across both temporal and spatial scales. Surprisingly, few studies have considered the effect of macroorganism-microbe interactions on the ecology and distribution dynamics of rare microbial taxa. In this review, we synthesize several lines of evidence that these relationships cannot be neglected any longer. First, we provide empirical support that the microbiota of macroorganisms represents a significant part of marine bacterial biodiversity and that host-microbe interactions benefit to certain microbial populations which are part of the rare biosphere (i.e., opportunistic copiotrophic organisms). Second, we reveal the major role that macroorganisms may have on the dispersal and the geographic distribution of microbes. Third, we introduce an innovative and integrated view of the interactions between microbes and macroorganisms, namely sustaining the rares, which suggests that macroorganisms favor the maintenance of marine microbial diversity and are involved in the regulation of its richness and dynamics. Finally, we show how this hypothesis complements existing theories in microbial ecology and offers new perspectives about the importance of macroorganisms for the microbial biosphere, particularly the rare members.
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2016 |
Bettarel, Yvan, et al. "Flow cytometric enumeration of bacterial in the coral surface mucus layer." Journal of Microbiological Methods. 128 (2016): 16–19.
Résumé: Abstract
The direct counts of bacteria inhabiting coral mucus were performed by flow cytometry testing four fluorescent dyes (SYBR®Green I, HCS, TOPRO®3, SYTO®62) with three different scleractinian species. Results obtained with SYTO62 were the most reliable based on the comparison with standardized epifluorescence counts and the resolution of cytograms.
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Gounand, I., et al. "Size evolution in microorganisms masks trade-offs predicted by the growth rate hypothesis." Proc. R. Soc. B-Biol. Sci.. 283.1845 (2016): 20162272.
Résumé: Adaptation to local resource availability depends on responses in growth rate and nutrient acquisition. The growth rate hypothesis (GRH) suggests that growing fast should impair competitive abilities for phosphorus and nitrogen due to high demand for biosynthesis. However, in microorganisms, size influences both growth and uptake rates, which may mask trade-offs and instead generate a positive relationship between these traits (size hypothesis, SH). Here, we evolved a gradient of maximum growth rate (mu(max)) from a single bacterium ancestor to test the relationship among mu(max), competitive ability for nutrients and cell size, while controlling for evolutionary history. We found a strong positive correlation between mu(max) and competitive ability for phosphorus, associated with a trade-off between mu(max) and cell size: strains selected for high mu(max) were smaller and better competitors for phosphorus. Our results strongly support the SH, while the trade-offs expected under GRH were not apparent. Beyond plasticity, unicellular populations can respond rapidly to selection pressure through joint evolution of their size and maximum growth rate. Our study stresses that physiological links between these traits tightly shape the evolution of competitive strategies.
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Roux, S., et al. "Analysis of metagenomic data reveals common features of halophilic viral communities across continents." Environ Microbiol. 18.3 (2016): 889–903.
Résumé: 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.
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2015 |
Bettarel, Y., et al. "The versatile nature of coral-associated viruses." Environ Microbiol. 17.10 (2015): 3433–3439.
Résumé: 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.
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Bouvy, M., et al. "Importance of predation and viral lysis for bacterial mortality in a tropical western Indian coral-reef ecosystem (Toliara, Madagascar)." Mar. Freshwater Res. (2015).
Résumé: 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.
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Brauer, V. S., et al. "Competition and facilitation between the marine nitrogen-fixing cyanobacteriunn Cyanothece and its associated bacterial community." Frontiers in Microbiology. 5 (2015).
Résumé: N-2-fixing cyanobacteria represent a major source of new nitrogen and carbon for marine microbial communities, but little is known about their ecological interactions with associated microbiota. In this study we investigated the interactions between the unicellular N-2-fixing cyanobacterium Cyanothece sp. Miami BG043511 and its associated free-living chemotrophic bacteria at different concentrations of nitrate and dissolved organic carbon and different temperatures. High temperature strongly stimulated the growth of Cyanothece, but had less effect on the growth and community composition of the chemotrophic bacteria. Conversely, nitrate and carbon addition did not significantly increase the abundance of Cyanothece, but strongly affected the abundance and species composition of the associated chemotrophic bacteria. In nitrate-free medium the associated bacterial community was co-dominated by the putative diazotroph Mesorhizobium and the putative aerobic anoxygenic phototroph Erythrobacter and after addition of organic carbon also by the Flavobacterium Muricauda. Addition of nitrate shifted the composition toward co-dominance by Erythrobacter and the Gammaproteobacterium Marinobacter. Our results indicate that Cyanothece modified the species composition of its associated bacteria through a combination of competition and facilitation. Furthermore, within the bacterial community, niche differentiation appeared to play an important role, contributing to the coexistence of a variety of different functional groups. An important implication of these findings is that changes in nitrogen and carbon availability due to, e.g., eutrophication and climate change are likely to have a major impact on the species composition of the bacterial community associated with N-2-fixing cyanobacteria.
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Chiarello, M., et al. "High diversity of skin-associated bacterial communities of marine fishes is promoted by their high variability among body parts, individuals and species." FEMS Microbiology Ecology (2015): fiv061.
Résumé: 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).
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De Wit, R., et al. "Viruses Occur Incorporated in Biogenic High-Mg Calcite from Hypersaline Microbial Mats." PLoS ONE. 10.6 (2015): e0130552.
Résumé: Using three different microscopy techniques (epifluorescence, electronic and atomic force microscopy), we showed that high-Mg calcite grains in calcifying microbial mats from the hypersaline lake “La Salada de Chiprana”, Spain, contain viruses with a diameter of 50–80 nm. Energy-dispersive X-ray spectrometer analysis revealed that they contain nitrogen and phosphorus in a molar ratio of ~9, which is typical for viruses. Nucleic acid staining revealed that they contain DNA or RNA. As characteristic for hypersaline environments, the concentrations of free and attached viruses were high (>1010 viruses per g of mat). In addition, we showed that acid treatment (dissolution of calcite) resulted in release of viruses into suspension and estimated that there were ~15 × 109 viruses per g of calcite. We suggest that virus-mineral interactions are one of the possible ways for the formation of nano-sized structures often described as “nanobacteria” and that viruses may play a role in initiating calcification.
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Mostajir, B., et al. "Microbial food web structural and functional responses to oyster and fish as top predators." Mar Ecol Prog Ser. 535 (2015): 11–27.
Résumé: ABSTRACT: The impact of fish and oysters on components of the pelagic microbial food web (MFW) was studied in a 10 d mesocosm experiment using Mediterranean coastal waters. Two mesocosms contained natural water only , 2 contained natural water with Crassostrea gigas (Oyster), and 2 contained natural water with Atherina spp. (Fish). Abundances and biomasses of microorganisms (viruses, bacteria, phytoplankton, heterotrophic flagellates, and ciliates) were measured to estimate their contribution to the total microbial carbon biomass. Two MFW indices, the microbial autotroph:heterotroph C biomass ratio (A:H) structural index and the gross primary production:respiration ratio (GPP:R) functional index, were defined. In the Fish mesocosms, selective predation on zooplankton led to a trophic cascade with 51% higher phytoplankton C biomass and consequently higher A:H and GPP:R than in the Controls. By the end of the experiment, the Oyster mesocosms had a bacterial C biomass 87% higher and phytoplankton C biomass 93% lower than the Controls, giving significantly lower A:H and GPP:R (<1). Overall, the results showed that wild zooplanktivorous fish had a cascading trophic effect, making the MFW more autotrophic (both indices gt;1), whereas oyster activities made the MFW more heterotrophic (both indices lt;1). These MFW indices can therefore be used to assess the impact of multiple local and global forcing factors on the MFW. The results presented here also have implications for sustainable management of coastal environments, suggesting that intense cultivation of filter feeders can be coupled with management to encourage wild local zooplanktivorous fishes to maintain a more resilient system and preserve the equilibrium of the MFW.
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Nguyen-Kim, H., et al. "Coral Mucus Is a Hot Spot for Viral Infections." Appl. Environ. Microbiol.. 81.17 (2015): 5773–5783.
Résumé: 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.
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Nguyen-Kim, H., et al. "Viral and Bacterial Epibionts in Thermally-Stressed Corals." Journal of Marine Science and Engineering. 3.4 (2015): 1272–1286.
Résumé: The periodic rise in seawater temperature is one of the main environmental determinants of coral bleaching. However, the direct incidence of these episodic thermal anomalies on coral-associated microbiota and their subsequent effects on coral health are still not completely understood. In this study, we investigated the dynamics of three main microbial communities of the coral holobiont (e.g., Symbiodinium, bacteria and viruses), during an experimental thermal stress (+4 °C) conducted on the scleractinian Fungia repanda. The heat-treatment induced coral bleaching after 11 days and resulted in a final elevation of ca. 9, 130 and 250-fold in the abundance of mucosal viruses, bacteria, and Symbiodinium, respectively. On the contrary, the proportion of actively respiring bacterial cells declined by 95% in heat-stressed corals. The community composition of epibiotic bacteria in healthy corals also greatly differed from bleached ones, which also exhibited much higher production rates of viral epibionts. Overall, our results suggest that the shift in temperature induced a series of microbial changes, including the expulsion and transfer of Symbiodinium cells from the coral polyps to the mucus, the collapse of the physiological state of the native bacterial associates, a substantial alteration in their community structure, and accompanied by the development of a cortege of highly active virulent phages. Finally, this study provides new insights into the environmentally-driven microbial and viral processes responsible for the dislocation of the coral holobiont.
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Pham, T. T., et al. "Coral-associated viruses and bacteria in the Ha Long Bay, Vietnam." Aquat Microb Ecol. 76.2 (2015): 149–161.
Résumé: ABSTRACT: Viruses inhabiting the surface mucus layer of scleractinian corals have received little ecological attention so far. Yet they have recently been shown to be highly abundant and could even play a pivotal role in coral health. A fundamental aspect that remains unresolved is whether their abundance and diversity change with the trophic state of their environment. The present study examined the variability in the abundance of viral and bacterial epibionts on 13 coral species collected from 2 different sites in the Ha Long Bay, Vietnam: one station heavily affected by anthropogenic activity (Cat Ba Island) and one protected offshore station (Long Chau Island). In general, viral abundance was significantly higher in coral mucus (mean = 10.6 ± 2.0 × 107 virus-like particles ml–1) than in the surrounding water (5.2 ± 1.3 × 107 virus-like particles ml–1). Concomitantly, the abundance and community diversity (inferred from phylogenetic and morphological analyses) of their mucosal bacterial hosts strongly differed from their planktonic counterparts. Surprisingly, despite large differences in water quality and nutrient concentrations between Cat Ba and Long Chau, there were no significant differences in the concentrations of epibiotic viruses and bacteria measured in the only 2 coral species (i.e. Pavona decussata and Lobophyllia flabelliformis) that were common at both sites. The ability of corals to shed bacteria to compensate for their fast growth in nutrient-rich mucus is questioned here.
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2014 |
Chu, T. V., et al. "Nutrient ratios and the complex structure of phytoplankton communities in a highly turbid estuary of Southeast Asia." Environ Monit Assess. 186.12 (2014): 8555–8572.
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Doan, T. T., et al. "Influence of buffalo manure, compost, vermicompost and biochar amendments on bacterial and viral communities in soil and adjacent aquatic systems." Applied Soil Ecology. 73 (2014): 78–86.
Résumé: 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.
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Fouilland, E., et al. "Bacterial carbon dependence on freshly produced phytoplankton exudates under different nutrient availability and grazing pressure conditions in coastal marine waters." FEMS microbiology ecology. 87.3 (2014): 757–769.
Résumé: The effects of grazing pressure and inorganic nutrient availability on the direct carbon transfer from freshly produced phytoplankton exudates to heterotrophic bacteria biomass production were studied in Mediterranean coastal waters. The short-term incorporation of (1)(3)C (H(1)(3)CO(3)) in phytoplankton and bacterial lipid biomarkers was measured as well as the total bacterial carbon production (BP), viral lysis and the microbial community structure under three experimental conditions: (1) High inorganic Nutrient and High Grazing (HN + HG), (2) High inorganic Nutrient and Low Grazing (HN + LG) and (3) under natural in situ conditions with Low inorganic Nutrient and High Grazing (LN + HG) during spring. Under phytoplankton bloom conditions (HN + LG), the bacterial use of freshly produced phytoplankton exudates as a source of carbon, estimated from (1)(3)C enrichment of bacterial lipids, contributed more than half of the total bacterial production. However, under conditions of high grazing pressure on phytoplankton with or without the addition of inorganic nutrients (HN + HG and LN + HG), the (1)(3)C enrichment of bacterial lipids was low compared with the high total bacterial production. BP therefore seems to depend mainly on freshly produced phytoplankton exudates during the early phase of phytoplankton bloom period. However, BP seems mainly relying on recycled carbon from viral lysis and predators under high grazing pressure.
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Nguyen-Kim, H., et al. "High occurrence of viruses in the mucus layer of scleractinian corals." Environmental Microbiology Reports. 6.6 (2014): 675–682.
Résumé: Viruses attract increasing interest from environmental microbiologists seeking to understand their function and role in coral health. However, little is known about their main ecological traits within the coral holobiont. In this study, a quantitative and qualitative characterization of viral and bacterial communities was conducted on the mucus of seven different coral species of the Van Phong Bay (Vietnam). On average, the concentrations of viruses and bacteria were, respectively, 17- and twofold higher in the mucus than in the surrounding water. The examination of bacterial community composition also showed remarkable differences between mucus and water samples. The percentage of active respiring cells was nearly threefold higher in mucus (m=24.8%) than in water (m=8.6%). Interestingly, a positive and highly significant correlation was observed between the proportion of active cells and viral abundance in the mucus, suggesting that the metabolism of the bacterial associates is probably a strong determinant of the distribution of viruses within the coral holobiont. Overall, coral mucus, given its unique physicochemical characteristics and sticking properties, can be regarded as a highly selective biotope for abundant, diversified and specialized symbiotic microbial and viral organisms.
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2013 |
Amossé, J., et al. "The flows of nitrogen, bacteria and viruses from the soil to water compartments are influenced by earthworm activity and organic fertilization (compost vs. vermicompost)." Soil Biology & Biochemistry. 66 (2013): 197–203.
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Combe, M., et al. "Freshwater prokaryote and virus communities can adapt to a controlled increase in salinity through changes in their structure and interactions." Estuarine Coastal and Shelf Science. 133 (2013): 58–66.
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Escalas, A., et al. "A unifying quantitative framework for exploring the multiple facets of microbial biodiversity across diverse scales." Environmental microbiology. 15.10 (2013): 2642–2657.
Résumé: Recent developments of molecular tools have revolutionized our knowledge of microbial biodiversity by allowing detailed exploration of its different facets and generating unprecedented amount of data. One key issue with such large datasets is the development of diversity measures that cope with different data outputs and allow comparison of biodiversity across different scales. Diversity has indeed three components: local (alpha), regional (gamma) and the overall difference between local communities (beta). Current measures of microbial diversity, derived from several approaches, provide complementary but different views. They only capture the beta component of diversity, compare communities in a pairwise way, consider all species as equivalent or lack a mathematically explicit relationship among the alpha, beta and gamma components. We propose a unified quantitative framework based on the Rao quadratic entropy, to obtain an additive decomposition of diversity (gamma = alpha + beta), so the three components can be compared, and that integrate the relationship (phylogenetic or functional) among Microbial Diversity Units that compose a microbial community. We show how this framework is adapted to all types of molecular data, and we highlight crucial issues in microbial ecology that would benefit from this framework and propose ready-to-use R-functions to easily set up our approach.
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Maurice, C. F., et al. "Linking the lytic and lysogenic bacteriophage cycles to environmental conditions, host physiology and their variability in coastal lagoons." Environmental microbiology. 15.9 (2013): 2463–2475.
Résumé: Changes in environmental conditions and prokaryote physiology can strongly affect the dynamics of both the lysogenic and lytic bacteriophage replication cycles in aquatic systems. However, it remains unclear whether it is the nature, amplitude or frequency of these changes that alter the phage replication cycles. We performed an annual survey of three Mediterranean lagoons with contrasting levels of chlorophyll a concentration and salinity to explore how these cues and their variability influence either replication cycle. The lytic cycle was always detected and showed seasonal patterns, whereas the lysogenic cycle was often undetected and highly variable. The lytic cycle was influenced by environmental and prokaryotic physiological cues, increasing with concentrations of dissolved organic carbon, chlorophyll a, and the proportion of respiring cells, and decreasing with the proportion of damaged cells. In contrast, lysogeny was not explained by the magnitude of any environmental or physiological parameter, but increased with the amplitude of change in prokaryote physiology. Our study suggests that both cycles are regulated by distinct factors: the lytic cycle is dependent on environmental parameters and host physiology, while lysogeny is dependent on the variability of prokaryote physiology. This could lead to the contrasting patterns observed between both cycles in aquatic systems.
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2012 |
Bettarel, Y., et al. "Observation of virus-like particles in thin sections of the bleaching scleractinian coral Acropora cytherea." Journal of the Marine Biological Association of the United Kingdom. FirstView (2012): 1–4.
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Bouvier, T., et al. "Contrasted Effects of Diversity and Immigration on Ecological Insurance in Marine Bacterioplankton Communities." PLoS One. 7.6 (2012).
Résumé: The ecological insurance hypothesis predicts a positive effect of species richness on ecosystem functioning in a variable environment. This effect stems from temporal and spatial complementarity among species within metacommunities coupled with optimal levels of dispersal. Despite its importance in the context of global change by human activities, empirical evidence for ecological insurance remains scarce and controversial. Here we use natural aquatic bacterial communities to explore some of the predictions of the spatial and temporal aspects of the ecological insurance hypothesis. Addressing ecological insurance with bacterioplankton is of strong relevance given their central role in fundamental ecosystem processes. Our experimental set up consisted of water and bacterioplankton communities from two contrasting coastal lagoons. In order to mimic environmental fluctuations, the bacterioplankton community from one lagoon was successively transferred between tanks containing water from each of the two lagoons. We manipulated initial bacterial diversity for experimental communities and immigration during the experiment. We found that the abundance and production of bacterioplankton communities was higher and more stable (lower temporal variance) for treatments with high initial bacterial diversity. Immigration was only marginally beneficial to bacterial communities, probably because microbial communities operate at different time scales compared to the frequency of perturbation selected in this study, and of their intrinsic high physiologic plasticity. Such local “physiological insurance” may have a strong significance for the maintenance of bacterial abundance and production in the face of environmental perturbations.
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Domaizon, I., et al. "Short-term responses of unicellular planktonic eukaryotes to increases in temperature and UVB radiation." BMC Microbiology. 12.1 (2012).
Résumé: 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 (<6mum; from a coastal Mediterranean lagoon) to a warming treatment (+3degreesC) and UVB radiation increases (+20%) at two different nutrient levels. Interestingly, the increase in temperature resulted in higher pigmented eukaryotes abundances and in community structure changes clearly illustrated by molecular analyses. For most of the phylogenetic groups, some rearrangements occurred at the OTUs level even when their relative proportion (microscope counting) did not change significantly. Temperature explained almost 20% of the total variance of the small eukaryote community structure (while UVB explained only 8.4%). However, complex cumulative effects were detected. Some antagonistic or non additive effects were detected between temperature and nutrients, especially for Dinophyceae and Cryptophyceae.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.
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Leruste, A., T. Bouvier, and Y. Bettarel. "Enumerating Viruses in Coral Mucus." Applied and Environmental Microbiology. 78.17 (2012): 6377–6379.
Résumé: 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.
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Mari, X., et al. "Aggregation dynamics along a salinity gradient in the Bach Dang estuary, North Vietnam." Estuarine Coastal and Shelf Science. 96 (2012): 151–158.
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Mouchet, M. A., et al. "Genetic difference but functional similarity among fish gut bacterial communities through molecular and biochemical fingerprints." FEMS Microbiology Ecology. 79.3 (2012): 568–580.
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2011 |
Bettarel, Y., et al. "Viral distribution and life strategies in the Bach Dang Estuary, Vietnam." Microbial Ecology. 62.1 (2011): 143–154.
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Bettarel, Y., et al. "Ecological traits of planktonic viruses and prokaryotes along a full-salinity gradient." FEMS Microbiology Ecology. 76.2 (2011): 360–372.
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Bouvier, T., and C. F. Maurice. "A single-cell analysis of virioplankton adsorption, infection, and intracellular abundance in different bacterioplankton physiologic categories." Microbial Ecology. 62.3 (2011): 669–678.
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Bouvy, M., et al. "Trophic interactions between viruses, bacteria and nanoflagellates under various nutrient conditions and simulated climate change." Environmental microbiology. 13.7 (2011): 1842–1857.
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Condon, R. H., et al. "Jellyfish blooms result in a major microbial respiratory sink of carbon in marine systems." Proceedings of the National Academy of Sciences of the United States of America. 108.25 (2011): 10225–10230.
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del Giorgio, P. A., et al. "Coherent patterns in bacterial growth, growth efficiency, and leucine metabolism along a northeastern Pacific inshore-offshore transect." Limnology and Oceanography. 56.1 (2011): 1–16.
Résumé: We investigated the patterns in bacterial growth, production, respiration, growth efficiency (BGE), and bacterial leucine respiration and C-to-leucine yield (i.e., conversion factor [CF]) along a transect off the coast of Oregon. Plankton respiration along the transect averaged 1.15 +/- 0.16 mu g C L-1 h(-1), peaking in the coastal upwelling region. The respiration in the filtered fraction, which was dominated by bacterial biomass, accounted for 79% of the total respiration. The different approaches that we used converged to an average BGE of 13% +/- 1%, with peaks of over 20% in the more productive coastal areas and values declining to below 5% toward the oligotrophic gyre waters. There was overall coherence between the various aspects of bacterial C metabolism: communities with low BGE also tended to have low growth rates and high leucine-to-thymidine incorporation ratios. The patterns in BGE were mirrored at the single compound level, and in the most oligotrophic sites, bacteria tended to quickly respire a large fraction (20-75%) of the leucine that was taken up and had the lowest C-to-leucine yield, suggesting that the patterns in bulk BGE and growth also apply to individual substrates. Bacterial growth was a function of both C consumption and BGE; these two aspects of bacterial C metabolism do not necessarily covary, and they are regulated differently. The patterns in C consumption, growth, BGE, and leucine metabolism all reflect the basic physiological response of bacteria to energy limitation due to high maintenance costs associated with life in oligotrophy.
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Gravel, D., et al. "Experimental niche evolution alters the strength of the diversity-productivity relationship." Nature. 469.7328 (2011): 89–U1601.
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Maurice, C. F., et al. "Disentangling the relative influence of bacterioplankton phylogeny and metabolism on lysogeny in reservoirs and lagoons." ISME Journal. 5.5 (2011): 831–842.
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Rochelle Newall, E., et al. "Phytoplankton distribution and productivity in a highly turbid, tropical coastal system (Bach Dang Estuary, Vietnam)." Marine Pollution Bulletin. 62.11 (2011): 2317–2329.
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Vidussi, F., et al. "Effects of experimental warming and increased ultraviolet B radiation on the Mediterranean plankton food web." Limnology and Oceanography. 56.1 (2011): 206–218.
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2010 |
Maurice, C. F., et al. "Seasonal variations of phage life strategies and bacterial physiological states in three northern temperate lakes." Environmental microbiology. 12.3 (2010): 628–641.
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Winter, C., et al. "Trade-offs between competition and defense specialists among unicellular planktonic organisms : the “Killing the Winner” hypothesis revisited." Microbiology and Molecular Biology Reviews. 74.1 (2010): 42–57.
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2009 |
Bettarel, Y., T. Bouvier, and M. Bouvy. "Viral persistence in water as evaluated from a tropical/temperate cross-incubation." Journal of Plankton Research. 31.8 (2009): 909–916.
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2008 |
Bettarel, Y., et al. "Virioplankton distribution and activity in a tropical eutrophicated bay." Estuarine Coastal and Shelf Science. 80.3 (2008): 425–429.
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Venail, P. A., et al. "Diversity and productivity peak at intermediate dispersal rate in evolving metacommunities." Nature. 452.7184 (2008): 210–257.
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