Publications by authors named "Yvan Bettarel"

33 Publications

Microbial Shift in the Enteric Bacteriome of Coral Reef Fish Following Climate-Driven Regime Shifts.

Microorganisms 2021 Aug 11;9(8). Epub 2021 Aug 11.

UMR MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France.

Replacement of coral by macroalgae in post-disturbance reefs, also called a "coral-macroalgal regime shift", is increasing in response to climate-driven ocean warming. Such ecosystem change is known to impact planktonic and benthic reef microbial communities but few studies have examined the effect on animal microbiota. In order to understand the consequence of coral-macroalgal shifts on the coral reef fish enteric bacteriome, we used a metabarcoding approach to examine the gut bacteriomes of 99 individual fish representing 36 species collected on reefs of the Inner Seychelles islands that, following bleaching, had either recovered to coral domination, or shifted to macroalgae. While the coral-macroalgal shift did not influence the diversity, richness or variability of fish gut bacteriomes, we observed a significant effect on the composition (R2 = 0.02; = 0.001), especially in herbivorous fishes (R2 = 0.07; = 0.001). This change is accompanied by a significant increase in the proportion of fermentative bacteria (, , ) and associated metabolisms (carbohydrates metabolism, DNA replication, and nitrogen metabolism) in relation to the strong turnover of and fishes. Predominance of fermentative metabolisms in fish found on macroalgal dominated reefs indicates that regime shifts not only affect the taxonomic composition of fish bacteriomes, but also have the potential to affect ecosystem functioning through microbial functions.
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http://dx.doi.org/10.3390/microorganisms9081711DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8398123PMC
August 2021

Fishing for the Virome of Tropical Tuna.

Viruses 2021 07 2;13(7). Epub 2021 Jul 2.

MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France.

While planktonic viruses have received much attention in recent decades, knowledge of the virome of marine organisms, especially fish, still remains rudimentary. This is notably the case with tuna, which are among the most consumed fish worldwide and represent considerable economic, social and nutritional value. Yet the composition of the tuna virome and its biological and environmental determinants remain unknown. To begin to address this gap, we investigated the taxonomic diversity of viral communities inhabiting the skin mucus, gut and liver of two major tropical tuna species (skipjack and yellowfin) in individuals fished in the Atlantic and Indian Oceans. While we found significant differences in the virome composition between the organs, this was totally independent of the tuna species or sex. The tuna virome was mainly dominated by eukaryotic viruses in the digestive organs (gut and liver), while bacteriophages were predominant in the mucus. We observed the presence of specific viral families in each organ, some previously identified as fish or human pathogens (e.g., , , ). Interestingly, we also detected a 'core virome' that was shared by all the organs and was mainly composed of , and . These results show that tuna host a mosaic of viral niches, whose establishment, role and circulation remain to be elucidated.
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http://dx.doi.org/10.3390/v13071291DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8310200PMC
July 2021

Does the Composition of the Gut Bacteriome Change during the Growth of Tuna?

Microorganisms 2021 May 27;9(6). Epub 2021 May 27.

MARBEC, University Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France.

In recent years, a growing number of studies sought to examine the composition and the determinants of the gut microflora in marine animals, including fish. For tropical tuna, which are among the most consumed fish worldwide, there is scarce information on their enteric bacterial communities and how they evolve during fish growth. In this study, we used metabarcoding of the 16S rDNA gene to (1) describe the diversity and composition of the gut bacteriome in the three most fished tuna species (skipjack, yellowfin and bigeye), and (2) to examine its intra-specific variability from juveniles to larger adults. Although there was a remarkable convergence of taxonomic richness and bacterial composition between yellowfin and bigeyes tuna, the gut bacteriome of skipjack tuna was distinct from the other two species. Throughout fish growth, the enteric bacteriome of yellowfin and bigeyes also showed significant modifications, while that of skipjack tuna remained relatively homogeneous. Finally, our results suggest that the gut bacteriome of marine fish may not always be subject to structural modifications during their growth, especially in species that maintain a steady feeding behavior during their lifetime.
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http://dx.doi.org/10.3390/microorganisms9061157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8229391PMC
May 2021

Exceptional but vulnerable microbial diversity in coral reef animal surface microbiomes.

Proc Biol Sci 2020 05 13;287(1927):20200642. Epub 2020 May 13.

MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Montpellier, France.

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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http://dx.doi.org/10.1098/rspb.2020.0642DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7287350PMC
May 2020

Therapeutic Potential of a New Jumbo Phage That Infects , a Widespread Coral Pathogen.

Front Microbiol 2018 24;9:2501. Epub 2018 Oct 24.

Sorbonne Universités UPMC Paris 06, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France.

Biological control using bacteriophages is a promising approach for mitigating the devastating effects of coral diseases. Several phages that infect , 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 phage, which was isolated from the coral reef in Van Phong Bay (Vietnam). BONAISHI appears to be strictly lytic for several pathogenic strains of 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 . A preliminary therapy test showed that adding BONAISHI to an infected culture of sp. cells reduced the impact of on sp. photosynthetic activity. This study showed that BONAISHI is able to mitigate infections, making it a good candidate for phage therapy for coral disease.
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http://dx.doi.org/10.3389/fmicb.2018.02501DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6207643PMC
October 2018

Skin microbiome of coral reef fish is highly variable and driven by host phylogeny and diet.

Microbiome 2018 08 24;6(1):147. Epub 2018 Aug 24.

Marine Biodiversity, Exploitation and Conservation (MARBEC), Université de Montpellier, CNRS, IRD, IFREMER, Place Eugène Bataillon, Case 093, 34 095, Montpellier Cedex 5, France.

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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http://dx.doi.org/10.1186/s40168-018-0530-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6109317PMC
August 2018

Hordes of Phages in the Gut of the Tilapia Sarotherodon melanotheron.

Sci Rep 2018 07 27;8(1):11311. Epub 2018 Jul 27.

MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, Montpellier, France.

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‰, 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 × 10 viruses ml), 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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http://dx.doi.org/10.1038/s41598-018-29643-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6063890PMC
July 2018

Corallivory and the microbial debacle in two branching scleractinians.

ISME J 2018 04 16;12(4):1109-1126. Epub 2018 Jan 16.

Aix-Marseille Université, CNRS 7278, IRD 198, INSERM 1095, Assistance-Publique des Hôpitaux de Marseille, Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), IHU Méditerranée Infection, Marseille, France.

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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http://dx.doi.org/10.1038/s41396-017-0033-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5864218PMC
April 2018

Procarcinogens - Determination and Evaluation by Yeast-Based Biosensor Transformed with Plasmids Incorporating RAD54 Reporter Construct and Cytochrome P450 Genes.

PLoS One 2016 22;11(12):e0168721. Epub 2016 Dec 22.

Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany.

In Vietnam, a great number of toxic substances, including carcinogens and procarcinogens, from industrial and agricultural activities, food production, and healthcare services are daily released into the environment. In the present study, we report the development of novel yeast-based biosensor systems to determine both genotoxic carcinogens and procarcinogens by cotransformation with two plasmids. One plasmid is carrying human CPR and CYP (CYP3A4, CYP2B6, or CYP2D6) genes, while the other contains the RAD54-GFP reporter construct. The three resulting coexpression systems bearing both CPR-CYP and RAD54-GFP expression cassettes were designated as CYP3A4/CYP2B6/CYP2D6 + RAD54 systems, respectively and used to detect and evaluate the genotoxic potential of carcinogens and procarcinogens by selective activation and induction of both CPR-CYP and RAD54-GFP expression cassettes in response to DNA damage. Procarcinogens were shown to be predominantly, moderately or not bioactivated by one of the CYP enzymes and thus selectively detected by the specific coexpression system. Aflatoxin B1 and benzo(a)pyrene were predominantly detected by the CYP3A4 + RAD54 system, while N-nitrosodimethylamine only moderately activated the CYP2B6 + RAD54 reporter system and none of them was identified by the CYP2D6 + RAD54 system. In contrast, the genotoxic carcinogen, methyl methanesulfonate, was detected by all systems. Our yeast-reporter system can be performed in 384-well microplates to provide efficient genotoxicity testing to identify various carcinogenic compounds and reduce chemical consumption to about 53% as compared with existing 96-well genotoxicity bioassays. In association with a liquid handling robot, this platform enables rapid, cost-effective, and high-throughput screening of numerous analytes in a fully automated and continuous manner without the need for user interaction.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0168721PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5179006PMC
July 2017

Flow cytometric enumeration of bacterial in the coral surface mucus layer.

J Microbiol Methods 2016 09 11;128:16-19. Epub 2016 Jun 11.

UMR MARBEC (IRD, CNRS, UM, IFREMER) Marine Biodiversity, Exploitation and Conservation, Montpellier, France.

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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http://dx.doi.org/10.1016/j.mimet.2016.05.032DOI Listing
September 2016

Colonization and release processes of viruses and prokaryotes on artificial marine macroaggregates.

FEMS Microbiol Lett 2016 Jan 13;363(1):fnv216. Epub 2015 Nov 13.

CNRS, UMR 7093, LOV, Observatoire Océanologique, 06230 Villefranche-sur-Mer, France Sorbonne Universités, UPMC, Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, 06230 Villefranche-sur-Mer, France Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, 13288, Marseille, France.

Marine organic aggregates are sites of high of viral accumulation; however, still little is known about their colonization processes and interactions with their local bacterial hosts. By taking advantage of a novel approach (paramagnetic functionalized microsphere method) to create and incubate artificial macroaggregates, we examined the small-scale movements of viruses and bacteria between such marine snow particles and the surrounding water. The examination of the codynamics of both free-living and attached viral and bacterial abundance, over 12 hours of incubation in virus-free water, suggests that aggregates are rather comparable to viral factories than to viral traps where a significant part of the virions production might be locally diverted to the water column. Also, the near-zero proportion of lysogenized cells measured in aggregates after mitomycin-C induction seems to indicate that lysogeny is not a prominent viral reproduction pathway in organic aggregates where most viruses might rather be virulent. Finally, we hypothesize that, contrary to bacteria, which can use both strong attachment and detachment from aggregates (two-way motion of bacteria), the adsorption of planktonic viruses appears to be numerically negligible compared to their massive export from the aggregates into the water column (one-way motion of viruses).
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http://dx.doi.org/10.1093/femsle/fnv216DOI Listing
January 2016

Analysis of metagenomic data reveals common features of halophilic viral communities across continents.

Environ Microbiol 2016 Mar 10;18(3):889-903. Epub 2015 Dec 10.

Université Blaise Pascal, Laboratoire 'Microorganismes: Génome et Environnement', Clermont Université, Clermont-Ferrand, France.

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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http://dx.doi.org/10.1111/1462-2920.13084DOI Listing
March 2016

Viruses Occur Incorporated in Biogenic High-Mg Calcite from Hypersaline Microbial Mats.

PLoS One 2015 26;10(6):e0130552. Epub 2015 Jun 26.

Centre for Marine Biodiversity, Exploitation and Conservation (MARBEC),Université de Montpellier, CNRS, IRD, Ifremer, Place Eugène Bataillon, Case 093, 34095, Montpellier, France.

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 (>10(10) 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 × 10(9) 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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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130552PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4482595PMC
April 2016

Coral Mucus Is a Hot Spot for Viral Infections.

Appl Environ Microbiol 2015 Sep 19;81(17):5773-83. Epub 2015 Jun 19.

Institute of Research for Development (IRD), UMR MARBEC, Montpellier, France/Hanoi, Vietnam.

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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http://dx.doi.org/10.1128/AEM.00542-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4551247PMC
September 2015

High diversity of skin-associated bacterial communities of marine fishes is promoted by their high variability among body parts, individuals and species.

FEMS Microbiol Ecol 2015 Jul 5;91(7). Epub 2015 Jun 5.

UMR 9190 Marine Biodiversity, Exploitation and Conservation (MARBEC), Université de Montpellier, CNRS, IRD, IFREMER, Place Eugène Bataillon, Case 093, 34 095 Montpellier Cedex 5, France.

Animal-associated microbiotas 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, has been scarcely studied, especially in case of skin-associated communities. In addition, the intraindividual 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, interindividual and intraindividual 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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http://dx.doi.org/10.1093/femsec/fiv061DOI Listing
July 2015

High occurrence of viruses in the mucus layer of scleractinian corals.

Environ Microbiol Rep 2014 Dec;6(6):675-82

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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http://dx.doi.org/10.1111/1758-2229.12185DOI Listing
December 2014

Genotoxicity of chemical compounds identification and assessment by yeast cells transformed with GFP reporter constructs regulated by the PLM2 or DIN7 promoter.

Int J Toxicol 2015 Jan-Feb;34(1):31-43

Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany

Yeast cells transformed with high-copy number plasmids comprising a green fluorescent protein (GFP)-encoding gene optimized for yeast under the control of the new DIN7 or PLM2 and the established RNR2 and RAD54 promoters were used to assess the genotoxic potential of chemical compounds. The activity of potential DNA-damaging agents was investigated by genotoxicity assays and by OxoPlate assay in the presence of various test compounds. The fluorescence signal generated by GFP in response to DNA damage was related to the different concentrations of analytes and the analyte-dependent GFP synthesis. The use of distinct DNA damage-inducible promoters presents alternative genotoxicity testing strategies by selective induction of promoters in response to DNA damage. The new DIN7 and PLM2 systems show higher sensitivity than the RNR2 and RAD54 systems in detecting 4-nitroquinoline-N-oxide and actinomycin D. Both DIN7 and PLM2 systems are able to detect camptothecin while RNR2 and RAD54 systems are not. Automated laboratory systems with assay performance on 384-well microplates provide for cost-effective high-throughput screening of DNA-damaging agents, reducing compound consumption to about 53% as compared with existing eukaryotic genotoxicity bioassays.
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http://dx.doi.org/10.1177/1091581814566870DOI Listing
October 2015

Nutrient ratios and the complex structure of phytoplankton communities in a highly turbid estuary of Southeast Asia.

Environ Monit Assess 2014 Dec 10;186(12):8555-72. Epub 2014 Sep 10.

Institute of Marine Environment and Resources (IMER), Vietnam Academy of Science and Technology (VAST), Haiphong, Viet Nam.

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.
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http://dx.doi.org/10.1007/s10661-014-4024-yDOI Listing
December 2014

Off-site impacts of agricultural composting: role of terrestrially derived organic matter in structuring aquatic microbial communities and their metabolic potential.

FEMS Microbiol Ecol 2014 Dec 30;90(3):622-32. Epub 2014 Sep 30.

UMR CNRS 5557, USC 1364 INRA, Ecologie Microbienne, Université Lyon1, Université de Lyon, Villeurbanne, France.

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 with soil alone. Leachates from these additions, either with or without biochar, were highly bioavailable to aquatic microbial communities, although reducing the metabolic potential of the community and harbouring 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.
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http://dx.doi.org/10.1111/1574-6941.12421DOI Listing
December 2014

The versatile nature of coral-associated viruses.

Environ Microbiol 2015 Oct 29;17(10):3433-9. Epub 2014 Aug 29.

Institute of Marine Environment and Resources, Haiphong, Vietnam.

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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http://dx.doi.org/10.1111/1462-2920.12579DOI Listing
October 2015

Short-term responses of unicellular planktonic eukaryotes to increases in temperature and UVB radiation.

BMC Microbiol 2012 Sep 11;12:202. Epub 2012 Sep 11.

INRA, UMR 42 CARRTEL, Thonon-les-bains, France.

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 (<6 μm; from a coastal Mediterranean lagoon) to a warming treatment (+3°C) 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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http://dx.doi.org/10.1186/1471-2180-12-202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3478981PMC
September 2012

Enumerating viruses in coral mucus.

Appl Environ Microbiol 2012 Sep 22;78(17):6377-9. Epub 2012 Jun 22.

UMR 5119 ECOSYM-Université Montpellier 2-IRD-IFREMER-CNRS, Montpellier, France.

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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http://dx.doi.org/10.1128/AEM.01141-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416620PMC
September 2012

Uncoupled viral and bacterial distributions in coral reef waters of Tuamotu Archipelago (French Polynesia).

Mar Pollut Bull 2012 28;65(10-12):506-15. Epub 2012 Jan 28.

UMR 5119, ECOSYM - Ecologie des systèmes marins côtiers (UM2, CNRS, IRD, Ifremer, UM1), Université Montpellier 2, Place Eugène Bataillon, Case 093, 34095 Montpellier Cedex 5, France.

This study examined the distribution of virioplankton and bacterioplankton in two coral reef systems (Ahe and Takaroa atolls) in the Tuamotu Archipelago, in comparison with the surrounding oligotrophic ocean. Mean concentrations of 4.8×10(5) and 6.2×10(5) cells ml(-1) for bacteria and 8.1×10(6) and 4.3×10(6) VLP(virus-like particle) ml(-1) were recorded in Ahe and Takaroa lagoons, respectively. Chlorophyll-a concentrations and dissolved organic matter were higher in Ahe whereas (3)H thymidine incorporation rates were higher in Takaroa. First data on lytic and lysogenic strategies of phages in coral reef environments were discussed in this paper. The fraction of visibly infected cells by viruses was negligible regardless of the lagoon station (mean=0.15%). However, the fraction of lysogenic cells ranged between 2.5% and 88.9%. Our results suggest that the distribution patterns of virioplankton are apparently not coupled to the spatial dynamics of the bacterioplankton communities.
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http://dx.doi.org/10.1016/j.marpolbul.2012.01.001DOI Listing
November 2012

Viral distribution and life strategies in the Bach Dang Estuary, Vietnam.

Microb Ecol 2011 Jul 9;62(1):143-54. Epub 2011 Mar 9.

UMR 5119, ECOSYM, Montpellier 2 University, CNRS, IRD, IFREMER, Montpellier, France.

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 <60 nm and 60 to 90 nm tailless viruses (92% and 80%, respectively), and in the Myoviridae (73%). Also, 60% of the variance of the tailless larger viruses (>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.
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http://dx.doi.org/10.1007/s00248-011-9835-6DOI Listing
July 2011

Ecological traits of planktonic viruses and prokaryotes along a full-salinity gradient.

FEMS Microbiol Ecol 2011 May 14;76(2):360-72. Epub 2011 Feb 14.

IRD, UMR 5119 ECOSYM, Montpellier, France.

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.
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http://dx.doi.org/10.1111/j.1574-6941.2011.01054.xDOI Listing
May 2011

Disentangling the relative influence of bacterioplankton phylogeny and metabolism on lysogeny in reservoirs and lagoons.

ISME J 2011 May 2;5(5):831-42. Epub 2010 Dec 2.

Laboratoire Ecosystèmes Lagunaires, Université de Montpellier 2, CNRS-Ifremer-IRD-UMR5119, Montpellier cedex 5, France.

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.
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http://dx.doi.org/10.1038/ismej.2010.181DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105773PMC
May 2011

Diversity of virus-host systems in hypersaline Lake Retba, Senegal.

Environ Microbiol 2011 Aug 25;13(8):1956-72. Epub 2010 Aug 25.

Laboratoire Microorganismes: Génome et Environnement, Université Blaise Pascal (Clermont-Ferrand II), UMR CNRS 6023, F-63177, Aubière Cedex, France.

Remarkable morphological diversity of virus-like particles was observed by transmission electron microscopy in a hypersaline water sample from Lake Retba, Senegal. The majority of particles morphologically resembled hyperthermophilic archaeal DNA viruses isolated from extreme geothermal environments. Some hypersaline viral morphotypes have not been previously observed in nature, and less than 1% of observed particles had a head-and-tail morphology, which is typical for bacterial DNA viruses. Culture-independent analysis of the microbial diversity in the sample suggested the dominance of extremely halophilic archaea. Few of the 16S sequences corresponded to known archeal genera (Haloquadratum, Halorubrum and Natronomonas), whereas the majority represented novel archaeal clades. Three sequences corresponded to a new basal lineage of the haloarchaea. Bacteria belonged to four major phyla, consistent with the known diversity in saline environments. Metagenomic sequencing of DNA from the purified virus-like particles revealed very few similarities to the NCBI non-redundant database at either the nucleotide or amino acid level. Some of the identifiable virus sequences were most similar to previously described haloarchaeal viruses, but no sequence similarities were found to archaeal viruses from extreme geothermal environments. A large proportion of the sequences had similarity to previously sequenced viral metagenomes from solar salterns.
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http://dx.doi.org/10.1111/j.1462-2920.2010.02323.xDOI Listing
August 2011

Lytic failure in cross-inoculation assays between phages and prokaryotes from three aquatic sites of contrasting salinity.

FEMS Microbiol Lett 2010 Oct 23;311(2):113-8. Epub 2010 Aug 23.

IRD, UMR 5119 ECOLAG, Montpellier, France.

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.
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http://dx.doi.org/10.1111/j.1574-6968.2010.02074.xDOI Listing
October 2010

Virus-bacterium interactions in water and sediment of West African inland aquatic systems.

Appl Environ Microbiol 2006 Aug;72(8):5274-82

UR 167 CYROCO, Centre de Bel Air, Route des Hydrocarbures, BP 1386, Dakar, Senegal.

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.
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http://dx.doi.org/10.1128/AEM.00863-06DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538746PMC
August 2006

Infection paradox: high abundance but low impact of freshwater benthic viruses.

Appl Environ Microbiol 2006 Jul;72(7):4893-8

Department of Aquatic Ecology, Eawag (Swiss Federal Institute of Aquatic Science and Technology), and Institute of Integrative Biology (IBZ), ETH Zurich, 6047 Kastanienbaum, Switzerland.

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 approximately 15,000 bacterial cells inspected in these three habitats; for comparison, nearly 300 of approximately 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.
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http://dx.doi.org/10.1128/AEM.00319-06DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1489317PMC
July 2006
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