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Bettarel, Y., Combe, M., Adingra, A., Ndiaye, A., Bouvier, T., Panfili, J., et al. (2018). Hordes of Phages in the Gut of the Tilapia Sarotherodon melanotheron. Sci Rep, 8, 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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Bouvier, T., Venail, P., Pommier, T., Bouvier, C., Barbera, C., & Mouquet, N. (2012). Contrasted Effects of Diversity and Immigration on Ecological Insurance in Marine Bacterioplankton Communities. PLoS One, 7(6).
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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Chiarello, M., Auguet, J. - C., Bettarel, Y., Bouvier, C., Claverie, T., Graham, N. A. J., et al. (2018). Skin microbiome of coral reef fish is highly variable and driven by host phylogeny and diet. Microbiome, 6, 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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Escalas, A., Hale, L., Voordeckers, J. W., Yang, Y., Firestone, M. K., Alvarez-Cohen, L., et al. (2019). Microbial functional diversity: From concepts to applications. Ecol. Evol., 9(20), 12000–12016.
Résumé: Functional diversity is increasingly recognized by microbial ecologists as the essential link between biodiversity patterns and ecosystem functioning, determining the trophic relationships and interactions between microorganisms, their participation in biogeochemical cycles, and their responses to environmental changes. Consequently, its definition and quantification have practical and theoretical implications. In this opinion paper, we present a synthesis on the concept of microbial functional diversity from its definition to its application. Initially, we revisit to the original definition of functional diversity, highlighting two fundamental aspects, the ecological unit under study and the functional traits used to characterize it. Then, we discuss how the particularities of the microbial world disallow the direct application of the concepts and tools developed for macroorganisms. Next, we provide a synthesis of the literature on the types of ecological units and functional traits available in microbial functional ecology. We also provide a list of more than 400 traits covering a wide array of environmentally relevant functions. Lastly, we provide examples of the use of functional diversity in microbial systems based on the different units and traits discussed herein. It is our hope that this paper will stimulate discussions and help the growing field of microbial functional ecology to realize a potential that thus far has only been attained in macrobial ecology.
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Goni-Urriza, M., Moussard, H., Lafabrie, H., Carré, C., Bouvy, M., Sakka Hlaili, A., et al. (2018). Consequences of contamination on the interactions between phytoplankton and bacterioplankton. Chemosphere, 195, 212–222.
Résumé: Sediment resuspension can provoke strong water enrichment in nutrients, contaminants, and microorganisms. Microcosm incubations were performed in triplicate for 96 h, with lagoon and offshore waters incubated either with sediment elutriate or with an artificial mixture of contaminants issued from sediment resuspension. Sediment elutriate provoked a strong increase in microbial biomass, with little effects on the phytoplankton and bacterioplankton community structures. Among the pool of contaminants released, few were clearly identified as structuring factors of phytoplanktdn and bacterioplankton communities, namely simazine, Cu, Sn, Ni, and Cr. Effects were more pronounced in the offshore waters, suggesting a relative tolerance of the lagoon microbial communities to contamination. The impacts of contamination on the microbial community structure were direct or indirect, depending on the nature and the strength of the interactions between phytoplankton and bacterioplankton. (C) 2017 Elsevier Ltd. All rights reserved.
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