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Bouchez, A., Pascault, N., Chardon, C., Bouvy, M., Cecchi, P., Lambs, L., et al. (2013). Mangrove microbial diversity and the impact of trophic contamination. Marine pollution bulletin, 66(1–2), 39–46.
Résumé: Mangroves are threatened ecosystems that provide numerous ecosystem services, especially through their wide biodiversity, and their bioremediation capacity is a challenging question in tropical areas. In a mangrove in Mayotte, we studied the potential role of microbial biofilm communities in removing nutrient loads from pre-treated wastewater. Microbial community samples were collected from tree roots, sediments, water, and from a colonization device, and their structure and dynamics were compared in two areas: one exposed to sewage and the other not. The samples from the colonization devices accurately reflected the natural communities in terms of diversity. Communities in the zone exposed to sewage were characterized by more green algae and diatoms, higher bacteria densities, as well as different compositions. In the area exposed to sewage, the higher cell densities associated with specific diversity patterns highlighted adapted communities that may play a significant role in the fate of nutrients.
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Compte-Port, S., Borrego, C. M., Moussard, H., Jeanbille, M., Restrepo-Ortiz, C. X., de Diego, A., et al. (2018). Metal contaminations impact archaeal community composition, abundance and function in remote alpine lakes. Environ. Microbiol., 20(7), 2422–2437.
Résumé: Using the 16S rRNA and mcrA genes, we investigated the composition, abundance and activity of sediment archaeal communities within 18 high-mountain lakes under contrasted metal levels from different origins (bedrock erosion, past-mining activities and atmospheric depositions). Bathyarchaeota, Euryarchaeota and Woesearchaeota were the major phyla found at the meta-community scale, representing 48%, 18.3% and 15.2% of the archaeal community respectively. Metals were equally important as physicochemical variables in explaining the assemblage of archaeal communities and their abundance. Methanogenesis appeared as a process of central importance in the carbon cycle within sediments of alpine lakes as indicated by the absolute abundance of methanogen 16S rRNA and mcrA gene transcripts (10(5) to 10(9) copies g(-1)). We showed that methanogen abundance and activity were significantly reduced with increasing concentrations of Pb and Cd, two indicators of airborne metal contaminations. Considering the ecological importance of methanogenesis in sediment habitats, these metal contaminations may have system wide implications even in remote area such as alpine lakes. Overall, this work was pioneer in integrating the effect of long-range atmospheric depositions on archaeal communities and indicated that metal contamination might significantly compromise the contribution of Archaea to the carbon cycling of the mountain lake sediments.
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Escalas, A., Bouvier, T., Mouchet, M. A., Leprieur, F., Bouvier, C., Troussellier, M., et al. (2013). A unifying quantitative framework for exploring the multiple facets of microbial biodiversity across diverse scales. Environmental microbiology, 15(10), 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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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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Escalas, A., Troussellier, M., Yuan, T., Bouvier, T., Bouvier, C., Mouchet, M. A., et al. (2017). Functional diversity and redundancy across fish gut, sediment and water bacterial communities. Environ. Microbiol., 19(8), 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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