Sébastien Personnic

Assessing the Diversity and Specificity of Two Freshwater Viral Communities through Metagenomics

Transitions between saline and fresh waters have been shown to be infrequent for microorganisms. Based on host-specific interactions, the presence of specific clades among hosts suggests the existence of freshwater-specific viral clades. Yet, little is known about the composition and diversity of the temperate freshwater viral communities, and even if freshwater lakes and marine waters harbor distinct clades for particular viral sub-families, this distinction remains to be demonstrated on a community scale. To help identify the characteristics and potential specificities of freshwater viral communities, such communities from two lakes differing by their ecological parameters were studied through metagenomics. Both the cluster richness and the species richness of the Lake Bourget virome were significantly higher that those of the Lake Pavin, highlighting a trend similar to the one observed for microorganisms (i.e. the specie richness observed in mesotrophic lakes is greater than the one observed in oligotrophic lakes). Using 29 previously published viromes, the cluster richness was shown to vary between different environment types and appeared significantly higher in marine ecosystems than in other biomes. Furthermore, significant genetic similarity between viral communities of related environments was highlighted as freshwater, marine and hypersaline environments were separated from each other despite the vast geographical distances between sample locations within each of these biomes. An automated phylogeny procedure was then applied to marker genes of the major families of single-stranded (Microviridae, Circoviridae, Nanoviridae) and double-stranded (Caudovirales) DNA viruses. These phylogenetic analyses all spotlighted a very broad diversity and previously unknown clades undetectable by PCR analysis, clades that gathered sequences from the two lakes. Thus, the two freshwater viromes appear closely related, despite the significant ecological differences between the two lakes. Furthermore, freshwater viral communities appear genetically distinct from other aquatic ecosystems, demonstrating the specificity of freshwater viruses at a community scale for the first time.

An ecosystem-based approach to assess the status of a Mediterranean ecosystem, the Posidonia oceanica seagrass meadow.

Biotic indices, which reflect the quality of the environment, are widely used in the marine realm. Sometimes, key species or ecosystem engineers are selected for this purpose. This is the case of the Mediterranean seagrass Posidonia oceanica, widely used as a biological quality element in the context of the European Union Water Framework Directive (WFD). The good quality of a water body and the apparent health of a species, whether or not an ecosystem engineer such as P. oceanica, is not always indicative of the good structure and functioning of the whole ecosystem. A key point of the recent Marine Strategy Framework Directive (MSFD) is the ecosystem-based approach. Here, on the basis of a simplified conceptual model of the P. oceanica ecosystem, we have proposed an ecosystem-based index of the quality of its functioning, compliant with the MSFD requirements. This index (EBQI) is based upon a set of representative functional compartments, the weighting of these compartments and the assessment of the quality of each compartment by comparison of a supposed baseline. The index well discriminated 17 sites in the north-western Mediterranean (French Riviera, Provence, Corsica, Catalonia and Balearic Islands) covering a wide range of human pressure levels. The strong points of the EBQI are that it is easy to implement, non-destructive, relatively robust, according to the selection of the compartments and to their weighting, and associated with confidence indices that indicate possible weakness and biases and therefore the need for further field data acquisition.

Do small grazers influence virus-induced mortality of bacteria in Lake Bourget (France)?

We performed simple tests to assess the importance of the presence or absence of small flagellated predators on the stimulation of viral-induced bacterial mortality (VIBM) in Lake Bourget (France) during three periods of the year (March-April, May and August 2003). To achieve this goal, samples were filtered either through < 5 or < 1.2 μm filters in order to keep or eliminate the smallest predators. We found that the VIBM was always enhanced in the presence of the predators after only 24 h. The viral impact was multiplied by about 8-fold at the end of March, 2.5-fold in May and 7-fold in August in the < 5 μm compared to the < 1.2 μm treatment. A clear and positive relationship was found between flagellates concentrations and the VIBM (r = 0.99, n = 3, p< 0.05). Our results highlight a tight coupling between the different compartments of the aquatic microbial loop, and more especially what could be a synergistic cooperation between grazing- and virus-induced mortality of bacteria.

An ecosystem-based approach to assess the status of Mediterranean algae-dominated shallow rocky reefs

A conceptual model was constructed for the functioning the algae-dominated rocky reef ecosystem of the Mediterranean Sea. The Ecosystem-Based Quality Index (reef-EBQI) is based upon this model. This index meets the objectives of the EU Marine Strategy Framework Directive. It is based upon (i) the weighting of each compartment, according to its importance in the functioning of the ecosystem; (ii) biological parameters assessing the state of each compartment; (iii) the aggregation of these parameters, assessing the quality of the ecosystem functioning, for each site; (iv) and a Confidence Index measuring the reliability of the index, for each site. The reef-EBQI was used at 40 sites in the northwestern Mediterranean. It constitutes an efficient tool, because it is based upon a wide set of functional compartments, rather than upon just a few species; it is easy and inexpensive to implement, robust and not redundant with regard to already existing indices.

Where seaweed forests meet animal forests: the examples of macroalgae in coral reefs and the Mediterranean coralligene ecosystem

Where seaweed forests meet animal forests: the examples of macroalgae in coral reefs and the Mediterranean coralligene ecosystem

Ecosystem-Based Versus Species-Based Approach for Assessment of the Human Impact on the Mediterranean Seagrass Posidonia oceanica

Biotic indices, which reflect the quality of the environment, are widely used in the marine realm. The Posidonia oceanica seagrass meadow is a benthic sublittoral habitat characteristic of the Mediterranean Sea. The Ecosystem-Based Quality Index (EBQI) is based upon the overall functioning of the Posidonia oceanica ecosystem, from primary producers and the litter to top predators. It is compliant with the Marine Strategy Framework Directive (MSFD) of the European Union (EU). It provides managers with a response that is very different from that of the indices only based upon the key species P. oceanica and a few affiliate species. While the species-based indices are mainly designed for assessing the water quality of a waterbody (e.g. pollution), the EBQI provides a picture of the actual status of the ecosystem functioning, including not only pollution but also the whole range of human impacts, from anchoring to overfishing.