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1. The extent to which stochastic and deterministic processes influence variations in species communities across space and time remains a central question in theoretical and applied ecology. Despite their high dispersal ability, the composition of phytoplankton communities displays striking spatial variations among lakes even at small spatial scale. 2. To investigate the mechanisms underlying the distribution of phytoplankton species, we evaluate the contribution of stochastic, spatial and environmental processes in determining b-diversity patterns of phytoplankton at a regional scale. Phytoplankton communities were surveyed in 50 different lakes from north-central France, a region characterised by strong environmental heterogeneity. 3. The regional species pool was characterised by extremely high b-diversity levels, which were mainly explained by species replacement (i.e. turnover) rather than by differences in species richness (i.e. nestedness). Null models of random species distribution and spatial processes failed to explain observed b-diversity patterns. At the opposite, local environmental conditions strongly influenced the degree of uniqueness of local phytoplankton communities, with the most contrasted environments, including human-dominated areas, promoting highly distinct phytoplankton communities. 4. Our results suggest that species-sorting mechanisms that arise from variations in local environmental conditions drive high species turnover at the region scale. Thus, in a landscape strongly impacted by cultural eutrophication, further anthropogenic impacts on aquatic ecosystems would likely induce regional homogenisation of phytoplankton communities. Overall, our study supports the fact that the management of lakes and reservoirs in anthropic landscapes should aim at maintaining environmental heterogeneity while preventing further eutrophication in order to favour the maintenance of high phytoplankton b-and c-diversity.

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HAL is a multidisciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

Metatranscriptome analysis relates to the transcriptome of microbial communities directly sampled in the environment. Accessing the mRNA pool in natural bacterial communities presents some technical challenges such as the RNA extraction, rRNA depletion, and the choice of the high-throughput sequencing technique. The lack of technical details in scientific articles is a major problem to correctly obtained mRNA from a microbial community and thus the corresponding sequencing data. In our study, we present the methodological procedure that was developed in order to access to the metatranscriptome of the microbial communities during two cyanobacterial blooms successively occurring in a freshwater eutrophic lake. Each procedure step was detailed and discussed with regard to the choices and difficulties encountered and to the recent literature. Finally, the two major limits for metatranscriptomic approaches targeting bacterial communities from natural environments were (i) the removal of rRNA in order to increase the putative mRNA reads number after sequencing, and (ii) for most of the bacterial communities living in natural environments, the lack of reference genomes in databases that leads to the non-assignation of numerous reads. Once these challenges overcome, we managed to access putative mRNA of dominant species, i.e. cyanobacteria (from 6 to 72 % of mRNA assigned), and of the surrounding bacteria (from 1 to 5 % of mRNA assigned).

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As the human population grows, the demand for living space and supplies of resources also increases, which may induce rapid change in land-use/land-cover (LULC) and associated pressures exerted on aquatic habitats. We propose a new approach to forecast the impact of regional land cover change and water management policies (i.e., targets in nutrient loads reduction) on lake and reservoir water eutrophication status using a model that requires minimal parameterisation compared with alternative methods. This approach was applied to a set of 48 periurban lakes located in the Ile de France region (IDF, France) to simulate catchment-scale management scenarios. Model outputs were subsequently compared to governmental agencies’ 2030 forecasts. Our model indicated that the efforts made to reduce pressure in the catchment of seepage lakes might be expected to be proportional to the gain that might be obtained, whereas drainage lakes will display little improvement until a critical level of pressure reduction is reached. The model also indicated that remediation measures, as currently planned by governmental agencies, might only have a marginal impact on improving the eutrophication status of lakes and reservoirs within the IDF region. Despite the commitment to appropriately managing the water resources in many countries, prospective tools to evaluate the potential impacts of global change on freshwater ecosystems integrity at medium to large spatial scales are lacking. This study proposes a new approach to investigate the impact of region-scale human-driven changes on lake and reservoir ecological status and could be implemented elsewhere with limited parameterisation. Issues are discussed that relate to model uncertainty and to its relevance as a tool applied to decision-making.

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