Impacts of large and small barriers on fish assemblage composition assessed using environmental DNA metabarcoding

River fragmentation caused by instream barriers is a leading cause of biodiversity loss, particularly for freshwater migratory fish, the vertebrate group that has suffered the steepest decline. However, most studies have tended to focus on the impacts of large dams on only a few taxa. We estimated the cumulative impact of both large and small barriers on fish species richness and relative abundance along an altitudinal gradient in the main stem of the River Allier (France). Using eDNA metabarcoding, we identified 24 fish zero-radius operational taxonomic units (zOTUs), corresponding to 26 species distributed along the main stem of the river. Elevation explained the greatest amount of variation in fish distribution, together with average flow, barrier density and its interaction with cumulative barrier height. Based on eDNA, the largest discontinuity in species richness was not related to the location of Poutès, the largest dam in the system, but located downstream from it. Our results indicate that, in addition to the more obvious effects of large dams on migratory fish such as the Atlantic salmon, the cumulative effects of small barriers can have widespread impacts on fish species richness and relative abundance, which should not be overlooked. We suggest that, as for other fragmented rivers, acting on numerous small barriers might bring about greater benefits in fish species richness than focusing only on the largest dams

Growing concentrations of phenol increasingly modify microbial communities' dynamics and performances' stability of anaerobic digesters

13th World Congress on Anaerobic Digestion : Recovering (bio) Ressources for the World, Santiago de Compostella, ESP, 25-/06/2013 - 28/06/2013International audienceAnaerobic degradation requires a complex network of interacting and competing microorganisms. Waste anaerobic digesters are based on the intensive use of this flora. Consequently, functioning and stability of digesters are directly related to microbial populations' dynamics. The latter may be subject to external disturbances, such as the arrival of micropollutants with waste, causing malfunction of bioprocesses. In this context, we questioned the influence of phenol addition on microbial communities degrading cellulose under anaerobic conditions. For that purpose, cellulose batch digesters were set-up and inoculated with municipal solid waste digester sludge. Modifications of microbial dynamics and degradation performances after addition of phenol were evaluated in triplicates (nine different concentrations tested, from 0 to 4g.L-1). Gas production, reaction pathways and phenol concentration were followed over time. These results were linked to the monitoring of microorganisms' dynamics (automated-ribosomal-intergenic-spacer-analysis method, ARISA and qPCR on functional gene and on total Archaea and Bacteria) and of their spatial organisation (fluorescent-in-situ-hybridization, FISH). With increasing phenol concentrations, increasing disruption of digesters' performances (gas production, intermediates accumulation) was observed. EC50 (half-maximal effective-concentration) values for phenol was calculated from the dose/effect curve obtained by plotting degradation parameters as a function of phenol concentration. With increasing concentration, intermediates pathways were modified; Archaea activity was totally inhibited from 1.5g.L-1, Bacteria activity from 2.0g.L-1. Moreover, phenol degradation was observed in several digesters after several weeks. ARISA monitoring revealed an important influence of phenol concentration on microbial dynamics in general. qPCR gave more specific information. Physico-chemical and microbial results were linked to establish patterns of communities' perturbation by phenol. A phenol inhibition threshold was established for several microorganisms. Subdominant microorganisms that used phenol perturbation to settle and phenol degrading microorganisms were identified. This study gives important insights in the understanding of micropollutants effect on complex microbial communities' dynamics and their influence on digesters' stability

Représentativité spatiale d'un signal d'ADN environnemental pour l'évaluation de la biodiversité piscicole dans un écosystème naturel d'eau douce

[Departement_IRSTEA]Eaux [TR1_IRSTEA]QUASAREInternational audienceIn the last few years, the study of environmental DNA (eDNA) has drawn attention for many reasons, including its advantages for monitoring and conservation purposes. So far, in aquatic environments, most of eDNA research has focused on the detection of single species using species-specific markers. Recently, species inventories based on the analysis of a single generalist marker targeting a larger taxonomic group (eDNA metabarcoding) have proven useful for bony fish and amphibian biodiversity surveys. This approach involves in situ filtering of large volumes of water followed by amplification and sequencing of a short discriminative fragment from the 12S rDNA mitochondrial gene. In this study, we went one step further by investigating the spatial representativeness (i.e. ecological reliability and signal variability in space) of eDNA metabarcoding for large-scale fish biodiversity assessment in a freshwater system including lentic and lotic environments. We tested the ability of this approach to characterize large-scale organization of fish communities along a longitudinal gradient, from a lake to the outflowing river. First, our results confirm that eDNA metabarcoding is more efficient than a single traditional sampling campaign to detect species presence, especially in rivers. Second, the species list obtained using this approach is comparable to the one obtained when cumulating all traditional sampling sessions since 1995 and 1988 for the lake and the river, respectively. In conclusion, eDNA metabarcoding gives a faithful description of local fish biodiversity in the study system, more specifically within a range of a few kilometers along the river in our study conditions, i.e. longer than a traditional fish sampling site