Characterizing the spatial signal of environmental DNA in river systems using a community ecology approach.

Environmental DNA (eDNA) is gaining a growing popularity among scientists but its applicability to biodiversity research and management remains limited in river systems by the lack of knowledge about the spatial extent of the downstream transport of eDNA. Here, we assessed the ability of eDNA inventories to retrieve spatial patterns of fish assemblages along two large and species-rich Neotropical rivers. We first examined overall community variation with distance through the distance decay of similarity and compared this pattern to capture-based samples. We then considered previous knowledge on individual species distributions, and compared it to the eDNA inventories for a set of 53 species. eDNA collected from 28 sites in the Maroni and 25 sites in the Oyapock rivers permitted to retrieve a decline of species similarity with increasing distance between sites. The distance decay of similarity derived from eDNA was similar and even more pronounced than that obtained with capture-based methods (gill-nets). In addition, the species upstream-downstream distribution range derived from eDNA matched to the known distribution of most species. Our results demonstrate that environmental DNA does not represent an integrative measure of biodiversity across the whole upstream river basin but provides a relevant picture of local fish assemblages. Importantly, the spatial signal gathered from eDNA was therefore comparable to that gathered with local capture-based methods, which describes fish fauna over a few hundred metres.

Low level of anthropization linked to harsh vertebrate biodiversity declines in Amazonia.

Assessing the impact of human activity on ecosystems often links local biodiversity to disturbances measured within the same locality. However, remote disturbances may also affect local biodiversity. Here, we used environmental DNA metabarcoding to evaluate the relationships between vertebrate biodiversity (fish and mammals) and disturbance intensity in two Amazonian rivers. Measurements of anthropic disturbance -here forest cover losses- were made from the immediate vicinity of the biodiversity sampling sites to up to 90 km upstream. The findings suggest that anthropization had a spatially extended impact on biodiversity. Forest cover losses of <11% in areas up to 30 km upstream from the biodiversity sampling sites were linked to reductions of >22% in taxonomic and functional richness of both terrestrial and aquatic fauna. This underscores the vulnerability of Amazonian biodiversity even to low anthropization levels. The similar responses of aquatic and terrestrial fauna to remote disturbances indicate the need for cross-ecosystem conservation plans that consider the spatially extended effects of anthropization.

Amazonian mammal monitoring using aquatic environmental DNA.

Environmental DNA (eDNA) metabarcoding has emerged as one of the most efficient methods to assess aquatic species presence. While the method can in theory be used to investigate nonaquatic fauna, its development for inventorying semi-aquatic and terrestrial fauna is still at an early stage. Here we investigated the potential of aquatic eDNA metabarcoding for inventorying mammals in Neotropical environments, be they aquatic, semi-aquatic or terrestrial. We collected aquatic eDNA in 96 sites distributed along three Guianese watersheds and compared our inventories to expected species distributions and field observations derived from line transects located throughout French Guiana. Species occurrences and emblematic mammalian fauna richness patterns were consistent with the expected distribution of fauna and our results revealed that aquatic eDNA metabarcoding brings additional data to line transect samples for diurnal nonaquatic (terrestrial and arboreal) species. Aquatic eDNA also provided data on species not detectable in line transect surveys such as semi-aquatic, aquatic and nocturnal terrestrial and arboreal species. Although the application of eDNA to inventory mammals still needs some developments to optimize sampling efficiency, it can now be used as a complement to traditional surveys.

Aquatic eDNA for monitoring French Guiana biodiversity.

BACKGROUND: Environmental DNA [eDNA] metabarcoding has recently emerged as a non-destructive alternative to traditional sampling for characterising species assemblages. NEW INFORMATION: We here provide a consistent dataset synthetising all eDNA sampling sites in French Guiana to date. Field collections have been initiated in 2014 and have continued until 2019. This dataset is however a work in progress and will be updated after each collecting campaign. We also provide a taxon by site matrix for fishes presence / absence as inferred from eDNA. Our aim is to allow a transparent communication to the stakeholders and provide the foundation for a monitoring programme based on eDNA. The lastest version of the dataset is publicly and freely accessible through the CEBA geoportal (http://vmcebagn-dev.ird.fr) or through the French Guiana geographic portal (https://www.geoguyane.fr).