Aquatic eDNA for monitoring French Guiana biodiversity

Abstract

Environmental DNA [eDNA] metabarcoding has recently emerged as a non-destructive alternative to traditional sampling for characterising species assemblages. 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).

eDNA in a bottleneck: obstacles to fish metabarcoding studies in megadiverse freshwater systems

“…CC-BY-NC 4.0 International license available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint this version posted January 7, 2021. ; https://doi.org/10.1101/2021.01.05.425493 doi: bioRxiv preprint been made publicly available, even when a larger fragment of the gene has been sequenced for the reference database (Cilleros et al, 2019). This study highlights that the expansion of eDNA studies in megadiverse areas depends on better collaborative efforts focused on building more publicly available datasets.…”

“…Understanding community compositions and species distributions within a target area is a crucial step to inform conservation management strategies. This requires cost-effective and robust methods for surveying biodiversity in a timely manner and eDNA metabarcoding has emerged as a promising method for surveying whole ecosystems (Lacoursière-Roussel et al, 2018;Murienne et al, 2019;Valdez-Moreno et al, 2019). As the use of genetic approaches to biodiversity monitoring relies on accurate, precise species identifications, the lack of appropriate taxonomic resolution and, consequently, detailed reference databases prevents the use of eDNA for biomonitoring from reaching its full potential.…”

“…CC-BY-NC 4.0 International license available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint this version posted January 7, 2021. ; https://doi.org/10.1101/2021.01.05.425493 doi: bioRxiv preprint 4 several limiting factors prevent its full application (Cilleros et al, 2019;Doble el al., 2020;Sales et al, 2021). Although challenges associated with the collection and preservation of samples have already been addressed (Sales et al, 2019), obstacles in taxonomic assignments remain understudied.…”

“…Furthermore, the proportion of species sequenced is lower in species-rich regions, such as the Neotropics with poorly sampled habitats and taxa. As it stands now, only a limited number of fish species can be found in DNA databases, hindering the potential of eDNA metabarcoding as a biomonitoring method in these regions (Cilleros et al, 2019;Sales et al, 2019Sales et al, , 2021.…”

“…Recent studies display its efficiency in different aquatic environments and show how it compares favourably to, or even outperforms, traditional sampling methods in terms of species detections (McDevitt et al, 2019;McElroy et al, 2020) and facilitates investigations into patterns of extirpation, invasive species detection, and dynamics of species richness (Lacoursière-Roussel et al, 2018;Sales et al, 2021). Despite the increase of eDNA surveys in megadiverse systems, several limiting factors prevent its full application (Cilleros et al, 2019;Doble el al., 2020;Sales et al, 2021). Although challenges associated with the collection and preservation of samples have already been addressed (Sales et al, 2019), obstacles in taxonomic assignments remain understudied.…”