Space-time dynamics in monitoring neotropical fish communities using eDNA metabarcoding

Abstract

The biodiverse Neotropical ecoregion remains insufficiently assessed, poorly managed, and threatened by unregulated human activities. Novel, rapid and cost-effective DNA-based approaches are valuable to improve understanding of the biological communities and for biomonitoring in remote areas. Here, we evaluate the potential of environmental DNA (eDNA) metabarcoding for assessing the structure and distribution of fish communities by analysing sediments and water from 11 locations along the Jequitinhonha River catchment (Brazil). Each site was sampled twice, before and after a major rain event in a five-week period and fish diversity was estimated using high-through-put sequencing of 12S rRNA amplicons. In total, 252 Molecular Operational Taxonomic Units (MOTUs) and 34 fish species were recovered, including endemic, introduced, and previously unrecorded species for this basin. Spatiotemporal variation of fish assemblages was detected, richness during the first campaign was nearly twice as high as in the second sampling round; though peaks of diversity were primarily associated with only four locations. No correlation between β-diversity and longitudinal distance or presence of dams was detected, but low species richness observed at sites located near dams indicates that these anthropogenic barriers might have an impact on local fish diversity. Unexpectedly high α-diversity levels recorded at the river mouth suggest that these sections should be further evaluated as putative "eDNA reservoirs" for rapid monitoring. By uncovering spatio-temporal changes, unrecorded biodiversity components, and putative anthropogenic impacts on fish assemblages, we further strengthen the potential of eDNA metabarcoding as a biomonitoring tool, especially in regions often neglected or difficult to access.

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

“…Advances in next-generation sequencing (NGS) have unlocked the potential use of eDNA metabarcoding for monitoring whole communities within specific taxonomic groups (e.g., fishes; Miya et al, 2020). Recent studies display its efficiency in different aquatic environments and show how it compares favorably 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 et al, 2020;Sales et al, 2021).…”

“…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.…”

“…Besides the well-known obstacles posed by incomplete reference databases, the sometimes scarce taxonomic resolution of target amplicons can hinder the inference of species occurrence. For example, the current fixed general threshold used for species assignment (e.g., > 97% similarity- Sales et al, 2021;>98% similarity-Marques et al, 2020) assumes the existence of a barcoding gap (i.e., presence of a gap between the highest intraspecific and the lowest interspecific variation within the analyzed taxonomic group; Meyer & Paulay, 2005). The accuracy of selected markers in detecting species relies on the separation between the intra-and inter-specific divergences, and the greater the overlap between these variations, the less effective DNA barcoding becomes (Meyer & Paulay, 2005).…”

More Than Expected From Old Sponge Samples: A Natural Sampler DNA Metabarcoding Assessment of Marine Fish Diversity in Nha Trang Bay (Vietnam)

“…Environmental DNA (eDNA) refers to the DNA extracted directly form an environmental sample without the need of isolating the target organisms (Thomsen and Willerslev, 2015;Creer et al, 2016;Cristescu and Hebert, 2018). Environmental DNA metabarcoding is emerging as a fast and efficient method for biodiversity monitoring that provides increased sensitivity and reduced costs compared to conventional surveys (Kelly et al, 2014b;Thomsen and Willerslev, 2015;Creer et al, 2016;Boussarie et al, 2018;Sales et al, 2020). Using eDNA provides different opportunities, such as the detection of cryptic taxa or different life stages, the rapid quantification of species richness and the non-invasiveness of sampling procedures, among others (Deiner et al, 2017).…”

Using Optimal Environmental DNA Method to Improve the Fish Diversity Survey—From Laboratory to Aquatic Life Reserve

“…The eDNA metabarcoding detected more fish species than that captured by traditional surveys, like electrofishing [23] and underwater visual censuses [24]. In addition, the eDNA metabarcoding was proved to be an efficient bio-monitoring tool for surveying fish diversity, especially in regions often ignored or difficult to access [25].…”