Inferring functional diversity from environmental DNA metabarcoding

Abstract

Environmental DNA (eDNA) metabarcoding is a reliable method to assess taxonomic diversity, but the incompleteness of genetic reference databases prevents the assignation of many sequences to a given species. Functional diversity (FD) is a key biodiversity facet to monitor, but it requires the identification of all species within communities to account for their trait values. So, the ability of eDNA‐based inventories to estimate the “true” level of FD is unknown. Here, using fish surveys in two representative temperate and tropical rivers, with a quasi‐exhaustive genetic and trait database, we measured the bias and variability of different FD indices when calculated with uncertainty in taxonomic assignment at the genus and family level. Our results show that when measuring FD indices with species randomly chosen within genera and families, the bias cannot exceed 30% from real observed FD values. The variability is higher for species‐poorer communities and when those communities are composed of genera and families with high functional heterogeneity. Despite taxonomic uncertainty, our results demonstrate the potential of eDNA surveys to estimate reliable FD values.

The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves

“…Therefore, seaports and reserves depending on the present communities would have different ecological functions. Characterizing seaports and reserves functions based on identified taxonomic groups based on traits databases would give additional knowledge by indirectly assess ecological functioning of the habitats sampled (Aglieri et al., 2021; Condachou et al., 2023; Marques et al., 2021). This approach would require wide taxonomic coverage and resolution, and would allow to point out which functions are altered in urbanized habitats.…”

First application of digital-PCR in oenology for the specific detection of intact cells ofBrettanomyces bruxellensisin the winemaking process

“…Digital-PCR, the latest generation of PCR technology, emerges as a promising candidate among available techniques. dPCR undergoes continuous development in human biology and is increasingly utilized in environmental biology (Condachou et al 2024), offering reliable and absolute quantification, resilient to PCR-reaction inhibitors (Kuypers and Jerome 2017).…”

Beyond species detection—leveraging environmental DNA and environmental RNA to push beyond presence/absence applications

“…An interesting simulation on the variability of estimates of functional diversity for fish communities based on eDNA metabarcoding was carried out by Condachou et al (2023). By employing eDNA analysis to infer species composition, they demonstrate that it may be possible to estimate the functional characteristics of a community in conjunction with another database containing functional attributes of the inhabiting organisms.…”

“…The assessment of functional diversity, however, may be influenced by uncertainty in the taxonomic assignment of species due to variations in taxonomic granularity. Condachou et al (2023) manipulate the uncertainty in the taxonomic assignment for fish species and found that misidentification of species within the same genus or family did not cause variability in functional diversity higher than 30% in comparison with a case with perfect taxonomic identification at the species level. This is a case study focusing on two sample rivers, but it raises warning flags for the general functional diversity estimation based on metabarcoding data.…”