Assessing environmental DNA metabarcoding and camera trap surveys as complementary tools for biomonitoring of remote desert water bodies

Abstract

Biodiversity assessments are indispensable tools for planning and monitoring conservation strategies. Camera traps (CT) are widely used to monitor wildlife and have proven their usefulness. Environmental DNA (eDNA)‐based approaches are increasingly implemented for biomonitoring, combining sensitivity, high taxonomic coverage and resolution, non‐invasiveness and easiness of sampling, but remain challenging for terrestrial fauna. However, in remote desert areas where scattered water bodies attract terrestrial species, which release their DNA into the water, this method presents a unique opportunity for their detection. In order to identify the most efficient method for a given study system, comparative studies are needed. Here, we compare CT and DNA metabarcoding of water samples collected from two desert ecosystems, the Trans‐Altai Gobi in Mongolia and the Kalahari in Botswana. We recorded with CT the visiting patterns of wildlife and studied the correlation with the biodiversity captured with the eDNA approach. The aim of the present study was threefold: (a) to investigate how well waterborne eDNA captures signals of terrestrial fauna in remote desert environments, which have been so far neglected in terms of biomonitoring efforts; (b) to compare two distinct approaches for biomonitoring in such environments; and (c) to draw recommendations for future eDNA‐based biomonitoring. We found significant correlations between the two methodologies and describe a detectability score based on variables extracted from CT data and the visiting patterns of wildlife. This supports the use of eDNA‐based biomonitoring in these ecosystems and encourages further research to integrate the methodology in the planning and monitoring of conservation strategies.

Constructing ecological indices for urban environments using species distribution models

“…Using eDNA from soil, sediment, water, or air sample inventories, we can complement existing species monitoring efforts through the identification of thousands of species at once, including plants, animals, and microbes (Stat et al 2019;Lin et al 2021;Nørgaard et al 2021). Use of eDNA can greatly complement traditional species monitoring by enabling greater taxonomic resolution (Deiner et al 2017;Ruppert et al 2019), the detection of species which tend to avoid the presence of humans (Yonezawa et al 2020;Mas-Carrió et al 2021), or organisms such as bacteria and fungi which can be difficult to monitor using traditional observations (Frøslev et al 2019;Liddicoat et al 2022). Comparisons of eDNA with observational methods have also indicated their potential to help capture additional elements of ecologically relevant information, such as the functional diversity of various groups of species (Aglieri et al, 2021;Donald et al 2021;Sigsgaard et al 2021), particularly with regards to identifying ecological indicators (Yan et al 2018;Blattner et al 2021;Seymour et al 2021).…”

A review of applications of environmental DNA for reptile conservation and management

“…eDNA methods for detecting terrestrial reptiles are not limited to soil and sediment samples. Several recent studies have shown the potential of using water samples to detect terrestrial mammals (Harper, Griffiths, et al, 2019 ; Lyet et al, 2021 ; Mas‐Carrió et al, 2021 ; Mena et al, 2021 ), and birds (Mas‐Carrió et al, 2021 ). Terrestrial animals visit water bodies, and their DNA can be transferred to aquatic systems directly through behaviors such as foraging, drinking, swimming, defecation, and bathing, or indirectly via rain and soil drainage (Coutant et al, 2021 ).…”

“…Terrestrial animals visit water bodies, and their DNA can be transferred to aquatic systems directly through behaviors such as foraging, drinking, swimming, defecation, and bathing, or indirectly via rain and soil drainage (Coutant et al, 2021 ). Mas‐Carrió et al ( 2021 ) used the 12S primer VERT01 (Taberlet et al, 2018 ) to target terrestrial birds, reptiles, and mammals in remote desert water bodies, although they did not detect any reptiles through eDNA or through camera trap surveys.…”

“…eDNA methods for detecting terrestrial reptiles are not limited to soil and sediment samples. Several recent studies have shown the potential of using water samples to detect terrestrial mammals (Harper, Griffiths, et al, 2019;Lyet et al, 2021;Mas-Carrió et al, 2021;Mena et al, 2021), and birds (Mas-Carrió et al, 2021).…”

Holistic monitoring of freshwater and terrestrial vertebrates by camera trapping and environmental DNA

“…Similarly, metabarcoding analysis of eDNA from stream water (Lyet et al, 2021) and terrestrial sediments (Leempoel et al, 2020) combined with CTs has been found to be efficient for monitoring terrestrial mammals. The number of such vertebrate studies combining water eDNA and CTs is growing rapidly, in covering all sorts of habitats from reefs (Stat et al, 2018; Boussarie et al, 2018) to ponds (Mas-Carrió et al, 2022; Harper et al, 2019).…”