Environmental DNA - An emerging tool in conservation for monitoring past and present biodiversity

By P. F. Thomsen, Eske Willerslev. 2015

1,888 citations recorded by the source corpus.

The continuous decline in Earth’s biodiversity represents a major crisis and challenge for the 21st century, and there is international political agreement to slow down or halt this decline. The challenge is in large part impeded by the lack of knowledge on the state and distribution of biodiversity – especially since the majority of species on Earth are un-described by science. All conservation efforts to save biodiversity essentially depend on the monitoring of species and populations to obtain reliable distribution patterns and population size estimates. Such monitoring has traditionally relied on physical identification of species by visual surveys and counting of individuals. However, traditional monitoring techniques remain problematic due to difficulties associated with correct identification of cryptic species or juvenile life stages, a continuous decline in taxonomic expertise, non-standardized sampling, and the invasive nature of some survey techniques. Hence, there is urgent need for alternative and efficient techniques for large-scale biodiversity monitoring. Environmental DNA (eDNA) – defined here as: genetic material obtained directly from environmental samples (soil, sediment, water, etc.) without any obvious signs of biological source material – is an efficient, non-invasive and easy-to-standardize sampling approach. Coupled with sensitive, cost-efficient and ever-advancing DNA sequencing technology, it may be an appropriate candidate for the challenge of biodiversity monitoring. Environmental DNA has been obtained from ancient as well as modern samples and encompasses single species detection to analyses of ecosystems. The research on eDNA initiated in microbiology, recognizing that culture-based methods grossly misrepresent the microbial diversity in nature. Subsequently, as a method to assess the diversity of macro-organismal communities, eDNA was first analyzed in sediments, revealing DNA from extinct and extant animals and plants, but has since been obtained from various terrestrial and aquatic environmental samples. Results from eDNA approaches have provided valuable insights to the study of ancient environments and proven useful for monitoring contemporary biodiversity in terrestrial and aquatic ecosystems. In the future, we expect the eDNA-based approaches to move from single-marker analyses of species or communities to meta-genomic surveys of entire ecosystems to predict spatial and temporal biodiversity patterns. Such advances have applications for a range of biological, geological and environmental sciences. Here we review the achievements gained through analyses of eDNA from macro-organisms in a conservation context, and discuss its potential advantages and limitations for biodiversity monitoring.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1dce750bdd7ba63a034c62c9681fbf44fee3fee3

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Citations in the corpus

A practical guide to DNA metabarcoding for entomological ecologists (2020, background): “However, sampling DNA metabarcoding workflow sediments raises the issue of whether the sample represents the present community or a previously existing community, and there is little agreement regarding the boundary separating present-day and historical DNA in sediments (Thomsen & Willerslev, 2015).”
Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates (2017, background): “(3) OTU table and match list is fed to the LULU”
Environmental DNA detects Critically Endangered largetooth sawfish in the wild (2016, background): “Environmental DNA (eDNA) is a relatively new and emerging technique that detects trace amounts of DNA from an aquatic species within water samples taken from putative habitats (Ficetola et al. 2008, Rees et al. 2014, Thomsen & Willerslev 2015).”
Extinction risk and threats to plants and fungi (2020, neutral): “Environmental DNA (eDNA) sampling is now an important conservation tool (Thomsen & Willerslev, 2015).”
Environmental DNA monitoring and management of invasive fish: comparison of eDNA and fyke netting (2017, methodology): “Recent publications have suggested that temporal factors such as breeding and migratory seasons should also be considered in eDNA surveys to increase the likelihood of detection (Barnes and Turner 2016; Thomsen and Willerslev 2015).”
Fish community assessment with eDNA metabarcoding: effects of sampling design and bioinformatic filtering (2017, background): “2014) and capable of detecting multiple species (Thomsen and Willerslev 2015).”
DNA metabarcoding in diet studies: Unveiling ecological aspects in aquatic and terrestrial ecosystems (2019, methodology): “This technique has considerable importance, for example, in the assessment of the diversity of macro‐organismal communities (Thomsen & Willerslev, 2015) and soil monitoring (e.g., for agroecosystem evaluation, assess overall taxonomic richness and relative biomass of indicator spe‐ cies)…”
The ecologist's field guide to sequence‐based identification of biodiversity (2016, methodology): “…environmental DNA (eDNA) is isolated directly from an environmental sample without ﬁrst isolating any type of organism (e.g. soil, sediment, faeces, water, air) and has been the topic of many recent reviews and special issues (Taberlet et al. 2012b; Bohmann et al. 2014; Thomsen & Willerslev 2015).”