Environmental DNA-Based Methods in Biodiversity Monitoring of Protected Areas: Application Range, Limitations, and Needs

Abstract

Novel methods for species detection based on collection of environmental DNA (eDNA) are not only important in biodiversity assessment in a scientific context, but are also increasingly being applied in conservation practice. The eDNA-based biodiversity detection methods have significant potential for regular use in biodiversity status assessments and conservation actions in protected areas (PAs) and other effective area-based conservation measures (OECMs) worldwide. Species detection based on DNA from environmental samples, such as water, sediment, soil, air, or organic material, has a broad application scope with precise, comprehensive, and rapid species identification. Here, we provide an overview of the application range of eDNA-based methods for biodiversity monitoring in PAs, evaluate environmental assessments in which this technology has already been implemented for nature conservation, and examine the challenges that can hamper further application in real world practice. Based on the outcomes of two projects, practical experience, and current scientific literature focusing on their application, we conclude that eDNA-based species detection methods provide promising novel approaches that have strong potential as supplement methods, or in some cases even as substitutes for the conventional monitoring methods used for PAs. This advancement is expected to affect decision-making in biodiversity conservation efforts in PAs and OECMs.

PROTAX-GPU: a scalable probabilistic taxonomic classification system for DNA barcodes

“…Our implementation achieved over a 1000 × speedup compared with the optimized CPU version, fitting within the 7.8 GB of VRAM of a standard consumer-grade GPU. This advance in computational efficiency has significant implications for environmental DNA (eDNA) analysis, which often involves processing large volumes of sequence data [27]. This tool enhances our ability to identify elusive or threatened species, detect invasive species, and improve biodiversity assessments with minimal habitat disturbance.…”

Environmental DNA revealed high accuracy in detection of the Eurasian otter in Himalaya

“…Owing to the challenging conditions, very few studies have addressed the issue of biodiversity monitoring in the Himalayan region (Laxmi, Sehgal & Rawat, 2022; Lim et al, 2022; Pascher, Švara & Jungmeier, 2022). This study suggests that the integration of traditional field survey and eDNA‐based approaches can play a key role in assessing freshwater biodiversity in this fragile and challenging ecosystem.…”

“…Environmental DNA (eDNA)‐based investigations can help overcome the limits of traditional species detection methods and have immense potential for understanding population ecology and distribution trends (Rees et al, 2014; Goldberg, Strickler & Pilliod, 2015). eDNA studies rely on DNA fragments released in the environment (soil, water, air) from faeces, mucus, skin cells, or other sources of organism DNA to infer the presence of a target species (Taberlet et al, 2012; Harrison, Sunday & Rogers, 2019; Prié et al, 2020; Pascher, Švara & Jungmeier, 2022). The application of molecular‐based techniques targeting eDNA has proven to be particularly useful for detecting rare and elusive species in aquatic environments (Hinlo et al, 2018; Valsecchi et al, 2022; Valsecchi et al, 2023), including the Eurasian otter ( Lutra lutra ) (Jamwal et al, 2021).…”

New-Generation Sequencing Technology in Diagnosis of Fungal Plant Pathogens: A Dream Comes True?

“…They can alter their lifestyle, such as in the adaptation of endophytes into parasites, and vice versa, by omics, tools new methods for exploring plant-microbe interaction and elucidating the different behaviors are developing [68]. Finally, microbiome studies are widely used in environmental studies, i.e., to define biodiversity status and implement conservation actions in protected areas [69,70], to define the role of several factors (host taxon and tissues, seasonality) in shaping the composition of both fungi and bacteria in tropical forests [71], or to compare the microbiomes of trees and of associated herbaceous plants used as phytoremediation [72]. Oomycetes are the causal agents of outbreaks especially in natural environments.…”