Utilizing the state of environmental DNA (eDNA) to incorporate time-scale information into eDNA analysis

Abstract

Environmental DNA (eDNA) analysis allows cost-effective and non-destructive biomonitoring with a high detection sensitivity in terrestrial and aquatic environments. However, the eDNA results can sometimes include false-positive inferences of target organisms owing to the detection of aged eDNA that has long since been released from the individual and is more likely to be detected at a site further away from its source. In order to address the issue, this manuscript focuses on the state of eDNA, proposing new methodologies to estimate the age of eDNA: (1) DNA damage rate, (2) eDNA particle size distribution, and (3) viable cell-derived eDNA. In addition, the manuscript also focuses on the shorter persistence of environmental RNA (eRNA) compared with eDNA, highlighting the application of eRNA and environmental nucleic acid ratio for assessing the age of the genetic materials in water. Although substantial further research is essential to support the feasibility of these methodologies, incorporating time-scale information into eDNA analysis would update current eDNA analysis, improve the accuracy and reliability of eDNA-based monitoring, and further refine eDNA analysis as a useful monitoring tool in ecology, fisheries and various environmental sciences.

Developing an eDNA approach for wetland biomonitoring: Insights on technical and conventional approaches

“…Understanding the persistence and transport of eDNA signals is important because it indicates the relative age of the deposited DNA (Jo, 2023) and its spatial representativeness (Civade et al, 2016) wetland environments, DNA persistence is likely to be significantly impacted by abiotic factors (e.g., pH <5, water temperature > 25°C, limited dispersion; Goldberg et al, 2018). However, different environments have varying intensities of physicochemical parameters and hydrological processes, which may be attributed to varying eDNA decay rates (Jo & Minamoto, 2021;Seymour et al, 2018).…”

A review of data collection methods used to monitor the associations of wild species with marine aquaculture sites

“…Finally, similar methods targeting RNA are emerging. Environmental RNA (eRNA) degrades faster than DNA in environmental matrices and the ratio of eDNA and eRNA may be an appealing approach because it potentially enhances ability to discriminate between live (or very recently alive) species and locally‐present organisms versus detections resulting from non‐local or transient sources 256–258 …”

Advancing River Health Assessments: Integrating Microscopy and Molecular Techniques through Diatom Indices

“…Therefore, the integration of microscopic examination with molecular analysis in diatom research signifies a major advancement in our ability to assess and monitor river ecosystem health. By leveraging the benefits of both traditional and modern methods, researchers and environmental managers can achieve a more nuanced and effective water quality assessment methods [25,62,65]. This integrated approach underscores the ongoing need for advanced bioinformatics expertise, collaborative research, and continuous innovation in the pursuit of sustainable water management and conservation strategies.…”

“…Despite their importance, traditional methods for benthic diatombased water quality assessment in river ecosystems are hampered by challenges including subjective interpretations, the need for specialized taxonomic expertise, and difficulties in processing samples. These issues mirror the technical obstacles encountered in environmental DNA (eDNA) analysis, such as contamination and taxonomic inconsistencies [24][25][26][27].…”