Linking the state of environmental DNA to its application for biomonitoring and stock assessment: Targeting mitochondrial/nuclear genes, and different DNA fragment lengths and particle sizes

Abstract

Environmental DNA (eDNA) analysis is a revolutionary tool for non‐invasive, cost‐effective, and highly sensitive monitoring of species distribution and abundance; however, there remain some uncertainties related to eDNA detection and quantification, as well as limitations in terms of its ecological interpretation. Although these may be elucidated by better understanding the characteristics and dynamics of eDNA, insight into such basic eDNA information has been limited in this decade, contrary to the advancements in eDNA applications targeting various taxa and environments. This review compiled previous findings regarding the characteristics and dynamics of macrobial eDNA and provides insights into how the basic knowledge of eDNA can contribute to the refinement and development of eDNA analysis for biomonitoring and stock assessment. A literature survey revealed that studies on the cellular and molecular state of eDNA were particularly lacking (18/728 papers from 2008 to 2020), resulting in a limited understanding regarding the process of eDNA transport and degradation. This review highlighted a number of studies targeting various types of eDNA beyond short mitochondrial DNA fragments (nuclear eDNA, longer eDNA fragments, and larger eDNA particles) to show how information on the state of eDNA improves the reliability of species detection and accuracy of abundance estimation, as well as provide more detailed information on individuals other than their presence and abundance. Linking the state of eDNA to its application will advance the analysis of eDNA and improve its application as a tool for monitoring biodiversity, ecosystem function, and fisheries resources.

Fine-tuning the performance of abundance estimation based on environmental DNA (eDNA) focusing on eDNA particle size and marker length

“…Alternatively, visualization of eDNA particles via fluorescence in situ hybridization (FISH) techniques and immunostaining (e.g., Kogure et al, 2006;Amann & Fuchs, 2008) may directly offer information on its cellular and the molecular structure. Although different particle sizes of eDNA can result in other transport and diffusion dynamics, the effect of the eDNA state (e.g., particle size, weight) on its transport and diffusion dynamics has not been elucidated (Shogren et al, 2016;Jo et al, 2021a). The additional information would explain the heterogeneous distribution of eDNA in water, associating its multiple states, and help support our hypothesis above.…”

“…The target eDNA, which is detected by a polymerase chain reaction (PCR), allows to evaluate species presence and relative abundance, making eDNA analysis a non-disruptive, cost-effective, and high-sensitivity monitoring tool compared with traditional capture-based surveys (e.g., Thomsen et al, 2012;Miya et al, 2015;Jo et al, 2020a;Lopes et al, 2021). Although there is potential for eDNA-based biomonitoring to become an essential approach for biodiversity and ecosystem conservation, knowledge on the production source and persistence state of eDNA, as well as its transport and degradation, is lacking (Barnes & Turner, 2016;Harrison et al, 2019;Jo et al, 2021a). The lack of or scarcity in understanding the characteristics and dynamics of eDNA causes uncertainty in eDNA-based species inferences, often resulting in ecological interpretation difficulty (Hansen et al, 2018).…”

Analysis of the persistence and particle size distributional shift of sperm-derived environmental DNA to monitor Jack Mackerel spawning activity

“…Moreover, as the sperm nucleus is only overlayed with the plasma membrane and a thin cytoplasmic layer, it is likely to be degraded more rapidly by microbes and extracellular enzymes, being supplied to the smaller fractions. Additionally, if these speculations are correct, then the sperm-derived eDNA may have short-lived persistence in larger size fractions, which may allow for the selective collection of sperm derived-eDNA based only on size fraction for some time after spawning 28 . Time-limited and/or selective collection of sperm-derived DNA would help to detect spawning activity with higher sensitivity on the basis of the observation of spikes in concentration or ratio caused by sperm release.…”

The multiple states of environmental DNA and what is known about their persistence in aquatic environments

“…When organisms shed DNA into the water column, this gives rise to extra-organismal eDNA (i.e. DNA no longer associated with its organism of origin) and can take the form of at least four states 9,10 . These four states include: dissolved DNA, DNA bound to the surfaces of suspended particles 3,6,10 , and DNA still encapsulated in either a cell or an organelle 11 .…”

“…DNA no longer associated with its organism of origin) and can take the form of at least four states 9,10 . These four states include: dissolved DNA, DNA bound to the surfaces of suspended particles 3,6,10 , and DNA still encapsulated in either a cell or an organelle 11 . What we currently lack is a robust understanding of how water chemistry and other environmental parameters affect which eDNA state(s) predominate in specific aquatic environments and how they persist.…”