Harnessing decay rates for coastal marine biosecurity applications: A review of environmental DNA and RNA fate

Abstract

Marine nonindigenous species (NIS) are spreading at an alarming rate internationally through anthropogenic activities such as shipping and aquaculture, affecting local biodiversity and negatively impacting the ecosystem and human well‐being. Countries and international organizations have recognized this global threat and have begun implementing biosecurity management programs to ensure early detection, effective surveillance, and mitigation of marine NIS spread. Molecular techniques based on environmental DNA and RNA (eDNA/eRNA), collectively referred to as environmental nucleic acids (eNAs), have become a popular noninvasive tool for detecting NIS and monitoring biodiversity locally and globally. However, uncertainties about eNAs detection probabilities and the location of the source population impede the broad uptake of this tool in marine biosecurity programs. It's been hypothesized that most of these uncertainties can be explained by studying the molecules' dynamics within a marine environment and implementing eNAs distribution models. To contribute to further knowledge development in this area, our study reviews data from 20 recent reports on the degradation mechanisms and fate of eNAs in the marine environment. We classified the critical factors influencing eNAs' persistence that should be considered by biosecurity practitioners, outlining the complex interaction between the molecules' degradation processes and particular environmental conditions. To help guide the parameterization of eNAs distribution models, this review also summarizes and standardizes the marine decay rates of eDNA/eRNA from the literature. Finally, this manuscript outlines guidelines to help calculate accurate decay rates to build appropriate “fit‐for‐purpose” marine biosecurity tools for improved target detectability and greater resolution in assessing biodiversity.

Environmental DNA–RNA dynamics provide insights for effective monitoring of marine invasive species

“…These increases in extracellular DNA may lead to increases in eDNA signal, which could account for the sporadic spikes we observed in our in-situ samples and tissue control samples. Though we began to investigate this pattern using an electrophoretic assessment (Agilent 2100 Bioanalyzer ® ) for eDNA, the need to delve into the ecological properties and fate of eDNA and eRNA remains evident, particularly for eRNA in marine settings, where essential factors such as common eRNA forms (particulate, cellular, or extracellular), persistence, and degradation mechanisms are still unclear (Jo et al, 2022;Scriver et al, 2023;Yates et al, 2021). This phenomenon might not be restricted to in-situ samples alone; it could also explain the inconsistent eDNA/eRNA signal patterns in field-stored (ice) samples.…”

Beyond species detection—leveraging environmental DNA and environmental RNA to push beyond presence/absence applications

“…Additionally, the authors show that Antarctic krill eDNA is unlikely to be detected via metabarcoding if a sample was classified as containing "older" eDNA with the qPCR assays. Scriver et al (2023) review eDNA and eRNA persistence with a focus on potential applications of these processes to coastal marine biosecurity monitoring.…”

“…They conclude that the comparability of estimates of community diversity recovered from different eNAs may be marker and context-specific, highlighting the need for further comparative research and careful consideration during application. Scriver et al (2023) again highlight the potential of eRNA to detect "living" assemblages but note that a myriad of factors can potentially impact eRNA degradation (e.g., environmental conditions, genomic source, taxon, and physiology of source organisms) and thus the interpretation of data generated from it.…”

Environmental DNA and RNA in aquatic community ecology: Toward methodological standardization

“…The ecology of eRNA, including its origin, state, transport, and fate, remains poorly understood (Kagzi et al, 2022;Marshall et al, 2021;Wood et al, 2020). Before proceeding with exclusive eRNA applications, we need to establish a comprehensive understanding of these aspects (Scriver et al, 2023).…”

“…For example, some of the purported advantages of using eRNA, such as the ability to detect organisms with higher resolution compared to eDNA due to its shorter persistence and higher turnover, lack examination across aquatic systems and nonmodel organisms (Jo et al, 2023;Scriver et al, 2023).…”