Environmental DNA: State-of-the-art of its application for fisheries assessment in marine environments

Abstract

Fisheries management involves a broad and complex set of tasks that are necessary to prevent overfishing and to help the recovery of overfished stock. Monitoring fishing activities based on two main sources, landings data and scientific surveys, is a challenging task. Fisheries collection data is often limited, which compromises the accuracy of the results obtained. Therefore, several emerging applications of molecular methods have the potential to provide unique understanding of ecological processes in marine environments and to build stronger empirical underpinnings for the Ecosystem-Based Fisheries Management. Environmental DNA (eDNA) is a complex mixture of genetic material shed by those organisms that inhabit a given environment, whereby DNA is extracted from an environmental sample without accessing the target organism. eDNA studies can be categorized into two main approaches, i) eDNA metabarcoding or semi-targeted (community) approaches and ii) species-specific or targeted approaches (single). Although both categories are often discussed, they differ drastically in their methodology, interpretations and accuracy. Both approaches involve a series of steps that include eDNA capture, preservation, extraction and amplification. This detection will depend on the affinity to the targeted taxa sequences and completeness and accuracy of DNA reference collection databases. The eDNA method applied in marine environments are probably the most challenging aquatic environments for applying this technique. This is because of the extreme relationship between water-volume to biomass, dynamics and the physical and chemical properties of seawater that affect dispersion, dilution and preservation. Here, we review the present application of this novel method in fishery assessment in marine environments. To date, many studies suggest that this method offers the potential to revolutionize fisheries monitoring, which will contribute to improving the range of tasks involved in fisheries management. The compelling conclusion is that the methodological steps including in eDNA surveys should be standardized and that research efforts should focus on developing appropriately validated tests to address environmental and sampling factors that may affect eDNA detection in marine environments in order to draw reliable conclusions. This bioassessment tool can assist fisheries professionals in achieve their research, management, and conservation objectives, but not as a replacement for time-proven assessment methods.

Age estimation in fishes using epigenetic clocks: Applications to fisheries management and conservation biology

“…Epigenetic clocks constitute a new age estimation tool that is less than 10 years old taking into account that the human epigenetic clock, the first one, was published in December of 2013 (Horvath, 2013). Further, in contrast to other molecular approaches that can be applied to fisheries management such as environmental DNA (eDNA) or Close-kin mark-recapture (CKMR), reviewed elsewhere in this volume (Ramıŕez-Amaro et al, 2022), no literature reviews exist on the subject of epigenetic clocks to estimate age in fishes, although genomic predictors of lifespan do exist for vertebrates (Mayne et al, 2020). Also, to the best of our knowledge, there are only epigenetic clocks for eight fish species so far (Table 1).…”

Unlocking Antarctic molecular time-capsules – recovering historical environmental DNA from museum-preserved sponges

“…This resolution has been linked to high degradation rates of DNA in the environment and influenced by biotic, e.g., bacterial activity (Tsuji et al 2017), and abiotic factors including pH and temperature (Strickler et al 2015; Tsuji et al 2017). The rapid degradation of eDNA in the open marine environment, however, also limits aquatic eDNA surveys to monitoring contemporary biodiversity patterns (Ramírez-Amaro et al 2022).…”

State-of-the-art of data analyses in environmental DNA approaches towards its applicability to sustainable fisheries management

“…As fisheries science is urgently needing to collect an increasing amount of data to assess the long-term sustainability of fish resources, environmental DNA approaches (eDNA, Taberlet et al, 2012) have become a promising technology in simplifying survey tasks. Hence, studies using eDNA to investigate marine species richness, distribution, and abundance expanded in the very last years (reviewed Gilbey et al, 2021;Jo et al, 2022;Miya, 2022;Ramıŕez-Amaro et al, 2022;Rourke et al, 2022). eDNA refers to DNA that can be extracted from environmental samples (such as soil, water, or air), without first isolating any target organisms.…”

“…Both strategies share the key characteristic of non-invasive indirect sampling but differ in their purpose, methodology, and interpretations. The current state of the art of sequencing and quantification technologies makes both eDNA approaches very powerful in helping sustainable marine fisheries surveys and monitoring (Gilbey et al, 2021;Ramıŕez-Amaro et al, 2022;Rourke et al, 2022). On the one hand, the metabarcoding or community eDNA approach is intended to characterize the species community living in a given environment (Alberdi et al, 2017).…”

“…Since the sea is a highly variable environment, and applications of eDNA cover a wide spectrum of scientific questions (Barnes & Turner, 2016), it is noted disparity among results of eDNA analyses. Such incongruencies have raised concerns on the potential applicability of eDNA surveys to help fisheries sustainable management (Hansen et al, 2018;Ramıŕez-Amaro et al, 2022). It has been highlighted that part of the disparate results found among studies could be explained by the heterogeneity across pipelines and bioinformatics tools used for data processing and analyses (Creedy et al, 2022).…”