Forensics Meets Ecology – Environmental DNA Offers New Capabilities for Marine Ecosystem and Fisheries Research

Abstract

Climatic changes and anthropogenic pressures affect biodiversity and community composition. These biodiversity shifts are recognized in marine ecosystems, but the underlying processes are barely understood so far. Importantly, human well-being highly relies on oceanic services, which are affected by anthropogenic pressures. Here, we review how interdisciplinary research approaches, with the incorporation of eDNA (environmental DNA) analyses, can help increase the understanding of complex ecosystem processes and dynamics, and how they affect ecosystem services. We discuss marine conservation issues in the light of life cycle aspects and conclude that eDNA can improve our ecological knowledge in some instances, for example, in tracking migration patterns. We also illustrate and discuss the application of eDNA analysis within the context of population genetics, epigenetics, geochemistry and oceanography. Embedded into an interdisciplinary context, eDNA can be exploited by a huge variety of methodological techniques, and can resolve spatio-temporal patterns of diversity, species, or even populations within ecological, evolutionary, and management frameworks.

Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward

“…With continuous method development, validation, refinement, and standardization, as well as with improved reference sequence databases and accessible eDNA data repositories, the eDNA approach will be able to greatly streamline routine biodiversity surveys of fish and other aquatic organisms. It will also become an indispensable tool for wildlife ecologists, conservation biologists, and fisheries managers, enabling them to uncover timely information about fish community responses to ongoing environmental changes at local, regional, and global scales (Evans & Lamberti, 2018; Hansen et al, 2018; Schadewell & Adams, 2021). In the near future, global integration of autonomous eDNA samplers and analysers, real‐time sequencing devices, machine‐learning algorithms, big data, and cloud computing are expected to enable automated biomonitoring and reconstruction of the Earth's ecological networks, hence allowing both sensitive detection of biodiversity patterns and credible predictions of ecological state shifts (Arribas et al, 2021; Bohan et al, 2017; Cordier et al, 2021; Keck et al, 2017).…”

“…The topics have included sample collection, eDNA enrichment and extraction, primer choices, polymerase chain reaction (PCR) techniques, bioinformatics filtering and processing of sequence reads, and statistical treatments of eDNA data (Kumar et al, 2020; Miya, 2022; Miya et al, 2020; Shu et al, 2020; Tsuji et al, 2019; Wang et al, 2021). In addition, several recent reviews have specifically focused on eDNA applications in freshwater and marine fisheries science (Evans & Lamberti, 2018; Hansen et al, 2018; Jerde, 2021; Schadewell & Adams, 2021). To avoid reiterating much of the laboratory processing procedures that have already been extensively reviewed, our primary focus is on more ecologically relevant aspects of eDNA techniques and applications in fish‐related research.…”

“…Although studies so far have invariably relied on tissue samples for epigenetic sequencing, they have firmly established the relationship between the physiological state and epigenetic patterns and have paved the way for eDNA-based epigenetic analysis of wild fish populations.But before eDNA epigenetic analysis can be applied in the field, a number of technical challenges still must be addressed (e.g., uneven contributions of different individuals to the total eDNA pool, mixed DNA source tissue types [different tissues can contain different epigenetic patterns], and degradation of epigenetic modifications over time). Those variables can bias and obscure correlations between particular epigenetic signals and physiological characteristics(Schadewell & Adams, 2021;Sigsgaard et al, 2020). With careful methodological validation, eDNA epigenetics may provide an exciting avenue for non-invasive measurements of age composition, stress response, health condition, and other valuable information that are important for conservation assessments and fishery stock management.…”

Using environmental DNA method to clarify the distribution of Pampus echinogaster in the East China Sea

“…For example, seasonal and vertical migrations may be affected by hydrodynamic movements that affect animal behavior. These behavior changes may in turn affect the eDNA signal (Croll et al, 2005;Schadewell and Adams, 2021). P. echinogaster is a migratory fish in the middle and upper layers (Oh et al, 2010).…”

Benthic invertebrates in Svalbard fjords—when metabarcoding does not outperform traditional biodiversity assessment

“…, Tautz et al, 2003 ), and identification with DNA-barcodes ( Hebert et al, 2003 ) been used as efficient alternatives to traditional methods. The technological developments of high throughput DNA sequencing have offered new tools to study biodiversity based on environmental DNA (eDNA) ( Taberlet et al, 2012a , 2012b ; Ji et al, 2013 ; Gibson et al, 2015 ; Lacoursière-Roussel et al, 2018 ; Wangensteen & Turon, 2017 ; Schadewell & Adams, 2021 ; Bohmann et al, 2021 ; Mugnai et al, 2021 ). Whilst some applications in marine environments have been relatively open-end inventories of metazoan diversity ( e.g.…”