Observing Life in the Sea Using Environmental DNA

Abstract

The use of environmental DNA (eDNA) for studying the ecology and variability of life in the sea is reviewed here in the context of US interagency Marine Biodiversity Observation Network (MBON) projects. Much of the information in this paper comes from samples collected within US National Marine Sanctuaries. The field of eDNA is relatively new but growing rapidly, and it has the potential to disrupt current paradigms developed on the basis of existing measurement methods. After a general review of the field, we provide specific examples of the type of information that eDNA provides regarding the changing distribution of life in the sea over space (horizontally and vertically) and time. We conclude that eDNA analyses yield results that are similar to those collected using traditional observation methods, are complementary to them, and because of the breadth of information provided, have the potential to improve conservation and management practices. Moreover, through technology development and standardization of methods, eDNA offers a means to scale biological observations globally to a level similar to those currently made for ocean physics and biogeochemistry. This scaling can ultimately result in a far better understanding of global marine biodiversity and contribute to better management and sustainable use of the world ocean. Improved information management systems that track methods and associated metadata, together with international coordination, will be needed to realize a global eDNA observation network.

Expanding the temporal and spatial scales of environmental DNA research with autonomous sampling

“…DNA extraction concentrations were quantified using a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific). Differences in yields between samples collected by manual and autonomous methods were evaluated by running Student's t test in R. The primer sequences, thermocycling parameters, purification of PCR products, equimolar pooling of PCR products, quantification of pool concentration, and library preparation methods for all of the metabarcoding primer sets used in this study are in the supporting information section Supplemental Methods and are also described in Chavez et al, 2021.…”

“…Molecular metabarcoding of eDNA is now used routinely to survey community composition and estimate diversity in freshwater and marine habitats (e.g., Berry et al, 2019; Jerde et al, 2019; Stoeckle et al, 2020). However, the development of optimal sampling protocols is crucial for accurate and reproducible eDNA results (Deiner et al, 2015) that can be integrated globally (Chavez et al, 2021). Improvements in collection methods, DNA extractions, gene target choice, and bioinformatic databases have led to increasingly powerful eDNA studies in the marine environment showing good agreement with visual and trawl surveys (Cilleros, 2019; Stoeckle et al, 2020; Thomsen et al, 2016; Yamamoto et al, 2017).…”

FathomNet: A global image database for enabling artificial intelligence in the ocean

“…The promising field of eDNA allows for identification of biological communities based on their shed DNA in the water column. While eDNA studies provide broad-scale views of biological communities with only a few discrete samples, determining the spatial source of the DNA, relating the measurements to population sizes, and the presence of confounding non-marine biological markers in samples are active areas of research that still need to be addressed 9 . Ultimately, -omics and acoustics approaches rely on visual observations for verification.…”

Biodiversity and Interannual Variation of Harmful Algal Bloom Species in the Coastal Sea of Qinhuangdao, China

“…The metabarcoding approach is an important complement to traditional observational methods. With the perfection of technology and standardization of sampling methods, it could even bring global biomonitoring to a level of observation similar to that of ocean physics and biogeochemistry [ 51 ]. In recent decades, metabarcoding methods, particularly Amplicon Sequence Variants (ASVs)-based metabarcoding analysis methods with the Divisive Amplicon Denoising Algorithm (DADA2), have been widely used to investigate the composition and distribution of plankton species [ 52 , 53 , 54 ].…”