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Environmental DNA (eDNA) is helping to explore the deep ocean

Researchers have found that environmental DNA (eDNA) concentrations can be used to reliably reveal information about migration patterns of organisms in the deep ocean.

The mesopelagic zone, or the twilight zone, is the largest habitat on earth. It describes the area of the sea between 200 and 1,000 metres deep. The mesopelagic zone supports considerable biomass and biodiversity. The ecosystem also has an important role in the global carbon cycle and marine food webs. However, to date it still remains poorly understood. This is largely because studying such a vast and remote area is extremely difficult. Many marine creatures found in the mesopelagic zone are easily destroyed during sampling and almost impossible to catch with traditional nets. Although advances in acoustic technologies have enabled more accurate estimates of biomass over time, questions about the diversity and distribution of species still remain unanswered.

Studying the ocean using eDNA

To answer some of these questions, scientists are focussed on developing new tools to investigate the mesopelagic zone and monitor its inhabitants. One such promising method is the analysis of environmental DNA (eDNA) captured from water samples. Molecular tools such as quantitative PCR (qPCR) or metabarcoding can be used to provide information about the presence of species, even from small volumes of water. This genetic analysis can be conducted on a range of materials, including scales, faecal pellets or tissue residue.

Using eDNA for biomass surveys is easier than collecting organisms, especially in less accessible habitats, and it enables scientists to detect species that are rare or traditionally hard to sample. However, little is understood about how eDNA is distributed in the ocean. This is because marine life is mobile and physical processes in the sea can transport eDNA after it is released by a host. This is especially true in the mesopelagic zone, where species vertically migrate hundreds of metres each day to and from the surface. Therefore, it is crucial to link the location at which eDNA has been shed to the place where it was collected in a water sample.

Simulating eDNA distribution

Recently, researchers at the Woods Hole Oceanographic Institution (WHOI) developed a mechanistic model to simulate the distribution of eDNA after it has been shed from a host organism. They did this by monitoring the impact of key biological and physical parameters on the spatial and temporal variability in eDNA concentration. The results were published in Scientific Reports.

The team found that physical processes, such as currents, wind and ocean mixing did not have a significant impact on the distribution of the eDNA. Instead, changes in the concentration of eDNA accurately reflected the movement of creatures as they travelled between the mesopelagic zone and the surface. In fact, it was revealed that most eDNA signals remained within 20 metres of where they were first shed.

This means that eDNA concentration could be used to reliably answer ecological questions about marine organisms, including what depths species are located at during the day and throughout the night. In addition, eDNA concentration variability could also be used to explain migration patterns between the mesopelagic zone and the surface.

Elizabeth Andruszkiewicz Allen, a Postdoctoral Fellow at WHOI during the study, explained:

“A major finding of our paper is that the eDNA signal doesn’t go away immediately if the animal moves up or down in the water column. That helps us answer some big questions we can’t answer with net tows or acoustic data. Which species are migrating? What percentage of them migrate each day? And who is an early or late migrator?”

Future eDNA sampling of ocean habitats

This was one of the first studies to model eDNA concentration in the ocean. The findings are promising and show how useful eDNA could be for studying animal migration and the presence of marine organisms in difficult-to-access parts of the ocean, as well as in other aquatic environments. There is also the potential for eDNA field sampling to be used in combination with other more traditional sampling methods, including nets and acoustics, to accelerate our understanding of ocean habitats.

Weifeng Zhang, a Physical Oceanographer at WHOI and co-author of the study, said:

“Before this work, we couldn’t confidently say what happened to the eDNA shed by mesopelagic zone species. But a very clear pattern showed up in the model, providing a baseline understanding of the concentration of eDNA between the surface and deep layers over time. With this new knowledge, field researchers will be able to target where they take the precious water samples so they can identify the migrating species and estimate the percentage of animals in each species group that migrate each day.”

Image credit: IDDRI

More on these topics

eDNA / Environment / Population Genetics

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