Course: Environmental DNA in oceanic survey

Japanese URL
Prof. Ahn's research theme
Program-Specific Assistant Professor Ahn retired from Hokkaido University in March 2023.
Prof. Hyojin Ahn Page

Environmental DNA (eDNA) is genetic material released from organisms into the environment, and it has been developed as an alternative species monitoring technique in the last decade. Its merits include convenience and noninvasiveness compared with directly sampling organisms, and eDNA has now become a valuable tool for various surveys, including biodiversity assessment and detection of alien, rare, or endangered species.
About environmental DNA URL

Environmental DNA analysis can be broadly used by sampling soil, sediment, water and ice, and a wide range of studies on eDNA in aquatic environments have been reported. However, most studies were conducted in rivers, lakes or coastal areas within 10 km from land and oceanic surveys with eDNA are still rare.
[Open Access] Yates et al., 2019, Environmental DNA URL

　　
Water sampling in the offshore ocean is not easy because it requires a ship or research vessel with proper equipment (e.g., Niskin bottles). In addition, since the spatial dimension is larger and DNA is likely more diluted in the ocean, large volumes of water are necessary to detect DNA in low densities in the water column. Bessey et al. (2020) investigated how water sample volume affects the detections of species in a fish community by using various water sample volumes from 25 to 2000 ml, and more species were detected as more water was filtered.
[Open Access] Bessey et al., 2020, Environmental DNA URL

　
Here I introduce the methods of water sampling and filtration for eDNA collection in ship.

There are two ways to sample a large amount of water on board.
1) Using water sampler (e.g. Niskin bottles): Water in specific depth(s) can be sampled. Also, environmental data can be obtained in combination with CTD.
2) From pump of ship: Surface water can be obtained from a tap the ship's continuous flow-through seawater system that is connected to a pump drawing water through the system in real time.
(Caution! Not every ship or vessel has this pump system.)
Sampled water should either be filtered immediately or treated with benzalkonium, kept cool until back to laboratory.
English subtitle is available!

Surface water from off Hokkaido was sampled following methods shown above video, and stored in six of 10 L-tank as evenly as possible.
We tried to increase detections of eDNA with the experimental design described below.
In present study, we hypothesized that the oceanic water is comparably clear and does not contain any materials so eDNA cannot attach.
And this may cause the low detection rate that eDNA pass through the filter cartridge.
Therefore we added four materials (sediment, diatomite, zicronia bead, molecular sieve) during filtration, and tried 0.22 um pore size filter in comparison with 0.45 um filter, expecting a higher detection rate.
Each experimental treatment had 5 replicates with 2-L filtered samples.
The experiment was conducted twice in summer and winter, and the results differed by season.
In the summer trial, Exp4 which added diatomite was significantly higher than others, while Exp5 which added zirconia bead was the highest in the winter trial.
From the result of GLM (generalized linear model), all additive materials affect the detection rate significantly.
On the other hand, the pore size showed no significant difference.
Seasonal change of fish community URL

Environmental DNA in oceanic survey