Due to massive economic importance (Figure 1.0), much of marine research is focused on commercial fish and shellfish stock surveys. In recent light, the methods of these surveys are under scrutiny due to the expensive and environmentally damaging strategies they employ.
Figure 1.0 Amount of fish caught worldwide (orange) and how many fish produced through aquaculture (blue) measured in million tonnes from 1950 to 2015. FAO The state of world fisheries and aquaculture review, 2018.
In response, governments and marine surveyors are investigating novel ways to mitigate these impacts, and one recently developed tool for biomonitoring is using environmental DNA (eDNA). My research is centered around investigating whether eDNA can be used efficiently, effectively and accurately during such stock surveys. Here I summarise my methods and challenges of collecting eDNA in the field from my most recent campaign of collecting eDNA for marine pelagic stock assessments.
PELTIC 2018 Stock Assessment Survey
The PELTIC survey is carried out by Cefas with their research vessel the Cefas Endeavour and is one of the UK’s largest pelagic stock surveys. The survey itself starts from the Bristol Channel and covers the entire English Channel within the time frame of 1 month.
During this survey I collected water samples from 51 different locations (Figure 2.0), 29 of which were at different depths in the water column and the rest were collected at the surface of the sea.
Figure 2.0 Map of the area sampled (blue), within this area 51 sample sites were sampled from. 29 (yellow) primary stations where different depths were taken dependent on stratification and 21 (red)stations were sampled at during trawling. Each sample site is separated by at least 2.2 nautical miles
How the Samples were Collected
There are two main methods of collection that I used;
1. Rosette sampling
A rosette (Image 1.0) refers to a metal framework that within it holds niskin bottles that can remotely trap water from varying depth and return to the surface. For my sampling at each of the 29 depth stations this sampling strategy was used. To determine the sampling depths, I used a combination of the total depth and stratification information (Figure 3.0) given from a CTD, equipment attached to the rosette. If the information showed stratification was present in the water column then I would sample 20m above and 20m below the given stratification point. However, if no stratification was present samples were taken 20m from the surface and 20m above the sea bed.
Image 1.0 A Rosette sampling tool, the rosette being the metal framework around the outside which holds 10 litre bottles on this inside. These bottles are lowered into the water column open, at desired depths these bottles can be remotely closed to capture the water from that depth. Also, on the rosette is a CTD that records salinity, temperature and dissolved oxygen.
Figure 3.0 The output graph of the CTD showing the water column temperature profile (from 4-8 degrees C). In this example there is very little variance in temperature from surface to the bottom, meaning that the water column is not stratified (has more than one water body) and that the water is mixed.
2. Surface Water Sampling
At the other 22 stations, surface water, from the 4m flow through, was sampled. This water was only sampled if weather was too rough for rosette sampling or if the boat was trawling for assessments.
How Do You Catch eDNA in the Water?
Post collection the sampled water is then pumped through cartridges (Image 2.0) that contained filters with tiny (0.22um) pores which separate out particles and cellular material that contain DNA or that DNA has bound itself to. These filters are then immediately frozen once the whole sample has passed through and then later the DNA is extracted using a new technique called mu-DNA (Sellers et al, 2018).
Image 2.0 Sample water pumped through tubing, using a peristaltic pump, and into a 0.22µm Sterivex™ filter and anything not collected by the filter flows into the sink. It is ensured that the filter cartridge does not touch anything apart from the package it was taken from and the sterile whirl-pak bag it is put into in post filtration of the sample.
Challenges with eDNA on a Research Vessel
Using eDNA presents a different set of problems, this is because DNA is EVERYWHERE; on our skin, in our hair, on most surfaces and even in the air we breathe- but most is human- which normally doesn’t present to much of a problem when looking for fish DNA. However, working on a research vessel presented a unique challenge especially with active fishing taking place. Meaning that fish DNA may be abundant all over the place.
This meant: decontamination, decontamination and then more decontamination!!!
Every step followed a rigorous cleaning cycle with hydrogen peroxide, to remove previous DNA contaminating a new sample, then a vigorous washing step with DNA-free water to ensure none of the DNA degrading chemicals are left.
Environmental DNA is fast becoming an advanced tool for detecting species in all sorts of environments. Through new protocols and intensive sampling from my study we should be able to further improve the applications and different types of practices of eDNA collection for the marine environment. Furthermore, through my endeavour of challenges my study should help optimise the decontamination protocols and field work applications in commercial use for governing bodies and surveying organisations.