Dawn of the eDNA era

New tool can help scientists map the locations of marine animals from the water they’ve been swimming through.

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eDNA could be a game changer in Marine Biology

Marine ecosystems can be one of the most expensive, time consuming and logistically infuriating places to research for scientists. The oceans around the world are vast and searching through them to find a particular species is like playing the world’s biggest game of ‘find the needle in the haystack’. It often requires hiring boats and expensive equipment, hours of fieldwork and frequent disappointment for researchers. However a new game changing technique could allow scientists to tell which animals have visited an area from as little as a litre of water!

What is eDNA?

Within every cell of an organisms body is the genetic code for making new cells in the form of DNA.  Just like how you and I lose dead skin cells to the air which become dust, marine animals also lose cells to their environment which remain as ‘dust’ in the water. This is better known as marine environmental DNA (eDNA). As well as dead cells eDNA can also be made up of mucus, blood and other secretions which when analysed in a lab can indicate which species it belongs to. This is not just limited to one species, a large cup of seawater may contain the eDNA of over a hundred species, meaning an entire ecosystem can be studied at once. It can also be used to estimate the abundance of each species which helps to assess population levels.  The eDNA can remain in the water column for around 24 hours and sometimes longer. This means eDNA can be used to map a species in both space and time. The potential uses of eDNA include monitoring the effects of human impacts such as fishing, shipping, renewable energy and climate change.

How does it work?

There are 3 basic steps to any eDNA study 1) water collection 2) filtering 3) genetic analysis.

Whilst there is no universal set way of doing an eDNA study it invariably requires first collecting samples from the water column. This can vary based on target species, taking samples at the surface is the easier option and gives a good representation of phytoplankton levels and some megafauna. However samples taken at varying depths using Niskin bottles gives a better picture of the whole ecosystem, but is a more expensive collection method. The most important thing is that the method is consistent and the containers used have been sterilized. Once the seawater sample is collected it is then vacuum filtered using extremely fine mesh that can not only collect dead cells but also partial fragments as small as 45 micrometres (0.001mm). Once the desired eDNA has been isolated it is then genetically analysed.

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Niskin bottles are used to collect seawater samples at varying depths

The most common form of genetic analysis is metabarcoding where an eDNA sample is sequenced and compared to an existing reference database. Certain genetic markers in DNA are unique to each species and machines can read these markers and see if they match with any known species in the database. This will usually require the sample to first undergo a polymerase chain reaction (PCR) where the eDNA is replicated so researchers have enough to work with.

What are the benefits of eDNA?

  • A sample of seawater can cost anywhere between $20 and $50 to collect and be analysed in the lab. This is a fraction of some of the more advanced forms of monitoring such as satellite tracking which can cost thousands.
  • It is easy to do and even untrained volunteers can collect samples.
  • Most samples can be analysed within 24 hours of reaching the lab meaning results can be produced quickly.
  • A sample of seawater contains eDNA of every animal over a set period of time which produces a more complete picture of an ecosystem.
  • Genetics don’t lie. Unlike observational studies there can be no false identifications which reduces human error.
  • It is non-invasive and completely harmless making it more ethically sound than other studies.

What are the problems?

  • eDNA provides no information on an individual’s age, size, sex, health and behavioural traits, this still requires observation or capture.
  • Only partial understanding of how eDNA levels relate to abundance of each species as can vary with species and environment.
  • Genetic reference libraries may be incomplete, especially marine species as it’s harder to obtain original samples. There is also no centralized global database for eDNA results.
  • No way of performing analysis on research vessels meaning samples must be sent to labs which can take weeks or months on a long voyage, this can reduce quality of results.
  • No agreed upon sampling process based on depth and areas of habitats.

Increasing popularity

Although the technique has been around since 2015 it has become increasingly popular with marine biologists. So much so that on 29-30 November 2018 the first National Conference on Marine Environmental DNA in America was hosted at Rockefeller University in New York. This presented the first real opportunity for scientists, government agencies and private companies to meet and discuss this newly emerging field of research. The goals of the conference were to raise awareness of the benefits of eDNA whilst also trying to address some of the issues regarding sampling, sharing data and making the process cheaper and more portable.

During the conference several high profile researchers praised the use and innovation of eDNA sampling. Martin Stoeckle a senior research associate at Rockefeller University and designer of the GoFish eDNA sampling kit (yes it really is named after the card game) described it as “a breakthrough with major environmental and economic implications”. Renowned Stanford marine scientist Barbara Block highlighted the ease at which she and her team were able to identify the presence of White sharks over 1,000 miles offshore within 48 hours. Jesse Ausubel, director of the Program for the Human Environment at Rockefeller University also claimed “In a few years’ time an early morning water sample from a beach could tell lifeguards by midmorning if tiger or white sharks were around”.

The use of eDNA as a sampling method in published papers has also increased in the last 2-3 years. Such as a 2018 study led by Kim Parsons from NOAA (National Oceanic and Atmospheric Administration in America) which mapped the population structure of Harbour porpoises in Alaska. The Harbour porpoise is a small cetacean renowned for its highly elusive nature and Alaska can be a particularly hard place to study. Such a study may not have been possible without the use of eDNA and is an excellent example of just how effective it can be.

To sum up 

Using eDNA as a method of locating marine species and estimating their abundance is relatively cheap, completely harmless and a lot easier than having to find the animals themselves. Whilst it has limitations, like most studies, it could be a game changing technology especially when used in conjunction with other techniques. Working together and given time scientists should also be able to perfect eDNA and make it much more effective and accessible to use. It has become a popular technique with scientists and moving forward it is likely to play a larger role in marine research and conservation.

Links

https://www.nationalgeographic.com/environment/2018/12/edna-environmental-dna-counts-fish-changes-marine-science/

https://phe.rockefeller.edu/eDNAmarine2018/meetings/

http://rsos.royalsocietypublishing.org/content/5/8/180537


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