Using eDNA to Avoid Being Eaten on the Job

Image Credit: pxfuel, CC0 1.0, Image Cropped

Monitoring the silver carp invasion in Africa: a case study using environmental DNA (eDNA) in dangerous watersheds (2020) Crookes et al., NeoBiota, http://doi.org/10.3897/neobiota.56.47475

The Crux

One thing the last two months have taught us all is that testing for a problem is crucial. The earlier you catch a problem, the more of a chance you have to stop that problem spreading. Coronavirus is one example, invasive species is another. Detecting an invader arriving early on means you can potentially remove it before it has become properly established, saving millions of dollars down the line.

But often testing isn’t practical. Take freshwater environments. Sometimes a river may be hard to get to. Sometimes it may be infested with crocodiles and hippos. Makes regular testing methods like electrofishing or gillnetting a bit tricky.

That’s where eDNA comes in. eDNA stands for environmental DNA, a type of DNA we can use to identify which species are present in an ecosystem simply by filling a bottle full of stream water. This week’s researchers wanted to test how well they could detect signs of the invasive silver carp (Hypophthalmichthys molitrix) by using eDNA collection in dangerous rivers.

What They Did

The Olifants watershed is located along the border between Mozambique and South Africa. It is occupied both by the Nile crocodile and the common hippopotamus. The researchers sampled nine sites in the Olifants watershed, both upstream and downstream of a large hydroelectric dam. They tested another three sites in a neighbouring watershed to see whether the carp had spread beyond the borders of the Olifants watershed. They filled three 2L water bottles from each site, from each of which two eDNA results were extracted to see whether the carp was present at the site, giving a total of six replicates at each site, 72 eDNA results in total.

Did You Know: Polymerase Chain Reactions

Guest section by Vanessa Bieker

PCR (short for Polymerase Chain Reaction) is a process which copies DNA, giving you enough to sequence or even make visible. The enzyme doing the job is called polymerase, and it’s the same type of enzyme animals and plants use to copy DNA before cell division. In the first step, the double-stranded DNA is heated up to about 95 ºC to make it single-stranded (this is called denaturation). Then small pieces of DNA, called primers, are attached to the DNA once temperatures have lowered. The primer you use determines which part of the genome will be multiplied. There are some universal primers for different regions of the DNA strand that can work across many species, but it is also possible to design primers that are specific to one organism you are interested in. In the next step, the reaction is heated up to a temperature where the polymerase is working well (usually around 72 ºC) and the DNA is copied from one strand, resulting in a new double stranded DNA fragment. Then those steps are repeated a couple of times to increase the DNA. qPCR, which was used here to detect the presence of silver carp, is a technique which detects DNA as the PCR process runs, giving an indication of the strength of the signal in real-time.

What They Found

All sites tested positive for silver carp, with all except one testing positive in at least three of the six replicates. Using the probability of obtaining a false absence, the number of samples subjected to PCR (see Did You Know), and the proportion of samples that yielded a positive detection of silver carp, they were able to calculate that the minimum number of samples needed for a result in which one could have 95% confidence in silver carp detection – in this case two.

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The Silver Carp, which has already been introduced to Europe and North America, is now starting to spread throughout Africa (Image Credit: Asian Carp Regional Coordinating Committee, CC BY 2.0)

Problems

One of my issues here is that the test was performed in an area were silver carp is already though to have been well established. Areas with lower levels of the carp would have made a welcome addition to the study, however finding these would not have been easy, nor relevant – if a river system was too far removed from the Olifants watershed it may have made the comparison invalid.

So What?

That this research proves the value of using eDNA in situations where normal sampling methods are risky is without doubt. The detection rate was high, and is in line with both local reports of the carp presence and occupancy modelling recorded on site. The technique could make for a great early warning system for the invasion of other species in dangerous areas throughout the world.

On a less positive note, it’s also an indication that the silver carp population in the Olifants watershed is going strong, and capable of spreading into other regions. There was no real difference between the populations upstream and downstream of the dam, so the potential dispersal barrier seems to make no difference to the species.

Sam Perrin is a freshwater ecologist currently completing his PhD at the Norwegian University of Science and Technology who is supportive of more people not getting eaten by crocodiles. You can read more about his research on his Ecology for the Masses profile here, and follow him on Twitter here.

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