eDNA use in the Tropics

The best method for managing the spread of invasive aquatic species is through the prevention of new incursions, rather than post-infestation eradication. To avoid widespread establishment of invasive species it is crucial to detect infestations early when their density is lowest. Recent advances in our understanding of the movement of environmental DNA (eDNA) and particle size through streams and capture methods continue to validate and optimize the reliability of eDNA techniques for detecting the presence of low-density aquatic species, including invasive species.

eDNA allows us to detect the presence of organisms without direct observation. Plants and animals shed cellular material into their surrounding environment, and this material can be collected and analyzed. Traces of DNA extracted from environmental samples can be used to determine if a target species has been in the vicinity of a sampling site.

There have been a number of studies with promising results especially with respect to the detection of invasive fish species. The most advanced field of study deals with the ongoing invasion of the Great Lakes by Asian Carp. However, most studies were conducted in temperate regions and not in tropical freshwater environments which come with additional challenges such as high turbidity, higher temperatures and higher ultra-violet light intensity most of which can have a profound destructive effect on eDNA. 

A new study from Australia put some of the parameters to the test. The researchers used Mozambique tilapia (Oreochromis mossambicus) as a detection model for the effect of modifications of conventional eDNA protocols for use in tropical environments.

Large–pore filters (20 μm) were effective in filtering turbid waters and retaining sufficient eDNA, whilst achieving filtration times of 2-3 minutes per 2-L sample. High water temperatures, often experienced in the tropics (23, 29, 35 °C), did not affect eDNA degradation rates, although high temperatures (35 °C) did significantly increase fish eDNA shedding rates.  We established a minimum detection limit for tilapia (1 fish/ 0.4 megalitres/ after 4 days) and found that low water flow (3.17 L/s) into ponds with high fish density (>16 fish/ 0.4 megalitres) did not affect eDNA detection. These results demonstrate that eDNA technology can be effectively used in tropical ecosystems to detect invasive fish species.

The only thing I don't understand is the use of 16S rRNA as marker system for this study. It is a rather unusual choice as it is not very commonly used for fish. Earlier studies that looked into 16S as a potential marker for a microarray based identification system showed that it is not very suitable for this purpose, one problem being the secondary structure of the molecule. There are also not as many sequences available as for COI barcodes or even cytb. It is fairly easy to find sequences that help with qPCR probe design for tilapia as this species has been subject to thorough analysis over the years but in order to go after real invaders one would need to move to a different system. Luckily, most of the suggested protocol changes and amendments are not with respect to the choice of markers which makes this a minor issue.