Using DNA for Environmental Management

Main Club Friday, 7th May 2021

Our speaker, Dr Oliver Berry, is the leader of the Environomics Future Science Platform, a Research and Development program at the CSIRO. Oliver was previously a post-doctoral researcher and Fellow at UWA. He told us that that he once worked with Rick How and John Dell, and that one of his first published articles was in our Western Australian Naturalist journal.

26/1 January 31, 2008 26-41
“Herpetofauna of four remnant bushland isolates in the City of Nedlands, Perth.” By P.F. Berry and O.F. Berry

“Environomics” (environment + genomics) is applied ecological research, linking genomics with environmental studies. One function of this research is to find new resources in nature. Oliver talked to us about how DNA and genomics technologies are transforming how we discover, monitor and manage biodiversity.

Three quarters of Australia’s biodiversity is found nowhere else, and much of that is not described or named. Monitoring all of this would take too long by conventional means but making use of environmental DNA can speed this up enormously. It can identify a wide range of species quickly and accurately. And analysis of the DNA in a sample of seawater, for example, can reveal not only what species exist in that locality, but potentially, how many of each species.

DNA is coded information, and just as genomics (the study of genomes) has transformed agriculture and medicine (e.g. Covid vaccines), it can be used to give information to land managers that would otherwise not be available. This “big data” can be used to measure any changes occurring in the environment and any threats to the health of ecosystems.

Genomics is currently being used in “blue carbon” projects (i.e. carbon captured by marine ecosystems) to restore seagrass meadows. This is important because seagrasses are major carbon-capturing systems. They use microbes (e.g. nitrogen-fixers) to enhance their resilience, and CSIRO is using genomics to test whether adding specific bacteria can help with that resilience in the face of pollution and climate change.

Knowing how intensively to harvest fish is critical to maintaining sustainable fisheries. To do that, we have to know what age the various fish species live to. This can be done by analysing their DNA. Oliver explained how measuring DNA methylation can be used to do this. This process correlates very closely with the old method of measuring the fish’s otoliths (ear-bones). The genomic process is much quicker and easier, doesn’t involve killing any fish, and has excellent predictive accuracy. (Incidentally, this can be done with ancient DNA, and has shown that Neanderthals lived to about 38 years.)

Oliver sees the use of genomic methods for bio-monitoring as a re-invention of how we measure ecosystem health, change and threats. The monitoring needed to manage Australia’s marine parks, the most extensive in the world, would be impossible if based on sampling by divers. Instead, a bucket of seawater can tell us all the organisms present in the water in that locality, and much more. Monitoring with e-DNA is very effective, and there is lots of science to validate it. In marine environments the method has caught on quickly. It has limitations, but it has been shown to have a close correlation with the evidence from video cameras and other more conventional ways to measure the environment. Methods have improved to make eDNA easy to collect, such as the development of “passive DNA”, which is a simple method of dipping filter membranes directly into the water, rather than using pumps.

On land, bees can be used as “bio-drones”, because they sample pollen from many plants, and that can be collected in pollen-traps at the hives. DNA can then be extracted from the pollen to create a database of plant species. In one experiment this method could detect five times the number of genera as human sampling could. The drawback is that bees are selective in what plants they collect from, but it is a very useful complement to other methods of sampling.

Oliver pointed out that to make the most of new DNA-based ways of measuring the environment we need a library or database of the DNA sequences of all Australian species. There are very few at present. Even old DNA from museum specimens that has broken down can now be used, because a method has recently been developed to sequence the broken-off fragments in the right order. A goal of CSIRO is to develop a barcode library of all Australian species. This would probably cost over $30 million for all 190,000 recognised species. The question is where to begin – endangered species? commercially important fish? special habitats such as Kakadu or the Great Barrier Reef?

So environomics is using the information contained in DNA to better understand, manage and make use of the environment. It opens up new possibilities for fast and accurate monitoring of the environment at a time when that is urgently needed. Oliver reminded us that since we all depend absolutely on our natural environment, we need to manage it well.

Mike Gregson