Mining waste is often buried underground or beneath man-made lakes. For reclamation to be successful, it is really important that the water and soil that covers the waste has a healthy microbiome to support the growth of plants and animals. When we want to study this, we start by taking a sample of the soil or water. Whenever microbes interact with their habitat— whether it's to eat, hide, or grow— they often leave behind DNA evidence in the same way that humans can leave DNA evidence at crime scenes. We use DNA sequencing to find these traces of microbial life in the environmental samples without having to try to grow the microbes and identify them by microscopy in a lab. I'm currently working on reclamation sites in Northern Alberta, where industrial engineers are developing new technologies to more efficiently dispose of mining waste. I study the microbes present in these sites to ensure that they are able to support a biodiverse reclaimed environment.
Modern DNA sequencing technology is extremely powerful, and we can get a lot of information from a very small sample. From a pea-sized piece of soil I can extract, on average, one thousandth of a milligram of DNA. That's enough to produce approximately 75,000 individual sequenced DNA fragments, called reads. Because only a tiny amount of soil and water is needed, this method of sampling does not disturb the environment too much, which is ideal for a site undergoing reclamation.
Once these reads have been sequenced, I compare the DNA, which is unique in every microbe, to databases of all known microbial species. This gives us a list of microbes which left their DNA in the sample, and, by counting the number of reads corresponding to each species of microbe, we can also make an estimate of how prevalent they are compared to the other microbes. We can get SO much information from such a small sample, the amount of data builds up very quickly! A huge part of my job is checking these huge datasets and making sure that only the highest quality data ends up being used in the final analysis. This is mostly done automatically, and requires a lot of computational power. I use the Canadian supercomputer network Compute Canada to run most of my experiments.

After the analyses are completed, we have a full picture of the microbes present in the environment. In my current study, we are following a man-made lake built on top of mining waste that has been processed using a new tailings treatment technology. This year marks our first full summer of sampling on this project, and I'm very excited to follow what the microbes get up to over the next couple of years! From previous research in this area, we know that there are likely to be all sorts of interesting bacteria feeding off any leftover bitumen in the mine waste, and I'm also very curious to see what sorts of microbes are feeding on those bacteria. Because environmental DNA can be used to study anything living, it means we can build up complex networks of interactions between the levels of the microbial food chain. Bitumen is an extremely energy-rich food source for bacteria, so I'm expecting a lot of microbial activity. We might even find some new species!
Scientific innovation is a huge part of my work, and most of the research I do relies upon technologies that have only existed for a couple of decades. Without access to highly accurate DNA sequencing technologies, supercomputers, or internet species databases, none of this would be possible. Innovation provides tools which scientists can use to investigate their own specialities - I use these techniques to study reclamation of mining waste, but I have friends and colleagues who use the same techniques to study the spread of diseases, or efficiency of agriculture, or ocean conservation. The development of technology is an essential part of the development of science.
The University of Alberta's inaugural Digital Innovation Showcase features the research of graduate students and postdoctoral fellows. View posters and engage the presenters on Twitter May 10-14, 2021 #UAlbertaInnovationShowcase.

Dr. Beth Richardson
Dr. Beth Richardson is a postdoctoral researcher in the School of Public Health at the University of Alberta. She received a Bachelor's and a Master's degree in Biochemistry at the University of Cambridge in her home country of the United Kingdom before joining the University of Alberta as a PhD student in 2014. Outside of the lab, she enjoys talking to the public about science, watching hockey, and trying to grow plants in a Zone 3 climate.