I had to take a brain break yesterday, but you can find my day 3 highlights after the jump:
The major theme of day 3 was the role of genomics and researchers in mitigating the downsides of non-renewable resource development. We heard from Terry Hazen, Julia Foght, and Lesley Warren, who all microbial genomics to help make non-renewable resources more sustainable. David Wheeler joined them to discuss the reconciliation of natural resource development with ecological and traditional practices.
Drs. Hazen, Foght, and Warren each talked about a different application of genomics in non-renewable resources. Dr. Hazen from the Oak Ridge National Laboratory in the US spoke about his work in the Deepwater Horizon oil spill (aka the BP oil spill) cleanup. This oil spill was completely unlike anything that had been seen before - since it happened at the sea floor, most of the oil was carried away by an underwater current, creating a plume of oil far below the surface. While the rest of the world was trying to stop the leak and clean it up, Dr. Hazen and his team used what they called an oil-spill systems biology approach: they wanted to know how the oil changed the microorganisms in the various environments at different ocean depths. Looking at a 300 km radius around the spill, the team collected genomics and transcriptomics data over a period of months (and made all their data immediately available as well). The team found 951 subfamilies of bacteria in non-contaminated water, but only 16 in the oil-contaminated water. By sequencing the 16S rRNA of the microorganisms, the team found that the plume was dominated by proteobacteria, many of which are hydrocarbon degraders. One type of bacteria in particular, Oceanospirillales, was common in the oil-contaminated water. Meta-genomics and meta-transcriptomics showed that these bacteria thrive in this environment with high expression of genes involved in chemotaxis, nutrient acquisition, and motility, essentially making them "oil-seeking missiles" (Dr. Hazen's words). His team also found that the community of microorganisms changed as oil began to dissipate - where once oil-degrading bacteria were predominant, soon came those that could degrade the oil-degrading bacteria. The implications of this research being that genomics can be used to enhance bioremediation, but also to detect locations of previous oil spills, even after oil is no longer detectable.
Microbial genomics can also be used to improve the way the oil and mining industries dispose of waste. Julia Foght from the University of Alberta studies the tailings ponds in the Alberta oil sands. The bitumen is separated from the sand using alkaline water, agitation, and a hydrocarbon solvent. While 99.5% of the solvent is recycled, the remaining 0.5% ends up in the tailings ponds. Naturally, bacteria live in these ponds, predominantly anaerobic bacteria. The microorganisms in these ponds produce greenhouse gases, including 40 L of methane per day. Interestingly, bacteria degrade hydorcarbons, but are unable to produce methane - that's the job of Archaea. That means there's actually a community of microorganisms living together, with the bacteria producing the metabolites for the Archaea. In her work, Dr. Foght has found 8700 different genera of bacteria and Archaea, some of which have never been characterized because they can't be cultured! Of these, only 5 make up the core microbiome of the tailings ponds. By using meta-genomics and meta-transcriptomics, she and her team found that the two types of microorganisms work together, upregulating and downregulating genes according to which species is doing what.
Lesley Warren of McMaster also works in the oil sands, but mostly with metal mines. Canadian mines generate 950 000 tons of tailings per day, and uses half of our renewable freshwater supply each year. In fact, one gold ring produces 20 tons of mine waste! She studies the microbes that are involved in the remediation of acid mine drainage. She and her team have also found communities of microbes in the tailings that are working together. In fact, she believes that the key to sustainable mining is in thinking of mines as bioreactors, of metals and ores as having biofilms, and that engineers should start thinking like biologists and biogeochemists. By using genomics and meta-genomics, Dr. Warren is able to show mining companies just what types of microorganisms are in their tailings and why they're important, as well as giving them the tools they need to see their own roles in managing tailings ecosystems.
So there you have it, that was the 2014 Genomics: the Power and the Promise conference! I'm sure I speak for just about everyone who attended when I say that I'm already looking forward to the next one (in 2016). Genome Canada will have a huge job ahead of them trying to top this one.