SRI’s BioCyc platform is giving a bioinformatic startup an edge in mine-related research.
When mining companies shut down a mining operation, regulations often require them to return the site to a more-or-less natural state. Mines can leach toxic minerals like arsenic, copper, and zinc into the surrounding environment. Enclosed spaces can fill with methane, creating very real explosion risks.
While the risks themselves are chemical, the underlying processes are often microbial: Microbes can accelerate mineral leaching, and some microbes are also responsible for synthesizing raw materials into methane. To develop effective interventions at a mine site, the remediation team needs to understand the mine’s microbial population.
Koonkie, a bioinformatics firm based in Vancouver, BC, views mine remediation as a prime area where cutting-edge bioinformatics research can make a real impact. Leveraging SRI’s BioCyc platform, the startup is leading the way in providing a more detailed picture of the microbes that live in mine sites and their impact on mining activities.
Mine site microbes: diverse and ill-understood
“Eighty percent of the microbes we find at mine sites are uncharacterized,” says Koonkie COO Erin Marshall, who holds a PhD in interdisciplinary oncology from the University of British Columbia, where she focused on the role of microbes in cancer development. “They haven’t been discovered by science.”
The first challenge is simply identifying these novel microbes. But the more important work, from a practical perspective, is sorting through a literal microbial soup to figure out which specific microbes might be impacting the chemical balance of a mine site.
Understanding the function of these microbes means understanding their metabolic pathways. That’s where SRI’s BioCyc platform comes in, and specifically BioCyc’s Pathway Tools.
How Koonkie leverages BioCyc to understand mine microbes
Working with a partner at a decommissioned gold mine, the Koonkie team recently demonstrated how BioCyc’s Pathway Tools can play a role in specific mine remediation projects.
In their work at the site, the Koonkie team identified an organism of particular interest: a novel and abundant archaea that shares a lineage with organisms found in ocean hydrothermal vents. Clearly, it was thriving at the mine site. The question: Did it play an important role in producing (or, alternatively, detoxifying) unwanted chemicals?
To find out, the team first sequenced and annotated the organism’s genome, then fed it into the Pathway Tools software. The SRI software computationally generated a pathway genome database for the organism, drawing on SRI’s MetaCyc database of metabolic reactions to model how this particular organism worked. The Pathway Tools algorithm produced an interconnected map showing the organization of genes into biochemical pathways that process substances at mine sites through multi-step chemical conversions. By building this metabolic overview, Koonkie could look beyond individual genes and understand the functional capabilities of the organism.
“Building pathway genome databases helps us understand the genetic blueprints of these tiny miners so that we can use them to solve industry-wide challenges related to critical mineral yield, tailings stabilization, and more.” — Erin Marshall
The results indicated that the organism in question contained a group of genes typically found in archaea that produce methane. Utilizing the map generated by Pathway Tools, the Koonkie team then took a more holistic look at how the entire metabolic network functioned. In this case, methane was not a predicted output of this particular organism’s metabolism, despite the presence of these genes.
In addition to learning that this organism did not increase the risk of methane gas generation at the mine site, the team identified metabolic pathways that could be beneficial to the remediation process. The pathway genome database predicted two pathways for arsenic detoxification, including one that converts arsenic from a highly toxic form to a more tolerable one — a function that is promising for remediation.
In other words, Pathway Tools helped Koonkie identify a potential risk at a mine site, analyze that risk to mitigate environmental concerns, and identify beneficial processes in the organism that could be functionalized in the future to bolster reclamation efforts.
The future of bioinformatics in mining
Understanding a mine’s unique microbiome, explains Marshall, is integral to remediation activities. But bioinformatics tools, she points out, also have a powerful role to play in mineral extraction, given the role that microbes play in freeing metals like copper from raw ore.
“Once you understand the metabolic pathway,” she says, “you can tune a bug’s favorability in the environment.”
If the organism is making mineral extraction more efficient, you might increase the amount of its choice nutrient in the environment. If the organism is associated with a toxic output, you might reduce the amount of its choice nutrient. You could also treat the site to change the pH, or explore more complicated chemical means of encouraging or discouraging particular microbial species.
“Since most mine microbes aren’t known, we need to build detailed maps of their DNA to understand how they operate,” Marshall concludes. “Building pathway genome databases helps us understand the genetic blueprints of these tiny miners so that we can use them to solve industry-wide challenges related to critical mineral yield, tailings stabilization, and more.”
Learn more about SRI’s BioCyc genome database collection or contact us.
