Volume 2, Issue 8
Mining For Microbes
Every time UC Berkeley professor Jillian Banfield descends into the abandoned Richmond Mine in Iron Mountain, California, she's fascinated by the strange beauty of the pink films floating on pools of green water. Those highly-acidic films are what make Richmond Mine, one of the country's largest Superfund sites, such an environmental nightmare. For nearly a decade, Banfield has studied the communities of microbes in those films, the source of the hazardous acid mine drainage. Someday, her research might even lead to new ways to remediate the ecological damage.
Professor Jill Banfield is also affiliated with the Lawrence Berkeley National Laboratory's Earth Sciences Division.
"I was trained as a geologist and I'm very interested in the environment," says Banfield, a professor of Earth and Planetary Science and of Environmental Science, Policy and Management. "So I looked for an environmental problem that involves interactions between microorganisms and minerals, and I found the mine."
More than a quarter mile into the mountain's darkness, various species of microbes grow from the air, water, and minerals in the extreme environment. They form a self-contained ecosystem, Banfield says, with specific members of the community contributing particular functions.
The microbe community's metabolic processes transform the iron sulfide ore into sulfuric acid. Indeed, the drainage from the mine is the most acidic groundwater ever measured. Indeed, if it weren't for a massive on-site treatment effort by the Environmental Protection Agency, the runoff could eventually make its way into the Sacramento River. Meanwhile, the genetic secrets that control how the microbes form a community and interact with their environment to produce the acid mine drainage have been something of a mystery.
A researcher collects samples of the pink biofilm floating atop hot, green, acidic pools in the Richmond Mine at Iron Mountain, California. (Brett Baker/UC Berkeley)
"In the past we could really only study microorganisms by growing them in the lab and characterizing them in vitro," Banfield says. "The limitation is that we don't know how to cultivate most of them."
Last year, Banfield, graduate student Gene W. Tyson from UC Berkeley's Department of Environmental Science, Policy and Management, and their colleagues borrowed a technique from the Human Genome Project to reconstruct whole genomes directly from samples gathered in the mine. Rather than separate out each kind of microbe and sequence its genes, the scientists — including postdoctoral researchers Eric Allen and Rachna Ram, biologist Philip Hugenholtz, and collaborators from the U.S. Department of Energy's Joint Genome Institute (JGI) — used "shotgun" sequencing to obtain the genomes of the whole community at once.
"We break the DNA into small pieces, clone it, and sequence it," Banfield says. "It's like taking five jigsaw puzzles, mixing them all together in a box, and then reconstructing them. Doing that enabled us to pretty comprehensively sample the genomes of these communities' dominant populations."
Acid mine drainage in Spring Creek downstream from the Richmond Mine, part of the Iron Mountain Mine Superfund Site. (Gene Tyson/UC Berkeley)
The novel approach resulted in two microbial genomes that are almost entirely complete and three that are ninety percent there. The data enabled the researchers to identify many of the genes' functions and determine the role of each microbe in the community. For example, only one organism has the cellular machinery to convert nitrogen gas into biologically-available nitrogen that supplies the entire population. Another spews out the biofilm that the community calls home. The "community genomics" technique, published in the scientific journal Nature, was also lauded by Science magazine as a "Breakthrough of the Year."
With the genomes in hand, Banfield and her collaborators at Oak Ridge National Laboratory are studying the proteins encoded by the genes — a process called proteomics — to help unravel the biological processes at play in the mine. Banfield believes that this may be the first time that proteomics has ever been applied to natural communities.
A deep understanding of the metabolic dependencies and characteristics of the organisms could eventually aid environmental scientists in the development of remediation techniques, she says. For instance, adding certain organic constituents, comparable to increasing the community's food supply, might optimize the microbes' functions and speed up the formation of acid mine drainage.
The blue and yellow fluorescent dots represent two kinds of microbes in a sample from the mine.
"That would reduce the cost of remediation at the site in the long-term and make it more practical to extract the metal from the runoff to offset the cost," Banfield says.
Interestingly, the research is also informing scientists who are seeking life in other extreme environments, including Mars. Banfield is principal investigator on a large NASA grant to study the Mars biosphere. If life has existed on the red planet, or still does, it's feasible that the extraterrestrials might actually be microbes that thrive on the planet's iron and sulfur-rich surface, she says. The key is to know what the signs of life might look like.
"The mine provides us with a microcosm to study, and its simplicity makes it manageable," Banfield says. "This work is opening the door to understanding microbial function in the environment, almost in real time."