Microbe Miners

Mention bacteria and most people generally think of dirt and disease. Fair enough; bacteria cause cholera, strep throat, salmonella, and a host of other ailments we’d all rather avoid. We spend enormous amounts on antibacterial soaps, and we worry about the dire consequences when bacteria evolve to evade our defenses.

Yet the vast majority of bacteria are harmless, and some, according to Cecilia Martinez-Gomez, an assistant professor in the Department of Plant and Microbial Biology, can actually become powerhouse cleaning agents. Martinez-Gomez is engineering bacteria that are likely some of the most efficient “scrubbers” ever discovered, able to protect the environment—and potentially our bodies—from heavy metals and medical waste products. She’s also developed bacteria that can be used to “mine” valuable elements from discarded electronics, an approach that could have important impacts for the production of everything from smartphones to military equipment.

Recovering rare earth elements

Down at the bottom of the periodic table, set aside from the elements we all remember from high school, you’ll find fifteen elements known as lanthanides. These metallic elements with unfamiliar names like ytterbium and dysprosium are collectively known as Rare Earth Elements (REEs) and are found in many products and materials we use daily. REEs are in the magnets that power up our laptops and other electric motors; they’re in the polishing agents for windshields and mirrors; and, crucially, they’re in the smartphones upon which we all increasingly rely. These elements are also essential for our military, making up critical components of guidance, night vision, and stealth systems.

Unfortunately, all this technology is not without cost. Lanthanides have toxic effects on humans, and, although our use of them has exploded in recent decades, we’ve barely studied the long-term effects of constant exposure. The process by which they’re extracted from the ground is also chemically intensive, often fouling groundwater and soil near mine sites.

With the demand for REEs on the rise, it’s imperative that we figure out how to recycle them, rather than adding them to landfills every time we swap out our phones for the latest model. That’s exactly the effort that’s going on in Martinez-Gomez’s lab, and, fascinatingly, she’s using genetically modified bacteria to hunt down and retrieve these valuable metals. “No matter how much chemistry we know,” she says, “we can’t compare to the incredible machinery the microbes have developed on their own over millions of years.” For years, REEs were largely dismissed as having no significant role in biological processes, perhaps due to their toxicity. But Martinez-Gomez and other pioneers in her field weren’t convinced. They began to research whether microbes could act as “micro-miners” that are able to extract and bioaccumulate REEs in pure form from parts of phones and batteries.

What followed was a series of experiments and genetic manipulations to find (and enhance) species of bacteria that could process lanthanides. “We don’t know exactly how microbes are sensing them, but we do know that they secrete molecules that combine with the lanthanides,” says Martinez-Gomez. Those molecules recognize gates in the membranes that allow them to selectively bring the lanthanides in. The mechanism for how these microbes bring in the metals is tightly regulated by inherent biology; each microbe can only bring in so much material. “What we’re doing is modifying the genome in order to make the process more selective, and also much more efficient, so that they can really hyper-accumulate pure metals into the cell,” says Martinez-Gomez.

Revolutionary advances

In the beginning, Martinez-Gomez and her colleagues broke up cell phones and speakers with a hammer in order to gather the parts that contained REEs. Now, they partner with a recycling company that delivers the electronics already ground into a fine powder. That e-waste goes into a bioreactor with sterile water, a few phosphates and sulfates, and the microbe Methylobacterium extorquens at very high concentrations. “Then we have millions and millions of cells accumulating metals,” she explains, “and afterward we break the cells and do a very simple purification from there.”

Creating a cellphone-eating bacteria that can produce purified REEs sounds easy when Martinez-Gomez describes it. But the concept is actually the kind of revolutionary advance that leapfrogs the quest for sustainability wildly forward. It’s so audacious that Martinez-Gomez and her colleagues from San Jose State University and Lawrence Livermore National Lab recently received a million-dollar grant from the Advanced Research Projects Agency-Energy (ARPA-E), the government agency dedicated to rapid progress in advanced energy technology.

The government’s interest is no surprise given the geopolitical implications of Martinez-Gomez’s work. The domestic supply of these vital materials depends on the largesse of rival superpowers like China, currently the largest producer of REEs. Though U.S. extraction of rare earth elements has increased over the last decade, a recent U.S. Geological Survey report identified China as the source of 78% of all refined REEs imported between 2017 and 2020. That makes the ability to recycle and preserve REEs a tantalizing prospect for our domestic economy. “I want to contribute to helping the United States be independent from a foreign supply,” says Martinez-Gomez.

To be clear, the technology is not yet ready to digest and repurpose all our castoff electronics. But for a radically new process, that day is closer than one might think. “Our max is still currently ten liters,” says Martinez-Gomez. “We’re not yet at the point where we can scale it to the level we would need to have constant production and be profitable.” However, with the ARPA-E funding, Martinez-Gomez’s lab is staffing up and making plans to move quickly. She has patents in various stages of approval, and the goal is to have a viable product to release to the public in four years.

A myriad of potential applications

The underlying science has promise even beyond capturing e-waste. The rare earth metal gadolinium, for example, is widely used in contrasting agents during MRIs. While largely harmless to patients during those brief clinical scans, once expelled via urine, the lanthanide accumulates at high concentrations in the water supply and can become harmful to people. Working with her graduate students, Martinez-Gomez established a fast-paced series of selective pressures on bacteria, making them mutate faster than normal. “Essentially we fed them gadolinium and made that the only source they had available to them,” she says. Not only did the bacteria evolve to tolerate this toxic compound, they mutated to prefer it, hyper-accumulating large quantities. Gadolinium-loving microbes can potentially be deployed in wastewater facilities, gobbling up heavy metals before they can pose a threat to human health.

Martinez-Gomez is doing similar work to coax bacteria to bind up methane—a greenhouse gas eighty times more potent than carbon dioxide—so that it is not released to the atmosphere where it can contribute to climate change. “These are emergent areas that not many people are working on,” Martinez-Gomez says. “We’re discovering mechanisms that nobody has described before and that’s incredibly exciting.” Far from being territorial, Martinez-Gomez eagerly hopes more scientists will join the field of lanthanide chemistry to help discover other possible applications.

Known as a generous collaborator and enthusiastic mentor, Martinez-Gomez recalls her first exposure to science as a kid roaming the halls of the National University of Mexico in Mexico City where her father was an administrator. “During the summers I was so bored, but I saw these researchers and everybody seemed so happy, so I got up the nerve to knock and say “I’m here every day anyway, so can I do anything to help?” A series of scientists opened their doors, let her sit in on lab meetings, and explained their research in terms she could understand. By her senior year of high school, she was working on high-level projects. From there, she kept adding disciplines to her skill set, becoming proficient as a biochemist, microbiologist, geneticist, and chemical engineer.

Martinez-Gomez continues to deepen the pure scientific understanding of how microbes behave, always keeping her eye on the real-world implications of her work. “I really believe in the idea of a circular bioeconomy,” she says. “We need to think of the world like people going on a mission to Mars. Our resources are connected—even our waste should be used to produce something of value.” With the insatiable desire for growth ingrained in today’s global economy, Martinez-Gomez’s work helps us see bacteria not as something dirty, but as an important contributor to our effort to create a sustainable future.