Mobilizing microbes: How can mining rare-earth elements become more sustainable?

Postdoctoral researcher Alexa Schmitz joined Barstow’s effort when, as a Cornell grad student earning her doctorate in plant pathology and plant-microbe biology, she was in a biofuels seminar presented by Barstow. But in the discussion afterward, he also talked about bioleaching and its potential in the mining and recovery of rare earths.

“It felt like risky, cutting-edge work,” says Schmitz, “but at the same time I thought ‘Yes. This can definitely work.’”

Schmitz was finishing her Ph.D. and looking for a postdoctoral position, and Barstow was looking for help on his biomining project after receiving an Academic Venture Fund seed grant from the Cornell Atkinson Center for Sustainability.

Schmitz got to work right away with a bacterium called Gluconobacter oxydans. It had already been shown to have potential as a bioleaching microbe through initial work done at the U.S. Department of Energy’s Idaho National Laboratory. Schmitz used a method developed by Barstow called Knockout Sudoku to selectively inactivate one gene at a time and then build a collection of several thousand variants of G. oxydans. Each of these variants will be tested as a bioleaching agent for rare earths, and then those that perform best will be further developed.

As she gathers data, Schmitz – who is continuing the work with help from the Cornell Atkinson Small Grants Program – says she will be compiling a roster of genes that could be key to the development of an efficient and sustainable system to extract rare earths.

Monazite is one of the ores known to contain rare earths in sufficient quantities to be worth mining. Schmitz can’t just throw a chunk of monazite and some bacteria into a beaker and wait to see what happens. Rather, the initial screening for genes that may be related to leaching of rare earths will happen in microplates that can be read spectroscopically.

Schmitz explains, “Once we know which genes are most important for bioleaching, we will target those genes – and genetic elements controlling those genes – for mutagenesis. This can be done in combination, targeting several genes at once, and the resulting modified strains are screened for changes in bioleaching.”

Mutagenesis is a process whereby the genetic information of an organism changes by mutation. That mutation can be spontaneous or it can be controlled in a laboratory. Schmitz and Barstow will force mutations on the genes that are most involved in bioleaching and then measure how effective the mutated organism is at gathering available rare earths. Their hope is that with a high-throughput method for evolving G. oxydans, they will be able to engineer an organism that can leach rare earths more efficiently and sustainably than existing industrial methods.

This is where Mingming Wu comes in. Wu, a professor of biological and environmental engineering (CALS), is an expert in microfluidic devices. Traditional methods of identifying, isolating, and mutating microbes are labor and time intensive, requiring a lot of careful and repetitive pipetting.

“Buz and I started to talk about his work,” says Wu, “and we realized that in microfluidics there already exists an established way of identifying and selecting ‘super-bugs’ that exhibit a desired characteristic.”

This existing process is called directed evolution. Together with Sean Medin, a second-year Ph.D. student in Barstow’s lab, the team is in the process of designing a microfluidic device that forces individual bacteria through a channel, with several “stations” along the way.

“We can put sensors in the device so that when a bacterium binds with a rare-earth element, it changes color and we can see it,” says Wu. “Those that bind will be sent down one route in the device, and those that don’t bind will be sent down another route.”

The bacteria that worked will be directed back through the device to a station where they will be mutagenized and then sent through the device again. In this way, Barstow’s team can create an improved variant of the bacterium that Medin will be using to adsorb rare earths.

In addition to helping to craft the microfluidic device the group will use in their process, Medin is also working on an essential step in biomining rare earths – separation.

Once the rare earths have been leached out of the monazite or other ores, they still need to be separated from each other and from the impurities that make it through the leaching process. Current methods of separation, such as liquid-liquid solvent extraction and the ion-exchange process, are energy-intensive and result in large amounts of dangerous waste products.

Medin will instead use a bacterium called Shewanella oneidensis MR-1, and he will subject it to a similar directed evolution process that Schmitz is using with G. oxydans. Medin will be selecting for variants that show higher than average ability to adsorb rare earths. These variants will be subjected to several rounds of mutagenesis with the aim of creating a bacterium that is able to adsorb specific rare earths in high quantity.

Medin joined the Barstow Lab with the express intent of working on this project, and he hopes to someday start a company to commercialize some of the processes honed in the lab. However, his focus would be on recycling existing rare earths from electronics, mine tailings and fly ash, which is one of the waste products of coal combustion.

“Ideally,” says Medin, “I’d like to be able to take fly ash or permanent magnets or other recycled sources of rare-earth elements, bioleach them, and then extract the rare earths out for reuse. And I’d like to do all of that in the U.S. and make sure it is environmentally friendly.”

Currently, the United States imports most of the rare earths it uses, and recycles just a tiny percentage of rare-earth-containing products.

Sabrina Marecos, a first-year Ph.D. student in the Barstow Lab, is working to validate the genetic models being used. Previous research at Cornell and elsewhere supports the theory that Barstow’s Knockout Sudoku process should work with Gluconobacter oxydans.

“At the moment,” says Marecos, “I am working on the verification of the knockout of the membrane-bound glucose dehydrogenase gene. This would confirm that it is possible to knock out genes in Gluconobacter. After that, I will proceed to try and validate the over-expression of another gene to confirm it can be done and which method is most suitable.”

Once Marecos validates the methods Barstow, Schmitz and Medin plan to use, the resultant tools will supplement the relatively few that already exist. “This would allow us to engineer the bacteria using data indicating that some genes are more involved than others in the production of important acids,” says Marecos. “By modifying the bacteria and observing its behavior, we will better understand the bioleaching process and how to enhance it.”

Barstow makes a point of highlighting the importance of Cornell’s culture of collaboration in enabling biomining research. In addition to his lab member’s individual projects, there is one pivotal piece of the work none of them can do: synthesize monazite containing precisely quantified amounts of various rare earths.

In order to know exactly how effective and efficient the bacteria are at leaching and separating rare-earth elements, the team needs to know exactly how much of each element there is in the initial ore. After all, it does not help to know how many grams of lanthanum have been collected through bioleaching if you have no idea how many grams were there to start.

Lucky for Barstow, there are two recent faculty hires who can synthesize and characterize monazite in exactly the way he requires. It was a chance encounter at a Cornell Atkinson brown-bag lunch that would eventually bring the three Atkinson Faculty Fellows together.

Assistant Professor Megan Holycross’s (ENG) specialty is understanding the processes that have differentiated the chemistry of earth’s solid interior. “The instruments in my lab in Snee Hall are capable of achieving temperatures and pressures that recreate the conditions up to 120 kilometers deep in the earth,” says Holycross. “I am studying what happens in the lower crust and the upper mantle of the earth.”

Serendipitously, some of Holycross’s lab equipment can also be used to create homogeneous samples of ores. “Buz and his team are running experiments to extract rare-earth elements from rocks using acids produced by microbes,” says Holycross. “And in order for them to quantify the efficiency of their microbes, they need to quantify their inputs and their outputs precisely.”

Holycross is growing synthetic monazite samples with Associate Professor Esteban Gazel (ENG) and postdoc Brian Balta. Gazel will use his geochemical expertise to characterize the samples, and he will also carry out mass balance calculations to help Barstow determine which mutant version of G. oxydans is most efficient – and therefore most commercializable.

“This is an idea that I believe could only happen at Cornell,” says Gazel. “There is this culture of interdisciplinary collaboration here that is very hard to find elsewhere."

Gazel adds, "Buz and Mingming knew as little about monazite as Megan and I knew about synthetic biology before collaborating.”

Holycross agrees. “This is why I came to Cornell – to do interdisciplinary things like this and work on exciting problems with colleagues.”

“The powerful perspective of our work is not only the fact that we are open to crossing the boundaries of disciplines,” Gazel says, “but that we are all open to learning new areas and communicating with each other. It is in these interdisciplinary spaces where solutions to old and new problems can be found.”

This article originally appeared on the Cornell Engineering website.