Q&A with Brian Sanders: Tiny spores for a big critical minerals challenge

Scientists at the Department of Energy's (DOE) Oak Ridge National Laboratory (ORNL) are exploring how durable, customizable bacterial spores could capture rare earth elements (REE) from acid mine drainage and other metal-containing waste streams. The project supports new methods of sourcing critical minerals essential for the nation's economic strength and national security.

The Spore Platform for REE Recovery (SpoREE) project combines biological engineering, artificial intelligence (AI)-aided protein design, advanced imaging and chemical analysis to develop biological materials that can identify and bind to rare earth ions in liquid waste streams. The goal is a highly efficient process in which concentrated elements are stripped from the spores and converted into valuable materials, while the spores are cleaned and reused.

SpoREE began as a critical minerals and materials pilot project supported by the DOE Office of Science Biological and Environmental Research program, and was recently approved for a two-year extension based on its initial successes.

Project lead Brian Sanders discussed what the pilot project accomplished, what researchers will investigate next and where the technology could lead.

Q: What is the basic idea behind SpoREE?

A: Certain bacteria produce spores-dormant, highly durable structures that protect their genetic material under harsh conditions. We are engineering the surfaces of those spores to display proteins that bind REEs.

You can think of the spore as a robust biological bead. We can customize its surface for a particular metal and then assemble many spores into a material that could filter metals from water.

Q:Why are bacterial spores well suited to this application?

A: Spores are compact biological particles with tough, multilayered surfaces. They can withstand dehydration, temperature changes, ultraviolet radiation and challenging chemical conditions, including the highly acidic conditions found in some mine drainage.

They also offer three important advantages: robustness, scalability and engineerability. Bacterial spores can potentially be produced in large quantities through fermentation, and we can use genetic tools to modify proteins on their surfaces or within their different layers.

Q: Why is the project focusing on acid mine drainage?

A: Acid mine drainage is water that flows from or collects near mines and becomes highly acidic through geochemical and microbial processes. Under those conditions, metals can be released from surrounding rock and soil and accumulate in the water.

Appalachia has large volumes of acid mine drainage associated with coal mines. The challenge is that rare earth elements are present at very low concentrations among much larger quantities of iron, manganese, aluminum and other elements.

Biology could offer a solution because proteins can distinguish among different metals. This selectivity-the ability to capture a desired metal while leaving others behind-is important when the target elements are so dilute.

Q: Which rare earth elements are the highest priorities?

A: Rare earth elements used in high-performance magnets, including neodymium and dysprosium, are among the highest priorities. However, we need to test several elements to understand how selective each biological design is.

Although we are demonstrating the approach with rare earth elements, the longer-term goal is a customizable platform. By changing the proteins displayed on the spores, it may be possible to target other critical materials, such as gallium.

Q: What did the pilot project accomplish?

A: Broadly speaking, we reduced some of the uncertainty surrounding the concept of displaying metal-binding proteins on spore surfaces to capture and potentially separate rare earth elements. The properties of the spores and the results we obtained indicate that this is a viable strategy worth continuing to investigate.

A major accomplishment was establishing the analytical pipeline needed to evaluate different biological designs. We can create many variations of the spores, but we also need efficient ways to determine how each change affects metal binding. The team developed and applied methods to screen many samples, measure very small quantities of metals and use advanced imaging to examine where metals are located around individual spores.

We also learned that metal binding involves more than simply placing a protein on a spore. The surrounding proteins and the spore's overall structure and composition can also influence performance. Those features give us additional design levers that we may be able to adjust to create better materials.

Q: What broadly useful research tools have resulted from the pilot?

A: The team used AI tools to advance REE-binding protein design. We also developed a method that can screen roughly 80 biological samples at once and rapidly determine their metal fingerprints. We are applying it to spores, but the approach could also be useful for studying cells, microparticles and other small beads used in metal recovery research.

Researchers have also advanced AI-enabled image analysis methods that can examine hundreds of spores and quickly measure their dimensions, size distribution and surface area. These characteristics are important when engineering spores to function as biological beads.

Some of the project's early contributions are therefore analytical tools and techniques that could be useful to the broader research community.

Q: What will scientists explore in the next phase?

A: The next phase will examine the system at several interconnected scales. At the molecular level, researchers will study how a protein's binding sites interact with individual metal ions and what controls selectivity.

At the spore level, the team will investigate where a designed protein should be attached, how the spore's different layers affect stability and reproducibility, and how changes to surrounding proteins alter metal binding.

At the materials level, researchers will study how multiple spores interact when they are assembled into a larger network. The team plans to immobilize or cross-link the spores, essentially binding them together, into materials that can be packed into laboratory columns. Researchers could then flow realistic solutions, including actual acid mine drainage, through the columns and measure which metals are captured and the reproducibility of this process.

This would be a laboratory-scale demonstration, but it would provide important evidence about whether the approach can work under more realistic conditions.

Q: What are the main scientific challenges?

A: Reliably measuring how proteins bind metals is difficult, even before those proteins are placed on a complex spore surface. Computational methods such as AI can design thousands of potential metal-binding proteins, but researchers must experimentally test those designs and feed the results back into the next design cycle. We will rely on our analytical workflows to address these challenges.

Actual acid mine drainage presents another challenge because it contains many competing elements and other substances. Testing under those conditions will help ensure that researchers are engineering the biology toward a meaningful application rather than toward an idealized laboratory solution.

Q: What could the project ultimately make possible?

A: Rare earth elements occur at low concentrations in acid mine drainage, but the water exists in very large volumes. A system that repeatedly processes those flows could recover useful quantities of the elements while drawing resources from an existing waste stream.

More broadly, the research would establish principles for designing spores as customizable materials. The longer-term vision is to predict how changing a protein or a spore's structure and composition will affect its performance, allowing scientists to design biological materials for different metals and recovery environments.

The project is still establishing that scientific foundation, and the pilot results provide a basis for continued research and future demonstrations.

Q: Why is ORNL particularly well suited to the research?

A: This is simultaneously a biology, chemistry, materials and analytical measurement challenge. ORNL brings to bear its unique multidisciplinary environment, including synthetic biology, computational protein design, trace-metal measurement, electron microscopy, image analysis and materials science.

That combination is important because faster, more reliable measurements enable faster biological design. The project's progress has depended on researchers across multiple disciplines working together to understand the system from individual protein-binding sites to networks containing many spores.

UT-Battelle manages ORNL for DOE's Office of Science, the single largest supporter of basic research in the physical sciences in the United States. DOE's Office of Science is working to address some of the most pressing challenges of our time. For more information, visit energy.gov/science. - Stephanie Seay