Harvesting the critical minerals future

Scientists are betting on a resource-efficient, highly effective strategy: Using engineered plants and symbiotic microbes to absorb critical minerals directly from the Earth in a process called phytomining.

OPAL partners include Oak Ridge, Argonne, Lawrence Berkeley and Pacific Northwest national laboratories. The project combines AI, robotics and automated experimentation to create an interconnected network of labs to learn, adapt and accelerate breakthroughs across biology, biotechnology and energy science. ORNL researchers’ initial focus is biodesign for critical minerals and materials recovery. Proactively sharing and integrating AI-ready data, models and agents to guide experiments at the four labs can significantly speed experimentation and time to analysis for faster solutions.

With the OPAL co-scientist, ORNL researchers conducting an experiment on the ability of plants to absorb nickel were able to reduce the time to analysis for more than 1,000 physical plant traits from hundreds of hours of manual labor to a few minutes of interaction with the AI agent.

With the OPAL co-scientist, ORNL researchers conducting an experiment on the ability of plants to absorb nickel were able to reduce the time to analysis for more than 1,000 physical plant traits from hundreds of hours of manual labor to a few minutes of interaction with the AI agent.

Phytomining is not a new concept. Plants have been used for years to help remediate soils at former industrial and mining sites. It is ideal for areas with large, low-grade mineral deposits unsuitable for conventional mining or for growing food crops. Deployment is aimed at rural areas with marginal lands, in warmer regions where plants grow larger faster, and in rehabilitation zones for existing or planned mining operations.

ORNL researchers investigated how 12 unique lines of the pennycress plant collected from varied growing regions across the world accumulated nickel. The plant is fast-growing, and in the same family as a known nickel accumulator. Nickel is used in lithium-ion batteries and is essential to making stainless steel and superalloys for jet engines, military hardware and weapons systems.

Researchers observed a total of 360 pennycress plants growing in soils treated with varying nickel concentrations using ORNL’s Advanced Plant Phenotyping Laboratory (APPL).

Day and night, the plants traveled through APPL on automated conveyers, where high-resolution cameras recorded tiny changes in leaf color, plant architecture, growth, stress response and mineral content. By the end of the experiment, more than 24,000 observations revealed how each individual plant responded to increasing nickel concentrations.

The OPAL co-scientist was developed on Frontier, the world’s fastest supercomputer for open science, at ORNL’s Oak Ridge Leadership Computing Facility, which is supported by DOE’s Advanced Scientific Computing Research program. OPAL uses Frontier’s processing speed to perform massive computation on the fly. The co-scientist also uses agentic AI modules developed by OPAL partner Argonne.

The co-scientist previously demonstrated its ability to cut the time for analysis of plants from hundreds of hours to minutes. Since then, the OPAL team has significantly increased the functionality of the agentic AI system and established automated workflows.

The co-scientist quickly delivered insights on pennycress performance and suggested next steps by:

• Identifying the top nickel-tolerant plant varieties in the experiment,
• Assessing which plants had superior growth and stress resilience and
• Pinpointing which early-stage traits best predicted final nickel accumulation.

The co-scientist also rapidly identified anomalies and alerted researchers to check the experiment for potential corrective action, reducing downtime and risk. It suggested follow-on experiments to confirm the plants’ growth dynamics, uncover underlying nickel tolerance biology and to refine biodesign strategies for enhanced nickel phytomining.

Automating repetitive, time-consuming tasks

“Instead of waiting until the end of the experiment for a single endpoint measurement, this unique computational platform created a dynamic record of how each plant responds to nickel over time during live experiments to enable real-time analysis and decision-making,” said David Weston, principal investigator for ORNL’s OPAL initiative. “Rather than requiring scientists to manually record and search through images, spreadsheets, model outputs and metadata, the co-scientist uses specialized agent skills to divide the work.”

As part of the experiment, scientists also collected some data by the traditional manual method, with two researchers measuring by hand plant traits, including greenness and bolting — the time when plants experience a growth spurt just before flowering and producing seed. The researchers took six hours to record the data for all plants on a given day using paper forms, then transferred the information to computers.

“The purpose of these agents is to collaborate with the scientist by reducing the technical burden of analyzing data across files, scripts and query tools, so the scientist can focus on interpretation, judgment and experimental design,” said Renan Souza, who led the ORNL experiment’s computational work.

“Even with extensive context, fully contextualized interpretation still requires human judgment,” said Daniel Rosendo, ORNL lead for OPAL’s Genesis Mission platform deployment. “The scientist remains in control, while the OPAL co-scientist’s agentic workflow helps shorten the path from data generation to scientific insight.”

“Agentic AI has the potential to become a true scientific collaborator by automating phenotyping, interpreting complex biological datasets and accelerating biodesign,” Sedbrook said. “For crops like pennycress and Odontarrhena, this could compress years of discovery into months and help bring DOE mission-focused agricultural and bioindustrial innovations to the field much faster.”

In the project’s next steps, ORNL scientists will integrate plant experiments with the proteins and microbes being developed by OPAL partners to aid phytomining. 

Argonne is developing pH-optimized proteins for enhanced bioleaching enzymes that can increase rare-earth element extraction, using AI and advanced robotics to accelerate the design, build, test and learn cycles. Pacific Northwest and Lawrence Berkeley national laboratories are using robotics and agentic AI approaches to develop microbes such as the metal-tolerant Pseudomonas putida that exude organic acids to release soil-bound critical minerals, enhancing uptake in plants. 

OPAL takes the highest-impact approach for successful phytomining by co-engineering plants, microbes and proteins, turning the resulting multi-scale, multi-kingdom biological system into a programmable platform that accumulates valuable minerals in plants for harvest and processing.