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DARPA EMBER employing Microbes for bioproduction of Rare Earth Elements (REEs)

REEs are a series of chemical elements found in the Earth’s crust that are essential components of many technologies, including electronics, computer and communication systems, transportation, health care, and national defense. Rare Earths Elements (REE) are incorporated into many sophisticated technologies with both commercial and defense applications including smartphones and flatscreen televisions to hybrid cars, wind-turbine power systems to communications equipment. These are referred to as “rare” because although relatively abundant in total quantity, they appear in low concentrations in the earth’s crust and extraction and processing is both difficult and costly.


Rare earth elements — a group of 17 metals, including neodymium — are used in lasers, precision-guided weapons, magnets for motors and other devices that are at the heart of many critical technologies the Defense Department depends on.


The top rare earth producing countries are China (105,000 tons), Australia (10,000 tons), US(4,100 tons), Russia(2,500 tons), Thailand(1,100 tons) and Malaysia (200 tons). Some estimates are that China now produces about 90- 95% of the world’s rare earth oxides and is the majority producer of the world’s two strongest magnets, samarium cobalt (SmCo) and neodymium iron boron (NeFeB) permanent, rare earth magnet.


The 70% of the world’s light rare earths coming from a single mining operation at the Bayan Obo deposit in Inner Mongolia.China imposes several different types of unfair export restraints on the materials at issue in today’s consultations request, including export duties, export quotas, export pricing requirements as well as related export procedures and requirements.


While the U.S. has domestic access to rare earth elements, it doesn’t have a strong domestic base for processing that supply, Stefanie Tompkins, director of the Defense Advanced Research Projects Agency, said during an online discussion today at the 5th Annual Defense News Conference. To get after that, Tompkins said DARPA embarked on a new program called the Environmental Microbes as a BioEngineering Resource, or EMBER program, to secure America’s rare earth elements supply chain.


“From a DARPA perspective what we’re looking at are what are some of the barriers that have made it difficult for the U.S. to maintain dominance in rare earth processing,” she said. “One of the things we just launched a new program in is related to bio-mining. The program is called EMBER, and that is about actually designing microbes who can more efficiently and at scale and in an environmentally sound way, separate out these rare earth elements from the ore in which they’re actually found.”



Right now, the most common practices for processing rare earth elements are chemically intensive and frequently toxic to the environment, she said. “Because of all of that, it’s caused the U.S. to sort of back away … from those sort of expensive and environmentally painful processes. And so we need to find new ways,” she said. “Biological is one of the things that we’re exploring.”


DARPA launched the  Environmental Microbes as a BioEngineering Resource (EMBER) program in Sep 2021 with aim to develop novel, bio-based technologies to overcome key challenges facing domestic supply of Rare Earth Elements (REEs) critical to the U.S. and Department of Defense.


The EMBER program will leverage the diversity, specificity, and customizability of environmental microbiology to enable new biomining methods for separation, purification, and conversion of REEs into manufacturing-ready forms. Microbes (and/or biomolecules), including those from extreme or metal-rich environments, can be biologically engineered or adapted to bind, assimilate, and manipulate individual REEs.


These biological components, once developed, may be assembled into an in-line separation, purification, and recovery workflow resulting in individual, purified REEs. Scalability of EMBER’s approach will be demonstrated with proof-of-concept, pilot scale studies aligned with existing mining/waste treatment infrastructure.


EMBER Program

REE purification is challenging – similarities between the 17 REEs require many physical and chemical extraction steps that are energy-intensive, hazardous to the environment and personnel, and often inefficient. As a group, these elements exhibit only modest differences between their Lewis acidities, molecular weights, and atomic radii; subsequently, separation of mixtures of these species into distinct concentrates of isolated elements remains technically challenging.


Biomining is an alternative approach that utilizes microbes to recover metals (e.g., copper, gold) from source materials, often using redox processes to liberate the target metal from a mineral source. Biosorbent and biofiltration approaches show promise in the extraction or removal of metals from contaminated milieu (e.g., for bioremediation) but need to be able to function with complex REE source materials and enable efficient recovery of the bound metals. Using microbes or biomolecules to separate REEs from mixtures is under study, but this approach currently lacks the required specificity to separate all individual REEs, is slow, and is not yet viable at scale.


Advances in microbial and biomolecular engineering could help address these limitations. While synthetic biology tools are well-developed for conventional lab-adapted chassis organisms, and may be suitable for production of organic molecules at circumneutral pH and moderate temperatures (T°), these approaches are underdeveloped for environmental and extremophile microbes, including those known to tolerate and utilize heavy metals. Engineering of organisms that thrive at acidic or alkaline pH and elevated T°, and those that bind, uptake, or store metals, has been impeded by cultivation and isolation challenges. Pathway design and engineering to produce organic molecules are informed by vast libraries of enzymes and regulatory parts, but a lack of annotated genomes, regulatory components, and genome integration tools has impeded advances to develop organisms that specifically utilize inorganic elements, including REEs.

Lastly, current assays for precise measurement of organism-associated REEs are low-throughput, destructive, and, thus, incompatible with typical synthetic biology pipelines. Overcoming these deficiencies could enable selective, specific, and high-capacity biomining of individual REEs.


The Environmental Microbes as a BioEngineering Resource (EMBER) program will develop a biotechnology-based separation and purification strategy for REEs from under-utilized domestic sources such as phosphate mine waste, acid mine drainage, and electronics recycling processes.

The program aims to deliver multiple capabilities such as the separation of REE mixtures into individual elements using aqueous processes; inter-conversion of REE salts/oxides to facilitate production of manufacturing-ready forms (e.g., halides, phosphates, nitrates); and new assays for high-throughput analysis of REE-containing cells and biomolecules.


Performers for the EMBER program will develop bioengineered organism/biomolecular approaches for REE separation and purification, then translate these to practical platforms for biomining (e.g., biosorbent, biofiltration, bioleaching) modules that will be used to extract REEs from domestic REE sources.

Some of the key technical challenges to be addressed by EMBER include:
 Design and engineering of chassis organisms tolerant of pH and temperature extremes, and high metal concentrations.
 Selective and specific biologically-driven extraction of individual REEs from complex mixtures.
 Development of high-throughput, sensitive, non-destructive assays for REEs associated with cells/biomolecules.
 Optimization of REE accumulation, rates, and regenerability/reuse of the bio-extraction process.
 Process engineering to integrate the chosen REE source material (e.g., mine waste, acid mine drainage, recycled electronics) with bio-based REE extraction modules to form a complete REE purification system. Demonstration of the developed technology at the pilot scale will likely require co-location at the facility that provides the REE source
 Techno-economic analysis of the developed bio-based approach that supports its scalability and commercial viability


Developing these REE separation and purification solutions will require two Technical Areas (TAs) – Bioengineering for REE Utilization (TA1) and REE Biomining (TA2).


Bioengineering for REE Utilization (TA1)

The overall goal of TA1 is to create the tools, both organismal and biomolecular, that will enable the TA2 effort to develop efficient REE biomining processes. Teams will need to establish a  design-build-test-learn (DBTL) platform for engineering organisms and/or biomolecules that manipulate REEs and enable their separation and purification from complex mixtures.

“Organisms” envisioned for this TA include microbes, fungi, or bacteriophage; use of photosynthetic organisms (cyanobacteria, microalgae) as chassis must include justification of the additional energy demands that these organisms require.


TA2: REE Biomining

The overall goal for TA2 is to develop technology and processes to utilize organisms, biomolecules, or biopolymers as the key means to separate, purify, and recover individual REEs from domestic REE source materials. Recovered REE materials may be in the form of salts (e.g., halides or nitrates), phosphates, oxides/hydroxides, or reduced metals, and should be devoid of biomass and impurities. Teams will develop and test a biomining workflow to purify individual REEs from complex source mixtures, likely using a combination of geological, chemical, and/or process engineering steps. Studies will progress from the laboratory bench scale to a pilot scale demonstration capable of generating at least 700 grams total REEs (tREE) per week. It is anticipated that the pilot scale demo will need to be co-located with the REE source material site.


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