7 ways ORNL is accelerating the biotechnology revolution

Microbes play a foundational role in modern biotechnology as an efficient means of producing new fuels, chemicals, materials and critical minerals to bolster the nation’s domestic supply chains. By harnessing cutting-edge platforms in synthetic biology and AI-driven design, scientists at the Department of Energy’s Oak Ridge National Laboratory are reprogramming the genetic makeup  of microorganisms at unprecedented speed and scale, building microbial powerhouses that will dominate the future of next-generation materials. 

What sets ORNL apart? The ability to work with a wide range of “wild” microbes — the ones that aren’t so well studied but possess unique abilities and tolerance of extreme conditions that make them ideal biological factories. Current biotechnology practices rely mostly on a small number of extensively researched model microorganisms such as E. coli and yeast. But by augmenting wild, non-model microbes or by transferring some of their genes to model organisms, scientists can give the U.S. biotechnology sector a remarkable advantage. 

Check out seven ways ORNL is expanding the toolbox to redefine what’s possible in industrial biotechnology:

1) Creating a SAGE method for modifying microbes

ORNL led a project adapting the DNA-editing SAGE tool, or Serine recombinase-Assisted Genome Engineering system, to quickly insert and test new DNA designs in virtually any microorganism. The tool is now widely used to accomplish microbial engineering in non-model microbes. 

ORNL scientists have used SAGE to produce biological materials licensed by several companies, including a project for biotechnology firm Kiverdi as part of the DOE Agile BioFoundry.

2) Expanding CRISPR frontiers to tame the wild ones

A multidisciplinary team of ORNL scientists used AI, quantum biology and bioengineering to improve how CRISPR-Cas9 genome editing tools work on non-model microbes. They developed an AI model to analyze tens of thousands of potential guide RNAs targeting a bacterial genome, including key quantum chemistry features about nucleotides that led them to better predictions of guide RNAs for CRISPR-Cas9 editing. In another project, ORNL used high-density screening and the CRISPR-interference gene-silencing tool to devise a new method to influence traits in photosynthetic bacteria. 

ORNL created a tool for modifying wild microbes by finding a way to trick them into accepting bioengineered DNA. The method identified and generated methylated DNA sequences that are unique to each microbe and act as a signature. Using these signature patterns, scientists ensured the target organism would accept and use the new DNA. ORNL researchers have successfully used the technique to engineer at least 25 other microorganisms. 

4) Finding, analyzing wild types

In the search for microbes that thrive in extreme environments, ORNL scientists have discovered hardy thermophiles that exist in undersea volcanic environments and in hot springs across the world. Researchers have also devised new techniques to analyze these valuable microorganisms, including the use of computational models and reverse genomics. In another project, ORNL scientists were able to create and analyze diverse microbial variants that let them more easily map the microorganism’s genome to desired physical traits. The trait mapping capability accelerates the design of custom microbes for various applications. 

5) Converting biomass with amped-up microbes 

With their newly expanded biotechnological toolbox, ORNL scientists have been successful in developing augmented microbes that are good at converting plant material to new fuels and products. Researchers engineered a microbe to turn lignin waste into the valuable industrial chemical itaconic acid, providing a pathway for additional revenue for biorefineries while ensuring every part of the plant is used. In another project, scientists modified a single microbe to simultaneously digest five of the most abundant components of lignocellulosic biomass. The “one-tank” innovation can eliminate several steps in biofuels production, significantly raising efficiency and lowering costs.

6) Discovering, engineering microbial enzymes

ORNL scientists have also discovered and engineered numerous enzymes from microorganisms for use as biological catalysts. Customized enzymes can be used to break down matter into smaller pieces, making them ideal for biotechnology applications such as processing and reusing waste to create new sources of primary materials for manufacturing. Scientists discovered a microbial enzyme that efficiently degrades leftover lignin from biofuels factories for conversion into a valuable biochemical. In another project, a multidisciplinary ORNL team combined synthetic biology, chemistry, materials science, neutrons and AI expertise to identify a new family of enzymes that can selectively break down nylon for reuse much more efficiently than a process using chemistry alone.

7) Biomining critical materials

Along with capabilities in AI, supercomputing, neutrons, chemistry and materials science, ORNL’s expertise in microbial and plant engineering can be leveraged to develop enhanced microbes and plants for the recovery of rare earths and minerals, securing new domestic supply chains for these critical materials. Microorganisms can be engineered to selectively extract or concentrate valuable metals, creating a more efficient method to source these critical materials. Similarly, plants can be modified to enhance their natural ability to hyperaccumulate metals from soil, effectively turning plants into functional phytomines. ORNL won an R&D Magazine MICRO/NANO award for its low-cost NanoFermentation process that uses bacteria for large-scale production of controlled magnetic nanoparticles containing critical minerals and materials, for use in applications ranging from MRI systems to magnetic storage devices.