CMI Researcher Receives $7.3M DOE Grant to Address National Crop Productivity Through Soil Microbes

Multi-year research project will explore how to reduce microbial competition for organic Nitrogen and increase plant efficiency for long-term sustainable bioenergy production

SAN DIEGO, CA – August 14, 2020 -- UC San Diego Center for Microbiome Innovation (CMI) Faculty Member Karsten Zengler and a team of researchers have been awarded a $7.3 million grant over a five-year period from the U.S. Department of Energy (DOE) with a goal of making bioenergy feedstock crops more productive and resilient.

With a shortage of suitable land for growing feedstock crops that are necessary for sustainable bioenergy production, the DOE grants will accelerate research to develop crops with greater productivity and survivability in stressful environments. The grant awards will focus on the complex interactions among crops, soil, and soil microbes that impact productivity and stress resistance.

Zengler, a professor of pediatrics and bioengineering at UC San Diego, in collaboration with co-principal investigators, was awarded the grant in August by competitive peer review under a DOE Funding Opportunity Announcement for Systems Biology Research to Advance Sustainable Bioenergy Crop Developmentand sponsored by the Office of Biological and Environmental Research (BER) within DOE’s Office of Science.

Co-principal investigators include Trent Northen and John Vogel of Lawrence Berkeley National Laboratory and Amélie Gaudin of UC Davis.

“To avoid competition with food crops and maximize economic and environmental benefits, bioenergy crops should be grown on marginal soils with minimal inputs, especially energy-intensive synthetic nitrogen fertilizer,” said Zengler. “For long-term sustainability, we need bioenergy crops to be more reliant on microbial-driven organic nitrogen for nutrition. Principles identified for bioenergy crops might also translate to food crops, increasing land that can be use agriculture in general.”

Root exudates, the variety of substances secreted by the roots of living plants and exist in the surrounding soil called the rhizosphere, are thought to play a critical role in recruiting and maintaining beneficial microbes, including those that make nitrogen available to the plant and provide a critical source of nutrition for diverse microorganisms. 

Using funds from the multi-year grant, Zengler and team will explore if this exchange of exudates for plant benefits continues through the night when plants are not photosynthesizing with initial research that exudate composition indicates strong circadian rhythms. Understanding the nature of plant and microbial drivers behind these dynamic interactions is crucial for putting together a complete picture of nitrogen cycling and the uptake process in the rhizosphere.

“By using predictive models to understand the complexity of these processes and optimize sustainable bioenergy systems, exudate and bacterial community engineering will enable enhanced nitrogen supplies,” said Zengler. “Our goal is to reduce microbial competition for organic nitrogen and thereby increase plant nitrogen use efficiency.”

Zengler is one of over 130 CMI Faculty Members working to advance innovative collaborations between UC San Diego Microbiome experts and industry partners that will accelerate microbiome discovery and create innovative technologies to advance the field and enable major clinical breakthroughs. 

“Zengler’s highly innovative and interdisciplinary study will unveil findings in plant productivity at a very mechanistic level and advance microbiome knowledge that is currently lacking,” said CMI Executive Director Andrew Bartko, Ph.D. “The Center for Microbiome Innovation is committed to this work to develop new methods for manipulating microbiomes that will benefit the environment and ultimately improve human health.”

The study will unveil new knowledge in the field and greatly improve the ability to increase the productivity of bioenergy and other crops grown under low input conditions. Research efforts will be enabled by advanced techniques developed by this group, which include model ecosystems, absolute microbial abundance measurements, community modeling, 24,000 grass mutant lines, state-of-the-art metabolomics, and isotope dilution methods. 

Using these systems biology and multi-omics tools, the researchers will further weave together the intricate network between plants and microbes across time and space and allow for the first genome-scale computational model of the rhizosphere. Additionally, it will enable design of nutrient and microbial variants that are optimized for specific plant lines and provide a significant research advancement for the field of biosustainable biotechnology.

Zengler’s research focus at UC San Diego is using omics tools to understand how microbes interact with their partners, and the use of computational models to analyze and integrate the data.


About Center for Microbiome Innovation at University of California San Diego:
The UC San Diego Center for Microbiome Innovation leverages the university's strengths in clinical medicine, bioengineering, computer science, the biological and physical sciences, data sciences, and more to coordinate and accelerate microbiome research. We also develop methods for manipulating microbiomes for the benefit of human and environmental health. Learn more at and follow @CMIDigest

Media Contact:
Erin Bateman
Communications Officer
Center for Microbiome Innovation, Jacobs School of Engineering
UC San Diego

Media Contacts

Erin Bateman
Center for Microbiome Innovation

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