Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Unleashing Photosynthesis and Nitrogen Fixation for Carbon Neutral Production of Nitrogen-Rich Compounds


Himadri B. Pakrasi1* (, Anindita Bandyopadhyay1, Michelle Liberton1, Christopher M. Jones1, Runyu Zhao1, Wenyu Li1, Jacob Sebesta2, Eric Schaedig2, Foteini Davrazou2, Ibrahim Alamin3, Lydia Davies3, Victory Obele3, Khadijah Taite3, Yinjie J. Tang1, Yixin Chen1, Jianping Yu2, Wei Xiong2, Harvey J. M. Hou3, Vida A. Dennis3


1Washington University in St. Louis; 2National Renewable Energy Laboratory; 3Alabama State University


Address basic research challenges in developing and advancing technologies for green fertilizer production.


Nitrogen is essential for life on Earth. Today, most of life’s nitrogen need is met by chemical conversion of atmospheric nitrogen into readily usable forms, but such conversion comes at a massive environmental cost. It is conducted under high temperature and pressure, generating a massive carbon footprint. An alternative approach is based on biological conversion of nitrogen at ambient temperature, a greener process restricted to only a few select groups of microbes. Of these, cyanobacteria are uniquely capable of driving the energetically expensive nitrogen fixation reaction solely with solar power while simultaneously capturing carbon, and thus reducing the carbon footprint (Liberton et al. 2019; Bandyopadhyay et al. 2021).

The use of cyanobacteria, non-model microbes, as chassis for the conversion of atmospheric nitrogen into valuable N-rich compounds, however, requires significant fundamental research, including development of robust growth conditions and systems level understanding of the biology of these photosynthetic autotrophs. This project addresses foundational research challenges that stand in the way of developing nitrogen-fixing cyanobacteria as cell factories for the production of nitrogen-rich compounds. This group focuses on the production of guanidine, ammonia and urea, three nitrogen-rich compounds that can serve as substitutes for synthetic fertilizers (Wang et al. 2019) (Fig. 1). Specifically, researchers are (1) designing and building functional modules for the production of guanidine, urea, and ammonia; (2) designing and building nitrogen-fixing chassis strains for optimal carbon and nitrogen capture and product formation; and (3) optimizing the production chassis.

This team is using two strains representing the two contrasting paradigms that cyanobacteria use to accommodate the mutually antagonistic processes of oxygenic photosynthesis and nitrogen fixation: temporal separation in a unicell (Cyanothece 51142) and spatial separation in a multicellular filament (Anabaena 33047). Researchers are working to engineer novel enzymes capable of catalyzing the conversion of atmospheric nitrogen into guanidine, ammonia and urea, and membrane transporters that will secrete the products out of the cell. Multiomics studies and machine learning tools will unravel the fundamental principles underlying the regulation of carbon and nitrogen fixation in cyanobacteria and their channelization towards the products of interest. The research team’s goal is to develop chassis strains that can produce sufficient quantities of fertilizer compounds for pilot scale-up geared towards commercialization of the concept. In the longer term, this group envisions future deployment of such strains in soil as a local source of nitrogen for bioenergy and other crops, and also in ocean fertilization for carbon dioxide (CO2) removal. This technology, when fully developed, has the potential to replace the use of synthetic fertilizers. The fundamental knowledgebase this research generates will also have broader scientific impact on carbon neutral biomanufacturing of nitrogen-containing petrochemical replacement compounds.

This research team of seven investigators from Washington University, National Renewable Energy Laboratory, and Alabama State University brings together significant interdisciplinary expertise in cyanobacterial systems biology, metabolic modeling, machine learning and synthetic biology. An important mission of this project is to train a number of students from underprivileged communities, equipping a future workforce with modern biomanufacturing technologies.


Potential Bottlenecks

Fig. 1: Schematic representation of our strategy. Proteins/pathways that are known bottlenecks and are the central engineering targets in this project are marked with red asterisks. Pathways that generate the substrates for products of interest and harbor potential bottlenecks are marked with blue asterisks. These are targets for omics-level investigation followed by AI-prediction-based rewiring of the metabolism of cyanobacteria.


Bandyopadhyay, A., et al. 2021. “Antenna Modification Leads to Enhanced Nitrogenase Activity in a High Light-Tolerant Cyanobacterium,” mBio 12(6). DOI:10.1128/mbio.03408-21.

Liberton, M., et al. 2019. “Enhanced Nitrogen Fixation in a glgX-Deficient Strain of Cyanothece sp. Strain ATCC 51142, a Unicellular Nitrogen-Fixing Cyanobacterium,” Applied and Environmental Microbiology 85(7). DOI:10.1128/AEM.02887-18.

Wang, B., et al. 2019. “Photosynthetic Production of the Nitrogen-Rich Compound Guanidine,” Green Chemistry 21(11), 2928–37. DOI:10.1039/C9GC01003C.

Funding Information

This work is supported by the U.S. DOE, Office of Science, under Award Number DE-SC0024702.