September 2, 2020
Journal Article

Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth

Cristal Zuniga
Tingting Li
Michael Guarnieri
Jackson Jenkins
Kerem Bingol
Michael Betenbaugh
Karsten Zengler
Chien-Ting Li

Abstract

Microbial communities comprised of phototrophs and heterotrophs hold great promise for sustainable biotechnology. Successful application of these communities relies on the selection of appropriate partners. We constructed four community metabolic models to guide strain selection of synthetic communities, pairing phototrophic, sucrose-secreting Synechococcus elongatus with heterotrophic Escherichia coli K-12, Escherichia coli W, Yarrowia lipolytica, or Bacillus subtilis. Metabolic exchanges that sustain the heterotrophs in minimal media devoid of any organic carbon source were elucidated. Model simulations pointed to S. elongatus-E. coli K-12 as the most active community. Reaction flux predictions were validated, confirming metabolic interactions and potential production capabilities. We determined member-specific metabolic bottlenecks (e.g. histidine- and transport-related reactions) that are bypassed in communities. Additionally, we calculated compensation for lethal genetic traits, achieving up to 27% recovery from lethal knockouts. The study provides a robust workflow for the rational design of synthetic communities with optimized growth sustainability using phototrophic partners.

Revised: September 2, 2020 | Published: July 30, 2020

Citation

Zuniga C., T. Li, M. Guarnieri, J. Jenkins, C. Li, A.K. Bingol, and Y. Kim, et al. 2020. "Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth." Nature Communications 11. PNNL-SA-152360. doi:10.1038/s41467-020-17612-8