Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth

Cristal Zuñiga,Michael J Betenbaugh,Chien-Ting Li,Michael T Guarnieri,Tingting Li,Karsten Zengler,Jackson P Jenkins,Kerem Bingol,Young-Mo Kim

doi:10.1038/s41467-020-17612-8

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. Here we construct four community metabolic models to guide strain selection, pairing phototrophic, sucrose-secreting Synechococcus elongatus with heterotrophic Escherichia coli K-12, Escherichia coli W, Yarrowia lipolytica, or Bacillus subtilis. Model simulations reveae metabolic exchanges that sustain the heterotrophs in minimal media devoid of any organic carbon source, pointing to S. elongatus-E. coli K-12 as the most active community. Experimental validation of flux predictions for this pair confirms metabolic interactions and potential production capabilities. Synthetic communities bypass member-specific metabolic bottlenecks (e.g. histidine- and transport-related reactions) and compensate for lethal genetic traits, achieving up to 27% recovery from lethal knockouts. The study provides a robust modelling framework for the rational design of synthetic communities with optimized growth sustainability using phototrophic partners.

Highlights

Microbial communities comprised of phototrophs and heterotrophs hold great promise for sustainable biotechnology
We focus on established microbial cell factories, i.e., Escherichia coli, Bacillus subtilis, and the fungus
We found community-specific production potential in all Synthetic phototrophic communities (SPCs); the SPC containing E. coli K-12 was capable of producing the most metabolites (111 metabolites), followed by E. coli W (106 metabolites), Y. lipolytica (60 metabolites), and B. subtilis (39 metabolites)

Summary

Introduction

Microbial communities comprised of phototrophs and heterotrophs hold great promise for sustainable biotechnology. The study provides a robust modelling framework for the rational design of synthetic communities with optimized growth sustainability using phototrophic partners. Phototrophic microbial communities exhibit symbiosis between photoautotrophic and heterotrophic organisms supported primarily by solar energy and the fixation of carbon dioxide (CO2). This type of association dominates many biofilms, microbial mats, and lichens[1,2,3], thriving in desiccation, nutrient starvation, and salinity or temperature extremes[4]. Photoautotrophic members, classically either cyanobacteria or eukaryotic algae, convert CO2 into organic carbon for growth and maintenance of the heterotrophic partner(s) Exchange of these metabolites can sustain the heterotrophs under conditions devoid of any organic carbon source. The first three steps (a–c) are important drivers for implementation of successful bioproduction processes that can be optimized and guided using metabolic modeling

Methods

Results

Conclusion