Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth
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.
- Publication Date:
- Research Org.:
- Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); National Renewable Energy Laboratory (NREL), Golden, CO (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF); Mexican National Research Council
- OSTI Identifier:
- 1644138
- Alternate Identifier(s):
- OSTI ID: 1657205; OSTI ID: 1677454
- Report Number(s):
- PNNL-SA-152360; NREL/JA-2700-74826
Journal ID: ISSN 2041-1723; 3803; PII: 17612
- Grant/Contract Number:
- AC05-76RL01830; AC36-08GO28308; SC0012658; SC0019388; 1332344; CBET-1804187; 237897
- Resource Type:
- Published Article
- Journal Name:
- Nature Communications
- Additional Journal Information:
- Journal Name: Nature Communications Journal Volume: 11 Journal Issue: 1; Journal ID: ISSN 2041-1723
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; computational biology and bioinformatics; computer modelling; environmental microbiology; bioenergy; photobiology; synthetic biology; genomics; 93 SC - Biological and Environmental Research (BER) (SC-23)
Citation Formats
Zuñiga, Cristal, Li, Tingting, Guarnieri, Michael T., Jenkins, Jackson P., Li, Chien-Ting, Bingol, Kerem, Kim, Young-Mo, Betenbaugh, Michael J., and Zengler, Karsten. Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth. United Kingdom: N. p., 2020.
Web. doi:10.1038/s41467-020-17612-8.
Zuñiga, Cristal, Li, Tingting, Guarnieri, Michael T., Jenkins, Jackson P., Li, Chien-Ting, Bingol, Kerem, Kim, Young-Mo, Betenbaugh, Michael J., & Zengler, Karsten. Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth. United Kingdom. https://doi.org/10.1038/s41467-020-17612-8
Zuñiga, Cristal, Li, Tingting, Guarnieri, Michael T., Jenkins, Jackson P., Li, Chien-Ting, Bingol, Kerem, Kim, Young-Mo, Betenbaugh, Michael J., and Zengler, Karsten. Thu .
"Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth". United Kingdom. https://doi.org/10.1038/s41467-020-17612-8.
@article{osti_1644138,
title = {Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth},
author = {Zuñiga, Cristal and Li, Tingting and Guarnieri, Michael T. and Jenkins, Jackson P. and Li, Chien-Ting and Bingol, Kerem and Kim, Young-Mo and Betenbaugh, Michael J. and Zengler, Karsten},
abstractNote = {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.},
doi = {10.1038/s41467-020-17612-8},
journal = {Nature Communications},
number = 1,
volume = 11,
place = {United Kingdom},
year = {Thu Jul 30 00:00:00 EDT 2020},
month = {Thu Jul 30 00:00:00 EDT 2020}
}
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https://doi.org/10.1038/s41467-020-17612-8
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