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November 29, 2016

Microbial interactions, including mutualistic nutrient exchange, underpin the flow of energy and materials in all ecosystems. [Image courtesy J. B. McKinlay]

A synthetic microbial ecosystem helps understand the behavior of bacterial communities

A bacterial co-culture was engineered to force two bacterial species to depend on each other to grow, shedding light on mutualism dynamics.

The Science
Researchers designed a stable co-culture in which Escherichia coli consumed sugar and produced organic acids to feed a Rhodopseudomonas palustris mutant strain that fixed and provided nitrogen for both microbes. A mathematical model was developed for this system, and the model accurately predicted how the co-culture would reach a new equilibrium when one of the microbes was genetically modified.

The Impact
Artificial co-cultures of two or more microbial species are useful tools for understanding how microbial communities behave in their natural habitat. However, the instability of co-culture systems has limited their utility for both fundamental and biotechnological studies. This research developed a microbial cross-feeding system that maintains its species composition over multiple generations, constituting a novel and important tool for understanding mutualistic relationships in natural environments and how to manipulate microbial communities for useful purposes.     

A mutant strain of R. palustris that can fix nitrogen gas and excrete ammonium was cultured together with E. coli in the presence of glucose as the only carbon source. R. palustris cannot consume glucose, but it feeds on the organic acids excreted by E. coli after it metabolizes glucose. In turn, E. coli obtains its nitrogen from the ammonium excreted by the R. palustris mutant. This cross-feeding dependency forced the co-culture to stabilize at a ratio of one E. coli cell to nine R. palustris cells, regardless of the proportion of each strain in the initial inoculum. The researchers at Indiana University also developed a mathematical model that enabled them to successfully predict the co-culture composition if the amounts of nutrients excreted by the microbes were altered. To test the model's accuracy, the investigators made a new R. palustris mutant that excreted three times more ammonium than the original strain. When this new mutant was co-cultured with E. coli, the system reached equilibrium at a ratio of one-to-one, as the model predicted. These results demonstrate the utility of stable co-cultures to understand cross-feeding relationships in ecosystems relevant for the global carbon cycle, or to engineer microbial systems for practical applications.

Contact (BER PM)
Pablo Rabinowicz
Office of Biological and Environmental Research
Office of Science
U.S. Department of Energy

(PI Contact)
James McKinlay
Joint BioEnergy Institute
Department of Biology
Indiana University
Bloomington, IN

This work was supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research Early Career Research Program award number DE-SC0008131 to James McKinlay. Authors also acknowledge partial support from the U.S. Army Research Office.

LaSarre, B., A. McCully, J. Lennon, and J. McKinlay. 2017. “Microbial Mutualism Dynamics Governed by Dose-Dependent Toxicity of Cross-Fed Nutrients,” The ISME Journal 11, 337–48. DOI: 10.1038/ismej.2016.141.

Reference link:

Topic Areas:

  • Research Area: Microbes and Communities
  • Research Area: DOE Bioenergy Research Centers (BRC)
  • Research Area: Biological Engineering
  • Research Area: Computational Biology, Bioinformatics, Modeling
  • Mission Science: Sustainable Biofuels
  • Mission Science: Climate

Division: SC-23.2 Biological Systems Science Division, BER


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