Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between bacteria in a synthetic community


Interactive microbial communities are ubiquitous, influencing biogeochemical cycles and host health. One widespread interaction is nutrient exchange, or cross-feeding, wherein metabolites are transferred between microbes. Some cross-fed metabolites, such as vitamins, amino acids, and ammonium (NH4+), are communally valuable and impose a cost on the producer. The mechanisms that enforce cross-feeding of communally valuable metabolites are not fully understood. Previously we engineered a cross-feeding coculture between N2-fixing Rhodopseudomonas palustris and fermentative Escherichia coli. Engineered R. palustris excretes essential nitrogen as NH4+ to E. coli, while E. coli excretes essential carbon as fermentation products to R. palustris. Here, we sought to determine whether a reciprocal cross-feeding relationship would evolve spontaneously in cocultures with wild-type R. palustris, which is not known to excrete NH4+. Indeed, we observed the emergence of NH4+ cross-feeding, but driven by adaptation of E. coli alone. A missense mutation in E. coli NtrC, a regulator of nitrogen scavenging, resulted in constitutive activation of an NH4+ transporter. This activity likely allowed E. coli to subsist on the small amount of leaked NH4+ and better reciprocate through elevated excretion of fermentation products from a larger E. coli population. Our results indicate that enhanced nutrient uptake by recipients, rather than increased excretion by producers, is an underappreciated yet possibly prevalent mechanism by which cross-feeding can emerge.

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Fig. 1: Synergistic cross-feeding between E. coli and R. palustris is facilitated by NH4+ excretion.
Fig. 2: Coculture doubling times decreased during experimental evolution of WT-based and NifA*-based cocultures.
Fig. 3: Final populations in WT-based cocultures show large increases through serial transfers.
Fig. 4: WT-based and NifA*-based cocultures exhibit distinct metabolic phenotypes.
Fig. 5: Adaptation by E. coli is sufficient to enable growth of WT-based cocultures.
Fig. 6: A missense mutation in E. coli ntrC enables emergent NH4+ cross-feeding by conferring constitutive expression of nitrogen acquisition genes.


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This work was supported in part by the US Army Research Office grants W911NF-14–1–0411 and W911NF-17–1–0159, a National Science Foundation CAREER award MCB-1749489, the US Department of Energy, Office of Science, Office of Biological and Environmental Research, under award DE-SC0008131, and the Joint Genome Institute Community Science Program, CSP 502893. The work conducted by the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the US Department of Energy under Contract No. DE-AC02–05CH11231. We thank A.L. Posto, J.R. Gliessman, and M.C. Onyeziri for coculture passaging and initial characterizations, J.T. Lennon and B.K. Lehmkuhl for equipment and assistance with qRT-PCR, and J. Ford and A.M. Buechlein at the IU Center for Genomics and Bioinformatics.

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Fritts, R.K., Bird, J.T., Behringer, M.G. et al. Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between bacteria in a synthetic community. ISME J 14, 2816–2828 (2020). https://doi.org/10.1038/s41396-020-00737-5

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