Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment

Blount, Z. D.; Maddamsetti, R.; Grant, N. A.; Ahmed, S. T.; Jagdish, T.; Sommerfeld, B. A.; Tillman, A.; Moore, J. P.; Slonczewski, J. L.; Barrick, J. E.; Lenski, R. E.

doi:10.1101/2020.01.22.915975

bioRxiv · 10.1101/2020.01.22.915975

Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment

Blount, Z. D.·Maddamsetti, R.·Grant, N. A.·Ahmed, S. T.·Jagdish, T.·Sommerfeld, B. A.·Tillman, A.·Moore, J. P.·Slonczewski, J. L.·Barrick, J. E.·Lenski, R. E.

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Abstract

Evolutionary innovations allow populations to colonize new, previously inaccessible ecological niches. We previously reported that aerobic growth on citrate (Cit+) evolved in a population of Escherichia coli during adaptation to a minimal glucose medium containing citrate (DM25). Cit+ can grow in citrate-only medium (DM0), which is a novel environment for E. coli. To study adaptation to this new niche, we evolved one set of Cit+ populations for 2,500 generations in DM0 and a control set in DM25. We identified numerous parallel mutations, many mediated by transposable elements. Several lineages evolved multi-copy amplifications containing the maeA gene, constituting up to [~]15% of the genome. We also found substantial cell death in ancestral and evolved clones. Our results demonstrate the importance of copy-number variation and transposable elements in the refinement of the Cit+ trait. However, the observed mortality suggests a persistent evolutionary mismatch between E. coli physiology and a citrate-only environment.

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Blount, Z. D., Maddamsetti, R., Grant, N. A., Ahmed, S. T., Jagdish, T., Sommerfeld, B. A., Tillman, A., Moore, J. P., Slonczewski, J. L., Barrick, J. E., Lenski, R. E.. 2020-01-23. Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment. https://doi.org/10.1101/2020.01.22.915975

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