Genomic and phenotypic evolution ofEscherichia coliin a novel citrate-only resource environment

Author:

Blount Zachary D.ORCID,Maddamsetti RohanORCID,Grant Nkrumah A.,Ahmed Sumaya T.,Jagdish TanushORCID,Sommerfeld Brooke A.,Tillman Alice,Moore Jeremy,Slonczewski Joan L.ORCID,Barrick Jeffrey E.ORCID,Lenski Richard E.ORCID

Abstract

ABSTRACTEvolutionary innovations allow populations to colonize new, previously inaccessible ecological niches. We previously reported that aerobic growth on citrate (Cit+) evolved in a population ofEscherichia coliduring adaptation to a minimal glucose medium containing citrate (DM25). Cit+can grow in citrate-only medium (DM0), which is a novel environment forE. 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 themaeAgene, 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 betweenE. coliphysiology and a citrate-only environment.

Publisher

Cold Spring Harbor Laboratory

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