Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment
Open Access
- 29 May 2020
- journal article
- research article
- Published by eLife Sciences Publications, Ltd in eLife
Abstract
Evolutionary innovations allow populations to colonize new ecological niches. We previously reported that aerobic growth on citrate (Cit+) evolved in an Escherichia coli population during adaptation to a minimal glucose medium containing citrate (DM25). Cit+ variants can also grow in citrate-only medium (DM0), a novel environment for E. coli. To study adaptation to this niche, we founded two sets of Cit+ populations and evolved them for 2500 generations in DM0 or DM25. The evolved lineages acquired numerous parallel mutations, many mediated by transposable elements. Several also evolved amplifications of regions containing the maeA gene. Unexpectedly, some evolved populations and clones show apparent declines in fitness. We also found evidence of substantial cell death in Cit+ clones. Our results thus demonstrate rapid trait refinement and adaptation to the new citrate niche, while also suggesting a recalcitrant mismatch between E. coli physiology and growth on citrate.Keywords
Funding Information
- Michigan State University (Ralph Evans Award)
- Kenyon College (Individual Faculty Development Award)
- Michigan State University (Rudolph Hugh Award)
- National Science Foundation (DEB-1451740)
- National Science Foundation (DBI-0939454)
- USDA National Institute of Food and Agriculture (MICL02253)
- National Science Foundation (MCB-1923077)
This publication has 91 references indexed in Scilit:
- Genomic analysis of a key innovation in an experimental Escherichia coli populationNature, 2012
- Ecological and evolutionary dynamics of coexisting lineages during a long-term experiment withEscherichia coliProceedings of the National Academy of Sciences of the United States of America, 2012
- Experimental evolution of multicellularityProceedings of the National Academy of Sciences of the United States of America, 2012
- Niche adaptation by expansion and reprogramming of general transcription factorsMolecular Systems Biology, 2011
- Genetics and ecological speciationProceedings of the National Academy of Sciences of the United States of America, 2009
- Historical contingency and the evolution of a key innovation in an experimental population ofEscherichia coliProceedings of the National Academy of Sciences of the United States of America, 2008
- Identification ofEscherichia coliYgaF as anl-2-Hydroxyglutarate OxidaseJournal of Bacteriology, 2008
- Multicopy Suppression Underpins Metabolic EvolvabilityMolecular Biology and Evolution, 2007
- Balancing Robustness and EvolvabilityPLoS Biology, 2006
- Long-Term Experimental Evolution in Escherichia coli. I. Adaptation and Divergence During 2,000 GenerationsThe American Naturalist, 1991