Genome Evolution of Acinetobacter baylyi ADP1 During Laboratory Domestication: Acquired Mutations Impact Competence and Metabolism

Abstract The bacterium Acinetobacter baylyi is a model organism known for its extreme natural competence and metabolic versatility. It is capable of transforming environmental DNA at a high frequency across all growth phases. The type strain ADP1 was created by random mutagenesis of a precursor strain, BD4, to prevent it from forming cell chains in culture. ADP1 has since been distributed between research groups over several decades and acquired subsequent mutations during this time. In this study we compare the genome sequences of Acinetobacter baylyi BD4 and its modern descendants to identify and understand the effects of mutations acquired and engineered during its domestication. We demonstrate that ADP1 variants in use today differ in their competence, growth on different carbon sources, and autoaggregation. Additionally, we link the global carbon storage regulator CsrA and a transposon insertion that removes its C-terminal domain specifically to changes in both overall competence and an almost complete loss of competence during stationary phase. Reconstructing the history of ADP1 and the diversity that has evolved in the variants currently in use improves our understanding of the desirable properties of this experimentally and industrially important bacterium and suggests ways that its reliability can be improved through further genome engineering. Significance Acinetobacter baylyi ADP1 is a bacterial chassis of interest to microbiologists in academia and industry due to its extreme natural competence and wide metabolic range. Its ability to take up DNA from its environment makes it straightforward to efficiently edit its chromosome. We identify and characterize mutations that have been passed down to modern strains of ADP1 from the initial work on ADP1 in the 1960s as well as subsequent mutations and genome edits separating strains in use by different research groups today. These mutations, including ones in a global regulator, have significant phenotypic consequences that have affected the reproducibility and consistency of experiments reported in the literature. We link a mutation in this global regulator to unexpected changes in natural competence. We also show that domesticated A. baylyi strains have impaired growth on a variety of carbon sources. Data Availability Genome sequencing data is available from the NCBI Sequence Read Archive (PRJNA1256545).