Genotype-by-environment interactions due to antibiotic resistance and adaptation in Escherichia coli

Mutations that are beneficial in one environment can have different fitness effects in other environments. In the context of antibiotic resistance, the resulting genotype-by-environment interactions potentially make selection on resistance unpredictable in heterogeneous environments. Furthermore, resistant bacteria frequently fix additional mutations during evolution in the absence of antibiotics. How do these two types of mutations interact to determine the bacterial phenotype across different environments? To address this, I used Escherichia coli as a model system, measuring the effects of nine different rifampicin resistance mutations on bacterial growth in 31 antibiotic-free environments. I did this both before and after approximately 200 generations of experimental evolution in antibiotic-free conditions (LB medium), and did the same for the antibiotic-sensitive wild type after adaptation to the same environment. The following results were observed: (i) bacteria with and without costly resistance mutations adapted to experimental conditions and reached similar levels of competitive fitness; (ii) rifampicin resistance mutations and adaptation to LB both indirectly altered growth in other environments; and (iii) resistant-evolved genotypes were more phenotypically different from the ancestor and from each other than resistant-nonevolved and sensitive-evolved genotypes. This suggests genotype-by-environment interactions generated by antibiotic resistance mutations, observed previously in short-term experiments, are more pronounced after adaptation to other types of environmental variation, making it difficult to predict long-term selection on resistance mutations from fitness effects in a single environment.