The insect-killing bacterium Photorhabdus luminescens has the lowest mutation rate among bacteria

Mutation is a primary source of genetic variation that is used to power evolution. Many studies, however, have shown that most mutations are deleterious and, as a result, extremely low mutation rates might be beneficial for survival. Using a mutation accumulation experiment, an unbiased method for mutation study, we found an extremely low base-substitution mutation rate of 5.94 × 10(–11) per nucleotide site per cell division (95% Poisson confidence intervals: 4.65 × 10(–11), 7.48 × 10(–11)) and indel mutation rate of 8.25 × 10(–12) per site per cell division (95% confidence intervals: 3.96 × 10(–12), 1.52 × 10(–11)) in the bacterium Photorhabdus luminescens ATCC29999. The mutations are strongly A/T-biased with a mutation bias of 10.28 in the A/T direction. It has been hypothesized that the ability for selection to lower mutation rates is inversely proportional to the effective population size (drift-barrier hypothesis) and we found that the effective population size of this bacterium is significantly greater than most other bacteria. This finding further decreases the lower-bounds of bacterial mutation rates and provides evidence that extreme levels of replication fidelity can evolve within organisms that maintain large effective population sizes. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s42995-020-00060-0) contains supplementary material, which is available to authorized users.