Growth phase-specific evolutionary benefits of natural transformation in Acinetobacter baylyi

Abstract

Natural transformation in bacteria facilitates the uptake and genomic integration of exogenous DNA. This allows horizontal exchange of adaptive traits not easily achieved by point mutations, and has a major role in the acquisition of adaptive traits exemplified by antibiotic resistance determinants and vaccination escape. Mechanisms of DNA uptake and genomic integration are well described for several naturally transformable bacterial species; however, the selective forces responsible for its evolution and maintenance are still controversial. In this study we evolved transformation-proficient and -deficient Acinetobacter baylyi for 175 days in serial transfer cultures where stress was included. We found that natural transformation-proficient populations adapted better to active growth and early stationary phase. This advantage was offset by the reduced performance in the late stationary/death phase. We demonstrate fitness trade-offs between adaptation to active growth and survival in stationary/death phase caused by antagonistic pleiotropy. The presented data suggest that the widely held assumption that recombination speeds up adaptation by rapid accumulation of multiple adaptive mutations in the same genetic background is not sufficient to fully account for the maintenance of natural transformation in bacteria.

Figure 1

Comparison of groups Com−, Com+ and Com+DNA at different time points during serial transfers based on mixed competition experiments with their respective ancestors. (a) The selection rate constant (r) calculated between 0 and 90 h of competition. (b) Relative fitness (w) calculated between 0 and 24 h of competition. (c) Relative survival (su) calculated between 24 and 90 h of competition. Each circle represents one competition and each group is made up of six replicate populations. Note that all median values indicated by horizontal lines in the box plots are descriptive and not adjusted for uneven sample distribution and repeated measurements. * Indicates a significant difference (P <0.05) compared with the Com− group at each time point derived from the linear quantile mixed model. The relationships between individual competitions and replicate populations from each group is presented in Supplementary Table SI 5.

Figure 2

Calculated growth rates (a) and growth curves including 95% confidence intervals (b) of groups Com−, Com+ and Com+DNA after 175 days of serial transfers and the ancestor. In (a) each circle represents one of six populations per group. The growth rate of Com+ is significantly different from Com− (P= 0.011), whereas Com+DNA is not different from that of Com− (P=0.059).

Figure 3

Direct competitions between the evolved populations of Com+ (open symbols and dotted line) and Com− (filled symbols and solid line). Selected populations are fitness representatives from their respective groups. Com+ populations (open triangles/circles) were in competition with Com− populations (filled triangles/circles). Both competitions were done in triplicates and each symbol is the result of one competition. The lines represent the central tendency of Com− (solid) and Com+ (dotted) in the competitions. Estimated mean fitness parameters with 95% confidence intervals in these competitions: w_Com+=1.45±0.34), su_Com+=−0.013 (±0.006), r_Com+=−0.22 /passage (±1.2).

Figure 4

Negative association between relative fitness (log₁₀ (w)) and survival (su) in competitions from the Com− group (circles) and Com+ group (crosses). Competitions are between all the populations from groups Com− and Com+ serially passaged for 175 days and competed with the appropriate ancestor. (β₁=−0.056, t=−2.78, P=0.007).

Figure 5

Mutation-fixation pattern of six mutations that were fixed (or partially fixed) after 175 days of serial transfers. Mutations are from Com+ (dotted) or Com− (solid) populations and listed in Table 2. Mutations: znuA-atp1 (filled squares), ACIAD3547 (open circles), ppc (open diamonds), ACIAD3006 (open triangles), ACIAD3007 (stars).