Experimental Evolution of Bacillus subtilis Reveals the Evolutionary Dynamics of Horizontal Gene Transfer and Suggests Adaptive and Neutral Effects

Shai Slomka, Itamar Françoise, Gil Hornung, Omer Asraf, Tammy Biniashvili, Yitzhak Pilpel, Orna Dahan
2020 Genetics  
Tracing evolutionary processes that lead to fixation of genomic variation in wild bacterial populations is a prime challenge in molecular evolution. In particular, the relative contribution of Horizontal Gene Transfer (HGT) versus de novo mutations during adaptation to a new environment is poorly understood. To gain a better understanding of the dynamics of HGT and its effect on adaptation, we subjected several populations of competent Bacillus subtilis to a serial dilution evolution on a high
more » ... alt containing medium, either with or without foreign DNA from diverse pre-adapted or naturally salt tolerant species. Following 504 generations of evolution, all populations improved growth yield on the medium. Sequencing of evolved populations revealed extensive acquisition of foreign DNA from close Bacillus donors but not from more remote donors. HGT occurred in bursts, whereby a single bacterial cell appears to have acquired dozens of fragments at once. In the largest burst, close to 2% of the genome has been replaced by HGT. Acquired segments tend to be clustered in integration "hot spots". Other than HGT, genomes also acquired spontaneous mutations. Many of these mutations occurred within, and seem to alter, the sequence of flagellar proteins. Finally, we show that while some HGT fragments could be neutral, others are adaptive and accelerate evolution.
doi:10.1534/genetics.120.303401 pmid:32847815 pmcid:PMC7536860 fatcat:rged3z3k3rc3zlibgf7tyuiu34