Experimental evolution of Bacillus subtilis

Abstract

Summary The endospore‐forming bacteria have persisted on earth perhaps 3Ga, leveraging the flexibility of their distinctive lifestyle to adapt to a remarkably wide range of environments. This process of adaptation can be investigated through the simple but powerful technique of laboratory evolution. Evolved strains can be analyzed by whole genome sequencing and an array of omics technologies. The intensively studied, genetically tractable endospore‐former, Bacillus subtilis, is an ideal subject for laboratory evolution experiments. Here, we describe the use of the B. subtilis model system to study the adaptation of these bacteria to reduced and stringent selection for endospore formation, as well as to novel environmental challenges of low atmospheric pressure, high ultraviolet radiation, and unfavourable growth temperatures. In combination with other approaches, including comparative genomics and environmental field work, laboratory evolution may help elucidate how these bacteria have so successfully adapted to life on earth, and perhaps beyond.

Rampant loss of social traits during domestication of a Bacillus subtilis natural isolate

“…2c). Similar colony morphology changes were previously observed during the domestication of other B. subtilis strains 3, [13][14][15]18 . Colonies are biofilms formed at the solid/air interface 1 .…”

“…Sporulation is, however, a time and energetically costly process, requiring the differential expression of over 10% of the genome over a period of 7-8 h 12,69 . Hence, the propagation of B. subtilis in the laboratory in the absence of selection for sporulation results in a reduction in the ability to sporulate [13][14][15][16] . B. subtilis has been used in laboratory conditions for more than 50 years and has accumulated mutations likely to be adaptive in that environment and which, relative to wild strains, lead to the attenuation of phenotypic traits which include swarming motility 41,42 , poly-γglutamate synthesis 31 , production of antibiotics, the secretion of degradative enzymes 70 or the formation of robust www.nature.com/scientificreports/ biofilms 6,31,71 .…”

“…The precocious and increased sporulation of BSP1 is due to the lack of two genes coding for Rap phosphatases, able to drain phosphoryl groups from the phosphorelay, through the dephosphorylation of Spo0F, a phosphorelay component 12 . Interestingly, continuous evolution under laboratory conditions leads to a decrease and loss of sporulating ability [13][14][15][16] .…”

“…The large number of traits that can potentially be lost during the continuous growth of B. subtilis in classical laboratory environments and the lack of knowledge regarding the first steps of adaptation makes it imperative to understand when and how the domestication occurs. Experimental evolution offers a powerful methodology to study the dynamics of the repeatability of evolutionary change under the same laboratory conditions and to study domestication 13,17,18 . When coupled with genome sequencing, it allows a real-time assessment of the tempo and genetic basis of adaptation to novel environments, as well as the order with which adaptive mutations fix in evolving populations 15,[19][20][21][22][23] .…”

Directed evolution by UV-C treatment of Bacillus cereus spores

“…Directed (laboratory) evolution approaches are becoming increasingly fruitful in food microbiology research to examine the adaptive potential of foodborne pathogens and spoilage organisms (Elena and Lenski, 2003;Gayán et al, 2016;Vanlint et al, 2012;Zeigler and Nicholson, 2017). In contrast to the evolution of vegetative cell properties, the impact of the selection pressure on the evolution and properties of spores has not yet been addressed.…”