Experimental evolution in biofilm populations

Abstract

Biofilms are a major form of microbial life in which cells form dense surface associated communities that can persist for many generations. The long-life of biofilm communities means that they can be strongly shaped by evolutionary processes. Here, we review the experimental study of evolution in biofilm communities. We first provide an overview of the different experimental models used to study biofilm evolution and their associated advantages and disadvantages. We then illustrate the vast amount of diversification observed during biofilm evolution, and we discuss (i) potential ecological and evolutionary processes behind the observed diversification, (ii) recent insights into the genetics of adaptive diversification, (iii) the striking degree of parallelism between evolution experiments and real-life biofilms and (iv) potential consequences of diversification. In the second part, we discuss the insights provided by evolution experiments in how biofilm growth and structure can promote cooperative phenotypes. Overall, our analysis points to an important role of biofilm diversification and cooperation in bacterial survival and productivity. Deeper understanding of both processes is of key importance to design improved antimicrobial strategies and diagnostic techniques.

Evolution of exploitative interactions during diversification in Bacillus subtilis biofilms

“…Experimental evolution studies continuously deepen our understanding of microbial adaptation, revealing common evolutionary scenarios such as genome reduction (Nilsson et al 2005) or genome rearrangements (Martin et al 2017), hypermutability (Flynn et al 2016;Tenaillon et al 2016), or diversification (Rainey and Travisano 1998;Poltak and Cooper 2011;Koch et al 2014;Flynn et al 2016;Kim, Levy and Foster 2016). The last one, where microbes diversify into distinct variants (typically referred to as morphotypes as they are identified based on distinct colony morphology), appears to be very common, especially in structured environments which offer alternative niches varying in nutrient and oxygen content (Martin et al 2016;Steenackers et al 2016). Biofilms, where microbes grow in tightly packed assemblies, represent an example of such an environment.…”

Pervasive and diverse collateral sensitivity profiles inform optimal strategies to limit antibiotic resistance

“…http://dx.doi.org/10.1101/241075 doi: bioRxiv preprint first posted online Dec. 30, 2017; evolutionarily short timescales 55 . On longer timescales, elegant experimental approaches to biofilm evolution have revealed that spatial structure can give rise to rich evolutionary dynamics 56,57 , though to date, little is known about collateral drug effects in these systems.…”

Laboratory Evolution of Microbial Interactions in Bacterial Biofilms

“…Importantly, evolutionary changes in microbial communities may be driven by a set of abiotic factors (e.g., fluctuations in the environment) or biotic components other than microbes (e.g., plant, animal, and human host or symbiont), which are not discussed in the paper. The study of evolutionary dynamics within biofilms and the origin of microbial interactions are significant for several reasons (26). First, biotic interactions among neighbors generate major selective forces that drive the development of many important traits of microbes, such as antibiotic resistance (27).…”