Connecting environmental and evolutionary microbiology for the development of new agrobiotechnological tools

We all are familiar with Theodosius Dobzhansky’s famous sentence: ‘Nothing in biology makes sense except in the light of evolution’, which is actually the title of a short essay he published in The American Biology Teacher (Dobzhansky, 1973). With that title, he was exposing a fundamental truth that even us biologists sometimes tend to obviate: Life means evolution. Genetic changes provide the diversity required for any form of evolution to take place, while the environment will ‘decide’ if those changes are successful or not. Dobzhansky viewed evolution as a process by which life tends to fill all available ecological niches. Microorganisms seem determined to prove him right; in fact, truly vacant ecological niches appear to be rare on our planet, as evidences of bacterial colonization keep being found even in environments where conditions are too extreme for other forms of life (Merino et al., 2019). If life is evolution, microbial life can be considered evolution on the fast lane. Under favourable growth conditions, a bacterial population duplicates in a very short time, a fact that has been exploited to study evolution under laboratory conditions. Besides the early, pioneering work on mutations and selection in bacteria (Atwood et al., 1951; Lederberg & Lederberg, 1952), perhaps one of the best-known examples is that of the long-term evolution experiment (LTEE) started in 1988 by Richard Lenski: parallel batch cultures of Escherichia coli grown overnight in defined medium and then transferred (1% of each population) to fresh medium every day, with periodical storage of cryopreserved samples of each culture (Lenski et al., 1991). These allow detailed phenotypic and genetic analysis and serve as intermediate ‘camps’ from where the experiment can be resumed if something goes wrong, without having to start all over (pretty much as the ‘save’ button of a videogame). The LTEE, maintained for 34 years by the Lenski group and recently transferred to Jeffrey Barrick’s lab at the University of Texas (Austin), has reached over 75,000 generations, and has been a source of relevant insights regarding the dynamics and repeatability of adaptation to particular growth conditions (Lenski, 2017). Additional approaches to study bacterial evolution in laboratory conditions include, among others, long-term adaptation of Escherichia coli to starvation and stationary phase (Finkel & Kolter, 1999), which results in the selection of specific mutants that take over the parental population (Zinser & Kolter, 2004); or static cultures of Pseudomonas fluorescens on the air-liquid interface, where nutrient and oxygen gradients lead to phenotypic and genetic differentiation as the result of adaptive radiation (Rainey & Travisano, 1998). Adaptive radiation also takes place in long-term biofilm populations of Pseudomonas putida (Yousef-Coronado and Espinosa-Urgel, unpublished). Further examples and experimental setups have been nicely reviewed by Van den Bergh and coworkers (Van den Bergh et al., 2018). Despite some obvious limitations, such as the use of single-species cultures and the rather specific and well-controlled environmental conditions (limitations which on the other hand are necessary to ensure reproducibility and to extract proper conclusions), all these Received: 26 August 2022 Accepted: 31 August 2022