The effect of recombination on incipient speciation in bacteria

Understanding what forces shape the tremendous diversity observed on our planet is one of the main goals of evolutionary biology. This requires a detailed understanding of how new species arise, as species form the basic unit of biodiversity. Nowhere is our lack of understanding of species formation more apparent than for the most diverse component of global biodiversity: the bacteria. This is problematic, because bacteria play fundamental roles not only in global biogeochemistry and ecosystem functioning, but also in health and disease and many industrial sectors, from agriculture to biotechnology. It is therefore vital to be able to identify bacteria, to understand how they originate, and how and why they are functionally different, and to know whether functions can potentially be transferred between them.

A popular model describing the divergence of bacterial types is the 'Stable Ecotype Model'. In this model, successive beneficial mutations allow a population to adapt to its environment. Two populations inhabiting different ecological niches will accumulate different beneficial mutations and so both 'ecotypes' will gradually diverge through differential adaptation. However, bacteria are known to not be purely clonal; they can also engage in 'parasex', transferring short fragments of DNA between different individuals. This 'bacterial sex' is often very important, being able to create more genetic variation than does point mutation in many species. One important way in which bacteria engage in parasex is transformation: the uptake of free DNA from the environment, followed by recombination of that DNA into the genome. Recombination has important implications for the Stable Ecotype Model for two reasons. First, adaptation within an ecotype is expected to proceed faster because different beneficial mutations arising at the same time in the population can be combined into a single most fit (i.e. well-adapted) genome (rather than the beneficial mutations competing against each other in different individuals). Recombination could thus speed up adaptive divergence (i.e. formation of novel ecotypes). However conversely, recombination could also slow down adaptive divergence when an ecotype takes up DNA originating from a different ecotype to create hybrid genotypes that are not well-adapted to either niche. This proposal will for the first time experimentally test the hypotheses:

1) whether transformation within an emerging ecotype promotes adaptation

2) whether transformation between two different emerging ecotypes hinders adaptive divergence

In collaboration with my proposed international project partners Dr. Pal Jarle Johnsen (University of Tromso, Norway) and Dr. Gabriel Perron ((University of Ottawa, Canada), a real-time evolution experiment will be used to evolve the frequently transforming species Acinetobacter baylyi in two distinct resources (niches). The availability of DNA for transformation will be manipulated to 1) increase the diversity of DNA from bacteria adapting to the same environment and 2) provide bacteria with DNA from bacteria adapting to the other environment. Subsequent competition experiments will be able to reveal whether adaptive divergence is promoted or hindered respectively. Understanding what ecological and evolutionary mechanisms cause a common bacterial ancestor to diversify into ecologically and genetically distinct types is of crucial importance to microbiology. Real-time controlled evolution of evolved phenotypes will enable us for the first time to test the influence of the key evolutionary variable, recombination, on the first steps in bacterial speciation.

Non-academic impact:
Although the fundamental nature of the proposed research means it is unlikely to lead to direct impact for end users, there is great potential for data collected on processes fundamental to bacteriology to inform and benefit the non-academic sector. First, our experiments will shed light on the process by which novel types of bacteria emerge, which will inform the study of emergent, opportunistic pathogens that increasingly lead to strain on the healthcare system (e.g. the important emerging pathogen Acinetobacter baumannii, which is related to the Acinetobacter species I propose to study). Understanding how bacteria that cause problems in hospitals differ from closely related but harmless bacteria isolated from the environment is important in clinical microbiology, but requires study of fundamental mechanisms not generally studied by clinical microbiologists. Second, transformation-mediated recombination is an important mechanism by which bacteria acquire multi-drug resistance, as has been demonstrated by my proposed collaborator Gabriel Perron (Perron et al. 2012; Proc Roy Soc B) in the Acinetobacter model system described in this proposal. The need for more study in this area was highlighted by the UK chief medical officer Dame Sally Davies, who stated: "There are few public health issues of potentially greater importance for society than antibiotic resistance" (The Guardian; 23rd Jan 2013).

Impact on the general public:
The European Centre for Environment and Human Health (European Centre) where I work is committed to dissemination of its research and employs two fulltime Knowledge Transfer Officers and a Communications Officer. This leads to a host of opportunities to interact with the media, local businesses and the general public, which I will engage with when opportunities arise during the proposed project. Approaches routinely used by European Centre include the distribution of videos, media interviews, press articles and newsletters. In addition, results will be highlighted on the European Centre website using short videos (as demonstrated by my current grant: http://vimeo.com/45693670) and my group's blog (www. http://coastalpathogens.wordpress.com/).
I participated in the 2013 'Science in the Square' event in Falmouth (http://www.exeter.ac.uk/cornwall/scienceinthesquare/) in the 'marine zone' and plan to organize a 'microbe zone' with colleagues for the 2014 event, highlighting the strange and wondrous world of microbes that fully deserve to be brought to the attention of the lay public. As well as generating interest in microbes in general, increased understanding of how antibiotic resistant bacteria arise is important in facilitating compliance with public health measures to tackle this issue. The real-time evolution experiments proposed here are also excellently suited to explain to a lay audience how the process of evolution 'works'. To further popularize the important and interesting life styles of bacteria, I am writing a paper for the journal Evolution: Education and Outreach highlighting similarities between the ecology and evolution of bacteria and animals.