Abstract
Phages have a major impact on microbial populations. In this work, we discuss how predation, transduction, lysogeny, and phage domestication lead to symbio-centric genomic interactions between bacteria and phage, ranging from antagonistic to mutualistic. Furthermore, these interactions influence bacterial diversification and ecotype formation. We then propose an additional consideration in the form of symbio-centric ecological speciation framework for bacteria. Our framework builds upon classical morphological and molecular taxonomy by also considering bacteria and their phages as a unit of evolutionary selection. This framework acknowledges the considerable effect that phage interaction has on bacterial genomic content, regulation, and evolution, and will advance our understanding of bacterial evolution.
Highlights
The work of microbiology pioneers Anton van Leeuwenhoek, Ferdinand Cohn, Albert Koch, Julius Petri, and Martinus Beijerinck, revealed the immense diversity of the microbial world and enabled the formulation of the first hypotheses about bacterial ubiquity and diversification
We will discuss how microbial genomic diversity eventually leads to ecological speciation, and we propose that considering the interaction of bacteria and their phage symbionts (Koonin, 2011) will lead to a deeper understanding of the mechanisms driving microbial evolution
We demonstrate how phages may modulate bacterial evolution by influencing fluctuating selection and evolutionary processes driven by Horizontal gene transfer (HGT), and play a relevant role in bacterial ecological speciation
Summary
The work of microbiology pioneers Anton van Leeuwenhoek, Ferdinand Cohn, Albert Koch, Julius Petri, and Martinus Beijerinck, revealed the immense diversity of the microbial world and enabled the formulation of the first hypotheses about bacterial ubiquity and diversification. We discuss the implications for genetic diversity in a microbial population that result from each of the categories of phage-bacterial symbioses Antagonistic coevolution such as predator-prey dynamics is considered one of the major ecological drivers of genetic variation through fluctuating selection (Thompson, 2013). Besides selecting for a more diverse population, phage predation can increase mutation rates in their hosts (Pal et al, 2007; Paterson et al, 2010), driving genome-wide evolution (i.e., in loci associated with resistance to phages), and FIGURE 1 | Bacterial diversification in the absence of phage interactions. The clades evolving outside evolutionary pressure (lower fitness) become extinct (B) following a diversity-purging process (C), i.e., periodic selection According to this model ecological speciation in the absence of phages is constrained. Through selection that leads to retention of genes that promote the replicative potential of the host
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