Explaining microbial population genomics through phage predation

By F. Rodríguez-Valera, Ana-Belen Martin-Cuadrado, Beltran Rodriguez-Brito, L. Pasic, T. Thingstad, Forest Rohwer, A. Mira. Nature Reviews Microbiology, 2009

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The remarkable differences that have been detected by metagenomics in the genomes of strains of the same bacterial species are difficult to reconcile with the widely accepted paradigm that periodic selection within bacterial populations will regularly purge genomic diversity by clonal replacement. We have found that many of the genes that differ between strains affect regions that are potential phage recognition targets. We therefore propose the constant-diversity dynamics model, in which the diversity of prokaryotic populations is preserved by phage predation. We provide supporting evidence for this model from metagenomics, mathematical analysis and computer simulations. Periodic selection and phage predation dynamics are not mutually exclusive; we compare their predictions to shed light on the ecological circumstances under which each type of dynamics could predominate.

Subfields: Ecology, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/3f40f74a0024059f1e079c1c544c3e90b24df71c

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Citations in the corpus

Phages in nature (2011, background): “The relationship between phages and their hosts has been modeled, and in a simple environment if there is no cost to host resistance the same oscillation in populations occurs.(46) However, if there is a cost to phage resistance, then bacteriophages have been theoretically and experimentally shown t”
The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates (2012, background): “, 2010), in combination with the recently proposed role of phages in sustaining microbial diversity via the ‘killing-the-winner’ principle (Rodriguez-Valera et al., 2009).”
Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus (2014, background): “predation, in the context of temporal and spatial environmental variation, helps explain their coexistence (28, 29).”
Species concepts and speciation factors in cyanobacteria, with connection to the problems of diversity and classification (2015, background): “The shell genome genes do not seem to be randomly dispersed over the chromosome, but rather concentrated within genomic islands with frequent HGT and HR events (Hacker and Carniel 2001; Rodriguez-Valera et al. 2009).”
Where less may be more: how the rare biosphere pulls ecosystems strings (2017, background): “Bacteriophages and protists often show frequencydependent predation and tend to over-consume abundant prey species (Jousset et al., 2009; Winter et al., 2010), preventing them from dominating the community and creating space for rare species (Rodriguez-Valera et al., 2009; Figure 1d).”
Computational approaches to predict bacteriophage–host relationships (2015, background): “The ecology of phage–host interactions, especially predator prey-like dynamics such as Kill-the-Winner (Rodriguez-Valera et al. 2009), can lead to very dynamic changes in abundance of both the phages and their host bacteria that violate the straightforward correlation of their occurrence profiles.”
Bacteria–phage coevolution as a driver of ecological and evolutionary processes in microbial communities (2014, background): “Final version published online 27 March 2014.”
RNA-guided genetic silencing systems in bacteria and archaea (2012, background): “However, viruses outnumber their microbial hosts in every ecological setting, and the selective pressures imposed by these rapidly evolving parasites has driven the diversification of microbial defence system”