Phage-Host Interaction in Nature

Citation

Tadmor, Arbel David (2011) Phage-Host Interaction in Nature. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/68Q5-D532. https://resolver.caltech.edu/CaltechTHESIS:05252011-233927917

Abstract

Though viruses may be the most abundant biological entities on the planet, very little is known about phage-host interaction in the wild due to the absence of proper experimental tools. In the present work we report of a method to pair environmental phages with their bacterial hosts at the single-cell level without having to culture either host or virus. The method utilizes microfluidic digital PCR in conjunction with a metagenome data mining tool that was developed to find a viral marker gene in an unknown environment. We implemented this technique on the microbial community residing in the hindgut of termites. Consequently, we discovered genus-wide infection patterns displaying remarkable intra-genus selectivity, with viral alleles displaying limited lateral gene transfer and/or host switching despite host proximity. To try and explain phage-host interactions from a theoretical perspective, we formulated a simple biophysical model describing the interaction of bacteria and viruses in aqueous environments. We predict that the radius r of a bacterium is the most critical parameter determining its fixed point concentration, which scales as r^-4. Given the hypothesis that there is no selection pressure on bacterial radii, our model predicts that the size spectrum of marine bacteria follows a power law with slope -1, close to the observed average spectrum. Moreover, given the total concentration of bacteria in the ocean, our model enables us to estimate the total number of bacterial “species” per volume of water providing a lower and upper bound on the total number of species in the oceans. To elucidate the concept of a “species”, we consider a bacterial-viral co-speciation model, which is consistent with the observed narrow host range of phages. Our model hints that the bacterial-viral “arms race” may be a critical component in the process of co-speciation. We suggest further experiments to test both models. Finally, we consider a recent high resolution measurement of the force as a function of time generated by stress fibers within a single fibroblast cell and suggest a stochastic model that is capable of accounting for the observed data.

Thesis Files