Carlos Ruiz-Perez, Thesis Defense

In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Bioinformatics
in the School of Biological Sciences

Carlos A. Ruiz Perez Defends his thesis:
Bacteriophages in the Chattahoochee: Novel bioinformatics approaches to characterize viral ecology in freshwater systems

Thursday, June 10th, 2021
1:00 PM EST

Thesis Advisor: Dr. Konstantinos T. Konstantinidis Civil and Environmental Engineering Georgia Institute of Technology

Committee Members:
Dr. James Cole Department of Plant, Soil and Microbial Sciences Michigan State University
Dr. King Jordan School of Biological Sciences Georgia Institute of Technology
Dr. Frank J. Stewart Department of Microbiology and Immunology Montana State University
Dr. Joshua Weitz School of Biological Sciences School of Physics Georgia Institute of Technology

Abstract: Bacteriophages (or phages) play a significant role in biogeochemical cycling by infecting and re-programming millions of host bacterial cells daily. Large-scale studies in marine environments have revealed that viral communities exhibit similar seasonality and biogeographical patterns as their hosts. However, seasonal and biogeographic patterns in freshwater viral communities remain comparatively much less characterized. To this end, we performed a metagenomic survey of five interconnected lakes and one estuarine location along the Chattahoochee River in the Southeast US in the late summertime over five years. Our analysis revealed endemic viral species and microbial provinces together with a substantial fraction of cosmopolitan viral populations (35%). The interactions between phages and their hosts, inferred based on interaction network reconstructions, provided further support for these findings, revealing that phages and hosts preferentially interact in smaller sub-communities with similar endemicity preferences. A closer look at phages infecting Cyanobacteria (cyanophages) revealed photosynthesis-related, bacterial-derived metabolic genes in the viral genomes that are evolutionarily distinct from their marine counterparts and can serve as biomarkers of the geographic origin (or preference) of freshwater cyanophages. Finally, hundreds of viral and bacterial genomes were recovered from the Chattahoochee samples representing novel species or higher taxonomic ranks. To efficiently assess the genomic relatedness among these genomes and taxonomically classify them, we developed FastAAI, a tool that estimates traditional whole-genome-based Average Amino-acid Identities (AAI) >1,000 times faster and with higher resolution at the phylum and domain levels than existing implementations based on the fraction of k-mers shared in protein-coding genes.