In partial fulfillment of the requirements for the degree of

Doctor of Philosophy in Ocean Science & Engineering

In the

School of Biological Sciences

Roth Conrad

Will defend his dissertation

Toward Advancing the Definitions of Sequence-Discrete Prokaryotic Species and Intra-Species Units, and Quantifying Their Distribution Patterns in Marine Environments

Thursday, July 18th, 2024

3 PM

(online only)

Zoom: https://gatech.zoom.us/j/91370832525

 Thesis Advisor:

Konstantinos (Kostas) Konstantinidis, Ph.D.

Civil and Environmental Engineering

& School of Biological Sciences (by courtesy)

Georgia Institute of Technology

Committee Members:

Dr. Joel Kostka, Ph.D.

School of Biological Sciences

& School of Earth and Atmospheric Sciences

Georgia Institute of Technology

Dr. Thomas DiChristina, Ph.D.

School of Biological Sciences

Georgia Institute of Technology

Dr. Thomas DiChristina, Ph.D.

School of Biological Sciences

Georgia Institute of Technology

Dr. Frank Stewart

Department of Microbiology & Cell Biology

Montana State University

Dr. Andrew Huang

The Centers for Disease Control (CDC)

ABSTRACT: Although sequence-discrete species appear to dominate natural microbial communities, the mechanism(s) that maintain such species and whether or not discrete intra-species units exist represent unanswered questions with major practical implications for communicating about microbial diversity. In this thesis, novel analytical approaches were developed to answer these questions, including a method to identified recently recombined genes between genomes. Application of this method to the 330 best sampled bacterial species by genome sequences identified a new intra-species ANI discontinuity between 99.2% and 99.8% (midpoint 99.5%) that can be used to identify genomovars (>99.5% ANI) and strains (>99.99% ANI) more reliably and robustly than the current practice. Further, this analysis showed that high ecological cohesiveness and unbiased horizontal gene flow, mediated by homologous recombination, underpin the sequence-discrete species and intra-species units. We also developed a new algorithm, employing the kernel density estimation (KDE) and a peak finding module, to determine when a population is identical or not between two metagenomes based on a read recruitment plot against a representative genome of the population. Application of this algorithm to available marine metagenomes allowed us to quantify how populations within a species diverge between ocean depths and basins and, interestingly, identified a few populations that are truly cosmopolitan across depths in the Gulf of Mexico. Therefore, this thesis provided novel means to integrated genomic and metagenomic data for identifying and tracking microbial species and intra-species units in situ, and has answered a major question for microbiology; that is, what is a species and what a strain.