Yellowstone, 2017

The Whitaker Lab studies the dynamics of microbes and their viruses using a combination of genomics, experimental evolution, modeling, and molecular biology. 

Viruses are obligate parasites, but the way they infect their hosts can be extraordinarily diverse and result in dynamic symbioses which protect their hosts from other viral predation and confer enormous benefits. Not much is known how this symbiosis contributes to the evolution of the communities they infect. We study this in several systems, including highly structured archaeal hot springs communities.

Viruses are increasingly found to be far from purely predatory. They often exhibit multi-dimensional relationships with the microbes they infect. In highly structured archaeal populations, complex viral infection dynamics arise from a mix of viral types (purely lytic viruses exist alongside chronic viruses which non-lethally extrude virion particles at a low rate) and immunity profiles of host cells. These infection dynamics have an enormous consequence on the host cells, where the chronic virus mediates death of uninfected cells. Infection with a chronic virus thus is an advantage to the hosts in this system, but may also provide evolutionary pressure on the transmission of the virus.

Mobile genetic elements blur the line between other and self. Our lab is interested in the way these symbioses evolve and how these elements affect the evolution of microbial populations.

Our lab is grounded in the population and genetics of Sulfolobus islandicus. The questions surrounding viral infection, evolution, and symbiosis are not unique to this organism, and we now have many projects going in the lab that all center around similar questions.

S. islandicus is a hyperthermophilic archaeon of the phylum Crenarcheota which lives in the acidic hot springs (pH of 2-3 at around 80 degrees C) found in volcanically active regions. We collect wild isolates largely from Yellowstone National Park (see our Pictures tab) in order to ask questions about population dynamics, virus-host interactions, symbiosis and speciation. Hot springs are an ideal system in which to study these eco-evolutionary phenomena. The extreme environment hosts a lower species diversity, and the springs’ physical separation presents a barrier to migration. These qualities lend tractability to the system, and lack of gene flow promotes independent adaptation among different populations.

S. islandicus is also of especial interest as a model organism for crenarchaeal cell biology. A robust set of genetic methods exist for probing its physiology, several of which have been developed in our own lab by Changyi. In addition to the inherent interest of these unique organisms, studying crenarchaeal genetics can shed light on eukaryal-archaeal evolution. With the discovery of the Asgard archaea in recent years, increasing evidence favors the exciting hypothesis that eukaryotes evolved from within the archaeal domain. The Asgards, however, are extremely difficult or impossible to cultivate and are not genetically tractable. Crenarchaeota are relatively closely related, and share central cellular systems with both the Asgards and eukaryotes. S. islandicus is thus well positioned to aid in unraveling this profound evolutionary question.

Virus-Host Interactions of Sulfolobus islandicus

We are investigating local adaptation in the coevolutionary interactions between Sulfolobus islandicus and mobile genetic elements such as plasmids, viruses and transposable elements. We are identifying to what extent the biogeographic distribution of mobile elements is determined by the biogeography of its hosts. We are investigating variation in the Sulfolobus immune systems that may be responsible for defining the patterns of coevolutionary interactions.

“Killer Archaea”

Our lab has recently shown that several Sulfolobus Spindle-Shaped Viruses (SSVs) confer a fitness benefit upon their host whereby it outcompetes uninfected cells in culture.  Interestingly, this effect is mediated by a toxic protein released by infected cells which kills off competitors, including ones with CRISPR-Cas immunity against the virus. The infected cells are protected against this toxicity by a yet-unknown mechanism. It is hypothesized that this phenotype may allow the virus to remove non-permissive hosts from the population, and could represent an emerging mutualism between S. islandicus and its virus.

Genomics of speciation in the model archaeon Sulfolobus islandicus

Sulfolobus islandicus has been developed as a novel model system to study the evolutionary process of speciation in domain Archaea. Genomic analysis of two sympatric S. islandicus species from one single hot spring located in Mutnovsky Volcano in Kamchatka, Russia revealed that although they can exchange genes recombination occurs at a higher frequency within than between species. We are interested in investigating the recombination rates among distinct S. islandicus species in lab as well as testing for and identifying the barriers to genetic exchange in S. islandicus by using genetic and genomic approach.

Population genomics of Sulfolobus islandicus

We are investigating the tempo and mode of archaeal genome evolution through comparative genomics of eight closely related Sulfolobus islandicus strains from biogeographically isolated geothermal environments. We are using this data to quantify the rate of horizontal gene transfer and other genome level dynamics over geologically-defined time scales.

We welcome you to explore these genomes yourself at 

Sulfolobus islandicus cell biology

A more recent endeavor, our lab has started to investigate certain cell physiological factors extant in Sulfolobus islandicus that could be linked to ancestral eukaryotic traits such as the rudiments of meiosis and the eukaryotic cell division process. We are pursuing these questions using a mix of approaches such as state-of-the-art high temperature live imaging and high resolution microscopic techniques, combined with what we observe on the genomic side to produce exciting new models detailing phenotypes of interest.

Other systems in the lab:

Pseudomonas aeruginosa

P. aeruginosa is common in human-associated environments and opportunistically infects immunocompromised people. The leading cause of morbidity in cystic fibrosis patients, P. aeruginosa has been widely studied in the context of within-patient long-term evolution, where it exhibits well-described adaptation to its new environment. P. aeruginosa is infected by a wide variety of bacterial viruses (also known as bacteriophages), and we are interested in the contribution of these viruses to the evolution of P. aeruginosa in the wild – as well as the contribution of P. aeruginosa to the evolution of its viruses.

Just as virus particles are more numerous than the microbes they infect, it comes as no surprise to find that the majority of microbes themselves harbor viral sequences in their chromosome. Many of these viral sequences are complete, latent viral chromosomes which are also known as proviruses (in bacteria as prophages), and may be activated to cause death to its host cell in an abrupt frenzy of viral particle production.  Prophages are often overlooked in considering the epidemiological impacts of microbes, even as the exogenous application of lytic phages on antibiotic-resistant infections is being increasingly recognized as an effective way to regulate the bacterial load.

Escherichia coli plasmid dynamics

How plasmids and mobile elements evolve and spread is central to understanding the spread of antibiotic resistance.


Rhizobia plasmid symbioses

Infection Genomics for One Health (IGOH)

Infectious agents cause problems for human health – but what about the infectious agents that infect the infectious agents? Viruses and other mobile genetic elements are often-overlooked pieces to the puzzle, producing nested genomes that shape the evolution of the host. We explore viral transmission dynamics in long-term P. aeruginosa infections of the CF lung using both evolutionary and bioinformatic approaches.  We take advantage of active CRISPR-Cas systems which can act as an immune “memory” for the viruses the host has encountered and use them to develop predictive models for infection in these communities.

The Infection Genomics for One Health (IGOH) theme is housed in the Carl R. Woese Institute of Genomic Biology and is under the fearless leadership of none other than Rachel Whitaker herself! You can find more information about research in the other labs and the theme as a whole here.


Our lab is a part of the Genomics and Eco-evolution of Multi-Scale Symbioses (GEMS) Institute, a Biology Integration Institute funded by the National Science Foundation. GEMS aims to break down barriers between biological disciplines in the pursuit of fundamental rules that underlie symbiosis evolution.