Britt Koskella, Professor

Closed (1) The costs and benefits of using phage cocktails to treat a bacterial plant pathogen

Closed. This professor is continuing with Fall 2018 apprentices on this project; no new apprentices needed for Spring 2019.

With the increasing threat of antibiotic resistance, scientists are turning to alternative solutions for treating antibiotic-resistant bacterial infections. One possible alternative involves the use of lytic bacteriophages (phages), which are obligate killers of their bacterial hosts. Phage therapy (the use of phages to treat bacterial infections) was first employed prior to antibiotic discovery but fell mostly out of use once antibiotics were easily mass-produced. While phages have been considered for use in treating bacterial infections of plants and animals, much is still unknown about bacteria-phage interactions and coevolution as they happen within the eukaryotic host, making it difficult to predict success, as well as the long-term impact of phage treatment.

In the Koskella lab, we work on a tritrophic system: tomato plants, the bacterial plant pathogen Pseudomonas syringae, and lytic phages of P. syringae. For this URAP project, we are interested in asking the following question: does treatment of P. syringae-infected plants with multiple phages lead to different ecological and evolutionary dynamics than treatment with a single phage? The student will use experimental evolution to determine:
(1) how combining multiple phages can impact bacterial growth in tomato leaves, and
(2) how exposure to multiple phages affects the evolution of bacterial resistance to phage.
The outcome of this project will be important in moving forward our understanding of phage cocktails in treating bacterial infections and has direct relevance for both medical and agricultural practices.

The student working on this project will be involved in experimental design, running the experiment (preparing inocula using standard microbiological techniques, growing and infecting plants), and collecting data (sampling plants, measuring bacteria and phage densities using a newly developed digital droplet PCR approach, and preparing assays for phage resistance). The student will also learn how to analyze and interpret data and, if desired, bioinformatic skills in whole genome sequencing and comparative genomics.


Day-to-day supervisor for this project: Catherine Hernandez, Ph.D. candidate

Qualifications: Enthusiasm for microbiology, ecology, and/or evolution and a desire to learn new skills. Commitment to work the required 9-12 hours per week, and the ability to stay focused when performing occasionally tedious lab work. It would be helpful (but not required) if the student has some background in microbiology lab work (particularly sterile technique), and exposure to evolutionary thinking. But desire to acquire and apply these skills is more important.

Weekly Hours: 6-8 hrs

Related website: https://naturesmicrocosm.com/

Closed (2) Experimental evolution of biofilm formation and its impacts on pathogen virulence and bacteria-phage interactions within a plant host

Closed. This professor is continuing with Fall 2018 apprentices on this project; no new apprentices needed for Spring 2019.

Biofilms, collections of cells that adhere to various surfaces, are a common virulence strategy of pathogenic bacteria both in animals and in plants. They are notoriously difficult to treat and remove due to the sticky substances produced by cells within the biofilm. One potential avenue of biofilm removal involves bacteriophages (phages), which are viruses that infect and kill bacteria. However, access of phage to cells within a biofilm is dependent on both the biofilm composition and phage type. While phage therapy is a growing field in medicine and agriculture, much is still unknown about the mechanisms of bacteria-phage interactions when within a eukaryotic host infected by a biofilm-producing pathogen.

The plant pathogen Pseudomonas syringae forms biofilms when growing in the apoplast (intercellular internal spaces) of leaves. We aim to investigate how biofilm formation of P. syringae impacts its interactions with phage, as well as its virulence on tomato plants. Agricultural phage therapy has had mixed success, and results from this project may lead to a better understanding of one factor that may be impacting therapeutic effectiveness.

In this project, we will generate high and low biofilm formation populations of bacteria and determine whether they differ in susceptibility to phage and virulence on plants. The project will involve classic microbiological techniques (including bacteria and phage plating), experimental evolution, plant infection assays, and use of the novel droplet digital PCR technique to quantify phage and bacterial replication in the plant environment. There will be ample opportunity to become involved beyond performing the hands-on laboratory work – we are happy to work with the student to develop experimental design, literature reading, and data analysis skills as desired.


We are seeking a highly motivated student with interest in the following research areas: microbiology, ecology, evolution, bacteria-phage interactions, and plant pathology. Previous research experience in microbiology is a plus, but not required. Most importantly, we are interested in someone excited about this project and willing to commit to 9-12 hours per week. Students of all years are welcome to apply.

The student working on this project will be involved in experimental design, running the experiment, and collecting data (sampling plants, measuring bacteria and phage densities using a newly developed digital droplet PCR approach, and preparing assays for phage resistance). The student will also learn how to analyze and interpret data and, if desired, bioinformatic skills in whole genome sequencing and comparative genomics.

Day-to-day supervisor for this project: Catherine Hernandez, Ph.D. candidate

Qualifications: Enthusiasm for microbiology, ecology, and/or evolution and a desire to learn new skills. Commitment to work the required 9-12 hours per week, and the ability to stay focused when performing occasionally tedious lab work. It would be helpful (but not required) if the student has some background in microbiology lab work (particularly sterile technique), and exposure to evolutionary thinking. But desire to acquire and apply these skills is far more important.

Weekly Hours: 6-8 hrs

Related website: https://naturesmicrocosm.com/

Closed (3) Tracking bacteria-phage dynamics in a natural tree disease system

Closed. This professor is continuing with Fall 2018 apprentices on this project; no new apprentices needed for Spring 2019.

We are building a new system (fire blight of pear trees) to better understand how bacteriophage viruses might impact the ability of a bacterial pathogen (Erwinia amylovora) to colonize and infect pear trees. We are tracking bacteria-phage interactions through time by isolating individual phages from each of 25 diseased pear trees across the growing season. We are also asking which bacteria each phage is capable of infecting in order to gain a broad understanding of the potential role phages have in shaping the pear tree microbiome.

The undergraduate researcher would be involved in helping to isolate phages from the Pear tree phyllosphere by culturing bacteria, growing bacterial lawns, isolating and amplifying phages, and testing the host range of each isolated phage using bacterial growth curve assays.

Qualifications: A keen interest in science, some experience with sterile technique and bacterial/phage culturing, good organizational habits, and ability to work well with others.

Weekly Hours: 6-8 hrs

Related website: https://naturesmicrocosm.com/