Britt Koskella, Professor

Closed (1) Understanding the importance of the seed-associated microbiome

Applications for fall 2021 are now closed for this project.

Seeds are the fundamental unit for plant life. Seed-associated microbes provide the initial inoculum for a developing plant and affect critical processes involved with seedling development, resilience, and defense against pathogens and herbivores. These microorganisms can determine successful seedling establishment and thus the trajectory of future plant life stages.Maternal plants can selectively transmit beneficial microbes to their seeds through the vascular tissue or floral pathway, providing their offspring a competitive advantage. Understanding the dynamics that determine seedling success can give us better insight into best seed production practices and provide novel seed inoculation techniques that are sustainable and long-term solutions to increasing crop production. In this project, we will be using tomato plants and bacteria/fungi isolated from tomato seeds to assess the assembly of seed microbial communities during seed morphogenesis. Additionally, wewill inoculate flowers with these microbial isolates at different densities to test transmission requirements and transmission efficacy of individual taxa. Specifically, we will be testing the following questions:1)What microbial taxa can be vertically transmitted?2)What are the mechanisms necessary for vertical transmission to occur?3)How does vertical transmission affect progeny fitness?Students will learn and implement a wide array of techniques involved with microbiology (preparing media, plating bacteria, quantifying bacterial density, creating bacterial inoculum), genetics (PCR), horticulture (germination, transplanting, plant microbial inoculations, sterile sampling), and bioinformatics. We are seeking an undergraduate student interested in the research areas of microbiology, ecology, evolution, coevolution, and plant physiology.

Students should be interested in plant microbiome research and will be expected to commit 6-8 hours per week on this project. Tasks include plant inoculations, plant care and physiological measurements, bacterial isolations and measurements of bacterial density and types. Learning outcomes include sterile technique, plant growth and care, microbiome analyses, data collection, statistical analysis, preparation of manuscripts for publication.

Day-to-day supervisor for this project: Mason “Kama” Chock, Ph.D. Candidate, Ph.D. candidate

Qualifications: Some microbiology lab work experience is helpful but enthusiasm, passion, and thoughtfulness towards the scientific process is most important.

Weekly Hours: 6-8 hrs

Related website: https://naturesmicrocosm.com/
Related website: https://kamalanichock.weebly.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 Spring 2021 apprentices on this project; no new apprentices needed for Fall 2021.

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: Kyle Meyer, 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

Applications for fall 2021 are now closed for this project.

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/

Closed (4) The role of inter-host transmission in structuring the evolution of phyllosphere communities

Closed. This professor is continuing with Spring 2021 apprentices on this project; no new apprentices needed for Fall 2021.

We are interested to learn how 'switching' among plant hosts influences the evolution of microbial communities on leaves. To do so we will repeatedly passage microbial innocula on the surface of tomato, pepper, and bean leaves. To ask how host-switching affects microbiome evolution, we will perform a treatment whereby tomato-passaged communities will alternate generations across either peppers or beans.

The undergraduate would assist with the organization and sample processing at each experimental passage. The work will be periodic; requiring slightly more effort during key points. Organizational tasks could include seed sterilization and germination, transplantation, labeling experimental tubes and bags, assistance during microbiome harvest, and assistance during microbial inoculation. , Post-Doc

Qualifications: Students should be detail oriented, organized, and enthusiastic to learn!

Weekly Hours: 9-11 hrs

Related website: https://naturesmicrocosm.com/