Plant-Microbiome Co-Occurrence
Ellen Simms, Professor
Integrative Biology
Closed. This professor is continuing with Spring 2024 apprentices on this project; no new apprentices needed for Fall 2024.
Until recently there was still the idea that when it comes to the microbial world, since it is so small, everything must be everywhere. Much current research is showing this claim does not hold water. Few things are truly everywhere and most things, even on the micro scale, have very preferred habitat and conditions in which they thrive. Microbiome research is still relatively young, and many projects have looked at diversity of microbiomes within a community (in one specific habitat and location) or across locations but using one species of host plant. Understanding large-scale patterns of distribution and association of microbiomes across different plant hosts and different locations will be critical to understanding their roles in ecosystem function and in making predictions about impacts of climate change or other disturbance. The aim of this study is to contribute to our understanding of the distribution patterns of plant microbiomes and their relatedness to other distributions and to build a functional co-occurrence dataset.
Role: With guidance and support from the project supervisor, (Graduate Student Anna Scharnagl), students will learn how to search the scientific literature, read and extract necessary data from scientific papers, and build and manage a cohesive database. We will also compile one or more analysis pipelines to reveal large-scale patterns (students with background in database management and skills in R are encouraged to apply). Students are expected to check in weekly with the group, sometimes by email and sometimes by Zoom or in person meeting. Check ins should include touching base about progress and bringing up any questions or problems encountered along the way. This project is a large-scale literature search and data mining venture to map plant and microbiome occurrences to date, so most of the work is done independently and remote. Open communication and honesty is critical to the project success. This project also includes opportunities to learn to use ImageJ to calculate leaf area, the possibility of learning how to input and interpret data in the QIIME pipeline (classic microbiome analysis pipeline), and some possibilities of lab work or fieldwork (including prepping materials in the lab for field projects).
Qualifications: You must have a good work ethic and be driven. While this project promises to build something great eventually, the road there is a bit slow. You must maintain good communication with your supervisor and your teammates in addition to the weekly check ins. We are in the fine tuning and maintenance phases of this project - clear communication and attention to detail are critical. Ideally you already have an interest in microbes or plants or ecology or staring at incredibly large datasets (large-scale patterns), or have skills to contribute to cleaning and maintaining large databases.
Day-to-day supervisor for this project: Anna Scharnagl, Graduate Student
Hours: to be negotiated
Off-Campus Research Site: Dept of Integrative Biology, University of California 3040 Valley Life Sciences Bldg. #3140 This project is designed as remote research done with guidance and support from the project supervisor and requiring meeting with a team of peers by Zoom regularly.
Biological & Health Sciences