Ellen Simms, Professor

Closed (1) Global biogeography of Rhizobium bacteria

Applications for fall 2021 are now closed for this project.

Microbial organisms were believed to have unlimited dispersal capabilities: that they passively disperse and their establishment in a location depends purely on broad environmental factors that filter out less well-adapted microbes (Everything is everywhere, but the environment selects). Lately, these dispersal capabilities have been challenged, especially by evidence suggesting that geographically distant microbes are less likely to be related to each other than are nearby microbes, a pattern known as “isolation by distance”.

Legumes benefit from symbiotic relationships with nitrogen-fixing bacteria called rhizobia, which colonize nodules in legume roots. Rhizobium genes involved in host plant interaction are located on either a plasmid or “island,” which is distinct from the rest of the genome, and can be more easily exchanged among rhizobia. Rhizobia are believed to adhere to the classic tenets of microbiological dispersal, with legume host species identity as the main environmental filter. However, even within the rhizobia associating with a single plant species, genotypes appear to be unevenly distributed across the world, suggesting that other factors could be at work.

We are interested in three important ecological questions: (1) Is the relatedness of rhizobial genotypes across space determined more strongly by their geographic distance or by the presence of a shared legume host; (2) Is the geographic distribution of genes located on the symbiotic plasmid more restricted than that of chromosomal genes; and (3) Is the distribution of some rhizobium genotypes more spatially restricted than others?

With guidance and support from the project supervisor, you will participate in data collection and bioinformatic and statistical analyses. Over the course of the semester, you will learn the basics of genetic analyses (DNA alignment, phylogenetic tree construction, recombination rate analyses) and statistical methods that are fundamental to population and community ecology (diversity analysis, multivariate analyses, Mantel tests, rarefaction).

There are ample opportunities for independent projects for students who demonstrate dedication and/or plan to stay on for multiple semesters.

This project does not require on-campus presence.

Day-to-day supervisor for this project: Jannick Van Cauwenberghe, Post-Doc

Qualifications: You must be dedicated to the project, which involves attention to detail, curiosity about novel techniques, and being results oriented. There is the potential for you to work on this project independently on your own time. We prefer that you be at least a sophomore in a Biological Science major.

Weekly Hours: 6-8 hrs

Related website: http://www.simmslab.org/

Closed (2) Have invasive rhizobia escaped their bacteriophage enemies? And how prevalent are prophages in rhizobia?

Applications for fall 2021 are now closed for this project.

Introduced plants can become invasive when they escape the insect and microbial enemies that control native plant populations. Legumes benefit from symbiotic relationships with nitrogen-fixing bacteria called rhizobia, which colonize nodules in legume roots. We have found that three invasive leguminous plant species (French broom, Spanish broom, and Scotch broom) host rhizobia more closely related to European rhizobia than to California rhizobia, which suggests that European rhizobia may have co-invaded California with their legume hosts.

Invasion theory predicts that invasive species might proliferate in a novel habitat if they have escaped the natural enemies that control their populations in their native range. Bacteriophages (phages, for short) are viruses that attack bacteria and can control bacterial population densities.

In this project, we first ask: Are introduced rhizobia less often attacked by phages than are native rhizobia? If so, then introduced rhizobia might also enjoy enemy escape. However, phages might be co-introduced into new habitats while integrated in their host's genome as a 'prophage'. Due to this possibility, we also ask: How prevalent are prophages in rhizobium genomes?

Students can participate either on or off campus:

On campus: With guidance and support from the project supervisor, you will participate in experimental design, culturing bacteria, isolating and characterizing bacteriophages, and collecting and analyzing data. Over the course of the semester, you may learn sterile technique, initiation and maintenance of bacterial cultures, phage isolation, DNA extraction and handling, and proper data management techniques.

Off campus: With guidance and support from the project supervisor and in collaboration with a team of your peers, you will learn how to compile and manage databases, align nucleotide and amino acid sequences, construct phylogenetic trees, detect prophages, and genomic analyses (e.g. annotation and comparative genomics).

Day-to-day supervisor for this project: Jannick Van Cauwenberghe, Post-Doc

Qualifications: You must have a strong work ethic and an interest in microbiology and ecology. You must be dedicated to learning from and contributing to the project, which involves meticulous laboratory procedures, attention to detail, continuous care of bacteria, and sometimes boring and repetitive protocols, but exciting and rewarding results. Experience with phage DNA extraction, sterile technique, bacterial culturing or programming (e.g. python) is a definite plus. Applicants with a genuine interest in biology will be favored. We prefer that you be at least a sophomore in a Biological Science major with a minimum GPA of 3.0.

Weekly Hours: 9-11 hrs

Off-Campus Research Site: Dept of Integrative Biology, University of California 3040 Valley Life Sciences Bldg. #3140

Related website: http://www.simmslab.org/

Closed (3) Do rhizobia adapt to herbicide exposure?

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

Legumes benefit from symbiotic relationships with nitrogen-fixing bacteria called rhizobia, which colonize nodules in legume roots. Chemical herbicides are used to control weeds in both agriculture and horticulture. Rhizobia are exposed to these chemicals when they are used to control weeds in leguminous crops or to control leguminous weeds. The goal of this project is to determine whether rhizobia exposed to herbicides adapt to this stress by evolving the ability to grow in the presence of these chemicals. If we find evidence that rhizobia have adapted to herbicide exposure, we might also test if herbicide adaptation involves a fitness trade-off, i.e., whether rhizobia able to grow in the presence of herbicides grow more slowly in the absence of herbicide.

You will collect rhizobia from legume populations that differ in their history of exposure to herbicides and test these rhizobia for their ability to grow in the presence of one or more herbicides. If you identify rhizobia that differ in their ability to grow in the presence of herbicide, you will then test for a fitness trade-off by comparing their growth rates in the absence of herbicide.

You will be expected to keep meticulous field and laboratory notebooks, attend lab group meetings, and write a project report by the end of the semester.

The project includes a small amount of field research (digging up plants) on campus and in city parks, followed by a large amount of laboratory work (isolating and growing rhizobia).
, Post-Doc

Qualifications: You must have a strong work ethic and an interest in microbiology and ecology. You must be dedicated to learning from and contributing to the project, which involves meticulous laboratory procedures, attention to detail, continuous care of bacteria, and sometimes boring and repetitive protocols, but exciting and rewarding results. Experience with sterile technique and bacterial culturing is a plus, but not required. Applicants with a genuine interest in biology will be favored. We prefer that you be at least a sophomore in a Biological Science major with a minimum GPA of 3.0.

Weekly Hours: 9-11 hrs

Related website: http://www.simmslab.org

Closed (4) Plant-Microbiome Co-Occurrence

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

Up 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.

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 (this likely will include training in use of GitHub and R). Students are expected to attend weekly meetings via Zoom with the group, which can include specific trainings, 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.
, Graduate Student

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 in addition to attending the weekly group meetings. Ideally you already have an interest in microbes or plants or ecology (large-scale patterns).

Weekly Hours: to be negotiated

Off-Campus Research Site: Off-campus: 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.