Ellen Simms, Professor

Closed (1) Drivers of Legume Invasions in the Bay Area

Closed. This professor is continuing with Spring 2017 apprentices on this project; no new apprentices needed for Fall 2017.

Microbes drive vital processes in all ecosystems, yet are often overlooked. Invading plants can fundamentally alter plant-microbial feedback loops that stabilize native ecosystems; so microbial community dynamics must be considered when choosing management methods. Invasive legumes exhibit particularly strong plant-microbial feedbacks. Legumes benefit from symbiotic relationships with nitrogen-fixing bacteria called rhizobia, which colonize nodules in legume roots. Drs. Kim La Pierre and Ellen Simms are working on a project that addresses three important ecological questions: (1) how does invasion by three leguminous plant species (French broom, Spanish broom, and Scotch broom) affect soil rhizobial community structure in Marin County parks and open space; (2) how do three common management techniques (hand–pulling, prescribed burning, and herbicide) affect the soil rhizobial community; and (3) does the state of the soil rhizobial community influence the success of native and/or invasive legumes in these landscapes?

With guidance and support from the project supervisor, you will participate in experimental design, collection of field samples around the Bay Area, culturing bacteria and growing plants for greenhouse experiments, maintaining greenhouse experiments, and collecting and analyzing data. Over the course of the semester, you may learn sterile technique, DNA extraction and handling, and initiation and maintenance of bacterial cultures, and proper greenhouse and data management techniques.

Day-to-day supervisor for this project: Kimberly La Pierre, Post-Doc

Qualifications: You must be dedicated to the project, which involves meticulous laboratory procedures, attention to detail, continuous care of plants and bacteria, sometimes boring and repetitive protocols, but exciting and rewarding results. We are looking for students who are team players. Experience with sterile technique, molecular work, and bacterial culturing is a plus, but not a requirement. We prefer that you be at least a sophomore in a Biological Science major with a minimum GPA of 3.0.

Weekly Hours: 9-12 hrs

Related website: http://www.simmslab.org
Related website: http://kimberlylapierre.weebly.com/

Closed (2) Mutualism theory predicts how legumes influence biodiversity-ecosystem function relationships under global change

Closed. This professor is continuing with Spring 2017 apprentices on this project; no new apprentices needed for Fall 2017.

Ecological theory predicts that niche and relative fitness differences among plant species underlie variation in the biodiversity-productivity relationship. However, the mechanisms underlying this variation among plant species are rarely experimentally quantified, leaving causal connections between plant variation and the biodiversity-productivity relationship elusive. Plants in the legume family are infected by beneficial soil bacteria called rhizobia, which fix atmospheric nitrogen (N) in exchange for carbon (C) from their plant hosts. As most plants obtain N from the soil, access to atmospheric N via this mutualism can differentiate legumes from non-legumes, thus influencing the productivity-diversity relationship. Increased atmospheric carbon dioxide (CO2) and soil N will likely influence the effect legume species have on the productivity-diversity relationship by altering the legume-rhizobia mutualism. We are experimentally examining the biotic processes that differentiate four legume species from each other and from non-legumes to understand how these differences cause variation in patterns of primary productivity within the BioCON experiment at Cedar Creek LTER.

First, we are assessing niche differences (ND) and relative fitness differences (RFD) among legume species by determining the composition and density of, and plant benefit from, the species-specific nodulating rhizobial community (NRC) in soil samples from the ambient condition BioCON biodiversity plots. Second, evolution of the NRC in response to enhanced CO2 and/or N, and its consequences for the richness-productivity relationship, will be examined by determining the composition and density of, and plant benefit derived from, the NRC of each BioCON diversity, CO2, and N treatment combination. Finally, variation among legume species in how CO2- and/or N-availability shifts enforcement of rhizobial cooperation (partner choice and sanctions), and the consequences of this variation for the richness-productivity relationship, will be examined through mixed-inoculation experiments. This research will inform management of ecosystem function under current and future global change scenarios, with important implications for human well-being.


With guidance and support from the project supervisor, you will participate in experimental design, culturing bacteria and growing plants for greenhouse experiments, maintaining greenhouse experiments, and collecting and analyzing data. Over the course of the semester, you may learn sterile technique, DNA extraction and handling, and initiation and maintenance of bacterial cultures, and proper greenhouse and data management techniques.

Day-to-day supervisor for this project: Kimberly La Pierre, Post-Doc

Qualifications: You must be dedicated to the project, which involves meticulous laboratory procedures, attention to detail, continuous care of plants and bacteria, sometimes boring and repetitive protocols, but exciting and rewarding results. We are looking for students who are team players. Experience with sterile technique, molecular work, and bacterial culturing is a plus, but not a requirement. We prefer that you be at least a sophomore in a Biological Science major with a minimum GPA of 3.0.

Weekly Hours: 9-12 hrs

Open (3) Have invasive rhizobia escaped their bacteriophage enemies?

Open. Apprentices needed for the fall semester. Please do NOT contact faculty before September 11th (the start of the 4th week of classes)! Enter your application on the web beginning August 16th. The deadline to apply is Tuesday, August 29th at 8 AM.

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.

Bacteriophages ("phage", for short) are viruses that attack bacteria and can control bacterial population densities. In this project, we ask if introduced rhizobia are less often attacked by phages than are native rhizobia. If so, then introduced rhizobia might also enjoy enemy escape.

With guidance and support from the project supervisor, you will participate in experimental design, culturing bacteria, isolating and characterizing bacteriophage, 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.

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


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.

Weekly Hours: 6-9 hrs

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

Open (4) Non-rhizobia in legume nodules and their use as biofertilizers

Open. Apprentices needed for the fall semester. Please do NOT contact faculty before September 11th (the start of the 4th week of classes)! Enter your application on the web beginning August 16th. The deadline to apply is Tuesday, August 29th at 8 AM.

It is well known that legumes benefit by hosting nitrogen-fixing bacteria called rhizobia in root nodules. However, many other bacteria also invade nodules as they are formed. Many non-rhizobial endophytic (NRE) bacteria are unable to fix nitrogen inside the nodule, but can promote plant growth by phytohormone production, nutrient mobilization and pathogen destruction. This study will investigate the occurrence of NRE bacteria in the root nodules of chickpea, soybean and alfalfa. The non-rhizobial nature of isolated bacteria will be confirmed by nodulation assay and PCR amplification of nodulation genes.
NRE isolates will also be characterized in vitro for plant growth promoting properties including indole acetic acid production, phosphate solubilization, nitrogen fixation and biofilm formation. Plant assays will test the potential of NRE isolates alone and in combination with rhizobia to improve plant agronomic characteristics.

Work and Tasks:

You will learn sterile culture technique, culturing of bacteria on solid and liquid media, husbandry and maintenance of plant hosts. You will learn experimental design by participating in set up, harvest and documentation of lab and greenhouse experiments. You may learn how to quantify and analyze microbial phenotypic traits and such molecular techniques as DNA extraction, PCR, and gel electrophoresis.





Day-to-day supervisor for this project: Mohsin Tariq, Post-Doc

Qualifications: Qualifications: A strong work ethic and a firm dedication to the project, which involves meticulous laboratory procedures, attention to detail, continuous care of plants and bacteria, sometimes boring and repetitive protocols, but exciting and rewarding results. Scientific engagement, curiosity, self motivation and independence (once you are trained) is essential. People who work easily with others in addition to independently are preferred. Required: Six to twelve hours per week, or negotiable for good candidates. Previous lab experience is preferred but not required. Dedication and completion of weekly hours is required. Two semester commitment.

Weekly Hours: 6-9 hrs

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