Rodrigo Almeida, Professor

Open (1) Biology and evolution of an emerging vector-borne plant pathogen

Open. Apprentices needed for the fall semester. Enter your application on the web beginning August 18th. The deadline to apply is Monday, August 30th at 9 AM.

Xylella fastidiosa is an economically important plant pathogen in California and globally. This insect transmitted bacterium causes Pierce’s Disease (PD) in grapevines and Almond Leaf Scorch (ALS) in almonds. Across the state, there are two subspecies–subsp. fastidiosa and subsp. multiplex; each subspecies includes multiple strains from different climates. Previous genomic research in our lab has shown that strains vary genetically by climate, but greenhouse and field experiments are necessary to understand how each strain may perform in alternative climates. Our lab is currently running field experiments in a vineyard in Northern California, as well as greenhouse manipulations in grapevine and almond. We also perform disease transmission experiments coupled with real-time monitoring of insect behavior and microscopy, at the Oxford Tract Greenhouse in Berkeley. Research questions include: (1) how quickly does the pathogen colonize grapevines under field conditions?; (2) do strains from different climates colonize plants at the same rate under controlled conditions?; (3) did this pathogen adapt to different climates in California?; and (4) does this pathogen impact the behavior and metabolism of its insect vectors in a way conducive to transmission?. These questions have important applications for pest management in viticulture and agriculture.

The URAP student will use molecular biology and microbiology techniques to quantify X. fastidiosa in field- and greenhouse-collected plant and insect samples. This will include sample processing, DNA extraction, qPCR, and bacterial culturing techniques. Training in all laboratory techniques will be provided. Additionally, there are opportunities to perform research with plant and insect samples and set up greenhouse experiments at Oxford Tract. If there is interest in field work, we can arrange for students to visit the experimental vineyard and collect plant samples and observational symptom data. Finally, our lab has expertise in genomics and bioinformatics, and can provide training in Python, R, and Bash scripting to students interested in bacterial genomics. Ultimately, the project and responsibilities will be shaped by the interests of the student.

Day-to-day supervisor for this project: Monica Donegan, Ph.D. candidate

Qualifications: Prior academic research or laboratory experience is not required. A keen attention to detail, willingness to ask questions, and respect for colleagues are required. The ideal student should be excited about biology, molecular ecology, evolution, and plant diseases.

Weekly Hours: 6-8 hrs

Related website: http://nature.berkeley.edu/~rodrigo/Lab%20page/index.html

Related website: https://www.researchgate.net/publication/316602562_Museum_specimen_data_reveal_emergence_of_a_plant_disease_may_be_linked_to_increases_in_the_insect_vector_population

Related website: http://nature.berkeley.edu/~rodrigo/Lab%20page/index.html

Closed (4) Determinants of Xylella fastidiosa host specificity

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

Xylella fastidiosa is an emerging xylem-limited vector-borne bacterium associated with several important diseases in a wide range of plants including crops (e.g. grapevines, almonds, sweet orange, peach), ornamentals (e.g. oleander, hibiscus), and trees (e.g. oak, sycamore, elm). The species is capable of infecting over 300 plant species in 69 families; only few plant species tested have proved to be inadequate as hosts both under experimental conditions and in the field. However, for most host plant species, X. fastidiosa does not cause disease. Thus, colonization does not necessarily equal disease. Importantly, the minimal genomic diversity of X. fastidiosa available suggests different phylogenetic groups have similar pathogenicity mechanisms. Despite its importance as a plant pathogen, there are no hypotheses on the determinants of X. fastidiosa host specificity. This project aims to address this very important knowledge gap.

The student will learn how to do some DNA extraction, qPCR besides learning some techniques such as preparing bacterial media and culturing Xylella fastidiosa., Ph.D. candidate

Qualifications: Desirable but not essential: experience and/or interest in plant pathology and/or microbiology.

Weekly Hours: 6-8 hrs