Microbiology and Environmental Toxicology

2015-16 General Catalog

430 Physical Sciences Building
Telephone (831) 459-4719
FAX (831) 459-3524

Faculty | Course Descriptions

Program Description

The Microbiology and Environmental Toxicology Department (METX) sponsors undergraduate and graduate courses in microbiology and environmental toxicology, both within the department and through affiliated departments. The curriculum offers a strong foundation in fundamental and applied toxicology and microbiology to provide the breadth and depth of perspective required for this interdisciplinary science. Research interests of students and faculty in METX span the fields of biology, microbiology, chemistry, Earth sciences, ocean sciences, environmental studies, and human health.

Undergraduate Programs

While the METX Department only awards graduate degrees, it does offer a select number of undergraduate courses to prepare and attract promising undergraduates for advanced studies in microbiology and environmental toxicology or related disciplines. Students interested in microbiology and environmental toxicology should major in a field such as biology; marine biology; molecular, cell, and developmental biology; biochemistry; chemistry; Earth sciences; engineering; or environmental studies while taking microbiology and environmental toxicology electives.

In addition, the program provides unique opportunities for exceptional undergraduates to conduct research in microbiology and environmental toxicology. These opportunities are limited to students who have demonstrated their potential in undergraduate courses in the basic sciences and environmental toxicology. With department approval, these undergraduates may also take graduate courses in microbiology and environmental toxicology. That coursework will be applied toward a graduate degree in microbiology and environmental toxicology if they are accepted into the program.

Graduate Programs

Graduate training in the METX Department prepares students to solve important problems in the field of environmental health by providing stimulating coursework, extensive scientific presentation training, and in-depth research that culminates in a thesis. There is no other program in the world that educates students to appreciate the interplay between microbes, chemical toxins, and health and provides the training students require to work effectively in a complex world. Graduate training in the METX department prepares students to become leaders in the field, following career paths in academia, teaching, industry, and government. Master of science (M.S.) students typically finish in two years and doctor of philosophy (Ph.D.) students in four to six years.

Key components of our graduate training include:

  • Interdisciplinary core course that teaches critical thinking and how to approach problems: METX 200, Interdisciplinary Approaches to Problems at the Interface of Microbiology and Environmental Toxicology.

  • Core course devoted to grant-writing skills: METX 205, Scientific Skills, Ethics, and Writing.
  • Personalized class plan for the remaining three courses to fit the student’s background and research goals. Possible courses include METX 201, Sources and Fates of Pollutants, METX 202, Cell and Molecular Toxicology, METX 206A, Advanced Microbiology, METX 210, Molecular and Cellular Basis of Bacterial Pathogenesis, METX 238, Pathogenesis: Molecular Mechanisms of Disease, and METX 250, Environmental Microbiology, as well as courses in other departments such as Ocean Sciences 220, Chemical Oceanography, and Molecular Cell and Developmental Biology 200B, Advanced Molecular Genetics. Speaking presentation skills training through coursework and yearly departmental presentations. Scientific writing and literature mastery through the writing of a literature review in the first year. Weekly seminars expose students to the breadth of our fields and provide students with opportunities to interact closely with speakers to form connections and collaborations.

  • Qualifying examinations designed to perfect the student’s ability to craft research plans.

  • Extensive laboratory research training that starts immediately upon entering the program and culminates in the student’s master’s thesis or Ph.D. dissertation.

Sample Pathways

Pathways within the microbiology and environmental toxicology graduate program focus on interdisciplinary approaches to addressing problems in environmental and public health.  We offer several defined training pathways, and also encourage students to create their own.

Metals in the Environment

Research includes how organisms are exposed to metals, how these metals cause toxicity, and investigating the concentration, speciation, and isotopic composition of contaminant metals and metalloids.


Microbiology provides research training on molecular genetic analysis of both non-pathogenic and pathogenic microbes. Students study host-pathogen interactions, ecology and evolution of pathogenic microorganisms, adaptation of pathogenic and non-pathogenic microorganisms to environmental stresses, and mechanisms of microbial biotransformation of pollutants and toxic metals.

Cellular and Organismal Toxicology

This pathway provides training in the biochemical, molecular, cellular, and physiological processes that are impacted by exposures to such contaminants as toxic metals. Research includes exposure pathways and toxicity of contaminants and pathogens within humans, with emphasis on the molecular and cellular mechanisms underlying toxicity.

Program Requirements

The METX student’s curriculum is tailored to the individual, creating a graduate experience that combines essential background material with coursework at the frontiers of science. The student, in conjunction with a faculty committee, chooses classes to complement the Ph.D. or master’s thesis work that each student is performing. Students are encouraged to explore new areas and bring this expertise back to their thesis research.

Requirements for both Master’s and Ph.D. Students in Microbiology and Environmental Toxicology

  1. Core coursework. METX 200 Interdisciplinary Approaches to Problems at the Interface of Microbiology and Environmental Toxicology, and METX 205, Scientific Skills, Ethics, and Writing, must be taken and passed with at least a B.

  2. Three additional courses. Two courses from the following: METX 201, 202, 206A, 210, 238, 250, and at least one additional approved graduate-level course within Microbiology and Environmental Toxicology or another department. Students must enroll in METX 281, 292, and 297 or 299 each quarter. Additional courses as recommended by your first-year advising committee. Must be passed with at least a B.

  3. Literature review. Under direction of the student’s adviser, write a literature review of the current state of the field of the proposed dissertation research. The written review will be handed in to the student’s adviser at the end of the summer of the first year.

  4. Department seminar. Give a 20-minute departmental seminar each academic year, and one 50-minute departmental seminar during the fall quarter of the third year if a doctoral student, or in spring of the second year if a master’s student.

Requirements specific to the Ph.D. degree

  1. Teaching assistant. Doctoral students are required to work as teaching assistants (TA) for at least one quarter. Priority for TA positions is given to first-year doctoral students, then to current doctoral students who have not yet worked as a teaching assistant.

  2. Ph.D. qualifying examination (QE1—microbiology and environmental toxicology internal). Part I of the qualifying examination consists of two portions: preparation and defense of an independent research proposal, and knowledge of material presented in the microbiology and environmental toxicology core courses taken by the student.  The student must complete QE1 no later than spring quarter of the second year.

  3. Third-year seminar and thesis proposal. The student will present a 50-minute seminar on his/her dissertation research proposal no later than the end of fall quarter in the third year.

  4. Ph.D. qualifying examination (QE2). Present and defend a dissertation research proposal to the student’s Ph.D. qualifying examination (QE) committee. The student must complete QE2 no later than fall quarter of the third year.

  5. Advancement to candidacy. The student advances to candidacy after completing all coursework, completing the literature review, giving the third-year seminar and passing the Ph. D. qualifying examination parts I and II.

  6. Dissertation defense. The student must submit their doctoral dissertation to the dissertation committee for tentative approval at least one month before presenting a formal, public doctoral research seminar.

Requirements specific to the Master’s degree

  1. Master’s comprehensive examination. The master’s comprehensive exam is a presentation and defense of the student’s master’s research proposal, including relevant background knowledge. The examination will not be specifically course-based, but will draw on knowledge from courses. This examination is taken in the fall quarter of the second year.

  2. Second-year seminar. The student will present a 50-minute seminar on his/her thesis work in spring quarter of the second year.

  3. Thesis. Students are required to submit a thesis for fulfillment of the degree requirements. The thesis should be submitted to the student’s master’s reading committee one month before the due date.

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Revised: 09/01/15