Microbiology and Environmental Toxicology Ph.D.


Key components of our graduate training include:

  • Interdisciplinary core course that teaches critical thinking and how to approach complex problems in environmental health: METX 200, Interdisciplinary Approaches to Problems at the Interface of Microbiology and Environmental Toxicology.
  • Core course devoted to grant-writing and scientific-writing skills: METX 205, Scientific Grant 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; METX 250: Environmental Microbiology; and METX 270, Frontiers in Drug Action and Discovery. Courses in other departments include OCEA 220, Chemical Oceanography; and BIOL 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 and form connections and collaborations.
  • Qualifying examinations designed to perfect the student’s ability to craft and defend research plans.
  • For Ph.D. and Plan I (research thesis) M.S. students, extensive laboratory research training that starts immediately upon entering the program and culminates in the student’s Ph.D. dissertation or master's thesis.

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 support students who want to create their own.

Metals in the Environment

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


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 contaminants such 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.

Microbial Biology and Pathogenesis Track within the Program in Biomedical Sciences and Engineering (PBSE)

The METX Department also admits students through the PBSE program Microbial Biology and Pathogenesis (MICRO) Ph.D. track. The PBSE track is a rotation-based graduate umbrella program. This training program emphasizes the application of diverse approaches, including biochemistry, genetics, genomics, ecology, and imaging to address questions at the forefront of microbial biology. Interdisciplinary research is encouraged and supported by a diverse group of faculty from the METX Department as well as from the Departments of Biomolecular Engineering; Ocean Sciences; Molecular, Cell, and Developmental Biology; Evolutionary and Ecology Biology; and Chemistry and Biochemistry.

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.

Course Requirements

Required core courses (2):

METX 200Interdisciplinary Approaches in Environmental Toxicology


METX 205Scientific Grant Writing


Two courses from the following:

METX 201Sources and Fates of Pollutants


METX 202Cell and Molecular Toxicology


METX 206AAdvanced Microbiology


METX 210Molecular and Cellular Basis of Bacterial Pathogenesis


METX 238Pathogenesis: Molecular Mechanisms of Disease


METX 250Environmental Microbiology


METX 270
/CHEM 270/BME 270
Drug Action and Development


Any additional courses as recommended by your first-year advising committee.

Each quarter, students must enroll in at least the following:
METX 292Introductory Graduate Seminar


METX 297Independent Study

METX 297AIndependent Study


METX 297BIndependent Study


METX 297CIndependent Study


Plus a topical seminar from the METX 281 series
METX 281ATopics in Environmental Toxicology


METX 281CTopics in Environmental Microbiology


METX 281MTopics in Molecular Toxicology


/BIOL 280O
Topics in Bacterial Pathogenesis


METX 281SCellular and Organismal Responses to Toxicants


METX 281VTopics in Bacterial Pathogenesis and Innate Immunity


METX 281YBiofilms: Processes and Regulation


Teaching Requirement

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. Fulfilling this requirement may happen pre- or post-candidacy.

Qualifying Examination

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 prepared by the student, 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.

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

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.

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.

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.


Dissertation and 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.