Plant & Microbial Biology

University of California, Berkeley

Overview

The Department of Plant and Microbial Biology consists of the Division of Plant Biology and the Division of Microbial Biology. Programs at both the undergraduate and graduate levels have been designed to offer students maximum flexibility in defining their own areas of interest. In addition to departmental resources that are available in Koshland Hall, the facilities of the College of Natural Resources Biological Imaging Facility and the United States Department of Agriculture Plant Gene Expression Center are available for the programs of the department.

The Division of Plant Biology

The Division of Plant Biology program emphasizes basic research and its application to plants and promotes the design of plant biotechnologies. With an increasing awareness of environmental problems, global changes, and emerging food needs, plants are a focal point for new research initiatives and educational training programs. Understanding the biology of plants, their development, their responses to the environment, and the impact of human activities on the plant biosphere are many of the challenges that will continue to fuel the expansion of plant biology research well into the twenty-first century.

The Division of Microbial Biology

The Division of Microbial Biology was established within the department to provide a focus for microbial biology at UC Berkeley. There is a growing awareness that microbes and microbial activities are essential to maintaining a high quality of life for all eukaryotes. Moreover, understanding the microbial world is necessary if we are to comprehend the global ecosystem, evolutionary history, and diversity of life on earth. The twenty-first century will bring a new understanding of the workings of the global ecosystem and a wealth of new technologies derived from the microbial world. The new microbial biology research programs are designed to meet this challenge.

Undergraduate Programs

Genetics and Plant Biology: BS
Microbial Biology: BS

Graduate Programs

The department and affiliated graduate group offer the following graduate degrees:
Microbiology: PhD
Plant Biology: PhD

Visit Department Website

Related Courses

Plant and Microbial Biology

PLANTBI 200A Plant Developmental Genetics 1.5 Unit

Terms offered: Fall 2017, Fall 2016, Fall 2015
The students will be provided with both the basic framework and current topics of plant developmental genetics.

Plant Developmental Genetics: Read More [+]

PLANTBI 200B Genomics and Computational Biology 1.5 Unit

Terms offered: Spring 2017, Spring 2016, Spring 2015
Principles of computational and genomic biology. Covers evolutionary, algorithmic, and statistical foundations of sequence analysis, allowing students to understand concepts underlying modern computational methods. Practical applications wil be pursued in student-coordinated sessions. Combined lecture with 220B.

Genomics and Computational Biology: Read More [+]

PLANTBI 200C Plant Diversity and Evolution 1.5 Unit

Terms offered: Spring 2017, Spring 2016, Spring 2015
This course will introduce the students to the diversity of plant form and function and provide them with a basic understanding of the tools and techniques used to study plant diversification and evolution. Molecular and morphological data will be discussed and plant diversity will be introduced at molecular, population, organismal, and ecological levels.

Plant Diversity and Evolution: Read More [+]

PLANTBI 200D Plant Cell Biology 1.5 Unit

Terms offered: Fall 2017, Fall 2016, Fall 2015
The course will describe the conceptual framework of plant cell biology followed by in-depth discussion of several active areas of research including cell wall biology, membrane transport, cellular trafficking, and cell signaling.

Plant Cell Biology: Read More [+]

PLANTBI 200E Plant Biochemistry 1.5 Unit

Terms offered: Fall 2017, Fall 2016, Fall 2015
The aim of this course is to augment the student's knowledge of key plant-specific (or particularly relevant) biochemical processes focusing on the underlying experiments used to deduce key cycles coupled with current areas of exploration and debate surrounding a given topic area. In addition, this section will broaden and deepen the student's knowledge of biochemistry in general including basic enzyme kinetics, assessment of enzymatic (biochemical)
function, and modes of regulation.
Plant Biochemistry: Read More [+]

PLANTBI 200F Plant-Environment Interactions 1.5 Unit

Terms offered: Spring 2017, Spring 2016, Spring 2015
Students will be provided with both the historical framework and current topics in the molecular mechanisms underlying plant dynamic responses to external signals and stresses.

Plant-Environment Interactions: Read More [+]

PLANTBI 201 Faculty Research Review 2 Units

Terms offered: Fall 2017, Fall 2016, Fall 2015
Presentation and discussion of faculty research in the areas of plant and microbial biology. Faculty speakers review recent advances in their area of expertise and present an outlook of current research activities in their laboratories. The format of the class is designed to stimulate a dialogue between instructor and students in the course of each presentation.

Faculty Research Review: Read More [+]

PLANTBI 202 Faculty Research Review 2 Units

Terms offered: Fall 2017, Fall 2016, Fall 2015
Presentation and discussion of faculty research in the area of microbial biology. Faculty speakers review recent advances in their area of expertise and present an outlook of current research activities in their laboratories. The format of the class is designed to stimulate a dialogue between instructor and students in the course of each presentation.

Faculty Research Review: Read More [+]

PLANTBI 205A Introduction to Research 2 - 12 Units

Terms offered: Fall 2017, Fall 2016
Closely supervised experimental work under the direction of an individual faculty member; an introduction to experimental methods and research approaches in particular areas of plant and microbial biology.

Introduction to Research: Read More [+]

PLANTBI 205B Introduction to Research 2 - 12 Units

Terms offered: Spring 2017
Closely supervised experimental work under the direction of an individual faculty member; an introduction to experimental methods and research approaches in particular areas of plant and microbial biology.

Introduction to Research: Read More [+]

PLANTBI 210 Scientific Reasoning and Logic 1 Unit

Terms offered: Fall 2017, Fall 2016, Fall 2015
The objectives of this class are to teach students to critically read and interpret scientific papers. Students will read and discuss strongly and poorly reasoned papers. At the end of the class the student should understand the logic and reasoning which make a paper strong, often classic, contribution.

Scientific Reasoning and Logic: Read More [+]

PLANTBI C216 Microbial Diversity Workshop 1 Unit

Terms offered: Fall 2017, Fall 2016, Fall 2015
This workshop for graduate students will parallel C116, Microbial Diversity, which should be taken concurrently. Emphasis in the workshop will be on review of research literature and formulation of paper pertinent to research in microbial diversity.

Microbial Diversity Workshop: Read More [+]

PLANTBI 220A Microbial Genetics 1.5 Unit

Terms offered: Fall 2017, Fall 2016, Fall 2015
The students will learn fundamental principles and advanced techniques in microbial genetics. The use of genetics in deducing biochemical pathways, protein interactions, and signal transduction pathways will be explores through reading and discussion of current and classic papers from the primary literature. Experimental design and interpretation will be the focus of problem sets solved in student-coordinated sessions.

Microbial Genetics: Read More [+]

PLANTBI 220B Genomics and Computational Biology 1.5 Unit

Terms offered: Spring 2017, Spring 2016, Spring 2015
Principles of computational and genomic biology. Covers evolutionary, algorithmic, and statistical foundations of sequence analysis, allowing students to understand concepts underlying modern computational methods. Practical applications will be pursued in student-coordinated sessions. Combined lecture with 200B.

Genomics and Computational Biology: Read More [+]

PLANTBI 220C Microbial Diversity and Evolution 1.5 Unit

Terms offered: Spring 2017, Spring 2016, Spring 2015
The students will be provided with both the basic framework and current topics of microbial diversity and evolution.

Microbial Diversity and Evolution: Read More [+]

PLANTBI 220D Cell Structure and Function 1.5 Unit

Terms offered: Fall 2017, Fall 2016, Fall 2015
The students will be provided with both the basic framework and current topics of cell structure and function.

Cell Structure and Function: Read More [+]

PLANTBI 220E Microbial Physiology 1.5 Unit

Terms offered: Fall 2017, Fall 2016, Fall 2015
The students will be provided with both the basic framework and current topics of microbial physiology.

Microbial Physiology: Read More [+]

PLANTBI 220F Microbial Ecology 1.5 Unit

Terms offered: Spring 2017, Spring 2016, Spring 2015
The students will be provided with both the basic framework and current topics of microbial ecology.

Microbial Ecology: Read More [+]

PLANTBI 222 Biochemistry of Biofuels: Concepts and Foundations 1 Unit

Terms offered: Spring 2015, Spring 2014, Spring 2013
This course offers a consideration of genes, enzymes, metabolic pathways and biochemical processes leading to the generation of hydrogen, bio-oils, ethanol, and other biofuels. Discussion of biochemistry is extended to cover product yields and techno-economic analyses of commercial viability of the various biofuel products. Lectures are based on historical and contemporary papers in plant and microbial biochemistry, integrating structure
, function and evolution of the molecular, cellular, and organismal levels, and discussing how this knowledge can be applied in the generation of renewable biofuels.
Biochemistry of Biofuels: Concepts and Foundations: Read More [+]

PLANTBI C224 The Berkeley Lectures on Energy: Energy from Biomass 3 Units

Terms offered: Fall 2015, Fall 2014, Fall 2013
After an introduction to the different aspects of our global energy consumption, the course will focus on the role of biomass. The course will illustrate how the global scale of energy guides the biomass research. Emphasis will be places on the integration of the biological aspects (crop selection, harvesting, storage, and distribution, and chemical composition of biomass) with the chemical aspects to convert biomass to energy. The course aims
to engage students in state-of-art research.
The Berkeley Lectures on Energy: Energy from Biomass: Read More [+]

PLANTBI 238 Readings in Environmental Microbiology 1 Unit

Terms offered: Fall 2014, Spring 2014, Fall 2013
Special Topics and Advanced Seminars in Plant Pathology. Seminar/discussion by graduate students of current research in the field of plant pathogenic bacteria.

Readings in Environmental Microbiology: Read More [+]

PLANTBI 290 Seminar 1 - 2 Units

Terms offered: Fall 2017, Spring 2017, Fall 2016
Advanced study in various fields of plant biology and microbial biology. Topics will be announced in advance of each semester. Enrollment in more than one section permitted.

Seminar: Read More [+]

PLANTBI 292 Research Review in Plant and Microbial Biology 1 Unit

Terms offered: Fall 2017, Spring 2017, Fall 2016
Lectures, reports, and discussions on current research in plant and microbial biology. Sections are operated independently and directed toward different topics.

Research Review in Plant and Microbial Biology: Read More [+]

PLANTBI 296 Graduate Supervised Independent Study 1 - 12 Units

Terms offered: Fall 2014, Spring 2014, Fall 2013
Graduate student independent study under the supervision of a faculty member. Sections are operated independently and directed toward different topics.

Graduate Supervised Independent Study: Read More [+]

PLANTBI 297 Grant Writing and Research Presentations 2 Units

Terms offered: Spring 2016, Spring 2015, Spring 2014
Each student will write a grant proposal in three steps: a one page outline, a three-page pre-proposal, and a complete 10-page grant proposal. There will be feedback at each step in the process -- each participant will review the other grant proposals. Some of the scheduled classes will include discussion of the outlines and pre-proposals, and the last class will be organized as a grant panel, with students assigned as primary and secondary
reviewers.
Grant Writing and Research Presentations: Read More [+]

PLANTBI 298 Plant Biology Group Studies 1 - 6 Units

Terms offered: Fall 2017, Spring 2017, Fall 2016
Advanced study of research topics which will vary semester to semester. Enrollment in more than one section permitted.

Plant Biology Group Studies: Read More [+]

PLANTBI 299 Graduate Research 1 - 12 Units

Terms offered: Fall 2017, Spring 2017, Fall 2016
Graduate student research.

Graduate Research: Read More [+]

PLANTBI 375 Workshop on Teaching 2 Units

Terms offered: Fall 2017, Fall 2016, Fall 2015
Designed for all graduate students. This course has two goals: discussion of questions and problems relating to the GSI's teaching, and learning how to design and execute a whole course. Effective teaching methods will be introduced by experienced GSIs and faculty. Students will participate in reciprocal classroom visits, visitation and critique of faculty lectures, course design, lecture preparation, sample lecture presentation, and discussion
of current literature on teaching.
Workshop on Teaching: Read More [+]

PLANTBI 602 Individual Study for Graduate Students 1 - 2 Units

Terms offered: Fall 2017, Spring 2017, Fall 2016
Individual study in consultation with the major field advisor, intended to provide an opportunity for qualified students to prepare for examinations required of Ph.D. candidates

Individual Study for Graduate Students: Read More [+]

Faculty and Instructors

+ Indicates this faculty member is the recipient of the Distinguished Teaching Award.

Faculty

Barbara Baker, Adjunct Professor. Biochemistry, genetics, signal transduction, plant and microbial biology, biolomolecular mechanisms of plant resistance to microbial disease, plant pathogen recognition, plant resistance to pathogen diseases, tobacco mosaic virus, agriculture and crops.
Research Profile

Benjamin Blackman, Assistant Professor.

Rachel B. Brem, Associate Adjunct Professor. Genetics of regulatory variation.
Research Profile

Steven Brenner, Professor. Molecular biology, computational biology, evolutionary biology, bioengineering, structural genomics, computational genomics, cellular activity, cellular functions, personal genomics.
Research Profile

Thomas D. Bruns, Professor. Microbial biology, plant biology, fungi, nucleic acid sequences, basidomycetes, ectomycorrhizal fungi communities.
Research Profile

John Coates, Professor.

Devin Coleman-Derr, Assistant Adjunct Professor. Plant, Microbiome, Environmental Stress, Drought, Sorghum.
Research Profile

+ Lewis J. Feldman, Professor. Microbial biology, plant biology.
Research Profile

Robert L. Fischer, Professor. Plant and microbial biology.
Research Profile

Jennifer C. Fletcher, Adjunct Professor. Molecular biology, genetics, gene regulation, stem cells, plant development.
Research Profile

Michael Freeling, Professor. Genetics, genomics, plants, trends in evolution.
Research Profile

N. Louise Glass, Professor. Biofuels, biotechnology, fungal genetics, fungal cell biology.
Research Profile

Britt Glaunsinger, Associate Professor. Virology, gene expression, herpesvirus.
Research Profile

Igor V. Grigoriev, Adjunct Professor. Genomics, fungi, algae, eukaryotes, computational biology, bioinformatics, genome annotation.
Research Profile

Sarah Hake, Adjunct Professor.

Frank Harmon, Associate Adjunct Professor.

Russell L. Jones, Professor. Plant and microbial biology.
Research Profile

Cheryl Kerfeld, Associate Adjunct Professor. Bacterial microcompartments, bioinformatics, photosynthesis, synthetic biology, Structural Biology, carboxysome, cyanobacteria, photoprotection.
Research Profile

Arash Komeili, Associate Professor. Microbiology, Biomineralization, bacterial organelles, Magnetic Nanoparticles.
Research Profile

Peggy G. Lemaux, Cooperative Extension Specialist.

Jennifer Lewis, Assistant Adjunct Professor. Plant-pathogen interactions, plant immunity, type III effector proteins.
Research Profile

Steven E. Lindow, Professor. Microbial ecology, microbial biology, plant biology, plant frost control, bacterial plant diseases, plant disease epidemiology.
Research Profile

Sheng Luan, Professor. Microbial biology, plant biology.
Research Profile

Sheila Mccormick, Adjunct Professor. Molecular biology, genetics, pollen, plant reproduction.
Research Profile

Anastasios Melis, Professor. Photosynthesis, Metabolic Engineering, bioenergy.
Research Profile

Krishna K. Niyogi, Professor. Genetics, plant and microbial biology, algae, photosynthesis, antioxidants.
Research Profile

Markus Pauly, Professor. Cell walls, extracellular matrix, plants, polysaccharides, carbohydrates, lignin, nucleotide sugars, analytical carbohydrate chemistry, plant genomics, enzyme biochemistry.
Research Profile

Daniel A. Portnoy, Professor. Mammalian cells, molecular and cellular basis of microbial pathogenesis, defense against infection, listeria monocytogenes, cell biology of infection, mechanisms of secretion.
Research Profile

Peter Quail, Professor. Plant biology, plant and microbial biology.
Research Profile

Kathleen Ryan, Associate Professor. Bacterial cell cycle regulation, signal transduction, and regulated proteolysis.
Research Profile

Henrik Scheller, Adjunct Professor. Biofuels, polysaccharides, plant cell walls, biochemistry, plant biotechnology, glycosylation.
Research Profile

Kimberly Seed, Assistant Professor.

Kimmen Sjolander, Professor. Computational biology, algorithms, phylogenetic tree reconstruction, protein structure prediction, multiple sequence alignment, evolution, bioinformatics, hidden Markov models, metagenomics, statistical modeling, phylogenomics, emerging and neglected diseases, machine-learning, genome annotation, metagenome annotation, systems biology, functional site prediction, ortholog identification.
Research Profile

Chris Somerville, Professor. Biochemistry, biotechnology, bioenergy, cell biology, biofuels, cell walls, polysaccharides, cellulose, arabidopsis, cellulose synthase.
Research Profile

Shauna Somerville, Professor. Powdery mildew disease, cell wall integrity sensing, plant-fungal interactions, plant cell walls.
Research Profile

Chelsea Specht, Associate Professor. Molecular evolution, adaptation, plant systematics, evolution of development (evo-devo), evolution of form and function, plant morphology, comparative phylogenetics, floral developmental evolution, diversification rates.
Research Profile

Brian J. Staskawicz, Professor. Biotechnology, plant and microbial biology.
Research Profile

Zinmay Sung, Professor. Plant biology, plant and microbial biology.
Research Profile

Michiko Taga, Assistant Professor. Molecular biology, genetics, microbial biology, chemical biology, cofactors, nutrient exchange, microbial communities.
Research Profile

John Taylor, Professor. Evolution, fungi, phylogenomics, mycology, population genomics.
Research Profile

Norman Terry, Professor. Phytoremediation, Bioremediation, environmental cleanup, soil and water, plant biology, microbial biology.
Research Profile

Matthew Traxler, Assistant Professor.

John Vogel, Adjunct Professor.

Mary Wildermuth, Associate Professor.

Patricia Zambryski, Professor. Microbial biology, plant biology, plant intercellular communication via plasmodesmata, Agrobacterium, bacterial type IV secretion.
Research Profile

Daniel Zilberman, Associate Professor.

Emeritus Faculty

Bob B. Buchanan, Professor Emeritus. Biotechnology, environmental policy, plant biology, thioredoxin.
Research Profile

Andrew Jackson, Professor Emeritus.

Contact Information

Department of Plant and Microbial Biology

111 Koshland Hall

Phone: 510-642-9999

Visit Department Website

Department Chair

Krishna K. Niyogi

371A Koshland Hall

Phone: 510-643-6602

Fax: 510-642-4995

niyogi@berkeley.edu

Associate Chair and Head Graduate Adviser

Pat Zambryski

Phone: 510-643-9203

Fax: 510-642-4995

zambrysk@berkeley.edu

Graduate Program Coordinator

Rocio Sanchez

Phone: 510-642-5167

rocio_s@berkeley.edu

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