Plant Microbiology- Prof Doty

ESRM 325/SEFS 523

ENVIRONMENTAL USES OF TREES:  Bioenergy and Bioremediation

The course provides students with information about pressing environmental issues and many possible “green” solutions. In the two main topics of the course, both the advantages and disadvantages of each method are covered with the goal that the students will learn critical thinking skills. The course includes a discussion of global climate change and carbon sequestration by plants, since it links to both of the main topics of the course- phytoremediation and bioenergy. The students will learn about how plants remove and detoxify organic pollutants and sequester metal pollutants. They will learn the advantages and disadvantages of using phytoremediation compared to current engineering methods, and how the process can be improved. One lecture will focus on genetic engineering of plants, followed by lectures describing how this method can lead to increased degradation of pollutants. The bioenergy part of the course covers bioethanol, biomethanol, and biodiesel as alternative fuels. This overview is then followed by several lectures on the latest research on how current practices are being improved to make biofuel production economically and biologically feasible.

Required Texts

Since the course covers the latest material on phytoremediation and bioenergy, some of which is not yet published, the reading is based on reviews and current scientific papers, not text books. Students are expected to read the reviews prior to class to engage effectively in class discussions.


There will be one midterm (150 pts) and one final examination (200 pts). The questions require essay style answers. To aid in the exams in the undergraduate version of the course (ESRM325), students may bring one note page (2-sided) of their own making (to be turned in with the exams). The graduate student version of the course (SEFS 523) has take-home exams rather than in-class exams with the expectation of more thorough answers based on both lectures and current literature.  There are two writing assignments, each worth 25 points.

Syllabus for 2018 (NOTE: Prof. Doty is on Sabbatical; course will be offered next in autumn 2020)

Sept 27- Overview on environmental applications of plants; standard remediation methods

Oct 2- Phytoremediation of organic chemicals (guest lecture by Robert Tournay)

Oct 4- Phytoremediation of inorganic chemicals

Oct 9- Genetic engineering

Oct 11- Enhancing phytoremediation using g.e.

Oct 16- Enhancing phytoremediation using endophytes

Oct 18- Phytoremediation- Local opportunities and strategies

Oct 23- Exam 1 (phytoremediation)

Oct 25- Bioenergy overview

Oct 30- Bioethanol and cellulosic bioethanol

Nov 1- Biodiesel, biomethanol, and biohydrogen

Nov 6- Biochemicals (guest lecture by Prof. Fernando Resende’s grad student, Gabriel Seufitelli)

Paper 1 is due

Nov 8- Improving the efficiency of biofuel production

Nov 13- Improving the efficiency of biofuel production (continued)

Nov 15- USDA/AFRI PNW Bioenergy Projects: AHB (guest lecture by Prof. Gustafson)

Nov 20- USDA/AFRI PNW Bioenergy Projects: NARA (guest lecture by Prof. Ganguly)

Nov 22- Thanksgiving Day holiday

Nov 27- Global climate change

Nov 29- Photosynthesis and carbon sequestration

Dec 4- Plant responses to climate change; tying together the course

Dec 6- Final Exam (last day of class)

Dec 11- Paper 2 is due

Dec 12- We are not using our assigned final exam day


Disability Accommodations

To request academic accommodations due to a disability, please contact Disabled Student Services, 448 Schmitz, (206) 543-8924 (V/TTY). If you have a letter from Disabled Student Services indicating that you have a disability which requires academic accommodations, please present the letter to the instructor so we can arrange the accommodations needed for this class.

Academic Integrity

Plagiarism, cheating, and other misconduct are serious violations of your contract as a student. We expect that you will know and follow the University’s policies on cheating and plagiarism. Any suspected cases of academic misconduct will be handled according to University regulations. More information, including definitions and examples of Academic Misconduct, is available at

Washington state law requires that UW develop a policy for accommodation of student absences or significant hardship due to reasons of faith or conscience, or for organized religious activities. The UW’s policy, including more information about how to request an accommodation, is available at Religious Accommodations Policy ( Accommodations must be requested within the first two weeks of this course using the Religious Accommodations Request form (