2019 Environmental Microbiology

Font size  SML

Register update notification mail Add to favorite lecture list
Academic unit or major
Graduate major in Life Science and Technology
Tanji Yasunori  Nakamura Satoshi  Wachi Masaaki  Hongoh Yuichi  Yatsunami Rie 
Class Format
Media-enhanced courses
Day/Period(Room No.)
Tue1-2(J233,S223)  Fri1-2(J233,S223)  
Course number
Academic year
Offered quarter
Syllabus updated
Lecture notes updated
Language used
Access Index

Course description and aims

Microorganisms living on earth are involved in the circulation of mass and energy on earth. Microorganisms express their own unique characteristics and functions depending on their environmental habitats, including natural environment, extreme environment, and internal environment of animals. Prof. Tanji provides analytical methods of microbial flora in environments and its practical application. Prof. Nakamura and Asoc. Prof. Yatsunami provide extremophiles, structures, and functions of enzymes produced by extremophiles. Prof. Wachi provides isolation and identification of soil microbes, and its application, including screening of antibiotics and bioremediation. Prof. Hongoh provides metagenomics and single-cell genomics of uncultured microbes.

Student learning outcomes

By the end of this course, students will be able to:
1. Understand the effect of material and energy circulation on the earth environment
2. Application of microbial functions on bioremediation, agriculture, and mass production
3. Understand the function and application of extremophiles
4. Understand how to analyze the structure and functions of environmental microbial communities


Microbial flora, Wastewater treatment, Microbial corrosion, Pathogenic micoorganism, Extremophiles, Bioremediation, Uncultured microbes, Metagenomics

Competencies that will be developed

Specialist skills Intercultural skills Communication skills Critical thinking skills Practical and/or problem-solving skills

Class flow

In the first half of the class, a summary of the previous lecture is given. In the latter half, the main points of the day’s lecture are discussed in detail. Students are recommended to check the required learning for each class as part of preparation and review.

Course schedule/Required learning

  Course schedule Required learning
Class 1 Culture-independent analysis of uncultured microbes Explain how to analyze the community structure of uncultured microbiota
Class 2 Metagenomics and single-cell genomicsbriefly Explain what are the metagenomics and single-cell genomics
Class 3 Functional analysis of uncultured gut microbes Explain the physiology and ecology of the gut microbiota
Class 4 Circulation of material and energy in surface of the earth Understanding of material and energy balance between reservoirs and effects on the environment
Class 5 Dynamic models of ecosystem Understanding of population dynamics in the ecosystem
Class 6 Wastewater treatment process and microbiologically influenced corrosion Understanding of mechanism and process of wastewater treatment, and microbiologically influenced corrosion
Class 7 Pathogenic microbes and its control Students must be able to recognize the variation pathogenic microbes and their control
Class 8 Introduction; Thermophiles, alkaliphiles, halophiles and their enzymes Explain the thermotolerant, alkalitolerant and halotolerant mechanisms of thermophiles, alkaliphiles, halophiles and their enzymes
Class 9 Organic solvent–tolerant microbes and their application Explain the organic-solvent-tolerant mechanisms of organic-solvent-tolerant
Class 10 Piezophiles and their enzymes Explain the piezophilic mechanism of piezophiles and their enzymes
Class 11 The mechanism of extreme desiccation tolerance in the midge Polypedilum vanderplanki Explain the mechanism of extreme desiccation tolerance in the midge Polypedilum vanderplanki
Class 12 Isolation and identification of soil microbes Understand the methods of isolation and determination of soil microbes
Class 13 Screening of antibiotics (1) Understand isolation of antibiotics and its application
Class 14 Screening of antibiotics (2) Explain the piezotolerant mechanisms of piezophiles and their enzymes
Class 15 Application of microorganisms in industry Understand microbial fermentation


None required.

Reference books, course materials, etc.

Brock Biology of Microorganisms (14th edition)
Handouts will be distributed at the beginning of class when necessary and elaborated on using PowerPoint slides.

Assessment criteria and methods

Reports or exams by each instructor.

Related courses

  • LST.A345 : Microbiology
  • LST.A336 : Genetic Engineering
  • LST.A208 : Molecular Biology I
  • LST.A213 : Molecular Biology II

Prerequisites (i.e., required knowledge, skills, courses, etc.)

No prerequisites are necessary, but enrollment in the related courses is desirable.

Contact information (e-mail and phone)    Notice : Please replace from "[at]" to "@"(half-width character).

Yasunori Tanji (ytanji[at]bio.titech.ac.jp, 5763), Stoshi Nakamura (snakamur[at]bio.titech.ac.jp, 5765), Masaaki Wachi (mwachi[at]bio.titech.ac.jp, 5770), Yuichi Hongoh (yhongo[at]bio.titech.ac.jp, 2865)

Office hours

Students may approach the instructors at the end of class or visit their offices upon securing an appointment through e-mail.

Page Top