2016 Environmental Microbiology

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Academic unit or major
Graduate major in Life Science and Technology
Tanji Yasunori  Nakamura Satoshi  Wachi Masaaki  Hongoh Yuichi 
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, internal environment of animals. Prof. Tanji provides analytical methods of microbial flora in environments and its practical application. Prof. Nakamura provides extremophiles and 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 the structure of environmental microbes and its analysis


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 Circulation of material and energy in surface of the earth concerned with microbial activities Students must be able to recognize the reservoirs involved material circulation in the earth surface and evaluate effect of material and energy balance between reservoirs on the environment
Class 2 Dynamic models of ecosystem Understanding of population ecology of single and double species
Class 3 Wastewater treatment process and microbiologically influenced corrosion Understanding of mechanism and process of wastewater treatment, and microbiologically influenced corrosion
Class 4 Pathogenic microbes and its control Students must be able to recognize the variation pathogenic microbes and their control
Class 5 Extreme environments and extremophiles Explain extremophiles living under extreme environments
Class 6 Thermophiles and their enzymes Explain the thermotolerant mechanisms of thermophiles and their enzymes
Class 7 Halophiles and their enzymes Explain the halotolerant mechanisms of halophiles and their enzymes
Class 8 Alkaliphiles and their enzymes Explain the alkalitolerant mechanisms of alkaliphiles and their enzymes
Class 9 Isolation and identification of soil microbes Understand the methods of isolation and determination of soil microbes
Class 10 Microorganisms producing medicines: Actinomycetes and fungi Understand antibiotics production by actinomycetes and fungi
Class 11 Microbial bioremediation Understand the bioremediation
Class 12 Application of microorganisms for agriculture Understand what microbial pesticides are
Class 13 Culture-independent analysis of uncultured microbes Understand the uncultured microbes
Class 14 Metagenomics and single-cell genomics Understand the metagenomics
Class 15 Functional analysis of uncultured gut micobes Unserstand the gut micobes


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.

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