2025 (Current Year) Faculty Courses School of Life Science and Technology Department of Life Science and Technology Graduate major in Life Science and Technology
Environmental Microbiology
- Academic unit or major
- Graduate major in Life Science and Technology
- Instructor(s)
- Yuichi Hongoh / Masaaki Wachi / Rie Yatsunami / Shawn Mcglynn
- Class Format
- Lecture (Livestream)
- Media-enhanced courses
- -
- Day of week/Period
(Classrooms) - 1-2 Tue / 1-2 Fri
- Class
- -
- Course Code
- LST.A503
- Number of credits
- 200
- Course offered
- 2025
- Offered quarter
- 2Q
- Syllabus updated
- Mar 19, 2025
- Language
- English
Syllabus
Course overview and goals
On Earth, diverse environments respectively accommodate unique microbiota, and the microbial communities greatly contribute to the global material cycle. In this course, the physiology, ecology, and phylogenetic diversity of environmental microbes, as well as how to investigate them, are outlined, and the applications of environmental microbes are also explained. Prof. Wachi explains how to isolate and cultivate soil microbes and their application in industry. Prof. Yatsunami explains the ecology of extremophiles and the structures and functions of their enzymes. Prof. Hongoh outlines metagenomics and single-cell genomics of uncultured microbes. Prof. McGlynn explains diverse energy conserving strategies of environmental microbes and outlines arguments on the Last universal common ancestor of extant organisms.
Course description and aims
By the end of this course, students will understand and be able to explain the outline of:
1. The functions and application of soil microbes and extremophiles.
2. The phylogenetic diversity, physiology, and ecology of microbes in diverse environments.
3. The material and energy cycle by environmental microbial communities.
Keywords
extremophiles, soil microbes, applied microbiology, uncultured microbes, metagenomics, energy conservation, origins of life
Competencies
- Specialist skills
- Intercultural skills
- Communication skills
- Critical thinking skills
- Practical and/or problem-solving skills
Class flow
The lectures are given in English by using PowerPoint slides (ZOOM), which will be uploaded prior to each lecture.
Course schedule/Objectives
| Course schedule | Objectives | |
|---|---|---|
| Class 1 | Isolation (cultivation) and identification of soil microbes |
Understand how to isolate and identify soil microbes |
| Class 2 | Screening of antibiotics from environmental microbes |
Understand how to isolate microbes producing antibiotics |
| Class 3 | Application of microorganisms in industry |
Understand the outline of applied microbiology, especially microbial fermentation |
| Class 4 | Halophiles and their enzymes |
Understand the functional mechanisms of halophiles and their enzymes |
| Class 5 | Piezophiles and their enzymes |
Understand the functional mechanism of piezophiles and their enzymes |
| Class 6 | Organic solvent–tolerant microbes and their enzymes |
Understand the functional mechanisms of organic-solvent-tolerant microbes and their enzymes |
| Class 7 | Application of extremophiles and their enzyme in industry |
Understand the outline of the application of extremophiles and their enzyme in industry |
| Class 8 | "Species" in bacteria and microbial community structure analysis |
Understand a hypothetical definition of "species" in bacteria and how to analyze microbial community structures |
| Class 9 | FISH and metagenomics |
Understand the outlines of fluorescence in situ hybridization and metagenomics |
| Class 10 | Single-cell genomics and functional genome analysis |
Understand the outline of single-cell genomics and functional genomics |
| Class 11 | Phenotypic heterogeneity |
Understand that isogenic populations are not homogeneous in activity, and be able to suggest some possible reasons why |
| Class 12 | Energy conserving strategies |
Understand the diversity of conservation strategies used in biology, and be able to suggest some that may yet be discovered in the future |
| Class 13 | What is the low energy limit for life? |
From the previous lecture, construct theoretical arguments of what might be the low energy limit of life on Earth, and compare this with observation |
| Class 14 | How old is biology, and what do we know about the earliest life? |
Understand uncertainties with the Last universal common ancestor (LUCA); its potential phenotype and its timing |
Study advice (preparation and review)
To enhance effective learning, students are encouraged to spend approximately 100 minutes preparing for class and another 100 minutes reviewing class content afterwards (including assignments) for each class.
They should do so by referring to textbooks and other course material.
Textbook(s)
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.
Evaluation methods and criteria
Assignments, online exams or others by each instructor.
If your reports are found to contain materials plagiarized from literature, including the Internet, or reports by other students, your grade will be marked zero, and the University may take further disciplinary action.
Related courses
- LST.A345 ： Microbiology
- LST.A347 ： Evolutionary Biology
Prerequisites
No prerequisites are necessary.
Contact information (e-mail and phone) Notice : Please replace from ”[at]” to ”@”(half-width character).
Masaaki Wachi (wachi.m.4123[at]m.isct.ac.jp), Rie Yatsunami (yatsunami.r.dfe1[at]m.isct.ac.jp), Yuichi Hongoh (yhongo[at]life.isct.ac.jp), Sahwn McGlynn (mcglynn[at]elsi.jp)
Office hours
Students may approach the instructors through e-mail.