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2023　Environmental Microbiology

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Academic unit or major
Graduate major in Life Science and Technology
Instructor(s)
Hongoh Yuichi  Wachi Masaaki  Yatsunami Rie  Mcglynn Shawn  Tanji Yasunori  Matsuura Katsumi 
Class Format
Lecture    (Livestream)
Media-enhanced courses
Day/Period(Room No.)
Tue1-2()  Fri1-2()  
Group
-
Course number
LST.A503
Credits
2
Academic year
2023
Offered quarter
2Q
Syllabus updated
2023/6/26
Lecture notes updated
-
Language used
English
Access Index

Course description and aims

On Earth, diverse environments respectively accommodate unique microbiota, and the microbial communities greatly contribute to the global material and energy 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. Hongoh outlines metagenomics and single-cell genomics of uncultured microbes. Prof. Yatsunami explains the ecology of extremophiles and the structures and functions of their enzymes. Prof. McGlynn explains diverse energy conserving strategies of environmental microbes and outlines arguments on the Last universal common ancestor of extant organisms. Prof. Matsuura introduces thermophilic microbiota and outlines the material and energy cycle. Prof Tanji outlines the bacteriophage communities in environments.

Student learning outcomes

By the end of this course, students will understand and be able to explain the outline of:
1. The phylogenetic diversity, physiology, and ecology of microbes in diverse environments
2. The functions and application of extremophiles
3. The material and energy cycle by environmental microbial communities

Keywords

extremophiles, applied microbiology, uncultured microbes, metagenomics, energy conservation, origins of life, bacteriophage

Competencies that will be developed

✔ 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/Required learning

  Course schedule Required learning
Class 1 "Species" in bacteria and microbial community structure analysis Understand a hypothetical definition of "species" in bacteria and how to analyze microbial community structures
Class 2 FISH and metagenomics Understand the outlines of fluorescence in situ hybridization and metagenomics
Class 3 Single-cell genomics and functional genome analysis Understand the outline of single-cell genomics and functional genomics
Class 4 Halophiles and their enzymes Understand the functional mechanisms of halophiles and their enzymes
Class 5 Desiccation tolerant organisms and their desiccation tolerance mechanisms Understand the functional mechanisms of desiccation tolerant organisms and their desiccation tolerance mechanisms
Class 6 Characteristics of bacteriophage and its use for controlling pathogenic bacteria Understand the characteristics of phages and can explain an example of its application
Class 7 Organic solvent–tolerant microbes and their enzymes Understand the functional mechanisms of organic-solvent-tolerant microbes and their enzymes
Class 8 Application of extremophiles and their enzyme in industry Understand the outline of the application of extremophiles and their enzyme in industry
Class 9 Thermophilic microbial communities and early life on earth Understand thermophilic microbial communities and their metabolism, and can discuss their possible relationship to the early evolution of life on earth
Class 10 Electron and material cycling and energy in life Understand and can discuss the electron cycling through carbon, oxygen, nitrogen, and sulfur in microbial communities and ecosystems.
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

Out-of-Class Study Time (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.

Assessment criteria and methods

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

No prerequisites are necessary.

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

Yuichi Hongoh (yhongo[at]bio.titech.ac.jp), Rie Yatsunami (yatsunami.r.aa[at]m.titech.ac.jp), Sahwn McGlynn (mcglynn[at]elsi.jp), Katsumi Matsuura (katsumimatsuura[at]gmail.com), Yasunori Tanji (ytanji1110[at]gmail.com)

Office hours

Students may approach the instructors through e-mail.

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