Advanced Biogeoscience Teaching Syllabus
Course Title: Advanced Biogeoscience Course Type: Elective / Special Topics Course Recommended Credits: 3 Credits Prerequisites: General Biology, General Geology, Basic Chemistry

I. Course Objectives
This course aims to explore the interactions between microorganisms and geochemical processes. It covers the roles of microorganisms in the lithosphere, hydrosphere, and biosphere, and delves into their critical functions in elemental cycles, mineral formation and degradation, and the generation of fossil fuels. Students will learn the application of traditional and molecular biological methods in geomicrobiological research and understand how microorganisms influence the evolution and changes of the Earth system.

II. Course Outline and Schedule
Week 1: Course Introduction and Overview
Explanation of course objectives and assessment methods
Scope and importance of Biogeoscience
Overview of microorganism-geological environment interactions

Weeks 2-3: Introduction to Geomicrobiological Processes (Chapter 6)
Classification and function of microbial physiological groups
Energy and carbon source mechanisms in catabolism and anabolism
Aerobic/anaerobic respiration, fermentation, and chemolithoautotrophy
Metabolic diversity of phototrophic microorganisms and mixotrophs

Week 4: Research Methods in Geomicrobiology (Chapter 7)
Non-molecular methods: in situ observation, cultivation and isolation, sample storage
Laboratory reconstruction and quantitative study of surface growth
Distinguishing between enzymatic and non-enzymatic reactions

Week 5: Application of Molecular Methods in Microbial Identification and Functional Analysis (Chapter 8)
Culture-independent techniques (e.g., 16S rRNA sequencing)
Single-cell isotope and metabolite techniques
Genomics and analysis of metabolic gene expression

Weeks 6-7: Microorganisms and Carbonate Geochemistry (Chapter 9)
Mechanisms of carbonate formation and degradation
Role of cyanobacteria and other microorganisms in carbonate precipitation
Microbial formation of various metal carbonates (e.g., Mn, Fe, Sr)
Relationship between carbonates and the carbon cycle

Weeks 8-9: Geomicrobiology of Iron (Chapter 16)
Iron redox reactions and energy metabolism
Metabolic strategies of acidophilic/iron-oxidizing bacteria, archaea, and mesophiles
Microbially induced iron precipitation and mobilization
Iron cycle and biogenic ore formation

Weeks 10-11: Geomicrobiology of Manganese (Chapter 17)
Manganese-oxidizing and -reducing microorganisms
Enzymatic and non-enzymatic reaction mechanisms
Manganese deposition and mobilization in soils, rocks, freshwater, and marine environments
Role of microorganisms in the manganese cycle

Weeks 12-13: Geomicrobiology of Sulfur (Chapter 19)
Sulfur redox reactions and microbial types
Sulfate reduction and elemental sulfur oxidation
Sulfur isotope fractionation and biogenic deposition
Sulfur cycle and environmental applications (e.g., acid mine drainage)

Weeks 14-15: Geomicrobiology of Fossil Fuels (Chapter 22)
Methanogenesis and methane oxidation (aerobic/anaerobic)
Microbial formation mechanisms of peat, coal, and petroleum
Applications of microorganisms in petroleum degradation and desulfurization
Microbial prospecting and enhanced oil recovery techniques

Week 16: Course Summary and Project Presentations
Review of key course concepts
Student project presentations and discussions
Future research directions and application prospects

III. Teaching Methods
Lectures
Literature review and discussion
Introduction to laboratory techniques
Independent research projects and presentations

IV. Assessment Methods
Class Participation and Discussion: 20%
Mid-term Project Report: 30%
Final Research Project and Oral Presentation: 30%
Literature Review Essay or Short Paper: 20%

V. Recommended References
Course materials derived from chapters of Advanced Biogeoscience (Chapters 6, 7, 8, 9, 16, 17, 19, 22)
Supplementary literature will be provided during the course