Course Coordinator: 
Filip Husnik
Microbial Evolution and Cell Biology
The students should have a background in biology and biochemistry and be interested in learning more about single-celled organisms. Apart from students with background in evolutionary biology, molecular cell biology, ecology, marine biology, microbiology, biochemistry, developmental biology, etc., the course can be taken also by out-of-field students who would like to get a glimpse of evolution of life and microbial diversity.
Most of the genetic, cellular, and biochemical diversity of life rests within single-celled organisms, prokaryotes (bacteria and archaea) and microbial eukaryotes (protists). Bacteria and archaea not only account for over 3.5 billion years of evolution, but also played a crucial role in the origin of the first eukaryotic-like (protist) cells approximately two billion years ago. However, most of our knowledge about evolution and cell biology (and how we frame it) comes from a small subset of eukaryotic diversity -- multicellular animals and plants. During the course, we will take a broad view of the immense diversity of single-celled organisms (both prokaryotes and eukaryotes), focusing on their evolution, ecology, genetics, biochemistry, and cell biology. We will explore their evolutionary history and highlight major cellular innovations that occurred in single-celled organisms during the evolution of life.
The successful student will be able to describe differences in evolution and cell biology of single-celled organisms as opposed to multicellular organisms. The course is designed partly to fix biases that students often acquire from working with ‘model organisms’ that are mostly multicellular (animals and plants) and partly to showcase the immense diversity of microorganisms. It is thus not a traditional microbiology course, but it rather focuses on selected broadly interesting aspects of microbial evolution and cell biology such as major evolutionary transitions and cellular innovations. The students should gain knowledge about the evolutionary ‘baggage’ from our single-celled history that constrains the functioning of any modern cell, and be able to apply the knowledge in their own projects.
At the end of the course, a successful student will be able to: SLO #1: Analyze and critically evaluate a scientific paper about single-celled organisms, explain its main results to its peers, and reply to questions. Deliverable: student presentation on a selected evolutionary cell biology article Assessment criteria: understanding the main take home messages of the paper (30%), clear presentation (20%), critically evaluating potential issues in the methods-results-discussion sections (20%), and responding to questions from the audience (30%) SLO #2: Design a scientific project (using literature review) that would target a fundamental question concerning single-celled organisms. Deliverable: written student project (3 pages, incl. 1-2 small figures) in the form of a small grant application (introduction, hypothesis, key question, 2-3 main goals, methods, broad implications) Assessment criteria: the grant application follows requirements (40%), literature review (20%), main goals target the key question (20%), methods and feasibility (20%) SLO #3: Analyze own results from laboratory work on microorganisms and contrast the results with data from other students. Deliverable: written protocols from laboratory exercises, including figures and discussion about negative/poor results Assessment criteria: main results clearly highlighted (50%), figures/drawings/plots represent main findings and include correct legends (25%), discussion about potential issues and troubleshooting (25%) SLO #4: Describe the main differences in evolution and cell biology of single-celled organisms as opposed to multicellular organisms. Deliverable: final exam Assessment criteria: 10 simple questions requiring a short answer (70%), 2 questions requiring a longer answer and/or a drawing (30%)
Course Content: 

Theoretical part
1. What are cells and how they came to be the way they are (Evolutionary Cell Biology)
2. Origin of life, RNA world, genetic codes, and first ‘prokaryotic’ cells (LUCA)
3. Introduction to population genetics and phylogenetics (selection, mutation, drift, Muller’s ratchet, constructive neutral evolution, interpreting phylogenetic trees)
4. Evolution and diversity of bacteria and archaea
5. Asgard archaea, mitochondria, and the origin of the eukaryotic cell (LECA)
6. Mitochondrial evolution (ATP, hydrogenosomes/mitosomes, etc.)
7. Photosynthesis and diversification of plastids
8. Tree of life and eukaryotic supergroups (SAR, Excavata, Amoebozoa, Opisthokonta, Archaeplastida, and orphan clades)
9. Chemosynthesis and life in deep sea and hydrothermal vents
10. Prokaryotic vs. eukaryotic metabolism and lifestyles (phototrophy, heterotrophy, mixotrophy)
11. Major eukaryotic innovations (endomembrane system, nucleus, phagocytosis, cytoskeleton)
12. Microbial genomics, sex, and horizontal gene transfer
13. Evolution of multicellularity

Student Presentations
15 min presentation by every student about a selected paper (+10 min discussion). Students will be provided with a list of possible papers to present, including options for out-of-field students.

Laboratory exercises
Cultivation-dependent and cultivation-independent methods for studying microorganisms
a) Sampling microorganisms (marine, fresh-water, soil, animal-associated, etc.)
b) Culturing single-celled eukaryotes (phototrophs and predators)
c) Preparing a Winogradsky column with prokaryotes
d) Light and fluorescent microscopy (microorganisms sampled during field work and/or cultured)
e) Genome-resolved metagenomics: Nanopore/Illumina sequencing and real-time bioinformatics analysis of microbial diversity

Course Type: 
30% participation and discussion, 20% presentation, 25% mid-term project, 25% final exam
Reference Book: 
One plus one equals one; John Archibald, Oxford University Press 2014
The tangled tree: A radical new history of life; David Quammen, Simon & Schuster 2018
I contain multitudes: The microbes within us and a grander view of life; Ed Yong, Ecco Press 2016
Prior Knowledge: 

Basic understanding of evolutionary and cell biology at the undergraduate level is assumed. The following courses offered at OIST are recommended to students who first want to review their knowledge: Molecular Biology of the Cell (B27) and Evolution (B43) [or Molecular Evolution (B23)].