SIO 123, Environmental Systems Biology, Syllabus Fall 2014


SIO 123, Microbial Environmental Systems Biology

Environmental systems biology is the study of the genomic basis for patterns of microbial diversity and adaptation in relation to habitat. This course introduces the microbial genome as a unit of study and surveys introductory principles in microbial genomics and bioinformatics that underlay a range of contemporary research in diverse marine habitats, such as the deep sea and polar regions, as well as studies of biomedical importance including the human microbiome. Three hours of lecture and one hour of recitation. Prerequisites: BILD 1 or 2, or ESYS 101, or equivalent coursework in cell biology, biochemistry, or genetics, or consent of instructor.


1) 25% class participation

2) 15% final exam

3) 30% 3 (2-3 page papers) (pick any 3 topics below)

4) 30% 1 (8-12 page paper)


Key Dates

Short Papers Due 1) Friday October 24 2) Friday November 14 3) Friday December 12

8-12 page paper due, Friday December 5 (proposed topic due Friday October 31)

Friday Presentations and Short Papers (Short papers can be on 3 of any of the 9 Friday topics and associated papers). Complete course reading list (PDFs) are organized by topic on TED.

  1. Biogeography Distribution Ecology
  2. Sar11 (or heterotrophic bacterioplankton)
  3. Prochlorococcos (or photosynthetic microbes)
  4. Metagenomics
  5. Single Cell Genomics
  6. Metatranscriptomics
  7. Proteomics
  8. Nitrogen Cycle Related and Metabolomics
  9. Phytoplankton Bacteria Networks Linkages

Week 1 (Monday October 6)

M:          Darwin to Woese (rRNA diversity and evolution)

W:          Woese to Venter (and a brief introduction to Microbiology)

F:            Reading/Presentation: Biogeography_Distribution_Ecology

Week 2 (Monday October 13)

M:          Bacterioplankton (heterotrophs)

W:          Photosynthetic Microbes

F:            Reading/Presentation: Sar11 (heterotrophic bacterioplankton)

Week 3 (Monday October 20)

M:          DNA Sequencing

W:          Metagenomics (prokaryotes)

F:            Reading/Presentation: Prochlorococcus (microalgae) ***short paper due***

Week 4 (Monday October 27)

M:          Genomics/Diversity/Metagenomics (Eukaryotes)

W:          Metagenomics (viruses)

F:            Reading Presentation: Metagenomics

Week 5 (Monday November 3)

M:          Single Cell Genomics (prokaryotic cells)

W:          Single Cell Genomics (eukaryotic cells)

F:            Reading/Presentation: Single Cell Genomics

Week 6 (Monday November 10)

M:          Gene Expression and Regulation

W:          Gene Expression in the Environment

F:            Reading/Presentation: Metatranscriptomics ***short paper due***

Week 7 (Monday November 17)

M:          Proteomics

W:          Functional Genomics

F:            Reading /Presentation: Proteomics

Week 8 (Monday November 24)

M:          Metabolomics, Genomics and Nitrogen Biogeochemistry

W:          Genomics and Nitrogen Biogeochemistry

F:            Reading/Presentation: Nitrogen Cycle Related and Metabolomics

Week 9 (Monday December 1)

M:          Networks and Linkages

W:          Networks and Linkages

F:            Reading/Presentation: Phytoplankton Bacteria Networks and Linkages *8-12 page paper due*

Week 10 (Monday December 9)

M:          Environmental Genomics of Southern Ocean Microbes

W:          Deep Sea/Hydrothermal Vent Environmental Genomics

F:            The Secret Life of Diatoms ***short paper due***