Marine Microbial Genomics BISC 599
Spring 2009
Instructors: John Heidelberg
Ph: 310-510-4064
e-mail: jheidelb@usc.edu
Eric Webb
Ph: 213-740-7954
e-mail: eawebb@usc.edu
Location: UPC campus; TBA
Units: 2
The field of marine microbial genomics has changed our perspective on how fundamental
processes in the ocean work (e.g. light and energy in the euphotic zone). The goal of this
course is to give you the required background, perspective, and methodology to
implement genomic techniques into your own research. This class will focus on the
major, recent findings in marine and environmental genomics and strive to fill in the
background on how this research is actually done. Additionally there will be tutorials on
the freely available tools on the internet (e.g. NCBI, IMG, etc) that can be used to mine
existing genomic data, as well as a short course on programming in PERL.
Guest Lectures: William Nelson, Karla Heidelberg, Eric Allen
Grading: The scoring will come from student presentation (50%) of key papers as well
as class participation. Additionally students will be graded on a short PERL program of
their own design (50%).
Statement for Students with Disabilities
Any student requesting academic accommodations based on a disability is required to
register with Disability Services and Programs (DSP) each semester. A letter of
verification for approved accommodations can be obtained from DSP. Please be sure the
letter is delivered to me (or to TA) as early in the semester as possible. DSP is located in
STU 301 and is open 8:30 a.m.–5:00 p.m., Monday through Friday. The phone number
for DSP is (213) 740-0776.
Statement on Academic Integrity
USC seeks to maintain an optimal learning environment. General principles of academic
honesty include the concept of respect for the intellectual property of others, the
expectation that individual work will be submitted unless otherwise allowed by an
instructor, and the obligations both to protect one’s own academic work from misuse by
others as well as to avoid using another’s work as one’s own. All students are expected to
understand and abide by these principles. Scampus, the Student Guidebook, contains the
Student Conduct Code in Section 11.00, while the recommended sanctions are located in
Appendix A: http://www.usc.edu/dept/publications/SCAMPUS/gov/. Students will be
referred to the Office of Student Judicial Affairs and Community Standards for further
review, should there be any suspicion of academic dishonesty. The Review process can
be found at: http://www.usc.edu/student-affairs/SJACS/.
Lecture #1: Introduction to the course (Webb)/ History of genomics (Heidelberg)
Readings: Historical Introduction and Overview of Bioinformatics. Chapter 1,
Bioinformatics. Sequence and genome analysis.
Lecture #2: Pure culture genomics / High throughput culturing. Sequencing, assembly,
annotation. (Heidelberg)
Paper - Whole-genome random sequencing and assembly of Haemophilus
influenzae Rd
The metagenomics RAST server - a public resource for the automatic
phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 2008,
9:386
Discussion:
Lecture #3: Ecological Context. Standing stock vs bloomers (Webb)
Paper: Giovannoni, S. & Stingl, U. (2005). Molecular diversity and ecology of
microbial plankton. Nature, 437(7057), 343-348.
Discussion:
Giovannoni, S. J., Tripp, H. J., Givan, S., Podar, M., Vergin, K. L., Baptista, D. et
al. (2005). Genome streamlining in a cosmopolitan oceanic bacterium. Science,
309(5738), 1242-1245.
Moran, M. A., Buchan, A., Gonzalez, J. M., Heidelberg, J. F., Whitman, W. B.,
Kiene, R. P. et al. (2004). Genome sequence of Silicibacter pomeroyi reveals
adaptations to the marine environment. Nature, 432(7019), 910-913.
Lecture #4: Single Cell Genomics (Heidelberg).
Papers: Genomic DNA Amplification from a Single Bacterium. Arumugham
Raghunathan, Harley R. Ferguson Jr., Carole J. Bornarth, Wanmin Song, Mark
Driscoll, and Roger S. Lasken
Applied and Environmental Microbiology,
June 2005, p. 3342-3347, Vol. 71
Mußmann M, Hu FZ, Richter M, de Beer D, Preisler A, et al. (2007) Insights into
the Genome of Large Sulfur Bacteria Revealed by Analysis of Single Filaments.
PLoS Biol 5(9): e230 doi:10.1371/journal.pbio.0050230
Discussion:
Lecture #5: Comparative genomics methods. ACT, Mummer, glass slide comparative
hybridization (not sure)
Paper: Complete genome sequence and comparative genomic analysis of an
emerging human pathogen, serotype V Streptococcus agalactiae. Tettelin et al.
PNAS September 17, 2002 vol. 99 no. 19 12391-12396
Population level functional diversity in a microbial community revealed by
comparative genomic and metagenomic analyses. The ISME Journal (2007) 1,
703–713
Discussion:
Lecture #6: IMG, IMG-ER workshop (Webb)
Markowitz, V. M., Korzeniewski, F., Palaniappan, K., Szeto, E., Werner, G.,
Padki, A. et al. (2006). The integrated microbial genomes (IMG) system. Nucleic
Acids Research, 34(Database Issue), D344.
Lecture #7: Ecological context. What did the cyanobacterial genomes show us” (Webb)
Paper: Rocap, G., Larimer, F. W., Lamerdin, J., Malfatti, S., Chain, P., Ahlgren,
N. A. et al. (2003). Genome divergence in two Prochlorococcus ecotypes reflects
oceanic niche differentiation. Nature, 424(6952), 1042-1047.
Palenik, B., Brahamsha, B., Larimer, F. W., Land, M., Hauser, L., Chain, P. et al.
(2003). The genome of a motile marine Synechococcus. Nature, 424(6952), 10371042.
Discussion:
Zehr, J. P., Bench, S. R., Carter, B. J., Hewson, I., Niazi, F., Shi, T. et al. (2008).
Globally Distributed Uncultivated Oceanic N2-Fixing Cyanobacteria Lack
Oxygenic Photosystem II. Science, 322(5904), 1110.
Lecture #8: YACs, BACs, and Fosmids. Methods – building, screening, functional
screens (Heidelberg)
Paper: Uncultured soil bacteria are a reservoir of new antibiotic resistance genes.
Christian S. Riesenfeld , Robert M. Goodman, and Jo Handelsman.
Environmental Microbiology. Volume 6, Issue 9, Pages 981-989
Isolation of Antibiotics Turbomycin A and B from a Metagenomic Library of Soil
Microbial DNA. oreen E. Gillespie,1 Sean F. Brady,2 Alan D. Bettermann,1
Nicholas P. Cianciotto,3 Mark R. Liles,1 Michelle R. Rondon,1,{dagger} Jon
Clardy,2 Robert M. Goodman,1 and Jo Handelsman. Applied and Environmental
Microbiology, September 2002, p. 4301-4306, Vol. 68
Discussion:
Lecture #9: Ecological perspective. How microbes interact with lights AAP and
rhodopsin (Webb)
Paper: Beja, O., Aravind, L., Koonin, E. V., Suzuki, M. T., Hadd, A., Nguyen, L.
P. et al. (2000). Bacterial rhodopsin: evidence for a new type of phototrophy in
the sea. Science, 289(5486), 1902-1906.
Beja, O., Suzuki, M. T., Heidelberg, J. F., Nelson, W. C., Preston, C. M.,
Hamada, T. et al. (2002). Unsuspected diversity among marine aerobic
anoxygenic phototrophs. Nature, 415(6872), 630-633.
Discussion:
Gómez-Consarnau, L., González, J. M., Coll-Lladó, M., Gourdon, P., Pascher, T.,
Neutze, R. et al. (2007). Light stimulates growth of proteorhodopsin-containing
marine Flavobacteria. Nature, 445(7124), 210-213.
Lecture #10 – Guest lecture. Karla and the differences with Euks
Lecture #11 and #12: PERL - short course on programming and Existing genome
services and interpretation. led by Dr. William Nelson
Lecture #13: Iron Mountain – Guest lecture Eric Allen
Paper:
Discussion:
Lecture 14 and #15 : Metagenomics – Long reads vs. Short reads and deep sequencing
vs low pass sequencing. Sargasso vs. Forest and Sargasso vs. GOS (Heidelberg and/or
Webb)
Paper:
Discussion: