BISC209/S11:Assignments

Lab Graded Assignments

Lab Assigned	Lab Due	Assignment description	Point Value (Total 200)
1	2	Turn in at the beginning of Lab 2, a Discussion with References of how the enrichment culture techniques and media you will use will select soil bacteria of the specific groups we seek and differentiate them from other microbes in the community. Start with a topic paragraph that, first, gets your reader interested in the context and significance of your semester long project: Investigating the Diversity and Abundance of Bacteria in a Soil Community. Be sure to read the directions for this assignment found at: Assignment: Enrichment for culturable bacteria of specific groups.	5
2	3	Make or Fill out a Table of the relevant morphologic, physical, and useful metabolic characteristics of expected genera of soil bacterial that you are attempting to find in your habitat. Use the Excel file template, Soil Bacteria Culture Characteristics Spread Sheet S11, found in the Resources section of Sakai. Morphologic or physical characteristics should include: shape (coccus, bacillus, spirillum, vibrio, etc), arrangement (strep, staph, palisades, individual, diplo, etc), colony morphology, motility, Gram stain or other stain-reveling cell wall characteristic, motility, capsule, sporulation, . Metabolic characteristics should include expected reactions on SIMs media tests (H2S and indol production), unusual carbon-source utilization information, any nitrogen-cycling capacity, or other interesting or unusual metabolic capabilities or incapabilities. Other metabolic capabilities to include are: cellulose and starch degradation and phosphate recycling. Include an appropriate enrichment medium and conditions (preferred temperature and oxygen gas requirement or sensitivity) and if the bacteria will grow on a general purpose medium such as NA. Include the following genera: Caulobacter, Asticcacaulis, Hyphomicrobium, Pedomicrobium, Hyphomonas, Thiodendron, Azotobacter, Bacillus, Streptomyces, Nitrobacter, Nitrosomonas, and 3-5 other genera likely to be found in your soil community. You will are likely to find this information in The Prokaryotes or Bergy's Manual. Directions for how to access the Wellesley library's electronic version of these books are in the Resources section of this wiki.	5
3	4	M&M Amplification of 16S rDNA in a soil sample	5
4	5	Introduction section of final paper. Read over the Introduction to the Project page in the wiki to identify the topic and experimental questions addressed. Include the history of the "Great Plate Count Anomaly" (the disparity between culturable and unculturable soil community bacteria). Use and cite references in journal Cell format. A reference that may be helpful is :| Uncultivated Microorganisms by Slava Epstein in Microbiology Monographs Vol. 10, 2009 DOI: 10.1007/978-3-540-85465-4 available as an e-book through Springerlink at the Wellesley College Library or as a pdf file in the Resources section of the lab Sakai site.	15
5	6	M&M Isolation of soil bacteria to pure culture & Identification of bacteria by 16S rRNA gene sequencing from soil genomic DNA	5
6	7	Write a brief summary of the theory behind the following techniques that we used to identify our bacterial species by molecular tools: genomic DNA isolation, polymerase chain amplification of part of the 16s rRNA genes, use of the Zero Blunt® TOPO® PCR Cloning Kit to create a library of unique plasmid vector with our 16S rRNA gene inserts and then select, One Shot® TOP10 Competent E. coli Cells that allowed us to select and separate our 16S rRNA genes for sequencing, and DNA sequencing by the Sanger method.	5
7	8	Study for Lab Practical
8	8	Lab practical	45
8	9	Results section with figures/tables: Identification of Culturable Soil Bacteria by Physical and Metabolic Characteristics	10
9	10	Partial Results section with figure(s)/table(s) Soil Community Diversity Results from 16S rDNA sequencing	10
10	11	Group "Virtual" Poster Presentation Note that the 25pt includes 10 points of Individual Contribution to Group points--assigned by consensus of your project and presentation group	25
11	12	Lab notebook	5
12	12	Final Paper	60
Other		CLEAN-UP points	5

Assignments

Lab 1 Assignment: Assignment: Enrichment for culturable bacteria of specific groups
Lab 2 Assignment: Assignment: Table of Cultured Soil Bacteria Characteristics
Lab 3 Assignment: Assignment3 ????
Lab 4 Assignment: Assignment4 ????
Lab 5 Assignment: Assignment5 ???
Lab 6 Assignment: Assignment6 ???
Lab 7 Assignment: Assignment7 ???
Lab 8 Assignment: Assignment8 ???
Lab 9 Assignment: Assignment9 ???
Lab 10 Assignment: Assignment10 ???
Lab 11 Assignment: Assignment11 ???
Lab 12 Assignment: Assignment12 ???

Links to Labs

Lab 1
Lab 2
Lab 3
Lab 4
Lab 5
Lab 6
Lab 7
Lab 8
Lab 9
Lab 10
Lab11
Lab 12