Community-level microbial diversity in soil
The activity is under development as part of a July 2007 workshop
This introductory laboratory course is designed to teach freshmen and sophomores the process of scientific investigation and basic laboratory and analytic skills. The course challenges students to address the question of how environmental conditions affect biological diversity at
the community, physiological and genetic levels. Students will specifically examine the effects of Ph on soil microbes, in order to understand how genome level impacts are related to ecological processes.
Students use molecular tools to assess microbial diversity under different environmental conditions. This leads to a genomic analysis of metabolic capabilities and can draw on published microarray and proteomic data.
Learning Goals
Attitude:
- Biological research is integrative and incorporates both field and lab, I don't feel affiliated with just one
- Biologists address questions at different levels of biological organization
- Different techniques have different limitations
Performance Skills:
- Experimental design
- Sterile technique
- DNA isolation
- PCR
- Recombinant DNA Technology and Cloning
- Plasmid Isolation
- Interpretation of chromatogram - vector trimming
- BLAST
- Multiple alignment
- Tree building
- Accessing information from a whole genome databases
- How environmental variable affect Biodiversity
- Microbial Ecology
- Biochemistry: DNA and PCR
- Understanding Recombinant DNA
- Sequence Conservation and divergence and Evolution
- Microbial Genome Structure
- Microbial Metabolism
Context for Use
Introductory Microbiology
Environment Physiology
Molecular Biology
Description and Teaching Materials
Set up experimental conditions (in pots and expose to different conditions -- pH, nutrients, etc)
Week 2: Extract DNA from soil (Epicentre Soil Extraction $185 for 50 reactions)
PCR using 16S primers --Archaeal and bacterial primers
Week 3: Clone -- (vector and bacteria and media)
Week 4: Plasmid isolation --- (Qiagen kit)
Sequencing --- sequencing Retrogen
Week 5: 16S analysis to identify clade --- bioinformatic
Each student has a few sequences
Blast searches --- ncbi
Week 6: Multiple Alignment --- clustalW
Phylogeny -- MEGA, Phylip, TreeView
Week 7: Genome-level analysis --- JGI img site?
Teaching Notes and Tips
Assessment
Skill:
binary: is there an output from each skill?
classroom observation
Performance:
paper and pencil
Lab report written in different sections (knowledge)
Attitude:
Likert scale
References and Resources
16 S rDNA primers and the unbiased assessment
of thermophile diversity
G.C. Baker1 and D.A. Cowan
Fierer and Jackson 2006 PNAS The diversity and biogeography of soil microbial communities.
citation for papers about soil pH
