a town on fire! metagenomic analysis of bacterial communities in soils overlying the centralia,...
TRANSCRIPT
A Town on Fire!
Metagenomic Analysis of Bacterial Communities in Soils Overlying the Centralia, Pennsylvania Coal Mine Fire
Case Study Overview
Class 1: Introduction to Centralia and Metagenomic Analysis
Activity #1: Introduction to Linux and QIIME (If you have a Mac, you can download the QIIME program..it takes around ½ hour, so do not try to do it during class). See me for help.
Activity #2: Who lives there?? Proposing and testing hypotheses regarding Centralia’s resident microbes.
Activity #3: Statistical and Phylogenetic Analysis, Part 1
Activity #5: Statistical and Phylogenetic Analysis, Part 2
Final Presentations
Overview
Historical Perspective
What Do We Know About the Environment?
What Do We Know About the Microbes?
Where is Centralia?
A Short History of the Centralia Mine Fire
May, 1962: The Fire Begins
A Short History of the Centralia Mine Fire, Continued…
The Fire Continues To Burn…….
A Short History of the Centralia Mine Fire, Continued…
1962-1978: Unsuccessful attempts to put out fire
1979-1983 OSM estimates $663 million needed to put out fire
DEP determines fumes and subsidence unsafe
1983 Route 61 collapses
1984 Congress provides $42 million to relocate residents
Centralia, Then and Now
What Do We Know About the Environment?
Earth and Environmental Sciences: Composition and Structure
of the Anthracite Coal Seams
Predict and Measure the Fire’s Spread
Nature of “Anthracite Smokers”
What Do We Know About the Environment?
Chemistry Temperatures
range to over 300°C (60°C Common)
High levels of SOx, NOx, As, CO, Al2(SO4)3, NH4Al(SO4)2, and NH4Cl compounds
What Do We Know About the Microbes?
Prediction, Exploration, Experimentation … and Serendipity
Predictions
Resident Microbes Should Include: Thermophiles- some similar to those in other
geothermal environments, some novel Nitrogen-Cycling Bacteria Sulfur-Cycling Bacteria
Experimental Approach Collect Soil From Boreholes Near
Active Vents (37°C, 52°C, 65°C)
Culture-Independent Methods Metagenomic Analysis of 16S
rRNA genes, Functional Metagenomics, Transcriptomics
Culture-Dependent Methods Physiological Assays Microscopy Staining Genome Sequencing
Metagenomic Analysis of Bacterial 16S rRNA Genes
What are the 16S rRNA genes?
Why use them?
Pyrosequencing
Questions?