a town on fire! metagenomic analysis of bacterial communities in soils overlying the centralia,...
TRANSCRIPT
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A Town on Fire!
Metagenomic Analysis of Bacterial Communities in Soils Overlying the Centralia, Pennsylvania Coal Mine Fire
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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
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Overview
Historical Perspective
What Do We Know About the Environment?
What Do We Know About the Microbes?
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Where is Centralia?
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A Short History of the Centralia Mine Fire
May, 1962: The Fire Begins
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A Short History of the Centralia Mine Fire, Continued…
The Fire Continues To Burn…….
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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
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Centralia, Then and Now
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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”
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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
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What Do We Know About the Microbes?
Prediction, Exploration, Experimentation … and Serendipity
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Predictions
Resident Microbes Should Include: Thermophiles- some similar to those in other
geothermal environments, some novel Nitrogen-Cycling Bacteria Sulfur-Cycling Bacteria
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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
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Metagenomic Analysis of Bacterial 16S rRNA Genes
What are the 16S rRNA genes?
Why use them?
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Pyrosequencing
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Questions?