A Town on Fire Metagenomic Analysis of Bacterial
A Town on Fire! Metagenomic Analysis of Bacterial Communities in Soils Overlying the Centralia, Pennsylvania Coal Mine Fire
Ü Class 1: Introduction to Centralia and Metagenomic Analysis Ü Activity #1: Introduction to Linux and QIIME (If you have a laptop, go ahead and bring it. Ü Activity #2: Who lives there? ? Proposing and testing hypotheses regarding Centralia’s resident microbes. Ü Activity #3: Statistical and Phylogenetic Analysis Ü Final Presentations and Papers
Overview Ü Historical Perspective Ü What Do We Know About the Environment? Ü What Do We Know About the Microbes?
Where is Centralia?
A Short History of the Centralia Mine Fire Ü May, 1962: The Fire Begins
A Short History of the Centralia Mine Fire, Continued… Ü The Fire Continues To Burn…….
A Short History of the Centralia Mine Fire, Continued… Ü 1962 -1978: Unsuccessful attempts to put out fire Ü 1979 -1983 OSM estimates $663 million needed to put out fire Ü DEP determines fumes and subsidence unsafe Ü 1983 Route 61 collapses Ü 1984 Congress provides $42 million to relocate residents
Centralia, Then and Now
What Do We Know About the Environment? Ü Earth and Environmental Sciences: Ü Composition and Structure of the Anthracite Coal Seams Ü Predict and Measure the Fire’s Spread Ü Nature of “Anthracite Smokers”
What Do We Know About the Environment? Ü Chemistry Ü Temperatures range to over 300°C (60°C Common) Ü High levels of SOx, NOx, As, CO, Al 2(SO 4)3, NH 4 Al(SO 4)2, and NH 4 Cl compounds
What Do We Know About the Microbes? Ü Prediction, Exploration, Experimentation … and Serendipity
Predictions Ü Resident Microbes Should Include: Ü Thermophiles- some similar to those in other geothermal environments, some novel Ü Nitrogen-Cycling Bacteria Ü Sulfur-Cycling Bacteria
Experimental Approach Ü Collect Soil From Boreholes Near Active Vents (37°C, 52°C, 65°C) Ü Culture-Independent Methods Ü Metagenomic Analysis of 16 S r. RNA genes, Functional Metagenomics, Transcriptomics Ü Culture-Dependent Methods Ü Physiological Assays Ü Microscopy Ü Staining Ü Genome Sequencing
Metagenomic Analysis of Bacterial 16 S r. RNA Genes Ü What are the 16 S r. RNA genes? Ü Why use them?
Pyrosequencing
Questions?
- Slides: 16