A Town on Fire! Metagenomic Analysis of Bacterial Communities in Soils Overlying the Centralia,...

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?