Microbial Ecology Program
The Microbial Ecology Program (MEP) uses sequencing-based technologies to understand microbial communities via a combination of computational and experimental methods. To date, molecular microbial ecology has relied heavily on small-subunit ribosomal RNA sequences for culture-independent characterization of microbial communities. We continue this proud tradition in the group, and have established a high-throughput pipeline for analysis of 16S rRNA PCR clone libraries and use fluorescence in-situ hybridization (FISH) to visualize phylogenetic groups under the microscope. A natural progression of 16S rRNA-based culture-independent methods is to clone and sequence genomic DNA extracted directly from environmental samples (metagenomics) in order to obtain an overview of community function and population dynamics. Since environmental shotgun sequencing is in its infancy, we are exploring ways to analyze and visualize metagenomic data together with the Genome Biology Program. In particular, methods are being developed to
- accurately bin (classify) metagenomic fragments into their corresponding species populations
- reconstruct metabolic pathways by comparative analysis to reference isolate genomes
- model ecosystem dynamics using metabolic reconstructions of metagenomic data
- visualize point mutations and genomic rearrangements within population data
There are thousands of microbial communities that would be interesting to study via metagenomics (and hopefully will be). However, we have chosen to initially focus on communities that are relatively simple and can be perturbed under controlled conditions. These include both environmental and clinical ecosystems, including
- Enhanced Biological Phosphorus Removal (EBPR) sludge (CSP project). Collaborators: Trina McMahon, Linda Blackall, Thomas Huber
- Ventilator-associated pneumonia. Collaborators: Jim Bristow, Jeanine Wiener-Kronish
- Termite hindguts. Collaborators: Jared Leadbetter, Eric Mathur
- Terephthalate-degrading bioreactor. Collaborators: Wen-Tso Liu, Joe Zhou
- Guerrero Negro hypersaline microbial mat. Collaborator: Norman Pace
Members
Microbial Ecology Group: (left to right) Falk Warnecke, Martin Allgaier, Anna Engelbrektson, Phil Hugenholtz, Suzan Yilmaz, Victor Kunin.
Links
Time Magazine (June 13, 2005): Mother Nature's DNA
East Bay Express (September 7, 2005): Bug Juice
Der Spiegel (September 12, 2005): Schatztruhe der Biochemie
Living on Earth (February 23, 2007): Can Termites Save the World?
San Francisco Chronicle (March 6, 2007): Unlocking clean, cheap energy
Reuters UK (November 21, 2007): Termite guts may hold key to better biofuels
GenomeWeb Daily News (November 21, 2007): Metagenomic Study of Termite's 'Bioreactor' Hindgut Shows Promise for Biofuel Apps
Chicago Tribune (May 19, 2008): Termites hold clue to replace corn in ethanol
