Metagenomics of Acid Mine Drainage at Iron Mountain California, Expanding Our View from Individual Genes and Cultures to Entire Communities
Brett J. Baker and Jillian F. Banfield
from: Acidophiles: Life in Extremely Acidic Environments (Edited by: Raquel Quatrini and D. Barrie Johnson). Caister Academic Press, U.K. (2016) Pages: 221-232.
The microbial world is vast and complex, which makes addressing fundamental questions related to ecology and evolution challenging. Until recently, microbial ecology relied on cultivation-based methods, which can only target a tiny faction of the diversity of microorganisms present in the environment. Therefore, microbiologists have turned to new tools to interrogate natural communities. This revolution has been fuelled by new DNA sequencing technologies that probe community composition and metabolic potential (metagenomics), and linked "omics" approaches, such as such as metaproteomics and metatranscriptomics that provide metrics for activity. Metagenomic and metaproteomics methods were first applied to study natural microbial communities at an acid mine drainage site (Richmond Mine at Iron Mountain, California). Research conducted there demonstrated that it is possible to obtain complete genomes representing natural populations and to track their metabolic activity in situ. As a result dozens of novel genomes (down to the strain level) of uncultured acidophiles are now available. These genomes have provided a robust framework upon which it has been possible to address fundamental questions related to ecological processes such as colonization and to document the modes and rate of genome evolution read more ...