Acid mine drainage (AMD) is a major worldwide environmental problem associated with the mining of energy resources (coal and uranium) and metals (eg., iron and copper), thus of direct DOE relevance. The processes that underpin AMD formation can be harnessed for bioleaching and bioremediation. Many scientific and industrial groups are studying various aspects of the biogeochemistry of AMD generation.
Random shotgun sequencing of an extremely acidic (pH <0.9) chemolithotrophic subsurface AMD biofilm community (from the Richmond Mine in Iron Mountain, California) recovered a genome fragment from a novel euryarchaeon, named WTF-1. This novel lineage was previously missed by common broad-specificity primers used for PCR-based surveys. Further study revealed two more groups, WTF-2 and WTF-3, which are highly divergent from WTF-1 sequences (8% and 17% respectively, at the rRNA gene level). Microscopic analyses of these archaea have shown that they are much smaller than other cells in the environment and that they are ubiquitous to AMD generation at the Richmond Mine site.
Whole-genome sequencing of these microorganisms, as a community, is of broad interest because these groups lie in a region of the tree of life characterized solely by rRNA gene clones. Currently, these novel microbes are missing from models of AMD systems. The genome sequences generated in this project will be used for evolutionary studies by researchers interested in archaeal biology and evolution. The data will also enable metabolic predictions and subsequent proteomic analyses needed to define the ecological roles of these tiny, enigmatic, uncultivated microorganisms.
CSP project participants: Brett J. Baker (proposer), Eric E. Allen, and Jillian F. Banfield (UC Berkeley).