PROTEOGENOMICS OF COMMUNITIES: IN SITU STUDY OF THE STRUCTURE AND FUNCTION OF NATURAL BIOGEOCHEMICAL SYSTEMS

Microbes impact their environments and microbial communities are shaped by the geochemistry of their surroundings. This connection is especially clear in the case of extremely acidophilic microorganisms that live in association with weathered metal sulfide deposits. In these environments, microorganisms establish self-sustaining communities that fix carbon and nitrogen from air and derive energy primarily from iron oxidation. The ferric iron byproduct of metabolism is an effective pyrite oxidant. Thus, microbial activity drives pyrite dissolution and formation of metal-rich, very low pH solutions. Because this process is commonly associated with metal sulfide ore deposits, the solutions are referred to as acid mine drainage (AMD).

The communities that colonize AMD habitats are typically characterized by relatively low species diversity. In the Richmond Mine system studied in the collaboration involving UC Berkeley, ORNL, and LLNL, the biofilms are dominated by around five dominant species populations. Frequently, the dominant bacteria are closely related to Leptospirillum ferriphilum (Leptospirillum group II), Letospirilum diazotrophum (Leptospirillum group III), and the dominant archaea are related to Ferroplasma acidarmanus, Ferroplasma type II, and Gplasma. Other bacteria and archaea, as well as Eukaryotes (protists and fungi), are also present in some communities. Community membership and species abundance varies with biofilm growth stage and geochemical conditions.      Images

Because these communities comprise species populations (not necessarily clonal), and given difficulties with cultivation of microbes from many lineages, the Banfield lab initiated study of community structure and function via cultivation-independent analyses. Near complete and partial genomes were reconstructed from DNA extracted directly from the environment (Tyson et al. 2004, Nature). In the current phase of research, we have used these genomic data to enable identification of proteins from protein mixtures extracted directly from environmentally-derived biofilms. The long term objectives of this project are to resolve, at the molecular pathway level, the ways in which cellular resources are invested, the nature of the major environmental challenges, how functions are distributed amongst community members, and how these allocations vary with environmental conditions.