“In this paper we reconstructed near complete genomes of uncultivated and, in one case, a previously undetected organism, directly from an environmental sample.”

The paper describes the first application of shotgun sequencing to characterize the microorganisms in a natural sample. I think that people are excited by the approach because it enables analysis of the metabolic potential of uncultivated microbial species that dominate most of the Earth's environments. There is also considerable current interest in organisms that grow in extreme environments, such as the metal contaminated, pH<1 environment studied here, and in population structure and dynamics. These data enable proteomic approaches to directly assay microbial activity in natural systems (as was accomplished in "Community Proteomics of a Natural Microbial Biofilm," (Rachna J. Ram et al., Science, 2005).

It had been necessary to isolate a microorganism prior to sequencing its genome, yet the vast majority of microbes are difficult or impossible to isolate. In this paper we reconstructed near-complete genomes of uncultivated and, in one case, a previously undetected organism, directly from an environmental sample. In our study we looked at a microbial community with relatively low diversity, but the possibility that the approach could be applied to more complex environments was intriguing. Subsequently, at least two other shotgun sequence-based studies of other relatively high diversity systems were published; one of these attained significant genomic coverage for a few species.

Microorganisms underpin most of the Earth's biological and geochemical cycles, yet we know little about them. We used a new approach to learn about the metabolism of organisms present in a biofilm that is involved in the formation of acid mine drainage, a major environmental problem associated with metal and energy resources. Our work revealed rampant exchange of genetic information (analogous to sex) amongst members of one archaeal species population.

We are interested in developing a detailed understanding of how microbial communities function, adapt, and evolve, as well as the ways in which they contribute to a major environmental problem. Organisms that populate acid mine drainage (AMD) systems were chosen for study because there is a clear coupling between microbial energy generation via iron oxidation and environmental acidification. We focused on AMD biofilms because it is consortia, and not single species, which exist in natural systems, and these biofilms are simple enough that they can be characterized comprehensively.