Reconstructing the Iron Mountain Community

The Microbe Mix Matters

Microbial communities, though often undetected by the naked eye, play integral roles in the ecosystems where they reside. Examination of such actors, good or bad, has been difficult because the vast majority of microorganisms resist cultivation in the laboratory, so their actual function within the environment may remain cryptic. Now, however, by applying the shotgun sequencing strategy to the problem, information about these communities and their interactions with their environment is surfacing.

The microbial community studied here is an excellent example of the value of such research. Decades of earthmoving activity at the Richmond Mine in Iron Mountain, California, created opportunities for microbes to colonize the site. The complex interaction of various microbes, water, and exposed ore has generated dangerously high levels of sulfuric acid and toxic heavy metals that ultimately find their way into the upper Sacramento River ecosystem. Sequencing the community will likely prove to be an important step toward a successful remediation strategy.

An EPA superfund site nasty enough to eat away an iron shovel over night may get some help from new genomic research. Scientists from JGI and the University of California, Berkeley, have succeeded in reconstructing the genomes of organisms in an Iron Mountain, California, acid mine drainage (AMD) microbial community. The work, published in Nature, represents the first sequencing of a microbial community directly from the environment.

Leptosprillum group II accounted for the majority of the acid mine drainage community.

After initial characterization by fluorescence in-situ hybridization (FISH), DNA extracted from the pink biofilm was sequenced by the whole-genome shotgun method. Because the biofilm contained few separate species with relatively little genomic rearrangement, it was possible to reconstruct the genomes of five distinct organisms. The resulting genomes of Leptospirillum group II and a new Ferroplasma species (designated type II) are nearly complete, and those of three other organisms are partial. The trick to assigning sequenced reads to the correct organisms was to group assembled scaffolds first by G+C content and then by read depth (coverage). Comparison to the previously sequenced genome of Ferroplasma acidarmanus fer1 aided assignment of scaffolds to that species and to G-plasma.

Acid mine drainage (AMD) witih the pink biofilm on its surface

The sequence information yielded important clues to the population structure at the site. The number of ecological niches appears to be small, as relatively few distinct genome types were found in the biofilm. By far the most common species was Leptospirillum group II. A very low rate of nucleotide polymorphisms (0.08%) in this genome indicated that the researchers sequenced essentially a single strain, suggesting strong environmental selection for this species, or a founder effect. In the Ferroplasma type II composite genome, the scientists found evidence that three ancestral strains, probably derived from a relatively recent common ancestor, have undergone homologous recombination to form mosaic genomes.

Phylogenetic tree for mosaic genomes

Metabolic analysis gave new insights into the ecological roles of community members. Contrary to expectation, Leptospirillum group III rather than group II is likely the primary fixer of nitrogen in the biofilm. Being a low-abundance member of the community, Leptospirillum group III may well be a keystone species that can be targeted for remediation purposes. Information was also gleaned about essential systems including electron transport, biofilm formation, motility, and resistance to toxic metals.

The sequence data for Leptospirillum group II is of particular significance, as it is the first genomic characterization of a member of the phylum Nitrospora. Community genome reconstruction holds great promise for the study of the vast majority of microbes that are not culturable. Besides offering important clues to metabolic networks and community structure, such reconstructions may reveal the conditions that would make culturing possible. The data may also allow production of DNA microarrays for monitoring gene expression in microbial communities.

Authors

G.W. Tyson, P. Hugenholtz, E.E. Allen, R.J. Ram, and J.F. Banfield (University of California, Berkeley); P.M. Richardson, V.V. Solovyev, and E.M. Rubin (JGI); and J. Chapman and D.S. Rokhsar (University of California, Berkeley, and JGI).

Publication

"Community Structure and Metabolism through Reconstruction of Microbial Genomes from the Environment," Nature 428, 37-43 (2004), doi: 10.1038/nature02340.

Funding

This research was funded by the U.S. Department of Energy Microbial Genomics Program and the National Science Foundation Biocomplexity Program.