Reconstructing the Iron Mountain Community
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.
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.
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.
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.