Highlights of Research Progress
Metagenomics: Opening a New Window onto Natural Microbial Communities
Our understanding of microbial diversity and function has been limited severely by the inability to grow the vast majority of microbes in the laboratory. High-throughput DNA sequencing and other biotechnology tools now offer a new avenue for obtaining this knowledge. Genome fragments can be isolated and analyzed after being collected directly from environmental samples, whether liters of water from the open sea or a scraping from a slick film at the bottom of a highly acidic mine. Such environmental genomic (metagenomic) approaches have been applied to studying entire microbial communities in a specific locale as well as single genes, pathways, and whole organisms. Analyses of these data have revealed a broad spectrum of genomes, genes, and previously undiscovered functions.1
These studies will result in a multitude of new insights into the dynamics between microbes and their environments and will have the potential to catalyze development of numerous practical applications. Effective mining of the environment for fundamental knowledge and products, however, will require substantial investments in new high-throughput technologies. These biophysical and physiological techniques can help reveal the functions of new microbial proteins and compare the properties of large collections of genes of a particular type or function.1,2
GTL supported the first sequencing of a microbial community directly from the environment at Iron Mountain, California,3 and the first comprehensive study of gene expression in such a community,4 as well as the vast environmental sample data set of large DNA fragments collected from the Sargasso Sea.5 Some highlights of these studies are described below, and all data are available to the research community.6 GTL also supports 11 other studies of natural microbial communities from sites as diverse as a boiling thermal pool in Yellowstone National Park, former uranium mining sites, and complex soil environments.
Microbial Community Thriving in Acid Mine Drainage
Direct environmental sampling led to the characterization of members of a microbial community in highly acidic water from an abandoned gold mine at Iron Mountain, one of the nation’s worst Superfund sites (see bottom right). Acid mine drainage is caused by the complex interaction of various microbes with exposed iron ore and water, resulting in a mix so toxic (pH 0.83) that it can completely corrode shovels accidentally left overnight.
Samples were taken from a pink microbial biofilm growing on the surface of acid mine drainage hundreds of feet underground within a pyrite ore body. A scanning electron microscope image of a piece of the biofilm revealed a tight association of microbial cells. After extracting and cloning DNA from the biofilm, investigators were able to reconstruct the genomes of two hardy microbes and parts of three others capable of withstanding the harsh conditions. Four of the microbes had never been cultivated. Using genomic and mass spectrometry-based proteomic methods, the team later identified over 2000 proteins from the 5 most abundant species, including 48% of the predicted proteins from the dominant biofilm organism. One of the proteins (a cytochrome) from a minor organism is key in the production of acid mine drainage. More than 500 of the proteins seem to be unique to the biofilm bacteria.
Further analyses of these data and future studies on each of the species will provide insights into their metabolic pathways, the ecological roles they play, and how they survive in such an extreme environment. Obtaining this knowledge can help in developing future cleanup strategies. [Jillian Banfield, University of California, Berkeley]
Snapshot of the Complex Microbial Communities in the Sargasso Sea
Environmental investigations in the nutrient-poor waters near Bermuda in the Sargasso Sea led to the discovery of 1800 new species of bacteria and more than 1.2 million new genes. Scientists used a whole-genome shotgun sequencing technique to clone random DNA fragments from the many microbes present in the sample. The resulting data represent the largest genomic data set for any community on earth and offer a first glimpse into the broad ensemble of adaptations underlying diversity in the oceans. Because microbes generally are not preserved in the fossil record, genomic studies provide the key to understanding how their biochemical pathways evolved.
Hundreds of the new genes have similarities to the known genes called rhodopsins that capture light energy from the sun. Bacterial rhodopsins couple light-energy harvesting with carbon cycling in the ocean through nonchlorophyll-based pathways.7 Future studies will allow more insights into how these molecules function as well as opportunities for mining and screening the data for specific applications. The vast data set provides a foundation for many new studies by other researchers. Analyses using iron-sulfur proteins as benchmarks led one researcher, for example, to conclude that these data reflect diversity equal to that in all the currently available databases, suggesting that microbial diversity thus far has been vastly underestimated.8 [J. Craig Venter Institute]
References
1. C. S. Riesenfeld, P. D. Schloss, and J. Handelsman, “Metagenomics: Genomic Analysis of Microbial Communities,”Annu. Rev. Genet. 38, 525–52 (2004).
2. P. G. Falkowski and C. deVargas, “Shotgun Sequencing in the Sea: A Blast from the Past?”Science 304, 58–60 (2004).
3. G. W. Tyson et al., “Community Structure and Metabolism Through Reconstruction of Microbial Genomes from the Environment,”Nature 428, 37–43 (2004).
4. R. J. Ram et al., “Community Proteomics of a Natural Microbial Biofilm,”Science 308, 1915–20 (2005).
5. J. C. Venter et al., “Environmental Genome Shotgun Sequencing of the Sargasso Sea,”Science 304, 58–60 (2004).
6. Whole-genome shotgun sequencing project data from Iron Mountain and the Sargasso Sea available on the web (www.ncbi.nlm.nih.gov/Web/Newsltr/Spring04/sargasso.html).
7. J. Meyer, “Miraculous Catch of Iron-Sulfur Protein Sequences in the Sargasso Sea,”FEBS Lett. 570, 1–6 (2004).
8. O. Beja et al., “Bacterial Rhodopsin: Evidence for a New Type of Phototrophy in the Sea,”Science 289, 1902–6 (2000).
