Helping improve microbes’ ability to remediate toxic metal contamination

into the groundwater and eventually into the river. Some microbes “breathe” the metals like we breathe oxygen, chemically altering them so they become insoluble and remain in the sediment, Wrighton said.

Banfield refers to microbe communities like these as the “dark matter” of biology, an analogy to the missing mass in the universe that has stumped astronomers for decades. The bacterial tree of life can be divided into about sixty phylum-level branches, but essentially nothing is known about half of them, she said.

“This new study provides new knowledge about the ecology as well as the evolution of a significant chunk of what could be considered the dark matter of the microbial world,” she said.

Before now, Banfield had performed metagenomic analyses of eight microbes coexisting in highly acidic underground streams in a former California mine and current Superfund clean-up site. Such an analysis involves grinding up all organisms in a sample, sequencing all the genes and then matching each with a unique microbial species.

The new study involved the genomes of ten times more organisms. All are anaerobic — they do not breathe oxygen like most organisms on Earth — and most, while not new to science, are totally unstudied because they cannot be cultured in the laboratory. Many are only a few hundred nanometers across, making them among the smallest known microbes.

Scientists at the Rifle site spread acetate — essentially diluted vinegar — in the subsurface to feed the underground bacteria that convert soluble metals to insoluble metals. They had assumed that they were culturing a colony comprised mostly of Geobacter bemidjiensis, a well-known metal-reducing bacterium.

Instead, Wrighton said, analysis of three samples obtained within ten days of acetate application showed a healthy population of Geobacter, but a throng of other bacteria presumably feeding on dead Geobacter and other carbon in the soil from previous additions of acetate. These organisms use or ferment complex carbon, such as dead plants and dead microbes, and produce hydrogen, small organic carbon compounds and carbon dioxide.

“The fermenters producing hydrogen after multiple additions of acetate may be more important to the underlying microbial community than we once thought,” said Philip E. Long, an LBNL geologist who manages research at the Rifle study site.

Wrighton, Banfield and their team are continuing metagenomic analyses of samples from the Rifle site, including some obtained before nutrients are added to determine what the natural population looks like.

— Read more in Kelly C. Wrighton et al., “Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla,” Science 337, no. 6102 (28 September 2012): 1661-65 (DOI: 10.1126/science.1224041)