ORNL, UC Berkeley unravel real-world clues to Earth’s mysteries

A microbial community thriving under bizarre natural conditions in California could be a gold mine to researchers in their quest to understand the complex biological relationships and how these inner workings might apply on a grander scale.

In a paper to appear today on Science Online, researchers from the Department of Energy’s Oak Ridge National Laboratory and the University of California Berkeley describe a bacterial community that flourishes in the iron sulfide-rich runoff of the Richmond Mine near Redding. A pH level of 7 is considered neutral and most proteins prefer pH levels between 5 and 7. The water trickling from the mine has a pH of about 0.8 and a temperature of 107 degrees Fahrenheit.

“This microbial community is thriving at the extreme edge,” said Bob Hettich, a co-author and member of ORNL’s Chemical Sciences Division. “A pH level of 0.8 is like swimming in sulfuric acid, so we’d like to know how this community can survive and how we might be able to use this information to better understand microbial systems in real-world conditions.”

The work is significant on a number of levels, according to the research team, which noted that while microbial communities play key roles in the Earth’s bio-geochemical cycles, scientists know little about the structure and activities within these communities. This is because the commonly used artificially cultivated organisms lack the diversity found in nature, so potentially critical community and environmental interactions go unsampled.

Raymond Orbach, director of DOE’s Office of Science, noted that this research offers a glimpse of what will be possible in the near future. “This work illustrates the power of the genome sequencing done at the Department of Energy’s Joint Genome Institute to contribute to understanding the microbiological communities living at contaminated sites,” Orbach said. “Now scientists can investigate not only the ’community genome,’ but also the resulting ’community proteome’ for enzymes and pathways that can help clean up some of the worst environmental sites in the nation. This underscores the value of basic research carried out by the DOE Genomics: Genomes to Life program that can develop novel approaches and solutions to national challenges.”

Hettich said their results would not have been possible without the collaboration with UC Berkeley, where Jill Banfield is an expert in natural microbial communities. Banfield, a professor in the Department of Environmental Science, Policy and Management, has studied this particular acid mine drainage community for several years. Meanwhile, ORNL boasts world-class mass spectrometry instrumentation and its researchers have demonstrated success in obtaining proteome information on simple microbial organisms grown in the laboratory. Working as a team, UC Berkeley and ORNL have struck it rich.

“Through this collaboration, Jill Banfield has been able to take her research up a quantum step by obtaining the first glimpse into the complex proteome dataset of this microbial community,” Hettich said. “To do this, it was critical that we bring together researchers with expertise in biology and ecology of microbial communities, analytical technologies and bioinformatics.”

Banfield and colleagues at UC Berkeley supplied the bacterial samples and characterized genome information while Hettich and Nathan VerBerkmoes, a post-doctoral student in ORNL’s Chemical Sciences Division, performed the mass spectrometry work. Manesh Shah of ORNL’s Life Sciences Division was responsible for the informatics related to database searching and data dissemination. The team detected 2,036 proteins from the five most abundant species in the bio-film, including 48 percent of the predicted proteins from the most abundant bio-film organism, Leptosprillum group II.

Researchers noted that this work represents the first large-scale proteomics-level examination of a natural microbial community.

“As such, we are really among the leaders in this area, as evidenced by the strong interest in Science,” Hettich said. “This is an area in which there is keen interest by many research groups; however, our team has been the most successful in obtaining detailed information from actual measurements.”

Of particular interest to DOE is how this effort relates to its Genomes to Life program, which is focused on identifying and characterizing protein complexes, the molecular machines of life.

“Most of the current work looks at single microbial organisms grown under controlled laboratory conditions, but the longer-term plans are to extend this work to real-world microbial communities — the natural state of these systems in the environment,” Hettich said. “This goal is particularly difficult to reach due to the complexity and heterogeneity of the communities.

“However, the acid mine drainage microbial colony is an excellent starting point because it is a real-life natural world community with a limited number of members. Thus, we can measure and learn about microbial interactions and function distribution in a natural setting without being overwhelmed by an extremely large number of organisms.”

The research team acknowledges that, although this study provides interesting details of microbial community structure and function, a great deal of work remains to more fully explore the spatial and temporal aspects of how such a community grows, ages and adapts to its environment.

Funding for this research was provided by DOE’s Office of Science, Office of Biological and Environmental Research, and by the National Science Foundation. Oak Ridge National Laboratory is managed for DOE by UT-Battelle.