Metal Mechanisms

Released: February 27, 2015
Bacteria breathe metals in different ways

The Science

Geobacter bacterial species use metal reduction pathways to respire metals such as uranium, rendering it insoluble. This is of interest for bioremediation of contaminated groundwater. However, mechanisms of metal reduction by Geobacter species found in subsurface environments have not been clear. This study addresses this question through proteomic analysis of Geobacter bemidjiensis, which is a major species that uses acetate to reduce uranium in aquifers and thus is particularly important for potential bioremediation applications.

The Impact

The results suggest there is not just one mechanism of metal reduction in microbes and Geobacter bemidjiensis exists with distinct physiological states in different ecological niches. Shedding light on metal reduction pathways in key microbial species paves the way for future widespread bioremediation efforts.


Researchers from Pacific Northwest National Laboratory (PNNL); The Ohio State University; University of California, Berkeley; Lawrence Berkeley National Laboratory and University of Washington carried out proteomics studies of Geobacter bemidjiensis grown with acetate as the electron donor and either fumarate, ferric citrate or one of two hydrous ferric oxide mineral types as the electron acceptor. Led by investigators funded by the Office of Science Office of Biological and Environmental Research (BER) Pan-omics project, the team carried out peptide-based liquid chromatography-mass spectrometry proteomics measurements on lab-grown cultures of Geobacter bemidjiensis at EMSL, the Environmental Molecular Sciences Laboratory, a Department of Energy (DOE) Office of Science national scientific user facility.

The major class of proteins whose expression changed across these conditions was c-type cytochromes, many of which are involved in metal reduction in other, better characterized Geobacter species. However, some c-type cytochromes in Geobacter bemidjiensis and Geobacter sulfurreducens had different expression profiles under similar growth conditions. This finding hints at divergent functions between homologous proteins and suggests there are multiple metal reduction pathways in microbes. The proteins that are differentially expressed across Geobacter species provide interesting targets for future studies aimed at exploring different mechanisms of metal reduction.

The researchers also compared laboratory proteomics data to previous proteomic analyses of biomass recovered from a uranium-contaminated aquifer at DOE’s Integrated Field Research Challenge site in Rifle, Colo. The microbial community there is dominated by strains closely related to Geobacter bemidjiensis. Researchers detected an increased number of proteins with functions related to motility, chemotaxis and signal transduction in Colorado field samples compared to laboratory samples, highlighting the importance of motility for metal reduction in the environment. This finding suggests Geobacter bemidjiensis existing in the subsurface may actively travel to insoluble iron(III) electron acceptors for cellular respiration required for growth and survival because such nutrients are present at lower concentrations in the field than in the lab. Moreover, results pave the way for future investigation of distinct physiological states of Geobacter bemidjiensis found in various ecological niches.

Contact: Mary Lipton

Funding: DOE Office of Biological and Environmental Research for Pan-Omics Technologies Development, Implementation and Applications, and a Subsurface Biogeochemical Research grant.

Publication: Merkley ED, K Wrighton, CJ Castelle, BJ Anderson, MJ Wilkins, V Shah, T Arbour, JN Brown, SW Singer, RD Smith, and MS Lipton. 2014. "Changes in protein expression across laboratory and field experiments in Geobacter bemidjiensis." Journal of Proteome Research.   DOI:10.1021/pr500983v

Program: Office of Biological and Environmental Research