DOE Human Genome Program Contractor-Grantee Workshop VIII
February 27-March 2, 2000  Santa Fe, NM

123. Diversity of Metal Reducing Bacteria from Ecological, Physiological and Genomic Perspectives

Jizhong Zhou^1,2, Guangshan Li¹, Alison Murray², Yul Roh¹, Heshu Huang¹, Ray Stapleton¹, Qiaoyun Qiu², John Heidelberg³, Claire Fraser³, Douglas Lies⁴, Kenneth H. Nealson⁴, and James M. Tiedje²

¹Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831; ²Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824; ³The Institute for Genomic Research, Rockville, MD 20850; and ⁴Department of Geology and Planetary Sciences, Jet Propulsion Laboratory and California Institute of Technology, Pasadena, CA 91109

zhouj@ornl.gov

Microbial metal reduction plays an important role in biogeochemical cycling of carbon and nitrogen as well as in bioremediation of metals, radionuclides and organic contaminants. To further investigate their diversity, metal-reducing bacteria were isolated from a variety of extreme environments including the deep terrestrial subsurface, Siberia and Alaska permafrost soils, continental margin marine sediments and Hawaii deep-sea water. Thermophilic isolates from terrestrial subsurface formations that had been geologically and hydrologically isolated for about 200 million years were able to use glucose, pyruvate, lactate, acetate and hydrogen as electron donors, and were able to reduce iron, manganese, chromium and uranium, as well as produce magnetite at 50-75 °C. The psychrotrophic isolates were able to use iron, manganese, and cobalt as electron acceptors, and were able to produce magnetite at 0 °C. A few isolates were able to reduce cobalt at - 4 °C and produce siderite using CO₂. Phylogenetic analyses indicated that the thermophilic iron-reducing bacteria were closely related to Thermoanaerobacter ethanolicus whereas the psychrotrophic iron-reducing bacteria were related to the members of the Shewanella genus. Although the psychrotrophic metal-reducing bacteria were able to use nitrate as electron acceptor, physiological studies and the comparisons of whole genome sequences from Shewanella oneidensis MR-1 (formerly S. putrefaciens MR-1) indicated that MR-1, and possibly the other psychrotrophic bacteria isolated appear to not be dissimilatory denitrifiers. In addition, whole genome sequence comparison indicated that MR-1 is more closely related to Vibrio cholerae O1 than to Escherichia coli K12. Finally, a partial microarray containing about 200 genes involved in energy metabolism and regulation were constructed and used to monitor gene expression patterns under anaerobic conditions. Substantial differences in gene expression patterns were observed under aerobic and anaerobic conditions. One interesting observation is that the genes (mtrA, B, and C) involved in metal reduction were highly expressed under both aerobic conditions and anaerobic metal reducing and denitrifying conditions, suggesting that the expression of these genes is not specific to metal reduction. The iron reduction rates in the deletion mutants of mtrB generated by newly developed suicide vectors were much slower than in the wild type strain. The partial microarrays were also used to assess the genome diversity among different metal-reducing bacteria. The results indicated that S. onedensis DLM7 is more closely related to MR-1 than Shewanella sp. W3-6-1. Housing keeping genes and the genes involved in metal reduction appear to be highly conserved between MR-1 and W3-6-1 although the overall genomic diversity is low.