Earth's microbes live in staggeringly diverse environments, colonizing habitats with extremes of temperature, pH, salt concentration, or presence of toxic compounds. Archaea, a domain of single-celled microbes sharing traits with bacteria and simple eukaryotes, are well known for their ability to thrive in harsh environments. How this impressive adaptive capability is achieved has remained a mystery. Now, a team of investigators at the Institute for Systems Biology has completed a groundbreaking study on the role of gene regulation in environmental niche adaptation by , an archaeal microbe that grows in high salt environments. Using a combination of comparative genomics and hypothesis-driven molecular biology experiments, the team found that a specific class of regulatory genes had been duplicated during the archaea's evolution and controls a nested set of "niche adaptation programs." These programs control cascades of gene expression essential for adaptation to particular environments. Diversification of these control elements has resulted in a "division of labor" such that overlapping regulatory networks flexibly balance large-scale functional shifts under changing conditions, where rapid adaptation increases fitness. Describing mechanisms that control niche adaptation in microbes allows us to better understand how microbial communities function in natural environments, and provides an intriguing glimpse into fundamental design rules governing biological systems.
Reference: Turkarslan, S., D. J. Reiss, G. Gibbins, W. L. Su, M. Pan, J. C. Bare, C. L. Plaisier, and N. S. Baliga. 2011. “Niche Adaptation by Expansion and Reprogramming of General Transcription Factors,” Molecular Systems Biology 7, Article 554. DOI:10.1038/msb.2011.87. ()
Sulfate-reducing bacteria (SRB), commonly found in oxygen-deprived habitats, are known for their involvement in the corrosion of metals and the formation of toxic sulfide; however, they also are involved in controlling the transformations and transport of a number of toxic metal contaminants in soils and groundwater. Effective use of SRBs to control metal contaminants requires a better understanding of their bioenergetic pathways for sulfate reduction. A team of scientists from the University of Missouri, Oak Ridge National Laboratory, and Environmental Molecular Sciences Laboratory (EMSL) used a mutant form of an SRB, Desulfovibrio alaskensis, to test the hypothesis that the sulfate reduction that occurs in the cell’s interior cytoplasm relies on a flow of electrons from the cell’s periplasm, found between the cell’s two exterior membranes. The researchers characterized bacterial growth and examined gene expression using proteomic and transcriptomic analyses at EMSL. Their results indicate that a protein that spans the inner membrane from the periplasm to the cytoplasm and another protein found only in the periplasm are essential for transferring electrons from the periplasm to the cytoplasm to drive sulfate reduction. These research results also are consistent with another recently discovered biochemical pathway involving hydrogen cycling that increases the efficiency of energy use in many SRBs. Together, these findings could be important in designing pathways for biofuels production.
Reference: Keller, K. L., B. J. Rapp-Giles, E. S. Semkiw, I. Porat, S. D. Brown, and J. D. Wall. 2014. “A New Model for Electron Flow for Sulfate Reduction in Desulfovibrio alaskensis G20,” Applied and Environmental Microbiology 80(3), 855-68. DOI:10.1128/AEM.02963-13.()
LabBench Activity Plant Pigments and Photosynthesis
NABIR investigators had a major impact on the annual meeting of the American Society of Microbiology which was attended by over 15,000 scientists. NABIR research was presented in 12 invited talks and over 50 additional scientific papers. NABIR researchers reported their findings in two sessions on "Bioreduction of Metals and Bioremediation of Metal-Contaminated Soils," as well as at sessions on "Subsurface Microbiology," "Anaerobic Respiration," "Molecular Microbiology Ecology," and "Gene Expression in the Environment." Dr. Gil Geesey, a NABIR investigator from Montana State University, won the most prestigious award in environmental microbiology, the 2001 Procter & Gamble Applied and Environmental Microbiology Award. Dr. Geesey was recognized for his research on bacterial-surface interactions, and he presented a lecture entitled "Surfaces: Catalysts of diverse bacterial cell behavior." Other highlights include a report by Dr. James Fredrickson of Pacific Northwest National Laboratory that the highly radiation-resistant bacterium is endemic to subsurface soils beneath radioactive waste storage tanks at the Hanford reservation, making this microbe especially promising for in situ bioremediation approaches. Dr. Derek Lovley from the University of Massachusetts reported that during active metal reduction, subsurface microbial communities are dominated by metal- and radionuclide-reducing bacteria called . Genomes of both and Deinococcus have been sequenced by the BER Microbial Genome Program, and researchers are using this information to better understand the potential of these bacteria for bioremediation of metals and radionuclides at DOE sites.