Sulfate-reducing bacteria (SRB) are ubiquitously found in soil, sediment and subsurface environments. The genome of the mesophilic sulfate-reducing bacterium Desulfovibrio vulgaris(3.2 Mbp) has been sequenced by The Institiute for Genomic Research (TIGR, www.tigr.org). The genomic sequence of the sulfate-reducing thermophilic archaeon Archaeoglobus fulgidus(2.2 Mbp) has also been determined. We have extensively studied the molecular biology of D. vulgarisin the past 15 years. Availability of the D. vulgaris genome sequence allows research in functional genomics and proteomics. These studies have led to a better understanding of two areas:
(i) The energy metabolism of these bacteria, particularly their ability to use hydrogen as an energy source for sulfate reduction. Electrons are transported from hydrogen to sulfate by a chain of redox proteins involving sequentially periplasmic hydrogenases, periplasmic c-type cytochromes, a membrane-bound redox protein complex (the Hmc complex) and cytoplasmic sulfate reduction enzymes of which the last one, dissimilatory sulfite reductase, is strongly conserved in all sulfate reducers. We have been frontrunners in the cloning and seqencing of most of the genes involved in this chain. Now that the complete genomic sequence is available we use proteomic and functional genomic approaches to define more globally genes that are crucial for metabolism of hydrogen and a variety of other energy substrates by D. vulgaris.This research is important and exciting because these bacteria have been present on Earth since the very beginning, are ubiquitously present in the subsurface and form a model for possible life forms on other planets. Yet many aspects of the basic metabolism of these bacteria remain unknown.
(ii) The oxygen defense system of these bacteria. SRB are anaerobes that can withstand long periods of oxygen exposure, but are eventually killed by exposure to air. We have identified both classical (superoxide dismutase or Sod, catalase or Cat) and novel (rubredoxin oxidoreductase or Rbo, also referred to as superoxide reductase or Sor and rubrerythrin or Rbr) components of the oxygen defense system of D. vulgaris.The novel components, Rbo and Rbr, appear to be generally present as oxygen defense proteins in anaerobes. They act by reducing superoxide or hydrogen peroxide to water, whereas the classical components found in all aerobic bacteria dismutate superoxide and hydrogen peroxide to water and oxygen. We define the roles of these various components by studying the properties (e.g. survival in air) of mutants in selected genes. D. vulgarisalso has a variety of sensor molecules of which some appear to register the presence of oxygen. The behaviour of mutants in these sensory genes, i.e. their ability to avoid oxygen by chemotaxis is also evaluated.