Prokaryotes are the dominant form of life on earth, representing an enormous biomass and number of individual cells. They are so diverse that it is misleading to give them a common name. In one way, they are really just what are left after the familiar plants, animals, fungi and protists are named. Nevertheless, they are the engines that make the biosphere and the ancestors to all modern life. Their evolution established the central plan for the living cell and shaped the biogeochemistry of the planet. Research in our laboratory uses an integrated approach to understand the nature of free-living prokaryotes. We believe that studying the ecology, systematics, physiology, biochemistry, and molecular biology together provides the best understanding for microorganisms. Likewise, the history or evolution of an organism provides insight into the modern organism. We have used these approaches to study the carbon and sulfur metabolism of the methane-producing archaeon Methanococcus, the sulfur metabolism of the marine alphaproteobacterium Ruegeria, and the impact of agriculture on soil bacterial communities.