Molecular maps of archaeal physiology and ecology: A transcriptional map of crenarchaeal respiratory versatility, and quantitative ecology of anaerobic methane-oxidizing communities

The Archaea are the third, and least understood major evolutionary lineage of cellular life. They are diverse, and widespread in nature, occupying niches at the physical and chemical extremes of life, as well as more temperate environments. Progress in understanding the biology of archaea and their ecological roles is limited in part by a limited physiological and phylogenetic diversity of archaeal model organisms, and by limited means for studying their growth and activities in natural environments.;The first part of this work focuses on archaeal respiration, about which relatively little is known. The hyperthermophilic crenarchaeal genus Pyrobaculum is remarkable among cultivated archaea for respiratory versatility, and provides a potential model system for studying the genetics and physiology of archaeal respiration using a wide variety of terminal electron acceptors. To identify genes involved in specific respiratory pathways in Pyrobaculum we compared global transcriptional patterns in one of the most metabolically flexible species in the genus, Pyrobaculum aerophilum, during growth with oxygen, nitrate, arsenate and ferric iron. In addition we compared the genome sequences of five Pyrobaculum species with diverse respiratory characteristics to identify conserved gene clusters and regulatory motifs associated with different respiratory pathways. Together these analyses were used to make a number of functional and regulatory predictions, identifying specific and in some cases novel roles for genes in aerobic respiration, denitrification, arsenate respiration, and iron homeostasis.;Progress in understanding the roles of archaea in global biogeochemical cycles ultimately depends on our ability to relate the growth of specific groups to geochemical parameters. Relatives of euryarchaeal methanogens, together with sulfate reducing bacteria, form consortia that couple the anaerobic oxidation of methane to sulfate reduction in marine sediments, which is a globally important process. Thus far efforts to isolate these organisms in pure cultures have been unsuccessful, and therefore their physiology is not well understood. We developed quantitative assays to measure the abundance of anaerobic methane oxidizing archaea and associated sulfate reducing bacteria in environmental samples, and used these to generate quantitative profiles of methane oxidizing microbial consortia in marine sediments in and around methane seeps in the Gulf of California.