They can function in energy conservation, generating a chemiosmotic gradient for ATP production by sodium ion export. This allows energy generation buy CAL-101 over a more negative redox range than oxidative phosphorylation does. They may also function in the reverse direction to produce reduced ferredoxin, or in other as yet unknown roles; protons rather than sodium may be pumped in some cases. The six or seven Rnf genes (rnfH

is not always present) are found in different arrangements in a variety of Bacteria and Archaea, usually but not always in a cluster. At least two bacteria (Azotobacter vinelandii and Desulfobacterium autotrophicum HRM2) have two different Rnf gene clusters. The BOGUAY genome encodes two possible copies of genes for five of the seven Rnf subunits (Table S8), and one each for RnfF and RnfH. selleck compound Perhaps significantly, these are the two least-characterized subunits, and rnfH is not always found in genomes possessing the other six (putative) genes. BLASTP searches (not shown) suggest that where the BOGUAY genome has two copies of an Rnf gene, they have different phylogenies. From this analysis, the BOGUAY genome has both expected and unexpected features. Pathways for sulfide oxidation and nitrate reduction are both present, although we cannot yet explain all aspects of the possible nitrogen respiration pathways. Some experiments addressing this are

suggested in MacGregor et al. (2013b). The answer to the

question whether orange-pigmented Beggiatoaceae are autotrophs or heterotrophs is, so far, “possibly both”. Genome sequences from additional pigmented and unpigmented filaments collected in different environments may provide some insights. Experimental work will be needed to clarify Beggiatoaceae physiology, however. For example, seafloor or shipboard incubations with isotopically labeled carbon substrates could be attempted, to determine which are incorporated directly into Beggiatoaceae biomass under particular conditions. Carbon dioxide and oxygen concentrations are likely important variables, as well as sulfide, organic acid, and perhaps hydrocarbon availability. The size of the filaments L-NAME HCl might make autoradiography feasible, or phylogenetically specific RNA or lipids could be isolated for stable or radiocarbon isotopic determinations. Removal of epibionts might be attempted to minimize cross-feeding, although they may be required for nutrient supply or waste removal. Gene expression studies might be used to ask which carbon acquisition pathways are activated under a given set of conditions. As in all microbial genomes, there also remain hundreds of hypothetical proteins of unknown function, providing for any amount of future experimentation. Thanks to the Captain and crews of the RV Atlantis and HOV Alvin, and to the shipboard parties of legs AT 15-40 and AT 15-56. Genome sequencing was performed by the J.