Deciphering the evolution and metabolism of an anammox bacterium from a community genome

Ten years ago a fortuitous discovery led to the identification of oceanic bacteria capable of anaerobic ammonium oxidation (anammox). It was soon recognized that the anammox reaction has great ecological significance, as it is responsible for removing up to 50% of fixed nitrogen from the oceans. The genome of the anammox bacterium Kuenenia stuttgartiensis has now been sequenced in a remarkable feat of what is called environmental genomics. Anammox bacteria grow very slowly and are not available in pure culture. For genome analysis an inoculum of wastewater sludge was grown in a bioreactor for one year, clocking up 10–15 generations. The DNA of the whole microbial community was sequenced and the genome of this one anammox bacterium was deduced from the results. With the genome sequence known, it will be possible to gain insight into the metabolism and evolution of these important bacteria. The genome of Kuenenia stuttgartiensis has been sequenced to learn more about anaerobic ammonium oxidation. Anaerobic ammonium oxidation (anammox) has become a main focus in oceanography and wastewater treatment1,2. It is also the nitrogen cycle's major remaining biochemical enigma. Among its features, the occurrence of hydrazine as a free intermediate of catabolism3,4, the biosynthesis of ladderane lipids5,6 and the role of cytoplasm differentiation7 are unique in biology. Here we use environmental genomics8,9—the reconstruction of genomic data directly from the environment—to assemble the genome of the uncultured anammox bacterium Kuenenia stuttgartiensis10 from a complex bioreactor community. The genome data illuminate the evolutionary history of the Planctomycetes and allow us to expose the genetic blueprint of the organism's special properties. Most significantly, we identified candidate genes responsible for ladderane biosynthesis and biological hydrazine metabolism, and discovered unexpected metabolic versatility.