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Ten years ago, an anaerobic ammonium oxidation (‘anammox’) process was discovered in a denitrifying pilot plant reactor. From this system, a highly enriched microbial community was obtained, dominated by a single deep-branching planctomycete, Candidatus Brocadia anammoxidans. Phylogenetic inventories of different wastewater treatment plants with anammox activity have suggested that at least two genera in Planctomycetales can catalyse the anammox process. Electron microscopy of the ultrastructure of B. anammoxidans has shown that several membrane-bounded compartments are present inside the cytoplasm. Hydroxylamine oxidoreductase, a key anammox enzyme, is found exclusively inside one of these compartments, tentatively named the ‘anammoxosome’.