Anaerobic ammonium oxidation (anammox) involves the microbiological oxidation of ammonium with nitrite as the electron acceptor and dinitrogen gas as the main product. The Scalindua species, an anammox genus that dominates natural habitats, plays an important role in catalysing the loss of nitrogen from marine environments. Until now, a few Scalindua species have been reported to be enriched from sea sediments. The objective of this study is to enrich marine anammox bacteria with coastal sediments in Hiroshima Bay as the inocula. The enrichment was achieved using a continuous upflow column reactor with synthetic sea water containing ammonium and nitrite. After 48 days of incubation, a simultaneous decrease in ammonium and nitrite was observed. A total nitrogen removal rate of 1.16 kg-N m−3 day−1 was attained after 306 days of incubation when the nitrogen loading rate was 1.32 kg-N m−3 day−1. Phylogenetic analysis revealed that the sequence similarity between the marine anammox-like bacteria in this reactor and the unidentified Candidatus Scalindua sp. was 96–98%. We successfully enriched marine anammox bacteria in the sediments of Hiroshima Bay by using synthetic sea water. Further studies are needed to investigate the characteristics of marine anammox bacteria, including optimal pH, temperature, and nitrogen loading rate.

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