Uary, 2012; revised 11 April, 2012; accepted 12 April, 2012. *For correspondence. E-mail [email protected]; Tel. (+31) 24 365 2940; Fax (+31) 24 365 2830. Present addresses: Springer, Dordrecht, the Netherlands; TNO Food Zeist, the Netherlands; �Department of Pathology, Utrecht University, Utrecht, the Netherlands; nalytical Development and Validation Department, MSD, Molenstraat 110, 5342 CC Oss, the Netherlands; Department of Microbial Ecology, University of Vienna, Austria. Re-use of this article is permitted in accordance using the Terms and Conditions set out at http://wileyonlinelibrary/ onlineopen#OnlineOpen_TermsDepartment of Biotechnology, Delft University of Technology, Delft, the Netherlands. Summary Anaerobic ammonium-oxidizing (anammox) bacteria are responsible for a significant portion of your loss of fixed nitrogen from the oceans, making them critical players in the global nitrogen cycle. To date, marine anammox bacteria found in marine water columns and sediments worldwide belong almost exclusively for the `Candidatus Scalindua’ species, but the molecular basis of their metabolism and competitive fitness is presently unknown. We applied community sequencing of a marine anammox enrichment culture dominated by `Candidatus Scalindua profunda’ to construct a genome assembly, which was subsequently used to analyse one of the most abundant gene transcripts and proteins. Inside the S. profunda assembly, 4756 genes were annotated, and only about half of them showed the highest identity towards the only other anammox bacterium of which a metagenome assembly had been constructed so far, the freshwater `Candidatus Kuenenia stuttgartiensis’. In total, 2016 genes of S. profunda could not be matched towards the K. stuttgartiensis metagenome assembly at all, and a similar number of genes in K. stuttgartiensis could not be found in S. profunda. Most of these genes did not have a known function but 98 expressed genes could be attributed to oligopeptide transport, amino acid metabolism, use of organic acids and electron transport. Around the basis of the S. profunda metagenome, and environmental metagenome data, we observed pronounced differences within the gene organization and expression of critical anammox enzymes, such as hydrazine synthase (HzsAB), nitrite reductase (NirS) and inorganic nitrogen transport proteins. Adaptations of Scalindua for the substrate limitation of the ocean may possibly include highly expressed ammonium, nitrite and oligopeptide transport systems and pathways for the transport, oxidation, and assimilation of small?2012 Society for Applied Microbiology and Blackwell Publishing Ltd1276 J.Buy1398507-82-8 van de Vossenberg et al.1-(4-Aminophenyl)-2-bromoethan-1-one Chemscene organic compounds that may allow a more versatile lifestyle contributing to the competitive fitness of Scalindua within the marine realm.PMID:33478281 Introduction Anaerobic ammonium oxidation (anammox) is a microbially mediated process that was predicted in 1977 as an important missing link in nature (Broda, 1977). In this exergonic process, ammonium is oxidized by equimolar amounts of nitrite to nitrogen gas (N2) because the final product. In 1995 the process was discovered in a nitrogenremoving bioreactor (Mulder et al., 1995), and the responsible group of bacteria was identified a few years later (Strous et al., 1999). The first anammox bacterial cultures had been enriched from wastewater treatment environments, and therefore the initial focus of anammox research was on the application of these bacteria (Kartal et al., 2010a). However, it soon became clear th.