title: The metagenome of the marine anammox bacterium 'Candidatus Scalindua profunda' illustrates the versatility of this globally important nitrogen cycle bacterium.
abstract: Anaerobic ammonium-oxidizing (anammox) bacteria are responsible for a significant portion of the loss of fixed nitrogen from the oceans, making them important players in the global nitrogen cycle. To date, marine anammox bacteria found in marine water columns and sediments worldwide belong almost exclusively to 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 the most abundant gene transcripts and proteins. In the S. profunda assembly, 4756 genes were annotated, and only about half of them showed the highest identity to 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 to 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. On the basis of the S. profunda metagenome, and environmental metagenome data, we observed pronounced differences in the gene organization and expression of important anammox enzymes, such as hydrazine synthase (HzsAB), nitrite reductase (NirS) and inorganic nitrogen transport proteins. Adaptations of Scalindua to the substrate limitation of the ocean may include highly expressed ammonium, nitrite and oligopeptide transport systems and pathways for the transport, oxidation, and assimilation of small organic compounds that may allow a more versatile lifestyle contributing to the competitive fitness of Scalindua in the marine realm.
authors.affiliation: Department of Microbiology, IWWR, Radboud University Nijmegen, 6525 AJ Nijmegen, the Netherlands.
authors.forename: Jack
authors.initials: J
authors.lastname: van de Vossenberg
authors.forename: Dagmar
authors.initials: D
authors.lastname: Woebken
authors.forename: Wouter J
authors.initials: WJ
authors.lastname: Maalcke
authors.forename: Hans J C T
authors.initials: HJ
authors.lastname: Wessels
authors.forename: Bas E
authors.initials: BE
authors.lastname: Dutilh
authors.forename: Boran
authors.initials: B
authors.lastname: Kartal
authors.forename: Eva M
authors.initials: EM
authors.lastname: Janssen-Megens
authors.forename: Guus
authors.initials: G
authors.lastname: Roeselers
authors.forename: Jia
authors.initials: J
authors.lastname: Yan
authors.forename: Daan
authors.initials: D
authors.lastname: Speth
authors.forename: Jolein
authors.initials: J
authors.lastname: Gloerich
authors.forename: Wim
authors.initials: W
authors.lastname: Geerts
authors.forename: Erwin
authors.initials: E
authors.lastname: van der Biezen
authors.forename: Wendy
authors.initials: W
authors.lastname: Pluk
authors.forename: Kees-Jan
authors.initials: KJ
authors.lastname: Francoijs
authors.forename: Lina
authors.initials: L
authors.lastname: Russ
authors.forename: Phyllis
authors.initials: P
authors.lastname: Lam
authors.forename: Stefanie A
authors.initials: SA
authors.lastname: Malfatti
authors.forename: Susannah Green
authors.initials: SG
authors.lastname: Tringe
authors.forename: Suzanne C M
authors.initials: SC
authors.lastname: Haaijer
authors.forename: Huub J M
authors.initials: HJ
authors.lastname: Op den Camp
authors.forename: Henk G
authors.initials: HG
authors.lastname: Stunnenberg
authors.forename: Rudi
authors.initials: R
authors.lastname: Amann
authors.forename: Marcel M M
authors.initials: MM
authors.lastname: Kuypers
authors.forename: Mike S M
authors.initials: MS
authors.lastname: Jetten
mesh_terms: D059001:Aquatic Organisms / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D016680:Genome, Bacterial; D054892:Metagenome; D009572:Nitrite Reductases / Q000378:metabolism; D058458:Nitrogen Cycle; D009792:Oceans and Seas; D010084:Oxidation-Reduction; D061328:Planctomycetales / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D000644:Quaternary Ammonium Compounds / Q000378:metabolism; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D014871:Water Microbiology
chemical_list: D000644:Quaternary Ammonium Compounds; D012336:RNA, Ribosomal, 16S; D009572:Nitrite Reductases