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.

Nitrate-Dependent Ferrous Iron Oxidation by Anaerobic Ammonium Oxidation (Anammox) Bacteria

“…DNRA is the likely pathway for NO 3 Ϫ reduction to NH 4 ϩ via NO 2 Ϫ , as previously demonstrated by anammox bacteria other than "Ca. Brocadia sinica" (21,22,51). Indeed, we found that "Ca.…”

Microbial oceanography of anoxic oxygen minimum zones

“…4), dominate the gene expression libraries in the upper oxic waters (50 m), in the lower oxic zone (85 m), and in the transition zone (110 m). Transcripts of these aerobic organisms, however, are essentially absent in the core of the open-ocean AMZ at 200 m, where sequences matching the anammox bacterium "Candidatus Scalindua profunda" (30) are prominent (Fig. 3).…”

Anaerobic ammonium-oxidising bacteria: A biological source of the bacteriohopanetetrol stereoisomer in marine sediments

“…Kuenenia stuttgartiensis' by Strous et al (2006) and Pearson et al, (2007), and in the genome of 'Ca. Scalindua profunda' by van de Vossenberg et al (2013). Thus, anammox bacteria are capable of synthesising hopanoids, including BHT, in anoxic environments.…”