The metagenome of the marine anammox bacterium 'Candidatus Scalindua profunda' illustrates the versatility of this globally important nitrogen cycle bacterium.

Jack Van De Vossenberg,Phyllis Lam,Bas E Dutilh,Wendy Pluk,Mike S M Jetten,Erwin Van Der Biezen,Dagmar Woebken,Jolein Gloerich,Guus Roeselers,Boran Kartal,Wim Geerts,Huub J M Op Den Camp,Lina Russ,Jia Yan,Marcel M M Kuypers,Wouter J Maalcke,Suzanne Caroline Marianne Haaijer ,Rudolf Amann ,Eva M Janssen-Megens ,Stephanie Malfatti ,Daan R Speth ,Henk Stunnenberg ,Susannah G Tringe ,Hans Wessels ,Kees−Jan Françoijs

doi:10.1111/j.1462-2920.2012.02774.x

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.

Highlights

Anaerobic ammonium oxidation is a microbially mediated process that was predicted in 1977 as an important missing link in nature (Broda, 1977)
It soon became clear that marine anammox bacteria are responsible for a significant portion of nitrogen loss from stratified seas and from oceanic oxygen minimum zones (OMZs) where up to half of global marine nitrogen loss takes place (Kuypers et al, 2003; 2005; Lam et al, 2007; Jensen et al, 2011)
This agreed well with the fluorescence in situ hybridization (FISH) results and suggested that the large majority of the genomic DNA was derived from S. profunda

Summary

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. 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

Introduction

Method

Results and discussion

Conclusion

Experimental procedures