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Deciphering the evolution and metabolism of an anammox bacterium from a community genome

Abstract

Anaerobic ammonium oxidation (anammox) has become a main focus in oceanography and wastewater treatment1,2. It is also the nitrogen cycle's major remaining biochemical enigma. Among its features, the occurrence of hydrazine as a free intermediate of catabolism3,4, the biosynthesis of ladderane lipids5,6 and the role of cytoplasm differentiation7 are unique in biology. Here we use environmental genomics8,9—the reconstruction of genomic data directly from the environment—to assemble the genome of the uncultured anammox bacterium Kuenenia stuttgartiensis10 from a complex bioreactor community. The genome data illuminate the evolutionary history of the Planctomycetes and allow us to expose the genetic blueprint of the organism's special properties. Most significantly, we identified candidate genes responsible for ladderane biosynthesis and biological hydrazine metabolism, and discovered unexpected metabolic versatility.

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Acknowledgements

Preliminary sequence data from G. obscuriglobus was obtained from The Institute for Genomic Research through the website at http://www.tigr.org. Sequencing of G. obscuriglobus was accomplished with support from the United States Department of Energy. A. Cabezas is acknowledged for technical assistance. M.H., A.C. and M.W. were supported by the Austrian Ministry for Science and Education. M.T. was funded by the German Federal Ministry for Education and Research (Biolog II). H.D. was supported by the Wiener Wissenschafts-, Forschungs- und Technologiefonds (WWTF). We thank B. Anneser, F. Maixner, M. Leitner, A. Pol and B. Meijerink for help in the first round annotation and M. Ott for his effort in high performance phylogenetic treeing. The Dutch anammox research was supported by the Netherlands Science Foundation for Earth and Life Science (ALW), the Foundation for Applied Research (STW) and the European Union. The Radboud University and S. Wendelaar Bonga financially supported the initial phase of the project.

Author information

Correspondence to Mike S. M. Jetten or Michael Wagner.

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Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.

Supplementary information

Supplementary Figure legends

(DOC 27 kb)

Supplementary Methods

(PDF 127 kb)

Supplementary Figure 1

Maximum-likelihood tree displaying the16S rRNA gene diversity in the anammox enrichment culture from which the K. stuttgartiensis genome was reconstructed. (PDF 57 kb)

Supplementary Figure 2

Representation of the K. stuttgartiensis chromosome including annotated coding sequences and RNA genes. (PDF 425 kb)

Supplementary Figure 3

Functional redundancy in catabolism and respiration in K. stuttgartiensis compared to other bacteria. (PDF 130 kb)

Supplementary Figure 4

Phylogenetic consensus tree based on concatenated 5S-16S-23S rRNA sequences, showing the phylogenetic positioning of K. stuttgartiensis within the Bacteria. (PDF 15 kb)

Supplementary Figure 5

Distance (FITCH with the Dayhoff-PAM model), maximum parsimony (MP) and maximum likelihood (PHYML with the Dayhoff-PAM model) phylogenetic trees based on 26 concatenated ribosomal protein sequences (see Supplementary Methods), showing the phylogenetic positioning of K. stuttgartiensis within the Bacteria. (PDF 25 kb)

Supplementary Table 1

General features of the Kuenenia stuttgartiensis genome and comparison with Rhodopirellula baltica. (PDF 16 kb)

Supplementary Table 2

Genes with known homologues involved in respiration. (PDF 24 kb)

Supplementary Table 3

Iron and manganese respiration by the anammox bacterium Kuenenia stuttgartiensis. (PDF 82 kb)

Supplementary Table 4

Genes with known homologues involved in carbon metabolism. (PDF 16 kb)

Supplementary Table 5

CO2 fixation pathway in Kuenenia stuttgartiensis. (PDF 29 kb)

Supplementary Table 6

Proteins (gene names) used for phylogenetic analysis. (PDF 18 kb)

Supplementary Table 7

List of orthologous groups (OG) in which both Chlamydiae and Planctomycetes are heavily represented, to the exclusion of most other sequenced bacteria. (PDF 39 kb)

Supplementary Table 8

Genes with homologues involved in peptidoglycan biosynthesis and cell division. (PDF 12 kb)

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Further reading

Figure 1: Metabolic pathways of K. stuttgartiensis inferred from the present genomic data, previous experimental evidence and thermodynamic calculations.
Figure 2: The operons representing the best candidates to encode hydrazine hydrolase (hh) and hydrazine dehydrogenase (hd).
Figure 3: The largest of four operons encoding fatty acid biosynthesis in K. stuttgartiensis (ORFs kuste3352 kuste3335).
Figure 4: Unrooted phylogenetic consensus tree based on 49 concatenated protein sequences, showing the phylogenetic positioning of K. stuttgartiensis within the Bacteria.

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