The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1
Ralf Rabus (1) , Michael Kube (2), Johann Heider (3), Alfred Beck (2), Katja Heitmann (2), Friedrich Widdel (1) and Richard Reinhardt (2)

(1) Max Planck Institut fuer Marine Mikrobiologie, Celsiusstrasse 1, 28359 Bremen, Germany
(2) Max Planck Institut fuer Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, Germany
(3) Institut fuer Biologie II, Mikrobiologie, Universität Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
The original publication is available at www.springerlink.com.

Recent research on microbial degradation of aromatic and other refractory compounds in anoxic waters and soils has revealed that nitrate-reducing bacteria belonging to the Betaproteobacteria contribute substantially to this process. Here we present the first complete genome of a metabolically versatile representative, strain EbN1, which metabolizes various aromatic compounds, including hydrocarbons. A circular chromosome (4.3 Mb) and two plasmids (0.21 and 0.22 Mb) encode 4603 predicted proteins. Ten anaerobic and four aerobic aromatic degradation pathways were recognized, with the encoding genes mostly forming clusters. The presence of paralogous gene clusters (e.g., for anaerobic phenylacetate oxidation), high sequence similarities to orthologs from other strains (e.g., for anaerobic phenol metabolism) and frequent mobile genetic elements (e.g., more than 200 genes for transposases) suggest high genome plasticity and extensive lateral gene transfer during metabolic evolution of strain EbN1. Metabolic versatility is also reflected by the presence of multiple respiratory complexes. A large number of regulators, including more than 30 two-component and several FNR-type regulators, indicate a finely tuned regulatory network able to respond to the fluctuating availability of organic substrates and electron acceptors in the environment. The absence of genes required for nitrogen fixation and specific interaction with plants separates strain EbN1 ecophysiologically from the closely related nitrogen-fixing plant symbionts of the Azoarcus cluster. Supplementary material on sequence and annotation are provided at the Web page http://www.micro-genomes.mpg.de/ebn1/.

Electronic Supplementary Material Supplementary material is available for this article at http://dx.doi.org/10.1007/s00203-004-0742-9.

Keywords: Complete genome - Anaerobic degradation - Aromatic compounds - Denitrifying bacterium - Betaproteobacteria

Dedicated to Prof. Dr. Dr. h.c. Gerhard Gottschalk on the occasion of his 70th birthday.