Rabus R, Kube M, Heider J, Beck A, Heitmann K, Widdel F et al.. The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1. Arch Microbiol 183: 27-36

Max Planck Institut für Marine Mikrobiologie, Celsiusstrasse 1, 28359, Bremen, Germany.
Archives of Microbiology (Impact Factor: 1.67). 02/2005; 183(1):27-36. DOI: 10.1007/s00203-004-0742-9
Source: PubMed


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

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    • "Even with the complete genome sequences of microorganisms with the potential for bioremediation studies are not accelerating in a rapid manner (Heidelberg et al., 2002; Tiedje and Shewanella, 2002; Golyshin et al., 2003; Rabus et al., 2005; Seshadri et al., 2005). With the completed genome sequences, it is possible to analyze the expression of all genes in each genome under various environmental conditions using wholegenome DNA microarrays (Muffler et al., 2002; Schut et al., 2003; Gao et al., 2004). "
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    • "BclA activates benzoate aerobically and anaerobically but also catalyses 2-aminobenzoyl-CoA formation in T. aromatica (Schühle et al., 2003). In contrast, in other denitrifying microorganisms, such as Azoarcus/'Aromatoleum' strains (Rabus et al., 2005; Carmona et al., 2009), as well as in the phototroph R. palustris (Egland et al., 1995), every catabolic cluster appears to have its own specific CoA ligase gene, e.g. the bzdA and bclA genes from the "
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