Bioinformática

The ISME Journal (2009) 3, 1335–1348
& 2009 International Society for Microbial Ecology All rights reserved 1751-7362/09 $32.00 www.nature.com/ismej ORIGINAL ARTICLE

Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis
Hikaru Suenaga1, Yoshinori Koyama1, Masatoshi Miyakoshi2, Ryo Miyazaki2,5, Hirokazu
Yano2,6, Masahiro Sota3, Yoshiyuki Ohtsubo2, Masataka Tsuda2 and Kentaro Miyazaki1,4
1

Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and
Technology (AIST), Tsukuba Central 6, Tsukuba, Ibaraki, Japan; 2Department of Environmental Life Sciences,
Graduate School of Life Sciences, Tohoku University, Katahira, Sendai, Japan; 3Integrated Technology
Development Team, R & D Center, Nagase Co. Ltd., Nishi-ku, Kobe, Japan and 4Department of Medical
Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tsukuba Central 6,
Tsukuba, Ibaraki, Japan

Several types of environmental bacteria that can aerobically degrade various aromatic compounds have been identified. The catabolic genes in these bacteria have generally been found to form operons, which promote efficient and complete degradation. However, little is known about the degradation pathways in bacteria that are difficult to culture in the laboratory. By functionally screening a metagenomic library created from activated sludge, we had earlier identified 91 fosmid clones carrying genes for extradiol dioxygenase (EDO), a key enzyme in the degradation of aromatic compounds. In this study, we analyzed
38 of these fosmids for the presence and organization of novel genes for aromatics degradation. Only two of the metagenomic clones contained complete degradation pathways similar to those found in known aromatic compound-utilizing bacteria. The rest of the clones contained only subsets of the pathway genes, with novel gene arrangements. A circular 36.7-kb