title: Impact of dibenzofuran/dibenzo-p-dioxin amendment on bacterial community from forest soil and ring-hydroxylating dioxygenase gene populations.
abstract: The impact of dibenzofuran (DF) and dibenzo-p-dioxin (DD) on the changes in bacterial community structure and the transition of catabolic genes were studied using forest soil. The bacterial community structure of soil suspensions amended with 1 microg/g of either DF or DD was analyzed by 16S rRNA and functional gene sequencing. To analyze the functional genes in the communities, we targeted a gene sequence that functions as the binding site of Rieske iron sulfur center common to ring-hydroxylating dioxygenases (RHDs) for monocyclic, bicyclic, and tricyclic aromatic compounds. The gene fragments were polymerase chain reaction-amplified from DNAs extracted from soil suspensions spiked with either DF or DD, cloned, and sequenced (70 clones). Bacterial community analysis based on 16S rRNA genes revealed that specific 16S rRNA gene sequences, in particular, phylotypes within alpha-Proteobacteria, increased in the soil suspension amended with DF or DD. RHD gene-based functional community analysis showed that, in addition to two groups of RHD genes that were also detected in unamended soil suspensions, another two groups of RHD genes, each of which is specific to DF- and DD-amended soil, respectively, emerged to a great extent. The DD-specific genotype is phylogenetically distant from any known RHDs. These results strongly suggest that soil microbial community potentially harbors a wide array of organisms having diverse RHDs including those previously unknown, and that they could quickly respond to an impact of contamination of hazardous chemicals by changing the microbial community and gene diversity.
authors.affiliation: Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan. n-kimura@aist.go.jp
authors.forename: Nobutada
authors.initials: N
authors.lastname: Kimura
authors.forename: Yoichi
authors.initials: Y
authors.lastname: Kamagata
mesh_terms: D001419:Bacteria / Q000145:classification / Q000187:drug effects / Q000201:enzymology / Q000235:genetics*; D001483:Base Sequence; D001572:Benzofurans / Q000494:pharmacology*; D044822:Biodiversity; D004147:Dioxins / Q000494:pharmacology*; D049308:Dioxygenases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D014450:Electron Transport Complex III / Q000737:chemistry; D005798:Genes, Bacterial / Q000187:drug effects; D006900:Hydroxylation / Q000187:drug effects; D008969:Molecular Sequence Data; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000378:metabolism; D012987:Soil / Q000032:analysis; D012988:Soil Microbiology; D014197:Trees
chemical_list: D001572:Benzofurans; D004147:Dioxins; D012336:RNA, Ribosomal, 16S; C037989:Rieske iron-sulfur protein; D012987:Soil; C023614:dibenzofuran; D049308:Dioxygenases; D014450:Electron Transport Complex III; C020887:dibenzo(1,4)dioxin