Functional soil metagenomics: elucidation of polycyclic aromatic hydrocarbon degradation potential following 12 years of in situ bioremediation.
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Authors
Duarte, MárciaNielsen, Agnes
Camarinha-Silva, Amélia
Vilchez Vargas, Ramiro
Bruls, Thomas
Wos-Oxley, Melissa L
Jauregui, Ruy
Pieper, Dietmar H.
Issue Date
2017-08
Metadata
Show full item recordAbstract
A culture-independent function-based screening approach was used to assess the microbial aerobic catabolome for polycyclic aromatic hydrocarbons degradation of a soil subjected to 12 years of in situ bioremediation. A total of 422 750 fosmid clones were screened for key aromatic ring-cleavage activities using 2,3-dihydroxybiphenyl as substrate. Most of the genes encoding ring-cleavage enzymes on the 768 retrieved positive fosmids could not be identified using primer-based approaches and, thus, 205 fosmid inserts were sequenced. Nearly two hundred extradiol dioxygenase encoding genes of three different superfamilies could be identified. Additional key genes of aromatic metabolic pathways were identified, including a high abundance of Rieske non-heme iron oxygenases that provided detailed information on enzymes activating aromatic compounds and enzymes involved in activation of the side chain of methylsubstituted aromatics. The gained insights indicated a complex microbial network acting at the site under study, which comprises organisms similar to recently identified Immundisolibacter cernigliae TR3.2 and Rugosibacter aromaticivorans Ca6 and underlined the great potential of an approach that combines an activity-screening, a cost-effective high-throughput sequencing of fosmid clones and a phylogenomic-routed and manually curated database to carefully identify key proteins dedicated to aerobic degradation of aromatic compounds.Citation
Functional soil metagenomics: elucidation of polycyclic aromatic hydrocarbon degradation potential following 12 years of in situ bioremediation. 2017, 19 (8):2992-3011 Environ. Microbiol.Affiliation
Helmholtz Centre for infection research GmbH, Inhoffenstr.7, 38124 Braunschweig, Germany.Journal
Environmental microbiologyPubMed ID
28401633Type
ArticleLanguage
enISSN
1462-2920ae974a485f413a2113503eed53cd6c53
10.1111/1462-2920.13756
Scopus Count
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Except where otherwise noted, this item's license is described as http://creativecommons.org/licenses/by-nc-sa/4.0/