Functional soil metagenomics: elucidation of polycyclic aromatic hydrocarbon degradation potential following 12 years of in situ bioremediation.

2.50
Hdl Handle:
http://hdl.handle.net/10033/621086
Title:
Functional soil metagenomics: elucidation of polycyclic aromatic hydrocarbon degradation potential following 12 years of in situ bioremediation.
Authors:
Duarte, Márcia; Nielsen, Agnes; Camarinha-Silva, Amélia; Vilchez-Vargas, Ramiro ( 0000-0002-7220-258X ) ; Bruls, Thomas; Wos-Oxley, Melissa L; Jauregui, Ruy; Pieper, Dietmar H.
Abstract:
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.
Affiliation:
Helmholtz Centre for infection research GmbH, Inhoffenstr.7, 38124 Braunschweig, Germany.
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.
Journal:
Environmental microbiology
Issue Date:
Aug-2017
URI:
http://hdl.handle.net/10033/621086
DOI:
10.1111/1462-2920.13756
PubMed ID:
28401633
Type:
Article
Language:
en
ISSN:
1462-2920
Appears in Collections:
publications of the research group microbial interactions and processes (MINP)

Full metadata record

DC FieldValue Language
dc.contributor.authorDuarte, Márciaen
dc.contributor.authorNielsen, Agnesen
dc.contributor.authorCamarinha-Silva, Améliaen
dc.contributor.authorVilchez-Vargas, Ramiroen
dc.contributor.authorBruls, Thomasen
dc.contributor.authorWos-Oxley, Melissa Len
dc.contributor.authorJauregui, Ruyen
dc.contributor.authorPieper, Dietmar H.en
dc.date.accessioned2017-09-01T14:37:32Z-
dc.date.available2017-09-01T14:37:32Z-
dc.date.issued2017-08-
dc.identifier.citationFunctional soil metagenomics: elucidation of polycyclic aromatic hydrocarbon degradation potential following 12 years of in situ bioremediation. 2017, 19 (8):2992-3011 Environ. Microbiol.en
dc.identifier.issn1462-2920-
dc.identifier.pmid28401633-
dc.identifier.doi10.1111/1462-2920.13756-
dc.identifier.urihttp://hdl.handle.net/10033/621086-
dc.description.abstractA 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.en
dc.language.isoenen
dc.rights.urihttp://creativecommons.org/licenses/by-nc-sa/4.0/*
dc.titleFunctional soil metagenomics: elucidation of polycyclic aromatic hydrocarbon degradation potential following 12 years of in situ bioremediation.en
dc.typeArticleen
dc.contributor.departmentHelmholtz Centre for infection research GmbH, Inhoffenstr.7, 38124 Braunschweig, Germany.en
dc.identifier.journalEnvironmental microbiologyen

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