title: Functional soil metagenomics: elucidation of polycyclic aromatic hydrocarbon degradation potential following 12 years of in situ bioremediation.
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.
authors.affiliation: Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124, Germany.
authors.forename: Márcia
authors.initials: M
authors.lastname: Duarte
authors.affiliation: Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124, Germany.
authors.forename: Agnes
authors.initials: A
authors.lastname: Nielsen
authors.affiliation: Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124, Germany.
authors.forename: Amélia
authors.initials: A
authors.lastname: Camarinha-Silva
authors.affiliation: Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124, Germany.|Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University, Magdeburg, Germany.
authors.forename: Ramiro
authors.initials: R
authors.lastname: Vilchez-Vargas
authors.affiliation: Institut de Génomique, Genoscope, UMR8030 (CNRS, CEA, Université d'Evry), Evry, France.
authors.forename: Thomas
authors.initials: T
authors.lastname: Bruls
authors.affiliation: Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124, Germany.
authors.forename: Melissa L
authors.initials: ML
authors.lastname: Wos-Oxley
authors.affiliation: Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124, Germany.|AgResearch Grasslands, Tennent drive, Palmerston North, New Zealand.
authors.forename: Ruy
authors.initials: R
authors.lastname: Jauregui
authors.affiliation: Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124, Germany.
authors.forename: Dietmar H
authors.initials: DH
authors.lastname: Pieper
mesh_terms: D001483:Base Sequence; D001673:Biodegradation, Environmental; D001713:Biphenyl Compounds / Q000737:chemistry; D002396:Catechols / Q000737:chemistry; D004269:DNA, Bacterial / Q000235:genetics; D020563:Gammaproteobacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism*; D059014:High-Throughput Nucleotide Sequencing; D056186:Metagenomics / Q000379:methods; D010105:Oxygenases / Q000235:genetics; D010802:Phylogeny; D011084:Polycyclic Aromatic Hydrocarbons / Q000378:metabolism*; D043362:Rhodocyclaceae / Q000145:classification / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism*; D012987:Soil; D012988:Soil Microbiology
chemical_list: D001713:Biphenyl Compounds; D002396:Catechols; D004269:DNA, Bacterial; D011084:Polycyclic Aromatic Hydrocarbons; D012987:Soil; C454813:2,3-dihydroxybiphenyl; D010105:Oxygenases; C439587:extradiol dioxygenase