Volume 19, Issue 8 p. 2992-3011
Research article

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

Márcia Duarte

Márcia Duarte

Microbial Interactions and Processes Research Group, HZI – Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124 Germany

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Agnes Nielsen

Agnes Nielsen

Microbial Interactions and Processes Research Group, HZI – Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124 Germany

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Amélia Camarinha-Silva

Amélia Camarinha-Silva

Microbial Interactions and Processes Research Group, HZI – Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124 Germany

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Ramiro Vilchez-Vargas

Ramiro Vilchez-Vargas

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

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Thomas Bruls

Thomas Bruls

Institut de Génomique, Genoscope, UMR8030 (CNRS, CEA, Université d'Evry), Evry, France

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Melissa L. Wos-Oxley

Melissa L. Wos-Oxley

Microbial Interactions and Processes Research Group, HZI – Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124 Germany

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Ruy Jauregui

Ruy Jauregui

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

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Dietmar H. Pieper

Corresponding Author

Dietmar H. Pieper

Microbial Interactions and Processes Research Group, HZI – Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124 Germany

For correspondence. E-mail [email protected]; Tel. (+49) 531 6181 4200;Search for more papers by this author
First published: 12 April 2017
Citations: 35

Summary

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.