title: Elucidation of in situ polycyclic aromatic hydrocarbon degradation by functional metaproteomics (protein-SIP).
abstract: Current knowledge of the physiology and phylogeny of polycyclic aromatic hydrocarbon (PAH) degrading bacteria often relies on laboratory enrichments and isolations. In the present study, in situ microcosms consisting of activated carbon pellets (BACTRAP®s) were loaded with either (13) C-naphthalene or (13) C-fluorene and were subsequently exposed in the contaminant source and plume fringe region of a PAH-contaminated aquifer. Metaproteomic analysis and protein-stable isotope probing revealed Burkholderiales, Actinomycetales, and Rhizobiales as the most active microorganisms in the groundwater communities. Proteins identified of the naphthalene degradation pathway showed a relative (13) C isotope abundance of approximately 50 atom% demonstrating that the identified naphthalene-degrading bacteria gained at least 80% of their carbon by PAH degradation. Although the microbial community grown on the fluorene-BACTRAPs showed a structure similar to the naphthalene-BACTRAPs, the identification of fluorene degraders and degradation pathways failed in situ. In complementary laboratory microcosms, a clear enrichment in proteins related to Rhodococcus and possible fluorene degradation enzymes was observed. This result demonstrates the impact of laboratory conditions on microbial community structure and activity of certain species and underlines the need on in situ exploration of microbial community functions. In situ microcosms in combination with protein-stable isotope probing may be a significant tool for in situ identification of metabolic key players as well as degradation pathways.
authors.affiliation: Department of Proteomics, UFZ - Helmholtz Centre for Environmental Research, Leipzig, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany.
authors.forename: Florian-Alexander
authors.initials: FA
authors.lastname: Herbst
authors.forename: Arne
authors.initials: A
authors.lastname: Bahr
authors.forename: Marcia
authors.initials: M
authors.lastname: Duarte
authors.forename: Dietmar H
authors.initials: DH
authors.lastname: Pieper
authors.forename: Hans-Hermann
authors.initials: HH
authors.lastname: Richnow
authors.forename: Martin
authors.initials: M
authors.lastname: von Bergen
authors.forename: Jana
authors.initials: J
authors.lastname: Seifert
authors.forename: Petra
authors.initials: P
authors.lastname: Bombach
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism; D001673:Biodegradation, Environmental; D005449:Fluorenes; D007553:Isotope Labeling; D056186:Metagenomics; D064307:Microbiota; D009281:Naphthalenes / Q000737:chemistry / Q000378:metabolism; D011084:Polycyclic Aromatic Hydrocarbons / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*
chemical_list: D001426:Bacterial Proteins; D005449:Fluorenes; D009281:Naphthalenes; D011084:Polycyclic Aromatic Hydrocarbons; C031721:naphthalene; C041509:fluorene
keywords: Aerobic PAH degradation; BACTRAP; Functional metaproteomics; Groundwater natural attenuation; Microbiology; Protein-SIP