title: Diversity of benzyl- and alkylsuccinate synthase genes in hydrocarbon-impacted environments and enrichment cultures.
abstract: Hydrocarbon-degrading microorganisms play an important role in the natural attenuation of spilled petroleum in a variety of anoxic environments. The role of benzylsuccinate synthase (BSS) in aromatic hydrocarbon degradation and its use as a biomarker for field investigations are well documented. The recent discovery of alkylsuccinate synthase (ASS) allows the opportunity to test whether its encoding gene, assA, can serve as a comparable biomarker of anaerobic alkane degradation. Degenerate assA- and bssA-targeted PCR primers were designed in order to survey the diversity of genes associated with aromatic and aliphatic hydrocarbon biodegradation in petroleum-impacted environments and enrichment cultures. DNA was extracted from an anaerobic alkane-degrading isolate (Desulfoglaeba alkenexedens ALDC), hydrocarbon-contaminated river and aquifer sediments, a paraffin-degrading enrichment, and a propane-utilizing mixed culture. Partial assA and bssA genes were PCR amplified, cloned, and sequenced, yielding several novel clades of assA genes. These data expand the range of alkane-degrading conditions for which relevant gene sequences are available and indicate that considerable diversity of assA genes can be found in hydrocarbon-impacted environments. The detection of genes associated with anaerobic alkane degradation in conjunction with the in situ detection of alkylsuccinate metabolites was also demonstrated. Comparable molecular signals of assA/bssA were not found when environmental metagenome databases of uncontaminated sites were searched. These data confirm that the assA gene is a useful biomarker for anaerobic alkane metabolism.
authors.affiliation: Department of Botany and Microbiology and Institute for Energy and the Environment, University of Oklahoma, Norman, Oklahoma 73019, USA. acallaghan@ou.edu
authors.forename: Amy V
authors.initials: AV
authors.lastname: Callaghan
authors.forename: Irene A
authors.initials: IA
authors.lastname: Davidova
authors.forename: Kristen
authors.initials: K
authors.lastname: Savage-Ashlock
authors.forename: Victoria A
authors.initials: VA
authors.lastname: Parisi
authors.forename: Lisa M
authors.initials: LM
authors.lastname: Gieg
authors.forename: Joseph M
authors.initials: JM
authors.lastname: Suflita
authors.forename: Jerome J
authors.initials: JJ
authors.lastname: Kukor
authors.forename: Boris
authors.initials: B
authors.lastname: Wawrik
mesh_terms: D001483:Base Sequence; D001673:Biodegradation, Environmental; D019755:Carbon-Carbon Lyases / Q000235:genetics*; D017931:DNA Primers; D004785:Environmental Pollutants / Q000378:metabolism / Q000633:toxicity*; D006838:Hydrocarbons / Q000378:metabolism / Q000633:toxicity*; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D020560:Proteobacteria / Q000201:enzymology* / Q000235:genetics / Q000378:metabolism; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D017931:DNA Primers; D004785:Environmental Pollutants; D006838:Hydrocarbons; D012336:RNA, Ribosomal, 16S; D019755:Carbon-Carbon Lyases; C114354:benzylsuccinate synthase