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.

Biodegradation of toxic organic compounds using a newly isolated Bacillus sp. CYR2

“…The USEPA has identified 16 PAH compounds as the priority pollutants [12]. Duarte et al (2017) used a culture-independent screening approach to analyse the aerobic microbial catabolome for PAHs degradation of a soil subjected to 12 years of in situ bioremediation [13]. A total of 422,750 fosmid clones were screened for key aromatic Wastewaters with high concentration of these organic compounds can be treated mainly by physicochemical processes such as Fenton's reagent, ozonation, UV, and H2O2 treatment.…”

From Functional Potential of Soil Bacterial Communities Towards Petroleum Hydrocarbons Bioremediation

“…Metagenomics, a technology based on shotgun sequencing, allows the study of total genomes from a microbial community. The assemblage of functional groups is essential to predict for example pathways that mediate key reactions in the hydrocarbon biodegradation process (Duarte et al 2017;Sharpton 2014). Metabarcoding and metagenomics analyses can be combined with targeted functional gene analyses to characterize the metabolic potential of uncultured organisms.…”

Identification by MALDI-TOF MS of Environmental Bacteria with High Potential to Degrade Pyrene

“…have been reported and their degradation pathways have subsequently been studied through chemical and omics analyses [23,[26][27][28]. Biodegradation by bacteria has been further advanced through the documentation of new isolates that represent diverse bacterial types that have been isolated from different environments and that possess different metabolic capabilities [18,29,30]. Therefore, in this work we carried out the isolation of indigenous bacteria from seawater and marine sediments samples through the enrichment method using pyrene as the sole carbon and energy source.…”