Bacterial metabolic networks channeling the biodegradation of PAHs in contaminated soils. Oxy-PAHs as catabolic nodes

Abstract

Polycyclic aromatic hydrocarbons (PAHs) are major environmental pollutants in a number of point source contaminated sites, where they are found embedded in complex mixtures containing different polyaromatic compounds. The application of bioremediation technologies is often constrained by unpredictable end-point concentrations, enriched in recalcitrant high molecular weight (HMW)-PAHs, and by the formation of generally overlooked PAH transformation products, such as oxygenated-PAHs (oxy-PAHs). The starting hypothesis of the Thesis was that cometabolic interactions and partial oxidation processes could play an essential role in channeling PAH carbon fluxes, with oxy-PAHs acting as potential catabolic nodes. The general objective is to expand the knowledge on the metabolic networks that drive the biological removal of PAHs in contaminated soils. Benz(a)anthracene (BaA) was used as a model to unravel the microbial populations and functions involved in the biodegradation of HMW-PAHs. The combination of DNA-SIP and shotgun metagenomics of 13C-labeled DNA allowed the unequivocal identification and functional analysis of the key BaA-degrading phylotype, a member of the novel genus Immundisolibacter. Analysis of the corresponding metagenome assembled genome (MAG) revealed a highly conserved genetic organization unique within this genus, including novel aromatic ring-hydroxylating dioxygenases. The influence of other HMW-PAHs on BaA degradation was ascertained in soil microcosms spiked with BaA and fluoranthene (FT), pyrene (PY) or chrysene (CHY) in binary mixtures. Co-incubation of PAHs resulted in a major delay in the removal of the less soluble PAHs and an increased formation of benz(a)anthracene-7,12-dione (BaAQ), the ready oxidation product from BaA, which was associated to relevant microbial interactions. To elucidate the mechanisms driving oxy-PAH biodegradation we isolated a 9,10-anthraquinone (ANTQ)-degrading bacterial strain, Sphingobium sp. AntQ-1. The metabolomic, genomic and transcriptomic characterization of the isolate served to reconstruct the ANTQ catabolic pathway, initiated by two sequential Baeyer-Villiger oxidations. Essential genes for the biodegradation of ANTQ were located in the megaplasmid pANTQ-1. The environmental relevance of the strain and the identified degradative mechanisms were confirmed by qPCR assessment during a previous biostimulation experiment of the creosote- contaminated soil. The metabolic networks involved in oxy-PAH biodegradation were investigated using a BaAQ-degrading microbial consortium obtained by enrichment in sand-in-liquid cultures with BaAQ as sole carbon source. The integration of data from metabolomic and metagenomic functional gene analyses revealed that the BaAQ metabolic pathway was probably initiated by the Baeyer-

Villiger monooxygenases encoded in pANTQ-1, indicating horizontal gene transfer phenomena. Our results suggest that Baeyer-Villiger oxidations, infrequent during PAH-biodegradation, could be a relevant mechanism for the processing of oxy-PAHs in contaminated sites, thus contributing to mitigate the potential risk of their accumulation. Further analysis of the BaAQ-degrading community MAGs also provided an insight into the potential roles and interactions within the consortium members. Several potential auxotrophies were detected, indicating that relevant interactions were taking place within the community members, not only to provide suitable carbon and energy sources, but also to supply essential nutrients and cofactors.