Bacterial benz(a)anthracene catabolic networks in contaminated soils and their modulation by other co-occurring HMW-PAHs

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. The aim of this study was to elucidate the microbial populations and potential interactions involved in the biodegradation of benz(a)anthracene (BaA) in PAH-contaminated soils. The combination of DNA stable isotope probing (DNA-SIP) and shotgun metagenomics of 13C-labeled DNA identified a member of the recently described genus Immundisolibacter as the key BaA-degrading population. Analysis of the corresponding metagenome assembled genome (MAG) revealed a highly conserved and unique genetic organization in this genus, including novel aromatic ring-hydroxylating dioxygenases (RHD). 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. The co-occurrence of PAHs resulted in a significant delay in the removal of PAHs that were more resistant to biodegradation, and this delay was associated with relevant microbial interactions. Members of Immundisolibacter, associated with the biodegradation of BaA and CHY, were outcompeted by Sphingobium and Mycobacterium, triggered by the presence of FT and PY, respectively. Our findings highlight that interacting microbial populations modulate the fate of PAHs during the biodegradation of contaminant mixtures in soils

Multi-omic profiling of a newly isolated Oxy-PAH degrading specialist from PAH-contaminated soil reveals bacterial mechanisms to mitigate the risk posed by polar transformation products

Polar biotransformation products have been identified as causative agents for the eventual increase in genotoxicity observed after the bioremediation of PAH-contaminated soils.Their further biodegradation has been described under certain biostimulation conditions; however, the underlying microorganisms and mechanisms remain to be elucidated. 9,10-Anthraquinone (ANTQ), a transformation product from anthracene (ANT), is the most commonly detected oxygenated PAH (oxy-PAH) in contaminated soils. Sand-in-liquid microcosms inoculated with creosote-contaminated soil revealed the existence of a specialized ANTQ degrading community, and Sphingobium sp. AntQ-1 was isolated for its ability to grow on this oxy-PAH. Combining the metabolomic, genomic, and transcriptomic analyses of strain AntQ-1, we comprehensively reconstructed the ANTQ biodegradation pathway. Novel mechanisms for polyaromatic compound degradation were revealed, involving the cleavage of the central ring catalyzed by Baeyer−Villiger monooxygenases (BVMO). Abundance of strain AntQ-1 16S rRNA and its BVMO genes in the sandin-liquid microcosms correlated with maximum ANTQ biodegradation rates, supporting the environmental relevance of this mechanism. Our results demonstrate the existence of highly specialized microbial communities in contaminated soils responsible for processing oxy-PAHs accumulated by primary degraders. Also, they underscore the key role that BVMO may play as a detoxification mechanism to mitigate the risk posed by oxy-PAH formation during bioremediation of PAH-contaminated soils

Rhizosphere-enhanced biosurfactant action on slowly desorbing PAHs incontaminated soil

We studied how sunflower plants affect rhamnolipid biosurfactant mobilization of slowly desorbing fractions of polycyclic aromatic hydrocarbons (PAHs) in soil froma creosote-contaminated site. Desorption kinetics of 13 individual PAHs revealed that the soil contained initially up to 50% slowly desorbing fractions. A rhamnolipid biosurfactantwas applied to the soil at the completion of the sunflower cycle (75 days in greenhouse conditions). After this period, the PAHs that remained in the soil were mainly present in a slowly desorbing form as a result of the efficient biodegradation of fast-desorbing PAHs by native microbial populations. The rhamnolipid enhanced the bioavailable fraction of the remaining PAHs by up to 30%, as evidenced by a standardized desorption extraction with Tenax, but the enhancement occurredwith only planted soils. The enhanced bioavailability did not decrease residual PAH concentrations under greenhouse conditions, possibly due to ecophysiological limitations in the biodegradation process thatwere independent of the bioavailability. However, biodegradationwas enhanced during slurry treatment of greenhouse planted soils that received the biosurfactant. The addition of rhamnolipids caused a dramatic shift in the soil bacterial community structure, which was magnified in the presence of sunflower plants. The stimulated groups were identified as fast-growing and catabolically versatile bacteria. This new rhizosphere microbial biomass possibly interacted with the biosurfactant to facilitate intra-aggregate diffusion of PAHs, thus enhancing the kinetics of slow desorption. Our results show that the usually limited biosurfactant efficiency with contaminated field soils can be significantly enhanced by integrating the sunflower ontogenetic cycle into the bioremediation design

Multi-Omic Profiling of a Newly Isolated Oxy-PAH Degrading Specialist from PAH-Contaminated Soil Reveals Bacterial Mechanisms to Mitigate the Risk Posed by Polar Transformation Products

Polar biotransformation products have been identified as causative agents for the eventual increase in genotoxicity observed after the bioremediation of PAH-contaminated soils. Their further biodegradation has been described under certain biostimulation conditions; however, the underlying microorganisms and mechanisms remain to be elucidated. 9,10-Anthraquinone (ANTQ), a transformation product from anthracene (ANT), is the most commonly detected oxygenated PAH (oxy-PAH) in contaminated soils. Sand-in-liquid microcosms inoculated with creosote-contaminated soil revealed the existence of a specialized ANTQ degrading community, and Sphingobium sp. AntQ-1 was isolated for its ability to grow on this oxy-PAH. Combining the metabolomic, genomic, and transcriptomic analyses of strain AntQ-1, we comprehensively reconstructed the ANTQ biodegradation pathway. Novel mechanisms for polyaromatic compound degradation were revealed, involving the cleavage of the central ring catalyzed by Baeyer-Villiger monooxygenases (BVMO). Abundance of strain AntQ-1 16S rRNA and its BVMO genes in the sand-in-liquid microcosms correlated with maximum ANTQ biodegradation rates, supporting the environmental relevance of this mechanism. Our results demonstrate the existence of highly specialized microbial communities in contaminated soils responsible for processing oxy-PAHs accumulated by primary degraders. Also, they underscore the key role that BVMO may play as a detoxification mechanism to mitigate the risk posed by oxy-PAH formation during bioremediation of PAH-contaminated soils