Nontarget Analysis Reveals a Bacterial Metabolite of Pyrene Implicated in the Genotoxicity of Contaminated Soil after Bioremediation

Fingerprinting of emerging contaminants in L'Albufera natural park (Valencia, Spain): Implications for wetland ecosystem health

Wetlands are crucial ecosystems that are increasingly threatened by anthropogenic activities. L'Albufera Natural Park, the second-largest coastal wetland in Spain, faces significant pressures from surrounding agricultural lands, industrial activities, human settlements, and associated infrastructures, including treated wastewater inputs. This study aimed at (i) establishing pathways of emerging pollutants entering the natural wetland using both target and non-target screening (NTS) for management purposes, (ii) distinguishing specific contamination hotspots through Geographic Information System (GIS) and (iii) performing basic ecological risk assessment to evaluate ecosystem health. Two sampling campaigns were conducted in the spring and summer of 2019, coinciding with the start and end of the rice cultivation season, the region's primary agricultural activity. Each campaign involved the collection of 51 samples. High-resolution mass spectrometry (HRMS) was employed, using a simultaneous NTS approach with optimized gradients for pesticides and moderately polar compounds, along with complementary NTS methods for polar compounds, to identify additional contaminants of emerging concern (CECs). Quantitative analysis revealed that fungicides comprised a substantial portion of detected CECs, constituting approximately 50% of the total quantified pesticides. Tebuconazole emerged as the predominant fungicide, with the highest mean concentration (>16.9 μg L-1), followed by azoxystrobin and tricyclazole. NTS tentatively identified 16 pesticides, 43 pharmaceuticals and personal care products (PPCPs), 24 industrial compounds, and 12 other CECs with high confidence levels. Spatial distribution analysis demonstrated significant contamination predominantly in the southwestern region of the park, gradually diminishing towards the north-eastern outlet. The composition of contaminants varied between water and sediment samples, with pharmaceuticals predominating in water and industrial compounds in sediments. Risk assessment, evaluated through risk quotient calculations based on parent compound concentrations, revealed a decreasing trend towards the outlet, suggesting wetland degradation capacity. However, significant risk levels persist throughout much of the Natural Park, highlighting the urgent need for mitigation measures to safeguard the integrity of this vital ecosystem.

Neural network establishes co-occurrence links between transformation products of the contaminant and the soil microbiome

It remains challenging to establish reliable links between transformation products (TPs) of contaminants and corresponding microbes. This challenge arises due to the sophisticated experimental regime required for TP discovery and the compositional nature of 16S rRNA gene amplicon sequencing and mass spectrometry datasets, which can potentially confound statistical inference. In this study, we present a new strategy by combining the use of 2H-labeled Stable Isotope-Assisted Metabolomics (2H-SIAM) with a neural network-based algorithm (i.e., MMvec) to explore links between TPs of pyrene and the soil microbiome. The links established by this novel strategy were further validated using different approaches. Briefly, a metagenomic study provided indirect evidence for the established links, while the identification of pyrene degraders from soils, and a DNA-based stable isotope probing (DNA-SIP) study offered direct evidence. The comparison among different approaches, including Pearson's and Spearman's correlations, further confirmed the superior performance of our strategy. In conclusion, we summarize the unique features of the combined use of 2H-SIAM and MMvec. This study not only addresses the challenges in linking TPs to microbes but also introduces an innovative and effective approach for such investigations. Environmental Implication: Taxonomically diverse bacteria performing successive metabolic steps of the contaminant were firstly depicted in the environmental matrix.

Metagenomic insights into the microbial cooperative networks of a benz(a)anthracene-7,12-dione degrading community from a creosote-contaminated soil

Genotoxicity of PAH-contaminated soils can eventually increase after bioremediation due to the formation and accumulation of polar transformation products, mainly oxygenated PAHs (oxy-PAHs). Biodegradation of oxy-PAHs has been described in soils, but information on the microorganisms and mechanisms involved is still scarce. Benz(a)anthracene-7,12-dione (BaAQ), a transformation product from benz(a)anthracene frequently detected in soils, presents higher genotoxic potential than its parent PAH. Here, using sand-in-liquid microcosms we identified a specialized BaAQ-degrading subpopulation in a PAH-contaminated soil. A BaAQ-degrading microbial consortium was obtained by enrichment in sand-in-liquid cultures with BaAQ as sole carbon source, and its metagenomic analysis identified members of Sphingobium, Stenotrophomonas, Pusillimonas, Olivibacter, Pseudomonas, Achromobacter, and Hyphomicrobiales as major components. The integration of data from metabolomic and metagenomic functional gene analyses of the consortium revealed that the BaAQ metabolic pathway was initiated by Baeyer-Villiger monooxygenases (BVMOs). The presence of plasmid pANTQ-1 in the metagenomic sequences, identified in a previous multi-omic characterization of a 9,10-anthraquinone-degrading isolate recovered from the same soil, suggested the occurrence of a horizontal gene transfer event. Further metagenomic analysis of the BaAQ-degrading consortium also provided insights into the potential roles and interactions within the consortium members. Several potential auxotrophies were detected, indicating that relevant nutritional interdependencies and syntrophic associations were taking place within the community members, not only to provide suitable carbon and energy sources, but also to supply essential nutrients and cofactors. Our work confirms the essential role that BVMO may play as a detoxification mechanism to mitigate the risk posed by oxy-PAH formation during bioremediation of contaminated soils.

Low-temperature thermally enhanced bioremediation of polycyclic aromatic hydrocarbon-contaminated soil: Effects on fate, toxicity and bacterial communities

Remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated soil using thermal desorption technology typically requires very high temperatures, necessitating coupled microbial treatment for energy and cost reduction. This study investigated the fate and toxicity of PAHs as well as the responses of microbial communities following thermal treatment within a low temperature range. The optimal temperature for PAH mineralization was 20-28 °C, within the growth range of most mesophilic microorganisms. By contrast, 50 °C treatment almost completely inhibited PAH mineralization but resulted in the greatest detoxification effect particularly for cardiotoxicity and nephrotoxicity. A potential increase in toxicity was observed at 28 °C. Co-metabolism and non-extractable residue formation may play an interdependent role in thermally enhanced bioremediation. Moreover, alterations in bacterial communities were strongly associated with PAH mineralization and zebrafish toxicity, revealing that soil microorganisms play a direct role in PAH mineralization and served as ecological receptors reflecting changes in toxicity. Network analysis revealed that Firmicutes formed specific ecological communities at high temperature, whereas Acidobacteria and Proteobacteria act as primary PAH degraders at moderate temperature. These findings will enable better integration of strategies for thermal and microbial treatments in soil remediation.

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.

Transformation Products of Tire Rubber Antioxidant 6PPD in Heterogeneous Gas-Phase Ozonation: Identification and Environmental Occurrence

6PPD, a tire rubber antioxidant, poses substantial ecological risks because it can form a highly toxic quinone transformation product (TP), 6PPD-quinone (6PPDQ), during exposure to gas-phase ozone. Important data gaps exist regarding the structures, reaction mechanisms, and environmental occurrence of TPs from 6PPD ozonation. To address these data gaps, gas-phase ozonation of 6PPD was conducted over 24-168 h and ozonation TPs were characterized using high-resolution mass spectrometry. The probable structures were proposed for 23 TPs with 5 subsequently standard-verified. Consistent with prior findings, 6PPDQ (C18H22N2O2) was one of the major TPs in 6PPD ozonation (∼1 to 19% yield). Notably, 6PPDQ was not observed during ozonation of 6QDI (N-(1,3-dimethylbutyl)-N'-phenyl-p-quinonediimine), indicating that 6PPDQ formation does not proceed through 6QDI or associated 6QDI TPs. Other major 6PPD TPs included multiple C18H22N2O and C18H22N2O2 isomers, with presumptive N-oxide, N,N'-dioxide, and orthoquinone structures. Standard-verified TPs were quantified in roadway-impacted environmental samples, with total concentrations of 130 ± 3.2 μg/g in methanol extracts of tire tread wear particles (TWPs), 34 ± 4 μg/g-TWP in aqueous TWP leachates, 2700 ± 1500 ng/L in roadway runoff, and 1900 ± 1200 ng/L in roadway-impacted creeks. These data demonstrate that 6PPD TPs are likely an important and ubiquitous class of contaminants in roadway-impacted environments.

Risk reductions during pyrene biotransformation and mobilization in a model plant-bacteria-biochar system

The productive application of motile microorganisms for degrading hydrophobic contaminants in soil is one of the most promising processes in modern remediation due to its sustainability and low cost. However, the incomplete biodegradation of the contaminants and the formation of the intermediary metabolites in the process may increase the toxicity in soil during bioremediation, and motile inoculants may mobilize the pollutants through biosorption. Therefore, controlling these factors should be a fundamental part of soil remediation approaches. The aim of this study was to evaluate the sources of risk associated with the cometabolism-based transformation of ¹⁴C-labeled pyrene by inoculated Pseudomonas putida G7 and identify ways to minimize risk. Our model scenario examined the increase in bioaccessibility to a distant source of contamination facilitated by sunflower (Helianthus annuus L.) roots. A biochar trap for mobilized pollutant metabolites and bacteria has also been employed. The experimental design consisted of pots filled with a layer of sand with ¹⁴C-labeled pyrene (88 mg kg^-1) as a contamination focus located several centimeters from the inoculation point. Half of the pots included a biochar layer at the bottom. The pots were incubated in a greenhouse with sunflower plants and P. putida G7 bacteria. Pots with sunflower plants showed a higher biodegradation of pyrene, its mobilization as metabolites through the percolate and the roots, and bacterial mobilization toward the source of contamination, also resulting in increased pyrene transformation. In addition, the biochar layer efficiently reduced the concentrations of pyrene metabolites collected in the leachates. Therefore, the combination of plants, motile bacteria and biochar safely reduced the risk caused by the biological transformation of pyrene.

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.

Non-targeted screening of volatile organic compounds in a museum in China Using GC-Orbitrap mass spectrometry

Non-targeted analysis (NTA) was used in identifying volatile organic compounds (VOCs) in a museum in China with the gas chromatograph (GC)-Orbitrap-mass spectrometer (MS). Approximately 230 VOCs were detected, of which 117 were observed at 100% frequency across all sampling sites. Although some were common in indoor environments, most of the detected VOCs were rarely reported in previous studies on museum environments. Some of the detected VOCs were found to be associated with the materials used in furnishings and the chemicals applied in conservation treatment. Spearman's correlation analysis showed that several classes of VOCs were well correlated, suggesting their common sources. Compared with compounds in outdoor air, indoor VOCs had a lower level of unsaturation and more portions of chemically reduced compounds. Hierarchical cluster analysis (HCA) were performed. The results suggested that the sampling adsorbents chosen may have a large impact and that a single type of adsorbent may not be sufficient to cover a wide range of compounds in NTA studies. The MonoTrap adsorbent containing octadecylsilane (ODS) and activated carbon (AC) is suitable for aliphatic polar compounds that contain low levels of oxygen, whereas the MonoTrap ODS and silica gel are good at sampling aliphatic and aromatic hydrocarbons with limited polarity. Principle component analysis (PCA) showed that the indoor VOCs changed significantly at different times in the museum; this may have been caused by the removal of artifacts and refurbishment of the gallery between sampling events. A comparison with compounds identified by chamber emission tests showed that decorative materials may have been one of the main sources of indoor VOCs in the museum. The VOCs identified in the present study are likely to be present in other similar museums; therefore, further examination may be warranted of their potential impacts on cultural heritage artifacts, museum personnel, and visitors.

Occurrence and Ecological Impact of Chemical Mixtures in a Semiclosed Sea by Suspect Screening Analysis

Stress from mixtures of synthetic chemicals is among the key issues that have significant adverse impacts on the marine ecosystems. A robust screening workflow integrating toxicological-based ranking schemes is still deficient for comprehensive investigation on the main constituents in chemical mixtures that contribute to the ecological risks. In this study, the presence and compositions of a collection of priority pollutants were monitored by suspect screening analysis of seawater and estuarine water samples from the semiclosed Bohai Sea. In total, 108 organic pollutants in nine use categories were identified. Pesticides, intermediates, plastic additives, and per- and polyfluoroalkyl substances were the extensively detected chemical groups. Varied distribution patterns of the pollutants were illustrated intuitively in distinctive sampling areas by hierarchical cluster analysis, which were mainly influenced by run-off inputs, ocean currents, and chemical use history. Ecological risks of chemicals with quantified residue levels were first assessed by the toxicity-weighted concentration ranking scheme, and pentachlorophenol was found as the main contributor in the investigating areas. By optimization of multiple alternative variables (e.g., instrumental response and detection frequency), extended ranking of all the identified pollutants was plausible under the toxicological priority index framework. Similarity in toxicological endpoints of the prioritized pollutants could further been screened by ToxAlerts. Aromatic amine was highlighted as the most frequently detected structural alert (SA) for genotoxic carcinogenicity and mutagenicity. These findings fully demonstrate rationality of the ranking schemes integrated into the suspect screening analysis for profiling contamination characteristics, assessing ecological risk potentials, and prioritizing SAs.

Effects of polycyclic aromatic hydrocarbon structure on PAH mineralization and toxicity to soil microorganisms after oxidative bioremediation by laccase

While bioremediation using soil microorganisms is considered an energy-efficient and eco-friendly approach to treat polycyclic aromatic hydrocarbon (PAH)-contaminated soils, a variety of polar PAH metabolites, particularly oxygenated ones, could increase the toxicity of the soil after biodegradation. In this study, a typical bio-oxidative transformation of PAH into quinones was investigated in soil amended with laccase using three PAHs with different structures (anthracene, benzo[a]anthracene, and benzo[a]pyrene) to assess the toxicity after oxidative bioremediation. The results show that during a 2-month incubation period the oxidation process promoted the formation of non-extractable residues (NERs) of PAHs, and different effects on mineralization were observed among the three PAHs. Oxidation enhanced the mineralization of the high-molecular-weight (HMW) PAHs (benzo[a]anthracene and benzo[a]pyrene) but inhibited the mineralization of the low-molecular-weight (LMW) PAH (anthracene). The inhibition of anthracene suggests increased toxicity after oxidative bioremediation, which coincided with a decrease in soil nitrification activity, bacterial diversity and PAH-ring hydroxylating dioxygenase gene copies. The analysis of PAH metabolites in soil extract indicated that oxidation by laccase was competitive with the natural transformation processes of PAHs and revealed that intermediates other than quinone metabolites increased the toxicity of soil during subsequent degradation. The different metabolic profiles of the three PAHs indicated that the toxicity of soil after PAH oxidation by laccase was strongly affected by the PAH structure. Despite the potential increase in toxicity, the results suggest that oxidative bioremediation is still an eco-friendly method for the treatment of HMW PAHs since the intermediates from HMW PAHs are more easily detoxified via NER formation than LMW PAHs.

Recognition and Prioritization of Chemical Mixtures and Transformation Products in Chinese Estuarine Waters by Suspect Screening Analysis

Chemical mixtures in surface waters could have significant impacts on exposure risks to human beings and pollution stress to aquatic system. By suspect screening analysis of high-resolution mass spectrometry data, occurrence, and compositions of ToxCast chemicals were investigated in grab estuarine water samples from a combination of 20 rivers that represents approximately 70% of the total river flow discharge along the east coast of China. In total, 59 ToxCast chemicals in seven use categories were identified, in which pesticides, intermediates, and pharmaceuticals were the abundant analogues. Significant differences in pollutant composition profiles were noticed, which possibly reflected singular release pattern and geographical-relevant usage preference (especially for herbicides and fungicides in the pesticide category). With the aid of tentative quantitative/semiquantitative measurement, essential contributors to the cumulative pollutant mass discharges and aquatic acute toxicity potentials were focused onto few particular chemicals. Existence of transformation products was further explored, which indicated that the fates of the selected parent ToxCast chemicals could be influenced by dominating transformation reactions (e.g., N-dealkylation and hydroxylation) and possible environmental factors (i.e., microbial activity). The results emphasize the necessity of suspect screening analysis for assessing the influence of terrestrial emissions of pollutants to the surrounding environment.

Chemo-metric engineering designs for deciphering the biodegradation of polycyclic aromatic hydrocarbons

Polycyclic aromatic hydrocarbons (PAHs) are non-polar organic compounds that are omnipresent in the environment and released due to anthropogenic activities through emissions and discharges. PAHs, being xenobiotic and exerts health impacts, thus they attract serious concern by the environmentalists. The stringent regulations and the need of sustainable development urges the hunt for a technically feasible and cost-effective wastewater treatment. Although the conventional physico-chemical treatment are widely preferred, they cause secondary pollution problems and demand subsequent treatment options. This comprehensive review intends to address the (a) different PAHs and their associated toxicity, (b) the remedial strategies, particularly biodegradation. The biological wastewater treatment techniques that involve microbial systems are highly influenced by the different physio-chemical and environmental parameters. Therefore, suitable optimization techniques are prerequisite for effective functioning of the biological treatment that sustains judiciously and interpreted in a lesser time. Here we have aimed to discuss (a) different chemo-metric tools involved in the design of experiments (DoE), (b) design equations and models, (c) tools for evaluating the model's adequacy and (d) plots for graphically interpreting the chemo-metric designs. However, to best of our knowledge, this is a first review to discuss the PAHs biodegradation that are tailored by chemo-metric designs. The associated challenges, available opportunities and techno-economic aspects of PAHs degradation using chemo-metric engineering designs are explained. Additionally, the review highlights how well these DoE tools can be suited for the sustainable socio-industrial sectors. Concomitantly, the futuristic scope and prospects to undertake new areas of research exploration were emphasized to unravel the least explored chemo-metric designs.

Targeting the right parameters in PAH remediation studies

Contaminated land burdens the economy of many countries and must be dealt with. Researchers have published thousands of documents studying and developing soil and sediment remediation treatments. Amongst the targeted pollutants are the polycyclic aromatic hydrocarbons (PAHs), described as a class of persistent organic compounds, potentially harmful to ecosystems and living organisms. The present paper reviews and discusses three scientific trends that are leading current PAH-contaminated soil/sediment remediation studies and management. First, the choice of compounds that are being studied and targeted in the scientific literature is discussed, and we suggest that the classical 16 US-EPA PAH compounds might no longer be sufficient to meet current environmental challenges. Second, we discuss the choice of experimental material in remediation studies. Using bibliometric measures, we show the lack of PAH remediation trials based on co-contaminated or aged-contaminated material. Finally, the systematic use of the recently validated bioavailability measurement protocol (ISO/TS 16751) in remediation trials is discussed, and we suggest it should be implemented as a tool to improve remediation processes and management strategies.

Effect of biostimulation and bioaugmentation on hydrocarbon degradation and detoxification of diesel-contaminated soil: a microcosm study

Soil contamination with diesel oil is quite common during processes of transport and storage. Bioremediation is considered a safe, economical, and environmentally friendly approach for contaminated soil treatment. In this context, studies using hydrocarbon bioremediation have focused on total petroleum hydrocarbon (TPH) analysis to assess process effectiveness, while ecotoxicity has been neglected. Thus, this study aimed to select a microbial consortium capable of detoxifying diesel oil and apply this consortium to the bioremediation of soil contaminated with this environmental pollutant through different bioremediation approaches. Gas chromatography (GC-FID) was used to analyze diesel oil degradation, while ecotoxicological bioassays with the bioindicators Artemia sp., Aliivibrio fischeri (Microtox), and Cucumis sativus were used to assess detoxification. After 90 days of bioremediation, we found that the biostimulation and biostimulation/bioaugmentation approaches showed higher rates of diesel oil degradation in relation to natural attenuation (41.9 and 26.7%, respectively). Phytotoxicity increased in the biostimulation and biostimulation/bioaugmentation treatments during the degradation process, whereas in the Microtox test, the toxicity was the same in these treatments as that in the natural attenuation treatment. In both the phytotoxicity and Microtox tests, bioaugmentation treatment showed lower toxicity. However, compared with natural attenuation, this approach did not show satisfactory hydrocarbon degradation. Based on the microcosm experiments results, we conclude that a broader analysis of the success of bioremediation requires the performance of toxicity bioassays.

Toxicity Testing of Effluent-Dominated Stream Using Predictive Molecular-Level Toxicity Signatures Based on High-Resolution Mass Spectrometry: A Case Study of the Lubbock Canyon Lake System

Current aquatic toxicity assessments usually focus on targeted analyses coupled with toxicity testing to determine the impacts of complex mixtures on aquatic organisms. However, based on this approach alone, it is sometimes difficult to explain observed toxicity from the selected chemical analytes. Recent analytical advances such as high-resolution mass spectrometry (HRMS) can improve the characterizations of the chemical composition of complex mixtures, but the intensive labor required to produce confident identifications limits its utility in high-throughput screening. In the present study, we evaluated a rapid workflow to predict potential toxicity signatures of complex water samples based on high-throughput, tentative HRMS identifications derived from database matching, followed by identification of chemical-ligand interactions and pathway identification. We tested the workflow with water samples from the effluent-dominated Lubbock Canyon Lake System (LCLS). Results across all sites showed that predicted toxicity signatures had little variation when correcting for HRMS false-positive rates. The most common pathways across sites were gonadotropin-releasing hormone receptor and α-adrenergic receptor signaling. Alterations to the predicted pathways were successfully observed in larval zebrafish exposures to LCLS water samples. These results may allow researchers to better utilize rapid assessments of HRMS data for the assessment of adverse impacts on aquatic organisms.

Recent Advances in the Study of the Remediation of Polycyclic Aromatic Compound (PAC)-Contaminated Soils: Transformation Products, Toxicity, and Bioavailability Analyses

Polycyclic aromatic compounds (PACs) encompass a diverse group of compounds, often found in historically contaminated sites. Different experimental techniques have been used to remediate PACs-contaminated soils. This brief review surveyed over 270 studies concerning remediation of PACs-contaminated soils and found that, while these studies often measured the concentration of 16 parent polycyclic aromatic hydrocarbons (PAHs) pre- and post-remediation, only a fraction of the studies included the measurement of PAC-transformation products (PAC-TPs) and other PACs (n = 33). Only a few studies also incorporated genotoxicity/toxicity/mutagenicity analysis pre- and post-remediation (n = 5). Another aspect that these studies often neglected to include was bioavailability, as none of the studies that included measurement of PAH-TPs and PACs included bioavailability investigation. Based on the literature analysis, future remediation studies need to consider chemical analysis of PAH-TPs and PACs, genotoxicity/toxicity/mutagenicity, and bioavailability analyses pre- and post-remediation. These assessments will help address numerous concerns including, among others, the presence, properties, and toxicity of PACs and PAH-TPs, risk assessment of soil post-remediation, and the bioavailability of PAH-TPs. Other supplementary techniques that help assist these analyses and recommendations for future analyses are also discussed.

Network Analysis for Prioritizing Biodegradation Metabolites of Polycyclic Aromatic Hydrocarbons

Polycyclic aromatic hydrocarbons (PAHs) are a diverse group of environmental contaminants released during the combustion of organic materials and the production and utilization of fossil fuels. Once released, PAHs deposit in soil and water bodies where they are subjected to environmental transport and transformations. As they degrade, intermediate transformation products may play an important role in their environmental impact. However, studying the effects of these degradation products has proven challenging because of the complexity, transience, and low concentration of many intermediates. Herein, a novel integration of a pathway prediction system and network theory was developed and applied to a set of four PAHs to demonstrate a possible solution to this challenge. Network analysis techniques were employed to refine the thousands of potential outputs and elucidate compounds of interest. Using these tools, we determined correlations between PAH degradation network data and intermediate metabolite structures, gaining information about the chemical characteristics of compounds based on their placement within the degradation network. Upon applying our developed filtering algorithm, we are able to predict up to 48% of the most common transformation products identified in a comprehensive empirical literature review. Additionally, our integrated approach uncovers potential metabolites which connect those found by past empirical studies but are currently undetected, thereby filling in the gaps of information in PAH degradation pathways.

Isomer-selective biodegradation of high-molecular-weight azaarenes in PAH-contaminated environmental samples

Polycyclic aromatic nitrogen heterocycles, or azaarenes, normally co-occur with polycyclic aromatic hydrocarbons (PAHs) in contaminated soils. We recently reported that nontarget analysis using high resolution mass spectrometry of samples from four PAH-contaminated sites revealed a previously unrecognized diversity and abundance of azaarene isomers and their methylated derivatives. Here we evaluated their biodegradability by natural microbial communities from each site in aerobic microcosm incubations under biostimulated conditions. The removal of total quantifiable azaarenes ranged from 15 to 85%, and was related to the initial degree of weathering for each sample. While three-ring azaarenes were readily biodegradable, the five-ring congeners were the most recalcitrant. Microbial-mediated removal of four-ring congeners varied for different isomers, which might be attributed to the position of the nitrogen atom that also influences the physicochemical properties of azaarenes and possibly the susceptibility to transformation by relevant microbial enzymes. The presence of methyl groups also influenced azaarene biodegradability, which decreased with increasing degree of methylation. Several oxidation products of azaarenes were detected, including ketones and dioxygenated derivatives of three- and four-ring compounds. Our results indicate the susceptibility of some azaarenes to bioremediation, while suggesting the potential implications for risk from the persistence of less-biodegradable isomers and the formation of oxidized-azaarene derivatives.

Hydrocarbon Removal by Two Differently Developed Microbial Inoculants and Comparing Their Actions with Biostimulation Treatment

Bioremediation of soils polluted with petroleum compounds is a widely accepted environmental technology. We compared the effects of biostimulation and bioaugmentation of soil historically contaminated with aliphatic and polycyclic aromatic hydrocarbons. The studied bioaugmentation treatments comprised of the introduction of differently developed microbial inoculants, namely: an isolated hydrocarbon-degrading community C1 (undefined-consisting of randomly chosen degraders) and a mixed culture C2 (consisting of seven strains with well-characterized enhanced hydrocarbon-degrading capabilities). Sixty days of remedial treatments resulted in a substantial decrease in total aliphatic hydrocarbon content; however, the action of both inoculants gave a significantly better effect than nutrient amendments (a 69.7% decrease for C1 and 86.8% for C2 vs. 34.9% for biostimulation). The bioaugmentation resulted also in PAH removal, and, again, C2 degraded contaminants more efficiently than C1 (reductions of 85.2% and 64.5%, respectively), while biostimulation itself gave no significant results. Various bioassays applying different organisms (the bacterium Vibrio fischeri, the plants Sorghum saccharatum, Lepidium sativum, and Sinapis alba, and the ostracod Heterocypris incongruens) and Ames test were used to assess, respectively, potential toxicity and mutagenicity risk after bioremediation. Each treatment improved soil quality, however only bioaugmentation with the C2 treatment decreased both toxicity and mutagenicity most efficiently. Illumina high-throughput sequencing revealed the lack of (C1) or limited (C2) ability of the introduced degraders to sustain competition from indigenous microbiota after a 60-day bioremediation process. Thus, bioaugmentation with the bacterial mixed culture C2, made up of identified, hydrocarbon-degrading strains, is clearly a better option for bioremediation purposes when compared to other treatments.

Suspect and Nontarget Screening for Contaminants of Emerging Concern in an Urban Estuary

This study used suspect and nontarget screening with high-resolution mass spectrometry to characterize the occurrence of contaminants of emerging concern (CECs) in the nearshore marine environment of Puget Sound (WA). In total, 87 non-polymeric CECs were identified; those confirmed with reference standards (45) included pharmaceuticals, herbicides, vehicle-related compounds, plasticizers, and flame retardants. Eight polyfluoroalkyl substances were detected; perfluorooctanesulfonic acid (PFOS) concentrations were as high as 72-140 ng/L at one location. Low levels of methamphetamine were detected in 41% of the samples. Transformation products of pesticides were tentatively identified, including two novel transformation products of tebuthiuron. While a hydrodynamic simulation, analytical results, and dilution calculations demonstrated the prevalence of wastewater effluent to nearshore marine environments, the identity and abundance of selected CECs revealed the additional contributions from stormwater and localized urban and industrial sources. For the confirmed CECs, risk quotients were calculated based on concentrations and predicted toxicities, and eight CECs had risk quotients >1. Dilution in the marine estuarine environment lowered the risks of most wastewater-derived CECs, but dilution alone is insufficient to mitigate risks of localized inputs. These findings highlighted the necessity of suspect and nontarget screening and revealed the importance of localized contamination sources in urban marine environments.

Nontarget profiling of organic compounds in a temporal series of hydraulic fracturing flowback and produced waters

Hydraulic fracturing (HF) flowback and produced water (FPW) can be toxic to aquatic life but its chemical content is largely unknown, variable and complex. Seven FPW samples were collected from a HF operation in the Duvernay Formation (Alberta, Canada) over 30 days of flowback and characterized by a nontarget workflow based on high performance liquid chromatography - high resolution mass spectrometry (HRMS). A modified Kendrick mass defect plot and MS/MS spectral interpretation revealed seven series of homologues composed of ethylene oxide (i.e. -CH₂CH₂O-), among which a series of aldehydes was proposed as degradation products of polyethylene glycols, and two series of alkyl ethoxylate carboxylates could be proprietary HF additives. Many other ions were confidently assigned a formula by accurate mass measurement and were subsequently prioritized for identification by matching to records in ChemSpider and the US EPA's CompTox Chemistry Dashboard. Quaternary ammonium compounds, amine oxides, organophosphorous compounds, phthalate diesters and hydroxyquinoline were identified with high confidence by MS/MS spectra (Level 3), matching to reference spectra in MassBank (Level 2) or to authentic standards (Level 1). Temporal trends showed that most of the compounds declined in abundance over the first nine days of flowback, except for phthalate diesters and hydroxyquinoline that were still observed on Day 30 and had disappearance half-lives of 61 and 91 days, respectively. All the compounds followed first-order disappearance kinetics in flowback, except for polyoxygenated acids which followed second-order kinetics. This analysis and the workflow, based largely on public on-line databases, enabled profiling of complex organic compounds in HF-FPW, and will likely be useful for further understanding the toxicity and chemical fate of HF-FPW.

Towards Mass Spectrometry-Based Chemical Exposome: Current Approaches, Challenges, and Future Directions

The proposal of the “exposome” concept represents a shift of the research paradigm in studying exposure-disease relationships from an isolated and partial way to a systematic and agnostic approach. Nevertheless, exposome implementation is facing a variety of challenges including measurement techniques and data analysis. Here we focus on the chemical exposome, which refers to the mixtures of chemical pollutants people are exposed to from embryo onwards. We review the current chemical exposome measurement approaches with a focus on those based on the mass spectrometry. We further explore the strategies in implementing the concept of chemical exposome and discuss the available chemical exposome studies. Early progresses in the chemical exposome research are outlined, and major challenges are highlighted. In conclusion, efforts towards chemical exposome have only uncovered the tip of the iceberg, and further advancement in measurement techniques, computational tools, high-throughput data analysis, and standardization may allow more exciting discoveries concerning the role of exposome in human health and disease.

Simplify: A Mass Spectrometry Metabolomics Approach to Identify Additives and Synergists from Complex Mixtures

In fields ranging from environmental toxicology to drug discovery, it is critical to identify how multiple chemical compounds interact to perturb biological systems. Isolation-based approaches fail to incorporate multiconstituent interactions, such as synergy. We have developed an approach called "Simplify", which identifies mixture constituents that interact to achieve biological effects. Simplify combines biological and mass spectrometric data sets and uses an "activity index" to predict mixture interactions. Using the plant Salvia miltiorrhiza as a case study, we employed Simplify to identify four individual constituents that contribute to antimicrobial activity, three additives and one synergist. Our study is the first to enable identification of unknown synergists prior to isolating them, demonstrating the ability of the Simplify workflow to predict key contributors to the biological effect of a complex mixture. While utilized for natural products discovery in this study, this approach is expected to prove useful across multiple disciplines that rely on mixture analysis.

Tracing the Biotransformation of Polycyclic Aromatic Hydrocarbons in Contaminated Soil Using Stable Isotope-Assisted Metabolomics

Biotransformation of organic pollutants may result in the formation of oxidation products more toxic than the parent contaminants. However, to trace and identify those products, and the metabolic pathways involved in their formation, is still challenging within complex environmental samples. We applied stable isotope-assisted metabolomics (SIAM) to PAH-contaminated soil collected from a wood treatment facility. Soil samples were separately spiked with uniformly ¹³C-labeled fluoranthene, pyrene, or benzo[a]anthracene at a level below that of the native contaminant, and incubated for 1 or 2 weeks under aerobic biostimulated conditions. Combining high-resolution mass spectrometry and automated SIAM workflows, chemical structures of metabolites and metabolic pathways in the soil were proposed. Ring-cleavage products, including previously unreported intermediates such as C₁₁H₁₀O₆ and C₁₅H₁₂O₅, were detected originating from fluoranthene and benzo[a]anthracene, respectively. Sulfate conjugates of dihydroxy compounds were found as major metabolites of pyrene and benzo[a]anthracene, suggesting the potential role of fungi in their biotransformation in soils. A series of unknown N-containing metabolites were identified from pyrene, but their structural elucidation requires further investigation. Our results suggest that SIAM can be successfully applied to understand the fate of organic pollutants in environmental samples, opening lines of evidence for novel mechanisms of microbial transformation within such complex matrices.

Diversity and Abundance of High-Molecular-Weight Azaarenes in PAH-Contaminated Environmental Samples

Azaarenes are N-heterocyclic polyaromatic pollutants that co-occur with polycyclic aromatic hydrocarbons (PAHs) in contaminated soils. Despite the known toxicity of some high-molecular-weight azaarenes, their diversity, abundance, and fate in contaminated soils remain to be elucidated. We applied high-resolution mass spectrometry and mass-defect filtering to four PAH-contaminated samples from geographically distant sites and detected 232 azaarene congeners distributed in eight homologous series, including alkylated derivatives and two hitherto unknown series. Four- and five-ring azaarenes were detected among these series, and the most abundant nonalkylated congeners groups (C₁₃H₉N, C₁₅H₉N, C₁₇H₁₁N, C₁₉H₁₁N, and C₂₁H₁₃N) were quantified. The profiles of congener groups varied among different sites. Three-ring azaarenes presented higher concentrations in unweathered sites, while four- and five-ring azaarenes predominated in weathered sites. Known toxic and carcinogenic azaarenes, such as benzo[c]acridine and dibenzo[a,h]acridine, were detected along with their multiple isomers. Our results highlight a previously unrecognized diversity and abundance of azaarenes in PAH-contaminated sites, with corresponding implications for environmental monitoring and risk assessment.