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

Bioremediation of petroleum-contaminated soil based on both toxicity risk control and hydrocarbon removal-progress and prospect

Petroleum contamination remains a worldwide issue requiring cost-effective bioremediation techniques. However, establishing a universal bioremediation strategy for all types of oil-polluted sites is challenging. This difficulty arises from the heterogeneity of soil textures, the complexity of oil products, and the variations in local climate and environment across different oil-contaminated regions. Several factors can impede bioremediation efficacy: (i) differences in bioavailability and biodegradability between aliphatic and aromatic fractions of crude oil; (ii) inconsistencies between hydrocarbon removal efficiency and toxicity attenuation during remediation; (iii) varying adverse effect of aliphatic and aromatic fractions on soil microorganisms. This review examines the ecotoxicity risk of petroleum contamination to soil fauna and flora. It also discusses three primary bioremediation strategies: biostimulation with nutrients, bioaugmentation with petroleum degraders, and phytoremediation with plants. Based on current research and state-of-the-art challenges, we highlighted future research scopes should focus on (i) exploring the ecotoxicity differentiation of aliphatic and aromatic fractions of crude oil, (ii) establishing unified risk factors and indicators for evaluating oil pollution toxicity, (iii) determining the fate and transformation of aliphatic and aromatic fractions of crude oil using advanced analytical techniques, and (iv) developing combined bioremediation techniques that improve petroleum removal and ecotoxicity attenuation.

Proteomic stable isotope probing with an upgraded Sipros algorithm for improved identification and quantification of isotopically labeled proteins

BACKGROUND

Proteomic stable isotope probing (SIP) is used in microbial ecology to trace a non-radioactive isotope from a labeled substrate into de novo synthesized proteins in specific populations that are actively assimilating and metabolizing the substrate in a complex microbial community. The Sipros algorithm is used in proteomic SIP to identify variably labeled proteins and quantify their isotopic enrichment levels (atom%) by performing enrichment-resolved database searching.

RESULTS

In this study, Sipros was upgraded to improve the labeled protein identification, isotopic enrichment quantification, and database searching speed. The new Sipros 4 was compared with the existing Sipros 3, Calisp, and MetaProSIP in terms of the number of identifications and the accuracy and precision of atom% quantification on both the peptide and protein levels using standard E. coli cultures with 1.07 atom%, 2 atom%, 5 atom%, 25 atom%, 50 atom%, and 99 atom% 13C enrichment. Sipros 4 outperformed Calisp and MetaProSIP across all samples, especially in samples with ≥ 5 atom% 13C labeling. The computational speed on Sipros 4 was > 20 times higher than Sipros 3 and was on par with the overall speed of Calisp- and MetaProSIP-based pipelines. Sipros 4 also demonstrated higher sensitivity for the detection of labeled proteins in two 13C-SIP experiments on a real-world soil community. The labeled proteins were used to trace 13C from 13C-methanol and 13C-labeled plant exudates to the consuming soil microorganisms and their newly synthesized proteins.

CONCLUSION

Overall, Sipros 4 improved the quality of the proteomic SIP results and reduced the computational cost of SIP database searching, which will make proteomic SIP more useful and accessible to the border community. Video Abstract.

Unlocking the potential of soil microbial communities for bioremediation of emerging organic contaminants: omics-based approaches

The remediation of emerging contaminants presents a pressing environmental challenge, necessitating innovative approaches for effective mitigation. This review article delves into the untapped potential of soil microbial communities in the bioremediation of emerging contaminants. Bioremediation, while a promising method, often proves time-consuming and requires a deep comprehension of microbial intricacies for enhancement. Given the challenges presented by the inability to culture many of these microorganisms, conventional methods are inadequate for achieving this goal. While omics-based methods provide an innovative approach to understanding the fundamental aspects, processes, and connections among microorganisms that are essential for improving bioremediation strategies. By exploring the latest advancements in omics technologies, this review aims to shed light on how these approaches can unlock the hidden capabilities of soil microbial communities, paving the way for more efficient and sustainable remediation solutions.

Low dose phosphorus supplementation is conducive to remediation of heavily petroleum-contaminated soil-From the perspective of hydrocarbon removal and ecotoxicity risk control

Biostimulation by supplementing of nitrogen and phosphorus nutrients is a common strategy for remediation of petroleum-polluted soils. However, the dosage influence of exogenous nitrogen or phosphorus on petroleum hydrocarbon removal and soil ecotoxicity and microbial function remain unclear. In this study, we compared the efficiencies of hydrocarbon degradation and ecotoxicity control by experiment conducted over addition of inorganic nitrogen or phosphorus at C/N ratio of 100/10, C/N/P ratio of 100/10/1, and C/P ratio of 100/1 in a heavily petroleum-contaminated loessal soil with 12,320 mg/kg of total petroleum hydrocarbon (TPH) content. A 90-day incubation study revealed that low-dose of phosphorus addition with the C/P ratio of 100/1 promoted hydrocarbon degradation and reduced soil ecotoxicity. Microbial community composition analysis suggested that phosphorus addition enriched hydrocarbon degrader Gordonia and Mycolicibacterium genus. The key enzymes EC 5.3.3.8, EC 6.2.1.20 and EC 6.4.1.1 which referred to degradation of long-chain hydrocarbons, unsaturated fatty acids and pyruvate metabolism were abundance by phosphorus supplementation. While nitrogen addition at C/N ratio of 100/10 or C/N/P ratio of 100/10/1 inhibited hydrocarbon degradation and exacerbated soil ecotoxicity due to promoting denitrification and coupling reactions with hydrocarbons. Our results suggested that low-dose phosphorus addition served as a favorable strategy to promote crude oil remediation and ecotoxicity risk control in heavily petroleum-contaminated soil. Hence, the application of suitable doses of exogenous biostimulants is an efficient approach to restore the ecological functions of organically contaminated soils.

Degradation and humification of steroidal estrogens in the soil environment: A review

Emerging pollutants are toxic and harmful chemical substances characterized by environmental persistence, bioaccumulation and biotoxicity, which can harm the ecological environment and even threaten human health. There are four categories of emerging pollutants that are causing widespread concern, namely, persistent organic pollutants, endocrine disruptors, antibiotics, and microplastics. The distribution of emerging pollutants has spatial and temporal heterogeneity, which is influenced by factors such as geographical location, climatic conditions, population density, emission amount, etc. Steroidal estrogens (SEs) discussed in this paper belong to the category of endocrine disruptors. There are generally three types of fate for SEs in the soil environment: sorption, degradation and humification. Humification is a promising pathway for the removal of SEs, especially for those that are difficult to degrade. Through humification, these difficult-to-degrade SEs can be effectively transferred or fixed, thus reducing their impact on the environment and organisms. Contrary to the well-studied process of sorption and degradation, the role and promise of the humification process for the removal of SEs has been underestimated. Based on the existing research, this paper reviews the sources, classification, properties, hazards and environmental behaviors of SEs in soil, and focuses on the degradation and humification processes of SEs and the environmental factors affecting their processes, such as temperature, pH, etc. It aims to provide references for the follow-up research of SEs, and advocates further research on the humification of organic pollutants in future studies.

Metabolomics perspectives of the ecotoxicological risks of polycyclic aromatic hydrocarbons: A scoping review

Polycyclic Aromatic Hydrocarbons (PAHs) represent persistent environmental pollutants ubiquitously distributed in the environment. Their presence alongside various other contaminants gives rise to intricate interactions, culminating in profound deleterious consequences. The combination effects of different PAH mixtures on biota remains a relatively unexplored domain. Recent studies have harnessed the exceptional sensitivity of metabolomic techniques to unveil the significant ecotoxicological perils of PAH pollution confronting both human populations and ecosystems. This article furnishes a comprehensive overview of current literature focused on the metabolic repercussions stemming from exposure to complex mixtures of PAHs or PAH-pollution sources using metabolomics approaches. These insights are obtained through a wide range of models, including in vitro assessments, animal studies, investigations on human subjects, botanical specimens, and soil environments. The findings underscore that PAH mixtures induce cellular stress responses and systemic effects, leading to metabolic dysregulations in amino acids, carbohydrates, lipids, and other key metabolites (e.g., organic acids, purines), with specific variations observed based on the organism and PAH compounds involved. Additionally, the ecological consequences of PAH pollutants on plant and soil microbial responses are emphasized, revealing significant changes in stress-related metabolites and nutrient cycling in soil ecosystems. The complex interplay of various PAHs and their metabolic effects on several models, as elucidated through metabolomics, highlight the urgency of further research and the need for comprehensive strategies to mitigate the risks posed by these widespread environmental pollutants.

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.

H/D Exchange Coupled with 2H-labeled Stable Isotope-Assisted Metabolomics Discover Transformation Products of Contaminants of Emerging Concern

Stable isotope-assisted metabolomics (SIAM) is a powerful tool for discovering transformation products (TPs) of contaminants. Nevertheless, the high cost or lack of isotope-labeled analytes limits its application. In-house H/D (hydrogen/deuterium) exchange reactions enable direct 2H labeling to target analytes with favorable reaction conditions, providing intuitive and easy-to-handle approaches for environmentally relevant laboratories to obtain cost-effective 2H-labeled contaminants of emerging concern (CECs). We first combined the use of in-house H/D exchange and 2H-SIAM to discover potential TPs of 6PPD (N-1,3-dimethylbutyl-N'-phenyl-p-phenylenediamine), providing a new strategy for finding TPs of CECs. 6PPD-d9 was obtained by in-house H/D exchange with favorable reaction conditions, and the impurities were carefully studied. Incomplete deuteride, for instance, 6PPD-d8 in this study, constitutes a major part of the impurities. Nevertheless, it has few adverse effects on the 2H-SIAM pipeline in discovering TPs of 6PPD. The 2H-SIAM pipeline annotated 9 TPs of 6PPD, and commercial standards further confirmed the annotated 6PPDQ (2-anilino-5-(4-methylpentan-2-ylamino)cyclohexa-2,5-diene-1,4-dione) and PPPD (N-phenyl-p-phenylenediamine). Additionally, a possible new formation mechanism for 6PPDQ was proposed, highlighting the performance of the strategy. In summary, this study highlighted a new strategy for discovering the TPs of CECs and broadening the application of SIAM in environmental studies.

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.

Diverse positional 14C labeling-assisted metabolic analysis of pesticides in rats: The case of vanisulfane, a novel vanillin-derived pesticide

Information on pesticide metabolites is crucial for accurate environmental risk assessment. However, identifying the various metabolites of a novel pesticide is challenging since the potential metabolic pathways are unknown. In this study, we coupled diverse positional ¹⁴C labeling with high-resolution mass spectrometry to quantitatively and qualitatively study pesticide metabolism in rats. With the unique M/(M + 2) ratios derived from ¹⁴C, precursor compounds of metabolites could be better distinguished from impurity ions. Additionally, the use of diverse ¹⁴C labeling positions is a powerful tool to elucidate the complete metabolic fate of novel contaminants. Vanisulfane is a novel vanillin-derived antiviral agent with encouraging prospects for the efficient control of cucumber mosaic virus in China, but its metabolic pathways in mammals are still poorly understood. Thus, the metabolism of vanisulfane was studied in rats of both sexes by this strategy. The results showed that phase I and phase II metabolism occurred in both sexes. The former included mainly oxidation reactions, and the latter involved binding reactions that formed glucuronide, sulfate and amino acid conjugates. Sex-related differences were observed in the experiment, with earlier appearance of downstream metabolites and a preference for sulfate conjugate formation in males compared to females. This research facilitates the risk evaluation of vanisulfane, and offers an effective framework for screening unknown pesticide metabolic pathways, which could be applied to establish the metabolic profiles of other novel contaminants with limited information.

Global Tracking of Transformation Products of Environmental Contaminants by 2H-Labeled Stable Isotope-Assisted Metabolomics

Stable isotope-assisted metabolomics (SIAM) enables global tracking of isotopic labels in nontargeted metabolomics in living organisms. However, its application in tracking transformation products (TPs, as metabolites of contaminants) of environmental contaminants is still a challenge due to limits in methodology, unmatured algorithms, and the high cost of ¹³C-labeled contaminants. Therefore, we developed a ²H-SIAM pipeline coupled with a highly flexible algorithm ²H-SIAM(1.0) (https://github.com/kechen1984/2H-SIAM), facilitating tracking TPs of contaminants in the environmental matrix. A detailed discussion illustrates the theory, behavior, and prospect of ²H-SIAM. We demonstrate that the proposed ²H-SIAM pipeline has unique advantages over ¹³C-SIAM, for example, cost-effective ²H-labeled contaminants, easy synthesis of ²H-labeled emerging contaminants, and providing more structural information. A pyrene soil degradation study further confirmed its high performance. It efficiently discarded 99% of noise signals and extracted 52 features from the nontargeted high resolution mass spectrometry (HRMS) data. Among them, 13 features were annotated as TPs of pyrene with identification confidence from Level 2a to Level 5, and 5 TPs were reported for the first time. In conclusion, the proposed ²H-SIAM pipeline is powerful in tracking potential TPs of environmental contaminants with unique advantages.

Humic acid enhanced pyrene degradation by Mycobacterium sp. NJS-1

The search for nature-based tools to enhance bioremediation is essential for the sustainable restoration of contaminated ecosystems. Humic acid (HA) is an important component of organic matter in soil and water, but its effect on the microbial degradation of organic pollutants remains unclear. In this study, the biodegradation of pyrene by Mycobacterium sp. NJS-1 with and without HA was investigated. Only around 10.5% of pyrene was biodegraded in the pyrene treatment alone, whereas the addition of HA significantly enhanced biodegradation to the point where over 90% of pyrene was biodegraded. The production of 4,5-dihydropyrene-4,5-diol and phenanthrene-3,4-diol indicated the metabolic pathway via attacking of 4,5-positions of pyrene. Interestingly, 1,2-dimethoxypyrene was detected with the addition of HA, suggesting that HA induced a new ring-opening pathway involving the attack on the 1,2-positions of pyrene. The addition of HA first induced protein self-cleavage behavior with a significant increase in phenylalanine, tyrosine, and tryptophan containing large numbers of COO^- groups. Furthermore, it altered the intracellular and extracellular ultrastructure of bacterial cells, promoting their growth in size and number as well as reducing the space between them. Overall, HA increased the ring-opening positions of pyrene and facilitated its interaction with bacterial cells, thus improving its biodegradability. Building upon the findings of this study to further research is conducive to the sustainable solution of environmental pollution.

Iron nanoparticles supported on N-doped carbon foam with honeycomb microstructure: An efficient potassium peroxymonosulfate activator for the degradation of fluoranthene in water and soil

A promising technology was developed for the remediation of fluoranthene (FLT) contaminated water and soil. Specifically, iron nanoparticles supported on N-doped carbon foam (Fe@CF-N) was synthesized by in-situ impregnation and a unique calcination process using pine cone as the precursor. The obtained Fe@CF-N was used as an activator of potassium peroxymonosulfate (PMS) to degrade FLT in water and soil. According to experimental results, Fe@CF-N had a three-dimensional network structure with a large specific surface area of 249.0 m² g^-1, displaying excellent catalytic performance. The maximum removal efficiency of FLT in water and soil reached 81.83% and 78.12% within 180 min, respectively. After four consecutive degradation cycles, the removal efficiency of FLT in water was still 55%. Electron spin resonance (ESR) measurements showed that hydroxyl radicals (·OH), sulfate radical (SO₄^-·) and ¹O₂ were the major reactive oxygen species (ROS). A series of low molecular weight intermediates were generated during the FLT degradation progress, such as C₆H₆O₃ and C₃H₈O₂. The effect of Fe@CF-N/PMS system on the phytotoxicity was evaluated via bioassay based on peas. The results indicated that seed germination rate and root shoot elongation of remediated soil by Fe@CF-N/PMS system were not significantly different from those of noncontaminated soil. This study provided a cost-effective remediation option for PAHs contaminated water and soil.

Combination of high specific activity carbon-14 labeling and high resolution mass spectrometry to study pesticide metabolism in crops: Metabolism of cycloxaprid in rice

The study of pesticide metabolism in crops is critical for assessing the mode of action and environmental risks of pesticides. However, the study of pesticide metabolism in crops is usually complicated and it is often a daunting challenge to accurately screen the metabolites of novel pesticides in complex matrices. This study demonstrated a combined use of high-specific activity carbon-14 labeling and high-resolution mass spectrometry (HSA-¹⁴C-HRMS) for metabolism profiling of a novel neonicotinoid cycloxaprid in rice. By generating the characteristic radioactive peaks on the liquid chromatogram, the use of ¹⁴C can eliminate the severe interference of complex matrices and quickly probe target compounds; by producing ion pairs with unique abundance ratios on HRMS, high-specific activity labeling can effectively exclude false matrix positives and promote the elucidation of metabolite structure. The structures of 15 metabolites were identified, three of which were further confirmed by authentic standards. Based on these metabolites, a metabolic profile of cycloxaprid was established, which includes denitrification, demethylation, imidazolidine hydroxylation and ring cleavage olefin formation, oxidation and carboxylation reactions. The strategy of combining high-specific activity ¹⁴C labeling and HRMS offers unique advantages and provides a powerful solution for profiling unknown metabolites of novel pesticides in complex matrices, especially when traditional non-labeling methods are not feasible.

Anaerobic phenanthrene biodegradation by a newly isolated sulfate-reducer, strain PheS1, and exploration of the biotransformation pathway

Phenanthrene is a widespread and harmful polycyclic aromatic hydrocarbon that is difficult to anaerobically biodegrade. Current challenges in anaerobic phenanthrene bioremediation are a lack of degrading cultures and limited knowledge of biotransformation pathways. Under sulfate-reducing conditions, pure-cultures and biotransformation processes for anaerobic phenanthrene biodegradation are poorly understood. In this study, strain PheS1, which is phylogenetically closely related to Desulfotomaculum, was found to be a sulfate-reducing phenanthrene-degrading bacterium. Anaerobic phenanthrene biodegradation using PheS1 was proposed based on metabolite and genome analyses, and the initial step was identified as carboxylation based on the detection of 2-phenanthroic acid, [¹³C]-2-phenanthroic acid, and [D9]-2- phenanthroic acid when phenanthrene+HCO₃^-, phenanthrene+H¹³CO₃^-, and [D10]-phenanthrene+HCO₃^- were used as the substrate, respectively. PheS1 genome ubiD gene encoding of carboxylase putatively involved in the biodegradation was performed. Next, benzene ring reduction and cleavage that produced benzene compounds and cyclohexane derivative were reported to occur in the downstream biotransformation processes. Additionally, benzene, naphthalene, benz[a]anthracene, and anthracene can be utilised by PheS1, whereas pyrene and benz[a]pyrene cannot. We discovered a new phenanthrene-degrading sulfate-reducer and provided the anaerobic phenanthrene biotransformation pathway under sulfate-reducing conditions, which can act as a reference for practical applications in bioremediation and for studying the molecular mechanisms of phenanthrene in anaerobic zones.

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.

Hydrocarbon transformation pathways and soil organic carbon stability in the biostimulation of oil-contaminated soil: Implications of 13C natural abundance

Mineralization, assimilation, and humification are key processes to detoxify oil-contaminated soil by biostimulation remediation strategies, and these processes are affected by stimulants. In this study, we investigated the effects of either inorganic salts or organic stimulants (organic compost and sawdust) on hydrocarbon transformation. Total petroleum hydrocarbons (TPH) and hydrocarbon components were determined by gravimetry and gas chromatography, and the ¹³C of CO₂, microbial biomass carbon (MBC), and humus were measured by stable isotope mass spectrometry. The results showed that organic compost was the most beneficial for the dissipation of hydrocarbons. After 60 days of remediation, the removal rates of TPH, saturates, aromatics, C7-C30 n-alkanes, and 16 PAHs were 35.7%, 39.6%, 15.9%, 80.5%, and 8.8%, respectively. A total of 84.7%-88.5% of the removed hydrocarbons were mineralized in all the treatments. The hydrocarbon degradation pathway in the control soil (without stimulant addition) was "assimilation → humification → mineralization". The hydrocarbon transformation pathways in the biostimulation treatments were "assimilation → mineralization → humification". The soil organic carbon (SOC) stability decreased during remediation, which was attributed to the enhanced microbial activity and the removal of recalcitrant hydrocarbons.

Elucidating degradation mechanisms of florfenicol in soil by stable-isotope assisted nontarget screening

Antibiotics in soil environments are a growing concern. Identifying transformation products is key to elucidating degradation pathways and mechanisms of antibiotics and other organic micropollutants. The primary challenge of transformation product identification is the interference of matrices. In this study, stable-isotope assisted nontarget screening was used to identify biodegradation products of florfenicol in soil. A total of 74 candidates were prioritized from thousands of mass features observed by a tiered peak filtering approach. Moreover, with the support of in silico prediction tools, the structures of 12 transformation products were elucidated, and 9 of them were reported for the first time. A biodegradation map of florfenicol consisting of amide hydrolysis, dechlorination, dehydration, defluorination, and sulfone reduction was established based on these identified products. A total of 8 products were also found in 6 field soil samples with manure application. Because of the structural similarity to florfenicol, some transformation products might still keep antimicrobial activity toward a variety of bacterial species. The strategies demonstrated in this study provide a basis for efficient identification of transformation products of other organic micropollutants in a variety of environmental matrices. The results also shed light on the degradation mechanisms, risk assessments, and regulations of these compounds.

Bioelectrochemically enhanced degradation of bisphenol S: mechanistic insights from stable isotope-assisted investigations

Electroactive microbes is the driving force for the bioelectrochemical degradation of organic pollutants, but the underlying microbial interactions between electrogenesis and pollutant degradation have not been clearly identified. Here, we combined stable isotope-assisted metabolomics (SIAM) and 13C-DNA stable isotope probing (DNA-SIP) to investigate bisphenol S (BPS) enhanced degradation by electroactive mixed-culture biofilms (EABs). Using SIAM, six 13C fully labeled transformation products were detected originating via hydrolysis, oxidation, alkylation, or aromatic ring-cleavage reactions from 13C-BPS, suggesting hydrolysis and oxidation as the initial and key degradation pathways for the electrochemical degradation process. The DNA-SIP results further displayed high 13C-DNA accumulation in the genera Bacteroides and Cetobacterium from the EABs and indicated their ability in the assimilation of BPS or its metabolites. Collectively, network analysis showed that the collaboration between electroactive microbes and BPS assimilators played pivotal roles the improvement in bioelectrochemically enhanced BPS degradation.

Insights into the mechanisms underlying efficient Rhizodegradation of PAHs in biochar-amended soil: From microbial communities to soil metabolomics

The combined effects of biochar amendment and the rhizosphere on the soil metabolic microbiome during the remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated soil remain unknown. In this study, we attempted to characterize a PAH degradation network by coupling the direct PAH degradation with soil carbon cycling. From microbial community structure and functions to metabolic pathways, we revealed the modulation strategies by which biochar and the rhizosphere benefited PAH degradation in soil. Firstly, some PAH degraders were enriched by biochar and the rhizosphere, and their combination promoted the cooperation among these PAH degraders. Simultaneously, under the combined effects of biochar and the rhizosphere, the functional genes participating in upstream PAH degradation were greatly upregulated. Secondly, there were strong co-occurrences between soil microbial community members and metabolites, in particular, some PAH degraders and the metabolites, such as PAH degradation products or common carbon resources, were highlighted in the networks. It shows that the overall downstream carbon metabolism of PAH degradation was also greatly upregulated by the combined effects of biochar and plant roots, showing good survival of the soil microbiome and contributing to PAH biodegradation. Taken together, both soil carbon metabolism and direct contaminant biodegradation are likely to be modulated by the combined effects of biochar and plant roots, jointly benefitting to PAH degradation by soil microbiome. Our study is the first to link PAH degradation with native carbon metabolism by coupling sequencing and soil metabolomics technology, providing new insights into a systematic understanding of PAH degradation by indigenous soil microbiome and their networks.

Metabolism of mono-(2-ethylhexyl) phthalate in Arabidopsis thaliana: Exploration of metabolic pathways by deuterium labeling

Mono-(2-ethylhexyl) phthalate (MEHP) is the primary monoester transformation product of the commonly used plasticizer, di-2-ethylhexyl phthalate (DEHP), and has been frequently detected in various environmental compartments (e.g., soil, biosolids, plants). Plants growing in contaminated soils can take up MEHP, and consumption of the contaminated plants may result in unintended exposure for humans and other organisms. The metabolism of MEHP in plants is poorly understood, but critical for evaluating the potential human and environmental health risks. The present study represents the first attempt to explore the metabolic fate of MEHP in plants. We used Arabidopsis thaliana cells as a plant model and explored metabolic pathways of MEHP using deuterium stable isotope labelling (SIL) coupled with time-of-flight high resolution mass spectrometer (TOF-HRMS). A. thaliana rapidly took up MEHP from the culture medium and mediated extensive metabolism of MEHP. Combining SIL with TOF-HRMS analysis was proved as a powerful method for identification of unknown MEHP metabolites. Four phase Ⅰ and three phase Ⅱ metabolites were confirmed or tentatively identified. Based on the detected transformation products, hydroxylation, oxidation, and malonylation are proposed as the potential MEHP metabolism pathways. In cells, the maximum fraction of each transformation product accounted for 2.8-56.5% of the total amount of metabolites during the incubation. For individual metabolites, up to 2.9-100% was found in the culture medium, suggesting plant excretion. The results in the cell culture experiments were further confirmed in cabbage and A. thaliana seedlings. The findings suggest active metabolism of MEHP in plants and highlight the need to include metabolites in refining environmental risk assessment of plasticizers in the agro-food systems.

Fungal bioremediation of soil co-contaminated with petroleum hydrocarbons and toxic metals

Abstract

Much research has been carried out on the bacterial bioremediation of soil contaminated with petroleum hydrocarbons and toxic metals but much less is known about the potential of fungi in sites that are co-contaminated with both classes of pollutants. This article documents the roles of fungi in soil polluted with both petroleum hydrocarbons and toxic metals as well as the mechanisms involved in the biotransformation of such substances. Soil characteristics (e.g., structural components, pH, and temperature) and intracellular or excreted extracellular enzymes and metabolites are crucial factors which affect the efficiency of combined pollutant transformations. At present, bioremediation of soil co-contaminated with petroleum hydrocarbons and toxic metals is mostly focused on the removal, detoxification, or degradation efficiency of single or composite pollutants of each type. Little research has been carried out on the metabolism of fungi in response to complex pollutant stress. To overcome current bottlenecks in understanding fungal bioremediation, the potential of new approaches, e.g., gradient diffusion film technology (DGT) and metabolomics, is also discussed.

Key points

• Fungi play important roles in soil co-contaminated with TPH and toxic metals.

• Soil characteristics, enzymes, and metabolites are major factors in bioremediation.

• DGT and metabolomics can be applied to overcome current bottlenecks.

Bisphenol A attenuation in natural microcosm: Contribution of ecological components and identification of transformation pathways through stable isotope tracing

Residues of bisphenol A (BPA) are ubiquitously detected in the surface water due to its widespread usage. This study systematically investigated the dissipation and kinetics of BPA under simulated hydrolysis, direct and indirect photolysis, bacterial degradation, microbial degradation and natural attenuation in microcosm. Structural equation modeling (SEM) by using partial least square method in path coefficient analysis suggested that the microbial degradation was the major factor involved in the natural attenuation of BPA. The potential transformation products were identified by using liquid chromatography high-resolution mass spectrometry (LC-HRMS) and stable isotope tracing technique by simultaneous performing gas chromatography combustion isotope ratio mass spectrometry (GC-C-IRMS) and gas chromatography mass spectrometry (GC-MS). A total of fourteen including three novel transformation products of BPA were identified to indicate five possible pathways. An increased yield of labeled (δ¹³C) CO₂ and detection of ¹³C-labeled phospholipid fatty acids (PLFAs) indicated the mineralization of BPA and possible utilization of BPA or its transformation products by microbes for cellular membrane synthesis, respectively.

Local Phenomena Shape Backyard Soil Metabolite Composition

Soil covers most of Earth's continental surface and is fundamental to life-sustaining processes such as agriculture. Given its rich biodiversity, soil is also a major source for natural product drug discovery from soil microorganisms. However, the study of the soil small molecule profile has been challenging due to the complexity and heterogeneity of this matrix. In this study, we implemented high-resolution liquid chromatography-tandem mass spectrometry and large-scale data analysis tools such as molecular networking to characterize the relative contributions of city, state and regional processes on backyard soil metabolite composition, in 188 soil samples collected from 14 USA States, representing five USA climate regions. We observed that region, state and city of collection all influence the overall soil metabolite profile. However, many metabolites were only detected in unique sites, indicating that uniquely local phenomena also influence the backyard soil environment, with both human-derived and naturally-produced (plant-derived, microbially-derived) metabolites identified. Overall, these findings are helping to define the processes that shape the backyard soil metabolite composition, while also highlighting the need for expanded metabolomic studies of this complex environment.

Tracing the mass flow from glucose and phenylalanine to pinoresinol and its glycosides in Phomopsis sp. XP-8 using stable isotope assisted TOF-MS

Phomopsis sp. XP-8, an endophytic fungus from the bark of Tu-Chung (Eucommia ulmoides Oliv) showed capability to biosynthesize pinoresinol (Pin) and pinoresinol diglucoside (PDG) from glucose (glu) and phenylalanine (Phe). To verify the mass flow in the biosynthesis pathway, [¹³C₆]-labeled glu and [¹³C₆]-labeled Phe were separately fed to the strain as sole substrates and [¹³C₆]-labeled products were detected by ultra-high-performance liquid chromatography-quadrupole time of flight mass spectrometry. As results, [¹³C₆]-labeled Phe was incorporated into [¹³C₆]-cinnamylic acid (Ca) and p-coumaric acid (p-Co), and [¹³C₁₂]-labeled Pin, which revealed that the Pin benzene ring came from Phe via the phenylpropane pathway. [¹³C₆]-Labeled Ca and p-Co, [¹³C₁₂]-labeled Pin, [¹³C₁₈]-labeled pinoresinol monoglucoside (PMG), and [¹³C₁₈]-labeled PDG products were found when [¹³C₆]-labeled glu was used, demonstrating that the benzene ring and glucoside of PDG originated from glu. It was also determined that PMG was not the direct precursor of PDG in the biosynthetic pathway. The study identified the occurrence of phenylalanine- lignan biosynthesis pathway in fungi at the level of mass flow.

Fungal laccase-mediated humification of estrogens in aquatic ecosystems

Estrogens are a category of non-degradable organic pollutants prevalent in aquatic environments with reported health risks in human and wildlife reproduction. A biotechnological approach is proposed for utilizing fungal laccase-mediated humification reactions (L-MHRs) to remove estrogens from water. Through a reactive radical-mediated C-C, C-O-C, or C-N-C covalent coupling mechanism, multifarious complex polymeric structures are generated having limited solubilities, which significantly reduces their estrogenic activity and ecotoxicity. This review highlights the available literature associated with the self/cross-coupling mechanism of fungal L-MHRs in catalyzing the single-electron oxidation of estrogens and humic acid (HA). Advances in identifying unknown estrogen-HA cross-coupling products using high-resolution mass spectrometry combined with ¹³C-isotope labeling and ¹³C NMR may provide key research directions beneficial to aquatic ecological restoration measures.

Applicability of in vitro methods in evaluating the biotransformation of polycyclic aromatic hydrocarbons (PAHs) in fish: Advances and challenges

The biotransformation of polycyclic aromatic hydrocarbons (PAHs) and the biochemical mechanisms involved in such process continue to be intensively studied in the fields of environmental science and toxicology. The investigation of PAH biotransformation in fish is fundamental to understand how piscine species cope with PAH exposure, as these compounds are ubiquitous in aquatic ecosystems and impact different levels of biological organization. New approaches are continuously developed in the field of ecotoxicology, allowing live animal testing to be combined with and, in some cases, replaced with novel in vitro systems. Many in vitro techniques have been developed and effectively applied in the investigation of the biochemical pathways driving the biotransformation of PAH in fish. In vitro experimentation has been fundamental in the advancement of not only understanding PAH-mediated toxicity, but also in highlighting suitable cell-based models for such investigations. Therefore, the present review highlights the value and applicability of in vitro systems for PAH biotransformation studies, and provides up-to-date information on the use of in vitro fish models in the evaluation of PAH biotransformation, common biomarkers, and challenges encountered when developing and applying such systems.