Network Analysis for Prioritizing Biodegradation Metabolites of Polycyclic Aromatic Hydrocarbons

Identification of Potentially Toxic Transformation Products Produced in Polycyclic Aromatic Hydrocarbon Bioremediation Using Suspect and Non-Target Screening Approaches

Polycyclic aromatic hydrocarbons (PAHs) are a class of ubiquitous environmental contaminants that can be remediated through physical, chemical, or biological means. Treatment strategies can lead to the formation of PAH-transformation products (PAH-TPs) that, despite having the potential for adverse ecological and human health effects, are unregulated and understudied in environmental monitoring and remediation. Unavailability of reference standards for PAH-TPs limits the ability to identify PAH-TPs by targeted methods. This study utilized suspect and nontarget screening approaches to identify PAH-TPs produced by a bacterial culture, Rhodococcus rhodochrous ATCC 21198, using liquid chromatography-high resolution mass spectrometry. Open-source tools were used to predict biotransformation products, predict potential PAH-TP structures from mass spectra, and estimate health hazards of potential PAH-TPs. The workflow developed in this study allowed for the tentative identification of 16 PAH-TPs (confidence levels 2a to 3), seven of which were not previously detected by targeted analysis. Several new potential transformation pathways for our bacterial pure culture were suggested by the PAH-TPs, including carboxylation, sulfonation and up to three hydroxylation reactions. A computational toxicity assessment indicated that the PAH-TPs shared many hazard characteristics with their parent compounds, including genotoxicity and endocrine disruption, highlighting the importance of considering PAH-TPs in future PAH studies.

Comparative genomic analysis and functional investigations for MCs catabolism mechanisms and evolutionary dynamics of MCs-degrading bacteria in ecology

Microcystins (MCs) significantly threaten the ecosystem and public health. Biodegradation has emerged as a promising technology for removing MCs. Many MCs-degrading bacteria have been identified, including an indigenous bacterium Sphingopyxis sp. YF1 that could degrade MC-LR and Adda completely. Herein, we gained insight into the MCs biodegradation mechanisms and evolutionary dynamics of MCs-degrading bacteria, and revealed the toxic risks of the MCs degradation products. The biochemical characteristics and genetic repertoires of strain YF1 were explored. A comparative genomic analysis was performed on strain YF1 and six other MCs-degrading bacteria to investigate their functions. The degradation products were investigated, and the toxicity of the intermediates was analyzed through rigorous theoretical calculation. Strain YF1 might be a novel species that exhibited versatile substrate utilization capabilities. Many common genes and metabolic pathways were identified, shedding light on shared functions and catabolism in the MCs-degrading bacteria. The crucial genes involved in MCs catabolism mechanisms, including mlr and paa gene clusters, were identified successfully. These functional genes might experience horizontal gene transfer events, suggesting the evolutionary dynamics of these MCs-degrading bacteria in ecology. Moreover, the degradation products for MCs and Adda were summarized, and we found most of the intermediates exhibited lower toxicity to different organisms than the parent compound. These findings systematically revealed the MCs catabolism mechanisms and evolutionary dynamics of MCs-degrading bacteria. Consequently, this research contributed to the advancement of green biodegradation technology in aquatic ecology, which might protect human health from MCs.

Integrated data-driven cross-disciplinary framework to prevent chemical water pollution

Access to a clean and healthy environment is a human right and a prerequisite for maintaining a sustainable ecosystem. Experts across domains along the chemical life cycle have traditionally operated in isolation, leading to limited connectivity between upstream chemical innovation to downstream development of water-treatment technologies. This fragmented and historically reactive approach to managing emerging contaminants has resulted in significant externalized societal costs. Herein, we propose an integrated data-driven framework to foster proactive action across domains to effectively address chemical water pollution. By implementing this integrated framework, it will not only enhance the capabilities of experts in their respective fields but also create opportunities for novel approaches that yield co-benefits across multiple domains. To successfully operationalize the integrated framework, several concerted efforts are warranted, including adopting open and FAIR (findable, accessible, interoperable, and reusable) data practices, developing common knowledge bases/platforms, and staying vigilant against new substance "properties" of concern.

Bio-polysaccharide composites mediated degradation of polyaromatic hydrocarbons in a sandy soil using free and immobilized consortium of Kocuria rosea and Aspergillus sydowii

Based on our previous study in minimal medium, Kocuria rosea and Aspergillus sydowii were identified as the best microbes for degradation of mixture of polyaromatic hydrocarbons (PAHs). The present study reports PAH degradation potential of these microbes in free and immobilized form. PAHs were extracted using QuEChERS-mediated process followed by quantification by high performance liquid chromatography. The microbial consortium of Kocuria rosea + Aspergillus sydowii was formulated in three bio-formulations, namely (i) bentonite-alginate composite beads; (ii) water dispersible granule composite using guar gum-nanobentonite; and (iii) composites of carboxymethyl cellulose-bentonite and were applied in PAH fortified (100 µg g-1) sandy loam soil. Results suggested that degradation data fitted well to first order kinetics as in most of the cases, the values of correlation coefficient (r) were > 0.95. The half-life (t1/2) values for PAHs in the uninoculated control soil were: naphthalene (10.43 d), fluorene (22.43 d), phenanthrene (24.64 d), anthracene (38.47 d), and pyrene (34.34 d). Inoculation of soil with free culture microbial consortium (without or with nutrient) and bio-formulation of degrading cultures enhanced degradation of all PAHs and half-life values were significantly reduced for each PAH: naphthalene (1.76-2.00 d), fluorene (2.52-6.65 d), phenanthrene (4.61-6.37 d), anthracene (9.01-12.22 d), and pyrene (10.98-15.55 d). Among different bio-formulations, guar gum-nanobentonite-based composite exhibited better efficacy for degradation of naphthalene, fluorene, phenanthrene, anthracene, and pyrene. The addition of microbial consortium in PAH fortified soil increased 16S rRNA gene copies of Alphaproteobacteria and Bacteroidetes, compared to the uninoculated, PAH-fortified control. The microbial functional gene assays showed that the gene copies of amoA, nirK, nirS, and anammox increased, suggesting nitrogen regulation in the PAH-fortified soil.

Degradation or humification: rethinking strategies to attenuate organic pollutants

The fate of organic pollutants in environmental matrices can be determined by degradation and humification. The humification process represents a promising strategy to remove organic pollutants, particularly those resistant to degradation. In contrast to the well-studied degradation process, the contribution and application prospects of the humification process for organic pollutant removal has been underestimated. The recent progress in synthesizing artificial humic substances (HS) has made directed humification of recalcitrant organic pollutants possible. This review focuses on degradation and humification of organic matter, especially recalcitrant organic pollutants. Challenges in understanding the contribution, underlying mechanisms, and artificial synthesis of HS for removing organic pollutants are also critically discussed. We advocate further investigating the humification of organic pollutants in future studies.

Performance analysis of Pseudomonas sp. strain SA3 in naphthalene degradation using phytotoxicity and microcosm studies

The present study is aimed to develop a microbial system for efficient naphthalene bioremediation. A phytotoxicity study was carried out to check the naphthalene detoxification efficiency of Pseudomonas sp. strain SA3 in mung bean (Vigna radiata). For this, administration of the degraded product (supernatant) of 500 mg L^-1 naphthalene by Pseudomonas sp. strain SA3 was studied on V. radiata till 168 h. The growth parameters of mung bean seedlings exposed to treated naphthalene solution were statistically similar to distilled water but a twofold decrease when exposed to untreated naphthalene solution. Further, through the soil microcosm study, the naphthalene degradation by pure colonies of Pseudomonas sp. strain SA3 was 6.8% higher as compared to when the natural microflora was mixed with Pseudomonas sp. strain SA3. Further naphthalene degradation by a microcosm model revealed that with an increased concentration of glucose, the carbon dioxide trap rate decreases.

Development of a highly efficient in-tube solid-phase microextraction system coupled with UHPLC-MS/MS for analyzing trace hydroxyl polycyclic aromatic hydrocarbons in biological samples

Hydroxyl polycyclic aromatic hydrocarbons are considered active mutagenic and carcinogenic substances and are found in extremely low levels (ng/g) in biological samples. As a result, their determination in urine and blood samples is challenging, and a sensitive and effective method for the analysis of trace hydroxyl polycyclic aromatic hydrocarbons in complex biological matrices is required. In this work, a novel macroporous in-tube solid-phase microextraction monolith was prepared via a thiol-yne click reaction, and a highly efficient analytical method based on in-tube solid-phase microextraction coupled with UHPLC-MS/MS was developed to determine hydroxyl polycyclic aromatic hydrocarbons with low detection limits of 0.137-11.0 ng/L in complex biological samples. Four hydroxyl polycyclic aromatic hydrocarbons, namely, 2-hydroxyanthraquinone, 1-hydroxypyrene, 1,8-dihydroxyanthraquinone, and 6-hydroxychrysene, were determined in the urine samples of smokers, non-smokers, and whole blood samples of mice. Satisfactory recoveries were achieved in the range of 83.1-113% with relative standard deviations of 3.2-9.7%. It was found that implementation of the macroporous monolith gave a highly efficient approach for enriching trace hydroxyl polycyclic aromatic hydrocarbons in biological samples.

A Classification Model to Identify Direct-Acting Mutagenic Polycyclic Aromatic Hydrocarbon Transformation Products

Polycyclic aromatic hydrocarbons (PAHs) are a complex group of environmental contaminants, many having long environmental half-lives. As these compounds degrade, the changes in their structure can result in a substantial increase in mutagenicity compared to the parent compound. Over time, each individual PAH can potentially degrade into several thousand unique transformation products, creating a complex, constantly evolving set of intermediates. Microbial degradation is the primary mechanism of their transformation and ultimate removal from the environment, and this process can result in mutagenic activation similar to the metabolic activation that can occur in multicellular organisms. The diversity of the potential intermediate structures in PAH-contaminated environments renders hazard assessment difficult for both remediation professionals and regulators. A mixture of structural and energetic descriptors has proven effective in existing studies for classifying which PAH transformation products will be mutagenic. However, most existing studies of environmental PAH mutagens primarily focus on nitrogenated derivatives, which are prevalent in the atmosphere and not as relevant in soil. Additionally, PAH products commonly found in the environment can range from as large as five rings to as small as a single ring, requiring a broadly inclusive methodology to comprehensively evaluate mutagenic potential. We developed a combination of supervised and unsupervised machine learning methods to predict environmentally induced PAH mutagenicity with improved performance over currently available tools. K-means clustering with principal component analysis allows us to identify molecular clusters that we hypothesize to have similar mechanisms of action. Recursive feature elimination identifies the most influential descriptors. The cluster-specific regression outperforms available classifiers in predicting direct-acting mutagens resulting from the microbial biodegradation of PAHs and provides direction for future studies evaluating the environmental hazards resulting from PAH biodegradation.