Investigating Biodegradation of 1,4-Dioxane by Groundwater and Soil Microbiomes: Insights into Microbial Ecology and Process Prediction

Although microorganisms play significant roles in bioremediation, their contributions to long-term site characteristics during and after active treatment need to be fully elucidated. This study described microbial ecology dynamics in 1,4-dioxane- and chlorinated solvents-contaminated groundwater in laboratory microcosms. Bioaugmented Pseudonocardia dioxanivorans CB1190 improved 1,4-dioxane removal, with increased carbohydrate and amino acid metabolism, but was eventually outcompeted by native microbes. The original microbiomes were perturbed and divergent but tended to be similar over time. Dechlorinating bacteria co-existed in the same niche, whereas CB1190 had more negative interactions in the shared niche. Multiple regression and classification machine learning models were built by using microbial taxa to predict the degradation process; the ensemble regression model provided most accurate prediction of 1,4-dioxane concentrations (R2 = 0.81 ± 0.17). Among the classification models, the support vector machine performed the best in differentiating the contamination levels (accuracy at 0.67 ± 0.07, kappa at 0.56 ± 0.10). The ensemble model predicted the 1,4-dioxane concentrations and relative duration of contamination with independent microbial datasets from a field study, and the results aligned with the geographic and hydrological information from monitoring wells. This study introduces the application of machine learning in microbiome-based diagnostics for groundwater remediation and evaluation, providing valuable methods for future research and practice

Biotransformation of 6:2 Fluorotelomer Alcohol (6:2 FTOH) by a Wood-Rotting Fungus

Biotransformation of 6:2 FTOH [F­(CF₂)₆CH₂CH₂OH] by the white-rot fungus, <i>Phanerochaete chrysosporium</i>, was investigated in laboratory studies. 6:2 FTOH is a raw material increasingly being used to replace products that can lead to long-chain perfluoroalkyl carboxylic acids (PFCAs, ≥ 8 carbons). During a product’s life cycle and after final disposal, 6:2 FTOH-derived compounds may be released into the environment and potentially biotransformed. In this study, <i>P. chrysosporium</i> transformed 6:2 FTOH to perfluorocarboxylic acids (PFCAs), polyfluorocarboxylic acids, and transient intermediates within 28 days. 5:3 Acid [F­(CF₂)₅CH₂CH₂COOH] was the most abundant transformation product, accounting for 32–43 mol % of initially applied 6:2 FTOH in cultures supplemented with lignocellulosic powder, yeast extract, cellulose, and glucose. PFCAs, including perfluoropentanoic (PFPeA) and perfluorohexanoic (PFHxA) acids, accounted for 5.9 mol % after 28-day incubation. Furthermore, four new transformation products as 6:2 FTOH conjugates or 5:3 acid analogues were structurally confirmed. These results demonstrate that <i>P. chrysosporium</i> has the necessary biochemical mechanisms to drive 6:2 FTOH biotransformation pathways toward more degradable polyfluoroalkylcarboxylic acids, such as 5:3 acid, with lower PFCA yields compared to aerobic soil, sludge, and microbial consortia. Since bacteria and fungi appear to contribute differently toward the environmental loading of FTOH-derived PFCAs and polyfluorocarboxylic acids, wood-rotting fungi should be evaluated as potential candidates for the bioremediation of wastewater and groundwater contaminated with fluoroalkyl substances

Evidence of 1,4-Dioxane Attenuation at Groundwater Sites Contaminated with Chlorinated Solvents and 1,4-Dioxane

There is a critical need to develop appropriate management strategies for 1,4-dioxane (dioxane) due to its widespread occurrence and perceived recalcitrance at groundwater sites where chlorinated solvents are present. A comprehensive evaluation of California state (GeoTracker) and Air Force monitoring records was used to provide significant evidence of dioxane attenuation at field sites. Temporal changes in the site-wide maximum concentrations were used to estimate source attenuation rates at the GeoTracker sites (median length of monitoring period = 6.8 years). While attenuation could not be established at all sites, statistically significant positive attenuation rates were confirmed at 22 sites. At sites where dioxane and chlorinated solvents were present, the median value of all statistically significant dioxane source attenuation rates (equivalent half-life = 31 months; <i>n </i>= 34) was lower than 1,1,1-trichloroethane (TCA) but similar to 1,1-dichloroethene (1,1-DCE) and trichloroethene (TCE). Dioxane attenuation rates were positively correlated with rates for 1,1-DCE and TCE but not TCA. At this set of sites, there was little evidence that chlorinated solvent remedial efforts (e.g., chemical oxidation, enhanced bioremediation) impacted dioxane attenuation. Attenuation rates based on well-specific records from the Air Force data set confirmed significant dioxane attenuation (131 out of 441 wells) at a similar frequency and extent (median equivalent half-life = 48 months) as observed at the California sites. Linear discriminant analysis established a positive correlation between dioxane attenuation and increasing concentrations of dissolved oxygen, while the same analysis found a negative correlation with metals and CVOC concentrations. The magnitude and prevalence of dioxane attenuation documented here suggest that natural attenuation may be used to manage some but not necessarily all dioxane-impacted sites

Vault Nanoparticles Packaged with Enzymes as an Efficient Pollutant Biodegradation Technology

Vault nanoparticles packaged with enzymes were synthesized as agents for efficiently degrading environmental contaminants. Enzymatic biodegradation is an attractive technology for <i>in situ</i> cleanup of contaminated environments because enzyme-catalyzed reactions are not constrained by nutrient requirements for microbial growth and often have higher biodegradation rates. However, the limited stability of extracellular enzymes remains a major challenge for practical applications. Encapsulation is a recognized method to enhance enzymatic stability, but it can increase substrate diffusion resistance, lower catalytic rates, and increase the apparent half-saturation constants. Here, we report an effective approach for boosting enzymatic stability by single-step packaging into vault nanoparticles. With hollow core structures, assembled vault nanoparticles can simultaneously contain multiple enzymes. Manganese peroxidase (MnP), which is widely used in biodegradation of organic contaminants, was chosen as a model enzyme in the present study. MnP was incorporated into vaults <i>via</i> fusion to a packaging domain called INT, which strongly interacts with vaults’ interior surface. MnP fused to INT and vaults packaged with the MnP-INT fusion protein maintained peroxidase activity. Furthermore, MnP-INT packaged in vaults displayed stability significantly higher than that of free MnP-INT, with slightly increased <i>K</i>_m value. Additionally, vault-packaged MnP-INT exhibited 3 times higher phenol biodegradation in 24 h than did unpackaged MnP-INT. These results indicate that the packaging of MnP enzymes in vault nanoparticles extends their stability without compromising catalytic activity. This research will serve as the foundation for the development of efficient and sustainable vault-based bioremediation approaches for removing multiple contaminants from drinking water and groundwater

Synergistic Treatment of Mixed 1,4-Dioxane and Chlorinated Solvent Contaminations by Coupling Electrochemical Oxidation with Aerobic Biodegradation

Biodegradation of the persistent groundwater contaminant 1,4-dioxane is often hindered by the absence of dissolved oxygen and the co-occurrence of inhibiting chlorinated solvents. Using flow-through electrolytic reactors equipped with Ti/IrO₂–Ta₂O₅ mesh electrodes, we show that combining electrochemical oxidation with aerobic biodegradation produces an overadditive treatment effect for degrading 1,4-dioxane. In reactors bioaugmented by <i>Pseudonocardia dioxanivorans</i> CB1190 with 3.0 V applied, 1,4-dioxane was oxidized 2.5 times faster than in bioaugmented control reactors without an applied potential, and 12 times faster than by abiotic electrolysis only. Quantitative polymerase chain reaction analyses of CB1190 abundance, oxidation–reduction potential, and dissolved oxygen measurements indicated that microbial growth was promoted by anodic oxygen-generating reactions. At a higher potential of 8.0 V, however, the cell abundance near the anode was diminished, likely due to unfavorable pH and/or redox conditions. When coupled to electrolysis, biodegradation of 1,4-dioxane was sustained even in the presence of the common co-contaminant trichloroethene in the influent. Our findings demonstrate that combining electrolytic treatment with aerobic biodegradation may be a promising synergistic approach for the treatment of mixed contaminants

Genome-Wide Assessment in Escherichia coli Reveals Time-Dependent Nanotoxicity Paradigms

The use of engineered nanomaterials (eNM) in consumer and industrial products is increasing exponentially. Our ability to rapidly assess their potential effects on human and environmental health is limited by our understanding of nanomediated toxicity. High-throughput screening (HTS) enables the investigation of nanomediated toxicity on a genome-wide level, thus uncovering their novel mechanisms and paradigms. Herein, we investigate the toxicity of zinc-containing nanomaterials (Zn-eNMs) using a time-resolved HTS methodology in an arrayed Escherichia coli genome-wide knockout (KO) library. The library was screened against nanoscale zerovalent zinc (nZn), nanoscale zinc oxide (nZnO), and zinc chloride (ZnCl₂) salt as reference. Through sequential screening over 24 h, our method identified 173 sensitive clones from diverse biological pathways, which fell into two general groups: early and late responders. The overlap between these groups was small. Our results suggest that bacterial toxicity mechanisms change from pathways related to general metabolic function, transport, signaling, and metal ion homeostasis to membrane synthesis pathways over time. While all zinc sources shared pathways relating to membrane damage and metal ion homeostasis, Zn-eNMs and ZnCl₂ displayed differences in their sensitivity profiles. For example, ZnCl₂ and nZnO elicited unique responses in pathways related to two-component signaling and monosaccharide biosynthesis, respectively. Single isolated measurements, such as MIC or IC₅₀, are inadequate, and time-resolved approaches utilizing genome-wide assays are therefore needed to capture this crucial dimension and illuminate the dynamic interplay at the nano-bio interface

Genome-Wide Assessment in Escherichia coli Reveals Time-Dependent Nanotoxicity Paradigms

The use of engineered nanomaterials (eNM) in consumer and industrial products is increasing exponentially. Our ability to rapidly assess their potential effects on human and environmental health is limited by our understanding of nanomediated toxicity. High-throughput screening (HTS) enables the investigation of nanomediated toxicity on a genome-wide level, thus uncovering their novel mechanisms and paradigms. Herein, we investigate the toxicity of zinc-containing nanomaterials (Zn-eNMs) using a time-resolved HTS methodology in an arrayed Escherichia coli genome-wide knockout (KO) library. The library was screened against nanoscale zerovalent zinc (nZn), nanoscale zinc oxide (nZnO), and zinc chloride (ZnCl₂) salt as reference. Through sequential screening over 24 h, our method identified 173 sensitive clones from diverse biological pathways, which fell into two general groups: early and late responders. The overlap between these groups was small. Our results suggest that bacterial toxicity mechanisms change from pathways related to general metabolic function, transport, signaling, and metal ion homeostasis to membrane synthesis pathways over time. While all zinc sources shared pathways relating to membrane damage and metal ion homeostasis, Zn-eNMs and ZnCl₂ displayed differences in their sensitivity profiles. For example, ZnCl₂ and nZnO elicited unique responses in pathways related to two-component signaling and monosaccharide biosynthesis, respectively. Single isolated measurements, such as MIC or IC₅₀, are inadequate, and time-resolved approaches utilizing genome-wide assays are therefore needed to capture this crucial dimension and illuminate the dynamic interplay at the nano-bio interface

A Multisite Survey To Identify the Scale of the 1,4-Dioxane Problem at Contaminated Groundwater Sites

1,4-Dioxane (dioxane) is an emerging groundwater contaminant that has significant regulatory implications and potential remediation costs, but our current understanding of its occurrence and behavior is limited. This study used intensive data mining to identify and evaluate >2000 sites in California where groundwater has been impacted by chlorinated solvents and/or dioxane. Dioxane was detected at 194 of these sites, with 95% containing one or more chlorinated solvents. Dioxane frequently co-occurs with 1,1,1-trichloroethene (1,1,1-TCA) (76% of the study sites), but despite this, no dioxane analyses were conducted at 332 (67%) of the sites where 1,1,1-TCA was detected. At sites where dioxane has been identified, plumes are dilute but not large (median maximal concentration of 365 μg/L; median plume length of 269 m) and have been delineated to a similar extent as typically co-occurring chlorinated solvents. Furthermore, at sites where dioxane and chlorinated solvents co-occur, dioxane plumes are frequently shorter than the chlorinated solvent plumes (62%). The results suggest that dioxane has not migrated beyond chlorinated solvent plumes and existing monitoring networks at the majority of sites, and that the primary risk is the large number of sites where dioxane is likely to be present but has yet to be identified