Toluene biodegradation in the vadose zone of a poplar phytoremediation system identified using metagenomics and toluene-specific stable carbon isotope analysis

Insights into the characteristics of changes in dissolved organic matter fluorescence components on the natural attenuation process of toluene

Natural attenuation (NA) is of great significance for the remediation of contaminated groundwater, and how to identify NA patterns of toluene in aquifers more quickly and effectively poses an urgent challenge. In this study, the NA of toluene in two typical soils was conducted by means of soil column experiment. Based on column experiments, dissolved organic matter (DOM) was rapidly identified using fluorescence spectroscopy, and the relationship between DOM and the NA of toluene was established through structural equation modeling analysis. The adsorption rates of toluene in clay and sandy soil were 39 % and 26 %, respectively. The adsorption capacity and total NA capacity of silty clay were large. The occurrence of fluorescence peaks of protein-like components and specific products indicated the occurrence of biodegradation. Arenimonas, Acidovorax and Brevundimonas were the main degrading bacteria identified in Column A, while Pseudomonas, Azotobacter and Mycobacterium were the main ones identified in Column B. The pH, ORP, and Fe(II) were the most important factors affecting the composition of microbial communities, which in turn affected the NA of toluene. These results provide a new way to quickly identify NA of toluene.

Quantifying remediation of chlorinated volatile compounds by sulfidated nano zerovalent iron treatment using numerical modeling and CSIA

Sulfidated nanoscale zerovalent iron (S-nZVI) has demonstrated promising reactivity and longevity for remediating chlorinated volatile compounds (cVOC) contaminants in laboratory tests. However, its effectiveness in field applications remains inadequately evaluated. This study provides the first quantitative evaluation of the long-term effectiveness of carboxymethyl cellulose-stabilized S-nZVI (CMC-S-nZVI) at a cVOC-contaminated field site. A reactive transport model-based numerical approach delineates the change in cVOC concentrations and carbon isotope values (i.e., δ13C from compound-specific stable isotope analysis (CSIA)) caused by dissolution of dense non-aqueous phase liquid, sorption, and pathway-specific degradation and production, respectively. This delineation reveals quantitative insights into remediation effectiveness typically difficult to obtain, including extent of degradation, contributions of different degradation pathways, and degradation rate coefficients. Significantly, even a year after CMC-S-nZVI application, degradation remains an important process effectively removing various cVOC contaminants (i.e., chlorinated ethenes, 1,2-dichloroethanes, and chlorinated methanes) at an extent varying from 5 %-62 %. Although the impacts of CMC-S-nZVI abundance on degradation vary for different cVOC and for different sampling locations at the site, for the primary site contaminants of tetrachloroethene and trichloroethene, their predominance of dichloroelimination pathway (≥ 88 %), high degradation rate coefficient (0.4-1.7 d-1), and occurrence at locations with relatively high CMC-S-nZVI abundance strongly indicate the effectiveness of abiotic remediation. These quantitative assessments support that CMC-S-nZVI supports sustainable ZVI-based remediation. Further, the novel numerical approach presented in this study provides a powerful tool for quantitative cVOC remediation assessments at complex field sites where multiple processes co-occur to control both concentration and CSIA data.

Compatibility of polar organic chemical integrative sampler (POCIS) with compound specific isotope analysis (CSIA) of substituted chlorobenzenes

Compound specific isotope analysis (CSIA) is a powerful technique to demonstrate in situ degradation of traditional groundwater contaminants when concentrations are typically in the mg/L range. Currently, an efficient preconcentration method is lacking to expand CSIA to low aqueous concentration environmental samples. Specially for the H- and N-CSIA of heteroatom-bearing non-traditional compounds, the CSIA analytical detection limits are significantly higher than that of the C-CSIA. This work demonstrates the compatibility of polar organic chemical integrative sampler (POCIS) with C-, H-, and N-CSIA using four nitro- and amino-substituted chlorobenzenes that are common industrial feedstocks for numerous applications and are commonly detected in the environment at mg/L to μg/L range. Using lab experiments, we showed isotopic equilibrium in POCIS was achieved after 30 days with either a negligible (<0.5 ‰) or a constant shift for C (<1 ‰) and N (<2 ‰). Similar negligible (<5 ‰) or constant shift (<20 ‰) was evident for H isotope except for 3,4-dichloroaniline. The method quantification limits for the combined sorbent and membrane of one POCIS were comparable to that of the solid phase extraction (SPE) using 10 L water. Next, we demonstrated the field applicability of POCIS for C- and N-CSIA after a 60-day deployment in a pilot constructed wetland by showing <1 ‰ difference between the δ13C and δ15N obtained from POCIS and SPE. Finally, we evaluated whether the biofilm development on POCIS membrane could affect the isotope signature of the sampled compounds during field deployment. Although a diverse microbial community was identified on the membrane after a 60-day deployment, we did not observe significant isotope fractionation. This was likely due to either slower diffusion in the biofilm or microbial degradation of the sampled compounds. This work demonstrates the potential of using POCIS-CSIA as a simple, fast, and sensitive method for low-concentration contaminants, such as pesticides, pharmaceuticals, and flame-retardants.

Effects of freeze-thaw cycles on methanogenic hydrocarbon degradation: Experiment and modeling

Cold regions are warming much faster than the global average, resulting in more frequent and intense freeze-thaw cycles (FTCs) in soils. In hydrocarbon-contaminated soils, FTCs modify the biogeochemical and physical processes controlling petroleum hydrocarbon (PHC) biodegradation and the associated generation of methane (CH₄) and carbon dioxide (CO₂). Thus, understanding the effects of FTCs on the biodegradation of PHCs is critical for environmental risk assessment and the design of remediation strategies for contaminated soils in cold regions. In this study, we developed a diffusion-reaction model that accounts for the effects of FTCs on toluene biodegradation, including methanogenic biodegradation. The model is verified against data generated in a 215 day-long batch experiment with soil collected from a PHC contaminated site in Ontario, Canada. The fully saturated soil incubations with six different treatments were exposed to successive 4-week FTCs, with temperatures oscillating between -10 °C and +15 °C, under anoxic conditions to stimulate methanogenic biodegradation. We measured the headspace concentrations and ¹³C isotope compositions of CH₄ and CO₂ and analyzed the porewater for pH, acetate, dissolved organic and inorganic carbon, and toluene. The numerical model represents solute diffusion, volatilization, sorption, as well as a reaction network of 13 biogeochemical processes. The model successfully simulates the soil porewater and headspace concentration time series data by representing the temperature dependencies of microbial reaction and gas diffusion rates during FTCs. According to the model results, the observed increases in the headspace concentrations of CH₄ and CO₂ by 87% and 136%, respectively, following toluene addition are explained by toluene fermentation and subsequent methanogenesis reactions. The experiment and the numerical simulation show that methanogenic degradation is the primary toluene attenuation mechanism under the electron acceptor-limited conditions experienced by the soil samples, representing 74% of the attenuation, with sorption contributing to 11%, and evaporation contributing to 15%. Also, the model-predicted contribution of acetate-based methanogenesis to total produced CH₄ agrees with that derived from the ¹³C isotope data. The freezing-induced soil matrix organic carbon release is considered as an important process causing DOC increase following each freezing period according to the calculations of carbon balance and SUVA index. The simulation results of a no FTC scenario indicate that, in the absence of FTCs, CO₂ and CH₄ generation would decrease by 29% and 26%, respectively, and that toluene would be biodegraded 23% faster than in the FTC scenario. Because our modeling approach represents the dominant processes controlling PHC biodegradation and the associated CH₄ and CO₂ fluxes, it can be used to analyze the sensitivity of these processes to FTC frequency and duration driven by temperature fluctuations.

Metagenome analyses of microbial population in geotextile fabrics used in permeable reactor barriers for toluene biodegradation

Toluene is one of the hydrocarbons that contaminate soil and groundwater, and has a high cost to remediate, which makes it an environmental pollutant of concern. This study aimed to find bacterial distribution from nonwoven geotextile (GT) fabric specimens in a pilot-scale permeable reactive barrier (PRB). Upon 167 days of incubation with the addition of toluene, the microbial community on the GT surfaces (n = 12) was investigated by the 16S rRNA metagenome sequencing approach. According to taxonomic classification, the Proteobacteria phylum dominated the metagenomes of all the geotextile samples (80-90%). Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway database search of the toluene degradation mechanism revealed the susceptible toluene-degrading species. For the toluene-to-benzoate degradation, the Cupriavidus genus, particularly C. gilardii, C. metallidurans, and C. taiwanensis, are likely to be functional. In addition to these species, the Novosphingobium genus was abundantly localized in the GTs, in particular Novosphingobium sp. ABRDHK2. The results suggested the biodegradation potential of these species in toluene remediation. Overall, this work sheds light on the variety of microorganisms found in the geotextile fabrics used in PRBs and the species involved in the biodegradation of toluene from several sources, including soil, sediment, and groundwater.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03460-y.

Response of environmental factors to attenuation of toluene in vadose zone

Contaminated groundwater migrates in reverse direction under capillary force in vadose zone, and the attenuation process of pollutant adsorption and microbial degradation changes the environment of vadose zone. In this study, the response of toluene to environmental factors during reverse migration and attenuation of toluene from aquifer to vadose zone was studied by column experiment and experimental data analysis. The changes of environmental factors, including potential of hydrogen (pH), dissolved oxygen (DO), and oxidation-reduction potential (ORP), and toluene concentration were monitored by soil column experiment under sterilized and non-sterilized conditions. The 16S rRNA molecular biological detection technology was used to quantitatively analyze the impact of microbial degradation on the environment. Finally, the correlation between environmental factors and concentration in the attenuation process of toluene in the vadose zone was quantitatively studied by Pearson Correlation Coefficient (PCC) and multivariate statistical equation. The results showed that pH was primarily affected by microbial degradation, and DO and ORP were primarily affected by both adsorption and microbial degradation. The attenuation of toluene was divided into two stages: adsorption dominated (0~26 d) and microbial degradation dominated (26~55 d). The degradation amounts of microorganisms at each position in the non-sterilized column from bottom to top were 9.37%, 55.34%, 68.64%, 75.70%, 66.03% and 42.50%. At the same time, the article proposes for the first time that there is an obvious functional relationship between environmental factors (DO, ORP, pH), time (t) and concentration (C_Toluene):C_Toluene=C₀+A100t+Bα+Cβ+D100γ, (α,β,γ are the pH, DO and ORP of capillary water, respectively; A, B, C and D are all undetermined coefficients), R² > 0.95. The results of this study may facilitate the use of simple and easy-to-obtain environmental factors to characterize the dynamic process of pollutant concentration changes.

Identification of degrader bacteria and fungi enriched in rhizosphere soil from a toluene phytoremediation site using DNA stable isotope probing

Improved knowledge of the ecology of contaminant-degrading organisms is paramount for effective assessment and remediation of aromatic hydrocarbon-impacted sites. DNA stable isotope probing was used herein to identify autochthonous degraders in rhizosphere soil from a hybrid poplar phytoremediation system incubated under semi-field-simulated conditions. High-throughput sequencing of bacterial 16S rRNA and fungal internal transcribed spacer (ITS) rRNA genes in metagenomic samples separated according to nucleic acid buoyant density was used to identify putative toluene degraders. Degrader bacteria were found mainly within the Actinobacteria and Proteobacteria phyla and classified predominantly as Cupriavidus, Rhodococcus, Luteimonas, Burkholderiaceae, Azoarcus, Cellulomonadaceae, and Pseudomonas organisms. Purpureocillium lilacinum and Mortierella alpina fungi were also found to assimilate toluene, while several strains of the fungal poplar endophyte Mortierella elongatus were indirectly implicated as potential degraders. Finally, PICRUSt2 predictive taxonomic functional modeling of 16S rRNA genes was performed to validate successful isolation of stable isotope-labeled DNA in density-resolved samples. Four unique sequences, classified within the Bdellovibrionaceae, Intrasporangiaceae, or Chitinophagaceae families, or within the Sphingobacteriales order were absent from PICRUSt2-generated models and represent potentially novel putative toluene-degrading species. This study illustrates the power of combining stable isotope amendment with advanced metagenomic and bioinformatic techniques to link biodegradation activity with unisolated microorganisms. Novelty statement: This study used emerging molecular biological techniques to identify known and new organisms implicated in aromatic hydrocarbon biodegradation from a field-scale phytoremediation system, including organisms with phyto-specific relevance and having potential for downstream applications (amendment or monitoring) in future and existing systems. Additional novelty in this study comes from the use of taxonomic functional modeling approaches for validation of stable isotope probing techniques. This study provides a basis for expanding existing reference databases of known aromatic hydrocarbon degraders from field-applicable sources and offers technological improvements for future site assessment and management purposes.

Quantification of toluene phytoextraction rates and microbial biodegradation functional profiles at a fractured bedrock phytoremediation site

This field study evaluated the efficacy of a mature hybrid poplar phytoremediation system for the remediation of toluene in a fractured bedrock aquifer site. Phytoextraction activity of the trees and the ecology and biodegradation potential of root-colonizing bacteria that ultimately influence how much toluene is transported from the roots and phytoextracted to the aboveground point of measurement were explored. Peak-season toluene mass removal rates ranging from 313 to 743 μg/day were quantified using passive in planta contaminant sampling techniques and continuous heat dissipation transpiration measurements in tree stems. Root bacterial microbiome structure and biodegradation potential were evaluated via high-throughput sequencing and predictive metagenomic functional modelling of bacterial 16S rRNA genes in roots. Poplar roots were colonized mostly by Proteobacteria, Actinobacteria, and Bacteroidetes. Distinct, more uniform communities were observed in roots associated with trees planted in the toluene source area compared to other areas, with differences apparent at lower taxonomic levels. Significant enrichment of Streptomyces in roots was observed in the source area, implicating that genus as a potentially important poplar endophyte at toluene-impacted sites. Moreover, significantly greater aerobic toluene biodegradation capacity was predicted in these roots compared to other areas using taxonomic functional modelling. Together with passive sampling, the molecular results provided supporting evidence of biodegradation activity in the source area and contextualized the detected phytoextraction patterns. These results support the application of phytoremediation systems for aromatic hydrocarbons in environments with complex geology and demonstrate field-validated monitoring techniques to assess phytoextraction and biodegradation in these systems.