Browsing by Author "Li, Mengyan"

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    1, 4-Dioxane biodegradation at low temperatures in Arctic groundwater samples
    (2010) Li, Mengyan; Alvarez, Pedro J.
    1,4-Dioxane is an emerging groundwater contaminant and a probable human carcinogen. Its biodegradation was investigated in microcosms prepared with groundwater and soil from an impacted site in Alaska. In addition to natural attenuation conditions (i.e., no amendments), the following treatments were tested: (a) biostimulation by addition of 1-butanol (a readily available auxiliary substrate) and inorganic nutrients; and (b) bioaugmentation with Pseudonocardia dioxanivorans CB1190, a well-characterized dioxane degrading bacterium, or with Pseudonocardia antarctica DVS 5a1, a bacterium isolated from Antarctica. Biostimulation enhanced the degradation of 50 mg L-1 dioxane by indigenous microorganisms (about 0.01 mg dioxane d-1 mg protein-1) at both 4 and 14°C, with a simultaneous increase in biomass. A more pronounced enhancement was observed through bioaugmentation. Microcosms with 50 mg L -1 initial dioxane (representing source zone contamination) and augmented with CB1190 degraded dioxane fastest (0.155 +/- 0.038 mg dioxane d-1 mg protein-1) at 14°C, and the degradation rate decreased dramatically at 4°C (0.021 +/- 0.007 mg dioxane d-1 mg protein-1). In contrast, microcosms with DVS 5a1 degraded dioxane at similar rates at 4 and 14°C (0.018 +/- 0.004 and 0.015 +/- 0.006 mg dioxane d-1 mg protein-1, respectively). DVS 5a1 outperformed CB1190 when the initial dioxane concentration was low (500 microg L-1). This indicates differences in competitive advantages of these two strains. Natural attenuation microcosms also showed significant degradation over 6 months when the initial dioxane concentration was 500 microg L-1. This is the first study to report the potential for dioxane bioremediation and natural attenuation of contaminated groundwater in sensitive cold-weather ecosystems such as the Arctic.
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    1,4-Dioxane-degrading consortia can be enriched from uncontaminated soils: prevalence of Mycobacterium and soluble di-iron monooxygenase genes
    (Wiley, 2017) He, Ya; Mathieu, Jacques; da Silva, Marcio L.B.; Li, Mengyan; Alvarez, Pedro J.J.
    Two bacterial consortia were enriched from uncontaminated soil by virtue of their ability to grow on 1,4-dioxane (dioxane) as a sole carbon and energy source. Their specific dioxane degradation rates at 30°C, pH = 7 (i.e. 5.7 to 7.1 g-dioxane per g-protein per day) were comparable to those of two dioxane-metabolizing archetypes: Pseudonocardia dioxanivoransCB1190 and Mycobacterium dioxanotrophicusPH-06. Based on 16S rRNA sequencing, Mycobacterium was the dominant genus. Acetylene inhibition tests suggest that dioxane degradation was mediated by monooxygenases. However, qPCR analyses targeting the tetrahydrofuran/dioxane monooxygenase gene (thmA/dxmA) (which is, to date, the only sequenced dioxane monooxygenase gene) were negative, indicating that other (as yet unknown) catabolic gene(s) were responsible. DNA sequence analyses also showed threefold to sevenfold enrichment of group 5 and group 6 soluble di-iron monooxygenase (SDIMO) genes relative to the original soil samples. Whereas biodegradation of trace levels of dioxane is a common challenge at contaminated sites, both consortia degraded dioxane at low initial concentrations (300 μg l−1) below detectable levels (5 μg l−1) in bioaugmented microcosms prepared with impacted groundwater. Overall, this work shows that dioxane-degrading bacteria (and the associated natural attenuation potential) exist even in some uncontaminated soils, and may be enriched to broaden bioaugmentation options for sites experiencing insufficient dioxane catabolic capacity.
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    Genetic Catabolic Probes to Assess the Natural Attenuation of 1,4-Dioxane
    (2013-12-06) Li, Mengyan; Alvarez, Pedro J.; Li, Qilin; Bennett, George N.; Fiorenza, Stephanie
    Remediation of aquifers contaminated with 1,4-dioxane (dioxane) is a difficult task because dioxane can be recalcitrant to biodegradation, is not easily removed by volatilization or adsorption, and is highly mobile in groundwater. Monitored natural attenuation (MNA), which relies primarily on biodegradation, is often the most cost-effective approach to manage large and dilute groundwater plumes of priority pollutants, such as those formed by dioxane. However, the burden of proof that MNA is an appropriate solution lies on the proponent, which requires demonstration of the presence and expression of relevant biodegradation capabilities. Therefore, an innovative micro-extraction of aqueous samples coupled with gas chromatography/mass spectrometry (GC/MS) was developed to monitor dioxane attenuation with low part-per-billion detection sensitivity. Soluble di-iron monooxygenases (SDIMOs), especially group-5 SDIMOs (e.g., tetrahydrofuran [THF]/dioxane monooxygenases), are of significant interest due to their potential role in the initializing the cleavage of cyclic ethers. In this study, seven gene clusters encoding SDIMOs were annotated in the genome of Pseudonocardia dioxanivorans CB1190, a well-characterized bacterial dioxane degrader. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) results revealed that only the dxmA gene encoding the large hydroxylase of the putative dioxane monooxygenase was significantly up-regulated when fed with dioxane and its structural analog, THF, compared to controls fed with acetate. This is in accordance with previous evidence implicating the key role of dioxane/THF in initiating the oxidation of cyclic ethers. Additional efforts to evaluate the presence of SDIMO genes in groundwater samples were undertaken using advanced molecular tools, such as functional gene array (i.e. GeoChip) and PCR-DGGE. Both assays demonstrated the widespread distribution of various dioxane-degrading SDIMO genes at a dioxane-impacted site in Alaska. Notably, a group-5 thmA-like gene was enriched in source-zone samples with higher dioxane concentrations, suggesting selective pressure by dioxane. Microcosm assays with 14C-labeled dioxane showed that the highest mineralization capacity corresponded to the source area, which was presumably more acclimated and contained a higher abundance of SDIMO genes. Thus, converging lines of evidence based on both pure bacterial cultures and complex environmental samples corroborate the usefulness of THF/dioxane monooxygenases as biomarkers of dioxane natural attenuation. A primer/probe set was then developed to target bacterial genes encoding the large hydroxylase subunits of THF/dioxane monooxygenases using Taqman (5’-nuclease) chemistry. The probe targets conserved regions surrounding the active site, thus enabling detection of multiple dioxane degraders. Real-time PCR using reference strain genomic DNA demonstrated the high selectivity (no false positives) and sensitivity of this probe. Microcosm tests prepared with groundwater samples from 16 monitoring wells at five different dioxane-impacted sites showed that enrichment of this catabolic gene (up to 114-fold) was significantly correlated to the amount of dioxane degraded. A significant correlation was also found between biodegradation rates and the abundance of thmA/dxmA genes, suggesting them as reliable indicators of dioxane biodegradation activity. Furthermore, pyrosequencing-based metagenomics and 16S rDNA profiling was used to understand how dioxane contamination incidents along with chlorinated solvents and other hydrocarbons have affected the indigenous microbial communities and the microbes that are critical to carbon cycling at the site in Alaska. Actinobacteria and Proteobacteria were the dominant bacterial phyla. However, shifting of the microbial communities structures among various sampling locations was significantly related to the types and presence of external carbon sources (e.g., synthetic chemicals and naturally released gases) at the site. This indicates that the indigenous microbes have adapted to the local environment probably due to long term of acclimation, and may be contributing to the presence of natural attenuation. This study comprehensively evaluated the essential roles of THF/dioxane monooxygenases in dioxane degradation in dioxane-degrading bacterial strains and environment samples. This is the first report to elicit the impact from dioxane and other co-contaminants on shaping functional and phylogenetic structures of microbial communities at a dioxane-impacted site. The development of the novel catabolic biomarker (thmA/dxmA) is of great research and engineering value to unequivocally characterize both dioxane biodegradation potential and activity for enhanced MNA forensics.
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    Whole-Genome Sequence of the 1,4-Dioxane-Degrading Bacterium Mycobacterium dioxanotrophicus PH-06
    (American Society for Microbiology, 2017) He, Ya; Wei, Kangfei; Si, Kaiwei; Mathieu, Jacques; Li, Mengyan; Alvarez, Pedro J.J.
    We report here the complete genome sequence of Mycobacterium dioxanotrophicus PH-06, which is capable of using 1,4-dioxane as a sole source of carbon and energy. The reported sequence will enable the elucidation of this novel metabolic pathway and the development of molecular biomarkers to assess bioremediation potential at contaminated sites.