When chemistry meets microbiology: Biotransformation of emerging organic contaminants

Yu, Yaochun

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https://hdl.handle.net/2142/114092 Copy

Description

Title

When chemistry meets microbiology: Biotransformation of emerging organic contaminants

Author(s)

Yu, Yaochun

Issue Date

2021-12-02

Director of Research (if dissertation) or Advisor (if thesis)

Men, Yujie

Doctoral Committee Chair(s)

Men, Yujie

Committee Member(s)

• Liu, Wen-Tso
• Nguyen, Thanh H.
• Liu, Jinyong Liu

Department of Study

Civil & Environmental Eng

Discipline

Environ Engr in Civil Engr

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

Ph.D.

Degree Level

Dissertation

Keyword(s)

• Biotransformation
• Emerging organic contaminants
• Nitrifiers
• Microbial reductive defluorination
• Per- and polyfluoroalkyl substances (PFAS)

Abstract

In recent years, with the increasing use of organic chemicals such as pesticides, pharmaceuticals, personal care products, and many other types of anthropogenic chemicals, there have been emerging concerns about the potential risk of these compounds to natural environments and public health. The release of such emerging organic contaminants (EOCs) into the environment threatens the ecosystem’s health and functioning. Microbial biotransformation shows its potential in alleviating the environmental detections of many EOCs. However, limited studies tackle the EOCs biotransformation mechanisms from both pathways’ elucidation and responsible microorganisms’ identification aspects. Thus, the primary focus of this study aims to build a framework to comprehensively study the fate of EOCs as well as their biotransformation patterns under the different environmental conditions, specifically focusing on investigating the transformation products, the biotransformation pathways, the responsible microorganisms, and ultimately the responsible genes and enzymes. I started the project by investigating the EOCs biotransformation capabilities of nitrifiers (i.e., nitrite-oxidizing bacterium Nitrobacter sp. and ammonia-oxidizing bacterium Nitrosomonas europaea). The results showed that the experimental used nitrite-oxidizing bacteria could not biotransform any investigated EOCs, whereas N. europaea showed the biotransformation capabilities for several EOCs. Notably, the results present strong evidence favoring ammonia monooxygenase (AMO) responsible for EOCs biotransformation, which likely occurred via co-metabolism. Furthermore, for the first time, we demonstrated that abiotic EOCs transformation by hydroxylamine, the product of AMO-mediated ammonia oxidation, likely represents another transformation mechanism of EOCs by ammonia oxidizers. I then compared the abilities of three phylogenetically distant ammonia oxidizers, Nitrososphaera gargensis, an ammonia-oxidizing archaeon; Nitrosomomas nitrosa Nm90, an ammonia-oxidizing bacterium; and Nitrospira inopinata, the only complete ammonia oxidizer available as a pure culture, to biotransform the selected EOCs. The results exhibited that among three ammonia oxidizers, only N. inopinata was able to biotransform carbendazim when ammonia was supplied as the energy source. The exclusive biotransformation of carbendazim by N. inopinata is likely enabled by an enhanced substrate promiscuity of its unique AMO and its much higher substrate (for ammonia) affinity compared with the other two ammonia oxidizers. Among various EOCs, organofluorine compounds (e.g., per- and polyfluoroalkyl substances, PFAS) have caused increasing global concerns due to their persistence in the environment, bioaccumulation in organisms, and toxicity to human beings and ecosystems. Therefore, I further investigated the microbial biotransformation and biodefluorination of structurally different per- and polyfluorinated compounds. Surprisingly, under the anaerobic condition, the microbial cleavage of C‒F bonds in PFAS was demonstrated for the first time by the release of F‒ and the formation of the corresponding defluorination products. Moreover, I found that the α, β-unsaturation was crucial for fluorinated compounds biotransformation by the defluorinating enrichment culture. Furthermore, the defluorination activity was significantly enhanced along with the enrichment processes, indicating the growth of defluorinating microorganisms. Given the toxicity of fluoride ion (F‒), the enhanced defluorination activity also suggested that the responsible microorganisms must defend themselves against the intracellular F‒ buildup. Taken together, the fluoride ion efflux transporter and the reductase responsible for α, β-unsaturated double bonds reduction were proposed as two biomarkers for selecting the responsible defluorinating microorganisms. By 16S rRNA gene amplicon sequencing and metagenomic sequencing, the community dynamics of the defluorinating enrichment culture were elucidated. One anaerobic bacterium isolate that met both selection criteria was then chosen as a representative for the biotransformation experiments. The results showed that the selected microorganism could biotransform the selected perfluorinated compound via the same biotransformation and biodefluorination pathways as observed in the enrichment community. Based on the differential gene expression, the electron transferring trajectory, the defluorination pattern, and the possible responsible genes/enzymes for fluorinated compound defluorination and hydrogenation were further elucidated. Overall, this work advances the fundamental understanding of the fate of various EOCs in natural and engineered environments and opens up diverse venues for both fundamental science and engineering applications. Those include identifying and characterizing the responsible microorganisms/genes/enzymes for EOCs removal, establishing novel EOCs

Graduation Semester

2021-12

Type of Resource

Thesis

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Copyright 2021 Yaochun Yu

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