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Yang Z, Zhang B, Zhang Y, Bartlam M, Wang Y. Stereoisomer-specific bacterial mechanisms for hexabromocyclododecane biotransformation. JOURNAL OF HAZARDOUS MATERIALS 2025; 489:137589. [PMID: 39954446 DOI: 10.1016/j.jhazmat.2025.137589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2024] [Revised: 01/20/2025] [Accepted: 02/10/2025] [Indexed: 02/17/2025]
Abstract
Hexabromocyclododecane (HBCD), a flame retardant classified as a Persistent Organic Pollutant (POP), undergoes stereoisomer-specific microbial transformation with significant environmental and health implications. However, the underlying mechanisms of this stereoisomer-specific microbial transformation remain poorly understood. In this study, high-purity HBCD chiral isomers were isolated using an optimized high-performance liquid chromatography (HPLC) method and their transformation by Acinetobacter hemolyticum sp. strain HW-2 was investigated through transcriptomic analysis. Within three days, strain HW-2 removed (+) α-, (-) α-, (+) β-, (-) β-, (+) γ-, and (-) γ-HBCD with respective removal efficiencies of 52.38 %, 71.08 %, 71.07 %, 63.34 %, 47.47 %, and 77.05 %. Transcriptomic data revealed stereoisomer-specific processes in HBCD transport, response, and transformation. Strain HW-2 upregulated major facilitator superfamily (MFS) transport genes for HBCD uptake, with distinct genes activated for different diastereoisomers. Compared to γ-HBCD, α- and β-HBCD exerted greater stress on strain HW-2, leading to increased expression of efflux genes and antioxidant-related genes. The transformation of HBCD stereoisomers involved distinct functional enzymes, with only (-) γ-HBCD metabolized via the aromatic compound metabolic pathway. This study elucidates the stereoisomeric-specific transformation mechanisms underlying HBCD transformation by strain HW-2, offering valuable insights for theoretical and practical applications in HBCD remediation.
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Affiliation(s)
- Zhao Yang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin 300350, China
| | - Bidan Zhang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin 300350, China
| | - Yi Zhang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin 300350, China
| | - Mark Bartlam
- College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin 300071, China.
| | - Yingying Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin 300350, China.
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Lin YJ, Hsieh PH, Mao CC, Shih YH, Chen SH, Lin CY. Interpretation of machine learning-based prediction models and functional metagenomic approach to identify critical genes in HBCD degradation. JOURNAL OF HAZARDOUS MATERIALS 2025; 486:136976. [PMID: 39740553 DOI: 10.1016/j.jhazmat.2024.136976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Revised: 11/01/2024] [Accepted: 12/22/2024] [Indexed: 01/02/2025]
Abstract
Hexabromocyclododecane (HBCD) poses significant environmental risks, and identifying HBCD-degrading microbes and their enzymatic mechanisms is challenging due to the complexity of microbial interactions and metabolic pathways. This study aimed to identify critical genes involved in HBCD biodegradation through two approaches: functional annotation of metagenomes and the interpretation of machine learning-based prediction models. Our functional analysis revealed a rich metabolic potential in Chiang Chun soil (CCS) metagenomes, particularly in carbohydrate metabolism. Among the machine learning algorithms tested, random forest models outperformed others, especially when trained on datasets reflecting the degradation patterns of species like Dehalococcoides mccartyi and Pseudomonas aeruginosa. These models highlighted enzymes such as EC 1.8.3.2 (thiol oxidase) and EC 4.1.1.43 (phenylpyruvate decarboxylase) as inhibitors of degradation, while EC 2.7.1.83 (pseudouridine kinase) was linked to enhanced degradation. This dual-methodology approach not only deepens our understanding of microbial functions in HBCD degradation but also provides an unbiased view of the microbial and enzymatic interactions involved, offering a more targeted and effective bioremediation strategy.
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Affiliation(s)
- Yu-Jie Lin
- Institute of Information Science, Academia Sinica, No. 128, Section 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Ping-Heng Hsieh
- Institute of Information Science, Academia Sinica, No. 128, Section 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Chun-Chia Mao
- Institute of Information Science, Academia Sinica, No. 128, Section 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Yang-Hsin Shih
- Department of Agricultural Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Shu-Hwa Chen
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, No. 250, Wuxing St., Taipei 11031, Taiwan
| | - Chung-Yen Lin
- Institute of Information Science, Academia Sinica, No. 128, Section 2, Academia Road, Nankang, Taipei 11529, Taiwan; Institute of Fisheries Science, National Taiwan University, No. 1, Section 4, Roosevelt Rd., Taipei 10617, Taiwan.
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Yu F, Zhang B, Liu Y, Luo W, Chen H, Gao J, Ye X, Li J, Xie Q, Peng T, Wang H, Huang T, Hu Z. Biotransformation of HBCDs by the microbial communities enriched from mangrove sediments. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:134036. [PMID: 38493623 DOI: 10.1016/j.jhazmat.2024.134036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/29/2024] [Accepted: 03/12/2024] [Indexed: 03/19/2024]
Abstract
1,2,5,6,9,10-Hexabromocyclododecanes (HBCDs) are a sort of persistent organic pollutants (POPs). This research investigated 12 microbial communities enriched from sediments of four mangroves in China to transform HBCDs. Six microbial communities gained high transformation rates (27.5-97.7%) after 12 generations of serial transfer. Bacteria were the main contributors to transform HBCDs rather than fungi. Analyses on the bacterial compositions and binning genomes showed that Alcanivorax (55.246-84.942%) harboring haloalkane dehalogenase genes dadAH and dadBH dominated the microbial communities with high transformation rates. Moreover, expressions of dadAH and dadBH in the microbial communities and Alcanivorax isolate could be induced by HBCDs. Further, it was found that purified proteins DadAH and DadBH showed high conversion rates on HBCDs in 36 h (91.9 ± 7.4 and 101.0 ± 1.8%, respectively). The engineered Escherichia coli BL21 strains harbored two genes could convert 5.7 ± 0.4 and 35.1 ± 0.1% HBCDs, respectively, lower than their cell-free crude extracts (61.2 ± 5.2 and 56.5 ± 8.7%, respectively). The diastereoisomer-specific transforming trend by both microbial communities and enzymes were γ- > α- > β-HBCD, differed from α- > β- > γ-HBCD by the Alcanivorax isolate. The identified transformation products indicated that HBCDs were dehalogenated via HBr elimination (dehydrobromination), hydrolytic and reductive debromination pathways in the enriched cultures. Two enzymes converted HBCDs via hydrolytic debromination. The present research provided theoretical bases for the biotransformation of HBCDs by microbial community and the bioremediation of HBCDs contamination in the environment.
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Affiliation(s)
- Fei Yu
- Department of Biology, College of Science, Shantou University, Shantou 515063, Guangdong Province, China
| | - Bing Zhang
- Department of Biology, College of Science, Shantou University, Shantou 515063, Guangdong Province, China
| | - Yongjin Liu
- Department of Biology, College of Science, Shantou University, Shantou 515063, Guangdong Province, China
| | - Wenqi Luo
- Department of Biology, College of Science, Shantou University, Shantou 515063, Guangdong Province, China
| | - Haonan Chen
- Department of Biology, College of Science, Shantou University, Shantou 515063, Guangdong Province, China
| | - Jun'na Gao
- Department of Biology, College of Science, Shantou University, Shantou 515063, Guangdong Province, China
| | - Xueying Ye
- School of Life Sciences, Huizhou University, Huizhou 516007, Guangdong Province, China
| | - Jin Li
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou 515063, Guangdong Province, China
| | - Qingyi Xie
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Tao Peng
- Department of Biology, College of Science, Shantou University, Shantou 515063, Guangdong Province, China
| | - Hui Wang
- Department of Biology, College of Science, Shantou University, Shantou 515063, Guangdong Province, China
| | - Tongwang Huang
- Department of Biology, College of Science, Shantou University, Shantou 515063, Guangdong Province, China
| | - Zhong Hu
- Department of Biology, College of Science, Shantou University, Shantou 515063, Guangdong Province, China.
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Hou R, Zhang S, Huang Q, Lin L, Li H, Li J, Liu S, Sun C, Xu X. Role of Gastrointestinal Microbiota from Crucian Carp in Microbial Transformation and Estrogenicity Modification of Novel Plastic Additives. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:11476-11488. [PMID: 37462611 DOI: 10.1021/acs.est.3c03595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Ingestion is a major exposure route for hydrophobic organic pollutants in fish, but the microbial transformation and estrogenic modification of the novel plastic additives by the gut microbiota of fish remain obscure. Using an in vitro approach, we provide evidence that structure-related transformation of various plastic additives by the gastric and intestinal (GI) microbiota from crucian carp, with the degradation ratio of bisphenols and triphenyl phosphate faster than those of brominated compounds. The degradation kinetics for these pollutants could be limited by oxygen and cometabolic substrates (i.e., glucose). The fish GI microbiota could utilize the vast majority of carbon sources in a Biolog EcoPlate, suggesting their high metabolic potential and ability to transform various organic compounds. Unique microorganisms associated with transformation of the plastic additives including genera of Citrobacter, Klebsiella, and some unclassified genera in Enterobacteriaceae were identified by combining high-throughput genetic analyses and metagenomic analyses. Through identification of anaerobic transformation products by high-resolution mass spectrometry, alkyl-cleavage was found the common transformation mechanism, and hydrolysis was the major pathway for ester-containing pollutants. After anaerobic incubation, the estrogenic activities of triphenyl phosphate and bisphenols A, F, and AF declined, whereas that of bisphenol AP increased.
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Affiliation(s)
- Rui Hou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Siqi Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qianyi Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lang Lin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Hengxiang Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Sanya 572100, China
| | - Jingxi Li
- Key Laboratory of Marine Eco-environmental Science and Technology, Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Shan Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Sanya 572100, China
| | - Chengjun Sun
- Key Laboratory of Marine Eco-environmental Science and Technology, Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Xiangrong Xu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Sanya 572100, China
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