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Xie Y, Feng NX, Huang L, Wu M, Li CX, Zhang F, Huang Y, Cai QY, Xiang L, Li YW, Zhao HM, Mo CH. Improving key gene expression and di-n-butyl phthalate (DBP) degrading ability in a novel Pseudochrobactrum sp. XF203 by ribosome engineering. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174207. [PMID: 38914327 DOI: 10.1016/j.scitotenv.2024.174207] [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: 04/30/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 06/26/2024]
Abstract
Di-n-butyl phthalate (DBP) is one of the important phthalates detected commonly in soils and crops, posing serious threat to human health. Pseudochrobactrum sp. XF203 (XF203), a new strain related with DBP biodegradation, was first identified from a natural habitat lacking human disturbance. Genomic analysis coupled with gene expression comparison assay revealed this strain harbors the key aromatic ring-cleaving gene catE203 (encoding catechol 2,3-dioxygenase/C23O) involved DBP biodegradation. Following intermediates identification and enzymatic analysis also indicated a C23O dependent DBP lysis pathway in XF203. The gene directed ribosome engineering was operated and to generate a desirable mutant strain XF203R with highest catE203 gene expression level and strong DBP degrading ability. The X203R removed DBP in soil jointly by reassembling bacterial community. These results demonstrate a great value of XF203R for the practical DBP bioremediation application, highlighting the important role of the key gene-directed ribosome engineering in mining multi-pollutants degrading bacteria from natural habitats where various functional genes are well conserved.
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Affiliation(s)
- Yunchang Xie
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; Jiangxi Key Laboratory of Organic Chemistry, Institute of Organic Functional Molecules, Jiangxi Science and Technology Normal University, Nanchang 330013, Jiangxi, China
| | - Nai-Xian Feng
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Li Huang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Miaoer Wu
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Cheng-Xuan Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Fantao Zhang
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Yunhong Huang
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Quan-Ying Cai
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Lei Xiang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yan-Wen Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Hai-Ming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Ce-Hui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
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2
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Hu CJ, Lv YQ, Xian WD, Jiao JY, Lian ZH, Tan S, Li MM, Luo ZH, Liu ZT, Lv AP, Liu L, Ali M, Liu WQ, Li WJ. Multi-omics insights into the function and evolution of sodium benzoate biodegradation pathway in Benzoatithermus flavus gen. nov., sp. nov. from hot spring. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135017. [PMID: 38936185 DOI: 10.1016/j.jhazmat.2024.135017] [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: 03/21/2024] [Revised: 06/06/2024] [Accepted: 06/22/2024] [Indexed: 06/29/2024]
Abstract
Biodegradation stands as an eco-friendly and effective approach for organic contaminant remediation. However, research on microorganisms degrading sodium benzoate contaminants in extreme environments remains limited. In this study, we report to display the isolation of a novel hot spring enriched cultures with sodium benzoate (400 mg/L) as the sole carbon source. The results revealed that the phylum Pseudomonadota was the potential sodium benzoate degrader and a novel genus within the family Geminicoccaceae of this phylum. The isolated strain was named Benzoatithermus flavus SYSU G07066T and was isolated from HNT-2 hot spring samples. Genomic analysis revealed that SYSU G07066T carried benABC genes and physiological experiments indicated the ability to utilize sodium benzoate as a sole carbon source for growth, which was further confirmed by transcriptomic data with expression of benABC. Phylogenetic analysis suggested that Horizontal Gene Transfer (HGT) plays a significant role in acquiring sodium benzoate degradation capability among prokaryotes, and SYSU G07066T might have acquired benABC genes through HGT from the family Acetobacteraceae. The discovery of the first microorganism with sodium benzoate degradation function from a hot spring enhances our understanding of the diverse functions within the family Geminicoccaceae. This study unearths the first novel genus capable of efficiently degrading sodium benzoate and its evolution history at high temperatures, holding promising industrial applications, and provides a new perspective for further exploring the application potential of hot spring "microbial dark matter".
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Affiliation(s)
- Chao-Jian Hu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; School of Ecology, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yi-Qing Lv
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Wen-Dong Xian
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316000, China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Zheng-Han Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Sha Tan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Zhen-Hao Luo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Ze-Tao Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Ai-Ping Lv
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
| | - Mukhtiar Ali
- Advanced Water Technology Laboratory, National University of Singapore (Suzhou) Research Institute, Suzhou, Jiangsu 215123, China.
| | - Wei-Qiu Liu
- School of Ecology, Sun Yat-Sen University, Guangzhou 510275, China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China.
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3
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Zhou Y, Wang Y, Yao S, Zhao X, Kong Q, Cui L, Zhang H. Driving mechanisms for the adaptation and degradation of petroleum hydrocarbons by native microbiota from seas prone to oil spills. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135060. [PMID: 38943887 DOI: 10.1016/j.jhazmat.2024.135060] [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: 02/15/2024] [Revised: 06/15/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Offshore waters have a high incidence of oil pollution, which poses an elevated risk of ecological damage. The microbial community composition and metabolic mechanisms influenced by petroleum hydrocarbons vary across different marine regions. However, research on metabolic strategies for in-situ petroleum degradation and pollution adaptation remains in its nascent stages. This study combines metagenomic techniques with gas chromatography-mass spectrometry (GC-MS) analysis. The data show that the genera Pseudoalteromonas, Hellea, Lentisphaera, and Polaribacter exhibit significant oil-degradation capacity, and that the exertion of their degradation capacity is correlated with nutrient and oil pollution stimuli. Furthermore, tmoA, badA, phdF, nahAc, and fadA were found to be the key genes involved in the degradation of benzene, polycyclic aromatic hydrocarbons, and their intermediates. Key genes (INSR, SLC2A1, and ORC1) regulate microbial adaptation to oil-contaminated seawater, activating oil degradation processes. This process enhances the biological activity of microbial communities and accounts for the geographical variation in their compositional structure. Our results enrich the gene pool for oil pollution adaptation and degradation and provide an application basis for optimizing bioremediation intervention strategies.
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Affiliation(s)
- Yumiao Zhou
- College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Ying Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
| | - Shudi Yao
- College of Geography and Environment, Shandong Normal University, Jinan 250014, China
| | - Xinyu Zhao
- Laoshan Laboratory, Qingdao 266237, China
| | - Qiang Kong
- College of Geography and Environment, Shandong Normal University, Jinan 250014, China
| | - Lihua Cui
- College of Geography and Environment, Shandong Normal University, Jinan 250014, China
| | - Huanxin Zhang
- College of Geography and Environment, Shandong Normal University, Jinan 250014, China.
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Ji T, Liaqat F, Khazi MI, Liaqat N, Nawaz MZ, Zhu D. Lignin biotransformation: Advances in enzymatic valorization and bioproduction strategies. INDUSTRIAL CROPS AND PRODUCTS 2024; 216:118759. [DOI: 10.1016/j.indcrop.2024.118759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
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5
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Ngo ACR, Celebi B, Hermann Hadewig SN, Mügge C, Tischler D. Selective pressure leads to an improved synthetic consortium fit for dye degradation. CHEMOSPHERE 2024; 361:142489. [PMID: 38825247 DOI: 10.1016/j.chemosphere.2024.142489] [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: 03/18/2024] [Revised: 05/17/2024] [Accepted: 05/29/2024] [Indexed: 06/04/2024]
Abstract
Microorganisms have great potential for bioremediation as they have powerful enzymes and machineries that can transform xenobiotics. The use of a microbial consortium provides more advantages in application point of view than pure cultures due to cross-feeding, adaptations, functional redundancies, and positive interactions among the organisms. In this study, we screened about 107 isolates for their ability to degrade dyes in aerobic conditions and without additional carbon source. From our screening results, we finally limited our synthetic consortium to Gordonia and Rhodococcus isolates. The synthetic consortium was trained and optimized for azo dye degradation using sequential treatment of small aromatic compounds such as phenols that act as selective pressure agents. After four rounds of optimization with different aims for each round, the consortium was able to decolorize and degrade various dyes after 48 h (80%-100% for brilliant black bn, methyl orange, and chromotrop 2b; 50-70% for orange II and reactive orange 16; 15-30% for chlorazol black e, reactive red 120, and allura red ac). Through rational approaches, we can show that treatment with phenolic compounds at micromolar dosages can significantly improve the degradation of bulky dyes and increase its substrate scope. Moreover, our selective pressure approach led to the production of various dye-degrading enzymes as azoreductase, laccase-like, and peroxidase-like activities were detected from the phenol-treated consortium. Evidence of degradation was also shown as metabolites arising from the degradation of methyl red and brilliant black bn were detected using HPLC and LC-MS analysis. Therefore, this study establishes the importance of rational and systematic screening and optimization of a consortium. Not only can this approach be applied to dye degradation, but this study also offers insights into how we can fully maximize microbial consortium activity for other applications, especially in biodegradation and biotransformation.
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Affiliation(s)
| | - Beyzanur Celebi
- Microbial Biotechnology, Ruhr Universität Bochum, Bochum, Germany
| | | | - Carolin Mügge
- Microbial Biotechnology, Ruhr Universität Bochum, Bochum, Germany
| | - Dirk Tischler
- Microbial Biotechnology, Ruhr Universität Bochum, Bochum, Germany
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6
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Pei Y, Lei A, Yang S, Chen H, Liu X, Liu L, Kang X. Biodegradation and bioaugmentation of tetracycline by Providencia stuartii TX2: Performance, degradation pathway, genetic background, key enzymes, and application risk assessment. JOURNAL OF HAZARDOUS MATERIALS 2024; 477:135231. [PMID: 39032181 DOI: 10.1016/j.jhazmat.2024.135231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/07/2024] [Accepted: 07/15/2024] [Indexed: 07/22/2024]
Abstract
The antibiotic tetracycline (TC) is an emerging pollutant frequently detected in various environments. Biodegradation is a crucial approach for eliminating TC contamination. However, only a few efficient TC-degrading bacteria have been isolated, and the molecular mechanisms of TC degradation, as well as their application potential, remain poorly understood. This study isolated a novel TC-degrading bacterium, Providencia stuartii TX2, from the intestine of black soldier fly larvae. TX2 exhibited remarkable performance, degrading 72.17 % of 400 mg/L TC within 48 h. Genomic analysis of TX2 unveiled the presence of antibiotic resistance genes and TC degradation enzymes. Transcriptomic analysis highlighted the roles of proteins related to efflux pumps, enzymatic transformation, adversity resistance, and unknown functions. Three TC degradation pathways were proposed, with TC being transformed into 27 metabolites through epimerization, hydroxylation, oxygenation, ring opening, and de-grouping, reducing TC toxicity. Additionally, TX2 significantly enhanced TC biodegradation in four TC-contaminated environmental samples and reduced antibiotic resistance genes and mobile genetic elements in chicken manure. This research provides insights into the survival and biodegradation mechanisms of Providencia stuartii TX2 and evaluates its potential for environmental bioremediation.
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Affiliation(s)
- Yaxin Pei
- Key Laboratory of Enzyme Engineering of Agricultural Microbiology (Ministry of Agriculture), School of Life Sciences, Henan Agricultural University, Zhengzhou, Henan Province, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, School of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan Province, 450046, China.
| | - Aojie Lei
- Key Laboratory of Enzyme Engineering of Agricultural Microbiology (Ministry of Agriculture), School of Life Sciences, Henan Agricultural University, Zhengzhou, Henan Province, 450046, China
| | - Sen Yang
- Key Laboratory of Enzyme Engineering of Agricultural Microbiology (Ministry of Agriculture), School of Life Sciences, Henan Agricultural University, Zhengzhou, Henan Province, 450046, China
| | - Hongge Chen
- Key Laboratory of Enzyme Engineering of Agricultural Microbiology (Ministry of Agriculture), School of Life Sciences, Henan Agricultural University, Zhengzhou, Henan Province, 450046, China
| | - Xinyu Liu
- Key Laboratory of Enzyme Engineering of Agricultural Microbiology (Ministry of Agriculture), School of Life Sciences, Henan Agricultural University, Zhengzhou, Henan Province, 450046, China
| | - Liangwei Liu
- Key Laboratory of Enzyme Engineering of Agricultural Microbiology (Ministry of Agriculture), School of Life Sciences, Henan Agricultural University, Zhengzhou, Henan Province, 450046, China
| | - Xiangtao Kang
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, School of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan Province, 450046, China
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7
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Fan Y, Zhou Z, Liu F, Qian L, Yu X, Huang F, Hu R, Su H, Gu H, Yan Q, He Z, Wang C. The vertical partitioning between denitrification and dissimilatory nitrate reduction to ammonium of coastal mangrove sediment microbiomes. WATER RESEARCH 2024; 262:122113. [PMID: 39032335 DOI: 10.1016/j.watres.2024.122113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 07/13/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024]
Abstract
Mangrove aquatic ecosystems receive substantial nitrogen (N) inputs from both land and sea, playing critical roles in modulating coastal N fluxes. The microbially-mediated competition between denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in mangrove sediments significantly impacts the N fate and transformation processes. Despite their recognized role in N loss or retention in surface sediments, how these two processes vary with sediment depths and their influential factors remain elusive. Here, we employed a comprehensive approach combining 15N isotope tracer, quantitative PCR (qPCR) and metagenomics to verify the vertical dynamics of denitrification and DNRA across five 100-cm mangrove sediment cores. Our results revealed a clear vertical partitioning, with denitrification dominated in 0-30 cm sediments, while DNRA played a greater role with increasing depths. Quantification of denitrification and DNRA functional genes further explained this phenomenon. Taxonomic analysis identified Pseudomonadota as the primary denitrification group, while Planctomycetota and Pseudomonadota exhibited high proportion in DNRA group. Furthermore, genome-resolved metagenomics revealed multiple salt-tolerance strategies and aromatic compound utilization potential in denitrification assemblages. This allowed denitrification to dominate in oxygen-fluctuating and higher-salinity surface sediments. However, the elevated C/N in anaerobic deep sediments favored DNRA, tending to generate biologically available NH4+. Together, our results uncover the depth-related variations in the microbially-mediated competition between denitrification and DNRA, regulating N dynamics in mangrove ecosystems.
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Affiliation(s)
- Yijun Fan
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhengyuan Zhou
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Fei Liu
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Lu Qian
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Xiaoli Yu
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Fangjuan Huang
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Ruiwen Hu
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Hualong Su
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Hang Gu
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Qingyun Yan
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhili He
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China.
| | - Cheng Wang
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China.
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8
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Bopp C, Bernet NM, Meyer F, Khan R, Robinson SL, Kohler HPE, Buller R, Hofstetter TB. Elucidating the Role of O 2 Uncoupling for the Adaptation of Bacterial Biodegradation Reactions Catalyzed by Rieske Oxygenases. ACS ENVIRONMENTAL AU 2024; 4:204-218. [PMID: 39035869 PMCID: PMC11258757 DOI: 10.1021/acsenvironau.4c00016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 07/23/2024]
Abstract
Oxygenation of aromatic and aliphatic hydrocarbons by Rieske oxygenases is the initial step of various biodegradation pathways for environmental organic contaminants. Microorganisms carrying Rieske oxygenases are able to quickly adapt their substrate spectra to alternative carbon and energy sources that are structurally related to the original target substrate, yet the molecular events responsible for this rapid adaptation are not well understood. Here, we evaluated the hypothesis that reactive oxygen species (ROS) generated by unproductive activation of O2, the so-called O2 uncoupling, in the presence of the alternative substrate exert a selective pressure on the bacterium for increasing the oxygenation efficiency of Rieske oxygenases. To that end, we studied wild-type 2-nitrotoluene dioxygenase from Acidovorax sp. strain JS42 and five enzyme variants that have evolved from adaptive laboratory evolution experiments with 3- and 4-nitrotoluene as alternative growth substrates. The enzyme variants showed a substantially increased oxygenation efficiency toward the new target substrates concomitant with a reduction of ROS production, while mechanisms and kinetics of enzymatic O2 activation remained unchanged. Structural analyses and docking studies suggest that amino acid substitutions in enzyme variants occurred at residues lining both substrate and O2 transport tunnels, enabling tighter binding of the target substrates in the active site. Increased oxygenation efficiencies measured in vitro for the various enzyme (variant)-substrate combinations correlated linearly with in vivo changes in growth rates for evolved Acidovorax strains expressing the variants. Our data suggest that the selective pressure from oxidative stress toward more efficient oxygenation by Rieske oxygenases was most notable when O2 uncoupling exceeded 60%.
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Affiliation(s)
- Charlotte
E. Bopp
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute
of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Nora M. Bernet
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute
of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Fabian Meyer
- Competence
Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland
| | - Riyaz Khan
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Serina L. Robinson
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Hans-Peter E. Kohler
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Rebecca Buller
- Competence
Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland
| | - Thomas B. Hofstetter
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute
of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
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9
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Mrnjavac N, Nagies FSP, Wimmer JLE, Kapust N, Knopp MR, Trost K, Modjewski L, Bremer N, Mentel M, Esposti MD, Mizrahi I, Allen JF, Martin WF. The radical impact of oxygen on prokaryotic evolution-enzyme inhibition first, uninhibited essential biosyntheses second, aerobic respiration third. FEBS Lett 2024; 598:1692-1714. [PMID: 38750628 PMCID: PMC7616280 DOI: 10.1002/1873-3468.14906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/12/2024] [Accepted: 04/19/2024] [Indexed: 07/15/2024]
Abstract
Molecular oxygen is a stable diradical. All O2-dependent enzymes employ a radical mechanism. Generated by cyanobacteria, O2 started accumulating on Earth 2.4 billion years ago. Its evolutionary impact is traditionally sought in respiration and energy yield. We mapped 365 O2-dependent enzymatic reactions of prokaryotes to phylogenies for the corresponding 792 protein families. The main physiological adaptations imparted by O2-dependent enzymes were not energy conservation, but novel organic substrate oxidations and O2-dependent, hence O2-tolerant, alternative pathways for O2-inhibited reactions. Oxygen-dependent enzymes evolved in ancestrally anaerobic pathways for essential cofactor biosynthesis including NAD+, pyridoxal, thiamine, ubiquinone, cobalamin, heme, and chlorophyll. These innovations allowed prokaryotes to synthesize essential cofactors in O2-containing environments, a prerequisite for the later emergence of aerobic respiratory chains.
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Affiliation(s)
- Natalia Mrnjavac
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Falk S P Nagies
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Jessica L E Wimmer
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Nils Kapust
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Michael R Knopp
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Katharina Trost
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Luca Modjewski
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Nico Bremer
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Marek Mentel
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | | | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev and The National Institute for Biotechnology in the Negev, Be'er-Sheva, Israel
| | - John F Allen
- Research Department of Genetics, Evolution and Environment, University College London, UK
| | - William F Martin
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
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10
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Šelo G, Planinić M, Tišma M, Klarić AM, Bucić-Kojić A. Effects of Fungal Solid-State Fermentation on the Profile of Phenolic Compounds and on the Nutritional Properties of Grape Pomace. Microorganisms 2024; 12:1310. [PMID: 39065079 PMCID: PMC11279339 DOI: 10.3390/microorganisms12071310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
Grape pomace (GP) is considered a natural source of bioactive compounds. To improve the extractability of bioactive compounds, in this work, GP was biologically treated for 15 days with the white-rot fungus Trametes versicolor in laboratory jars and a tray bioreactor under solid-state fermentation (SSF) conditions. During SSF, the activity of lignolytic (laccase and manganese peroxidase) and hydrolytic (xylanase, cellulase, β-glucosidase, and invertase) enzymes was measured, with the activities of laccase (2.66 U/gdb in jars and 0.96 U/gdb in the bioreactor) and xylanase (346.04 U/gdb in jars and 200.65 U/gdb in the bioreactor) being the highest. The effect of the complex enzyme system was reflected in the changes in the chemical composition of GP with increasing ash, crude protein, and free fat content: 28%, 10%, and 17% in the laboratory jars, and 29%, 11%, and 7% in the bioreactor, respectively. In addition, the biological treatment improved the extractability of 13 individual phenolic compounds. Therefore, the applied SSF technique represents an effective strategy to improve the profile of phenolic compounds and the nutritional composition of GP, promoting their valorization and opening the door for potential applications in the food industry and other sectors.
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Affiliation(s)
| | | | | | | | - Ana Bucić-Kojić
- Faculty of Food Technology Osijek, Josip Juraj Strossmayer University of Osijek, F. Kuhača 18, HR-31 000 Osijek, Croatia; (G.Š.); (M.P.); (M.T.)
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11
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Pan L, Yuan B, Li Q, Ouyang J, Yang J, Zhou Y, Cui C. Efficient biodegradation of chlorobenzene via monooxygenation pathways by Pandoraea sp. XJJ-1 with high potential for groundwater bioremediation. Int Microbiol 2024:10.1007/s10123-024-00544-4. [PMID: 38900217 DOI: 10.1007/s10123-024-00544-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/15/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024]
Abstract
Chlorobenzene (CB), extensively used in industrial processes, has emerged as a significant contaminant in soil and groundwater. The eco-friendly and cost-effective microbial remediation has been increasingly favored to address this environmental challenge. In this study, a degrading bacterium was isolated from CB-contaminated soil at a pesticide plant, identified as Pandoraea sp. XJJ-1 (CCTCC M 2021057). This strain completely degraded 100 mg·L-1 CB and showed extensive degradability across a range of pH (5.0-9.0), temperature (10-37 °C), and CB concentrations (100-600 mg·L-1). Notably, the degradation efficiency was 85.2% at 15 °C, and the strain could also degrade six other aromatic hydrocarbons, including benzene, toluene, ethylbenzene, and xylene (o-, m-, p-). The metabolic pathway of CB was inferred using ultraperformance liquid chromatography, gas chromatography-mass spectrometry, and genomic analysis. In strain XJJ-1, CB was metabolized to o-chlorophenol and 3-chloroxychol by CB monooxygenase, followed by ortho-cleavage by the action of 3-chlorocatechol 1,2-dioxygenase. Moreover, the presence of the chlorobenzene monooxygenation pathway metabolism in strain XJJ-1 is reported for the first time in Pandoraea. As a bacterium with low-temperature resistance and composite pollutant degradation capacity, strain XJJ-1 has the potential application prospects in the in-situ bioremediation of CB-contaminated sites.
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Affiliation(s)
- Lixu Pan
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control On Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Bo Yuan
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control On Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Qingqing Li
- State Environment Protection Engineering Center for Urban Soil Contamination Control and Remediation, Shanghai Academy of Environmental Sciences, Shanghai, 200233, China
| | - Ji Ouyang
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control On Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Jie Yang
- State Environment Protection Engineering Center for Urban Soil Contamination Control and Remediation, Shanghai Academy of Environmental Sciences, Shanghai, 200233, China
| | - Yan Zhou
- Sinopec Fifth Construction Co., Ltd, Guangzhou, 510145, China
| | - Changzheng Cui
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control On Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China.
- Institute of Pollution Control and Ecological Security, Shanghai, 200092, China.
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12
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Moreno R, Yuste L, Morales G, Rojo F. Inactivation of Pseudomonas putida KT2440 pyruvate dehydrogenase relieves catabolite repression and improves the usefulness of this strain for degrading aromatic compounds. Microb Biotechnol 2024; 17:e14514. [PMID: 38923400 PMCID: PMC11196380 DOI: 10.1111/1751-7915.14514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/09/2024] [Indexed: 06/28/2024] Open
Abstract
Pyruvate dehydrogenase (PDH) catalyses the irreversible decarboxylation of pyruvate to acetyl-CoA, which feeds the tricarboxylic acid cycle. We investigated how the loss of PDH affects metabolism in Pseudomonas putida. PDH inactivation resulted in a strain unable to utilize compounds whose assimilation converges at pyruvate, including sugars and several amino acids, whereas compounds that generate acetyl-CoA supported growth. PDH inactivation also resulted in the loss of carbon catabolite repression (CCR), which inhibits the assimilation of non-preferred compounds in the presence of other preferred compounds. Pseudomonas putida can degrade many aromatic compounds, most of which produce acetyl-CoA, making it useful for biotransformation and bioremediation. However, the genes involved in these metabolic pathways are often inhibited by CCR when glucose or amino acids are also present. Our results demonstrate that the PDH-null strain can efficiently degrade aromatic compounds even in the presence of other preferred substrates, which the wild-type strain does inefficiently, or not at all. As the loss of PDH limits the assimilation of many sugars and amino acids and relieves the CCR, the PDH-null strain could be useful in biotransformation or bioremediation processes that require growth with mixtures of preferred substrates and aromatic compounds.
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Affiliation(s)
- Renata Moreno
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología, CSICMadridSpain
| | - Luis Yuste
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología, CSICMadridSpain
| | - Gracia Morales
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología, CSICMadridSpain
- Present address:
European UniversityMadridSpain
| | - Fernando Rojo
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología, CSICMadridSpain
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13
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Dornelles HS, Sabatini CA, Adorno MAT, Silva EL, Lee PH, Varesche MBA. Microbial synergies drive simultaneous biodegradation of ethoxy and alkyl chains of Nonylphenol Ethoxylate in fluidized bed reactors. CHEMOSPHERE 2024; 358:142084. [PMID: 38642772 DOI: 10.1016/j.chemosphere.2024.142084] [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: 02/17/2024] [Revised: 04/02/2024] [Accepted: 04/18/2024] [Indexed: 04/22/2024]
Abstract
The widely-used surfactant Nonylphenol Ethoxylate (NPEO) produces endocrine-disrupting compounds during biodegradation, with these byproducts being more harmful than untreated NPEO. This study investigates the effectiveness of a Fluidized Bed Reactor (FBR) in reducing the production of 4-Nonylphenol (4-NP) during the biodegradation of NPEO. Two identical FBR filled with sand were used to assess the NPEO degradation and to enhance the microbial consortia capable of breaking down the complex byproducts, ethanol and fumarate were introduced as co-substrates. Our findings demonstrate the significant potential of the FBR, especially when coupled with fumarate, for enhancing the surfactant degradation. It outperforms the efficiency achieved with ethanol as the primary electron donor, albeit with a higher rate of byproduct production. Microbial community taxonomy and metabolic prediction revealed the high abundance of Geobacter (1.51-31.71%) and Methanobacterium (1.08-13.81%) in non-conductive sand. This may hint a new metabolic interaction and expand our understanding of Direct Interspecies Electron Transfer (DIET) in bioreactors applied to micropollutants degradation. Such an intricate relationship between facultative and anaerobes working together to simultaneously biodegrade the ethoxy and alkyl chains presents a new perspective on NPEO degradation and can potentially be extended to other micropollutants.
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Affiliation(s)
- Henrique S Dornelles
- Department of Hydraulics and Sanitation, School of Engineering, University of São Paulo, Av. João Dagnone - 1100, 13563-120, São Carlos, São Paulo, Brazil; Department of Civil and Environmental Engineering, Imperial College London, South Kensington Campus, Imperial College Road, SW7 2BU, London, England, United Kingdom
| | - Carolina A Sabatini
- Department of Hydraulics and Sanitation, School of Engineering, University of São Paulo, Av. João Dagnone - 1100, 13563-120, São Carlos, São Paulo, Brazil
| | - Maria A T Adorno
- Department of Hydraulics and Sanitation, School of Engineering, University of São Paulo, Av. João Dagnone - 1100, 13563-120, São Carlos, São Paulo, Brazil
| | - Edson L Silva
- Department of Chemical Engineering, Federal University of São Carlos, Rod. Washington Luiz, Km 235, SP 310, 13565-905, São Carlos, São Paulo, Brazil
| | - Po-Heng Lee
- Department of Civil and Environmental Engineering, Imperial College London, South Kensington Campus, Imperial College Road, SW7 2BU, London, England, United Kingdom
| | - Maria Bernadete A Varesche
- Department of Hydraulics and Sanitation, School of Engineering, University of São Paulo, Av. João Dagnone - 1100, 13563-120, São Carlos, São Paulo, Brazil.
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14
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Zhao P, Jiang Y, Wang Q, Chen J, Yao F, Cong Z. Crucial gating residues govern the enhancement of peroxygenase activity in an engineered cytochrome P450 O-demethylase. Chem Sci 2024; 15:8062-8070. [PMID: 38817576 PMCID: PMC11134341 DOI: 10.1039/d4sc02418d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 05/02/2024] [Indexed: 06/01/2024] Open
Abstract
P450-catalyzed O-demethylation reactions have recently attracted particular attention because of their potential applications in lignin bioconversion. We recently enabled the peroxygenase activity of CYP199A4, a NADH-dependent cytochrome P450 monooxygenase from Rhodopseudomonas palustris, by engineering a hydrogen peroxide (H2O2) tunnel. In this report, we reveal by crystallography and molecule dynamics simulations that key residues located at one of the water tunnels in CYP199A4 play a crucial gating role, which enhances the peroxygenase activity by regulating the inflow of H2O2. These results provide a more complete understanding of the mechanism by which monooxygenase is converted into peroxygenase activity through the H2O2 tunnel engineering (HTE) strategy. Furthermore, a library of engineered CYP199A4 peroxygenases was constructed to explore their application potentials for O-demethylation of various methoxy-substituted benzoic acid derivatives. The engineered CYP199A4 peroxygenases showed good functional group tolerance and preferential O-demethylation at the meta- or para-position, indicating potential O-demethylation of H- and G-type lignin monomers. This work reveals the feasibility of the HTE strategy in creating P450 peroxygenase from a mechanistic perspective, laying the foundation for developing an effective P450 O-demethylase applicable in lignin bioconversion.
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Affiliation(s)
- Panxia Zhao
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences Qingdao Shandong P. R. China
- University of Chinese Academy of Sciences (UCAS) Beijing 100049 P. R. China
| | - Yiping Jiang
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences Qingdao Shandong P. R. China
- Shandong Energy Institute Qingdao Shandong 266101 China
- Qingdao New Energy Shandong Laboratory Qingdao Shandong P. R. China
| | - Qian Wang
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences Qingdao Shandong P. R. China
| | - Jie Chen
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences Qingdao Shandong P. R. China
- Shandong Energy Institute Qingdao Shandong 266101 China
- Qingdao New Energy Shandong Laboratory Qingdao Shandong P. R. China
| | - Fuquan Yao
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences Qingdao Shandong P. R. China
| | - Zhiqi Cong
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences Qingdao Shandong P. R. China
- Shandong Energy Institute Qingdao Shandong 266101 China
- University of Chinese Academy of Sciences (UCAS) Beijing 100049 P. R. China
- Qingdao New Energy Shandong Laboratory Qingdao Shandong P. R. China
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15
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Vural C, Ettadili H. Biodegradation of phthalic acid and terephthalic acid by Comamonas testosteroni strains. Folia Microbiol (Praha) 2024:10.1007/s12223-024-01176-x. [PMID: 38809402 DOI: 10.1007/s12223-024-01176-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 05/20/2024] [Indexed: 05/30/2024]
Abstract
Phthalic acid isomers are the monomers of phthalate molecules, also known as phthalic acid esters, widely employed in the plastics industry. This study aims to investigate the biodegradation of phthalic acid (PA) and terephthalic acid (TPA) by five industry-borne Comamonas testosteroni strains: 3APTOL, 3ABBK, 2B, 3A1, and C8. To assess the ability of C. testosteroni strains to biodegrade phthalic acid isomers in fermentation media, an analytical method was employed, consisting of high-performance liquid chromatography (HPLC) analyses. Subsequently, molecular screening of the genomic and plasmid DNA was conducted to identify the degradative genes responsible for the breakdown of these chemicals. The genes of interest, including ophA2, tphA2, tphA3, pmdA, and pmdB, were screened by real-time PCR. The five C. testosteroni strains effectively degraded 100% of 100 mg/L PA (p = 0.033) and TPA (p = 0.0114). Molecular analyses indicated that all C. testosteroni strains contained the pertinent genes at different levels within their genomes and plasmids, as reflected in the threshold cycle (Ct) values. Additionally, DNA temperature of melting (Tm) analyses uncovered minor differences between groups of genes in genomic and plasmid DNA. C. testosteroni strains could be excellent candidates for the removal of phthalic acid isomers from environmental systems.
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Affiliation(s)
- Caner Vural
- Department of Biology, Molecular Biology Section, Pamukkale University, 20160, Denizli, Turkey.
| | - Hamza Ettadili
- Department of Biology, Molecular Biology Section, Pamukkale University, 20160, Denizli, Turkey
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16
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Ali NS, Thakur S, Ye M, Monteil-Rivera F, Pan Y, Qin W, Yang TC. Uncovering the lignin-degrading potential of Serratia quinivorans AORB19: insights from genomic analyses and alkaline lignin degradation. BMC Microbiol 2024; 24:181. [PMID: 38789935 PMCID: PMC11127350 DOI: 10.1186/s12866-024-03331-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Lignin is an intricate phenolic polymer found in plant cell walls that has tremendous potential for being converted into value-added products with the possibility of significantly increasing the economics of bio-refineries. Although lignin in nature is bio-degradable, its biocatalytic conversion is challenging due to its stable complex structure and recalcitrance. In this context, an understanding of strain's genomics, enzymes, and degradation pathways can provide a solution for breaking down lignin to unlock the full potential of lignin as a dominant valuable bioresource. A gammaproteobacterial strain AORB19 has been isolated previously from decomposed wood based on its high laccase production. This work then focused on the detailed genomic and functional characterization of this strain based on whole genome sequencing, the identification of lignin degradation products, and the strain's laccase production capabilities on various agro-industrial residues. RESULTS Lignin degrading bacterial strain AORB19 was identified as Serratia quinivorans based on whole genome sequencing and core genome phylogeny. The strain comprised a total of 123 annotated CAZyme genes, including ten cellulases, four hemicellulases, five predicted carbohydrate esterase genes, and eight lignin-degrading enzyme genes. Strain AORB19 was also found to possess genes associated with metabolic pathways such as the β-ketoadipate, gentisate, anthranilate, homogentisic, and phenylacetate CoA pathways. LC-UV analysis demonstrated the presence of p-hydroxybenzaldehyde and vanillin in the culture media which constitutes potent biosignatures indicating the strain's capability to degrade lignin. Finally, the study evaluated the laccase production of Serratia AORB19 grown with various industrial raw materials, with the highest activity detected on flax seed meal (257.71 U/L), followed by pea hull (230.11 U/L), canola meal (209.56 U/L), okara (187.67 U/L), and barley malt sprouts (169.27 U/L). CONCLUSIONS The whole genome analysis of Serratia quinivorans AORB19, elucidated a repertoire of genes, pathways and enzymes vital for lignin degradation that widens the understanding of ligninolytic metabolism among bacterial lignin degraders. The LC-UV analysis of the lignin degradation products coupled with the ability of S. quinivorans AORB19 to produce laccase on diverse agro-industrial residues underscores its versatility and its potential to contribute to the economic viability of bio-refineries.
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Affiliation(s)
- Nadia Sufdar Ali
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Ottawa, ON, Canada
- Department of Biology, Lakehead University, Thunder Bay, ON, Canada
| | - Subarna Thakur
- Department of Bioinformatics, University of North Bengal, Siliguri, India
| | - Mengwei Ye
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Fanny Monteil-Rivera
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Youlian Pan
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Wensheng Qin
- Department of Biology, Lakehead University, Thunder Bay, ON, Canada.
| | - Trent Chunzhong Yang
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Ottawa, ON, Canada.
- BioWise Technologies Inc, Ottawa, Canada.
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17
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Ling H, Lv Y, Zhang Y, Zhou NY, Xu Y. Widespread and active piezotolerant microorganisms mediate phenolic compound degradation under high hydrostatic pressure in hadal trenches. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:331-348. [PMID: 38827128 PMCID: PMC11136905 DOI: 10.1007/s42995-024-00224-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/20/2024] [Indexed: 06/04/2024]
Abstract
Phenolic compounds, as well as other aromatic compounds, have been reported to be abundant in hadal trenches. Although high-throughput sequencing studies have hinted at the potential of hadal microbes to degrade these compounds, direct microbiological, genetic and biochemical evidence under in situ pressures remain absent. Here, a microbial consortium and a pure culture of Pseudomonas, newly isolated from Mariana Trench sediments, efficiently degraded phenol under pressures up to 70 and 60 MPa, respectively, with concomitant increase in biomass. By analyzing a high-pressure (70 MPa) culture metatranscriptome, not only was the entire range of metabolic processes under high pressure generated, but also genes encoding complete phenol degradation via ortho- and meta-cleavage pathways were revealed. The isolate of Pseudomonas also contained genes encoding the complete degradation pathway. Six transcribed genes (dmpKLMNOPsed) were functionally identified to encode a multicomponent hydroxylase catalyzing the hydroxylation of phenol and its methylated derivatives by heterogeneous expression. In addition, key catabolic genes identified in the metatranscriptome of the high-pressure cultures and genomes of bacterial isolates were found to be all widely distributed in 22 published hadal microbial metagenomes. At microbiological, genetic, bioinformatics, and biochemical levels, this study found that microorganisms widely found in hadal trenches were able to effectively drive phenolic compound degradation under high hydrostatic pressures. This information will bridge a knowledge gap concerning the microbial aromatics degradation within hadal trenches. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-024-00224-2.
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Affiliation(s)
- Hao Ling
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Yongxin Lv
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200240 China
- State Key of Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Yu Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200240 China
- State Key of Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Ying Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
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18
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Shrestha S, Goswami S, Banerjee D, Garcia V, Zhou E, Olmsted CN, Majumder ELW, Kumar D, Awasthi D, Mukhopadhyay A, Singer SW, Gladden JM, Simmons BA, Choudhary H. Perspective on Lignin Conversion Strategies That Enable Next Generation Biorefineries. CHEMSUSCHEM 2024:e202301460. [PMID: 38669480 DOI: 10.1002/cssc.202301460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/14/2024] [Indexed: 04/28/2024]
Abstract
The valorization of lignin, a currently underutilized component of lignocellulosic biomass, has attracted attention to promote a stable and circular bioeconomy. Successful approaches including thermochemical, biological, and catalytic lignin depolymerization have been demonstrated, enabling opportunities for lignino-refineries and lignocellulosic biorefineries. Although significant progress in lignin valorization has been made, this review describes unexplored opportunities in chemical and biological routes for lignin depolymerization and thereby contributes to economically and environmentally sustainable lignin-utilizing biorefineries. This review also highlights the integration of chemical and biological lignin depolymerization and identifies research gaps while also recommending future directions for scaling processes to establish a lignino-chemical industry.
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Affiliation(s)
- Shilva Shrestha
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21205, United States
| | - Shubhasish Goswami
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Deepanwita Banerjee
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Valentina Garcia
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Biomanufacturing and Biomaterials, Sandia National Laboratories, Livermore, CA 94550, United States
| | - Elizabeth Zhou
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
| | - Charles N Olmsted
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Erica L-W Majumder
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Deepak Kumar
- Department of Chemical Engineering, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, United States
| | - Deepika Awasthi
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - John M Gladden
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Biomanufacturing and Biomaterials, Sandia National Laboratories, Livermore, CA 94550, United States
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Hemant Choudhary
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Bioresource and Environmental Security, Sandia National Laboratories, Livermore, CA 94550, United States
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19
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Zhao Y, Liu D, Zhang J, Shen J, Cao J, Gu H, Cui M, He L, Chen G, Liu S, Shi K. Improving Soluble Phenolic Profile and Antioxidant Activity of Grape Pomace Seeds through Fungal Solid-State Fermentation. Foods 2024; 13:1158. [PMID: 38672831 PMCID: PMC11049521 DOI: 10.3390/foods13081158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 03/31/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Abstract
Grape pomace seeds contain abundant phenolic compounds, which are also present in both soluble and insoluble forms, similar to many other plant matrices. To further increase the extractable soluble phenolics and their antioxidant activities, grape pomace seeds were fermented with different fungi. Results showed that solid-state fermentation (SSF) with Aspergillus niger, Monascus anka, and Eurotium cristatum at 28 °C and 65% humidity had a significantly positive impact on the release of soluble phenolics in grape pomace seeds. Specifically, SSF with M. anka increased the soluble phenolic contents by 6.42 times (calculated as total phenolic content) and 6.68 times (calculated as total flavonoid content), leading to an overall improvement of antioxidant activities, including DPPH (increased by 2.14 times) and ABTS (increased by 3.64 times) radical scavenging activity. Furthermore, substantial changes were observed in the composition and content of individual phenolic compounds in the soluble fraction, with significantly heightened levels of specific phenolics such as chlorogenic acid, syringic acid, ferulic acid, epicatechin gallate, and resveratrol. Notably, during M. anka SSF, positive correlations were identified between the soluble phenolic content and hydrolase activities. In particular, there is a strong positive correlation between glycosidase and soluble phenols (r = 0.900). The findings present an effective strategy for improving the soluble phenolic profiles and bioactivities of grape pomace seeds through fungal SSF, thereby facilitating the valorization of winemaking by-products.
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Affiliation(s)
- Yuzhu Zhao
- College of Enology, College of Life Sciences, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain’s East Foothill Wine Experiment and Demonstration Station, Life Science Research Core Services, Northwest A&F University, Xianyang 712100, China; (Y.Z.); (D.L.); (J.Z.); (J.S.); (J.C.); (H.G.); (M.C.); (L.H.); (S.L.)
| | - Doudou Liu
- College of Enology, College of Life Sciences, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain’s East Foothill Wine Experiment and Demonstration Station, Life Science Research Core Services, Northwest A&F University, Xianyang 712100, China; (Y.Z.); (D.L.); (J.Z.); (J.S.); (J.C.); (H.G.); (M.C.); (L.H.); (S.L.)
| | - Jiaxuan Zhang
- College of Enology, College of Life Sciences, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain’s East Foothill Wine Experiment and Demonstration Station, Life Science Research Core Services, Northwest A&F University, Xianyang 712100, China; (Y.Z.); (D.L.); (J.Z.); (J.S.); (J.C.); (H.G.); (M.C.); (L.H.); (S.L.)
| | - Jiaxin Shen
- College of Enology, College of Life Sciences, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain’s East Foothill Wine Experiment and Demonstration Station, Life Science Research Core Services, Northwest A&F University, Xianyang 712100, China; (Y.Z.); (D.L.); (J.Z.); (J.S.); (J.C.); (H.G.); (M.C.); (L.H.); (S.L.)
| | - Jiamin Cao
- College of Enology, College of Life Sciences, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain’s East Foothill Wine Experiment and Demonstration Station, Life Science Research Core Services, Northwest A&F University, Xianyang 712100, China; (Y.Z.); (D.L.); (J.Z.); (J.S.); (J.C.); (H.G.); (M.C.); (L.H.); (S.L.)
| | - Huawei Gu
- College of Enology, College of Life Sciences, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain’s East Foothill Wine Experiment and Demonstration Station, Life Science Research Core Services, Northwest A&F University, Xianyang 712100, China; (Y.Z.); (D.L.); (J.Z.); (J.S.); (J.C.); (H.G.); (M.C.); (L.H.); (S.L.)
| | - Mengqing Cui
- College of Enology, College of Life Sciences, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain’s East Foothill Wine Experiment and Demonstration Station, Life Science Research Core Services, Northwest A&F University, Xianyang 712100, China; (Y.Z.); (D.L.); (J.Z.); (J.S.); (J.C.); (H.G.); (M.C.); (L.H.); (S.L.)
| | - Ling He
- College of Enology, College of Life Sciences, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain’s East Foothill Wine Experiment and Demonstration Station, Life Science Research Core Services, Northwest A&F University, Xianyang 712100, China; (Y.Z.); (D.L.); (J.Z.); (J.S.); (J.C.); (H.G.); (M.C.); (L.H.); (S.L.)
| | - Gong Chen
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China;
| | - Shuwen Liu
- College of Enology, College of Life Sciences, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain’s East Foothill Wine Experiment and Demonstration Station, Life Science Research Core Services, Northwest A&F University, Xianyang 712100, China; (Y.Z.); (D.L.); (J.Z.); (J.S.); (J.C.); (H.G.); (M.C.); (L.H.); (S.L.)
| | - Kan Shi
- College of Enology, College of Life Sciences, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain’s East Foothill Wine Experiment and Demonstration Station, Life Science Research Core Services, Northwest A&F University, Xianyang 712100, China; (Y.Z.); (D.L.); (J.Z.); (J.S.); (J.C.); (H.G.); (M.C.); (L.H.); (S.L.)
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20
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Liu Y, Guo W, Wei C, Huang H, Nan F, Liu X, Liu Q, Lv J, Feng J, Xie S. Rainfall-induced changes in aquatic microbial communities and stability of dissolved organic matter: Insight from a Fen river analysis. ENVIRONMENTAL RESEARCH 2024; 246:118107. [PMID: 38181848 DOI: 10.1016/j.envres.2024.118107] [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: 11/12/2023] [Revised: 12/25/2023] [Accepted: 01/02/2024] [Indexed: 01/07/2024]
Abstract
Microbial communities are pivotal in aquatic ecosystems, as they affect water quality, energy dynamics, nutrient cycling, and hydrological stability. This study explored the effects of rainfall on hydrological and photosynthetic parameters, microbial composition, and functional gene profiles in the Fen River. Our results demonstrated that rainfall-induced decreases in stream temperature, dissolved oxygen, pH, total phosphorus, chemical oxygen demand, and dissolved organic carbon concentrations. In contrast, rainfall increased total dissolved solids, salinity, and ammonia-nitrogen concentrations. A detailed microbial community structure analysis revealed that Cyanobacteria was the dominant microbial taxon in the Fen River, accounting for approximately 75% and 25% of the microalgal and bacterial communities, respectively. The abundance of Chlorophyta and Bacillariophyta increased by 47.66% and 29.92%, respectively, whereas the relative abundance of Bacteroidetes decreased by 37.55% under rainfall conditions. Stochastic processes predominantly affected the assembly of the bacterial community on rainy days. Functional gene analysis revealed variations in bacterial functions between sunny (Sun) and rainy (Rain) conditions, particularly in genes associated with the carbon cycle. The 3-oxoacyl-[acyl-carrier-protein] reductase gene was more abundant in the Fen River bacterial community. Particular genes involved in metabolism and environmental information processing, including the acetyl-CoA C-acetyltransferase (atoB), enoyl-CoA hydratase (paaF), and branched-chain amino acid transport system gene (livK), which are integral to environmental information processing, were more abundant in Sun than the Rain conditions. In contrast, the phosphate transport system gene, the galactose metabolic gene, and the pyruvate metabolic gene were more abundant in Rain. The excitation-emission matrix analysis with parallel factor analysis identified four fluorescence components (C1-C4) in the river, which were predominantly protein- (C1) and humic-like (C2-C4) substances. Rainfall affected organic matter production and transport, leading to changes in the degradation and stability of dissolved organic matter. Overall, this study offers insight into how rainfall affects aquatic ecosystems.
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Affiliation(s)
- Yang Liu
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Weinan Guo
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Caihua Wei
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Hanjie Huang
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Fangru Nan
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Xudong Liu
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Qi Liu
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Junping Lv
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Jia Feng
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Shulian Xie
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China.
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21
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Li M, Cao L, Liu D, Su T, Cheng W, Li G, Ma T. Efficient bio-remediation of multiple aromatic hydrocarbons using different types of thermotolerant, ring-cleaving dioxygenases derived from Aeribacillus pallidus HB-1. BIORESOURCE TECHNOLOGY 2024; 398:130472. [PMID: 38387841 DOI: 10.1016/j.biortech.2024.130472] [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: 11/06/2023] [Revised: 02/17/2024] [Accepted: 02/18/2024] [Indexed: 02/24/2024]
Abstract
As toxic contaminants, aromatic compounds are widespread in most environmental matrices, and bioenzymatic catalysis plays a critical role in the degradation of xenobiotics. Here, a thermophillic aromatic hydrocarbon degrader Aeribacillus pallidus HB-1 was found. Bioinformatic analysis of the HB-1 genome revealed two ring-cleaving extradiol dioxygenases (EDOs), among which, EDO-0418 was assigned to a new subfamily of type I.1 EDOs and exhibited a broad substrate specificity, particularly towards biarylic substrate. Both EDOs exhibited optimal activities at elevated temperatures (55 and 65 °C, respectively) and showed remarkable thermostability, pH stability, metal ion resistance and tolerance to chemical reagents. Most importantly, simulated wastewater bioreactor experiments demonstrated efficient and uniform degradation performance of mixed aromatic substrates under harsh environments by the two enzymes combined for potential industrial applications. The unveiling of two thermostable dioxygenases with broad substrate specificities and stress tolerance provides a novel approach for highly efficient environmental bioremediation using composite enzyme systems.
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Affiliation(s)
- Mingchang Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Lu Cao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Dakun Liu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Tianqi Su
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Wei Cheng
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Guoqiang Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; Tianjin Engineering Technology Center of Green Manufacturing Biobased Materials, Tianjin 300071, China.
| | - Ting Ma
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; Tianjin Engineering Technology Center of Green Manufacturing Biobased Materials, Tianjin 300071, China.
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22
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Zito P, Sihota N, Mohler RE, Podgorski DC. The formation, reactivity, and fate of oxygen-containing organic compounds in petroleum-contaminated groundwaters: A state of the science review and future research directions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170619. [PMID: 38311075 DOI: 10.1016/j.scitotenv.2024.170619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/06/2024]
Abstract
Hydrocarbon (HC) contamination in groundwater (GW) is a widespread environmental issue. Dissolved hydrocarbons in water are commonly utilized as an energy source by natural microbial communities, which can produce water soluble intermediate metabolite compounds, herein referred to as oxygen containing organic compounds (OCOCs), before achieving complete mineralization. This review aims to provide a comprehensive assessment of the literature focused on the state of the science for OCOCs detected and measured in GW samples collected from petroleum contaminated aquifers. In this review, we discuss and evaluate two hypotheses investigating OCOC formation, which are major points of contention in the freshwater oil spill community that need to be addressed. We reviewed over 150 articles compiling studies investigating OCOC formation and persistence to uncover knowledge gaps in the literature and studies that recommend quantitative and qualitative measurements of OCOCs in petroleum-contaminated aquifers. This review is essential because no consensus exists regarding specific compounds and related concerns. We highlight the knowledge gaps to progressing the discussion of hydrocarbon conversion products.
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Affiliation(s)
- Phoebe Zito
- Department of Chemistry, Chemical Analysis & Mass Spectrometry Facility, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148, USA; Department of Chemistry, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK 99508, USA.
| | - Natasha Sihota
- Chevron Technical Center, 6001 Bollinger Canyon Road, San Ramon, CA 94583, USA
| | - Rachel E Mohler
- Chevron Technical Center, 100 Chevron Way, Richmond, CA 94801, USA
| | - David C Podgorski
- Department of Chemistry, Chemical Analysis & Mass Spectrometry Facility, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148, USA; Pontchartrain Institute of Environmental Science, Shea Penland Coastal Education and Research Facility, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148, USA; Department of Chemistry, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK 99508, USA
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23
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Yang Y, Zhong W, Wang Y, Yue Z, Zhang C, Sun M, Wang Z, Xue X, Gao Q, Wang D, Zhang Y, Zhang J. Isolation, identification, degradation mechanism and exploration of active enzymes in the ochratoxin A degrading strain Acinetobacter pittii AP19. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133351. [PMID: 38150759 DOI: 10.1016/j.jhazmat.2023.133351] [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: 08/23/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 12/29/2023]
Abstract
Ochratoxin A (OTA) is a polyketide mycotoxin that commonly contaminates agricultural products and causes significant economic losses. In this study, the efficient OTA-degrading strain AP19 was isolated from vineyard soil and was identified as Acinetobacter pittii. Compared with growth in nutrient broth supplemented with OTA (OTA-NB), strain AP19 grew faster in nutrient broth (NB), but the ability of the resulting cell lysates to remove OTA was weaker. After cultivation in NB, the cell lysate of strain AP19 was able to remove 100% of 1 mg/L OTA within 18 h. The cell lysate fraction > 30 kDa degraded 100% of OTA within 12 h, while the fractions < 30 kDa were practically unable to degrade OTA. Further anion exchange chromatography of the > 30 kDa fraction yielded two peaks exhibiting significant OTA degradation activity. The degradation product was identified as OTα. Amino acid metabolism exhibited major transcriptional trends in the response of AP19 to OTA. The dacC gene encoding carboxypeptidase was identified as one of the contributors to OTA degradation. Soil samples inoculated with strain AP19 showed significant OTA degradation. These results provide significant insights into the discovery of novel functions in A. pittii, as well as its potential as an OTA decomposer.
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Affiliation(s)
- Yan Yang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Weitong Zhong
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yanning Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zhiwen Yue
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Chen Zhang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Mi Sun
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zhao Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xianli Xue
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Qiang Gao
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Depei Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Ying Zhang
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Jian Zhang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China.
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24
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Wakjira T, Gemta AB, Kassahun GB, Andoshe DM, Tadele K. Bismuth-Based Z-Scheme Heterojunction Photocatalysts for Remediation of Contaminated Water. ACS OMEGA 2024; 9:8709-8729. [PMID: 38434902 PMCID: PMC10905724 DOI: 10.1021/acsomega.3c08939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/27/2024] [Accepted: 01/31/2024] [Indexed: 03/05/2024]
Abstract
Agricultural runoff, fuel spillages, urbanization, hospitalization, and industrialization are some of the serious problems currently facing the world. In particular, byproducts that are hazardous to the ecosystem have the potential to mix with water used for drinking. Over the last three decades, various techniques, including biodegradation, advanced oxidation processes (AOPs), (e.g., photocatalysis, photo-Fenton oxidation, Fenton-like oxidation, and electrochemical oxidation process adsorption), filtration, and adsorption techniques, have been developed to remove hazardous byproducts. Among those, AOPs, photocatalysis has received special attention from the scientific community because of its unusual properties at the nanoscale and its layered structure. Recently, bismuth based semiconductor (BBSc) photocatalysts have played an important role in solving global energy demand and environmental pollution problems. In particular, bismuth-based Z-scheme heterojunction (BBZSH) is considered the best alternative route to overhaul the limitations of single-component BBSc photocatalysts. This work aims to review recent studies on a new type of BBZSH photocatalysts for the treatment of contaminated water. The general overview of the synthesis methods, efficiency-enhancing strategies, classifications of BBSc and Z-scheme heterojunctions, the degradation mechanisms of Z- and S-schemes, and the application of BBZSH photocatalysts for the degradation of organic dyes, antibiotics, aromatics compounds, endocrine-disrupting compounds, and volatile organic compounds are reviewed. Finally, challenges and the future perspective of BBZSH photocatalysts are discussed.
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Affiliation(s)
- Tadesse
Lemma Wakjira
- Department
of Applied Physics, Adama Science and Technology
University, Adama 1888, Ethiopia
| | - Abebe Belay Gemta
- Department
of Applied Physics, Adama Science and Technology
University, Adama 1888, Ethiopia
| | - Gashaw Beyene Kassahun
- Department
of Applied Physics, Adama Science and Technology
University, Adama 1888, Ethiopia
| | - Dinsefa Mensur Andoshe
- Department
of Material Engineering, Adama Science and
Technology University, Adama 1888, Ethiopia
| | - Kumneger Tadele
- Department
of Applied Physics, Adama Science and Technology
University, Adama 1888, Ethiopia
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25
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Li X, Mu L, Zhang Y, Zhu Z, Xiao Y, Fang Z. Sphingomicrobium clamense sp. nov., Isolated from Sediment of Clam Island Beach in China. Curr Microbiol 2024; 81:104. [PMID: 38393394 DOI: 10.1007/s00284-024-03639-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 02/13/2024] [Indexed: 02/25/2024]
Abstract
A Gram-stain-negative, non-flagellated, aerobic, ovoid or rod-shaped bacterium with motility, designated B8T, was isolated from the sediment of Clam Island beach, Liaoning province, China. The optimum growth of strain B8T occurred at 35 oC, pH 7.0, and in the presence of 4.0-5.0% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B8T formed a distinct lineage within the genus Sphingomicrobium and was closely related to Sphingomicrobium nitratireducens O-35T (98.3% sequence similarity), Sphingomicrobium aestuariivivum KCTC 42286T (96.9%), and Sphingomicrobium astaxanthinifaciens JCM 18551T (96.5%). The digital DNA-DNA hybridization and average nucleotide identity values between strain B8T and closely related strains were lower than 21.0% and 78.0%, much lower than the cutoff values of 70.0% and 95.0%, respectively, for bacterial species delineation. The dominant respiratory quinone of strain B8T was ubiquinone-10. The major fatty acids were Sum In Feature 8 (C18:1ω7c and/or C18:1ω6c), Sum In Feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C17:1ω6c, C18:1 2-OH, and C16:0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, glycolipids, and four unknown polar lipids. The DNA G + C content of strain B8T was 63.9%. Based on the phenotypic, phylogenetic, and chemotaxonomic analyses, strain B8T is considered a new species of Sphingomicrobium, for which the name Sphingomicrobium clamense sp. nov. is proposed. The type strain is B8T (= CGMCC 1.19486T = KCTC 92052T).
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Affiliation(s)
- Xing Li
- School of Life Sciences, Anhui University, Hefei, Anhui, 230601, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, 230601, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, 230601, China
| | - Lulu Mu
- School of Life Sciences, Anhui University, Hefei, Anhui, 230601, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, 230601, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, 230601, China
| | - Yanfeng Zhang
- Institute of Soil and Fertilizer, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Zimu Zhu
- School of Life Sciences, Anhui University, Hefei, Anhui, 230601, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, 230601, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, 230601, China
| | - Yazhong Xiao
- School of Life Sciences, Anhui University, Hefei, Anhui, 230601, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, 230601, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, 230601, China
| | - Zemin Fang
- School of Life Sciences, Anhui University, Hefei, Anhui, 230601, China.
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, 230601, China.
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, 230601, China.
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26
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Guan J, Huang J, Sun Y, Li C, Wan Y, Wei G, Kang R, Pang H, Shi Q, McHugh T, Ma J. Understanding petroleum vapor fate and transport through high resolution analysis of two distinct vapor plumes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169464. [PMID: 38123082 DOI: 10.1016/j.scitotenv.2023.169464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/09/2023] [Accepted: 12/16/2023] [Indexed: 12/23/2023]
Abstract
No field study has provided a detailed characterization of the molecular composition and spatial distribution of a vadose zone plume of petroleum volatile organic compounds (VOCs), which is critical to improve the current understanding of petroleum VOC transport and fate. This is study reports a high-resolution analysis of two distinct vapor plumes emanating from two different light non-aqueous phase liquid (LNAPL) sources (an aliphatic-rich LNAPL for Zone #1vs an aromatic-rich LNAPL for Zone #2) at a large petrochemical site. Although deep soil vapor signatures were similar to the source zone LNAPL signatures, the composition of the shallow soil vapors reflected preferential attenuation of certain hydrocarbons over others during upward transport in the vadose zone. Between deeper and shallower soil gas samples, attenuation of aromatics was observed under all conditions, but important differences were observed in attenuation to aliphatic compound classes. Attenuation of all aliphatic compounds was observed under aerobic conditions but little attenuation of any aliphatics was observed under anoxic conditions without methane. In contrast, under methanogenic conditions, paraffins attenuated more than isoparaffins and naphthenes. These results suggest that isoparafins and naphthenes may present more of a vapor intrusion risk than benzene or other aromatic hydrocarbons commonly considered to be petroleum vapor intrusion risk drivers. While the overall vapor composition changed significantly within the vadose zone, diagnostic ratios of relatively recalcitrant alkylcyclopentanes were preserved in shallow soil vapor samples. These alkylcyclopentanes may be useful for distinguishing between petroleum vapor intrusion and other sources of petroleum VOCs detected in indoor air.
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Affiliation(s)
- Junjie Guan
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum-Beijing, Beijing 102249, China; College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing 102249, China
| | - Jierui Huang
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum-Beijing, Beijing 102249, China; College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing 102249, China
| | - Yue Sun
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum-Beijing, Beijing 102249, China; College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing 102249, China
| | - Chong Li
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum-Beijing, Beijing 102249, China; College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing 102249, China
| | - Yuruo Wan
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum-Beijing, Beijing 102249, China; College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing 102249, China
| | - Guo Wei
- Beijing Beitou Eco-environment Co., Ltd, Canal East St. 6th, Beijing 101117, China
| | - Rifeng Kang
- Beijing Beitou Eco-environment Co., Ltd, Canal East St. 6th, Beijing 101117, China
| | - Hongwei Pang
- Beijing Beitou Eco-environment Co., Ltd, Canal East St. 6th, Beijing 101117, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum-Beijing, Beijing 102249, China; College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing 102249, China
| | - Thomas McHugh
- GSI Environmental Inc., 2211 Norfolk Street, Suite 1000, Houston, TX 77098, USA
| | - Jie Ma
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum-Beijing, Beijing 102249, China; College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing 102249, China.
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Pardhe BD, Paudel L, Han SR, Oh TJ. Genomic insight into O-demethylation of 4-methoxybenzoate by a two-component system from Amycolatopsis magusensis KCCM40447. Heliyon 2024; 10:e25083. [PMID: 38317971 PMCID: PMC10838780 DOI: 10.1016/j.heliyon.2024.e25083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/07/2024] Open
Abstract
Cytochrome P450 monooxygenases perform a multitude of roles, including the generation of hydroxylated aromatic compounds that might be utilized by microorganisms for their survival. WGS data of Amycolatopsis magusensis KCCM40447 revealed a complete circular genome of 9,099,986 base pairs and functionally assigned 8601 protein-encoding genes. Genomic analysis confirmed that the gene for 4-methoxybenzoate monoxygenase (CYP199A35) was conserved in close proximity to the gene for 4-hydroxybenzoate transporter (PcaK). The co-localized genes encoding CYP199A35, and ferredoxin-NAD(P) reductase (Mbr) represent a two-component system for electron transfer. CYP199A35 was specific for O-demethylation of para O-methyl substituted benzoic acid derivatives, 4-methoxybenzoate (4 MB), and 4-methoxycinnamic acid (4MCA) using the native redox partner (Mbr); two-component system and non-physiological redox partners (Pdr/Pdx); three-component system. The catalytic efficiency for O-demethylation of 4 MB using Mbr and Pdr/Pdx was 0.02 ± 0.006 min-1 μM-1 and 0.07 ± 0.02 min-1 μM-1 respectively. Further, sequence annotation and function prediction by RAST and KEEG analysis revealed a complete catabolic pathway for the utilization of 4 MB by strain KCCM40447, which was also proved experimentally.
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Affiliation(s)
- Bashu Dev Pardhe
- Department of Life Science and Biochemical Engineering, Sun Moon University, Asan, Republic of Korea
| | - Lakshan Paudel
- Department of Life Science and Biochemical Engineering, Sun Moon University, Asan, Republic of Korea
| | - So-Ra Han
- Genome-based BioIT Convergence Institute, Asan, Republic of Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Sun Moon University, Asan, Republic of Korea
- Genome-based BioIT Convergence Institute, Asan, Republic of Korea
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, Republic of Korea
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Bharali P, Gogoi B, Sorhie V, Acharjee SA, Walling B, Alemtoshi, Vishwakarma V, Shah MP. Autochthonous psychrophilic hydrocarbonoclastic bacteria and its ecological function in contaminated cold environments. Biodegradation 2024; 35:1-46. [PMID: 37436665 DOI: 10.1007/s10532-023-10042-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/30/2023] [Indexed: 07/13/2023]
Abstract
Petroleum hydrocarbon (PH) pollution has mostly been caused by oil exploration, extraction, and transportation activities in colder regions, particularly in the Arctic and Antarctic regions, where it serves as a primary source of energy. Due to the resilience feature of nature, such polluted environments become the realized ecological niches for a wide community of psychrophilic hydrocarbonoclastic bacteria (PHcB). In contrast, to other psychrophilic species, PHcB is extremely cold-adapted and has unique characteristics that allow them to thrive in greater parts of the cold environment burdened with PHs. The stated group of bacteria in its ecological niche aids in the breakdown of litter, turnover of nutrients, cycling of carbon and nutrients, and bioremediation. Although such bacteria are the pioneers of harsh colder environments, their growth and distribution remain under the influence of various biotic and abiotic factors of the environment. The review discusses the prevalence of PHcB community in colder habitats, the metabolic processes involved in the biodegradation of PH, and the influence of biotic and abiotic stress factors. The existing understanding of the PH metabolism by PHcB offers confirmation of excellent enzymatic proficiency with high cold stability. The discovery of more flexible PH degrading strategies used by PHcB in colder environments could have a significant beneficial outcome on existing bioremediation technologies. Still, PHcB is least explored for other industrial and biotechnological applications as compared to non-PHcB psychrophiles. The present review highlights the pros and cons of the existing bioremediation technologies as well as the potential of different bioaugmentation processes for the effective removal of PH from the contaminated cold environment. Such research will not only serve to investigate the effects of pollution on the basic functional relationships that form the cold ecosystem but also to assess the efficacy of various remediation solutions for diverse settings and climatic conditions.
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Affiliation(s)
- Pranjal Bharali
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India.
| | - Bhagyudoy Gogoi
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India
| | - Viphrezolie Sorhie
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India
| | - Shiva Aley Acharjee
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India
| | - Bendangtula Walling
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India
| | - Alemtoshi
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India
| | - Vinita Vishwakarma
- Centre for Nanoscience and Nanotechnology, Galgotias University, Greater Noida, NCR Delhi, India
| | - Maulin Pramod Shah
- Industrial Waste Water Research Lab, Division of Applied and Environmental Microbiology Lab at Enviro Technology Ltd., Ankleshwar, Gujarat, India
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Luo P, Tang Y, Lu J, Jiang L, Huang Y, Jiang Q, Chen X, Qin T, Shiels HA. Diesel degradation capability and environmental robustness of strain Pseudomonas aeruginosa WS02. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 351:119937. [PMID: 38159304 DOI: 10.1016/j.jenvman.2023.119937] [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: 08/18/2023] [Revised: 11/12/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024]
Abstract
Petroleum hydrocarbon (PHC) degrading bacteria have been frequently discovered. However, in practical application, a single species of PHC degrading bacterium with weak competitiveness may face environmental pressure and competitive exclusion due to the interspecific competition between petroleum-degrading bacteria as well as indigenous microbiota in soil, leading to a reduced efficacy or even malfunction. In this study, the diesel degradation ability and environmental robustness of an endophytic strain Pseudomonas aeruginosa WS02, were investigated. The results show that the cell membrane surface of WS02 was highly hydrophobic, and the strain secreted glycolipid surfactants. Genetic analysis results revealed that WS02 contained multiple metabolic systems and PHC degradation-related genes, indicating that this strain theoretically possesses the capability of oxidizing both alkanes and aromatic hydrocarbons. Gene annotation also showed many targets which coded for heavy metal resistant and metal transporter proteins. The gene annotation-based inference was confirmed by the experimental results: GC-MS analysis revealed that short chain PHCs (C10-C14) were completely degraded, and the degradation of PHCs ranging from C15-C22 were above 90% after 14 d in diesel-exposed culture; Heavy metal (Mn2+, Pb2+ and Zn2+) exposure was found to affect the growth of WS02 to some extent, but not its ability to degrade diesel, and the degradation efficiency was still maintained at 39-59%. WS02 also showed a environmental robustness along with PHC-degradation performance in the co-culture system with other bacterial strains as well as in the co-cultured system with the indigenous microbiota in soil fluid extracted from a PHC-contaminated site. It can be concluded that the broad-spectrum diesel degradation efficacy and great environmental robustness give P. aeruginosa WS02 great potential for application in the remediation of PHC-contaminated soil.
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Affiliation(s)
- Penghong Luo
- School of Resources, Environment and Materials, Guangxi University, Nanning, 530004, China; Key Laboratory of Environmental Protection, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China; Guangxi Key Laboratory of Emerging Contaminants Monitoring, Early Warning and Environmental Health Risk Assessment, Guangxi University, Nanning, 530004, China
| | - Yankui Tang
- School of Resources, Environment and Materials, Guangxi University, Nanning, 530004, China; Key Laboratory of Environmental Protection, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China; Guangxi Key Laboratory of Petrochemical Resource Processing and Process Intensification Technology, Guangxi University, Nanning, 530004, China; College of Civil Engineering and Architecture, Guangxi University, Nanning, 530004, China; Guangxi Key Laboratory of Emerging Contaminants Monitoring, Early Warning and Environmental Health Risk Assessment, Guangxi University, Nanning, 530004, China.
| | - Jiahua Lu
- School of Resources, Environment and Materials, Guangxi University, Nanning, 530004, China; Key Laboratory of Environmental Protection, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China
| | - Lu Jiang
- School of Resources, Environment and Materials, Guangxi University, Nanning, 530004, China; Key Laboratory of Environmental Protection, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China; Guangxi Key Laboratory of Emerging Contaminants Monitoring, Early Warning and Environmental Health Risk Assessment, Guangxi University, Nanning, 530004, China
| | - Yiting Huang
- College of Civil Engineering and Architecture, Guangxi University, Nanning, 530004, China
| | - Qiming Jiang
- School of Resources, Environment and Materials, Guangxi University, Nanning, 530004, China; Key Laboratory of Environmental Protection, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China; Guangxi Key Laboratory of Emerging Contaminants Monitoring, Early Warning and Environmental Health Risk Assessment, Guangxi University, Nanning, 530004, China
| | - Xuemin Chen
- School of Resources, Environment and Materials, Guangxi University, Nanning, 530004, China; Key Laboratory of Environmental Protection, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China; Guangxi Key Laboratory of Emerging Contaminants Monitoring, Early Warning and Environmental Health Risk Assessment, Guangxi University, Nanning, 530004, China
| | - Tianfu Qin
- School of Resources, Environment and Materials, Guangxi University, Nanning, 530004, China; Key Laboratory of Environmental Protection, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China; Guangxi Key Laboratory of Emerging Contaminants Monitoring, Early Warning and Environmental Health Risk Assessment, Guangxi University, Nanning, 530004, China
| | - Holly Alice Shiels
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, M13 9PL, United Kingdom
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Li D, Wen Q, Chen Z. Effects of Fe/Fe-Mn oxides loaded biochar on anaerobic degradation of typical phenolic compounds in coal gasification wastewater: Performance and mechanism. BIORESOURCE TECHNOLOGY 2024; 394:130308. [PMID: 38199441 DOI: 10.1016/j.biortech.2024.130308] [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: 10/30/2023] [Revised: 01/06/2024] [Accepted: 01/07/2024] [Indexed: 01/12/2024]
Abstract
In this study, two kinds of magnetic biochar (BC) were synthesized by loading Fe (FeBC) and Fe-Mn oxides (FMBC) and their effects on anaerobic phenolics degradation were investigated. Compared with BC/FMBC, FeBC addition achieved the superior phenolics biodegradation even for 3,5-xylenol. Compared with control, FeBC addition enhanced CH4 production by 100.1 % with the lag time shortened from 9.5 days to 6.6 days while it increased to 11.2 days with FMBC addition. FeBC addition activated adsorption-biodegradation and Fe (III) reduction with the improved electron transfer activity, adenosine triphosphate and cytochrome C concentrations. Abundant phenol degrading bacteria, electroactive bacteria, syntrophic partners could be enriched by FeBC addition, contributing to the enhanced benzoyl-CoA and methanogenesis pathways. However, this enhancement was inhibited by FMBC addition owing to the accumulation of reactive oxygen species. This study provided novel insights into the application of magnetic BC to enhanced anaerobic treatment of phenolic wastewater.
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Affiliation(s)
- Da Li
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin 150090, PR China
| | - Qinxue Wen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin 150090, PR China
| | - Zhiqiang Chen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin 150090, PR China.
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Li X, Li Z, Li M, Li J, Wang Q, Wang S, Li S, Li H. Transcriptomic and metabolomic analysis reveals the influence of carbohydrates on lignin degradation mediated by Bacillus amyloliquefaciens. Front Microbiol 2024; 15:1224855. [PMID: 38333584 PMCID: PMC10850570 DOI: 10.3389/fmicb.2024.1224855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 01/05/2024] [Indexed: 02/10/2024] Open
Abstract
Introduction Ligninolytic bacteria can secrete extracellular enzymes to depolymerize lignin into small-molecular aromatics that are subsequently metabolized and funneled into the TCA cycle. Carbohydrates, which are the preferred carbon sources of bacteria, influence the metabolism of lignin-derived aromatics through bacteria. Methods In this study, untargeted metabolomics and transcriptomics analyses were performed to investigate the effect of carbohydrates on lignin degradation mediated by Bacillus amyloliquefaciens MN-13, a strain with lignin-degrading activity that was isolated in our previous work. Results The results demonstrated that the cell growth of the MN-13 strain and lignin removal were promoted when carbohydrates such as glucose and sodium carboxymethyl cellulose were added to an alkaline lignin-minimal salt medium (AL-MSM) culture. Metabolomics analysis showed that lignin depolymerization took place outside the cells, and the addition of glucose regulated the uptake and metabolism of lignin-derived monomers and activated the downstream metabolism process in cells. In the transcriptomics analysis, 299 DEGs were screened after 24 h of inoculation in AL-MSM with free glucose and 2 g/L glucose, respectively, accounting for 8.3% of the total amount of annotated genes. These DEGs were primarily assigned to 30 subcategories, including flagellar assembly, the PTS system, RNA degradation, glycolysis/gluconeogenesis, the TCA cycle, pyruvate metabolism, and tryptophan metabolism. These subcategories were closely associated with the cell structure, generation of cellular energy, and precursors for biosynthetic pathways, based on a - log 10 (P adjust) value in the KEGG pathway analysis. Conclusion In summary, the addition of glucose increased lignin degradation mediated by the MN-13 strain through regulating glycolysis, TCA cycle, and central carbon metabolism.
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Affiliation(s)
- Xiaodan Li
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Zhuofan Li
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Ming Li
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Jingwen Li
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Quan Wang
- College of Life Sciences, Hebei Agricultural University, Baoding, China
- Hebei Forage Microbial Technology Innovation Center, Baoding, Hebei, China
| | - Shuxiang Wang
- College of Life Sciences, Hebei Agricultural University, Baoding, China
- Hebei Forage Microbial Technology Innovation Center, Baoding, Hebei, China
| | - Shuna Li
- College of Life Sciences, Hebei Agricultural University, Baoding, China
- Hebei Forage Microbial Technology Innovation Center, Baoding, Hebei, China
| | - Hongya Li
- College of Life Sciences, Hebei Agricultural University, Baoding, China
- Hebei Forage Microbial Technology Innovation Center, Baoding, Hebei, China
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Vilbert AC, Kontur WS, Gille D, Noguera DR, Donohue TJ. Engineering Novosphingobium aromaticivorans to produce cis,cis-muconic acid from biomass aromatics. Appl Environ Microbiol 2024; 90:e0166023. [PMID: 38117061 PMCID: PMC10807440 DOI: 10.1128/aem.01660-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/13/2023] [Indexed: 12/21/2023] Open
Abstract
The platform chemical cis,cis-muconic acid (ccMA) provides facile access to a number of monomers used in the synthesis of commercial plastics. It is also a metabolic intermediate in the β-ketoadipic acid pathway of many bacteria and, therefore, a current target for microbial production from abundant renewable resources via metabolic engineering. This study investigates Novosphingobium aromaticivorans DSM12444 as a chassis for the production of ccMA from biomass aromatics. The N. aromaticivorans genome predicts that it encodes a previously uncharacterized protocatechuic acid (PCA) decarboxylase and a catechol 1,2-dioxygenase, which would be necessary for the conversion of aromatic metabolic intermediates to ccMA. This study confirmed the activity of these two enzymes in vitro and compared their activity to ones that have been previously characterized and used in ccMA production. From these results, we generated one strain that is completely derived from native genes and a second that contains genes previously used in microbial engineering synthesis of this compound. Both of these strains exhibited stoichiometric production of ccMA from PCA and produced greater than 100% yield of ccMA from the aromatic monomers that were identified in liquor derived from alkaline pretreated biomass. Our results show that a strain completely derived from native genes and one containing homologs from other hosts are both capable of stoichiometric production of ccMA from biomass aromatics. Overall, this work combines previously unknown aspects of aromatic metabolism in N. aromaticivorans and the genetic tractability of this organism to generate strains that produce ccMA from deconstructed biomass.IMPORTANCEThe production of commodity chemicals from renewable resources is an important goal toward increasing the environmental and economic sustainability of industrial processes. The aromatics in plant biomass are an underutilized and abundant renewable resource for the production of valuable chemicals. However, due to the chemical composition of plant biomass, many deconstruction methods generate a heterogeneous mixture of aromatics, thus making it difficult to extract valuable chemicals using current methods. Therefore, recent efforts have focused on harnessing the pathways of microorganisms to convert a diverse set of aromatics into a single product. Novosphingobium aromaticivorans DSM12444 has the native ability to metabolize a wide range of aromatics and, thus, is a potential chassis for conversion of these abundant compounds to commodity chemicals. This study reports on new features of N. aromaticivorans that can be used to produce the commodity chemical cis,cis-muconic acid from renewable and abundant biomass aromatics.
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Affiliation(s)
- Avery C. Vilbert
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Wayne S. Kontur
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Derek Gille
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Daniel R. Noguera
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Timothy J. Donohue
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Kleemann K, Bolduan P, Battagliarin G, Christl I, McNeill K, Sander M. Molecular Structure and Conformation of Biodegradable Water-Soluble Polymers Control Adsorption and Transport in Model Soil Mineral Systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:1274-1286. [PMID: 38164921 PMCID: PMC10795197 DOI: 10.1021/acs.est.3c05770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 01/03/2024]
Abstract
Water-soluble polymers (WSPs) are used in diverse applications, including agricultural formulations, that can result in the release of WSPs to soils. WSP biodegradability in soils is desirable to prevent long-term accumulation and potential associated adverse effects. In this work, we assessed adsorption of five candidate biodegradable WSPs with varying chemistry, charge, and polarity characteristics (i.e., dextran, diethylaminoethyl dextran, carboxymethyl dextran, polyethylene glycol monomethyl ether, and poly-l-lysine) and of one nonbiodegradable WSP (poly(acrylic acid)) to sand and iron oxide-coated sand particles that represent important soil minerals. Combined adsorption studies using solution-depletion measurements, direct surface adsorption techniques, and column transport experiments over varying solution pH and ionic strengths revealed electrostatics dominating interactions of charged WSPs with the sorbents as well as WSP conformations and packing densities in the adsorbed states. Hydrogen bonding controls adsorption of noncharged WSPs. Under transport in columns, WSP adsorption exhibited fast and slow kinetic adsorption regimes with time scales of minutes to hours. Slow adsorption kinetics in soil may lead to enhanced transport but also shorter lifetimes of biodegradable WSPs, assuming more rapid biodegradation when dissolved than adsorbed. This work establishes a basis for understanding the coupled adsorption and biodegradation dynamics of biodegradable WSPs in agricultural soils.
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Affiliation(s)
- Kevin Kleemann
- Institute
of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
| | - Patrick Bolduan
- BASF
SE, Materials and Formulation Research, Carl-Bosch-Strasse 38, 67056 Ludwigshafen, Germany
| | - Glauco Battagliarin
- BASF
SE, Materials and Formulation Research, Carl-Bosch-Strasse 38, 67056 Ludwigshafen, Germany
| | - Iso Christl
- Institute
of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
| | - Kristopher McNeill
- Institute
of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
| | - Michael Sander
- Institute
of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
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Godínez-Pérez CM, Loza A, Hurtado JM, Gutiérrez-Ríos RM. The benzoyl-CoA pathway serves as a genomic marker to identify the oxygen requirements in the degradation of aromatic hydrocarbons. Front Microbiol 2024; 14:1308626. [PMID: 38264488 PMCID: PMC10803450 DOI: 10.3389/fmicb.2023.1308626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/22/2023] [Indexed: 01/25/2024] Open
Abstract
The first step of anaerobic benzoate degradation is the formation of benzoyl-coenzyme A by benzoate-coenzyme A ligase (BCL). The anaerobic route is steered by benzoyl-CoA reductase, which promotes benzoyl-CoA breakdown, which is subsequently oxidized. In certain bacteria at low oxygen conditions, the aerobic metabolism of monoaromatic hydrocarbons occurs through the degradation Box pathway. These pathways have undergone experimental scrutiny in Alphaproteobacteria and Betaproteobacteria and have also been explored bioinformatically in representative Betaproteobacteria. However, there is a gap in our knowledge regarding the distribution of the benzoyl-CoA pathway and the evolutionary forces propelling its adaptation beyond that of representative bacteria. To address these questions, we used bioinformatic procedures to identify the BCLs and the lower pathways that transform benzoyl-CoA. These procedures included the identification of conserved motifs. As a result, we identified two motifs exclusive to BCLs, describing some of the catalytic properties of this enzyme. These motifs helped to discern BCLs from other aryl-CoA ligases effectively. The predicted BCLs and the enzymes of lower pathways were used as genomic markers for identifying aerobic, anaerobic, or hybrid catabolism, which we found widely distributed in Betaproteobacteria. Despite these enhancements, our approach failed to distinguish orthologs from a small cluster of paralogs exhibiting all the specified features to predict an ortholog. Nonetheless, the conducted phylogenetic analysis and the properties identified in the genomic context aided in formulating hypotheses about how this redundancy contributes to refining the catabolic strategy employed by these bacteria to degrade the substrates.
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Affiliation(s)
| | | | | | - Rosa-María Gutiérrez-Ríos
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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Gu J, Qiu Q, Yu Y, Sun X, Tian K, Chang M, Wang Y, Zhang F, Huo H. Bacterial transformation of lignin: key enzymes and high-value products. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:2. [PMID: 38172947 PMCID: PMC10765951 DOI: 10.1186/s13068-023-02447-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024]
Abstract
Lignin, a natural organic polymer that is recyclable and inexpensive, serves as one of the most abundant green resources in nature. With the increasing consumption of fossil fuels and the deterioration of the environment, the development and utilization of renewable resources have attracted considerable attention. Therefore, the effective and comprehensive utilization of lignin has become an important global research topic, with the goal of environmental protection and economic development. This review focused on the bacteria and enzymes that can bio-transform lignin, focusing on the main ways that lignin can be utilized to produce high-value chemical products. Bacillus has demonstrated the most prominent effect on lignin degradation, with 89% lignin degradation by Bacillus cereus. Furthermore, several bacterial enzymes were discussed that can act on lignin, with the main enzymes consisting of dye-decolorizing peroxidases and laccase. Finally, low-molecular-weight lignin compounds were converted into value-added products through specific reaction pathways. These bacteria and enzymes may become potential candidates for efficient lignin degradation in the future, providing a method for lignin high-value conversion. In addition, the bacterial metabolic pathways convert lignin-derived aromatics into intermediates through the "biological funnel", achieving the biosynthesis of value-added products. The utilization of this "biological funnel" of aromatic compounds may address the heterogeneous issue of the aromatic products obtained via lignin depolymerization. This may also simplify the separation of downstream target products and provide avenues for the commercial application of lignin conversion into high-value products.
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Affiliation(s)
- Jinming Gu
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Qing Qiu
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Yue Yu
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Xuejian Sun
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Kejian Tian
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Menghan Chang
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Yibing Wang
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Fenglin Zhang
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Hongliang Huo
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China.
- Engineering Lab for Water Pollution Control and Resources Recovery of Jilin Province, Changchun, 130117, China.
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Changchun, 130117, China.
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Gao L, Wang S, Xu X, Zheng J, Cai T, Jia S. Metagenomic analysis reveals the distribution, function, and bacterial hosts of degradation genes in activated sludge from industrial wastewater treatment plants. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 340:122802. [PMID: 37913976 DOI: 10.1016/j.envpol.2023.122802] [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: 08/10/2023] [Revised: 10/12/2023] [Accepted: 10/23/2023] [Indexed: 11/03/2023]
Abstract
For comprehensive insights into the bacterial community and its functions during industrial wastewater treatment, with a particular emphasis on its pivotal role in the bioremediation of organic pollutants, this study utilized municipal samples as a control group for metagenomic analysis. This approach allowed us to investigate the distribution, function, and bacterial hosts of biodegradation genes (BDGs) and organic degradation genes (ODGs), as well as the dynamics of bacterial communities during the industrial wastewater bioprocess. The results revealed that BDGs and ODGs associated with the degradation of benzoates, biphenyls, triazines, nitrotoluenes, and chlorinated aromatics were notably more abundant in the industrial samples. Specially, genes like clcD, linC, catE, pcaD, hbaB, hcrC, and badK, involved in the peripheral pathways for the catabolism of aromatic compounds, benzoate transport, and central aromatic intermediates, showed a significantly higher abundance of industrial activated sludge (AS) than municipal AS. Additionally, the BDG/ODG co-occurrence contigs in industrial samples exhibited a higher diversity in terms of degradation gene carrying capacity. Functional analysis of Clusters of Orthologous Groups (COGs) indicated that the primary function of bacterial communities in industrial AS was associated with the category of "metabolism". Furthermore, the presence of organic pollutants in industrial wastewater induced alterations in the bacterial community, particularly impacting the abundance of key hosts harboring BDGs and ODGs (e.g. Bradyrhizobium, Hydrogenophaga, and Mesorhizobium). The specific hosts of BDG/ODG could explain the distribution characteristics of degradation genes. For example, the prevalence of the Adh1 gene, primarily associated with Mesorhizobium, was notably more prevalent in the industrial AS. Overall, this study provides valuable insights into the development of more effective strategies for the industrial wastewater treatment and the mitigation of organic pollutant contamination.
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Affiliation(s)
- Linjun Gao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shuya Wang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xu Xu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinli Zheng
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tianming Cai
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shuyu Jia
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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Hernández-Rocamora VM, Molina R, Alba A, Carrasco-López C, Rojas-Altuve A, Panjikar S, Medina A, Usón I, Alfonso C, Galán B, Rivas G, Hermoso JA, Sanz JM. Structural characterization of PaaX, the main repressor of the phenylacetate degradation pathway in Escherichia coli W: A novel fold of transcription regulator proteins. Int J Biol Macromol 2024; 254:127935. [PMID: 37949283 DOI: 10.1016/j.ijbiomac.2023.127935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/30/2023] [Accepted: 11/05/2023] [Indexed: 11/12/2023]
Abstract
PaaX is a transcriptional repressor of the phenylacetic acid (PAA) catabolic pathway, a central route for bacterial aerobic degradation of aromatic compounds. Induction of the route is achieved through the release of PaaX from its promoter sequences by the first compound of the pathway, phenylacetyl-coenzyme A (PA-CoA). We report the crystal structure of PaaX from Escherichia coli W. PaaX displays a novel type of fold for transcription regulators, showing a dimeric conformation where the monomers present a three-domain structure: an N-terminal winged helix-turn-helix domain, a dimerization domain similar to the Cas2 protein and a C-terminal domain without structural homologs. The domains are separated by a crevice amenable to harbour a PA-CoA molecule. The biophysical characterization of the protein in solution confirmed several hints predicted from the structure, i.e. its dimeric conformation, a modest importance of cysteines and a high dependence of solubility and thermostability on ionic strength. At a moderately acidic pH, the protein formed a stable folding intermediate with remaining α-helical structure, a disrupted tertiary structure and exposed hydrophobic patches. Our results provide valuable information to understand the stability and mechanism of PaaX and pave the way for further analysis of other regulators with similar structural configurations.
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Affiliation(s)
- Víctor M Hernández-Rocamora
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, Av. Universidad, s/n, E-03202 Elche, Alicante, Spain; Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Rafael Molina
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - Alejandra Alba
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - César Carrasco-López
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - Alzoray Rojas-Altuve
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, Clayton, Australia; Department of Molecular Biology and Biochemistry, Monash University, Melbourne, Australia
| | - Ana Medina
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Baldiri Reixach 15, 08028 Barcelona, Spain
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Baldiri Reixach 15, 08028 Barcelona, Spain; ICREA: Institució Catalana de Recerca i Estudis Avançats, Pg. Lluis Companys 23, 08010 Barcelona, Spain
| | - Carlos Alfonso
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28049 Madrid, Spain
| | - Beatriz Galán
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28049 Madrid, Spain
| | - Germán Rivas
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28049 Madrid, Spain
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain.
| | - Jesús M Sanz
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28049 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.
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38
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Walker BJJ, Letnic M, Bucknall MP, Watson L, Jordan NR. Male dingo urinary scents code for age class and wild dingoes respond to this information. Chem Senses 2024; 49:bjae004. [PMID: 38319120 DOI: 10.1093/chemse/bjae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Indexed: 02/07/2024] Open
Abstract
Chemical information in canid urine has been implicated in territoriality and influences the spacing of individuals. We identified the key volatile organic compound (VOC) components in dingo (Canis lupus dingo) urine and investigated the potential role of scents in territorial spacing. VOC analysis, using headspace gas chromatography-mass spectrometry (GC-MS), demonstrated that the information in fresh urine from adult male dingoes was sufficient to allow statistical classification into age categories. Discriminant function analyses demonstrated that the relative amounts or combinations of key VOCs from pre-prime (3-4 years), prime (5-9 years), and post-prime (≥10 years) males varied between these age categories, and that scents exposed to the environment for 4 (but not 33) days could still be classified to age categories. Further, a field experiment showed that dingoes spent less time in the vicinity of prime male dingo scents than other scents. Collectively, these results indicate that age-related scent differences may be discriminable by dingoes. Previous authors have suggested the potential to use scent as a management tool for wild canids by creating an artificial territorial boundary/barrier. Our results suggest that identifying the specific signals in prime-age male scents could facilitate the development of scent-based tools for non-lethal management.
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Affiliation(s)
- Benjamin J J Walker
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW Sydney, NSW 2052, Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, NSW 2052, Australia
| | - Mike Letnic
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW Sydney, NSW 2052, Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, NSW 2052, Australia
| | - Martin P Bucknall
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, UNSW Sydney, NSW 2052, Australia
| | - Lyn Watson
- Dingo Discovery Sanctuary and Research Centre, Australian Dingo Foundation, P.O. Box 502, Gisborne, VIC, Australia
| | - Neil R Jordan
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW Sydney, NSW 2052, Australia
- Taronga Institute of Science and Learning, Taronga Western Plains Zoo, Taronga Conservation Society, Dubbo, NSW 2830, Australia
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Dai S, Harnisch F, Morejón MC, Keller NS, Korth B, Vogt C. Microbial electricity-driven anaerobic phenol degradation in bioelectrochemical systems. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 17:100307. [PMID: 37593528 PMCID: PMC10432169 DOI: 10.1016/j.ese.2023.100307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 07/06/2023] [Accepted: 07/22/2023] [Indexed: 08/19/2023]
Abstract
Microbial electrochemical technologies have been extensively employed for phenol removal. Yet, previous research has yielded inconsistent results, leaving uncertainties regarding the feasibility of phenol degradation under strictly anaerobic conditions using anodes as sole terminal electron acceptors. In this study, we employed high-performance liquid chromatography and gas chromatography-mass spectrometry to investigate the anaerobic phenol degradation pathway. Our findings provide robust evidence for the purely anaerobic degradation of phenol, as we identified benzoic acid, 4-hydroxybenzoic acid, glutaric acid, and other metabolites of this pathway. Notably, no typical intermediates of the aerobic phenol degradation pathway were detected. One-chamber reactors (+0.4 V vs. SHE) exhibited a phenol removal rate of 3.5 ± 0.2 mg L-1 d-1, while two-chamber reactors showed 3.6 ± 0.1 and 2.6 ± 0.9 mg L-1 d-1 at anode potentials of +0.4 and + 0.2 V, respectively. Our results also suggest that the reactor configuration certainly influenced the microbial community, presumably leading to different ratios of phenol consumers and microorganisms feeding on degradation products.
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Affiliation(s)
- Shixiang Dai
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany
| | - Falk Harnisch
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany
| | - Micjel Chávez Morejón
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany
| | - Nina Sophie Keller
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany
| | - Benjamin Korth
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany
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Zhao ZM, Liu ZH, Zhang T, Meng R, Gong Z, Li Y, Hu J, Ragauskas AJ, Li BZ, Yuan YJ. Unleashing the capacity of Rhodococcus for converting lignin into lipids. Biotechnol Adv 2024; 70:108274. [PMID: 37913947 DOI: 10.1016/j.biotechadv.2023.108274] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/11/2023] [Accepted: 10/22/2023] [Indexed: 11/03/2023]
Abstract
Bioconversion of bioresources/wastes (e.g., lignin, chemical pulping byproducts) represents a promising approach for developing a bioeconomy to help address growing energy and materials demands. Rhodococcus, a promising microbial strain, utilizes numerous carbon sources to produce lipids, which are precursors for synthesizing biodiesel and aviation fuels. However, compared to chemical conversion, bioconversion involves living cells, which is a more complex system that needs further understanding and upgrading. Various wastes amenable to bioconversion are reviewed herein to highlight the potential of Rhodococci for producing lipid-derived bioproducts. In light of the abundant availability of these substrates, Rhodococcus' metabolic pathways converting them to lipids are analyzed from a "beginning-to-end" view. Based on an in-depth understanding of microbial metabolic routes, genetic modifications of Rhodococcus by employing emerging tools (e.g., multiplex genome editing, biosensors, and genome-scale metabolic models) are presented for promoting the bioconversion. Co-solvent enhanced lignocellulose fractionation (CELF) strategy facilitates the generation of a lignin-derived aromatic stream suitable for the Rhodococcus' utilization. Novel alkali sterilization (AS) and elimination of thermal sterilization (ETS) approaches can significantly enhance the bioaccessibility of lignin and its derived aromatics in aqueous fermentation media, which promotes lipid titer significantly. In order to achieve value-added utilization of lignin, biodiesel and aviation fuel synthesis from lignin and lipids are further discussed. The possible directions for unleashing the capacity of Rhodococcus through synergistically modifying microbial strains, substrates, and fermentation processes are proposed toward a sustainable biological lignin valorization.
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Affiliation(s)
- Zhi-Min Zhao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Department of Chemical & Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, United States; Key Laboratory of Ecology and Resource Use of the Mongolian Plateau (Ministry of Education), School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Zhi-Hua Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Tongtong Zhang
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau (Ministry of Education), School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Rongqian Meng
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau (Ministry of Education), School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Zhiqun Gong
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau (Ministry of Education), School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Yibing Li
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau (Ministry of Education), School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Jing Hu
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau (Ministry of Education), School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Arthur J Ragauskas
- Department of Chemical & Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, United States; Joint Institute of Biological Science, Biosciences Division, Oak Ridge National Laboratory (ORNL), Oak Ridge, TN 37831, United States; Department of Forestry, Wildlife, and Fisheries, Center for Renewable Carbon, University of Tennessee Institute of Agriculture, Knoxville, TN 37996, United States.
| | - Bing-Zhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
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41
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Seshan H, Santillan E, Constancias F, Chandra Segaran US, Williams RBH, Wuertz S. Metagenomics and metatranscriptomics suggest pathways of 3-chloroaniline degradation in wastewater reactors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166066. [PMID: 37549699 DOI: 10.1016/j.scitotenv.2023.166066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 07/23/2023] [Accepted: 08/03/2023] [Indexed: 08/09/2023]
Abstract
Biological wastewater treatment systems are often affected by shifts in influent quality, including the input of toxic chemicals. Yet the mechanisms underlying the adaptation of activated sludge process performance are rarely studied in a controlled and replicated experimental setting, particularly when challenged with a sustained toxin input. Three replicate bench-scale bioreactors were subjected to a chemical disturbance in the form of 3-chloroaniline (3-CA) over 132 days, after an acclimation period of 58 days, while three control reactors received no 3-CA input. Ammonia oxidation was initially affected by 3-CA. Within three weeks of the experiment, microbial communities in all three treatment reactors adapted to biologically degrade 3-CA resulting in partial ammonia oxidation recovery. Combining process and microbial community data from amplicon sequencing with potential functions gleaned from assembled metagenomics and metatranscriptomics data, two putative degradation pathways for 3-CA were identified. The first pathway, determined from metagenomics data, involves a benzoate dioxygenase and subsequent meta-cleavage of the aromatic ring. The second, determined from intensive short-term sampling for gene expression data in tandem with 3-CA degradation, involves a phenol monooxygenase followed by ortho-cleavage of the aromatic ring. The relative abundances of amplicon sequence variants associated with the genera Gemmatimonas, OLB8, and Taibaiella correlated significantly with 3-CA degradation. Metagenome-assembled genome data also showed the genus OLB8 to be differentially enriched in treatment reactors, making it a strong candidate as 3-CA degrader. Using replicated reactors, this study has demonstrated the impact of a sustained stress on the activated sludge process. The unique and novel features of this study include the identification of putative pathways and potential degraders of 3-CA using long-term and short-term sampling in tandem with multiple methods in a controlled and replicated experiment.
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Affiliation(s)
- Hari Seshan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; Department of Civil and Environmental Engineering, University of California, Davis, CA 95616, USA
| | - Ezequiel Santillan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; Department of Civil and Environmental Engineering, University of California, Davis, CA 95616, USA
| | - Florentin Constancias
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore
| | - Uma Shankari Chandra Segaran
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, 119077, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; Department of Civil and Environmental Engineering, University of California, Davis, CA 95616, USA; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798, Singapore..
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Li D, Wen Q, Chen Z. Enhanced anaerobic biodegradation of typical phenolic compounds in coal gasification wastewater (CGW) using biochar: Focusing on the hydrolysis-acidification process and microbial community succession. ENVIRONMENTAL RESEARCH 2023; 237:116964. [PMID: 37619633 DOI: 10.1016/j.envres.2023.116964] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/19/2023] [Accepted: 08/22/2023] [Indexed: 08/26/2023]
Abstract
The aim of this research is to investigate the effects of biochar (BC) on treatment performance (especially hydrolysis-acidification process) and microbial community shifts during anaerobic degradation of typical phenolic compounds in coal gasification wastewater. Compared to the control group, the removal of phenol, p-cresol and 3, 5-xylenol was gradually enhanced when increasing the BC addition within the test dosage (1-5 g/L). The biodegradation of phenol and p-cresol was significantly enhanced by BC addition while limited improvement for 3, 5-xylenol. The addition of BC significantly accelerated the hydrolysis-acidification process with the hydrolytic removal of phenol improved by 69.14%, the microbial activity was enhanced by 57.01%, and the key hydrolase bamA gene was enriched by 117.27%, respectively. Compared to 1-2 g/L dose, more protein-like and humic acid-like substances were secreted with 5 g/L BC, which probably contributed to higher extracellular electron transfer efficiency. In addition, phenol degrading bacteria (Syntrophorhabdus, Dysgonomonas, Holophaga, etc.) and electroactive microorganisms (Geobacter, Syntrophorhabdus, Methanospirillum, etc.) were enriched by BC addition. The functional genes related to carboxylation, benzoylation and ring cleavage processes of benzoyl-CoA pathway were potentially activated by BC.
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Affiliation(s)
- Da Li
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin, 150090, PR China.
| | - Qinxue Wen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin, 150090, PR China.
| | - Zhiqiang Chen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin, 150090, PR China; School of Civil Engineering, Lanzhou University of Technology, Lanzhou, 730070, PR China.
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Falk N, Droppo IG, Drouillard KG, Weisener CG. Biogeochemical Processes and Microbial Dynamics Governing Phosphorus Retention and Release in Sediments: A Case Study in Lower Great Lakes Headwaters. ENVIRONMENTAL MANAGEMENT 2023; 72:932-944. [PMID: 37505273 PMCID: PMC10509119 DOI: 10.1007/s00267-023-01859-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/10/2023] [Indexed: 07/29/2023]
Abstract
The ability of headwater bed and suspended sediments to mitigate non-point agricultural phosphorus (P) loads to the lower Great Lakes is recognized, but the specific biogeochemical processes promoting sediment P retention or internal P release remain poorly understood. To elucidate these mechanisms, three headwater segments located within priority watersheds of Southern Ontario, Canada, were sampled through the growing season of 2018-2020. The study employed equilibrium P assays along with novel assessments of legacy watershed nutrients, nitrogen (N) concentrations, sediment redox, and microbial community composition. 20-year data revealed elevated total P (TP) and total Nitrogen (TN) at an inorganic fertilizer and manure fertilizer-impacted site, respectively. Overall, sampled sites acted as P sinks; however, agricultural sediments exhibited significantly lower buffering capacity compared to a reference forested watershed. Collection of fine suspended sediment (<63 µm) through time-integrated sampling showed the suspended load at the inorganic-fertilized site was saturated with P, indicating a greater potential for P release into surface waters compared to bed sediments. Through vertical microsensor profiling and DNA sequencing of the sediment microbial community, site-specific factors associated with a distinct P-source event were identified. These included rapid depletion of dissolved oxygen (DO) across the sediment water interface (SWI), as well as the presence of nitrate-reducing bacterial and ammonia-oxidizing archaeal (AOA) genera. This research provides valuable insights into the dynamics of P in headwaters, shedding light on P retention and release. Understanding these processes is crucial for effective management strategies aimed at mitigating P pollution to the lower Great Lakes.
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Affiliation(s)
- Nicholas Falk
- Flinders Accelerator for Microbiome Research, College of Science and Engineering, Flinders University, Sturt Rd, Adelaide, SA, 5042, Australia.
- Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Avenue, Windsor, ON, N9B 3P4, Canada.
| | - Ian G Droppo
- Canada Centre for Inland Waters, Environment and Climate Change Canada, 867 Lakeshore Rd, Burlington, ON, L7R 4A6, Canada
| | - Ken G Drouillard
- Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Avenue, Windsor, ON, N9B 3P4, Canada
| | - Christopher G Weisener
- Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Avenue, Windsor, ON, N9B 3P4, Canada
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Ke Z, Zhu Q, Zhang M, Gao S, jiang M, Zhou Y, Qiu J, Cheng M, Yan X, Wang J, Hong Q. Unveiling the regulatory mechanisms of salicylate degradation gene cluster cehGHIR4 in Rhizobium sp. strain X9. Appl Environ Microbiol 2023; 89:e0080223. [PMID: 37800922 PMCID: PMC10617420 DOI: 10.1128/aem.00802-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/19/2023] [Indexed: 10/07/2023] Open
Abstract
In a previous study, the novel gene cluster cehGHI was found to be involved in salicylate degradation through the CoA-mediated pathway in Rhizobium sp. strain X9 (Mol Microbiol 116:783-793, 2021). In this study, an IclR family transcriptional regulator CehR4 was identified. In contrast to other regulators involved in salicylate degradation, cehR4 forms one operon with the gentisyl-CoA thioesterase gene cehI, while cehG and cehH (encoding salicylyl-CoA ligase and salicylyl-CoA hydroxylase, respectively) form another operon. cehGH and cehIR4 are divergently transcribed, and their promoters overlap. The results of the electrophoretic mobility shift assay and DNase I footprinting showed that CehR4 binds to the 42-bp motif between genes cehH and cehI, thus regulating transcription of cehGH and cehIR4. The repeat sequences IR1 (5'-TTTATATAAA-3') and IR2 (5'-AATATAGAAA-3') in the motif are key sites for CehR4 binding. The arrangement of cehGH and cehIR4 and the conserved binding motif of CehR4 were also found in other bacterial genera. The results disclose the regulatory mechanism of salicylate degradation through the CoA pathway and expand knowledge about the systems controlled by IclR family transcriptional regulators.IMPORTANCEThe long-term residue of aromatic compounds in the environment has brought great threat to the environment and human health. Microbial degradation plays an important role in the elimination of aromatic compounds in the environment. Salicylate is a common intermediate metabolite in the degradation of various aromatic compounds. Recently, Rhizobium sp. strain X9, capable of degrading the pesticide carbaryl, was isolated from carbaryl-contaminated soil. Salicylate is the intermediate metabolite that appeared during the degradation of carbaryl, and a novel salicylate degradation pathway and the involved gene cluster cehGHIR4 have been identified. This study identified and characterized the IclR transcription regulator CehR4 that represses transcription of cehGHIR4 gene cluster. Additionally, the genetic arrangements of cehGH and cehIR4 and the binding sites of CehR4 were also found in other bacterial genera. This study provides insights into the biodegradation of salicylate and provides an application in the bioremediation of aromatic compound-contaminated environments.
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Affiliation(s)
- Zhijian Ke
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
- School of Biological and Chemical Engineering, Ningbo Tech University, Ningbo, Zhejiang, China
| | - Qian Zhu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Mingliang Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Siyuan Gao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Mingli jiang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yidong Zhou
- School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Jiguo Qiu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Minggen Cheng
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Xin Yan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jinbo Wang
- School of Biological and Chemical Engineering, Ningbo Tech University, Ningbo, Zhejiang, China
| | - Qing Hong
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
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Liu T, Ning L, Mei C, Li S, Zheng L, Qiao P, Wang H, Hu T, Zhong W. Synthetic bacterial consortia enhanced the degradation of mixed priority phthalate ester pollutants. ENVIRONMENTAL RESEARCH 2023; 235:116666. [PMID: 37453507 DOI: 10.1016/j.envres.2023.116666] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
Dimethyl phthalate (DMP), diethyl phthalate (DEP), di-n-butyl phthalate (DBP), butyl benzyl phthalate (BBP), bis(2-ethylhexyl) phthalate (DEHP), and di-n-octyl phthalate (DOP) are hazardous chemicals listed as priority pollutants that disrupt endocrine systems. According to available reports, these six priority phthalate esters (PAEs) are considered the most polluting; however, no studies have been conducted on the efficient remediation of these PAEs. We therefore designed and constructed a synthetic bacterial consortium capable of the simultaneous and efficient degradation of six priority PAEs in minimal inorganic salt medium (MSM) and soil. The consortium comprised Glutamicibacter sp. ZJUTW, which demonstrates priority for degrading short-chain PAEs; Cupriavidus sp. LH1, which degrades phthalic acid (PA) and protocatechuic acid (PCA), intermediates of the PAE biodegradation process; and Gordonia sp. GZ-YC7, which efficiently degrades long-chain priority PAEs, including DEHP and DOP. In MSM containing the six mixed PAEs (250 mg/L each), the ZJUTW + YC + LH1 consortium completely degraded the four short-chain PAEs within 48 h, and DEHP (100%) and DOP (62.5%) within 72 h. In soil containing the six mixed PAEs (DMP, DEP, BBP, and DOP, 400 mg/kg each; DBP and DEHP, 500 mg/kg, each), the ZJUTW + YC + LH1 consortium completely degraded DMP, DEP, BBP, and DBP within 6 days, and 70.84% of DEHP and 66.24% of DOP within 2 weeks. The consortium efficiently degraded the six mixed PAEs in both MSM and soil. We thus believe that this synthetic microbial consortium is a strong candidate for the bioremediation of environments contaminated with mixed PAE pollutants.
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Affiliation(s)
- Tengfei Liu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032, Zhejiang, China
| | - Lixiao Ning
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032, Zhejiang, China
| | - Chengyu Mei
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032, Zhejiang, China
| | - Shuang Li
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032, Zhejiang, China
| | - Lianbao Zheng
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032, Zhejiang, China
| | - Pei Qiao
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032, Zhejiang, China
| | - Haixia Wang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032, Zhejiang, China
| | - Tong Hu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032, Zhejiang, China
| | - Weihong Zhong
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032, Zhejiang, China.
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46
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Bai B, Zhang L, Dong H, Huang Y. Coupled Fe(III) reduction and phenanthrene degradation by marine-derived Kocuria oceani FXJ8.057 under aerobic condition. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132237. [PMID: 37595472 DOI: 10.1016/j.jhazmat.2023.132237] [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: 03/02/2023] [Revised: 06/29/2023] [Accepted: 08/04/2023] [Indexed: 08/20/2023]
Abstract
Diverse aerobic actinobacteria possess the capacity to degrade polycyclic aromatic hydrocarbons (PAHs) and have recently been shown to reduce Fe(III). However, the coupling of the two processes under oxic conditions remains unclear. Here, the co-metabolism of phenanthrene (PHE) and Fe(III) by marine-derived Kocuria oceani FXJ8.057 was realized under aerobic condition. In the presence of both PHE and Fe(III), the rates of PHE degradation (83.91 %) and Fe(III) reduction (50.00 %) were synchronously enhanced, compared to those with PHE (67.34 %) or Fe(III) (38.00 %) alone. Transcriptome analysis detected upregulation of PHE biodegradation and riboflavin biosynthesis in the strain cultured with both PHE and Fe(III) compared to that with PHE alone. Metabolite analysis indicated that, with the addition of Fe(III), the strain could efficiently degrade PHE via three pathways. Moreover, the strain secreted riboflavin, which acted as a shuttle to promote electron transfer from PHE to Fe(III). It also secreted organic acids that could delay Fe(II) reoxidation. Finally, H2O2 secreted by the strain caused extracellular Fenton reaction to generate •OH, which also played a minor role in the PHE degradation. These findings provide the first example of an aerobic bacterium that couples PAH degradation to Fe(III) reduction and extend our understanding of Fe(III)-reducing microorganisms.
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Affiliation(s)
- Bingbing Bai
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Limin Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Hailiang Dong
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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47
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Pimviriyakul P, Buttranon S, Soithongcharoen S, Supawatkon C, Disayabootr K, Watthaisong P, Tinikul R, Jaruwat A, Chaiyen P, Chitnumsub P, Maenpuen S. Structure and biochemical characterization of an extradiol 3,4-dihydroxyphenylacetate 2,3-dioxygenase from Acinetobacter baumannii. Arch Biochem Biophys 2023; 747:109768. [PMID: 37769893 DOI: 10.1016/j.abb.2023.109768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/23/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023]
Abstract
3,4-Dihydroxyphenylacetate (DHPA) 2,3-dioxygenase (EC 1.13.11.15) from Acinetobacter baumannii (AbDHPAO) is an enzyme that catalyzes the 2,3-extradiol ring-cleavage of DHPA in the p-hydroxyphenylacetate (HPA) degradation pathway. While the biochemical reactions of various DHPAOs have been reported, only structures of DHPAO from Brevibacterium fuscum and their homologs are available. Here, we report the X-ray structure and biochemical characterization of an Fe2+-specific AbDHPAO that shares 12% sequence identity to the enzyme from B. fuscum. The 1.8 Å X-ray structure of apo-AbDHPAO was determined with four subunits per asymmetric unit, consistent with a homotetrameric structure. Interestingly, the αβ-sandwiched fold of the AbDHPAO subunit is different from the dual β-barrel-like motif of the well-characterized B. fuscum DHPAO structures; instead, it is similar to the structures of non-DHPA extradiol dioxygenases from Comamonas sp. and Sphingomonas paucimobilis. Similarly, these extradiol dioxygenases share the same chemistry owing to a conserved 2-His-1-carboxylate catalytic motif. Structure analysis and molecular docking suggested that the Fe2+ cofactor and substrate binding sites consist of the conserved residues His12, His57, and Glu238 forming a 2-His-1-carboxylate motif ligating to Fe2+ and DHPA bound with Fe2+ in an octahedral coordination. In addition to DHPA, AbDHPAO can also use other 3,4-dihydroxyphenylacetate derivatives with different aliphatic carboxylic acid substituents as substrates, albeit with low reactivity. Altogether, this report provides a better understanding of the structure and biochemical properties of AbDHPAO and its homologs, which is advancing further modification of DHPAO in future applications.
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Affiliation(s)
- Panu Pimviriyakul
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Supacha Buttranon
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi, 20131, Thailand; School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | - Sahachat Soithongcharoen
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi, 20131, Thailand; School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | - Cheerapat Supawatkon
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi, 20131, Thailand; School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | - Kasidis Disayabootr
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi, 20131, Thailand
| | - Pratchaya Watthaisong
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | - Ruchanok Tinikul
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Aritsara Jaruwat
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | - Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand.
| | - Somchart Maenpuen
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi, 20131, Thailand.
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Tian J, Boggs DG, Donnan PH, Barroso GT, Garcia AA, Dowling DP, Buss JA, Bridwell-Rabb J. The NADH recycling enzymes TsaC and TsaD regenerate reducing equivalents for Rieske oxygenase chemistry. J Biol Chem 2023; 299:105222. [PMID: 37673337 PMCID: PMC10579966 DOI: 10.1016/j.jbc.2023.105222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 08/22/2023] [Accepted: 08/31/2023] [Indexed: 09/08/2023] Open
Abstract
Many microorganisms use both biological and nonbiological molecules as sources of carbon and energy. This resourcefulness means that some microorganisms have mechanisms to assimilate pollutants found in the environment. One such organism is Comamonas testosteroni, which metabolizes 4-methylbenzenesulfonate and 4-methylbenzoate using the TsaMBCD pathway. TsaM is a Rieske oxygenase, which in concert with the reductase TsaB consumes a molar equivalent of NADH. Following this step, the annotated short-chain dehydrogenase/reductase and aldehyde dehydrogenase enzymes TsaC and TsaD each regenerate a molar equivalent of NADH. This co-occurrence ameliorates the need for stoichiometric addition of reducing equivalents and thus represents an attractive strategy for integration of Rieske oxygenase chemistry into biocatalytic applications. Therefore, in this work, to overcome the lack of information regarding NADH recycling enzymes that function in partnership with Rieske non-heme iron oxygenases (Rieske oxygenases), we solved the X-ray crystal structure of TsaC to a resolution of 2.18 Å. Using this structure, a series of substrate analog and protein variant combination reactions, and differential scanning fluorimetry experiments, we identified active site features involved in binding NAD+ and controlling substrate specificity. Further in vitro enzyme cascade experiments demonstrated the efficient TsaC- and TsaD-mediated regeneration of NADH to support Rieske oxygenase chemistry. Finally, through in-depth bioinformatic analyses, we illustrate the widespread co-occurrence of Rieske oxygenases with TsaC-like enzymes. This work thus demonstrates the utility of these NADH recycling enzymes and identifies a library of short-chain dehydrogenase/reductase enzyme prospects that can be used in Rieske oxygenase pathways for in situ regeneration of NADH.
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Affiliation(s)
- Jiayi Tian
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - David G Boggs
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Patrick H Donnan
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Gage T Barroso
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Daniel P Dowling
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, USA
| | - Joshua A Buss
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
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49
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Zehnle H, Otersen C, Benito Merino D, Wegener G. Potential for the anaerobic oxidation of benzene and naphthalene in thermophilic microorganisms from the Guaymas Basin. Front Microbiol 2023; 14:1279865. [PMID: 37840718 PMCID: PMC10570749 DOI: 10.3389/fmicb.2023.1279865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 09/13/2023] [Indexed: 10/17/2023] Open
Abstract
Unsubstituted aromatic hydrocarbons (UAHs) are recalcitrant molecules abundant in crude oil, which is accumulated in subsurface reservoirs and occasionally enters the marine environment through natural seepage or human-caused spillage. The challenging anaerobic degradation of UAHs by microorganisms, in particular under thermophilic conditions, is poorly understood. Here, we established benzene- and naphthalene-degrading cultures under sulfate-reducing conditions at 50°C and 70°C from Guaymas Basin sediments. We investigated the microorganisms in the enrichment cultures and their potential for UAH oxidation through short-read metagenome sequencing and analysis. Dependent on the combination of UAH and temperature, different microorganisms became enriched. A Thermoplasmatota archaeon was abundant in the benzene-degrading culture at 50°C, but catabolic pathways remained elusive, because the archaeon lacked most known genes for benzene degradation. Two novel species of Desulfatiglandales bacteria were strongly enriched in the benzene-degrading culture at 70°C and in the naphthalene-degrading culture at 50°C. Both bacteria encode almost complete pathways for UAH degradation and for downstream degradation. They likely activate benzene via methylation, and naphthalene via direct carboxylation, respectively. The two species constitute the first thermophilic UAH degraders of the Desulfatiglandales. In the naphthalene-degrading culture incubated at 70°C, a Dehalococcoidia bacterium became enriched, which encoded a partial pathway for UAH degradation. Comparison of enriched bacteria with related genomes from environmental samples indicated that pathways for benzene degradation are widely distributed, while thermophily and capacity for naphthalene activation are rare. Our study highlights the capacities of uncultured thermophilic microbes for UAH degradation in petroleum reservoirs and in contaminated environments.
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Affiliation(s)
- Hanna Zehnle
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Carolin Otersen
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - David Benito Merino
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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50
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Liu WW, Pan P, Zhou NY. The presence of benzene ring activating CoA ligases for aromatics degradation in the ANaerobic MEthanotrophic (ANME) archaea. Microbiol Spectr 2023; 11:e0176623. [PMID: 37754561 PMCID: PMC10581246 DOI: 10.1128/spectrum.01766-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/03/2023] [Indexed: 09/28/2023] Open
Abstract
Petroleum-source and black carbon-source aromatic compounds are present in the cold seep environments, where ANaerobic MEthanotrophic (ANME) archaea as the dominant microbial community mediates the anaerobic oxidation of methane to produce inorganic and organic carbon. Here, by predicting the aromatics catabolic pathways in ANME metagenome-assembled genomes, we provide genomic and biochemical evidences that ANME have the potential of metabolizing aromatics via the strategy of CoA activation of the benzene ring using phenylacetic acid and benzoate as the substrates. Two ring-activating enzymes phenylacetate-CoA ligase (PaaKANME) and benzoate-CoA ligase (BadAANME) are able to convert phenylacetate to phenylacetyl-CoA and benzoate to benzoyl-CoA in vitro, respectively. They are mesophilic, alkali resistance, and with broad substrate spectra showing different affinity with various substrates. An exploration of the relative gene abundance in ANME genomes and cold seep environments indicates that about 50% of ANME genomes contain PCL genes, and various bacteria and archaea contain PCL and BCL genes. The results provide evidences for the capability of heterotrophic metabolism of aromatic compounds by ANME. This has not only enhanced our understanding of the nutrient range of ANME but also helped to explore the additional ecological and biogeochemical significance of this ubiquitous sedimentary archaea in the carbon flow in the cold seep environments. IMPORTANCE ANaerobic MEthanotrophic (ANME) archaea is the dominant microbial community mediating the anaerobic oxidation of methane in the cold seep environments, where aromatic compounds are present. Then it is hypothesized that ANME may be involved in the metabolism of aromatics. Here, we provide genomic and biochemical evidences for the heterotrophic metabolism of aromatic compounds by ANME, enhancing our understanding of their nutrient range and also shedding light on the ecological and biogeochemical significance of these ubiquitous sedimentary archaea in carbon flow within cold seep environments. Overall, this study offers valuable insights into the metabolic capabilities of ANME and their potential contributions to the global carbon cycle.
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Affiliation(s)
- Wei-Wei Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Piaopiao Pan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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