1
|
Wei J, Luo J, Peng T, Zhou P, Zhang J, Yang F. Comparative genomic analysis and functional investigations for MCs catabolism mechanisms and evolutionary dynamics of MCs-degrading bacteria in ecology. ENVIRONMENTAL RESEARCH 2024; 248:118336. [PMID: 38295970 DOI: 10.1016/j.envres.2024.118336] [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: 08/21/2023] [Revised: 01/06/2024] [Accepted: 01/27/2024] [Indexed: 02/07/2024]
Abstract
Microcystins (MCs) significantly threaten the ecosystem and public health. Biodegradation has emerged as a promising technology for removing MCs. Many MCs-degrading bacteria have been identified, including an indigenous bacterium Sphingopyxis sp. YF1 that could degrade MC-LR and Adda completely. Herein, we gained insight into the MCs biodegradation mechanisms and evolutionary dynamics of MCs-degrading bacteria, and revealed the toxic risks of the MCs degradation products. The biochemical characteristics and genetic repertoires of strain YF1 were explored. A comparative genomic analysis was performed on strain YF1 and six other MCs-degrading bacteria to investigate their functions. The degradation products were investigated, and the toxicity of the intermediates was analyzed through rigorous theoretical calculation. Strain YF1 might be a novel species that exhibited versatile substrate utilization capabilities. Many common genes and metabolic pathways were identified, shedding light on shared functions and catabolism in the MCs-degrading bacteria. The crucial genes involved in MCs catabolism mechanisms, including mlr and paa gene clusters, were identified successfully. These functional genes might experience horizontal gene transfer events, suggesting the evolutionary dynamics of these MCs-degrading bacteria in ecology. Moreover, the degradation products for MCs and Adda were summarized, and we found most of the intermediates exhibited lower toxicity to different organisms than the parent compound. These findings systematically revealed the MCs catabolism mechanisms and evolutionary dynamics of MCs-degrading bacteria. Consequently, this research contributed to the advancement of green biodegradation technology in aquatic ecology, which might protect human health from MCs.
Collapse
Affiliation(s)
- Jia Wei
- Xiangya School of Public Health, Central South University, Changsha, Hunan, 410078, China
| | - Jiayou Luo
- Xiangya School of Public Health, Central South University, Changsha, Hunan, 410078, China.
| | - Tangjian Peng
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, University of South China, Hengyang, Hunan, 421001, China
| | - Pengji Zhou
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, University of South China, Hengyang, Hunan, 421001, China
| | - Jiajia Zhang
- Xiangya School of Public Health, Central South University, Changsha, Hunan, 410078, China
| | - Fei Yang
- Xiangya School of Public Health, Central South University, Changsha, Hunan, 410078, China; Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, University of South China, Hengyang, Hunan, 421001, China.
| |
Collapse
|
2
|
Ateia M, Sigmund G, Bentel MJ, Washington JW, Lai A, Merrill NH, Wang Z. Integrated data-driven cross-disciplinary framework to prevent chemical water pollution. ONE EARTH (CAMBRIDGE, MASS.) 2023; 6:10.1016/j.oneear.2023.07.001. [PMID: 38264630 PMCID: PMC10802893 DOI: 10.1016/j.oneear.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Access to a clean and healthy environment is a human right and a prerequisite for maintaining a sustainable ecosystem. Experts across domains along the chemical life cycle have traditionally operated in isolation, leading to limited connectivity between upstream chemical innovation to downstream development of water-treatment technologies. This fragmented and historically reactive approach to managing emerging contaminants has resulted in significant externalized societal costs. Herein, we propose an integrated data-driven framework to foster proactive action across domains to effectively address chemical water pollution. By implementing this integrated framework, it will not only enhance the capabilities of experts in their respective fields but also create opportunities for novel approaches that yield co-benefits across multiple domains. To successfully operationalize the integrated framework, several concerted efforts are warranted, including adopting open and FAIR (findable, accessible, interoperable, and reusable) data practices, developing common knowledge bases/platforms, and staying vigilant against new substance "properties" of concern.
Collapse
Affiliation(s)
- Mohamed Ateia
- United States Environmental Protection Agency, Center for Environmental Solutions & Emergency Response, Cincinnati, OH 45220, USA
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Gabriel Sigmund
- Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, University of Vienna, Josef-Holaubeck-Platz 2, 1090 Vienna, Austria
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 AA Wageningen, the Netherlands
| | - Michael J. Bentel
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC 29634, USA
| | - John W. Washington
- United States Environmental Protection Agency, Center for Environmental Measurement and Modeling, Athens, GA 30605, USA
| | - Adelene Lai
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367 Belvaux, Luxembourg
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University, 07743 Jena, Germany
| | - Nathaniel H. Merrill
- United States Environmental Protection Agency, Center for Environmental Measurement and Modeling, Narragansett, RI, USA
| | - Zhanyun Wang
- Empa Swiss – Federal Laboratories for Materials Science and Technology, Technology and Society Laboratory, 9014 St. Gallen, Switzerland
| |
Collapse
|
3
|
Khandelwal A, Sugavanam R, Ramakrishnan B, Dutta A, Varghese E, Banerjee T, Nain L, Singh SB, Singh N. Bio-polysaccharide composites mediated degradation of polyaromatic hydrocarbons in a sandy soil using free and immobilized consortium of Kocuria rosea and Aspergillus sydowii. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:80005-80020. [PMID: 35220535 DOI: 10.1007/s11356-022-19252-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/12/2022] [Indexed: 06/14/2023]
Abstract
Based on our previous study in minimal medium, Kocuria rosea and Aspergillus sydowii were identified as the best microbes for degradation of mixture of polyaromatic hydrocarbons (PAHs). The present study reports PAH degradation potential of these microbes in free and immobilized form. PAHs were extracted using QuEChERS-mediated process followed by quantification by high performance liquid chromatography. The microbial consortium of Kocuria rosea + Aspergillus sydowii was formulated in three bio-formulations, namely (i) bentonite-alginate composite beads; (ii) water dispersible granule composite using guar gum-nanobentonite; and (iii) composites of carboxymethyl cellulose-bentonite and were applied in PAH fortified (100 µg g-1) sandy loam soil. Results suggested that degradation data fitted well to first order kinetics as in most of the cases, the values of correlation coefficient (r) were > 0.95. The half-life (t1/2) values for PAHs in the uninoculated control soil were: naphthalene (10.43 d), fluorene (22.43 d), phenanthrene (24.64 d), anthracene (38.47 d), and pyrene (34.34 d). Inoculation of soil with free culture microbial consortium (without or with nutrient) and bio-formulation of degrading cultures enhanced degradation of all PAHs and half-life values were significantly reduced for each PAH: naphthalene (1.76-2.00 d), fluorene (2.52-6.65 d), phenanthrene (4.61-6.37 d), anthracene (9.01-12.22 d), and pyrene (10.98-15.55 d). Among different bio-formulations, guar gum-nanobentonite-based composite exhibited better efficacy for degradation of naphthalene, fluorene, phenanthrene, anthracene, and pyrene. The addition of microbial consortium in PAH fortified soil increased 16S rRNA gene copies of Alphaproteobacteria and Bacteroidetes, compared to the uninoculated, PAH-fortified control. The microbial functional gene assays showed that the gene copies of amoA, nirK, nirS, and anammox increased, suggesting nitrogen regulation in the PAH-fortified soil.
Collapse
Affiliation(s)
- Ashish Khandelwal
- Division of Agricultural Chemicals, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012, India
- Division of Environment Science, ICAR- Indian Agricultural Research Institute, New Delhi, 110 012, India
| | - Ramya Sugavanam
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012, India
| | | | - Anirban Dutta
- Division of Agricultural Chemicals, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012, India
| | - Eldho Varghese
- Fishery Resources Assessment Division, ICAR-Central Marine Fisheries Research Institute, Kochi, 682 018, Kerala, India
| | - Tirthankar Banerjee
- Division of Agricultural Chemicals, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012, India
| | - Lata Nain
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012, India
| | - Shashi Bala Singh
- Division of Agricultural Chemicals, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012, India
| | - Neera Singh
- Division of Agricultural Chemicals, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012, India.
| |
Collapse
|
4
|
Degradation or humification: rethinking strategies to attenuate organic pollutants. Trends Biotechnol 2022; 40:1061-1072. [PMID: 35339288 DOI: 10.1016/j.tibtech.2022.02.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 02/14/2022] [Accepted: 02/22/2022] [Indexed: 11/19/2022]
Abstract
The fate of organic pollutants in environmental matrices can be determined by degradation and humification. The humification process represents a promising strategy to remove organic pollutants, particularly those resistant to degradation. In contrast to the well-studied degradation process, the contribution and application prospects of the humification process for organic pollutant removal has been underestimated. The recent progress in synthesizing artificial humic substances (HS) has made directed humification of recalcitrant organic pollutants possible. This review focuses on degradation and humification of organic matter, especially recalcitrant organic pollutants. Challenges in understanding the contribution, underlying mechanisms, and artificial synthesis of HS for removing organic pollutants are also critically discussed. We advocate further investigating the humification of organic pollutants in future studies.
Collapse
|
5
|
Tirkey SR, Ram S, Mitra M, Mishra S. Performance analysis of Pseudomonas sp. strain SA3 in naphthalene degradation using phytotoxicity and microcosm studies. Biodegradation 2022; 33:169-180. [PMID: 35103887 DOI: 10.1007/s10532-022-09972-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/18/2022] [Indexed: 11/30/2022]
Abstract
The present study is aimed to develop a microbial system for efficient naphthalene bioremediation. A phytotoxicity study was carried out to check the naphthalene detoxification efficiency of Pseudomonas sp. strain SA3 in mung bean (Vigna radiata). For this, administration of the degraded product (supernatant) of 500 mg L-1 naphthalene by Pseudomonas sp. strain SA3 was studied on V. radiata till 168 h. The growth parameters of mung bean seedlings exposed to treated naphthalene solution were statistically similar to distilled water but a twofold decrease when exposed to untreated naphthalene solution. Further, through the soil microcosm study, the naphthalene degradation by pure colonies of Pseudomonas sp. strain SA3 was 6.8% higher as compared to when the natural microflora was mixed with Pseudomonas sp. strain SA3. Further naphthalene degradation by a microcosm model revealed that with an increased concentration of glucose, the carbon dioxide trap rate decreases.
Collapse
Affiliation(s)
- Sushma Rani Tirkey
- Academy of Scientific and Innovative Research Headquarters, CSIR-HRDC Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad, 201002, India.,Applied Phycology and Biotechnology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364002, India
| | - Shristi Ram
- Department of Microbiology, School of Basic and Applied Sciences, Dayananda Sagar University, Bengaluru, 560111, India
| | - Madhusree Mitra
- Academy of Scientific and Innovative Research Headquarters, CSIR-HRDC Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad, 201002, India.,Applied Phycology and Biotechnology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364002, India
| | - Sandhya Mishra
- Applied Phycology and Biotechnology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364002, India.
| |
Collapse
|
6
|
Zhang Q, Zhang X, Yang B, Liu S, Wen M, Bao L, Jiang L. Development of a highly efficient in-tube solid-phase microextraction system coupled with UHPLC-MS/MS for analyzing trace hydroxyl polycyclic aromatic hydrocarbons in biological samples. J Sep Sci 2021; 45:919-928. [PMID: 34923746 DOI: 10.1002/jssc.202100751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/08/2021] [Accepted: 12/11/2021] [Indexed: 12/20/2022]
Abstract
Hydroxyl polycyclic aromatic hydrocarbons are considered active mutagenic and carcinogenic substances and are found in extremely low levels (ng/g) in biological samples. As a result, their determination in urine and blood samples is challenging, and a sensitive and effective method for the analysis of trace hydroxyl polycyclic aromatic hydrocarbons in complex biological matrices is required. In this work, a novel macroporous in-tube solid-phase microextraction monolith was prepared via a thiol-yne click reaction, and a highly efficient analytical method based on in-tube solid-phase microextraction coupled with UHPLC-MS/MS was developed to determine hydroxyl polycyclic aromatic hydrocarbons with low detection limits of 0.137-11.0 ng/L in complex biological samples. Four hydroxyl polycyclic aromatic hydrocarbons, namely, 2-hydroxyanthraquinone, 1-hydroxypyrene, 1,8-dihydroxyanthraquinone, and 6-hydroxychrysene, were determined in the urine samples of smokers, non-smokers, and whole blood samples of mice. Satisfactory recoveries were achieved in the range of 83.1-113% with relative standard deviations of 3.2-9.7%. It was found that implementation of the macroporous monolith gave a highly efficient approach for enriching trace hydroxyl polycyclic aromatic hydrocarbons in biological samples.
Collapse
Affiliation(s)
- Qianchun Zhang
- School of Biology and Chemistry, Key Laboratory for Analytical Science of Food and Environment Pollution of Qian Xi Nan, Xingyi Normal University for Nationalities, Xingyi, P. R. China
| | - Xiaolan Zhang
- School of Biology and Chemistry, Key Laboratory for Analytical Science of Food and Environment Pollution of Qian Xi Nan, Xingyi Normal University for Nationalities, Xingyi, P. R. China
| | - Bingnian Yang
- School of Biology and Chemistry, Key Laboratory for Analytical Science of Food and Environment Pollution of Qian Xi Nan, Xingyi Normal University for Nationalities, Xingyi, P. R. China
| | - Shan Liu
- School of Biology and Chemistry, Key Laboratory for Analytical Science of Food and Environment Pollution of Qian Xi Nan, Xingyi Normal University for Nationalities, Xingyi, P. R. China
| | - Ming Wen
- School of Biology and Chemistry, Key Laboratory for Analytical Science of Food and Environment Pollution of Qian Xi Nan, Xingyi Normal University for Nationalities, Xingyi, P. R. China
| | - Linchun Bao
- Clinical Laboratory, Qian Xi Nan People's Hospital, Xingyi, P. R. China
| | - Li Jiang
- School of Biology and Chemistry, Key Laboratory for Analytical Science of Food and Environment Pollution of Qian Xi Nan, Xingyi Normal University for Nationalities, Xingyi, P. R. China
| |
Collapse
|
7
|
Sleight TW, Sexton CN, Mpourmpakis G, Gilbertson LM, Ng CA. A Classification Model to Identify Direct-Acting Mutagenic Polycyclic Aromatic Hydrocarbon Transformation Products. Chem Res Toxicol 2021; 34:2273-2286. [PMID: 34662518 DOI: 10.1021/acs.chemrestox.1c00187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are a complex group of environmental contaminants, many having long environmental half-lives. As these compounds degrade, the changes in their structure can result in a substantial increase in mutagenicity compared to the parent compound. Over time, each individual PAH can potentially degrade into several thousand unique transformation products, creating a complex, constantly evolving set of intermediates. Microbial degradation is the primary mechanism of their transformation and ultimate removal from the environment, and this process can result in mutagenic activation similar to the metabolic activation that can occur in multicellular organisms. The diversity of the potential intermediate structures in PAH-contaminated environments renders hazard assessment difficult for both remediation professionals and regulators. A mixture of structural and energetic descriptors has proven effective in existing studies for classifying which PAH transformation products will be mutagenic. However, most existing studies of environmental PAH mutagens primarily focus on nitrogenated derivatives, which are prevalent in the atmosphere and not as relevant in soil. Additionally, PAH products commonly found in the environment can range from as large as five rings to as small as a single ring, requiring a broadly inclusive methodology to comprehensively evaluate mutagenic potential. We developed a combination of supervised and unsupervised machine learning methods to predict environmentally induced PAH mutagenicity with improved performance over currently available tools. K-means clustering with principal component analysis allows us to identify molecular clusters that we hypothesize to have similar mechanisms of action. Recursive feature elimination identifies the most influential descriptors. The cluster-specific regression outperforms available classifiers in predicting direct-acting mutagens resulting from the microbial biodegradation of PAHs and provides direction for future studies evaluating the environmental hazards resulting from PAH biodegradation.
Collapse
Affiliation(s)
- Trevor W Sleight
- Civil & Environmental Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Caitlin N Sexton
- Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Giannis Mpourmpakis
- Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Leanne M Gilbertson
- Civil & Environmental Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States.,Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Carla A Ng
- Civil & Environmental Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States.,Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| |
Collapse
|