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Verma H, Kaur J, Thakur V, Dhingra GG, Lal R. Comprehensive review on Haloalkane dehalogenase (LinB): a β-hexachlorocyclohexane (HCH) degrading enzyme. Arch Microbiol 2024; 206:380. [PMID: 39143366 DOI: 10.1007/s00203-024-04105-1] [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: 06/05/2024] [Revised: 08/02/2024] [Accepted: 08/05/2024] [Indexed: 08/16/2024]
Abstract
Haloalkane dehalogenase, LinB, is a member of the α/β hydrolase family of enzymes. It has a wide range of halogenated substrates, but, has been mostly studied in context of degradation of hexachlorocyclohexane (HCH) isomers, especially β-HCH (5-12% of total HCH isomers), which is the most recalcitrant and persistent among all the HCH isomers. LinB was identified to directly act on β-HCH in a one or two step transformation which decreases its toxicity manifold. Thereafter, many studies focused on LinB including its structure determination using X-ray crystallographic studies, structure comparison with other haloalkane dehalogenases, substrate specificity and kinetic studies, protein engineering and site-directed mutagenesis studies in search of better catalytic activity of the enzyme. LinB was mainly identified and characterized in bacteria belonging to sphingomonads. Detailed sequence comparison of LinB from different sphingomonads further revealed the residues critical for its activity and ability to catalyze either one or two step transformation of β-HCH. Association of LinB with IS6100 elements is also being discussed in detail in sphingomonads. In this review, we summarized vigorous efforts done by different research groups on LinB for developing better bioremediation strategies against HCH contamination. Also, kinetic studies, protein engineering and site directed mutagenesis studies discussed here forms the basis of further exploration of LinB's role as an efficient enzyme in bioremediation projects.
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Affiliation(s)
| | - Jasvinder Kaur
- Gargi College, University of Delhi, Delhi, 110007, India
| | | | | | - Rup Lal
- INSA, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi, 110019, India.
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2
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Zhang D, Jiang J, Shi H, Lu L, Zhang M, Lin J, Lü T, Huang J, Zhong Z, Zhao H. Nonionic surfactant Tween 80-facilitated bacterial transport in porous media: A nonmonotonic concentration-dependent performance, mechanism, and machine learning prediction. ENVIRONMENTAL RESEARCH 2024; 251:118670. [PMID: 38493849 DOI: 10.1016/j.envres.2024.118670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/06/2024] [Accepted: 03/09/2024] [Indexed: 03/19/2024]
Abstract
The surfactant-enhanced bioremediation (SEBR) of organic-contaminated soil is a promising soil remediation technology, in which surfactants not only mobilize pollutants, but also alter the mobility of bacteria. However, the bacterial response and underlying mechanisms remain unclear. In this study, the effects and mechanisms of action of a selected nonionic surfactant (Tween 80) on Pseudomonas aeruginosa transport in soil and quartz sand were investigated. The results showed that bacterial migration in both quartz sand and soil was significantly enhanced with increasing Tween 80 concentration, and the greatest migration occurred at a critical micelle concentration (CMC) of 4 for quartz sand and 30 for soil, with increases of 185.2% and 27.3%, respectively. The experimental results and theoretical analysis indicated that Tween 80-facilitated bacterial migration could be mainly attributed to competition for soil/sand surface sorption sites between Tween 80 and bacteria. The prior sorption of Tween 80 onto sand/soil could diminish the available sorption sites for P. aeruginosa, resulting in significant decreases in deposition parameters (70.8% and 33.3% decrease in KD in sand and soil systems, respectively), thereby increasing bacterial transport. In the bacterial post-sorption scenario, the subsequent injection of Tween 80 washed out 69.8% of the bacteria retained in the quartz sand owing to the competition of Tween 80 with pre-sorbed bacteria, as compared with almost no bacteria being eluted by NaCl solution. Several machine learning models have been employed to predict Tween 80-faciliated bacterial transport. The results showed that back-propagation neural network (BPNN)-based machine learning could predict the transport of P. aeruginosa through quartz sand with Tween 80 in-sample (2 CMC) and out-of-sample (10 CMC) with errors of 0.79% and 3.77%, respectively. This study sheds light on the full understanding of SEBR from the viewpoint of degrader facilitation.
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Affiliation(s)
- Dong Zhang
- College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou, 310018, Zhejiang, China
| | - Jiacheng Jiang
- College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou, 310018, Zhejiang, China
| | - Huading Shi
- Technical Centre for Soil, Agricultural and Rural Ecology and Environment, Ministry of Ecology and Environment, Beijing, 100012, China.
| | - Li Lu
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310018, Zhejiang, China
| | - Ming Zhang
- Department of Environmental Science and Engineering, China Jiliang University, Hangzhou, 310018, Zhejiang, China
| | - Jun Lin
- Institute of Carbon Neutrality and New Energy, School of Electronics and Information, Hangzhou Dianzi University, Hangzhou, 310018, Zhejiang, China
| | - Ting Lü
- College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou, 310018, Zhejiang, China
| | - Jingang Huang
- College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou, 310018, Zhejiang, China
| | - Zhishun Zhong
- Guangdong Jiandi Agriculture Technology Co. Ltd., Foshan, Guangdong, 528200, China
| | - Hongting Zhao
- College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou, 310018, Zhejiang, China.
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Guo Y, Askari N, Smets I, Appels L. A review on co-metabolic degradation of organic micropollutants during anaerobic digestion: Linkages between functional groups and digestion stages. WATER RESEARCH 2024; 256:121598. [PMID: 38663209 DOI: 10.1016/j.watres.2024.121598] [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: 03/13/2024] [Accepted: 04/09/2024] [Indexed: 05/12/2024]
Abstract
The emerging presence of organic micropollutants (OMPs) in water bodies produced by human activities is a source of growing concern due to their environmental and health issues. Biodegradation is a widely employed treatment method for OMPs in wastewater owing to its high efficiency and low operational cost. Compared to aerobic degradation, anaerobic degradation has numerous advantages, including energy efficiency and superior performance for certain recalcitrant compounds. Nonetheless, the low influent concentrations of OMPs in wastewater treatment plants (WWTPs) and their toxicity make it difficult to support the growth of microorganisms. Therefore, co-metabolism is a promising mechanism for OMP biodegradation in which co-substrates are added as carbon and energy sources and stimulate increased metabolic activity. Functional microorganisms and enzymes exhibit significant variations at each stage of anaerobic digestion affecting the environment for the degradation of OMPs with different structural properties, as these factors substantially influence OMPs' biodegradability and transformation pathways. However, there is a paucity of literature reviews that explicate the correlations between OMPs' chemical structure and specific metabolic conditions. This study provides a comprehensive review of the co-metabolic processes which are favored by each stage of anaerobic digestion and attempts to link various functional groups to their favorable degradation pathways. Furthermore, potential co-metabolic processes and strategies that can enhance co-digestion are also identified, providing directions for future research.
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Affiliation(s)
- Yutong Guo
- KU Leuven, Department of Chemical Engineering, Chemical and Biochemical Reactor Engineering and Safety (CREaS) Campus De Nayer, Jan Pieter De Nayerlaan 5, Sint-Katelijne-Waver 2860, Belgium
| | - Najmeh Askari
- KU Leuven, Department of Chemical Engineering, Chemical and Biochemical Reactor Engineering and Safety (CREaS) Campus De Nayer, Jan Pieter De Nayerlaan 5, Sint-Katelijne-Waver 2860, Belgium
| | - Ilse Smets
- KU Leuven, Department of Chemical Engineering, Chemical and Biochemical Reactor Engineering and Safety (CREaS), Celestijnenlaan 200F box 2424, Heverlee 3001, Belgium
| | - Lise Appels
- KU Leuven, Department of Chemical Engineering, Chemical and Biochemical Reactor Engineering and Safety (CREaS) Campus De Nayer, Jan Pieter De Nayerlaan 5, Sint-Katelijne-Waver 2860, Belgium.
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Ibbini J, Al-Kofahi S, Davis LC, Alrousan D, Elshebli M. Investigating the Potential of Fusarium solani and Phanerochaete chrysosporium in the Removal of 2,4,6-TNT. Appl Biochem Biotechnol 2024; 196:2713-2727. [PMID: 37782454 DOI: 10.1007/s12010-023-04735-z] [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] [Accepted: 09/15/2023] [Indexed: 10/03/2023]
Abstract
Past and recent applications of 2,4,6-trinitrotoluene (TNT) in military and civilian industries have led to contamination of soil and marine ecosystems. Among various TNT remediation techniques, biological remediation is widely accepted for its sustainability, low cost, and scalable applications. This study was designed to isolate a fungus strain from a TNT-contaminated soil to investigate its tolerance to and potential for removal of TNT. Thus, a soil column with a history of periodic TNT amendment was used to isolate dominant strains of fungi Fusarium solani isolate, which is not commonly reported for TNT mineralization and was found predominant in the subsurface layer of the TNT-amended soil. F. solani was investigated for TNT concentration tolerance at 30, 70, and 100 mg/L on agar plates and for TNT removal in liquid cultures at the same given concentrations. F. solani activity was compared with that of a reference soil-born fungus that has been intensively studied for TNT removal (Phanerochaete chrysosporium) obtained from the American Type Culture Collection. On agar media, F. solani showed a larger colony diameter than P. chrysosporium at similar TNT concentrations, indicating its high potential to tolerate toxic levels of TNT as found in contaminated sites. In the liquid culture medium, F. solani was able to significantly produce higher biomass than P. chrysosporium in all TNT concentrations. The TNT removal percentage from the liquid culture at the highest TNT concentration of 100 mg/L reached about 85% with F. solani, while P. chrysosporium was no better than 25% at the end of an 84-h incubation period. Results indicate a significant potential of using F. solani in the bioremediation of polluted TNT soils that overcome the high concentration barrier in the field. However, further investigation is needed to identify enzymatic potential and the most effective applications and possible limitations of this method on a large scale.
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Affiliation(s)
- Jwan Ibbini
- Department of Land Management and Environment, Prince El-Hassan Bin Talal Faculty of Natural Resources and Environment, The Hashemite University, Zarqa, Jordan
| | - Salman Al-Kofahi
- Department of Land Management and Environment, Prince El-Hassan Bin Talal Faculty of Natural Resources and Environment, The Hashemite University, Zarqa, Jordan
| | - Lawrence C Davis
- Department of Biochemistry, Kansas State University, Manhattan, KS, USA
| | - Dheaya Alrousan
- Department of Water Management and Environment, Prince El-Hassan Bin Talal Faculty of Natural Resources and Environment, The Hashemite University, Zarqa, Jordan
| | - Marwa Elshebli
- Boone Pickens School of Geology, Oklahoma State University, Stillwater, OK, USA.
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Umar A, Mubeen M, Ali I, Iftikhar Y, Sohail MA, Sajid A, Kumar A, Solanki MK, Kumar Divvela P, Zhou L. Harnessing fungal bio-electricity: a promising path to a cleaner environment. Front Microbiol 2024; 14:1291904. [PMID: 38352061 PMCID: PMC10861785 DOI: 10.3389/fmicb.2023.1291904] [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: 09/10/2023] [Accepted: 12/20/2023] [Indexed: 02/16/2024] Open
Abstract
Integrating fungi into fuel cell systems presents a promising opportunity to address environmental pollution while simultaneously generating energy. This review explores the innovative concept of constructing wetlands as fuel cells for pollutant degradation, offering a practical and eco-friendly solution to pollution challenges. Fungi possess unique capabilities in producing power, fuel, and electricity through metabolic processes, drawing significant interest for applications in remediation and degradation. Limited data exist on fungi's ability to generate electricity during catalytic reactions involving various enzymes, especially while remediating pollutants. Certain species, such as Trametes versicolor, Ganoderma lucidum, Galactomyces reessii, Aspergillus spp., Kluyveromyce smarxianus, and Hansenula anomala, have been reported to generate electricity at 1200 mW/m3, 207 mW/m2, 1,163 mW/m3, 438 mW/m3, 850,000 mW/m3, and 2,900 mW/m3, respectively. Despite the eco-friendly potential compared to conventional methods, fungi's role remains largely unexplored. This review delves into fungi's exceptional potential as fuel cell catalysts, serving as anodic or cathodic agents to mitigate land, air, and water pollutants while simultaneously producing fuel and power. Applications cover a wide range of tasks, and the innovative concept of wetlands designed as fuel cells for pollutant degradation is discussed. Cost-effectiveness may vary depending on specific contexts and applications. Fungal fuel cells (FFCs) offer a versatile and innovative solution to global challenges, addressing the increasing demand for alternative bioenergy production amid population growth and expanding industrial activities. The mechanistic approach of fungal enzymes via microbial combinations and electrochemical fungal systems facilitates the oxidation of organic substrates, oxygen reduction, and ion exchange membrane orchestration of essential reactions. Fungal laccase plays a crucial role in pollutant removal and monitoring environmental contaminants. Fungal consortiums show remarkable potential in fine-tuning FFC performance, impacting both power generation and pollutant degradation. Beyond energy generation, fungal cells effectively remove pollutants. Overall, FFCs present a promising avenue to address energy needs and mitigate pollutants simultaneously.
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Affiliation(s)
- Aisha Umar
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Institute of Botany, University of the Punjab, Lahore, Pakistan
| | - Mustansar Mubeen
- Department of Plant Pathology, College of Agriculture, University of Sargodha, Sargodha, Pakistan
| | - Iftikhar Ali
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, United States
| | - Yasir Iftikhar
- Department of Plant Pathology, College of Agriculture, University of Sargodha, Sargodha, Pakistan
| | - Muhammad Aamir Sohail
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Ashara Sajid
- Department of Plant Pathology, College of Agriculture, University of Sargodha, Sargodha, Pakistan
| | - Ajay Kumar
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | - Manoj Kumar Solanki
- Department of Life Sciences and Biological Sciences, IES University, Bhopal, Madhya Pradesh, India
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | | | - Lei Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Wang X, Teng Y, Wang X, Xu Y, Li R, Sun Y, Dai S, Hu W, Wang H, Li Y, Fang Y, Luo Y. Nitrogen transfer and cross-feeding between Azotobacter chroococcum and Paracoccus aminovorans promotes pyrene degradation. THE ISME JOURNAL 2023; 17:2169-2181. [PMID: 37775536 PMCID: PMC10689768 DOI: 10.1038/s41396-023-01522-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 10/01/2023]
Abstract
Nitrogen is a limiting nutrient for degraders function in hydrocarbon-contaminated environments. Biological nitrogen fixation by diazotrophs is a natural solution for supplying bioavailable nitrogen. Here, we determined whether the diazotroph Azotobacter chroococcum HN can provide nitrogen to the polycyclic aromatic hydrocarbon-degrading bacterium Paracoccus aminovorans HPD-2 and further explored the synergistic interactions that facilitate pyrene degradation in nitrogen-deprived environments. We found that A. chroococcum HN and P. aminovorans HPD-2 grew and degraded pyrene more quickly in co-culture than in monoculture. Surface-enhanced Raman spectroscopy combined with 15N stable isotope probing (SERS - 15N SIP) demonstrated that A. chroococcum HN provided nitrogen to P. aminovorans HPD-2. Metabolite analysis and feeding experiments confirmed that cross-feeding occurred between A. chroococcum HN and P. aminovorans HPD-2 during pyrene degradation. Transcriptomic and metabolomic analyses further revealed that co-culture significantly upregulated key pathways such as nitrogen fixation, aromatic compound degradation, protein export, and the TCA cycle in A. chroococcum HN and quorum sensing, aromatic compound degradation and ABC transporters in P. aminovorans HPD-2. Phenotypic and fluorescence in situ hybridization (FISH) assays demonstrated that A. chroococcum HN produced large amounts of biofilm and was located at the bottom of the biofilm in co-culture, whereas P. aminovorans HPD-2 attached to the surface layer and formed a bridge-like structure with A. chroococcum HN. This study demonstrates that distinct syntrophic interactions occur between A. chroococcum HN and P. aminovorans HPD-2 and provides support for their combined use in organic pollutant degradation in nitrogen-deprived environments.
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Affiliation(s)
- Xia Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
- University of the Chinese Academy of Sciences, 100049, Beijing, China.
| | - Xiaomi Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Yongfeng Xu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Ran Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Yi Sun
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Shixiang Dai
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Wenbo Hu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Hongzhe Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Yanning Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Yan Fang
- University of the Chinese Academy of Sciences, 100049, Beijing, China
- Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Yongming Luo
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
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Buffi M, Cailleau G, Kuhn T, Li Richter XY, Stanley CE, Wick LY, Chain PS, Bindschedler S, Junier P. Fungal drops: a novel approach for macro- and microscopic analyses of fungal mycelial growth. MICROLIFE 2023; 4:uqad042. [PMID: 37965130 PMCID: PMC10642649 DOI: 10.1093/femsml/uqad042] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023]
Abstract
This study presents an inexpensive approach for the macro- and microscopic observation of fungal mycelial growth. The 'fungal drops' method allows to investigate the development of a mycelial network in filamentous microorganisms at the colony and hyphal scales. A heterogeneous environment is created by depositing 15-20 µl drops on a hydrophobic surface at a fixed distance. This system is akin to a two-dimensional (2D) soil-like structure in which aqueous-pockets are intermixed with air-filled pores. The fungus (spores or mycelia) is inoculated into one of the drops, from which hyphal growth and exploration take place. Hyphal structures are assessed at different scales using stereoscopic and microscopic imaging. The former allows to evaluate the local response of regions within the colony (modular behaviour), while the latter can be used for fractal dimension analyses to describe the hyphal network architecture. The method was tested with several species to underpin the transferability to multiple species. In addition, two sets of experiments were carried out to demonstrate its use in fungal biology. First, mycelial reorganization of Fusarium oxysporum was assessed as a response to patches containing different nutrient concentrations. Second, the effect of interactions with the soil bacterium Pseudomonas putida on habitat colonization by the same fungus was assessed. This method appeared as fast and accessible, allowed for a high level of replication, and complements more complex experimental platforms. Coupled with image analysis, the fungal drops method provides new insights into the study of fungal modularity both macroscopically and at a single-hypha level.
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Affiliation(s)
- Matteo Buffi
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Guillaume Cailleau
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Thierry Kuhn
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
- Laboratory of Eco-Ethology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Xiang-Yi Li Richter
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
- Laboratory of Eco-Ethology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Claire E Stanley
- Department of Bioengineering, Imperial College London, B304, Bessemer Building, South Kensington Campus, SW7 2AZ, London, United Kingdom
| | - Lukas Y Wick
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Patrick S Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, P.O. Box 1663, NM 87545, United States
| | - Saskia Bindschedler
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
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Tyumina E, Subbotina M, Polygalov M, Tyan S, Ivshina I. Ketoprofen as an emerging contaminant: occurrence, ecotoxicity and (bio)removal. Front Microbiol 2023; 14:1200108. [PMID: 37608946 PMCID: PMC10441242 DOI: 10.3389/fmicb.2023.1200108] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/25/2023] [Indexed: 08/24/2023] Open
Abstract
Ketoprofen, a bicyclic non-steroidal anti-inflammatory drug commonly used in human and veterinary medicine, has recently been cited as an environmental contaminant that raises concerns for ecological well-being. It poses a growing threat due to its racemic mixture, enantiomers, and transformation products, which have ecotoxicological effects on various organisms, including invertebrates, vertebrates, plants, and microorganisms. Furthermore, ketoprofen is bioaccumulated and biomagnified throughout the food chain, threatening the ecosystem function. Surprisingly, despite these concerns, ketoprofen is not currently considered a priority substance. While targeted eco-pharmacovigilance for ketoprofen has been proposed, data on ketoprofen as a pharmaceutical contaminant are limited and incomplete. This review aims to provide a comprehensive summary of the most recent findings (from 2017 to March 2023) regarding the global distribution of ketoprofen in the environment, its ecotoxicity towards aquatic animals and plants, and available removal methods. Special emphasis is placed on understanding how ketoprofen affects microorganisms that play a pivotal role in Earth's ecosystems. The review broadly covers various approaches to ketoprofen biodegradation, including whole-cell fungal and bacterial systems as well as enzyme biocatalysts. Additionally, it explores the potential of adsorption by algae and phytoremediation for removing ketoprofen. This review will be of interest to a wide range of readers, including ecologists, microbiologists, policymakers, and those concerned about pharmaceutical pollution.
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Affiliation(s)
- Elena Tyumina
- Perm Federal Research Center of the Ural Branch of the Russian Academy of Sciences, Perm, Russia
- Microbiology and Immunology Department, Perm State University, Perm, Russia
| | - Maria Subbotina
- Perm Federal Research Center of the Ural Branch of the Russian Academy of Sciences, Perm, Russia
- Microbiology and Immunology Department, Perm State University, Perm, Russia
| | - Maxim Polygalov
- Perm Federal Research Center of the Ural Branch of the Russian Academy of Sciences, Perm, Russia
- Microbiology and Immunology Department, Perm State University, Perm, Russia
| | - Semyon Tyan
- Perm Federal Research Center of the Ural Branch of the Russian Academy of Sciences, Perm, Russia
- Microbiology and Immunology Department, Perm State University, Perm, Russia
| | - Irina Ivshina
- Perm Federal Research Center of the Ural Branch of the Russian Academy of Sciences, Perm, Russia
- Microbiology and Immunology Department, Perm State University, Perm, Russia
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9
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Villalobos-Escobedo JM, Mercado-Esquivias MB, Adams C, Kauffman WB, Malmstrom RR, Deutschbauer AM, Glass NL. Genome-wide fitness profiling reveals molecular mechanisms that bacteria use to interact with Trichoderma atroviride exometabolites. PLoS Genet 2023; 19:e1010909. [PMID: 37651474 PMCID: PMC10516422 DOI: 10.1371/journal.pgen.1010909] [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: 04/23/2023] [Revised: 09/22/2023] [Accepted: 08/07/2023] [Indexed: 09/02/2023] Open
Abstract
Trichoderma spp. are ubiquitous rhizosphere fungi capable of producing several classes of secondary metabolites that can modify the dynamics of the plant-associated microbiome. However, the bacterial-fungal mechanisms that mediate these interactions have not been fully characterized. Here, a random barcode transposon-site sequencing (RB-TnSeq) approach was employed to identify bacterial genes important for fitness in the presence of Trichoderma atroviride exudates. We selected three rhizosphere bacteria with RB-TnSeq mutant libraries that can promote plant growth: the nitrogen fixers Klebsiella michiganensis M5aI and Herbaspirillum seropedicae SmR1, and Pseudomonas simiae WCS417. As a non-rhizosphere species, Pseudomonas putida KT2440 was also included. From the RB-TnSeq data, nitrogen-fixing bacteria competed mainly for iron and required the siderophore transport system TonB/ExbB for optimal fitness in the presence of T. atroviride exudates. In contrast, P. simiae and P. putida were highly dependent on mechanisms associated with membrane lipid modification that are required for resistance to cationic antimicrobial peptides (CAMPs). A mutant in the Hog1-MAP kinase (Δtmk3) gene of T. atroviride showed altered expression patterns of many nonribosomal peptide synthetase (NRPS) biosynthetic gene clusters with potential antibiotic activity. In contrast to exudates from wild-type T. atroviride, bacterial mutants containing lesions in genes associated with resistance to antibiotics did not show fitness defects when RB-TnSeq libraries were exposed to exudates from the Δtmk3 mutant. Unexpectedly, exudates from wild-type T. atroviride and the Δtmk3 mutant rescued purine auxotrophic mutants of H. seropedicae, K. michiganensis and P. simiae. Metabolomic analysis on exudates from wild-type T. atroviride and the Δtmk3 mutant showed that both strains excrete purines and complex metabolites; functional Tmk3 is required to produce some of these metabolites. This study highlights the complex interplay between Trichoderma-metabolites and soil bacteria, revealing both beneficial and antagonistic effects, and underscoring the intricate and multifaceted nature of this relationship.
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Affiliation(s)
- José Manuel Villalobos-Escobedo
- Plant and Microbial Biology Department, The University of California, Berkeley, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Maria Belen Mercado-Esquivias
- Plant and Microbial Biology Department, The University of California, Berkeley, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Catharine Adams
- Plant and Microbial Biology Department, The University of California, Berkeley, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - W. Berkeley Kauffman
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Rex R. Malmstrom
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Adam M. Deutschbauer
- Plant and Microbial Biology Department, The University of California, Berkeley, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - N. Louise Glass
- Plant and Microbial Biology Department, The University of California, Berkeley, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
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Taglialegna A. Fungi feed bacteria for biodegradation. Nat Rev Microbiol 2023; 21:220. [PMID: 36792888 DOI: 10.1038/s41579-023-00869-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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