1
|
Amirbekov A, Vrchovecka S, Riha J, Petrik I, Friedecky D, Novak O, Cernik M, Hrabak P, Sevcu A. Assessing HCH isomer uptake in Alnus glutinosa: implications for phytoremediation and microbial response. Sci Rep 2024; 14:4187. [PMID: 38378833 PMCID: PMC10879209 DOI: 10.1038/s41598-024-54235-1] [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: 12/06/2023] [Accepted: 02/10/2024] [Indexed: 02/22/2024] Open
Abstract
Although the pesticide hexachlorocyclohexane (HCH) and its isomers have long been banned, their presence in the environment is still reported worldwide. In this study, we investigated the bioaccumulation potential of α, β, and δ hexachlorocyclohexane (HCH) isomers in black alder saplings (Alnus glutinosa) to assess their environmental impact. Each isomer, at a concentration of 50 mg/kg, was individually mixed with soil, and triplicate setups, including a control without HCH, were monitored for three months with access to water. Gas chromatography-mass spectrometry revealed the highest concentrations of HCH isomers in roots, decreasing towards branches and leaves, with δ-HCH exhibiting the highest uptake (roots-14.7 µg/g, trunk-7.2 µg/g, branches-1.53 µg/g, leaves-1.88 µg/g). Interestingly, α-HCH was detected in high concentrations in β-HCH polluted soil. Phytohormone analysis indicated altered cytokinin, jasmonate, abscisate, and gibberellin levels in A. glutinosa in response to HCH contamination. In addition, amplicon 16S rRNA sequencing was used to study the rhizosphere and soil microbial community. While rhizosphere microbial populations were generally similar in all HCH isomer samples, Pseudomonas spp. decreased across all HCH-amended samples, and Tomentella dominated in β-HCH and control rhizosphere samples but was lowest in δ-HCH samples.
Collapse
Affiliation(s)
- Aday Amirbekov
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, 460 01, Liberec, Czech Republic
- Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Technical University of Liberec, 461 17, Liberec, Czech Republic
| | - Stanislava Vrchovecka
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, 460 01, Liberec, Czech Republic
- Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Technical University of Liberec, 461 17, Liberec, Czech Republic
| | - Jakub Riha
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, 460 01, Liberec, Czech Republic
| | - Ivan Petrik
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Faculty of Science, Palacký University Olomouc, 78371, Olomouc, Czech Republic
| | - David Friedecky
- Laboratory for Inherited Metabolic Disorders, Department of Clinical Biochemistry, University Hospital Olomouc and Faculty of Medicine and Dentistry, Palacký University Olomouc, 775 20, Olomouc, Czech Republic
| | - Ondrej Novak
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Faculty of Science, Palacký University Olomouc, 78371, Olomouc, Czech Republic
| | - Miroslav Cernik
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, 460 01, Liberec, Czech Republic
| | - Pavel Hrabak
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, 460 01, Liberec, Czech Republic.
- Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Technical University of Liberec, 461 17, Liberec, Czech Republic.
| | - Alena Sevcu
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, 460 01, Liberec, Czech Republic.
- Faculty of Science, Humanities and Education, Technical University of Liberec, 460 01, Liberec, Czech Republic.
| |
Collapse
|
2
|
Yan PF, Dong S, Manz KE, Woodcock MJ, Liu C, Mezzari MP, Abriola LM, Pennell KD, Cápiro NL. Aerobic biotransformation of 6:2 fluorotelomer sulfonate in soils from two aqueous film-forming foam (AFFF)-impacted sites. WATER RESEARCH 2024; 249:120941. [PMID: 38070347 DOI: 10.1016/j.watres.2023.120941] [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: 07/28/2023] [Revised: 11/14/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024]
Abstract
Although 6:2 fluorotelomer sulfonate (6:2 FTS) is a common ingredient in aqueous film-forming foam (AFFF) formulations, its environmental fate at AFFF-impacted sites remains poorly understood. This study investigated the biotransformation of 6:2 FTS in microcosms prepared with soils collected from two AFFF-impacted sites; the former Loring Air Force Base (AFB) and Robins AFB. The half-life of 6:2 FTS in Loring soil was 43.3 days; while >60 mol% of initially spiked 6:2 FTS remained in Robins soil microcosms after a 224-day incubation. Differences in initial sulfate concentrations and the depletion of sulfate over the incubation likely contributed to the different 6:2 FTS biotransformation rates between the two soils. At day 224, stable transformation products, i.e., C4C7 perfluoroalkyl carboxylates, were formed with combined molar yields of 13.8 mol% and 1.2 mol% in Loring and Robins soils, respectively. Based on all detected transformation products, the biotransformation pathways of 6:2 FTS in the two soils were proposed. Microbial community analysis suggests that Desulfobacterota microorganisms may promote 6:2 FTS biotransformation via more efficient desulfonation. In addition, species from the genus Sphingomonas, which exhibited higher tolerance to elevated concentrations of 6:2 FTS and its biotransformation products, are likely to have contributed to 6:2 FTS biotransformation. This study demonstrates the potential role of biotransformation processes on the fate of 6:2 FTS at AFFF-impacted sites and highlights the need to characterize site biogeochemical properties for improved assessment of 6:2 FTS biotransformation behavior.
Collapse
Affiliation(s)
- Peng-Fei Yan
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA.
| | - Sheng Dong
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | | | | | - Chen Liu
- School of Engineering, Brown University, Providence, RI, USA
| | - Melissa P Mezzari
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Linda M Abriola
- School of Engineering, Brown University, Providence, RI, USA
| | - Kurt D Pennell
- School of Engineering, Brown University, Providence, RI, USA
| | - Natalie L Cápiro
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA.
| |
Collapse
|
3
|
Sharma M, Singh DN, Uttam G, Sharma P, Meena SA, Verma AK, Negi RK. Adaptive evolution of Sphingopyxis sp. MC4 conferred degradation potential for persistent β- and δ-Hexachlorocyclohexane (HCH) isomers. JOURNAL OF HAZARDOUS MATERIALS 2024; 461:132545. [PMID: 37757562 DOI: 10.1016/j.jhazmat.2023.132545] [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: 02/20/2023] [Revised: 09/09/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023]
Abstract
Hexachlorocyclohexane (HCH), an organochlorine pesticide imposes several harmful impacts on the ecosystem. β- and δ-isomers of HCH are highly toxic, persistent, and recalcitrant to biodegradation, slow and incomplete degradation of β- and δ- isomers have been reported in a few strains. We have isolated a strain designated as Sphingopyxis strain MC4 that can tolerate and degrade high concentrations of α-, β-, γ- and δ-HCH isomers. To date, no other Sphingopyxis strain has been reported to degrade β- and δ-isomers. To understand the underlying genetic makeup contributing to adaptations, the whole genome of strain MC4 was sequenced. Comparative genome analysis showed that strain MC4 harbors the complete pathway (lin genes) required for HCH degradation. Genetic footprints such as presence of lin genes on genomic islands, IS6100 elements in close proximity of lin genes, and synteny in lin flanking regions with other strains reflects the horizontal gene transfer in strain MC4. Positive selection and HGT drive the adaptive evolution of strain MC4 under the pressure of HCH contamination that it experienced in its surrounding niche. In silico analyses showed efficient binding of β- and δ-isomers with enzymes leading to rapid degradation that need further validation by cloning and biochemical experiments.
Collapse
Affiliation(s)
- Monika Sharma
- Department of Zoology, University of Delhi, Delhi 110007, India
| | - Durgesh Narain Singh
- Department of Zoology, University of Delhi, Delhi 110007, India; BioNEST-BHU, InnoResTech Foundation, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Gunjan Uttam
- Zoology section, MMV, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Poonam Sharma
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Shivam A Meena
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Akhilesh K Verma
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Ram Krishan Negi
- Department of Zoology, University of Delhi, Delhi 110007, India.
| |
Collapse
|
4
|
Amirbekov A, Strojsova M, Nemecek J, Riha J, Hrabak P, Arias C, Sevcu A, Černík M. Biodiversity in wetland+ system: a passive solution for HCH dump effluents. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2023; 88:3095-3109. [PMID: 38154796 PMCID: wst_2023_395 DOI: 10.2166/wst.2023.395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2023]
Abstract
The hexachlorocyclohexane isomers (HCH) are long-banned pesticides. Even though their use has been prohibited for decades, their presence in the environment is still reported worldwide. Wetland + is a registered trademark of the remedial treatment technology consisting of an aerobic sedimentary tank, a permeable reactive barrier, a biosorption system, and an aerobic wetland. This proven method combines a reductive treatment known from PRBs with the natural wetland self-cleaning processes. The average efficiency of the system is 96.8% for chlorobenzenes (ClB) and 81.7% for HCH, during the first 12 months of the system operation. The presence of the genes encoding enzymes involved in the degradation of the HCH compounds indicates that the removal of HCH and ClB occurs not only by chemical removal but also through aerobic and anaerobic combining biodegradation. Changes in abundance and the composition of the diatom community were found to be suitable indicators of the water quality and of the impact of the Wetland + operation on the water ecosystem. The system's annual operation exhibited a markedly higher number of diatom species in the closing profiles of the Ostrovský Creek, the Wetland + effluent recipient.
Collapse
Affiliation(s)
- Aday Amirbekov
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 7, Liberec 460 01, Czech Republic E-mail:
| | - Martina Strojsova
- Faculty of Science, Humanities and Education, Technical University of Liberec, Trebízskeho 1244/2, Liberec 460 01, Czech Republic
| | - Jan Nemecek
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 7, Liberec 460 01, Czech Republic
| | - Jakub Riha
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 7, Liberec 460 01, Czech Republic
| | - Pavel Hrabak
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 7, Liberec 460 01, Czech Republic
| | - Carlos Arias
- Department of Biology, Aquatic Biology, Ole Worms Allé 1, Aarhus University, Aarhus C 8000, Denmark; WATEC Aarhus University Centre for Water Technology, Aarhus University, Ole Worms Allé 3, Building 1171, Aarhus C 8000, Denmark
| | - Alena Sevcu
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 7, Liberec 460 01, Czech Republic; Faculty of Science, Humanities and Education, Technical University of Liberec, Trebízskeho 1244/2, Liberec 460 01, Czech Republic
| | - Miroslav Černík
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 7, Liberec 460 01, Czech Republic
| |
Collapse
|
5
|
Guío J, Fillat MF, Peleato ML, Sevilla E. Responses of Anabaena sp. PCC7120 to lindane: Physiological effects and differential expression of potential lin genes. Microbiologyopen 2023; 12:e1355. [PMID: 37379427 DOI: 10.1002/mbo3.1355] [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: 03/09/2023] [Revised: 04/10/2023] [Accepted: 04/13/2023] [Indexed: 06/30/2023] Open
Abstract
Lindane (γ-HCH) is an organochlorine pesticide that causes huge environmental concerns worldwide due to its recalcitrance and toxicity. The use of the cyanobacterium Anabaena sp. PCC 7120 in aquatic lindane bioremediation has been suggested but information relative to this process is scarce. In the present work, data relative to the growth, pigment composition, photosynthetic/respiration rate, and oxidative stress response of Anabaena sp. PCC 7120 in the presence of lindane at its solubility limit in water are shown. In addition, lindane degradation experiments revealed almost a total disappearance of lindane in the supernatants of Anabaena sp. PCC 7120 culture after 6 days of incubation. The diminishing in lindane concentration was in concordance with an increase in the levels of trichlorobenzene inside the cells. Furthermore, to identify potential orthologs of the linA, linB, linC, linD, linE, and linR genes from Sphingomonas paucimobilis B90A in Anabaena sp. PCC 7120, a whole genome screening was performed allowing the identification of five putative lin orthologs (all1353 and all0193 putative orthologs of linB, all3836 putative orthologs of linC, and all0352 and alr0353 putative orthologs of linE and linR, respectively) which could be involved in the lindane degradation pathway. Differential expression analysis of these genes in the presence of lindane revealed strong upregulation of one of the potential lin genes of Anabaena sp. PCC 7120.
Collapse
Affiliation(s)
- Jorge Guío
- Departamento de Bioquímica y Biología Molecular y Celular and Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Zaragoza, Spain
| | - Maria F Fillat
- Departamento de Bioquímica y Biología Molecular y Celular and Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Zaragoza, Spain
| | - Maria L Peleato
- Departamento de Bioquímica y Biología Molecular y Celular and Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Zaragoza, Spain
| | - Emma Sevilla
- Departamento de Bioquímica y Biología Molecular y Celular and Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Zaragoza, Spain
| |
Collapse
|
6
|
Li YJ, Chuang CH, Cheng WC, Chen SH, Chen WL, Lin YJ, Lin CY, Shih YH. A metagenomics study of hexabromocyclododecane degradation with a soil microbial community. JOURNAL OF HAZARDOUS MATERIALS 2022; 430:128465. [PMID: 35739659 DOI: 10.1016/j.jhazmat.2022.128465] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/27/2022] [Accepted: 01/27/2022] [Indexed: 06/15/2023]
Abstract
Hexabromocyclododecanes (HBCDs) are globally prevalent and persistent organic pollutants (POPs) listed by the Stockholm Convention in 2013. They have been detected in many environmental media from waterbodies to Plantae and even in the human body. Due to their highly bioaccumulative characterization, they pose an urgent public health issue. Here, we demonstrate that the indigenous microbial community in the agricultural soil in Taiwan could decompose HBCDs with no additional carbon source incentive. The degradation kinetics reached 0.173 day-1 after the first treatment and 0.104 day-1 after second exposure. With additional C-sources, the rate constants decreased to 0.054-0.097 day-1. The hydroxylic debromination metabolites and ring cleavage long-chain alkane metabolites were identified to support the potential metabolic pathways utilized by the soil microbial communities. The metagenome established by Nanopore sequencing showed significant compositional alteration in the soil microbial community after the HBCD treatment. After ranking, comparing relative abundances, and performing network analyses, several novel bacterial taxa were identified to contribute to HBCD biotransformation, including Herbaspirillum, Sphingomonas, Brevundimonas, Azospirillum, Caulobacter, and Microvirga, through halogenated / aromatic compound degradation, glutathione-S-transferase, and hydrolase activity. We present a compelling and applicable approach combining metagenomics research, degradation kinetics, and metabolomics strategies, which allowed us to decipher the natural attenuation and remediation mechanisms of HBCDs.
Collapse
Affiliation(s)
- Yi-Jie Li
- Department of Agricultural Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Chia-Hsien Chuang
- Institute of Information Science, Academia Sinica, No. 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Wen-Chih Cheng
- Institute of Information Science, Academia Sinica, No. 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Shu-Hwa Chen
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University (TMU), No. 250 Wu-Hsing St., Taipei, Taiwan
| | - Wen-Ling Chen
- Department of Agricultural Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan; Institute of Food Safety and Health, College of Public Health, National Taiwan University, No. 17, Xuzhou Rd., Taipei 100, Taiwan; Department of Public Health, College of Public Health, National Taiwan University, No. 17, Xuzhou Rd., Taipei 100, Taiwan
| | - Yu-Jie Lin
- Department of Agricultural Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Chung-Yen Lin
- Institute of Information Science, Academia Sinica, No. 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan.
| | - Yang-Hsin Shih
- Department of Agricultural Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan.
| |
Collapse
|
7
|
Biodegradation of technical hexachlorocyclohexane by Cupriavidus malaysiensis. World J Microbiol Biotechnol 2022; 38:108. [DOI: 10.1007/s11274-022-03284-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/11/2022] [Indexed: 10/18/2022]
|
8
|
Singh V, Srivastava S, Singh N, Srivastava S, Lehri A, Singh N. Study on the characterization of endosulfan-degrading bacterial strains isolated from contaminated rhizospheric soil. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, TOXICOLOGY AND CARCINOGENESIS 2022; 40:68-85. [PMID: 35895931 DOI: 10.1080/26896583.2022.2050155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In the present study, we have isolated endosulfan tolerant bacterial strains from the rhizosphere of plants growing in a pesticide-contaminated area. The tolerance capacities of these strains were tested up to 50,000 µg ml-1 of endosulfan. It was found that out of nineteen, four strains (EAG-EC-12, EAG-EC-13, EAG-EC-14, and EAG-EC-15) were capable of surviving up to 50,000 µg ml-1 endosulfan concentration in the media; thus, these four strains were selected for the characterization. Among four, two strains were identified as Serratia liquefaciens, while the other two strains were Bacillus sp. and Brevibacterium halotolerans. The result shows that growth of strain Serratia liquefaciens 1 and Serratia liquefaciens 2 in treated medium was statistically similar to that of control (cfu 6.8 × 107) after 24 h, while strains Bacillus sp. and Brevibacterium halotolerans have shown growth significantly less than the control. The degradation potential of these strains was analyzed against 100 to 250 µg ml-1 of endosulfan in a Minimal Broth Medium (MBM), and it was recorded that only 9, 2, 7, and 19% of endosulfan (100 µg ml-1) remain after a 72 h incubation period of Bacillus sp., Serratia liquefaciens 1, Serratia liquefaciens 2, and Brevibacterium halotolerans, respectively. This endosulfan removal potential of studied strains was decreased with an increase in concentration of endosulfan.
Collapse
Affiliation(s)
- Vandana Singh
- Central Instrumentation Facility, National Botanical Research Institute, Lucknow, India
| | | | - Namrata Singh
- Eco Auditing Group, National Botanical Research Institute, Lucknow, India
| | - Suchi Srivastava
- Division of Plant Microbe Interaction, National Botanical Research Institute, Lucknow, India
| | - Alok Lehri
- Central Instrumentation Facility, National Botanical Research Institute, Lucknow, India
| | - Nandita Singh
- Eco Auditing Group, National Botanical Research Institute, Lucknow, India
| |
Collapse
|
9
|
Abstract
This study evaluated the efficiency of two biofilter systems, with and without biochar chambers installed, at degrading and removing HCH and its isomers in natural drainage water. The biochar biofilter proved to be 96% efficient at cleaning HCH and its transformation products from drainage water, a significant improvement over classic biofilter that remove, on average, 68% of HCH. Although iron- and sulfur-oxidizing bacteria, such as Gallionella and Sulfuricurvum, were dominant in the biochar bed outflows, they were absent in sediments, which were rich in Simplicispira, Rhodoluna, Rhodoferax, and Flavobacterium. The presence of functional genes involved in the biodegradation of HCH isomers and their byproducts was confirmed in both systems. The high effectiveness of the biochar biofilter displayed in this study should further encourage the use of biochar in water treatment solutions, e.g., for temporary water purification installations during the construction of other long-term wastewater treatment technologies, or even as final solutions at contaminated sites.
Collapse
|
10
|
Mazur A, Grinkevich P, Chaloupkova R, Havlickova P, Kascakova B, Kuty M, Damborsky J, Kuta Smatanova I, Prudnikova T. Structural Analysis of the Ancestral Haloalkane Dehalogenase AncLinB-DmbA. Int J Mol Sci 2021; 22:ijms222111992. [PMID: 34769421 PMCID: PMC8584953 DOI: 10.3390/ijms222111992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/27/2021] [Accepted: 11/02/2021] [Indexed: 11/16/2022] Open
Abstract
Haloalkane dehalogenases (EC 3.8.1.5) play an important role in hydrolytic degradation of halogenated compounds, resulting in a halide ion, a proton, and an alcohol. They are used in biocatalysis, bioremediation, and biosensing of environmental pollutants and also for molecular tagging in cell biology. The method of ancestral sequence reconstruction leads to prediction of sequences of ancestral enzymes allowing their experimental characterization. Based on the sequences of modern haloalkane dehalogenases from the subfamily II, the most common ancestor of thoroughly characterized enzymes LinB from Sphingobium japonicum UT26 and DmbA from Mycobacterium bovis 5033/66 was in silico predicted, recombinantly produced and structurally characterized. The ancestral enzyme AncLinB-DmbA was crystallized using the sitting-drop vapor-diffusion method, yielding rod-like crystals that diffracted X-rays to 1.5 Å resolution. Structural comparison of AncLinB-DmbA with their closely related descendants LinB and DmbA revealed some differences in overall structure and tunnel architecture. Newly prepared AncLinB-DmbA has the highest active site cavity volume and the biggest entrance radius on the main tunnel in comparison to descendant enzymes. Ancestral sequence reconstruction is a powerful technique to study molecular evolution and design robust proteins for enzyme technologies.
Collapse
Affiliation(s)
- Andrii Mazur
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; (A.M.); (P.G.); (P.H.); (B.K.); (M.K.)
| | - Pavel Grinkevich
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; (A.M.); (P.G.); (P.H.); (B.K.); (M.K.)
| | - Radka Chaloupkova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (R.C.); (J.D.)
- Enantis Ltd., Kamenice 771/34, 625 00 Brno, Czech Republic
| | - Petra Havlickova
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; (A.M.); (P.G.); (P.H.); (B.K.); (M.K.)
| | - Barbora Kascakova
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; (A.M.); (P.G.); (P.H.); (B.K.); (M.K.)
| | - Michal Kuty
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; (A.M.); (P.G.); (P.H.); (B.K.); (M.K.)
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (R.C.); (J.D.)
- International Clinical Research Center, St Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Ivana Kuta Smatanova
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; (A.M.); (P.G.); (P.H.); (B.K.); (M.K.)
- Correspondence: (I.K.S.); (T.P.)
| | - Tatyana Prudnikova
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; (A.M.); (P.G.); (P.H.); (B.K.); (M.K.)
- Correspondence: (I.K.S.); (T.P.)
| |
Collapse
|
11
|
Knobloch MC, Schinkel L, Kohler HPE, Mathis F, Kern S, Bleiner D, Heeb NV. Transformation of short-chain chlorinated paraffins and olefins with the bacterial dehalogenase LinB from Sphingobium Indicum - Kinetic models for the homologue-specific conversion of reactive and persistent material. CHEMOSPHERE 2021; 283:131199. [PMID: 34153917 DOI: 10.1016/j.chemosphere.2021.131199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/12/2021] [Accepted: 06/09/2021] [Indexed: 06/13/2023]
Abstract
Structure, reactivity and physico-chemical properties of polyhalogenated compounds determine their up-take, transport, bio-accumulation, transformation and toxicity and their environmental fate. In technical mixtures of chlorinated paraffins (CPs), these properties are distributed due to the presence of thousands of homologues. We hypothesized that roles of CP dehalogenation reactions, catalyzed by the haloalkane dehalogenase LinB, depend on structural properties of the substrates, e.g. chlorination degree and carbon-chain length. We exposed mixtures of chlorinated undecanes, dodecanes and tridecanes in-vitro to LinB from Sphingobium Indicum bacteria. These single-chain CP-materials also contain small amounts of chlorinated olefins (COs), which can be distinct by mathematical deconvolution of respective mass-spectra. With this procedure, we obtained homologue-specific transformation kinetics of substrates differing in saturation degree, chlorination degree and carbon chain-length. For all homologues, two-stage first-order kinetic models were established, which described the faster conversion of reactive material and the slower transformation of more persistent material. Half-lifes of 0.5-3.2 h and 56-162 h were determined for more reactive and more persistent CP-material. Proportions of persistent material increased steadily from 18 to 67% for lower (Cl6) to higher (Cl11) chlorinated paraffins and olefins. Conversion efficiencies decreased with increasing chlorination degree from 97 to 70%. Carbon-chain length had only minor effects on transformation rates. Hence, the conversion was faster and more efficient for lower-chlorinated material, and slower for higher-chlorinated and longer-chained CPs and COs. Current legislation has banned short-chain chlorinated paraffins (SCCPs) and forced a transition to longer-chain CPs. This may be counterproductive with regard to enzymatic transformation with LinB.
Collapse
Affiliation(s)
- Marco C Knobloch
- Laboratory for Advanced Analytical Technologies, Swiss Federal Institute for Materials Science and Technology Empa, Überlandstrasse 129, 8600, Dübendorf, Switzerland; Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland.
| | - Lena Schinkel
- Laboratory for Advanced Analytical Technologies, Swiss Federal Institute for Materials Science and Technology Empa, Überlandstrasse 129, 8600, Dübendorf, Switzerland; Swiss Federal Institute of Aquatic Research and Technology Eawag, Überlandstrasse 129, 8600, Dübendorf, Switzerland
| | - Hans-Peter E Kohler
- Swiss Federal Institute of Aquatic Research and Technology Eawag, Überlandstrasse 129, 8600, Dübendorf, Switzerland
| | - Flurin Mathis
- Zürich University of Applied Sciences ZHAW, Unterstrass 31, 8820, Wädenswil, Switzerland
| | - Susanne Kern
- Zürich University of Applied Sciences ZHAW, Unterstrass 31, 8820, Wädenswil, Switzerland
| | - Davide Bleiner
- Laboratory for Advanced Analytical Technologies, Swiss Federal Institute for Materials Science and Technology Empa, Überlandstrasse 129, 8600, Dübendorf, Switzerland; Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Norbert V Heeb
- Laboratory for Advanced Analytical Technologies, Swiss Federal Institute for Materials Science and Technology Empa, Überlandstrasse 129, 8600, Dübendorf, Switzerland
| |
Collapse
|
12
|
Yuan J, Shentu J, Ma B, Lu Z, Luo Y, Xu J, He Y. Microbial and abiotic factors of flooded soil that affect redox biodegradation of lindane. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 780:146606. [PMID: 34030285 DOI: 10.1016/j.scitotenv.2021.146606] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 03/14/2021] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
Pollution induces pressure to soil microorganism; and conversely, the degradation of pollutants is reported largely regulated by the soil microbiome assembly in situ. However, the specific-dependent core taxa of degraders were barely confirmed, which is not conducive to improving the soil remediation strategy. Taking pollution of a typical organochlorine pesticide (OCP), lindane, as an example, we explored the microbial community assembly in flooded soils and simultaneously quantified the corresponding dynamics of typical soil redox processes. Contrasting initial status of microbial diversity was set up by gamma irradiation or not, with additives (acetate, NaNO3, acetate + NaNO3) capable of modifying microbial growth employed simultaneously. Microorganism under lindane stress was reflected by microbial adaptability within complex co-occurrence networks, wherein some environment-dependent core taxa (e.g., Clostridia, Bacteroidia, Bacilli) were highly resilient to pollution and sterilization disturbances. Lindane had higher degradation rate in irradiated soil (0.96 mg kg-1 d-1) than non-irradiated soil (0.83 mg kg-1 d-1). In non-irradiated soil, addition of acetate promoted lindane degradation and methanogenesis, whereas nitrate inhibited lindane degradation but promoted denitrification. No significant differences in lindane degradation were observed in irradiated soils, which exhibited low-diversity microbiomes in parallel to stronger Fe reduction and methanogenesis. The varied corresponding trigger effects on soil redox processes are likely due to differences of soil microbiome, specifically, deterministic or stochastic assembly, in response to pollution stress under high or low initial microbial diversity conditions. Our results improve the knowledge of the adaptability of disturbed microbiomes and their feedback on microbial functional development in OCP-polluted soils, achieving for a more reliable understanding with respect to the ecological risk of soils resided with OCPs under the fact of global microbial diversity loss.
Collapse
Affiliation(s)
- Jing Yuan
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Jue Shentu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Zhijiang Lu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Yu Luo
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Yan He
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China.
| |
Collapse
|
13
|
Sharma M, Singh DN, Budhraja R, Sood U, Rawat CD, Adrian L, Richnow HH, Singh Y, Negi RK, Lal R. Comparative proteomics unravelled the hexachlorocyclohexane (HCH) isomers specific responses in an archetypical HCH degrading bacterium Sphingobium indicum B90A. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:41380-41395. [PMID: 33783707 DOI: 10.1007/s11356-021-13073-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 02/17/2021] [Indexed: 06/12/2023]
Abstract
Hexachlorocyclohexane (HCH) is a persistent organochlorine pesticide that poses threat to different life forms. Sphingobium indicum B90A that belong to sphingomonad is well-known for its ability to degrade HCH isomers (α-, β-, γ-, δ-), but effects of HCH isomers and adaptive mechanisms of strain B90A under HCH load remain obscure. To investigate the responses of strain B90A to HCH isomers, we followed the proteomics approach as this technique is considered as the powerful tool to study the microbial response to environmental stress. Strain B90A culture was exposed to α-, β-, γ-, δ-HCH (5 mgL-1) and control (without HCH) taken for comparison and changes in whole cell proteome were analyzed. In β- and δ-HCH-treated cultures growth decreased significantly when compared to control, α-, and γ-HCH-treated cultures. HCH residue analysis corroborated previous observations depicting the complete depletion of α- and γ-HCH, while only 66% β-HCH and 34% δ-HCH were depleted from culture broth. Comparative proteome analyses showed that β- and δ-HCH induced utmost systemic changes in strain B90A proteome, wherein stress-alleviating proteins such as histidine kinases, molecular chaperons, DNA binding proteins, ABC transporters, TonB proteins, antioxidant enzymes, and transcriptional regulators were significantly affected. Besides study confirmed constitutive expression of linA, linB, and linC genes that are crucial for the initiation of HCH isomers degradation, while increased abundance of LinM and LinN in presence of β- and δ-HCH suggested the important role of ABC transporter in depletion of these isomers. These results will help to understand the HCH-induced damages and adaptive strategies of strain B90A under HCH load which remained unravelled to date.
Collapse
Affiliation(s)
- Monika Sharma
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India
| | | | - Rohit Budhraja
- Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Utkarsh Sood
- Department of Zoology, University of Delhi, Delhi, 110007, India
- The Energy and Resources Institute, Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi, 110003, India
| | - Charu Dogra Rawat
- Department of Zoology, Ramjas College, University of Delhi, Delhi, 110007, India
| | - Lorenz Adrian
- Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | | | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Ram Krishan Negi
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India.
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, 110007, India.
- The Energy and Resources Institute, Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi, 110003, India.
| |
Collapse
|
14
|
Ara T, Nisa WU, Anjum M, Riaz L, Saleem AR, Hayat MT. Hexachlorocyclohexane toxicity in water bodies of Pakistan: challenges and possible reclamation technologies. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2021; 83:2345-2362. [PMID: 34032614 DOI: 10.2166/wst.2021.120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Pakistan is an agro-economy country where hexachlorocyclohexane (HCH) pesticides are being used to improve crop productivity, as a result the risk of contamination of soil and sediment has been increased. HCH exhibits all the characteristics of persistent organic pollutants (POP), and was therefore added to the list of 'new POPs' in 2009. This review report revealed that the major rivers of Pakistan such as the Indus Basin, River Ravi, River Chenab and their tributaries all are contaminated with HCH and the highest residual concentration (4,090 ng/g) was detected in a pesticide burial ground in Hyderabad city. Major sources of HCH contamination were identified as agricultural runoff, discharge of untreated industrial effluents and surface runoff. In order to manage HCH pollution, various ex-situ and in-situ remediation techniques along with their merits and demerits are thoroughly reviewed. Among these, microbial bioremediation is a low cost, environment friendly, effective in-situ remediation technique for remediation of HCH. Overall, the information provided in this manuscript will provide a future reference to the scientific community and bridge the knowledge gap between HCH release in the environment and their mitigation through proper treatment methods.
Collapse
Affiliation(s)
- Talat Ara
- Department of Environmental Science, International Islamic University Islamabad, Islamabad, Pakistan
| | - Waqar-Un Nisa
- Center for Interdisciplinary Research in Basic Sciences (SA-CIRBS), International Islamic University Islamabad, Islamabad, Pakistan
| | - Muzammil Anjum
- Department of Environmental Sciences, PMAS Arid Agriculture University, Rawalpindi 46300, Pakistan and School of Materials Science and Engineering, Sun Yat-sen University, Guangzhou, China E-mail: ;
| | - Luqman Riaz
- College of Life Sciences, Henan Normal University, Xinxiang, China and Department of Environmental Sciences, University of Narowal, Narowal, Pakistan
| | - Aansa Rukya Saleem
- Department of Earth and Environmental Sciences, Bahria University, Islamabad, Pakistan
| | - Malik Tahir Hayat
- Department of Environmental Sciences, COMSATS Institute of Information and Technology, Abbotabad 22010, Pakistan
| |
Collapse
|
15
|
Heeb NV, Hubeli J, Fleischmann T, Lienemann P, Nayyar N, Lal R, Kohler HPE. Transformation of ε-HBCD with the Sphingobium Indicum enzymes LinA1, LinA2 and LinATM, a triple mutant of LinA2. CHEMOSPHERE 2021; 267:129217. [PMID: 33321275 DOI: 10.1016/j.chemosphere.2020.129217] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
Hexabromocyclododecanes (HBCDs) were used as flame-retardants until their ban in 2013. Among the 16 stereoisomers known, ε-HBCD has the highest symmetry. This makes ε-HBCD an interesting substrate to study the selectivity of biotransformations. We expressed three LinA dehydrohalogenase enzymes in E. coli bacteria, two wild-type, originating from Sphingobium indicum B90A bacteria and LinATM, a triple mutant of LinA2, with mutations of L96C, F113Y and T133 M. These enzymes are involved in the hexachlorocyclohexane (HCH) metabolism, specifically of the insecticide γ-HCH (Lindane). We studied the reactivity of those eight HBCD stereoisomers found in technical HBCD. Furthermore, we compared kinetics and selectivity of these LinA variants with respect to ε-HBCD. LC-MS data indicate that all enzymes converted ε-HBCD to pentabromocyclododecenes (PBCDens). Transformations followed Michaelis-Menten kinetics. Rate constants kcat and enzyme specificities kcat/KM indicate that ε-HBCD conversion was fastest and most specific with LinA2. Only one PBCDen stereoisomer was formed by LinA2, while LinA1 and LinATM produced mixtures of two PBCDE enantiomers at three times lower rates than LinA2. In analogy to the biotransformation of (-)β-HBCD, with selective conversion of dibromides in R-S-configuration, we assume that 1E,5S,6R,9S,10R-PBCDen is the ε-HBCD transformation product from LinA2. Implementing three amino acids of the LinA1 substrate-binding site into LinA2 resulted in a triple mutant with similar kinetics and product specificity like LinA1. Thus, point-directed mutagenesis is an interesting tool to modify the substrate- and product-specificity of LinA enzymes and enlarge their scope to metabolize other halogenated persistent organic pollutants regulated under the Stockholm Convention.
Collapse
Affiliation(s)
- Norbert V Heeb
- Empa, Swiss Federal Laboratories for Materials Testing and Research, Laboratory for Advanced Analytical Technologies, Überlandstrasse 129, CH-8600, Dübendorf, Switzerland.
| | - Jasmin Hubeli
- Empa, Swiss Federal Laboratories for Materials Testing and Research, Laboratory for Advanced Analytical Technologies, Überlandstrasse 129, CH-8600, Dübendorf, Switzerland; ZHAW, Zurich University of Applied Sciences, Institute of Chemistry and Biological Chemistry, Reidbach, CH-8820, Wädenswil, Switzerland; Current Address: Cantonal Pharmacy Zürich, Südstrasse 3, CH-8952, Schlieren, Switzerland
| | - Thomas Fleischmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - Peter Lienemann
- ZHAW, Zurich University of Applied Sciences, Institute of Chemistry and Biological Chemistry, Reidbach, CH-8820, Wädenswil, Switzerland
| | - Namita Nayyar
- Sri Venkateswara College, University of Delhi, Delhi, 1110021, India
| | - Rup Lal
- The Energy and Resources Institute, India Habitat Center, New Delhi, Delhi, 110003, India
| | - Hans-Peter E Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| |
Collapse
|
16
|
Knobloch MC, Schinkel L, Schilling I, Kohler HPE, Lienemann P, Bleiner D, Heeb NV. Transformation of short-chain chlorinated paraffins by the bacterial haloalkane dehalogenase LinB - Formation of mono- and di-hydroxylated metabolites. CHEMOSPHERE 2021; 262:128288. [PMID: 33182101 DOI: 10.1016/j.chemosphere.2020.128288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/04/2020] [Accepted: 09/05/2020] [Indexed: 06/11/2023]
Abstract
Short-chain chlorinated paraffins (SCCPs) are listed as persistent organic pollutants (POPs) under the Stockholm Convention. Such substances are toxic, bioaccumulating, transported over long distances and degrade slowly in the environment. Certain bacterial strains of the Sphingomonadacea family are able to degrade POPs, such as hexachlorocyclohexanes (HCHs) and hexabromocyclododecanes (HBCDs). The haloalkane dehalogenase LinB, expressed in certain Sphingomonadacea, is able to catalyze the transformation of haloalkanes to hydroxylated compounds. Therefore, LinB is a promising candidate for conversion of SCCPs. Hence, a mixture of chlorinated tridecanes was exposed in vitro to LinB, which was obtained through heterologous expression in Escherichia coli. Liquid chromatography mass spectrometry (LC-MS) was used to analyze chlorinated tridecanes and their transformation products. A chloride-enhanced soft ionization method, which favors the formation of chloride adducts [M+Cl]- without fragmentation, was applied. Mathematical deconvolution was used to distinguish interfering mass spectra of paraffinic, mono-olefinic and di-olefinic compounds. Several mono- and di-hydroxylated products including paraffinic, mono-olefinic and di-olefinic compounds were found after LinB exposure. Mono- (rt = 5.9-6.9 min) and di-hydroxylated (rt = 3.2-4.5 min) compounds were separated from starting material (rt = 7.7-8.5 min) by reversed phase LC. Chlorination degrees of chlorinated tridecanes increased during LinB-exposure from nCl = 8.80 to 9.07, indicating a preferential transformation of lower chlorinated (Cl<9) tridecanes. Thus, LinB indeed catalyzed a dehalohydroxylation of chlorinated tridecanes, tridecenes and tridecadienes. The observed hydroxylated compounds are relevant CP transformation products whose environmental and toxicological effects should be further investigated.
Collapse
Affiliation(s)
- Marco C Knobloch
- Laboratory for Advanced Analytical Technologies, Swiss Federal Institute for Materials Science and Technology Empa, Überlandstrasse 129, 8600, Dübendorf, Switzerland; Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland.
| | - Lena Schinkel
- Swiss Federal Institute of Aquatic Research and Technology Eawag, Überlandstrasse 129, 8600, Dübendorf, Switzerland
| | - Iris Schilling
- Swiss Federal Institute of Aquatic Research and Technology Eawag, Überlandstrasse 129, 8600, Dübendorf, Switzerland
| | - Hans-Peter E Kohler
- Swiss Federal Institute of Aquatic Research and Technology Eawag, Überlandstrasse 129, 8600, Dübendorf, Switzerland
| | - Peter Lienemann
- Zürich University of Applied Sciences ZHAW, Einsiedlerstrasse 3, 8820, Wädenswil, Switzerland
| | - Davide Bleiner
- Laboratory for Advanced Analytical Technologies, Swiss Federal Institute for Materials Science and Technology Empa, Überlandstrasse 129, 8600, Dübendorf, Switzerland; Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Norbert V Heeb
- Laboratory for Advanced Analytical Technologies, Swiss Federal Institute for Materials Science and Technology Empa, Überlandstrasse 129, 8600, Dübendorf, Switzerland
| |
Collapse
|
17
|
Pino-Otín MR, Val J, Ballestero D, Navarro E, Sánchez E, Mainar AM. Impact of Artemisia absinthium hydrolate extracts with nematicidal activity on non-target soil organisms of different trophic levels. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 180:565-574. [PMID: 31129435 DOI: 10.1016/j.ecoenv.2019.05.055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 05/14/2019] [Accepted: 05/16/2019] [Indexed: 06/09/2023]
Abstract
Natural pesticides are considered a good alternative to synthetic pesticides to reduce environmental impacts. However, biopesticides may have unknown effects on the environment, and can affect non-target organisms. In this study, the ecotoxicological effects of an aqueous extract (hydrolate) from Spanish populations of Artemisia absinthium (var. Candial) showing a promising biopesticide activity, were evaluated on non-target soil organisms from different trophic levels (natural microbial communities characterized through 16S rRNA gene sequencing, the earthworm Eisenia fetida and the plant Allium cepa). The hydrolate usually was considered as a by-product of the distillation to obtain essential oils. However, recently has been found to have nematicide properties. The hydrolate caused acute toxicity at values of LC50 of 3.87% v/v for A. cepa and 0.07 mL/g for E. fetida. All the concentrations except for the most diluted (1% v/v) reduced the bacterial physiological activity compared to controls (LC50 = 25.72% v/v after 24 h of exposure). The hydrolate also slightly altered the ability of the microbial community to degrade carbon substrates. These results indicate that the hydrolate from A. absinthium may affect the survival and metabolic abilities of key soil organisms.
Collapse
Affiliation(s)
- M Rosa Pino-Otín
- Universidad San Jorge, Villanueva de Gállego, 50830, Zaragoza, Spain.
| | - Jonatan Val
- Universidad San Jorge, Villanueva de Gállego, 50830, Zaragoza, Spain; Colegio Internacional Ánfora, c/ Pirineos, 8, 50410, Cuarte de Huerva, Zaragoza, Spain
| | - Diego Ballestero
- Universidad San Jorge, Villanueva de Gállego, 50830, Zaragoza, Spain
| | - Enrique Navarro
- Instituto Pirenaico de Ecología, Consejo Superior de Investigaciónes Científicas, Av. Montañana 1005, 50059, Zaragoza, Spain
| | - Esther Sánchez
- Colegio Internacional Ánfora, c/ Pirineos, 8, 50410, Cuarte de Huerva, Zaragoza, Spain
| | - Ana M Mainar
- I3A, Universidad de Zaragoza, c/ Mariano Esquillor s/n, 50018, Zaragoza, Spain
| |
Collapse
|
18
|
Regar RK, Gaur VK, Bajaj A, Tambat S, Manickam N. Comparative microbiome analysis of two different long-term pesticide contaminated soils revealed the anthropogenic influence on functional potential of microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 681:413-423. [PMID: 31108361 DOI: 10.1016/j.scitotenv.2019.05.090] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 05/07/2019] [Accepted: 05/07/2019] [Indexed: 05/17/2023]
Abstract
Microbial communities play a crucial role in bioremediation of pollutants in contaminated ecosystem. In addition to pure culture isolation and bacterial 16S rRNA based community studies, the focus has now shifted employing the omics technologies enormously for understanding the microbial diversity and functional potential of soil samples. Our previous report on two pesticide-contaminated sites revealed the diversity of both culturable and unculturable bacteria. In the present study, we have observed distinct taxonomic and functional communities in contaminated soil with respect to an uncontaminated soil as control by using shotgun metagenomic sequencing method. Our data demonstrated that Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Acidobacteria significantly dominated the microbial diversity with their cumulative abundance percentage in the range of 98.61, 87.38, and 80.52 for Hindustan Insecticides Limited (HIL), India Pesticides Limited (IPL), and control respectively. Functional gene analysis demonstrated the presence of large number of both substrate specific upper pathway and common lower pathway degradative genes. Relatively lower number of genes was found encoding the degradation of styrene, atrazine, bisphenol, dioxin, and naphthalene. When three bacteria were augumentated with rhamnolipid (20-100 μM) and Triton X-100 (84-417 μM) surfactants in HIL soil, an enhanced degradation to 76%, 70%, and 58% of HCH, Endosulfan, and DDT respectively was achieved. The overall data obtained from two heavily contaminated soil suggest the versatility of the microbial communities for the xenobiotic pollutant degradation which may help in exploiting their potential applications in bioremediation.
Collapse
Affiliation(s)
- Raj Kumar Regar
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31 Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, India; Department of Biochemistry, School of Dental Sciences, Babu Banarsi Das University, Lucknow, Uttar Pradesh, India
| | - Vivek Kumar Gaur
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31 Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, India; Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, India
| | - Abhay Bajaj
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31 Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, India
| | - Subodh Tambat
- Bionivid Technology Pvt. Ltd., Bengaluru, Karnataka, India
| | - Natesan Manickam
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31 Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, India.
| |
Collapse
|
19
|
Liu Y, Wu L, Kohli P, Kumar R, Stryhanyuk H, Nijenhuis I, Lal R, Richnow HH. Enantiomer and Carbon Isotope Fractionation of α-Hexachlorocyclohexane by Sphingobium indicum Strain B90A and the Corresponding Enzymes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:8715-8724. [PMID: 31266304 DOI: 10.1021/acs.est.9b01233] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Chiral organic contaminants, like α-hexachlorocyclohexane (α-HCH), showed isotope fractionation and enantiomer fractionation during biodegradation. This study aims to understand the correlation between these two processes. Initial tests of α-HCH degradation by six Sphingobium strains (with different LinA variants) were conducted. Results showed variable enantiomer selectivity over the time course. In contrast, constant enantiomer selectivity was observed in experiments employing (i) cell suspensions, (ii) crude extracts, or (iii) LinA1 and LinA2 enzymes of strain B90A for α-HCH degradation in enzyme activity assay buffer. The average value of enantioselectivity (ES) were -0.45 ± 0.03 (cell suspensions), -0.60 ± 0.05 (crude extracts), and 1 (LinA1) or -1 (LinA2). The average carbon isotope enrichment factors (εc) of (+)α- and (-)α-HCH were increased from cells suspensions (-6.3 ± 0.1‰ and -2.3 ± 0.03‰) over crude extracts (-7.7 ± 0.4‰ and -3.4 ± 0.02‰) to purified enzymes (-11.1 ± 0.3‰ and -3.8 ± 0.2‰). The variability of ES and the εc were discussed based on the effect of mass transport and degradation rates. Our study demonstrates that enantiomer and isotope fractionation of α-HCH are two independent processes and both are affected by underlying reactions of individual enzymes and mass transport to a different extent.
Collapse
Affiliation(s)
- Yaqing Liu
- Department of Isotope Biogeochemistry , Helmholtz Centre for Environmental Research-UFZ , Permoserstraße 15 , 04318 Leipzig , Germany
| | - Langping Wu
- Department of Isotope Biogeochemistry , Helmholtz Centre for Environmental Research-UFZ , Permoserstraße 15 , 04318 Leipzig , Germany
| | - Puneet Kohli
- Molecular Biology Laboratory, Department of Zoology , University of Delhi , Delhi - 110007 , India
| | - Roshan Kumar
- Molecular Biology Laboratory, Department of Zoology , University of Delhi , Delhi - 110007 , India
| | - Hryhoriy Stryhanyuk
- Department of Isotope Biogeochemistry , Helmholtz Centre for Environmental Research-UFZ , Permoserstraße 15 , 04318 Leipzig , Germany
| | - Ivonne Nijenhuis
- Department of Isotope Biogeochemistry , Helmholtz Centre for Environmental Research-UFZ , Permoserstraße 15 , 04318 Leipzig , Germany
| | - Rup Lal
- Molecular Biology Laboratory, Department of Zoology , University of Delhi , Delhi - 110007 , India
| | - Hans-Hermann Richnow
- Department of Isotope Biogeochemistry , Helmholtz Centre for Environmental Research-UFZ , Permoserstraße 15 , 04318 Leipzig , Germany
| |
Collapse
|
20
|
Heeb NV, Schalles S, Lehner S, Schinkel L, Schilling I, Lienemann P, Bogdal C, Kohler HPE. Biotransformation of short-chain chlorinated paraffins (SCCPs) with LinA2: A HCH and HBCD converting bacterial dehydrohalogenase. CHEMOSPHERE 2019; 226:744-754. [PMID: 30965245 DOI: 10.1016/j.chemosphere.2019.03.169] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/19/2019] [Accepted: 03/24/2019] [Indexed: 06/09/2023]
Abstract
Short-chain chlorinated paraffins (SCCPs) are polyhalogenated hydrocarbons as are hexachlorocyclohexanes (HCHs) and hexabromocyclododecanes (HBCDs). They all have been classified as persistent organic pollutants (POPs) under the UN Stockholm Convention. Per se such compounds are transformed slowly in the environment, transported over long distances and accumulate in biota. Several Sphingomonadacea strains isolated from HCH dump sites have evolved to express enzymes that can transform HCHs and HBCDs. We hypothesized that LinA2, a dehydrohalogenase expressed in such bacteria, may also transform CPs to chlorinated olefins (COs). Three mixtures of penta- to deca-chlorinated undecanes (C11), dodecanes (C12) and tridecanes (C13) were exposed to LinA2. High-resolution full-scan mass spectra (R∼8'000) of CPs and COs were obtained applying a soft ionization method, enhancing chloride-adduct [M+Cl]- formation. A mathematical deconvolution procedure was used to separate interfering spectra to verify that LinA2 indeed catalyzed the conversion of CPs to COs. About 20-40% of the material was transformed in 24 h, about 50-70% was converted in 200 h. A bimodal first-order kinetic model could describe transformations of reactive and persistent CPs. Under the given conditions reactive CPs (τ1/2 = 1.4-6.9 h) were converted 30 to 190-times faster than the persistent ones (τ1/2 = 150-260 h). Proportions of persistent isomers (pp) varied from 60 to 80%. Lower chlorinated homologues contained higher proportions of persistent isomers. In conclusion, SCCP mixtures contain both, material that is readily converted by LinA2, and persistent material that is not or only slowly transformed.
Collapse
Affiliation(s)
- Norbert V Heeb
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Advanced Analytical Technologies, Überlandstrasse 129, CH-8600, Dübendorf, Switzerland.
| | - Simone Schalles
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Advanced Analytical Technologies, Überlandstrasse 129, CH-8600, Dübendorf, Switzerland; RWTH, Aachen University, Institute for Environmental Sciences, Worringerweg 1, D-52074, Aachen, Germany; ETH, Swiss Federal Institute of Technology, Institute of Biogeochemistry and Pollutant Dynamic, Universitätsstrasse 16, CH-8092, Zurich, Switzerland
| | - Sandro Lehner
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Advanced Analytical Technologies, Überlandstrasse 129, CH-8600, Dübendorf, Switzerland; ZHAW, Zurich University of Applied Sciences, Institute of Chemistry and Biological Chemistry, Reidbach, CH-8820, Wädenswil, Switzerland
| | - Lena Schinkel
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Advanced Analytical Technologies, Überlandstrasse 129, CH-8600, Dübendorf, Switzerland; ETH, Swiss Federal Institute of Technology, Institute of Chemical and Bioengineering, Vladimir-Prelog-Weg 1, CH-8093, Zurich, Switzerland
| | - Iris Schilling
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - Peter Lienemann
- ZHAW, Zurich University of Applied Sciences, Institute of Chemistry and Biological Chemistry, Reidbach, CH-8820, Wädenswil, Switzerland
| | - Christian Bogdal
- ETH, Swiss Federal Institute of Technology, Institute of Biogeochemistry and Pollutant Dynamic, Universitätsstrasse 16, CH-8092, Zurich, Switzerland; present address: FOR, Zurich Forensic Science Institute, Zeughausstrasse 11, CH-8004, Zurich, Switzerland
| | - Hans-Peter E Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| |
Collapse
|
21
|
Schilling IE, Hess R, Bolotin J, Lal R, Hofstetter TB, Kohler HPE. Kinetic Isotope Effects of the Enzymatic Transformation of γ-Hexachlorocyclohexane by the Lindane Dehydrochlorinase Variants LinA1 and LinA2. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:2353-2363. [PMID: 30674184 DOI: 10.1021/acs.est.8b04234] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Compound-specific isotope analysis (CSIA) can provide insights into the natural attenuation processes of hexachlorocyclohexanes (HCHs), an important class of persistent organic pollutants. However, the interpretation of HCH stable isotope fractionation is conceptually challenging. HCHs exist as different conformers that can be converted into each other, and the enzymes responsible for their transformation discriminate among those HCH conformers. Here, we investigated the enzyme specificity of apparent 13C- and 2H-kinetic isotope effects (AKIEs) associated with the dehydrochlorination of γ-HCH (lindane) by two variants of the lindane dehydrochlorinases LinA1 and LinA2. While LinA1 and LinA2 attack γ-HCH at different trans-1,2-diaxial H-C-C-Cl moieties, the observed C and H isotope fractionation was large, typical for bimolecular eliminations, and was not affected by conformational mobility. 13C-AKIEs for transformation by LinA1 and LinA2 were the same (1.024 ± 0.001 and 1.025 ± 0.001, respectively), whereas 2H-AKIEs showed minor differences (2.4 ± 0.1 and 2.6 ± 0.1). Variations of isotope effects between LinA1 and LinA2 are small and in the range reported for different degrees of C-H bond cleavage in transition states of dehydrochlorination reactions. The large C and H isotope fractionation reported here for experiments with pure enzymes contrasts with previous observations from whole cell experiments and suggests that specific uptake processes by HCH-degrading microorganisms might modulate the observable HCH isotope fractionation at contaminated sites.
Collapse
Affiliation(s)
- Iris E Schilling
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , CH-8600 Dübendorf , Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics , ETH Zürich , CH-8092 Zürich , Switzerland
| | - Ramon Hess
- Institute of Biogeochemistry and Pollutant Dynamics , ETH Zürich , CH-8092 Zürich , Switzerland
| | - Jakov Bolotin
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , CH-8600 Dübendorf , Switzerland
| | - Rup Lal
- Department of Zoology , University of Delhi , Delhi 110007 , India
| | - Thomas B Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , CH-8600 Dübendorf , Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics , ETH Zürich , CH-8092 Zürich , Switzerland
| | - Hans-Peter E Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , CH-8600 Dübendorf , Switzerland
| |
Collapse
|
22
|
Sineli PE, Herrera HM, Cuozzo SA, Dávila Costa JS. Quantitative proteomic and transcriptional analyses reveal degradation pathway of γ-hexachlorocyclohexane and the metabolic context in the actinobacterium Streptomyces sp. M7. CHEMOSPHERE 2018; 211:1025-1034. [PMID: 30223317 DOI: 10.1016/j.chemosphere.2018.08.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/07/2018] [Accepted: 08/08/2018] [Indexed: 06/08/2023]
Abstract
Highly contaminated γ-hexachlorocyclohexane (lindane) areas were reported worldwide. Low aqueous solubility and high hydrophobicity make lindane particularly resistant to microbial degradation. Physiological and genetic Streptomyces features make this genus more appropriate for bioremediation compared with others. Complete degradation of lindane was only proposed in the genus Sphingobium although the metabolic context of the degradation was not considered. Streptomyces sp.M7 has demonstrated ability to remove lindane from culture media and soils. In this study, we used MS-based label-free quantitative proteomic, RT-qPCR and exhaustive bioinformatic analysis to understand lindane degradation and its metabolic context in Streptomyces sp. M7. We identified the proteins involved in the up-stream degradation pathway. In addition, results demonstrated that mineralization of lindane is feasible since proteins from an unusual down-stream degradation pathway were also identified. Degradative steps were supported by an active catabolism that supplied energy and reducing equivalents in the form of NADPH. To our knowledge, this is the first study in which degradation steps of an organochlorine compound and metabolic context are elucidate in a biotechnological genus as Streptomyces. These results serve as basement to study other degradative actinobacteria and to improve the degradation processes of Streptomyces sp. M7.
Collapse
Affiliation(s)
- Pedro E Sineli
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Tucumán, Argentina
| | - Hector M Herrera
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Tucumán, Argentina
| | - Sergio A Cuozzo
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Tucumán, Argentina; Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Tucumán, Argentina
| | - José S Dávila Costa
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Tucumán, Argentina.
| |
Collapse
|
23
|
Xu Y, Niu L, Qiu J, Zhou Y, Lu H, Liu W. Stereoselective accumulations of hexachlorocyclohexanes (HCHs) are correlated with Sphingomonas spp. in agricultural soils across China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 240:27-33. [PMID: 29729566 DOI: 10.1016/j.envpol.2018.04.078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/17/2018] [Accepted: 04/18/2018] [Indexed: 06/08/2023]
Abstract
The wide usage of hexachlorocyclohexanes (HCHs) as pesticides has caused soil pollution and adverse health effects through direct contact or bioaccumulation in the food chain. This study quantified major HCH isomers in farmland topsoils across China, and evaluated their correlations with microbial community structure, function, and abiotic variables (e.g., moisture, pH, and temperature). Recalcitrant β-HCH was more abundant than α-, γ-, and δ-HCHs, and α-HCH enantiomeric fractions (EF) were larger than 0.5, indicating preferential degradation of (-)-α-HCH. Sphingomonas was not only a predominant population (especially in samples collected in the south), but also a promising biomarker indicating total- and β-HCH residuals, and EF values of α-HCH. Soil moisture and temperature were among the most influential factors that structured the diversity and function of soil microbial communities. The results suggested that increasing soil moisture (in the range of 5-45%) would benefit the growth of HCH-degrading populations and the enrichment of HCH-degradation related pathways. Revealing the site-specific relationships between topsoil physical, chemical, and microbial properties will benefit the in situ bioremediation of farmlands with relatively low HCH residuals across the world.
Collapse
Affiliation(s)
- Yang Xu
- International Joint Research Center for Persistent Toxic Substances (IJRC-PTS), MOE Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Lili Niu
- International Joint Research Center for Persistent Toxic Substances (IJRC-PTS), MOE Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Jiguo Qiu
- International Joint Research Center for Persistent Toxic Substances (IJRC-PTS), MOE Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Yuting Zhou
- International Joint Research Center for Persistent Toxic Substances (IJRC-PTS), MOE Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Huijie Lu
- International Joint Research Center for Persistent Toxic Substances (IJRC-PTS), MOE Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Department of Civil and Environmental Engineering, University of Vermont, 33 Colchester Ave, Burlington, VT 05405, USA.
| | - Weiping Liu
- International Joint Research Center for Persistent Toxic Substances (IJRC-PTS), MOE Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| |
Collapse
|
24
|
Heeb NV, Mazenauer M, Wyss S, Geueke B, Kohler HPE, Lienemann P. Kinetics and stereochemistry of LinB-catalyzed δ-HBCD transformation: Comparison of in vitro and in silico results. CHEMOSPHERE 2018; 207:118-129. [PMID: 29793023 DOI: 10.1016/j.chemosphere.2018.05.057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 05/04/2018] [Accepted: 05/09/2018] [Indexed: 06/08/2023]
Abstract
LinB is a haloalkane dehalogenase found in Sphingobium indicum B90A, an aerobic bacterium isolated from contaminated soils of hexachlorocyclohexane (HCH) dumpsites. We showed that this enzyme also converts hexabromocyclododecanes (HBCDs). Here we give new insights in the kinetics and stereochemistry of the enzymatic transformation of δ-HBCD, which resulted in the formation of two pentabromocyclododecanols (PBCDols) as first- (P1δ, P2δ) and two tetrabromocyclododecadiols (TBCDdiols) as second-generation products (T1δ, T2δ). Enzymatic transformations of δ-HBCD, α1-PBCDol, one of the transformation products, and α2-PBCDol, its enantiomer, were studied and modeled with Michaelis-Menten (MM) kinetics. Respective MM-parameters KM, vmax, kcat/KM indicated that δ-HBCD is the best LinB substrate followed by α2- and α1-PBCDol. The stereochemistry of these transformations was modeled in silico, investigating respective enzyme-substrate (ES) and enzyme-product (EP) complexes. One of the four predicted ES-complexes led to the PBCDol product P1δ, identical to α2-PBCDol with the 1R,2R,5S,6R,9R,10S-configuration. An SN2-like substitution of bromine at C6 of δ-HBCD by Asp-108 of LinB and subsequent hydrolysis of the alkyl-enzyme led to α2-PBCDol. Modeling results further indicate that backside attacks at C1, C9 and C10 are reasonable too, selectively binding leaving bromide ions in a halide pocket found in LinB. Docking with α2-PBCDol, also allowed productive enzyme binding. A TBCD-1,5-diol with the 1S,2S,5R,6R,9S,10R-configuration is the predicted second-generation product T1δ. In conclusion, in vitro- and in silico findings now allow a detailed description of step-wise enzymatic dehalohydroxylation reactions of δ-HBCD to specific PBCDols and TBCDdiols at Å-resolution and predictions of their stereochemistry.
Collapse
Affiliation(s)
- Norbert V Heeb
- Swiss Federal Institute for Materials Science and Technology (Empa), Laboratory of Advanced Analytical Technologies, Überlandstrasse 129, CH-8600, Dübendorf, Switzerland.
| | - Manuel Mazenauer
- Swiss Federal Institute for Materials Science and Technology (Empa), Laboratory of Advanced Analytical Technologies, Überlandstrasse 129, CH-8600, Dübendorf, Switzerland; Zurich University of Applied Sciences, Institute of Chemistry and Biological Chemistry, Reidbach, 8820 Wädenswil, Switzerland
| | - Simon Wyss
- Swiss Federal Institute for Materials Science and Technology (Empa), Laboratory of Advanced Analytical Technologies, Überlandstrasse 129, CH-8600, Dübendorf, Switzerland; Zurich University of Applied Sciences, Institute of Chemistry and Biological Chemistry, Reidbach, 8820 Wädenswil, Switzerland
| | - Birgit Geueke
- Swiss Federal Institute of Aquatic Research and Technology (Eawag), Überlandstrasse 129, 8600 Dübendorf, Switzerland
| | - Hans-Peter E Kohler
- Swiss Federal Institute of Aquatic Research and Technology (Eawag), Überlandstrasse 129, 8600 Dübendorf, Switzerland
| | - Peter Lienemann
- Zurich University of Applied Sciences, Institute of Chemistry and Biological Chemistry, Reidbach, 8820 Wädenswil, Switzerland
| |
Collapse
|
25
|
Kumar D, Pannu R. Perspectives of lindane (γ-hexachlorocyclohexane) biodegradation from the environment: a review. BIORESOUR BIOPROCESS 2018. [DOI: 10.1186/s40643-018-0213-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
26
|
|
27
|
Cuozzo SA, Sineli PE, Davila Costa J, Tortella G. Streptomyces sp. is a powerful biotechnological tool for the biodegradation of HCH isomers: biochemical and molecular basis. Crit Rev Biotechnol 2017; 38:719-728. [PMID: 29124958 DOI: 10.1080/07388551.2017.1398133] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Actinobacteria are well-known degraders of toxic materials that have the ability to tolerate and remove organochloride pesticides; thus, they are used for bioremediation. The biodegradation of organochlorines by actinobacteria has been demonstrated in pure and mixed cultures with the concomitant production of metabolic intermediates including γ-pentachlorocyclohexene (γ-PCCH); 1,3,4,6-tetrachloro-1,4-cyclohexadiene (1,4-TCDN); 1,2-dichlorobenzene (1,2-DCB), 1,3-dichlorobenzene (1,3-DCB), or 1,4-dichlorobenzene (1,4-DCB); 1,2,3-trichlorobenzene (1,2,3-TCB), 1,2,4-trichlorobenzene (1,2,4-TCB), or 1,3,5-trichlorobenzene (1,3,5-TCB); 1,3-DCB; and 1,2-DCB. Chromatography coupled to mass spectrometric detection, especially GC-MS, is typically used to determine HCH-isomer metabolites. The important enzymes involved in HCH isomer degradation metabolic pathways include hexachlorocyclohexane dehydrochlorinase (LinA), haloalkane dehalogenase (LinB), and alcohol dehydrogenase (LinC). The metabolic versatility of these enzymes is known. Advances have been made in the identification of actinobacterial haloalkane dehydrogenase, which is encoded by linB. This knowledge will permit future improvements in biodegradation processes using Actinobacteria. The enzymatic and genetic characterizations of the molecular mechanisms involved in these processes have not been fully elucidated, necessitating further studies. New advances in this area suggest promising results. The scope of this paper encompasses the following: (i) the aerobic degradation pathways of hexachlorocyclohexane (HCH) isomers; (ii) the important genes and enzymes involved in the metabolic pathways of HCH isomer degradation; and (iii) the identification and quantification of intermediate metabolites through gas chromatography coupled to mass spectrometry (GC-MS).
Collapse
Affiliation(s)
- S A Cuozzo
- a Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET) , Tucumán , Argentina.,b Facultad de Ciencias Naturales e Instituto Miguel Lillo , Universidad Nacional de Tucumán , Tucumán , Argentina
| | - P E Sineli
- a Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET) , Tucumán , Argentina
| | - J Davila Costa
- a Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET) , Tucumán , Argentina
| | - G Tortella
- c Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA) , Universidad de La Frontera , Temuco , Chile.,d Departamento de Ingeniería Química , Universidad de La Frontera , Temuco , Chile
| |
Collapse
|
28
|
Heeb NV, Grubelnik A, Geueke B, Kohler HPE, Lienemann P. Biotransformation of hexabromocyclododecanes with hexachlorocyclohexane-transforming Sphingobium chinhatense strain IP26. CHEMOSPHERE 2017; 182:491-500. [PMID: 28521164 DOI: 10.1016/j.chemosphere.2017.05.047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 05/05/2017] [Accepted: 05/08/2017] [Indexed: 06/07/2023]
Abstract
Bacterial evolution has resulted in the appearance of several Sphingomonadacea strains that gained the ability to metabolize hexachlorocyclohexanes (HCHs). HCHs have been widely used as pesticides but were banned under the Stockholm Convention on persistent organic pollutants (POPs) in 2009. Here we present evidence for bacterial transformation reactions of hexabromocyclododecanes (HBCDs), which are structurally related to HCHs. HBCDs were used as flame retardants. They are now also considered as POPs and their production and use is restricted since 2013. Racemic α-, β-, and γ-HBCDs and their mixture were exposed to Sphingobium chinhatense IP26 in resting cell assays in parallel to β-HCH. All HBCD stereoisomers were converted with (-)β-HBCD being the best and both α-HBCD enantiomers the poorest substrates. HBCD conversion rates were 27-430 times slower than that of β-HCH. Three generations of hydroxylated transformation products were observed, 7 pentabromocyclododecanol isomers (PeBCD-ols), 11 tetrabromocyclododecadiols (TeBCD-diols) and 3 tribromocyclododecatriols (TrBCD-triols). The conversion of (+)α-, (-)β- and (-)γ-HBCD was faster than those of their enantiomers. Therefore the respective enantiomeric excess increased to 3 ± 1%, 36 ± 1% and 6 ± 2% during 48 h of bacterial exposure. PeBCD-ols appeared first, followed by TeBCD-diols and TrBCD-triols indicating stepwise hydrolytic dehalogenation reactions. In conclusion, severe HCH pollution at geographically distinct dumpsites triggered bacterial evolution to express enzymes transforming such compounds. We used S. chinhatense IP26 bacteria to transform structurally related HBCDs, also regulated under the Stockholm Convention. Such bacteria might be useful for bioremediation but the toxicity of the numerous transformation products observed must be assessed in advance.
Collapse
Affiliation(s)
- Norbert V Heeb
- Empa, Swiss Federal Laboratories for Materials Testing and Research, Laboratory for Advanced Analytical Technologies, Überlandstrasse 129, CH-8600, Dübendorf, Switzerland.
| | - Andreas Grubelnik
- Empa, Swiss Federal Laboratories for Materials Testing and Research, Laboratory for Advanced Analytical Technologies, Überlandstrasse 129, CH-8600, Dübendorf, Switzerland
| | - Birgit Geueke
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - Hans-Peter E Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - Peter Lienemann
- ZHAW, Zurich University of Applied Sciences, Institute of Chemistry and Biological Chemistry, Reidbach, CH-8820, Wädenswil, Switzerland
| |
Collapse
|
29
|
Verma H, Bajaj A, Kumar R, Kaur J, Anand S, Nayyar N, Puri A, Singh Y, Khurana JP, Lal R. Genome Organization of Sphingobium indicum B90A: An Archetypal Hexachlorocyclohexane (HCH) Degrading Genotype. Genome Biol Evol 2017; 9:2191-2197. [PMID: 28922869 PMCID: PMC5737386 DOI: 10.1093/gbe/evx133] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2017] [Indexed: 12/23/2022] Open
Abstract
Among sphingomonads, Sphingobium indicum B90A is widely investigated for its ability to degrade a manmade pesticide, γ-hexachlorocyclohexane (γ-HCH) and its isomers (α-, β-, δ-, and ε-HCH). In this study, complete genome of strain B90A was constructed using Single Molecule Real Time Sequencing (SMRT) and Illumina platform. The complete genome revealed that strain B90A harbors four replicons: one chromosome (3,654,322 bp) and three plasmids designated as pSRL1 (139,218 bp), pSRL2 (108,430 bp) and pSRL3 (43,761 bp). The study determined the precise location of lin genes (genes associated with the degradation of HCH isomers), for example, linA2, linB, linDER, linF, linGHIJ, and linKLMN on the chromosome; linA1, linC, and linF on pSRL1 and linDEbR on pSRL3. Strain B90A contained 26 copies of IS6100 element and most of them (15 copies) was found to be associated with lin genes. Duplication of several lin genes including linA, linDER, linGHIJ, and linF along with two variants of linE, that is, linEa (hydroquinone 1,2-dioxygenase) and linEb (chlorohydroquinone/hydroquinone 1,2-dioxygenase) were identified. This suggests that strain B90A not only possess efficient machinery for upper and lower HCH degradation pathways but it can also act on both hydroquinone and chlorohydroquinone metabolites produced during γ-HCH degradation. Synteny analysis revealed the duplication and transposition of linA gene (HCH dehydrochlorinase) between the chromosome and pSRL1, possibly through homologous recombination between adjacent IS6100 elements. Further, in silico analysis and laboratory experiments revealed that incomplete tyrosine metabolism was responsible for the production of extracellular brown pigment which distinguished strain B90A from other HCH degrading sphingomonads. The precise localization of lin genes, and transposable elements (IS6100) on different replicons now opens up several experimental avenues to elucidate the functions and regulatory mechanism of lin genes acquisition and transfer that were not completely known among the bacterial population inhabiting the HCH contaminated environment.
Collapse
Affiliation(s)
- Helianthous Verma
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, India
| | - Abhay Bajaj
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, India
| | - Roshan Kumar
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, India
| | - Jasvinder Kaur
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, India
| | - Shailly Anand
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, India
| | - Namita Nayyar
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, India
| | - Akshita Puri
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, India
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, India
| | - Yogendra Singh
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, India
| | - Jitendra P. Khurana
- Department of Plant Molecular Biology, Interdisciplinary Centre for Plant Genomics, University of Delhi South Campus, India
| | - Rup Lal
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, India
| |
Collapse
|
30
|
Asemoloye MD, Ahmad R, Jonathan SG. Synergistic rhizosphere degradation of γ-hexachlorocyclohexane (lindane) through the combinatorial plant-fungal action. PLoS One 2017; 12:e0183373. [PMID: 28859100 PMCID: PMC5578508 DOI: 10.1371/journal.pone.0183373] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/02/2017] [Indexed: 11/19/2022] Open
Abstract
Fungi are usually involved in degradation/deterioration of many anthropogenic wastes due to their verse enzyme secretions and adaptive capabilities. In this study, five dominant fungal strains were isolated from an aged lindane polluted site, they were all mixed (100 mg each) together with pent mushroom compost (SMC) and applied to lindane polluted soil (5 kg) at 10, 20, 30, 40% and control 0% (soil with no treatment), these were used to grow M. maximus Jacq for 3 months. To establish lindane degradation, deductions such as Degradation rate (K1), Half-life (t1/2) and Degradation efficiency (DE) were made based on the analyzed lindane concentrations before and after the experiment. We also tested the presence and expressions of phosphoesterases (mpd and opd-A) and catechol 1,2-dioxygenases (efk2 and efk4) genes in the strains. The stains were identified as Aspergillus niger (KY693970); Talaromyces atroroseus (KY488464), Talaromyces purpurogenus (KY488468), Yarrowia lipolytica (KY488469) and Aspergillus flavus (KY693973) through morphological and molecular methods. Combined rhizospheric action of M. maximus and fungi speed up lindane degradation rate, initially detected lindane concentration of 45 mg/kg was reduced to 11.26, 9.34 and 11.23 mg/kg in 20, 30 and 40% treatments respectively making 79.76, 85.93 and 88.67% degradation efficiencies. K1 of 1.29 was recorded in control while higher K1 of 1.60, 1.96 and 2.18 /day were recorded in 20, 30 and 40% treatments respectively. The best t1/2 of 0.32 and 0.35 /day were recorded in 40 and 30% compared to control (0.54 /day). All the strains were also affirmed to possess the tested genes; opd was overexpressed in all the strains except KY693973 while mpd was overexpressed in KY693970, KY488464 but moderately expressed in KY488468, KY488469 and KY693973. However, efk genes were under-expressed in most of the strains except KY488469 and KY693973 which showed moderate expression of efk4. This work suggests that the synergistic association of the identified rhizospheric fungi and M. maximus roots could be used to remove lindane in soil at a limited time period and this combination could be used at large scale.
Collapse
Affiliation(s)
- Michael Dare Asemoloye
- Food and Environmental Mycology/Biotechnology Unit, Department of Botany, University of Ibadan, Ibadan, Nigeria
| | - Rafiq Ahmad
- Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Segun Gbolagade Jonathan
- Food and Environmental Mycology/Biotechnology Unit, Department of Botany, University of Ibadan, Ibadan, Nigeria
| |
Collapse
|
31
|
Novel Three-Component Phenazine-1-Carboxylic Acid 1,2-Dioxygenase in Sphingomonas wittichii DP58. Appl Environ Microbiol 2017; 83:AEM.00133-17. [PMID: 28188209 DOI: 10.1128/aem.00133-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 02/06/2017] [Indexed: 11/20/2022] Open
Abstract
Phenazine-1-carboxylic acid, the main component of shenqinmycin, is widely used in southern China for the prevention of rice sheath blight. However, the fate of phenazine-1-carboxylic acid in soil remains uncertain. Sphingomonas wittichii DP58 can use phenazine-1-carboxylic acid as its sole carbon and nitrogen sources for growth. In this study, dioxygenase-encoding genes, pcaA1A2, were found using transcriptome analysis to be highly upregulated upon phenazine-1-carboxylic acid biodegradation. PcaA1 shares 68% amino acid sequence identity with the large oxygenase subunit of anthranilate 1,2-dioxygenase from Rhodococcus maanshanensis DSM 44675. The dioxygenase was coexpressed in Escherichia coli with its adjacent reductase-encoding gene, pcaA3, and ferredoxin-encoding gene, pcaA4, and showed phenazine-1-carboxylic acid consumption. The dioxygenase-, ferredoxin-, and reductase-encoding genes were expressed in Pseudomonas putida KT2440 or E. coli BL21, and the three recombinant proteins were purified. A phenazine-1-carboxylic acid conversion capability occurred in vitro only when all three components were present. However, P. putida KT2440 transformed with pcaA1A2 obtained phenazine-1-carboxylic acid degradation ability, suggesting that phenazine-1-carboxylic acid 1,2-dioxygenase has low specificities for its ferredoxin and reductase. This was verified by replacing PcaA3 with RedA2 in the in vitro enzyme assay. High-performance liquid chromatography-mass spectrometry (HPLC-MS) and nuclear magnetic resonance (NMR) analysis showed that phenazine-1-carboxylic acid was converted to 1,2-dihydroxyphenazine through decarboxylation and hydroxylation, indicating that PcaA1A2A3A4 constitutes the initial phenazine-1-carboxylic acid 1,2-dioxygenase. This study fills a gap in our understanding of the biodegradation of phenazine-1-carboxylic acid and illustrates a new dioxygenase for decarboxylation.IMPORTANCE Phenazine-1-carboxylic acid is widely used in southern China as a key fungicide to prevent rice sheath blight. However, the degradation characteristics of phenazine-1-carboxylic acid and the environmental consequences of the long-term application are not clear. S. wittichii DP58 can use phenazine-1-carboxylic acid as its sole carbon and nitrogen sources. In this study, a three-component dioxygenase, PcaA1A2A3A4, was determined to be the initial dioxygenase for phenazine-1-carboxylic acid degradation in S. wittichii DP58. Phenazine-1-carboxylic acid was converted to 1,2-dihydroxyphenazine through decarboxylation and hydroxylation. This finding may help us discover the pathway for phenazine-1-carboxylic acid degradation.
Collapse
|
32
|
Horemans B, Breugelmans P, Saeys W, Springael D. Soil-Bacterium Compatibility Model as a Decision-Making Tool for Soil Bioremediation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:1605-1615. [PMID: 28001051 DOI: 10.1021/acs.est.6b04956] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Bioremediation of organic pollutant contaminated soil involving bioaugmentation with dedicated bacteria specialized in degrading the pollutant is suggested as a green and economically sound alternative to physico-chemical treatment. However, intrinsic soil characteristics impact the success of bioaugmentation. The feasibility of using partial least-squares regression (PLSR) to predict the success of bioaugmentation in contaminated soil based on the intrinsic physico-chemical soil characteristics and, hence, to improve the success of bioaugmentation, was examined. As a proof of principle, PLSR was used to build soil-bacterium compatibility models to predict the bioaugmentation success of the phenanthrene-degrading Novosphingobium sp. LH128. The survival and biodegradation activity of strain LH128 were measured in 20 soils and correlated with the soil characteristics. PLSR was able to predict the strain's survival using 12 variables or less while the PAH-degrading activity of strain LH128 in soils that show survival was predicted using 9 variables. A three-step approach using the developed soil-bacterium compatibility models is proposed as a decision making tool and first estimation to select compatible soils and organisms and increase the chance of success of bioaugmentation.
Collapse
Affiliation(s)
- Benjamin Horemans
- KU Leuven , Division of Soil and Water Management, Kasteelpark Arenberg 20, 3001 Heverlee, Belgium
| | - Philip Breugelmans
- KU Leuven , Division of Soil and Water Management, Kasteelpark Arenberg 20, 3001 Heverlee, Belgium
| | - Wouter Saeys
- KU Leuven , Department of Biosystems, MeBioS, Kasteelpark Arenberg 30, 3001 Leuven, Belgium
| | - Dirk Springael
- KU Leuven , Division of Soil and Water Management, Kasteelpark Arenberg 20, 3001 Heverlee, Belgium
| |
Collapse
|
33
|
Kaushik S, Prokop Z, Damborsky J, Chaloupkova R. Kinetics of binding of fluorescent ligands to enzymes with engineered access tunnels. FEBS J 2016; 284:134-148. [DOI: 10.1111/febs.13957] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 09/30/2016] [Accepted: 11/04/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Shubhangi Kaushik
- Loschmidt Laboratories Department of Experimental Biology Research Centre for Toxic Compounds in the Environment (RECETOX) Masaryk University Brno Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories Department of Experimental Biology Research Centre for Toxic Compounds in the Environment (RECETOX) Masaryk University Brno Czech Republic
- International Clinical Research Center St. Anne's University Hospital Brno Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories Department of Experimental Biology Research Centre for Toxic Compounds in the Environment (RECETOX) Masaryk University Brno Czech Republic
- International Clinical Research Center St. Anne's University Hospital Brno Czech Republic
| | - Radka Chaloupkova
- Loschmidt Laboratories Department of Experimental Biology Research Centre for Toxic Compounds in the Environment (RECETOX) Masaryk University Brno Czech Republic
- International Clinical Research Center St. Anne's University Hospital Brno Czech Republic
| |
Collapse
|
34
|
Kohli P, Richnow HH, Lal R. Compound-Specific Stable Isotope Analysis: Implications in Hexachlorocyclohexane in-vitro and Field Assessment. Indian J Microbiol 2016; 57:11-22. [PMID: 28148976 DOI: 10.1007/s12088-016-0630-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 10/27/2016] [Indexed: 11/30/2022] Open
Abstract
Assessment of biotic and abiotic degradation reactions by studying the variation in stable isotopic compositions of organic contaminants in contaminated soil and aquifers is being increasingly considered during the last two decades with development of Compound specific stable isotope analysis (CSIA) technique. CSIA has been recognized as a potential tool for evaluating both qualitative and quantitative degradation with measurement of shifts in isotope ratios of contaminants and their degradation products as its basis. Amongst a wide variety of environmental pollutants including monoaromatics, chlorinated ethenes and benzenes etc., it is only recently that its efficacy is being tested for assessing biodegradation of a noxious pollutant namely hexachlorocyclohexane (HCH), by pure microbial cultures as well as directly at the field site. Anticipating the increase in demand of this technique for monitoring the microbial degradation along with natural attenuation, this review highlights the basic problems associated with HCH contamination emphasizing the applicability of emerging CSIA technique to absolve the major bottlenecks in assessment of HCH. To this end, the review also provides a brief overview of this technique with summarizing the recent revelations put forward by both in vitro and in situ studies by CSIA in monitoring HCH biodegradation.
Collapse
Affiliation(s)
- Puneet Kohli
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Hans H Richnow
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Rup Lal
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007 India
| |
Collapse
|
35
|
Sineli PE, Tortella G, Dávila Costa JS, Benimeli CS, Cuozzo SA. Evidence of α-, β- and γ-HCH mixture aerobic degradation by the native actinobacteria Streptomyces sp. M7. World J Microbiol Biotechnol 2016; 32:81. [PMID: 27038951 DOI: 10.1007/s11274-016-2037-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 02/23/2016] [Indexed: 11/27/2022]
Abstract
The organochlorine insecticide γ-hexachlorocyclohexane (γ-HCH, lindane) and its non-insecticidal α- and β-isomers continue to pose serious environmental and health concerns, although their use has been restricted or completely banned for decades. In this study we report the first evidence of the growth ability of a Streptomyces strain in a mineral salt medium containing high doses of α- and β-HCH (16.6 mg l(-1)) as a carbon source. Degradation of HCH isomers by Streptomyces sp. M7 was investigated after 1, 4, and 7 days of incubation, determining chloride ion release, and residues in the supernatants by GC with µECD detection. The results show that both the α- and β-HCH isomers were effectively metabolized by Streptomyces sp. M7, with 80 and 78 % degradation respectively, after 7 days of incubation. Moreover, pentachlorocyclohexenes and tetrachlorocyclohexenes were detected as metabolites. In addition, the formation of possible persistent compounds such as chlorobenzenes and chlorophenols were studied by GC-MS, while no phenolic compounds were detected. In conclusion, we have demonstrated for the first time that Streptomyces sp. M7 can degrade α- and β-isomers individually or combined with γ-HCH and could be considered as a potential agent for bioremediation of environments contaminated by organochlorine isomers.
Collapse
Affiliation(s)
- P E Sineli
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, T40001 MVB, Tucumán, Argentina
| | - G Tortella
- Departamento de Ingeniería Química, Universidad de La Frontera, Casilla 54-D, Temuco, Chile
| | - J S Dávila Costa
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, T40001 MVB, Tucumán, Argentina
| | - C S Benimeli
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, T40001 MVB, Tucumán, Argentina
- Universidad del Norte Santo Tomás de Aquino (UNSTA), 9 de Julio 165, 4000, Tucumán, Argentina
| | - S A Cuozzo
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, T40001 MVB, Tucumán, Argentina.
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, 4000, Tucumán, Argentina.
| |
Collapse
|
36
|
Tang X, Zhang R, Zhang Q, Wang W. Dehydrochlorination mechanism of γ-hexachlorocyclohexane degraded by dehydrochlorinase LinA from Sphingomonas paucimobilis UT26. RSC Adv 2016. [DOI: 10.1039/c5ra21461k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The biotransformation pathway from γ-HCH to 1,3,4,6-TCDN catabolized by dehydrochlorinase LinA contains two discontinuous dehydrochlorination reactions and a conformational transition for the product of the first dehydrochlorination reaction.
Collapse
Affiliation(s)
- Xiaowen Tang
- Environment Research Institute
- Shandong University
- Jinan 250100
- P. R. China
| | - Ruiming Zhang
- Environment Research Institute
- Shandong University
- Jinan 250100
- P. R. China
| | - Qingzhu Zhang
- Environment Research Institute
- Shandong University
- Jinan 250100
- P. R. China
| | - Wenxing Wang
- Environment Research Institute
- Shandong University
- Jinan 250100
- P. R. China
| |
Collapse
|
37
|
Ruffner B, Péchy-Tarr M, Höfte M, Bloemberg G, Grunder J, Keel C, Maurhofer M. Evolutionary patchwork of an insecticidal toxin shared between plant-associated pseudomonads and the insect pathogens Photorhabdus and Xenorhabdus. BMC Genomics 2015; 16:609. [PMID: 26275815 PMCID: PMC4542124 DOI: 10.1186/s12864-015-1763-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 07/09/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Root-colonizing fluorescent pseudomonads are known for their excellent abilities to protect plants against soil-borne fungal pathogens. Some of these bacteria produce an insecticidal toxin (Fit) suggesting that they may exploit insect hosts as a secondary niche. However, the ecological relevance of insect toxicity and the mechanisms driving the evolution of toxin production remain puzzling. RESULTS Screening a large collection of plant-associated pseudomonads for insecticidal activity and presence of the Fit toxin revealed that Fit is highly indicative of insecticidal activity and predicts that Pseudomonas protegens and P. chlororaphis are exclusive Fit producers. A comparative evolutionary analysis of Fit toxin-producing Pseudomonas including the insect-pathogenic bacteria Photorhabdus and Xenorhadus, which produce the Fit related Mcf toxin, showed that fit genes are part of a dynamic genomic region with substantial presence/absence polymorphism and local variation in GC base composition. The patchy distribution and phylogenetic incongruence of fit genes indicate that the Fit cluster evolved via horizontal transfer, followed by functional integration of vertically transmitted genes, generating a unique Pseudomonas-specific insect toxin cluster. CONCLUSIONS Our findings suggest that multiple independent evolutionary events led to formation of at least three versions of the Mcf/Fit toxin highlighting the dynamic nature of insect toxin evolution.
Collapse
Affiliation(s)
- Beat Ruffner
- Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, CH-8092, Zurich, Switzerland.
| | - Maria Péchy-Tarr
- Department of Fundamental Microbiology, University of Lausanne, Biophore Building, CH-1015, Lausanne, Switzerland.
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Crop Protection, Ghent University, Ghent, Belgium.
| | - Guido Bloemberg
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
| | - Jürg Grunder
- Natural Resources Sciences, University of Applied Sciences ZHAW, Wädenswil, Switzerland
| | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Biophore Building, CH-1015, Lausanne, Switzerland.
| | - Monika Maurhofer
- Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, CH-8092, Zurich, Switzerland.
| |
Collapse
|
38
|
Heeb NV, Wyss SA, Geueke B, Fleischmann T, Kohler HPE, Bernd Schweizer W, Moor H, Lienemann P. Stereochemistry of enzymatic transformations of (+)β- and (-)β-HBCD with LinA2--a HCH-degrading bacterial enzyme of Sphingobium indicum B90A. CHEMOSPHERE 2015; 122:70-78. [PMID: 25434265 DOI: 10.1016/j.chemosphere.2014.11.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 10/21/2014] [Accepted: 11/02/2014] [Indexed: 06/04/2023]
Abstract
LinA2, a bacterial enzyme expressed in various Sphingomonadaceae, catalyzes the elimination of HCl from hexachlorocyclohexanes (HCHs) and, as discussed here, the release of HBr from certain hexabromocyclododecanes (HBCDs). Both classes of compounds are persistent organic pollutants now regulated under the Stockholm Convention. LinA2 selectively catalyzes the transformation of β-HBCDs; other stereoisomers like α-, γ-, and δ-HBCDs are not converted. The transformation of (-)β-HBCD is considerably faster than that of its enantiomer. Here, we present the XRD crystal structure of 1E,5S,6S,9R,10S-pentabromocyclododecene (PBCDE) and demonstrate that its enantiomer with the 1E,5R,6R,9S,10R-configuration is the only metabolite formed during LinA2-catalyzed dehydrobromination of (-)β-HBCD. Formation of this product can be rationalized by HBr elimination at C5 and C6. A reasonable enzyme-substrate complex with the catalytic dyad His-73 and Asp-25 approaching the hydrogen at C6 and a cationic pocket of Lys-20, Try-42 and Arg-129 binding the leaving bromine at C5 was found from in silico docking experiments. A second PBCDE of yet unknown configuration was obtained from (+)β-HBCD. We predicted its stereochemistry to be 1E,5S,6S,9S,10R-PBCDE from docking experiments. The enzyme-substrate complex obtained from LinA2 and an activated conformation of (+)β-HBCD allows the HBr elimination at C9 and C10 leading to the predicted product. Both modeled enzyme-substrate complexes are in line with 1,2-diaxial HBr eliminations. In conclusion, LinA2, a bacterial enzyme of the HCH-degrading strain Sphingobium indicum B90A was able to stereoselectively convert β-HBCDs. Configurations of both PBCDE metabolites were predicted by molecular docking experiments and confirmed in one case by XRD data.
Collapse
Affiliation(s)
- Norbert V Heeb
- Empa, Swiss Federal Laboratories for Materials Testing and Research, Laboratory for Analytical Chemistry, Überlandstrasse 129, CH-8600 Dübendorf, Switzerland.
| | - Simon A Wyss
- Empa, Swiss Federal Laboratories for Materials Testing and Research, Laboratory for Analytical Chemistry, Überlandstrasse 129, CH-8600 Dübendorf, Switzerland; ZHAW, Zurich University of Applied Sciences, Institute of Chemistry and Biological Chemistry, Reidbach, CH-8820 Wädenswil, Switzerland
| | - Birgit Geueke
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
| | - Thomas Fleischmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
| | - Hans-Peter E Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
| | - W Bernd Schweizer
- ETH, Swiss Federal Institute of Technology, Laboratory for Organic Chemistry, Hönggerberg, CH-8093 Zürich, Switzerland
| | - Heidi Moor
- Empa, Swiss Federal Laboratories for Materials Testing and Research, Laboratory for Analytical Chemistry, Überlandstrasse 129, CH-8600 Dübendorf, Switzerland; ZHAW, Zurich University of Applied Sciences, Institute of Chemistry and Biological Chemistry, Reidbach, CH-8820 Wädenswil, Switzerland
| | - Peter Lienemann
- ZHAW, Zurich University of Applied Sciences, Institute of Chemistry and Biological Chemistry, Reidbach, CH-8820 Wädenswil, Switzerland
| |
Collapse
|
39
|
Verma H, Kumar R, Oldach P, Sangwan N, Khurana JP, Gilbert JA, Lal R. Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways. BMC Genomics 2014; 15:1014. [PMID: 25418849 PMCID: PMC4289293 DOI: 10.1186/1471-2164-15-1014] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 10/23/2014] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Sphingobium spp. are efficient degraders of a wide range of chlorinated and aromatic hydrocarbons. In particular, strains which harbour the lin pathway genes mediating the degradation of hexachlorocyclohexane (HCH) isomers are of interest due to the widespread persistence of this contaminant. Here, we examined the evolution and diversification of the lin pathway under the selective pressure of HCH, by comparing the draft genomes of six newly-sequenced Sphingobium spp. (strains LL03, DS20, IP26, HDIPO4, P25 and RL3) isolated from HCH dumpsites, with three existing genomes (S. indicum B90A, S. japonicum UT26S and Sphingobium sp. SYK6). RESULTS Efficient HCH degraders phylogenetically clustered in a closely related group comprising of UT26S, B90A, HDIPO4 and IP26, where HDIPO4 and IP26 were classified as subspecies with ANI value >98%. Less than 10% of the total gene content was shared among all nine strains, but among the eight HCH-associated strains, that is all except SYK6, the shared gene content jumped to nearly 25%. Genes associated with nitrogen stress response and two-component systems were found to be enriched. The strains also housed many xenobiotic degradation pathways other than HCH, despite the absence of these xenobiotics from isolation sources. Additionally, these strains, although non-motile, but posses flagellar assembly genes. While strains HDIPO4 and IP26 contained the complete set of lin genes, DS20 was entirely devoid of lin genes (except linKLMN) whereas, LL03, P25 and RL3 were identified as lin deficient strains, as they housed incomplete lin pathways. Further, in HDIPO4, linA was found as a hybrid of two natural variants i.e., linA1 and linA2 known for their different enantioselectivity. CONCLUSION The bacteria isolated from HCH dumpsites provide a natural testing ground to study variations in the lin system and their effects on degradation efficacy. Further, the diversity in the lin gene sequences and copy number, their arrangement with respect to IS6100 and evidence for potential plasmid content elucidate possible evolutionary acquisition mechanisms for this pathway. This study further opens the horizon for selection of bacterial strains for inclusion in an HCH bioremediation consortium and suggests that HDIPO4, IP26 and B90A would be appropriate candidates for inclusion.
Collapse
Affiliation(s)
- Helianthous Verma
- />Molecular Biology Laboratory, Department of Zoology, University of Delhi, Room No. 115, Delhi, 110007 India
| | - Roshan Kumar
- />Molecular Biology Laboratory, Department of Zoology, University of Delhi, Room No. 115, Delhi, 110007 India
| | - Phoebe Oldach
- />Molecular Biology Laboratory, Department of Zoology, University of Delhi, Room No. 115, Delhi, 110007 India
| | - Naseer Sangwan
- />Molecular Biology Laboratory, Department of Zoology, University of Delhi, Room No. 115, Delhi, 110007 India
| | - Jitendra P Khurana
- />Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, India
| | - Jack A Gilbert
- />Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439 USA
- />Department of Ecology and Evolution, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637 USA
| | - Rup Lal
- />Molecular Biology Laboratory, Department of Zoology, University of Delhi, Room No. 115, Delhi, 110007 India
| |
Collapse
|
40
|
Heeb NV, Wyss SA, Geueke B, Fleischmann T, Kohler HPE, Lienemann P. LinA2, a HCH-converting bacterial enzyme that dehydrohalogenates HBCDs. CHEMOSPHERE 2014; 107:194-202. [PMID: 24444415 DOI: 10.1016/j.chemosphere.2013.12.035] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 11/28/2013] [Accepted: 12/11/2013] [Indexed: 06/03/2023]
Abstract
Hexabromocyclododecanes (HBCDs) and hexachlorocyclohexanes (HCHs) are lipophilic, polyhalogenated hydrocarbons with comparable stereochemistry. Bacterial evolution in HCH-contaminated soils resulted in the development of several Spingomonadaceae which express a series of HCH-converting enzymes. We showed that LinB, a haloalkane dehalogenase from Sphingobium indicum B90A, also transforms various HBCDs besides HCHs. Here we present evidence that LinA2, another dehalogenase from S. indicum also converts certain HBCDs to pentabromocyclododecenes (PBCDEs). Racemic mixtures of α-, β-, γ-HBCDs, a mixture of them, and δ-HBCD, a meso form, were exposed to LinA2. Substantial conversion of (-)β-HBCD was observed, but all other stereoisomers were not transformed significantly. The enantiomeric excess (EE) of β-HBCDs increased up to 60% in 32 h, whereas EE values of α- and γ-HBCDs were not affected. Substrate conversion and product formation were described with second-order kinetic models. One major (P1β) and possibly two minor (P2β, P3β) metabolites were detected. Respective mass spectra showed the characteristic isotope pattern of PBCDEs, the HBr elimination products of HBCDs. Michaelis-Menten parameters KM=0.47 ± 0.07 μM and vmax=0.17 ± 0.01 μmoll(-1)h(-1) were deduced from exposure data with varying enzyme/substrate ratios. LinA2 is more substrate specific than LinB, the latter converted all tested HBCDs, LinA2 only one. The widespread HCH pollution favored the selection and evolution of bacteria converting these compounds. We found that LinA2 and LinB, two of these HCH-converting enzymes expressed in S. indicum B90A, also dehalogenate HBCDs to lower brominated compounds, indicating that structural similarities of both classes of compounds are recognized at the level of substrate-protein interactions.
Collapse
Affiliation(s)
- Norbert V Heeb
- Empa, Swiss Federal Laboratories for Materials Testing and Research, Laboratory for Analytical Chemistry, Überlandstrasse 129, CH-8600 Dübendorf, Switzerland.
| | - Simon A Wyss
- Empa, Swiss Federal Laboratories for Materials Testing and Research, Laboratory for Analytical Chemistry, Überlandstrasse 129, CH-8600 Dübendorf, Switzerland; ZHAW, Zurich University of Applied Sciences, Institute of Chemistry and Biological Chemistry, Reidbach, CH-8820 Wädenswil, Switzerland
| | - Birgit Geueke
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
| | - Thomas Fleischmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
| | - Hans-Peter E Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
| | - Peter Lienemann
- ZHAW, Zurich University of Applied Sciences, Institute of Chemistry and Biological Chemistry, Reidbach, CH-8820 Wädenswil, Switzerland
| |
Collapse
|
41
|
Endo R, Ohtsubo Y, Tsuda M, Nagata Y. Growth Inhibition by Metabolites of γ-Hexachlorocyclohexane inSphingobium japonicumUT26. Biosci Biotechnol Biochem 2014; 70:1029-32. [PMID: 16636477 DOI: 10.1271/bbb.70.1029] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The growth of a gamma-hexachlorocyclohexane (gamma-HCH)-degrading bacterium Sphingobium japonicum (formerly Sphingomonas paucimobilis) UT26 in rich medium was inhibited by gamma-HCH. This growth inhibition was not observed in a mutant that lacked the initial or second step enzymatic activity for gamma-HCH degradation, suggesting that metabolites of gamma-HCH are toxic to UT26. Two metabolites of gamma-HCH, 2,5-dichlorophenol (2,5-DCP) and 2,5-dichlorohydroquinone (2,5-DCHQ), showed a direct toxic effect on UT26 and other sphingomonad strains. Because only 2,5-DCP accumulated during gamma-HCH degradation, 2,5-DCP is thought to be a main compound for growth inhibition.
Collapse
Affiliation(s)
- Ryo Endo
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | | | | | | |
Collapse
|
42
|
Nayyar N, Sangwan N, Kohli P, Verma H, Kumar R, Negi V, Oldach P, Mahato NK, Gupta V, Lal R. Hexachlorocyclohexane: persistence, toxicity and decontamination. REVIEWS ON ENVIRONMENTAL HEALTH 2014; 29:49-52. [PMID: 24622782 DOI: 10.1515/reveh-2014-0015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 01/16/2014] [Indexed: 06/03/2023]
Abstract
Hexachlorocyclohexane (HCH), a persistent organochlorine insecticide, has been extensively used in the past for control of agricultural pests and vector borne diseases. The use of HCH has indeed accrued benefits, however the unusual production of the insecticidal isomer; γ-HCH (lindane) and unregulated disposal of HCH muck has created various dumpsites all over the world, leading to serious environmental concerns. HCH isomers have been ranked as possible human carcinogens and endocrine disruptors with proven teratogenic, mutagenic and genotoxic effects, hence making its decontamination mandatory. Efforts in this direction have led to the isolation of various HCH degrading bacteria from the dumpsites, reflecting their role in HCH bioremediation. This review summarizes the problem of environmental persistence of HCH isomers along with their toxicity and possible solutions for their decontamination.
Collapse
|
43
|
Enantioselective dehydrochlorination of δ-Hexachlorocyclohexane and δ-Pentachlorocyclohexene by LinA1 and LinA2 from Sphingobium indicum B90A. Appl Environ Microbiol 2013; 79:6180-3. [PMID: 23872559 DOI: 10.1128/aem.01770-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
δ-Hexachlorocyclohexane (δ-HCH), one of the prevalent isomers of technical HCH, was enantioselectively dehydrochlorinated by the dehydrochlorinases LinA1 and LinA2 from Sphingobium indicum B90A to the very same δ-pentachlorocyclohexene enantiomer. Racemic δ-pentachlorocyclohexene, however, was transformed with opposite enantioselectivities by the two enzymes. A transformation pathway based on an anti-1,2-elimination, followed by a syn-1,4-elimination and a subsequent syn-1,2-elimination is postulated.
Collapse
|
44
|
Manna RN, Dybala-Defratyka A. Insights into the elimination mechanisms employed for the degradation of different hexachlorocyclohexane isomers using kinetic isotope effects and docking studies. J PHYS ORG CHEM 2013. [DOI: 10.1002/poc.3163] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Rabindra Nath Manna
- Institute of Applied Radiation Chemistry, Faculty of Chemistry; Lodz University of Technology; Zeromskiego 116 Lodz Poland
| | - Agnieszka Dybala-Defratyka
- Institute of Applied Radiation Chemistry, Faculty of Chemistry; Lodz University of Technology; Zeromskiego 116 Lodz Poland
| |
Collapse
|
45
|
De Paolis MR, Lippi D, Guerriero E, Polcaro CM, Donati E. Biodegradation of α-, β-, and γ-hexachlorocyclohexane by Arthrobacter fluorescens and Arthrobacter giacomelloi. Appl Biochem Biotechnol 2013; 170:514-24. [PMID: 23553101 DOI: 10.1007/s12010-013-0147-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 02/18/2013] [Indexed: 11/30/2022]
Abstract
The organochlorine pesticide γ-hexachlorocyclohexane (γ-HCH, lindane) and its non-insecticidal isomers α-, β-, and δ- continue to pose serious environmental and health concerns, although their use has been restricted or completely banned for decades. The present study reports the first results on the ability of two Arthrobacter strains, not directly isolated from a HCH-polluted site, to grow in a mineral salt medium containing α-, β-, or γ-HCH (100 mgl(-1)) as sole source of carbon. Growth of cultures and HCHs degradation by Arthrobacter fluorescens and Arthrobacter giacomelloi were investigated after 1, 2, 3, 4, and 7 days of incubation by enumerating colony forming units and GC with ECD detection, respectively. Both bacteria are able to metabolize the HCHs: A. giacomelloi is the most effective one, as after 72 h of incubation it produces 88 % degradation of α-, 60 % of β-, and 56 % of γ-HCH. The formation of possible persistent compounds was studied by GC/MS and by HPLC analysis. Pentachlorocyclohexenes and tetrachlorocyclohexenes have been detected as metabolites, which are almost completely eliminated after 72 h of incubation, while no phenolic compounds were found.
Collapse
Affiliation(s)
- M R De Paolis
- Institute of Agro-environmental and Forest Biology, Research Area of Rome 1, National Research Council, Via Salaria Km. 29,300, 00015 Monterotondo (Roma), Italy
| | | | | | | | | |
Collapse
|
46
|
Alvarez A, Benimeli CS, Saez JM, Fuentes MS, Cuozzo SA, Polti MA, Amoroso MJ. Bacterial bio-resources for remediation of hexachlorocyclohexane. Int J Mol Sci 2012; 13:15086-106. [PMID: 23203113 PMCID: PMC3509629 DOI: 10.3390/ijms131115086] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 09/29/2012] [Accepted: 10/17/2012] [Indexed: 11/25/2022] Open
Abstract
In the last few decades, highly toxic organic compounds like the organochlorine pesticide (OP) hexachlorocyclohexane (HCH) have been released into the environment. All HCH isomers are acutely toxic to mammals. Although nowadays its use is restricted or completely banned in most countries, it continues posing serious environmental and health concerns. Since HCH toxicity is well known, it is imperative to develop methods to remove it from the environment. Bioremediation technologies, which use microorganisms and/or plants to degrade toxic contaminants, have become the focus of interest. Microorganisms play a significant role in the transformation and degradation of xenobiotic compounds. Many Gram-negative bacteria have been reported to have metabolic abilities to attack HCH. For instance, several Sphingomonas strains have been reported to degrade the pesticide. On the other hand, among Gram-positive microorganisms, actinobacteria have a great potential for biodegradation of organic and inorganic toxic compounds. This review compiles and updates the information available on bacterial removal of HCH, particularly by Streptomyces strains, a prolific genus of actinobacteria. A brief account on the persistence and deleterious effects of these pollutant chemical is also given.
Collapse
Affiliation(s)
- Analía Alvarez
- Pilot Plant of Industrial and Microbiological Processes (PROIMI), CONICET, Av. Belgrano y Pasaje Caseros, 4000 Tucumán, Argentina; E-Mails: (A.A.); (C.S.B.); (J.M.S.); (M.S.F.); (S.A.C.); (M.A.P.)
- Natural Sciences College and Miguel Lillo Institute, National University of Tucumán, Miguel Lillo 205, 4000 Tucumán, Argentina
| | - Claudia S. Benimeli
- Pilot Plant of Industrial and Microbiological Processes (PROIMI), CONICET, Av. Belgrano y Pasaje Caseros, 4000 Tucumán, Argentina; E-Mails: (A.A.); (C.S.B.); (J.M.S.); (M.S.F.); (S.A.C.); (M.A.P.)
- North University of Saint Thomas Aquines, 9 de Julio 165, 4000 Tucumán, Argentina
| | - Juliana M. Saez
- Pilot Plant of Industrial and Microbiological Processes (PROIMI), CONICET, Av. Belgrano y Pasaje Caseros, 4000 Tucumán, Argentina; E-Mails: (A.A.); (C.S.B.); (J.M.S.); (M.S.F.); (S.A.C.); (M.A.P.)
| | - María S. Fuentes
- Pilot Plant of Industrial and Microbiological Processes (PROIMI), CONICET, Av. Belgrano y Pasaje Caseros, 4000 Tucumán, Argentina; E-Mails: (A.A.); (C.S.B.); (J.M.S.); (M.S.F.); (S.A.C.); (M.A.P.)
| | - Sergio A. Cuozzo
- Pilot Plant of Industrial and Microbiological Processes (PROIMI), CONICET, Av. Belgrano y Pasaje Caseros, 4000 Tucumán, Argentina; E-Mails: (A.A.); (C.S.B.); (J.M.S.); (M.S.F.); (S.A.C.); (M.A.P.)
- Natural Sciences College and Miguel Lillo Institute, National University of Tucumán, Miguel Lillo 205, 4000 Tucumán, Argentina
| | - Marta A. Polti
- Pilot Plant of Industrial and Microbiological Processes (PROIMI), CONICET, Av. Belgrano y Pasaje Caseros, 4000 Tucumán, Argentina; E-Mails: (A.A.); (C.S.B.); (J.M.S.); (M.S.F.); (S.A.C.); (M.A.P.)
- Natural Sciences College and Miguel Lillo Institute, National University of Tucumán, Miguel Lillo 205, 4000 Tucumán, Argentina
| | - María J. Amoroso
- Pilot Plant of Industrial and Microbiological Processes (PROIMI), CONICET, Av. Belgrano y Pasaje Caseros, 4000 Tucumán, Argentina; E-Mails: (A.A.); (C.S.B.); (J.M.S.); (M.S.F.); (S.A.C.); (M.A.P.)
- North University of Saint Thomas Aquines, 9 de Julio 165, 4000 Tucumán, Argentina
- Biochemistry, Chemistry and Pharmacy College, National University of Tucumán, Ayacucho 471, 4000 Tucumán, Argentina
| |
Collapse
|
47
|
Manickam N, Bajaj A, Saini HS, Shanker R. Surfactant mediated enhanced biodegradation of hexachlorocyclohexane (HCH) isomers by Sphingomonas sp. NM05. Biodegradation 2012; 23:673-82. [PMID: 22302596 DOI: 10.1007/s10532-012-9543-z] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 01/21/2012] [Indexed: 12/01/2022]
Abstract
Environmental biodegradation of several chlorinated pesticides is limited by their low solubility and sorption to soil surfaces. To mitigate this problem we quantified the effect of three biosurfactant viz., rhamnolipid, sophorolipid and trehalose-containing lipid on the dissolution, bioavailability, and biodegradation of HCH-isomers in liquid culture and in contaminated soil. The effect of biosurfactants was evaluated through the critical micelle concentration (CMC) value as determined for each isomer. The surfactant increased the solubilization of HCH isomers by 3-9 folds with rhamnolipid and sophorolipid being more effective and showing maximum solubilization of HCH isomers at 40 μg/mL, compared to trehalose-containing lipid showing peak solubilization at 60 μg/mL. The degradation of HCH isomers by Sphingomonas sp. NM05 in surfactant-amended liquid mineral salts medium showed 30% enhancement in 2 days as compared to degradation in 10 days in the absence of surfactant. HCH-spiked soil slurry incubated with surfactant also showed around 30-50% enhanced degradation of HCH which was comparable to the corresponding batch culture experiments. Among the three surfactants, sophorolipid offered highest solubilization and enhanced degradation of HCH isomers both in liquid medium and soil culture. The results of this study suggest the effectiveness of surfactants in improving HCH degradation by increased bioaccessibility.
Collapse
Affiliation(s)
- Natesan Manickam
- Environmental Biotechnology, Indian Institute of Toxicology Research, Council of Scientific & Industrial Research, Lucknow 226001, India.
| | | | | | | |
Collapse
|
48
|
Geueke B, Garg N, Ghosh S, Fleischmann T, Holliger C, Lal R, Kohler HPE. Metabolomics of hexachlorocyclohexane (HCH) transformation: ratio of LinA to LinB determines metabolic fate of HCH isomers. Environ Microbiol 2012; 15:1040-9. [PMID: 23121161 DOI: 10.1111/1462-2920.12009] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 09/18/2012] [Accepted: 09/26/2012] [Indexed: 11/26/2022]
Abstract
Although the production and use of technical hexachlorocyclohexane (HCH) and lindane (the purified insecticidal isomer γ-HCH) are prohibited in most countries, residual concentrations still constitute an immense environmental burden. Many studies describe the mineralization of γ-HCH by bacterial strains under aerobic conditions. However, the metabolic fate of the other HCH isomers is not well known. In this study, we investigated the transformation of α-, β-, γ-, δ-, ε-HCH, and a heptachlorocyclohexane isomer in the presence of varying ratios of the two enzymes that initiate γ-HCH degradation, a dehydrochlorinase (LinA) and a haloalkane dehalogenase (LinB). Each substrate yielded a unique metabolic profile that was strongly dependent on the enzyme ratio. Comparison of these results to those of in vivo experiments with different bacterial isolates showed that HCH transformation in the tested strains was highly optimized towards productive metabolism of γ-HCH and that under these conditions other HCH-isomers were metabolized to mixtures of dehydrochlorinated and hydroxylated side-products. In view of these results, bioremediation efforts need very careful planning and toxicities of accumulating metabolites need to be evaluated.
Collapse
Affiliation(s)
- Birgit Geueke
- Department of Environmental Microbiology, Swiss Federal Institute for Aquatic Science and Technology (Eawag), 8600, Dübendorf, Switzerland
| | | | | | | | | | | | | |
Collapse
|
49
|
Heeb NV, Zindel D, Geueke B, Kohler HPE, Lienemann P. Biotransformation of Hexabromocyclododecanes (HBCDs) with LinB--an HCH-converting bacterial enzyme. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:6566-6574. [PMID: 22578084 DOI: 10.1021/es2046487] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Hexabromocyclododecanes (HBCDs) and hexachlorocyclohexanes (HCHs) are polyhalogenated hydrocarbons with similar stereochemistry. Both classes of compounds are considered biologically persistent and bioaccumulating pollutants. In 2009, the major HCH stereoisomers came under regulation of the Stockholm convention. Despite their persistence, HCHs are susceptible to bacterial biotransformations. Here we show that LinB, an HCH-converting haloalkane dehalogenase from Sphingobium indicum B90A, is also able to transform HBCDs. Racemic mixtures of α-, β-, and γ-HBCDs were exposed to LinB under various conditions. All stereoisomers were converted, but (-)α-, (+)β-, and (+)γ-HBCDs were transformed faster by LinB than their enantiomers. The enantiomeric excess increased to 8 ± 4%, 27 ± 1%, and 20 ± 2% in 32 h comparable to values of 7.1%, 27.0%, and 22.9% as obtained from respective kinetic models. Initially formed pentabromocyclododecanols (PBCDOHs) were further transformed to tetrabromocyclododecadiols (TBCDDOHs). At least, seven mono- and five dihydroxylated products were distinguished by LC-MS so far. The widespread occurrence of HCHs has led to the evolution of bacterial degradation pathways for such compounds. It remains to be shown if LinB-catalyzed HBCD transformations in vitro can also be observed in vivo, for example, in contaminated soils or in other words if such HBCD biotransformations are important environmental processes.
Collapse
Affiliation(s)
- Norbert V Heeb
- Laboratory for Analytical Chemistry, Swiss Federal Laboratories for Materials Testing and Research, Empa, Überlandstrasse 129, CH-8600 Dübendorf, Switzerland.
| | | | | | | | | |
Collapse
|
50
|
Bala K, Geueke B, Miska ME, Rentsch D, Poiger T, Dadhwal M, Lal R, Holliger C, Kohler HPE. Enzymatic conversion of ε-hexachlorocyclohexane and a heptachlorocyclohexane isomer, two neglected components of technical hexachlorocyclohexane. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:4051-4058. [PMID: 22385211 DOI: 10.1021/es204143x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
α-, β, γ-, and δ-Hexachlorocyclohexane (HCH), the four major isomers of technical HCH, are susceptible to biotic transformations, whereby only α- and γ-HCH undergo complete mineralization. Nevertheless, LinA and LinB catalyzing HCl elimination and hydrolytic dehalogenations, respectively, as initial steps in the mineralization also convert β- and δ-HCH to a variety of mainly hydroxylated metabolites. In this study, we describe the isolation of two minor components of technical HCH, ε-HCH, and heptachlorocyclohexane (HeCH), and we present data on enzymatic transformations of both compounds by two dehydrochlorinases (LinA1 and LinA2) and a haloalkane dehalogenase (LinB) from Sphingobium indicum B90A. In contrast to reactions with α-, γ-, and δ-HCH, both LinA enzymes converted ε-HCH to a mixture of 1,2,4-, 1,2,3-, and 1,3,5-trichlorobenzenes without the accumulation of pentachlorocyclohexene as intermediate. Furthermore, both LinA enzymes were able to convert HeCH to a mixture of 1,2,3,4- and 1,2,3,5-tetrachlorobenzene. LinB hydroxylated ε-HCH to pentachlorocyclohexanol and tetrachlorocyclohexane-1,4-diol, whereas hexachlorocyclohexanol was the sole product when HeCH was incubated with LinB. The data clearly indicate that various metabolites are formed from minor components of technical HCH mixtures. Such metabolites will contribute to the overall toxic potential of HCH contaminations and may constitute serious, yet unknown environmental risks and must not be neglected in proper risk assessments.
Collapse
Affiliation(s)
- Kiran Bala
- Department of Environmental Microbiology, Swiss Federal Institute for Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
| | | | | | | | | | | | | | | | | |
Collapse
|