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Wani SR, Jain V. Deciphering the molecular mechanism and regulation of formaldehyde detoxification in Mycobacterium smegmatis. Appl Environ Microbiol 2024; 90:e0203923. [PMID: 38259108 PMCID: PMC10880627 DOI: 10.1128/aem.02039-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/11/2023] [Indexed: 01/24/2024] Open
Abstract
The build-up of formaldehyde, a highly reactive molecule is cytotoxic and must be eliminated for the organism's survival. Formaldehyde detoxification system is found in nearly all organisms including both pathogenic and non-pathogenic mycobacteria. MscR, a formaldehyde dehydrogenase from Mycobacterium smegmatis (Msm), is an indispensable part of this system and forms a bicistronic operon with its downstream uncharacterized gene, fmh. We here show that Fmh, a putative metallo-beta-lactamase, is essential in tolerating higher amounts of formaldehyde when co-overexpressed with mscR in vivo. Our NMR studies indicate that MscR, along with Fmh, enhances formate production through a mycothiol (MSH)-dependent pathway, emphasizing the importance of Fmh in detoxifying formaldehyde. Although another aldehyde dehydrogenase, MSMEG_1543, induces upon formaldehyde addition, it is not involved in its detoxification. We also show that the expression of the mscR operon is constitutive and remains unchanged upon formaldehyde addition, as displayed by the promoter activity of PmscR and by the transcript and protein levels of MscR. Furthermore, we establish the role of a thiol-responsive sigma factor SigH in formaldehyde detoxification. We show that SigH, and not SigE, is crucial for formaldehyde detoxification, even though it does not directly regulate mscR operon expression. In addition, sensitivity to formaldehyde in sigH-knockout could be alleviated by overexpression of mscR. Taken together, our data demonstrate the importance of MSH-dependent pathways in detoxifying formaldehyde in a mycobacterial system. An absence of such MSH-dependent proteins in eukaryotes and its complete conservation in M. tuberculosis, the causative agent of tuberculosis, further unravel new drug targets for this pathogen.IMPORTANCEExtensive research has been done on formaldehyde detoxification in different bacteria. However, our current understanding of the mechanisms underlying this process in mycobacteria remains exceedingly little. We previously showed that MscR, a formaldehyde dehydrogenase from Mycobacterium smegmatis, plays a pivotal role in this detoxification pathway. Here, we present a potential S-formyl-mycothiol hydrolase named Fmh, thought to be a metallo-beta-lactamase, which functions along with mycothiol (MSH) and MscR to enhance formate production within this detoxification pathway. Co-expression of Fmh with MscR significantly enhances the efficiency of formaldehyde detoxification in M. smegmatis. Our experiments establish that Fmh catalyzes the final step of this detoxification pathway. Although an alternative sigma factor SigH was found to be involved in formaldehyde detoxification, it did not directly regulate the expression of mscR. Since formaldehyde detoxification is essential for bacterial survival, we envisage this process to be a potential drug target for M. tuberculosis eradication.
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Affiliation(s)
- Saloni Rajesh Wani
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh, India
| | - Vikas Jain
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh, India
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Zhang L, Cheng Y, Qian Y, Ding T, Li J. Bisphenol S degradation in soil and the dynamics of microbial community associated with degradation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 846:157451. [PMID: 35868379 DOI: 10.1016/j.scitotenv.2022.157451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/10/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Bisphenol S (BPS) has been widely applied as a replacement for BPA in industrial application, leading to the frequent detection in the environment. However, its impact on soil microbial communities has not been well reported. Here, effects of BPS exposure on soil microbial communities in the presence of polystyrene (PS) microplastics were revealed. Rapid degradation of BPS occurred with a degradation rate of up to 98.9 ± 0.001 % at 32 d. The presence of BPS reduced the diversity of soil microbial communities, and changed community structures. After BPS treatment, Proteobacteria, and its members Methylobacillus, Rhodobacteraceae and Mesorhizobium became dominant, and were considered as potential biomarkers indicating BPS contamination. Co-occurrence network analysis revealed the increased relationships of certain groups of microbes after BPS treatment. The resultant low stability and resilience towards environment disturbance of microbial community networks implied the biotoxicity of BPS towards soil ecosystems. The degradation and biotoxicity of BPS (p > 0.05) in soil was not affected by the presence of PS. Our findings showed that exposure to BPS could reshape soil microbial communities and impair the robustness of microbial co-occurrence networks.
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Affiliation(s)
- Lili Zhang
- Shenzhen Key Laboratory of Environmental Chemistry and Ecological Remediation, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Yanan Cheng
- Shenzhen Key Laboratory of Environmental Chemistry and Ecological Remediation, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Yiguang Qian
- Shenzhen Key Laboratory of Environmental Chemistry and Ecological Remediation, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Tengda Ding
- Shenzhen Key Laboratory of Environmental Chemistry and Ecological Remediation, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Juying Li
- Shenzhen Key Laboratory of Environmental Chemistry and Ecological Remediation, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China.
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3
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Wani SR, Jain V. Molecular dissection of a dedicated formaldehyde dehydrogenase from Mycobacterium smegmatis. Protein Sci 2022; 31:628-638. [PMID: 34904319 PMCID: PMC8862421 DOI: 10.1002/pro.4258] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/08/2021] [Accepted: 12/10/2021] [Indexed: 11/07/2022]
Abstract
Accumulation of formaldehyde, a highly reactive molecule, in the cell is toxic, and requires detoxification for the organism's survival. Mycothiol-dependent formaldehyde dehydrogenase or S-nitrosomycothiol reductase (MscR) from Mycobacterium smegmatis and Mycobacterium tuberculosis was previously known for detoxifying formaldehyde and protecting the cell against nitrosative stress. We here show that M. smegmatis MscR exhibits a mycothiol-independent formaldehyde dehydrogenase (FDH) activity in vitro. Presence of zinc in the reaction enhances MscR activity, thus making it a zinc-dependent FDH. Interestingly, MscR utilizes only formaldehyde and no other primary aldehydes as its substrate in vitro, and M. smegmatis lacking mscR (ΔmscR) shows sensitivity exclusively toward formaldehyde. Bioinformatics analysis of MscRs from various bacteria reveals 10 positionally conserved cysteines, whose importance in structural stability and biological activity is not yet investigated. To explore the significance of these cysteines, we generated MscR single Cys variants by systematically replacing each cysteine with serine. All of the Cys variants except C39S and C309S are unable to show a complete rescue of ΔmscR on formaldehyde, show a significant loss of enzymatic activity in vitro, pronounced structural alterations as probed by circular dichroism, and loss of homotetramerization on size exclusion chromatography. Our data thus reveal the importance of intact cysteines in the structural stability and biological activity of MscR, which is a dedicated FDH in M. smegmatis, and shows ~84% identity with M. tuberculosis MscR. We believe that this knowledge will further help in the development of FDH as a potential drug target against M. tuberculosis infections.
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Affiliation(s)
- Saloni Rajesh Wani
- Microbiology and Molecular Biology Laboratory, Department of Biological SciencesIndian Institute of Science Education and Research (IISER)BhopalIndia
| | - Vikas Jain
- Microbiology and Molecular Biology Laboratory, Department of Biological SciencesIndian Institute of Science Education and Research (IISER)BhopalIndia
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4
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Jin C, Geng Z, Pang X, Zhang Y, Wang G, Ji J, Li X, Guan C. Isolation and characterization of a novel benzophenone-3-degrading bacterium Methylophilus sp. strain FP-6. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 186:109780. [PMID: 31627096 DOI: 10.1016/j.ecoenv.2019.109780] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 09/09/2019] [Accepted: 10/06/2019] [Indexed: 06/10/2023]
Abstract
Benzophenone-3 (BP-3) is extensively applied in sunscreens and some other related cosmetic products. It is necessary to efficiently and safely remove BP-3 from environments by application of various treatment technologies. However, to the authors' knowledge, BP-3 biodegradation by a single bacterial strain has not been reported before. In this study, a Gram-negative aerobic bacterium capable of degrading BP-3 as a sole carbon source was isolated from a municipal wastewater treatment plant and classified as Methylophilus sp. FP-6 according to BIOLOG GEN III and 16S rDNA analysis. Methanol was chosen for further experiments as a co-metabolic carbon source to enhance the microbial degradation efficiency of BP-3. Orthogonal and one-way experiments were all performed to investigate the optimal culture conditions for degradation of BP-3 by Methylophilus sp. FP-6. The degradation rate of BP-3 reached about 65% after 8 days of incubation with strain FP-6 under optimal culture conditions. The half-life (t1/2) of BP-3 biodegradation by strain FP-6 was estimated as 2.95 days according to the BP-3 degradation curve. The metabolite intermediates generated during the BP-3 degradation process were analyzed by LC-MS/MS and three metabolite products were identified. According to the analysis of metabolic intermediates, three pathways for degradation of BP-3 by strain FP-6 were proposed. The results from this study gave first insights into the potential of BP-3 biodegradation by a single bacterial strain.
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Affiliation(s)
- Chao Jin
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Zhenlong Geng
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Xintong Pang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Yue Zhang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Gang Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Jing Ji
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Xiaozhou Li
- Tianjin Prenatal Diagnosis Center, Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, 300070, China
| | - Chunfeng Guan
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China.
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Firsova YE, Torgonskaya ML. Different roles of two groEL homologues in methylotrophic utiliser of dichloromethane Methylorubrum extorquens DM4. Antonie van Leeuwenhoek 2019; 113:101-116. [PMID: 31463590 DOI: 10.1007/s10482-019-01320-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 08/19/2019] [Indexed: 11/28/2022]
Abstract
The genome of methylotrophic bacteria Methylorubrum extorquens DM4 contains two homologous groESL operons encoding the 60-kDa and 10-kDa subunits of GroE heat shock chaperones with highly similar amino acid sequences. To test a possible functional redundancy of corresponding GroEL proteins we attempted to disrupt the groEL1 and groEL2 genes. Despite the large number of recombinants analysed and the gentle culture conditions the groEL1-lacking mutant was not constructed suggesting that the loss of GroEL1 was lethal for cells. At the same time the ∆groEL2 strain was viable and varied from the wild-type by increased sensitivity to acid, salt and desiccation stresses as well as by the impaired growth with a toxic halogenated compound-dichloromethane (DCM). The evaluation of activity of putative PgroE1 and PgroE2 promoters using the reporter gene of green fluorescent protein (GFP) showed that the expression of groESL1 operon greatly prevails (about two orders of magnitude) over those of groESL2 under all tested conditions. However the above promoters demonstrated differential regulation in response to stresses. The expression from PgroE1 was heat-inducible, while the activity of PgroE2 was upregulated upon acid shock and cultivation with DCM. Based on these results we conclude that the highly conservative groESL1 operon (old locus tags METDI5839-5840) encodes the housekeeping chaperone essential for fundamental cellular processes. On the contrary the second pair of paralogues (METDI4129-4130) is dispensable, but corresponding GroE2 chaperone promotes the tolerance to acid and salt stresses, in particular, during the growth with DCM.
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Affiliation(s)
- Yulia E Firsova
- Laboratory of Radioactive Isotopes, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC Pushchino Center for Biological Research of Russian Academy of Sciences, Pushchino, Russia, 142290
| | - Maria L Torgonskaya
- Laboratory of Radioactive Isotopes, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC Pushchino Center for Biological Research of Russian Academy of Sciences, Pushchino, Russia, 142290.
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6
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Habibi A, Nalband M, Jalilnejad E. Experimentation and CFD modeling of continuous degradation of formaldehyde by immobilized Ralstonia eutropha in a semi-pilot-scale plug flow bioreactor. Bioprocess Biosyst Eng 2018; 42:485-497. [PMID: 30539242 DOI: 10.1007/s00449-018-2052-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 11/30/2018] [Indexed: 11/29/2022]
Abstract
This study focuses on continuous formaldehyde (FA) biodegradation by Ralstonia eutropha immobilized on polyurethane foam in a semi-pilot-scale plug flow packed-bed bioreactor. The stepwise increasing of the influent FA concentration from 43.9 to 1325.1 mg L-1 was studied in the bioreactor during 70 days of operation. A complete removal of FA was achieved for inlet concentration up to 425.5 mg L-1 and the initial specific biodegradation rate reached to its maximum value about 44.3 mg gcell-1 h-1 at 425.5 mg L-1. However, further increase of inlet concentration resulted in decrease of the biodegradation performance of the immobilized cells due to the inhibitory effect of FA on the enzymatic system involved in the biodegradation process. Based on kinetic modeling results, the Luong equation with the following constants could best describe the behavior of the bio-system: maximum specific FA biodegradation rate (qmax) of 124 mg gcell-1 h-1, half-saturation constant (KS) of 337.2 mg L-1, maximum degradable FA concentration (Smax) of 1582 mg L-1, and shape factor (n) of 1.49. Also, three-dimensional simulation of the bioreactor was performed using an integrated computational fluid dynamics (CFD) approach that takes into account both the biokinetic constants of the immobilized system as well as the fluid properties under steady-state condition. Eulerian computations successfully anticipated the concentration gradients through the reactor for different inlet FA concentrations, and uniform vertical velocity pathlines and non-dispersed plug flow inside the reactor were verified by the presented velocity distribution and flow streamlines.
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Affiliation(s)
- Alireza Habibi
- Faculty of Petroleum and Chemical Engineering, Razi University, Kermanshah, Iran
| | - Mehran Nalband
- Faculty of Chemical Engineering, Urmia University of Technology, Urmia, Iran
| | - Elham Jalilnejad
- Faculty of Chemical Engineering, Urmia University of Technology, Urmia, Iran.
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Xu W, Zhang Y, Cao H, Sheng Y, Li H, Li Y, Zhao H, Gui X. Metagenomic insights into the microbiota profiles and bioaugmentation mechanism of organics removal in coal gasification wastewater in an anaerobic/anoxic/oxic system by methanol. BIORESOURCE TECHNOLOGY 2018; 264:106-115. [PMID: 29793117 DOI: 10.1016/j.biortech.2018.05.064] [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: 03/16/2018] [Revised: 05/15/2018] [Accepted: 05/17/2018] [Indexed: 06/08/2023]
Abstract
Coal gasification wastewater is a typical high phenol-containing, toxic and refractory industrial wastewater. Here, lab-scale anaerobic-anoxic-oxic system was employed to treat real coal gasification wastewater, and methanol was added to oxic tank as the co-substrate to enhance the removal of refractory organic pollutants. The results showed that the average COD removal in oxic effluent increased from 24.9% to 36.0% by adding methanol, the total phenols concentration decreased from 54.4 to 44.9 mg/L. GC-MS analysis revealed that contents of phenolic components and polycyclic aromatic hydrocarbons (PAHs) were decreased compared to the control and their degradation intermediates were observed. Microbial community revealed that methanol increased the abundance of phenolics and PAHs degraders such as Comamonas, Burkholderia and Sphingopyxis. Moreover, functional analysis revealed the relative abundance of functional genes associated with toluene, benzoate and PAHs degradation pathways was higher than that of control based on KEGG database.
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Affiliation(s)
- Weichao Xu
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, PR China; Beijing Engineering Research Centre of Process Pollution Control, Division of Environmental Engineering and Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Yuxiu Zhang
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, PR China.
| | - Hongbin Cao
- Beijing Engineering Research Centre of Process Pollution Control, Division of Environmental Engineering and Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Yuxing Sheng
- Beijing Engineering Research Centre of Process Pollution Control, Division of Environmental Engineering and Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Haibo Li
- Beijing Engineering Research Centre of Process Pollution Control, Division of Environmental Engineering and Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Yuping Li
- Beijing Engineering Research Centre of Process Pollution Control, Division of Environmental Engineering and Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - He Zhao
- Beijing Engineering Research Centre of Process Pollution Control, Division of Environmental Engineering and Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Xuefei Gui
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, PR China; Beijing Engineering Research Centre of Process Pollution Control, Division of Environmental Engineering and Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
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8
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A Novel Methylotrophic Bacterial Consortium for Treatment of Industrial Effluents. Appl Biochem Biotechnol 2018; 185:691-704. [PMID: 29292474 DOI: 10.1007/s12010-017-2680-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 12/14/2017] [Indexed: 10/18/2022]
Abstract
Considering the importance of methylotrophs in industrial wastewater treatment, focus of the present study was on utilization of a methylotrophic bacterial consortium as a microbial seed for biotreatment of a variety of industrial effluents. For this purpose, a mixed bacterial methylotrophic AC (Ankleshwar CETP) consortium comprising of Bordetella petrii AC1, Bacillus licheniformis AC4, Salmonella subterranea AC5, and Pseudomonas stutzeri AC8 was used. The AC consortium showed efficient biotreatment of four industrial effluents procured from fertilizer, chemical and pesticide industries, and common effluent treatment plant by lowering their chemical oxygen demand (COD) of 950-2000 mg/l to below detection limit in 60-96 h in 6-l batch reactor and 9-15 days in 6-l continuous reactor. The operating variables of wastewater treatment, viz. COD, BOD, pH, MLSS, MLVSS, SVI, and F/M ratio of these effluents, were also maintained in the permissible range in both batch and continuous reactors. Therefore, formation of the AC consortium has led to the development of an efficient microbial seed capable of treating a variety of industrial effluents containing pollutants generated from their respective industries.
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Habibi A, Vahabzadeh F, Zaiat M. Dynamic mathematical models for biodegradation of formaldehyde by Ralstonia eutropha in a batch bioreactor. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2013; 129:548-554. [PMID: 24018119 DOI: 10.1016/j.jenvman.2013.08.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 08/07/2013] [Indexed: 06/02/2023]
Abstract
Degradation of formaldehyde by Ralstonia eutropha was studied in a batch bioreactor operated in recycling mode (30 °C, initial pH of 6.5, aeration rate 0.5 vvm, and a recycling flow rate of 6 mL min(-1)). Growth kinetics equations were described using four substrate inhibition models, and the initial formaldehyde concentration ranged from 54.5 to 993.0 mg L(-1). In each case, model parameters were estimated interactively using nonlinear regression analysis and on the basis of the goodness of fit, the fitness of the model to the experimental data was obtained (i.e., the coefficient of determination and the percent of standard deviation). The estimated parameters according to the Luong equation were μmax = 0.101 h(-1), KS = 54.1 mg L(-1), Sm = 1329 mg L(-1), and n = 2.07. According to the maintenance energies explained by Pirt, cell maintenance was quantified with q = Aμ + B; where A and B are the associated and non-associated growth parts of substrate consumption, respectively. The importance of these terms was verified using the developed models, which would efficiently describe the dynamic nature of growth and formaldehyde biodegradation.
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Affiliation(s)
- Alireza Habibi
- Chemical Engineering Department, Faculty of Engineering, Razi University, Kermanshah, Iran
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Khan F, Pal D, Ghosh A, Cameotra SS. Degradation of 2,4-dinitroanisole (DNAN) by metabolic cooperative activity of Pseudomonas sp. strain FK357and Rhodococcus imtechensis strain RKJ300. CHEMOSPHERE 2013; 93:2883-2888. [PMID: 24075532 DOI: 10.1016/j.chemosphere.2013.09.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 08/26/2013] [Accepted: 09/01/2013] [Indexed: 06/02/2023]
Abstract
2,4-Dinitroanisole (DNAN) is an insensitive explosive ingredient used by many defense agencies as a replacement for 2,4,6-trinitrotoluene. Although the biotransformation of DNAN under anaerobic condition has been reported, aerobic microbial degradation pathway has not been elucidated. An n-methyl-4-nitroaniline degrading bacterium Pseudomonas sp. strain FK357 transformed DNAN into 2,4-dinitrophenol (2,4-DNP) as an end product. Interestingly, when strain FK357 was co-cultured with a 2,4-DNP degrading Rhodococcus imtechensis strain RKJ300, complete and high rate of DNAN degradation was observed with no accumulation of intermediates. Enzyme assay using cell extracts of strain FK357 demonstrated that O-demethylation reaction is the first step of DNAN degradation with formation of 2,4-DNP and formaldehyde as intermediates. Subsequently, 2,4-DNP was degraded by strain RKJ300 via the formation of hydride-Meisenheimer complex. The present study clearly demonstrates that complete degradation of DNAN occurs as a result of the metabolic cooperative activity of two members within a bacterial consortium.
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Affiliation(s)
- Fazlurrahman Khan
- Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India
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Khan F, Vyas B, Pal D, Cameotra SS. Aerobic degradation of N-methyl-4-nitroaniline (MNA) by Pseudomonas sp. strain FK357 isolated from soil. PLoS One 2013; 8:e75046. [PMID: 24116023 PMCID: PMC3792944 DOI: 10.1371/journal.pone.0075046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 08/08/2013] [Indexed: 11/18/2022] Open
Abstract
N-Methyl-4-nitroaniline (MNA) is used as an additive to lower the melting temperature of energetic materials in the synthesis of insensitive explosives. Although the biotransformation of MNA under anaerobic condition has been reported, its aerobic microbial degradation has not been documented yet. A soil microcosms study showed the efficient aerobic degradation of MNA by the inhabitant soil microorganisms. An aerobic bacterium, Pseudomonas sp. strain FK357, able to utilize MNA as the sole carbon, nitrogen, and energy source, was isolated from soil microcosms. HPLC and GC-MS analysis of the samples obtained from growth and resting cell studies showed the formation of 4-nitroaniline (4-NA), 4-aminophenol (4-AP), and 1, 2, 4-benzenetriol (BT) as major metabolic intermediates in the MNA degradation pathway. Enzymatic assay carried out on cell-free lysates of MNA grown cells confirmed N-demethylation reaction is the first step of MNA degradation with the formation of 4-NA and formaldehyde products. Flavin-dependent transformation of 4-NA to 4-AP in cell extracts demonstrated that the second step of MNA degradation is a monooxygenation. Furthermore, conversion of 4-AP to BT by MNA grown cells indicates the involvement of oxidative deamination (release of NH2 substituent) reaction in third step of MNA degradation. Subsequent degradation of BT occurs by the action of benzenetriol 1, 2-dioxygenase as reported for the degradation of 4-nitrophenol. This is the first report on aerobic degradation of MNA by a single bacterium along with elucidation of metabolic pathway.
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Affiliation(s)
- Fazlurrahman Khan
- Environmental Biotechnology and Microbial Biochemistry Laboratory, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39-A, Chandigarh, India
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13
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Degradation of formaldehyde in packed-bed bioreactor by kissiris-immobilized Ralstonia eutropha. BIOTECHNOL BIOPROC E 2013. [DOI: 10.1007/s12257-012-0200-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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14
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Draft genome sequence of the methane-oxidizing bacterium Methylococcus capsulatus (Texas). J Bacteriol 2013; 194:6626. [PMID: 23144383 DOI: 10.1128/jb.01656-12] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methanotrophic bacteria perform major roles in global carbon cycles via their unique enzymatic activities that enable the oxidation of one-carbon compounds, most notably methane. Here we describe the annotated draft genome sequence of the aerobic methanotroph Methylococcus capsulatus (Texas), a type strain originally isolated from sewer sludge.
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15
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Fulazzaky MA, Talaiekhozani A, Hadibarata T. Calculation of optimal gas retention time using a logarithmic equation applied to a bio-trickling filter reactor for formaldehyde removal from synthetic contaminated air. RSC Adv 2013. [DOI: 10.1039/c3ra22753g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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16
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Habibi A, Vahabzadeh F. Degradation of formaldehyde at high concentrations by phenol-adapted Ralstonia eutropha closely related to pink-pigmented facultative methylotrophs. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2013; 48:279-292. [PMID: 23245303 DOI: 10.1080/10934529.2013.726829] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The ability of the phenol-adapted Ralstonia eutropha to utilize formaldehyde (FD) as the sole source of carbon and energy was studied. Adaptation to FD was accomplished by substituting FD for glucose in a stepwise manner. The bacterium in the liquid test culture could tolerate concentrations of FD up to 900 mg L(-1). Degradation of FD was complete in 528 h at 30°C with shaking at 150 rpm (r = 1.67 mg L(-1) h(-1)), q = 0.035 g(FD) g(cell) (-1) h(-1). Substrate inhibition kinetics (Haldane and Luong equations) are used to describe the experimental data. At non-inhibitory concentrations of FD, the Monod equation was used. According to the Luong model, the values of the maximum specific growth rate (μ(max)), half-saturation coefficient (k(S)), the maximum allowable formaldehyde concentration (S(m)), and the shape factor (n) were 0.117 h(-1), 47.6 mg L(-1), 900 mg L(-1), and 2.2, respectively. The growth response of the test bacterium to consecutive FD feedings was examined, and the FD-adapted R. eutropha cells were able to degrade 1000 mg L(-1) FD in 150 h through 4 cycles of FD feeds. During FD degradation, formic acid metabolite was formed. Assimilation of FD, methanol, formic acid, and oxalate by the test bacterium was accompanied by the formation of a pink pigment. The carotenoid nature of the cellular pigment has been confirmed and the test bacterium appeared to be closely related to pink-pigmented facultative methylotrophs (PPFM). The extent of harm to soil exposed to biotreated wastewaters containing FD may be moderated due to the association between methylotrophic/oxalotrophic bacteria and plants.
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Affiliation(s)
- Alireza Habibi
- Chemical Engineering Department, Amirkabir University of Technology, Tehran, Iran
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Lolas IB, Chen X, Bester K, Nielsen JL. Identification of triclosan-degrading bacteria using stable isotope probing, fluorescence in situ hybridization and microautoradiography. MICROBIOLOGY-SGM 2012; 158:2796-2804. [PMID: 22956759 DOI: 10.1099/mic.0.061077-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Triclosan is considered a ubiquitous pollutant and can be detected in a wide range of environmental samples. Triclosan removal by wastewater treatment plants has been largely attributed to biodegradation processes; however, very little is known about the micro-organisms involved. In this study, DNA-based stable isotope probing (DNA-SIP) combined with microautoradiography-fluorescence in situ hybridization (MAR-FISH) was applied to identify active triclosan degraders in an enrichment culture inoculated with activated sludge. Clone library sequences of 16S rRNA genes derived from the heavy DNA fractions of enrichment culture incubated with (13)C-labelled triclosan showed a predominant enrichment of a single bacterial clade most closely related to the betaproteobacterial genus Methylobacillus. To verify that members of the genus Methylobacillus were actively utilizing triclosan, a specific probe targeting the Methylobacillus group was designed and applied to the enrichment culture incubated with (14)C-labelled triclosan for MAR-FISH. The MAR-FISH results confirmed a positive uptake of carbon from (14)C-labelled triclosan by the Methylobacillus. The high representation of Methylobacillus in the (13)C-labelled DNA clone library and its observed utilization of (14)C-labelled triclosan by MAR-FISH reveal that these micro-organisms are the primary consumers of triclosan in the enrichment culture. The results from this study show that the combination of SIP and MAR-FISH can shed light on the networks of uncultured micro-organisms involved in degradation of organic micro-pollutants.
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Affiliation(s)
- Ihab Bishara Lolas
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark
| | - Xijuan Chen
- Department of Environmental Science, Aarhus University, Frederiksborgsvej 399, 4000 Roskilde, Denmark.,Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark
| | - Kai Bester
- Department of Environmental Science, Aarhus University, Frederiksborgsvej 399, 4000 Roskilde, Denmark
| | - Jeppe Lund Nielsen
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark
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Boden R, Kelly DP, Murrell JC, Schäfer H. Oxidation of dimethylsulfide to tetrathionate by Methylophaga thiooxidans sp. nov.: a new link in the sulfur cycle. Environ Microbiol 2011; 12:2688-99. [PMID: 20482741 DOI: 10.1111/j.1462-2920.2010.02238.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new pathway of dimethylsulfide (DMS) metabolism was identified in a novel species of Gammaproteobacteria, Methylophaga thiooxidans sp. nov., in which tetrathionate (S(4)O(6)(2-)) was the end-product of DMS oxidation. Inhibitor evidence indicated that DMS degradation was initiated by demethylation, catalysed by a corrinoid demethylase. Thiosulfate was an intermediate, which was oxidized to tetrathionate by a cytochrome-linked thiosulfate dehydrogenase. Thiosulfate oxidation was coupled to ATP synthesis, and M. thiooxidans could also use exogenous thiosulfate as an energy source during chemolithoheterotrophic growth on DMS or methanol. Cultures grown on a variety of substrates oxidized thiosulfate, indicating that thiosulfate oxidation was constitutive. The observations have relevance to interactions among sulfur-metabolizing bacteria in the marine environment. The production of tetrathionate from an organosulfur precursor is previously undocumented and represents a potential step in the biogeochemical sulfur cycle, providing a 'shunt' across the cycle.
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Affiliation(s)
- Rich Boden
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
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Purification and characterization of dimethylsulfide monooxygenase from Hyphomicrobium sulfonivorans. J Bacteriol 2011; 193:1250-8. [PMID: 21216999 DOI: 10.1128/jb.00977-10] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Dimethylsulfide (DMS) is a volatile organosulfur compound which has been implicated in the biogeochemical cycling of sulfur and in climate control. Microbial degradation is a major sink for DMS. DMS metabolism in some bacteria involves its oxidation by a DMS monooxygenase in the first step of the degradation pathway; however, this enzyme has remained uncharacterized until now. We have purified a DMS monooxygenase from Hyphomicrobium sulfonivorans, which was previously isolated from garden soil. The enzyme is a member of the flavin-linked monooxygenases of the luciferase family and is most closely related to nitrilotriacetate monooxygenases. It consists of two subunits: DmoA, a 53-kDa FMNH₂-dependent monooxygenase, and DmoB, a 19-kDa NAD(P)H-dependent flavin oxidoreductase. Enzyme kinetics were investigated with a range of substrates and inhibitors. The enzyme had a K(m) of 17.2 (± 0.48) μM for DMS (k(cat) = 5.45 s⁻¹) and a V(max) of 1.25 (± 0.01) μmol NADH oxidized min⁻¹ (mg protein⁻¹). It was inhibited by umbelliferone, 8-anilinonaphthalenesulfonate, a range of metal-chelating agents, and Hg²(+), Cd²(+), and Pb²(+) ions. The purified enzyme had no activity with the substrates of related enzymes, including alkanesulfonates, aldehydes, nitrilotriacetate, or dibenzothiophenesulfone. The gene encoding the 53-kDa enzyme subunit has been cloned and matched to the enzyme subunit by mass spectrometry. DMS monooxygenase represents a new class of FMNH₂-dependent monooxygenases, based on its specificity for dimethylsulfide and the molecular phylogeny of its predicted amino acid sequence. The gene encoding the large subunit of DMS monooxygenase is colocated with genes encoding putative flavin reductases, homologues of enzymes of inorganic and organic sulfur compound metabolism, and enzymes involved in riboflavin synthesis.
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Viggi CC, Dionisi D, Miccheli A, Valerio M, Majone M. Metabolic analysis of the removal of formic acid by unacclimated activated sludge. WATER RESEARCH 2010; 44:3393-3400. [PMID: 20417951 DOI: 10.1016/j.watres.2010.03.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Revised: 03/22/2010] [Accepted: 03/26/2010] [Indexed: 05/29/2023]
Abstract
This paper investigates the removal of formic acid by unacclimated biomass from a municipal activated sludge wastewater treatment plant. The biomass was initially able to remove formic acid, but its removal rate and Oxygen Uptake Rate (OUR) decreased with time, until formic acid removal stopped before the formic acid had been exhausted. Formaldehyde was removed in a similar way, whereas the same biomass was simultaneously able to grow and store PHAs when acetic acid was used as substrate. Batch tests with glycine and (13)C NMR analysis were performed, showing that unacclimated biomass was not able to synthesize all the metabolic intermediates from formic acid alone. At least glycine needed to be externally supplemented, in order to activate the serine synthesis pathway. A small amount of formic acid removal in the absence of growth was also possible through formaldehyde formation and its further conversion to formalin (1,2-formaldehyde dimer), whereas no PHAs were formed.
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Affiliation(s)
- Carolina Cruz Viggi
- Department of Chemistry, University of Rome La Sapienza, p.le A. Moro 5, 00185 Rome, Italy.
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Yoshida K, Ishii H, Ishihara Y, Saito H, Okada Y. Bioremediation potential of formaldehyde by the marine microalga Nannochloropsis oculata ST-3 strain. Appl Biochem Biotechnol 2008; 157:321-8. [PMID: 18663415 DOI: 10.1007/s12010-008-8314-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2008] [Accepted: 07/01/2008] [Indexed: 10/21/2022]
Abstract
The present work is intended to investigate biodegradation of formaldehyde by the marine microalga Nannochloropsis oculata ST-3 strain. Formaldehyde concentration in the medium decreased with the growth of the ST-3 strain. It is observed that the degradation of formaldehyde concentration depends on the increased cell number of the ST-3 strain. The ST-3 strain which was adapted to formaldehyde stepwise was able to tolerate to 19.9 ppm formaldehyde and degrade 99.3% of it in the medium for 22 days. Tolerance and degradation ability of formaldehyde by the ST-3 strain was improved by stepwise increasing of the formaldehyde concentration. Transformation of [13C]formaldehyde in the medium with the passage of incubation was monitored by using a nuclear magnetic resonance (NMR) spectrometer. Formaldehyde was transformed into formate, and these two substances degraded in the medium with the passage of incubation as clearly shown by the NMR spectrum.
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Affiliation(s)
- Kosuke Yoshida
- School of Marine Science and Technology, Tokai University, 3-20-1 Orido, Shimizu-ku, Shizuoka city, Shizuoka 424-8610, Japan.
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