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Ahmadi F, Lackner M. Recent findings in methanotrophs: genetics, molecular ecology, and biopotential. Appl Microbiol Biotechnol 2024; 108:60. [PMID: 38183483 DOI: 10.1007/s00253-023-12978-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/08/2023] [Accepted: 10/01/2023] [Indexed: 01/08/2024]
Abstract
The potential consequences for mankind could be disastrous due to global warming, which arises from an increase in the average temperature on Earth. The elevation in temperature primarily stems from the escalation in the concentration of greenhouse gases (GHG) such as CO2, CH4, and N2O within the atmosphere. Among these gases, methane (CH4) is particularly significant in driving alterations to the worldwide climate. Methanotrophic bacteria possess the distinctive ability to employ methane as both as source of carbon and energy. These bacteria show great potential as exceptional biocatalysts in advancing C1 bioconversion technology. The present review describes recent findings in methanotrophs including aerobic and anaerobic methanotroph bacteria, phenotypic characteristics, biotechnological potential, their physiology, ecology, and native multi-carbon utilizing pathways, and their molecular biology. The existing understanding of methanogenesis and methanotrophy in soil, as well as anaerobic methane oxidation and methanotrophy in temperate and extreme environments, is also covered in this discussion. New types of methanogens and communities of methanotrophic bacteria have been identified from various ecosystems and thoroughly examined for a range of biotechnological uses. Grasping the processes of methanogenesis and methanotrophy holds significant importance in the development of innovative agricultural techniques and industrial procedures that contribute to a more favorable equilibrium of GHG. This current review centers on the diversity of emerging methanogen and methanotroph species and their effects on the environment. By amalgamating advanced genetic analysis with ecological insights, this study pioneers a holistic approach to unraveling the biopotential of methanotrophs, offering unprecedented avenues for biotechnological applications. KEY POINTS: • The physiology of methanotrophic bacteria is fundamentally determined. • Native multi-carbon utilizing pathways in methanotrophic bacteria are summarized. • The genes responsible for encoding methane monooxygenase are discussed.
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Affiliation(s)
- Fatemeh Ahmadi
- School of Agriculture and Environment, University of Western Australia, Crawley, 6009, Australia
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, 7001, Australia
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Keun Kang C, Eun Yang J, Jo JH, Sun Kim M, Kim MS, Jun Choi Y. Microbial upcycling of methane to phytoene using metabolically engineered Methylocystis sp. MJC1 strain. BIORESOURCE TECHNOLOGY 2024; 407:131116. [PMID: 39019197 DOI: 10.1016/j.biortech.2024.131116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 07/13/2024] [Accepted: 07/13/2024] [Indexed: 07/19/2024]
Abstract
Methane, a potent greenhouse gas, requires sustainable mitigation strategies. Here, the microbial upcycling of methane to phytoene, a valuable colorless carotenoid with applications in the cosmeceutical industry was demonstrated. To achieve this goal, a stepwise metabolic engineering approach was employed in Methylocystis sp. MJC1, a methane-oxidizing bacterium. The incorporation of crtE and crtB genes from Deinococcus radiodurans R1 established the phytoene biosynthetic pathway. This pathway was fine-tuned through promoter optimization, resulting in a phytoene production of 450 μg/L from 37 mmol/L methane. Disrupting the ackA gene reduced a by-product, acetate, by 50 % and increased phytoene production by 56 %. Furthermore, overexpressing the dxs gene boosted phytoene titer 3-fold. The optimized strain produced 15 mg/L phytoene from 2 mol/L methane in fed-batch fermentation, a 4-fold increase in phytoene titer and 4-fold in yield. This demonstrates Methylocystis sp. MJC1's potential for efficient phytoene production and presents a novel approach for greenhouse gas reduction.
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Affiliation(s)
- Chang Keun Kang
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdae-ro, Dongdaemun-gu, Seoul 02504, Republic of Korea
| | - Jung Eun Yang
- Department of Advanced Process Technology and Fermentation, World Institute of Kimchi, Gwangju 61755, Republic of Korea
| | - Jae-Hwan Jo
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, 25 Samso-ro 270beon-gil, Buk-gu, Gwangju 61003, Republic of Korea; Interdisciplinary Program of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Min Sun Kim
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdae-ro, Dongdaemun-gu, Seoul 02504, Republic of Korea
| | - Min-Sik Kim
- Energy Resources Upcycling Research Laboratory, Korea Institute of Energy Research, Daejeon, 34129, Republic of Korea
| | - Yong Jun Choi
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdae-ro, Dongdaemun-gu, Seoul 02504, Republic of Korea.
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Bhat EH, Henard JM, Lee SA, McHalffey D, Ravulapati MS, Rogers EV, Yu L, Skiles D, Henard CA. Construction of a broad-host-range Anderson promoter series and particulate methane monooxygenase promoter variants expand the methanotroph genetic toolbox. Synth Syst Biotechnol 2024; 9:250-258. [PMID: 38435708 PMCID: PMC10909576 DOI: 10.1016/j.synbio.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024] Open
Abstract
Methanotrophic bacteria are currently used industrially for the bioconversion of methane-rich natural gas and anaerobic digestion-derived biogas to valuable products. These bacteria may also serve to mitigate the negative effects of climate change by capturing atmospheric greenhouse gases. Several genetic tools have previously been developed for genetic and metabolic engineering of methanotrophs. However, the available tools for use in methanotrophs are significantly underdeveloped compared to many other industrially relevant bacteria, which hinders genetic and metabolic engineering of these biocatalysts. As such, expansion of the methanotroph genetic toolbox is needed to further our understanding of methanotrophy and develop biotechnologies that leverage these unique microbes for mitigation and conversion of methane to valuable products. Here, we determined the copy number of three broad-host-range plasmids in Methylococcus capsulatus Bath and Methylosinus trichosporium OB3b, representing phylogenetically diverse Gammaproteobacterial and Alphaproteobacterial methanotrophs, respectively. Further, we show that the commonly used synthetic Anderson series promoters are functional and exhibit similar relative activity in M. capsulatus and M. trichosporium OB3b, but the synthetic series had limited range. Thus, we mutagenized the native M. capsulatus particulate methane monooxygenase promoter and identified variants with activity that expand the activity range of synthetic, constitutive promoters functional not only in M. capsulatus, but also in Escherichia coli. Collectively, the tools developed here advance the methanotroph genetic engineering toolbox and represent additional synthetic genetic parts that may have broad applicability in Pseudomonadota bacteria.
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Affiliation(s)
| | | | | | - Dustin McHalffey
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Mahith S. Ravulapati
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Elle V. Rogers
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Logan Yu
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - David Skiles
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Calvin A. Henard
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
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Yuan CY, Yan WJ, Sun FY, Tu HH, Lu JJ, Feng L, Dong WY. Management of biofilm by an innovative layer-structured membrane for membrane biofilm reactor (MBfR) to efficient methane oxidation coupled to denitrification (AME-D). WATER RESEARCH 2024; 251:121107. [PMID: 38218075 DOI: 10.1016/j.watres.2024.121107] [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: 09/12/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/15/2024]
Abstract
Aerobic methane oxidation coupled with denitrification (AME-D) has garnered significant attention as a promising technology for nitrogen removal from water. Effective biofilm management on the membrane surface is essential to enhance the efficiency of nitrate removal in AME-D systems. In this study, we introduce a novel and scalable layer-structured membrane (LSM) developed using a meticulously designed polyurethane sponge. The application of the LSM in advanced biofilm management for AME-D resulted in a substantial enhancement of denitrification performance. Our experimental results demonstrated remarkable improvements in nitrate-removal flux (92.8 mmol-N m-2 d-1) and methane-oxidation rate (325.6 mmol m-2 d-1) when using an LSM in a membrane biofilm reactor (L-MBfR) compared with a conventional membrane reactor (C-MBfR). The l-MBfR exhibited 12.4-, 6.8- and 3.4-fold increases in nitrate-removal rate, biomass-retention capacity, and methane-oxidation rate, respectively, relative to the control C-MBfR. Notably, the l-MBfR demonstrated a 3.5-fold higher abundance of denitrifying bacteria, including Xanthomonadaceae, Rhodocyclaceae, and Methylophilaceae. In addition, the denitrification-related enzyme activity was twice as high in the l-MBfR than in the C-MBfR. These findings underscore the LSM's ability to create anoxic/anaerobic microenvironments conducive to biofilm formation and denitrification. Furthermore, the LSM exhibited a unique advantage in shaping microbial community structures and facilitating cross-feeding interactions between denitrifying bacteria and aerobic methanotrophs. The results of this study hold great promise for advancing the application of MBfRs in achieving efficient and reliable nitrate removal through the AME-D pathway, facilitated by effective biofilm management.
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Affiliation(s)
- Chun-Yan Yuan
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, PR China
| | - Wei-Jia Yan
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, PR China
| | - Fei-Yun Sun
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, PR China; Shenzhen Key Laboratory of Water Resource Utilization and Environmental Pollution Control, Shenzhen 518055, PR China.
| | - Hong-Hua Tu
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, PR China
| | - Jian-Jiang Lu
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, PR China; College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266590, PR China; Institute of Yellow River Delta Earth Surface Processes and Ecological Integrity, Shandong University of Science and Technology, Qingdao 266590, PR China.
| | - Liang Feng
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, PR China
| | - Wen-Yi Dong
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, PR China; Shenzhen Key Laboratory of Water Resource Utilization and Environmental Pollution Control, Shenzhen 518055, PR China
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Cheon H, Kim JH, Kim JS, Park JB. Valorization of single-carbon chemicals by using carboligases as key enzymes. Curr Opin Biotechnol 2024; 85:103047. [PMID: 38128199 DOI: 10.1016/j.copbio.2023.103047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023]
Abstract
Single-carbon (C1) biorefinery plays a key role in the consumption of global greenhouse gases and a circular carbon economy. Thereby, we have focused on the valorization of C1 compounds (e.g. methanol, formaldehyde, and formate) into multicarbon products, including bioplastic monomers, glycolate, and ethylene glycol. For instance, methanol, derived from the oxidation of CH4, can be converted into glycolate, ethylene glycol, or erythrulose via formaldehyde and glycolaldehyde, employing C1 and/or C2 carboligases as essential enzymes. Escherichia coli was engineered to convert formate, produced from CO via CO2 or from CO2 directly, into glycolate. Recent progress in the design of biotransformation pathways, enzyme discovery, and engineering, as well as whole-cell biocatalyst engineering for C1 biorefinery, was addressed in this review.
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Affiliation(s)
- Huijin Cheon
- Department of Food Science and Biotechnology, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jun-Hong Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea.
| | - Jin-Byung Park
- Department of Food Science and Biotechnology, Ewha Womans University, Seoul 03760, Republic of Korea.
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Tikhonova EN, Suleimanov RZ, Oshkin IY, Konopkin AA, Fedoruk DV, Pimenov NV, Dedysh SN. Growing in Saltwater: Biotechnological Potential of Novel Methylotuvimicrobium- and Methylomarinum-like Methanotrophic Bacteria. Microorganisms 2023; 11:2257. [PMID: 37764101 PMCID: PMC10538026 DOI: 10.3390/microorganisms11092257] [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: 08/15/2023] [Revised: 09/02/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Methanotrophic bacteria that possess a unique ability of using methane as a sole source of carbon and energy have attracted considerable attention as potential producers of a single-cell protein. So far, this biotechnology implied using freshwater methanotrophs, although many regions of the world have limited freshwater resources. This study aimed at searching for novel methanotrophs capable of fast growth in saltwater comparable in composition with seawater. A methane-oxidizing microbial consortium containing Methylomarinum- and Methylotuvimicrobium-like methanotrophs was enriched from sediment from the river Chernavka (water pH 7.5, total salt content 30 g L-1), a tributary river of the hypersaline Lake Elton, southern Russia. This microbial consortium, designated Ch1, demonstrated stable growth on natural gas in a bioreactor in media with a total salt content of 23 to 35.9 g L-1 at a dilution rate of 0.19-0.21 h-1. The highest biomass yield of 5.8 g cell dry weight (CDW)/L with a protein content of 63% was obtained during continuous cultivation of the consortium Ch1 in a medium with a total salt content of 29 g L-1. Isolation attempts resulted in obtaining a pure culture of methanotrophic bacteria, strain Ch1-1. The 16S rRNA gene sequence of strain Ch1-1 displayed 97.09-97.24% similarity to the corresponding gene fragments of characterized representatives of Methylomarinum vadi, methanotrophs isolated from marine habitats. The genome of strain Ch1-1 was 4.8 Mb in size and encoded 3 rRNA operons, and about 4400 proteins. The genome contained the gene cluster coding for ectoine biosynthesis, which explains the ability of strain Ch1-1 to tolerate high salt concentration.
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Affiliation(s)
| | | | | | | | | | | | - Svetlana N. Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (E.N.T.); (R.Z.S.); (I.Y.O.); (A.A.K.); (D.V.F.); (N.V.P.)
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