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Eam H, Ko D, Lee C, Myung J. Methylosinus trichosporium OB3b bioaugmentation unleashes polyhydroxybutyrate-accumulating potential in waste-activated sludge. Microb Cell Fact 2024; 23:160. [PMID: 38822346 PMCID: PMC11140957 DOI: 10.1186/s12934-024-02442-w] [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: 01/29/2024] [Accepted: 05/27/2024] [Indexed: 06/02/2024] Open
Abstract
BACKGROUND Wastewater treatment plants contribute approximately 6% of anthropogenic methane emissions. Methanotrophs, capable of converting methane into polyhydroxybutyrate (PHB), offer a promising solution for utilizing methane as a carbon source, using activated sludge as a seed culture for PHB production. However, maintaining and enriching PHB-accumulating methanotrophic communities poses challenges. RESULTS This study investigated the potential of Methylosinus trichosporium OB3b to bioaugment PHB-accumulating methanotrophic consortium within activated sludge to enhance PHB production. Waste-activated sludges with varying ratios of M. trichosporium OB3b (1:0, 1:1, 1:4, and 0:1) were cultivated. The results revealed substantial growth and methane consumption in waste-activated sludge with M. trichosporium OB3b-amended cultures, particularly in a 1:1 ratio. Enhanced PHB accumulation, reaching 37.1% in the same ratio culture, indicates the dominance of Type II methanotrophs. Quantification of methanotrophs by digital polymerase chain reaction showed gradual increases in Type II methanotrophs, correlating with increased PHB production. However, while initial bioaugmentation of M. trichosporium OB3b was observed, its presence decreased in subsequent cycles, indicating the dominance of other Type II methanotrophs. Microbial community analysis highlighted the successful enrichment of Type II methanotrophs-dominated cultures due to the addition of M. trichosporium OB3b, outcompeting Type I methanotrophs. Methylocystis and Methylophilus spp. were the most abundant in M. trichosporium OB3b-amended cultures. CONCLUSIONS Bioaugmentation strategies, leveraging M. trichosporium OB3b could significantly enhance PHB production and foster the enrichment of PHB-accumulating methanotrophs in activated sludge. These findings contribute to integrating PHB production in wastewater treatment plants, providing a sustainable solution for resource recovery.
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Affiliation(s)
- Hyerim Eam
- Department of Civil and Environmental Engineering, KAIST, Daejeon, 34141, Republic of Korea
| | - Dayoung Ko
- Department of Civil, Urban, Earth, and Environmental Engineering, UNIST, Ulsan, 44919, Republic of Korea
| | - Changsoo Lee
- Department of Civil, Urban, Earth, and Environmental Engineering, UNIST, Ulsan, 44919, Republic of Korea
| | - Jaewook Myung
- Department of Civil and Environmental Engineering, KAIST, Daejeon, 34141, Republic of Korea.
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2
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Lienhart PH, Rohra V, Clement C, Toppen LC, DeCola AC, Rizzo DM, Scarborough MJ. Landfill intermediate cover soil microbiomes and their potential for mitigating greenhouse gas emissions revealed through metagenomics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 925:171697. [PMID: 38492594 DOI: 10.1016/j.scitotenv.2024.171697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/09/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
Landfills are a major source of anthropogenic methane emissions and have been found to produce nitrous oxide, an even more potent greenhouse gas than methane. Intermediate cover soil (ICS) plays a key role in reducing methane emissions but may also result in nitrous oxide production. To assess the potential for microbial methane oxidation and nitrous oxide production, long sequencing reads were generated from ICS microbiome DNA and reads were functionally annotated for 24 samples across ICS at a large landfill in New York. Further, incubation experiments were performed to assess methane consumption and nitrous oxide production with varying amounts of ammonia supplemented. Methane was readily consumed by microbes in the composite ICS and all incubations with methane produced small amounts of nitrous oxide even when ammonia was not supplemented. Incubations without methane produced significantly less nitrous oxide than those incubated with methane. In incubations with methane added, the observed specific rate of methane consumption was 0.776 +/- 0.055 μg CH4 g dry weight (DW) soil-1 h-1 and the specific rate of nitrous oxide production was 3.64 × 10-5 +/- 1.30 × 10-5 μg N2O g DW soil-1 h-1. The methanotrophs Methylobacter and an unclassified genus within the family Methlyococcaceae were present in the original ICS samples and the incubation samples, and their abundance increased during incubations with methane. Genes encoding particulate methane monooxygenase/ ammonia monooxygenase (pMMO) were much more abundant than genes encoding soluble methane monooxygenase (sMMO) across the landfill ICS. Genes encoding proteins that convert hydroxylamine to nitrous oxide were not highly abundant in the ICS or incubation metagenomes. In total, these results suggest that although ammonia oxidation via methanotrophs may result in low levels of nitrous oxide production, ICS microbial communities have the potential to greatly reduce the overall global warming potential of landfill emissions.
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Affiliation(s)
- Peyton H Lienhart
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States
| | - Venus Rohra
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States
| | - Courtney Clement
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Lucinda C Toppen
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States.
| | - Amy C DeCola
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States
| | - Donna M Rizzo
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States; Gund Institute for Environment, University of Vermont, Burlington, VT, United States.
| | - Matthew J Scarborough
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States; Gund Institute for Environment, University of Vermont, Burlington, VT, United States.
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3
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Ouyang MY, Wang S, Nie WH, Wang PH, Liao WX, Liu XH, Lin SS, Lin RP, Chen GY, Zhu B, Shen J. Methylomonas defluvii sp. nov., a type I methane-oxidizing bacterium from a secondary sedimentation tank of a wastewater treatment plant. Int J Syst Evol Microbiol 2024; 74. [PMID: 38607367 DOI: 10.1099/ijsem.0.006321] [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] [Indexed: 04/13/2024] Open
Abstract
An aerobic methanotroph was isolated from a secondary sedimentation tank of a wastewater treatment plant and designated strain OY6T. Cells of OY6T were Gram-stain-negative, pink-pigmented, motile rods and contained an intracytoplasmic membrane structure typical of type I methanotrophs. OY6T could grow at a pH range of 4.5-7.5 (optimum pH 6.5) and at temperatures ranging from 20 °C to 37 °C (optimum 30 °C). The major cellular fatty acids were C14 : 0, C16 : 1ω7c/C16 : 1ω6c and C16 : 1ω5c; the predominant respiratory quinone was MQ-8. The genome size was 5.41 Mbp with a DNA G+C content of 51.7 mol%. OY6T represents a member of the family Methylococcaceae of the class Gammaproteobacteria and displayed 95.74-99.64 % 16S rRNA gene sequence similarity to the type strains of species of the genus Methylomonas. Whole-genome comparisons based on average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) confirmed that OY6T should be classified as representing a novel species. The most closely related type strain was Methylomonas fluvii EbBT, with 16S rRNA gene sequence similarity, ANI by blast (ANIb), ANI by MUMmer (ANIm) and dDDH values of 99.64, 90.46, 91.92 and 44.5 %, respectively. OY6T possessed genes encoding both the particulate methane monooxygenase enzyme and the soluble methane monooxygenase enzyme. It grew only on methane or methanol as carbon sources. On the basis of phenotypic, genetic and phylogenetic data, strain OY6T represents a novel species within the genus Methylomonas for which the name Methylomonas defluvii sp. nov. is proposed, with strain OY6T (=GDMCC 1.4114T=KCTC 8159T=LMG 33371T) as the type strain.
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Affiliation(s)
- Ming-Yan Ouyang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Sai Wang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Wen-Han Nie
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Pei-Hong Wang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Wei-Xue Liao
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Xiao-Hui Liu
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Si-Si Lin
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Rong-Peng Lin
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Gong-You Chen
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Bo Zhu
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Jian Shen
- People's Hospital, Hangzhou 310014, Zhejiang, PR China
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4
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Liu C, Schmitz RA, Pol A, Hogendoorn C, Verhagen D, Peeters SH, van Alen TA, Cremers G, Mesman RA, Op den Camp HJM. Active coexistence of the novel gammaproteobacterial methanotroph 'Ca. Methylocalor cossyra' CH1 and verrucomicrobial methanotrophs in acidic, hot geothermal soil. Environ Microbiol 2024; 26:e16602. [PMID: 38454738 DOI: 10.1111/1462-2920.16602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 02/16/2024] [Indexed: 03/09/2024]
Abstract
Terrestrial geothermal ecosystems are hostile habitats, characterized by large emissions of environmentally relevant gases such as CO2 , CH4 , H2 S and H2 . These conditions provide a niche for chemolithoautotrophic microorganisms. Methanotrophs of the phylum Verrucomicrobia, which inhabit these ecosystems, can utilize these gases and grow at pH levels below 1 and temperatures up to 65°C. In contrast, methanotrophs of the phylum Proteobacteria are primarily found in various moderate environments. Previously, novel verrucomicrobial methanotrophs were detected and isolated from the geothermal soil of the Favara Grande on the island of Pantelleria, Italy. The detection of pmoA genes, specific for verrucomicrobial and proteobacterial methanotrophs in this environment, and the partially overlapping pH and temperature growth ranges of these isolates suggest that these distinct phylogenetic groups could coexist in the environment. In this report, we present the isolation and characterization of a thermophilic and acid-tolerant gammaproteobacterial methanotroph (family Methylococcaceae) from the Favara Grande. This isolate grows at pH values ranging from 3.5 to 7.0 and temperatures from 35°C to 55°C, and diazotrophic growth was demonstrated. Its genome contains genes encoding particulate and soluble methane monooxygenases, XoxF- and MxaFI-type methanol dehydrogenases, and all enzymes of the Calvin cycle. For this novel genus and species, we propose the name 'Candidatus Methylocalor cossyra' CH1.
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Affiliation(s)
- Changqing Liu
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Rob A Schmitz
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Arjan Pol
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Carmen Hogendoorn
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Daniël Verhagen
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Stijn H Peeters
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Theo A van Alen
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Geert Cremers
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Rob A Mesman
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
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5
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Furtak A, Szafranek-Nakonieczna A, Furtak K, Pytlak A. A review of organophosphonates, their natural and anthropogenic sources, environmental fate and impact on microbial greenhouse gases emissions - Identifying knowledge gaps. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 355:120453. [PMID: 38430886 DOI: 10.1016/j.jenvman.2024.120453] [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: 10/03/2023] [Revised: 01/26/2024] [Accepted: 02/20/2024] [Indexed: 03/05/2024]
Abstract
Organophosphonates (OPs) are a unique group of natural and synthetic compounds, characterised by the presence of a stable, hard-to-cleave bond between the carbon and phosphorus atoms. OPs exhibit high resistance to abiotic degradation, excellent chelating properties and high biological activity. Despite the huge and increasing scale of OP production and use worldwide, little is known about their transportation and fate in the environment. Available data are dominated by information concerning the most recognised organophosphonate - the herbicide glyphosate - while other OPs have received little attention. In this paper, a comprehensive review of the current state of knowledge about natural and artificial OPs is presented (including glyphosate). Based on the available literature, a number of knowledge gaps have been identified that need to be filled in order to understand the environmental effects of these abundant compounds. Special attention has been given to GHG-related processes, with a particular focus on CH4. This stems from the recent discovery of OP-dependent CH4 production in aqueous environments under aerobic conditions. The process has changed the perception of the biogeochemical cycle of CH4, since it was previously thought that biological methane formation was only possible under anaerobic conditions. However, there is a lack of knowledge on whether OP-associated methane is also formed in soils. Moreover, it remains unclear whether anthropogenic OPs affect the CH4 cycle, a concern of significant importance in the context of the increasing rate of global warming. The literature examined in this review also calls for additional research into the date of OPs in waste and sewage and in their impact on environmental microbiomes.
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Affiliation(s)
- Adam Furtak
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290, Lublin, Poland
| | - Anna Szafranek-Nakonieczna
- Department of Biology and Biotechnology of Microorganisms, Institute of Medical Sciences, The John Paul II Catholic University of Lublin, Konstantynów 1 I, 20-708, Lublin, Poland
| | - Karolina Furtak
- Department of Agricultural Microbiology, Institute of Soil Science and Plant Cultivation - State Research Institute, Krańcowa 8, INCBR Centre, 24-100, Puławy, Poland
| | - Anna Pytlak
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290, Lublin, Poland.
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6
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Tucci FJ, Rosenzweig AC. Direct Methane Oxidation by Copper- and Iron-Dependent Methane Monooxygenases. Chem Rev 2024; 124:1288-1320. [PMID: 38305159 PMCID: PMC10923174 DOI: 10.1021/acs.chemrev.3c00727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Methane is a potent greenhouse gas that contributes significantly to climate change and is primarily regulated in Nature by methanotrophic bacteria, which consume methane gas as their source of energy and carbon, first by oxidizing it to methanol. The direct oxidation of methane to methanol is a chemically difficult transformation, accomplished in methanotrophs by complex methane monooxygenase (MMO) enzyme systems. These enzymes use iron or copper metallocofactors and have been the subject of detailed investigation. While the structure, function, and active site architecture of the copper-dependent particulate methane monooxygenase (pMMO) have been investigated extensively, its putative quaternary interactions, regulation, requisite cofactors, and mechanism remain enigmatic. The iron-dependent soluble methane monooxygenase (sMMO) has been characterized biochemically, structurally, spectroscopically, and, for the most part, mechanistically. Here, we review the history of MMO research, focusing on recent developments and providing an outlook for future directions of the field. Engineered biological catalysis systems and bioinspired synthetic catalysts may continue to emerge along with a deeper understanding of the molecular mechanisms of biological methane oxidation. Harnessing the power of these enzymes will necessitate combined efforts in biochemistry, structural biology, inorganic chemistry, microbiology, computational biology, and engineering.
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Affiliation(s)
- Frank J Tucci
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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7
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Lim J, Wehmeyer H, Heffner T, Aeppli M, Gu W, Kim PJ, Horn MA, Ho A. Resilience of aerobic methanotrophs in soils; spotlight on the methane sink under agriculture. FEMS Microbiol Ecol 2024; 100:fiae008. [PMID: 38327184 PMCID: PMC10872700 DOI: 10.1093/femsec/fiae008] [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: 09/05/2023] [Revised: 01/19/2024] [Accepted: 02/06/2024] [Indexed: 02/09/2024] Open
Abstract
Aerobic methanotrophs are a specialized microbial group, catalyzing the oxidation of methane. Disturbance-induced loss of methanotroph diversity/abundance, thus results in the loss of this biological methane sink. Here, we synthesized and conceptualized the resilience of the methanotrophs to sporadic, recurring, and compounded disturbances in soils. The methanotrophs showed remarkable resilience to sporadic disturbances, recovering in activity and population size. However, activity was severely compromised when disturbance persisted or reoccurred at increasing frequency, and was significantly impaired following change in land use. Next, we consolidated the impact of agricultural practices after land conversion on the soil methane sink. The effects of key interventions (tillage, organic matter input, and cover cropping) where much knowledge has been gathered were considered. Pairwise comparisons of these interventions to nontreated agricultural soils indicate that the agriculture-induced impact on the methane sink depends on the cropping system, which can be associated to the physiology of the methanotrophs. The impact of agriculture is more evident in upland soils, where the methanotrophs play a more prominent role than the methanogens in modulating overall methane flux. Although resilient to sporadic disturbances, the methanotrophs are vulnerable to compounded disturbances induced by anthropogenic activities, significantly affecting the methane sink function.
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Affiliation(s)
- Jiyeon Lim
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Helena Wehmeyer
- Nestlè Research, Route du Jorat 57, CH 1000 Lausanne 26, Switzerland
| | - Tanja Heffner
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Meret Aeppli
- Environmental Engineering Institute IIE-ENAC, Laboratory SOIL, Ecole Polytechnique Fédérale de Lausanne (EPFL), Valais Wallis, CH 1950 Sion, Switzerland
| | - Wenyu Gu
- Environmental Engineering Institute IIE-ENAC, Laboratory MICROBE, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH 1015 Lausanne, Switzerland
| | - Pil Joo Kim
- Division of Applied Life Science, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Marcus A Horn
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Adrian Ho
- Nestlè Research, Route du Jorat 57, CH 1000 Lausanne 26, Switzerland
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8
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Zhu X, Deng Y, Liu Y. Methylocystis dominates methane oxidation in glacier foreland soil at elevated temperature. FEMS Microbiol Lett 2024; 371:fnae011. [PMID: 38366911 DOI: 10.1093/femsle/fnae011] [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: 09/27/2023] [Revised: 12/01/2023] [Accepted: 02/15/2024] [Indexed: 02/19/2024] Open
Abstract
Methane-oxidizing bacteria (methanotrophs) play an important role in mitigating methane emissions in various ecological environments, including cold regions. However, the response of methanotrophs in these cold environments to extreme temperatures above the in-situ temperature has not been thoroughly explored. Therefore, this study collected soil samples from Longxiazailongba (LXZ) and Qiangyong (QY) glacier forelands and incubated them with 13CH4 at 35°C under different soil water conditions. The active methanotroph populations were identified using DNA stable isotope probing (DNA-SIP) and high throughput sequencing techniques. The results showed that the methane oxidation potential in LXZ and QY glacier foreland soils was significantly enhanced at an unusually high temperature of 35°C during microcosm incubations, where abundant substrate (methane and oxygen) was provided. Moreover, the influence of soil water conditions on this potential was observed. Interestingly, Methylocystis, a type II and mesophilic methanotroph, was detected in the unincubated in-situ soil samples and became the active and dominant methanotroph in methane oxidation at 35°C. This suggests that Methylocystis can survive at low temperatures for a prolonged period and thrive under suitable growth conditions. Furthermore, the presence of mesophilic methanotrophs in cold habitats could have potential implications for reducing greenhouse gas emissions in warming glacial environments.
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Affiliation(s)
- Xinshu Zhu
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China
- College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yongcui Deng
- School of Geography, Nanjing Normal University, Nanjing 210023, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing 210023, China
| | - Yongqin Liu
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
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9
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Ma R, Li J, Tyagi RD, Zhang X. Carbon dioxide and methane as carbon source for the production of polyhydroxyalkanoates and concomitant carbon fixation. BIORESOURCE TECHNOLOGY 2024; 391:129977. [PMID: 37925086 DOI: 10.1016/j.biortech.2023.129977] [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: 10/11/2023] [Revised: 11/01/2023] [Accepted: 11/01/2023] [Indexed: 11/06/2023]
Abstract
The currently used plastics are non-biodegradable, and cause greenhouse gases (GHGs) emission as they are petroleum-based. Polyhydroxyalkanoates (PHAs) are biopolymers with excellent biodegradability and biocompatibility, which can be used to replace petroleum-based plastics. A variety of microorganisms have been found to synthesize PHAs by using typical GHGs: carbon dioxide and methane as carbon sources. Converting carbon dioxide (CO2) and methane (CH4) to PHAs is an attractive option for carbon capture and biodegradable plastic production. In this review, the microorganisms capable of using CO2 and CH4 to produce PHAs were summarized. The metabolic mechanism, PHAs production process, and the factors influencing the production process are illustrated. The currently used optimization techniques to improve the yield of PHAs are discussed. The challenges and future prospects for developing economically viable PHAs production using GHGs as carbon source are identified. This work provides an insight for achieving carbon sequestration and bioplastics based circular economy.
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Affiliation(s)
- Rui Ma
- School of Civil and Environmental Engineering, Shenzhen Key Laboratory of Water Resource Application and Environmental Pollution Control, Harbin Institute of Technology, Shenzhen, Shenzhen Guangdong 518055, PR China
| | - Ji Li
- School of Civil and Environmental Engineering, Shenzhen Key Laboratory of Water Resource Application and Environmental Pollution Control, Harbin Institute of Technology, Shenzhen, Shenzhen Guangdong 518055, PR China
| | - R D Tyagi
- Chief Scientific Officer, BOSK-Bioproducts, Quebec, Canada
| | - Xiaolei Zhang
- School of Civil and Environmental Engineering, Shenzhen Key Laboratory of Water Resource Application and Environmental Pollution Control, Harbin Institute of Technology, Shenzhen, Shenzhen Guangdong 518055, PR China.
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10
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Dong L, Chen M, Liu C, Lv Y, Wang X, Lei Q, Fang Y, Tong H. Microbe interactions drive the formation of floating iron films in circumneutral wetlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167711. [PMID: 37832684 DOI: 10.1016/j.scitotenv.2023.167711] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 10/04/2023] [Accepted: 10/07/2023] [Indexed: 10/15/2023]
Abstract
Floating iron (Fe) films are widely found in wetlands that can form oxic-anoxic boundaries under circumneutral conditions. These films play a crucial role in the redox transformations and bioavailability of nutrients and trace metals. Current studies mainly focus on chemical oxidation during Fe film formation under circumneutral conditions. The functional microorganisms and associated microbial processes involved in Fe film formation have yet to be investigated in detail. Here, we investigated the microbial communities and involved microbial processes for the formation of floating Fe films in wetlands. Ferrihydrite was the dominant Fe(III) phase in films, accompanied by moderate levels of carbon and silicon. The Fe species and microbial analysis indicated that Fe films contain mixed-valent Fe and can form biotically. Microbial community analysis showed that the dominant genera in these Fe films were Fe-oxidizing and reducing bacteria and methanotrophs, including Leptothrix, Ferriphasclus, Gallionella, Geobacter and Methylococcales. Leptothrix, Ferriphasclus and Gallionella, as classical Fe(II)-oxidizing bacteria (FeOB), can oxidize Fe(II) with limited oxygen and form special structures that are consistent with Fe film morphology. Geobacter can provide a source of Fe(II) for FeOB growth, and Methylococcales can perform methane oxidation to provide energy for Fe cycling. The high ratios of Gallionella- and Geobacter-related microorganisms and carbon fixation genes proved the contribution of potential of Fe cycling and autotrophic microbial communities to the formation of Fe films. The diversity of microbial community suggested that Fe(II) oxidation could trigger carbon fixation, while Fe(III) reduction accelerated Fe and carbon cycling through anaerobic respiration and autotrophic chemosynthesis. These results highlight the contribution of these multiple microbial processes to Fe and carbon cycling during the formation of floating Fe films in wetlands. However, further studies are required to fully elucidate the interaction of functional microorganisms involved in floating film formation and their biogeochemical role in wetlands.
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Affiliation(s)
- Leheng Dong
- College of Agriculture / Tree Peony, Henan University of Science and Technology, Luoyang 471023, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Manjia Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Chengshuai Liu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Yahui Lv
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Xugang Wang
- College of Agriculture / Tree Peony, Henan University of Science and Technology, Luoyang 471023, China
| | - Qinkai Lei
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Yujuan Fang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Hui Tong
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.
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11
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Pazos-Rojas LA, Cuellar-Sánchez A, Romero-Cerón AL, Rivera-Urbalejo A, Van Dillewijn P, Luna-Vital DA, Muñoz-Rojas J, Morales-García YE, Bustillos-Cristales MDR. The Viable but Non-Culturable (VBNC) State, a Poorly Explored Aspect of Beneficial Bacteria. Microorganisms 2023; 12:39. [PMID: 38257865 PMCID: PMC10818521 DOI: 10.3390/microorganisms12010039] [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: 11/17/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
Many bacteria have the ability to survive in challenging environments; however, they cannot all grow on standard culture media, a phenomenon known as the viable but non-culturable (VBNC) state. Bacteria commonly enter the VBNC state under nutrient-poor environments or under stressful conditions. This review explores the concept of the VBNC state, providing insights into the beneficial bacteria known to employ this strategy. The investigation covers different chemical and physical factors that can induce the latency state, cell features, and gene expression observed in cells in the VBNC state. The review also covers the significance and applications of beneficial bacteria, methods of evaluating bacterial viability, the ability of bacteria to persist in environments associated with higher organisms, and the factors that facilitate the return to the culturable state. Knowledge about beneficial bacteria capable of entering the VBNC state remains limited; however, beneficial bacteria in this state could face adverse environmental conditions and return to a culturable state when the conditions become suitable and continue to exert their beneficial effects. Likewise, this unique feature positions them as potential candidates for healthcare applications, such as the use of probiotic bacteria to enhance human health, applications in industrial microbiology for the production of prebiotics and functional foods, and in the beer and wine industry. Moreover, their use in formulations to increase crop yields and for bacterial bioremediation offers an alternative pathway to harness their beneficial attributes.
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Affiliation(s)
- Laura Abisaí Pazos-Rojas
- Faculty of Stomatology, Meritorious Autonomous University of Puebla (BUAP), Puebla 72570, Mexico; (L.A.P.-R.); (A.R.-U.)
- Monterrey Institute of Technology, School of Engineering and Sciences, Monterrey 64700, Mexico; (A.C.-S.); (A.L.R.-C.); (D.A.L.-V.)
| | - Alma Cuellar-Sánchez
- Monterrey Institute of Technology, School of Engineering and Sciences, Monterrey 64700, Mexico; (A.C.-S.); (A.L.R.-C.); (D.A.L.-V.)
| | - Ana Laura Romero-Cerón
- Monterrey Institute of Technology, School of Engineering and Sciences, Monterrey 64700, Mexico; (A.C.-S.); (A.L.R.-C.); (D.A.L.-V.)
| | - América Rivera-Urbalejo
- Faculty of Stomatology, Meritorious Autonomous University of Puebla (BUAP), Puebla 72570, Mexico; (L.A.P.-R.); (A.R.-U.)
| | - Pieter Van Dillewijn
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain;
| | - Diego Armando Luna-Vital
- Monterrey Institute of Technology, School of Engineering and Sciences, Monterrey 64700, Mexico; (A.C.-S.); (A.L.R.-C.); (D.A.L.-V.)
| | - Jesús Muñoz-Rojas
- Ecology and Survival of Microorganisms Group, Laboratory of Microbial Molecular Ecology (LEMM), Center for Research in Microbiological Sciences, Institute of Sciences, Meritorious Autonomous University of Puebla (BUAP), Puebla 72570, Mexico;
| | - Yolanda Elizabeth Morales-García
- Ecology and Survival of Microorganisms Group, Laboratory of Microbial Molecular Ecology (LEMM), Center for Research in Microbiological Sciences, Institute of Sciences, Meritorious Autonomous University of Puebla (BUAP), Puebla 72570, Mexico;
- Faculty of Biological Sciences, Meritorious Autonomous University of Puebla (BUAP), Puebla 72570, Mexico
| | - María del Rocío Bustillos-Cristales
- Ecology and Survival of Microorganisms Group, Laboratory of Microbial Molecular Ecology (LEMM), Center for Research in Microbiological Sciences, Institute of Sciences, Meritorious Autonomous University of Puebla (BUAP), Puebla 72570, Mexico;
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12
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Peng P, Yang J, DiSpirito AA, Semrau JD. MmoD regulates soluble methane monooxygenase and methanobactin production in Methylosinus trichosporium OB3b. Appl Environ Microbiol 2023; 89:e0160123. [PMID: 38014956 PMCID: PMC10734442 DOI: 10.1128/aem.01601-23] [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: 09/12/2023] [Accepted: 10/10/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Aerobic methanotrophs play a critical role in the global carbon cycle, particularly in controlling net emissions of methane to the atmosphere. As methane is a much more potent greenhouse gas than carbon dioxide, there is increasing interest in utilizing these microbes to mitigate future climate change by increasing their ability to consume methane. Any such efforts, however, require a detailed understanding of how to manipulate methanotrophic activity. Herein, we show that methanotrophic activity is strongly controlled by MmoD, i.e., MmoD regulates methanotrophy through the post-transcriptional regulation of the soluble methane monooxygenase and controls the ability of methanotrophs to collect copper. Such data are likely to prove quite useful in future strategies to enhance the use of methanotrophs to not only reduce methane emissions but also remove methane from the atmosphere.
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Affiliation(s)
- Peng Peng
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Junwon Yang
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Alan A. DiSpirito
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Jeremy D. Semrau
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
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13
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Wang S, Chen X, Li W, Gong W, Wang Z, Cao W. Grazing exclusion alters soil methane flux and methanotrophic and methanogenic communities in alpine meadows on the Qinghai-Tibet Plateau. Front Microbiol 2023; 14:1293720. [PMID: 38164400 PMCID: PMC10757936 DOI: 10.3389/fmicb.2023.1293720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024] Open
Abstract
Grazing exclusion (GE) is an effective measure for restoring degraded grassland ecosystems. However, the effect of GE on methane (CH4) uptake and production remains unclear in dominant bacterial taxa, main metabolic pathways, and drivers of these pathways. This study aimed to determine CH4 flux in alpine meadow soil using the chamber method. The in situ composition of soil aerobic CH4-oxidizing bacteria (MOB) and CH4-producing archaea (MPA) as well as the relative abundance of their functional genes were analyzed in grazed and nongrazed (6 years) alpine meadows using metagenomic methods. The results revealed that CH4 fluxes in grazed and nongrazed plots were -34.10 and -22.82 μg‧m-2‧h-1, respectively. Overall, 23 and 10 species of Types I and II MOB were identified, respectively. Type II MOB comprised the dominant bacteria involved in CH4 uptake, with Methylocystis constituting the dominant taxa. With regard to MPA, 12 species were identified in grazed meadows and 3 in nongrazed meadows, with Methanobrevibacter constituting the dominant taxa. GE decreased the diversity of MPA but increased the relative abundance of dominated species Methanobrevibacter millerae from 1.47 to 4.69%. The proportions of type I MOB, type II MOB, and MPA that were considerably affected by vegetation and soil factors were 68.42, 21.05, and 10.53%, respectively. Furthermore, the structural equation models revealed that soil factors (available phosphorus, bulk density, and moisture) significantly affected CH4 flux more than vegetation factors (grass species number, grass aboveground biomass, grass root biomass, and litter biomass). CH4 flux was mainly regulated by serine and acetate pathways. The serine pathway was driven by soil factors (0.84, p < 0.001), whereas the acetate pathway was mainly driven by vegetation (-0.39, p < 0.05) and soil factors (0.25, p < 0.05). In conclusion, our findings revealed that alpine meadow soil is a CH4 sink. However, GE reduces the CH4 sink potential by altering vegetation structure and soil properties, especially soil physical properties.
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Affiliation(s)
- Shilin Wang
- Key Laboratory of Grassland Ecosystem, Ministry of Education, College of Pratacultural Science, Gansu Agricultural University, Lanzhou, China
| | - Xindong Chen
- Key Laboratory of Grassland Ecosystem, Ministry of Education, College of Pratacultural Science, Gansu Agricultural University, Lanzhou, China
| | - Wen Li
- Key Laboratory of Development of Forage Germplasm in the Qinghai-Tibetan Plateau of Qinghai Province, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining, China
| | - Wenlong Gong
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Zhengwen Wang
- Key Laboratory of Grassland Ecosystem, Ministry of Education, College of Pratacultural Science, Gansu Agricultural University, Lanzhou, China
| | - Wenxia Cao
- Key Laboratory of Grassland Ecosystem, Ministry of Education, College of Pratacultural Science, Gansu Agricultural University, Lanzhou, China
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14
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Woern C, Grossmann L. Microbial gas fermentation technology for sustainable food protein production. Biotechnol Adv 2023; 69:108240. [PMID: 37647973 DOI: 10.1016/j.biotechadv.2023.108240] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 08/16/2023] [Accepted: 08/21/2023] [Indexed: 09/01/2023]
Abstract
The development of novel, sustainable, and robust food production technologies represents one of the major pillars to address the most significant challenges humanity is going to face on earth in the upcoming decades - climate change, population growth, and resource depletion. The implementation of microfoods, i.e., foods formulated with ingredients from microbial cultivation, into the food supply chain has a huge potential to contribute towards energy-efficient and nutritious food manufacturing and represents a means to sustainably feed a growing world population. This review recapitulates and assesses the current state in the establishment and usage of gas fermenting bacteria as an innovative feedstock for protein production. In particular, we focus on the most promising representatives of this taxon: the hydrogen-oxidizing bacteria (hydrogenotrophs) and the methane-oxidizing bacteria (methanotrophs). These unicellular microorganisms can aerobically metabolize gaseous hydrogen and methane, respectively, to provide the required energy for building up cell material. A protein yield over 70% in the dry matter cell mass can be reached with no need for arable land and organic substrates making it a promising alternative to plant- and animal-based protein sources. We illuminate the holistic approach to incorporate protein extracts obtained from the cultivation of gas fermenting bacteria into microfoods. Herein, the fundamental properties of the bacteria, cultivation methods, downstream processing, and potential food applications are discussed. Moreover, this review covers existing and future challenges as well as sustainability aspects associated with the production of microbial protein through gas fermentation.
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Affiliation(s)
- Carlos Woern
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA
| | - Lutz Grossmann
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA.
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15
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Park YR, Krishna S, Lee OK, Lee EY. Biosynthesis of chiral diols from alkenes using metabolically engineered type II methanotroph. BIORESOURCE TECHNOLOGY 2023; 389:129851. [PMID: 37813317 DOI: 10.1016/j.biortech.2023.129851] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 10/06/2023] [Accepted: 10/06/2023] [Indexed: 10/11/2023]
Abstract
Methanotrophs are environmentally friendly microorganisms capable of converting gas to liquid using methane monooxygenases (MMOs). In addition to methane-to-methanol conversion, MMOs catalyze the conversion of alkanes to alcohols and alkenes to epoxides. Herein, the efficacy of epoxidation by type I and II methanotrophs was investigated, and type II methanotrophs were observed to be more efficient in converting alkenes to epoxides. Subsequently, three (Epoxide hydrolase) EHs of different origins were overexpressed in the type II methanotroph Methylosinus trichosporium OB3b to produce 1,2-diols from epoxide. Methylosinus trichosporium OB3b expressing Caulobacter crescentus EH produced the highest amount of (R)-1,2-propanediol (251.5 mg/L) from 1-propene. These results demonstrate the possibility of using methanotrophs as a microbial platform for diol production and the development of a continuous bioreactor for industrial applications.
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Affiliation(s)
- Ye Rim Park
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Shyam Krishna
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Ok Kyung Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea.
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16
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Kurt E, Qin J, Williams A, Zhao Y, Xie D. Perspectives for Using CO 2 as a Feedstock for Biomanufacturing of Fuels and Chemicals. Bioengineering (Basel) 2023; 10:1357. [PMID: 38135948 PMCID: PMC10740661 DOI: 10.3390/bioengineering10121357] [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: 10/17/2023] [Revised: 11/20/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
Microbial cell factories offer an eco-friendly alternative for transforming raw materials into commercially valuable products because of their reduced carbon impact compared to conventional industrial procedures. These systems often depend on lignocellulosic feedstocks, mainly pentose and hexose sugars. One major hurdle when utilizing these sugars, especially glucose, is balancing carbon allocation to satisfy energy, cofactor, and other essential component needs for cellular proliferation while maintaining a robust yield. Nearly half or more of this carbon is inevitably lost as CO2 during the biosynthesis of regular metabolic necessities. This loss lowers the production yield and compromises the benefit of reducing greenhouse gas emissions-a fundamental advantage of biomanufacturing. This review paper posits the perspectives of using CO2 from the atmosphere, industrial wastes, or the exhausted gases generated in microbial fermentation as a feedstock for biomanufacturing. Achieving the carbon-neutral or -negative goals is addressed under two main strategies. The one-step strategy uses novel metabolic pathway design and engineering approaches to directly fix the CO2 toward the synthesis of the desired products. Due to the limitation of the yield and efficiency in one-step fixation, the two-step strategy aims to integrate firstly the electrochemical conversion of the exhausted CO2 into C1/C2 products such as formate, methanol, acetate, and ethanol, and a second fermentation process to utilize the CO2-derived C1/C2 chemicals or co-utilize C5/C6 sugars and C1/C2 chemicals for product formation. The potential and challenges of using CO2 as a feedstock for future biomanufacturing of fuels and chemicals are also discussed.
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Affiliation(s)
- Elif Kurt
- Department of Chemical Engineering, University of Massachusetts, Lowell, MA 01854, USA; (E.K.); (J.Q.); (A.W.)
| | - Jiansong Qin
- Department of Chemical Engineering, University of Massachusetts, Lowell, MA 01854, USA; (E.K.); (J.Q.); (A.W.)
| | - Alexandria Williams
- Department of Chemical Engineering, University of Massachusetts, Lowell, MA 01854, USA; (E.K.); (J.Q.); (A.W.)
| | - Youbo Zhao
- Physical Sciences Inc., 20 New England Business Ctr., Andover, MA 01810, USA;
| | - Dongming Xie
- Department of Chemical Engineering, University of Massachusetts, Lowell, MA 01854, USA; (E.K.); (J.Q.); (A.W.)
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17
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Chang J, Peng P, Farhan Ul-Haque M, Hira A, DiSpirito AA, Semrau JD. Inhibition of nitrous oxide reduction in forest soil microcosms by different forms of methanobactin. Environ Microbiol 2023; 25:2338-2350. [PMID: 37395163 DOI: 10.1111/1462-2920.16456] [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: 02/20/2023] [Accepted: 06/14/2023] [Indexed: 07/04/2023]
Abstract
Copper plays a critical role in controlling greenhouse gas emissions as it is a key component of the particulate methane monooxygenase and nitrous oxide reductase. Some methanotrophs excrete methanobactin (MB) that has an extremely high copper affinity. As a result, MB may limit the ability of other microbes to gather copper, thereby decreasing their activity as well as impacting microbial community composition. Here, we show using forest soil microcosms that multiple forms of MB; MB from Methylosinus trichosporium OB3b (MB-OB3b) and MB from Methylocystis sp. strain SB2 (MB-SB2) increased nitrous oxide (N2 O) production as well caused significant shifts in microbial community composition. Such effects, however, were mediated by the amount of copper in the soils, with low-copper soil microcosms showing the strongest response to MB. Furthermore, MB-SB2 had a stronger effect, likely due to its higher affinity for copper. The presence of either form of MB also inhibited nitrite reduction and generally increased the presence of genes encoding for the iron-containing nitrite reductase (nirS) over the copper-dependent nitrite reductase (nirK). These data indicate the methanotrophic-mediated production of MB can significantly impact multiple steps of denitrification, as well as have broad effects on microbial community composition of forest soils.
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Affiliation(s)
- Jin Chang
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Peng Peng
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Abid Hira
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan
| | - Alan A DiSpirito
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Jeremy D Semrau
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
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18
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Venetz J, Żygadłowska OM, Lenstra WK, van Helmond NAGM, Nuijten GHL, Wallenius AJ, Dalcin Martins P, Slomp CP, Jetten MSM, Veraart AJ. Versatile methanotrophs form an active methane biofilter in the oxycline of a seasonally stratified coastal basin. Environ Microbiol 2023; 25:2277-2288. [PMID: 37381163 DOI: 10.1111/1462-2920.16448] [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: 12/23/2022] [Accepted: 05/31/2023] [Indexed: 06/30/2023]
Abstract
The potential and drivers of microbial methane removal in the water column of seasonally stratified coastal ecosystems and the importance of the methanotrophic community composition for ecosystem functioning are not well explored. Here, we combined depth profiles of oxygen and methane with 16S rRNA gene amplicon sequencing, metagenomics and methane oxidation rates at discrete depths in a stratified coastal marine system (Lake Grevelingen, The Netherlands). Three amplicon sequence variants (ASVs) belonging to different genera of aerobic Methylomonadaceae and the corresponding three methanotrophic metagenome-assembled genomes (MOB-MAGs) were retrieved by 16S rRNA sequencing and metagenomic analysis, respectively. The abundances of the different methanotrophic ASVs and MOB-MAGs peaked at different depths along the methane oxygen counter-gradient and the MOB-MAGs show a quite diverse genomic potential regarding oxygen metabolism, partial denitrification and sulphur metabolism. Moreover, potential aerobic methane oxidation rates indicated high methanotrophic activity throughout the methane oxygen counter-gradient, even at depths with low in situ methane or oxygen concentration. This suggests that niche-partitioning with high genomic versatility of the present Methylomonadaceae might contribute to the functional resilience of the methanotrophic community and ultimately the efficiency of methane removal in the stratified water column of a marine basin.
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Affiliation(s)
- Jessica Venetz
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Olga M Żygadłowska
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Wytze K Lenstra
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Niels A G M van Helmond
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Guylaine H L Nuijten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Anna J Wallenius
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Paula Dalcin Martins
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Caroline P Slomp
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Annelies J Veraart
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
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19
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Zhong W, Li H, Wang Y. Design and Construction of Artificial Biological Systems for One-Carbon Utilization. BIODESIGN RESEARCH 2023; 5:0021. [PMID: 37915992 PMCID: PMC10616972 DOI: 10.34133/bdr.0021] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/05/2023] [Indexed: 11/03/2023] Open
Abstract
The third-generation (3G) biorefinery aims to use microbial cell factories or enzymatic systems to synthesize value-added chemicals from one-carbon (C1) sources, such as CO2, formate, and methanol, fueled by renewable energies like light and electricity. This promising technology represents an important step toward sustainable development, which can help address some of the most pressing environmental challenges faced by modern society. However, to establish processes competitive with the petroleum industry, it is crucial to determine the most viable pathways for C1 utilization and productivity and yield of the target products. In this review, we discuss the progresses that have been made in constructing artificial biological systems for 3G biorefineries in the last 10 years. Specifically, we highlight the representative works on the engineering of artificial autotrophic microorganisms, tandem enzymatic systems, and chemo-bio hybrid systems for C1 utilization. We also prospect the revolutionary impact of these developments on biotechnology. By harnessing the power of 3G biorefinery, scientists are establishing a new frontier that could potentially revolutionize our approach to industrial production and pave the way for a more sustainable future.
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Affiliation(s)
- Wei Zhong
- Westlake Center of Synthetic Biology and Integrated Bioengineering, School of Engineering,
Westlake University, Hangzhou 310000, PR China
| | - Hailong Li
- Westlake Center of Synthetic Biology and Integrated Bioengineering, School of Engineering,
Westlake University, Hangzhou 310000, PR China
- School of Materials Science and Engineering,
Zhejiang University, Zhejiang Province, Hangzhou 310000, PR China
| | - Yajie Wang
- Westlake Center of Synthetic Biology and Integrated Bioengineering, School of Engineering,
Westlake University, Hangzhou 310000, PR China
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20
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Qiu L, Lok KS, Lu Q, Zhong H, Guo X, Shim H. Zinc and copper supplements enhance trichloroethylene removal by Pseudomonas plecoglossicida in water. ENVIRONMENTAL TECHNOLOGY 2023; 44:3698-3709. [PMID: 35451932 DOI: 10.1080/09593330.2022.2069518] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
The effects of two microelements, zinc and copper, on the aerobic co-metabolic removal of trichloroethylene (10 mg/L) by the isolate Pseudomonas plecoglossicida were investigated. The strain was previously isolated from a petroleum-contaminated site using toluene (150 mg/L) as substrate. Different concentrations (1, 10 and 100 mg/L) of microelements provided with SO42- and Cl- were tested. The results showed the supplement of Zn2+ and Cu2+ at the low concentration (1 mg/L) significantly enhanced cell growth. The removal efficiencies for toluene and trichloroethylene were also enhanced at the low concentration (1 mg/L) of Zn2+ and Cu2+. Compared to the control without zinc supplement, higher concentrations of zinc (10 and 100 mg/L) enhanced the removal efficiencies for both toluene and trichloroethylene in the first three days but showed some inhibitory effect afterward. However, the higher concentrations of Cu2+ (10 and 100 mg/L) always showed inhibitory to the toluene removal while showing inhibitory to the TCE removal after three days. For both Zn2+ and Cu2+, the anions SO42- and Cl- did not show significant difference in their effects on the toluene removal. A possible mechanism for Zn2+ and Cu2+ to enhance the removal of toluene and trichloroethylene would be their involvement in toluene oxygenase-based transformation processes. In addition, high concentrations of Zn2+ and Cu2+ ions could be removed from the liquid by the cells accordingly. The results imply a potential of supplementing low concentrations of zinc and copper to enhance bioremediation of the sites co-contaminated with toluene and trichloroethylene.
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Affiliation(s)
- Lan Qiu
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau SAR, People's Republic of China
| | - Keng Seng Lok
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau SAR, People's Republic of China
| | - Qihong Lu
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau SAR, People's Republic of China
| | - Hua Zhong
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau SAR, People's Republic of China
| | - Xiaoyuan Guo
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau SAR, People's Republic of China
| | - Hojae Shim
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau SAR, People's Republic of China
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van den Bergh SG, Chardon I, Meima-Franke M, Costa OYA, Korthals GW, de Boer W, Bodelier PLE. The intrinsic methane mitigation potential and associated microbes add product value to compost. WASTE MANAGEMENT (NEW YORK, N.Y.) 2023; 170:17-32. [PMID: 37542791 DOI: 10.1016/j.wasman.2023.07.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/20/2023] [Accepted: 07/23/2023] [Indexed: 08/07/2023]
Abstract
Conventional agricultural activity reduces the uptake of the potent greenhouse gas methane by agricultural soils. However, the recently observed improved methane uptake capacity of agricultural soils after compost application is promising but needs mechanistic understanding. In this study, the methane uptake potential and microbiomes involved in methane cycling were assessed in green compost and household-compost with and without pre-digestion. In bottle incubations of different composts with both high and near-atmospheric methane concentrations (∼10.000 & ∼10 ppmv, respectively), green compost showed the highest potential methane uptake rates (up to 305.19 ± 94.43 nmol h-1 g dw compost-1 and 25.19 ± 6.75 pmol h-1 g dw compost-1, respectively). 16S, pmoA and mcrA amplicon sequencing revealed that its methanotrophic and methanogenic communities were dominated by type Ib methanotrophs, and more specifically by Methylocaldum szegediense and other Methylocaldum species, and Methanosarcina species, respectively. Ordination analyses showed that the abundance of type Ib methanotrophic bacteria was the main steering factor of the intrinsic methane uptake rates of composts, whilst the ammonium content was the main limiting factor, being most apparent in household composts. These results emphasize the potential of compost to contribute to methane mitigation, providing added value to compost as a product for industrial, commercial, governmental and public interests relevant to waste management. Compost could serve as a vector for the introduction of active methanotrophic bacteria in agricultural soils, potentially improving the methane uptake potential of agricultural soils and contributing to global methane mitigation, which should be the focus of future research.
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Affiliation(s)
- Stijn G van den Bergh
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700AB Wageningen, the Netherlands; Soil Biology Group, Wageningen University and Research, PO Box 47, 6700AA Wageningen, the Netherlands.
| | - Iris Chardon
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700AB Wageningen, the Netherlands.
| | - Marion Meima-Franke
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700AB Wageningen, the Netherlands.
| | - Ohana Y A Costa
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700AB Wageningen, the Netherlands.
| | - Gerard W Korthals
- Biointeractions and Plant Health, Wageningen Plant Research, PO Box 16, 6700AA Wageningen, the Netherlands.
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700AB Wageningen, the Netherlands; Soil Biology Group, Wageningen University and Research, PO Box 47, 6700AA Wageningen, the Netherlands.
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700AB Wageningen, the Netherlands.
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22
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Hwang Y, Na JG, Lee SJ. Transcriptional regulation of soluble methane monooxygenase via enhancer-binding protein derived from Methylosinus sporium 5. Appl Environ Microbiol 2023; 89:e0210422. [PMID: 37668365 PMCID: PMC10537576 DOI: 10.1128/aem.02104-22] [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: 12/15/2022] [Accepted: 07/07/2023] [Indexed: 09/06/2023] Open
Abstract
Methane is a major greenhouse gas, and methanotrophs regulate the methane level in the carbon cycle. Soluble methane monooxygenase (sMMO) is expressed in various methanotroph genera, including Alphaproteobacteria and Gammaproteobacteria, and catalyzes the hydroxylation of methane to methanol. It has been proposed that MmoR regulates the expression of sMMO as an enhancer-binding protein under copper-limited conditions; however, details on this transcriptional regulation remain limited. Herein, we elucidate the transcriptional pathway of sMMO depending on copper ion concentration, which affects the interaction of MmoR and sigma factor. MmoR and sigma-54 (σ54) from Methylosinus sporium 5 were successfully overexpressed in Escherichia coli and purified to investigate sMMO transcription in methanotrophs. The results indicated that σ54 binds to a promoter positioned -24 (GG) and -12 (TGC) upstream between mmoG and mmoX1. The binding affinity and selectivity are lower (Kd = 184.6 ± 6.2 nM) than those of MmoR. MmoR interacts with the upstream activator sequence (UAS) with a strong binding affinity (Kd = 12.5 ± 0.5 nM). Mutational studies demonstrated that MmoR has high selectivity to its binding partner (ACA-xx-TGT). Titration assays have demonstrated that MmoR does not coordinate with copper ions directly; however, its binding affinity to UAS decreases in a low-copper-containing medium. MmoR strongly interacts with adenosine triphosphate (Kd = 62.8 ± 0.5 nM) to generate RNA polymerase complex. This study demonstrated that the binding events of both MmoR and σ54 that regulate transcription in M. sporium 5 depend on the copper ion concentration. IMPORTANCE This study provides biochemical evidence of transcriptional regulation of soluble methane monooxygenase (sMMO) in methanotrophs that control methane levels in ecological systems. Previous studies have proposed transcriptional regulation of MMOs, including sMMO and pMMO, while we provide further evidence to elucidate its mechanism using a purified enhancer-binding protein (MmoR) and transcription factor (σ54). The characterization studies of σ54 and MmoR identified the promoter binding sites and enhancer-binding sequences essential for sMMO expression. Our findings also demonstrate that MmoR functions as a trigger for sMMO expression due to the high specificity and selectivity for enhancer-binding sequences. The UV-visible spectrum of purified MmoR suggested an iron coordination like other GAF domain, and that ATP is essential for the initiation of enhancer elements. Binding assays indicated that these interactions are blocked by the copper ion. These results provide novel insights into gene regulation of methanotrophs.
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Affiliation(s)
- Yunha Hwang
- Department of Chemistry, Jeonbuk National University , Jeonju, South Korea
| | - Jeong-Geol Na
- Department of Chemical Engineering, Sogang University , Seoul, South Korea
| | - Seung Jae Lee
- Department of Chemistry, Jeonbuk National University , Jeonju, South Korea
- Institute of Molecular Biology and Genetics, Jeonbuk National University , Jeonju, South Korea
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23
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Huang J, Zhao W, Ju J, Liu S, Ye J, Long Y. The existence of ferric hydroxide links the carbon and nitrogen cycles by promoting nitrite-coupled methane anaerobic oxidation. WATER RESEARCH 2023; 243:120192. [PMID: 37454463 DOI: 10.1016/j.watres.2023.120192] [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: 02/22/2023] [Revised: 06/04/2023] [Accepted: 06/06/2023] [Indexed: 07/18/2023]
Abstract
Microorganism-mediated anaerobic oxidation of methane can efficiently mitigate methane atmospheric emissions and is a key process linking the biogeochemical cycles of carbon, nitrogen, and iron. The results showed that methane oxidation and nitrite removal rates in the CF were 1.12 and 1.28 times higher than those in CK, respectively, suggesting that ferric hydroxide can enhance nitrite-driven AOM. The biochemical process was mediated by the enrichment of methanogens, methanotrophs, and denitrifiers. Methanobacterium and Methanosarcina were positively correlated with Fe3+ and Fe2+, whereas Methylocystis and Methylocaldum were positively correlated with methane, and denitrifiers were positively correlated with nitrite. Metagenomic analysis revealed that the genes related to methane oxidation, nitrogen reduction, and heme c-type cytochrome were upregulated in CF, indicating that a synergistic action of bacteria and methanogens drove AOM via diverse metabolic pathways, within which ferric hydroxide played a crucial role. This study provides novel insights into the synergistic mechanism of ferric iron and nitrite-driven AOM.
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Affiliation(s)
- Juan Huang
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Wurong Zhao
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Jinwei Ju
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Suifen Liu
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Jinshao Ye
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Yan Long
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China.
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24
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Mortensen AT, Goonesekera EM, Dechesne A, Elad T, Tang K, Andersen HR, Smets BF, Valverde-Pérez B. Methanotrophic oxidation of organic micropollutants and nitrogen upcycling in a hybrid membrane biofilm reactor (hMBfR) for simultaneous O 2 and CH 4 supply. WATER RESEARCH 2023; 242:120104. [PMID: 37348423 DOI: 10.1016/j.watres.2023.120104] [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: 02/24/2023] [Revised: 05/01/2023] [Accepted: 05/19/2023] [Indexed: 06/24/2023]
Abstract
Pharmaceuticals and other organic micropollutants (OMPs) present in wastewater effluents are of growing concern, as they threaten environmental and human health. Conventional biological treatments lead to limited removal of OMPs. Methanotrophic bacteria can degrade a variety of OMPs. By employing a novel bubble-free hybrid membrane biofilm bioreactor (hMBfR), we grew methanotrophic bacteria at three CH4 loading rates. Biomass productivity and CH4 loading showed a linear correlation, with a maximum productivity of 372 mg-VSS·L-1·d-1, with corresponding biomass concentration of 1117.6 ± 56.4 mg-VSS·L-1. Furthermore, the biodegradation of sulfamethoxazole and 1H-benzotriazole positively correlated with CH4 oxidation rates, with highest biodegradation kinetic constants of 3.58 L·g-1·d-1 and 5.42 L·g-1·d-1, respectively. Additionally, the hMBfR recovered nutrients as microbial proteins, with an average content 39% DW. The biofilm community was dominated by Methylomonas, while the bulk was dominated by aerobic heterotrophic bacteria. The hMBfR removed OMPs, allowing for safer water reuse while valorising CH4 and nutrients.
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Affiliation(s)
- Anders T Mortensen
- Department of Environmental and Resource Engineering, Technical University of Denmark, DTU, Building 115, Bygningstorvet, Lyngby 2800, Denmark
| | - Estelle M Goonesekera
- Department of Environmental and Resource Engineering, Technical University of Denmark, DTU, Building 115, Bygningstorvet, Lyngby 2800, Denmark
| | - Arnaud Dechesne
- Department of Environmental and Resource Engineering, Technical University of Denmark, DTU, Building 115, Bygningstorvet, Lyngby 2800, Denmark
| | - Tal Elad
- Department of Environmental and Resource Engineering, Technical University of Denmark, DTU, Building 115, Bygningstorvet, Lyngby 2800, Denmark
| | - Kai Tang
- Department of Environmental and Resource Engineering, Technical University of Denmark, DTU, Building 115, Bygningstorvet, Lyngby 2800, Denmark
| | - Henrik R Andersen
- Department of Environmental and Resource Engineering, Technical University of Denmark, DTU, Building 115, Bygningstorvet, Lyngby 2800, Denmark
| | - Barth F Smets
- Department of Environmental and Resource Engineering, Technical University of Denmark, DTU, Building 115, Bygningstorvet, Lyngby 2800, Denmark
| | - Borja Valverde-Pérez
- Department of Environmental and Resource Engineering, Technical University of Denmark, DTU, Building 115, Bygningstorvet, Lyngby 2800, Denmark.
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25
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Weng C, Peng X, Han Y. From methane to value-added bioproducts: microbial metabolism, enzymes, and metabolic engineering. ADVANCES IN APPLIED MICROBIOLOGY 2023; 124:119-146. [PMID: 37597946 DOI: 10.1016/bs.aambs.2023.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/21/2023]
Abstract
Methane is abundant in nature, and excessive emissions will cause the greenhouse effect. Methane is also an ideal carbon and energy feedstock for biosynthesis. In the review, the microorganisms, metabolism, and enzymes for methane utilization, and the advances of conversion to value-added bioproducts were summarized. First, the physiological characteristics, classification, and methane oxidation process of methanotrophs were introduced. The metabolic pathways for methane utilization and key intermediate metabolites of native and synthetic methanotrophs were summarized. Second, the enzymatic properties, crystal structures, and catalytic mechanisms of methane-oxidizing and metabolizing enzymes in methanotrophs were described. Third, challenges and prospects in metabolic pathways and enzymatic catalysis for methane utilization and conversion to value-added bioproducts were discussed. Finally, metabolic engineering of microorganisms for methane biooxidation and bioproducts synthesis based on different pathways were summarized. Understanding the metabolism and challenges of microbial methane utilization will provide insights into possible strategies for efficient methane-based synthesis.
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Affiliation(s)
- Caihong Weng
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, P.R. China; School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Xiaowei Peng
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, P.R. China; School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Yejun Han
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, P.R. China; School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, P.R. China.
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26
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Ouyang C, Qin Y, Liang Y, Gou Y. Community structure and network interaction of aerobic methane-oxidizing bacteria in Chongqing's central urban area in the Three Gorges Reservoir, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:56368-56381. [PMID: 36914933 DOI: 10.1007/s11356-023-26310-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
A reservoir is an important source of methane (CH4), which is consumed by aerobic methane-oxidizing bacteria (MOB), representing the main CH4 sink in water. The central urban area of Chongqing in the Three Gorges Reservoir (TGR) area was selected as the study area in 2021. High-throughput sequencing was used to analyze the community structure and abundance of MOBs. The results showed that Methylocystis (Type II) was the dominant MOB in water, whereas Methylococcus (Type I) and Methylocystis co-dominated the sediments. High water temperature in the study area largely accounted for the predominance of Type II MOBs in the two habitats. Moreover, the influence of environmental factors on MOB community and its interspecific relationship were significantly regulated by the operation of the TGR. In the low-water-level period, NO2--N and CO2 concentration significantly correlated with Methylocystis, whereas in the high-water-level period, the higher discharge and velocity weakened the influence of all environmental factors on Methylocystis. In addition, the scouring of sediments by increasing discharge in the high-water-level period caused a significant decrease in dissolved CH4 concentration. The decrease in substrate increased interspecific competition within the MOB community, especially between different types of MOBs, in the high-water-level period.
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Affiliation(s)
- Changyue Ouyang
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing, 400074, China
- Key Laboratory of Hydraulic and Waterway Engineering of the Ministry of Education, Chongqing Jiaotong University, Chongqing, 400074, China
| | - Yu Qin
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing, 400074, China.
- Key Laboratory of Hydraulic and Waterway Engineering of the Ministry of Education, Chongqing Jiaotong University, Chongqing, 400074, China.
| | - Yue Liang
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing, 400074, China
| | - Yujia Gou
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing, 400074, China
- Key Laboratory of Hydraulic and Waterway Engineering of the Ministry of Education, Chongqing Jiaotong University, Chongqing, 400074, China
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27
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Synergy effects of Methylomonas koyamae and Hyphomicrobium methylovorum under methanethiol stress. Appl Microbiol Biotechnol 2023; 107:3099-3111. [PMID: 36933079 DOI: 10.1007/s00253-023-12472-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/25/2023] [Accepted: 03/03/2023] [Indexed: 03/19/2023]
Abstract
Methanotrophs are able to metabolize volatile organic sulfur compounds (VOSCs), excrete organic carbon during CH4 oxidation, and influence microbial community structure and function of the ecosystem. In return, microbial community structure and environmental factors can affect the growth metabolism of methanotrophs. In this study, Methylomonas koyamae and Hyphomicrobium methylovorum were used for model organisms, and methanethiol (MT) was chosen for a typical VOSC to investigate the synergy effects under VOSC stress. The results showed that when Hyphomicrobium methylovorum was co-cultured with Methylomonas koyamae in the medium with CH4 used as the carbon source, the co-culture had better MT tolerance relative to Methylomonas koyamae and oxidized all CH4 within 120 h, even at the initial MT concentration of 2000 mg m-3. The optimal co-culture ratios of Methylomonas koyamae to Hyphomicrobium methylovorum were 4:1-12:1. Although MT could be converted spontaneously to dimethyl disulfide (DMDS), H2S, and CS2 in air, faster losses of MT, DMDS, H2S, and CS2 were observed in each strain mono-culture and the co-culture. Compared with Hyphomicrobium methylovorum, MT was degraded more quickly in the Methylomonas koyamae culture. During the co-culture, the CH4 oxidation process of Methylomonas koyamae could provide carbon and energy sources for the growth of Hyphomicrobium methylovorum, while Hyphomicrobium methylovorum oxidized MT to help Methylomonas koyamae detoxify. These findings are helpful to understand the synergy effects of Methylomonas koyamae and Hyphomicrobium methylovorum under MT stress and enrich the role of methanotrophs in the sulfur biogeochemical cycle. KEY POINTS: • The co-culture of Methylomonas and Hyphomicrobium has better tolerance to CH3SH. • Methylomonas can provide carbon sources for the growth of Hyphomicrobium. • The co-culture of Methylomonas and Hyphomicrobium enhances the removal of CH4 and CH3SH.
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28
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Mrudulakumari Vasudevan U, Mai DHA, Krishna S, Lee EY. Methanotrophs as a reservoir for bioactive secondary metabolites: Pitfalls, insights and promises. Biotechnol Adv 2023; 63:108097. [PMID: 36634856 DOI: 10.1016/j.biotechadv.2023.108097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/10/2022] [Accepted: 01/06/2023] [Indexed: 01/11/2023]
Abstract
Methanotrophs are potent natural producers of several bioactive secondary metabolites (SMs) including isoprenoids, polymers, peptides, and vitamins. Cryptic biosynthetic gene clusters identified from these microbes via genome mining hinted at the vast and hidden SM biosynthetic potential of these microbes. Central carbon metabolism in methanotrophs offers rare pathway intermediate pools that could be further diversified using advanced synthetic biology tools to produce valuable SMs; for example, plant polyketides, rare carotenoids, and fatty acid-derived SMs. Recent advances in pathway reconstruction and production of isoprenoids, squalene, ectoine, polyhydroxyalkanoate copolymer, cadaverine, indigo, and shinorine serve as proof-of-concept. This review provides theoretical guidance for developing methanotrophs as microbial chassis for high-value SMs. We summarize the distinct secondary metabolic potentials of type I and type II methanotrophs, with specific attention to products relevant to biomedical applications. This review also includes native and non-native SMs from methanotrophs, their therapeutic potential, strategies to induce silent biosynthetic gene clusters, and challenges.
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Affiliation(s)
- Ushasree Mrudulakumari Vasudevan
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Dung Hoang Anh Mai
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Shyam Krishna
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea.
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Rumah B, Claxton Stevens BH, Yeboah JE, Stead CE, Harding EL, Minton NP, Zhang Y. In Vivo Genome Editing in Type I and II Methanotrophs Using a CRISPR/Cas9 System. ACS Synth Biol 2023; 12:544-554. [PMID: 36688528 PMCID: PMC9942187 DOI: 10.1021/acssynbio.2c00554] [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] [Indexed: 01/24/2023]
Abstract
Methanotrophic bacteria are Gram-negative, aerobic organisms that use methane as their sole source of carbon and energy. In this study, we constructed and exemplified a CRISPR/Cas9 genome editing system and used it to successfully make gene deletions and insertions in the type I methanotroph Methylococcus capsulatus Bath and the type II methanotroph Methylocystis parvus OBBP. High frequencies of gene deletions and insertions were achieved in combination with homology-directed repair. In M. parvus OBBP, we also investigated the impact of several parameters on the CRISPR/Cas9 genome editing, where the ligD gene was targeted with various PAM sequences and guide RNA spacer sequences, homology arms of variable length, differences in the duration of mating during conjugation, and exploiting promoters of different strengths to control the expression of cas9 and sgRNA. Although not the first attempt to develop a CRISPR/Cas system in methanotrophs, this work demonstrated for the first time an efficient CRISPR/Cas9 system generating scarless clean gene deletions and insertions in methanotroph genomes.
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30
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Oudova-Rivera B, Crombie AT, Murrell JC, Lehtovirta-Morley LE. Alcohols as inhibitors of ammonia oxidizing archaea and bacteria. FEMS Microbiol Lett 2023; 370:fnad093. [PMID: 37698885 PMCID: PMC11025371 DOI: 10.1093/femsle/fnad093] [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: 05/26/2023] [Revised: 08/23/2023] [Accepted: 09/11/2023] [Indexed: 09/13/2023] Open
Abstract
Ammonia oxidizers are key players in the global nitrogen cycle and are responsible for the oxidation of ammonia to nitrite, which is further oxidized to nitrate by other microorganisms. Their activity can lead to adverse effects on some human-impacted environments, including water pollution through leaching of nitrate and emissions of the greenhouse gas nitrous oxide (N2O). Ammonia monooxygenase (AMO) is the key enzyme in microbial ammonia oxidation and shared by all groups of aerobic ammonia oxidizers. The AMO has not been purified in an active form, and much of what is known about its potential structure and function comes from studies on its interactions with inhibitors. The archaeal AMO is less well studied as ammonia oxidizing archaea were discovered much more recently than their bacterial counterparts. The inhibition of ammonia oxidation by aliphatic alcohols (C1-C8) using the model terrestrial ammonia oxidizing archaeon 'Candidatus Nitrosocosmicus franklandus' C13 and the ammonia oxidizing bacterium Nitrosomonas europaea was examined in order to expand knowledge about the range of inhibitors of ammonia oxidizers. Methanol was the most potent specific inhibitor of the AMO in both ammonia oxidizers, with half-maximal inhibitory concentrations (IC50) of 0.19 and 0.31 mM, respectively. The inhibition was AMO-specific in 'Ca. N. franklandus' C13 in the presence of C1-C2 alcohols, and in N. europaea in the presence of C1-C3 alcohols. Higher chain-length alcohols caused non-specific inhibition and also inhibited hydroxylamine oxidation. Ethanol was tolerated by 'Ca. N. franklandus' C13 at a higher threshold concentration than other chain-length alcohols, with 80 mM ethanol being required for complete inhibition of ammonia oxidation.
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Affiliation(s)
- Barbora Oudova-Rivera
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Andrew T Crombie
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
- School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
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Ray S, Jin JO, Choi I, Kim M. Recent trends of biotechnological production of polyhydroxyalkanoates from C1 carbon sources. Front Bioeng Biotechnol 2023; 10:907500. [PMID: 36686222 PMCID: PMC9852868 DOI: 10.3389/fbioe.2022.907500] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 12/06/2022] [Indexed: 01/09/2023] Open
Abstract
Growing concerns over the use of limited fossil fuels and their negative impacts on the ecological niches have facilitated the exploration of alternative routes. The use of conventional plastic material also negatively impacts the environment. One such green alternative is polyhydroxyalkanoates, which are biodegradable, biocompatible, and environmentally friendly. Recently, researchers have focused on the utilization of waste gases particularly those belonging to C1 sources derived directly from industries and anthropogenic activities, such as carbon dioxide, methane, and methanol as the substrate for polyhydroxyalkanoates production. Consequently, several microorganisms have been exploited to utilize waste gases for their growth and biopolymer accumulation. Methylotrophs such as Methylobacterium organophilum produced highest amount of PHA up to 88% using CH4 as the sole carbon source and 52-56% with CH3OH. On the other hand Cupriavidus necator, produced 71-81% of PHA by utilizing CO and CO2 as a substrate. The present review shows the potential of waste gas valorization as a promising solution for the sustainable production of polyhydroxyalkanoates. Key bottlenecks towards the usage of gaseous substrates obstructing their realization on a large scale and the possible technological solutions were also highlighted. Several strategies for PHA production using C1 gases through fermentation and metabolic engineering approaches are discussed. Microbes such as autotrophs, acetogens, and methanotrophs can produce PHA from CO2, CO, and CH4. Therefore, this article presents a vision of C1 gas into bioplastics are prospective strategies with promising potential application, and aspects related to the sustainability of the system.
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Affiliation(s)
- Subhasree Ray
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, South Korea,Department of Life Science, School of Basic Science and Research, Sharda University, Greater Noida, India,*Correspondence: Myunghee Kim, ; Subhasree Ray,
| | - Jun-O Jin
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea,Department of Food Science and Technology, Yeungnam University, Gyeongsan, South Korea
| | - Inho Choi
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea,Department of Food Science and Technology, Yeungnam University, Gyeongsan, South Korea
| | - Myunghee Kim
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, South Korea,Department of Food Science and Technology, Yeungnam University, Gyeongsan, South Korea,*Correspondence: Myunghee Kim, ; Subhasree Ray,
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Yao X, Wang J, Hu B. How methanotrophs respond to pH: A review of ecophysiology. Front Microbiol 2023; 13:1034164. [PMID: 36687570 PMCID: PMC9853399 DOI: 10.3389/fmicb.2022.1034164] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/09/2022] [Indexed: 01/08/2023] Open
Abstract
Varying pH globally affects terrestrial microbial communities and biochemical cycles. Methanotrophs effectively mitigate methane fluxes in terrestrial habitats. Many methanotrophs grow optimally at neutral pH. However, recent discoveries show that methanotrophs grow in strongly acidic and alkaline environments. Here, we summarize the existing knowledge on the ecophysiology of methanotrophs under different pH conditions. The distribution pattern of diverse subgroups is described with respect to their relationship with pH. In addition, their responses to pH stress, consisting of structure-function traits and substrate affinity traits, are reviewed. Furthermore, we propose a putative energy trade-off model aiming at shedding light on the adaptation mechanisms of methanotrophs from a novel perspective. Finally, we take an outlook on methanotrophs' ecophysiology affected by pH, which would offer new insights into the methane cycle and global climate change.
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Affiliation(s)
- Xiangwu Yao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China,Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China,*Correspondence: Baolan Hu ✉
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Xie R, Takashino M, Igarashi K, Kitagawa W, Kato S. Transcriptional Regulation of Methanol Dehydrogenases in the Methanotrophic Bacterium Methylococcus capsulatus Bath by Soluble and Insoluble Lanthanides. Microbes Environ 2023; 38:ME23065. [PMID: 38092408 PMCID: PMC10728633 DOI: 10.1264/jsme2.me23065] [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: 07/12/2023] [Accepted: 10/18/2023] [Indexed: 12/18/2023] Open
Abstract
The effects of soluble and insoluble lanthanides on gene expression in Methylococcus capsulatus Bath were investigated. Genes for lanthanide-containing methanol dehydrogenases (XoxF-MDHs) and their calcium-containing counterparts (MxaFI-MDHs) were up- and down-regulated, respectively, by supplementation with soluble lanthanide chlorides, indicating that M. capsulatus has the "lanthanide switch" observed in other methanotrophs. Insoluble lanthanide oxides also induced the lanthanide switch and were dissolved by the spent medium of M. capsulatus, suggesting the presence of lanthanide-chelating compounds. A transcriptome ana-lysis indicated that a gene cluster for the synthesis of an enterobactin-like metal chelator contributed to the dissolution of insoluble lanthanides.
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Affiliation(s)
- Ruoyun Xie
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060–8589, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 2–17–2–1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062–8517, Japan
| | - Motoko Takashino
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 2–17–2–1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062–8517, Japan
| | - Kensuke Igarashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 2–17–2–1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062–8517, Japan
| | - Wataru Kitagawa
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060–8589, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 2–17–2–1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062–8517, Japan
| | - Souichiro Kato
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060–8589, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 2–17–2–1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062–8517, Japan
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Wu Z, Man Q, Niu H, Lyu H, Song H, Li R, Ren G, Zhu F, Peng C, Li B, Ma X. Recent advances and trends of trichloroethylene biodegradation: A critical review. Front Microbiol 2022; 13:1053169. [PMID: 36620007 PMCID: PMC9813602 DOI: 10.3389/fmicb.2022.1053169] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
Trichloroethylene (TCE) is a ubiquitous chlorinated aliphatic hydrocarbon (CAH) in the environment, which is a Group 1 carcinogen with negative impacts on human health and ecosystems. Based on a series of recent advances, the environmental behavior and biodegradation process on TCE biodegradation need to be reviewed systematically. Four main biodegradation processes leading to TCE biodegradation by isolated bacteria and mixed cultures are anaerobic reductive dechlorination, anaerobic cometabolic reductive dichlorination, aerobic co-metabolism, and aerobic direct oxidation. More attention has been paid to the aerobic co-metabolism of TCE. Laboratory and field studies have demonstrated that bacterial isolates or mixed cultures containing Dehalococcoides or Dehalogenimonas can catalyze reductive dechlorination of TCE to ethene. The mechanisms, pathways, and enzymes of TCE biodegradation were reviewed, and the factors affecting the biodegradation process were discussed. Besides, the research progress on material-mediated enhanced biodegradation technologies of TCE through the combination of zero-valent iron (ZVI) or biochar with microorganisms was introduced. Furthermore, we reviewed the current research on TCE biodegradation in field applications, and finally provided the development prospects of TCE biodegradation based on the existing challenges. We hope that this review will provide guidance and specific recommendations for future studies on CAHs biodegradation in laboratory and field applications.
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Affiliation(s)
- Zhineng Wu
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, China
| | - Quanli Man
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, China
| | - Hanyu Niu
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, China
| | - Honghong Lyu
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, China
| | - Haokun Song
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, China
| | - Rongji Li
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, China
| | - Gengbo Ren
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, China
| | - Fujie Zhu
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, China
| | - Chu Peng
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Benhang Li
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, China
| | - Xiaodong Ma
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, China,*Correspondence: Xiaodong Ma,
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Koo CW, Hershewe JM, Jewett MC, Rosenzweig AC. Cell-Free Protein Synthesis of Particulate Methane Monooxygenase into Nanodiscs. ACS Synth Biol 2022; 11:4009-4017. [PMID: 36417751 PMCID: PMC9910172 DOI: 10.1021/acssynbio.2c00366] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Particulate methane monooxygenase (pMMO) is a multi-subunit membrane metalloenzyme used by methanotrophic bacteria to convert methane to methanol. A major hurdle to studying pMMO is the lack of a recombinant expression system, precluding investigation of individual residues by mutagenesis and hampering a complete understanding of its mechanism. Here, we developed an Escherichia coli lysate-based cell-free protein synthesis (CFPS) system that can be used to express pMMO in vitro in the presence of nanodiscs. We used a SUMO fusion construct to generate the native PmoB subunit and showed that the SUMO protease (Ulp1) cleaves the protein in the reaction mixture. Using an affinity tag to isolate the complete pMMO complex, we demonstrated that the complex forms without the need for exogenous translocon machinery or chaperones, confirmed by negative stain electron microscopy. This work demonstrates the potential for using CFPS to express multi-subunit membrane-bound metalloenzymes directly into lipid bilayers.
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Affiliation(s)
- Christopher W. Koo
- Department of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Jasmine M. Hershewe
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C. Rosenzweig
- Department of Molecular Biosciences and of Chemistry and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
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Howe KL, Seitz KW, Campbell LG, Baker BJ, Thrash JC, Rabalais NN, Rogener MK, Joye SB, Mason OU. Metagenomics and metatranscriptomics reveal broadly distributed, active, novel methanotrophs in the Gulf of Mexico hypoxic zone and in the marine water column. FEMS Microbiol Ecol 2022; 99:6909064. [PMID: 36520069 PMCID: PMC9874027 DOI: 10.1093/femsec/fiac153] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/17/2022] [Accepted: 12/20/2022] [Indexed: 12/23/2022] Open
Abstract
The northern Gulf of Mexico (nGOM) hypoxic zone is a shallow water environment where methane, a potent greenhouse gas, fluxes from sediments to bottom water and remains trapped due to summertime stratification. When the water column is destratified, an active planktonic methanotrophic community could mitigate the efflux of methane, which accumulates to high concentrations, to the atmosphere. To investigate the possibility of such a biofilter in the nGOM hypoxic zone we performed metagenome assembly, and metagenomic and metatranscriptomic read mapping. Methane monooxygenase (pmoA) was an abundant transcript, yet few canonical methanotrophs have been reported in this environment, suggesting a role for non-canonical methanotrophs. To determine the identity of these methanotrophs, we reconstructed six novel metagenome-assembled genomes (MAGs) in the Planctomycetota, Verrucomicrobiota and one putative Latescibacterota, each with at least one pmoA gene copy. Based on ribosomal protein phylogeny, closely related microbes (mostly from Tara Oceans) and isolate genomes were selected and co-analyzed with the nGOM MAGs. Gene annotation and read mapping suggested that there is a large, diverse and unrecognized community of active aerobic methanotrophs in the nGOM hypoxic zone and in the global ocean that could mitigate methane flux to the atmosphere.
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Affiliation(s)
- Kathryn L Howe
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, 32306, Tallahassee, United States
| | - Kiley W Seitz
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, 78373, Port Aransas, United States
| | - Lauren G Campbell
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, 32306, Tallahassee, United States
| | - Brett J Baker
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, 78373, Port Aransas, United States,Department of Integrative Biology, University of Texas at Austin, 78712, Austin, United States
| | - J Cameron Thrash
- Department of Biological Sciences, University of Southern California, 90089, Los Angeles, United States
| | - Nancy N Rabalais
- Department of Oceanography and Coastal Sciences, Louisiana State University, 70803, Baton Rouge, United States,Louisiana Universities Marine Consortium, 70344, Chauvin, United States
| | - Mary-Kate Rogener
- Department of Marine Sciences, University of Georgia, 30602, Athens, United States
| | - Samantha B Joye
- Department of Marine Sciences, University of Georgia, 30602, Athens, United States
| | - Olivia U Mason
- Corresponding author: Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL 32306, United States. E-mail:
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Goonesekera EM, Tsapekos P, Angelidaki I, Valverde-Pérez B. Impact of recovered phosphorus supply on methanotrophic cultivation and microbial protein production. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 322:115820. [PMID: 36058074 DOI: 10.1016/j.jenvman.2022.115820] [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: 03/23/2022] [Revised: 05/13/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Microbial protein is a promising dietary supplement alternative to traditional sources, being methane oxidising bacteria (MOB) an attractive option to produce it. Though current production processes rely on fossil resources, there is an increasing trend of using recovered residual nutrient streams, with most research focusing on nitrogen and methane, paying little attention to phosphorus. Struvite and precipitated calcium phosphate (PCP) were evaluated as potential residual P sources for microbial protein production after dissolved them with strong acids. MOB growth was studied in batch experiments. Yields ranged from 0.21 to 0.29 g CDW g CH4-1. Crude protein contents above 50% of dried weight were achieved, and neither the P nor the N source affected the amino acid profile significantly. The highest protein content (75%) was observed when using struvite as nutrient source, but also yielded cadmium and lead accumulation above limits set in legislation.
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Affiliation(s)
- Estelle Maria Goonesekera
- Department of Environmental and Resource Engineering, Bygningstorvet 115, Technical University of Denmark; DTU, 2800, Lyngby, Denmark
| | - Panagiotis Tsapekos
- Department of Chemical Engineering, Søltofts Plads 228A, Technical University of Denmark, DTU, 2800, Lyngby, Denmark
| | - Irini Angelidaki
- Department of Chemical Engineering, Søltofts Plads 228A, Technical University of Denmark, DTU, 2800, Lyngby, Denmark
| | - Borja Valverde-Pérez
- Department of Environmental and Resource Engineering, Bygningstorvet 115, Technical University of Denmark; DTU, 2800, Lyngby, Denmark.
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38
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Ecological Aerobic Ammonia and Methane Oxidation Involved Key Metal Compounds, Fe and Cu. Life (Basel) 2022; 12:life12111806. [PMID: 36362966 PMCID: PMC9693385 DOI: 10.3390/life12111806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
Interactions between metals and microbes are critical in geomicrobiology and vital in microbial ecophysiological processes. Methane-oxidizing bacteria (MOB) and ammonia-oxidizing microorganisms (AOM) are key members in aerobic environments to start the C and N cycles. Ammonia and methane are firstly oxidized by copper-binding metalloproteins, monooxygenases, and diverse iron and copper-containing enzymes that contribute to electron transportation in the energy gain pathway, which is evolutionally connected between MOB and AOM. In this review, we summarized recently updated insight into the diverse physiological pathway of aerobic ammonia and methane oxidation of different MOB and AOM groups and compared the metabolic diversity mediated by different metalloenzymes. The elevation of iron and copper concentrations in ecosystems would be critical in the activity and growth of MOB and AOM, the outcome of which can eventually influence the global C and N cycles. Therefore, we also described the impact of various concentrations of metal compounds on the physiology of MOB and AOM. This review study could give a fundamental strategy to control MOB and AOM in diverse ecosystems because they are significantly related to climate change, eutrophication, and the remediation of contaminated sites for detoxifying pollutants.
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Jiang L, Chu YX, Zhang X, Wang J, He X, Liu CY, Chen T, He R. Characterization of anaerobic oxidation of methane and microbial community in landfills with aeration. ENVIRONMENTAL RESEARCH 2022; 214:114102. [PMID: 35973464 DOI: 10.1016/j.envres.2022.114102] [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: 07/03/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
Landfills are the third largest source of anthropogenic CH4 emissions. Anaerobic oxidation of methane (AOM) activity and communities of methane-oxidizing bacteria were investigated in three informal landfills in this study, namely, BJ, CH and SZ landfills, among which BJ and CH represent traditional anaerobic landfills, while the SZ landfill was subjected to aeration to accelerate waste stabilization. The AOM rates of the investigated landfilled wastes ranged from 3.66 to 23.91 nmol g-1 h-1. Among the three landfills, the AOM rate was highest in the SZ-1-Top sample, which was closest to the aeration pipe. Among the possible electron acceptors for AOM, including NO3-, NO2-, SO42- and Fe3+, the NO2--N content was the only variable that was positively correlated with the AOM rate. Compared with α-Proteobacteria methanotrophs, γ-Proteobacteria methanotrophs were more abundant in the landfilled waste, especially Methylobacter, which was detected in nearly all samples. Members of the family Methylomirabilaceae, including Candidatus Methylomirabilis, were also detected in the SZ-1 and SZ-2-Bot samples. The relative abundance of the main methanotrophs in the families Methylomonadaceae, Methylococcaceae, Rokubacteriales and Methylomirabilaceae, the genus Methylocystis and the phylum NC10 were all positive correlations with the contents of NO2--N in the landfilled waste samples. Additionally, significantly positive correlations were observed between the AOM rates and the relative abundance of the main methanotrophs except for the family Methylococcaceae. This indicated that aeration could enhance the conversion of nitrogen compounds in the landfilled waste, in which the high contents of NO2--N could stimulate the growth of methanotrophs and increase AOM rate. These findings are helpful for understanding the mechanisms of CH4 oxidation in landfills and for taking effective measures to mitigate CH4 emissions from landfills.
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Affiliation(s)
- Lei Jiang
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China
| | - Yi-Xuan Chu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Xuan Zhang
- Eco-Environmental Science and Research Institute of Zhejiang Province, Hangzhou, 310061, China
| | - Jing Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Xiaosong He
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Chen-Yang Liu
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China
| | - Ting Chen
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China
| | - Ruo He
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China.
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Qin Y, Ouyang C, Gou Y, Jiang C, Li Z. The characteristics and influencing factors of dissolved methane concentrations in Chongqing's central urban area in the Three Gorges Reservoir, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:72045-72057. [PMID: 35608766 DOI: 10.1007/s11356-022-20822-w] [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: 01/26/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
Methane (CH4) emissions from reservoirs have received widespread attention. The central urban area of Chongqing in the Three Gorges Reservoir area was selected as the study area in 2020. The temporal and spatial distribution of dissolved CH4 concentration and flux, key generation pathways, and influencing factors have been studied. The dissolved CH4 concentration in low-water-level period and impoundment period varied from 0.037~0.12 μmol·L-1 and 0.11~0.23 μmol·L-1, with the average values of (0.066 ± 0.0067) μmol·L-1 and (0.13 ± 0.034) μmol·L-1. The CH4 flux was (0.941 ± 0.217) μmol·m-2·h-1 in low-water-level period and (1.915 ± 0.204) μmol·m-2·h-1 in impoundment period. CH4 was produced by CO2 reduction and acetic acid fermentation, accounting for 17.95% and 82.05% of the total CH4 production, respectively. The dissolved CH4 concentration was significantly positively correlated with DO and NO3--N, and it is opposite with dissolved inorganic carbon. The dissolved CH4 concentration in this study area is affected by water environment (33.42%), inorganic nitrogen (29.60%), organic carbon (23.88%), and inorganic carbon (13.10%), and anthropogenic influences promoted dissolved CH4 concentration.
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Affiliation(s)
- Yu Qin
- Key Laboratory of Hydraulic and Waterway Engineering of the Ministry of Education, Chongqing Jiaotong University, Chongqing, 400074, China.
| | - Changyue Ouyang
- Key Laboratory of Hydraulic and Waterway Engineering of the Ministry of Education, Chongqing Jiaotong University, Chongqing, 400074, China
| | - Yujia Gou
- Key Laboratory of Hydraulic and Waterway Engineering of the Ministry of Education, Chongqing Jiaotong University, Chongqing, 400074, China
| | - Chengyong Jiang
- Key Laboratory of Hydraulic and Waterway Engineering of the Ministry of Education, Chongqing Jiaotong University, Chongqing, 400074, China
| | - Zhe Li
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
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Multiple Mechanisms for Copper Uptake by Methylosinus trichosporium OB3b in the Presence of Heterologous Methanobactin. mBio 2022; 13:e0223922. [PMID: 36129259 PMCID: PMC9601215 DOI: 10.1128/mbio.02239-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methanotrophs require copper for their activity as it plays a critical role in the oxidation of methane to methanol. To sequester copper, some methanotrophs secrete a copper-binding compound termed methanobactin (MB). MB, after binding copper, is reinternalized via a specific outer membrane TonB-dependent transporter (TBDT). Methylosinus trichosporium OB3b has two such TBDTs (MbnT1 and MbnT2) that enable M. trichosporium OB3b to take up not only its own MB (MB-OB3b) but also heterologous MB produced from other methanotrophs, e.g., MB of Methylocystis sp. strain SB2 (MB-SB2). Here, we show that uptake of copper in the presence of heterologous MB-SB2 can either be achieved by initiating transcription of mbnT2 or by using its own MB-OB3b to extract copper from MB-SB2. Transcription of mbnT2 is mediated by the N-terminal signaling domain of MbnT2 together with an extracytoplasmic function sigma factor and an anti-sigma factor encoded by mbnI2 and mbnR2, respectively. Deletion of mbnI2R2 or excision of the N-terminal region of MbnT2 abolished induction of mbnT2. However, copper uptake from MB-SB2 was still observed in M. trichosporium OB3b mutants that were defective in MbnT2 induction/function, suggesting another mechanism for uptake copper-loaded MB-SB2. Additional deletion of MB-OB3b synthesis genes in the M. trichosporium OB3b mutants defective in MbnT2 induction/function disrupted their ability to take up copper in the presence of MB-SB2, indicating a role of MB-OB3b in copper extraction from MB-SB2.
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Rushworth DD, Christl I, Kumar N, Hoffmann K, Kretzschmar R, Lehmann MF, Schenkeveld WDC, Kraemer SM. Copper mobilisation from Cu sulphide minerals by methanobactin: Effect of pH, oxygen and natural organic matter. GEOBIOLOGY 2022; 20:690-706. [PMID: 35716154 PMCID: PMC9544142 DOI: 10.1111/gbi.12505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/03/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Aerobic methane oxidation (MOx) depends critically on the availability of copper (Cu) as a crucial component of the metal centre of particulate methane monooxygenase, one of the main enzymes involved in MOx. Some methanotrophs have developed Cu acquisition strategies, in which they exude Cu-binding ligands termed chalkophores under conditions of low Cu availability. A well-characterised chalkophore is methanobactin (mb), exuded by the microaerophilic methanotroph Methylosinus trichosporium OB3b. Aerobic methanotrophs generally reside close to environmental oxic-anoxic interfaces, where the formation of Cu sulphide phases can aggravate the limitation of bioavailable Cu due to their low solubility. The reactivity of chalkophores towards such Cu sulphide mineral phases has not yet been investigated. In this study, a combination of dissolution experiments and equilibrium modelling was used to examine the dissolution and solubility of bulk and nanoparticulate Cu sulphide minerals in the presence of mb as influenced by pH, oxygen and natural organic matter. In general, we show that mb is effective at increasing the dissolved Cu concentrations in the presence of a variety of Cu sulphide phases that may potentially limit Cu bioavailability. More Cu was mobilised per mole of mb from Cu sulphide nanoparticles compared with well-crystalline bulk covellite (CuS). In general, the efficacy of mb at mobilising Cu from Cu sulphides is pH-dependent. At lower pH, e.g. pH 5, mb was ineffective at solubilizing Cu. The presence of mb increased dissolved Cu concentrations between pH 7 and 8.5, where the solubility of all Cu sulphides is generally low, both in the presence and absence of oxygen. These results suggest that chalkophore-promoted Cu mobilisation from sulphide phases is an effective extracellular mechanism for increasing dissolved Cu concentrations at oxic-anoxic interfaces, particularly in the neutral to slightly alkaline pH range. This suggests that aerobic methanotrophs may be able to fulfil their Cu requirements via the exudation of mb in natural environments where the bioavailability of Cu is constrained by very stable Cu sulphide phases.
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Affiliation(s)
- Danielle D. Rushworth
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaAustria
| | - Iso Christl
- Soil ChemistryInstitute of Biogeochemistry and Pollutant Dynamics, ETHZurichSwitzerland
| | - Naresh Kumar
- Soil Chemistry and Chemical Soil Quality, Environmental SciencesWageningen UniversityWageningenThe Netherlands
| | - Kevin Hoffmann
- Soil ChemistryInstitute of Biogeochemistry and Pollutant Dynamics, ETHZurichSwitzerland
| | - Ruben Kretzschmar
- Soil ChemistryInstitute of Biogeochemistry and Pollutant Dynamics, ETHZurichSwitzerland
| | - Moritz F. Lehmann
- Department of Environmental GeosciencesUniversity of BaselBaselSwitzerland
| | - Walter D. C. Schenkeveld
- Soil Chemistry and Chemical Soil Quality, Environmental SciencesWageningen UniversityWageningenThe Netherlands
| | - Stephan M. Kraemer
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaAustria
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43
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Müller M, Germer P, Andexer JN. Biocatalytic One-Carbon Transfer – A Review. SYNTHESIS-STUTTGART 2022. [DOI: 10.1055/s-0040-1719884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
AbstractThis review provides an overview of different C1 building blocks as substrates of enzymes, or part of their cofactors, and the resulting functionalized products. There is an emphasis on the broad range of possibilities of biocatalytic one-carbon extensions with C1 sources of different oxidation states. The identification of uncommon biosynthetic strategies, many of which might serve as templates for synthetic or biotechnological applications, towards one-carbon extensions is supported by recent genomic and metabolomic progress and hence we refer principally to literature spanning from 2014 to 2020.1 Introduction2 Methane, Methanol, and Methylamine3 Glycine4 Nitromethane5 SAM and SAM Ylide6 Other C1 Building Blocks7 Formaldehyde and Glyoxylate as Formaldehyde Equivalents8 Cyanide9 Formic Acid10 Formyl-CoA and Oxalyl-CoA11 Carbon Monoxide12 Carbon Dioxide13 Conclusions
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Rodero MDR, Herrero-Lobo R, Pérez V, Muñoz R. Influence of operational conditions on the performance of biogas bioconversion into ectoines in pilot bubble column bioreactors. BIORESOURCE TECHNOLOGY 2022; 358:127398. [PMID: 35640813 DOI: 10.1016/j.biortech.2022.127398] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
The application of biogas as a low-priced substrate for the production of ectoines constitutes an opportunity to decrease their production costs and to enhance the viability of anaerobic digestion. The influence of operational conditions on CH4-biogas biodegradation and on ectoines production yields was assessed in continuous pilot bubble column bioreactors. The rise in biomass concentration from 1 to 3 g L-1 resulted in a decrease in the specific ectoine content from 42 ± 8 to 30 ± 4 mgectoine gVSS-1. The concentration of Cu2+ and Mg2+ did not impact process performance, while the use of ammonium as N source resulted in low CH4 biodegradation and ectoine yields (13 ± 7 mgectoine gVSS-1). The increase in CH4 content from 4.5 to 9 %v·v-1 enhanced CH4 removal efficiency. Process operation at NaCl concentrations of 3 %w·w-1 instead of 6 %w·w-1 decreased the ectoine yield to 17 mgectoine gVSS-1. Finally, Methylomicrobiumburyatense was identified as the dominant species.
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Affiliation(s)
- María Del Rosario Rodero
- Institute of Sustainable Processes, University of Valladolid, 47011, Valladolid, Spain; Department of Chemical Engineering and Environmental Technology, School of Industrial Engineerings. University of Valladolid, Dr. Mergelina s/n., 47011, Valladolid, Spain
| | - Raquel Herrero-Lobo
- Institute of Sustainable Processes, University of Valladolid, 47011, Valladolid, Spain; Department of Chemical Engineering and Environmental Technology, School of Industrial Engineerings. University of Valladolid, Dr. Mergelina s/n., 47011, Valladolid, Spain
| | - Víctor Pérez
- Institute of Sustainable Processes, University of Valladolid, 47011, Valladolid, Spain; Department of Chemical Engineering and Environmental Technology, School of Industrial Engineerings. University of Valladolid, Dr. Mergelina s/n., 47011, Valladolid, Spain
| | - Raúl Muñoz
- Institute of Sustainable Processes, University of Valladolid, 47011, Valladolid, Spain; Department of Chemical Engineering and Environmental Technology, School of Industrial Engineerings. University of Valladolid, Dr. Mergelina s/n., 47011, Valladolid, Spain.
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Wang J, Wei ZP, Chu YX, Tian G, He R. Eutrophic levels and algae growth increase emissions of methane and volatile sulfur compounds from lakes. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119435. [PMID: 35550131 DOI: 10.1016/j.envpol.2022.119435] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 05/02/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Eutrophic lakes are hot spots of CH4 and volatile sulfur compound (VSC) emissions, especially during algal blooms and decay. However, the response of CH4 and VSC emissions to lake eutrophication and algae growth as well as the underlying mechanisms remain unclear. In this study, the emissions of CH4 and VSCs from four regions of Lake Taihu with different eutrophic levels were investigated in four months (i.e., March, May, August and December). The CH4 emissions ranged from 20.4 to 126.9 mg m-2 d-1 in the investigated sites and increased with eutrophic levels and temperature. H2S and CS2 were the dominant volatile sulfur compounds (VSCs) emitted from the lake. The CH4 oxidation potential of water ranged from 2.1 to 14.9 μg h-1 L-1, which had positive correlations with trophic level index and the environmental variables except for the NH4+-N concentration. Eutrophic levels could increase the abundances of bacteria and methanotrophs in lake water. α-Proteobacteria methanotroph Methylocystis was more abundant than γ-Proteobacteria methanotrophs in March and May, while the latter was more abundant in August and November. The relative abundance of Cyanobacteria, including Microcystis, A. granulata var. angustissima and Cyanobium had significantly positive correlations with temperature, turbidity, SO42--S, and total sulfur. Partial least squares path modelling revealed that the algal growth could promote VSC emissions, which had a positive correlation with CH4 oxidation potential, likely due to the positive correlation between the CH4 and VSC emissions from lakes. These findings indicate that water eutrophication and algae growth could increase the emissions of CH4 and VSCs from lakes. Controlling algae growth might be an effective way to mitigate the emissions of CH4 and VSCs from freshwater lakes.
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Affiliation(s)
- Jing Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Zhi-Peng Wei
- Hohai University, State Key Laboratory Hydrology-Water Resources and Hydraulic Engineering, Nanjing, 210098, China
| | - Yi-Xuan Chu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Guangming Tian
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Ruo He
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China; College of Environmental and Resource Science, Zhejiang University, Hangzhou, 310058, China.
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Wang Y, Lu Y, Li X, Zhu G, Li N, Han J, Sun L, Yang Z, Zeng RJ. Light-dependent enhancement of sulfadiazine detoxification and mineralization by non-photosynthetic methanotrophs. WATER RESEARCH 2022; 220:118623. [PMID: 35665677 DOI: 10.1016/j.watres.2022.118623] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Co-metabolism and photodegradation are two approaches for remediating trace organic compounds (TOrCs), however, interactions between the two with regards to TOrCs degradation have not been elucidated. In this study, sulfadiazine (SDZ) was chosen as a representative TOrC and Methylocystis bryophila as a typical strain. Under light conditions, about 80.6% of SDZ was removed by M. bryophila, but only 7.6% or 28.9% of SDZ was eliminated by either individual photodegradation or by co-metabolism. The SDZ stimulated more extracellular organic matter (EOM) production by M. bryophila. The enhanced SDZ degradation was attributed to indirect photolysis caused by the excited triplet state of EOM (3EOM*) and co-metabolism. The UPLC-QTOF-MS analysis showed that due to co-metabolism, the pyrimidine ring was broken and could further be oxidized into smaller molecules under light conditions, such as formic and acetic acids. The SDZ mineralization ratio increased from 9.9% under the co-metabolic condition alone to 36.5% under co-metabolism coupled with photodegradation. The Ames tests confirmed that the SDZ degradation products by co-metabolism were mutagenic, however, their toxicity was ameliorated by light during co-metabolism. In conclusion, light plays a crucial role in co-metabolic processes of TOrCs.
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Affiliation(s)
- Yongzhen Wang
- School of Energy and Environment, Southeast University, No.2, Sipailou, Nanjing, Jiangsu 210096, China; State Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing 210096, China
| | - Yongze Lu
- School of Energy and Environment, Southeast University, No.2, Sipailou, Nanjing, Jiangsu 210096, China; State Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing 210096, China.
| | - Xin Li
- School of Energy and Environment, Southeast University, No.2, Sipailou, Nanjing, Jiangsu 210096, China; State Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing 210096, China
| | - Guangcan Zhu
- School of Energy and Environment, Southeast University, No.2, Sipailou, Nanjing, Jiangsu 210096, China; State Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing 210096, China
| | - Na Li
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Jing Han
- School of Energy and Environment, Southeast University, No.2, Sipailou, Nanjing, Jiangsu 210096, China; State Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing 210096, China
| | - Liwei Sun
- School of Energy and Environment, Southeast University, No.2, Sipailou, Nanjing, Jiangsu 210096, China; State Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing 210096, China
| | - Zhonglian Yang
- School of Energy and Environment, Southeast University, No.2, Sipailou, Nanjing, Jiangsu 210096, China; State Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing 210096, China
| | - Raymond Jianxiong Zeng
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Tentori EF, Fang S, Richardson RE. RNA Biomarker Trends across Type I and Type II Aerobic Methanotrophs in Response to Methane Oxidation Rates and Transcriptome Response to Short-Term Methane and Oxygen Limitation in Methylomicrobium album BG8. Microbiol Spectr 2022; 10:e0000322. [PMID: 35678574 PMCID: PMC9241951 DOI: 10.1128/spectrum.00003-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 05/21/2022] [Indexed: 11/26/2022] Open
Abstract
Methanotrophs, which help regulate atmospheric levels of methane, are active in diverse natural and man-made environments. This range of habitats and the feast-famine cycles seen by many environmental methanotrophs suggest that methanotrophs dynamically mediate rates of methane oxidation. Global methane budgets require ways to account for this variability in time and space. Functional gene biomarker transcripts are increasingly studied to inform the dynamics of diverse biogeochemical cycles. Previously, per-cell transcript levels of the methane oxidation biomarker pmoA were found to vary quantitatively with respect to methane oxidation rates in the model aerobic methanotroph Methylosinus trichosporium OB3b. In the present study, these trends were explored for two additional aerobic methanotroph pure cultures grown in membrane bioreactors, Methylocystis parvus OBBP and Methylomicrobium album BG8. At steady-state conditions, per-cell pmoA mRNA transcript levels strongly correlated with per-cell methane oxidation across the three methanotrophs across many orders of magnitude of activity (R2 = 0.91). The inclusion of both type I and type II aerobic methanotrophs suggests a universal trend between in situ activity level and pmoA RNA biomarker levels which can aid in improving estimates of both subsurface and atmospheric methane. Additionally, genome-wide expression data (obtained by transcriptome sequencing [RNA-seq]) were used to explore transcriptomic responses of steady-state M. album BG8 cultures to short-term CH4 and O2 limitation. These limitations induced regulation of genes involved in central carbon metabolism (including carbon storage), cell motility, and stress response. IMPORTANCE Methanotrophs are naturally occurring microorganisms capable of oxidizing methane, having an impact on global net methane emissions. Additionally, they have also gained interest for their biotechnological applications in single-cell protein production, biofuels, and bioplastics. Having better ways of measuring methanotroph activity and understanding how methanotrophs respond to changing conditions is imperative for both optimization in controlled-growth applications and understanding in situ methane oxidation rates. In this study, we explored the applicability of methane oxidation biomarkers as a universal indicator of methanotrophic activity and explored methanotroph transcriptomic response to short-term changes in substrate availability. Our results contribute to better understanding the activity of aerobic methanotrophs, their core metabolic pathways, and their stress responses.
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Affiliation(s)
- Egidio F. Tentori
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York, USA
| | - Shania Fang
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York, USA
| | - Ruth E. Richardson
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York, USA
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An Overview on Methanotrophs and the Role of Methylosinus trichosporium OB3b for Biotechnological Applications. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-022-0046-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Nguyen NA, Cong Y, Hurrell RC, Arias N, Garg N, Puri AW, Schmidt EW, Agarwal V. A Silent Biosynthetic Gene Cluster from a Methanotrophic Bacterium Potentiates Discovery of a Substrate Promiscuous Proteusin Cyclodehydratase. ACS Chem Biol 2022; 17:1577-1585. [PMID: 35666841 PMCID: PMC9746716 DOI: 10.1021/acschembio.2c00251] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Natural product-encoding biosynthetic gene clusters (BGCs) within microbial genomes far outnumber the known natural products; chemical products from such BGCs remain cryptic. These silent BGCs hold promise not only for the elaboration of new natural products but also for the discovery of useful biosynthetic enzymes. Here, we describe a genome mining strategy targeted toward the discovery of substrate promiscuous natural product biosynthetic enzymes. In the genome of the methanotrophic bacterium Methylovulum psychrotolerans Sph1T, we discover a transcriptionally silent natural product BGC that encoded numerous ribosomally synthesized and post-translationally modified peptide (RiPP) natural products. These cryptic RiPP natural products were accessed using heterologous expression of the substrate peptide and biosynthetic enzyme-encoded genes. In line with our genome mining strategy, the RiPP biosynthetic enzymes in this BGC were found to be substrate promiscuous, which allowed us to use them in a combinatorial fashion with a similarly substrate-tolerant cyanobactin biosynthetic enzyme to introduce head-to-tail macrocyclization in the proteusin family of RiPP natural products.
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Affiliation(s)
- Nguyet A. Nguyen
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta GA, USA 30332
| | - Ying Cong
- Department of Medicinal Chemistry, University of Utah, Salt Lake City UT, USA 84112
| | - Rachel C. Hurrell
- Department of Chemistry and the Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City UT, USA 84112
| | - Natalie Arias
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta GA, USA 30332
| | - Neha Garg
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta GA, USA 30332
| | - Aaron W. Puri
- Department of Chemistry and the Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City UT, USA 84112
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City UT, USA 84112
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta GA, USA 30332,School of Biological Sciences, Georgia Institute of Technology, Atlanta GA, USA 30332,correspondence:
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Tsai YF, Natarajan T, Lin ZH, Tsai IK, Janmanchi D, Chan SI, Yu SSF. Voltage-Gated Electrocatalysis of Efficient and Selective Methane Oxidation by Tricopper Clusters under Ambient Conditions. J Am Chem Soc 2022; 144:9695-9706. [PMID: 35622083 DOI: 10.1021/jacs.2c01169] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Selective methane oxidation is difficult chemistry. Here we describe a strategy for the electrocatalysis of selective methane oxidation by immobilizing tricopper catalysts on the cathodic surface. In the presence of dioxygen and methane, the activation of these catalysts above a threshold cathodic potential can initiate the dioxygen chemistry for O atom transfer to methane. The catalytic turnover is completed by facile electron injections into the tricopper catalysts from the electrode. This technology leads to dramatic enhancements in performance of the catalysts toward methane oxidation. Unprecedented turnover frequencies (>40 min-1) and high product throughputs (turnover numbers >30 000 in 12 h) are achieved for this challenging chemical transformation in water under ambient conditions. The technology is green and suitable for on-site direct conversion of methane into methanol.
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Affiliation(s)
- Yi-Fang Tsai
- Institute of Chemistry, Academia Sinica, Nangang, Taipei 11529, Taiwan
| | | | - Zhi-Han Lin
- Institute of Chemistry, Academia Sinica, Nangang, Taipei 11529, Taiwan.,Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program (TIGP), Academia Sinica, Taipei 11529, Taiwan
| | - I-Kuen Tsai
- Institute of Chemistry, Academia Sinica, Nangang, Taipei 11529, Taiwan
| | - Damodar Janmanchi
- Institute of Chemistry, Academia Sinica, Nangang, Taipei 11529, Taiwan
| | - Sunney I Chan
- Institute of Chemistry, Academia Sinica, Nangang, Taipei 11529, Taiwan
| | - Steve S-F Yu
- Institute of Chemistry, Academia Sinica, Nangang, Taipei 11529, Taiwan.,Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program (TIGP), Academia Sinica, Taipei 11529, Taiwan
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