201
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Xing Z, Zhao T, Zhang L, Gao Y, Liu S, Yang X. Effects of copper on expression of methane monooxygenases, trichloroethylene degradation, and community structure in methanotrophic consortia. Eng Life Sci 2018; 18:236-243. [PMID: 32624902 DOI: 10.1002/elsc.201700153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 12/12/2017] [Accepted: 12/29/2017] [Indexed: 11/08/2022] Open
Abstract
Copper plays a key role in regulating the expression of enzymes that promote biodegradation of contaminants in methanotrophic consortia (MC). Here, we utilized MC isolated from landfill cover to investigate cometabolic degradation of trichloroethylene (TCE) at nine different copper (Cu2+) concentrations. The results demonstrated that an increase in Cu2+ concentration from 0 to 15 μM altered the specific first-order rate constant k 1,TCE, the expression levels of methane monooxygenase (pmoA and mmoX) genes, and the specific activity of soluble methane monooxygenase (sMMO). High efficiency TCE degradation (95%) and the expression levels of methane monooxygenase (MMO) were detected at a Cu2+ concentration of 0.03 μM. Notably, sMMO-specific activity ranged from 74.41 nmol/(mgcell h) in 15 μM Cu2+ to 654.99 nmol/(mgcell h) in 0.03 μM Cu2+, which contrasts with cultures of pure methanotrophs in which sMMO activity is depressed at high Cu2+ concentrations, indicating a special regulatory role for Cu2+ in MC. The results of MiSeq pyrosequencing indicated that higher Cu2+ concentrations stimulated the growth of methanotrophic microorganisms in MC. These findings have important implications for the elucidation of copper-mediated regulatory mechanisms in MC.
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Affiliation(s)
- Zhilin Xing
- Faculty of Urban Construction and Environment Engineering Chongqing University Chongqing P. R. China.,School of Chemistry and Chemical Engineering Chongqing University of Technology Chongqing P. R. China
| | - Tiantao Zhao
- Faculty of Urban Construction and Environment Engineering Chongqing University Chongqing P. R. China.,School of Chemistry and Chemical Engineering Chongqing University of Technology Chongqing P. R. China
| | - Lijie Zhang
- School of Chemistry and Chemical Engineering Chongqing University of Technology Chongqing P. R. China
| | - Yanhui Gao
- Faculty of Urban Construction and Environment Engineering Chongqing University Chongqing P. R. China.,School of Chemistry and Chemical Engineering Chongqing University of Technology Chongqing P. R. China
| | - Shuai Liu
- School of Chemistry and Chemical Engineering Chongqing University of Technology Chongqing P. R. China
| | - Xu Yang
- School of Chemistry and Chemical Engineering Chongqing University of Technology Chongqing P. R. China
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202
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Methane utilization in Methylomicrobium alcaliphilum 20Z R: a systems approach. Sci Rep 2018; 8:2512. [PMID: 29410419 PMCID: PMC5802761 DOI: 10.1038/s41598-018-20574-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 01/22/2018] [Indexed: 12/20/2022] Open
Abstract
Biological methane utilization, one of the main sinks of the greenhouse gas in nature, represents an attractive platform for production of fuels and value-added chemicals. Despite the progress made in our understanding of the individual parts of methane utilization, our knowledge of how the whole-cell metabolic network is organized and coordinated is limited. Attractive growth and methane-conversion rates, a complete and expert-annotated genome sequence, as well as large enzymatic, 13C-labeling, and transcriptomic datasets make Methylomicrobium alcaliphilum 20ZR an exceptional model system for investigating methane utilization networks. Here we present a comprehensive metabolic framework of methane and methanol utilization in M. alcaliphilum 20ZR. A set of novel metabolic reactions governing carbon distribution across central pathways in methanotrophic bacteria was predicted by in-silico simulations and confirmed by global non-targeted metabolomics and enzymatic evidences. Our data highlight the importance of substitution of ATP-linked steps with PPi-dependent reactions and support the presence of a carbon shunt from acetyl-CoA to the pentose-phosphate pathway and highly branched TCA cycle. The diverged TCA reactions promote balance between anabolic reactions and redox demands. The computational framework of C1-metabolism in methanotrophic bacteria can represent an efficient tool for metabolic engineering or ecosystem modeling.
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203
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Hedegaard MJ, Deliniere H, Prasse C, Dechesne A, Smets BF, Albrechtsen HJ. Evidence of co-metabolic bentazone transformation by methanotrophic enrichment from a groundwater-fed rapid sand filter. WATER RESEARCH 2018; 129:105-114. [PMID: 29136518 DOI: 10.1016/j.watres.2017.10.073] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 10/27/2017] [Accepted: 10/31/2017] [Indexed: 06/07/2023]
Abstract
The herbicide bentazone is recalcitrant in aquifers and is therefore frequently detected in wells used for drinking water production. However, bentazone degradation has been observed in filter sand from a rapid sand filter at a waterworks with methane-rich groundwater. Here, the association between methane oxidation and removal of bentazone was investigated with a methanotrophic enrichment culture derived from methane-fed column reactors inoculated with that filter sand. Several independent lines of evidence obtained from microcosm experiments with the methanotrophic enrichment culture, tap water and bentazone at concentrations below 2 mg/L showed methanotrophic co-metabolic bentazone transformation: The culture removed 53% of the bentazone in 21 days in presence of 5 mg/L of methane, while only 31% was removed in absence of methane. Addition of acetylene inhibited methane oxidation and stopped bentazone removal. The presence of bentazone partly inhibited methane oxidation since the methane consumption rate was significantly lower at high (1 mg/L) than at low (1 μg/L) bentazone concentrations. The transformation yield of methane relative to bentazone normalized by their concentration ratio ranged from 58 to 158, well within the range for methanotrophic co-metabolic degradation of trace contaminants calculated from the literature, with normalized substrate preferences varying from 3 to 400. High-resolution mass spectrometry revealed formation of the transformation products (TPs) 6-OH, 8-OH, isopropyl-OH and di-OH-bentazone, with higher abundances of all TPs in the presence of methane. Overall, we found a suite of evidence all showing that bentazone was co-metabolically transformed to hydroxy-bentazone by a methanotrophic culture enriched from a rapid sand filter at a waterworks.
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Affiliation(s)
| | - Hélène Deliniere
- DTU Environment, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Carsten Prasse
- Department of Civil and Environmental, Engineering University of California, Berkeley, CA 94720, United States; Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Arnaud Dechesne
- DTU Environment, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Barth F Smets
- DTU Environment, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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204
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Methanobactin from Methylosinus trichosporium OB3b inhibits N 2O reduction in denitrifiers. ISME JOURNAL 2018; 12:2086-2089. [PMID: 29330532 DOI: 10.1038/s41396-017-0022-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/09/2017] [Accepted: 11/17/2017] [Indexed: 11/09/2022]
Abstract
Methanotrophs synthesize methanobactin, a secondary metabolite that binds copper with an unprecedentedly high affinity. Such a strategy may provide methanotrophs a "copper monopoly" that can inhibit the activity of copper-containing enzymes of other microbes, e.g., copper-dependent N2O reductases. Here, we show that methanobactin from Methylosinus trichosporium OB3b inhibited N2O reduction in denitrifiers. When Pseudomonas stutzeri DCP-Ps1 was incubated in cocultures with M. trichosporium OB3b or with purified methanobactin from M. trichosporium OB3b, stoichiometric N2O production was observed from NO3- reduction, whereas no significant N2O accumulation was observed in cocultures with a mutant defective in methanobactin production. Copper uptake by P. stutzeri DCP-Ps1 was inhibited by the presence of purified methanobactin, leading to a significant downregulation of nosZ transcription. Similar findings were observed with three other denitrifier strains. These results suggest that in situ stimulation of methanotrophs can inadvertently increase N2O emissions, with the potential for increasing net greenhouse gas emissions.
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205
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Technologies for the bioconversion of methane into more valuable products. Curr Opin Biotechnol 2018; 50:128-135. [PMID: 29316497 DOI: 10.1016/j.copbio.2017.12.021] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 11/22/2022]
Abstract
Methane, with a global warming potential twenty five times higher than that of CO2 is the second most important greenhouse gas emitted nowadays. Its bioconversion into microbial molecules with a high retail value in the industry offers a potential cost-efficient and environmentally friendly solution for mitigating anthropogenic diluted CH4-laden streams. Methane bio-refinery for the production of different compounds such as ectoine, feed proteins, biofuels, bioplastics and polysaccharides, apart from new bioproducts characteristic of methanotrophic bacteria, has been recently tested in discontinuous and continuous bioreactors with promising results. This review constitutes a critical discussion about the state-of-the-art of the potential and research niches of biotechnologies applied in a CH4 biorefinery approach.
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206
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E. Bjorck C, D. Dobson P, Pandhal J. Biotechnological conversion of methane to methanol: evaluation of progress and potential. AIMS BIOENGINEERING 2018. [DOI: 10.3934/bioeng.2018.1.1] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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207
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Martinez-Cruz K, Leewis MC, Herriott IC, Sepulveda-Jauregui A, Anthony KW, Thalasso F, Leigh MB. Anaerobic oxidation of methane by aerobic methanotrophs in sub-Arctic lake sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 607-608:23-31. [PMID: 28686892 DOI: 10.1016/j.scitotenv.2017.06.187] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 06/20/2017] [Accepted: 06/22/2017] [Indexed: 05/25/2023]
Abstract
Anaerobic oxidation of methane (AOM) is a biological process that plays an important role in reducing the CH4 emissions from a wide range of ecosystems. Arctic and sub-Arctic lakes are recognized as significant contributors to global methane (CH4) emission, since CH4 production is increasing as permafrost thaws and provides fuels for methanogenesis. Methanotrophy, including AOM, is critical to reducing CH4 emissions. The identity, activity, and metabolic processes of anaerobic methane oxidizers are poorly understood, yet this information is critical to understanding CH4 cycling and ultimately to predicting future CH4 emissions. This study sought to identify the microorganisms involved in AOM in sub-Arctic lake sediments using DNA- and phospholipid-fatty acid (PLFA)- based stable isotope probing. Results indicated that aerobic methanotrophs belonging to the genus Methylobacter assimilate carbon from CH4, either directly or indirectly. Other organisms that were found, in minor proportions, to assimilate CH4-derived carbon were methylotrophs and iron reducers, which might indicate the flow of CH4-derived carbon from anaerobic methanotrophs into the broader microbial community. While various other taxa have been reported in the literature to anaerobically oxidize methane in various environments (e.g. ANME-type archaea and Methylomirabilis Oxyfera), this report directly suggest that Methylobacter can perform this function, expanding our understanding of CH4 oxidation in anaerobic lake sediments.
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Affiliation(s)
- Karla Martinez-Cruz
- Water and Environmental Research Center, Institute of Northern Engineering, University of Alaska Fairbanks, 306 Tanana Loop, 99775 Fairbanks, AK, USA; Biotechnology and Bioengineering Department, Cinvestav, 2508 IPN Av, 07360, Mexico City, Mexico.
| | - Mary-Cathrine Leewis
- Institute of Arctic Biology, University of Alaska Fairbanks, 930 N Koyukuk Dr, 99775Fairbanks, AK, USA.
| | - Ian Charold Herriott
- Institute of Arctic Biology, University of Alaska Fairbanks, 930 N Koyukuk Dr, 99775Fairbanks, AK, USA.
| | - Armando Sepulveda-Jauregui
- Water and Environmental Research Center, Institute of Northern Engineering, University of Alaska Fairbanks, 306 Tanana Loop, 99775 Fairbanks, AK, USA.
| | - Katey Walter Anthony
- Water and Environmental Research Center, Institute of Northern Engineering, University of Alaska Fairbanks, 306 Tanana Loop, 99775 Fairbanks, AK, USA.
| | - Frederic Thalasso
- Water and Environmental Research Center, Institute of Northern Engineering, University of Alaska Fairbanks, 306 Tanana Loop, 99775 Fairbanks, AK, USA; Biotechnology and Bioengineering Department, Cinvestav, 2508 IPN Av, 07360, Mexico City, Mexico.
| | - Mary Beth Leigh
- Institute of Arctic Biology, University of Alaska Fairbanks, 930 N Koyukuk Dr, 99775Fairbanks, AK, USA.
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208
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Stone KA, Hilliard MV, He QP, Wang J. A mini review on bioreactor configurations and gas transfer enhancements for biochemical methane conversion. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2017.09.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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209
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Gómez-Borraz TL, González-Sánchez A, Bonilla-Blancas W, Revah S, Noyola A. Characterization of the biofiltration of methane emissions from municipal anaerobic effluents. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.08.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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210
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Kallistova AY, Merkel AY, Tarnovetskii IY, Pimenov NV. Methane formation and oxidation by prokaryotes. Microbiology (Reading) 2017. [DOI: 10.1134/s0026261717060091] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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211
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Vaksmaa A, van Alen TA, Ettwig KF, Lupotto E, Valè G, Jetten MSM, Lüke C. Stratification of Diversity and Activity of Methanogenic and Methanotrophic Microorganisms in a Nitrogen-Fertilized Italian Paddy Soil. Front Microbiol 2017; 8:2127. [PMID: 29180985 PMCID: PMC5693880 DOI: 10.3389/fmicb.2017.02127] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/18/2017] [Indexed: 11/30/2022] Open
Abstract
Paddy fields are important ecosystems, as rice is the primary food source for about half of the world's population. Paddy fields are impacted by nitrogen fertilization and are a major anthropogenic source of methane. Microbial diversity and methane metabolism were investigated in the upper 60 cm of a paddy soil by qPCR, 16S rRNA gene amplicon sequencing and anoxic 13C-CH4 turnover with a suite of electron acceptors. The bacterial community consisted mainly of Acidobacteria, Chloroflexi, Proteobacteria, Planctomycetes, and Actinobacteria. Among archaea, Euryarchaeota and Bathyarchaeota dominated over Thaumarchaeota in the upper 30 cm of the soil. Bathyarchaeota constituted up to 45% of the total archaeal reads in the top 5 cm. In the methanogenic community, Methanosaeta were generally more abundant than the versatile Methanosarcina. The measured maximum methane production rate was 444 nmol gdwh-1, and the maximum rates of nitrate-, nitrite-, and iron-dependent anaerobic oxidation of methane (AOM) were 57 nmol, 55 nmol, and 56 nmol gdwh-1, respectively, at different depths. qPCR revealed a higher abundance of 'Candidatus Methanoperedens nitroreducens' than methanotrophic NC10 phylum bacteria at all depths, except at 60 cm. These results demonstrate that there is substantial potential for AOM in fertilized paddy fields, with 'Candidatus Methanoperedens nitroreducens' archaea as a potential important contributor.
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Affiliation(s)
- Annika Vaksmaa
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Theo A. van Alen
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Katharina F. Ettwig
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Elisabetta Lupotto
- Research Centre for Food and Nutrition, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Rome, Italy
| | - Giampiero Valè
- Research Centre for Cereal and Industrial Crops, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Vercelli, Italy
| | - Mike S. M. Jetten
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Claudia Lüke
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
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212
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Nies DH. The biological chemistry of the transition metal "transportome" of Cupriavidus metallidurans. Metallomics 2017; 8:481-507. [PMID: 27065183 DOI: 10.1039/c5mt00320b] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review tries to illuminate how the bacterium Cupriavidus metallidurans CH34 is able to allocate essential transition metal cations to their target proteins although these metals have similar charge-to-surface ratios and chemical features, exert toxic effects, compete with each other, and occur in the bacterial environment over a huge range of concentrations and speciations. Central to this ability is the "transportome", the totality of all interacting metal import and export systems, which, as an emergent feature, transforms the environmental metal content and speciation into the cellular metal mélange. In a kinetic flow equilibrium resulting from controlled uptake and efflux reactions, the periplasmic and cytoplasmic metal content is adjusted in a way that minimizes toxic effects. A central core function of the transportome is to shape the metal ion composition using high-rate and low-specificity reactions to avoid time and/or energy-requiring metal discrimination reactions. This core is augmented by metal-specific channels that may even deliver metals all the way from outside of the cell to the cytoplasm. This review begins with a description of the basic chemical features of transition metal cations and the biochemical consequences of these attributes, and which transition metals are available to C. metallidurans. It then illustrates how the environment influences the metal content and speciation, and how the transportome adjusts this metal content. It concludes with an outlook on the fate of metals in the cytoplasm. By generalization, insights coming from C. metallidurans shed light on multiple transition metal homoeostatic mechanisms in all kinds of bacteria including pathogenic species, where the "battle" for metals is an important part of the host-pathogen interaction.
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Affiliation(s)
- Dietrich H Nies
- Molecular Microbiology, Institute for Biology/Microbiology, Martin-Luther-University Halle-Wittenberg, Germany.
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213
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Laskar F, Das Purkayastha S, Sen A, Bhattacharya MK, Misra BB. Diversity of methanogenic archaea in freshwater sediments of lacustrine ecosystems. J Basic Microbiol 2017; 58:101-119. [PMID: 29083035 DOI: 10.1002/jobm.201700341] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 09/25/2017] [Accepted: 09/27/2017] [Indexed: 12/15/2022]
Abstract
About half of the global methane (CH4 ) emission is contributed by the methanogenic archaeal communities leading to a significant increase in global warming. This unprecedented situation has increased the ever growing necessity of evaluating the control measures for limiting CH4 emission to the atmosphere. Unfortunately, research endeavors on the diversity and functional interactions of methanogens are not extensive till date. We anticipate that the study of the diversity of methanogenic community is paramount for understanding the metabolic processes in freshwater lake ecosystems. Although there are several disadvantages of conventional culture-based methods for determining the diversity of methanogenic archaeal communities, in order to understand their ecological roles in natural environments it is required to culture the microbes. Recently different molecular techniques have been developed for determining the structure of methanogenic archaeal communities thriving in freshwater lake ecosystem. The two gene based cloning techniques required for this purpose are 16S rRNA and methyl coenzyme M reductase (mcrA) in addition to the recently developed metagenomics approaches and high throughput next generation sequencing efforts. This review discusses the various methods of culture-dependent and -independent measures of determining the diversity of methanogen communities in lake sediments in lieu of the different molecular approaches and inter-relationships of diversity of methanogenic archaea.
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Affiliation(s)
- Folguni Laskar
- Advance Institutional Biotech Hub, Karimganj College, Karimganj, Assam, India
| | | | - Aniruddha Sen
- Advance Institutional Biotech Hub, Karimganj College, Karimganj, Assam, India
| | | | - Biswapriya B Misra
- Department of Genetics, Texas Biomedical Research Institute, San Antonio 78227, Texas, USA
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214
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Copper and cerium-regulated gene expression in Methylosinus trichosporium OB3b. Appl Microbiol Biotechnol 2017; 101:8499-8516. [DOI: 10.1007/s00253-017-8572-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 09/25/2017] [Accepted: 10/02/2017] [Indexed: 12/16/2022]
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215
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Xing Z, Zhao T, Gao Y, He Z, Zhang L, Peng X, Song L. Real-time monitoring of methane oxidation in a simulated landfill cover soil and MiSeq pyrosequencing analysis of the related bacterial community structure. WASTE MANAGEMENT (NEW YORK, N.Y.) 2017; 68:369-377. [PMID: 28532620 DOI: 10.1016/j.wasman.2017.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 04/30/2017] [Accepted: 05/03/2017] [Indexed: 06/07/2023]
Abstract
Real-time CH4 oxidation in a landfill cover soil was studied using automated gas sampling that determined biogas (CH4 and CO2) and O2 concentrations at various depths in a simulated landfill cover soil (SLCS) column reactor. The real-time monitoring system obtained more than 10,000 biogas (CH4 and CO2) and O2 data points covering 32 steady states of CH4 oxidation with 32 different CH4 fluxes (0.2-125mol·m-2·d-1). The kinetics of CH4 oxidation at different depths (0-20cm, 20-40cm, and 40-60cm) of SLCS were well fit by a CH4-O2 dual-substrate model based on 32 values (averaged, n=5-15) of equilibrated CH4 concentrations. The quality of the fit (R2 ranged from 0.90 to 0.96) was higher than those reported in previous studies, which suggests that real time monitoring is beneficial for CH4 oxidation simulations. MiSeq pyrosequencing indicated that CH4 flux events changed the bacterial community structure (e.g., increased the abundance of Bacteroidetes and Methanotrophs) and resulted in a relative increase in the amount of type I methanotrophs (Methylobacter and Methylococcales) and a decrease in the amount of type II methanotrophs (Methylocystis).
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Affiliation(s)
- Zhilin Xing
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China; Faculty of Urban Construction and Environment Engineering, Chongqing University, Chongqing 400045, China
| | - Tiantao Zhao
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China; Faculty of Urban Construction and Environment Engineering, Chongqing University, Chongqing 400045, China.
| | - Yanhui Gao
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China; Faculty of Urban Construction and Environment Engineering, Chongqing University, Chongqing 400045, China
| | - Zhi He
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China
| | - Lijie Zhang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China
| | - Xuya Peng
- Faculty of Urban Construction and Environment Engineering, Chongqing University, Chongqing 400045, China
| | - Liyan Song
- Environmental Microbiology and Ecology Research Center, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science (CAS), Chongqing 400714, China.
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216
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Molybdenum-Based Diazotrophy in a Sphagnum Peatland in Northern Minnesota. Appl Environ Microbiol 2017; 83:AEM.01174-17. [PMID: 28667112 DOI: 10.1128/aem.01174-17] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 06/28/2017] [Indexed: 11/20/2022] Open
Abstract
Microbial N2 fixation (diazotrophy) represents an important nitrogen source to oligotrophic peatland ecosystems, which are important sinks for atmospheric CO2 and are susceptible to the changing climate. The objectives of this study were (i) to determine the active microbial group and type of nitrogenase mediating diazotrophy in an ombrotrophic Sphagnum-dominated peat bog (the S1 peat bog, Marcell Experimental Forest, Minnesota, USA); and (ii) to determine the effect of environmental parameters (light, O2, CO2, and CH4) on potential rates of diazotrophy measured by acetylene (C2H2) reduction and 15N2 incorporation. A molecular analysis of metabolically active microbial communities suggested that diazotrophy in surface peat was primarily mediated by Alphaproteobacteria (Bradyrhizobiaceae and Beijerinckiaceae). Despite higher concentrations of dissolved vanadium ([V] 11 nM) than molybdenum ([Mo] 3 nM) in surface peat, a combination of metagenomic, amplicon sequencing, and activity measurements indicated that Mo-containing nitrogenases dominate over the V-containing form. Acetylene reduction was only detected in surface peat exposed to light, with the highest rates observed in peat collected from hollows with the highest water contents. Incorporation of 15N2 was suppressed 90% by O2 and 55% by C2H2 and was unaffected by CH4 and CO2 amendments. These results suggest that peatland diazotrophy is mediated by a combination of C2H2-sensitive and C2H2-insensitive microbes that are more active at low concentrations of O2 and show similar activity at high and low concentrations of CH4 IMPORTANCE Previous studies indicate that diazotrophy provides an important nitrogen source and is linked to methanotrophy in Sphagnum-dominated peatlands. However, the environmental controls and enzymatic pathways of peatland diazotrophy, as well as the metabolically active microbial populations that catalyze this process, remain in question. Our findings indicate that oxygen levels and photosynthetic activity override low nutrient availability in limiting diazotrophy and that members of the Alphaproteobacteria (Rhizobiales) catalyze this process at the bog surface using the molybdenum-based form of the nitrogenase enzyme.
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217
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Chidambarampadmavathy K, Karthikeyan OP, Huerlimann R, Maes GE, Heimann K. Responses of mixed methanotrophic consortia to variable Cu 2+/Fe 2+ ratios. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2017; 197:159-166. [PMID: 28365562 DOI: 10.1016/j.jenvman.2017.03.063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 03/14/2017] [Accepted: 03/21/2017] [Indexed: 05/22/2023]
Abstract
Methane mitigation in landfill top cover soils is mediated by methanotrophs whose optimal methane (CH4) oxidation capacity is governed by environmental and complex microbial community interactions. Optimization of CH4 remediating bio-filters need to take microbial responses into account. Divalent copper (Cu2+) and iron (Fe2+) are present in landfills at variable ratios and play a vital role in methane oxidation capacity and growth of methanotrophs. This study, as a first of its kind, therefore quantified effects of variable Cu2+ and Fe2+ (5:5, 5:25 and 5:50 μM) ratios on mixed methanotrophic communities enriched from landfill top cover (LB) and compost soils (CB). CH4 oxidation capacity, CH4 removal efficiencies, fatty acids content/profiles and polyhydroxybutyrate (PHB; a biopolymer) contents were also analysed to quantify performance and potential co-product development. Mixed methanotroph cultures were raised in 10 L continuous stirred tank reactors (CSTRs, Bioflo® & Celligen® 310 Fermentor/Bioreactor; John Morris Scientific, Chatswood, NSW, Australia). Community structure was determined by amplifying the V3-V4 region of 16s rRNA gene. Community structure and, consequently, fatty acid-profiles changed significantly with increasing Cu2+/Fe2+ ratios, and responses were different for LB and CB. Effects on methane oxidation capacities and PHB content were similar in the LB- and CB-CSTR, decreasing with increasing Cu2+/Fe2+ ratios, while biomass growth was unaffected. In general, high Fe2+ concentration favored growth of the type -II methanotroph Methylosinus in the CB-CSTR, but methanotroph abundances decreased in the LB-CSTR. Increase in Cu2+/Fe2+ ratio increased the growth of Sphingopyxis in both systems, while Azospirllum was co-dominant in the LB- but absent in the CB-CSTR. After 13 days, methane oxidation capacities and PHB content decreased by ∼50% and more in response to increasing Fe2+ concentrations. Although methanotroph abundance was ∼2% in the LB- (compared to >50% in CB-CSTR), methane oxidation capacities were comparable in the two systems, suggesting that methane oxidation capacity was maintained by the dominant Azospirllum and Sphingopyxis in the LB-CSTR. Despite similar methanotroph inoculum community composition and controlled environmental variables, increasing Cu2+/Fe2+ ratios resulted in significantly different microbial community structures in the LB- and CB-CSTR, indicative of complex microbial interactions. In summary, our results suggest that a detailed understanding of allelopathic interactions in mixed methanotrophic consortia is vital for constructing robust bio-filters for CH4 emission abatement.
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Affiliation(s)
- Karthigeyan Chidambarampadmavathy
- College of Science and Engineering, James Cook University, Townsville 4811, Queensland, Australia; Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville 4811, Queensland, Australia
| | - Obulisamy Parthiba Karthikeyan
- College of Science and Engineering, James Cook University, Townsville 4811, Queensland, Australia; Comparative Genomics Centre, James Cook University, Townsville 4811, Queensland, Australia; Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville 4811, Queensland, Australia; Sino-Forest Applied Research Centre for Pearl River Delta Environment (ARCPE), Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Roger Huerlimann
- College of Science and Engineering, James Cook University, Townsville 4811, Queensland, Australia; Comparative Genomics Centre, James Cook University, Townsville 4811, Queensland, Australia; Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville 4811, Queensland, Australia
| | - Gregory E Maes
- College of Science and Engineering, James Cook University, Townsville 4811, Queensland, Australia; Comparative Genomics Centre, James Cook University, Townsville 4811, Queensland, Australia; Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville 4811, Queensland, Australia
| | - Kirsten Heimann
- College of Science and Engineering, James Cook University, Townsville 4811, Queensland, Australia; Comparative Genomics Centre, James Cook University, Townsville 4811, Queensland, Australia; Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville 4811, Queensland, Australia; Centre for Bio-discovery and Molecular Development of Therapeutics, James Cook University, Townsville 4811, Queensland, Australia.
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218
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Lu X, Gu W, Zhao L, Farhan Ul Haque M, DiSpirito AA, Semrau JD, Gu B. Methylmercury uptake and degradation by methanotrophs. SCIENCE ADVANCES 2017; 3:e1700041. [PMID: 28580426 PMCID: PMC5451197 DOI: 10.1126/sciadv.1700041] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/30/2017] [Indexed: 05/22/2023]
Abstract
Methylmercury (CH3Hg+) is a potent neurotoxin produced by certain anaerobic microorganisms in natural environments. Although numerous studies have characterized the basis of mercury (Hg) methylation, no studies have examined CH3Hg+ degradation by methanotrophs, despite their ubiquitous presence in the environment. We report that some methanotrophs, such as Methylosinus trichosporium OB3b, can take up and degrade CH3Hg+ rapidly, whereas others, such as Methylococcus capsulatus Bath, can take up but not degrade CH3Hg+. Demethylation by M. trichosporium OB3b increases with increasing CH3Hg+ concentrations but was abolished in mutants deficient in the synthesis of methanobactin, a metal-binding compound used by some methanotrophs, such as M. trichosporium OB3b. Furthermore, addition of methanol (>5 mM) as a competing one-carbon (C1) substrate inhibits demethylation, suggesting that CH3Hg+ degradation by methanotrophs may involve an initial bonding of CH3Hg+ by methanobactin followed by cleavage of the C-Hg bond in CH3Hg+ by the methanol dehydrogenase. This new demethylation pathway by methanotrophs indicates possible broader involvement of C1-metabolizing aerobes in the degradation and cycling of toxic CH3Hg+ in the environment.
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Affiliation(s)
- Xia Lu
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Wenyu Gu
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Linduo Zhao
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Muhammad Farhan Ul Haque
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alan A. DiSpirito
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Jeremy D. Semrau
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Baohua Gu
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Corresponding author.
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219
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Liang Y, Cook LJ, Mattes TE. Temporal abundance and activity trends of vinyl chloride (VC)-degrading bacteria in a dilute VC plume at Naval Air Station Oceana. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:13760-13774. [PMID: 28401391 DOI: 10.1007/s11356-017-8948-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/27/2017] [Indexed: 06/07/2023]
Abstract
Assessment and monitoring of microbial community dynamics is useful when tracking the progress of vinyl chloride (VC) bioremediation strategies, particularly in dilute plumes where apparent VC attenuation rates are low. In a long-term field study, the abundance and the activity of microbial VC degraders were tracked in three monitoring wells (MW05, MW25, and MW19) along a dilute VC plume at Naval Air Station (NAS) Oceana. High-throughput sequencing of partial 16S ribosomal RNA (rRNA) genes and transcripts revealed diverse groundwater microbial communities and showed that methanotrophs and anaerobic respirers (e.g., methanogens, sulfate reducers, and iron reducers) were among the most active and abundant guilds. Quantitative PCR analysis showed that among bacterial guilds with a potential to contribute to VC biodegradation, methanotrophs were the most abundant and active microbial group. Ethene-oxidizing bacterial populations were less abundant and relatively inactive compared to methanotrophs. In MW19, expression of functional genes associated with both aerobic VC oxidation and anaerobic VC reduction was observed. Overall, our results reveal that the groundwater community contains various active bacterial guilds previously associated with metabolic and cometabolic VC degradation processes either under aerobic and anaerobic conditions that might have contributed to the slowly decreasing VC concentrations at the NAS Oceana site over the 6-year study period.
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Affiliation(s)
- Yi Liang
- Department of Civil and Environmental Engineering, University of Iowa, 4105 Seamans Center, Iowa City, IA, 52242, USA
| | - Laura J Cook
- CH2M 5701 Cleveland Street Suite 200, Virginia Beach, VA, 23462, USA
| | - Timothy E Mattes
- Department of Civil and Environmental Engineering, University of Iowa, 4105 Seamans Center, Iowa City, IA, 52242, USA.
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220
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He R, Chen M, Ma RC, Su Y, Zhang X. Ammonium conversion and its feedback effect on methane oxidation of Methylosinus sporium. J Biosci Bioeng 2017; 123:466-473. [DOI: 10.1016/j.jbiosc.2016.11.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 10/20/2016] [Accepted: 11/10/2016] [Indexed: 11/16/2022]
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221
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Ross MO, Rosenzweig AC. A tale of two methane monooxygenases. J Biol Inorg Chem 2017; 22:307-319. [PMID: 27878395 PMCID: PMC5352483 DOI: 10.1007/s00775-016-1419-y] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/15/2016] [Indexed: 11/24/2022]
Abstract
Methane monooxygenase (MMO) enzymes activate O2 for oxidation of methane. Two distinct MMOs exist in nature, a soluble form that uses a diiron active site (sMMO) and a membrane-bound form with a catalytic copper center (pMMO). Understanding the reaction mechanisms of these enzymes is of fundamental importance to biologists and chemists, and is also relevant to the development of new biocatalysts. The sMMO catalytic cycle has been elucidated in detail, including O2 activation intermediates and the nature of the methane-oxidizing species. By contrast, many aspects of pMMO catalysis remain unclear, most notably the nuclearity and molecular details of the copper active site. Here, we review the current state of knowledge for both enzymes, and consider pMMO O2 activation intermediates suggested by computational and synthetic studies in the context of existing biochemical data. Further work is needed on all fronts, with the ultimate goal of understanding how these two remarkable enzymes catalyze a reaction not readily achieved by any other metalloenzyme or biomimetic compound.
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Affiliation(s)
- Matthew O Ross
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, 60208, USA.
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222
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Stępniewska Z, Goraj W, Kuźniar A, Łopacka N, Małysza M. Enrichment culture and identification of endophytic methanotrophs isolated from peatland plants. Folia Microbiol (Praha) 2017; 62:381-391. [PMID: 28275945 PMCID: PMC5579069 DOI: 10.1007/s12223-017-0508-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 02/16/2017] [Indexed: 11/24/2022]
Abstract
Aerobic methane-oxidizing bacteria (MOB) are an environmentally significant group of microorganisms due to their role in the global carbon cycle. Research conducted over the past few decades has increased the interest in discovering novel genera of methane-degrading bacteria, which efficiently utilize methane and decrease the global warming effect. Moreover, methanotrophs have more promising applications in environmental bioengineering, biotechnology, and pharmacy. The investigations were undertaken to recognize the variety of endophytic methanotrophic bacteria associated with Carex nigra, Vaccinium oxycoccus, and Eriophorum vaginatum originating from Moszne peatland (East Poland). Methanotrophic bacteria were isolated from plants by adding sterile fragments of different parts of plants (roots and stems) to agar mineral medium (nitrate mineral salts (NMS)) and incubated at different methane values (1–20% CH4). Single colonies were streaked on new NMS agar media and, after incubation, transferred to liquid NMS medium. Bacterial growth dynamics in the culture solution was studied by optical density—OD600 and methane consumption. Changes in the methane concentration during incubation were controlled by the gas chromatography technique. Characterization of methanotrophs was made by fluorescence in situ hybridization (FISH) with Mg705 and Mg84 for type I methanotrophs and Ma450 for type II methanotrophs. Identification of endophytes was performed after 16S ribosomal RNA (rRNA) and mmoX gene amplification. Our study confirmed the presence of both types of methanotrophic bacteria (types I and II) with the predominance of type I methanotrophs. Among cultivable methanotrophs, there were different strains of the genus Methylomonas and Methylosinus. Furthermore, we determined the potential of the examined bacteria for methane oxidation, which ranged from 0.463 ± 0.067 to 5.928 ± 0.169 μmol/L CH4/mL/day.
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Affiliation(s)
- Zofia Stępniewska
- Department of Biochemistry and Environmental Chemistry, Institute of Biotechnology, The John Paul II Catholic University of Lublin, Konstantynow 1I, 20-708, Lublin, Poland
| | - Weronika Goraj
- Department of Biochemistry and Environmental Chemistry, Institute of Biotechnology, The John Paul II Catholic University of Lublin, Konstantynow 1I, 20-708, Lublin, Poland.
| | - Agnieszka Kuźniar
- Department of Biochemistry and Environmental Chemistry, Institute of Biotechnology, The John Paul II Catholic University of Lublin, Konstantynow 1I, 20-708, Lublin, Poland
| | - Natalia Łopacka
- Department of Biochemistry and Environmental Chemistry, Institute of Biotechnology, The John Paul II Catholic University of Lublin, Konstantynow 1I, 20-708, Lublin, Poland
| | - Magdalena Małysza
- Department of Biochemistry and Environmental Chemistry, Institute of Biotechnology, The John Paul II Catholic University of Lublin, Konstantynow 1I, 20-708, Lublin, Poland
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223
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Wang VCC, Maji S, Chen PPY, Lee HK, Yu SSF, Chan SI. Alkane Oxidation: Methane Monooxygenases, Related Enzymes, and Their Biomimetics. Chem Rev 2017; 117:8574-8621. [PMID: 28206744 DOI: 10.1021/acs.chemrev.6b00624] [Citation(s) in RCA: 249] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Methane monooxygenases (MMOs) mediate the facile conversion of methane into methanol in methanotrophic bacteria with high efficiency under ambient conditions. Because the selective oxidation of methane is extremely challenging, there is considerable interest in understanding how these enzymes carry out this difficult chemistry. The impetus of these efforts is to learn from the microbes to develop a biomimetic catalyst to accomplish the same chemical transformation. Here, we review the progress made over the past two to three decades toward delineating the structures and functions of the catalytic sites in two MMOs: soluble methane monooxygenase (sMMO) and particulate methane monooxygenase (pMMO). sMMO is a water-soluble three-component protein complex consisting of a hydroxylase with a nonheme diiron catalytic site; pMMO is a membrane-bound metalloenzyme with a unique tricopper cluster as the site of hydroxylation. The metal cluster in each of these MMOs harnesses O2 to functionalize the C-H bond using different chemistry. We highlight some of the common basic principles that they share. Finally, the development of functional models of the catalytic sites of MMOs is described. These efforts have culminated in the first successful biomimetic catalyst capable of efficient methane oxidation without overoxidation at room temperature.
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Affiliation(s)
- Vincent C-C Wang
- Institute of Chemistry, Academia Sinica , 128, Section 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Suman Maji
- School of Chemical Engineering and Physical Sciences, Lovely Professional University , Jalandhar-Delhi G. T. Road (NH-1), Phagwara, Punjab India 144411
| | - Peter P-Y Chen
- Department of Chemistry, National Chung Hsing University , 250 Kuo Kuang Road, Taichung 402, Taiwan
| | - Hung Kay Lee
- Department of Chemistry, The Chinese University of Hong Kong , Shatin, New Territories, Hong Kong
| | - Steve S-F Yu
- Institute of Chemistry, Academia Sinica , 128, Section 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Sunney I Chan
- Institute of Chemistry, Academia Sinica , 128, Section 2, Academia Road, Nankang, Taipei 11529, Taiwan.,Department of Chemistry, National Taiwan University , No. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan.,Noyes Laboratory, 127-72, California Institute of Technology , 1200 East California Boulevard, Pasadena, California 91125, United States
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224
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Farhan Ul Haque M, Gu W, Baral BS, DiSpirito AA, Semrau JD. Carbon source regulation of gene expression in Methylosinus trichosporium OB3b. Appl Microbiol Biotechnol 2017; 101:3871-3879. [PMID: 28108763 DOI: 10.1007/s00253-017-8121-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 01/03/2017] [Accepted: 01/10/2017] [Indexed: 01/06/2023]
Abstract
Gene expression in methanotrophs has been shown to be affected by the availability of a variety of metals, most notably copper regulating expression of alternative forms of methane monooxygenase. Here, we show that growth substrate also affects expression of genes encoding for enzymes responsible for the oxidation of methane to formaldehyde and the assimilation of carbon. Specifically, in Methylosinus trichosporium OB3b, expression of genes involved in the conversion of methane to methanol (pmoA and mmoX) and methanol to formaldehyde (mxaF, xoxF1, and xoxF2) as well as in carbon assimilation (fae1, fae2, metF, and sga) decreased when this strain was grown on methanol vs. methane, indicating that methanotrophs manipulate gene expression in response to growth substrate as well as the availability of copper. Interestingly, growth of M. trichosporium OB3b on methane vs. methanol was similar despite such large changes in gene expression. Finally, methanol-grown cultures of M. trichosporium OB3b also exhibited the "copper-switch." That is, expression of pmoA increased and mmoX decreased in the presence of copper, indicating that copper still controlled the expression of alternative forms of methane monooxygenase in M. trichosporium OB3b even though methane was not provided. Such findings indicate that methanotrophs can sense and respond to multiple environmental parameters simultaneously.
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Affiliation(s)
- Muhammad Farhan Ul Haque
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, 48109-2125, USA
| | - Wenyu Gu
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, 48109-2125, USA
| | - Bipin S Baral
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011-3260, USA
| | - Alan A DiSpirito
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011-3260, USA
| | - Jeremy D Semrau
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, 48109-2125, USA.
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225
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Deng Y, Liu Y, Dumont M, Conrad R. Salinity Affects the Composition of the Aerobic Methanotroph Community in Alkaline Lake Sediments from the Tibetan Plateau. MICROBIAL ECOLOGY 2017; 73:101-110. [PMID: 27878346 DOI: 10.1007/s00248-016-0879-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 10/12/2016] [Indexed: 06/06/2023]
Abstract
Lakes are widely distributed on the Tibetan Plateau, which plays an important role in natural methane emission. Aerobic methanotrophs in lake sediments reduce the amount of methane released into the atmosphere. However, no study to date has analyzed the methanotroph community composition and their driving factors in sediments of these high-altitude lakes (>4000 m). To provide new insights on this aspect, the abundance and composition in the sediments of six high-altitude alkaline lakes (including both freshwater and saline lakes) on the Tibetan Plateau were studied. The quantitative PCR, terminal restriction fragment length polymorphism, and 454-pyrosequencing methods were used to target the pmoA genes. The pmoA gene copies ranged 104-106 per gram fresh sediment. Type I methanotrophs predominated in Tibetan lake sediments, with Methylobacter and uncultivated type Ib methanotrophs being dominant in freshwater lakes and Methylomicrobium in saline lakes. Combining the pmoA-pyrosequencing data from Tibetan lakes with other published pmoA-sequencing data from lake sediments of other regions, a significant salinity and alkalinity effect (P = 0.001) was detected, especially salinity, which explained ∼25% of methanotroph community variability. The main effect was Methylomicrobium being dominant (up to 100%) in saline lakes only. In freshwater lakes, however, methanotroph composition was relatively diverse, including Methylobacter, Methylocystis, and uncultured type Ib clusters. This study provides the first methanotroph data for high-altitude lake sediments (>4000 m) and shows that salinity is a driving factor for the community composition of aerobic methanotrophs.
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Affiliation(s)
- Yongcui Deng
- College of Geographic Sciences, Nanjing Normal University, 1 Wenyuan Road, 210023, Nanjing, China
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043, Marburg, Germany
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, 1 Wenyuan Road, 210023, Nanjing, China
| | - Yongqin Liu
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, 100085, Beijing, China.
| | - Marc Dumont
- Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Ralf Conrad
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043, Marburg, Germany
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226
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Kim S, Lee W, Song I, Kwon Y, Yun S, Park S, Cho S, Oh BK, Oh HB, Lee J. Production of uracil from methane by a newly isolated Methylomonas sp. SW1. J Biotechnol 2016; 240:43-47. [DOI: 10.1016/j.jbiotec.2016.10.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 10/16/2016] [Accepted: 10/20/2016] [Indexed: 11/28/2022]
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227
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Lawton TJ, Rosenzweig AC. Biocatalysts for methane conversion: big progress on breaking a small substrate. Curr Opin Chem Biol 2016; 35:142-149. [PMID: 27768948 PMCID: PMC5161620 DOI: 10.1016/j.cbpa.2016.10.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/30/2016] [Accepted: 10/03/2016] [Indexed: 01/08/2023]
Abstract
Nature utilizes two groups of enzymes to catalyze methane conversions, methyl-coenzyme M reductases (MCRs) and methane monooxygenases (MMOs). These enzymes have been difficult to incorporate into industrial processes due to their complexity, poor stability, and lack of recombinant tractability. Despite these issues, new ways of preparing and stabilizing these enzymes have recently been discovered, and new mechanistic insight into how MCRs and MMOs break the C-H bond in nature's most inert hydrocarbon have been obtained. This review focuses on recent findings in the methane biocatalysis field, and discusses the impact of these finding on designing MMO and MCR-based biotechnologies.
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Affiliation(s)
- Thomas J Lawton
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208, USA.
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228
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Welte CU, Rasigraf O, Vaksmaa A, Versantvoort W, Arshad A, Op den Camp HJM, Jetten MSM, Lüke C, Reimann J. Nitrate- and nitrite-dependent anaerobic oxidation of methane. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:941-955. [PMID: 27753265 DOI: 10.1111/1758-2229.12487] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Microbial methane oxidation is an important process to reduce the emission of the greenhouse gas methane. Anaerobic microorganisms couple the oxidation of methane to the reduction of sulfate, nitrate and nitrite, and possibly oxidized iron and manganese minerals. In this article, we review the recent finding of the intriguing nitrate- and nitrite-dependent anaerobic oxidation of methane (AOM). Nitrate-dependent AOM is catalyzed by anaerobic archaea belonging to the ANME-2d clade closely related to Methanosarcina methanogens. They were named 'Candidatus Methanoperedens nitroreducens' and use reverse methanogenesis with the key enzyme methyl-coenzyme M (methyl-CoM) reductase for methane activation. Their major end product is nitrite which can be taken up by nitrite-dependent methanotrophs. Nitrite-dependent AOM is performed by the NC10 bacterium 'Candidatus Methylomirabilis oxyfera' that probably utilizes an intra-aerobic pathway through the dismutation of NO to N2 and O2 for aerobic methane activation by methane monooxygenase, yet being a strictly anaerobic microbe. Environmental distribution, physiological and biochemical aspects are discussed in this article as well as the cooperation of the microorganisms involved.
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Affiliation(s)
- Cornelia U Welte
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
- Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Olivia Rasigraf
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
- Netherlands Earth Systems Science Center, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Annika Vaksmaa
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Wouter Versantvoort
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Arslan Arshad
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
- Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
- Netherlands Earth Systems Science Center, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Claudia Lüke
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Joachim Reimann
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
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Malyan SK, Bhatia A, Kumar A, Gupta DK, Singh R, Kumar SS, Tomer R, Kumar O, Jain N. Methane production, oxidation and mitigation: A mechanistic understanding and comprehensive evaluation of influencing factors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 572:874-896. [PMID: 27575427 DOI: 10.1016/j.scitotenv.2016.07.182] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 07/02/2016] [Accepted: 07/25/2016] [Indexed: 06/06/2023]
Abstract
Methane is one of the critical greenhouse gases, which absorb long wavelength radiation, affects the chemistry of atmosphere and contributes to global climate change. Rice ecosystem is one of the major anthropogenic sources of methane. The anaerobic waterlogged soil in rice field provides an ideal environment to methanogens for methanogenesis. However, the rate of methanogenesis differs according to rice cultivation regions due to a number of biological, environmental and physical factors like carbon sources, pH, Eh, temperature etc. The interplay between the different conditions and factors may also convert the rice fields into sink from source temporarily. Mechanistic understanding and comprehensive evaluation of these variations and responsible factors are urgently required for designing new mitigation options and evaluation of reported option in different climatic conditions. The objective of this review paper is to develop conclusive understanding on the methane production, oxidation, and emission and methane measurement techniques from rice field along with its mitigation/abatement mechanism to explore the possible reduction techniques from rice ecosystem.
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Affiliation(s)
- Sandeep K Malyan
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Arti Bhatia
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Amit Kumar
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Dipak Kumar Gupta
- ICAR-Central Arid Zone Research Institute, Regional Research Station, Pali-Marwar, Rajasthan 342003, India
| | - Renu Singh
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Smita S Kumar
- Department of Environmental Science and Engineering, Guru Jambheshwar University of Science and Technology, Hisar, Haryana 125001, India
| | - Ritu Tomer
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Om Kumar
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Niveta Jain
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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230
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Oswald K, Jegge C, Tischer J, Berg J, Brand A, Miracle MR, Soria X, Vicente E, Lehmann MF, Zopfi J, Schubert CJ. Methanotrophy under Versatile Conditions in the Water Column of the Ferruginous Meromictic Lake La Cruz (Spain). Front Microbiol 2016; 7:1762. [PMID: 27891115 PMCID: PMC5104750 DOI: 10.3389/fmicb.2016.01762] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 10/20/2016] [Indexed: 11/13/2022] Open
Abstract
Lakes represent a considerable natural source of methane to the atmosphere compared to their small global surface area. Methanotrophs in sediments and in the water column largely control methane fluxes from these systems, yet the diversity, electron accepting capacity, and nutrient requirements of these microorganisms have only been partially identified. Here, we investigated the role of electron acceptors alternative to oxygen and sulfate in microbial methane oxidation at the oxycline and in anoxic waters of the ferruginous meromictic Lake La Cruz, Spain. Active methane turnover in a zone extending well below the oxycline was evidenced by stable carbon isotope-based rate measurements. We observed a strong methane oxidation potential throughout the anoxic water column, which did not vary substantially from that at the oxic/anoxic interface. Both in the redox-transition and anoxic zones, only aerobic methane-oxidizing bacteria (MOB) were detected by fluorescence in situ hybridization and sequencing techniques, suggesting a close coupling of cryptic photosynthetic oxygen production and aerobic methane turnover. Additions of nitrate, nitrite and to a lesser degree iron and manganese oxides also stimulated bacterial methane consumption. We could not confirm a direct link between the reduction of these compounds and methane oxidation and we cannot exclude the contribution of unknown anaerobic methanotrophs. Nevertheless, our findings from Lake La Cruz support recent laboratory evidence that aerobic methanotrophs may be able to utilize alternative terminal electron acceptors under oxygen limitation.
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Affiliation(s)
- Kirsten Oswald
- Department of Surface Waters - Research and Management, Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaum, Switzerland; Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Swiss Federal Institute of TechnologyZurich, Switzerland
| | - Corinne Jegge
- Department of Surface Waters - Research and Management, Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaum, Switzerland; School of Architecture, Civil and Environmental Engineering, EPFL, Swiss Federal Institute of TechnologyLausanne, Switzerland
| | - Jana Tischer
- Department of Environmental Sciences, University of Basel Basel, Switzerland
| | - Jasmine Berg
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Andreas Brand
- Department of Surface Waters - Research and Management, Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaum, Switzerland; Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Swiss Federal Institute of TechnologyZurich, Switzerland
| | - María R Miracle
- Department of Microbiology and Ecology, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia Burjassot, Spain
| | - Xavier Soria
- Department of Microbiology and Ecology, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia Burjassot, Spain
| | - Eduardo Vicente
- Department of Microbiology and Ecology, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia Burjassot, Spain
| | - Moritz F Lehmann
- Department of Environmental Sciences, University of Basel Basel, Switzerland
| | - Jakob Zopfi
- Department of Environmental Sciences, University of Basel Basel, Switzerland
| | - Carsten J Schubert
- Department of Surface Waters - Research and Management, Swiss Federal Institute of Aquatic Science and Technology Kastanienbaum, Switzerland
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231
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Abstract
Methanotrophic bacteria use methane, a potent greenhouse gas, as their primary source of carbon and energy. The first step in methane metabolism is its oxidation to methanol. In almost all methanotrophs, this chemically challenging reaction is catalyzed by particulate methane monooxygenase (pMMO), a copper-dependent integral membrane enzyme. Methanotrophs acquire copper (Cu) for pMMO by secreting a small ribosomally produced, posttranslationally modified natural product called methanobactin (Mbn). Mbn chelates Cu with high affinity, and the Cu-loaded form (CuMbn) is reinternalized into the cell via an active transport process. Bioinformatic and gene regulation studies suggest that two proteins might play a role in CuMbn handling: the TonB-dependent transporter MbnT and the periplasmic binding protein MbnE. Disruption of the gene that encodes MbnT abolishes CuMbn uptake, as reported previously, and expression of MbnT in Escherichia coli confers the ability to take up CuMbn. Biophysical studies of MbnT and MbnE reveal specific interactions with CuMbn, and a crystal structure of apo MbnE is consistent with MbnE's proposed role as a periplasmic CuMbn transporter. Notably, MbnT and MbnE exhibit different levels of discrimination between cognate and noncognate CuMbns. These findings provide evidence for CuMbn-protein interactions and begin to elucidate the molecular mechanisms of its recognition and transport.
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232
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Chu F, Beck DAC, Lidstrom ME. MxaY regulates the lanthanide-mediated methanol dehydrogenase switch in Methylomicrobium buryatense. PeerJ 2016; 4:e2435. [PMID: 27651996 PMCID: PMC5018670 DOI: 10.7717/peerj.2435] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 08/12/2016] [Indexed: 01/12/2023] Open
Abstract
Many methylotrophs, microorganisms that consume carbon compounds lacking carbon-carbon bonds, use two different systems to oxidize methanol for energy production and biomass accumulation. The MxaFI methanol dehydrogenase (MDH) contains calcium in its active site, while the XoxF enzyme contains a lanthanide in its active site. The genes encoding the MDH enzymes are differentially regulated by the presence of lanthanides. In this study, we found that the histidine kinase MxaY controls the lanthanide-mediated switch in Methylomicrobium buryatense 5GB1C. MxaY controls the transcription of genes encoding MxaFI and XoxF at least partially by controlling the transcript levels of the orphan response regulator MxaB. We identify a constitutively active version of MxaY, and identify the mutated residue that may be involved in lanthanide sensing. Lastly, we find evidence to suggest that tight control of active MDH production is required for wild-type growth rates.
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Affiliation(s)
- Frances Chu
- Department of Chemical Engineering, University of Washington , Seattle , WA , United States
| | - David A C Beck
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States; eScience Institute, University of Washington, Seattle, WA, United States
| | - Mary E Lidstrom
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States; Department of Microbiology, University of Washington, Seattle, WA, United States
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233
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Kenney GE, Sadek M, Rosenzweig AC. Copper-responsive gene expression in the methanotroph Methylosinus trichosporium OB3b. Metallomics 2016; 8:931-40. [PMID: 27087171 PMCID: PMC6195801 DOI: 10.1039/c5mt00289c] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Methanotrophic bacteria convert methane to methanol using methane monooxygenase (MMO) enzymes. In many strains, either an iron-containing soluble (sMMO) or a copper-containing particulate (pMMO) enzyme can be produced depending on copper availability; the mechanism of this copper switch has not been elucidated. A key player in methanotroph copper homeostasis is methanobactin (Mbn), a ribosomally produced, post-translationally modified natural product with a high affinity for copper. The Mbn precursor peptide is encoded within an operon that contains a range of putative transporters, regulators, and biosynthetic proteins, but the involvement of these genes in Mbn-related processes remains unclear. Extensive time-dependent qRT-PCR studies of Methylosinus trichosporium OB3b and the constitutive sMMO-producing mutant M. trichosporium OB3b PP358 show that the Mbn operon is indeed copper-regulated, providing experimental support for its bioinformatics-based identification. Moreover, the Mbn operon is co-regulated with the sMMO operon and reciprocally regulated with the pMMO operon. Within the Mbn and sMMO operons, a subset of regulatory genes exhibits a distinct and shared pattern of expression, consistent with their proposed functions as internal regulators. In addition, genome sequencing of the M. trichosporium OB3b PP358 mutant provides new evidence for the involvement of genes adjacent to the pMMO operon in methanotroph copper homeostasis.
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Affiliation(s)
- Grace E. Kenney
- Department of Molecular Biosciences, Northwestern University, Evanston,IL 60208, USA.
| | - Monica Sadek
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Amy C. Rosenzweig
- Department of Molecular Biosciences, Northwestern University, Evanston,IL 60208, USA.
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
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234
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Kenney GE, Goering AW, Ross MO, DeHart CJ, Thomas PM, Hoffman BM, Kelleher NL, Rosenzweig AC. Characterization of Methanobactin from Methylosinus sp. LW4. J Am Chem Soc 2016; 138:11124-7. [PMID: 27527063 DOI: 10.1021/jacs.6b06821] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Methanobactins (Mbns) are a growing family of ribosomally produced, post-translationally modified natural products. Characteristic nitrogen-containing heterocycles and neighboring thioamides allow these compounds to bind copper with high affinity. Genome mining has enabled the identification of Mbn operons in bacterial genomes and the prediction of diverse Mbn structures from operon content and precursor peptide sequence. Here we report the characterization of Mbn from Methylosinus (Ms.) species (sp.) LW4. The peptide backbone is distinct from all previously characterized Mbns, and the post-translational modifications correspond precisely to those predicted on the basis of the Ms. sp. LW4 Mbn operon. Thus, prediction based on genome analysis combined with isolation and structural characterization represents a phylogenetic approach to finding diverse Mbns and elucidating their biosynthetic pathways.
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Affiliation(s)
- Grace E Kenney
- Departments of †Molecular Biosciences and ‡Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Anthony W Goering
- Departments of †Molecular Biosciences and ‡Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Matthew O Ross
- Departments of †Molecular Biosciences and ‡Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Caroline J DeHart
- Departments of †Molecular Biosciences and ‡Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Paul M Thomas
- Departments of †Molecular Biosciences and ‡Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Brian M Hoffman
- Departments of †Molecular Biosciences and ‡Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Departments of †Molecular Biosciences and ‡Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Amy C Rosenzweig
- Departments of †Molecular Biosciences and ‡Chemistry, Northwestern University , Evanston, Illinois 60208, United States
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235
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Assessment of farm soil, biochar, compost and weathered pine mulch to mitigate methane emissions. Appl Microbiol Biotechnol 2016; 100:9365-9379. [DOI: 10.1007/s00253-016-7794-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 06/13/2016] [Accepted: 08/08/2016] [Indexed: 10/21/2022]
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236
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Vaksmaa A, Lüke C, van Alen T, Valè G, Lupotto E, Jetten MSM, Ettwig KF. Distribution and activity of the anaerobic methanotrophic community in a nitrogen-fertilized Italian paddy soil. FEMS Microbiol Ecol 2016; 92:fiw181. [PMID: 27562776 DOI: 10.1093/femsec/fiw181] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2016] [Indexed: 12/23/2022] Open
Abstract
In order to mitigate methane emissions from paddy fields, it is important to understand the sources and sinks. Most paddy fields are heavily fertilized with nitrite and nitrate, which can be used as electron acceptors by anaerobic methanotrophs. Here we show that slurry incubations of Italian paddy field soil with nitrate and 13C-labelled methane have the potential for nitrate-dependent anaerobic oxidation of methane (79.9 nmol g-1dw d-1). Community analysis based on 16S rRNA amplicon sequencing and qPCR of the water-logged soil and the rhizosphere showed that anaerobic oxidation of methane-associated archaea (AAA), including Methanoperedens nitroreducens, comprised 9% (bulk soil) and 1% (rhizosphere) of all archaeal reads. The NC10 phylum bacteria made up less than 1% of all bacterial sequences. The phylogenetic analysis was complemented by qPCR showing that AAA ranged from 0.28 × 106 to 3.9 × 106 16S rRNA gene copies g-1dw in bulk soil and 0.27 × 106 to 2.8 × 106 in the rhizosphere. The abundance of NC10 phylum bacteria was an order of magnitude lower. Revisiting published diversity studies, we found that AAA have been detected, but not linked to methane oxidation, in several paddy fields. Our data suggest an important role of AAA in methane cycling in paddy fields.
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Affiliation(s)
- A Vaksmaa
- Radboud University, Department of Microbiology, Institute of Water and Wetland Research, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - C Lüke
- Radboud University, Department of Microbiology, Institute of Water and Wetland Research, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - T van Alen
- Radboud University, Department of Microbiology, Institute of Water and Wetland Research, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - G Valè
- CREA - Council for Agricultural Research and Economics, Rice Research Unit, s.s.11 to Torino km 2.5, 13100 Vercelli, Italy
| | - E Lupotto
- CREA - Council for Agricultural Research and Economics, Rice Research Unit, s.s.11 to Torino km 2.5, 13100 Vercelli, Italy
| | - M S M Jetten
- Radboud University, Department of Microbiology, Institute of Water and Wetland Research, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - K F Ettwig
- Radboud University, Department of Microbiology, Institute of Water and Wetland Research, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
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237
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Ho A, Angel R, Veraart AJ, Daebeler A, Jia Z, Kim SY, Kerckhof FM, Boon N, Bodelier PLE. Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System. Front Microbiol 2016; 7:1285. [PMID: 27602021 PMCID: PMC4993757 DOI: 10.3389/fmicb.2016.01285] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 08/04/2016] [Indexed: 11/13/2022] Open
Abstract
Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic controls and interactions potentially steering microbial communities leading to altered functioning are less known. Yet, recent accumulating evidence suggests that the concerted actions of a community can be significantly different from the combined effects of individual microorganisms, giving rise to emergent properties. Here, we exemplify the importance of microbial interaction for ecosystem processes by analysis of a reasonably well-understood microbial guild, namely, aerobic methane-oxidizing bacteria (MOB). We reviewed the literature which provided compelling evidence for the relevance of microbial interaction in modulating methane oxidation. Support for microbial associations within methane-fed communities is sought by a re-analysis of literature data derived from stable isotope probing studies of various complex environmental settings. Putative positive interactions between active MOB and other microbes were assessed by a correlation network-based analysis with datasets covering diverse environments where closely interacting members of a consortium can potentially alter the methane oxidation activity. Although, methanotrophy is used as a model system, the fundamentals of our postulations may be applicable to other microbial guilds mediating other biogeochemical processes.
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Affiliation(s)
- Adrian Ho
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Roey Angel
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna Vienna, Austria
| | - Annelies J Veraart
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Anne Daebeler
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna Vienna, Austria
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences Nanjing, China
| | - Sang Yoon Kim
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Frederiek-Maarten Kerckhof
- Center for Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University Ghent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University Ghent, Belgium
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
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238
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Lawton TJ, Rosenzweig AC. Methane-Oxidizing Enzymes: An Upstream Problem in Biological Gas-to-Liquids Conversion. J Am Chem Soc 2016; 138:9327-40. [PMID: 27366961 PMCID: PMC5242187 DOI: 10.1021/jacs.6b04568] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Biological conversion of natural gas to liquids (Bio-GTL) represents an immense economic opportunity. In nature, aerobic methanotrophic bacteria and anaerobic archaea are able to selectively oxidize methane using methane monooxygenase (MMO) and methyl coenzyme M reductase (MCR) enzymes. Although significant progress has been made toward genetically manipulating these organisms for biotechnological applications, the enzymes themselves are slow, complex, and not recombinantly tractable in traditional industrial hosts. With turnover numbers of 0.16-13 s(-1), these enzymes pose a considerable upstream problem in the biological production of fuels or chemicals from methane. Methane oxidation enzymes will need to be engineered to be faster to enable high volumetric productivities; however, efforts to do so and to engineer simpler enzymes have been minimally successful. Moreover, known methane-oxidizing enzymes have different expression levels, carbon and energy efficiencies, require auxiliary systems for biosynthesis and function, and vary considerably in terms of complexity and reductant requirements. The pros and cons of using each methane-oxidizing enzyme for Bio-GTL are considered in detail. The future for these enzymes is bright, but a renewed focus on studying them will be critical to the successful development of biological processes that utilize methane as a feedstock.
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Affiliation(s)
- Thomas J Lawton
- 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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239
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Enrichment and characteristics of mixed methane-oxidizing bacteria from a Chinese coal mine. Appl Microbiol Biotechnol 2016; 100:10331-10341. [DOI: 10.1007/s00253-016-7738-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/11/2016] [Accepted: 07/13/2016] [Indexed: 10/21/2022]
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240
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Lichtmannegger J, Leitzinger C, Wimmer R, Schmitt S, Schulz S, Kabiri Y, Eberhagen C, Rieder T, Janik D, Neff F, Straub BK, Schirmacher P, DiSpirito AA, Bandow N, Baral BS, Flatley A, Kremmer E, Denk G, Reiter FP, Hohenester S, Eckardt-Schupp F, Dencher NA, Adamski J, Sauer V, Niemietz C, Schmidt HHJ, Merle U, Gotthardt DN, Kroemer G, Weiss KH, Zischka H. Methanobactin reverses acute liver failure in a rat model of Wilson disease. J Clin Invest 2016; 126:2721-35. [PMID: 27322060 DOI: 10.1172/jci85226] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 04/12/2016] [Indexed: 12/15/2022] Open
Abstract
In Wilson disease (WD), functional loss of ATPase copper-transporting β (ATP7B) impairs biliary copper excretion, leading to excessive copper accumulation in the liver and fulminant hepatitis. Current US Food and Drug Administration- and European Medicines Agency-approved pharmacological treatments usually fail to restore copper homeostasis in patients with WD who have progressed to acute liver failure, leaving liver transplantation as the only viable treatment option. Here, we investigated the therapeutic utility of methanobactin (MB), a peptide produced by Methylosinus trichosporium OB3b, which has an exceptionally high affinity for copper. We demonstrated that ATP7B-deficient rats recapitulate WD-associated phenotypes, including hepatic copper accumulation, liver damage, and mitochondrial impairment. Short-term treatment of these rats with MB efficiently reversed mitochondrial impairment and liver damage in the acute stages of liver copper accumulation compared with that seen in untreated ATP7B-deficient rats. This beneficial effect was associated with depletion of copper from hepatocyte mitochondria. Moreover, MB treatment prevented hepatocyte death, subsequent liver failure, and death in the rodent model. These results suggest that MB has potential as a therapeutic agent for the treatment of acute WD.
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241
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Printable enzyme-embedded materials for methane to methanol conversion. Nat Commun 2016; 7:11900. [PMID: 27301270 PMCID: PMC4912616 DOI: 10.1038/ncomms11900] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 05/10/2016] [Indexed: 01/29/2023] Open
Abstract
An industrial process for the selective activation of methane under mild conditions would be highly valuable for controlling emissions to the environment and for utilizing vast new sources of natural gas. The only selective catalysts for methane activation and conversion to methanol under mild conditions are methane monooxygenases (MMOs) found in methanotrophic bacteria; however, these enzymes are not amenable to standard enzyme immobilization approaches. Using particulate methane monooxygenase (pMMO), we create a biocatalytic polymer material that converts methane to methanol. We demonstrate embedding the material within a silicone lattice to create mechanically robust, gas-permeable membranes, and direct printing of micron-scale structures with controlled geometry. Remarkably, the enzymes retain up to 100% activity in the polymer construct. The printed enzyme-embedded polymer motif is highly flexible for future development and should be useful in a wide range of applications, especially those involving gas–liquid reactions. There is a need for small-scale reactors that convert methane emissions to more valuable products to reduce climate impacts. Here, the authors show that printing 3D structures of the pMMO enzyme enables continuous methane conversion under ambient conditions and reduces mass transfer limitations.
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242
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DiSpirito AA, Semrau JD, Murrell JC, Gallagher WH, Dennison C, Vuilleumier S. Methanobactin and the Link between Copper and Bacterial Methane Oxidation. Microbiol Mol Biol Rev 2016; 80:387-409. [PMID: 26984926 PMCID: PMC4867365 DOI: 10.1128/mmbr.00058-15] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Methanobactins (mbs) are low-molecular-mass (<1,200 Da) copper-binding peptides, or chalkophores, produced by many methane-oxidizing bacteria (methanotrophs). These molecules exhibit similarities to certain iron-binding siderophores but are expressed and secreted in response to copper limitation. Structurally, mbs are characterized by a pair of heterocyclic rings with associated thioamide groups that form the copper coordination site. One of the rings is always an oxazolone and the second ring an oxazolone, an imidazolone, or a pyrazinedione moiety. The mb molecule originates from a peptide precursor that undergoes a series of posttranslational modifications, including (i) ring formation, (ii) cleavage of a leader peptide sequence, and (iii) in some cases, addition of a sulfate group. Functionally, mbs represent the extracellular component of a copper acquisition system. Consistent with this role in copper acquisition, mbs have a high affinity for copper ions. Following binding, mbs rapidly reduce Cu(2+) to Cu(1+). In addition to binding copper, mbs will bind most transition metals and near-transition metals and protect the host methanotroph as well as other bacteria from toxic metals. Several other physiological functions have been assigned to mbs, based primarily on their redox and metal-binding properties. In this review, we examine the current state of knowledge of this novel type of metal-binding peptide. We also explore its potential applications, how mbs may alter the bioavailability of multiple metals, and the many roles mbs may play in the physiology of methanotrophs.
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Affiliation(s)
- 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
| | - J Colin Murrell
- Earth and Life Systems Alliance, School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | - Warren H Gallagher
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, USA
| | - Christopher Dennison
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Stéphane Vuilleumier
- Department of Microbiology, Genomics and the Environment, UMR 7156 UNISTRA-CNRS, Université de Strasbourg, Strasbourg, France
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Vavilin VA, Rytov SV, Shim N, Vogt C. Non-linear dynamics of stable carbon and hydrogen isotope signatures based on a biological kinetic model of aerobic enzymatic methane oxidation. ISOTOPES IN ENVIRONMENTAL AND HEALTH STUDIES 2016; 52:185-202. [PMID: 26513269 DOI: 10.1080/10256016.2016.1092965] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 08/02/2015] [Indexed: 06/05/2023]
Abstract
The non-linear dynamics of stable carbon and hydrogen isotope signatures during methane oxidation by the methanotrophic bacteria Methylosinus sporium strain 5 (NCIMB 11126) and Methylocaldum gracile strain 14 L (NCIMB 11912) under copper-rich (8.9 µM Cu(2+)), copper-limited (0.3 µM Cu(2+)) or copper-regular (1.1 µM Cu(2+)) conditions has been described mathematically. The model was calibrated by experimental data of methane quantities and carbon and hydrogen isotope signatures of methane measured previously in laboratory microcosms reported by Feisthauer et al. [ 1 ] M. gracile initially oxidizes methane by a particulate methane monooxygenase and assimilates formaldehyde via the ribulose monophosphate pathway, whereas M. sporium expresses a soluble methane monooxygenase under copper-limited conditions and uses the serine pathway for carbon assimilation. The model shows that during methane solubilization dominant carbon and hydrogen isotope fractionation occurs. An increase of biomass due to growth of methanotrophs causes an increase of particulate or soluble monooxygenase that, in turn, decreases soluble methane concentration intensifying methane solubilization. The specific maximum rate of methane oxidation υm was proved to be equal to 4.0 and 1.3 mM mM(-1) h(-1) for M. sporium under copper-rich and copper-limited conditions, respectively, and 0.5 mM mM(-1) h(-1) for M. gracile. The model shows that methane oxidation cannot be described by traditional first-order kinetics. The kinetic isotope fractionation ceases when methane concentrations decrease close to the threshold value. Applicability of the non-linear model was confirmed by dynamics of carbon isotope signature for carbon dioxide that was depleted and later enriched in (13)C. Contrasting to the common Rayleigh linear graph, the dynamic curves allow identifying inappropriate isotope data due to inaccurate substrate concentration analyses. The non-linear model pretty adequately described experimental data presented in the two-dimensional plot of hydrogen versus carbon stable isotope signatures.
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Affiliation(s)
- Vasily A Vavilin
- a Russian Academy of Sciences , Ecological Department of Water Problems Institute , Moscow , Russian Federation
| | - Sergey V Rytov
- a Russian Academy of Sciences , Ecological Department of Water Problems Institute , Moscow , Russian Federation
| | - Natalia Shim
- a Russian Academy of Sciences , Ecological Department of Water Problems Institute , Moscow , Russian Federation
- b College of Engineering , University of Georgia , Athens , GA , USA
| | - Carsten Vogt
- c Department of Isotope Biogeochemistry , Helmholtz Center for Environmental Research - UFZ , Leipzig , Germany
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244
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Gu W, Farhan Ul Haque M, DiSpirito AA, Semrau JD. Uptake and effect of rare earth elements on gene expression in Methylosinus trichosporium OB3b. FEMS Microbiol Lett 2016; 363:fnw129. [PMID: 27190151 DOI: 10.1093/femsle/fnw129] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2016] [Indexed: 11/13/2022] Open
Abstract
It is well known that Methylosinus trichosporium OB3b has two forms of methane monooxygenase (MMO) responsible for the initial conversion of methane to methanol, a cytoplasmic (soluble) methane monooxygenase and a membrane-associated (particulate) methane monooxygenase, and that copper strongly regulates expression of these alternative forms of MMO. More recently, it has been discovered that M. trichosporium OB3b has multiple types of the methanol dehydrogenase (MeDH), i.e. the Mxa-type MeDH (Mxa-MeDH) and Xox-type MeDH (Xox-MeDH), and the expression of these two forms is regulated by the availability of the rare earth element (REE), cerium. Here, we extend these studies and show that lanthanum, praseodymium, neodymium and samarium also regulate expression of alternative forms of MeDH. The effect of these REEs on MeDH expression, however, was only observed in the absence of copper. Further, a mutant of M. trichosporium OB3b, where the Mxa-MeDH was knocked out, was able to grow in the presence of lanthanum, praseodymium and neodymium, but was not able to grow in the presence of samarium. Collectively, these data suggest that multiple levels of gene regulation by metals exist in M. trichosporium OB3b, but that copper overrides the effect of other metals by an as yet unknown mechanism.
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Affiliation(s)
- Wenyu Gu
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI 48109-2125, USA
| | - Muhammad Farhan Ul Haque
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI 48109-2125, USA
| | - Alan A DiSpirito
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Jeremy D Semrau
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI 48109-2125, USA
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245
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Cantera S, Lebrero R, García-Encina PA, Muñoz R. Evaluation of the influence of methane and copper concentration and methane mass transport on the community structure and biodegradation kinetics of methanotrophic cultures. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2016; 171:11-20. [PMID: 26866670 DOI: 10.1016/j.jenvman.2016.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 01/22/2016] [Accepted: 02/01/2016] [Indexed: 06/05/2023]
Abstract
The environmental conditions during culture enrichment, which ultimately determine its maximum specific biodegradation rate (qmax) and affinity for the target pollutant (Ks), play a key role in the performance of bioreactors devoted to the treatment of methane emissions. This study assessed the influence of Cu(2+) and CH4 concentration and the effective CH4 supply rate during culture enrichment on the structure and biodegradation kinetics of methanotrophic communities. The results obtained demonstrated that an increase in Cu(2+) concentration from 0.05 to 25 μM increased the qmax and Ks of the communities enriched by a factor of ≈ 3, even if the Cu(2+) concentration did not seem to have an effect on the enzymatic "copper switch" and only pMMO was detected. In addition, high Cu(2+) concentrations supported lower diversity coefficients (Hs ≈ 1.5× lower) and apparently promoted the growth of more adapted methanotrophs such as Methylomonas. Despite no clear effect of CH4 concentration on the population structure or on the biodegradation kinetics of the communities enriched was recorded at the two low CH4 concentrations studied (1 and 8%), a higher agitation rate increased the qmax by a factor of ≈ 2.3 and Ks by a factor of ≈ 3.1.
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Affiliation(s)
- Sara Cantera
- Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina, s/n, 47011, Valladolid, Spain
| | - Raquel Lebrero
- Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina, s/n, 47011, Valladolid, Spain
| | - Pedro A García-Encina
- Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina, s/n, 47011, Valladolid, Spain
| | - Raúl Muñoz
- Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina, s/n, 47011, Valladolid, Spain.
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246
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Danilova OV, Suzina NE, Van De Kamp J, Svenning MM, Bodrossy L, Dedysh SN. A new cell morphotype among methane oxidizers: a spiral-shaped obligately microaerophilic methanotroph from northern low-oxygen environments. ISME JOURNAL 2016; 10:2734-2743. [PMID: 27058508 DOI: 10.1038/ismej.2016.48] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 02/05/2016] [Accepted: 02/25/2016] [Indexed: 12/29/2022]
Abstract
Although representatives with spiral-shaped cells are described for many functional groups of bacteria, this cell morphotype has never been observed among methanotrophs. Here, we show that spiral-shaped methanotrophic bacteria do exist in nature but elude isolation by conventional approaches due to the preference for growth under micro-oxic conditions. The helical cell shape may enable rapid motility of these bacteria in water-saturated, heterogeneous environments with high microbial biofilm content, therefore offering an advantage of fast cell positioning under desired high methane/low oxygen conditions. The pmoA genes encoding a subunit of particulate methane monooxygenase from these methanotrophs form a new genus-level lineage within the family Methylococcaceae, type Ib methanotrophs. Application of a pmoA-based microarray detected these bacteria in a variety of high-latitude freshwater environments including wetlands and lake sediments. As revealed by the environmental pmoA distribution analysis, type Ib methanotrophs tend to live very near the methane source, where oxygen is scarce. The former perception of type Ib methanotrophs as being typical for thermal habitats appears to be incorrect because only a minor proportion of pmoA sequences from these bacteria originated from environments with elevated temperatures.
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Affiliation(s)
- Olga V Danilova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Natalia E Suzina
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | | | - Mette M Svenning
- UiT The Arctic University of Norway, Department of Arctic and Marine Biology, Tromsø, Norway
| | | | - Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
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247
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Larsen Ø, Karlsen OA. Transcriptomic profiling of Methylococcus capsulatus (Bath) during growth with two different methane monooxygenases. Microbiologyopen 2016; 5:254-67. [PMID: 26687591 PMCID: PMC4831470 DOI: 10.1002/mbo3.324] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 11/04/2015] [Accepted: 11/06/2015] [Indexed: 11/23/2022] Open
Abstract
Methylococcus capsulatus (Bath) is a methanotroph that possesses both a membrane-embedded (pMMO) and a soluble methane monooxygenase (sMMO). The expression of these two MMO's is tightly controlled by the availability of copper in the growth medium, but the underlying mechanisms and the number of genes involved in this switch in methane oxidation is not yet fully elucidated. Microarray analyses were used to assess the transcriptome in cells producing either pMMO or sMMO. A total of 137 genes were differentially expressed, with 87 genes showing a significant up-regulation during sMMO production. The majority of the differentially expressed genes could be assigned to functional roles in the energy metabolism and transport. Furthermore, three copper responding gene clusters were discovered, including an extended cluster that also harbors the genes for sMMO. Our data also indicates that major changes takes place in the respiratory chain between pMMO- and sMMO-producing cells, and that quinone are predominantly used as the electron donors for methane oxidation by pMMO. Intriguingly, a large proportion of the differentially expressed genes between pMMO- and sMMO-producing cells encode c-type cytochromes. By combining microarray- and mass spectrometry data, a total of 35 c-type cytochromes are apparently expressed in M. capsulatus when grown in nitrate mineral salt medium with methane as sole energy and carbon source, and the expression of 21 of these respond to the availability of copper. Interestingly, several of these c-type cytochromes are recovered from the cell surface, suggesting that extracellular electron transfers may occur in M. capsulatus.
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Affiliation(s)
- Øivind Larsen
- Uni Research EnvironmentThormøhlensgate 49bBergen5006Norway
| | - Odd A. Karlsen
- Department of Molecular BiologyUniversity of BergenBergenNorway
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248
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Wei XM, He R, Chen M, Su Y, Ma RC. Conversion of methane-derived carbon and microbial community in enrichment cultures in response to O2 availability. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:7517-7528. [PMID: 26728286 DOI: 10.1007/s11356-015-6017-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 12/22/2015] [Indexed: 06/05/2023]
Abstract
Methanotrophs not only play an important role in mitigating CH4 emissions from the environment, but also provide a large quantity of CH4-derived carbon to their habitats. In this study, the distribution of CH4-derived carbon and microbial community was investigated in a consortium enriched at three O2 tensions, i.e., the initial O2 concentrations of 2.5 % (LO-2), 5 % (LO-1), and 21 % (v/v) (HO). The results showed that compared with the O2-limiting environments (2.5 and 5 %), more CH4-derived carbon was converted into CO2 and biomass under the O2 sufficient condition (21 %). Besides biomass and CO2, a high conversion efficiency of CH4-derived carbon to dissolved organic carbon was detected in the cultures, especially in LO-2. Quantitative PCR and Miseq sequencing both showed that the abundance of methanotroph increased with the increasing O2 concentrations. Type II methanotroph Methylocystis dominated in the enrichment cultures, accounting for 54.8, 48.1, and 36.9 % of the total bacterial 16S rRNA gene sequencing reads in HO, LO-1, and LO-2, respectively. Methylotrophs, mainly including Methylophilus, Methylovorus, Hyphomicrobium, and Methylobacillus, were also abundant in the cultures. Compared with the O2 sufficient condition (21 %), higher microbial biodiversity (i.e., higher Simpson and lower Shannon indexes) was detected in LO-2 enriched at the initial O2 concentration of 2.5 %. These findings indicated that compared with the O2 sufficient condition, more CH4-derived carbon was exuded into the environments and promoted the growth of non-methanotrophic microbes in O2-limiting environments.
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Affiliation(s)
- Xiao-Meng Wei
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Ruo He
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China.
| | - Min Chen
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Yao Su
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Ruo-Chan Ma
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
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249
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XoxF Acts as the Predominant Methanol Dehydrogenase in the Type I Methanotroph Methylomicrobium buryatense. J Bacteriol 2016; 198:1317-25. [PMID: 26858104 DOI: 10.1128/jb.00959-15] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 02/04/2016] [Indexed: 01/13/2023] Open
Abstract
UNLABELLED Many methylotrophic taxa harbor two distinct methanol dehydrogenase (MDH) systems for oxidizing methanol to formaldehyde: the well-studied calcium-dependent MxaFI type and the more recently discovered lanthanide-containing XoxF type. MxaFI has traditionally been accepted as the major functional MDH in bacteria that contain both enzymes. However, in this study, we present evidence that, in a type I methanotroph, Methylomicrobium buryatense, XoxF is likely the primary functional MDH in the environment. The addition of lanthanides increases xoxF expression and greatly reduces mxa expression, even under conditions in which calcium concentrations are almost 100-fold higher than lanthanide concentrations. Mutations in genes encoding the MDH enzymes validate our finding that XoxF is the major functional MDH, as XoxF mutants grow more poorly than MxaFI mutants under unfavorable culturing conditions. In addition, mutant and transcriptional analyses demonstrate that the lanthanide-dependent MDH switch operating in methanotrophs is mediated in part by the orphan response regulator MxaB, whose gene transcription is itself lanthanide responsive. IMPORTANCE Aerobic methanotrophs, bacteria that oxidize methane for carbon and energy, require a methanol dehydrogenase enzyme to convert methanol into formaldehyde. The calcium-dependent enzyme MxaFI has been thought to primarily carry out methanol oxidation in methanotrophs. Recently, it was discovered that XoxF, a lanthanide-containing enzyme present in most methanotrophs, can also oxidize methanol. In a methanotroph with both MxaFI and XoxF, we demonstrate that lanthanides transcriptionally control genes encoding the two methanol dehydrogenases, in part by controlling expression of the response regulator MxaB. Lanthanides are abundant in the Earth's crust, and we demonstrate that micromolar amounts of lanthanides are sufficient to suppress MxaFI expression. Thus, we present evidence that XoxF acts as the predominant methanol dehydrogenase in a methanotroph.
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250
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Lanthanide-Dependent Regulation of Methanol Oxidation Systems in Methylobacterium extorquens AM1 and Their Contribution to Methanol Growth. J Bacteriol 2016; 198:1250-9. [PMID: 26833413 DOI: 10.1128/jb.00937-15] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 01/28/2016] [Indexed: 01/16/2023] Open
Abstract
UNLABELLED Methylobacterium extorquens AM1 has two distinct types of methanol dehydrogenase (MeDH) enzymes that catalyze the oxidation of methanol to formaldehyde. MxaFI-MeDH requires pyrroloquinoline quinone (PQQ) and Ca in its active site, while XoxF-MeDH requires PQQ and lanthanides, such as Ce and La. Using MeDH mutant strains to conduct growth analysis and MeDH activity assays, we demonstrate that M. extorquens AM1 has at least one additional lanthanide-dependent methanol oxidation system contributing to methanol growth. Additionally, the abilities of different lanthanides to support growth were tested and strongly suggest that both XoxF and the unknown methanol oxidation system are able to use La, Ce, Pr, Nd, and, to some extent, Sm. Further, growth analysis using increasing La concentrations showed that maximum growth rate and yield were achieved at and above 1 μM La, while concentrations as low as 2.5 nM allowed growth at a reduced rate. Contrary to published data, we show that addition of exogenous lanthanides results in differential expression from the xox1 and mxa promoters, upregulating genes in the xox1 operon and repressing genes in the mxa operon. Using transcriptional reporter fusions, intermediate expression from both the mxa and xox1 promoters was detected when 50 to 100 nM La was added to the growth medium, suggesting that a condition may exist under which M. extorquens AM1 is able to utilize both enzymes simultaneously. Together, these results suggest that M. extorquens AM1 actively senses and responds to lanthanide availability, preferentially utilizing the lanthanide-dependent MeDHs when possible. IMPORTANCE The biological role of lanthanides is a nascent field of study with tremendous potential to impact many areas in biology. Our studies demonstrate that there is at least one additional lanthanide-dependent methanol oxidation system, distinct from the MxaFI and XoxF MeDHs, that may aid in classifying additional environmental organisms as methylotrophs. Further, our data suggest that M. extorquens AM1 has a mechanism to regulate which MeDH is transcribed, depending on the presence or absence of lanthanides. While the mechanism controlling differential regulation is not yet understood, further research into how methylotrophs obtain and use lanthanides will facilitate their cultivation in the laboratory and their use as a biomining and biorecycling strategy for recovery of these commercially valuable rare-earth elements.
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