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Tan X, Lu Y, Nie WB, Xie GJ, Evans P, Wang XW, Dang CC, Zhao ZC, Fan SQ, Ren N. Evidence for Nitrous Oxide Emissions by Nitrite-Dependent Anaerobic Methane Oxidizing Bacteria. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:16862-16872. [PMID: 37873608 DOI: 10.1021/acs.est.3c02805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Nitrite-dependent anaerobic methane oxidizing (n-DAMO) bacteria generally convert nitrite to dinitrogen and bypass the nitrous oxide (N2O) formation step. However, N2O is often detected in n-DAMO bacteria dominated cultures and it remains an open question as to the microbial origin of N2O in these enrichments. Using a stable nitrite consuming microbial community enriched for n-DAMO bacteria, we demonstrated that N2O production was coupled to methane oxidation and the higher initial nitrite concentrations led to increased quantities of N2O being formed. Moreover, continuous exposure of the enrichment culture to about 5 mg of N L-1 nitrite resulted in constant N2O being produced (12.5% of nitrite was reduced to N2O). Metatranscriptomic analyses revealed that nitrite reductase (nirS) and nitric oxide reductase (norZ) transcripts from n-DAMO bacteria increased in response to nitrite exposure. No other bacteria significantly expressed nor genes under these conditions, suggesting n-DAMO bacteria are responsible for N2O being produced. In a 35-day bioreactor experiment, N2O produced by the n-DAMO bacteria accumulated when nitrite was in excess; this was found to be up to 3.2% of the nitrogen that resulted from nitrite removal. Together, these results suggested that excess nitrite is an important driver of N2O production by n-DAMO bacteria. To this end, proper monitoring and control of nitrite levels in wastewater treatment plants would be effective strategies for mitigating N2O emissions to the atmosphere.
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Affiliation(s)
- Xin Tan
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yang Lu
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Wen-Bo Nie
- Key Laboratory of the Three Gorges Region's Eco-Environment, Ministry of Education, College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Guo-Jun Xie
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Paul Evans
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Xiao-Wei Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Cheng-Cheng Dang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Zhi-Cheng Zhao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Sheng-Qiang Fan
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
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Baublitz CB, Fiore AM, Ludwig SM, Nicely JM, Wolfe GM, Murray LT, Commane R, Prather MJ, Anderson DC, Correa G, Duncan BN, Follette-Cook M, Westervelt DM, Bourgeois I, Brune WH, Bui TP, DiGangi JP, Diskin GS, Hall SR, McKain K, Miller DO, Peischl J, Thames AB, Thompson CR, Ullmann K, Wofsy SC. An observation-based, reduced-form model for oxidation in the remote marine troposphere. Proc Natl Acad Sci U S A 2023; 120:e2209735120. [PMID: 37579162 PMCID: PMC10451388 DOI: 10.1073/pnas.2209735120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 06/26/2023] [Indexed: 08/16/2023] Open
Abstract
The hydroxyl radical (OH) fuels atmospheric chemical cycling as the main sink for methane and a driver of the formation and loss of many air pollutants, but direct OH observations are sparse. We develop and evaluate an observation-based proxy for short-term, spatial variations in OH (ProxyOH) in the remote marine troposphere using comprehensive measurements from the NASA Atmospheric Tomography (ATom) airborne campaign. ProxyOH is a reduced form of the OH steady-state equation representing the dominant OH production and loss pathways in the remote marine troposphere, according to box model simulations of OH constrained with ATom observations. ProxyOH comprises only eight variables that are generally observed by routine ground- or satellite-based instruments. ProxyOH scales linearly with in situ [OH] spatial variations along the ATom flight tracks (median r2 = 0.90, interquartile range = 0.80 to 0.94 across 2-km altitude by 20° latitudinal regions). We deconstruct spatial variations in ProxyOH as a first-order approximation of the sensitivity of OH variations to individual terms. Two terms modulate within-region ProxyOH variations-water vapor (H2O) and, to a lesser extent, nitric oxide (NO). This implies that a limited set of observations could offer an avenue for observation-based mapping of OH spatial variations over much of the remote marine troposphere. Both H2O and NO are expected to change with climate, while NO also varies strongly with human activities. We also illustrate the utility of ProxyOH as a process-based approach for evaluating intermodel differences in remote marine tropospheric OH.
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Affiliation(s)
- Colleen B. Baublitz
- Department of Earth and Environmental Sciences, Columbia University, New York, NY10027
- Division of Ocean and Climate Physics, Lamont-Doherty Earth Observatory of Columbia University, Palisades, NY10964
| | - Arlene M. Fiore
- Department of Earth and Environmental Sciences, Columbia University, New York, NY10027
- Division of Ocean and Climate Physics, Lamont-Doherty Earth Observatory of Columbia University, Palisades, NY10964
| | - Sarah M. Ludwig
- Department of Earth and Environmental Sciences, Columbia University, New York, NY10027
- Division of Ocean and Climate Physics, Lamont-Doherty Earth Observatory of Columbia University, Palisades, NY10964
| | - Julie M. Nicely
- Earth System Science Interdisciplinary Center, University of Maryland, College Park, MD20740
- Atmospheric Chemistry and Dynamics Laboratory, National Aeronautics and Space Administration Goddard Space Flight Center, Greenbelt, MD20771
| | - Glenn M. Wolfe
- Atmospheric Chemistry and Dynamics Laboratory, National Aeronautics and Space Administration Goddard Space Flight Center, Greenbelt, MD20771
| | - Lee T. Murray
- Department of Earth and Environmental Sciences, University of Rochester, Rochester, NY14627
| | - Róisín Commane
- Department of Earth and Environmental Sciences, Columbia University, New York, NY10027
- Division of Ocean and Climate Physics, Lamont-Doherty Earth Observatory of Columbia University, Palisades, NY10964
| | - Michael J. Prather
- Department of Earth System Science, University of California, Irvine, CA92697
| | - Daniel C. Anderson
- Atmospheric Chemistry and Dynamics Laboratory, National Aeronautics and Space Administration Goddard Space Flight Center, Greenbelt, MD20771
- Goddard Earth Sciences Technology and Research II, University of Maryland Baltimore County, Baltimore, MD21250
| | - Gustavo Correa
- Division of Ocean and Climate Physics, Lamont-Doherty Earth Observatory of Columbia University, Palisades, NY10964
| | - Bryan N. Duncan
- Atmospheric Chemistry and Dynamics Laboratory, National Aeronautics and Space Administration Goddard Space Flight Center, Greenbelt, MD20771
| | - Melanie Follette-Cook
- Atmospheric Chemistry and Dynamics Laboratory, National Aeronautics and Space Administration Goddard Space Flight Center, Greenbelt, MD20771
- Goddard Earth Sciences Technology and Research II, Morgan State University, Baltimore, MD21251
| | - Daniel M. Westervelt
- Division of Ocean and Climate Physics, Lamont-Doherty Earth Observatory of Columbia University, Palisades, NY10964
- National Aeronautics and Space Administration Goddard Institute for Space Studies, New York, NY10025
| | - Ilann Bourgeois
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO80309
- National Oceanic and Atmospheric Administration Chemical Sciences Laboratory, Boulder, CO80305
| | - William H. Brune
- Department of Meteorology and Atmospheric Science, Pennsylvania State University, University Park, PA16802
| | - T. Paul Bui
- Atmospheric Science Branch, National Aeronautics and Space Administration Ames Research Center, Moffett Field, CA94035
| | - Joshua P. DiGangi
- National Aeronautics and Space Administration Langley Research Center, Hampton, VA23666
| | - Glenn S. Diskin
- National Aeronautics and Space Administration Langley Research Center, Hampton, VA23666
| | - Samuel R. Hall
- Atmospheric Chemistry Observations & Modeling Laboratory, National Center for Atmospheric Research, Boulder, CO80307
| | - Kathryn McKain
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO80309
- National Oceanic and Atmospheric Administration Global Monitoring Laboratory, Boulder, CO80305
| | - David O. Miller
- Department of Meteorology and Atmospheric Science, Pennsylvania State University, University Park, PA16802
| | - Jeff Peischl
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO80309
- National Oceanic and Atmospheric Administration Chemical Sciences Laboratory, Boulder, CO80305
| | - Alexander B. Thames
- Department of Meteorology and Atmospheric Science, Pennsylvania State University, University Park, PA16802
| | - Chelsea R. Thompson
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO80309
- National Oceanic and Atmospheric Administration Chemical Sciences Laboratory, Boulder, CO80305
| | - Kirk Ullmann
- Atmospheric Chemistry Observations & Modeling Laboratory, National Center for Atmospheric Research, Boulder, CO80307
| | - Steven C. Wofsy
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA02138
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3
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Guo K, Glatter T, Paczia N, Liesack W. Asparagine Uptake: a Cellular Strategy of Methylocystis to Combat Severe Salt Stress. Appl Environ Microbiol 2023; 89:e0011323. [PMID: 37184406 PMCID: PMC10305061 DOI: 10.1128/aem.00113-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/17/2023] [Indexed: 05/16/2023] Open
Abstract
Methylocystis spp. are known to have a low salt tolerance (≤1.0% NaCl). Therefore, we tested various amino acids and other well-known osmolytes for their potential to act as an osmoprotectant under otherwise growth-inhibiting NaCl conditions. Adjustment of the medium to 10 mM asparagine had the greatest osmoprotective effect under severe salinity (1.50% NaCl), leading to partial growth recovery of strain SC2. The intracellular concentration of asparagine increased to 264 ± 57 mM, with a certain portion hydrolyzed to aspartate (4.20 ± 1.41 mM). In addition to general and oxidative stress responses, the uptake of asparagine specifically induced major proteome rearrangements related to the KEGG level 3 categories of "methane metabolism," "pyruvate metabolism," "amino acid turnover," and "cell division." In particular, various proteins involved in cell division (e.g., ChpT, CtrA, PleC, FtsA, FtsH1) and peptidoglycan synthesis showed a positive expression response. Asparagine-derived 13C-carbon was incorporated into nearly all amino acids. Both the exometabolome and the 13C-labeling pattern suggest that in addition to aspartate, the amino acids glutamate, glycine, serine, and alanine, but also pyruvate and malate, were most crucially involved in the osmoprotective effect of asparagine, with glutamate being a major hub between the central carbon and amino acid pathways. In summary, asparagine induced significant proteome rearrangements, leading to major changes in central metabolic pathway activity and the sizes of free amino acid pools. In consequence, asparagine acted, in part, as a carbon source for the growth recovery of strain SC2 under severe salinity. IMPORTANCE Methylocystis spp. play a major role in reducing methane emissions into the atmosphere from methanogenic wetlands. In addition, they contribute to atmospheric methane oxidation in upland soils. Although these bacteria are typical soil inhabitants, Methylocystis spp. are thought to have limited capacity to acclimate to salt stress. This called for a thorough study into potential osmoprotectants, which revealed asparagine as the most promising candidate. Intriguingly, asparagine was taken up quantitatively and acted, at least in part, as an intracellular carbon source under severe salt stress. The effect of asparagine as an osmoprotectant for Methylocystis spp. is an unexpected finding. It may provide Methylocystis spp. with an ecological advantage in wetlands, where these methanotrophs colonize the roots of submerged vascular plants. Collectively, our study offers a new avenue into research on compounds that may increase the resilience of Methylocystis spp. to environmental change.
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Affiliation(s)
- Kangli Guo
- Methanotrophic Bacteria and Environmental Genomics/Transcriptomics Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Timo Glatter
- Core Facility for Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Nicole Paczia
- Core Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Werner Liesack
- Methanotrophic Bacteria and Environmental Genomics/Transcriptomics Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
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4
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Zhu HZ, Jiang CY, Liu SJ. Microbial roles in cave biogeochemical cycling. Front Microbiol 2022; 13:950005. [PMID: 36246268 PMCID: PMC9554484 DOI: 10.3389/fmicb.2022.950005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 09/14/2022] [Indexed: 11/23/2022] Open
Abstract
Among fundamental research questions in subterranean biology, the role of subterranean microbiomes playing in key elements cycling is a top-priority one. Karst caves are widely distributed subsurface ecosystems, and cave microbes get more and more attention as they could drive cave evolution and biogeochemical cycling. Research have demonstrated the existence of diverse microbes and their participance in biogeochemical cycling of elements in cave environments. However, there are still gaps in how these microbes sustain in caves with limited nutrients and interact with cave environment. Cultivation of novel cave bacteria with certain functions is still a challenging assignment. This review summarized the role of microbes in cave evolution and mineral deposition, and intended to inspire further exploration of microbial performances on C/N/S biogeocycles.
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Affiliation(s)
- Hai-Zhen Zhu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- *Correspondence: Shuang-Jiang Liu,
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5
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Belova SE, Danilova OV, Ivanova AA, Merkel AY, Dedysh SN. Methane-Oxidizing Communities in Lichen-Dominated Forested Tundra Are Composed Exclusively of High-Affinity USCα Methanotrophs. Microorganisms 2020; 8:microorganisms8122047. [PMID: 33371270 PMCID: PMC7766663 DOI: 10.3390/microorganisms8122047] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 01/04/2023] Open
Abstract
Upland soils of tundra function as a constant sink for atmospheric CH4 but the identity of methane oxidizers in these soils remains poorly understood. Methane uptake rates of -0.4 to -0.6 mg CH4-C m-2 day-1 were determined by the static chamber method in a mildly acidic upland soil of the lichen-dominated forested tundra, North Siberia, Russia. The maximal CH4 oxidation activity was localized in an organic surface soil layer underlying the lichen cover. Molecular identification of methanotrophic bacteria based on retrieval of the pmoA gene revealed Upland Soil Cluster Alpha (USCα) as the only detectable methanotroph group. Quantification of these pmoA gene fragments by means of specific qPCR assay detected ~107pmoA gene copies g-1 dry soil. The pmoA diversity was represented by seven closely related phylotypes; the most abundant phylotype displayed 97.5% identity to pmoA of Candidatus Methyloaffinis lahnbergensis. Further analysis of prokaryote diversity in this soil did not reveal 16S rRNA gene fragments from well-studied methanotrophs of the order Methylococcales and the family Methylocystaceae. The largest group of reads (~4% of all bacterial 16S rRNA gene fragments) that could potentially belong to methanotrophs was classified as uncultivated Beijerinckiaceae bacteria. These reads displayed 96-100 and 95-98% sequence similarity to 16S rRNA gene of Candidatus Methyloaffinis lahnbergensis and "Methylocapsa gorgona" MG08, respectively, and were represented by eight species-level operational taxonomic units (OTUs), two of which were highly abundant. These identification results characterize subarctic upland soils, which are exposed to atmospheric methane concentrations only, as a unique habitat colonized mostly by USCα methanotrophs.
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6
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Gaubert B, Emmons LK, Raeder K, Tilmes S, Miyazaki K, Arellano AF, Elguindi N, Granier C, Tang W, Barré J, Worden HM, Buchholz RR, Edwards DP, Franke P, Anderson JL, Saunois M, Schroeder J, Woo JH, Simpson IJ, Blake DR, Meinardi S, Wennberg PO, Crounse J, Teng A, Kim M, Dickerson RR, He H, Ren X, Pusede SE, Diskin GS. Correcting model biases of CO in East Asia: impact on oxidant distributions during KORUS-AQ. ATMOSPHERIC CHEMISTRY AND PHYSICS 2020; 20:14617-14647. [PMID: 33414818 PMCID: PMC7786812 DOI: 10.5194/acp-20-14617-2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Global coupled chemistry-climate models underestimate carbon monoxide (CO) in the Northern Hemisphere, exhibiting a pervasive negative bias against measurements peaking in late winter and early spring. While this bias has been commonly attributed to underestimation of direct anthropogenic and biomass burning emissions, chemical production and loss via OH reaction from emissions of anthropogenic and biogenic volatile organic compounds (VOCs) play an important role. Here we investigate the reasons for this underestimation using aircraft measurements taken in May and June 2016 from the Korea-United States Air Quality (KORUS-AQ) experiment in South Korea and the Air Chemistry Research in Asia (ARIAs) in the North China Plain (NCP). For reference, multispectral CO retrievals (V8J) from the Measurements of Pollution in the Troposphere (MOPITT) are jointly assimilated with meteorological observations using an ensemble adjustment Kalman filter (EAKF) within the global Community Atmosphere Model with Chemistry (CAM-Chem) and the Data Assimilation Research Testbed (DART). With regard to KORUS-AQ data, CO is underestimated by 42% in the control run and by 12% with the MOPITT assimilation run. The inversion suggests an underestimation of anthropogenic CO sources in many regions, by up to 80% for northern China, with large increments over the Liaoning Province and the North China Plain (NCP). Yet, an often-overlooked aspect of these inversions is that correcting the underestimation in anthropogenic CO emissions also improves the comparison with observational O3 datasets and observationally constrained box model simulations of OH and HO2. Running a CAM-Chem simulation with the updated emissions of anthropogenic CO reduces the bias by 29% for CO, 18% for ozone, 11% for HO2, and 27% for OH. Longer-lived anthropogenic VOCs whose model errors are correlated with CO are also improved, while short-lived VOCs, including formaldehyde, are difficult to constrain solely by assimilating satellite retrievals of CO. During an anticyclonic episode, better simulation of O3, with an average underestimation of 5.5 ppbv, and a reduction in the bias of surface formaldehyde and oxygenated VOCs can be achieved by separately increasing by a factor of 2 the modeled biogenic emissions for the plant functional types found in Korea. Results also suggest that controlling VOC and CO emissions, in addition to widespread NO x controls, can improve ozone pollution over East Asia.
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Affiliation(s)
- Benjamin Gaubert
- Atmospheric Chemistry Observations and Modeling, National Center for Atmospheric Research, Boulder, CO, USA
| | - Louisa K. Emmons
- Atmospheric Chemistry Observations and Modeling, National Center for Atmospheric Research, Boulder, CO, USA
| | - Kevin Raeder
- Computational and Information Systems Laboratory, National Center for Atmospheric Research, Boulder, CO, USA
| | - Simone Tilmes
- Atmospheric Chemistry Observations and Modeling, National Center for Atmospheric Research, Boulder, CO, USA
| | - Kazuyuki Miyazaki
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Avelino F. Arellano
- Dept. of Hydrology and Atmospheric Sciences, University of Arizona, Tucson, AZ, USA
| | - Nellie Elguindi
- Laboratoire d’Aérologie, CNRS, Université de Toulouse, Toulouse, France
| | - Claire Granier
- Laboratoire d’Aérologie, CNRS, Université de Toulouse, Toulouse, France
- NOAA Chemical Sciences Laboratory-CIRES/University of Colorado, Boulder, CO, USA
| | - Wenfu Tang
- Advanced Study Program, National Center for Atmospheric Research, Boulder, CO, USA
| | - Jérôme Barré
- European Centre for Medium-Range Weather Forecasts, Shinfield Park, Reading, RG2 9AX, UK
| | - Helen M. Worden
- Atmospheric Chemistry Observations and Modeling, National Center for Atmospheric Research, Boulder, CO, USA
| | - Rebecca R. Buchholz
- Atmospheric Chemistry Observations and Modeling, National Center for Atmospheric Research, Boulder, CO, USA
| | - David P. Edwards
- Atmospheric Chemistry Observations and Modeling, National Center for Atmospheric Research, Boulder, CO, USA
| | - Philipp Franke
- Forschungszentrum Jülich GmbH, Institut für Energie und Klimaforschung IEK-8, 52425 Jülich, Germany
| | - Jeffrey L. Anderson
- Computational and Information Systems Laboratory, National Center for Atmospheric Research, Boulder, CO, USA
| | - Marielle Saunois
- Laboratoire des Sciences du Climat et de l’Environnement, LSCE-IPSL (CEA-CNRS-UVSQ), Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | | | - Jung-Hun Woo
- Department of Advanced Technology Fusion, Konkuk University, Seoul, South Korea
| | - Isobel J. Simpson
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Donald R. Blake
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Simone Meinardi
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | | | - John Crounse
- California Institute of Technology, Pasadena, CA, USA
| | - Alex Teng
- California Institute of Technology, Pasadena, CA, USA
| | - Michelle Kim
- California Institute of Technology, Pasadena, CA, USA
| | - Russell R. Dickerson
- Department of Atmospheric and Oceanic Science, University of Maryland, College Park, MD, USA
- Earth System Science Interdisciplinary Center, University of Maryland, College Park, MD, USA
| | - Hao He
- Department of Atmospheric and Oceanic Science, University of Maryland, College Park, MD, USA
- Earth System Science Interdisciplinary Center, University of Maryland, College Park, MD, USA
| | - Xinrong Ren
- Department of Atmospheric and Oceanic Science, University of Maryland, College Park, MD, USA
- Air Resources Laboratory, National Oceanic and Atmospheric Administration, College Park, MD, USA
| | - Sally E. Pusede
- Department of Environmental Sciences, University of Virginia, Charlottesville, VA, USA
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7
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Zhang G, Xiao X, Dong J, Xin F, Zhang Y, Qin Y, Doughty RB, Moore B. Fingerprint of rice paddies in spatial-temporal dynamics of atmospheric methane concentration in monsoon Asia. Nat Commun 2020; 11:554. [PMID: 31992693 PMCID: PMC6987195 DOI: 10.1038/s41467-019-14155-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/16/2019] [Indexed: 11/29/2022] Open
Abstract
Agriculture (e.g., rice paddies) has been considered one of the main emission sources responsible for the sudden rise of atmospheric methane concentration (XCH4) since 2007, but remains debated. Here we use satellite-based rice paddy and XCH4 data to investigate the spatial–temporal relationships between rice paddy area, rice plant growth, and XCH4 in monsoon Asia, which accounts for ~87% of the global rice area. We find strong spatial consistencies between rice paddy area and XCH4 and seasonal consistencies between rice plant growth and XCH4. Our results also show a decreasing trend in rice paddy area in monsoon Asia since 2007, which suggests that the change in rice paddy area could not be one of the major drivers for the renewed XCH4 growth, thus other sources and sinks should be further investigated. Our findings highlight the importance of satellite-based paddy rice datasets in understanding the spatial–temporal dynamics of XCH4 in monsoon Asia. The role of paddy rice agriculture in the spatial and temporal dynamics of atmospheric methane concentration remains unclear. Here, Zhang et al. show that regions with dense rice paddies have high satellite-based column averaged CH4 concentrations (XCH4), and that seasonal dynamics of XCH4 mirror those of paddy rice growth.
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Affiliation(s)
- Geli Zhang
- College of Land Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xiangming Xiao
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.
| | - Jinwei Dong
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Fengfei Xin
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, 200433, China
| | - Yao Zhang
- Department of Earth and Environmental Engineering, Columbia University, New York, NY, 10027, USA
| | - Yuanwei Qin
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Russell B Doughty
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Berrien Moore
- College of Atmospheric and Geographic Sciences, University of Oklahoma, Norman, OK, 73019, USA
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8
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Tveit AT, Hestnes AG, Robinson SL, Schintlmeister A, Dedysh SN, Jehmlich N, von Bergen M, Herbold C, Wagner M, Richter A, Svenning MM. Widespread soil bacterium that oxidizes atmospheric methane. Proc Natl Acad Sci U S A 2019; 116:8515-8524. [PMID: 30962365 PMCID: PMC6486757 DOI: 10.1073/pnas.1817812116] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The global atmospheric level of methane (CH4), the second most important greenhouse gas, is currently increasing by ∼10 million tons per year. Microbial oxidation in unsaturated soils is the only known biological process that removes CH4 from the atmosphere, but so far, bacteria that can grow on atmospheric CH4 have eluded all cultivation efforts. In this study, we have isolated a pure culture of a bacterium, strain MG08 that grows on air at atmospheric concentrations of CH4 [1.86 parts per million volume (p.p.m.v.)]. This organism, named Methylocapsa gorgona, is globally distributed in soils and closely related to uncultured members of the upland soil cluster α. CH4 oxidation experiments and 13C-single cell isotope analyses demonstrated that it oxidizes atmospheric CH4 aerobically and assimilates carbon from both CH4 and CO2 Its estimated specific affinity for CH4 (a0s) is the highest for any cultivated methanotroph. However, growth on ambient air was also confirmed for Methylocapsa acidiphila and Methylocapsa aurea, close relatives with a lower specific affinity for CH4, suggesting that the ability to utilize atmospheric CH4 for growth is more widespread than previously believed. The closed genome of M. gorgona MG08 encodes a single particulate methane monooxygenase, the serine cycle for assimilation of carbon from CH4 and CO2, and CO2 fixation via the recently postulated reductive glycine pathway. It also fixes dinitrogen and expresses the genes for a high-affinity hydrogenase and carbon monoxide dehydrogenase, suggesting that atmospheric CH4 oxidizers harvest additional energy from oxidation of the atmospheric trace gases carbon monoxide (0.2 p.p.m.v.) and hydrogen (0.5 p.p.m.v.).
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Affiliation(s)
- Alexander T Tveit
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, 9037 Tromsoe, Norway
| | - Anne Grethe Hestnes
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, 9037 Tromsoe, Norway
| | - Serina L Robinson
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, 9037 Tromsoe, Norway
| | - Arno Schintlmeister
- Center of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
| | - Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of Russian Academy of Sciences, 117312 Moscow, Russia
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany
- Faculty of Life Sciences, Institute of Biochemistry, University of Leipzig, 04109 Leipzig, Germany
| | - Craig Herbold
- Center of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
| | - Michael Wagner
- Center of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
| | - Andreas Richter
- Center of Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem Research, University of Vienna, 1090 Vienna, Austria
| | - Mette M Svenning
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, 9037 Tromsoe, Norway;
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9
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Sulzberger B, Austin AT, Cory RM, Zepp RG, Paul ND. Solar UV radiation in a changing world: roles of cryosphere-land-water-atmosphere interfaces in global biogeochemical cycles. Photochem Photobiol Sci 2019; 18:747-774. [PMID: 30810562 PMCID: PMC7418111 DOI: 10.1039/c8pp90063a] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 12/19/2018] [Indexed: 12/29/2022]
Abstract
Global change influences biogeochemical cycles within and between environmental compartments (i.e., the cryosphere, terrestrial and aquatic ecosystems, and the atmosphere). A major effect of global change on carbon cycling is altered exposure of natural organic matter (NOM) to solar radiation, particularly solar UV radiation. In terrestrial and aquatic ecosystems, NOM is degraded by UV and visible radiation, resulting in the emission of carbon dioxide (CO2) and carbon monoxide, as well as a range of products that can be more easily degraded by microbes (photofacilitation). On land, droughts and land-use change can reduce plant cover causing an increase in exposure of plant litter to solar radiation. The altered transport of soil organic matter from terrestrial to aquatic ecosystems also can enhance exposure of NOM to solar radiation. An increase in emission of CO2 from terrestrial and aquatic ecosystems due to the effects of global warming, such as droughts and thawing of permafrost soils, fuels a positive feedback on global warming. This is also the case for greenhouse gases other than CO2, including methane and nitrous oxide, that are emitted from terrestrial and aquatic ecosystems. These trace gases also have indirect or direct impacts on stratospheric ozone concentrations. The interactive effects of UV radiation and climate change greatly alter the fate of synthetic and biological contaminants. Contaminants are degraded or inactivated by direct and indirect photochemical reactions. The balance between direct and indirect photodegradation or photoinactivation of contaminants is likely to change with future changes in stratospheric ozone, and with changes in runoff of coloured dissolved organic matter due to climate and land-use changes.
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Affiliation(s)
- B Sulzberger
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland.
| | - A T Austin
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Agronomía, Universidad de Buenos Aires en las afiliations, Buenos Aires, Argentina
| | - R M Cory
- University of Michigan, Earth & Environmental Science, Ann Arbor, Michigan, USA
| | - R G Zepp
- United States Environmental Protection Agency, Athens, Georgia, USA
| | - N D Paul
- Lancaster Environment Centre, Lancaster University, LA1 4YQ, UK
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10
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Wilson SR, Madronich S, Longstreth JD, Solomon KR. Interactive effects of changing stratospheric ozone and climate on tropospheric composition and air quality, and the consequences for human and ecosystem health. Photochem Photobiol Sci 2019; 18:775-803. [PMID: 30810564 DOI: 10.1039/c8pp90064g] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The composition of the air we breathe is determined by emissions, weather, and photochemical transformations induced by solar UV radiation. Photochemical reactions of many emitted chemical compounds can generate important (secondary) pollutants including ground-level ozone (O3) and some particulate matter, known to be detrimental to human health and ecosystems. Poor air quality is the major environmental cause of premature deaths globally, and even a small decrease in air quality can translate into a large increase in the number of deaths. In many regions of the globe, changes in emissions of pollutants have caused significant changes in air quality. Short-term variability in the weather as well as long-term climatic trends can affect ground-level pollution through several mechanisms. These include large-scale changes in the transport of O3 from the stratosphere to the troposphere, winds, clouds, and patterns of precipitation. Long-term trends in UV radiation, particularly related to the depletion and recovery of stratospheric ozone, are also expected to result in changes in air quality as well as the self-cleaning capacity of the global atmosphere. The increased use of substitutes for ozone-depleting substances, in response to the Montreal Protocol, does not currently pose a significant risk to the environment. This includes both the direct emissions of substitutes during use and their atmospheric degradation products (e.g. trifluoroacetic acid, TFA).
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Affiliation(s)
- S R Wilson
- Centre for Atmospheric Chemistry, School of Earth, Atmosphere and Life Sciences, University of Wollongong, NSW, Australia.
| | - S Madronich
- National Center for Atmospheric Research, Boulder, CO, USA
| | - J D Longstreth
- The Institute for Global Risk Research, LLC, Bethesda, MD, USA and Emergent BioSolutions, Gaithersburg, MD, USA
| | - K R Solomon
- Centre for Toxicology and School of Environmental Sciences, University of Guelph, ON, Canada
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11
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Turner AJ, Frankenberg C, Kort EA. Interpreting contemporary trends in atmospheric methane. Proc Natl Acad Sci U S A 2019; 116:2805-2813. [PMID: 30733299 PMCID: PMC6386658 DOI: 10.1073/pnas.1814297116] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Atmospheric methane plays a major role in controlling climate, yet contemporary methane trends (1982-2017) have defied explanation with numerous, often conflicting, hypotheses proposed in the literature. Specifically, atmospheric observations of methane from 1982 to 2017 have exhibited periods of both increasing concentrations (from 1982 to 2000 and from 2007 to 2017) and stabilization (from 2000 to 2007). Explanations for the increases and stabilization have invoked changes in tropical wetlands, livestock, fossil fuels, biomass burning, and the methane sink. Contradictions in these hypotheses arise because our current observational network cannot unambiguously link recent methane variations to specific sources. This raises some fundamental questions: (i) What do we know about sources, sinks, and underlying processes driving observed trends in atmospheric methane? (ii) How will global methane respond to changes in anthropogenic emissions? And (iii), What future observations could help resolve changes in the methane budget? To address these questions, we discuss potential drivers of atmospheric methane abundances over the last four decades in light of various observational constraints as well as process-based knowledge. While uncertainties in the methane budget exist, they should not detract from the potential of methane emissions mitigation strategies. We show that net-zero cost emission reductions can lead to a declining atmospheric burden, but can take three decades to stabilize. Moving forward, we make recommendations for observations to better constrain contemporary trends in atmospheric methane and to provide mitigation support.
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Affiliation(s)
- Alexander J Turner
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720;
| | - Christian Frankenberg
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91226;
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109
| | - Eric A Kort
- Climate and Space Sciences and Engineering, University of Michigan, Ann Arbor, MI 48109
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12
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Schimmelmann A, Fernandez-Cortes A, Cuezva S, Streil T, Lennon JT. Radiolysis via radioactivity is not responsible for rapid methane oxidation in subterranean air. PLoS One 2018; 13:e0206506. [PMID: 30383783 PMCID: PMC6211692 DOI: 10.1371/journal.pone.0206506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 10/15/2018] [Indexed: 11/18/2022] Open
Abstract
Atmospheric methane is rapidly lost when it enters humid subterranean critical and vadose zones (e.g., air in soils and caves). Because methane is a source of carbon and energy, it can be consumed by methanotrophic methane-oxidizing bacteria. As an additional subterranean sink, it has been hypothesized that methane is oxidized by natural radioactivity-induced radiolysis that produces energetic ions and radicals, which then trigger abiotic oxidation and consumption of methane within a few hours. Using controlled laboratory experiments, we tested whether radiolysis could rapidly oxidize methane in sealed air with different relative humidities while being exposed to elevated levels of radiation (more than 535 kBq m-3) from radon isotopes 222Rn and 220Rn (i.e., thoron). We found no evidence that radiolysis contributed to methane oxidation. In contrast, we observed the rapid loss of methane when moist soil was added to the same apparatus in the absence of elevated radon abundance. Together, our findings are consistent with the view that methane oxidizing bacteria are responsible for the widespread observations of methane depletion in subterranean environments. Further studies are needed on the ability of microbes to consume trace amounts of methane in poorly ventilated caves, even though the trophic and energetic benefits become marginal at very low partial pressures of methane.
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Affiliation(s)
- Arndt Schimmelmann
- Department of Earth and Atmospheric Sciences, Indiana University, Bloomington, Indiana, United States of America
- * E-mail:
| | - Angel Fernandez-Cortes
- Department of Biology and Geology, University of Almeria, Almeria, Spain
- Department of Earth Sciences, Royal Holloway, University of London, Egham, Surrey, United Kingdom
| | - Soledad Cuezva
- Department of Biology and Geology, University of Almeria, Almeria, Spain
| | | | - Jay T. Lennon
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
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