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Michaud AB, Massé RO, Emerson D. Microbial iron cycling is prevalent in water-logged Alaskan Arctic tundra habitats, but sensitive to disturbance. FEMS Microbiol Ecol 2023; 99:7022315. [PMID: 36725207 DOI: 10.1093/femsec/fiad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/23/2023] [Accepted: 01/31/2023] [Indexed: 02/03/2023] Open
Abstract
Water logged habitats in continuous permafrost regions provide extensive oxic-anoxic interface habitats for iron cycling. The iron cycle interacts with the methane and phosphorus cycles, and is an important part of tundra biogeochemistry. Our objective was to characterize microbial communities associated with the iron cycle within natural and disturbed habitats of the Alaskan Arctic tundra. We sampled aquatic habitats within natural, undisturbed and anthropogenically disturbed areas and sequenced the 16S rRNA gene to describe the microbial communities, then supported these results with process rate and geochemical measurements. Undisturbed habitats have microbial communities that are significantly different than disturbed habitats. Microbial taxa known to participate in the iron and methane cycles are significantly associated with natural habitats, whereas they are not significantly associated with disturbed sites. Undisturbed habitats have significantly higher extractable iron and are more acidic than disturbed habitats sampled. Iron reduction is not measurable in disturbed aquatic habitats and is not stimulated by the addition of biogenic iron mats. Our study highlights the prevalence of Fe-cycling in undisturbed water-logged habitats, and demonstrates that anthropogenic disturbance of the tundra, due to legacy gravel mining, alters the microbiology of aquatic habitats and disrupts important biogeochemical cycles in the Arctic tundra.
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Affiliation(s)
- Alexander B Michaud
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544, United States
| | - Rémi O Massé
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544, United States
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544, United States
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Abstract
Methane (CH4) emissions from estuarine wetlands were proved to be influenced by tide movement and inundation conditions notably in many previous studies. Although there have been several researches focusing on the seasonal or annual CH4 emissions, the short-term CH4 emissions during the tide cycles were rarely studied up to now in this area. In order to investigate the CH4 emission pattern during a tide cycle in Yangtze Estuary salt marshes, frequent fixed-point observations of methane flux were carried out using the in-situ static closed chamber technique. The results indicated that the daily average CH4 fluxes varied from 0.68 mgCH4·m−2·h−1 to 4.22 mgCH4·m−2·h−1 with the average flux reaching 1.78 mgCH4·m−2·h−1 from small tide to spring tide in summer. CH4 fluxes did not show consistent variation with both tide levels and inundation time but increased steadily during almost the whole research period. By Pearson correlation analysis, CH4 fluxes were not correlated with both tide levels (R = −0.014, p = 0.979) and solar radiation (R = 0.024, p = 0.865), but significantly correlated with ambient temperature. It is temperature rather than the tide level mainly controlling CH4 emissions during the tide cycles. Besides, CH4 fluxes also showed no significant correlation with the underground pore-water CH4 concentrations, indicating that plant-mediated transport played a more important role in CH4 fluxes compared with its production and consumption.
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Edwards A, Cameron KA, Cook JM, Debbonaire AR, Furness E, Hay MC, Rassner SM. Microbial genomics amidst the Arctic crisis. Microb Genom 2020; 6:e000375. [PMID: 32392124 PMCID: PMC7371112 DOI: 10.1099/mgen.0.000375] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/16/2020] [Indexed: 12/16/2022] Open
Abstract
The Arctic is warming - fast. Microbes in the Arctic play pivotal roles in feedbacks that magnify the impacts of Arctic change. Understanding the genome evolution, diversity and dynamics of Arctic microbes can provide insights relevant for both fundamental microbiology and interdisciplinary Arctic science. Within this synthesis, we highlight four key areas where genomic insights to the microbial dimensions of Arctic change are urgently required: the changing Arctic Ocean, greenhouse gas release from the thawing permafrost, 'biological darkening' of glacial surfaces, and human activities within the Arctic. Furthermore, we identify four principal challenges that provide opportunities for timely innovation in Arctic microbial genomics. These range from insufficient genomic data to develop unifying concepts or model organisms for Arctic microbiology to challenges in gaining authentic insights to the structure and function of low-biomass microbiota and integration of data on the causes and consequences of microbial feedbacks across scales. We contend that our insights to date on the genomics of Arctic microbes are limited in these key areas, and we identify priorities and new ways of working to help ensure microbial genomics is in the vanguard of the scientific response to the Arctic crisis.
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Affiliation(s)
- Arwyn Edwards
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Karen A. Cameron
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Joseph M. Cook
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Aliyah R. Debbonaire
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Eleanor Furness
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Melanie C. Hay
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Sara M.E. Rassner
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
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Dynamics of microbial communities and CO 2 and CH 4 fluxes in the tundra ecosystems of the changing Arctic. J Microbiol 2019; 57:325-336. [PMID: 30656588 DOI: 10.1007/s12275-019-8661-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 12/20/2018] [Accepted: 12/24/2018] [Indexed: 10/27/2022]
Abstract
Arctic tundra ecosystems are rapidly changing due to the amplified effects of global warming within the northern high latitudes. Warming has the potential to increase the thawing of the permafrost and to change the landscape and its geochemical characteristics, as well as terrestrial biota. It is important to investigate microbial processes and community structures, since soil microorganisms play a significant role in decomposing soil organic carbon in the Arctic tundra. In addition, the feedback from tundra ecosystems to climate change, including the emission of greenhouse gases into the atmosphere, is substantially dependent on the compositional and functional changes in the soil microbiome. This article reviews the current state of knowledge of the soil microbiome and the two most abundant greenhouse gas (CO2 and CH4) emissions, and summarizes permafrost thaw-induced changes in the Arctic tundra. Furthermore, we discuss future directions in microbial ecological research coupled with its link to CO2 and CH4 emissions.
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Methanotrophy across a natural permafrost thaw environment. ISME JOURNAL 2018; 12:2544-2558. [PMID: 29955139 PMCID: PMC6155033 DOI: 10.1038/s41396-018-0065-5] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 01/08/2018] [Accepted: 01/09/2018] [Indexed: 11/09/2022]
Abstract
The fate of carbon sequestered in permafrost is a key concern for future global warming as this large carbon stock is rapidly becoming a net methane source due to widespread thaw. Methane release from permafrost is moderated by methanotrophs, which oxidise 20-60% of this methane before emission to the atmosphere. Despite the importance of methanotrophs to carbon cycling, these microorganisms are under-characterised and have not been studied across a natural permafrost thaw gradient. Here, we examine methanotroph communities from the active layer of a permafrost thaw gradient in Stordalen Mire (Abisko, Sweden) spanning three years, analysing 188 metagenomes and 24 metatranscriptomes paired with in situ biogeochemical data. Methanotroph community composition and activity varied significantly as thaw progressed from intact permafrost palsa, to partially thawed bog and fully thawed fen. Thirteen methanotroph population genomes were recovered, including two novel genomes belonging to the uncultivated upland soil cluster alpha (USCα) group and a novel potentially methanotrophic Hyphomicrobiaceae. Combined analysis of porewater δ13C-CH4 isotopes and methanotroph abundances showed methane oxidation was greatest below the oxic-anoxic interface in the bog. These results detail the direct effect of thaw on autochthonous methanotroph communities, and their consequent changes in population structure, activity and methane moderation potential.
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Hopcroft PO, Valdes PJ, Kaplan JO. Bayesian Analysis of the Glacial-Interglacial Methane Increase Constrained by Stable Isotopes and Earth System Modeling. GEOPHYSICAL RESEARCH LETTERS 2018; 45:3653-3663. [PMID: 29937607 PMCID: PMC6001704 DOI: 10.1002/2018gl077382] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 02/28/2018] [Accepted: 03/05/2018] [Indexed: 06/08/2023]
Abstract
The observed rise in atmospheric methane (CH4) from 375 ppbv during the Last Glacial Maximum (LGM: 21,000 years ago) to 680 ppbv during the late preindustrial era is not well understood. Atmospheric chemistry considerations implicate an increase in CH4 sources, but process-based estimates fail to reproduce the required amplitude. CH4 stable isotopes provide complementary information that can help constrain the underlying causes of the increase. We combine Earth System model simulations of the late preindustrial and LGM CH4 cycles, including process-based estimates of the isotopic discrimination of vegetation, in a box model of atmospheric CH4 and its isotopes. Using a Bayesian approach, we show how model-based constraints and ice core observations may be combined in a consistent probabilistic framework. The resultant posterior distributions point to a strong reduction in wetland and other biogenic CH4 emissions during the LGM, with a modest increase in the geological source, or potentially natural or anthropogenic fires, accounting for the observed enrichment of δ13CH4.
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Affiliation(s)
- Peter O. Hopcroft
- Bristol Research Initiative for the Dynamic Global Environment, School of Geographical SciencesUniversity of BristolBristolUK
- Cabot InstituteUniversity of BristolBristolUK
- Now at the School of Geography, Earth and Environmental SciencesUniversity of BirminghamEdgbastonUK
| | - Paul J. Valdes
- Bristol Research Initiative for the Dynamic Global Environment, School of Geographical SciencesUniversity of BristolBristolUK
- Cabot InstituteUniversity of BristolBristolUK
| | - Jed O. Kaplan
- Max Planck Institute for the Science of Human HistoryJenaGermany
- ARVE Research SARLPullySwitzerland
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Microbial and Environmental Controls of Methane Fluxes Along a Soil Moisture Gradient in a Pacific Coastal Temperate Rainforest. Ecosystems 2016. [DOI: 10.1007/s10021-016-0003-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Daebeler A, Gansen M, Frenzel P. Methyl fluoride affects methanogenesis rather than community composition of methanogenic archaea in a rice field soil. PLoS One 2013; 8:e53656. [PMID: 23341965 PMCID: PMC3544908 DOI: 10.1371/journal.pone.0053656] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 12/04/2012] [Indexed: 11/19/2022] Open
Abstract
The metabolic pathways of methane formation vary with environmental conditions, but whether this can also be linked to changes in the active archaeal community structure remains uncertain. Here, we show that the suppression of aceticlastic methanogenesis by methyl fluoride (CH3F) caused surprisingly little differences in community composition of active methanogenic archaea from a rice field soil. By measuring the natural abundances of carbon isotopes we found that the effective dose for a 90% inhibition of aceticlastic methanogenesis in anoxic paddy soil incubations was <0.75% CH3F (v/v). The construction of clone libraries as well as t-RFLP analysis revealed that the active community, as indicated by mcrA transcripts (encoding the α subunit of methyl-coenzyme M reductase, a key enzyme for methanogenesis), remained stable over a wide range of CH3F concentrations and represented only a subset of the methanogenic community. More precisely, Methanocellaceae were of minor importance, but Methanosarcinaceae dominated the active population, even when CH3F inhibition only allowed for aceticlastic methanogenesis. In addition, we detected mcrA gene fragments of a so far unrecognised phylogenetic cluster. Transcription of this phylotype at methyl fluoride concentrations suppressing aceticlastic methanogenesis suggests that the respective organisms perform hydrogenotrophic methanogenesis. Hence, the application of CH3F combined with transcript analysis is not only a useful tool to measure and assign in situ acetate usage, but also to explore substrate usage by as yet uncultivated methanogens.
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Affiliation(s)
- Anne Daebeler
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Martina Gansen
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Peter Frenzel
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- * E-mail:
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Flury S, McGinnis DF, Gessner MO. Methane emissions from a freshwater marsh in response to experimentally simulated global warming and nitrogen enrichment. ACTA ACUST UNITED AC 2010. [DOI: 10.1029/2009jg001079] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
The oxidation of methane by methane-oxidising microorganisms is an important link in the global methane budget. Oxic soils are a net sink while wetland soils are a net source of atmospheric methane. It has generally been accepted that the consumption of methane in upland as well as lowland systems is inhibited by nitrogenous fertiliser additions. Hence, mineral nitrogen (i.e. ammonium/nitrate) has conceptually been treated as a component with the potential to enhance emission of methane from soils and sediments to the atmosphere, and results from numerous studies have been interpreted as such. Recently, ammonium-based fertilisation was demonstrated to stimulate methane consumption in rice paddies. Growth and activity of methane-consuming bacteria in microcosms as well as in natural rice paddies was N limited. Analysing the available literature revealed that indications for N limitation of methane consumption have been reported in a variety of lowland soils, upland soils, and sediments. Obviously, depriving methane-oxidising bacteria of a suitable source of N hampers their growth and activity. However, an almost instantaneous link between the presence of mineral nitrogen (i.e. ammonium, nitrate) and methane-oxidising activity, as found in rice soils and culture experiments, requires an alternative explanation. We propose that switching from mineral N assimilation to the fixation of molecular nitrogen may explain this phenomenon. However, there is as yet no experimental evidence for any mechanism of instantaneous stimulation, since most studies have assumed that nitrogenous fertiliser is inhibitory of methane oxidation in soils and have focused only on this aspect. Nitrogen as essential factor on the sink side of the global methane budget has been neglected, leading to erroneous interpretation of methane emission dynamics, especially from wetland environments. The purpose of this minireview is to summarise and balance the data on the regulatory role of nitrogen in the consumption of methane by soils and sediments, and thereby stimulate the scientific community to embark on experiments to close the existing gap in knowledge.
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Affiliation(s)
- Dongqi Wang
- School of Resources and Environment Science; East China Normal University; Shanghai China
| | - Zhenlou Chen
- School of Resources and Environment Science; East China Normal University; Shanghai China
| | - Shiyuan Xu
- School of Resources and Environment Science; East China Normal University; Shanghai China
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Turetsky MR, Treat CC, Waldrop MP, Waddington JM, Harden JW, McGuire AD. Short-term response of methane fluxes and methanogen activity to water table and soil warming manipulations in an Alaskan peatland. ACTA ACUST UNITED AC 2008. [DOI: 10.1029/2007jg000496] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Rhew RC, Teh YA, Abel T. Methyl halide and methane fluxes in the northern Alaskan coastal tundra. ACTA ACUST UNITED AC 2007. [DOI: 10.1029/2006jg000314] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Wickland KP, Striegl RG, Neff JC, Sachs T. Effects of permafrost melting on CO2and CH4exchange of a poorly drained black spruce lowland. ACTA ACUST UNITED AC 2006. [DOI: 10.1029/2005jg000099] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | | | - Jason C. Neff
- University of Colorado; Department of Geological Sciences; Boulder Colorado USA
| | - Torsten Sachs
- Environmental Science Department; Alaska Pacific University; Anchorage Alaska USA
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Sowers T. Late Quaternary Atmospheric CH4 Isotope Record Suggests Marine Clathrates Are Stable. Science 2006; 311:838-40. [PMID: 16469923 DOI: 10.1126/science.1121235] [Citation(s) in RCA: 159] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
One explanation for the abrupt increases in atmospheric CH4, that occurred repeatedly during the last glacial cycle involves clathrate destabalization events. Because marine clathrates have a distinct deuterium/hydrogen (D/H) isotope ratio, any such destabilization event should cause the D/H ratio of atmospheric CH4 (deltaD(CH4)) to increase. Analyses of air trapped in the ice from the second Greenland ice sheet project show stable and/or decreasing deltaD(CH4) values during the end of the Younger and Older Dryas periods and one stadial period, suggesting that marine clathrates were stable during these abrupt warming episodes. Elevated glacial deltaD(CH4) values may be the result of a lower ratio of net to gross wetland CH4 emissions and an increase in petroleum-based emissions.
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Affiliation(s)
- Todd Sowers
- Department of Geosciences and the Earth and Environmental Systems Institute, Pennsylvania State University, University Park, PA 16802, USA.
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Oberlander EA. Trace gas measurements along the Trans-Siberian railroad: The TROICA 5 expedition. ACTA ACUST UNITED AC 2002. [DOI: 10.1029/2001jd000953] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Bréas O, Guillou C, Reniero F, Wada E. The global methane cycle: isotopes and mixing ratios, sources and sinks. ISOTOPES IN ENVIRONMENTAL AND HEALTH STUDIES 2001; 37:257-379. [PMID: 12723792 DOI: 10.1080/10256010108033302] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A review of the global cycle of methane is presented with emphasis on its isotopic composition. The history of methane mixing ratios, reconstructed from measurements of air trapped in ice-cores is described. The methane record now extends back to 420 kyr ago in the case of the Vostok ice cores from Antarctica. The trends in mixing ratios and in delta13C values are reported for the two Hemispheres. The increase of the atmospheric methane concentration over the past 200 years, and by 1% per year since 1978, reaching 1.7 ppmv in 1990 is underlined. The various methane sources are presented. Indeed the authors describe the methane emissions by bacterial activity under anaerobic conditions in wet environments (wetlands, bogs, tundra, rice paddies), in ruminant stomachs and termite guts, and that originating from fossil carbon sources, such as biomass burning, coal mining, industrial losses, automobile exhaust, sea floor vent, and volcanic emissions. Furthermore, the main sinks of methane in the troposphere, soils or waters via oxidation are also reported, and the corresponding kinetic isotope effects.
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Affiliation(s)
- O Bréas
- European Commission Joint Research Centre, Institute for Reference Materials and Measurements, Isotope Measurements Unit, B-2440 Geel, Belgium
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Kane DL, Reeburgh WS. Introduction to special section: Land-Air-Ice Interactions (LAII) Flux Study. ACTA ACUST UNITED AC 1998. [DOI: 10.1029/1998jd200017] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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