Activation of Methanogenesis in Arid Biological Soil Crusts Despite the Presence of Oxygen
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{"title"=>"Activation of methanogenesis in arid biological soil crusts despite the presence of oxygen", "type"=>"journal", "authors"=>[{"first_name"=>"Roey", "last_name"=>"Angel", "scopus_author_id"=>"26767524800"}, {"first_name"=>"Diethart", "last_name"=>"Matthies", "scopus_author_id"=>"7005737445"}, {"first_name"=>"Ralf", "last_name"=>"Conrad", "scopus_author_id"=>"54790610300"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-79957846434", "sgr"=>"79957846434", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0020453", "pmid"=>"21655270", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pui"=>"361862630"}, "id"=>"3e997482-e3e3-3a66-bac1-5e7aa46b544c", "abstract"=>"Methanogenesis is traditionally thought to occur only in highly reduced, anoxic environments. Wetland and rice field soils are well known sources for atmospheric methane, while aerated soils are considered sinks. Although methanogens have been detected in low numbers in some aerated, and even in desert soils, it remains unclear whether they are active under natural oxic conditions, such as in biological soil crusts (BSCs) of arid regions. To answer this question we carried out a factorial experiment using microcosms under simulated natural conditions. The BSC on top of an arid soil was incubated under moist conditions in all possible combinations of flooding and drainage, light and dark, air and nitrogen headspace. In the light, oxygen was produced by photosynthesis. Methane production was detected in all microcosms, but rates were much lower when oxygen was present. In addition, the δ13C of the methane differed between the oxic/oxygenic and anoxic microcosms. While under anoxic conditions methane was mainly produced from acetate, it was almost entirely produced from H2/CO2 under oxic/oxygenic conditions. Only two genera of methanogens were identified in the BSC-Methanosarcina and Methanocella; their abundance and activity in transcribing the mcrA gene (coding for methyl-CoM reductase) was higher under anoxic than oxic/oxygenic conditions, respectively. Both methanogens also actively transcribed the oxygen detoxifying gene catalase. Since methanotrophs were not detectable in the BSC, all the methane produced was released into the atmosphere. Our findings point to a formerly unknown participation of desert soils in the global methane cycle.", "link"=>"http://www.mendeley.com/research/activation-methanogenesis-arid-biological-soil-crusts-despite-presence-oxygen", "reader_count"=>132, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>6, "Researcher"=>27, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>43, "Student > Postgraduate"=>5, "Other"=>6, "Student > Master"=>21, "Student > Bachelor"=>11, "Professor"=>4}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>6, "Researcher"=>27, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>43, "Student > Postgraduate"=>5, "Other"=>6, "Student > Master"=>21, "Student > Bachelor"=>11, "Professor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>7, "Agricultural and Biological Sciences"=>57, "Business, Management and Accounting"=>1, "Chemical Engineering"=>4, "Chemistry"=>1, "Earth and Planetary Sciences"=>9, "Engineering"=>3, "Environmental Science"=>36, "Biochemistry, Genetics and Molecular Biology"=>8, "Nursing and Health Professions"=>1, "Medicine and Dentistry"=>1, "Social Sciences"=>1, "Immunology and Microbiology"=>3}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Unspecified"=>{"Unspecified"=>7}, "Environmental Science"=>{"Environmental Science"=>36}, "Chemical Engineering"=>{"Chemical Engineering"=>4}, "Engineering"=>{"Engineering"=>3}, "Chemistry"=>{"Chemistry"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>9}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>57}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>8}}, "reader_count_by_country"=>{"Saudi Arabia"=>1, "Sweden"=>1, "United States"=>7, "Japan"=>1, "Brazil"=>2, "Peru"=>1}, "group_count"=>2}

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  • {"files"=>["https://ndownloader.figshare.com/files/770124"], "description"=>"<p>Amino acid composition was deduced from DNA sequences and the tree was calculated with RAxML 7.04. Bootstrap values above 50% (out of a 100 trials) are displayed next to the nodes. Shaded clusters with diagonal lines contain sequences that were detected in the soil samples.</p>", "links"=>[], "tags"=>["phylogenetic", "aligned", "amino", "sequences", "methyl", "coenzyme", "reductase"], "article_id"=>440492, "categories"=>["Ecology", "Microbiology"], "users"=>["Roey Angel", "Diethart Matthies", "Ralf Conrad"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020453.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Maximum_likelihood_phylogenetic_tree_based_on_aligned_partial_amino_acid_sequences_of_the_methyl_coenzyme_M_reductase_gene_mcrA_/440492", "title"=>"Maximum likelihood phylogenetic tree based on aligned partial amino acid sequences of the methyl coenzyme M reductase gene (<i>mcrA</i>).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-05-31 00:08:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/770044"], "description"=>"<p>A. Accumulation of CH<sub>4</sub> in the microcosm headspaces B. mean production rate per day: means±1 SE; n = 3. Treatment codes are as follows: flooded-F, wet-drained-W, light-L, dark-d, N<sub>2</sub> headspace-N, air (21% O<sub>2</sub>) headspace-O.</p>", "links"=>[], "tags"=>["microcosms"], "article_id"=>440413, "categories"=>["Ecology", "Microbiology"], "users"=>["Roey Angel", "Diethart Matthies", "Ralf Conrad"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020453.g001", "stats"=>{"downloads"=>2, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Methane_production_in_the_microcosms_throughout_the_incubation_/440413", "title"=>"Methane production in the microcosms throughout the incubation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-05-31 00:06:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/770316"], "description"=>"<p>Isolines represent different apparent fractionation factors (ε<sub>app</sub>; eq.3). “Strictly anoxic” refers only to the anoxic microcosms in the dark while “oxic/oxygenic” refers to all the rest. The arrow in the “strictly anoxic” ellipse points to the direction of temporal development (d7 and d14 Refer to day 7 and 14th resp.). Treatment codes are as follows: flooded-F, wet-drained-W, light-L, dark-D, N<sub>2</sub> headspace-N, air (21% O2) headspace-O.</p>", "links"=>[], "tags"=>["carbon", "isotope", "formed", "methane", "microcosm", "headspaces"], "article_id"=>440692, "categories"=>["Ecology", "Microbiology"], "users"=>["Roey Angel", "Diethart Matthies", "Ralf Conrad"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020453.g004", "stats"=>{"downloads"=>1, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Stable_carbon_isotope_signature_13_C_of_the_CO_2_and_the_newly_formed_methane_in_the_microcosm_headspaces_see_Methods_means_177_1_SE_n_8202_8202_3_/440692", "title"=>"Stable carbon isotope signature (δ<sup>13</sup>C) of the CO<sub>2</sub> and the newly formed methane in the microcosm headspaces (see Methods): means±1 SE; n = 3.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-05-31 00:11:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/770390"], "description"=>"<p>Means±1 SE.</p><p>*Mean fold change in gene expression.</p><p>†Values above 1 represent upregulation in the second matched treatment compared to the first. Treatment codes are as follows: flooded-F, wet-drained-W, light-L, dark-D, N2 headspace-N, air (21% O<sub>2</sub>) headspace-O.</p>", "links"=>[], "tags"=>["paired"], "article_id"=>440765, "categories"=>["Ecology", "Microbiology"], "users"=>["Roey Angel", "Diethart Matthies", "Ralf Conrad"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020453.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Differences_in_relative_expression_2_8722_916_916_CT_of_katE_in_Methanocella_and_Methanosarcina_between_paired_treatments_/440765", "title"=>"Differences in relative expression (2<sup>−ΔΔCT</sup>)<sup>*</sup> of <i>katE</i> in <i>Methanocella</i> and <i>Methanosarcina</i> between paired treatments.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-05-31 00:12:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/770203"], "description"=>"<p>In situ refers to the dry BSC prior to any treatment. A. <i>mcrA</i> gene and transcript copy numbers. B. 16S rRNA gene copy numbers.</p>", "links"=>[], "tags"=>["transcript", "numbers", "quantified", "qpcr", "plotted", "methane"], "article_id"=>440569, "categories"=>["Ecology", "Microbiology"], "users"=>["Roey Angel", "Diethart Matthies", "Ralf Conrad"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020453.g003", "stats"=>{"downloads"=>2, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_and_transcript_copy_numbers_quantified_using_qPCR_plotted_against_methane_production_rates_means_177_1_SE_n_8202_8202_3_/440569", "title"=>"Gene and transcript copy numbers quantified using qPCR plotted against methane production rates: means±1 SE; n = 3.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-05-31 00:09:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/386757", "https://ndownloader.figshare.com/files/386820", "https://ndownloader.figshare.com/files/386864", "https://ndownloader.figshare.com/files/386916", "https://ndownloader.figshare.com/files/386949", "https://ndownloader.figshare.com/files/387023", "https://ndownloader.figshare.com/files/387050", "https://ndownloader.figshare.com/files/387087", "https://ndownloader.figshare.com/files/387148"], "description"=>"<div><p>Methanogenesis is traditionally thought to occur only in highly reduced, anoxic environments. Wetland and rice field soils are well known sources for atmospheric methane, while aerated soils are considered sinks. Although methanogens have been detected in low numbers in some aerated, and even in desert soils, it remains unclear whether they are active under natural oxic conditions, such as in biological soil crusts (BSCs) of arid regions. To answer this question we carried out a factorial experiment using microcosms under simulated natural conditions. The BSC on top of an arid soil was incubated under moist conditions in all possible combinations of flooding and drainage, light and dark, air and nitrogen headspace. In the light, oxygen was produced by photosynthesis. Methane production was detected in all microcosms, but rates were much lower when oxygen was present. In addition, the δ<sup>13</sup>C of the methane differed between the oxic/oxygenic and anoxic microcosms. While under anoxic conditions methane was mainly produced from acetate, it was almost entirely produced from H<sub>2</sub>/CO<sub>2</sub> under oxic/oxygenic conditions. Only two genera of methanogens were identified in the BSC-<em>Methanosarcina</em> and <em>Methanocella</em>; their abundance and activity in transcribing the <em>mcrA</em> gene (coding for methyl-CoM reductase) was higher under anoxic than oxic/oxygenic conditions, respectively. Both methanogens also actively transcribed the oxygen detoxifying gene catalase. Since methanotrophs were not detectable in the BSC, all the methane produced was released into the atmosphere. Our findings point to a formerly unknown participation of desert soils in the global methane cycle.</p> </div>", "links"=>[], "tags"=>["activation", "methanogenesis", "arid", "crusts"], "article_id"=>136357, "categories"=>["Ecology", "Microbiology"], "users"=>["Roey Angel", "Diethart Matthies", "Ralf Conrad"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0020453.s001", "https://dx.doi.org/10.1371/journal.pone.0020453.s002", "https://dx.doi.org/10.1371/journal.pone.0020453.s003", "https://dx.doi.org/10.1371/journal.pone.0020453.s004", "https://dx.doi.org/10.1371/journal.pone.0020453.s005", "https://dx.doi.org/10.1371/journal.pone.0020453.s006", "https://dx.doi.org/10.1371/journal.pone.0020453.s007", "https://dx.doi.org/10.1371/journal.pone.0020453.s008", "https://dx.doi.org/10.1371/journal.pone.0020453.s009"], "stats"=>{"downloads"=>19, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Activation_of_Methanogenesis_in_Arid_Biological_Soil_Crusts_Despite_the_Presence_of_Oxygen/136357", "title"=>"Activation of Methanogenesis in Arid Biological Soil Crusts Despite the Presence of Oxygen", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-05-31 01:45:57"}

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Relative Metric

{"start_date"=>"2011-01-01T00:00:00Z", "end_date"=>"2011-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Molecular biology", "average_usage"=>[295, 553, 688, 802, 914, 1017, 1108, 1194, 1278, 1351, 1419, 1500, 1570, 1633, 1712, 1774, 1839, 1903, 1970, 2033, 2101, 2162, 2228, 2291, 2352, 2418, 2486, 2547, 2610, 2680, 2737, 2799, 2859, 2919, 2974, 3029, 3082]}, {"subject_area"=>"/Ecology and environmental sciences/Ecosystems", "average_usage"=>[322, 507, 643, 742, 811, 883, 959, 1028, 1082, 1164, 1252, 1329, 1378, 1436, 1511, 1574, 1652, 1735, 1804, 1880, 1946, 2005, 2067, 2148, 2229]}, {"subject_area"=>"/Physical sciences/Chemistry", "average_usage"=>[272, 506, 626, 733, 837, 944, 1031, 1116, 1192, 1253, 1324, 1388, 1459, 1528, 1593, 1653, 1718, 1787, 1854, 1916, 1974, 2045, 2111, 2167, 2232, 2297, 2355, 2425, 2489, 2549, 2615, 2675, 2734, 2793, 2851, 2904, 2961]}]}
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Net::HTTPTooManyRequests

Source
Scopus
Time
2019-09-27 16:11:11 UTC
Target URL
https://api.elsevier.com/content/search/index:SCOPUS?query=DOI(10.1371%2Fjournal.pone.0020453)
Trace

/app/models/concerns/networkable.rb:21:in `get_result'
/app/models/source.rb:165:in `get_data'
/app/models/retrieval_status.rb:47:in `perform_get_data'
/app/jobs/source_job.rb:52:in `block (2 levels) in perform'
/app/jobs/source_job.rb:51:in `block in perform'
/app/jobs/source_job.rb:35:in `each'
/app/jobs/source_job.rb:35:in `perform'