{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,10]],"date-time":"2026-06-10T16:25:49Z","timestamp":1781108749586,"version":"3.54.1"},"reference-count":108,"publisher":"National Academy of Sciences","issue":"23","license":[{"start":{"date-parts":[[2019,11,16]],"date-time":"2019-11-16T00:00:00Z","timestamp":1573862400000},"content-version":"vor","delay-in-days":184,"URL":"https:\/\/www.pnas.org\/site\/aboutpnas\/licenses.xhtml"}],"content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2019,6,4]]},"abstract":"<jats:title>Significance<\/jats:title>\n                  <jats:p>Predicting biochemical processes driven by microbes in the environment remains challenging, because the \u201ckinetic\u201d parameters conventionally used to predict reaction rates are usually poorly known. Here we mathematically show that in poorly mixed systems, such as stagnant waters, bulk biochemical reaction rates can become limited by the slow transport of substrates across space and essentially independent of kinetic parameters. We demonstrate our arguments for a large and heavily studied ocean basin, where we accurately predict the microbially driven fluxes of various substances, across a depth range of hundreds of meters. Our work opens up avenues for predicting ecosystem processes without knowledge of kinetic parameters and without laborious chemical profile measurements.<\/jats:p>","DOI":"10.1073\/pnas.1819883116","type":"journal-article","created":{"date-parts":[[2019,5,16]],"date-time":"2019-05-16T20:25:37Z","timestamp":1558038337000},"page":"11329-11338","update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":17,"title":["Circumventing kinetics in biogeochemical modeling"],"prefix":"10.1073","volume":"116","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9216-5619","authenticated-orcid":false,"given":"Stilianos","family":"Louca","sequence":"first","affiliation":[{"name":"Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403;"},{"name":"Department of Biology, University of Oregon, Eugene, OR 97403;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mary I.","family":"Scranton","sequence":"additional","affiliation":[{"name":"School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6925-7571","authenticated-orcid":false,"given":"Gordon T.","family":"Taylor","sequence":"additional","affiliation":[{"name":"School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yrene M.","family":"Astor","sequence":"additional","affiliation":[{"name":"Estaci\u00f3n de Investigaciones Marinas de Margarita, Fundaci\u00f3n La Salle de Ciencias Naturales, Punta de Piedras, Estado Nueva Esparta, Venezuela;"},{"name":"Institute for Marine Remote Sensing, University of South Florida, Tampa, FL 33701;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sean A.","family":"Crowe","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada;"},{"name":"Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Doebeli","sequence":"additional","affiliation":[{"name":"Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada;"},{"name":"Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada;"},{"name":"Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"341","published-online":{"date-parts":[[2019,5,16]]},"reference":[{"key":"e_1_3_3_1_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1472-4669.2009.00214.x"},{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1042\/BST20120105"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1602897113"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/0016-7037(84)90301-6"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-642-60421-8"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.1061\/(ASCE)0733-9372(1990)116:5(945)"},{"key":"e_1_3_3_7_2","volume-title":"A Practical Guide to Ecological Modelling: Using R as a Simulation Platform","author":"Soetaert K","year":"2008","unstructured":"Soetaert K, Herman PM (2008) A Practical Guide to Ecological Modelling: Using R as a Simulation Platform (Springer Science & Business Media, Dordrecht, The Netherlands)."},{"key":"e_1_3_3_8_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1313713111"},{"key":"e_1_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.1029\/JC076i024p05877"},{"key":"e_1_3_3_10_2","doi-asserted-by":"publisher","DOI":"10.4319\/lo.2008.53.1.0319"},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.gca.2004.08.010"},{"key":"e_1_3_3_12_2","doi-asserted-by":"publisher","DOI":"10.1080\/01490451.2011.653084"},{"key":"e_1_3_3_13_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6941.2007.00332.x"},{"key":"e_1_3_3_14_2","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00055-18"},{"key":"e_1_3_3_15_2","volume-title":"Resource Competition and Community Structure","author":"Tilman D","year":"1982","unstructured":"Tilman D (1982) Resource Competition and Community Structure (Princeton Univ Press, Princeton)."},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1600359113"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1205009109"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.dsr2.2017.11.016"},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41559-018-0519-1"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-1694(98)00157-7"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1029\/WR019i005p01231"},{"key":"e_1_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-642-77862-9_14"},{"key":"e_1_3_3_23_2","doi-asserted-by":"publisher","DOI":"10.1038\/338411a0"},{"key":"e_1_3_3_24_2","doi-asserted-by":"publisher","DOI":"10.3354\/meps077157"},{"key":"e_1_3_3_25_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0611081104"},{"key":"e_1_3_3_26_2","doi-asserted-by":"publisher","DOI":"10.4319\/lo.2007.52.4.1336"},{"key":"e_1_3_3_27_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.dsr.2011.11.001"},{"key":"e_1_3_3_28_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.02087-06"},{"key":"e_1_3_3_29_2","unstructured":"Gies EA (2015) Illuminating phylogeny and function of microbial dark matter in Sakinaw Lake. PhD thesis (University of British Columbia Vancouver BC Canada)."},{"key":"e_1_3_3_30_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00248-015-0612-9"},{"key":"e_1_3_3_31_2","doi-asserted-by":"publisher","DOI":"10.4319\/lo.1985.30.5.0944"},{"key":"e_1_3_3_32_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.gca.2005.01.002"},{"key":"e_1_3_3_33_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro1838"},{"key":"e_1_3_3_34_2","doi-asserted-by":"publisher","DOI":"10.5670\/oceanog.2014.18"},{"key":"e_1_3_3_35_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-marine-010318-095150"},{"key":"e_1_3_3_36_2","doi-asserted-by":"publisher","DOI":"10.1016\/0016-7037(74)90145-8"},{"key":"e_1_3_3_37_2","doi-asserted-by":"publisher","DOI":"10.1357\/002224084788502756"},{"key":"e_1_3_3_38_2","doi-asserted-by":"publisher","DOI":"10.2475\/ajs.286.3.161"},{"key":"e_1_3_3_39_2","doi-asserted-by":"publisher","DOI":"10.1016\/0079-6611(88)90053-5"},{"key":"e_1_3_3_40_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.marchem.2007.02.001"},{"key":"e_1_3_3_41_2","doi-asserted-by":"publisher","DOI":"10.1029\/WR001i002p00325"},{"key":"e_1_3_3_42_2","doi-asserted-by":"publisher","DOI":"10.2307\/3546587"},{"key":"e_1_3_3_43_2","doi-asserted-by":"publisher","DOI":"10.1016\/0016-7037(96)00140-8"},{"key":"e_1_3_3_44_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.185.5.1485-1491.2003"},{"key":"e_1_3_3_45_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1258966"},{"key":"e_1_3_3_46_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-1694(01)00524-8"},{"key":"e_1_3_3_47_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.dsr.2004.08.005"},{"key":"e_1_3_3_48_2","first-page":"203","volume-title":"The Handbook of Environmental Chemistry","author":"Yakushev EV","year":"2013","unstructured":"Yakushev EV (2013) RedOx layer model: A tool for analysis of the water column oxic\/anoxic interface processes. The Handbook of Environmental Chemistry, ed Yakushev EV (Springer, Berlin), Vol 22, pp 203\u2013233."},{"key":"e_1_3_3_49_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ecolmodel.2016.05.011"},{"key":"e_1_3_3_50_2","doi-asserted-by":"publisher","DOI":"10.2307\/2258068"},{"key":"e_1_3_3_51_2","doi-asserted-by":"crossref","unstructured":"Berner R (1980) Early Diagenesis: A Theoretical Approach Princeton Series in Geochemistry (Princeton Univ Press Princeton).","DOI":"10.1515\/9780691209401"},{"key":"e_1_3_3_52_2","doi-asserted-by":"publisher","DOI":"10.1016\/0016-7061(89)90022-0"},{"key":"e_1_3_3_53_2","doi-asserted-by":"publisher","DOI":"10.1029\/94WR00955"},{"key":"e_1_3_3_54_2","doi-asserted-by":"publisher","DOI":"10.1016\/0016-7037(91)90407-V"},{"key":"e_1_3_3_55_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF00389209"},{"key":"e_1_3_3_56_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6941.1992.tb01661.x"},{"key":"e_1_3_3_57_2","doi-asserted-by":"publisher","DOI":"10.4319\/lo.2001.46.1.0148"},{"key":"e_1_3_3_58_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.71.11.7389-7400.2005"},{"key":"e_1_3_3_59_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01186-08"},{"key":"e_1_3_3_60_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-2920.2009.02058.x"},{"key":"e_1_3_3_61_2","doi-asserted-by":"publisher","DOI":"10.4319\/lo.2013.58.1.0001"},{"key":"e_1_3_3_62_2","doi-asserted-by":"publisher","DOI":"10.1016\/0016-7037(85)90172-3"},{"key":"e_1_3_3_63_2","unstructured":"Duffy D (2001) Green\u2019s Functions with Applications Applied Mathematics (Chapman & Hall\/CRC New York)."},{"key":"e_1_3_3_64_2","doi-asserted-by":"crossref","unstructured":"Nabighian M Corbett J (1988) Electromagnetic Methods in Applied Geophysics: Theory Electromagnetic Methods in Applied Geophysics (Soc Exploration Geophysics Tulsa OK).","DOI":"10.1190\/1.9781560802631"},{"key":"e_1_3_3_65_2","unstructured":"Steinkamp K (2011) Inverse modeling of the sources and sinks of atmospheric CO2: Joint constraints from the ocean and atmosphere. PhD thesis (ETH Z\u00fcrich Z\u00fcrich)."},{"key":"e_1_3_3_66_2","doi-asserted-by":"publisher","DOI":"10.2475\/ajs.286.3.199"},{"key":"e_1_3_3_67_2","first-page":"111","article-title":"Kinetics of weathering and diagenesis","volume":"8","author":"Berner RA","year":"1983","unstructured":"Berner RA (1983) Kinetics of weathering and diagenesis. Rev Mineral 8:111\u2013133.","journal-title":"Rev Mineral"},{"key":"e_1_3_3_68_2","doi-asserted-by":"publisher","DOI":"10.1016\/0016-7037(84)90252-7"},{"key":"e_1_3_3_69_2","doi-asserted-by":"publisher","DOI":"10.1029\/2000RG000081"},{"key":"e_1_3_3_70_2","doi-asserted-by":"publisher","DOI":"10.4319\/lo.1982.27.4.0610"},{"key":"e_1_3_3_71_2","doi-asserted-by":"publisher","DOI":"10.4319\/lo.1985.30.5.0956"},{"key":"e_1_3_3_72_2","doi-asserted-by":"publisher","DOI":"10.1357\/002224089785076154"},{"key":"e_1_3_3_73_2","doi-asserted-by":"publisher","DOI":"10.1016\/0016-7037(90)90293-T"},{"key":"e_1_3_3_74_2","doi-asserted-by":"publisher","DOI":"10.1016\/0304-4203(95)00081-X"},{"key":"e_1_3_3_75_2","doi-asserted-by":"publisher","DOI":"10.1029\/2006GC001442"},{"key":"e_1_3_3_76_2","doi-asserted-by":"publisher","DOI":"10.1016\/0278-4343(85)90031-7"},{"key":"e_1_3_3_77_2","doi-asserted-by":"publisher","DOI":"10.1016\/0198-0149(87)90047-1"},{"key":"e_1_3_3_78_2","doi-asserted-by":"publisher","DOI":"10.1357\/0022240943077091"},{"key":"e_1_3_3_79_2","doi-asserted-by":"publisher","DOI":"10.4319\/lo.1998.43.7.1500"},{"key":"e_1_3_3_80_2","doi-asserted-by":"publisher","DOI":"10.5194\/bg-8-1565-2011"},{"key":"e_1_3_3_81_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ecss.2011.01.012"},{"key":"e_1_3_3_82_2","doi-asserted-by":"crossref","unstructured":"Louca S Astor YM Doebeli M Taylor GT Scranton MI (May 2 2019) Microbial metabolite fluxes in a model marine anoxic ecosystem 10.1101\/625087.","DOI":"10.1101\/625087"},{"key":"e_1_3_3_83_2","doi-asserted-by":"publisher","DOI":"10.1016\/0304-4203(84)90043-4"},{"key":"e_1_3_3_84_2","doi-asserted-by":"publisher","DOI":"10.1357\/0022240963213808"},{"key":"e_1_3_3_85_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro2778"},{"key":"e_1_3_3_86_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.aam7240"},{"key":"e_1_3_3_87_2","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1614"},{"key":"e_1_3_3_88_2","doi-asserted-by":"publisher","DOI":"10.1002\/wsbm.60"},{"key":"e_1_3_3_89_2","doi-asserted-by":"publisher","DOI":"10.1002\/bit.21617"},{"key":"e_1_3_3_90_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.dsr.2012.09.001"},{"key":"e_1_3_3_91_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1207514109"},{"key":"e_1_3_3_92_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.67.4.1663-1674.2001"},{"key":"e_1_3_3_93_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.72.4.2679-2690.2006"},{"key":"e_1_3_3_94_2","doi-asserted-by":"publisher","DOI":"10.3354\/ame01817"},{"key":"e_1_3_3_95_2","doi-asserted-by":"publisher","DOI":"10.1093\/femsec\/fiv088"},{"key":"e_1_3_3_96_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0198-0149(10)80009-3"},{"key":"e_1_3_3_97_2","doi-asserted-by":"publisher","DOI":"10.1016\/0198-0149(80)90091-6"},{"key":"e_1_3_3_98_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.marchem.2003.11.002"},{"key":"e_1_3_3_99_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.marchem.2008.06.002"},{"key":"e_1_3_3_100_2","doi-asserted-by":"publisher","DOI":"10.1016\/0016-7037(89)90239-1"},{"key":"e_1_3_3_101_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-05159-8"},{"key":"e_1_3_3_102_2","doi-asserted-by":"publisher","DOI":"10.1029\/2003GL018756"},{"key":"e_1_3_3_103_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.65.8.3697-3704.1999"},{"key":"e_1_3_3_104_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature07540"},{"key":"e_1_3_3_105_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41559-016-0015"},{"key":"e_1_3_3_106_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.aaf4507"},{"key":"e_1_3_3_107_2","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2017.187"},{"key":"e_1_3_3_108_2","unstructured":"MATLAB (2015) MATLAB R2015b version 8.6.0 (The MathWorks Inc. Natick MA)."}],"container-title":["Proceedings of the National Academy of Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pnas.org\/doi\/pdf\/10.1073\/pnas.1819883116","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,4,13]],"date-time":"2022-04-13T04:13:18Z","timestamp":1649823198000},"score":1,"resource":{"primary":{"URL":"https:\/\/pnas.org\/doi\/full\/10.1073\/pnas.1819883116"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,5,16]]},"references-count":108,"journal-issue":{"issue":"23","published-print":{"date-parts":[[2019,6,4]]}},"alternative-id":["10.1073\/pnas.1819883116"],"URL":"https:\/\/doi.org\/10.1073\/pnas.1819883116","relation":{},"ISSN":["0027-8424","1091-6490"],"issn-type":[{"value":"0027-8424","type":"print"},{"value":"1091-6490","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,5,16]]},"assertion":[{"value":"2019-05-16","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}