{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,4]],"date-time":"2026-05-04T21:07:15Z","timestamp":1777928835715,"version":"3.51.4"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2021,11,2]],"date-time":"2021-11-02T00:00:00Z","timestamp":1635811200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100006370","name":"Small Business Innovation Research","doi-asserted-by":"crossref","award":["DE-SC0019619"],"award-info":[{"award-number":["DE-SC0019619"]}],"id":[{"id":"10.13039\/100006370","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Integrated Management and Analysis Platform for Multi Domain Site Data"},{"name":"Department of Energy (DOE) Biological and Environmental Research program"},{"name":"Department of Energy\u2019s Joint Genome Institute","award":["1781"],"award-info":[{"award-number":["1781"]}]},{"DOI":"10.13039\/100019109","name":"Environmental Molecular Sciences Laboratory","doi-asserted-by":"crossref","award":["50334"],"award-info":[{"award-number":["50334"]}],"id":[{"id":"10.13039\/100019109","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100006206","name":"Office of Biological and Environmental Research","doi-asserted-by":"publisher","award":["DE-AC02- 05CH11231"],"award-info":[{"award-number":["DE-AC02- 05CH11231"]}],"id":[{"id":"10.13039\/100006206","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006206","name":"Office of Biological and Environmental Research","doi-asserted-by":"publisher","award":["DE-AC05-76RL01830"],"award-info":[{"award-number":["DE-AC05-76RL01830"]}],"id":[{"id":"10.13039\/100006206","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Wrighton Laboratory: National Sciences Foundation Division of Biological Infrastructure","award":["1759874"],"award-info":[{"award-number":["1759874"]}]},{"name":"DOE Early Career","award":["DE-SC0018020"],"award-info":[{"award-number":["DE-SC0018020"]}]},{"name":"DOE Early Career","award":["FY21.1068.001"],"award-info":[{"award-number":["FY21.1068.001"]}]},{"name":"Scientific Focus Area (SFA) project at PNNL"},{"name":"U.S. Department of Energy, Office of Science, Environmental System Science (ESS) Program."},{"name":"ESS Scientific Focus Area (SFA) at the Pacific Northwest National Laboratory"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Nutrient and contaminant behavior in the subsurface are governed by multiple coupled hydrobiogeochemical processes which occur across different temporal and spatial scales. Accurate description of macroscopic system behavior requires accounting for the effects of microscopic and especially microbial processes. Microbial processes mediate precipitation and dissolution and change aqueous geochemistry, all of which impacts macroscopic system behavior. As \u2018omics data describing microbial processes is increasingly affordable and available, novel methods for using this data quickly and effectively for improved ecosystem models are needed.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We propose a workflow (\u2018Omics to Reactive Transport\u2014ORT) for utilizing metagenomic and environmental data to describe the effect of microbiological processes in macroscopic reactive transport models. This workflow utilizes and couples two open-source software packages: KBase (a software platform for systems biology) and PFLOTRAN (a reactive transport modeling code). We describe the architecture of ORT and demonstrate an implementation using metagenomic and geochemical data from a river system. Our demonstration uses microbiological drivers of nitrification and denitrification to predict nitrogen cycling patterns which agree with those provided with generalized stoichiometries. While our example uses data from a single measurement, our workflow can be applied to spatiotemporal metagenomic datasets to allow for iterative coupling between KBase and PFLOTRAN.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Interactive models available at https:\/\/pflotranmodeling.paf.subsurfaceinsights.com\/pflotran-simple-model\/. Microbiological data available at NCBI via BioProject ID PRJNA576070. ORT Python code available at https:\/\/github.com\/subsurfaceinsights\/ort-kbase-to-pflotran. KBase narrative available at https:\/\/narrative.kbase.us\/narrative\/71260 or static narrative (no login required) at https:\/\/kbase.us\/n\/71260\/258.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab753","type":"journal-article","created":{"date-parts":[[2021,10,28]],"date-time":"2021-10-28T15:14:33Z","timestamp":1635434073000},"page":"778-784","source":"Crossref","is-referenced-by-count":5,"title":["ORT: a workflow linking genome-scale metabolic models with reactive transport codes"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8142-6713","authenticated-orcid":false,"given":"Rebecca L","family":"Rubinstein","sequence":"first","affiliation":[{"name":"Subsurface Insights, LLC , Hanover, NH 03755, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mikayla A","family":"Borton","sequence":"additional","affiliation":[{"name":"Department of Soil and Crop Sciences, Colorado State University , Fort Collins, CO 80521, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haiyan","family":"Zhou","sequence":"additional","affiliation":[{"name":"Subsurface Insights, LLC , Hanover, NH 03755, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Shaffer","sequence":"additional","affiliation":[{"name":"Department of Soil and Crop Sciences, Colorado State University , Fort Collins, CO 80521, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David W","family":"Hoyt","sequence":"additional","affiliation":[{"name":"EMSL Biomolecular Pathways Group, Pacific Northwest National Laboratory , Richland, WA 99354, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James","family":"Stegen","sequence":"additional","affiliation":[{"name":"Ecosystem Science Team, Pacific Northwest National Laboratory, Richland, WA 99354, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christopher S","family":"Henry","sequence":"additional","affiliation":[{"name":"Data Science and Learning, Argonne National Laboratory , Lemont, IL 60439, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kelly C","family":"Wrighton","sequence":"additional","affiliation":[{"name":"Department of Soil and Crop Sciences, Colorado State University , Fort Collins, CO 80521, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roelof","family":"Versteeg","sequence":"additional","affiliation":[{"name":"Subsurface Insights, LLC , Hanover, NH 03755, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,11,2]]},"reference":[{"key":"2023020201174043100_btab753-B1","doi-asserted-by":"crossref","first-page":"13219","DOI":"10.1038\/ncomms13219","article-title":"Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system","volume":"7","author":"Anantharaman","year":"2016","journal-title":"Nat. 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