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Microbial denitrification is a primary contributor to biotic production of N2O in anoxic regions of soil, marine systems, and wastewater treatment facilities. Here, through comprehensive genome analysis, we show that pathway partitioning is a ubiquitous mechanism of complete denitrification within microbial communities. We have investigated mechanisms and consequences of process partitioning of denitrification through detailed physiological characterization and kinetic modeling of a synthetic community of Rhodanobacter thiooxydans FW510-R12 and Acidovorax sp. GW101-3H11. We have discovered that these two bacterial isolates, from a heavily nitrate (NO3\u2212) contaminated superfund site, complete denitrification through the exchange of nitrite (NO2\u2212) and nitric oxide (NO). The process partitioning of denitrification and other processes, including amino acid metabolism, contribute to increased cooperativity within this denitrifying community. We demonstrate that certain contexts, such as high NO3\u2212, cause unbalanced growth of community members, due to differences in their substrate utilization kinetics. The altered growth characteristics of community members drives accumulation of toxic NO2\u2212, which disrupts denitrification causing N2O off gassing.<\/jats:p>","DOI":"10.1093\/ismejo\/wraf093","type":"journal-article","created":{"date-parts":[[2025,5,9]],"date-time":"2025-05-09T08:09:17Z","timestamp":1746778157000},"source":"Crossref","is-referenced-by-count":19,"title":["Emergence and disruption of cooperativity in a denitrifying microbial community"],"prefix":"10.1093","volume":"19","author":[{"given":"Alex V","family":"Carr","sequence":"first","affiliation":[{"name":"Institute for Systems Biology , Seattle, WA 98109 ,","place":["United States"]},{"name":"Molecular Engineering Program, University of Washington , Seattle, WA 98195 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne E","family":"Otwell","sequence":"additional","affiliation":[{"name":"Institute for Systems Biology , Seattle, WA 98109 ,","place":["United States"]},{"name":"Department of Civil and Environmental Engineering, University of Washington , Seattle, WA 98195 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristopher A","family":"Hunt","sequence":"additional","affiliation":[{"name":"Institute for Systems Biology , Seattle, WA 98109 ,","place":["United States"]},{"name":"Department of Civil and Environmental Engineering, University of Washington , Seattle, WA 98195 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Chen","sequence":"additional","affiliation":[{"name":"Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory , Berkeley, CA 94720 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Wilson","sequence":"additional","affiliation":[{"name":"Institute for Systems Biology , Seattle, WA 98109 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos\u00e9 P","family":"Faria","sequence":"additional","affiliation":[{"name":"Data Science and Learning Division, Argonne National Laboratory , Lemont, IL 60439 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Filipe","family":"Liu","sequence":"additional","affiliation":[{"name":"Data Science and Learning Division, Argonne National Laboratory , Lemont, IL 60439 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Janaka N","family":"Edirisinghe","sequence":"additional","affiliation":[{"name":"Data Science and Learning Division, Argonne National Laboratory , Lemont, IL 60439 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacob J","family":"Valenzuela","sequence":"additional","affiliation":[{"name":"Institute for Systems Biology , Seattle, WA 98109 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Serdar","family":"Turkarslan","sequence":"additional","affiliation":[{"name":"Institute for Systems Biology , Seattle, WA 98109 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lauren M","family":"Lui","sequence":"additional","affiliation":[{"name":"Environmental Genomics and Systems Biology Division, Lawrence Berkeley National, Laboratory , Berkeley, CA 94720 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Torben N","family":"Nielsen","sequence":"additional","affiliation":[{"name":"Environmental Genomics and Systems Biology Division, Lawrence Berkeley National, Laboratory , Berkeley, CA 94720 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam P","family":"Arkin","sequence":"additional","affiliation":[{"name":"Environmental Genomics and Systems Biology Division, Lawrence Berkeley National, Laboratory , Berkeley, CA 94720 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher S","family":"Henry","sequence":"additional","affiliation":[{"name":"Data Science and Learning Division, Argonne National Laboratory , Lemont, IL 60439 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher J","family":"Petzold","sequence":"additional","affiliation":[{"name":"Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory , Berkeley, CA 94720 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David A","family":"Stahl","sequence":"additional","affiliation":[{"name":"Department of Civil and Environmental Engineering, University of Washington , Seattle, WA 98195 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nitin S","family":"Baliga","sequence":"additional","affiliation":[{"name":"Institute for Systems Biology , Seattle, WA 98109 ,","place":["United States"]},{"name":"Molecular Engineering Program, University of Washington , Seattle, WA 98195 ,","place":["United States"]},{"name":"Departments of Biology and Microbiology, University of Washington , Seattle, WA 98195 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,5,11]]},"reference":[{"key":"2025060900464098000_ref1","doi-asserted-by":"publisher","first-page":"636","DOI":"10.1038\/ngeo325","article-title":"How a century of ammonia synthesis changed the world","volume":"1","author":"Erisman","year":"2008","journal-title":"Nat Geosci"},{"key":"2025060900464098000_ref2","doi-asserted-by":"publisher","first-page":"e2121998119","DOI":"10.1073\/pnas.2215799119","article-title":"Exploring global changes in agricultural ammonia emissions and their contribution to 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