Substrate Affinity as a Key Adaptive Mechanism in Ammonia Oxidation under Acidification

Substrate Affinity as a Key Adaptive Mechanism in Ammonia Oxidation under Acidification | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Substrate Affinity as a Key Adaptive Mechanism in Ammonia Oxidation under Acidification Zhen-Zhen Zheng, Senwei Tong, Hui Shen, Li-Li Han, Jin-Ming Tang, and 2 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5909337/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 27 Jan, 2026 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Abstract Ammonia oxidation, mediated primarily by ammonia-oxidizing archaea (AOA) and bacteria (AOB), is a cornerstone of the nitrogen cycle of aquatic ecosystems. However, the impact of increasing acidification on this process remains unresolved, with field observations across diverse aquatic environments yielding contradictory results. Here, we present a comprehensive investigation combining pH manipulation experiments across multiple ecosystems—including a freshwater reservoir, estuaries, and the oligotrophic open ocean—and controlled laboratory experiments using the AOA isolate Nitrosopumilus maritimus SCM1. Our results reveal an unexpected adaptive response: both AOA and AOB enhance their substrate affinity under acidified conditions, counteracting the anticipated reduction in ammonia availability. This respense defies to traditional paradigm that predicts diminished ammonia oxidation under acidified conditions and highlights substrate affinity as a key regulator of microbial activity. Notably, in AOA-dominated environments, this adaptation sustains ammonia oxidation rates despite acidification-induced substrate scarcity. These results reconcile previously inconsistent observations and establish a mechanistic framework for predicting ammonia oxidizer dynamics in acidifying aquatic systems. By incorporating substrate affinity into predictive models of nitrogen cycling, this study offers critical insights into the resilience of biogeochemical processes under future acidification scenarios. Earth and environmental sciences/Biogeochemistry Biological sciences/Biochemistry/Biogeochemistry acidification affinity ammonia oxidation kinetics substrate concentration Full Text Additional Declarations There is NO Competing Interest. Supplementary Files SWTAcidificationonAOSupportinginformation25.1.25.docx supplementary information for Cite Share Download PDF Status: Published Journal Publication published 27 Jan, 2026 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-5909337","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":420822287,"identity":"daa6aaab-49c7-4a14-8c7f-40dcfccd8a76","order_by":0,"name":"Zhen-Zhen 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