{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T00:12:10Z","timestamp":1792023130930,"version":"4.4.0"},"reference-count":50,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T00:00:00Z","timestamp":1770249600000},"content-version":"vor","delay-in-days":35,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100014013","name":"UK Research and Innovation","doi-asserted-by":"publisher","award":["NE\/Y000889\/1"],"award-info":[{"award-number":["NE\/Y000889\/1"]}],"id":[{"id":"10.13039\/100014013","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,14]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Bacterial growth and respiration are fundamental metabolic processes that drive energy transformation and allocation within organisms and impact carbon sequestration at the ecosystem scale. However, these traits are usually measured independently; bacterial growth is quantified with endpoint biomass measurements, while respiration is determined by monitoring oxygen or carbon dioxide. Because the two physiological traits are collected at different temporal and volumetric scales (hours-to-days for growth versus minutes-to-hours for respiration), reconciling them is challenging and often introduces scale-mismatch bias, obscuring causal links between metabolism and environmental drivers. In this study, we develop a novel method for quantifying the rates of bacterial growth and respiration from a single dissolved-oxygen time series. Our approach introduces a model that couples exponential biomass growth with biomass-specific respiration, enabling simultaneous inference of growth rate and respiration rate from each oxygen trajectory. We applied our high-throughput method to 15 bacterial taxa isolated from natural environments. Our approach yielded growth estimates in close agreement with measurements based on popular methods using optical density or flow cytometry (${R}^2$ &amp;gt; 0.9) with no evidence of taxon-specific bias. We also tested our approach in quantifying the effects of temperature on respiration, growth, and carbon use-efficiency in Pseudomonas sp. Our method yielded typical unimodal thermal response curves for growth and respiration where rates were highest at moderate temperatures, while carbon use efficiency increased with temperature, peaked around the growth thermal optimum (\u223c30\u00b0C\u201335\u00b0C), and declined at the highest temperature. By quantifying respiration and growth within a single assay and in high throughput, our approach effectively enables measurement of microbial metabolic strategies and adaptations to stress. It offers a noninvasive and scalable tool for high-throughput phenotyping and studies of environmental perturbations, enabling a new class of trait-based microbial ecology that links cellular physiology to broader ecosystem function.<\/jats:p>","DOI":"10.1093\/ismeco\/ycag024","type":"journal-article","created":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T13:49:28Z","timestamp":1770299368000},"source":"Crossref","is-referenced-by-count":2,"title":["A novel method to simultaneously estimate bacterial respiration and growth from oxygen dynamics"],"prefix":"10.1093","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3930-8347","authenticated-orcid":false,"given":"Ilgaz","family":"Cakin","sequence":"first","affiliation":[{"name":"Living Systems Institute, University of Exeter , Stocker Road, Exeter EX4 4QD, England ,","place":["United Kingdom"]},{"name":"Department of Geography, University of Exeter , Amory Building, Rennes Drive, Exeter EX4 4RJ, England ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebecca","family":"Millington","sequence":"additional","affiliation":[{"name":"Plymouth Marine Laboratory , Prospect Pl, Plymouth PL1 3DH, England ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samraat","family":"Pawar","sequence":"additional","affiliation":[{"name":"Department of Life Sciences, Imperial College London , Silwood Park Campus, Ascot SL5 7PY, England ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Angus","family":"Buckling","sequence":"additional","affiliation":[{"name":"Centre for Ecology and Conservation, University of Exeter , SERFS, Penryn Campus, Penryn TR10 9FE, England ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5630-5602","authenticated-orcid":false,"given":"Nicholas","family":"Smirnoff","sequence":"additional","affiliation":[{"name":"Department of Biosciences, University of Exeter , Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, England ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6799-9670","authenticated-orcid":false,"given":"Daniel","family":"Padfield","sequence":"additional","affiliation":[{"name":"Department of Ecology and Conservation, Environment and Sustainability Institute, University of Exeter , Penryn Campus, Penryn TR10 9FE, England ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Duffy","sequence":"additional","affiliation":[{"name":"Living Systems Institute, University of Exeter , Stocker Road, Exeter EX4 4QD, England ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriel","family":"Yvon-Durocher","sequence":"additional","affiliation":[{"name":"Living Systems Institute, University of Exeter , Stocker Road, Exeter EX4 4QD, England ,","place":["United Kingdom"]},{"name":"Department of Geography, University of Exeter , Amory Building, Rennes Drive, Exeter EX4 4RJ, England ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,2,5]]},"reference":[{"key":"2026041609573568600_ref1","doi-asserted-by":"crossref","first-page":"5895","DOI":"10.1038\/s41467-023-41524-y","article-title":"Microbial growth under drought is confined to distinct taxa and modified by potential future climate conditions","volume":"14","author":"Metze","year":"2023","journal-title":"Nat Commun"},{"key":"2026041609573568600_ref2","doi-asserted-by":"crossref","first-page":"439","DOI":"10.3732\/ajb.1000498","article-title":"The generation and maintenance of diversity in microbial communities","volume":"98","author":"Fierer","year":"2011","journal-title":"Am J Bot"},{"key":"2026041609573568600_ref3","doi-asserted-by":"crossref","first-page":"406","DOI":"10.4319\/lom.2006.4.406","article-title":"A system to quantitatively recover bacterioplankton respiratory CO2 for isotopic analysis to trace sources and ages of organic matter consumed in freshwaters","volume":"4","author":"McCallister","year":"2006","journal-title":"Limnol Oceanogr Methods"},{"key":"2026041609573568600_ref4","doi-asserted-by":"crossref","first-page":"8106","DOI":"10.1029\/2018JC014277","article-title":"Bacterial carbon cycling in the river plume in the northern South China Sea during summer","volume":"123","author":"Xu","year":"2018","journal-title":"J Geophys Res Oceans"},{"key":"2026041609573568600_ref5","doi-asserted-by":"crossref","first-page":"3507","DOI":"10.1029\/2019JG005095","article-title":"Links of extracellular enzyme activities, microbial metabolism, and community composition in the river-impacted coastal waters","volume":"124","author":"Shi","year":"2019","journal-title":"J Geophys Res Biogeosci"},{"key":"2026041609573568600_ref6","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1098\/rspb.1965.0069","article-title":"The maintenance energy of bacteria in growing cultures","volume":"163","author":"Pirt","year":"1965","journal-title":"Proc R Soc Lond B Biol Sci"},{"key":"2026041609573568600_ref7","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1128\/mr.59.1.48-62.1995","article-title":"Energetics of bacterial growth: balance of anabolic and catabolic reactions","volume":"59","author":"Russell","year":"1995","journal-title":"Microbiol Rev"},{"key":"2026041609573568600_ref8","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1016\/0022-5193(79)90189-9","article-title":"A model of physiological adaptation in unicellular algae","volume":"78","author":"Shuter","year":"1979","journal-title":"J Theor Biol"},{"key":"2026041609573568600_ref9","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1111\/j.1469-8137.1989.tb00321.x","article-title":"Respiration and microalgal growth: a review of the quantitative relationship between dark respiration and growth","volume":"112","author":"J. Geider","year":"1989","journal-title":"New Phytol"},{"key":"2026041609573568600_ref10","article-title":"Recherches Sur la croissance des cultures bact\u00e9riennes","volume":"911","author":"Monod","year":"1958","journal-title":"Actualit\u00e9s Scientifiques et Industrielles"},{"key":"2026041609573568600_ref11","doi-asserted-by":"crossref","first-page":"6722","DOI":"10.1128\/AEM.00405-07","article-title":"New and fast method to quantify respiration rates of bacterial and plankton communities in freshwater ecosystems by using optical oxygen sensor spots","volume":"73","author":"Warkentin","year":"2007","journal-title":"Appl Environ Microbiol"},{"key":"2026041609573568600_ref12","doi-asserted-by":"publisher","journal-title":"J Vis Exp","DOI":"10.3791\/50262"},{"key":"2026041609573568600_ref13","doi-asserted-by":"publisher","first-page":"e0193748","DOI":"10.1371\/journal.pone.0193748","article-title":"Multiplexed chemostat system for quantification of biodiversity and ecosystem functioning in anaerobic digestion","volume":"13","author":"Plouchart","year":"2018","journal-title":"PLoS One"},{"key":"2026041609573568600_ref14","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1007\/s42995-022-00133-2","article-title":"Making comparable measurements of bacterial respiration and production in the subtropical coastal waters","volume":"4","author":"Guo","year":"2022","journal-title":"Mar Life Sci Technol"},{"key":"2026041609573568600_ref15","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1146\/annurev-biophys-112221-074832","article-title":"The effects of temperature on cellular physiology","volume":"51","author":"Knapp","year":"2022","journal-title":"Annu Rev Biophys"},{"key":"2026041609573568600_ref16","doi-asserted-by":"crossref","first-page":"15620","DOI":"10.3390\/ijms232415620","article-title":"Effects of salinity and temperature on the flexibility and function of a polyextremophilic enzyme","volume":"23","author":"Laye","year":"2022","journal-title":"Int J Mol Sci"},{"key":"2026041609573568600_ref17","doi-asserted-by":"crossref","first-page":"10989","DOI":"10.1073\/pnas.1805518115","article-title":"Changes in temperature alter the relationship between biodiversity and ecosystem functioning","volume":"115","author":"Garc\u00eda","year":"2018","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026041609573568600_ref18","doi-asserted-by":"publisher","volume":"178","journal-title":"Measurement","DOI":"10.1016\/j.measurement.2021.109323"},{"key":"2026041609573568600_ref19","doi-asserted-by":"publisher","first-page":"41","DOI":"10.29074\/ascls.24.1.41","article-title":"Introduction: pseudomonas aeruginosa","volume":"24","author":"Moore","year":"2011","journal-title":"Clin Lab Sci"},{"key":"2026041609573568600_ref20","doi-asserted-by":"crossref","first-page":"1375","DOI":"10.3389\/fmicb.2016.01375","article-title":"Size and carbon content of sub-seafloor microbial cells at Landsort Deep, Baltic Sea","volume":"7","author":"Braun","year":"2016","journal-title":"Front Microbiol"},{"key":"2026041609573568600_ref21","doi-asserted-by":"publisher","DOI":"10.1007\/978-0-387-98141-3","volume-title":"Ggplot2: Elegant Graphics for Data Analysis","author":"Wickham","year":"2009"},{"key":"2026041609573568600_ref22","doi-asserted-by":"publisher","author":"Pedersen","DOI":"10.32614\/CRAN.package.patchwork"},{"key":"2026041609573568600_ref23","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v067.i01","article-title":"Fitting linear mixed-effects models using lme4","volume":"67","author":"Bates","year":"2015","journal-title":"J Stat Softw"},{"key":"2026041609573568600_ref24","first-page":"p156","article-title":"Dplyr: a grammar of data manipulation","volume":"3","author":"Wickham","year":"2015","journal-title":"R package version 04"},{"key":"2026041609573568600_ref25","doi-asserted-by":"publisher","author":"","DOI":"10.32614\/CRAN.package.tidyr"},{"key":"2026041609573568600_ref26","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1016\/S0140-6736(86)90837-8","article-title":"Statistical methods for assessing agreement between two methods of clinical measurement","volume":"327","author":"Bland","year":"1986","journal-title":"Lancet"},{"key":"2026041609573568600_ref27","doi-asserted-by":"publisher","DOI":"10.32614\/CRAN.package.minpack.lm"},{"key":"2026041609573568600_ref28","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1016\/0022-5193(81)90246-0","article-title":"Non-linear regression of biological temperature-dependent rate models based on absolute reaction-rate theory","volume":"88","author":"Schoolfield","year":"1981","journal-title":"J Theor Biol"},{"key":"2026041609573568600_ref29","doi-asserted-by":"crossref","first-page":"906252","DOI":"10.3389\/fmicb.2022.906252","article-title":"Thermal traits govern the response of microbial community dynamics and ecosystem functioning to warming","volume":"13","author":"Garcia","year":"2022","journal-title":"Front Microbiol"},{"key":"2026041609573568600_ref30","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1111\/ele.12545","article-title":"Rapid evolution of metabolic traits explains thermal adaptation in phytoplankton","volume":"19","author":"Padfield","year":"2016","journal-title":"Ecol Lett"},{"key":"2026041609573568600_ref31","doi-asserted-by":"crossref","first-page":"100045","DOI":"10.1016\/j.gloepi.2020.100045","article-title":"Bland-Altman methods for comparing methods of measurement and response to criticisms","volume":"3","author":"Mansournia","year":"2021","journal-title":"Glob Epidemiol"},{"key":"2026041609573568600_ref32","doi-asserted-by":"crossref","first-page":"2123","DOI":"10.1111\/ele.13840","article-title":"Systematic variation in the temperature dependence of bacterial carbon use efficiency","volume":"24","author":"Smith","year":"2021","journal-title":"Ecol Lett"},{"key":"2026041609573568600_ref33","doi-asserted-by":"crossref","first-page":"7594","DOI":"10.1128\/AEM.01227-09","article-title":"Temporal variation of bacterial respiration and growth efficiency in tropical coastal waters","volume":"75","author":"Lee","year":"2009","journal-title":"Appl Environ Microbiol"},{"key":"2026041609573568600_ref34","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1016\/0168-1605(94)90165-1","article-title":"Estimation of bacterial growth rates from turbidimetric and viable count data","volume":"23","author":"Dalgaard","year":"1994","journal-title":"Int J Food Microbiol"},{"key":"2026041609573568600_ref35","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1016\/0003-2697(70)90174-0","article-title":"Turbidity measurements of bacterial cultures in some available commercial instruments","volume":"38","author":"Koch","year":"1970","journal-title":"Anal Biochem"},{"key":"2026041609573568600_ref36","doi-asserted-by":"crossref","first-page":"714","DOI":"10.1016\/j.ijheh.2015.04.001","article-title":"Application of flow cytometry and PMA-qPCR to distinguish between membrane intact and membrane compromised bacteria cells in an aquatic milieu","volume":"218","author":"Zacharias","year":"2015","journal-title":"Int J Hyg Environ Health"},{"key":"2026041609573568600_ref37","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1186\/s40168-017-0285-3","article-title":"Schr\u00f6dinger\u2019s microbes: tools for distinguishing the living from the dead in microbial ecosystems","volume":"5","author":"Emerson","year":"2017","journal-title":"Microbiome"},{"key":"2026041609573568600_ref38","doi-asserted-by":"publisher","first-page":"e2016810118","DOI":"10.1073\/pnas.2016810118","article-title":"Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns","volume":"118","author":"Weissman","year":"2021","journal-title":"Proc Natl Acad Sci"},{"key":"2026041609573568600_ref39","doi-asserted-by":"crossref","first-page":"1481","DOI":"10.1038\/ismej.2014.235","article-title":"The physiology and ecological implications of efficient growth","volume":"9","author":"Roller","year":"2015","journal-title":"ISME J"},{"key":"2026041609573568600_ref40","doi-asserted-by":"crossref","first-page":"20123","DOI":"10.1038\/s41598-022-21108-4","article-title":"Fertilization treatments affect soil CO2 emission through regulating soil bacterial community composition in the semiarid loess plateau","volume":"12","author":"Wang","year":"2022","journal-title":"Sci Rep"},{"key":"2026041609573568600_ref41","doi-asserted-by":"crossref","first-page":"243","DOI":"10.3354\/ame043243","article-title":"Temperature regulation of bacterial production, respiration, and growth efficiency in a temperate salt-marsh estuary","volume":"43","author":"Apple","year":"2006","journal-title":"Aquat Microb Ecol"},{"key":"2026041609573568600_ref42","doi-asserted-by":"crossref","first-page":"31","DOI":"10.3389\/fmicb.2017.00031","article-title":"Drivers of bacterial maintenance and minimal energy requirements","volume":"8","author":"Kempes","year":"2017","journal-title":"Front Microbiol"},{"key":"2026041609573568600_ref43","doi-asserted-by":"crossref","first-page":"930","DOI":"10.1111\/ele.12113","article-title":"Carbon use efficiency of microbial communities: stoichiometry, methodology and modelling","volume":"16","author":"Sinsabaugh","year":"2013","journal-title":"Ecol Lett"},{"key":"2026041609573568600_ref44","first-page":"21","article-title":"pH as a primary control in environmental microbiology: 1. Thermodynamic perspective. Frontiers in environmental","volume":"6","author":"Jin","year":"2018","journal-title":"Science"},{"key":"2026041609573568600_ref45","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1085\/jgp.201411296","article-title":"Bacterial responses to osmotic challenges","volume":"145","author":"Wood","year":"2015","journal-title":"J Gen Physiol"},{"key":"2026041609573568600_ref46","doi-asserted-by":"crossref","first-page":"1386","DOI":"10.1890\/06-0219","article-title":"Microbial stress-response physiology and its implications for ecosystem function","volume":"88","author":"Schimel","year":"2007","journal-title":"Ecology"},{"key":"2026041609573568600_ref47","doi-asserted-by":"crossref","first-page":"5333","DOI":"10.1111\/gcb.15168","article-title":"Quantifying microbial growth and carbon use efficiency in dry soil environments via 18O water vapor equilibration","volume":"26","author":"Canarini","year":"2020","journal-title":"Glob Chang Biol"},{"key":"2026041609573568600_ref48","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1016\/j.copbio.2016.06.007","article-title":"Tracking microbial interactions with NanoSIMS","volume":"41","author":"Musat","year":"2016","journal-title":"Curr Opin Biotechnol"},{"key":"2026041609573568600_ref49","doi-asserted-by":"crossref","first-page":"8010","DOI":"10.1038\/s41467-024-52160-5","article-title":"Emerging multiscale insights on microbial carbon use efficiency in the land carbon cycle","volume":"15","author":"He","year":"2024","journal-title":"Nat Commun"},{"key":"2026041609573568600_ref50","doi-asserted-by":"crossref","first-page":"1782","DOI":"10.1002\/2015GB005188","article-title":"Explicitly representing soil microbial processes in earth system models","volume":"29","author":"Wieder","year":"2015","journal-title":"Glob Biogeochem Cycles"}],"container-title":["ISME Communications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/ismecommun\/advance-article-pdf\/doi\/10.1093\/ismeco\/ycag024\/66781652\/ycag024.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ismecommun\/article\/doi\/10.1093\/ismeco\/ycag024\/8464200","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ismecommun\/article\/doi\/10.1093\/ismeco\/ycag024\/8464200","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T13:57:46Z","timestamp":1776347866000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/ismecommun\/article\/doi\/10.1093\/ismeco\/ycag024\/8464200"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1]]},"references-count":50,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,1,14]]}},"URL":"https:\/\/doi.org\/10.1093\/ismeco\/ycag024","relation":{},"ISSN":["2730-6151"],"issn-type":[{"value":"2730-6151","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,1]]},"published":{"date-parts":[[2026,1]]},"article-number":"ycag024"}}