Respiration from oxygen consumption: Difference between revisions

Latest revision as of 15:02, 11 May 2026

Community respiration
Approach: O₂ consumption in dark incubations
Context: incubation, lab; in situ
Spatial scale: point sample
Temporal scale: hours to days
Units: µmol O₂ L^-1 h^-1
Community captured: bulk
Co-measurements: initial and final O₂, temperature, volume, incubation time

Method Overview

Community respiration is measured by tracking the decrease in dissolved oxygen concentration in sealed, dark-incubated water samples. Two main analytical approaches are used: end-point assessment by Winkler titration, in which oxygen is fixed chemically at the start and end of the incubation and quantified by iodometric titration^[1]; and continuous measurement using optical oxygen sensors (optodes), which allow real-time tracking of O₂ dynamics throughout the incubation^[2].

Incubations can be performed on board (in vitro) or deployed in situ using purpose-built incubators such as RESPIRE^[3]. The change in oxygen concentration over the incubation period, normalized to volume and time, gives the community respiration rate.

Scale of measurement

Each incubation provides a point measurement in space. Multiple incubations across a depth profile or transect are typically combined to characterize spatial patterns. Temporal resolution is set by the incubation duration, which ranges from a few hours (optode-based) to 24 h (Winkler endpoint).

Data generated

The method yields bulk community respiration rate in µmol O₂ L^-1 h^-1, reflecting the combined metabolic activity of all organisms in the incubation. This integrates bacterial, microeukaryote, and (if present) zooplankton respiration.

Units & currency

Units are µmol O₂ L^-1 h^-1. The currency is oxygen; conversion to carbon requires a respiratory quotient (RQ), typically assumed to be ~0.8 but variable with substrate composition.

Sample size

Winkler titrations commonly use 125–300 mL BOD bottles.

Repositories & databases

Limitations

The method assumes that respiration in the dark equals respiration in the light, and that community composition and activity remain stable throughout the incubation. Bottle confinement can alter trophic interactions and the physico-chemical environment relative to ambient conditions. For optode-based continuous measurements, sensor drift and biofouling over longer incubations must be monitored. Conversion to carbon units is uncertain due to variability in RQ across different microbial substrates and communities.

Example Applications & Protocols

Classic examples

Carpenter (1965) The Chesapeake Bay Institute technique for the Winkler dissolved oxygen method ^[1]
Warkentin et al. (2007) New and fast method to quantify respiration rates of bacterial and plankton communities by using optical oxygen sensor spots ^[2]
Boyd et al. (2015) RESPIRE: An in situ particle interceptor for particle remineralization and microbial dynamics studies ^[3]

Recent applications

Common calculations/conversions

Respiration rate (µmol O₂ L^-1 h^-1) = (O_2,initial − O_2,final) / incubation time.
Carbon respiration = O₂ consumption / RQ; a community RQ of 0.8 is commonly assumed for mixed marine communities.

References

↑ ^1.0 ^1.1 Carpenter, J. H. (1965). The Chesapeake Bay Institute technique for the Winkler dissolved oxygen method. Limnology and Oceanography, 10(1), 141–143. https://doi.org/10.4319/lo.1965.10.1.0141
↑ ^2.0 ^2.1 Warkentin, M., Freese, H. M., Karsten, U., & Schumann, R. (2007). New and fast method to quantify respiration rates of bacterial and plankton communities in freshwater ecosystems by using optical oxygen sensor spots. Applied and Environmental Microbiology, 73(21), 6722–6729. https://doi.org/10.1128/AEM.00405-07
↑ ^3.0 ^3.1 Boyd, P. W., McDonnell, A., Valdez, J., LeFevre, D., & Gall, M. P. (2015). RESPIRE: An in situ particle interceptor to conduct particle remineralization and microbial dynamics studies in the oceans' twilight zone. Limnology and Oceanography: Methods, 13(9), 494–508. https://doi.org/10.1002/lom3.10043

[Carpenter1965-1] 1.0 ^1.1 Carpenter, J. H. (1965). The Chesapeake Bay Institute technique for the Winkler dissolved oxygen method. Limnology and Oceanography, 10(1), 141–143. https://doi.org/10.4319/lo.1965.10.1.0141

[Warkentin2007-2] 2.0 ^2.1 Warkentin, M., Freese, H. M., Karsten, U., & Schumann, R. (2007). New and fast method to quantify respiration rates of bacterial and plankton communities in freshwater ecosystems by using optical oxygen sensor spots. Applied and Environmental Microbiology, 73(21), 6722–6729. https://doi.org/10.1128/AEM.00405-07

[Boyd2015-3] 3.0 ^3.1 Boyd, P. W., McDonnell, A., Valdez, J., LeFevre, D., & Gall, M. P. (2015). RESPIRE: An in situ particle interceptor to conduct particle remineralization and microbial dynamics studies in the oceans' twilight zone. Limnology and Oceanography: Methods, 13(9), 494–508. https://doi.org/10.1002/lom3.10043

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
-{{BreadcrumbsSecondary Production Respiration}}
+{{BreadcrumbsSecondaryProduction}}
-* [[Page authors|Page authors]]: [[User:Melanie Cohn|Melanie Cohn]], [[New Contributor]]
+* [[Page authors|Page authors]]: [[PRIMO]]
-* [[Responsible curator|Responsible curator]]:  [[User:Pending]]
+* [[Responsible curator|Responsible curator]]:  [[User:Hagi BucknWise|Hagen Buck-Wiese]]
 ----
 __TOC__
 <div class="model-box">
-{| class="model-ib"
+{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
-! Oxygen-based Respiration
+! Community respiration
 |-
-| '''Approach:''' continuous mounted oxygen optode
+| '''Approach:''' O<sub>2</sub> consumption in dark incubations
 |-
-| '''Context:''' dark incubation
+| '''Context:''' incubation, lab; ''in situ''
 |-
-| '''Spatial scale:''' mL, discreet depths
+| '''Spatial scale:''' point sample
 |-
-| '''Temporal scale:''' hours to daily, discreet timepoints
+| '''Temporal scale:''' hours to days
 |-
-| '''Units:''' µmol O<sub>2</sub> L<sup>-1</sup> day<sup>-1</sup>
+| '''Units:''' µmol O<sub>2</sub> L<sup>-1</sup> h<sup>-1</sup>
 |-
-| '''Community captured:''' <br>''"Community"'' (unfiltered) <br>''"Bacterial"'' (<0.7 µm, <1.2 µm, <3 µm)<br>''Other'' (<5 µm, <200 µm, etc.)
+| '''Community captured:''' bulk
 |-
-| '''Co-measurements:''' Required: temperature, salinity <br> Often Included: cell abundance, DOC, TOC
+| '''Co-measurements:''' initial and final O<sub>2</sub>, temperature, volume, incubation time
 |}
 </div>
@@ Line 28: / Line 28: @@
 == Method Overview ==
-Seawater is incubated in biological oxygen demand (BOD) bottles for 12-48 hours in the dark. Opitacal sensor spots are mounted inside the BOD bottle and measured through the glass wall via fiber optics. The change in oxygen concentration over the incubation period is the oxygen consumption rate (respiration), which can be converted to carbon units (CO<sub>2</sub> produced) via a respiratory quotient.
-'''Detailed Methods:'''
+Community respiration is measured by tracking the decrease in dissolved oxygen concentration in sealed, dark-incubated water samples. Two main analytical approaches are used: end-point assessment by Winkler titration, in which oxygen is fixed chemically at the start and end of the incubation and quantified by iodometric titration<ref name="Carpenter1965">Carpenter, J. H. (1965). The Chesapeake Bay Institute technique for the Winkler dissolved oxygen method. ''Limnology and Oceanography'', 10(1), 141–143. https://doi.org/10.4319/lo.1965.10.1.0141</ref>; and continuous measurement using optical oxygen sensors (optodes), which allow real-time tracking of O<sub>2</sub> dynamics throughout the incubation<ref name="Warkentin2007">Warkentin, M., Freese, H. M., Karsten, U., & Schumann, R. (2007). New and fast method to quantify respiration rates of bacterial and plankton communities in freshwater ecosystems by using optical oxygen sensor spots. ''Applied and Environmental Microbiology'', 73(21), 6722–6729. https://doi.org/10.1128/AEM.00405-07</ref>.
-Seawater is collected following carbon-clean protocols and kept dark. If desired, the seawater is fractionated using filtration. For bacterial or phytoplankton studies, grazers are commonly removed with a 200 m mesh or smaller. The [filtered] water is transferred to a gas-tight bottle with an internally-mounted planar optode ("sensor spot", such as [https://www.presens.de/products/o2 Precision Sensing]), or immersion probe (such as [https://unisense.com/products/o2-microsensor/ UniSens]). The bottles must incubated in the dark, as the sensor spots are light sensitive and will decrease precision and the lifetime of the sensor. In the case of PreSens, a fiber optic cable (POF) runs from the oxygen meter and can be mounted to the exterior of the sample bottle for high-resolution continuous measurements (e.g. every 30 seconds for 24 hours) or may be manual held up to each bottle at regular intervals (e.g. every 2 hours over 2 days) if the number of samples exceeds the number of available oxygen meters. A killed control (HgCl<sub>2</sub> or MilliQ control should be co-incubated. Corrections for deviations in temperature (>0.2 deg. Celsius should be considered) are applied to the oxygen data.<ref name = "Cohn2024" /> A linear regression is fit to the continuous oxygen data, the slope is taken to be the oxygen drawdown rate. The oxygen-based rate may be converted to carbon using a respiratory quotient (RQ).
-== Output ==
+Incubations can be performed on board (''in vitro'') or deployed ''in situ'' using purpose-built incubators such as RESPIRE<ref name="Boyd2015">Boyd, P. W., McDonnell, A., Valdez, J., LeFevre, D., & Gall, M. P. (2015). RESPIRE: An ''in situ'' particle interceptor to conduct particle remineralization and microbial dynamics studies in the oceans' twilight zone. ''Limnology and Oceanography: Methods'', 13(9), 494–508. https://doi.org/10.1002/lom3.10043</ref>. The change in oxygen concentration over the incubation period, normalized to volume and time, gives the community respiration rate.
 === Scale of measurement ===
-''Discreet Measurements'' <br>
-Incubations are required in order to produce a measurable respiration signal. Therefore, samples are discreet and often sparse. Respiration is under sampled in oceanography compared to in situ oxygen concentrations or primary production rates regionally and globally.
+Each incubation provides a point measurement in space. Multiple incubations across a depth profile or transect are typically combined to characterize spatial patterns. Temporal resolution is set by the incubation duration, which ranges from a few hours (optode-based) to 24 h (Winkler endpoint).
 === Data generated ===
+The method yields bulk community respiration rate in µmol O<sub>2</sub> L<sup>-1</sup> h<sup>-1</sup>, reflecting the combined metabolic activity of all organisms in the incubation. This integrates bacterial, microeukaryote, and (if present) zooplankton respiration.
 === Units & currency ===
-O<sub>2</sub> L<sup>-1</sup> day<sup>-1</sup><br>
-CO<sub>2</sub> L<sup>-1</sup> day<sup>-1</sup>
+Units are µmol O<sub>2</sub> L<sup>-1</sup> h<sup>-1</sup>. The currency is oxygen; conversion to carbon requires a respiratory quotient (RQ), typically assumed to be ~0.8 but variable with substrate composition.
 === Sample size ===
-mL, 300 mL, 1 L, etc.
+Winkler titrations commonly use 125–300 mL BOD bottles.
 === Repositories & databases ===
-* ''A global dataset of marine pelagic microbial respiration (v1)'' [[https://www.bodc.ac.uk/data/published_data_library/catalogue/10.5285/4b2a5ac6-b6db-c98e-e063-7086abc040c6]] <ref>
-Robinson C.; Seguro I.; Dall'Olmo G.; Moncoiffé G.; Aranguren-Gassis M.; Arístegui J.; Azzaro M.; Baek Y.; Baltar F.; Cohn M.R.; Eissler Y.; Evans C.; Fennel K.; Fernández-Urruzola I.; Ferrón S.; Fukuda H.; García-Martín E.E.; Gifford S.; Goddard-Dwyer M.; Hernández-Hernández N.; Herndl G.; Hill P.; Huang B.; Huang Y.; Hyun J.; Kim B.; Kirchman D.; Kitidis V.; LaBrie R.; Lefèvre D.; Lønborg C.; Maranger R.; Martínez-García S.; Montero M.F.; Mouriño-Carballido B.; Nagata T.; Osma N.; Panton A.; Regaudie de Gioux A.; Reinthaler T.; Serret P.; Sulpis O.; Uchimiya M.; Wang B.; Wang Q.; Yokokawa T.(2026). A global dataset of marine pelagic microbial respiration. NERC EDS British Oceanographic Data Centre NOC. https://doi:10.5285/4b2a5ac6-b6db-c98e-e063-7086abc040c6</ref>
 == Limitations ==
-* Assumption of linearity
-* Optode precision
-* Respiratory Quotients
+The method assumes that respiration in the dark equals respiration in the light, and that community composition and activity remain stable throughout the incubation. Bottle confinement can alter trophic interactions and the physico-chemical environment relative to ambient conditions. For optode-based continuous measurements, sensor drift and biofouling over longer incubations must be monitored. Conversion to carbon units is uncertain due to variability in RQ across different microbial substrates and communities.
 == Example Applications & Protocols ==
 === Classic examples ===
-* ''Microbial respiration in contrasting ocean provinces via high-frequency optode assays'' Cohn et al. (2024) <ref name = "Cohn2024">Cohn, M. R., Stephens, B. M., Meyer, M. G., Sharpe, G., Niebergall, A. K., Graff, J. R., Cassar, N., Marchetti, A., Carlson, C. A., & Gifford, S. M. (2024). Microbial respiration in contrasting ocean provinces via high-frequency optode assays. Frontiers in Marine Science, 11. https://doi.org/10.3389/fmars.2024.1395799</ref> <br>
+* Carpenter (1965) ''The Chesapeake Bay Institute technique for the Winkler dissolved oxygen method'' <ref name="Carpenter1965" />
-* ''Rapid microbial respiration of oil from the Deepwater Horizon spill in offshore surface waters of the Gulf of Mexico'' Edwards et al. (2011) <ref>Edwards, B. R., Reddy, C. M., Camilli, R., Carmichael, C. A., Longnecker, K., & Van Mooy, B. A. S. (2011). Rapid microbial respiration of oil from the Deepwater Horizon spill in offshore surface waters of the Gulf of Mexico. Environmental Research Letters, 6(3), 035301. https://doi.org/martG</ref>
+* Warkentin et al. (2007) ''New and fast method to quantify respiration rates of bacterial and plankton communities by using optical oxygen sensor spots'' <ref name="Warkentin2007" />
+* Boyd et al. (2015) ''RESPIRE: An in situ particle interceptor for particle remineralization and microbial dynamics studies'' <ref name="Boyd2015" />
 === Recent applications ===
-* Devices such as the AutoBOD by Van Mooy Lab at Woods Hole use a rotating carousel to pass the sample bottles past a single POF, increasing sample throughput with limited number of oxygen meters <ref>Stephens, B. M., Stincone, P., Petras, D., English, C. J., Opalk, K., Giovannoni, S., & Carlson, C. A. (2025). Oxidation state of bioavailable dissolved organic matter influences bacterioplankton respiration and growth efficiency. Communications Biology, 8(1), 1–14. https://doi.org/10.1038/s42003-025-07574-2
+*
-</ref>.
-* For more information on the function of oxygen optodes, see Bitting et al. (2017)<ref>Bittig HC, Körtzinger A, Neill C, van Ooijen E, Plant JN, Hahn J, Johnson KS, Yang B and Emerson SR (2018) Oxygen Optode Sensors: Principle, Characterization, Calibration, and Application in the Ocean. Front. Mar. Sci. 4:429. doi: 10.3389/fmars.2017.00429</ref>
 === Common calculations/conversions ===
-* ''Respiration Rate:'' The slope of the linear regression over the incubation period is the respiration rate in oxygen units (e.g. µmol O<sub>2</sub> L<sup>-1</sup> day<sup>-1</sup>. Assumes linearity.
+* Respiration rate (µmol O<sub>2</sub> L<sup>-1</sup> h<sup>-1</sup>) = (O<sub>2,initial</sub> − O<sub>2,final</sub>) / incubation time.
+* Carbon respiration = O<sub>2</sub> consumption / RQ; a community RQ of 0.8 is commonly assumed for mixed marine communities.
-* ''Temperature correction:'' temperature affects dissolved gas concentration, the optode fluorescence relationship with oxygen concentration, and even metabolic activity. It is essential to maintain a stable temperature, whether that is in situ temperature or experimental (e.g. standardized to 20 deg. Celsius). Temperature must be monitored closely; much variation in oxygen concentration during the incubation period can be attributed to temperature fluctuations. One approach to temperature corrections is to subtract out a co-incubated MilliQ or killed control from the samples.
-*''Respiratory Quotients (RQ):'' respiration should really be in units of CO2 produced rather than oxygen consumed. However, respiration is often measured in oxygen units due to instrumental limitation of CO<sub>2</sub> sensors. A quotient of molecules of carbon dioxide produced per oxygen molecule consumed is assumed to convert O<sub>2</sub> to CO<sub>2</sub>. RQs generally range from 0.8 to 1.4 CO<sub>2</sub>:O<sub>2</sub> and are dependent upon the organic matter substrate and metabolic capabilities of the microbes.<ref>Robinson, C., Serret, P., Tilstone, G., Teira, E., Zubkov, M. V., Rees, A. P., & Woodward, E. M. S. (2002). Plankton respiration in the Eastern Atlantic Ocean. Deep Sea Research Part I: Oceanographic Research Papers, 49(5), Article 5. https://doi.org/10.1016/S0967-0637(01)00083-8</ref><ref>del Giorgio, P. A., & Duarte, C. M. (2002). Respiration in the open ocean. Nature (London), 420(6914), 379–384. https://doi.org/10.1038/nature01165</ref><ref>Berggren, M., Lapierre, J., & Del Giorgio, P. A. (2012). Magnitude and regulation of bacterioplankton respiratory quotient across freshwater environmental gradients. The ISME Journal, 6(5), 984–993. https://doi.org/10.1038/ismej.2011.157
-</ref>
 == References ==
 [[Category:Main Pages|Model types]]