Respiration from oxygen consumption - Revision history

Melanie Cohn: Blanked the page

2026-02-24T00:23:30Z

Blanked the page

← Older revision		Revision as of 17:23, 23 February 2026
Line 1:		Line 1:
	~~{{BreadcrumbsSecondary Production Respiration}}~~

	* [[Page authors\|Page authors]]: [[User:Melanie Cohn\|Melanie Cohn]], [[New Contributor]]
	* [[Responsible curator\|Responsible curator]]: [[User:Pending]]
	~~----~~

	~~__TOC__~~
	~~<div class="model-box">~~
	~~{\| class="model-ib"~~
	~~! Oxygen-based Respiration~~
	\|-
	~~\| '''Approach:''' continuous mounted oxygen optode~~
	\|-
	~~\| '''Context:''' dark incubation~~
	\|-
	~~\| '''Spatial scale:''' mL, discreet depths~~
	\|-
	~~\| '''Temporal scale:''' hours to daily, discreet timepoints~~
	\|-
	~~\| '''Units:''' µmol O<sub>2</sub> L<sup>-1</sup> day<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.)~~
	\|-
	~~\| '''Co-measurements:''' Required: temperature, salinity <br> Often Included: cell abundance, DOC, TOC~~
	\|}
	~~</div>~~
	~~<div style="clear:both"></div>~~

	~~== 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:'''~~
	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 ==~~


	~~=== 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.


	~~=== Data generated ===~~


	~~=== 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>~~


	~~=== Sample size ===~~
	~~60 mL, 300 mL, 1 L, etc.~~


	~~=== 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


	~~== 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>
	* ''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>


	~~=== 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.

	* ''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]]~~

Melanie Cohn at 00:17, 24 February 2026

2026-02-24T00:17:35Z

← Older revision		Revision as of 17:17, 23 February 2026
Line 55:		Line 55:
	=== Repositories & databases ===		=== 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>		* ''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. doi: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>

Melanie Cohn at 00:16, 24 February 2026

2026-02-24T00:16:24Z

← Older revision		Revision as of 17:16, 23 February 2026
Line 34:		Line 34:

	== Output ==		== Output ==


	=== Scale of measurement ===		=== Scale of measurement ===
	''Discreet Measurements'' <br>		''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.		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.


	=== Data generated ===		=== Data generated ===


	=== Units & currency ===		=== Units & currency ===
	O<sub>2</sub> L<sup>-1</sup> day<sup>-1</sup><br>		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>		CO<sub>2</sub> L<sup>-1</sup> day<sup>-1</sup>


	=== Sample size ===		=== Sample size ===
	60 mL, 300 mL, 1 L, etc.		60 mL, 300 mL, 1 L, etc.


	=== Repositories & databases ===		=== Repositories & databases ===
Line 57:		Line 62:
	* Optode precision		* Optode precision
	* Respiratory Quotients		* Respiratory Quotients


	== Example Applications & Protocols ==		== Example Applications & Protocols ==


	=== Classic examples ===		=== Classic examples ===
Line 69:		Line 76:
	</ref>.		</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>		* 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 ===		=== Common calculations/conversions ===
Line 75:		Line 83:
	* ''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.		* ''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>		*''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>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>		</ref>


	== References ==		== References ==

	[[Category:Main Pages\|Model types]]		[[Category:Main Pages\|Model types]]

Melanie Cohn: Respiration via continuous oxygen optodes

2026-02-24T00:12:10Z

Respiration via continuous oxygen optodes

New page

{{BreadcrumbsSecondary Production Respiration}}

* [[Page authors|Page authors]]: [[User:Melanie Cohn|Melanie Cohn]], [[New Contributor]]
* [[Responsible curator|Responsible curator]]: [[User:Pending]]
----

__TOC__
<div class="model-box">
{| class="model-ib"
! Oxygen-based Respiration
|-
| '''Approach:''' continuous mounted oxygen optode
|-
| '''Context:''' dark incubation
|-
| '''Spatial scale:''' mL, discreet depths
|-
| '''Temporal scale:''' hours to daily, discreet timepoints
|-
| '''Units:''' µmol O2 L-1 day-1
|-
| '''Community captured:''' ''"Community"'' (unfiltered) ''"Bacterial"'' (<0.7 µm, <1.2 µm, <3 µm) ''Other'' (<5 µm, <200 µm, etc.)
|-
| '''Co-measurements:''' Required: temperature, salinity Often Included: cell abundance, DOC, TOC
|}
</div>
<div style="clear:both"></div>

== 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 (CO2 produced) via a respiratory quotient.

'''Detailed Methods:'''
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 (HgCl2 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 ==

=== Scale of measurement ===
''Discreet Measurements'' 
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.

=== Data generated ===

=== Units & currency ===
O2 L-1 day-1 
CO2 L-1 day-1

=== Sample size ===
60 mL, 300 mL, 1 L, etc.

=== 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. doi:10.5285/4b2a5ac6-b6db-c98e-e063-7086abc040c6</ref>

== Limitations ==
* Assumption of linearity
* Optode precision
* Respiratory Quotients

== 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> 
* ''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>

=== 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 O2 L-1 day-1. Assumes linearity.

* ''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 CO2 sensors. A quotient of molecules of carbon dioxide produced per oxygen molecule consumed is assumed to convert O2 to CO2. RQs generally range from 0.8 to 1.4 CO2:O2 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]]