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Respiration from oxygen consumption: optodes

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Template:BreadcrumbsSecondary Production Respiration

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

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 Precision Sensing), or immersion probe (such as 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.[1] 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) [[1]] [2]


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) [1]
  • Rapid microbial respiration of oil from the Deepwater Horizon spill in offshore surface waters of the Gulf of Mexico Edwards et al. (2011) [3]


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 [4].
  • For more information on the function of oxygen optodes, see Bitting et al. (2017)[5]


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.[6][7][8]


References

  1. ↑ 1.0 1.1 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
  2. ↑ 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
  3. ↑ 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
  4. ↑ 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
  5. ↑ 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
  6. ↑ 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
  7. ↑ 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
  8. ↑ 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
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