Benthic Ecosystem Calcification Measured with Coupled pH and O2 Aquatic Eddy Covariance

Abstract

We present a method to quantify benthic ecosystem calcification from simultaneous pH (proton) and \(O_{2}\) eddy covariance flux measurements. In benthic ecosystems, photosynthesis is a proton sink, while calcification is a proton source. Where calcification is the dominant nonmetabolic proton source, it can be isolated as the residual between the measured proton flux and the flux predicted from O2-derived metabolism. We demonstrate this technique in Posidonia oceanica seagrass meadows near Ischia, Italy, where coralline algae epiphytes are the primary calcifiers. The method resolved a diurnal calcification signal consistent in magnitude with previous estimates for seagrass epiphytes. However, our pH measurements and proton fluxes also revealed widespread, diffusive \(CO_2\) vent influence at both the vent-adjacent site and the control site (670 m away), demonstrating that control sites near natural \(CO_2\) vents may not provide the stable baseline often assumed. Excluding the vent-affected data removed substantial portions of the data set, resulting in high uncertainty, while also illustrating the insights that high-speed multiparameter sensing provides. Our error analysis identifies accuracy in pH, alkalinity, and the ecosystem photosynthetic quotient as critical constraints on this and other pH-\(O_2\) based calcification measurements, particularly in environments where calcification rates are small relative to metabolic fluxes.

Citation

BibTeX citation:

@online{koopmans2026,
  author = {Koopmans, D. and Schaap, A. and Meyer, V. and Färber, P. and
    Queiss, L. and Montilla, L. M. and Loucaides, S. and Ahmerkamp, S.
    and Cardini, U.},
  title = {Benthic {Ecosystem} {Calcification} {Measured} with {Coupled}
    {pH} and {O2} {Aquatic} {Eddy} {Covariance}},
  date = {2026-04-21},
  url = {https://www.luismmontilla.com/papers/koopmans2026/},
  doi = {10.1021/acsestwater.5c00481},
  langid = {en},
  abstract = {We present a method to quantify benthic ecosystem
    calcification from simultaneous pH (proton) and \$O\_\{2\}\$ eddy
    covariance flux measurements. In benthic ecosystems, photosynthesis
    is a proton sink, while calcification is a proton source. Where
    calcification is the dominant nonmetabolic proton source, it can be
    isolated as the residual between the measured proton flux and the
    flux predicted from O2-derived metabolism. We demonstrate this
    technique in \_Posidonia oceanica\_ seagrass meadows near Ischia,
    Italy, where coralline algae epiphytes are the primary calcifiers.
    The method resolved a diurnal calcification signal consistent in
    magnitude with previous estimates for seagrass epiphytes. However,
    our pH measurements and proton fluxes also revealed widespread,
    diffusive \$CO\_2\$ vent influence at both the vent-adjacent site
    and the control site (670 m away), demonstrating that control sites
    near natural \$CO\_2\$ vents may not provide the stable baseline
    often assumed. Excluding the vent-affected data removed substantial
    portions of the data set, resulting in high uncertainty, while also
    illustrating the insights that high-speed multiparameter sensing
    provides. Our error analysis identifies accuracy in pH, alkalinity,
    and the ecosystem photosynthetic quotient as critical constraints on
    this and other pH-\$O\_2\$ based calcification measurements,
    particularly in environments where calcification rates are small
    relative to metabolic fluxes.}
}

For attribution, please cite this work as:

Koopmans, D., A. Schaap, V. Meyer, et al. 2026. “Benthic Ecosystem Calcification Measured with Coupled pH and O2 Aquatic Eddy Covariance.” ACS ES&T Water, April 21. https://doi.org/10.1021/acsestwater.5c00481.