Development of an ecophysiology module in the GEOS-Chem chemical transport model version 12.2.0 to represent biosphere–atmosphere fluxes relevant for ozone air quality
Authors: Lam Joey C. Y. , Tai Amos P. K. , Ducker Jason A. , Holmes Christopher D. 
Published: May 2023

Abstract. Ground-level ozone (O3) is a major air pollutant that adversely affects human health and ecosystem productivity. Removal of tropospheric
O3 by plant stomatal uptake can in turn cause damage to plant tissues with ramifications for ecosystem and crop health. In many
atmospheric and land surface models, the functionality of stomata opening is represented by a bulk stomatal conductance, which is often
semi-empirically parameterized and highly fitted to historical observations. A lack of mechanistic linkage to ecophysiological processes such as
photosynthesis may render models inadequate to represent plant-mediated responses of atmospheric chemistry to long-term changes in CO2,
climate, and short-lived air pollutant concentrations. A new ecophysiology module was thus developed to mechanistically simulate land−atmosphere
exchange of important gas species in GEOS-Chem, a chemical transport model widely used in atmospheric chemistry studies. The implementation not only
allows for dry deposition to be coupled with plant ecophysiology but also enables plant and crop productivity and functions to respond dynamically to
atmospheric chemical changes. We conduct simulations to evaluate the effects of the ecophysiology module on simulated dry deposition velocity and
concentration of surface O3 against an observation-derived dataset known as SynFlux. Our estimated stomatal conductance and dry deposition
velocity of O3 are close to SynFlux with root-mean-squared errors (RMSEs) below 0.3 cm s−1 across different plant functional
types (PFTs), despite an overall positive bias in surface O3 concentration (by up to 16 ppbv). Representing ecophysiology was
found to reduce the simulated biases in deposition fluxes from the prior model but worsen the positive biases in simulated O3
concentrations. The increase in positive concentration biases is mostly attributable to the ecophysiology-based stomatal conductance being generally
smaller (and closer to SynFlux values) than that estimated by the prior semi-empirical formulation, calling for further improvements in non-stomatal
depositional and non-depositional processes relevant for O3 simulations. The estimated global O3 deposition flux is
864 Tg O3 yr−1 with GEOS-Chem, and the new module decreases this estimate by 92 Tg O3 yr−1. Estimated global gross
primary production (GPP) without O3 damage is 119 Pg C yr−1. O3-induced reduction in GPP is 4.2 Pg C yr−1
(3.5 %). An elevated CO2 scenario (580 ppm) yields higher global GPP (+16.8 %) and lower global O3
depositional sink (−3.3 %). Global isoprene emission simulated with a photosynthesis-based scheme is 317.9 Tg C yr−1, which is
31.2 Tg C yr−1 (−8.9 %) less than that calculated using the MEGAN
(Model of Emissions of Gases and Aerosols from Nature) emission algorithm. This new model development dynamically
represents the two-way interactions between vegetation and air pollutants and thus provides a unique capability in evaluating vegetation-mediated
processes and feedbacks that can shape atmospheric chemistry and air quality, as well as pollutant impacts on vegetation health, especially for any
timescales shorter than the multidecadal timescale.