Calibrating soybean parameters in JULES 5.0 from the US- Ne2/3 FLUXNET sites and the SoyFACE-O3 experiment

Tropospheric ozone (O3) is the third most important anthropogenic greenhouse gas. O3 is detrimental to plant productivity, and it has a significant impact on crop yield. Currently, the Joint UK Land Environment 15 Simulator (JULES) land surface model includes a representation of global crops (JULES-crop), but does not have crop-specific O3 damage parameters, and applies default C3 grass O3 parameters for soybean that underestimates O3 damage. Physiological parameters for O3 damage in soybean in JULES-crop were calibrated against leaf gasexchange measurements from the Soybean Free-Air-Concentration-Enrichment (SoyFACE) with O3 experiment in Illinois, USA. Other plant parameters were calibrated using an extensive array of soybean observations such 20 as crop height, leaf carbon, etc. and meteorological data from FLUXNET sites near Mead, Nebraska, USA. The yield, aboveground carbon and leaf area index (LAI) of soybean from the SoyFACE experiment were used to evaluate the newly calibrated parameters. The result shows good performance for yield, with the modelled yield being within the spread of the SoyFACE observations. Although JULES-crop is able to reproduce observed LAI seasonality, its magnitude is underestimated. The newly calibrated version of JULES will be applied regionally 25 and globally in future JULES simulations. This study helps to build a state-of-the-art impact assessment model and contribute to a more complete understanding of the impacts of climate change on food production. https://doi.org/10.5194/gmd-2020-97 Preprint. Discussion started: 3 June 2020 c © Author(s) 2020. CC BY 4.0 License.


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Surface ozone (O3) pollution is one of the major threats to global food security due to the detrimental effects of ozone exposure on crops Avnery et al., 2011b;Leung et al., 2020;Long et al., 2005;Tai et al., 2014;Tai and Val Martin, 2017). In the United States alone, crop loss due to tropospheric O3 costs more than $5 billion USD annually Avnery et al., 2011a;Van Dingenen et al., 2009).

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Soybean is one of the main staple crops for human consumption; it also serves as an important source of animal feed. It is a cheap source of proteins and therefore soybean products are consumed around the world. The impact of O3 on soybean physiology and growth has been studied extensively Betzelberger et al., 2012;Dermody et al., 2008;Morgan et al., 2003). Crop yield losses to tropospheric O3 have been quantified using model projection and experiments. The National Crop Loss Assessment Network and European Open Top 40 Chamber programs have established the air quality guideline, which derived dose-response relationships from comparable experimental data. These campaigns provided critical information such as the O3 response relationship and estimated yield loss due to O3 damage that enabled regional projections of O3 effects on crop yields (Fuhrer, 2009). However, open top chambers modify plant response to O3 due to the 'chamber effects' which create microclimates (Elagöz and Manning, 2005) and environmental differences between the chamber and open air 45 micrometeorology in which yield loss is underestimated (Van Dingenen et al., 2009). Recently the introduction of Free-Air-Concentration-Enrichment (FACE) technology avoids the artefacts from enclosed chambers, a nd O3 fumiga tion w as ada pte d to FA C E fac ilities (M orga n e t a l., 2004). The application of FACE experiment on crops took place in China (Zhu et al., 2011) and USA, including experiments with soybean at the SoyFACE experiment in Champaign, Illinois (Morgan et al., 2004;Betzelberger et al. 2010;2012). 50 Crops are a significant component of the land surface; e.g., croplands and pasturelands represent 12% and 26% of the global terrestrial land, respectively (Van den Hoof et al., 2011). Moreover, the phenology of crops is very different from that of natural vegetation, and is characterized by high growth, turnover rate, and strong seasonality. It is thus necessary to include a crop-specific parameterization scheme to improve simulations of 55 land surface fluxes and regional climate in agroecosystems ( Van den Hoof et al., 2011). The Joint UK Land Environment Simulator with crops (JULES-crop) is a crop parameterisation (Osborne et al., 2015) within the land surface model, JULES (Best et al., 2011;Clark et al., 2011). Global simulations have been performed with JULES-crop for rice, wheat, maize and soybean (Osborne et al., 2015). These four crop types contribute more https://doi.org/10.5194/gmd-2020-97 Preprint. Discussion started: 3 June 2020 c Author(s) 2020. CC BY 4.0 License. grains of cereal, fruits, and root) and stem reserves, respectively. Carbon pools for stem and leaves are determined from the existing prognostic variables, LAI (Leaf area index) and canopy height. In Osborne et al. (2015), global runs of maize, wheat, soybean and rice were carried out using JULES-crop. Site runs were performed at four FLUXNET sites with soybean-maize rotation: Bondville (US-Bo1), Fermi (US-IB1) and Mead (US-Ne2 and US-Ne3). Simulated yield was compared against country and global FAO crop yields. Osborne et al. (2015) 70 used generic representations for each of the crops in their global study. For the plant parameters that are needed outside the crop model such as leaf nitrogen and leaf respiration parameters, these are set to those of the C3 or C4 grass functional types. Osborne et al. (2015) suggested that these parameters could be tuned to be more crop specific to improve fit to observations. These JULES parameters have been calibrated against observations for maize, using data from the Mead FLUXNET sites in Nebraska (Williams et al., 2017). However, to date, these 75 parameters have not been calibrated to soybean data.
There are many crop models developed by institutions / organisations around the world. Most are designed for application to an individual field up to the regional scale and do not include O3 impacts on vegetation.
(Appendix Table A1) compares a selection of land surface models which include crop tiles and have the 80 functions to model climate impact on crop productivity. JULES-crop is of particular interest because it is a development of the global land surface component JULES of the Met Office numerical weather prediction and climate models, and contains a detailed representation of plant physiological processes at sub-diurnal timescales, including consideration of O3 effects on natural vegetation, thus making it suitable for this study.
JULES-Crop has been accepted into the JULES trunk with the intention to be coupled with the Hadley Centre 85 Global Environment Model (HadGEM) in the near future. HadGEM is recognised as one of the best performing climate models with smaller errors than typical climate models (Gleckler et al., 2008;Knutti et al., The calibration of O3 damage on soybean would allow land surface and crop models to more realistically and reliably simulate present-day and future O3 damage, and subsequently to quantify its economic impacts. The objective of this study is to calibrate soybean representation for JULES-crop, with a particular focus on the response of soybean to O3 exposure.

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This paper is organised as follows: Section 2 describes the model set-up and observations used for the JULES calibration. Section 3 compares the results from the calibrated JULES runs against independent observations. Section 4 assesses the suitability of the model for modelling soybean under O3 damage and discusses ways of future model improvement. This is consistent with Mills et al. (2007), who reviewed over 700 published papers and conference proceedings and found that O3 level of AOT40 over 3 months of 5 ppm-h reduced soybean yield by less than 5%. Then we 110 calibrated specifically the soybean O3 response using leaf gas exchange measurements from soybean grown under elevated O3 concentrations at SoyFACE.
Finally, we applied JULES-crop newly calibrated for soybean and its O3 sensitivity at the leaf-level and evaluated model performance against observed yield and leaf area index from SoyFACE, taken for the full range of rings 115 and cultivars (Figure 1, step 7).

Calibration of soybean in the absence of ozone damage, using observations from Mead
We followed the standard tuning procedure performed on maize by Williams et al., (2017) but applied to 120 soybean ( Figure 1, steps1-5). This method is described in detail in the Supplementary Material, and the resulting https://doi.org/10.5194/gmd-2020-97 Preprint. Discussion started: 3 June 2020 c Author(s) 2020. CC BY 4.0 License. parameters are given in Table 1-3. These are compared to the parameters used in Osborne et al. (2015), which we refer to as the "Osborne 2015 tuning". Note that the parameters in Table 3 in the Osborne 2015 tuning are typical defaults for C3 grass, rather than soybean-specific.

Ozone effects on vegetation (exposure-response)
Many studies have shown that the impacts of O3 are closely related to accumulated exposure above a threshold concentration rather than the mean growing season concentration (Forestry Commission, 2016;Gerosa et al. 2012;Mills et al. 2007). An index of accumulated exposure above a threshold concentration of x ppb (AOTx) has thus 130 been developed as a measure of assessing O3 pollution effects on vegetation. AOTx is calculated as the summed product of the concentration above the threshold concentration and time (T), with values expressed in ppb h or ppm h. (Mills et al. 2007;Forestry Commission, 2016).
The O3 exposure index AOT40: Accumulated O3 exposure over a threshold of 40 parts per billion (Equation 1) 135 has been widely used by crop impact models in the forestry and agriculture industry and was used at SoyFACE.
The metric ensures only O3 concentrations above 40 ppb are included. The integral is taken over daytime hours.
AOT40 does not account for the actual uptake of O3 by plants and how this varies with ontogenetic (life span of the plant) and climatic factors such as temperature, irradiance, vapour pressure deficit, and/or soil moisture 140 (Ashmore, 2005;Fuhrer et al. 1997).
There is a drawback of the cumulative O3 exposure indices (Pleijel et al. 2000), which assume an instantaneously fixed threshold flux below which there is no effect of O3, which may not be realistic. Also in nature, the threshold value is unlikely to be constant (Ashmore, 2005) since the capacity of detoxification of O3 varies with climate and 145 plant species. To improve these indices, the Stockholm Environment Institute developed the Deposition of Ozone for Stomatal Exchange model (DO3SE) . DO3SE was developed to estimate the risk of O3 damage to European vegetation and is capable of providing O3 flux estimation by evaluating the soil water deficits and their influence on stomatal conductance which affect plant O3 uptake. Phyto-toxic O3 dose (POD) above a stomatal threshold over a growing season (the accumulated stomatal flux above threshold Y) PODy can 150 differentiate species sensitivity to rising background concentration, while AOT40 can only incorporate the effect https://doi.org/10.5194/gmd-2020-97 Preprint. Discussion started: 3 June 2020 c Author(s) 2020. CC BY 4.0 License. of rising global background O3 above the threshold 40ppb. This difference means AOT40 metric is less sensitive to O3 peaks, and stomatal flux based metric (e.g. PODy and DO3SE) perform better on O3 damage estimation in general (Büker et al., 2012;Dentener, F., Keating, T., and Akimoto, 2010;Pleijel et al., 2007). 155

Description of ozone response scheme in JULES
The current O3 scheme in JULES uses a dose-response approach to model O3 damage Clark et al., 2011). It uses the O3 concentration in the atmosphere to modify net photosynthesis Ap by an O3 uptake factor f : (2)  160 where f represents the fractional reduction of plant production: f = 1 − aUO>F O3crit (3) It assumes that O3 suppresses the potential net leaf photosynthesis in proportion to the O3 flux through stomata 165 above a specified critical threshold (Clark et al., 2011). UO>F O3crit is the instantaneous leaf uptake of O3 over a plant functional type specific threshold (FO3crit) (nmol m −2 s −1 ) and the plant type specific parameter a is the fractional reduction of photosynthesis with O3 uptake by leaves (Clark et al., 2011;Sitch et al., 2007).
From equations 3 & 4, F depends on the O3 uptake rate by stomata (FO3) over a critical (plant functional type specific) threshold for damage. It uses an analogy of Ohm's law, the O3 flux through stomata, FO3 (nmol O3 m-2 s-1), is given by, 175 where [O3] is the molar concentration of O3 at reference level (nmol m-3), Ra is the combined aerodynamic and boundary layer resistance between leaf surface and reference level (s m-1). gl is the leaf conductance for H2O (m 180 s-1), and κO3 = 1.67 is the ratio of leaf resistance for O3 to leaf resistance for water vapour . The uptake flux is dependent on the stomatal conductance, which is reliant on the photosynthetic rate in JULES. Given that gl and photosynthetic rate A are linear related [Cox et al., 1999], gl is given by, Where gp is the leaf conductance in the absence of O3 effects. The set of equations (3,5,6) produces a quadratic relationship as a function of , that can be solved analytically .
Fractional reduction of photosynthesis with the instanteneous uptake of O3 by leaves (mmol m-2) (dfp_dcuo_io) determines the sensitivity of soybean to O3 and the PFT-specific O3 critical level (FO3 crit) determines the 190 threshold O3 flux which would cause damage to photosynthesis (Oliver et al., 2018;Sitch et al., 2007). The higher the sensitivity of plants to O3 the lower photosynthesis the plant has at a given constant critical threshold. Sitch et al. (2007) configured plant functional types with two different O3 sensitivities (fractional reduction of photosynthesis by O3, F, equation 1, 2), where F = 1.40 is high sensitivity, and F = 0.25 is lower sensitivity for C3 grass (Sitch, 2007), using monthly average O3 data and calibration to yield observations. 195

Calibrating the ozone effects on crop leaf photosynthesis in JULES using SoyFACE
The SoyFACE experiment in Illinois allows controlled CO2 or O3 enrichment across large plots within a soybean field without an enclosure. SoyFACE O3 fumigation typically began after the emergence of soybean, and the plots were fumigated with O3 for 8-9 hours daily except when leaves were wet. In 2009 and 2010, soybeans were 200 exposed to nine different concentrations of O3 ranging from the ambient level to a target level of 200 ppb ( Figure   A2). The fumigation ended when soybean was mature.
Plant damage from O3 is cumulative and the target concentration for the experiment was not always met (e.g., when wind speeds are low, during rain or when O3 generators or analyzers are down). Therefore, the 8-hour mean 205 and the AOT40 index (Accumulated Ozone exposure above the Threshold of 40 ppb) were used for the analysis in SoyFACE instead of using the target O3 concentration. The planting dates were June 6, 2009 (Day 159) and To calibrate the O3 parameters for soybean in JULES-crop, we used midday photosynthetic gas-exchange 215 measurements from Betzelberger et al. (2012). These were taken at four stages during the growing season, from seven soybean cultivars growing at 9 different O3 concentrations, using open gas exchange systems (LI-6400 and LI-6400-40). These observations were used in conjunction with the daytime 8-hour mean O3 concentration measurements and the parameters calibrated at the Mead site to drive the Leaf Simulator computer package, which reproduces the calculation of leaf photosynthesis within JULES. We then tuned the O3 parameterisation of 220 Fractional reduction of photosynthesis by O3 (sensitivity) and Threshold of O3 flux (mmol m-2 s-1) to match the modelled leaf photosynthesis rate to the observed rate ( Figure 2). The tuned parameters are showed in Table 4.

Model configuration for the JULES-crop SoyFACE runs
The meteorological forcing data measured at Champaign, Illinois in 2009 (Ainsworth et al., 2010) were used to drive the JULES-crop model. The downward longwave radiation and diffuse radiation data from NOAA at Bondville site (SURFRAD) were used as SoyFACE does not have these variables available. The driving data were 230 repeatedly applied (recycled 25 times) to spin up the model from an arbitrary starting point with soil temperature initially set to 278 K and soil moisture to 75% of saturation. A single crop type was modelledsoybeanusing a single plant tile. Observed CO2 (NOAA) and 8-hour mean observed O3 concentrations from the SoyFACE rings (averaged over a month) were used as the driving data of the model since natural O3 is produced around 8 hours in daytime and it is a typical temporal resolution for O3 fumigation. The soil ancillary parameters used in 235 SoyFACE were extracted from the global dataset of soil ancillary from the HadGEM2-ES model (a coupled Earth System Model that was used by the Met Office Hadley Centre for the CMIP5). Observed ambient O3 were used as the control. The new parameters for soybean were used, which we calibrated to observations from the Mead FLUXNET sites as described in the supplementary material. The exception is the initial carbon: since the row spacing at the SoyFACE experiment is half that used at the Mead sites, we doubled the initial carbon for SoyFACE compared to Mead. The resulting model yield, above ground carbon and LAI was compared to the SoyFACE observations. calibrated parameters overestimated the carbon at ambient ozone levels. One contributing factor could be that water stress is underestimated in the new configuration, since it was not possible to evaluate the response to soil water availability using the Mead site data, so we instead derived a value for p0 (parameterise in the calculation of the threshold for water stress, see Table 3) from literature. We tested the sensitivity to this choice by re-running this configuration with p0=0, and this caused a 12% reduction in aboveground carbon (plots not shown). In 255 addition, the representation of the soil properties in the JULES SoyFACE run could be improved by calibration to site measurements. In contrast, the "Osborne 2015 tuning" intersects the line fitted to observed aboveground carbon at zero ozone concentration (partially because of higher water stress), but then shows a sharp decrease from zero to ambient levels, which is not realistic. Note that no observations were taken for below-ambient ozone concentrations at SoyFACE, so this section of the fitted line is an extrapolation. The slope of the aboveground 260 carbon response to increasing ozone concentrations is similar for all three runs, and compares very well to the to yield observations. Therefore, they can be seen as 'effective' parameters in these configurations, since they incorporate the effect of the ozone damage processes that are not explicitly represented in JULES.
Note that we plot AOT40 on the x-axis for illustrative purposes only, to be comparable with results presented in Betzelberger et al 2012 -AOT40 was not used in the JULES run. An alternative would be to plot ring number or ring target concentration. Ideally, we would plot the x-axis with the metric Phytotoxic Ozone Dose (POD) for JULES and observed data, which account the dosage of O3 that get into the stomata of soybean, but is beyond the 285 scope of the present study. Figure 5 compares the model and observed LAI at SoyFACE for different O3 concentrations. JULES was able to reproduce LAI seasonality; however, it underestimated the amplitude. The maximum LAI for calibrated JULES peaked around day 240 in September and observations peaked at DOY 220~230. The peak LAI in the model runs 290 was less than half the observed LAI in all cases. While the Mead model runs also showed a slight underestimation of peak LAI compared to observation (Supplementary Materials), the majority of the underestimation of the modelled SoyFACE LAI is due to a difference between the observed relationships between peak LAI and yield at the Mead and SoyFACE sites. At both sites, observed maximum yield increases with observed peak LAI.
However, for similar observed yields, the observed SoyFACE yield tends to be higher than the observed Mead 295 LAI. Given that our calibration is based on Mead observations, it is therefore not surprising that our model runs at SoyFACE underestimate peak LAI compared to the SoyFACE observations. A contributing factor to the different relationship between observed peak LAI and observed yield at SoyFACE compared to Mead could be the different methods used to measure LAI at the Mead sites (which this parameter 300 set was tuned against) and at SoyFACE. At Mead, destructive measurements were taken, whereas at SoyFACE, LAI was measured indirectly, using radiation attenuation through the canopy. https://doi.org/10.5194/gmd-2020-97 Preprint. Discussion started: 3 June 2020 c Author(s) 2020. CC BY 4.0 License.
Another plausible contributing factor for the different relationship between observed peak LAI and observed yield at SoyFACE compared to Mead is the row density of the soybean. The SoyFACE row spacing was half that of 305 Mead so, as described above, we set the initial carbon to twice that observed at Mead. The denser planting allowed soybean at SoyFACE to reach higher LAI earlier in the growing season. If this also resulted in thinner leaves at the beginning of the season than with the Mead row spacing, then this could explain the difference in the peak LAI to yield relationship between the two sites. JULES also does not account for leaf age on leaf assimilation rate -in reality a lower leaf assimilation is observed in the late season associated with leaf aging, and it is plausible 310 that this could also be affected by row spacing.
Figure 5 also demonstrates that model LAI responds more to ozone concentrations than the observed LAI. One contributing factor is the observed decrease in specific leaf area at SoyFACE in increased ozone (Betzelberger et al 2012). As mentioned above, this process is not captured by JULES. This issue is particularly pronounced in the 315 Osborne 2015 tuning runs, where the modelled LAI in the ring with target 200ppb is roughly a third of the peak LAI in the ambient ring.

Conclusions 320
Climate change and air pollution are a great threat to food production. JULES-crop has been developed to represent crops in the land surface model and allow us to estimate the future climate and air pollution impact to crops. The O3 impact on crops could be quantified with an improved parameterization to the existing O3 damage scheme for C3 plants. The default soybean biochemical and respiratory parameters in JULES were based on C3 grass parameters. Characteristics of soybean are more similar to a shrub than grass, therefore parameter calibration 325 is needed to improve the performance of soybean in JULES-crop.
In this paper, the parameters needed to describe soybean in JULES-crop were first revised against observations from the Mead FLUXNET sites to ensure that the crop, biochemical and respiratory parameters explicitly represented soybean. Compared with observations from these sites showed that GPP and LAI were well 330 represented for irrigated soybean at Mead. The O3 damage parameterisation was subsequently calibrated against leaf gas exchange observations from the Soybean Free-Air-Concentration-Enrichment (FACE) experiment for the O3 damage, by tuning the sensitivity and critical threshold of O3 damage. On the whole, JULES-Crop reproduces https://doi.org/10.5194/gmd-2020-97 Preprint. Discussion started: 3 June 2020 c Author(s) 2020. CC BY 4.0 License. the observed negative correlation between yield and O3 exposure. It also reproduced the negative impacts of ozone on LAI, and the seasonality of phenology, although the simulated LAI was underestimated at SoyFACE. This 335 method of calibrating soybean could be replicated for other crops once data become available and would contribute to more accurate parameters for crop models. The calibration will be applied to a regional and transient run and eventually the newly calibrated JULES-crop for soybean and its sensitivity to O3 damage, coupled within an Earth System Model. https://code.metoffice.gov.uk/trac/roses-u/browser/a/r/8/6/6/trunk/driving_data https://code.metoffice.gov.uk/trac/roses-u/browser/a/r/8/6/6/trunk/bin/SoyFACE_gas_exchange_data_2009.csv https://code.metoffice.gov.uk/trac/roses-u/browser/a/r/8/6/6/trunk/ancil_data Accessing the MOSRS requires registration, but once you access into the system, there's no information about 360 who is downloading or viewing which pages.  Simulator with Crop module turned on (JULES-crop) using the Mead soybean tuning (red), Osborne et al. (2015) standard parameters with Sitch et al. (2007) low ozone sensitivity (blue), high ozone sensitivity (green) and observation from SoyFACE from Betzelberger et al. 2012. https://doi.org/10.5194/gmd-2020-97 Preprint. Discussion started: 3 June 2020 c Author(s) 2020. CC BY 4.0 License.  Division of sunlit and shaded leaves within each canopy level.
A modified version of inhibition of leaf respiration in the light. exponential decline of leaf N with canopy height proportional to LAI, following Beer's law.

L_irrid_dmd
Switch controlling the implementation of irrigation demand code.

Irr_crop
Irrigation season (i.e. season in which crops might be growing on the gridbox) lasts the entire year.
l_trait_phys Switch for using trait-based physiology. Vcmax is calculated based on parameters nl0 (kgN kgC-1) and neff.    Table 4. Summary of ozone parameter configurations employed in JULES-crop for the default Osborne et al., (2015) value and the tuned as calibrated to SoyFACE leaf gas-exchange measurements (note that these have been calibrated to daytime 8-hour concentrations and therefore will be different to parameters calibrated to 575 monthly 24hour means) JULES ozone damage Parameters