Review comments on the manuscript titled “Source specific bias correction of US background ozone modeled in CMAQ” by T. Nash Skipper et al.,

Background O₃ constitutes a significant portion of total surface O₃ and the contribution becomes higher when O₃ levels decline. This study used a measurement-model data fusion approach to assess CTM biases in USB O₃ and attribute these biases to different sources. Two sets of CMAQ simulations, PA and EQUATES, are conducted to analyze the contributions of different sources to USB O₃. While the study is of scientific significance in assessing model biases in background O₃ estimation, two major concerns need to be addressed by the authors.

(1) The two sets of simulations are for different years, the model configuration and inputs are different, different versions of emissions inventory are adopted, which will introduce substantial uncertainties. The PA simulations cover the year of 2016; while the EQUATES simulations span between 2002-2019. Additional simulations using the EQUATES modeling framework were conducted for 2016–2017 to estimate USB O₃ and USA O₃ using the zero-out method. CMAQ v5.2.1 was used for the PA simulations while CMAQ v5.3.2 was used for the EQUATES simulations. It seems this study is not outlined within a comprehensive framework but combine different modelling work to do the current study. The differences of biases caused by different model configurations and model setup between the two sets of scenarios need to be fully discussed. (2) While biases in the study are fully discussed, the reasons behind these biases remain ambiguous. Factors such as uncertainties in emissions inventory, meteorology simulations, and chemical mechanisms could contribute to biases. Providing insights into the main drivers of biases and offering suggestions for modelers to mitigate these biases would enhance the value of the study for readers seeking to improve background O₃ modeling accuracy.

Specific comments:

1. Abstract. The current form of the abstract is notably objective, it lacks quantitative results detailing the biases and their spatial-temporal characteristics. Additionally, what can we do to reduce these biases? The abstract could benefit from discussing potential strategies to mitigate these biases.
2. Methods. The overall model configuration needs to be briefly outlined in the main text, such as modelling domain, WRF configuration, CMAQ gas-phase mechanism, IC/BC, vertical layers, etc.
3. Table 1. The descriptions provided in Table 1 could benefit from clarification regarding emissions from other regions. For instance, in the case of "ZROW," where all international anthropogenic emissions are removed, it's unclear whether this includes emissions from the United States, Canada, and Mexico. To enhance clarity, it is recommended to use a clear table format that separates regions with emissions using symbols such as "√" to indicate the presence of emissions and "×" to denote the absence of emissions. This approach will facilitate a more straightforward understanding of the emission scenarios across different regions. Addtionally, Table 1 and Table S1 is exactly the same.

1. In the main text, Tables S4 and S5 (Line 95) comes before Table S3 (Line 101), this is strange.
2. Line 115, “STRAT” should be spelled out at the first time it appears.
3. CTM results: can you explain further why the 12km simulations have the best performance? Additionally, what about the model performance for NO2 simulations?
4. Table 2 and 3, what’s the unit of the data in this table?
5. section 3.3. The authors extensively compared the differences in deviations between different scenarios. Are these differences in deviations related to the zero-out method neglecting nonlinear ozone production?
6. section 3.4. The authors extensively described the results of model bias. These results seem to be an extension of section 3.3, but what can these results further illustrate?

Major comments: 

1. This study analyzed surface ozone from a suite of hemispheric and regional-scale CMAQ simulations for 2016 and 2017 and attempted to attribute the biases in model simulated total surface ozone to different components,  including ozone produced from US anthropogenic emissions, natural sources, intercontinental transport, and stratospheric intrusions. Understanding US background ozone and its components is of broad interest because they are directly relevant to the setting and implementation of US ozone air quality standards. However, the manuscript needs to be substantially revised before it can be published. Description of the methodology used and discussions in many sections are incomplete. The authors should also discuss the model biases in the context of published literature. The referee’s main concern is on the methodology used to attribute the model biases to different components. The description of the data fusion model in Section 2.3 is hard to understand. Is the data fusion model trained using one set of simulations and applied to another set of simulations for the bias attribution? How do you know the sources of biases in the two sets of simulations are the same? There are a couple of places where the authors refer to Skipper et al. (ES & T, 2021) for the method, but that study did not discuss the different USB components. 

2. The title of this paper is about the bias of US background ozone, but in the abstract and in the paper, there is substantial discussion on the biases of US anthropogenic O3 and the influence of model resolution. The authors stated “The estimated correction factors suggest a seasonally consistent positive bias in US anthropogenic O3 in the eastern US, with the bias becoming higher with coarser model resolution and with higher simulated total O3 though the bias does not increase much with higher observed O3.”  This statement seems to imply that coarser model resolution always produces higher US anthropogenic O3, which is not true. There is clearly a seasonal dependence. During winter when ozone production is in NOx-saturated regime, coarser model resolution leads to artificial dilution of NOx and thus higher O3 due to less NOx titration. During summer, however, when ozone production at most locations is in NOx-limited regime, coarser model resolution may lead to lower ozone concentrations produced from regional anthropogenic emissions. Increasing model resolution may lead to higher simulated US anthropogenic O3, leading to better agreement with observations, such as in the Central Valley of California. These seasonal characteristics of model resolution impacts on US anthropogenic ozone are clearly demonstrated in the published literature, including the recent studies of Schwantes et al. (2021) and Lin et a. (2024). 

Figure 6: the authors should present results for different seasons, not annual averages.  

Figure 13: What is the horizontal resolution of PA and EQUATES simulations presented in this figure? Are the differences driven by differences in model configurations or model resolution? The authors should show the comparison from the same configuration but at different resolutions. 

Schwantes, R. H., Lacey, F. G., Tilmes, S., Emmons, L. K., Lauritzen, P. H., Walters, S., et al. (2022). Evaluating the impact of chemical complexity and horizontal resolution on tropospheric ozone over the conterminous US with a global variable resolution chemistry model. Journal of Advances in Modeling Earth Systems, 14(6), e2021MS002889. https://doi.org/10.1029/2021MS002889

Lin, M., L. W. Horowitz, M. Zhao, L. Harris, P. Ginoux, J. P. Dunne, S. Malyshev, E. Shevliakova, H. Ahsan, S. Garner, F. Paulot, A. Pouyaei, S. J. Smith, Y. Xie, N. Zadeh, L. Zhou.  The GFDL Variable-Resolution Global Chemistry-Climate Model for Research at the Nexus of US Climate and Air Quality Extremes. Journal of Advances in Modeling Earth Systems, in press, https://doi.org/10.1029/2023MS003984, 2024

3.  Discussion on stratospheric contribution and CMAQ low-O3 bias in spring should be placed in the broader published literature, including those using dynamic stratospheric ozone tracers with explicit stratospheric chemistry and evaluation with intensive ozone profiling during western US field campaigns.  The stratospheric contribution estimated by CMAQ appears to be much lower than the estimates from these prior studies:

A.O. Langford, R.J. Alvarez II, J. Brioude, R. Fine, M. Gustin, J.S. Holloway, M.Y. Lin, R.D. Marchbanks, R.B. Pierce, S.P. Sandberg, C.J. Senff, A.M. Weickmann, E.J. Williams, Entrainment of stratospheric air and Asian pollution by the convective boundary layer in the Southwestern U.S., J. Geophys. Res., 122 (2), doi:10.1002/2016JD025987, 2017.

Lin M., A. M. Fiore , O. R. Cooper , L. W. Horowitz , A. O. Langford , Hiram Levy II , B. J. Johnson , V. Naik , S. J. Oltmans , C. Senff (2012): Springtime high surface ozone events over the western United States: Quantifying the role of stratospheric intrusions, Journal of Geophysical Research, 117, D00V22, doi:10.1029/2012JD018151

Langford, A.O., C.J. Senff, R.J. Alvarez II, J. Brioude, O.R. Cooper, J.S. Holloway, M.Y. Lin, R.D. Marchbanks, R.B. Pierce, S.P. Sandberg, A.M. Weickmann , E.J. Williams (2015): An overview of the 2013 Las Vegas Ozone Study (LVOS): Impact of stratospheric intrusions and long-range transport on surface air quality. Atmos. Environ, doi:10.1016/j.atmosenv.2014.08.040

Langford, A. O., Senff, C. J., Alvarez II, R. J., Aikin, K. C., Baidar, S., Bonin, T. A., Brewer, W. A., Brioude, J., Brown, S. S., Burley, J. D., Caputi, D. J., Conley, S. A., Cullis, P. D., Decker, Z. C. J., Evan, S., Kirgis, G., Lin, M., Pagowski, M., Peischl, J., Petropavlovskikh, I., Pierce, R. B., Ryerson, T. B., Sandberg, S. P., Sterling, C. W., Weickmann, A. W., and Zhang, L.: The Fires, Asian, and Stratospheric Transport-Las Vegas Ozone Study (FAST-LVOS), Atmos. Chem. Phys., https://doi.org/10.5194/acp-2021-690, 2022.

Other comments:

Lines 29-30: “USB O3 … is a larger portion of total observed O3 as anthropogenic precursor emissions decline”.  This statement needs a few references, such as Lin et al. (2017):

Lin, M.., W. Horowitz, R. Payton, A.M. Fiore, G. Tonnesen (2017). US surface ozone trends and extremes from 1980 to 2014: Quantifying the roles of rising Asian emissions, domestic controls, wildfires, and climate. Atmos. Chem. Phys., doi:10.5194/acp-17-2943-2017

Lines 38-48: Need references. Could also discuss the difficulty to separate the anthropogenic and natural driver of wildfire impacts on ozone air quality, as ozone production is enhanced due to mixing of wildfire VOC emissions with urban NOx? 

Table 1: The referee agrees with Referee #1 that the authors should list more detailed information regarding model version, simulations types, horizontal and vertical resolution, US anthropogenic emissions, international emissions, fire emissions (including temporal frequency and injection height), and other natural emissions. 

For all of the figures, please indicate in the figure caption whether MDA8 O3 or 24-h O3 is shown. There are some discussions of the metric in the first paragraph of Section 2.1. But it is much easier for readers if you label them as “MDA8 O3” directly in the figure captions. 

Figures 2 to 5: Results in the maps look pretty similar in their current form. Please use a different colorbar so that the spatial distribution of different model configurations can be better illustrated!