Review of ” Biosphere-atmosphere related processes influence trace-gas and aerosol satellite-model biases.” by Emma Sands, Ruth M. Doherty, Fiona M. O’Connor, Richard J. Pope, James Weber, and Daniel P. Grosvenor

This paper investigates the impact from different modifications to the UKESM model´s representation of biosphere-atmosphere interactions with a focus on evaluating the impact on certain gas-phase compounds and aerosol. The model is compared to satellite observations of the isoprene, formaldehyde and aerosol optical depth. The modifications to the model include changes to BVOC emission factors, chemical reaction rates, the atmospheric chemistry scheme, new particle formation, aerosol hygroscopicity and land cover changes. Simulations have been run to test the implications of the different modifications individually and then in combined in 3 different model configurations. These simulations are compared to the standard model configuration and satellite data to evaluate the different model configurations. Lastly, the implications for model configuration for the direct radiative effect is investigated.

The paper is well within the scope of ACP. The paper presents a novel overview of the results from individual and combined model modifications and compare these to satellite datasets, some which have not been used extensively before. The study finds substantial differences between the model configurations and can draw conclusions regarding their performance using the satellite validation.  The scientific methods and assumptions are valid and explained in a clear way. The descriptions of the model experiments and the model itself are well made. The text is well written and the paper is structured in a clear way. I recommend the paper for publication after the following comments has been addressed:

 Major comments:

 You mention the indirect effects from land use change and BVOCs in the introduction and you investigate the changes in aerosol radiative effects between the simulations in Section 3.7. Why have you not calculated the changes in the indirect effects between the simulations? Even if you don’t calculate them, I think it could be worth commenting on them in the paper and explaining why they are not calculated in this study.     

Minor comments:

Page 4, line 112: How do the monoterpenes form Sec_OrgMt? Are there yields for specific oxidants or is it a set fraction of the monoterpene concentrations?

Page 15, line 328: Should “lower” in the sentence be higher?

Page 19 Figure 8: The third column with the emissions ratio have a somewhat confusing color scale. The color scale is used for differences in other plots and it seems a little out of place in these figures. Please consider changing it.

Page 20, Figure 9. The last part of the figure caption should be removed. And please add subplot labels.

Page 21, line 420-422. Please consider dividing this sentence into two sentences.  

Page 27, line 529. What does Supplement 9 refer to?

Page 28, Figure 14. I find this figure hard to interpret. Would it not be easier to just make a figure of a comparison of the updated model version compared to the satellite data?

The manuscript by Sands et al. studies how making process-level changes concerning biosphere-atmosphere interactions to the standard setup of UKESM1.1 impacts modeled isoprene, formaldehyde (HCHO), and aerosol optical depth (AOD). Modeled isoprene, HCHO, and AOD are then subsequently compared against satellite measurements. The satellite-model bias is most greatly impacted by changing to a more detailed chemical mechanism (CS2). The authors also explore the impact of updated BVOC emission factors, reaction rates, organically-mediated boundary layer nucleation, hygroscopicity values, contributions to SOA from isoprene, and an observationally-derived land cover dataset. They report a significant difference in the aerosol direct radiative effect (+0.17 W m^-2) from the combined effects.

I believe this manuscript will be of relevance to the readership of ACP and recommend publication after attention to the following comments:

- Lines 252-262: Concerning the two-sampling methodologies, I am concerned that the 6-hourly method underestimates the isoprene column by up to 1.5 x 10¹⁶ molec cm^-2 over isoprene hotspots in the tropics (Fig S2). In some ways, I am not surprised since the model may sometimes be sampled nearly 3 hours away from the 13:30 LT satellite overpass (which also happens to coincide with peak isoprene emission)! At any rate, an underestimation of 1-1.5 x 10¹⁶ molec cm^-2 by the 6-hourly method compared to the 13:30 LT method is substantial over isoprene hotspots. To help address this concern, I would like the authors to comment in Section 3.6 how their satellite and model comparison would change had their sampling methodology used the model output from 13:30 and not the 6-hourly method. I would also think this could impact their HCHO comparison as well given that HCHO is a major oxidation product of isoprene.

- Lines 304-307: These lines give the impression that BVOC emissions are reducing atmospheric oxidation capacity, but Lines 334-338 suggest it is due to the choice of chemical mechanism between CS2 and ST (particularly with HO_x recycling in CS2 that would increase OH). I realize they're interrelated, but I would like the authors to clarify in the paper if they think the reduced atmospheric oxidation capacity is primarily due to increased BVOC emissions or the chemical mechanism.

- Lines 438-439: Could you show a figure in the supplement showing where the loss of crops and pastures in favor of high emitting grasses is taking place? It just seems odd to me that an observational dataset would simplify down like that.

- Figure 14: This is one of the main summary plots of the paper, but I found it confusing to report data as "new bias as a percentage of old bias." Why not compare Exp_CS2mLC to the satellite data directly for the different seasons since then the reader can see how far off in sign and magnitude the model (Exp_CS2mLC) is compared to satellite? The original Figure 14 could then be moved to supplemental for readers interested in comparison back to the baseline model.

- Line 522-523: Is the magnitude of the global mean difference for a particular season or annual?

- Line 601: In addition to missing sources of HCHO, do the authors think that the standard setup just does not get oxidants correct (considering that the standard mechanism does not have HO_x recycling)? That could also explain why the standard model greatly underestimates HCHO.

Technical Corrections:

- Line 245: "than" instead of "then"

- Line 365: "emissions" instead of "emisisons"

- Fix Figure 9 caption

- Fix Line 419 formatting

- Line 454: Double-check figure subsets. Figures 11a and 11b do not use the new EFs, correct?

- Line 501: "section" instead of "seciton"

- Line 505: Awkward phrasing of "...how processes involved in the biosphere impacts on atmospheric chemistry and aerosols have a wide range of effects..."

- Supplemental: Confusing to have section headers different than the figure numbers. For example, Figure S6 appears in S8.