Dear Author,

Thank you for having submitted a revised version of the manuscript. One referee still has concerns which need to be addressed. Below are the comments (from the referees and I) below. Please provide a point-by-point reply as well as a revised version. Referee #1 requested to be sent the revised version.

Regards,
Jean-Pierre Gattuso


-----------------------------------------------------------------------------
Can the authors put their finding in perspective with the SOCAT QC procedures ? In particular they show a relatively poor comparison of pCO2 measurements by two systems on board the same ship (+/- 20 µatm) while SOCAT QC procedures aim at cross-overs of VOS lines better than 5 µatm.
----
1.15. P 2804 L13: provide reference(s) to back statement “strong gradients in temperature,
salinity and pCO2“
The sentence now reads: “strong gradients in temperature, salinity and chemical
variables (Rérolle et al., 2014)”. (P. 11, 18-19)
* COMMENT : Please refer to indepedent references to back this statement, the paper by Rérolle et al. (2014) is an auto-citation, and strong gradients in temp, salinity and pCO2 in shelf seas were shown in publications at least one decade before the paper by Rérolle.
----
1.22. P2809: "complete shielding from light" will not prevent bacterial growth
We no longer mention microbial growth and now the sentence reads as follow: “c)
prevention of phototrophic growth in the equilibrator by complete shielding from
light.” (P. 17, 3)
* COMMENT : Yes, but the fact of shielding from light does not guaranty that there is no biological alteration of the measurements, since there can still be bacterial activity in absence of light in the pipes and equilibrator
-----
1.28. Finally, there are several papers that have raised the issue of the impact of organic
acids on computations of the CO2 system in coastal waters. I’m surprised these aspects
are not mentioned/discussed (Koeve & Oschlies 2012; Kim et al. 2006; Muller & Bleie
2008; Kim & Lee 2009; Hernández-Ayón et al. 2007).
We have added to the discussion: “Several papers have raised the issue of the impact of
organic acids on computations of the CO2 system in coastal waters (Kim et al., 2006;
Hernández-Ayón et al., 2007; Kim and Lee, 2009). Dissolved organic matter produced
by phytoplankton during photosynthesis can potentially make a significant contribution
to seawater total alkalinity although we saw no evidence for this in our study (analysis
not shown).” (P. 15, 10-14)
* COMMENT : This is an important issue regarding CO2 measurements in coastal waters, and if the authors can demonstration that in their data-set there was no influence of organic acids, then this fully deserves to be shown in the paper, and being set aside with an « analysis not shown »
-----
P1 lines 16-17: What is an "ocean acidification cruise"? Reword please!
-----
P12 lie 9: Brackets are confusing, are they really necessary?
-----
P14 lines 21-26: This seems not at all connected to the rest of the manuscript. How do your results compare to those of Lueker et al. (2000)? Also, the grammatical structure of the paragraph could get improved.
-----
P16 line 7: "some cruise" should read "same cruise".
-----
Please provide the link to your data in BODC.
-----
Whenever appropriate, make sure that you cite all the relevant papers of the special issue.


Regards,
Jean-Pierre Gattuso

Dear Author,

Thank you for submitting a revised version of your manuscript submitted to Biogeosciences, which I am glad to accept for publication.

I look forward to seeing this paper published and thank you for considering Biogeosciences to publish these interesting results.

Best regards,
Jean-Pierre Gattuso
BG Editor