Dear Authors,

Thank you for your detailed responses to three reviewer reports. Please revise your manuscript according to your responses and also considering my own suggestions provided below. To expedite the final review process, I would like to ask you to make all the changes “clearly visible” in a marked-up manuscript and a point-by-point reply to the reviewer and my own comments.

1. Contributing factors for large inter-laboratory discrepancies
In general agreement with the very positive evaluations provided by three reviewers, I think that your work would contribute greatly to raising awareness of inter-laboratory analytical discrepancies among research communities employing CH4 and N2O measurements not only in the marine environment but also in various freshwater systems. Many researchers, including myself, would be interested in understanding major contributing factors for the reported (surprisingly large) inter-laboratory differences. The current version (and also your responses) do not provide an easy-to-follow summary of inter-lab differences in major procedures (starting from sampling storage) and an in-depth discussion of the relative importance of sample storage, gas extraction methods, and analytical accuracy. Details are now scattered through the text and in supplementary tables, so it is very difficult to attribute major findings to inter-lab differences in sample storage/preparation/analysis. As reviewers indicated, this issue of relative contribution is not trivial, because sample preparation and storage could override analytical inaccuracies. I wondered if you could provide an overview diagram or table (in the main manuscript) showing major inter-lab differences in sample storage (including gas sample storage after headspace equilibration), the used gas extraction techniques, and GC analysis. In discussing large analytical discrepancies, you could refer to this overview to allow readers to do some self-assessment of contributing factors.

2. Technical recommendations
In your response to a second reviewer comment, you just described your future plan for a "Best Practice Guide", indicating that this is not the primary objective. However, providing recommendations was implicated as an important goal in one of your four research questions (Q3). Please consider providing more detailed and specific recommendations, particularly in the concluding paragraph. For example, you could be more quantitative in your statements like “it is recommended to keep storage time to a minimum”.

3. Uncertainties in addressing reviewer comments
Some of your responses might need more articulation in the revised text. For example, in your response to a first reviewer comment on stopper/septa contamination and leakage, you just mentioned potential contamination, not considering the leakage issue. Regarding a comment on preservative issue, you cited some potential problems but jumped to a TINA conclusion: “however pending a community-wide evaluation of their effectiveness over a range of microbial assemblages and environmental conditions for both methane and nitrous oxide, we recommend continuing with a long-established method.”. I wondered if this statement would be logically acceptable given the problems described in the preceding sentence. Please double check whether you have fully addressed all reviewer comments in preparing the revised version.

Sincerely,

Ji-Hyung Park
Associate Editor, Biogeosciences

Dear Authors,

Thank you for addressing reviewer comments carefully.

I am pleased to let you know that your manuscript can be published in Biogeosciences after some technical corrections as described below.

- Please include (“briefly mention in the text”) your responses to the following reviewer comments in the final version:

Page 18, line 512: What would be their maximum recommended storage time? For samples with very low or high concentrations, analysis within 2 months is recommended. For samples with concentrations equivalent to or exceeding atmospheric equilibrium, analysis could be conducted within a slightly longer timeframe e.g. 6 months


Line 220: Why is there such variation in equilibration time for the gases; between 20 min to 24 hours? Has anyone done a time series of equilibration times to show what the time needs to be? This could be part of the recommendations. The longer equilibration times are due to overnight equilibrations in water baths. All laboratories should test equilibration time for the headspace analysis or the sparge time for the purge-and-trap technique, when establishing their own personal protocols for different sample volumes, temperatures, and sampling habitat.

“Please check whether the revised Table S7 has been properly uploaded”
Can you add a column in the supplemental table for N2O for how each person dealt with water, like what was done for methane? Water is a huge issue for N2O precision, and there is no mention of how water was dealt with. This is now included in Supplementary Table 7. As a quick response, water vapor is removed by most laboratories using a drying agent frequently in combination with Nafion tubing.

- Please include relevant references in the following newly added sentences (L 88-91):
The 89 purge and trap technique is typically more sensitive by 2-3 orders of magnitude over headspace 90 equilibrium. However, the purge and trap technique requires more time for sample analysis and 91 it is more difficult to automate the injection of samples into the gas analyzer.

- Optional suggestion:
Your responses to the many reviewer comments on technical recommendations (as summarized in Section 4.3), together with implications for ocean CH4 and N2O study, could be summarized as a concluding remark in the very general last statement of the abstract. I just want to remind you of the fact that your efforts for responding to those comments have not been reflected in the “intact” abstract.

Sincerely,

Ji-Hyung Park
Associate Editor, Biogeosciences