Dear Dr. van Dam

Thank you for submitting this work to BG. I have read the material and believe that a throroughly revised manuscript might be suitable. I therefore invite you to resubmit. Your paper will be re-evaluated by (a subset of) the referees.

With best regards, Jack Middelburg

Dear Dr. van Dam:

Thank you for submitting your revised paper to Biogeosciences. Your paper has been re-evaluated by two referees (#1 and # 2): both identified issues that require further attention, but they also believe that your data are worthy of publication.

Referee # 2 remains rather critical and has a different view on TA generating processes. She/he argues that anaerobic processes generate substantial alkalinity and that this should be incorporated more prominently in the text and your interpretation.

Referee # 1 is more positive towards publication (and believes you have adequately dealt with most issues of referee # 2 as well). However, she/he believes that there is additional data processing to be done (metabolic rate estimates and their uncertainty). She/he provided a detailed review of your revised manuscript.

I therefore invite you to revise your manuscript another time. Please have a detailed look at the feedback: more explicit discussion/incorporation of uncertainties (conceptually and numerically) will strengthen the conclusiveness of your paper.

With best regards,

Jack Middelburg, Associate Editor

Dear Dr. Van Dam:

Thank you for submitting your revised version to Biogeosciences. One referee had another look at your paper and she/he made useful suggestions to further improve the quality of your presentation. I therefore invite you to submit another revision which incorporates these suggestions. Moreover, I would like you to screen your figures for colour blind issues (do not use red and green together like in Figure 6 (see below for tips). Your revised version will only be inspected by me.

With best regards, Jack Middelburg, Associate Editor

Please find here (http://betterfigures.org/2014/11/18/end-of-the-rainbow/) a plea to help rid science of colour scales that can distort, mislead and confuse. Colour scales that are often illegible to those who are colour blind. See also: http://geog.uoregon.edu/datagraphics/EOS/. Please make sure that the color palettes that you use follow the recommendations outlined in these sites. Importantly, green and red colors must not be used in the same figure. This means that you need to redraw several of your figures.

Dear Dr. van Dam:

Thank you for submitting another revision to Biogeosciences. Your paper addresses an important but difficult to grasp topic. Some of your findings require further work to be conclusive and your paper may stimulate others to do so. I am therefore happy to inform you that your paper is now accepted for publication pending technical corrections.

With best regards, Jack Middelburg, Associate Editor

Corrections:
p. 1, l. 14: you use NEC here, but introduce it only in line 17. Please rewrite
p. 1, l. 17: ..were net dissolving carbonate minerals…
p. 4, Figure 1: it may be my printer, but the FCE-LTER sites are not green, more brownish. Please resolve.
p. 7, l. 22: due to the consumption of NO3- (or . consumption of HNO3). HNO3- does not exist
p. 8, l. 18: may not hold or may not be valid would be better
p. 8, l. 19 and a couple of times more: replace advection of spatial concentration gradients with advection in combination with spatial concentration gradients
(same applies to p. 14, line 6; p. 24, l. 21).
p.9, l. 16:…. at the low-density site
p. 21, l. 5: epiphytes? (they do contribute to NEP, not to clipping based production)
p. 22, l.26: deleted lately
p. 23, l. 16-18, related to figure 9. Given that protons are buffered (buffer capacity of seawater) and oxygen is not, is not surprising that correlations in figure 9 are rather poor. I therefore advice you to mention that protons are rapidly recycled through buffering.
p. 25, l.7: assess