Dear Steve,

thank you very much for the revised version of your manuscript and the point-by-point reply to the concerns raised by the reviewers and other colleagues. I think your paper is almost ready for type setting and I’d like to conditionally accept it. However, there’s a few things left to do. What is missing here is any statement as to what the effect of using mixed coral- vs mono-species communities could be (I presume none except that you would have had to use many more flumes for incubating sediments alone, the different coral and the different algae species alone?). Furthermore, I missed in the intro and discussion/conclusion some sentences about the effects of OA on organisms beyond the reef-builders and sediments (cf eg Fabricius, K. E., De'ath, G., Noonan, S., and Uthicke, S.: Ecological effects of ocean acidification and habitat complexity on reef-associated macroinvertebrate communities, Proceedings of the Royal Society B: Biological Sciences, 281, 2014) and what your results will/could imply for the reef ecosystem.

In addition, there’s a few more, rather small issues that need to be addressed (see below).
Best, Helge (Editor)

Comment by Eyre on ripple formation etc. This probably addresses infiltration of SW into sediments when it flows over ripples, which is coupled to the upwellling of (reduced) pore water (ripples create a pressure gradient when overflown, similar to aeroplane wings; see papers by Huettel and colleagues).


L38 ff entire sentence reads odd. Check grammar (RE using “now”)
L 42: change “to studying” to “ for studying”
L 43: use adverb (ie “firstly”)
L 45: use adverb
L 46: change to “... and has not yet been used to..”
L 47: use adverb
L 47: reef communities can not be created, that would be a ‘divine’ act ;). Rephrase to “assemblages of reef communities can be monitored in ex situ experiments with (re)constructed reef communities” or the like.
L 64 ff. entire sentence. This belongs to the material and method section.
L 69 ff. This is far, far too much detail for an introductory section, and you repeat it in the M&M section. Lower level of detail to something like: We investigated the response of constructed reef communities to OA in flumes at ambient seawater- and elevated pCO2. Calcification rates (measured at three levels of biological function: whole community, sediments, and macro-calcifiers) showed... ADD ONE SENTENCE WITH THE MOST IMPORTANT RESULT
L 85: remove “2013”, this is redundant as you mentioned this before.
L 87: 2013 is redundant
L 90: do you mean “Richard B. Gump South Pacific Research Field Station”?
L96 ff: “it was not possible” reads oddly as if there were some technical constraints in sampling the sediments. It’s ok, that you didn’t measure redox gradients or the like, so rather write something like “....to allow chemical stratification to re-establish (note that chemical stratification was not monitored)....”
L102, add a comma after “flume”
L 104/L105: be consistent: either “XX cm (diameter - and rather use inner diameter)” or XX cm-diameter
L 140: as the total alkalinity method was the cause for some controversy in the reviews, I’d appreciate if you'd provide a very brief (!) description of the principal of this technique.
L 165: I presume you mean repeated “measures” ANOVA?
L 174: see above RE ANOVA
L 251: change to: “... 1996) was also ...”
L 253: change to: “...conditions are also similar...”
L 270: specify country to which Heron Island belongs to
L 281: “conditions of double ambient pCO2” reads oddly. Change to something like “..was detected at night when CO2 levels in the flume where equivalent to 2-fold elevated pCO2 in ambient air”
L 287 change to “has previously been shown to..”
L 293 change to: “..alone accounted for a decrease..” (exhibited a decrease doesn’t read well)
L 299 ff. This sentence doesn't read well and I don’t really understand what you wan to express (that your measurements of calcification rates of corals and coraline algae are similar and that this similarity underscores the validity of your approach to calculate calcification rates?)
L 311: “utility” doesn’t really fit here. I think that “suitability” or “usefulness” is better.
L 509: specify what each bar shows ( I presume Fx indicates different flumes?)

Dear Steve,

thank you very much for your revised MS, which I now accept in its current form.
You may, however, want to consider to think about the following two points (that I already addressed in the last round). These are rather minor, so I leave it up to you to judge whether theses points have been addressed sufficiently in the current MS.

The more important one is about the effects of OA on the community vs. single organism level. To make a definite statements about this, you would have had to compare, strictly speaking, incubations with constructed communities and parallel incubations of single organisms. I see that this would have been rather impractical as it'd have had implied using a lot of flumes, probably more that the the field station could have hosted. Instead, you have compared your results to previously published calcification rates mostly determined from the incubation of single organisms. This is ok, but you may want to add this information (in a very brief form in your discussion).

The second comment that might be relevant for your study is the one about ripple formation. When water flows over ripples it'll create a pressure gradient, which'll lead to the upwelling of reduced pore waters. The leaking of these reduced PW into the water column may then change alkalinity. One of the reviewers was wondering if this could have made an effect in your study. the same will be true for obstacles (like coral blocks), which may, in their lee, induce PW upwelling. However, I presume that the study design with respect to the arrangement of coral blocks etc was the same in low and high pCO2 treatments, so that any such effects would have similarly 'biased' your measurements. Again, I leave this up to you.

Best, Helge