Reply on RC3

Comment The present manuscript by Francois et al., 2022 presents a field study of Caribbean tropical foraminifera in the Puerto Morelos reef Lagoon. Six stations were sampled in October 2011 along a broad natural pH gradient generated by submarine springs. The study of spatial variability on foraminifera fauna driven by pH gradient is an original approach. This work shows interesting results that corroborate knowledge already known/suggested in previous studies. However, this manuscript deserves to be restructured and clarified on some major points before publication.

It should be kept in mind that specimens come from the natural environment (not a controlled experiment) so multiple stresses can potentially influence calcification (salinity, eutrophication, pollution, warming...) these other parameters should be further discussed according to what is known about the site in previous studies.
Reply: To address this comment, we now performed multiple regression analysis considering all measured variables (carbonate system, temperature, and salinity). They were compared according to their contribution to the model's Akaike Information Criterion (AIC), and the models with lowest AIC value (i.e., highest fit) were select to the analysis. Notably, consistent with previous studies we find the temperature and salinity have limited effects and the sites are not polluted so this is not a consideration.
We have added a discussion about salinity and for eutrophication/high nutrient concentration the following paragraph was already included in the manuscript: "The springs from PM also have high nutrient concentrations compared to the open waters in the region (Null et al., 2014;Crook et al., 2016), however, near spring assemblages did not change towards opportunistic dominated assemblages, suggesting that the nutrient availability does not exert a major control at this site. Rather, the high-pH assemblages heavily dominated by small calcareous forms were replaced by larger symbiont-bearing species near the springs (Fig. 4a-e). Symbiont-bearing species are known to be sensitive to high nutrient loading, likely because of changes in turbidity/light regimes and their dependence on algal symbionts to enhance growth and calcification (Hallock et al., 2003). At PM despite higher nutrient levels the waters at the springs are clear and light regimes are not reduced." Regarding warming, this is not considered to influence the species distribution as temperature changed very little and for pollution we have analyzed the concentrations of the metals (Paytan unpublished), and the concentrations were not significantly higher at the discharge sites when compared to the control sites. We do not have a lot of heavy metal data because it is a lot of work and when we found that the concentrations at the springs were not high, we did not analyze anymore. Thus, we decided to not include this information, but we could add a sentence along the lines -preliminary data for heavy metal concentrations did not show significant differences between ojo and control sites hence we do not attribute the changes in foraminifera calcification observed to impacts of heavy metals.
Comment -There is a need for the bibliography to be more up to date especially those published on LBF and µCT. I suggest this non-exhaustive list: Charrieau et al., (2022) Reply: The low number of fully stained foraminifera is probably not associated with seasonality since it is a common pattern in the Caribbean and even in pristine (off-shore) reef environments (Barbosa et al., 2009(Barbosa et al., , 2012, Marine Micropaleontology) as most reefdwelling taxa live on phytal or hard substrates rather than directly on the sediments.
About the use of total assemblages (live + dead tests), this approach has extensively been used in the literature in the last decades to assess mid-term responses of foraminiferal assemblages to environmental conditions (e.g., water and sediment quality), including for changes in carbonate system (e.g., Uthicke et al. 2013, Scientific reports, DOI: 10.1038/srep01769). It happens that the accumulation of foraminifera tests in the sediments integrate the effects of stressors over time (Hallock et al., 2003;Environmental Monitoring and Assessment, DOI: 10.1023/A:1021337310386), and also of small seasonal fluctuations of the assemblages, providing an ideal indicator of the foraminifera responses by reflecting the prevailing marine conditions. (Scott and Medioli, 1980; Journal of Paleoecology; DOI: http://www.jstor.org/stable/1304312).
It is important to note that the present research was also motivated by the results presented in Martinez et al., 2018(Biogeosciences, DOI: 10.5194/bg-15-6819-2018) that also used total assemblages from Puerto Morelos to investigate the effects of low pH/saturation state waters. To compare our results we followed the same approach.
About the study on phytal and rubble substrates it would rather address the species responses within a particular point in time, which wasn't our objective. However, to expand our discussion we briefly discussed the stained counts, i.e., mainly dead, recently deposited tests (most had some degree of staining but were not fully brightly stained) because as stated above the species don't live in the sediments. Specifically, we mentioned the behavior of the most abundant species, Rosalina globularis, comparing our results with Di Bella et al. (2022) that specifically observed a resilient behavior for this genus in the low pH venting sites of Panarea.
Comment -You need to clarify which data are common with the paper by Martinez et al., (2018). It seems to me that you have the same dataset or a selection of them. If you share other data from this previous paper, please indicate it clearly (this can also help to reduce the manuscript).
Reply: The carbonate chemistry, temperature, and salinity data from 7 samples were based on those presented in Martinez et al., 2018. Here the data set was complemented with 20 mid-ranges samples collected at the same day following the same protocols described by Martinez et al. (2018) but not reported there.
As suggested, this information was added to the manuscript.
Comment -Your data are related to the impacts of a natural pH gradient on a series of stations at a specific date (October 2011). You are therefore looking at spatial variability of foraminifera along a pH gradient and not at temporal variability. If you want to discuss temporal projections, I will discuss this in a discussion section. To discuss temporal projections, you need to be more nuanced because you need to know the seasonal variability of the living fauna and their interannual variability and species metabolisms (maybe you have some previous studies on this site).

Reply:
We agree with the referee that the assemblages response are associated to a spatial variability of the environmental data, but as explained above the use of total assemblages also imply a temporal (i.e., generational) factor to the assemblages response. That is the data represents the response of multiple generations of forams accumulated probably over decades (representing the upper ~ 1cm of sediment).