General comments:

In this manuscript, Díaz-Rosas et al. study the distribution of Emiliania huxleyi morphotypes in the Patagonian fjords and relate their distribution patterns to extensive oceanographic data. Most importantly, they aim to test whether the distribution of E. huxleyi morphotypes with different degrees of calcification relates to regional gradients in carbonate chemistry and calcite saturation state. In addition, the coccolithophore distribution is compared with the neighbouring coastal and oceanic areas and northern hemisphere fjords with similar hydrographic conditions. The results of this study contribute to the ongoing discussions on the fate of coccolithophores and pelagic calcification under the projected decrease in oceanic pH and calcite saturation state. The study will be of interest to a wide range of readers, from biological oceanographers to researchers focused on biology, biodiversity and ecology of coccolithophores.

The manuscript is very well-written and abounds with novel data presented in a well-structured and systematic way. The methods are described in-depth and are suitable for addressing the aims of the study. The results are appropriately presented, discussed in a balanced way, and the conclusions are in line with the presented data. I find this manuscript suitable for publication in Biogeosciences, following some minor revisions. Specific comments are written below.

Specific comments:

- The authors should discuss the possible origin of morphological variability within E. huxleyi (especially within the morphotype A) in more detail as it has implications for the niche analysis and the overall conclusion of the manuscript. The heavily calcified “A-CC” and “R/hyper-calcified” morphotypes have been reported as stable under different environmental conditions (e.g. Von Dassow et al. 2018) and seem to be also genetically distinct (e.g. Hagino et al. 2011). On the other hand, the “light”, “moderate”, and “robust” morphotypes could also represent the continuum of phenotypic plasticity within the same genotype or population, though there is evidence that they are also genetically distinct (Young et al. 2014). If they are indeed the same genotype, the results of the niche analysis suggest that E. huxleyi morphotype A has a remarkably broad niche and is highly adaptable to changing carbonate chemistry or calcite saturation state while exhibiting different phenotypes under different environmental conditions. If each morphotype represents a separate genotype or a population, then their individual niches are narrower (e.g. as seen for the “light” morphotype), and they are arguably less adaptable to environmental changes. In any case, the use of “light”, “moderate”, and “robust” morphotypes in this study is valid as it provides a detailed insight into the degree of calcification found under different environmental conditions. Finally, the overall conclusion on the high adaptability of E. huxleyi as a species holds regardless of the nature of its morphotypes.

- in Figures 4 and 6, it would be useful to have station names written above the plots a), b) and c) so that the readers can immediately see which stations the series of plots are referring to. Currently, this is not immediately clear, and the information is only found in the figure caption.

- Line 415-416: “The low diversity of coccolithophores assemblages, dominated by E. huxleyi, is common to both the Patagonian and Norwegian fjord systems.”

The dominance of E. huxleyi and apparent low coccolithophore diversity may also represent a seasonal feature of both systems, as is the case in well-studied areas such as the Mediterranean Sea, where winter communities are dominated by E. huxleyi, while summer communities can have a larger proportion of other species. Detailed seasonal studies, including sampling along the vertical profiles, would likely reveal significant additional coccolithophore diversity in the Patagonian and Norwegian fjords.

- Line 111-113: “iii) does the abundance and relative composition of E. huxleyi morphotypes reflect populations in adjacent Pacific, Atlantic, or Southern Ocean waters or instead exhibit similarities to the Norwegian fjord system, suggesting it is shaped by local factors?”

The authors can consider leaving out the part: “suggesting it is shaped by local factors?” at this point while listing the aims of the manuscript. The explanations for the similar community composition in Norwegian fjords and the studied area can be addressed later in the discussion section.

- Conclusion point 5 – “Niche analysis shows that the moderate A morphotype and A-CC morphotypes are generalists, whereas the R/hyper-calcified morphotype has a more marginal (specialized) realized niche.”

Can this observation indicate that the R/hyper-calcified morphotype is truly genetically distinct (as was shown earlier, e.g. by Hagino et al. 2011), while A-CC is a part of the same population as the “light”, “moderate” and “robust” morphotypes (i.e. morphotype A)?

- The lightly calcified genotype (LC) should be addressed in the conclusions, as it shows a narrower niche than the other (“moderate” and “robust”) type A-related morphotypes.

- It would be interesting to include the other E. huxleyi morphotypes (B, O and B/C) into the expanded niche analysis (Figure 7b) to show how their niches compare with the different type A morphotypes addressed in this study. Of course, if the data on their distribution and abundance is available in the expanded dataset when coastal/oceanic sites are included.

- Line 509: “Our study of how E. huxleyi populations and morphotypes respond to the highly dynamic physical and chemical environments”

The authors can omit the term “populations” here, as the populations in the genetic sense were not studied in this work.

- Line 451: “4.4 Comparison of E. huxleyi morphotypes in Patagonia to nearby oceans vs. Norwegian fjords”

Rephrase, e.g. “to nearby oceans and Norwegian fjords”

- Line 490: “…eastern South Pacific (Beaufort et al., 2011; Alvites, 2016; von Dassow et al., 2018), although it has seen (and reported as rare)”

Should read “although it has been seen…”

- Line 502: “…a genetic underpinning of E. huxleyi morphotype (Krueger-Hadfield et al., 2014)…”

Should read “morphotypes”

General comments:

In this manuscript Díaz-Rosas et al. use Patagonian fjords as a natural study system to investigate the influence of calcification status on the niche of the calcifying phytoplankton species Emiliania huxleyi. In the study multiple E. huxleyi morphotypes are investigated, and their niche breath and scope are quantified using an ordination method called OMI analysis. The authors find that the more heavily calcified 'R/hyper-calcified' morphotypes show a smaller realized niche, while the less calcified 'A morphotype' shows a larger realized niche. Additionally, it is found E. huxleyi shows much higher tolerance scores than other coccolithophore species. The OMI results suggest that carbonate chemistry is the main driver of this difference in realized niche size, which implies that there is an important relationship between coccolithophore calcification status and carbonate chemistry.

This work has important implications for coccolithophore ecology, and provides a novel angle to the role of calcification status in coccolithophore niche. However, I would like to see more discussion on the implications these findings have on global carbonate production, and what it might tell us about the response of coccolithophores to ocean acidification and global warming.

I would also like to see more contextualization of the work with laboratory results in the discussion. Specifically in the context of potential mechanistic reasons for the observed trends.

For the OMI analysis, there should be a bit more discussion about limitations of the method. For example, how would adding parameters like MLD, light, nutrients and grazers change the results?

Finally, I would strongly recommend that the authors upload their data to a FAIR-aligned reliable public data repository such as PANGAEA (specially Tables S1-S3).

Specific comments:

line 36: coccolithophores are the main phytoplankton group to contribute to CaCO3 production, but not necessarily the main calcifying plankton group (see Buitenhuis et al., 2019).

line 37: not sure what it is meant with functional roles?

line 38: expand this to add some discussion about impact of the PIC:POC ratio on global biogeochemical cycles. (e.g. Ridgewell et al., 2007; Ridgewell, et al., 2009).

line 40: define calcite.

line 50: see discussion in Kottmeier et al., 2016, Gafar., et al 2018, Gafar et al., 2019, Paul and Bach 2020.

line 51: please add a citation to back up this statement.

line 85: Fjord systems

line 233: mechanistically pH, CO2, and HCO3- would have been a better choice, as calcite saturation state only indirectly influences sensitivity. See Kottmeier et al 2016, Gafar et al 2018, Gafar et al 2019, Paul and Bach 2020.

line 265 “Thereby, a species having a low OMI (species score close to zero, located in the center of the multivariate space) and high Tol is one that utilizes a wider array of resources and maintains populations within a wider variety of conditions (i.e., generalist), when compared with the specialized and less resilient species with more restricted realized-niche associated to high OMI and low Tol (Dolédec et al., 2000).”

This needs clarification. Although generally true, low OMI values do not necessarily imply a large niche breath and vice versa.

line 270: which environmental parameters were used for the OMI analysis?

line 273: where does the number of this correction factor come from?

line 372: Add another section here summarizing the main trends from Sections 3.1 and 3.2.

line 387: Patagonian fjords.

line 398: What about the Moderate A morphotype? %Rtol suggests that over half of variance is not explained by the OMI analysis?

line 399: This analysis is very interesting and an important part of the manuscript. Consider replacing 'complementary' with 'interspecies'.

line 414: Add some biomass numbers here.

line 426: Is there any satellite data for the Fjords? Why not?

line 439: What are some of these potential environmental and biotic factors?

line 440: briefly define sigma calcite.

line 556: clarify what you mean with 'more subtle patterns'.

line 458: morphologically distinct.

line 463: “Although the moderate-calcified and robust-calcified A morphotypes have also been shown to be present in eastern South Pacific coastal and open ocean waters 465 (von Dassow et al., 2018), the dominance of these A morphotypes was particular to Patagonian interior waters, as revealed by the IndVal analysis (these A moderate-calcified and robust-calcified A morphotypes were consolidated for final statistical analyses as they are not easily distinguished by objective morphological characters and were present in all samples, and preliminary analysis revealed completely overlapping realized niches). “

This is a run-on sentence which should be split for readability.

line 497: This is a interesting observation. How does it fit in with coccolithophore calcification state? The first OMI analysis suggest that the calcification state might influence tolerance, but this result seems not to support that? Why? What are the implications of this wide niche breath on global E. huxleyi abundance relative to other species?

line 504: clarify that the study specifically considers temperature and carbonate chemistry, but future environmental change will also include shifts in nutrient availability, mixing rates, and shallowing of the phototic zone. There may also be community shifts which could change biotic pressures like grazing.

line 508: Add a section here contextualizing the results with previous work on coccolithophore calcification and potential biogeochemical implications. How do the omega calcite and pH parameters observed in the Patagonian fjords compare to the RCP 8.5 2100 ocean?

line 513: Remove or define SS for readers skipping straight to the conclusion.

line 514: How small? What is meant by moderate abundances? What are typical Norwegian stocks?

line 518: replace important with abundance and generally rephrase. Why does high E. hux abundance in lower macronutrients imply that E. hux is most abundant when large diatoms are absent?

line 518: briefly mention what the difference is.

line: 525: dominance in.

References:

Buitenhuis et al., 2019 (https://doi. org/10.1029/2018GB006110)

Gafar et al., 2018 (https://doi.org/10.3389/fmars.2017.00433)

Gafar et al., 2019 (https://doi.org/10.1002/lol2.10105)

Kottmeier et al., 2016 (https://doi.org/10.1111/nph.13885)

Paul and Bach 2020 (https://doi.org/10.1111/nph.16806)

Ridgwell et al. 2007 (https://doi.org/10.5194/bg-4-481-2007)

Ridgwell et al. 2009 (https://doi.org/10.5194/bg-6-2611-2009) 

Review of the manuscript “Abundances and morphotypes of the coccolithophore Emiliania huxleyi in southern Patagonia compared to neighboring oceans and northern-hemisphere fjords”

Summary

In this manuscript, Díaz-Rosas and co-authors study for first time the coccolithophore assemblages in the Patagonian fjords/channels using surface and CTD plankton samples retrieved during late (austral) spring 2015 (in 21 stations) and early-spring 2017 (in 11 stations). The authors evaluate how a suite of environmental variables (such as sea surface temperature, salinity, calcite saturation state, etc) influence the coccolithophore distribution, abundance, diversity and biomass.

Díaz-Rosas et al. show that Emiliania huxleyi is clearly the predominant taxa occurring across a wide range of physico-chemical conditions and they thoroughly assess the degree of calcification of different morphotypes dwelling in the Patagonian fjords. Using an outline mean index niche analysis, the authors find out that E. huxleyi moderately calcified A morphotype (which dominates the E. huxleyi assemblages) exhibits the widest niche, and that the R/hyper-calcified morphotype displays a more restricted niche in the study area. Because E. huxleyi is observed in low pH/ calcite saturation state environments, Díaz-Rosas et al. emphasize the high capacity of E. huxleyi for adaptation to environmental change, in contrast to other coccolithophore taxa.

In this piece of research, the authors briefly compare E. huxleyi and diatom abundances and biomass within the study area, and they also compare their coccolithophore findings in the Patagonian fjords to available plankton data from the Norwegian fjords, as well as to other areas such as the eastern South Pacific, Southern Ocean, Drake Passage and the Atlantic Patagonian Shelf.

General comments

This manuscript addresses relevant scientific questions within the scope of BG and it is definitely of interest for the coccolithophore and the micropalaeontological communities. It is well written, logically structured, and presents an invaluable coccolithophore dataset, which has been thoroughly analysed by the authors using robust statistical/ecological tools.

The title reflects the contents of the manuscript and the authors present a good summary of their work in the abstract. The state of the art and the main aims of this piece of research are properly introduced in the first section. The scientific methods used in this study seem adequate and are described in detail in section 2 of the manuscript. In my opinion, mathematical formulae, symbols, abbreviations and units are correctly defined and used through the text. The interpretations and substantial conclusions proposed here have been logically derived from their findings, and supported by the original data shown in section 3 (Results). Figures and tables are clear and of high quality, which notably helps the reader (Tables such as 1 and 4 are just great!). I just have minor suggestions regarding the figures (see specific comments/technical corrections). I find that the references cited in the manuscript are adequate and the authors give proper credit to already published work. The supplementary material is extensive and of high quality. I would probably move some of the supplementary figures/plates to the main manuscript (see specific comments).

Specific comments / minor suggestions

Line 76: Specify where was this observed.

Line 181: I find interesting the information regarding the malformed coccospheres, although they are just marginally mentioned in the introduction and here. Maybe the supplementary material Figure S2 (i.e. the plate) could be moved to the main text and the authors could mention a bit more about malformations in the results section.

Lines 202-205. I am not a diatom specialist, but I am aware that in the Southern Ocean, many diatoms are colonial and chain-forming, and thus it is difficult to enumerate at a quick glance. Can the authors specify if the diatoms were counted (or semiquantitatively estimated) as frustules or valves? can they specify if the diatoms were broken or intact? I think that only frustules (= cells) should be compared to coccospheres. Maybe the authors can elaborate more on this point.

Lines 374-375: I am aware that supplementary material Figure S10 contains a lot of information. It is up to the authors, but I consider that it could be also moved to section 3.3 of the manuscript.

The following point has already been mentioned by #Reviewer 2. The authors already uploaded all the scanning electron micrograph image datasets in https://doi.org/10.5281/zenodo.4292020 and they state that all data resulting from this study are available from the corresponding author upon request, which is great for the scientific community. However, I think it would be worthy to also upload the rest of the valuable data shown in some of the tables from the supplementary material in an Open Access library/repository such as PANGAEA.

Technical corrections

Line 69: I recommend using either CO₃^2- or [CO₃^2-], just for consistency (e.g., see lines 40, 449, Table 2…)

Line 100: “and” instead of “but”.

Line 111: “and” instead “Focusing on the cosmopolitan E. huxleyi”

Line 233: Double check if you need “in situ” here.

Line 235: “We also included CO₂, which was moderately correlated with pH (Spearman correlation = 0.8)…”

Line 244: Are diatom abundances cells/L? Can the authors specify?

Lines 277-278: Either: “the potential biases from comparing data from both SEM and Utermöhl counts were minimized” or “the potential bias from comparing data from both SEM and Utermöhl counts was minimized”.

Line 308: “were corrosive to calcite” sounds rather dramatic. I would use: “where undersaturated occurred”.

Line 309: Here and elsewhere in the text. Because it is the beginning of a sentence the whole name (i.e.“Emiliania huxleyi”) should be written instead of the abbreviation (“E. huxleyi”)

Line 344: Add “taxa” or “species” after coccolithophore.

Line 475: “Niche analysis of E. huxleyi morphotypes…”

Line 564: E. huxleyi (in italics)

Figure 1: Is it possible to make the station numbers lighter to see them more clearly?

Figure 2 (caption). Since there is a coccosphere of E. huxleyi morphotype O in this figure, I guess the authors mean “The main E. huxleyi morphotypes recorded…” (delete A)

Figures 4 and 6: In the text of the manuscript, salinity does not have any units, I would delete “(psu)” for consistency.