General comments

In this manuscript, Valentin Deteix and colleagues analyze the size structure of phytoplankton biomass and primary production in the Southern Indian Ocean during the austral summer of 2023. The authors partitioned the phytoplankton community into three size classes: picophytoplankton (< 3 μm), nanophytoplankton (3–20 μm), and microphytoplankton (> 20 μm). They then estimated the contribution of each size class to total Chlorophyll-a (TChl-a) and net primary production (NPP) across all stations analyzed. Furthermore, the authors estimated the contribution of major phytoplankton groups to Chl-a within each size class. Their findings indicate that TChla was primarily controlled by the nano- and microphytoplankton size classes, while integrated NPP was dominated by the microphytoplankton size class. Regarding phytoplankton group contributions to total Chl-a, the data revealed a latitudinal gradient consistent with previous reports in the Southern Ocean. These data are particularly interesting because phytoplankton studies often focus on specific groups rather than on the entire phytoplankton community. Moreover, the study area is an undersampled region of the global ocean, and therefore, the presented results are valuable and deserve to be published.

Overall, the manuscript is well-presented and reasonably well-written, the methodology is appropriate, and the figures are of good quality. However, several points require improvement. In general, the authors differentiate phytoplankton by size and major groups but scarcely mention the phytoplankton species or genera present in the region. Although their methodological approach does not allow for species-level identification, comparing their results with previously published information on the species present in the study area could aid in some of their interpretations. Additionally, the description of the results, which often refers to stations numerically, is sometimes difficult to follow. It would be helpful to refer to the zonal systems where they are located, as this would improve the readability of the text. Below, I include a series of more specific points that the authors should consider for the next version of the manuscript.

Abstract

Line 16. Could the authors specify the regions analyzed during the experiment?

Line 40. The term "irrelevant" is not the most appropriate here. Maybe "insufficient" or "too general"? Please rephrase.

Line 49. Please replace the comma with "and" before dissolved inorganic phosphorous.

Line 58. What about silicate concentrations in the AZ?

Line 60. "SIO". Please reduce the use of acronyms such as this one. It will facilitate understanding of the text.

Line 65. "Euphotic layer". Do the authors mean deeper layers of the euphotic zone, or subsurface layers of the photic zone? Please rephrase, as the upper surface layer (mentioned in the previous sentence) also belongs to the euphotic layer.

Line 69. Please add "and" before Heard and McDonald Islands.

Line 74. Please provide background information about the differing roles of the different phytoplankton groups and size classes in the biological pump. So far, it is not clear in the text why it is important to differentiate between phytoplankton size classes.

Line 79. "The long-term monitoring of oceanic CO2 parameters in the SIO". Please provide references.

Line 92. Could the authors relate these regimes to the stations shown in Figure 1? This could be done either here or later in this section.

Figure 1. Please identify the islands on the map.

Lines 99-103. So, this means that different depths were sampled at each station? Please clarify and provide specific depths somewhere in the text or as supplementary material.

Line 200. Please write SML in full the first time it is mentioned in the text.

Line 201. This information is very interesting, but it would be useful for the non-specialized reader if it were explained in further detail why values lower than the Redfield ratio are interpreted as N limitation. Please also extend your explanation to all the statements related to nutrients in this paragraph.

Line 209. What values are suboptimal and why? Please explain in further detail.

Lines 247-249. "By normalizing NPP to TChla (NPPTChla, mgC mgTChla-1 d-1) which can reflect photosynthesis efficiency under given environmental conditions (e.g. light/nutrient availability; Cermeño et al., 2005), NPPTChla TOTAL was maximal in the SML at all stations, except at O3 and O6 where it peaked below the SML, and decreased with depth (Fig. 2k-o; Fig. A3 in Appendix A)." Please rephrase this sentence.

Line 309. This is interesting because dinoflagellates are often relatively large. Do the authors have an idea of the species present in the study area? Could you refer to the existing bibliography to hypothesize possible components of this group of organisms within the study area?

Lines 311-312. "As expected, cyanobacteria (Prochlorococcus and Synechococcus) biomass was mainly distributed in the picophytoplankton, but also surprisingly detected in the nano- and microphytoplankton." Could the authors provide a possible explanation for these results? Was sieving not effective? Were they attached to larger phytoplankton? Did they form colonies? Please provide possible explanations in the discussion section.

Line 369. The title is vague; please rephrase.

Line 378. Could you please associate these stations with environments/zonal systems?

Line 390. The term "global" is misleading; please rephrase.

Line 392. I would suggest using the term "similar" instead of "are in agreement," as the regions are not directly comparable. The Atlantic and Indian oceans exhibit different physical and chemical distributions, which hamper direct comparisons between regions.

Lines 417-420. The relationships between pigments and phytoplankton groups should be presented in the Materials and Methods.

Line 419. Please, do not capitalize "diatoms."

Line 421. "Inter-zonal spatial variability of phytoplankton biomass…" The title of this section is unnecessarily complex. Why not simply "Geographical distribution of phytoplankton biomass"?

Line 424. Please provide references documenting similar changes in the size and/or composition of phytoplankton assemblages between the STZ and the Southern Ocean.

Lines 425-427. This part of the discussion is unclear. The authors list the main factors controlling the spatial distribution of phytoplankton, but in the second sentence, other parameters are addressed. I would suggest that the authors commence with their findings, then compare results with studies in the literature that found similar results, then with studies that do not match (if such studies exist), and then reach a conclusion based on all the evidence presented.

Line 426. Is salinity an important factor determining phytoplankton distribution in the study area, or is it just a spurious correlation? Please provide references that support the influence of salinity on the distribution of phytoplankton groups in environments similar to those analyzed here.

Line 449. "Phytoplankton chemotaxonomic groups biomass". How similar or different are the STZ of the Atlantic and Indian oceans in terms of physical and chemical parameter distributions? This should be mentioned somewhere in the text, as comparisons with the Atlantic sector are frequent.

Line 452. It would be interesting for the reader to mention some possible species that account for much of the biomass of the phytoplankton groups addressed in the discussion. This information would strengthen the interpretations. For example, there are several studies by Shramik Patil et al. that documented coccolithophore species distributions in this region, and there must be papers documenting diatom assemblages as well. Also, it is interesting that diatoms account for a substantial fraction of the nanoplankton. Diatom species are often larger than 20 micrometers, so the number of species smaller than 20 micrometers must be quite limited. The authors should revise the available bibliography in the study region to put their results into a broader context.

Lines 481-482. Please explain in further detail the findings of Lamont and Barlow mentioned here.

Line 482. It is the first time the authors refer to NPP fluxes; please explain the units when presenting this parameter either in the Introduction or Materials and Methods.

Line 511. Which value range is considered suboptimal and why?

Line 512. "Si availability hypothesis" — shouldn't this be "Si limitation" instead?

Line 512. Please replace "noticeable shift" with "noticeable difference."

Lines 517-518. Please rephrase this sentence, as you indicate the purpose of the ratio twice.

Line 567. Please do not capitalize "chlorophytes, dinoflagellates and cryptophytes."