This is an excellent, data-rich contribution that sheds new light on the vertical structure of the tropical Indian Ocean during the Piacenzian. The integration of δ¹³C and δ¹⁸O records from benthic and planktic foraminifera and bulk coccolith fractions, combined with assemblage data, is novel and highly relevant for understanding carbon cycling and stratification in a key low-latitude region.

The manuscript is generally well-written, and the interpretations are thoughtful and supported by the data. The findings on the role of Florisphaera profunda in biasing bulk coccolith isotope signals are particularly important for future proxy studies. The linkage between orbital-scale variability, stratification, and global carbon cycling is compelling.

I recommend minor revisions before acceptance. The main points below aim to improve clarity, strengthen interpretations, and enhance the broader impact of this study.

Major Comments

1. Novelty and Broader Context

The study fills an important spatial gap in Piacenzian reconstructions by providing a tropical Indian Ocean perspective. Emphasizing how these findings complement better-studied Atlantic and Pacific records (e.g., in the Abstract and Conclusions) would highlight the significance of this work for global carbon cycle reconstructions.

2. Age Model and Orbital Phasing

The age model, tuned to LR04, is robust but introduces potential circularity when discussing phase relationships with orbital forcing. Because the phasing between pCO₂, δ¹³C/δ¹⁸O, and insolation is a core conclusion, a brief discussion of age-model uncertainties (e.g., ±kyr at tie-points) and their implications for inferred leads/lags would be valuable (e.g., Section 3.4 and Fig. 4).

3. Coccolith Isotopic Interpretation

The discussion convincingly attributes the lower δ¹³C and heavier δ¹⁸O of the coccolith fraction to the dominance of deep-photic F. profunda. Still, the relative influence of vital effects versus habitat depth and any diagenetic alteration remains qualitative.

• Please clarify how smear-slide observations (≥95 % coccoliths) support the interpretation of minimal diagenetic overprint.
• A table or schematic summarizing expected δ¹³C–δ¹⁸O offsets for key taxa (e.g., F. profunda, Reticulofenestra, Calcidiscus, Helicosphaera) based on culture or core-top studies would help readers contextualize the bulk isotopic signal (can be in supplemental material)

4. Productivity and Export Efficiency

The inference that high surface productivity during the mPWP did not lead to efficient export due to stratification is plausible but indirect. Acknowledging the lack of independent export-production proxies (e.g., opal, Ba/Al, %Corg) and noting that this remains a hypothesis would make the discussion more balanced.

5. Conceptual Framework for Orbital Controls

The evidence for obliquity-dominated deep-water variability versus precession-dominated surface variability is compelling. A simple schematic summarizing the proposed mechanisms (linking Southern Ocean ventilation, Indian Ocean stratification, and orbital forcing) would help communicate these insights to a broad readership.

6. pCO₂ and Isotopic Gradients

The discussion of leads/lags between δ¹³C/δ¹⁸O and pCO₂ (Fig. 5) is rich but dense. A brief table summarizing the key intervals (e.g., MIS M2 onset, KM2 event, mPWP peak), the sign of isotopic shifts, and hypothesized drivers (e.g., AMOC weakening, Southern Ocean ventilation) would improve accessibility.

Minor Comments

• Ensure consistent use of “coccolith fraction” vs. “bulk fine fraction (<20 µm)”.
• Improve legibility of figure axes and legends (Figs. 3–5; Supplementary Figs. S1–S2) for print and grayscale viewing (ie. increase font size slightly)
• A few recent studies on Indo-Pacific upwelling and Plio-Pleistocene productivity (e.g., Ford et al., 2022) could be cited to further contextualize results.
• Language is generally excellent; only minor copy-editing is needed to shorten some long sentences.

Recommendation: Minor revisions

This manuscript is a substantial and timely contribution to understanding tropical controls on Pliocene carbon cycling and orbital-scale climate feedbacks. Addressing the points above (particularly clarifying age-model uncertainty, refining coccolith isotope interpretation, and contextualizing productivity–export relationships) will further strengthen an already strong study.

The article “Photic zone niche partitioning, stratification, and carbon cycling in the tropical Indian Ocean during the Piacenzian” present novel δ¹³C and δ¹⁸O records from benthic and planktic foraminifera, and bulk coccolith fraction, which combined with assemblage data provides a unique view of the vertical structure in a low-latitude key region during the Piacenzian. Furthermore, this study also provides new insights to broaden the knowledge on the carbon cycling and ocean stratification in this location.

Overall, the manuscript reads well and presents a solid structure as all the critical points are addressed. Furthermore, the interpretation, which is deeply developed and grounded on a strong literature background, is supported by the data presented in the study. Particularly, findings on the processes connecting and biasing the δ¹³C signal between the different water layers are of great interest, and represents an advance in the understanding of the carbon cycle. Moreover, uncovering the effect of having high abundances of certain nannofossil species (e.g., Florisphaera profunda) represents a step forward in the interpretation of future proxy studies.

Based on the above-mentioned statements I recommend minor revisions before acceptance. Following lines provide a series of suggestions intended to improve the clarity and readability of the manuscript.

General comments

Methodology

In section 2.3 Benthic foraminifera carbon and oxygen stable isotopes, the authors clearly state a step-by-step process to achieve the δ¹³C and δ¹⁸O records presented. However, I wonder if there were any further cleaning steps to ensure the usage pristine benthic and planktonic foraminifera species or if samples were already good enough after the disaggregation and subsequent sieving process. In this regard, I would recommend adding a plate with some images of the remaining specimens from some of the samples used (if possible). Otherwise, I would clearly state that samples condition was already good enough for the measurements without further cleaning protocols.

Results and discussion

First of all, I want to emphasise again how pleasant it was to read this section. It clearly expresses the authors hypotheses in a really narrative and natural way, which makes it easy for the reader to understand.

In section 3.1 Vertical water column plankton community structure, the authors present the δ¹³C values for the benthic and planktonic foraminifera, and the bulk coccolith fraction. Specifically, the authors express in Lines 203-204 that “This similarity in the range of δ¹³C values with the benthic record may indicate a partial integration of deep photic zone DIC signals, especially under stratified conditions.”. Despite that I absolutely agree with the fact that integration of deep waters signal within upper layers (specially during high stratified periods), I cannot happen but wonder, how is this relation working for getting lower δ¹³C values on the bulk coccolith fraction. Lately (Lines 209-211), the authors evoke recycling of organic carbon and stratification as potential mechanisms explaining the difference between the bulk coccolith fraction and the planktonic foraminifera. Could this be also the case for the lower values compared with the benthic δ¹³C?

As already stated by reviewer 1 (point 6 of major comments), I consider that adding a table with the δ¹³C, δ¹⁸O and the Dδ¹³C and Dδ¹⁸O values for key intervals would improve accessibility and serve as core for readers while going through the discussion. Furthermore, in section 3.5 Regional feedback and global context in a warm, high CO₂ world, the authors evoke a series of very specific processes and scenarios, such as MIS M2, which is characterised by a low productivity, enhanced stratification and low export efficiency according to their interpretations. In this regard, I would suggest to add a figure with a sketch to help the reader to visualize the conditions described in the text and guide them through this part of the discussion.

Specific comments

• As stated by reviewer 1, using both “coccolith fraction” and “bulk fine fraction (<20 µm)” can be confusing. Therefore, I suggest to use one of the terms consistently through the manuscript.
• The benthic foraminifera species wuellerstorfi has recently be renamed as Lobatula wuellerstorfi (please, for specific details refer to https://www.marinespecies.org/aphia.php?p=taxdetails&id=112890). However, I understand that most of the studies still consider the name C. wuellerstorfi when referring to this benthic species.
• Writing and grammar are excellent and only a quick check to correct typos need to be done.

Decision: Minor revisions

The manuscript provides a novel contribution to understanding the carbon cycle, and its relation to orbital-scale feedback processes during the Pliocene. I believe that implementing the above-mention comments within the manuscript will provide clarity and accessibility to a broader audience, and provide additional support for this work.

The manuscript of Tangunan et al. “Photic zone niche partitioning, stratification, and carbon cycling in the tropical Indian Ocean during the Piacenzian” constitutes a valuable paleoceanographic reconstruction that provides new insights into the vertical structure and water masses dynamics of the tropical Indian Ocean during the Piacenzian.  

The manuscript is well written, conceptually strong, and presents a novel dataset from a climatically critical but understudied region. The high quality of the research is expressed by the complex multiproxy approach based on high-resolution δ¹³C and δ¹⁸O records from benthic foraminifera and bulk coccolith fraction, low-resolution planktic foraminifera integrated with high resolution coccoliths assemblage data. The integration of multiple depth-habitat proxy and the calculation of isotopic gradients is a particular strength. The spectral and wavelet analyses clearly show the control of the different orbital parameters on stratification and global carbon cycling. The overall hypotheses are strongly supported by the data presented. The findings are significant for understanding low-latitude ocean dynamics and their role in global carbon cycling during intervals of global warmth and transient glaciation.

I believe the manuscript deserves to be published in Climate of the Past following minor revision before acceptance.

General comments

Introduction

• I would suggest to include a map to show the location of the site, the eddies and the pathway of the Agulhas Current.
• Please specify that even the coccolith assemblage data are at high resolution (Lines 86-91).

Methodology

• At the beginning of section 2.3 the author writes that “In intervals where there is not enough wuellerstorfi, other Cibicidoides species (i.e., Cibicidoides bradyii, Cibicidoides mundulus) or Uvigerina s pecies were chosen”. Can you please clarify why you excluded δ¹³C Uvigerina values? (Line 120)
• I suggest specifying the preservation state of the shells and/or if a cleaning procedure of the shells has been followed. Please specify even if the picked shells have been crushed before the measurements.
• Please add some information in section 2.7 concerning the slides preparation technique and how many coccoliths have been counted/ number of frames analyzed.

Results and discussion

The detailed discussion of the Florisphaera profunda dominance and its isotopic implications is remarkable, underscoring the role of deep-photic species in shaping bulk isotopic signature. However, I agree that the influence of the dominant taxon may obscure signals from shallower-dwelling forms. This might be the case of Reticulofenestra spp. which shows an important contribution not only in the assemblage, but also in the coccolith mass and especially in the carbonate contribution where the mean value (43%) is higher than F. profunda. I agree with the authors which state “This highlights the need for species-specific geochemical analyses to resolve the contributions of individual taxa to the bulk signal”. As pointed out by reviewer 1, the inclusion of a table summarizing expected δ¹³C–δ¹⁸O offsets for key taxa (e.g., F. profunda, Reticulofenestra, Calcidiscus, Helicosphaera) is recommended.

Conclusion

• I would specify that coccolith abundance data are at high resolution here as well.

Specific comments

• Using both “coccolith fraction” and “bulk fine fraction (<20 µm)” could confuse the reader. I also recommend adopting a single term and applying it consistently through the manuscript.

• Please add the reference for the orbital parameter curves in the figure captions 3 and S1 (obliquity).
• Overall, the language is excellent, requiring only minor copy-editing to improve sentence conciseness.

Recommendation: Minor revisions

The manuscript has clear scientific merit and represents an important contribution to understanding tropical ocean stratification and carbon cycling during Pliocene. Addressing the above-mentioned points will strengthen the paper and its clarity.