Review of Liniger et al.

This manuscript uses remote sensing data products, together with some model output, to investigate whether changes in glacial melt can account for variability in surface chlorophyll-a and net primary productivity in two Antarctic polynyas from 1998-2017 (Amundsen Sea Polynya and Pine Island Polynya). The authors report observational support for a positive relationship between surface chla and glacial melt (but no relationship with NPP) in ASP, and no significant relationship with either variable in PIP. Instead, local processes at PIP seem to impact the bloom phenology. The authors investigate and discuss plausible mechanisms that may be operating distinctly in each region. 

The authors provide a speculative discussion on why the relationship between glacial melt and chla differs between the two polynyas and why chla and NPP appear decoupled in ASP. The methods and statistical analyses are appropriate, the manuscript is logically structured, and the figures are generally insightful. Ultimately, the study points towards interesting signals and empirical results and is therefore appropriate for publication. However, there are general concerns about the mechanistic interpretation of some of the signals, as well as queries about the quality and reliability of the chla data product in this region. There are a few further specific suggestions to improve the manuscript. 

General comments

Discussion of Chla and NPP relationships

The decoupling of NPP and chla in the ASP is a central feature of the results but is not given much attention in the subsequent discussion. The explanation that it is due to the vertical mixing that may concurrently be promoted by glacial meltwater is somewhat unsatisfying. In the first instance, there is presumably a spatial separation between these processes – the meltwater plume will promote mixing at or near the glacier face, but to what extent is that enhanced mixing present across the rest of the polynya area? In contrast one might expect the meltwater to enhance stratification once it settles at a level of neutral buoyancy. Has this proposed enhancement of vertical mixing, and its spatial extent, been described elsewhere in the literature?  Secondly, is your explanation that deeper mixed layers limit light availability and reduce NPP relative to chla consistent with the VPGM algorithm? In what way does that algorithm take mixed layer depth into account, and is it likely to capture variations in mixed layer depth due to glacial melt in this region? This is presumably testable by looking more closely at the chla:NPP relationship directly, rather than through the lens of their relationship with TVF. 

The claim related to the possible role of phytoplankton community composition needs to be described in greater detail. 

Chla product and uncertainty

Ocean colour is influenced by absorption from pure water, dissolved compounds, phytoplankton, and suspended sediments. Globally tuned chla algorithms do not always perform optimally in optically complex waters. In the context of this study, glacial meltwater could impart an optical signature potentially affecting the accuracy of chla estimates. Could the authors comment on whether the chla algorithm used is expected to handle such conditions, and how confident they are in its performance in the study region? Some additional analysis looking at the uncertainty in the chla fields or comparison with other available chla products (that use different algorithms) would be useful to gauge the potential impact of additional optical influences on the results. 

What influence does the number of visible days in the region have on the results? Is there reason to be confident that, in this region, a fraction of the primary production is not missed prior to the return of sufficient light for ocean colour to be detected? See a couple of recent papers that have noted possible distinctions between what the satellite sees and what growth is taking place, both with respect to the solar angle and the sea ice cover (McLish and Bushinsky, 2023; Douglas et al., 2024). 

Oceanographic context

The introduction could be strengthened by providing some background on the regional circulation and major water masses influencing the study area and how this differs between the two polynyas. Similarly, the description of the meltwater pump was somewhat lacking in detail. Expanding this section would help better frame and qualify the later discussion. 

Additionally, there is some confusing use of terminology that could be clarified. In particular, “ice shelf meltwater” and “glacial meltwater” seem to be used interchangeably throughout the manuscript, while “subglacial discharge” is used only once in the discussion but is not defined anywhere. Suggest using consistent terminology and provide a clear distinction between terms. 

Figure presentation

Many of the maps are too small, leading to overlapping of labels, and obscuring of data with overlaid markings. Please make maps larger, especially for Figures 4 and 6. 

Data availability and reproducibility

Please make sure to provide all details needed to locate and access the versions of the data products used, rather than simply links to the general websites. DOI’s should be provided where available. 

Specific comments 

L79: what does “natural” mean in this context? 

L147-153: Given the NPP dataset is central to the main results of the manuscript, I suggest including a few lines on how NPP was derived in the model. This would also be useful for the later discussion. 

L274: Why highlight the relationship between chla in ASP and TVFasp and Dotson ice shelf but not Crosson ice shelf?   

L304-343: Table 1 and Figure 4 show opposing relationships between chla and TVF for ASP and PIP. While the relationship is positive for ASP it is negative for PIP (particularly for Cosgrove where the relationship is quite strong). How do you interpret this difference? 

L333. Comments for Figure 4; 

- Suggest using black crossing to indicate insignificant correlations rather than significant ones. At present, it is difficult to read the magnitude of the correlations because the colours are obscured by the black crosses. 

- Consider repeating the labels from Figure 1 to guide the reader (at least for the ice shelves) 

- Ensure longitudinal labels are legible and not overlapping 

L421-422: “IRT and OWP are significantly related in the PIP.” Is this also true for ASP? Where is this relationship shown? 

L443-444: Did you do any pretreatment of the data, e.g. mean centering and normalisation? Please specify or alternatively, argue for why you did not do this. 

L454-456: The loadings (vectors) for OWP and IRT are very similar in ASP and PIP, both in their projections onto Dim1 and Dim2 and in their magnitudes. The main difference between the two polynyas with regards to OWP and IRT lies in the variance explained by Dim1. I suggest using this difference to support the statement that “...physical conditions might play a stronger structuring role…” rather than how they project on Dim1 and Dim2. 

L457-458: which is in line with the earlier correlation analysis showing opposing relationships between chla and TFV between the two polynyas. 

L476: Comment for Figure 7: 

General: Please explain in more detail in the main text how to interpret this figure, and PCAs in general, for the uninitiated. 

- Figure 7 and the accompanying text heavily relies on the use of acronyms. You might consider providing a legend next to panel b for ease of interpretation. 

- Please ensure labels are not overlapping 

L546: “settling depth” is unclear. Do you mean the depth of neutral buoyancy? 

Minor/technical comments 

L50: Reference Figure 1. 

L276-277: Delete duplicate sentence. 

L278-279: This has already been stated. Delete. 

L446: Please make sure you define all acronyms. “BD” is currently not defined. 

L454: As above, please define “BM”. 

L498: change “… and the modelling…” to and models. 

L519: delete “related”. 

References 

McClish, S., Bushinsky, S.M., 2023. Majority of Southern Ocean Seasonal Sea Ice Zone Bloom Net Community Production Precedes Total Ice Retreat. Geophysical Research Letters 50, e2023GL103459. https://doi.org/10.1029/2023GL103459 

Douglas, C.C., Briggs, N., Brown, P., MacGilchrist, G., Naveira Garabato, A., 2024. Exploring the relationship between sea ice and phytoplankton growth in the Weddell Gyre using satellite and Argo float data. Ocean Science 20, 475–497. https://doi.org/10.5194/os-20-475-2024