General comments

The manuscript presents the results of a 3D coupled hydrodynamic-biogeochemical model over 2013-2020 period, investigating the seasonal and inter-annual variability of the pelagic ecosystem in Rhodes Gyre, a known site of Levantine Intermediate Water (LIW) formation. Given the lack of other 3D biogeochemical modelling studies in this area, the manuscript presents an important scientific interest. The biogeochemical model results are thoroughly validated and an extensive analysis is provided, adequately discussing different aspects of ecosystem dynamics, with regard to the impact of vertical mixing on phytoplankton growth, organic carbon fluxes and implications for carbon sequestration. Therefore, I recommend the manuscript acceptance for publication, following a minor to moderate revision, according to the comments listed below (in order of appearance).

Specific comments

L59

“Other studies have also reported LIW formations in the Gulf of Antalya (Sur et al., 1992; Kubin et al., 2019; Fach et al., 2021), in the southeastern margins of the basin or along the continental margins of the totality of the Levantine Basin (Brenner et al., 1991; Lascaratos et al. 1993; Özsoy et al. 1993).”

You could include the Cretan Sea, as a potential site for LIW formation, following Taillandier et al. (2022).

L192

“The position of the region respecting the set of criteria varying from year to year, we chose the smallest outline in order to cover the most of the gyre during the period of study.

Not totally clear how you specify the “smallest outline”. Please explain.

L206

“ The physical contribution of the budget is divided into two components: lateral transport and vertical

transport, both due to mixing and advection. “

In the lateral transport do you consider also horizontal mixing?

Because Eq.S3 probably refers only to advection by currents

L265

“Figure 2 shows the temporal variation of the satellite and modeled surface chlorophyll averaged all over the Levantine Sea”

Perhaps you could also show the model/satellite comparison for the Rhodes Gyre area. This would highlight the difference of this area, as compared to the Levantine basin and also validate the simulated inter-annual variability.

L281

“NRMSD (23%)”

I guess RMSD is normalized with data STD? Meaning that the error is 23% of the data STD.

You could clarify this in the figure caption and/or text

L299

“The model reproduces the general features of the nitrate and phosphate concentration profiles with an increase from the surface to 500-1000 m and a gradual, low decrease below (Fig. 3).”

Given that the model is initialized from observation profiles, isn’t that expected? Perhaps it would be more meaningful if the comparison focuses on the surface layer, as with Chl.

Also it is mentioned (section 2.1.3) that nutrients are initialized from summer CARIMED profiles, while summer nutrients are not included in Fig.3

L300

“The modeled phosphate and nitrate, concentrations in the transitional layer (500-1000), located between the intermediate and deep layers, are in the lower range values of observations.”

This can be seen mostly for phosphate.

L306

“PERLE 1 and PERLE 2 phosphate observations show high variability, with a SD ~ 0.065 and 0.062 mmol P m -3 respectively. “

The Taylor diagram seems a bit confusing. Blue dots should normally be the data points (correlation=1), not the model.

L370

“We display both nitrate and phosphate due to their role of limitation on primary production in this region (Moutin and Raimbault, 2002).”

Not sure what you mean here. Isn’t phosphate the main limiting nutrient?

L382

“Increases in plankton and DOC concentrations under the surface layer (0-150 m) are clearly visible during that period (Fig. 6). “

Not clear what you mean, as DOC follows a different pattern from phytoplankton (decreases during winter)

L386

“the surface nitrate concentration ranging between 0.3 and 1 mmol N m -3, in agreement with the observations of Yilmaz and Tugrul (1998)”

Does this refers to winter period? After April this is <0.1mmol/m3. Please clarify in the text

L422

“Lateral export is more important for POC, with values exceeding 10 mmol C m -2 d-1 over several months for some summer/fall, when the DOC lateral export shows little variation along the period (Fig. 7f). “

Any explanation for this?

L425

“in summer and autumn, when DOC can be injected into the surface layer.”

Not clear what you mean here. Please explain.

L436

“A secondary peak of OC respiration is visible in fall when the maximum POC concentration is the deepest.”

Not totally clear. Please explain.

L499

“The surface values fall in the lower range of observations (41-100 mmol C m-3), which could be partly explained by the locations of the observations, mostly outside the Rhodes Gyre in more stratified and less productive regions.“

Do you see such pattern (increase of DOC in less productive waters) in the model?

L507

“Regarding the organic carbon biological fluxes, the seven year averaged annual NPP that amounts to 115 ± 15 g”

Maybe you could add the mean NPP for the EM for comparison with other studies and also indicating the relatively higher magnitude in the RG area.

L515

“The mean annual POC export at 150 m depth is estimated in the model at 11.9 ± 3.4 g C m -2 year -1 .”

This refers to the Rhodes gyre area? Please clarify in the text.

L540

“The intensification of the cyclonic circulation in fall favors the shallowing of the nutriclines.”

I think part of this shallowing might be also related to the solar radiation seasonal variability and the deepening of the DCM.

Although this is partly illustrated based on the interannual variability, given that the study focuses on the Rhodes Gyre, it would be nice to show (maybe with a figure in the supplement) for comparison the difference from another area or an average over the Levantine where such shallowing of the nutriclines, related with the circulation does not occur.

L575

“On the other hand, the model PP relies at 30% on the uptake of nitrate, and at 70% on the uptake of ammonium (not shown). The former is significantly correlated with HL (R> 0.88, Fig. 10g) and MLD, whereas no correlation can be found between the latter and HL (R< 0.69, Fig. 10h) or winter mixing.”

This might be a bit misleading, as PP is generally well correlated with mixing/heat loss. I would suggest to rephrase

L601

“For example, the dates of maximum MLD and chlorophyll are in March during both the mild winter 2013-14 and the severe winter 2014-15 (Table S1).”

Not clear. Table S1 indicates 12Feb for Chl(2013-2014) and 20Feb for MLD(2014-2015). Please clarify.

Technical corrections

L74

“Ediger and Yilmaz (1996) highlighted interannual variability”

the interannual variability

L115

“we use a 3D hydrodynamic-biogeochemical coupled modeling”

we use 3-D ..coupled model simulations..

L146

“As for the Gibraltar Strait, a narrowing was conducted with a 1.3 km grid for a better representation of the exchange area between the Mediterranean Sea and Atlantic Ocean.”

Better rephrase

e.g. ..Strait, the model resolution was further increased…

L148

“and closer levels ranging near the surface.”

better rephrase e.g. and increased resolution near the surface

L151

“The SYMPHONIE simulation runs”

Better rephrase e.g ..simulation is performed from..

L154

“monthly discharges were based on the study of Poulos et al. (1997),”

you mean monthly climatology?

L156

“We used the daily 3D current velocity, temperature, salinity and vertical diffusivity outputs of the hydrodynamic simulations as forcing fields for the biogeochemical model run. “

Is salinity somehow involved in biogeochemical processes?

L175

“concentrations of nutrients were imposed at subbasin scale”

Not sure what you mean by subbasin

L211

“The internal variation of organic carbon inventory, biological term and lateral physical term were

calculated online,”

Please rephrase “online” e.g. calculated from model output

L259

“The hydrodynamical model was evaluated and validated “

“evaluated” and “validated” appear quite similar

L292

“could be attributed in part to an underestimation in winter of chlorophyll concentration in satellite data in the Levantine Sea”

rephrase to be more concise

e.g. an underestimation of satellite chl concentration during winter in the Levantine...

L318

“ In winter, the surface oxygen concentration is maximal coinciding with the peak of surface

chlorophyll.”

Rephrase e.g As with Chl-a, the surface oxygen concentration is maximum during winter..

L386

“Phytoplankton accumulation”

Not sure if accumulation is the wright word. Maybe phytoplankton growth?

L409

“the time series of the variation of the organic carbon inventory, of biogeochemical fluxes and

of vertical and horizontal exchanges at the limits of the two boxes.”

Rephrase

e.g. the variability of the organic carbon inventory, the biogeochemical fluxes and the vertical and horizontal exchanges at the limits of the two boxes.

L488

“We notice however an underestimation in the magnitude of the modeled maximum chlorophyll and dissolved oxygen concentration when comparing with both the BGC-Argo float and cruise data.”

You refer to the sub-surface maximum? Please clarify in the text

L561

“We found a significant correlation between nutrient injection and mean winter

HL (heat loss) or mean winter MLD (higher than 0.85)”

repeated above. Please rephrase or merge.

L700

“High interannual variability of annual”

The high…

FigS2

“Red dots represent the river mouths.” is repeated in the Fig.caption

This manuscript titled ‘Seasonal and interannual variability of the pelagic ecosystem and of the organic carbon budget in the Rhodes Gyre (Eastern Mediterranean): influence of winter mixing’ by Habib et al. presents a model description of the biogeochemistry and organic carbon budget of the Rhodes gyres. This gyre has a peculiar importance for the Mediterranean Sea since it is a major forming region of the Levantine Intermediate Water (LIW). The article is well written and thoroughly detailed. The research focus is original because of the lack of modeling studies focused on the eastern basin (and in particular on the Rhodes gyres). Overall, I recommend this article for publication after a few comments and questions detailed below are addressed.

The introduction gives rich background information, but the key research questions addressed by this study are not explicitly stated. I think the last paragraph of the intro (lines 112-116) could be reformulated to highlight the research gap that is addressed here and to make a short outline of the paper in a couple of sentences.

Methods are described in detail, yet, a few key information are missing. In particular, the time resolution of the model and the outputs are not described. Also, there is no mention of a model spin-up or of model drift (or absence of drift) in the biogeochemical variables. Some information is missing in 2.1.1 about the key features and the resolution of the model. Also, it is unclear from the Methods that the model is ran over the entire Mediterranean, which introduces some confusion in the results (see my comment below).

The paragraph in lines 141-150 relates to the model description and could go in 2.1.1.

Lines 156-158: did you do a spin-up of the model? Did you check for drift in the biogeochemical variables?

If I understand correctly, you used a model for the global Med basin and zoomed on the Rhodes gyres which you identified using the criteria you describe in 2.1.4?

In the introduction, the need for dedicated models of the Rhodes Gyres is highlighted (lines 99-103): “On the other hand, only one 1-D coupled hydrodynamic-biogeochemical model has been carried out in the Rhodes Gyre (Napolitano et al. 2000), while most 3D modeling studies investigated the whole Mediterranean Sea (Lazzari et al., 2012; Macias et al., 2014; Guyennon et al., 2016; Richon et al., 2017, 2018; Karaloni et al., 2020; Cossarini et al., 2021) or eastern Mediterranean Sea (Petihakis et al., 2009) without focusing on the LIW formation region of the Rhodes Gyre.” These sentences seem to imply that you are about to use a dedicated model of the Rhodes gyre. It's fine to use a model of the global basin, but I think it would be less misleading if the introduction and methods section mentioned explicitly your model domain. Maybe you could add a sentence at the end of the introduction saying that you are using a model for the global basin, as done in previous studies, but the originality is that you are using precise criteria for describing and analysing the Rhodes gyre?

The results are overall well described.

On Figure 7a, it looks like there is a drift in the OC inventory? Is that so? If yes, please discuss the reasons for it.

Although figure 7 is described in great details, I think the opposite trends seen between 7c and 7d could be mentioned and discussed. I find interesting that the NCP and total transport seem to compensate for each other during the cold winters (see the peaks at ~+60mmol/m2/d for NCP in 2015 that are outbalanced by the ~-60mmol/m2/d for total transport).

The paragraph on lines 437-445 could go after line 426 in order to group the results regarding the surface.

The discussion is overall well written and detailed, but some minor rearrangement could help making it easier to read.

The introductory paragraph on lines 476-489 can probably be discarded. This would help streamline the article.

Lines 515-522: You explain that your modelled estimates of POC export are different to those measured and those from other models. Can you give a short explanation of what may cause these discrepancies and the potential implication for your results?

Lines 575-580: Do you think the NH4 uptake could be linked with atmospheric deposition? Could the influence of atmospheric deposition of NH4 explain the absence of correlation between NH4 uptake and HL? (i.e. maybe NH4 uptake actually correlates with deposition).

There is a lot of information on Figure 11, but I’m wondering if all (or any) is necessary to the article. This figure focuses on 3 case studies over you time series and the long text associated is actually very descriptive. Maybe you could put this figure and the associated text (lines 582-607) in supplement and only keep in the main article a few sentences highlighting the key informations brought by those case studies.

Lines 609-629: this long text describing deep convection in other regions than the Rhodes gyre feels of place and can probably be discarded since they do not bring additional information.

Similarly on lines 639-646: this paragraph feels like a description of the figures 7 and 10 and should therefore go in the results.

Figure 12 focuses on a specific event over the time series and introduces some confusion. I think this example and the text associated could go in supplement.

Overall, maybe the discussion sections 4.3 and 4.4 can be merged and significantly streamlined. As it is presented, the text feels long and some paragraphs are very descriptive. Plus, the case studies of Figures 11 and 12 make it difficult to read the messages of the authors clearly. I think all text related with description of the figures should go either in the results section, or in supplement (for the text associated to Figs 11 and 12). The discussion should be limited to the key messages of the authors placing their results in the context of their research questions and the current state of knowledge regarding the carbon cycle in the Rhodes gyres.

Other minor points:

- Line 44: What do you mean by “after further transformations”, please reformulate.

- Line 91: ‘understanding its formation’, remove ‘of’

- Line 108: add a comma after ‘project’

- Lines 119-120: Either add references for the model, or discard these sentences because the model is described in detail right after.

-Line 215: “Because the number of observations in the Rhodes Gyre area are limited,...”

- Line 271, the equation does not display correctly.

- You could add a circle around the Rhodes gyre area on Figure 4b, similarly to the one on figure 1.

-Figure 6 precise that these are modelled results. I can’t see the green line in 6c. No mention of the C and M periods in the text.

- Line 356 replace “smaller” with “lower”.

- Line 377: “when the mixed layer depth increases” instead of “intensifies”

- Lines 635-636: I am not sure I understand this sentence. Please rephrase.

- Line 714-715: Is there other references for DIC budgets than this unplublished work?

The paper presents the results of a modelistic study in the Easterm Mediterranean sea with a specific focus on the Rodhes gyre, a permanent cyclonic structure playing an important role in the Mediterranean intermediate water formation (LIW) and displaying higher level of phytoplankton biomass during late winter-early spring in respect to the rest of the basin, which is well known for its extreme oligotrophy. The main aim of the study is to quantify the contribution, in terms of carbon fluxes in different forms, of the gyre activity to the Eastern Mediterranean basin biogeochemistry, and to connect their variability to physical forcing and the linked nutrient fluxes from different sources, with a key role played by the vertical transport. Most of the relevant processes and fluxes are included in the model whose simulations are build on the GCM Symphonie, already calibrated for the whole basin, whose daily averaged outputs are used for assessing the transport of tracers which react according to the formulations of Eco3-M model. The latter is a classical biogeochemical flux model validated in many previous studies (see refs in the text). Results are compared with different data sets, both from in situ measurements and from satellite observations. The match between data and model outputs is definitely good (see below for further comments) especially considering the differences in time and space resolutions among the compared data.

As the authors rightly comment (l.491) the resolution of in situ data does not provide a convincing test for a model performance, unless some macropatterns are missed. To some extent one would be tempted to rely more on the calibrated model outputs than on the interpolations/extrapolations of in situ data to assess global or regional fluxes. This is, indeed, the main contribution of the study, which flanks other recent modelistic studies carried out on the basin (cited in the text), though with the specific focus on the Rodhes gyre. The main conclusions of the study are: 1. that there is a net lateral export of fixed carbon from the gyre toward to the Eastern basin, in other words the gyre 'feeds' the basin, with the export being more significant than the utilization within the structure; 2. that the heat fluxes that drive the mixed layer dynamics correlate well with the nutrient fluxes and the main biological responses, suggesting that they are the dominant driver of biotic response.

While the latter is quite expected for the bottom-up structure of the model and for what is already well established, the former is the first quantitative assessment of the contribution of the gyre activity to the biogeochemstry of the basin and is an interesting result considering the closeness of gyres in respect to their boundaries.

The paper is quite long, likewise the discussion which is more focused on the comparison of the model outputs with other estimates than on the few observed discrepancies between the model and the observations.

From conceptual point of view there is a sort of circularity in these modelistic studies. The results of model simulations are consistent with the basic oceanographic processes, that are known since decades, which are at the base of their formulations. e.g., the sequence nutrient transport to the photic zone-mixed layer dynamics-phytoplankton growth. Since they do not include all the possible processes, and with the caveat of the difficulty to compare the results with observations carried out often at drastically different scales, e.g., Bio-ARGO data with model cells, what would deserve further analyses should be the mismatches. Instead, the focus is on the ability of the model to get as close as possible to the reality, which is certainly useful for operational purposes but not for a better understanding of the role of the many processes which are not included in the formulations. I am aware that the conclusion could be that they play a minor role but this is not tested. I consider this paper worth to be published because in all sections there is a comprehensive discussion of the existing information on the processes that the model simulates and because it provides useful results on the biogeochemistry of the Eastern Mediterranean.

My suggestion to the authors for this study or for its follow-ups is to analyze and discuss the following aspects: - The delimitation of the Rodhes gyre domain is based on hydrographical and geometric properties. Did they consider to delimit the domain using dynamic data, i.e., velocity fields?

- How do they interpret two evident mismatches, the vertical winter chl.a profile (fig.3 top left plot) and the systematic difference in the DCM depth (Fig.3 upper plots), and the overestimate of the model of the Chl.a maxima (Fig.2a).

- The model produces grazers maxima at the level of DCM, which is not what is generally observed especially considering that DCM phyto belong to the small size classes. Could they discuss this results analyzing which components of phyto and zoo are in those maxima?

- Table 1 reports interesting result on the interannual variability in carbon fluxes. These and the implications of the biogeochemistry of the basin are not discussed at all. Neither is discussed the weight of the gyre in the carbon fluxes of the whole basin.

- Both GPP and NPP display high values, for GPP maxima, in summer. Considering the water column structure and the position of the DCM, this should be mostly recycled production in the upper part of the water colums with, as a side effect, an accumulation of DOC (Figs. 7a, 7b and 11). Information on the players and comments on the mechanisms could be helpful.

Below minor suggestions/remarks

l.52 ...with surface temperature reaching 25 °C ..this value is an underestimate if the max considers all seasons (see El-Geziry, Acta Oceanol. Sin., 2021, Vol. 40, No. 3, P. 1–7, https://doi.org/10.1007/s13131-021-1709-2)

References

l.90 Palmiéri et al., 2015 wrong date or missing

l.140 Kessouri, 2015 either wrong date or missing see also l.967

l.713 & l.714 are they different? see ref. on l.1241 Otherwise Ulss et al. subm. is missing in the list