Dear Sergey and co-authors,

I have read the reports of the two reviewers and the answers you provided to their comments, based on that and on my own assessment of the work (please see my comments below), I recommend major revision of your work. I am convinced that the topic addressed in this manuscript (“impact of atmospheric extreme events (here cyclones) on the chlorophyll a dynamics and species composition”) is of high general relevance and in particular in the case of the Black Sea where it has not been very much investigated.
However, in its present form the manuscript needs substantial revisions.

Both reviewers have provided a list of extensive comments that I would like you to consider thoroughly.
In addition, I am providing an additional review. I would greatly appreciate that you address this list of comments.

Thank you in advance for your efforts,
Kind regards,
Marilaure

Editorial review (Marilaure Grégoire):
First, in the introduction, I missed an overview on the frequency of occurrence of such cyclones in the Black sea and current knowledge on how they modify the hydrodynamics and chla, RRS dynamics. Here only one year is investigated and I am convinced that the consideration of similar events would considerably strengthen the analysis and conclusions of the work. So my recommendation is to extend the analysis to other similar events.
Then, to better highlight the impact of such events I would suggest to compare the state of the system in two situations with and without cyclones (see my detailed comments below). For instance, Sur et al 1996 already evidenced the occurrence of strong coccolithophorids blooms in summer-fall due to baroclinic instabilities that are generated at the end of summer. Please demonstrate that the event induced by cyclones are really exceptional and how their impacts (on chla and RRs) are exceptional (in a quantitative manner).

In addition, as requested by one of the reviewers, I would appreciate that you better justify why an increase in Rrs is an indication of blooms of coccolithophores and not an increase of particles from deeper waters (e.g. the “suboxic zone” ) or from the shelf (as mentioned by the authors enhanced horizontal advection stimulates the transport of particles from the shelf to the southern coast).

After reading the whole manuscript, I am still puzzled by what is exactly the impact of such storms on the phytoplankton group composition. First, you mention that such events favor blooms of coccolithophorids but at the end of the paper, it is also mentioned that diatoms are stimulated. I would appreciate a clearer justification of the mechanisms at stake that explain why this storm favors the growth of coccolithophores and not diatoms. I also note that reviewer 1 does not clearly capture the mechanisms at stake, in some parts of the text we are told that the bloom is caused by an intensified vertical mixing but later in the text lateral advection from the shelf is evoked. So I really encourage the authors to significantly improve the writing.

Finally, the conclusion needs to be rewritten and more reflect the main messages from this manuscript. As it is now, it is a mixture of introduction (Lines 189-203) and results from the work and this dilutes the main messages.

Detailed comments:
Page 2, lines 58-60: please use a dot for a scalar product and bold symbols for vectors for clarity.
Please specify what is meant by “deep waters” e.g; page 4, line 81, line 96)
Line 85: nitracline? Nitrocline is used everywhere; please correct.
Line 112: I guess that your description mainly relates to surface chla or at least that seen from the satellite.
Legend figure 2: I would say “8-day averaged maps”.
It would be worth to compare with maps obtained for other years during which there is no cyclone (a climatological average).
Section 3.1: A figure illustrating how this (these?) tropical cyclones modify the Black Sea hydrodynamics (e.g. SST, Rim Current velocity, SSH, Ekman pumping) compared to climatological situation would be greatly helpful.
Section 3.2: Same remark as above: a figure highlighting how tropical cyclones modify the Chla dynamics and RRs compared to climatology would be needed here to convince the reader. For instance, you may add to Figure 3, the climatological average and show as in Figure 2 the spatial pattern in a climatological year.
Lines isobaths and not isobates
Line 179: deepening of the nitracline.
Line 208: a reference is needed after: “..promoting the favorable condition for the coccolithophores bloom”. Why an exec of phosphorus will favor coccolithophores compared to other phytoplankton species?
Lines 205-206: please explain how satellite date can show the development of the two types of phytoplankton blooms simultaneously (i.e. diatoms and coccolithophores). This does not appear in the results neither n the methodology.
Line 213: Please check the referencing throughout the manuscript: Kubryakov, Zatsepin et al., 2019 should be Kubryakov et al., 2019. You can use ‘a” and “b” if you have two similar references.

Dear Sergey and co-authors,
I have received the report of two reviewers who evaluated the revised version of your manuscript. One of the reviewers still raised important concerns that I would like you to address carefully. Reading the revised version of your work (before reading the comments of that reviewer), I have to say that I had very similar concerns. I find that you demonstrate quite robustly the impact of this tropical cyclone on the Black Sea physics and in particular on the intensity of the western gyre upwelling and Rim Current. However, the demonstration of the impact of this extreme event on the ecosystem is by far less robustly addressed and less convincing. In particular, the exceptional character of the coccolithophore bloom and on its dominance over other groups need to be more convincing. The reviewer also questions the algorithm that has been used to estimate the Chla and the abundance of coccolithophores. She/he underlines that the MODIS level 2 product is indeed not appropriate for Case2 waters and the Kubryakov et al (2019b) equation considers that the reflectance is due to coccolithophores only. Then, she/he asks to use specific algorithms 1) for case 2 waters for retrieving chla and 2) to retrieve TSM and then to clearly differentiate the contribution of coccolithophores to the Rrs. He/she made suggestions about algorithms that can be used.
I think that it is an important request that needs to be addressed because the novelty of this manuscript is the impact of the cyclone on the biology (and not on the physics since it has already been published). I am convinced that it would strengthened your message (please see the full review for details). She/he also requires a deeper investigation of the mechanisms that explain the dominance of coccolithophores during the event. I agree that as it is now it is still quite generic and that the absence of other species during this event (e.g. diatoms) needs to be better justified.
Then I would like that you address very carefully all the comments of the reviewer and that you provide a point by point answer to each comment with a clear explanation on how you plan to address them in a revised version. I have also provided a short review of your work here below. As said above, I urge you to give strong evidences of the impact of this cyclone on the biology. In a lot of places in the manuscript, this impact is described based on features that are not specific to this cyclone. A robust justification also requires an excellent data set on which the interpretation will be based.
In a lot of places, the manuscript is not clearly written and would strongly benefit from a careful reading and english editing. I am not a native speaker but I have tried to provide some suggestions (I realized that some suggestions that I made on the first version were not taken into account, so please check carefully).
Thank you so much for your efforts,
Kind regards,
Marilaure

Editor comment (Marilaure Grégoire)
Line 40 “Tropical cyclones mostly are observed at latitudes less than 30°” .. A reference is needed. Then, I will say “..an anomalous atmospheric cyclone ..” and not “the”
Lines 44-46: “Later, detailed statistics of cyclones of the basin on the base of the regional atmospheric model showed that eddies with similar intensity were detected over the Black Sea only 3 times over 30-year period 45 (Efimov et al., 2009)”. This sentence is not clear. What do you mean by “detailed statistics of cyclones of the basin” which regional atmospheric model? What do you mean by “eddies”?
Line 58: Please give the units of N and Bbp
Lines 60-61: “According to the used parameterization, the concentration value is more than 1.0∙106 cells l-1, i.e. bloom conditions, corresponds to the value of Rrs=0.005 sr-1. “. This sentence is not clear. Do you mean that the condition for having a bloom is a cell abundance higher than 106 cells/l which means, according to the parameterization linking Rrs and the cells abundance, a Rrs larger than 0.005sr-1?
Line 66: I would suggest to use v (and not  ) in vectoral form.
Line 67: please add a complete reference of the product
Line 87: “A quasi-tropical atmospheric cyclone…” why do you use “A” and not ‘The atmospheric cyclone..’ are you referring to the cyclone you are investigating in this manuscript? Or is it a generality of the effect of atmospheric cyclone? If this is the case then, a reference is needed
Line 92: “Such a divergence causes the compensating upward vertical motions and intense entrainment of cold waters from deep layers to the surface ..” I find this sentence confusing. First, upwelled waters are not coming from deep waters but from waters located at ~50-100 m depth (please specify) For a reader who does not know very well the Black Sea this needs to be clarified. Then, from what is written above (lines 87-90), the enhanced upwelling in the central part is created by Ekman pumping generated by the wind shear stress associated to the cyclone. Please clarify.
Lines 102-103: please be more specific. Why may? Do you have evidence that it happens? If yes, please gives a concrete example.
Line 109-110: I would say that it is the enhanced sea level anomaly gradient between the western central basin and the coast that intensified the Rim Current.
Lines 114-115: This delay in the response of the current to an intensification of the wind curl has also been evidenced in ..and is related to ..
Lines 116-118: please reformulate.
Line 133: Before the passage of the atmospheric cyclone..
Line 131: Chl as defined in the intro
Line 141: ..after the action of the atmospheric cyclone..
Line 146: “ .. which suggests the mainly mechanical nature of its increase…”. Please explain what is meant here.
Line 245: the number of cells associated with the maximum Rrs is still much lower than the value of 30 106 cells/l given in the introduction.
Lines 296: please reformulate
Line 301: the intense denitrification
Lines 307-308: I am confused. Do you think that there was photoinhibition in early October after the passage of the cyclone? Do you think that it was the photo-inhibition that could explain a (eventual) dominance of coccolithophores during this period of the year, especially after the passage of a cyclone that, as you show in the manuscript, considerably extended the mixed layer depth?
Line 309: do you mean heterotrophic dinoflagellates?
Lines 340-344: I do not understand the link between these 4 lines and the cyclones passage. This seems to be a generality about the occurrence of coccolithophores blooms in the Black Sea and in other areas. Please clarify the link or remove.
Line 340: I would say clacifiers or coccolithophores instead of calcified phytoplankton.
Line 356: correct the units
Lines 347-351: I would insist on the particular conditions associated with the passage of the cyclone that led to this anomalous boom. Here what is mentioned in (1) also happens when there is no cyclone. I would insist on the unusual Ekman transport that generated unusual upwelling, …
Figure 2: could you please add a legend for the arrow (length and velocity)? + give the source of the Seal level data in the legend.
Figure 3: I would reformulate the legend. “Temporal evolution during the passage of the cyclone of the SST, .., western cyclonic gyre .. extension of the coccolithophore bloom. Please specify what is meant by western cyclonic gyre (the black circle in Figure 2) same with the south continental slope (indicate on Figure 2 the region of averaging).
Figure 4: Chl
Figure 6: Instead of showing the RRs in December I would like to see snapshot in October because the coccolithophore bloom is usually observed at the end of summer (see e.g. Sur et al., 1994).


English editing
You use a mix of simple past, present perfect and preterit. Please check the manuscript and use consistently the same tense.
Line 8 : I would say “..causing a decrease in sea surface temperature of 15°C and an acceleration of the cyclonic ..”
Line 10: “Baroclinic instabilities of the plume boundary caused …”
Line 11: “These processes triggered ..” please use the same tense everywhere.
Line 37: “Weaker blooms are also observed in the cold period of the year .. ”,
Line 38: Kubryakov et al., 2019a
Line 40: “Tropical cyclones are mostly observed at latitudes less than 30° E”.
Line 41 “This cyclone had..”
Line 47: which led
Line 86: what is nitrocline? Please define. Is it nutricline or nitracline?
Line 91: rose by and dropped by
Line 94: “.. for September of..”
Line 95: felt
Line 96: “which was 13-15°C lower than the surrounding water SST (23-25°C) ..”
Line 96: The isotherm 10°C in the Black Sea in September was located ..”
Line 98: into the sea surface
Line 99: period of the year
Line 100: Nitroclyne? Check the whole manuscript
Line 110: the Rim Current
Line 119: was about
Line 135: spread of the Danube plume
Line 145 part of the sea
Line 148: transported
Line 151: Rim Current or Rim current? Please choose and use it consistently throughout the manuscript.
Line 159: caused
Line 184: remove however
Line 193: climatological values

Dear Sergey and co-authors,
I have read the revised version of your work and found that you significantly improve the manuscript. The reviewer is also satisfied with your replies to his/her concerns. Hence, I am happy to accept your manuscript for publication provided that you address the last concerns of the reviewer and a few more ones from my side.

Thank you so much for your efforts,

Kind regards,

Marilaure

Minor comments:
Abstract: line 10 cause an intense submesoscale process. Singular or plurial?
Line 85 : The Ekman transport “Wek” and the rotational (“rot”) are both vectors and should be either in bold or with an arrow (as chosen by the authors)
Line 106: Please replace “while in (Efimov et al., 2008), authors” by “Efimov et al., 2008 documented..”
Line 119: The Black Sea nutricline..;
Figure 1d, Please specify the convention for the sign of the velocity
Line 204: Please remove "however " since the section is starting.

Dear Sergey and co-authors,
I have read the last revised version of your manuscript and found that you successfully addressed the remaining concerns.

I am thus pleased to accept your work for publication in Biogeosciences,

Thank you so much for all your efforts during the review process,

Kind regards,
Marilaure