Dear Carolina Cisternas-Novoa,

First of all I would like to thank both reviewers for their insightful reviews and you for your comments. I agree with both reviewers that you need to streamline the text and reorganize it to get a better flow and the manuscript becomes easier to read. I think that the comments of reviewer #1 will be especially helpful for this. Unfortunately, your reply doesn’t make it easy for me. This big block of text in which I have to find out myself where the comments begin and end and your replies begin is a bit unclear. Especially replies that basically say that you will modify the manuscript according to the reviewers specifications, without actually stating how it might look in the modified manuscript. For quite a few comments I now have to trust you will actually make the changes the reviewer asked for without being able to judge now if you are on the right track. It would be great if you could include a better structured and easier to follow rebuttal with you modified manuscript, each comment and response separated by a blank line and, for instance, the comment in italics and the response just plain text.
As for the comment about line 297, I think the reviewer means that these percentages are a bit confusing. I assume you mean that chlorophytes represent 25% of the phytoplankton > 5µm and Planctonema 4%, right? There are methods of counting filaments other than just the number of filaments, using a counting grid and grid crossings for instance, bit old fashioned maybe. The thing is that comparing filaments and unicellular organisms based on just numbers is a bit meaningless, they have completely different number to biomass relationships. Something to think about.
As for the main comment of Dr. Tom Jilbert. I am not sure you can get away with this so easily. His suggestion is that mixing of different water masses and replacement of old water masses with new ones resulted in low Si(OH)4 and PO4 at depth independent of scavenging by MnOx. So the end result might be similar, low Si(OH)4 and PO4 at depth and high MnOx, the mechanism might very different. Both linked to water mass mixing and oxygenation, but without a causal connection between the two. You might need to put a little more attention to this comment than you have in the rebuttal so far.
I trust you will do a thorough reorganization and rewriting of the manuscript and a better organization of the rebuttal so it will be easier for me to keep track of everything. I am looking forward to the revised manuscript.

Marcel

BG-2018-360 decision

Dear Carolina Cisternas-Novoa,

First of all I would like to thank both reviewers again for their insightful reviews and you for your better organized comments. I think the manuscript has improved significantly, but do still have some smaller and perhaps bigger issues. I guess one of the more major comments has to do with your MnOx-like particles, they are MnOx-like up until page 31 and then they become MnOx? Looking at your M&M section, I am not entirely clear what they are. If the method you describe for measurement of these particles is known to target MnOx particles I would expect one or more references indicating this. If not, than how do you know what these particles are? If they do contain MnOx, please indicate how you know, is MnOx-like the best name for them? MnOx containing might be better?
What is CSP? I know what it stands for, but what is it? Proteins or particle containing relatively large amounts of proteins? Is CSP correlated to DI?

Minor comments:
Line 16: “Sinking particles are the main form in which photosynthetically fixed carbon is transported from the euphotic zone to the ocean interior, the so called biological pump (BCP)”. And of course you can discuss the Baltic being an ocean.
Line 22: GB, but not
Line 25: oxygenated by the inflow of relatively saline waters from the North Sea?
Line 28: POC has not been defined. Abbreviations and acronyms are typically defined the first time you use them in the abstract and again in the main text. If you only use them once, just use the full name.
Line 48: We’re in the main text now so define BCP again.
Line 49: POC is defined, great, do the same in the abstract.
Line 53-54: What do these authors mean with “higher refractory nature of sinking particles in the OMZ?
Line 58-60: Didn’t you just give that information?
Line 70: Gotland Basin (GB)
Line 73: Define OM or even POM
Line 84: “… would be necessary the bottom water….”?
Line 85: Gotland Basin, used before in line 70, define GB in line 70.
Line 87: just Kattegat should do I think.
Line 98: GB, it has been defined now.
Line 105: “Water column stratification…”
Line 108: Does that redoxcline still exists during/after the MB?
Line 109: this pelagic redoxcline is the original or the second redoxcline from the previous sentence?
Line 114-115: “…under oxic conditions OR in the presence of nitrate they react with O2 and …” They will get oxidized, but in the latter case there is no O2?
Line 127: TEP is or TEP particles are
Line 133: by Stokes law…
Line 161: special variability?
Line 173: filled up to 10 L? How much water did you have to add to get to 10 L. And why would you dilute your samples?
Line 174: swimmers were removed with a 500 µm mesh screen?
Line 185: Aliquots from the 10 L? So not only trapped material, but diluted trapped material?
Line 192: Did you define POP?
Line 200-209: Am I correct in thinking that everything between 5 and 20 µm is both counted by flow cytometer and microscopy? I am assuming the flow cytometer is counting cells containing chlorophyll and/or phycoerythrin?
Line 214: Explain what coomassie normally stains. Later on explain why that might be interesting.
Line 231-236: If this is a known method to measure particles containing MnOx, refer to these papers or methods. MnOx-like particles could basically be anything. Line 243-244 “…. Undergoes degradation…”
Line 272: The deepest point sampled in the LD (430 m)
Line 299: increased to 38.9
Line 301: the lowest concentration was not at 180 m?
Line 304: GB µg per liter, LD µg per liter and µM?
Line 304-312: There is overlap in your defined pico- and nanophytoplankton (< 20 µm) and large phytoplankton (> 5 µm)?
Line 314: Filament counts, so the actual biomass or even individual cell counts could be even way larger, right? This also means that the other spp are a percentage of the total counts or phytoplankton counts. Not of the total biomass or even cell counts. Completely dwarfed by the cyano’s therefore, right?
Line 315: total counts, so you could wonder if they are indeed significant based on biomass or cell counts taking into account you counted filaments rather than cyano cells.
Line 317: total phytoplankton counts
Line 318: phytoplankton counts
Line 331: TEP particles were counted right? So shouldn’t this be counts as well? Line 340: so here is a little indication of what CSP might be… gel like, the question what it is still remains.
Line 345: MnOx containing particles? But did you actually measure MnOx? Or just counted particles that looked and behave as MnOx?
Line 362-363: by 18%
Line 376: Fully oxygenated water depths
Line 384-387: IS the TAA related to CSP?
Line 398: SOM or DOM?
Line 406: indicate the Redfield ratio for Si.
Line 411: TCHO?
Line 427: biomass? Or counts?
Line 437: the overlap in size classes again?
Line 483: MnOx-like and in line 485 you are sure it is actually MnOx, what has changed?
Line 531-532: So in Glockzin et al they actually measure manganese?
Line 533: (H2S), pretty sure there is H2O.
Line 537-538: “… redox conditions favorable for the formation of MnOx resulting in the high MnOx flux measured …”
Line 547: containing or should it be like?
Line 590: we consider
Line 592: mixed
Line 598: mixed
Line 606: than rather than that?
Line 615: “… how similar the biogeochemical conditions were …”
Line 625: Hence the N2 fixing cyano’s?
Line 660: transporting solid material from the and ?
Line 662: for the comparison of POM

Dear Carolina Cisternas-Novoa and co-authors,

Thank you very much for the extensive amount of work you have put into answering my questions and improving your manuscript. I think it has improved significantly and I am very happy to accept this manuscript for publication.

Best regards,

Marcel