Review of bg-2017-206 by Brigolin et al.

Dear Dr. Brigolin,
Thanks for providing responses to reviewers regarding your article Modelling biogeochemical processes in sediments from the north western Adriatic Sea: response to enhanced POC fluxes.

1) Please avoid Acronyms. The scope of this journal is an integrative, and the excessive use of abbreviations, specially non-standards only makes the article more difficult t o read, unless you come from this specific field.. AE, TSS, TSM (only used twice…), etc.
2) Reviewer 1. AC1, C6. L18-19, p4: What is the impact of neglecting Fe and Mn biogeochemical related processes on the total biogeochemical processes? Are these processes really negligible? This could be the case as sulfate reduction process appear negligeable (from SO42- profiles and in spite what your modeling result tend to indicate). In addition you do not have any NO3- data that could also be an important process in the area studied. -
Response: Thanks. Including Mn and Fe related processes would definitely increase the EDM realism, but also its complexity. Mn and Fe dynamics were present in a previous modelling work applied in a close area, located in the Northern Adriatic (Brigolin et al., 2011, cited in the text). However, with respect to the present work, in this other case, a larger database was available for constraining the model (pg 4, lns 18-20 - initial version of the ms). This model limitation was stated explicitly in the methods section of the ms, and a remark concerning the potential development of the model was also present in the discussion (pg 9, lns 43-44 - initial version of the ms) " A more precise estimation of the fate of this oxygen could be obtained by introducing in the model FeS precipitation, for which at least Fe2+ measurements in pore waters would be required.".
Editor: This question needs to be properly answered. We need to know the impact of neglecting: overestimate, underestimate, by how much, is it still reliable without , etc.
Response: With respect to NO3, we acknowledge that this would be a relevant information for constraining nitrification/denitrification, and this was highlighted in the discussion (pg 10, lns 5-9 - initial version of the ms) " Higher NH4+ concentration predicted at station EST1 with respect to field data could be explained with a higher rate of nitrification at this station. However, in the calibration performed within this work, the kinetic constant for nitrification was kept at its original value (Table A4), due to the lack of data concerning NO3-."
Editor: Again, What is the impact…? (please see above)
3) Reviewer 1: C7 Last paragraph. L5-6, p5: what is the influence of the farm on the current within the farm? This is the current within the farm that will drive the transport and deposition of particulate from the farm. This is not explained within the deposition model section. I think this is important for the reader. Please explain.
Response: This engineering aspect, although of interest, has not been properly investigated yet*. To the best of our knowledge, multiple current meter measurements within the same longline suspended mussel farm are not available, and model predictions regarding the local effect of structures on currents would be complex to validate. Similar effects are currently neglected in most deposition models also for fish cages (which nets are expected to have more relevant impacts on the current flows). We added a synthetic remark on the fact that the aspect is not included in the model (model theory paragraph 2.2, ln 35 pg 3).
Editor: *There is information in the literature. See for instance:
Deposition beneath long-line mussel farms (http://www.sciencedirect.com/science/article/pii/S0144860905000166)
4) Reviewer: AC2, C4, Fifth paragraph. P4 L38: How do you address the problem of color particulate matter, optical shallow waters and water turbidity, where the river could have a major role to play? As example please see: * Cannizzaro and Carder (2006)â Ì ́lA ÌE ̨ a [optical shallow waters]
Response: Thanks, again, we believe that this is related with the use that was done of Chla data, which were provided as input to characterize the typical growth trajectory of a mussel over one decade, and in order to assess the mean Delta in POC flux induced by the presence of the farm. Based on this comment from the reviewer, we decided to add a specific sentence regarding the perspective use of the model (section 4.3 “Integrated model features”). The sentence reads as follows: “We underline that the application presented in this work could be extended, in order to include the evaluation of the uncertainties related to spatial inconsistencies of nearshore-offshore remote sensing products.”

Editor: I do not understand your answer. Please rephrase and address the problem
5) Page 2, Line 7. This sentence distracts, and does not add anything new to the introduction and its flow. “Biogeochemical and contaminant cycling associated to the presence of shellfish farming in a Mediterranean lagoon was the focus of a special issue (Estuarine Coastal and Shelf Science 72(3); Rabouille et al., 2007). ”

6) It is not clear if “…representative for the 2km2 study area the Chla and SST time series if they were constructed based on an area of app. 100Km2? ” (Reviewer 2), considering that in line 25, Page 3, is stated “…The individual growth model requires in input time series of daily values of sea water temperature, and concentrations of chlorophyll-a, particulate …”
Editor: This concerns needs a better explanation since averaged data (100 km2) is much bigger than farms and there several issues related to coastal calibration of chlorophyll, including reflection in shallow water (<40 m depth)
7) Other issues:
a) Fix “Chloophyll-
” in Fig. 2
b) Proposed conclusion:
“to characterize more strongly”. Do you mean, “better characterize”?
Those issues need to be addressed for publication in the journal.
Sincerely yours

Silvio Pantoja
Associate Editor

January 8, 2018
Dear Dr. Brigolin,
Thanks for your responses, that I found not satisfactory and require further clarification:

1. “The median daily value of faeces and pseudofaeces fluxes from the 10 simulations was used as an input for the deposition model. This step also had the effect of smoothing potential biases in chlorophyll-a estimation, induced by the interference caused by Colored Dissolved Organic Matter absorbance (see Cannizzaro and Carder, 2006).”

Please summarize the argument of Cannizzaro and Carder that diminishes interference with CDOM

2. One of the reviewers argued that satellite chlorophyll data was not well sustained. Your reply with supporting evidence should be in the text including reference “…according to Mauri et al. (2007), the area investigated in the present work lies at the edge of the zone under Po river…. ”. Reviewer also suggest that you revise “Lavigne et al. (2015) describe some observations near your study area. https://www.biogeosciences.net/12/5021/2015/ …” and incorporate in the text. Do data match?

Minor issues:
3. Delete word “see” in Cannizzaro and Carder, 2006 and in the rest of the text; not needed.

1. Abstract, line 6 “…linked to new data in…”. What is new data?
2. Abstract. “… by similar proportions between oxic and anoxic degradation pathways at the two stations… .”

Change “degradation pathways” to “degradation rates”


Sincerely yours

Silvio Pantoja
Associate editor