Bottom RedOx Model (BROM v.1.1): a coupled benthic–pelagic model for simulation of water and sediment biogeochemistry

Yakushev, Evgeniy V.; Protsenko, Elizaveta A.; Bruggeman, Jorn; Wallhead, Philip; Pakhomova, Svetlana V.; Yakubov, Shamil Kh.; Bellerby, Richard G. J.; Couture, Raoul-Marie

doi:https://doi.org/10.5194/gmd-10-453-2017

Articles | Volume 10, issue 1

https://doi.org/10.5194/gmd-10-453-2017

© Author(s) 2017. This work is distributed under
the Creative Commons Attribution 3.0 License.

https://doi.org/10.5194/gmd-10-453-2017

© Author(s) 2017. This work is distributed under
the Creative Commons Attribution 3.0 License.

Articles | Volume 10, issue 1

Model description paper

|

01 Feb 2017

Model description paper |

| 01 Feb 2017

Bottom RedOx Model (BROM v.1.1): a coupled benthic–pelagic model for simulation of water and sediment biogeochemistry

Evgeniy V. Yakushev, Elizaveta A. Protsenko, Jorn Bruggeman, Philip Wallhead, Svetlana V. Pakhomova, Shamil Kh. Yakubov, Richard G. J. Bellerby, and Raoul-Marie Couture

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Final revised paper (published on 01 Feb 2017)
Supplement to the final revised paper
Preprint (discussion started on 15 Jan 2016)

Interactive discussion

Status: closed

AC: Author comment | RC: Referee comment | SC: Short comment | EC: Editor comment

- Printer-friendly version

- Supplement

RC1: 'Evaluation of BROM', Jack Middelburg, 10 Feb 2016
- AC2: 'Reply to review by Jack Middelburg', Evgeniy Yakushev, 07 Sep 2016
RC2: 'Review', Oleg Savchuk, 23 Feb 2016
- AC1: 'Reply to 'Review' by Oleg Savchuk, 23 Feb 2016', Evgeniy Yakushev, 19 Jun 2016
RC3: 'Description to be completed, scope and limitation to be better discussed', Guy Munhoven, 04 Mar 2016
- AC3: 'Reply to review by Guy Munhoven', Evgeniy Yakushev, 07 Sep 2016

Peer-review completion

AR: Author's response | RR: Referee report | ED: Editor decision

AR by Evgeniy Yakushev on behalf of the Authors (04 Jul 2016) Author's response Manuscript

ED: Referee Nomination & Report Request started (26 Aug 2016) by Didier Roche

RR by Guy Munhoven (15 Sep 2016)

Suggestions for revision or reasons for rejection

The authors have made an in-depth revision of their paper. The English is just fine now -- this would have been the kind of quality I would have expected for the initial submission!

The replies to my comments and questions posted in the interactive discussion in GMDD are largely adequate.

After reading the revised manuscript, I find that the description of the model is much more satisfactory and comprehensive now. The code availability and localization description is also much more comprehensive (I have not verified the exactness, though). There remain a few minor problems to address before final publication. Except for one or two, I consider those, however, to be technical only. Please find the details below.

Main text

Throughout: please revise the citation style! All citations have been put within in brackets, whether they belong to the text or not. This is especially annoying when it is referred to particular places in the original papers (e.g., p. 9, ll. 14-15).

In a few instances, one reads the expression "nitrogen currency"; I suggest to change this to "nitrogen equivalents"

p. 2, l. 3: "variation" should read "variations"

p. 3, l. 4: strange sentence ("which latter" ? Split?

p. 4, l. 14: within FABM (discard "the")

p. 5, l. 1: would "built upon" not better read "integrated into"

p. 5, ll. 18-19: "This eliminates the need to include a separate state variable e.g. for pH." No, including such a variable would at best be redundant, possibly even inconsistent, since the evolution of such a variable is completely determined by the other variables (total concentrations) that are included.

p. 6, l. 5: "which is" should read "which are" or "which follow"?

p. 6, l. 19: what are "heterotrophic transfer functions" ?

p. 6, l. 31: it is not the boric alkalinity (more commonly called borate alkalinity) that is estimated from salinity, but the total dissolved boron. Borate alkalinity needs to be calculated together with all the other alkalinity contributions from total dissolved boron.

p. 10: re. bioirrigation: I think the important paper by Aller (2001) must be cited here - it was referred to in the discussion.

p. 11, l. 1: "Schluter" should read "Schlüter"

p. 11, l. 15: "calculated as" would better read "calculated by", "calculated from" or "calculated using"

p. 11, ll. 15-16: correct to "... using FABM ..." (delete "the")

p. 11, l. 21: incorrect sentence: "...if the maximum value on high on any given day"

p. 11, l. 23: "ability": I guess you mean "option" or "possibility"

p. 12, l. 16: "boundary conditions"

p. 12, l. 33: please provide a reference for k_660

p. 13, l. 5: please provide a reference for F_wind;
please correct "is the Schmidt number" (not "a")
Question: are these Sc the same for O2 and CO2? Please provide values and references.

p. 14, l. 18: please provide the chapter reference for this assertion (there are varying authors per chapter so the reference to the entire book is not relevant enough)

p. 14, l. 36 - p. 15, l. 2: The model does not seem to include a diffusive boundary layer (which would be typically 1 mm thick in the deep sea), and which impedes the exchange of solutes between sediment porewaters and the overlying seawater. Is this not necessary in the setting chosen here?

p. 16, l. 9: "an integrated"

p. 16, l. 20: "Chapter" would better read "Section"

p. 17, l. 19: what about BROM-biogeochemistry? Is it considered part of FABM and thus licensed under the same conditions as FABM?

p. 18, ll. 1-2: "at the BROM repository"

p. 18, l. 5: "from a text file"

p. 18, l. 19: "on 1st January"

p. 18, l. 34: incorrect formulation "For NetCDF output file can be used any software with NetCDF input"

p. 19: Eq. B2 is only correct if D_Bi^{intra} (please notice *intra*) is the same for all constituents of the solid phase, else D_Bi^{intra} does not cancel out.

Appendices C and D:

I recommend to put these sample brom.yaml and fabm.yaml files into supplementary material. Here, there are line-feed problems (lines are folded that should not, I suppose). T would be more helpful to have correctly formatted versions in separate files.

References:

Please delete the GMDD ref. to Butenschön et al. (2015) as the final paper Butenschön et al. (2016) - also cited anyway - has been published now in GMD.

p. 32, ll. 47-48: The reference Canfield et al. (2005) is ambiguous -- either incomplete or incorrect. The DOI provided points to the chapter "The Phosphorus Cycle", which extends only from pp. 419 to 440.
If the complete volume is referred to, the reference has to be adapted.

p. 35, ll. 28-30: duplicate reference to Roy et al. (1993).

p. 35, l. 34: "Phousphorus" --> "Phosphorus"

Tables:

Although I have not checked all the tables in full detail (this would really be too fastidious...), I have nevertheless spotted a few problems:

p. 39: "Nitrification 1 stage" would probably better read "Nitrification stage 1";
"Nitrification 2 stage" would probably better read "Nitrification stage 2"

p. 41: problem in the chemical reaction under "MnCO3 precipitation/dissolution" (right-hand side should probably hold a "Mn")

p. 42: various problems in the chemical reactions. Apparently not all of the characters come out correctly in the PDF.

p. 50: missing references for four entries (formation, dissolution of MnS, solubility products for MnS and MnCO3)

pp. 51-53: additional missing references

p. 61: the top and bottom parts better had to have the same horizontal scales, else, they are really difficult to interpret

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ED: Reconsider after major revisions (26 Oct 2016) by Didier Roche

AR by Evgeniy Yakushev on behalf of the Authors (17 Nov 2016) Author's response Manuscript

ED: Publish as is (13 Dec 2016) by Didier Roche

Short summary

This paper presents a new benthic–pelagic biogeochemical model (BROM) that combines a relatively simple pelagic ecosystem model with a detailed biogeochemical model of the coupled cycles of N, P, Si, C, O, S, Mn, Fe in the water column, benthic boundary layer, and sediments, with a focus on oxygen and redox state. BROM should be of interest for the study of a range of environmental applications in addition to hypoxia, such as benthic nutrient recycling, redox biogeochemistry, and eutrophication.