Use of remote-sensing reflectance to constrain a data assimilating marine biogeochemical model of the Great Barrier Reef

Jones, Emlyn M.; Baird, Mark E.; Mongin, Mathieu; Parslow, John; Skerratt, Jenny; Lovell, Jenny; Margvelashvili, Nugzar; Matear, Richard J.; Wild-Allen, Karen; Robson, Barbara; Rizwi, Farhan; Oke, Peter; King, Edward; Schroeder, Thomas; Steven, Andy; Taylor, John

doi:https://doi.org/10.5194/bg-13-6441-2016

Articles | Volume 13, issue 23

https://doi.org/10.5194/bg-13-6441-2016

© Author(s) 2016. This work is distributed under
the Creative Commons Attribution 3.0 License.

https://doi.org/10.5194/bg-13-6441-2016

© Author(s) 2016. This work is distributed under
the Creative Commons Attribution 3.0 License.

Articles | Volume 13, issue 23

Research article

| Highlight paper

|

07 Dec 2016

Research article | Highlight paper |

| 07 Dec 2016

Use of remote-sensing reflectance to constrain a data assimilating marine biogeochemical model of the Great Barrier Reef

Emlyn M. Jones, Mark E. Baird, Mathieu Mongin, John Parslow, Jenny Skerratt, Jenny Lovell, Nugzar Margvelashvili, Richard J. Matear, Karen Wild-Allen, Barbara Robson, Farhan Rizwi, Peter Oke, Edward King, Thomas Schroeder, Andy Steven, and John Taylor

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Final revised paper (published on 07 Dec 2016)
Preprint (discussion started on 09 May 2016)

Interactive discussion

Status: closed

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

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RC1: 'Review of: ‘Use of remote-sensing reflectance to constrain a data assimilating marine biogeochemical model of the Great Barrier Reef.’ By Jones et al.', Emmanuel Boss, 24 May 2016
- AC1: 'Response to RC1', E. Jones, 27 May 2016
RC2: 'Review of “Use of remote-sensing..." by Emlyn M. Jones et al', S. Ciavatta, 27 May 2016
- AC2: 'Preliminary response to RC2 general comments.', E. Jones, 30 Jun 2016
RC3: 'Review of "Use of remote-sensing reflectance to constrain a data assimilating marine biogeochemical model of the Great Barrier Reef" by Jones et al.', David Ford, 06 Jun 2016

Peer-review completion

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

ED: Reconsider after major revisions (05 Jul 2016) by Katja Fennel

AR by E. Jones on behalf of the Authors (05 Sep 2016) Author's response Manuscript

ED: Referee Nomination & Report Request started (08 Sep 2016) by Katja Fennel

RR by Emmanuel Boss (12 Sep 2016)

RR by David Ford (13 Sep 2016)

RR by Ciavatta Stefano (16 Sep 2016)

Suggestions for revision or reasons for rejection

Comments on the revised version of “Use of remote sensing reflectance …” by Emlyn Jones et al.

The authors addressed all my comments in a constructive way. Though they did not accept some recommendations (e.g. to include TSS and nutrients in the control vector of EXP1, or include more optically active variables in EXP2-4), they justified soundly their methodological choices and pointed out assumptions and limits of their work.
In particular, I am glad and grateful that the authors added EXP5, which demonstrated the feasibility and advantages of direct assimilation of reflectance data (R551).
Furthermore, the authors reorganized and polished the manuscript, such that the text flows much better in the current version.
Overall, this work represents a major step in biogeochemical data assimilation and, potentially, in our capability to simulate and predict crucial dynamics in marine ecosystems.
For the above reasons, I think that this revised manuscript is suitable for publication after a minor revision.
The most relevant comments are listed below; others were included in the pdf file.

1) I kindly insist that the author replace the current Appendix 1 with an appendix that lists the most important equations and parameterisation of the bio-optical model. This would increase the readability of the manuscript, as well as well as the reproducibility of the work. I do appreciate that the bio-optical model was published in a previous paper, but so was the biogeochemical model which is lengthy described in the current appendix;
2) The authors should be more objective in judging the results of the simulation shown in figure 4 (e.g. the overestimated OC3M south of Papua). Furthermore, in figure 4, the simulated OC3M matches better the NASA OC3M rather than the ANN OC3M, which has been assimilated. Please comment in the manuscript. See more comments in the pdf;
3) Figure 5: The non-linear relationship between the two simulated variables is an obvious result, because you have included in your model a non-linear relationship between the two variables. It would be more relevant a plot of in situ chlorophyll versus satellite OC3M, or, at least, simulated chlorophyll versus satellite OC3M. Weak or non-linear relationships in these plots would support better your point. Please add such plot to the manuscript;
4) Figure 6. The top graph does not provide a clear overall ranking of the performance of the experiments. It is not easy to assess which exp has the “best” mean forecast innovation (i.e. ~0 most of the analyses). The authors should plot the absolute values of the mean forecast innovations, or provide in a table the temporal average of the absolute values of the mean forecast innovations for each experiment;
5) Figure 11, top plot: you can reduce the y-scale to 10 mg m-3;
6) In the conclusion, section 4.2, I do agree with the authors that assimilation of reflectance has the benefit to use data with lower error, because data do not rely on empirical models. However, they should recognize that modelling (and assimilating) optical properties might increase the complexity and/or uncertainty of the ecosystem model. To a certain extent, the problem is moved from satellite retrievals into the structure of the marine model. One needs to add equations and parameterization that are rough approximation and highly uncertain. For example: which experimental phytoplankton absorption coefficient should I use for the “small phytoplankton” represented in the model? What are the implications of representing CDOM as a linear regression of salinity? Is this more accurate than retrieving CDOM absorption from satellite data?
Therefore, the authors should mention the above issues in the conclusions and list the most relevant bio-optical equations and parameterizations in the appendix.

With my compliments for this nice piece of work,
kind regards,
Stefano Ciavatta

Referee Report: PDF

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ED: Publish subject to minor revisions (Editor review) (26 Sep 2016) by Katja Fennel

AR by E. Jones on behalf of the Authors (06 Oct 2016) Author's response Manuscript

ED: Publish subject to technical corrections (17 Oct 2016) by Katja Fennel

AR by E. Jones on behalf of the Authors (11 Nov 2016) Manuscript

Short summary

Marine biogeochemical models are often used to understand water quality, nutrient and blue-carbon dynamics at scales that range from estuaries and bays, through to the global ocean. We introduce a new methodology allowing for the assimilation of observed remote sensing reflectances, avoiding the need to use empirically derived chlorophyll-a concentrations. This method opens up the possibility to assimilate of reflectances from a variety of missions and potentially non-satellite platforms.