the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 22 Oct 2024
Development and assessment of the physical-biogeochemical ocean regional model in the Northwest Pacific: NPRT v1.0 (ROMS v3.9–TOPAZ v2.0)
Abstract. The biogeochemical cycling system exhibits diverse characteristics in different regions owing to various factors. The Northwest Pacific is characterized by the presence of the warm and nutrient-depleted Kuroshio Current and the cold and nutrient-enriched Oyashio Current. In this region, surface primary production leads to increased nutrient consumption and CO2 exchange. The Yellow and East China Seas (YECS) are predominantly influenced by freshwater input. A high resolution regional numerical model tailored to the specific features of each area is required to reproduce the different characteristics of each region. Therefore, to accurately analyze the physical and biogeochemical system, this study developed a new coupled physical-biogeochemical model combining the three-dimensional Regional Ocean Modeling System (ROMS) and the Generic Ocean Turbulence Model Tracers of Phytoplankton with Allometric Zooplankton (TOPAZ) for the Northwest Pacific, including the YECS. The simulated physical and biogeochemical variables in the ROMS–TOPAZ (NPRT) were evaluated by comparing them with available observational data. The spatial correlation ranges of the various variables reproduced in the NPRT were 0.5–0.7. In the upper layer (0–20 m), NPRT successfully simulated the seasonal variability of chlorophyll, capturing two peaks in spring and summer, which were not captured by the CMIP6 data. Particularly in the YECS, NPRT effectively represented the biomass driven by riverine effect, which is difficult to reproduce in global biogeochemical model with low-resolution. However, NPRT still exhibits significant biases in the subarctic region and marginal seas. To minimize the uncertainties in biogeochemical variables, it is necessary to refine the initial and boundary conditions, adjust parameters, and apply discharge forcing based on observational data. Despite these limitations, NPRT is an important tool for studying the interaction between ocean physics and biogeochemistry at a high resolution.
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Status: open (until 17 Dec 2024)
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RC1: 'Comment on egusphere-2024-1509', Anonymous Referee #1, 28 Oct 2024
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I cannot recommend the editor accept the publication for the current manuscript. The reason is as follows.
Major comments
I think that the discussion is feeble and I think we need to deepen the discussion with more analysis. In addition, I suggest the authors reconstruct the section, especially after the biological parts (Section 3.2). The production of chlorophyll relies on the amount of nutrients and light. Therefore the turn of the sections for nutrients should be put before the chlorophyll and discussions should be more with the reproducibility of the nutrients. Furthermore, the purpose of this study is to show the reproducibility of the model. Since the ocean condition in the northwest Pacific is deeply affected by regional oceanic conditions seasonally, at least the authors should show and describe the reproducibility regionally and seasonally. How about making Tables to summarize the seasonal reproducibility for each parameter in the season (spring, summer, autumn, winter) at several depths in each region? If you put in such tables, it will help us and the authors to understand the advantages and disadvantages of the model, which will help us to improve it for the next opportunity.
Minor comments
Figures and Tables
- Figure resolutions are low, and the memory and contour labels are too small. (Figs 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 13, 14 16, 17). The memory size is too small to be easily identified. If printed, the diagram will be even smaller and should be noted in large size.
2) Fig 9 b, c d: The ranges of the x and y axis are too large, being not appropriate.
3) Fig.11: The authors examine the reproducibility in the Northwest Pacific, subarctic region, East Sea, and YECS in DIC and chlorophyll, but not in nutrients. The reproducibility of chlorophyll and DIC is connected to that of the nutrients. It is better to add the regional and seasonal variability in the nutrients.
4) Fig.12: Why don’t you include the figure of silicate?
Section1
- L57-l58 (However, in the Northwest Pacific …. PDO and ENSO (Jung et al., 2017; Ma et al. 2020).) : I don’t think so. I think the sentence could be misunderstood, so I think it should be reworded.
- L73 (simulation of high biomass) : ?
- L188 (1/12deg): It is helpful to add the distance as well.
- L211 (Each model is … ‘r1i1p1fl’.) : I could not understand this sentence.
Section 2
- L189-191: One of the interesting points in this model includes the climatological monthly mean discharges of 12 major rivers although the target region in the model is the Northwest Pacific. I checked the data availability of this data (L519-538), but there is no information. It is very helpful to write it.
Section 3
- L245-248 (In this study, the water …. WOA18 data): The sentence is not appropriate here. You can move to the section 2 (l211-212 in the current version).
- L261: Since the authors describe the NPIW between density 26.6 and 27.2 σθ. It is better to add the density contours, not the salinity contours in Fig. 5.
- L270-282: Instead of the distributions of the surface salinity in the Northwest Pacific, how about showing the expanded figure targeting the YECS, because the WOA18 does not include the data in the YECS very much (I mean that it is hard to get the data), although some of the readers wanted to know the situation.
- L414-415 “In particular, for the surface DIC concentration, regarding the latitude, the air-sea exchange and vertical mixing are balanced”: I checked Ishizu et al. (2021) and this sentence comes from the misunderstanding. In the subarctic region, biological processes are also impacted.
Section 4
- Since I suggested reconstructing Section 3 by dividing results and discussion separately, in this section conclusions would be written only.
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RC2: 'Comment on egusphere-2024-1509', Anonymous Referee #2, 18 Nov 2024
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I am writing for Kim et al “Development and assessment of the physical-biogeochemical ocean regional model in the Northwest Pacific: NPRT v1.0 (ROMS v3.9-TOPAZ v2.0)
In general, I’m very grateful to see sophisticated efforts to develop NPRT v1.0 in the early stage of manuscript as a reviewer. Regional setting of physical-biogeochemical model needs numerous efforts to tune up regional characteristics and setting boundary conditions. The authors newly coupled existing physical and biogeochemical models that methods have been described well in section 2.3. They found the better representations of plankton phenology which is not represented in the global model. I would like to recommend the manuscript would be suitable in the journal. However, I can give comments for clarification as below.
L17. I think it is unclear sentence with non-scientific words. I would recommend removing it or rephrase it to be an general explanation for Northwest Pacific rather than having unspecified words like “different regions” or “various factors” in scientific writing. But it seems second sentence would be the one to explain them in general.
L195. I don’t know what “las” stands for.
I think Fig. 3 represent a bias of large meandering of Kuroshio extenstion. Please refer Hayashida et al. (https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2023JC019697) and discuss it with biogeochemical properties of NPRT results.
In detail, based on Hayashida et al., several spin-up would be needed to catch Kuroshio large meandering despite of data assimilation. They found 4th cycles of spin-up initial condition can match large meander reliability. This could be a discussion point of view in physical and biogeochemical cycles in the Kuroshio regions. This can be also nice fit to your next potential topic by using NPRT v1.0 I guess. This is not recommendation for the review step so please don’t feel pressure to do it right away at this point.
I’m afraid to see chlorophyll bias in Yellow sea region but it could be natural due to dissolved organic matter influx. Could you describe them more in the manuscript if type I or type II water could be a matter of chlorophyll bias in the MODIS, the modeled chlorophyll, and CDOM.
CDOM could be very effective on shortwave heating scheme in the regional modeling setup. Author may want to add more discussion about the potential effects of CDOM, e.g., Grace Kim et al. (https://journals.ametsoc.org/view/journals/clim/29/24/jcli-d-16-0053.1.xml) or other potential effects there to be able to develop.
ERA5 forcing has been updated in MOM5-TOPAZ. NPRT also have ERA5 forcing? If they have, I think authors should show chlorophyll time series in regional domain and calculate correlation of modeled chlorophyll with satellite ocean color.
Temperature, salinity, and/or nutrient timeseries can be compared with KODC datasets as well as.
N:P ratio should be compared to see major limiting factors.
Please add references which nutrients are limited in those regions.
Describe primary productions and carbon cycles like air-sea co2 flux, pCO2, dissolved inorganic carbon, alkalinity, pH, aragnoite, calcium carbonate saturations and carbon exports (pe-ratio; laufkotter et al 2015, https://bg.copernicus.org/articles/12/6955/2015/bg-12-6955-2015.html).
Please describe differences between biogeochemical states of GFDL-ESM2M in Dunne et al 2013b (https://journals.ametsoc.org/view/journals/clim/26/7/jcli-d-12-00150.1.xml?tab_body=fulltext-display) and this result. ESM2M results published in IPCC AR5 should be enough to compare.
Please describe oceanic front locations and resolving eddies that would be typically strong enough in regional setting compared to global model ESM2M as well as phenology.
Citation: https://doi.org/10.5194/egusphere-2024-1509-RC2 -
RC3: 'Comment on egusphere-2024-1509', Anonymous Referee #3, 19 Nov 2024
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The authors develop a high-resolution regional ocean biogeochemical model for the Northwest Pacific Ocean using ROMS and TOPAZ. The model is run for the years 2000-2014 and the physical-biogeochemical results are compared to a number of observational data products. The comparison illustrates variables and regions where the model performs well, but also identifies some model biases, particularly in the biogeochemistry. Overall, I find the model results interesting, and I think the model-data comparison presented is somewhat basic, as each model variable comparison is performed in isolation, with no broader connection of the underlying model biases. There are also some sections that I think would benefit from a more detailed description. I’ve described these comments in more detail below.
The model comparisons to the observational datasets presented provide an overview of the model biases, but it’s a somewhat preliminary comparison without any substantive description of how the various biases connect and what that means for their use in future applications. Because it’s a physical-biogeochemically coupled model, the biases in 1 variable will direct translate to other, mechanistically connected variables. Thus, the authors can describe how the bias in something like surface temperature, may impact primary productivity and also surface oxygen due to thermal solubility. I’ve provided a more detailed example of this later on, when trying to deduce the source of the bias in DIC, but I would encourage the authors to delve a bit deeper into their model results. Especially considering that this is a model descriptive paper in a model descriptive journal, a more thorough description of the model biases and how they support or reinforce biases in other variables is warranted.
The description of the model spin-up for the initial and biogeochemical boundary conditions in section 2.4 is confusing to me. First, the terminology throughout the description appears to be inconsistent and not specific at points. There are various models described as MOM-TOPAZ, MOM5-TOPAZ, and NPRT, which itself is also MOM5-TOPAZ. It’s unclear to me if there are either 1, 2, or 3 total models here. My interpretation is that they are running a global simulation of MOM5-TOPAZ for 100 years, which is then used as the initial condition and boundary conditions for the NPRT run. But this is very unclear to me overall and I am likely incorrect in this interpretation. Considering the 100 year spin-up conducted, I think it’s appropriate to see some analysis of any drift in biogeochemical variables over this timeframe. As the authors mentioned, running a 100 year spin-up at potentially global resolution is a huge computational effort, and justifies some explanation and description of the results. I’m also curious to see this considering the large DIC bias that I discuss in more detail in the next paragraph. While longer spin-up times are recommended for biogeochemical variables, that doesn’t mean that the results will inherently be more accurate than a short spin-up time, given the possibility for significant model drift.
I’m a bit concerned with the apparent DIC bias in the model for a couple of reasons. First, it’s a relatively large bias, with a R value of 0.41 and a RMSE value of nearly 100 µmol/kg. In fact, the discrepancy is large enough that it’s easily visible, even without looking at the difference plot in Figure 13c. It’s the large, positive bias for nearly the entire model domain that I’m specifically concerned about, as opposed to the negative bias within the YECS (which will be tougher for the model to capture due to the freshwater influence, and the coarser GLODAP product itself is likely far less reliable there). Second, is that the positive DIC bias does not appear to align with some of the other biogeochemical biases described. For example, my first thought was that it was maybe due to a positive salinity bias, considering how relatively spatially homogenous it is. But, Figure 6 suggests that the model is actually fresher than the observations, which should impart a negative DIC bias. Thus, if Figure 13 was salinity normalized, the positive bias would be even greater. Looking at primary productivity next, it appears that, if anything, the model is biased high with respect to productivity. This is based on higher chlorophyll values (Figure 8a), a greater nutrient drawdown (Figure 11), and greater oxygen concentrations (Figure 16c) than the observations. But again, higher model productivity would generate a negative DIC bias, not positive. So, what exactly is going on here? Are the DIC boundary conditions too high? Are the alkalinity concentrations too high, thereby generating more negative ∆pCO2 concentrations and a large carbon accumulation from the atmosphere over the 100 year spin-up? Without a more mechanistic description and understanding of this bias and additional information regarding the model alkalinity, pCO2, and CO2 flux patterns, I would be really hesitant to use this output for any application involving the carbonate chemistry.
Overall, I suggest that the authors incorporate more specific language and examples into their analysis, and remove a number of generalized sentences that are either too broad and/or non-specific. I’ll cite some specific examples under the “specific comments” section below, but a number of occurrences are the first sentence of a new section (e.g. abstract, discussion and conclusion) and they can pretty much all be completely removed.
Figures 3-6 would greatly benefit by having difference plots included, as otherwise it’s difficult to see the comparison when the variability across the whole region is relatively large. The authors include difference plots for the remaining model-data comparisons, so it seems like it was missed for the earlier comparisons?
Specific comments:
The first sentences of the abstract and the introduction are overly generalized to the point of being meaningless.
Lines 154-157: mentions a surface flux from the atmosphere for alkalinity? I don’t recall this being a common process in NPZD models, so could the authors describe this a little more?
Lines 154-157: Where is the climatological data for these air-sea fluxes coming from and what are the seasonal variations? More description is required here.
Line 266-267: Suggest the authors expand on this statement. How are they attributing the inadequate dispersion to an insufficient model integration time?
Line 282: Missing a “respectively” at the end of this sentence.
Line 297-298: Do the authors have evidence to support the statement that the observational uncertainty for satellite-derived chlorophyll is lower than nutrients? I’m skeptical of this claim.
Lines 304-325: This is a confusing paragraph because it appears to be conflating previous literature assessments with the model results. It makes it difficult to understand whether the authors are describing their model’s phytoplankton dynamics, or what’s already been described in previous studies. Suggest removing the descriptions from prior work and placing it in the introduction and/or discussion.
Lines 330-334: The authors here are comparing how riverine nutrient fluxes are handled in global models vs. their model, but it’s very confusing what the actual difference is. “Similar to that adopted in the regional biogeochemical model”. Which model is this referring to? Here’s where more specific language would benefit the description.
Lines 340: Is an R value of 0.45 really sufficient for capturing the annual mean distribution? That seems somewhat low to me, so I would suggest providing more support here.
Lines 418-425: I’m not following the last couple sentences here. So, the model has a significant negative bias in DIC compared to GLODAP. But then the next sentence says the model results are consistent with observational data from ships? What observational data from ships is this referring to? The only comparison is to GLODAP, which does incorporate ship data, but the authors phrase this as if they are discussing a completely different product that the model does compare well with. Then the final sentence attributes this to the use of a high-resolution model? Why? Need to be more descriptive here.
Lines 450-451: This sentence is overly generalized to the point of being meaningless.
Line 472: Replace period with comma
Lines 485-489: This is an odd description to me, because it starts with a very targeted, tractable method for how model uncertainty within the YECS could be reduced by developing an improved understanding of the riverine runoff and nutrient concentrations. But then, states that this would be too difficult, and instead lists a number of vague strategies that could also apply for essentially any model application. Why would the first method be too difficult? Is it because the authors are already confident with what they’re currently using for the river outflow and nutrients here, and thereby think that they will have minimal gains by trying to incorporate more? If so, then this justification would be extremely helpful.
Line 642: Should the Jung et al., reference be 2019 rather than 2020? It’s listed as 2019 in the main text.
Citation: https://doi.org/10.5194/egusphere-2024-1509-RC3
Data sets
ROMS-TOPAZ (NPRT V1.0) input and output data Daehyuk Kim and Hyun-Chae Jung https://zenodo.org/records/13941078
Model code and software
physical-biogeochemical ocean regional ocean model: ROMS –TOPAZ (NPRT V1.0) Daehyuk Kim, Hyun-Chae Jung, and Jae-Hong Moon, https://doi.org/10.5281/zenodo.11218350
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