Nitrogen isotopes reveal a particulate-matter-driven biogeochemical reactor in a temperate estuary

Dähnke, Kirstin; Sanders, Tina; Voynova, Yoana; Wankel, Scott D.

doi:https://doi.org/10.5194/bg-19-5879-2022

Articles | Volume 19, issue 24

https://doi.org/10.5194/bg-19-5879-2022

© Author(s) 2022. This work is distributed under
the Creative Commons Attribution 4.0 License.

https://doi.org/10.5194/bg-19-5879-2022

© Author(s) 2022. This work is distributed under
the Creative Commons Attribution 4.0 License.

Articles | Volume 19, issue 24

Research article

|

21 Dec 2022

Research article |

| 21 Dec 2022

Nitrogen isotopes reveal a particulate-matter-driven biogeochemical reactor in a temperate estuary

Kirstin Dähnke, Tina Sanders, Yoana Voynova, and Scott D. Wankel

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Final revised paper (published on 21 Dec 2022)
Supplement to the final revised paper
Preprint (discussion started on 31 May 2022)

Interactive discussion

Status: closed

RC1:
'Comment on bg-2022-123', Anonymous Referee #1, 28 Jun 2022
General comments

This paper reports nitrogen transformation along the Elbe estuary and river by tracking concentration and the stable isotope composition of nitrogen compounds and particulate matter. The authors constructed a total nitrogen isotope mass balance to explore potential processes and controls on the evolution of riverine nitrogen along the estuarine reach. They also determine the nitrogen isotope effect of ammonium and nitrite oxidation and of remineralization.

The Elbe River is the most important source of reactive nitrogen to the Southern North Sea which regarded as a problem area of eutrophication. The topic of this study is important because they investigate contribution of complicated N recycling processes (e.g. remineralization, nitrification) for nitrate production based on obtained nitrogen isotope effects. In addition, they provided a novel insight into the potential control process of nitrification in the Elbe estuary.

Sampling and experimental procedures are clearly explained in detail. To confirm the activity of nitrification, the authors perform not only nutrient and isotope analysis but also nitrification rate measurement. Those combined approach is suitable for determination of contribution of nitrification.

For the most part, the results are clearly presented, and the biogeochemical data are well illustrated with figures. However, there are some specific comments on determination of isotope effect of nitrification and the total isotope mass balance modeling.

In summary, I recommend the publication of this paper if the authors add some discussions and make minor revisions as shown below.

Specific comments

Line: 62

The significance of evaluation of nitrogen transformation along Elbe estuary under “intense summer oxygen depletion” is a little vague. Why do sample the water column under unusual condition? Please revise them for clearer description.

Line: 70

In the explanation of study site, there is a lack of information where an agricultural catchment area and areas of nutrient discharge (Line 71-73) exist. Where is the input of N ? Those information helps us to understand the interpretation of geochemical data along Elbe Estuary.

Line: 128

As for nitrate isotope analysis, how was nitrite removed from the nitrate samples? Some samples contained enough nitrite for isotope measurements. Thus, the presence of nitrite interfered with nitrate isotope measurements.

Line: 150

It seems that both of ammonium oxidation and nitrite oxidation occur between stream km 641 and 656. Isotope compositions of nitrite could be affected by both of ammonium oxidation and nitrite oxidation. Do you consider the influence of ammonium oxidation on nitrite isotopes?

Line:261

How did you calculate and conclude that the drop of oxygen isotope values in the harbor region was due to nitrification? What is the value of oxygen composition of river water (¹⁸O_H2O) ?

Line:320

The authors constructed a total isotope mass balance by modeling. I understood the assumption of the model. However, the equation, parameters and calculation method were not presented in this text. Therefore, it is difficult to understand the conclusion that Total N fluctuations are driven by PN fluctuations. I’m not so familiar with this box model, but it seems better that the authors briefly explain equations and parameters in the box model and a modeling software in the method section or supplemental information.
Citation: https://doi.org/10.5194/bg-2022-123-RC1
- AC1: 'Reply on RC1', Kirstin Dähnke, 22 Jul 2022
  
  Response to Referee #1
  We thank the referee for feedback and the helpful and constructive comments on themanuscript. For a detailed response to the individual issues, please see the attached pdf (for formatting reasons).
  
  Citation: https://doi.org/10.5194/bg-2022-123-AC1
RC2:
'Comment on bg-2022-123', Anonymous Referee #2, 06 Jul 2022
In the manuscript , Dähnke and colleagues present a timely study to assess estuarine nitrogen processing, taking advantage of conditions that enabled the isotopic analysis of nitrate, nitrite, ammonium, and particulate nitrogen along the Elbe estuary. Overall, this is an interesting dataset, with a lot of potential, but additional details are needed in several places to allow the reader to validate your conclusions and place them in context, these areas are outlined below.

Throughout, language such as unusual, exceptional, and unique are used to describe the conditions encountered, so how applicable are your results, just to these conditions? How often do these conditions occur? Are your findings applicable to the conditions seen in Sanders et al, 2018? It would be nice to see more comparisons drawn to this dataset.

Nitrification rates: more details are needed both in the methods and data interpretation.

Nitrite and nitrate concentrations were stable, meaning all ammonium had been utilized?

room temperature, was this close to insitu conditions?

14 days seems a long time and that bottle effects would be likely, was there any sign of this in the data? Exponential behavior for example? It would be beneficial to show some of this data, maybe in a supplement. How representative are these rates of insitu, as there seem to be a number of caveats, none of which are mentioned and there is also no comparison of the rates determined to those in the literature to put them in context, it is only mentioned that they are high.

you mention in the methods that ammonia and nitrite oxidation rates were determined but this is not mentioned in the results/discussion.

Isotope mass balance box model: it is difficult to assess the outcomes of the model as no details are provided, equations, parameters etc, please provide this in the methods or supplement.

Line 34 to 36: it is not clear how the second half of the sentence links to the first

Line 106: How was chlorophyll analyzed

Line 126 / Nitrate Isotopes: There is no mention of a nitrite removal step, so are these actually N+N and not nitrate only? Please note the implications of this.

Line 137: You note here that high concentrations were needed for isotope analysis of nitrite and ammonium, please include what concentrations needed to be greater than for isotopic analysis

Line 225: For ammonium you use ε_amm to represent the isotope effect for ammonium removal and then go on to discuss uptake and oxidation, which is great, but why not the same for nitrite? Here you assume it is just nitrite oxidation (ε_nitox), but highlight later in the manuscript a potential role for denitrification in this system (e.g. Line 372), which would also consume nitrite, what would be the implications of this for your calculated isotope effect?

Figure 4 and associated text: it would be nice to see some errors on the calculated isotope effects.

Line 294 to 298: Across these lines, you discuss how nitrification scales / correlates with N content (%) and indicators of OM quality, where do I see this, you refer to Figure 4, but this is your isotope effects figure. These relationships need to clearly evident to support your conclusions.

Line 305 to 307 (and throughout this section): more explanation is needed for SPM reactivity, use the literature, for example, why does low C/N suggest its fresh and labile, references and details are needed for the reader to keep up with your line of thinking and confirm your conclusions.
Citation: https://doi.org/10.5194/bg-2022-123-RC2
- AC2: 'Reply on RC2', Kirstin Dähnke, 22 Jul 2022
  
  We thank the reviewer for the helpful and elaborate comments that will greatly inprove the manuscript. For a detailed point-by-point reply, please see the attached pdf.
  
  Citation: https://doi.org/10.5194/bg-2022-123-AC2

Peer review completion

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

ED: Reconsider after major revisions (08 Aug 2022) by Ji-Hyung Park

Dear Authors:

Thank you for providing detailed responses to the comments and suggestions offered by the two referees.

While both reviewers recognized the significance of your research, one reviewer suggested a major revision for better data presentation and interpretation. I agreed with the reviewers’ overall positive evaluation of your manuscript and also thought that several raised issues would require substantial efforts to improve clarity in data presentation and discussion and also to provide adequate methodological details. Please also take into consideration my additional suggestions as follows:

- N sources: In your response to the first reviewer’s comment (line 70), you focused on upstream “diffuse sources” (nonpoint sources). I wondered if you could also add some quantitative information about point sources such as wastewater effluents from big cities near and within the estuary.
- O2 level: In terms of, again, providing quantitative information, I thought you could better respond to the first comment of the second review on the extent of O2 depletion by providing the overall range of DO in the Elbe River (better citing papers that addressed the issue of O2 depletion in the same river system), or temporal variations of DO in the estuary if data are available.
- Lines 8-9: Do you mean “biogeochemical reactors that act to modify the loads and composition of nutrients transported to the coastal zone.”?
- Lines 14-18: Please remove the very general background information (e.g., “estuarine biogeochemistry is governed by settling, resuspension, and remineralization of particulate matter”); instead provide “actual findings” that you want to highlight in the abstract. It should be noted that the abstract requires a substantial revision to provide the key findings and their implications.
- Sampling and sample analysis: Please pay more attention to details during the revision. For example, “surface water samples” at what depth?; uniform descriptions of instruments (brand, company, country); QA/QC for water analyses (like blanks, replicates, reference materials,,,)
- Discussion also requires a substantial revision, because many general (background-like) descriptions are provided without clear linkages to the findings. Please consider a more focused discussion to highlight your points in a clearer way; for instance, when you begin a discussion section, you could articulate key findings in the context of your research questions.
- Figs. 2-6: Please pay attention to details about axis titles and legends (e.g start the titles with upper-case letters; The initial “f” in Fig. 4 can be noted in the caption.

I would like to ask you to make all the changes easily identifiable in a marked-up manuscript based on your point-by-point responses to the reviewer comments. If possible, please specify the line numbers of the revised parts in your responses accompanying the revised manuscript.

Sincerely,

Ji-Hyung Park
Associate Editor, Biogeosciences

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AR by Kirstin Dähnke on behalf of the Authors (06 Sep 2022) Author's response Author's tracked changes Manuscript

ED: Referee Nomination & Report Request started (08 Sep 2022) by Ji-Hyung Park

RR by Anonymous Referee #2 (20 Sep 2022)

Suggestions for revision or reasons for rejection

Firstly, I would like to thank the authors for the time and consideration they put into the revision and reviewer response, which I believe has resulted in an improved manuscript. However, while the overall message is clearer, clarity is still needed in some places. In addition to this I urge the authors to think about the readability of their manuscript, currently the majority of the manuscript is short paragraphs of 2 to 3 sentences, resulting in the text lacking flow and cohesiveness.

Line 45: some additional explanation / references are needed here, why does low oxygen result in the accumulation of ammonium and nitrite?

Line 67: The opening sentence of this paragraph where you refer to a key finding of Sanders et al, 2018 is totally disconnected from the following sentences where you introduce your study, I suggest you delete it or reword to incorporate it into the rest of the section.

Figure 1 (same is true for Figures 2 and 3): throughout you use the term harbour region and I suggest you use this language here in figure 1 instead of or in addition to Hamburg port. For clarity it would also be beneficial to mark the harbour region onto Figures 2 and 3 (and maybe also in Figure 3 the region you use to determine ammonium and nitrite isotope effects)

Line 142: the fact that you saw no significant differences between treatments, needs to be commented upon. Was sufficient inhibitor used? 0.5uM seems very low when looking at Belser and Mays, 1980.

Line 236: I find this text misleading and confusing regarding where you are defining the harbour region, as currently written here it sounds like the harbour region is from 618 to 656km, which I don’t think is the case. Please clarify.

Line 273 and 276: If you want to use the words rare and unusual as you do in this paragraph you need to provide some context and compare / contrast to the literature to demonstrate this is the case.

Line 308/309: See comment below on section 4.4 as well, this only makes sense once I get to the end of the manuscript. Here you need to comment directly on a potential role for sedimentary and water column denitrification.

Line 338: ‘where organic matter is fresh’ this statement comes too early as you don’t provide evidence for this until later in this section where you introduce the C/N results.

Line 343: What is your evidence for the statement remineralization is prominent, im actually not even sure what that means – this section is about determining an isotope effect and comparing it to the literature.

Line 359: potentially even denitrifying, where is the evidence for this prior to this statement? Or at this point of the manuscript are you relying on the literature, if so a reference is needed.

Section 4.4 : it is only here that things finally fall into place for the reader, you need to introduce the ideas of water column and sedimentary denitrification earlier and there impacts on N isotopes (maybe in the introduction along with where in the estuary you would expect to find each based on the literature?), as prior to this you just use the term denitrification. This is confusing for the reader as you conclude that your isotope effect is representative of only nitrite oxidation as it is unaffected by additional nitrite sinks or sources (line 308), but then mention a number of times in the text a role for denitrification in the Elbe and it is not 100% clear in all cases where in the estuary you are referring to (e.g. line 359). Would a cross plot of 18O and 15N of nitrate not be informative with respect to picking these processes apart – this seems typical for nitrification / denitrification in other studies so would be good to highlight why this method is not relevant here?

Line 435: a reference is needed to demonstrate that denitrification inside particles is feasible

Line 445 to 448: more explanation is needed here for the non-expert, and references are also needed, for example it should be highlighted how these ideas do / don’t differ from km 640 to 655 where you also postulate a role for sedimentary denitrification.

Line 457: language, produce used twice

Line 462: ‘alter the balance of nitrification and denitrification’ it is not clear to me where this was directly discussed in the manuscript with respect to OM.

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RR by Anonymous Referee #1 (23 Sep 2022)

ED: Reconsider after major revisions (26 Sep 2022) by Ji-Hyung Park

Dear Authors:

Thank you for revising the manuscript following the reviewers’ comments and suggestions.

The same reviewers of the first review round kindly provided their second reviews. While one reviewer considered your revision as adequate, another reviewer suggested a further major revision to improve the clarity and readability of the manuscript. I also think that your efforts to improve clarity would make your invaluable data sets more accessible to the readership of Biogeosciences. For your information, I enclose the two reviewers’ comments. Please also take into consideration my additional suggestions as follows:

- The main part of the abstract: Thanks for revising it in response to my suggestion, but I still find it difficult to figure out how you have derived your interpretations from the “actual findings”. For instance, what are the relevant results for “the estuarine nitrogen budget of the Elbe estuary is governed by settling, resuspension, and remineralization of particulate matter”? On which finding did you base your interpretation that “the reactivity and concentration of particulate matter in the estuary is the main control of nitrogen isotope dynamics and of remineralization”?
- Section 3.1 & Fig. 2: You repeatedly refer to the “harbor (port) region” and its entrance in Fig. 2. I wondered if you could indicate the area or a key location on the figure, like by using some shaded area or vertical line(s).
- As I requested earlier, please avoid general (introductory) statements in Discussion and focus on key findings and their implications in line with your research questions. For instance, the new first sentence doesn’t fit into the first paragraph. Rather you can start with the second paragraph, and put the first paragraph at the end of the second one to explain how your approach contrasts with previous studies. The third and fourth paragraphs, which repeat background information described in Introduction, can be removed or incorporated into the introductory sentences.
Another example of vague discussion point: “Based on C / N ratios and chlorophyll, we find that SPM is not equally reactive throughout the estuary. O2 saturation, an indicator for heterotrophic metabolism, reaches its minimum in the harbor region, after chlorophyll fluorescence decreased, suggesting active decomposition of limnic algal material (Fig. 2a)”. I guess you meant “depletion of labile agal material” in the low-oxygen harbor region by “active decomposition of limnic algal material”. However, this and the following sentence are confusing in the sense of active decomposition zone.
- As the first reviewer pointed out, I would also like to ask you to pay more attention to enhancing the cohesiveness of many short paragraphs (in contrast to the very long first paragraph of 4.4). And a thorough proofreading would reduce grammatical errors such as inconsistent use of tense (just to select one example: From 0.2 μmol L-1 at stream km 618, concentrations “decreased: to < 2 μmol L-1 (1.7 +/- 0.6) and “remains” relatively stable along the estuary.), many present tenses used in Results and Discussion, and some awkward sentences like that appearing in Conclusions (“Ammonium assimilation competes with nitrification and produces reactive organic matter is produced that can in turn increase reactivity in the estuary.”)

I would like to ask you to make all the changes easily identifiable in a marked-up manuscript based on your point-by-point responses to the reviewer comments. If possible, please specify the line numbers of the revised parts in your responses accompanying the revised manuscript.

Sincerely,

Ji-Hyung Park
Associate Editor, Biogeosciences

Firstly, I would like to thank the authors for the time and consideration they put into the revision and reviewer response, which I believe has resulted in an improved manuscript. However, while the overall message is clearer, clarity is still needed in some places. In addition to this I urge the authors to think about the readability of their manuscript, currently the majority of the manuscript is short paragraphs of 2 to 3 sentences, resulting in the text lacking flow and cohesiveness.

Line 45: some additional explanation / references are needed here, why does low oxygen result in the accumulation of ammonium and nitrite?

Line 67: The opening sentence of this paragraph where you refer to a key finding of Sanders et al, 2018 is totally disconnected from the following sentences where you introduce your study, I suggest you delete it or reword to incorporate it into the rest of the section.

Figure 1 (same is true for Figures 2 and 3): throughout you use the term harbour region and I suggest you use this language here in figure 1 instead of or in addition to Hamburg port. For clarity it would also be beneficial to mark the harbour region onto Figures 2 and 3 (and maybe also in Figure 3 the region you use to determine ammonium and nitrite isotope effects)

Line 142: the fact that you saw no significant differences between treatments, needs to be commented upon. Was sufficient inhibitor used? 0.5uM seems very low when looking at Belser and Mays, 1980.

Line 236: I find this text misleading and confusing regarding where you are defining the harbour region, as currently written here it sounds like the harbour region is from 618 to 656km, which I don’t think is the case. Please clarify.

Line 273 and 276: If you want to use the words rare and unusual as you do in this paragraph you need to provide some context and compare / contrast to the literature to demonstrate this is the case.

Line 308/309: See comment below on section 4.4 as well, this only makes sense once I get to the end of the manuscript. Here you need to comment directly on a potential role for sedimentary and water column denitrification.

Line 338: ‘where organic matter is fresh’ this statement comes too early as you don’t provide evidence for this until later in this section where you introduce the C/N results.

Line 343: What is your evidence for the statement remineralization is prominent, im actually not even sure what that means – this section is about determining an isotope effect and comparing it to the literature.

Line 359: potentially even denitrifying, where is the evidence for this prior to this statement? Or at this point of the manuscript are you relying on the literature, if so a reference is needed.

Section 4.4 : it is only here that things finally fall into place for the reader, you need to introduce the ideas of water column and sedimentary denitrification earlier and there impacts on N isotopes (maybe in the introduction along with where in the estuary you would expect to find each based on the literature?), as prior to this you just use the term denitrification. This is confusing for the reader as you conclude that your isotope effect is representative of only nitrite oxidation as it is unaffected by additional nitrite sinks or sources (line 308), but then mention a number of times in the text a role for denitrification in the Elbe and it is not 100% clear in all cases where in the estuary you are referring to (e.g. line 359). Would a cross plot of 18O and 15N of nitrate not be informative with respect to picking these processes apart – this seems typical for nitrification / denitrification in other studies so would be good to highlight why this method is not relevant here?

Line 435: a reference is needed to demonstrate that denitrification inside particles is feasible

Line 445 to 448: more explanation is needed here for the non-expert, and references are also needed, for example it should be highlighted how these ideas do / don’t differ from km 640 to 655 where you also postulate a role for sedimentary denitrification.

Line 457: language, produce used twice

Line 462: ‘alter the balance of nitrification and denitrification’ it is not clear to me where this was directly discussed in the manuscript with respect to OM.

This manuscript was thoroughly revised. In the revised manuscript, the isotope mass balance calculation was clearly described. The introduction was also revised appropriately to address the significance of capturing oxygen minimum condition. I have a specific comment, explained below.

Specific comment.

Line 273: In this study, we captured a “rare” event in the Elbe estuary
From the introduction and the author’s response, I understood that oxygen minimum condition occurs regularly in summer and it is recognized as an ecological problem. However, these events are “rarely” captured. This sentence might mislead to that event itself rarely occur.

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AR by Kirstin Dähnke on behalf of the Authors (28 Oct 2022) Author's response Author's tracked changes Manuscript

ED: Referee Nomination & Report Request started (03 Nov 2022) by Ji-Hyung Park

RR by Anonymous Referee #2 (15 Nov 2022)

ED: Publish subject to technical corrections (17 Nov 2022) by Ji-Hyung Park

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Short summary

Nitrogen is an important macronutrient that fuels algal production in rivers and coastal regions. We investigated the production and removal of nitrogen-bearing compounds in the freshwater section of the tidal Elbe Estuary and found that particles in the water column are key for the production and removal of water column nitrate. Using a stable isotope approach, we pinpointed regions where additional removal of nitrate or input from sediments plays an important role in estuarine biogeochemistry.