Reply on RC1

Reply on RC1 Gesa Schulz et al. Author comment on "Suspended particulate matter drives the spatial segregation of nitrogen turnover along the hyper-turbid Ems estuary" by Gesa Schulz et al., Biogeosciences Discuss., https://doi.org/10.5194/bg-2021-321-AC1, 2022 We thank the reviewer for their constructive and helpful review of our paper. In following, we will reply to the individual comments. Reviewer comments are written in italics, our answers are kept in plain font.


I was a bit confused when the methods section talked about FerryBox sampling (Line 92) and equilibrator measurements of nitrous oxide (Line 132), yet the datasets only show discrete samples for the sampling stations along the 100 km transect (Figure 2). To be clear, I like the data presentation in Figure 2 because its clear and easy to follow, but at the moment the Methods section highlights sampling that is not reflected in the results section.
We agree that the current presentation of the FerryBox and nitrous oxide data does not represent the continuous measurements during our campaigns. For nitrous oxide, we will change the figure by plotting data points for 1 min averages along the transect. For clarity, we decided to keep the current way of presentation for the FerryBox data (salinity and oxygen concentration) with plotting only data points for our 20 min sampling interval. In the revised manuscript version, we will clearly refer to the fact that the plot only shows discrete points of the continuous measurement to avoid confusion.

The only continual measurements are a snapshot of dissolved oxygen concentrations over a 2-3 day period for fixed locations (Figure 3). Also, Figure 3 is less easier to follow than the other figures in the manuscript and I think future readers would appreciate efforts to make it more interpretable.
We will modify the figure caption by adding a brief sentence on sampling points, i.e.: "In 2014, oxygen concentration was measured at two sampling stations at stream kilometers 11.8 and 24.5. In 2020, additional measurements were done at stream kilometers 18.2 and 33.0." We will further evaluate changes of the figure that may improve clarity.

It wasn't clear to me whether the authors interpret the datasets obtained six years apart (in 2014 and 2020) to be sufficiently similar that they can be considered a sampling replicate or whether there are differences between 2014 and 2020 that indicate changes to the N cycling. Looking at Figure 2, there appear to be differences in nitrite concentrations and also the isotopic composition of nitrate. Is this noteworthy to the readers? Discussion of this could be included when discussing differences in the PCA plots on Figure 5?
Thanks to the referee for the comment. We interpret the data of both sampling campaigns not as sampling replicates, but as sufficiently similar for comparison to evaluate the zonation of the estuary. With a six-year time difference, we cannot ensure identical sampling and measuring conditions for both cruises that would be necessary for true replicates. The PCA analysis showed that nitrogen turnover was comparable in both years. However, there are distinct differences (such as the occurrence of assimilation in the outer estuary, which is much more distinct in 2020) between the cruises that we tried to address in the manuscript.
Seasonal and interannual variation may cause differences in dissolved inorganic nitrogen distribution and nitrate stable isotope composition. Water temperature and discharge were significantly higher during our cruise in 2014 than in 2020. The offset of nitrate isotopes fits relatively well with the observed shift of salinity, oxygen and ammonium concentration. In the manuscript, we argue that these shifts may be driven by the increased discharge (Line 285 -290). The increased nitrite concentration in 2014 may be caused by enhanced temperature that fuels microbial turnover.
In general, we see the same nitrogen turnover processes along Ems estuary during both cruises. There is no evidence hinting significant changes that were not caused by seasonal or single effects. The PCA independently confirms the same zones of nitrogen turnover for each year. The loadings of the principle components were also similar for both cruises.
In summary, the two cruises allow a more robust assessment of general N-cycling patterns in the Ems than a single campaign would, but they can certainly not be regarded as replicates. We will briefly address similarities and differences in the revised manuscript where we see fit, most likely in the section addressing the PCA results, as suggested by the reviewer.

Line 362 The authors justify using an isotope effect of 10 ‰ based on unpublished data. This is should be changed. The authors can always deposit the data in a free public database e.g. zenodo, and cite the doi.
The data was presented at the EGU in 2014 (Sanders, T.; Daehnke, K.: N-Isotope fractionation of nitrification in the tidal influenced Elbe River estuary, Germany. In: European Geosciences Union General Assembly, EGU 2014. Wien (A), 27.04. -02.05.2014, 2014.). We will include the conference abstract with its doi as a reference. In addition, we are currently working on a publication of the data as a short communication. Inclusion of the data in a data base is difficult, as these are results from incubation experiments that needs further method explanation, and this format not easily included in a free public database like, e.g., PANGAEA.

Line 443 'Furthermore, our results as well as those from 1997 were obtained from a single survey in June making the comparison intruding' This is just a small language error, the authors should change intruding to intriguing or another word to better reflect their intention.
Thanks for the comment! We will correct this to intriguing in the revised version.

Figure 1. Is it possible for the authors to either indicate on the map, the four sections that are referred to in the text, or draw a transect below the map that indicates the four zones?
We will include indications for the four sections in a new version of our map.

Was the O2 sensor data included in the Supplementary Material? I don't think I saw it there.
The oxygen data is not part of the supplement materials. We did not include it, because we used data provided by the German Federal Institute of Hydrology (Bundesanstalt für Gewässerkunde -BfG). The BfG itself plans the publication of the data soon in "BfG-Report No. 2077". As soon as the report is published, we will provide links to the data. We hope this is sufficient, as all measured data points were presented in the figures 3 and S1.