Overall, this manuscript presents a well-compiled nitrification and nitrifiers database in the global ocean. Statistical analyses of the distribution patterns of nitrification rates and nitrifier abundance were provided, along with a brief summary of the influence of different environmental factors, such as temperature, pH, light, N concentration etc. This database has the potential to make significant contributions to the advancement of ecological and biogeochemical models.

Strengths:

1. The data and methods presented in the manuscript are new and have the potential to be useful in the future. The authors have compiled a database of nitrification rates and nitrifier abundance in the global ocean from published literature and unpublished datasets, which can be used to constrain the distribution of marine nitrification, evaluate and improve biogeochemical models of nitrification, and quantify the impact of nitrification on ecosystem functions like marine productivity and N₂O production.
2. The methods and materials are described in detail, allowing other researchers to replicate the study or use the database for their own research.
3. The references and citations to other data sets or articles appear to be appropriate and complete.
4. The article itself is appropriate to support the publication of a data set, as it provides a description of the data collection, processing, and analysis methods.
5. The data set itself appears to be of high quality, as it is accessible, and well-documented. The data set is usable in its current format, and the formal metadata is appropriate.

    Thus, I recommend accepting this manuscript after some major revisions based on the suggestions provided below.

Major:

(1)  Method. The rate values were mainly obtained by using isotope tracers. The incubation condition, preincubation environment, and calculating methods would have a large impact on the final result. In line 204-214, the author summarized the general incubation procedure for nitrification, which is appropriate in the main text. However, during the incubation, different controlling conditions existed in different studies, especially of temperature, light (or paired light and dark to calculate daily), N concentration, and tracer concentration. These essential information (if available) should be directly present in the data table (not only in metadata) for further interpretation and analysis. In addition, calculating equations should also be presented in the data file instead of only in the reference.

(2)  Data presentation. Some trends are “buried” in the scatter plot. This manuscript is actually too long for a dataset paper (32 figures and 66 pages). An overly lengthy analysis may turn off some interested readers. I have some suggestions:

1. a) Some “below detection limit” data should be also presented and marked in proper ways (like marked proportion).
2. b) This manuscript mainly analyzes the scattered points of nitrification data, and I did not see the analysis of water column integration, considering that each nitrification profile must go through the whole numerical "cycle" from 0 to the maximum value (Figure. 13). The analysis of scatter data can lead to a shot-gun situation. I suggest that the currently available profile data should be analyzed by water column integral processing under a certain standard, which may achieve better results. Alternatively, please consider merging the scatter plot and box plot in the text into a single one (such as Figures 4 and 5), where the scatter plot can serve as the background for the box plot. This will enhance the clarity and conciseness of the graphical presentation in the article. Or try to remove some into the appendix or supplementary.
3. c) Scatter plots should be color-classified by different regions to make the image more orderly
4. d) Subgraph numbers should be added in all combined graphs. This will help readers easily refer to specific panels in the graph and enhance clarity in the presentation of the data.
5. e) In Figures 16, 17, 21, and 22, it is unclear whether the amoA archaeal gene abundance corresponds only to the total AOA in the database. Additionally, certain categories such as “Shallow clade AOA”, “WCA”, “Deep clade AOA”, “low-ammonia group AOA”, and “high-ammonia group AOA” in Figure 21 are not specifically marked in the database. I suggest that all labels in figures to be consistent with the database to ensure direct access to the corresponding information in the database.

Minor:

1. Please note that the submission guidelines: Genus and species names are italic; high-order taxonomic ranks are roman. Thus, all graph Labels about the gene names and microbial names should be using italics, such as, "amoA" and "Nitrispina" in Figures 15-27 should be changed to "amoA" and "Nitrispina".
2. Line 77 and Line 80: There is inconsistency in the usage of nitrifiers or nitrifiers’. It is recommended to be consistent throughout the text.
3. Line 143 Table 1 and 147 Table 2, Should be changed to a three-line table format. These modifications will enhance visual clarity.
4. Line 628 p > 0.01 and Line 622 p>0.01, To ensure consistency in the formatting of symbols and text, it is recommended to include spaces between symbols and text throughout the entire text.
5. Table 3: Water Column ecotype A (WCB) should be Water Column ecotype B (WCB).
6. Make a consistent mark in the datasheet. For example, I see “light”, “in situ”, and “yes” in the “in-situ light simulation” column of “rate metadata”. Make sure you don't confuse your readers.

Review of “Database of nitrification and nitrifiers in the global ocean” by Tang et al.

Summary

The authors have compiled an impressive database of hundreds to thousands of environmental rate measurements on both ammonia and nitrite oxidation in the ocean, together with reports of quantitative measurements of the abundances of the major microbial groups presumed to be carrying out these processes.

The synthesis of such a dataset is exciting, necessary and offers the community an important tool for capturing the big picture of this important process. Despite the wide range of techniques and methodologies used, the synthesis provides good assessment of major patterns across the regions of the ocean where studies have been focused. In this sense, this synthesis also provides an excellent picture of where the biggest gaps are – and thereby offers a useful roadmap for the next set of studies that need to be conducted to close such gaps. Although there were no major ‘discoveries’ that dropped out of such a synthesis – this will prove to be a valuable contribution for sure.

I appreciated the attention given to the limitations in methodologies and approaches as well as the recommendations listed for how to optimize future work in this field. This will make a valuable contribution to the literature. I have a few recommendations below for areas that might be clarified or modestly expanded on, as well as a few typos and editorial comments throughout that I hope are useful.

Major comments:

1. My one primary observation that I feel was glossed over by the authors is in the attribution of nitrification rate regulation by light limitation. Both Figure 6c and Figure 11c clearly seem to indicate that rates are actually highest in that upper 10m of the sunlit ocean. For nitrite oxidation – it seems this was perhaps explained by the high rates reported by Clark et al., for the UK shelves, subpolar N Atlantic and Mauritaneian upwelling system. It is unclear whether these are the same studies that used the ¹⁵N dilution method which appears to have a systematic divergence from nitrite oxidation rates measured through ¹⁵NO₂^- addition (Lines 193-195). In Figure 13b, are these left out? If so – this would be good to clarify (i.e., clarify why Fig 13b appears to be a bit different from 11c)? For ammonia oxidation is there a similar explanation for why the highest rates of ammonia oxidation in the whisker-bar plot in Fig 6c ‘seem’ to be absent from the Figure 13a? All in all, I was just looking for a bit more clarity on this surface ocean nitrification dynamic from this database – and felt a little confused by some of how the data were represented.
2. Similarly, despite text that suggests that the distribution of AMO rates and AOA as well as nitrite oxidation rates and NOB were qualitatively similar, respectively, - I was struck by the distinction between Figures 20c and 6c, and 25c and 11c. In comparing these pairs of figures, rates appear to be quite elevated with respect to the clearly lower abundances of organisms at these shallowest depths above 60m. Some clarification on this dynamic might be useful for understanding nitrification in the surface ocean.
3. Given the large uncertainty associated with the stoichiometric conversion of C to biomass during nitrification – it is not clear to me whether rates derived from the ¹⁴HCO₃^- incorporation experiments are as justifiably included in this database. Personally, I would recommend leaving these out of the database to help keep the methodologically sourced ‘noise’ down.
4. This might be a useful forum for a couple paragraphs on the nuances underlying the calculations of these rates – as alluded to on L249-253. In particular, even just spelling out some of the basic sets of equations could be useful for helping guide readers through what aspects might underlie variability among the different studies.

 Minor comments:

Many of the figures did not clearly reproduce (blurry, fuzzy) in the PDF version – somewhat limiting the utility of their color coding and geographic distributions (e.g., Fig 2a; Figure 7).

L70:  group

L93: uptake

The headers for Table 1 are unclear. It seems likely there was a formatting error.

L321:  Wording: The quantification of nitrifier abundance starts to accumulate after 2002.

L323:  originates

L385: light limitation of nitrifiers

L390: missing period

Figure 15 – please explain what is implied by the lighter shaded nitrite oxidation rates (I assume that these refer to the ¹⁵N dilution method estimates which may be biased?).

Figure 16 – please explain the lighter shaded AOB bars.

L625:  I’m not sure that Figure 28c (PAR) supports the statement that ammonia oxidation rates decrease at high light intensity.

Figure 30 and 31:  The panels comparing AOA or Nitrospina abundances vs NO₃^- are not discussed.

Lines 678 – 682: There are some discrepancies in here with respect to correlation coefficients (r values).

L755: … and this group accounts…

in their manuscript entitled "Database of nitrification and nitrifiers in the ocean", Tang and colleagues have compiled a large set of previously published and several unpublished datasets of ammonia and nitrite oxidation rate measurements, as well as qPCR datasets on the abundance of the ammonia and nitrite oxidizing organisms. The authors briefly review the implications of the different methods used to generate the data, and use their compiled data to investigate trends in the activity and abundance of niitrifying organisms across ocean regions, depth, latitude, and seasons. Correlations between abundance of nitrite and ammonia oxidizers, and between organism abundance and activity are also shown. Finally, recommendations are made for future experimental design and target regions, to maximize the value that can be gained from comparative and synthesis studies.



Overall, this data synthesis is a valuable effort to show the state of our measurements of nitrification in the global ocean, and to guide future studies.

I have some recommendations that I hope can be addressed before final publication:



At the moment, it isn't immediately clear from the database which studies have coupled measurements of ammonia and nitrite oxidation, and which studies also include quantification of either ammonia or nitrite oxidizers. Table 2 and 3 cover in the manuscript cover this to a certain extent, but I think it would be beneficial to add this information to the database as well. This could be done in the form of a few extra columns in the "volumetric ammonia oxidation", "volumetric nitrite oxidation", "ammonia oxidizer", and "nitrite oxidizer" tabs, indicating whether coupled measurements are available or not (Y/N).



for the outlier removal, the authors use Chauvenet's criterion, but don't show whether the data is normal or lognormal distributed. As far as I can tell from the text, the only excluded values based where high and low outliers in the ammonia oxidizer qPCR quantification. Instead of listing the examples, I would recoomend listing how many observations were removed from each dataset, and for what reason (outlier or zero/below detection).



Please check the colors in figure 1 and 2 for colorblind friendliness



In figure 3a, it seems a 5th category (Thaumarcheaota 16S + archaeal amoA + bacterial amoA) seems to have been omitted, even though there seem to be several studies in the database that characterized all 3



In figure 5, 10, 19, and 24, please specify in the legend what the x-axis numbers refer to, or label the months by a 1 letter or 3 letter abbreviation. I assume 1 corresponds to january, but it is not stated anywhere.

for those same figures, I understand that the strip plots have been added here for consistency with all other figures, and I generally like the combination of scatter and box plot as used in the manuscript. However for the data by month both the strip plot and the box plots are categorical. if showing the strip plot, consider adding jitter to the data so the distribution is more clear.



Most figures that include depth information use an axis break at 500m, and show the deepest measurements at a different axis scale, please mention this in the legend where appropriate. Figure 8 and 14 do not use an axis break, instead showing the shallower samples (up to 500m depth) in a seperate panel. Either is fine, but I would suggest using one consistently throughout the manuscript.



I noticed figure 21 is not mentioned in the text, please check throughout that all figures are discussed in the text.



line 267: the phrase "partially encoded" struck me as odd, perhaps consider changing to "which is a multisubunit enzyme partially encoded by the amoA gene"



line 553-557: this paragraph seems to suggest that the lowest values are driven by geography and nutrient limitation, but it looks like depth plays a much bigger role overall, if the discussion of the lowest values is ment to refer primarily to the shallow depths, please explicitly state that in the text.



line 629 (and likely elsewhere): perhaps it is better to refer to previously unpublished data included in this work as "this study", or "previously unpublished"?



line 712-719: This paragraph reads as if the authors are going to recommend using the tracer addition methods over the product dilution methods, but then stop short and state a comparison is necessary. Most studies incorporated in the database seem to have been conducted with tracer addition methods, so is there a specific reason the authors would not want to recommend using these going forward?



line 792-793: the authors mention a data compilation template is available, but I could not find it. Perhaps add a link to the template under data availability