the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Version 2 of the global oceanic diazotroph database
Zhibo Shao
Yangchun Xu
Hua Wang
Weicheng Luo
Lice Wang
Yuhong Huang
Abstract. Marine diazotrophs convert dinitrogen (N2) in seawater into bioavailable nitrogen (N), contributing approximately half of the external input of bioavailable N to the global ocean. A global oceanic diazotroph database was previously published in 2012. Here, we compiled version 2 of the database by adding 23,095 in situ measurements of marine diazotrophic abundance and N2 fixation rates published in the past decade, increasing the number of N2 fixation rates and microscopic and qPCR-based diazotrophic abundance data by 140 %, 26 % and 443 %, respectively. Although the updated database expanded spatial coverage considerably, particularly in the Indian Ocean, the data distribution was still not uniform and most data were sampled in the surface Pacific and Atlantic Oceans. By summing the arithmetic means of the N2 fixation rates in each ocean basin, the updated database substantially increased the estimate of global oceanic N2 fixation from 137 ± 9 Tg N yr-1 using the old database to 260 ± 20 Tg N yr-1 (mean ± standard error). However, using geometric means instead, the updated database gave an estimate of global oceanic N2 fixation (60 Tg N yr-1) similar to that estimated from the old database (62 Tg N yr-1), while the new estimate had a larger uncertainty (confidence intervals based on one standard error: 47 – 107 Tg N yr-1 versus 52 – 73 Tg N yr-1), mostly attributable to elevated uncertainties in the Pacific Ocean. An analysis comparing N2 fixation rates measured at the same months and location (1° × 1° grids) showed that the new 15N2 dissolution method obtained N2 fixation rates higher than the conventional 15N2 bubble method in 65 % of cases, with this percentage increasing when the N2 fixation rates were high (> approximately 3 μmol N m-3 d-1 using the 15N2 dissolution method). With greatly increased data points, this version 2 of the global oceanic diazotrophic database can support future studies in marine ecology and biogeochemistry. The database is stored at the Figshare repository (https://doi.org/10.6084/m9.figshare.21677687) (Shao et al., 2022).
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Zhibo Shao et al.
Status: final response (author comments only)
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RC1: 'Comment on essd-2023-13', Anonymous Referee #1, 17 Feb 2023
The comment was uploaded in the form of a supplement: https://essd.copernicus.org/preprints/essd-2023-13/essd-2023-13-RC1-supplement.pdf
- AC1: 'Reply on RC1', Zhibo Shao, 14 Apr 2023
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RC2: 'Comment on essd-2023-13', Christopher Somes, 09 Mar 2023
This manuscript by Shao and Xu et al. describes an updated version 2 of the global oceanic diazotroph database. It build upon the previous version by adding additional measurements of marine diazotrophic abundance, N2 fixation rates, microscopic and qPCR-based diazotropic abundance. The spatial coverage significantly improved most notably in the Indian Ocean. The newly revised estimate for global N2 fixation rate is significantly higher (+123 Tg N yr-1, almost doubled) when calculating using a standard arithmetic mean, although surprisingly the geometric mean did not significantly change. A brief analysis and discussion of the 15N2 bubble vs. dissolution indicated a potential general underestimation from the bubble method particularly at high rates, however noting the comparison of samples were from different times so it is not a formal error analysis (which the authors acknowledge). The database is available to download from the provided link in the abstract.
Overall I find this to be an important update to the database mainly due to the significant increase in included measurements and spatial coverage. The database is transparent and mostly well described. The analysis and first preliminary quantification of the 15N2 bubble vs. dissolution is also an important contribution. Perhaps some additional details/analysis could be provided (see comments below), but additional analyses can also be performed independently by users who download the data for their specific interest. There is one important aspect that needs additional clarification in my view before I would endorse this manuscript for publication (global N2 fixation rate calculation, see below).
-Christopher Somes
GEOMAR Helmholtz Centre for Ocean Research Kiel
Major Comment: Global N2 fixation calculation description
Since this paper will likely often be cited for revising the global N2 fixation rate significantly upwards, the description of this calculation should be more transparent and comprehensive:
line 266 (Table 5 caption): “Data are first binned to 3x3 grids…”
This needs to be better described. For example, was there any type of interpolation method used or simple averaging of all measurements in each bin? It would be interesting to know what percentage of bins in each ocean basin has data coverage. How do you define the Southern Ocean region and is that area removed from the other southern regions?
How was the vertical coordinate handled? Is it evenly spaced or according to the depths ranges in Figure 7?
It is not clear to me how the “Areal sum” calculation was made based on the “Mean N2 fixation rate” (Table 5). Does the “Mean N2 fixation” rate include all measurements or only the “Depth-integrated N2 rates”, which requires 3 measurements in the vertical? If the vertical coordinate is uneven, do measurements that get binned into a larger volume in larger deeper layers have more weight on the depth-integrated rate than shallower layers?
When calculating the “Areal Sum”, do you assume that the “Mean N2 fixation rate” extrapolates across the entire region or do you only consider the area of the bins that have data coverage? For example, the Indian Ocean has about 36% of the bins compared to the South Pacific. Therefore I was expecting a much larger decrease when calculating the Areal Sum relative to the Mean N2 fixation rate for the Indian Ocean compared to the South Pacific. However this relative decrease is quite subtle in Table 5 between these regions. I acknowledge there is no truly perfect way to estimate a global ocean N2 fixation rate with the current coverage, but all of the assumptions and details that go into the calculation should be specifically stated and described.
The authors do not give much context on interpreting the geometric vs. arithmetic mean despite that it is mentioned multiple times throughout the manuscript and gives a significantly different result. From what I understand, geometric mean is less sensitive to the high-end rates compared to arithmetic mean. Does this mean that most of the increase in the arithmetic mean is driven by newly included high-end rates? It would be valuable to know how much of the large increase in the arithmetic areal sum is driven by additional spatial coverage versus generally higher rate values. I would suggest to include a histogram of the previous version in one of the supplementary figures for comparison. If newly included rate values tend to be significantly higher, it would be interesting to know how much of that may be attributable to growing numbers of the dissolution method compared to bubble method (i.e. based on Figure 10).
Minor Comments:
line 84 and data file: Metadata
In the data file, the meta data are titled “Surface …”, yet they are associated with a specific depth, so are they really surface? I am used to seeing chlorophyll expressed by volume not area.
lines 127-129: daily vs. daytime vs. nighttime normalization
I am still a little confused about the time normalization with this brief description. If the incubation is only performed during the day, you convert hours to day by 12 hr/day which assumes no rates at night? I see that incubation hours vary a lot and in some cases not a multiple of 12 hours or 1 day. Perhaps you can describe how individual studies typically convert to a daily rate depending on the incubation period. Would it make more sense to multiply by the daytime of each location during the time of sampling instead of assuming 12 hours?
Table 5.: “n” is missing in Indian Ocean
Figure 7:
Why do you choose geometric mean over the more commonly used arithmetic mean in this figure? Does it look significantly different if you use arithmetic means?
I would be interested to see a euphotic vs. aphotic depth-integrated rate. I am curious how much the generally low to moderate rates occurring below 100 meters contribute to the total depth-integrated rate since they can occupy more volume. Perhaps adding a <100m and >100m panel would be useful? At what depths are the deepest N2 fixation measurements?
Section 4.1/Figure 10:
As mentioned above, I think is a useful first investigation into methodological uncertainties on N2 fixation rates. Is there enough data coverage to do a similar analysis for acetylene reduction?
Citation: https://doi.org/10.5194/essd-2023-13-RC2 - AC2: 'Reply on RC2', Zhibo Shao, 14 Apr 2023
Zhibo Shao et al.
Data sets
Version 2 of the global oceanic diazotroph database Zhibo Shao, Yangchun Xu, Hua Wang, Weicheng Luo, Lice Wang, Yuhong Huang, and Ya-Wei Luo https://doi.org/10.6084/m9.figshare.21677687
Zhibo Shao et al.
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