the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Potential contributions of nitrifiers and denitrifiers to nitrous oxide sources and sinks in China’s estuarine and coastal areas
- 1State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
- 2Department of Geosciences, Princeton University, NJ 08540, USA
- 3State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, China
- 4Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
- 1State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
- 2Department of Geosciences, Princeton University, NJ 08540, USA
- 3State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, China
- 4Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
Abstract. Nitrous oxide (N2O) is an important ozone-depleting greenhouse gas produced and consumed by microbially mediated nitrification and denitrification pathways. Estuaries are intensive N2O emission regions in marine ecosystems. However, the potential contributions of nitrifiers and denitrifiers to N2O sources and sinks in China's estuarine and coastal areas are poorly understood. The abundance and transcription of six key microbial functional genes involved in nitrification and denitrification, as well as the clade II-type nosZ gene-bearing community composition of N2O reducers, were investigated in four estuaries spanning the Chinese coastline. The results showed that the ammonia-oxidizing archaeal amoA genes and transcripts were more dominant in the northern Bohai Sea (BS) and Yangtze River estuaries, which had low nitrogen concentrations, while the denitrifier nirS genes and transcripts were more dominant in the southern Jiulong River (JRE) and Pearl River estuaries, which had high levels of terrestrial nitrogen input. Notably, the nosZ clade II gene was more abundant than the clade I-type throughout the estuaries except for in the JRE and a few sites of the BS, while the opposite transcript distribution pattern was observed in these two estuaries. The gene and transcript distributions were significantly constrained by nitrogen and oxygen concentrations, as well as salinity, temperature, and pH. The nosZ clade II gene-bearing community composition along China’s coastline had a high diversity and was distinctly different from that in the soil and marine oxygen-minimum-zone waters. By comparing the gene distribution patterns across the estuaries with the distribution patterns of the N2O concentration and flux, we found that denitrification may principally control the N2O emissions pattern.
- Preprint
(1659 KB) -
Supplement
(519 KB) - BibTeX
- EndNote
Xiaofeng Dai et al.
Status: final response (author comments only)
-
RC1: 'Comment on bg-2022-43', Anonymous Referee #1, 12 May 2022
Dai et al. investigated the distribution of six key genes and transcripts related to N2O production and consumption in four main estuaries in China. The authors analyzed the correlation between these genes and N2O fluxes or concentrations obtained from previous literature and discussed what environmental factors might control the gene distribution pattern. This work implies denitrification might be essential for N2O emissions in these estuaries. This study provides new insight into microbial divers of N2O cycling in estuaries in China.
Here are some minor suggestions:
Line 70: cite (Frey et al., 2020 Biogeosciences) for the dominance of nitrate derived N2O in OMZs.
Lines 75-79: cite (Ji et al. 2018 Biogeosciences) for N2O production from denitrification in the Chesapeake Bay.
Line 82: cite Figure 1 for the location of the four estuaries.
Line 126: What were the minor modifications? Please elaborate.
Line 145: What kind of alpha diversity? (e.g. Shannon alpha diversity?)
Line 148: ‘The top 10 most similar sequences of each OTU were used as references.’ It is not clear how the taxonomy of the OTU was assigned. Did you use the taxonomy of the top 1 reference as the taxonomy of the OTU or the dominant taxonomy among all 10 references? Please explain this.
Line 235: accounting for % and % of N2O production-related gene abundance
Line 240: I believe you meant to say ‘one to two orders of magnitudes’.
Line 291: should be (Figure 4b). Abundance was not reflected in Figure 4a.
Line 376: need to tune down this sentence here since N2O emission is controlled by both N2O production and consumption. You could say ‘suggesting that acidification of the ocean may decrease N2O consumption potential.’
Line 345: Since the four estuaries were sampled in different seasons, it would be useful to see some discussion about how different seasons might affect the distribution of genes and transcripts.
Lines 388-404: nosZ clade I was transcribed more even though nosZ clade II genes were more abundant (Figure 3 i). The discrepancy between nosZ DNA and transcripts is worth discussing.
Lines 415-416: (a) are these datasets measured from the same months or years as the microbial samples? Or they are mean values of some sort? Please provide a little more detail here. (b) why use gene abundance as indicators but not transcripts? The latter shows ‘activity’ in some sense. Could you present the transcript data in Figure 6 or the supplement?
Line 456: additional citations should be included here: (Bertagnolli et al., 2020 Environmental Microbiology reports) and (Sun et al., 2017 Frontiers in Microbiology).
Figure 1: I suggest adding sampling time for each estuary in the figure.
Figure 2: please label the four estuaries (maybe as row names for all subplots). Latitudes and longitudes for the first few plots were missing. Please add latitudes and longitudes for all subplots. It is hard to tell ammonia, nitrite, and nitrate concentrations in three out of the four estuaries. You could use a different scale bar for PRE, so the other three plots could have a better resolution.
Figure S2: red and orange in the plots were too similar to each other, please choose another color to distinguish the two better.
-
RC2: 'Comment on bg-2022-43', Anonymous Referee #2, 02 Jun 2022
I have carefully read the manuscript “Potential contributions of nitrifiers and denitrifiers to nitrous oxide sources and sinks in China’s estuarine and coastal areas” by Dai et al. The manuscript describes the spatial distribution and abundance of marker genes and transcripts related to the production and consumption of nitrous oxide in four estuaries in coastal China. Moreover, the diversity of the clade II-type nosZ gene was further investigated along the same four estuaries. The manuscript is nicely written and provides valuable information on the potential mechanisms controlling nitrous oxide consumption/production in coastal China. Furthermore, the results are put in context by using water column physicochemical data and by previously published measurements of nitrous oxide fluxes in the same four estuaries. I have, however, the following minor comments on this manuscript:
- Line 39: add “the” before nitrification.
- In the introduction, between lines 52-59 the authors describe the physiology/ecology of microorganism possessing the clade II-type nosZ. How is that different from microbes containing the clade I-type?
- Check verb tense in the introduction. Usually, present tense is used.
- In material and methods please provide the depths from which samples were collected.
- Lines 125-126. What minor modifications?
- Was the same qPCR program (lines 178-180) used for all primer sets?
- Line 199: What characteristic of the community? (i.e., community assembly or structure?)
- Please add units to salinity values (ppt, I guess?)
- When reporting the qPCR/RT-qPCR copy numbers, it is nice that the authors provided the range for each site. However, the median could also be informative, since the extremes may be outliers.
- Line 241: Orders of magnitude?
- Line 283: It was not clear to me what did the authors mean by “sequencing coverage”?
- Line 311-313. NMDS is only a visualization approach, I think the authors measured the similarity level by performing pairwise comparisons of the Bray Curtis dissimilarity index.
- In the discussion, as well as in the introduction, when describing previous literature, the present tense is usually preferred.
- Lines 374-376: Authors mention that the nosZ gene/transcript abundance was correlated with pH. Could it also be a confounding effect of DIN concentration, since pH seems to have a similar spatial gradient as DIN, with higher pH and lower DIN in the open ocean (Fig. 2).
- As I mentioned above, it is a strength of the manuscript to use N2O flux, and deltaN2O data to put in context the results. However, greater background/information on where, when, and how that data was collected would be helpful to the reader.
- As reviewer 1 mentioned, I also wonder why the authors decided to use the gene abundance, and not the transcript abundance to correlate it with N2O flux and deltaN2O.
- Figure 2: What were the depth layers? Adding a label explaining which panel corresponds to which estuary may be helpful for the reader (same for Fig 3).
- Figure 6: Could it help to log transform the qPCR/RT-qPCR data to plot it in order to avoid breaking the y-axis?
Xiaofeng Dai et al.
Xiaofeng Dai et al.
Viewed
| HTML | XML | Total | Supplement | BibTeX | EndNote | |
|---|---|---|---|---|---|---|
| 348 | 100 | 13 | 461 | 27 | 2 | 2 |
- HTML: 348
- PDF: 100
- XML: 13
- Total: 461
- Supplement: 27
- BibTeX: 2
- EndNote: 2
Viewed (geographical distribution)
| Country | # | Views | % |
|---|
| Total: | 0 |
| HTML: | 0 |
| PDF: | 0 |
| XML: | 0 |
- 1