Seasonal and interannual dynamics of soil microbial biomass and available nitrogen in an alpine meadow in the eastern part of Qinghai–Tibet Plateau, China

Xu, Bo; Wang, Jinniu; Wu, Ning; Wu, Yan; Shi, Fusun

doi:https://doi.org/10.5194/bg-15-567-2018

Articles | Volume 15, issue 2

https://doi.org/10.5194/bg-15-567-2018

© Author(s) 2018. This work is distributed under
the Creative Commons Attribution 3.0 License.

https://doi.org/10.5194/bg-15-567-2018

© Author(s) 2018. This work is distributed under
the Creative Commons Attribution 3.0 License.

Articles | Volume 15, issue 2

Research article

|

29 Jan 2018

Research article |

| 29 Jan 2018

Seasonal and interannual dynamics of soil microbial biomass and available nitrogen in an alpine meadow in the eastern part of Qinghai–Tibet Plateau, China

Bo Xu, Jinniu Wang, Ning Wu, Yan Wu, and Fusun Shi

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Final revised paper (published on 29 Jan 2018)
Supplement to the final revised paper
Preprint (discussion started on 27 Mar 2017)

Interactive discussion

Status: closed

AC: Author comment | RC: Referee comment | SC: Short comment | EC: Editor comment

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- Supplement

RC1: 'review', Anonymous Referee #1, 06 Apr 2017
- RC3: 'Review bg-2017-66', Anonymous Referee #3, 21 Apr 2017
  - AC3: 'Responses to Anonymous Referee #3', Bo Xu, 22 May 2017
- AC1: 'Responses to Anonymous Referee #1', Bo Xu, 22 May 2017
RC2: 'bg-2017-66: Referee Comment', Anonymous Referee #2, 19 Apr 2017
- AC2: 'Responses to Anonymous Referee #2', Bo Xu, 22 May 2017
RC4: 'Seasonal and interannual dynamics of soil microbial biomass and available nitrogen in an alpine meadow in the eastern part of Qinghai-Tibet Plateau, China', Anonymous Referee #4, 22 Apr 2017
- AC4: 'Responses to Anonymous Referee #4', Bo Xu, 22 May 2017

Peer-review completion

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

ED: Reconsider after major revisions (25 May 2017) by Michael Weintraub

Thank you for your submission to Biogeosciences. Your MS generated considerable interest from potential reviewers and we received four reviews from highly qualified reviewers in this field. However, these reviewers consistently expressed significant concerns about the writing and data presentation and interpretation, and offered numerous substantive comments to improve the manuscript. While I could not access the revised version of the paper mentioned in the authors’ responses to the reviews in the MS records, it sounds as if the proposed revisions described in the Authors’ response to the reviewers will help to address the concerns raised. Thus, I will be happy to consider a revised submission that substantively addresses these reviewer comments as described in the Authors’ response to reviews. Please pay particular attention to addressing the comments about clarifying the research questions, providing the proper literature context for this work, and clarifying what is new and novel about this study, as well as the comments on the specific details of the research, when revising the text.

Additionally, I found some of the wording to be confusing. For example, "interannual" vs. "year to year" in lines 338 and 339; and what does "incompletely consistent" mean? Furthermore, it may be worth considering combining figures 2 and 3 into a single multipanel figure showing microbial biomass C and N temporal dynamics and growing season/non-growing season means. Also, in Figure 6, it would be nice to have every other season shaded in the top graph so it would be easier to see where each season ended.

Please be sure that the clarifications provided in the response to reviewers are also incorporated into the manuscript text. Please also clearly describe how the text was revised according to the reviewer comments when submitting your revised manuscript.

Thank you for your efforts, and for your support of Biogeosciences.

Sincerely,
Mike Weintraub
Associate Editor
Biogeosciences

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AR by Anna Wenzel on behalf of the Authors (04 Jul 2017) Author's response Manuscript

ED: Referee Nomination & Report Request started (19 Jul 2017) by Michael Weintraub

RR by Anonymous Referee #1 (02 Aug 2017)

Suggestions for revision or reasons for rejection

The authors have made substantial progress. Here I note the some comments that are, in my view, still not addressed adequately.

Correction factors: it's the 0.45 and 0.54 (now page 8, L8). I recommend not correcting these numbers using these factors.

There is still no reason given for the pseudoreplicative design (ie three non-independent sets of 5 samples that are then treated as independent). It's not ideal, but there are often acceptable reasons for it and so it's not a fatal flaw in the study. However, I'd like the know the authors' thinking here. The way I see it there are two possibilities: (1) logistically it was not possible to randomly sample across the entire area (meadow or meadow system) of interest, but the authors wanted 15 samples so this is how they were able to achieve that. (2) they were originally planning on comparing the sites, but there were not a lot of interesting differences so they pooled them together in order to achieve a better overall understanding of seasonal trends, which were perhaps not visible with n = 5 at each site. This was a point brought up by multiple reviewers and the authors need to provide a justification on why such a design was used.

Figures: having the bar graphs below the line graphs further emphasizes that the information is redundant. I'll leave it up to authors and editor, but I still recommend removing the bar graphs.

Inclusion of data in a publicly available repository: the authors did not address this request. I still recommend it.

Re: TDN vs. MBN numbers. Some ok points made in the reviewer response, but it's not in the paper. It warrants discussion in the paper.

Photograph and map are not the same thing. It helps to see what the ecosystem looks like on the ground. I still recommend this, even if in the supp materials.

A comment from another reviewer about unsubstantiated statements in the discussion is still relevant: "Finally, there isn’t direct support for many of the overall conclusions of the paper – this study can describe correlations, but not the types of conclusions described (e.g. soil microorganisms play a crucial role in accumulation of inorganic N pools)" Some examples of these statements:
"This period of active microbial activity and N mineralization benefited from substrates conducive for microbial growth, particularly those supplied by the fresh plant litter inputs in autumn."
"Snow melting during this period is an important source of NH4 +–N" This is only true with high deposition. Not sure if this region is susceptible to that.
"At the start of the growing season, NH4 +–N content sharply decreased, partly because alpine meadow plants prefer NH4 +–N" maybe change partly to possibly
"the seasonal dynamics of different available N pools showed significant complementarity with the nutrient supply process and play a crucial role in maintaining abundant biodiversity of alpine meadow ecosystem"
"However, they showed a divergent interannual pattern during the growing season, partly because of the plant and microbe uptakes and leaching effects." same use of partly. maybe authors mean to use possibly in these cases.
"According to our monitoring results, soil temperature and water condition are the primary environmental factors driving the seasonal and interannual dynamics of soil microbial biomass and available N pools." I would probably leave this out. It's something most would accept but at the same time, is not really shown by this study, which does not address mechanisms.

Finally, I would still axe the mentions of climate change from the conclusion. The contributions of this paper are on seasonal trends, not climate change. It's not a huge change. It's fine to mention it where it is mentioned just before the conclusion, but it should not be emphasized as the final statement in the paper. The authors justification in the response that because temperature and moisture appear to correlate with the other measured variables, climate change is important is not convincing. Temperature and moisture are always important for microbial processes, and it's a leap to then suggest that this paper provides particular insight on how this relationship will change with climate.

minor:
"An obviously trend of increasing NH4 + –N content was found during the early soil thaw" this revised sentence does not make sense

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RR by Anonymous Referee #2 (07 Aug 2017)

RR by Anonymous Referee #4 (18 Aug 2017)

Suggestions for revision or reasons for rejection

This paper describes both seasonal and interannual variability in soil microbial biomass and soil available N in alpine tundra with monthly resolution over a 3 year time period. This is an impressive data set which is worthy of publication. I reviewed an earlier version of this manuscript and made a number of suggestions. The writing is much improved but still requires further work. Further, some of my previous comments have not been dealt with to my satisfaction, as described below.

In the previous version I had questions about the MBC/MBN methods as well as the statistics. Neither of these have been dealt with satisfactorily. The methods for determining TDN are still not clear. The procedure for TDN is described on page 7 line 11-16. Line 9-11 describes the chloroform fumigation procedure which is not the methods for TDN but are part of the methods for MBN. TDN is determined on both fumigated and non-fumigated samples (the non-fumigated sample analysis is currently not described in the paper) and the difference is MBN. The chloroform fumigation methods could be moved to the paragraph beginning on page 8 line 6.

For the statistics, the response to reviewer 4 indicates that sample ID was included in the model to account for the lack of independence of samples across time. However, the stastistical analysis section of the manuscript does not describe any inclusion of sample ID in the model. Please clarify in the manuscript. Also, all F values throughout the manuscript should include the degrees of freedom.

Some parts of the result section are also not clear. For example, when describing DOC patterns, the seasons are described as being not significantly different from each other (page 11 line 18) and also significantly different (page 12 line 4). Also, the results section could be reduced – e.g. The two sentences from page 10 line 17 to page 11 line 1 say the same thing. Finally, just as a suggestion, figure 3 could also be presented with only part A and shading to indicate the different season – this way the data is only presented once rather than repeated in both parts of the figure. The same change could be applied to the other figures. The two types of presentations are presented in the same figure sometimes (Figure 3) and as separate figures in others (Figure 7 and 8).

In the discussion, the authors still need to be cautious about implying causality for some of the patterns they have measured. Some examples are below:
Page 13 Line 14 – indicate that the mechanism for the increase in soil MBC and available N are speculative. Also, the conclusion of this paragraph describes an accumulation of organic N which is not described in the remainder of the paragraph.
Page 15 Line 15 – Only describe what you have evidence for – e.g. an increase in microbial biomass and not activity

And lastly, a few clarifications are required in the discussion:
Page 15 line 9 – what do you mean by the “number of bacteria” increased just after thaw? The previous paragraph describes a crash in microbial biomass. Do you mean the proportion of bacteria to fungi? The number of bacterial phenotypes?
Page 15 line 2-5 The units for soil organic matter need an area (per m2?) for this comparison to be relevant. Is this sentence implying that the SOM in tundra is limiting to microbial growth in some circumstances?

The writing in this version is much improved over the last version. However, the writing still needs to be improved for clarity and grammar. A number of examples follow:
Page 1 Line 10 – replace “occurs seasonally” with “varies seasonally” as the activity occurs all the time
Page 1 Line 15 – replace “Topsoil samples were” with “Soil was” and “and were analyzed” with “and analyzed”
Page 1 Line 17 – replace “was measured” with “as measured”
Page 1 Line 18 – replace “ the number of” with “the proportion of”
Page 2 Line 1 – replace “induced by soil temperatures” with “induced by changes in soil temperatures”
Page 3 Line 11 – delete “apparently”
Page 4 Line 5 Delete “In alpine systems” as it is repeated later in the sentence
Page 5 line 8 Delete “and”
Page 6 line 10 – Delete “ and 15 soil samples… time” as this information is repeated from a few sentences earlier
Page 9 line 4 – “analysis of variance” not “variance analysis”
Page 14 line 17 – what does the a refer to in the units for biomass? Per year?

Similarly, the use of appropriate references is also much improved. A few more which need to be changed are:
Page 3, line 3: Mikan is not an alpine reference
Page 16 line 13 – Qin and Petechey/Gaston are general biodiversity –ecosystem functioning researchers and not appropriate for use in this sentence.

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ED: Reconsider after major revisions (22 Aug 2017) by Michael Weintraub

AR by Anna Wenzel on behalf of the Authors (06 Oct 2017) Author's response Manuscript

ED: Reconsider after major revisions (20 Oct 2017) by Michael Weintraub

I was disappointed to see that the authors chose to ignore some of the most important and valid points made by the reviewers in the last round of review. For example, multiple reviewers asked the authors to significantly revise or eliminate unsupported statements or conclusions, but the authors did little to address this issue. The problem of the authors ignoring the reviewers' comments was an issue even with the simplest points. For example, Reviewer 1 pointed out that the sentence ""An obviously trend of increasing NH4 + –N content was found during the early soil thaw" does not make sense (due to significant grammatical errors). Instead of fixing this issue, the authors chose to ignore this comment, missing the obvious writing correction that was needed.

Another instance is where the authors ignored Reviewer 1's recommendation to not use extraction efficiency correction factors for microbial biomass. The authors completely missed or ignored the point that extraction efficiency correction factors for microbial biomass should not be used unless they have been determined for the soil being studied or it can be demonstrated that the soil being studied is substantively similar to the limited range of mostly agriculture soils for which they were originally developed.

In one instance after another, it appears that authors did little to seriously consider the substance of and substantively address the most recent comments from the reviewers. Thus, I now encourage the authors to go back and give more careful serious consideration to every one the reviewers criticisms and address them more substantively (e.g. the request for a more meaningful discussion of the pseudo-replicated sampling design, which was also ignored). I emphasize to the authors that this problem is not restricted only to the specific examples mentioned here.

I especially am troubled by instances where the authors claim that they addressed reviewer comments, but did not. For example, reviewer 4 asked for more details on the procedure used for measuring TDN, and the authors responded that "Yes, the methods for determining TDN, MBC and MBN were rewrote according to your suggestion" but, after a careful analysis of the revised methods section, I could not find any of the additional requested methods details for TDN.

I also emphasize to the authors that where clarifications are requested by the reviewers, the clarifications need to be added to the manuscript text itself. These clarifications are not simply for the reviewers' knowledge (e.g. reviewer 2 asked "Page 38 line 18: what do you mean with a-1?" and the authors answered the reviewer's question in their response, but as far as I can tell they did not add the appropriate clarification to the manuscript. There is the same issue with the request for clarification of about site elevations). Similarly, Reviewer 4 requested an explanation of how and why Sample ID was included in their statistical model, but this explanation was not added, and the response to the reviewer's comment also does not satisfactorily address this point.

Finally, there are still significant grammatical and English usage errors throughout this manuscript, and the authors are asked to put significantly more effort into fixing them in order to make this manuscript acceptable for publication.

Please be sure to submit a new, revised authors' response along with your revised manuscript.

Thank you for your efforts, and for your support of Biogeosciences.

Sincerely,
Mike Weintraub
Associate Editor
Biogeosciences

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AR by Anna Mirena Feist-Polner on behalf of the Authors (24 Nov 2017) Author's response

ED: Publish as is (11 Dec 2017) by Michael Weintraub

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Short summary

The Qinghai–Tibet Plateau is sensitive to climate change. We documented seasonal and interannual dynamics of soil microbial and available N in an alpine meadow in this region. Consistently increasing trends of microbial biomass and available N pools were observed during the nongrowing season. Significant shifts in microbial communities largely contributed to microbial reduction during soil thaw. Divergent seasonal dynamics of different N forms showed a complementary nutrient supply pattern.