Diversity and distribution of nitrogen fixation genes in the oxygen minimum zones of the world oceans

Jayakumar, Amal; Ward, Bess B.

doi:https://doi.org/10.5194/bg-17-5953-2020

Articles | Volume 17, issue 23

https://doi.org/10.5194/bg-17-5953-2020

© Author(s) 2020. This work is distributed under
the Creative Commons Attribution 4.0 License.

Special issue:

Ocean deoxygenation: drivers and consequences – past, present...

https://doi.org/10.5194/bg-17-5953-2020

© Author(s) 2020. This work is distributed under
the Creative Commons Attribution 4.0 License.

Articles | Volume 17, issue 23

Research article

|

02 Dec 2020

Research article |

| 02 Dec 2020

Diversity and distribution of nitrogen fixation genes in the oxygen minimum zones of the world oceans

Amal Jayakumar and Bess B. Ward

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Final revised paper (published on 02 Dec 2020)
Supplement to the final revised paper
Preprint (discussion started on 13 Jan 2020)
Supplement to the preprint

Interactive discussion

Status: closed

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

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- Supplement

RC1: 'review of the manuscript by Jayakumar and Ward', Anonymous Referee #1, 27 Jan 2020
- AC1: 'Anonymous Referee #1', Amal Jayakumar, 08 May 2020
RC2: 'Comment on “Diversity and distribution of Nitrogen Fixation Genes in the Oxygen Minimum Zones of the World Oceans” by Amal Jayakumar and Bess B. Ward', Anonymous Referee #2, 02 Mar 2020
- AC2: 'Anonymous Referee #2', Amal Jayakumar, 08 May 2020

Peer-review completion

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

ED: Reconsider after major revisions (15 May 2020) by Anja Engel

ED: Reconsider after major revisions (15 May 2020) by Katja Fennel (Co-editor-in-chief)

AR by Amal Jayakumar on behalf of the Authors (20 May 2020) Manuscript

ED: Referee Nomination & Report Request started (07 Jun 2020) by Anja Engel

RR by Anonymous Referee #2 (22 Jun 2020)

Suggestions for revision or reasons for rejection

In this version, the authors have compared their results with those in the previous studies, which resulted in a more thorough discussion about the nifH phylotypes in OMZs of the world oceans. The manuscript has been improved significantly with these revisions.

Nevertheless, I still have a major concern about the insufficient dataset in this study. According to the information in Table 1, there were few sequences per sample, some samples even have only 3-4 clones being sequenced. This problem is exactly what I was worried about and that’s why I asked the authors to provide more details (Table 1) in the previous review. With such limited dataset, it is hard to say anything about the relative abundance of the OTUs or compare the nifH communities at different depth and OMZs. The authors need to either increase the sequencing depth or convince the audiences that their results can really represent “nifH phylotypes/community in the world OMZs”. In the current version, it is obvious that the authors could not draw any convincing conclusions. Besides, I have some specific comments as follows.

L16-17: “The OTUs were biogeographically distinct for the most part – there was little overlap among regions,” Would it be a result of limited sequencing depth in your study? Based on Table 1, only the most dominant phylotypes could be detected with 3-50 sequences per sample.

L54: I did not see 32 samples in Table 1.

L88: You should construct maximum-likelihood tree and choose the best-fit model using model test.

L149: How can you compare community composition and biogeography with 3-50 sequences per sample?

L405-408: It seems over-speculation to me. The “similar metabolic types” was not supported by the result. You only sequenced some clones of nifH gene fragments. Also, without the actual abundance (i.e. gene copy number), you cannot make any statement about “bloom”. “Most of the sites/depths, both in this study and in others from OMZ regions, are
dominated by one or a few OTUs” could be due to limited sequencing depth or low diversity of nifH phylotypes in the samples.

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RR by Anonymous Referee #3 (30 Jun 2020)

ED: Reconsider after major revisions (05 Jul 2020) by Anja Engel

ED: Reconsider after major revisions (07 Jul 2020) by Katja Fennel (Co-editor-in-chief)

AR by Amal Jayakumar on behalf of the Authors (20 Aug 2020) Author's response

ED: Referee Nomination & Report Request started (30 Aug 2020) by Anja Engel

RR by Anonymous Referee #2 (15 Sep 2020)

ED: Publish as is (15 Sep 2020) by Anja Engel

ED: Publish as is (15 Sep 2020) by Katja Fennel (Co-editor-in-chief)

AR by Amal Jayakumar on behalf of the Authors (23 Sep 2020)

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Short summary

Diversity and community composition of nitrogen-fixing microbes in the three main oxygen minimum zones of the world ocean were investigated using nifH clone libraries. Representatives of three main clusters of nifH genes were detected. Sequences were most diverse in the surface waters. The most abundant OTUs were affiliated with Alpha- and Gammaproteobacteria. The sequences were biogeographically distinct and the dominance of a few OTUs was commonly observed in OMZs in this (and other) studies.