Metagenomic analyses of the late Pleistocene permafrost – additional tools  for reconstruction of environmental conditions

Rivkina, Elizaveta; Petrovskaya, Lada; Vishnivetskaya, Tatiana; Krivushin, Kirill; Shmakova, Lyubov; Tutukina, Maria; Meyers, Arthur; Kondrashov, Fyodor

doi:https://doi.org/10.5194/bg-13-2207-2016

Articles | Volume 13, issue 7

https://doi.org/10.5194/bg-13-2207-2016

© Author(s) 2016. This work is distributed under
the Creative Commons Attribution 3.0 License.

https://doi.org/10.5194/bg-13-2207-2016

© Author(s) 2016. This work is distributed under
the Creative Commons Attribution 3.0 License.

Articles | Volume 13, issue 7

Research article

|

15 Apr 2016

Research article |

| 15 Apr 2016

Metagenomic analyses of the late Pleistocene permafrost – additional tools for reconstruction of environmental conditions

Elizaveta Rivkina, Lada Petrovskaya, Tatiana Vishnivetskaya, Kirill Krivushin, Lyubov Shmakova, Maria Tutukina, Arthur Meyers, and Fyodor Kondrashov

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Final revised paper (published on 15 Apr 2016)
Supplement to the final revised paper
Preprint (discussion started on 04 Aug 2015)
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

RC C4968: 'Review of "Metagenomic analyses of the late Pleistocene permafrost – additional tools for paleo-reconstructions"', Anonymous Referee #1, 06 Sep 2015
- AC C7046: 'Answers to comments of Rev#1', Elizaveta Rivkina, 26 Oct 2015
RC C8070: 'Review of manusrcript bg-2015-284', Anonymous Referee #2, 28 Nov 2015
RC C8527: 'Referee Comment', Anonymous Referee #3, 16 Dec 2015
- AC C8582: 'Answers to comments of Rev#1,2 and 3', Elizaveta Rivkina, 20 Dec 2015
  - AC C8589: 'The new version of ms aftre revission', Elizaveta Rivkina, 20 Dec 2015

Peer-review completion

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

ED: Reconsider after major revisions (16 Dec 2015) by Victor Brovkin

AR by Elizaveta Rivkina on behalf of the Authors (21 Dec 2015) Author's response Manuscript

ED: Referee Nomination & Report Request started (04 Jan 2016) by Victor Brovkin

RR by Anonymous Referee #1 (14 Jan 2016)

Suggestions for revision or reasons for rejection

The revised version of the manuscript takes several of the critical points into account, which were raised in the first review; however some fundamental issues were not met sufficiently.
First of all, the authors should clearly describe the rationale of the study in the introduction. It is still unclear why a metagenomic analysis is required when the authors aim to elucidate the reason for low methane concentrations and low methanogenic activity in permafrost samples of the late Pleistocene. The question is not if a metagenomic analysis gives valuable information (as the authors response implies) but why it is necessary to conduct a metagenomic analysis if only the methane cycle is of interest. The results on microorganisms of the sulfur and nitrogen cycle are prominently presented in the manuscript including two figures (none for the methane cycle), hence it seems that not only the methane cycle was of interest in this study and this should be considered when presenting the objectives.
Secondly, the authors cited further literature showing elevated methane concentrations, viable methanogens and methanogenic activity in syngenetic permafrost of the late Pleistocene Ice Complex, but they do not clearly consider these results in the introduction and discussion (see specific comments). The generalization that syngenetic Yedoma deposits do not contain methane (see l. 406) and viable or active methanogens is not correct considering current literature.
If the samples should be used for paleo-reconstructions the authors should comment in more detail on the climate 30.000 years ago in the area where the samples were taken. Currently the authors describe the climate in the late Pleistocene during Yedoma formation as “cold-arid” but this is a too general description. There were substantial changes in temperature and precipitation in northern Siberia over the ten-thousands of years during Yedoma formation. In particular 30.000 years ago, the age of the samples, the climate was more moderate and humid.
All these issues were raised in the review of the original submission but not considered sufficiently. Furthermore, several of the specific comments were not considered in the author’s response or the revised version. There is no comment on the concentration of methane in the pore water and no comment on the higher functional diversity of Eukaryotes in the anaerobic lake sediments, which is quite surprising.
Specific comments:
L48ff: Please clarify what you mean by “low concentrations”. Brouchkov & Fukuda 2002 call their methane concentrations in Yedoma (up to 6.000 ppm in air) “high” and methane concentrations in the Yedoma reported by Bischoff et al. 2013 are up to twice as high as in the sample IC4 of the current study. Hence the two cited publications do not support “low” methane concentrations in Yedoma. Furthermore Brouchkov & Fukuda 2002 did not study Yedoma in the Lena Delta.
L54ff: Please consider that Bischoff et al. 2013 reports elevated methane concentrations, viable methanogens and methanogenic activity in syngenetic permafrost of the late Pleistocene Ice Complex in the Lena River Delta. A general absence of methane and methanogenic archaea in late Pleistocene Yedoma deposits cannot be concluded from the current literature.
L86ff: This sentence is still unclear. Which response is referred to? Please explain how the description of a microbial community composition will help to elucidate the response (of this community?) to permafrost thawing.
L188: must read Table 2
L291ff: It is essential to discuss the implications of these potential changes in the permafrost community over a period of 30.000 years on paleo-reconstructions, which is based on this (potentially altered) community.
L394ff: Please clearly explain which role late Pleistocene Ice Complex deposits in the Kolyma lowland may play in climate warming, permafrost degradation and greenhouse gas emission.
L422ff: This sentence is unclear. Please clearly explain how a metagenomic analysis may characterize the contribution of a frozen community to climate warming and permafrost thaw.
L432f: the sampled Yedoma…

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RR by Victor Brovkin (07 Feb 2016)

ED: Reconsider after major revisions (07 Feb 2016) by Victor Brovkin

AR by Elizaveta Rivkina on behalf of the Authors (14 Mar 2016) Author's response Manuscript

ED: Referee Nomination & Report Request started (14 Mar 2016) by Victor Brovkin

RR by Anonymous Referee #1 (24 Mar 2016)

ED: Publish subject to minor revisions (Editor review) (25 Mar 2016) by Victor Brovkin

AR by Elizaveta Rivkina on behalf of the Authors (25 Mar 2016) Author's response Manuscript

ED: Publish subject to technical corrections (06 Apr 2016) by Victor Brovkin

AR by Elizaveta Rivkina on behalf of the Authors (06 Apr 2016) Author's response Manuscript

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Short summary

A comparative analysis of the metagenomes from two 30,000-year-old permafrost samples, one of lake-alluvial origin and the other from late Pleistocene Ice Complex sediments, revealed significant differences within microbial communities. The late Pleistocene Ice Complex sediments (which are characterized by the absence of methane with lower values of redox potential and Fe²⁺ content) showed both a low abundance of methanogenic archaea and enzymes from the carbon, nitrogen, and sulfur cycles.