Planktonic foraminifera-derived environmental DNA extracted from abyssal sediments preserves patterns of plankton macroecology

Morard, Raphaël; Lejzerowicz, Franck; Darling, Kate F.; Lecroq-Bennet, Béatrice; Winther Pedersen, Mikkel; Orlando, Ludovic; Pawlowski, Jan; Mulitza, Stefan; de Vargas, Colomban; Kucera, Michal

doi:https://doi.org/10.5194/bg-14-2741-2017

Articles | Volume 14, issue 11

Biogeosciences, 14, 2741–2754, 2017

https://doi.org/10.5194/bg-14-2741-2017

© Author(s) 2017. This work is distributed under
the Creative Commons Attribution 3.0 License.

Biogeosciences, 14, 2741–2754, 2017

https://doi.org/10.5194/bg-14-2741-2017

© Author(s) 2017. This work is distributed under
the Creative Commons Attribution 3.0 License.

Articles | Volume 14, issue 11

Research article 06 Jun 2017

Research article | 06 Jun 2017

Planktonic foraminifera-derived environmental DNA extracted from abyssal sediments preserves patterns of plankton macroecology

Raphaël Morard et al.

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Final revised paper (published on 06 Jun 2017)
Supplement to the final revised paper
Preprint (discussion started on 22 Nov 2016)
Supplement to the preprint

Interactive discussion

Status: closed

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

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RC1: 'Comments to the author', Anonymous Referee #1, 24 Dec 2016
RC2: 'Comments to the authors', Anonymous Referee #2, 10 Jan 2017
AC1: 'Reply to reviewers comments', Morard Raphael, 09 Feb 2017

Peer-review completion

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

ED: Reconsider after major revisions (10 Feb 2017) by Emilio Marañón

AR by Morard Raphael on behalf of the Authors (10 Feb 2017) Author's response Manuscript

ED: Referee Nomination & Report Request started (10 Feb 2017) by Emilio Marañón

RR by Anonymous Referee #2 (21 Feb 2017)

Suggestions for revision or reasons for rejection

General comments
The revised version of the manuscript, although clearer in some aspects, does not address some of the concerns. Even if the authors are convinced that the extremely different sequencing depth among samples (48 to 124,355 reads per library) does not affect their analyses and conclusions they should have made the exercise of testing such potential bias and adequately discuss the problem. This is particularly relevant considering that they are including clearly un-saturated samples (Caribbean samples). I think that the authors have to justify convincingly the inclusion of samples with such an extremely low library size (<100 reads) and clearly define which size they consider defective. I could agree that sub-sampling all the libraries to the lowest library size (once excluding those defective samples with extremely low number of reads) would imply a considerable loss of data. However, there are alternative methodologies to account for widely varying library sizes. Sequence counts can be also normalized, for example, with the r package deseq2 (Love et al. 2014). This method accounts for differential sample depth and is appropriate for normalizing high-variance data sets from high-throughput sequencing.
On the other hand, the authors must discuss in more detail why the transfer of organic matter to the deep ocean and the preservation of planktonic DNA in oceanic sediments “should apply” to other taxa, as affirmed by the authors. There are some literature to this respect that they could include. For example, Capo et al (2015) showed that Cryptophyta and Haptophyta are not well preserved in lake sediments; and Boere et al (2011) discussed the possible causes behind the variation in the level of DNA preservation among diatoms and dinoflagellates in oceanic sediments. I addition, I do not believe that “there are no have no reason to believe that the transfer of organic matter from the top to the bottom of the ocean acts differently depending on taxonomic group” as stated by the authors.

Specific comments
Figure 4. I do not see that “the Caribbean and Japan areas (red and purple) are perfectly disjoint” at the taxonomic level of morphospecies. The authors can conduct some statistical analysis to test that (e.g. PERMANOVA and ANOSIM). In addition, the separation observed based on absolute number or on Dice index mostly derives from the very different level of taxonomic saturation between Japan and Caribbean samples (figure 3), as the authors mention in the manuscript.

References
Boere, A. C., Damsté, J. S. S., Rijpstra, W. I. C., Volkman, J. K., & Coolen, M. J. (2011). Source-specific variability in post-depositional DNA preservation with potential implications for DNA based paleoecological records. Organic Geochemistry, 42(10), 1216-1225.
Capo, E., Debroas, D., Arnaud, F., & Domaizon, I. (2015). Is planktonic diversity well recorded in sedimentary DNA? Toward the reconstruction of past protistan diversity. Microbial ecology, 70(4), 865-875.
Love M, Anders S, Huber W (2014) Differential analysis of count data—the DESeq2 package.

Referee Report: PDF

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ED: Reconsider after major revisions (23 Feb 2017) by Emilio Marañón

AR by Morard Raphael on behalf of the Authors (05 Apr 2017) Author's response Manuscript

ED: Referee Nomination & Report Request started (06 Apr 2017) by Emilio Marañón

RR by Anonymous Referee #2 (26 Apr 2017)

ED: Publish subject to technical corrections (26 Apr 2017) by Emilio Marañón

AR by Morard Raphael on behalf of the Authors (02 May 2017) Author's response Manuscript

Short summary

The exploitation of deep-sea sedimentary archive relies on the recovery of mineralized skeletons of pelagic organisms. Planktonic groups leaving preserved remains represent only a fraction of the total marine diversity. Environmental DNA left by non-fossil organisms is a promising source of information for paleo-reconstructions. Here we show how planktonic-derived environmental DNA preserves ecological structure of planktonic communities. We use planktonic foraminifera as a case study.