Arctic microbial and next-generation sequencing approach for bacteria in snow and frost flowers: selected identification, abundance and freezing nucleation

Mortazavi, R.; Attiya, S.; Ariya, P. A.

doi:https://doi.org/10.5194/acp-15-6183-2015

Articles | Volume 15, issue 11

https://doi.org/10.5194/acp-15-6183-2015

© Author(s) 2015. This work is distributed under
the Creative Commons Attribution 3.0 License.

https://doi.org/10.5194/acp-15-6183-2015

© Author(s) 2015. This work is distributed under
the Creative Commons Attribution 3.0 License.

Articles | Volume 15, issue 11

Research article

|

05 Jun 2015

Research article |

| 05 Jun 2015

Arctic microbial and next-generation sequencing approach for bacteria in snow and frost flowers: selected identification, abundance and freezing nucleation

R. Mortazavi, S. Attiya, and P. A. Ariya

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Final revised paper (published on 05 Jun 2015)
Preprint (discussion started on 19 Dec 2014)

Interactive discussion

Status: closed

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

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- Supplement

RC C10457: 'A next generation sequencing of Arctic bacteria in snow and frost flowers: identification, abundance and freezing nucleation', Anonymous Referee #1, 24 Dec 2014
RC C10468: 'Referee Comment Next Generation Sequencing of Arctic Bacteria in Snow and Frost Flowers: Identification, Abundance and Freezing nucleation', Anonymous Referee #2, 24 Dec 2014
- SC C10494: 'Note on referee #2 comment', Jeff Bowman, 25 Dec 2014
SC C10490: 'Comments for A Next Generation Sequencing of Arctic Bacteria in Snow and Frost Flowers: Identification, Abundance and Freezing nucleation', Jeff Bowman, 25 Dec 2014
RC C10873: 'Interactive comment on “A next generation sequencing of Arctic bacteria in snow and frost flowers: identification, abundance and freezing nucleation” by R. Mortazavi et al.', Anonymous Referee #3, 05 Jan 2015
AC C12418: 'Authors' response + Modified paper', Roya Mortazavi, 27 Feb 2015
AC C12460: 'Letter to Editor', Roya Mortazavi, 27 Feb 2015
AC C12461: 'Letter to Editor', Roya Mortazavi, 27 Feb 2015

Peer-review completion

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

AR by Roya Mortazavi on behalf of the Authors (27 Feb 2015) Author's response

ED: Referee Nomination & Report Request started (04 Mar 2015) by Yinon Rudich

RR by Anonymous Referee #3 (04 Mar 2015)

RR by Anonymous Referee #2 (10 Mar 2015)

Suggestions for revision or reasons for rejection

The authors did a great job during their response to the reviewers remarks and significantly improved the manuscript entitled “Microbial and Next Generation Sequencing Approach for Bacteria in Snow and Frost Flowers: Selected Identification, Abundance and Freezing nucleation”. Nevertheless:

• The manuscript is still highly speculative. For instant, the authors discussed the role of Geobaccter species in uranium utilization (lines 330-336) but I didn’t find any support for presence of Geobacter species presented in the dataset (Table 2; Table 3; Table A.1 and Table A.2). Moreover, throughout the manuscript the authors attempt to infer about bacterial origin and physiological characteristics based on 16S gene similarity, however the percentage of similarity presented here range from 87 to 98%. It is well established that even bacteria with 100% of similarity of the 16S gene, may have completely different metabolic capacities. For instance, E. coli strains share 100% similarity however the physiological and metabolic characteristics among them have varied from harmful pathogens to commensal bacteria. Thus I suggest to authors more carefully rewrite the discussion.

• I have serious concerns about the authors’ choice for a DNA extraction method. According the extraction methods presented in section 2.4 (lines 209-213) the authors lose most of DNA from their samples. The 10 minutes of ultra-sonication will disturb the vast majority of bacteria in the sample, releasing genomic DNA into the aqueous phase. Released DNA will NOT precipitate from this phase during a 15 min centrifugation at 18000 g. For DNA to pellet, the solution needed to contain a sufficiently high concentration of salts. Here, the author’s will primarily pellet cell wall fragments, denatured proteins and small proportions of undisturbed cells. The DNA extracted using this method represents a tiny fraction of total DNA, only that from undisturbed cells and DNA that had happened to sorb to cell walls.

• All published data must be publicly available!!!

The author MUST deposit the generated sequencing data into a public access archive like NCBI and provide their accession numbers both for NGS and isolates.

WITHOUT THESE ACCESSION NUMBERS WE CAN NOT PUBLISH THE MANUSCRIPT.

Referee Report: PDF

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ED: Reconsider after major revisions (18 Mar 2015) by Yinon Rudich

AR by Roya Mortazavi on behalf of the Authors (29 Apr 2015) Author's response Manuscript

ED: Publish as is (03 May 2015) by Yinon Rudich

AR by Roya Mortazavi on behalf of the Authors (11 May 2015)

Short summary

Next-generation sequencing revealed the existence of diverse community of bacteria in the Arctic samples with many originating from distinct ecological environments. The observed varied range in ice nucleation of cultivable bacteria and in all of the melted samples further revealed the existence of the heterogeneous pool of bacteria. Changes in the microbial pool and its impact on the freezing and melting process may potentially lead to changing the Arctic environment and thus global climate.