Genetically controlled biomineralization in Cyanobacteria: diel fluctuations of ccyA transcript abundances and identification of neighboring genes putatively involved in the precipitation of intracellular amorphous calcium carbonates in Microcystis aeruginosa PCC7806

Dear Dr. Benzerara and co-authors,

Thank you very much for the submission of the revision this paper and for carefully considering the reviewers comments and suggestions. I have checked these points and consider that they have been carefully addressed and where possible correctly accommodated in the revision. Nevertheless, I have spotted a certain number of mainly editorial points that need correction. Therefore, I kindly ask you to post a new revised version with these corrections. This is the last step before I can agree on a recommendation. I am looking forward to receive the revision in due course and subsequently will write the recommendation as is the custom for PCI.

Best wishes, Rutger de Wit

Recommender PCI-Microbiology

Comments

1-    a) After reading again I consider that the statement (lines 30-31, “The ccyA gene shows a clear day/night expression pattern with a maximum transcript abundance at the end of the night.” Could be misleading as the maximum of expression concerns the whole of the second half of the night (see Fig. 3) and not just a single time point prior to “sunrise”. I suggest to change as follows:

“The ccyA gene shows a clear day/night expression pattern with maximum transcript abundances during the second half of the night.”

b) Same point lines 249-251 replace as follows: “A clear day/night pattern can be observed in the expression of ccyA, with maximum transcript abundances during the second half of the night (t7_N and t8_N, Table 1) and a minimum transcript abundance at 12 am during daytime (t3_D, Table 1)”.

c) Same point lines 256-258 replace as follows: “When compared with the mean expression of the 4440 genes of the whole transcriptome, the mean expression of the ccyA gene was significantly higher (p-value < 0.05) during the second half of the night, i.e., at the two-time points : 2 am (t7_N) and 7 am (t8_N) (Table 1).

2-    To make things a bit more clear I suggest that you replace (lines 73-75) “About the later hypothesis, we note that buoyancy is not just controlled by cell density but also by additional parameters such as cell aggregation. For example, Gu et al. (2020) showed that Ca induces EPS production by M. aeruginosa, which can increase buoyancy” by : 

“About the later hypothesis, we note that buoyancy is not just controlled by cell density but also by additional parameters such as EPS adhering to the cells and cell aggregation. For example, Gu et al. (2020) showed that Ca induces EPS production by M. aeruginosa, which particularly when incorporated in the cell aggregates, can increase buoyancy”. 

3-    Note the ref Gu et al (2020) is missing in the list.

4-    You may wish to change (line 111) “Overall, one way of gaining a better understanding” into “A first step of gaining a better understanding”, which makes the justification for your approach a bit stronger.

5-    Legend Fig. 7, replace “Figure 7 - Abundance profiles of three genomic neighbors of” by “Figure 7 – Time course of the Abundances of three genomic neighbors of” 

6-    a) Line 456, I think the “alternation” is a more appropriate term than “compartmentalization” in this context, as compartmentalization implies occurring in different spaces separated by some sort of boundaries.

b) Same point, lines 475-476, I suggest: “is compartmentalized” should be replaced by “alternates”

7-    There is an error in a name of a co-author in the Straub et al. publication

First name: Nicole

Family name: Tandeau de Marsac

Correct Reference:

Straub, C., Quillardet, P., Vergalli, J., Tandeau de Marsac, N., Humbert, J.-F., 2011. A day in the life of 830 Microcystis aeruginosa strain PCC 7806 as revealed by a transcriptomic analysis. PLOS ONE 831 6, e16208. https://doi.org/10.1371/journal.pone.0016208

                                                                                   Montpellier, 25 October 2024

Re: M/S submitted to PCI Microbiology 

Diel changes in the expression of a marker gene and candidate genes for intracellular amorphous CaCO3 biomineralization in Microcystis

by Bruley & Gaëtan et al.

Dear Drs Bruley, Gaëtan, Benzerara, Duprat and other co-authors.

Thank you very much for submitting the aforementioned M/S for evaluation to PCI-Microbiology. In the first place, I want to apologize for the delay of my response. I have had enormous problems in finding reviewers, among the more than 20 invited I only succeeded in obtaining one report, which to me appears very valuable and helpful. To advance the process I decided to do the second review myself, despite the fact that I only master this area only partially and I am not a specialist in transcriptomics. Nevertheless, I hope that you will find my report useful.

For the time-being, albeit promising, I cannot yet recommend this paper and thus advice formally “This preprint merits a revision” (considering the 3 possibilities for PCI recommendors). Hence, I ask you to prepare a carefully revised version. Please carefully consider the points raised by the reviewers and take them into account for the preparation of the revised version. I highly appreciate if you can prepare a reply where you pointwise address the issues raised by the reviewers and indicate how you have accommodated them in the revised version. I am looking forward to receiving the revised version with the reply in due course. Upon receipt, I will contact the other reviewer for additional assessment and also prepare my own assessment.

Yours sincerely,

Rutger De Wit

Recommender for PCI-Microbiology