Editor’s comments on bg-2017-514

Dear Dr. Wehking,

Thank you for submitting your manuscript “Community composition and seasonal changes of archaea in coarse and fine air particulate matter” to Biogeosciences. Three expert reviewers have assessed your submission and feel that it has potential for publication as your investigation of airborne Archaea from atmospheric particulate matter is interesting and a worthwhile topic for publication. However, the reviewers also identified numerous ways to improve the manuscript.

Based on the reviewers’ comments I am accepting the paper subject to minor revisions per your responses provided. The reviewers also suggest that the paper be edited again for English language and they have also made suggestions to improve the grammar.
At this point, I ask that you please revise your paper based on the reviewer’s comments. Once the manuscript is resubmitted it will be subject to editorial review prior to a final decision. To facilitate the process, please submit a version of your paper so all changes marked as track changes.
Please feel free to contact me with any questions.

Sincerely,
Dr. Denise M. Akob

Editor’s comments on bg-2017-514

Dear Dr. Wehking,

Thank you for revising your manuscript “Community composition and seasonal changes of archaea in coarse and fine air particulate matter” per the reviewers’ comments. I have now reviewed the manuscript in detail and looked over your revisions.

Based on your revisions I am accepting the paper subject to minor revisions as I identified some additional points that require revision/correction for accuracy and clarity. At this point, please revise your paper based on my comments below then I will do a final editorial review prior to acceptance. To facilitate the process, please submit a version of your paper so all changes marked as track changes.

Please feel free to contact me with any questions.

Sincerely,
Dr. Denise M. Akob



1. I think that Archaea should be capitalized throughout the paper since you are referring to a Domain of life. Same with Bacteria if you are referring to the Domain and not to all single-celled organisms.

2. The gene studied should always be written as “16S rRNA gene” and not abbreviated to “16S” or “16S rRNA”. “16S rRNA” would imply that your analysis was performed on a RNA level.

3. In SI and throughout the paper use “.” instead of “,” for decimal places.

4. Pg. 8, L. 22: change to 16S rRNA gene.

5. Pg. 9, l. 13: you definitely need to capitalize the domain names here

6. Pg. 10, l. 17: the units are not correct. It should be “gene cp kg-1” not DNA copies. In addition, you need to clarify if you mean Bacteria and Archaea gene copies. I also would not bother abbreviating copies.

7. Pg. 12, l. 14: add a “.” To the end of the sentence.

8. Pg. 12, l. 6-19: the sampling time frame is not clearly described in this section. “over a 7 day period isn’t clear” and 24 pairs doesn’t match a full year. The only way to know when samples were collected you have to go to the SI. One-2 sentences stating that samples were collected weekly over a 1 year time period by filtering for 7 days would be helpful. State that in some cases samples were not collected because …I presume weather?

9. Table S1 also has >24 samples but no information is provided about which filter each sample is. Add a column of what filter is presented. Also explain whether extracts from different filter types were combined. Provide details on which samples were which controls/blanks.

10. Pg. 12, l. 25: can you provide some more information on how DNA was extracted? A kit name would be sufficient

11. Pg. 12: l. 26: I don’t think this is correct. Illumina did not develop or have instruments that ran pyrosequencing chemistry. Illumina uses “sequencing by synthesis (SBS)” and according to this fact sheet the GAIIx instrument used SBS chemistry: https://support.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/datasheet_genome_analyzeriix.pdf. In addition, only Illumina protocols are listed on the EMP website. Please confirm the type of sequencing chemistry used and use correct language throughout the paper. I usually use “Illumina sequencing” or “next-generation sequencing”.

12. Pg. 13, l. 15: change to QIIME

13. Pg. 16, l. 7: change to “,” for 2,342 sequences

14. Make it clear that the sequences recovered from TSP are just a sum of the coarse and fine samples. State this in the figure legends.

15. Pg. 18, l. 14: remove “of”

16. Pg. 18, l. 26: were the exact same primers used? If not, that is another important factor that could have contributed to differences in the results.

17. Figure 3: consider putting your data first (upper left most location) and putting “this study” under the location. This way you can have the reader focus more on your findings than previous work.

18. Pg. 19, l. 15: if Yooseph et al. 2013 analyzed peptides then you can’t present the data as sequences in Figure 3. Revise as needed to present the data accurately.

19. Pg. 20, l. 20: is euryarchaeotic the correct term?

20. Pg. 20, l. 24 & 25: change to livestock

21. Figure 1: be mindful of whether this figure is legible by those that are color blind. Add “TSP” to the legend.

22. Figure 4: add RFO to the legend.

23. Figure 5: specify in the legend that the data are from this study.

24. Table 1: define the * after “S”

Dear Dr. Wehking,

Thank you for revising your manuscript. I have now reviewed the manuscript and revisions in detail and happy to accept the paper subject to technical corrections. The only correction needed is the legend for Figure 2. Please modify to:

"Figure 2: Rarefaction curve of species richness for total suspended (TSP), coarse, and fine particulate matter. TSP is a single airstream split into coarse and fine particulate matter. The solid curves represent the interpolated number of OTUs as a function against the number of samples. The dashed lines are according extrapolations and the dot marks the sample size of this study. The colored areas represent the 95 confidence intervals."

Please feel free to contact me with any questions.

Sincerely,
Dr. Denise M. Akob