Diversity of bacterial community in the rhizosphere and bulk soil of Artemisia annua grown in highlands of Uganda

Namuli Aidah; Ogwang Patrick Engeu; Tumuhairwe John Baptist; Vincent B. Muwanika; Mayega Johnson; Bazira Joel

doi:10.1371/journal.pone.0269662

Peer Review History

Original SubmissionAugust 30, 2021
18 Nov 2021 Decision Letter - Lorenzo Brusetti, Editor PONE-D-21-28060Diversity of bacterial community in the rhizosphere and bulk soil of Artemisia annua grown in highlands of UgandaPLOS ONE Dear Dr. namuli, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. In particular, most criticisms are related to the quality of the text and the figures and some minor, but important, points regarding analysis. Please ensure that your decision is justified on PLOS ONE’s publication criteria and not, for example, on novelty or perceived impact. 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Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols. We look forward to receiving your revised manuscript. Kind regards, Lorenzo Brusetti Academic Editor PLOS ONE Journal Requirements: When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? 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(Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: Review PONE-D- 21-28060 Diversity of bacterial community in the rhizosphere and bulk soil of Artemisia annua grown in highlands of Uganda Title: the specie name should be in italics Abstract: OTU is misspelled. Introduction: the first 2 paragraphs are a bit repetitive and can be shorten in one. Sometimes the wording is heavy and the same concept could be expressed in a clearer way (see the last paragraph of the introduction). Methods: Sequencing paragraph can be deleted. Analysis can also be omitted. Authors can start directly with assembly section. Processing and clustering OTU is misspelled. Taxonomic assignment Fig.1 does not show the rarefaction curves but the composition of the samples. Results: Fig.1 need to be changed. Pie charts are easily misread, and the use of bar-chart is recommended. It would be easier to read if next to T1, T2 etc is added the description itself such as T1 Beans only or even T1 B as the authors used this code for table 2 and in the text. It is also not clear which test has been applied to test the effect of treatment across the different phyla composition, this should be clearly stated in the text and more info should be provided than the p-value alone such as R2, F value etc based on the test used by the authors. Same for table 2, authors clearly state the number of samples and used mean and standard deviation but not info of the type of test used were given (and data were tested for normality and variance?) Species abundance: Authors should reconsider their ability to assign OTUs to species levels. The clustering at 97% of identity is to determine the genus and not the species so authors should analysis the data at one taxonomic order higher (genera) and not species. All this section needs to be re-written based on the new data analysis generated on genus level. Additional comments on this section: The description of how data were analysed for the PCA including KMO and Bartleets test should be moved to material and methods section. Here the authors should be presenting their results so for examples starting directly with the Principal compenten anyalis revelead etc... Again all the section talking about the varimax rotation should be moved to M&M section including the explanation why two species were removed (this part might not be any more present when data analysed at genus level). The section starting “Furthermore…” can be easily omitted and included in the M&M section. Section relating Figure 2 and table 3, authors try to find a connection between the different species and the chemistry and physical properties of the soil based on the general composition of the samples, why did they not include these properties in the PCA analysis? This would support their statement better than the present statements. Discussion: First paragraph needs to be rewritten. Hard to follow and not providing any information more than a repetition of the results itself. The paragraph about the species should be rewritten in the light of the use of genera. Conclusion: no changes needed General comments: Attention OTUs misspelled all over the manuscript. Phylum/phyla used in the wrong places. Name of the phyla sometimes with capital letter sometimes with lower letter. In general, the manuscript needs a revision to achieve a better fluidity in the text as many parts are disconnected and sometimes repetitive especially in the introduction. ****** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review?** For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. 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Revision 1
5 Apr 2022 Author Response Reviewer’s Comment Response Title: -The species name should be in italics -It was italicized Abstract: -OTU is misspelled. -Changing species to genus in the last section of the result affected this section as the reviewer stated that “The clustering at 97% of identity is to determine the genus and not the species so authors should analysis the data at one taxonomic order higher (genera) and not species.” -OUT changed to OTU -Different species replaced with different genera Introduction: The first 2 paragraphs are a bit repetitive and can be shorten in one. Sometimes the wording is heavy and the same concept could be expressed in a clearer way (see the last paragraph of the introduction). First two paragraphs omitted and only the beginning part of second paragraph embedded at the beginning of the last paragraph Methods: -Sequencing paragraph can be deleted. -Analysis can also be omitted. -Authors can start directly with assembly section. Processing and clustering OTU is misspelled. -Taxonomic assignment Fig.1 does not show the rarefaction curves but the composition of the samples. -Section of writing from result to be moved to this section (species abundance) -Sequencing paragraph deleted -Analysis paragraph omitted -Began directly with assembly - OUT changed to OTU in 2 positions i.e CD-HIT-OTU and a user-specified OTU -Figure 1 deleted. -Section of species abundance (changed to genus abundance) moved to this section. Results: Fig.1 Need to be changed. Pie charts are easily misread, and the use of bar-chart is recommended. It would be easier to read if next to T1, T2 etc is added the description itself such as T1 Beans only or even T1 B as the authors used this code for table 2 and in the text. It is also not clear which test has been applied to test the effect of treatment across the different phyla composition, this should be clearly stated in the text and more info should be provided than the p-value alone such as R2, F value etc based on the test used by the authors. Same for table 2, authors clearly state the number of samples and used mean and standard deviation but not info of the type of test used were given (and data were tested for normality and variance?) Species abundance: Authors should reconsider their ability to assign OTUs to species levels. The clustering at 97% of identity is to determine the genus and not the species so authors should analysis the data at one taxonomic order higher (genera) and not species. All this section needs to be re-written based on the new data analysis generated on genus level. Additional comments on this section: The description of how data were analysed for the PCA including KMO and Bartleets test should be moved to material and methods section. Here the authors should be presenting their results so for examples starting directly with the Principal compenten anyalis revelead etc... Again all the section talking about the varimax rotation should be moved to M&M section including the explanation why two species were removed (this part might not be any more present when data analysed at genus level). The section starting “Furthermore…” can be easily omitted and included in the M&M section. Section relating Figure 2 and table 3, authors try to find a connection between the different species and the chemistry and physical properties of the soil based on the general composition of the samples, why did they not include these properties in the PCA analysis? This would support their statement better than the present statements. ---bar chart used instead -T1/T2—Disregarded and the initials used in table 2 were used The test used was one way ANOVA, multiple comparison of means was done using LSD test. (Was included in the methods and below table 1) -R2 was not stated since the analysis used was ANOVA and not Ordinary least squares (OLS) regression -F-test is also under regression as it indicates whether the linear regression model provides a better fit to the data than a model that does not contain independent variables. (In this paper, the interest was to determine if significant mean variations existed) -Furthermore, one of the most essential requirements for use of ANOVA is the normality of the dependent variable. This assumption was checked and verified using histograms for all the variables. Generally, all the variables fulfilled the normality assumption because they had a normal distribution. As for the homogeneity of variance the Levene’s test was employed, all of which had insignificant values (p˃0.05) for Levene’s test i.e none of the variables violated the normality and homogeneity of variance tests. Genus abundance: -Reconsidered to genus level -All this section was re-written based on the new data analysis generated on genus level. Discussion: First paragraph needs to be rewritten. Hard to follow and not providing any information more than a repetition of the results itself. The paragraph about the species should be rewritten in the light of the use of genera. References -Paragraph one deleted -paragraphs relating to species rewriiten in relation to genus -Some few references were added as they were used to discuss the observations related to genera instead of species. -Some few references were deleted as they were used to as references for information that was deleted (in the introduction and discussion) Attachments Attachment Submitted filename: Rensponse to Reviewers.docx https://doi.org/10.1371/journal.pone.0269662.r002
26 May 2022 Decision Letter - Lorenzo Brusetti, Editor Diversity of bacterial community in the rhizosphere and bulk soil of Artemisia annua grown in highlands of Uganda PONE-D-21-28060R1 Dear Dr. namuli, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Lorenzo Brusetti Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0269662.r003
Formally Accepted
24 Aug 2022 Acceptance Letter - Lorenzo Brusetti, Editor PONE-D-21-28060R1 Diversity of bacterial community in the rhizosphere and bulk soil of Artemisia annua grown in highlands of Uganda Dear Dr. Aidah: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Lorenzo Brusetti Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0269662.r004

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