Actinomycetes isolated from rhizosphere of wild Coffea arabica L. showed strong biocontrol activities against coffee wilt disease

Mimi Nuguse; Tekalign Kejela

doi:10.1371/journal.pone.0306837

Peer Review History

Original SubmissionMarch 18, 2024
7 May 2024 Decision Letter - Ali Tan Kee Zuan, Editor Transfer Alert This paper was transferred from another journal. As a result, its full editorial history (including decision letters, peer reviews and author responses) may not be present. PONE-D-24-10862Actinomycetes Isolated from Rhizosphere of Wild Coffea arabica L. Showed Strong Biocontrol Activities against Coffee Wilt DiseasePLOS ONE Dear Dr. Geleta, 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. Please submit your revised manuscript by Jun 21 2024 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. 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The conclusions must be drawn appropriately based on the data presented. Reviewer #1: No Reviewer #2: Partly ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: No Reviewer #2: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: No ****** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The authors' diligent work has revealed the potential of Actinomycetes isolates as biocontrol agents for Coffee Wilt Disease (CWD). These findings are significant for the scientific community and hold great promise for implementing sustainable agricultural practices in the coffee industry. This manuscript does not clearly state the number of replications prepared for some tests conducted. In addition, data points behind the mean and variance measures of the results presented were unavailable in the manuscript. It needs improvement. The isolates were not deposited in any Microbial culture collection center - no information was provided in the manuscript. Additional results (if available) on molecular identification, phylogenetic analysis of the isolates and electron micrographs (SEM and TEM) of cell walls of treated plants will make the manuscript more interesting for publication in PLOS ONE. Reviewer #2: General comments: 1. This study is interesting and demanding for the sustainability of coffee industry. 2. English need to be improved. 3. Found many inconsistencies in words, spelling, formatting etc. 4. Lack of discussion on the findings. 5. No work done on molecular identification or any other appropriate identification on the selected actinomycetes isolates, therefore this manuscript should be rejected. Specific comments: Line 49, important export? Line 97, typo Fusarium Line 107, delete ‘root rhizosphere’, delete root Line 114, 1376–1890 mas, mas? Line 116, Mattu is located in the temperate zone Line 117, ideal for arabica coffee plantation Line 125-126, describe in detail how field samples can be collected aseptically? Line 147, fungal agar block, check 1 x 2 cm2? Wrong? Line 147 , what do you mean by leading margin of cultures, please explain. Line 148, check degree symbol, 25 °C Line 153, delete ‘free of charge’, was obtained from Line 162, delete rhizospheric, to actinomycetes isolates with the most..... Line 181, delete ‘test’ after Catalase, replace with tests after xanthine Line 183, delete test after methyl red and MacConkey. Typo ‘Methy’ Line 184, delete ‘Cliques’ Line 189, ‘clean? zones’, to ‘clear zones’ Line 199, delete ‘3’ at end line Line 241, small letter ‘a’ for ‘actinomycetes’ not capital Actinomycetes, and more throughout this manuscript, please check, unless use as starting word in a sentence. Line 269, typo, ‘seedlings’ Line 290, small letter ‘a’ for actinomycetes, delete ‘root’, rhizospheric soil ****** 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 Reviewer #2: 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. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. Attachments Attachment Submitted filename: CommentsAa.docx https://doi.org/10.1371/journal.pone.0306837.r001
Revision 1
20 Jun 2024 Author Response Date 20/06/2024 To The Editorial manager, PLOS ONE Subject: submission of revised manuscript for consideration of its publication in PLOS ONE Dear Sir/Madam, I am writing to submit our revised manuscript entitled, “Actinomycetes isolated from rhizosphere of wild Coffea arabica L. showed strong biocontrol activities against coffee wilt disease,” for consideration of its publication in the esteemed journal PLOS ONE. First of all, I would like to thank you for allowing us to revise and submit the manuscript. I appreciate the time and details the academic editor and reviewers provided to enrich our manuscript. Based on the comments, we have thoroughly revised the whole manuscript. As commented by the academic editor, the manuscript was edited based on PLOS ONE's style requirements. The full name of the authority that approved the field site access was included in the material method section under the sub-topic ‘study site’. All relevant data are within the manuscript and the details were also added as supporting information in a separate file. We hope you will be pleased with this revision and consider it for publication; we couldn't have done it without your input. Responds to each point raised by the reviewers are indicated below. Sincerely, Tekalign Kejela (Ph.D) Author response to reviewers' Comments Reviewer #1: The authors' diligent work has revealed the potential of Actinomycetes isolates as biocontrol agents for Coffee Wilt Disease (CWD). These findings are significant for the scientific community and hold great promise for implementing sustainable agricultural practices in the coffee industry. Authors' response: we appreciate the reviewer's commitment to critically reviewing our manuscript. We agree with the reviewer’s idea and thus why we conducted the study. This manuscript does not clearly state the number of replications prepared for some tests conducted. In addition, data points behind the mean and variance measures of the results presented were unavailable in the manuscript. It needs improvement. Authors' response: All the experiments were conducted in three replicates and this information was added as a footnote under each figure and table in the manuscript. In addition, data points behind the mean and variance were incorporated as necessary and uploaded as a separate file as suggested by the reviewer. The isolates were not deposited in any Microbial culture collection center - no information was provided in the manuscript. Authors' response: the isolate was deposited in the Applied microbiology laboratory of Mattu University, Mettu, Ethiopia. This information was incorporated in the MS as suggested by the reviewer. NB: No microbial culture collection center established so far in Ethiopia. Additional results (if available) on molecular identification, phylogenetic analysis of the isolates and electron micrographs (SEM and TEM) of cell walls of treated plants will make the manuscript more interesting for publication in PLOS ONE. Authors' response: we appreciate the reviewer’s comment, we performed the identification process to genus level based on morphological and biochemical characteristics. We don’t have the mentioned data to include in the MS. We performed the experiments to the best of our resources. We will consider it in our future work. Reviewer #2 General comments: This study is interesting and demanding for the sustainability of coffee industry. Authors' response: we appreciate the reviewer’s commitment to critically reviewing our manuscript. We agree with the reviewer’s idea and thus why we conducted the study. Using bioinoculants in the coffee industry is tremendously important due to emerging pesticide-resistant pathogens, and the difficulty of controlling soil-born pathogens including G. xylarioides using chemical pesticides as it affects non-targeted populations. Furthermore, the customer performance of chemical-free products and environmental safety concerns make biocontrol a demanding input in the sustainable coffee industry. English need to be improved. Authors' response: grammatical mistakes, spelling errors, punctuations, and other language issues checked throughout the manuscript and corrected. Found many inconsistencies in words, spelling, formatting etc. Authors' response: inconsistencies in words, spelling, and formatting throughout the manuscript checked and corrected Lack of discussion on the findings. Authors' response: The discussion on the findings was incorporated, and corrected as per the suggestion. No work done on molecular identification or any other appropriate identification on the selected actinomycetes isolates, therefore this manuscript should be rejected. Authors' response: we did not perform molecular identification of the isolates, but, we have performed the appropriate identification method of the isolates to genus level to the best of our resources as outlined below We used the selective isolation method of actinomycetes Primary identification of the isolates to the genus level was performed by morphological (macroscopic and microscopic) and biochemical characterization of the isolates based on Bergey’s Manual of Determinative Bacteriology. In addition, for the confirmation of genus-level taxonomic identification of the isolates, gram reaction, caisin, xanthine, and tyrosine tests were performed according to Taddie et al, 2006. Hence, we used an appropriate and scientifically acceptable method to classify the rhizobacteria isolates to genus level, and thus why we reported actinomycete isolates. We appreciate the reviewer's comment and will consider species-level identification using molecular methods in our future work. Specific comments: Line 49, important export? Authors' response: ‘important export’ corrected to ‘significant export’ Line 97, typo Fusarium Authors' response: ‘Fussarium’ corrected to ‘Fusarium’ Line 107, delete ‘root rhizosphere’, delete root Authors' response: ‘root rhizosphere’ corrected to ‘rhizosphere’ as per suggestion Line 114, 1376–1890 mas, mas? Authors' response: ‘1376–1890 mas’ corrected to ‘1376–1890 meters above sea level’ Line 116, Mattu is located in the temperate zone Authors' response: ‘Mattu is located in the temperate zone’ corrected to ‘Mattu has a relatively cool tropical monsoon climate under the Köppen climate classification’ Line 117, ideal for arabica coffee plantation Authors' response: ‘ideal for arabica coffee plantation’ corrected to “which is suitable for coffee cultivation” Line 125-126, describe in detail how field samples can be collected aseptically? Authors' response: details of how field samples collected were incorporated Line 147, fungal agar block, check 1 x 2 cm2? Wrong? Authors' response: ‘fungal agar block (1 x 2 cm2 )’ corrected to ‘fungal agar block (1 cm X 2 cm)’ Line 147 , what do you mean by leading margin of cultures, please explain. Authors' response: The leading margin of cultures refers to the actively growing edge of the culture. Explanation incorporated as per suggestion. Line 148, check degree symbol, 25 °C Authors' response: the incorrect symbol ‘ 0C’ corrected to ‘°C’ Line 153, delete ‘free of charge’, was obtained from Authors' response: the word was deleted Line 162, delete rhizospheric, to actinomycetes isolates with the most..... Authors' response: the word was deleted Line 181, delete ‘test’ after Catalase, replace with tests after xanthine Authors' response: corrected as per suggestion Line 183, delete test after methyl red and MacConkey. Typo ‘Methy’ Authors' response: corrected as per suggestion, ‘Methy’ corrected to ‘methyl” Line 184, delete ‘Cliques’ Authors' response: the word was deleted Line 189, ‘clean? zones’, to ‘clear zones’ Authors' response: ‘clean zones’ corrected to ‘clear zones’ Line 199, delete ‘3’ at end line Authors' response: the number ‘3’ was deleted Line 241, small letter ‘a’ for ‘actinomycetes’ not capital Actinomycetes, and more throughout this manuscript, please check, unless use as starting word in a sentence. Authors' response: throughout the manuscript ‘Actinomycetes ‘is corrected to ‘actinomycetes’ except when used as a starting word in a sentence. Line 269, typo, ‘seedlings’ Authors' response: The incorrect word ‘seedlidgs’ in the formula DI (% )=(No.of infected seedlidgs)/(Total No.of seedlings)×100 corrected to ‘seedlings’ and the formula corrected to DI (%)=(No.of infected seedlings)/(Total No.of seedlings)×100 Line 290, small letter ‘a’ for actinomycetes, delete ‘root’, rhizospheric soil Authors' response: ‘Actinomycetes ‘ corrected to ‘actinomycetes’ and the word ‘root’ deleted https://doi.org/10.1371/journal.pone.0306837.r002
25 Jun 2024 Decision Letter - Ali Tan Kee Zuan, Editor Actinomycetes isolated from rhizosphere of wild Coffea arabica L. showed strong biocontrol activities against coffee wilt disease PONE-D-24-10862R1 Dear Dr. Geleta, 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 will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, 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, Ali Tan Kee Zuan, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0306837.r003
Formally Accepted
28 Jun 2024 Acceptance Letter - Ali Tan Kee Zuan, Editor PONE-D-24-10862R1 PLOS ONE Dear Dr. Kejela, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps. Lastly, 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 customercare@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. Ali Tan Kee Zuan Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0306837.r004

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