PONE-D-21-28634The distribution and type B trichothecene chemotype of Fusarium species associated with head blight of wheat in South AfricaPLOS ONE

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Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

Additional Editor Comments (if provided):

Dear authors,

Based on the comments of one reviewer and my own review, I suggest to amend the paper with minor revisions.

Both the reviewer and myself appreciate the dimenssion of the sampling campaign.

some minor comments from my side:

1. Please (if necessary) change the significant numbers in table 3, when less than 100 samples are taken, you cannot have a % incidence of lower than 1%...so something like 36.36 is impossible, should be then 36

2. The chemotypes presented in a table is not clear. It would be better to somehow also include a pie diagram put on the geography map. It is known from previous work by Waalwijk and coworkers that geography (e.g. altitutde) can affect the chemotype.

3. There are quite some differences between the western cape , free state, and the rest...the reason for these differences are now somehow addressed in the discussion, but in my opinion would merit a section in the results.

4. DId you look at co-occurence? recent insights (study by tan et al., 2021 and some reports before by several authors) report on the tendency of some species to co-occur in disease complexes. Did you observe any of these co-occurences as they might be one of the important drivers explaining how the plasticity of a population works.

5. What about climatic conditions? can your report be put in a historic context? have you seen changes compared to previous report?

Please commend on these remarks and on the remarks raised by the second reviewer.

kind regards

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

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3. Have the authors made all data underlying the findings in their manuscript fully available?

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Reviewer #1: Yes

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Reviewer #1: Yes

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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: In many ways this is an excellent and comprehensive report on the FHB population in South Africa. The authors conducted a large scale survey on the main wheat producing areas and expand the knowledge of Fusarium species and trichothecene chemotype composition in different ecological regions. The study has an outstanding level and should be published with some revisions.

1. The high frequency of FIESC in this study seems strange for me. Normally it is a very weak pathogenic species to wheat and widely distributed in soil, plant debris, surface of rice and wheat grains and so on. In my experience, for the wheat head samples with obvious symptoms, the isolation frequency would be lower than 1%, which can be ignored in the field FHB management practice. To my knowledge, there is also no report of such high ratio of FIESC as FHB pathogen before in other place worldwide. So the author should be careful about if they are real the causal agent of FHB or just surface contamination on the heads. Details of the isolation procedure should be examined. For example, for the heads with very mild symptom (i.e. without red mold), it would be hard to find the infected spikelet when they were dried several days after sampling, this maybe influence the result of the isolation. Anyway, I suggest the authors discuss the reasons of the unusual observation, if they are the pathogen, the high frequency of FIESC should considered in the field control and mycotoxin contamination.

2. P14L283-285, FCSC1, FCSC5 and FSSC5 were found. Did they determine by EF1a blast? These species were identified by phylogenetic analysis of several conserved genes, only ef1a sequence is identical?

3. The introduction and discussion are a bit long. I suggest to reduce some content not well fit the key points.

4. I noticed that the sample size of the places where F. pseudograminearum was predominant are small. The authors should mention it in the discussion, because small sample size is easy to cause bias.

5. Adding line numbers after page 21 will facilitate review.

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Reviewer #1: Yes: Hao Zhang

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PONE-D-21-28634R1The distribution and type B trichothecene chemotype of Fusarium species associated with head blight of wheat in South AfricaPLOS ONE

Dear authors,

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 Feb 26 2022 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. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

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We look forward to receiving your revised manuscript.

Kind regards,

Kris Audenaert, Ph.D.

Academic Editor

PLOS ONE

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

Additional Editor Comments (if provided):

There is still one minor comment, in regard to table 3: the calculated incidence: "then calculated as follows: For FGSC: (30/35) x 100 = 85.71%, and for FIESC: (5/35) x

100 = 14.29%. This is also indicated in the subscript of Table 3." But my point is that when you have 100 sampels, you can never been more precise than 1%, so for example 1.567% is impossoble. This also accounts when you work with less samples, so everything lower than 1 shoudl definetely be removed....85.71% should be 85%...this is as precise as you can be when doing these types of calculation

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PONE-D-21-28634R2The distribution and type B trichothecene chemotype of Fusarium species associated with head blight of wheat in South AfricaPLOS ONE

Dear Dr. Van Coller,

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 Aug 18 2022 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. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. 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,

Yuefeng Ruan, Ph.D

Academic Editor

PLOS ONE

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #2: All comments have been addressed

Reviewer #3: All comments have been addressed

Reviewer #4: (No Response)

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: Yes

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #2: Yes

Reviewer #3: (No Response)

Reviewer #4: N/A

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4. 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 #2: Yes

Reviewer #3: Yes

Reviewer #4: (No Response)

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5. 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 #2: Yes

Reviewer #3: Yes

Reviewer #4: Yes

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6. 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 #2: Title and Abstract: a little bit misleading and unclear title. Since this survey was done in 14 years ago, it is better point out the time period in the title and abstract. Otherwise, audience will think this is a latest survey report.

Discussion: since this survey study is from 2008/09, almost 15 years ago. it is better to see if there is a latest survey report published recently and make a comparison.

Line 443: this is not a "current" study, but almost 15 years old

Reviewer #3: Dear Authors,

Your manuscript titled "The distribution and type B trichothecene chemotype of Fusarium species associated with head blight of wheat in South Africa" is a well written and structured manuscript that provides valuable information on the species associated with FHB infection. Unfortunately, the research and findings are outdated. Utilizing words such as "first report" is not accurate given that the sampling has been completed 13 and 14 years ago. The distribution pattern of species changes over the time while facing the changes of cropping system and practices, environment, the level of resistance of cultivars grown etc. I believe many changes could have happened in the last 14 years that could have changed the distribution pattern you are reporting in this study. Your manuscript still has a great value because it reports what species were predominant over a decade ago which could be a reference for newer studies. I strongly encourage you to address the findings as an overview research over the late 2000s.

Reviewer #4: This paper reports survey results conducted to determine the identity, distribution and type B trichothecene chemotype of Fusarium species associated with FHB of wheat in South Africa.

• General concern: The survey was in 2008 and 2009 which is about 13-14 year ago making it a historical data. So it doesn’t show recent developments although it still provides a good information if documented as a publication.

Abstract

o The finding shows chemotype diversity was limited (15-ADON=90.1%) and highly structure in terms of species difference. However, authors report for the first time six Fusarium species not recorded on wheat elsewhere which is a plus.

o Results were not indicated as related to production conditions – irrigated versus non-irrigated and province wise. One thing that should be addressed here is whether the species distribution under different farming conditions and provinces the same or different? Please describe it briefly.

Materials and methods

There is no mention if the locations overlapping across the two survey years. Please describe this as F. species differences between the years could be a factor of the sites of sample collection besides crop culture.

Results

o Line#273: What are the factors behind such large differences in the prevalence of FGSC between 2008 and 2009? This should be discussed in terms of sites of sample collection, weather condition, crop culture / rotation crops or species competition.

o Fig. 1. FGSC is common across all regions with one exception. In Western Cape and followed by Free State the proportion of F. pseudograminearum is exceptionally high. What makes this region so special. This needs discussing (seemingly due to bias in small sample size).

Discussion

o Lines#443-444: This sentence is confusing. Were these six Fusarium species not recorded on other crop species similar to wheat? If they reported on other plant species, they are not new species. They could be a new record on a wheat crop. Please reword the sentence.

Please check reference cited.

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Reviewer #2: No

Reviewer #3: No

Reviewer #4: Yes: Firdissa Bokore

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Attachments

Attachment

Submitted filename: PONE-D-21-28634_R2.pdf

The distribution and type B trichothecene chemotype of Fusarium species associated with head blight of wheat in South Africa during 2008 and 2009

PONE-D-21-28634R3

Dear Dr. Van Coller,

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.

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Kind regards,

Yuefeng Ruan, Ph.D

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Dear Authors:

Thank you for addressing reviewers’ comments and revising the manuscript.

Thank you for submitting to PLOS ONE again.

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #4: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #4: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #4: Yes

**********

4. 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 #4: Yes

**********

5. 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 #4: Yes

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6. 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 #4: The authors responded to my comments and made improvements to the previous version. I have no further comments to make.

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Reviewer #4: Yes: Firdissa Bokore

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