Isolates of the Nematophagous Fungus Pochonia chlamydosporia Are Endophytic in Banana Roots and Promote Plant Growth
Round 1
Reviewer 1 Report
New technologies for the improvement of agriculturally relevant crops are to be encouraged. Mainly in a more sustainable perspective. The manuscript is focused on the beneficial effects of Pochonia chlamydosporia endophyte on banana growth: the experimental design is clear and results are quite interesting.
However, I found that same manuscript was already pre-published on Biorxiv website:
https://www.biorxiv.org/content/10.1101/2020.06.10.144550v1
I have addressed to the Edito the question if such pre-publishing occurrence could be considerded a violation of the Journal principle "manuscripts must have not been published elsewere": personally, I'm not supportive in the pre-print habit.
In case of the Editor will decide to accept this occurrence, my comments on the manuscript are as follow:
English language editing is required: example or errors are listed below:
Line 13: "The biocontrol fungus, Pochonia chlamydosporia, colonizes" delete commas
Line 14: "found colonize" should be "colonized"
Line 15: "penetration of root cells" should be "penetration in root cells"
Line 17: "chamber experiments 30 days post-inoculation" instead of "chamber experiments at 30 days post-inoculation"
Line 217: "Growth promotion by Pc has also proven" should be "was also obtained/observed"
Other issues:
Many scientific names are not in italic (i.e. keywords, or Line 48)
Literature is insufficient: for example, in Line 29, sentence "Crop yield is conditioned by a set of biotic and abiotic factors.... rhizosphere [3]" was supported by a single citation. This is obviously not enough, considering the importance of the statement, as well as the following "Many important pest and diseases can affect banana plants....and plant-parasitic nematodes [4]"
Caption to Figures 2-C and 2-E seem to have been switched respect to the order in which the relevant images are presented.
Line 207: "Klamic ®" should be "Klamic®"
From Line 206 and 220, "In our study" is highly repeated; this is an unfair redundance. Please remove.
Author Response
We appreciate your comments and corrections, they have helped us a lot to improve the manuscript. Below I attach the file with the corrections.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
This paper investigates the potential of four strains of Pochonoa chlamydosporia (Pc21, Pc123, Pc399, and Pccat) in the development of root colonization as well as promote the plant growth in Banana. In general, the study is interesting however, there are many things to improve the manuscript see below under major comments and specific comments.
Major comments
The language used in the manuscript needs to improve or at least read by a native speaker.
Title
Authors have used only four strains of P. chlamydosporia to determine their role in root colonization and plant growth of banana, therefore, based on four strains authors cannot claim the word “worldwide strains”. This is a too strong word to be used only for four strains. Consider modifying the title.
Introduction
In the introduction significant portion covering the impact of P. chlamydosporia against plant-parasitic nematodes while authors didn’t study on nematodes, therefore, there is no point to emphasize the impact against nematodes. While authors didn’t cover a significant part of literature specifically on the root colonization and plant growth promotion by P. chlamydosporia. I would suggest enhancing this part instead of plant-parasitic nematodes.
Throughout the experiment, authors referred to a number of conidia or chlamydospores in a GENERAL notation (such as 5,000 chlamydospores/gram of substrate) instead of in scientific notation (such as 5 × 104 chlamydospores/gram of substrate). Revised this throughout the manuscript.
Use the accurate scientific notation of fungal pathogens, for example, Fusarium oxysporum, should be written with the full genus and species name at first mentioning, and later genus always abbreviated and with full species such as F. oxysporum. This scientific notation has not been followed in the manuscript, consider to revise this throughout the manuscript.
At the end of the introduction consider providing the hypotheses of the study
Close the introduction by providing a summary of the study in a 2-3 sentence.
Results
The presentation of the results needs to improve for example, section 3.3 needs to come first at the start which means section 3.1.
Section 3.3 author claimed that Pc 21 performed better in root colonization and plant growth then why authors choose strain Pc 123 in the experiment of banana plantlets (section 3.1) and greenhouse experiment (section 3.2)?
Authors measured the fresh weight of root, corm and leaves, why not dry weight? Since fresh weight is not an absolute way to measure the weight in the experiment.
Figure 1, Figure 2 and Figure3 some of the sections are wrongly labelled, which is differently mentioned the text as well as in figure captions.
Supplementary figure 1, figure 2 and figure 4, not explained throughout the experiment, while figures present in the manuscript.
Overall, all the figures provided in the manuscript have a low resolution, the quality of figures also needs to be improved.
Discussion
The overall discussion is weak and results not discussed in a very logical way. The discussion should look different than the literature review. The discussion needs to improve overall.
Specific comments
Abstract
L17: Remove (DPI)
L19-20: Don’t need to mention the origin of strains in the abstract, instead, give this information in the materials and method section
L 24: Italicize the scientific names of fungus and banana
L 39: replace 5,000 chlamydospores per gram with 5 × 103 chlamydospores/gram
L 45-46: Sentence needs to be rephrased
L 57: Pochonia chlamydosporia replaced with P. chlamydosporia (see above comment)
L 58-63: Keep the consistent style, either use “spp”. or “sp”., don’t mix the scientific style.
L 64: Why Pc123 used instead of other strains even Pc 21 performed better in root colonization.
L 70: “inoculated with 10,000 Pc123 conidia” replaced with “inoculated with 1 × 104 Pc123 conidia
L83: 50,000 replaced with 5 × 104
L88: see as in L83 commented
L96: see as in L83 commented
L123-124: How fold change in root colonization was calculated either using the Pfaffl or delta-delta Ct method?
Results
L133: change heading into “Effect of Pc inoculation on plant growth”
L 135: In the text, Fig 1a corresponds to length while in figure it corresponds to weight. Make it consistent
L 135: In the text, Fig 1b corresponds to weight while in figure it corresponds to the length. Make it consistent.
L 133-141: In section 3.1, how much per cent increase in weight was observed when inoculated with Pc123? Interpret the results by mentioning the percentage increased or decreased.
L 133-141: In section 3.1, why the fresh weight was taken instead of dry weight?
Figure 1b: letterings are missing on corm bars.
L 145: Figure 1 caption, 1a corresponds to length, while in figure 1a corresponds to weight. Make it consistent.
L 146: Figure 1 caption, 1b corresponds to weight, while in figure 1b corresponds to the length. Make it consistent.
L 152: “P. chlamydosporia” should be italics
L 152: In the text, Fig 2a corresponds to length while in figure it corresponds to weight. Same goes to figure 2 captions. Make it consistent.
L153-154: In the text, Fig 2b corresponds to weight while in figure it corresponds to the length. Same goes to figure 2 captions. Make it consistent.
L 157: You only mentioned Fig. S3 in the text, where are the Figure S1 and Figure S2? The authors never explained the supplementary figure S1, S2 and S4 throughout the manuscript.
L 152-159: Consider providing the per cent increase or decrease in weight.
Figure 2: 2a lettering is missing. 2b also lettering missing for corm. In the text, authors claimed the significant increase in root weight while figure 2b shows no significant difference with control, since sharing similar letters.
L 176: If Pc121 performed better, then why didn’t used in greenhouse experiment instead of Pc123?
Figure 3: Captions not matching with the figure labeling, for example, Figure 3a corresponds to weight while captions correspond to length, similar go figure 3b corresponds to length while in captions shows weight.
Discussion
L192: The word “paramount” is too strong, consider revising this word.
The discussion overall needs to be improved, the discussion should be different than the literature review.
Conclusions
Conclusions should be presented in a paragraph instead of points.
Author Response
We appreciate your comments and corrections, they have helped us a lot to improve the manuscript. Below I attach the file with the corrections
Author Response File: Author Response.pdf
Round 2
Reviewer 1 Report
Authors promptly answered to my issues and proceeded to follow provided suggestions.
However, the major concern about this manuscript still remains unsolved: the present work was already published online on Biorivx website, by same Authors; in my opinion, this occurrence represent a case of "previously published" that strongly contrasts with MDPI publishing ethics. Authors did not provided any comments in regard. As I declared in my previous revision, it is not my policy to support such behaviour. In absence of different Editor's guideline, my only suggestion is that this manuscript is not suitable for publication.
Author Response
Dear reviwer,
At the request of the editor I attach below the letter I wrote her when the problems with the preprint arose, in it there is a screenshot of the guide of authors in which the information related to the preprint is explained.
Thank you very much for the corrections and for the time invested.
Regards,
Cristina Mingot
Author Response File: Author Response.pdf
Reviewer 2 Report
Thank you for making the revision of the manuscript. The authors mainly revised and modified the manuscript however, there are some concerns yet needs to address as mentioned below.
Main concern
I have seen this paper already on the “bioRxiv” which you can access on the following link (https://doi.org/10.1101/2020.06.10.144550). If the MDPI publisher's rules allowed this and particularly the Agronomy journal allow to put manuscript before publishing then this paper can be accepted with minor revision.
Title
I have suggested modifying the title since based on four strains author cannot claim the word “worldwide” the author answered, “two were used from Europe, one from Asia, and one from America”, based on this, I think, still authors cannot use the word “worldwide” since it can be true if authors included the strains as representative from all the continent’s which are seven. Am not satisfied with this title and response.
General comments
Although authors have made significant changes in the revised version of the manuscript. However, the author has re-written the major portion with the same text as the text was in the original version it only has been typed by activating the track change which is marked with the red.
Hypotheses are not formulated as it should be in the Introduction section, rather it seems objective of the study.
Author Response
Dear reviewer,
At the request of the editor I attach below the letter I wrote her when the problems with the preprint arose. In this letter is explained all about preprints.
Thank you very much for the corrections and for the time invested.
---- Editor Letter-----
Monday, 17th August 2020
Dear Editor,
As you can follow in the revision track, reviewers criticize that we include or manuscript entitled “Worldwide strains of the nematophagous fungus Pochonia chlamydosporia are endophytic in banana roots and promote plant growth” because we have included our work in Biorxiv, a preprint platform. Our manuscript with ID is agronomy-886033, this article is hosted in a pre-print web (BioRxiv) (https://doi.org/10.1101/2020.06.10.144550). We informed about this during submission.
Our manuscript is still under review, I would like if you could clarify to the reviewers that we are following all the recommendations explained in your Guide for Authors.
Preprints and Conference Papers (Guide of Authors) https://www.mdpi.com/journal/agronomy/instructions#preprints
Agronomy accepts articles that have previously been made available as preprints provided that they have not undergone peer review. A preprint is a draft version of a paper made available online before submission to a journal.
MDPI operates Preprints, a preprint server to which submitted papers can be uploaded directly after completing journal submission. Note that Preprints operates independently of the journal and posting a preprint does not affect the peer review process. Check the Preprints instructions for authors for further information.
Kind regards,
Cristina Mingot-Ureta
Corresponding Author
Author Response File: Author Response.pdf
