Trichoderma: Population Structure and Genetic Diversity of Species with High Potential for Biocontrol and Biofertilizer Applications

Round 1

Reviewer 1 Report (Previous Reviewer 1)

Comments and Suggestions for Authors

Dear Authors, Unfortunately, I do not recommend this work for publication in JAM due to its non-innovative nature. The authors only performed a phylogenetic analysis of sequences of selected phylogenetic markers for selected Trichoderma species obtained by other authors, which were available in the NCBI database. Therefore, the work is not very original, because it is based on data that has already been published, neither verified personally nor obtained independently by re-identifying strains. The work does not contribute new knowledge, especially in the context of the potential goal set by the authors, which is to identify strains with potential for biocontrol and biofertilization. It is worth keeping in mind that the tested DNA regions/species affiliation do not determine the above ability. It is rather an isolate-specific feature. It is worth reading the available literature on this topic and planning further research, including a methodological approach, in order to reliably solve the problem of identifying strains with the ability to biocontrol and biofertilization, which bothers the Authors. First of all, it would be necessary to obtain Trichoderma strains that are of interest to the authors, re-identify the strains (confirm species affiliation) and assess their potential for biofertilization and biocontrol. Using such a characterized collection, it would be possible to develop a methodology for rapid identification of biotechnologically beneficial strains.

Comments for author File: Comments.pdf

Author Response

Please see the attachment

Author Response File: Author Response.pdf

Reviewer 2 Report (Previous Reviewer 2)

Comments and Suggestions for Authors

The manuscript has been improved, which can be accepted now.

Author Response

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Author Response File: Author Response.pdf

Reviewer 3 Report (Previous Reviewer 3)

Comments and Suggestions for Authors

In this manuscript (manuscript ID: applmicrobiol-2998521), the author's effort was to study Trichoderma literature to identify prevalent species in soil and plant endophytes.

Sequences from three loci, tef1α, rpb2, and ITS, including references were obtained from Genbank. They then used phylogenetic analysis based on combined DNA sequences of these loci following the recommendation of Cai et al. 2021 (Fungal Diversity, 107, 1–69) to assess genetic diversity and population structure. This is fine. The molecular identification of Trichoderma requires DNA barcodes analysis of at least ITS, tef1, and rpb2, which can also be supported by online tools (e.g. those available on https://www.trichokey.com/).

However, I have raised some questions on the presentation of the manuscript that need to be addressed before the manuscript can be considered for publication.

From the review perspective, it would be helpful to improve the presentation and the discussions of the results. For instance, in the manuscript the authors state the recognition of putative new Trichoderma species (some of which were delimitated within previously existing species complexes or clades, such as T. atroviride, T. hamatum, T. virens and T. asperellum).

Authors should consider their results in the context of the journal's scope. Did the themes of the journal cover the problem of molecular identification of Trichoderma at the species level, with the recognition of new Trichoderma species?

Moreover, the authors should consider contacting those who collected/identified the Trichoderma strains and deposited the respective DNA sequences in public databases then used in the manuscript. Are these new putative Trichoderma species awaiting their formal and accurate description?

Finally, the authors should explain to the readers why they did not consider the public availability of Trichoderma whole-genome sequences (WGS). The analysis of WGS for Trichoderma species (available in public databases including GenBank, NCBI), when deposited by Trichoderma researchers and specialists, provides insights into the recognition of putative new Trichoderma species.

I hope it helps.

Comments on the Quality of English Language

Minor editing of English language required.

Author Response

Please see the attachment

Author Response File: Author Response.pdf

This manuscript is a resubmission of an earlier submission. The following is a list of the peer review reports and author responses from that submission.

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The Authors of the manuscript proposed in the title to present the population structure and genetic diversity of Trichoderma species with high potential for biocontrol and applications as a biofertilizer. The title seems interesting and promising. Unfortunately, the Authors limited themselves solely to searching the literature data to identify Trichoderma isolates/species with the above properties, or rather the nucleotide sequences of a fragment of the tef1 gene as a phylogenetic marker. As a criterion, they set literature data that described Trichoderma fungi isolated from soil or plant tissues as endophytes. Nucleotide sequences selected from the NCBI database were used for phylogenetic analyses. Based on the obtained phylogenetic trees, based only on one DNA region (a fragment of the tef1 gene) and groupings, the authors formulated conclusions regarding the potential of isolates as BCAs and biofertilizers, which is a significant simplification. Due to the above, it is believed that the approach, research purpose and methodology should be revised significantly. The manuscript also lacks a discussion and reference to the literature that was the basis for selecting data for bioinformatics analyses. When redrafting the manuscript, it is also worth paying attention to making the Materials and Methods section more detailed and improving the quality of the tables. These main criticisms influence the decision not to recommend this work for publication in its current form. Detailed notes and comments are highlighted in the PDF file of the manuscript

  Comments on the Quality of English Language

It is recommended to pay attention to the grammar and style of the sentences. The spelling of Latin names and gene names should be revised throughout the manuscript.

Reviewer 2 Report

Comments and Suggestions for Authors

The manuscript mainly focused on the research of Trichoderma genus fungi, which have a wide range of applications in agriculture and ecology. The study involved multiple aspects, including the classification, genomics, biochemistry, physiology, and ecology of Trichoderma genus. In addition, the application of Trichoderma genus fungi in plant protection, biological control, and sustainable agriculture was explored. Finally, the authors provided a comprehensive overview of the potential research of Trichoderma fungi, demonstrating their important role in agriculture and ecology.

I have no special comments on the manuscript, which could be accepted after minor revision, but improve the quality of table and figure to meet the journal's high requirement. for example, Phylogenetic tree can be made in colour revision, and tables can be  changed into three-line table.

 

Comments on the Quality of English Language

   

Reviewer 3 Report

Comments and Suggestions for Authors

In this manuscript (manuscript ID: applmicrobiol-2868481), the author's effort was to study Trichoderma literature to identify prevalent species in soil and plant endophytes. They then used translation elongation factor 1α (tef1) gene sequences to assess genetic diversity and population structure.

However, I have raised some questions on the presentation of the manuscript that need to be addressed before the manuscript can be considered for publication.

Authors should consider the results in context of the journal's scope. Did the aim of the manuscript cover the main themes of the journal?

From the review perspective, it would be helpful to improve the presentation and the discussions of the results. For instance, the authors should explain to the readers why they focused on a single protein-coding gene for phylogenetic relationships, considering the public availability of Trichoderma sequencing/genome data.  

I hope it helps.

Comments on the Quality of English Language

Minor editing of English language required.