Review Reports - An Overview of the <i>Alternaria</i> Genus: Ecology, Pathogenicity and Importance for Agriculture and Human Health

Round 1

Reviewer 1 Report

This manuscript by Vinogradova et al. provides a broad narrative review of the genus Alternaria, covering taxonomy, ecology, morphology, plant pathogenicity, and control methods. Overall, the manuscript is well-organized and clearly falls within the scope of the JoF. However, the manuscript requires minor revisions to address inconsistencies and correct biological terminology.

It would be beneficial to explicitly state how this review differs from or updates recent similar reviews (justify why this review is important).
The review covers Azoles, Strobilurins, and Dithiocarbamates well. However, Succinate Dehydrogenase Inhibitors (SDHIs) are also a major class of fungicides widely used against Alternaria in modern agriculture. A brief mention of SDHIs would make the chemical control section more complete.
Line 153-"A. alternata, consisting of ergosterol...". This phrasing is incorrect. The fungus does not "consist of" these compounds; it produces or synthesizes them.

Minor suggestions are the followings:

Table 1: "Apium Graveolens" should be "Apium graveolens". Also, the author should italicize wheat (right next to A. tenuissima).
The Abstract mentions 27 sections, whereas the Taxonomy section states 29 sections have been identified.
The Introduction states the fungi produce "over 300 different secondary metabolites", but the Biotechnological Potential section states "more than 30 metabolites".

Author Response

Dear Reviewer. Thank you for your meticulous review of our manuscript and for your highly valuable comments and corrections. We have carefully addressed each point you raised, and all necessary revisions have been made to the manuscript, including a thorough review to improve the overall quality of the English language.

Comments 1: It would be beneficial to explicitly state how this review differs from or updates recent similar reviews (justify why this review is important).

Response 1: Thank you for this important and constructive comment. We fully agree with the necessity to clearly articulate the contribution and novelty of our review within the context of the existing literature.

In response to your suggestion, we have substantially revised the concluding paragraph of the "Introduction" section (lines 92–105) to explicitly formulate the aim, concept, and unique aspects of our work. The edits made clearly highlight how this article complements previously published reviews by offering an integrated synthesis of fundamental and applied aspects of research on the genus Alternaria.

We hope that the specific focus of our work, as well as its value within the current state of research, is now clear to the reader. Of course, no single review article can claim to provide a complete and exhaustive coverage of the entire topic. Therefore, we have consciously concentrated on what we consider to be the key interrelationships between taxonomy, molecular pathogenesis, and contemporary control strategies, including the biotechnological potential of these fungi.

Comments 2: The review covers Azoles, Strobilurins, and Dithiocarbamates well. However, Succinate Dehydrogenase Inhibitors (SDHIs) are also a major class of fungicides widely used against Alternaria in modern agriculture. A brief mention of SDHIs would make the chemical control section more complete.

Response 2: Thank you for your valuable comment. We fully agree that the class of SDHI fungicides is one of the key components in modern Alternaria control strategies. A corresponding paragraph has been added to the chemical control section (Lines 365-377). In it, we briefly outlined the mechanism of action of SDHI, and also highlighted the issue of resistance development to certain members of this class, which underscores the need for discovering new compounds and implementing rotation strategies.

Comments 3: Line 153-"A. alternata, consisting of ergosterol...". This phrasing is incorrect. The fungus does not "consist of" these compounds; it produces or synthesizes them.

Response 3: You are absolutely right. Thank you for catching this inaccuracy. We amend lines 190-193 to state that A. alternata produces these secondary metabolites.

Comments 4: Table 1: "Apium Graveolens" should be "Apium graveolens". Also, the author should italicize wheat (right next to A. tenuissima).

Response 4: Thank you very much. We have fixed this error.

Comments 5: The Abstract mentions 27 sections, whereas the Taxonomy section states 29 sections have been identified.

Response 5: We thank the reviewer for the careful reading of our manuscript and for identifying an important discrepancy in the data regarding the taxonomy of the genus Alternaria. We acknowledge that contradictory information was presented in the text, and we sincerely appreciate the opportunity to correct this. The mention of 27 sections is indeed based on earlier classification schemes. The current taxonomy of the genus Alternaria recognizes 29 sections as the up-to-date and generally accepted structure.

Comments 6: The Introduction states the fungi produce "over 300 different secondary metabolites", but the Biotechnological Potential section states "more than 30 metabolites".

Response 6: We thank you for your careful reading and for pointing out this important discrepancy in the numerical data. The figure of "over 300" refers to the total number of secondary metabolites described for the genus Alternaria in the scientific literature. We have rechecked the information and have now put it in proper order.

Reviewer 2 Report

There are some writing mistakes:

1.Incorrect chapter numbering: Chapter 5 Conclusions directly follows Chapter 8 with no proper sequential arrangement.

2.Inconsistent citation format: The literature citation styles at line 134 and line 177 are not uniform.

3.Incorrect subscript notation (line 159): "CO2" should be formatted as CO₂.

4.Redundant conjunction (line 231): Delete the word "and" before "etc.".

5.Incorrect superscript notation (line 451): "m3" should be formatted as m³.

6.Missing punctuation (line 167): No period is placed at the end of the paragraph.

7.Spelling error (line 455): "enuazonic acid" is misspelled and should be corrected to tenuazonic acid.

Major revisions:

1.The manuscript states that the genus Alternaria comprises 27 sections, yet refers to 29 sections in a later part. The authors are requested to clarify the reason for this discrepancy and standardize the classification system and its corresponding data sources.

2.The pathogenic mechanisms of Alternaria toxins (including AAL, ACR, AM, etc.) are currently presented only as descriptive summaries. Could the authors add an integrated schematic diagram or a comparative table to improve the readability and comprehensiveness of this part?

There are some writing mistakes:

1.Incorrect chapter numbering: Chapter 5 Conclusions directly follows Chapter 8 with no proper sequential arrangement.

2.Inconsistent citation format: The literature citation styles at line 134 and line 177 are not uniform.

3.Incorrect subscript notation (line 159): "CO2" should be formatted as CO₂.

4.Redundant conjunction (line 231): Delete the word "and" before "etc.".

5.Incorrect superscript notation (line 451): "m3" should be formatted as m³.

6.Missing punctuation (line 167): No period is placed at the end of the paragraph.

7.Spelling error (line 455): "enuazonic acid" is misspelled and should be corrected to tenuazonic acid.

Major revisions:

Author Response

Comments 1: Incorrect chapter numbering: Chapter 5 Conclusions directly follows Chapter 8 with no proper sequential arrangement.

Response 1: Thank you very much. We have fixed this error.

Comments 2: Inconsistent citation format: The literature citation styles at line 134 and line 177 are not uniform.

Response 2: Thank you. We've tried to standardize the citation format.

Comments 3: Incorrect subscript notation (line 159): "CO2" should be formatted as CO₂.

Response 3: Corrected.

Comments 4: Redundant conjunction (line 231): Delete the word "and" before "etc.".

Response 4: Corrected.

Comments 5: Incorrect superscript notation (line 451): "m3" should be formatted as m³.

Response 5: Corrected.

Comments 6: Missing punctuation (line 167): No period is placed at the end of the paragraph.

Response 6: Corrected.

Comments 7: Spelling error (line 455): "enuazonic acid" is misspelled and should be corrected to tenuazonic acid.

Response 7: Corrected.

Comments 8: The manuscript states that the genus Alternaria comprises 27 sections, yet refers to 29 sections in a later part. The authors are requested to clarify the reason for this discrepancy and standardize the classification system and its corresponding data sources.

Response 8: We thank the reviewer for the careful reading of our manuscript and for identifying an important discrepancy in the data regarding the taxonomy of the genus Alternaria. We acknowledge that contradictory information was presented in the text, and we sincerely appreciate the opportunity to correct this. The mention of 27 sections is indeed based on earlier classification schemes. The current taxonomy of the genus Alternaria recognizes 29 sections as the up-to-date and generally accepted structure.

Comments 9: The pathogenic mechanisms of Alternaria toxins (including AAL, ACR, AM, etc.) are currently presented only as descriptive summaries. Could the authors add an integrated schematic diagram or a comparative table to improve the readability and comprehensiveness of this part?

Response 9: We fully agree with your suggestion that a visual representation of the pathogenic mechanisms of Alternaria toxins would significantly enhance the accessibility of the material for readers. In response to your recommendation, we have prepared a schematic figure that clearly illustrates the mechanisms of action of the key host-specific toxins (AAL, ACR, AF, AM) at the subcellular level (Figure 2. Schematic model of Alternaria toxins action on plant cellular targets).

Reviewer 3 Report

Please refer to detailed comments

Comments to the author (JOF- 4038331)

Thank you for sharing the interesting paper. Overall, I feel that the manuscript does not have any novelty but only some reported and compiled studies of the genus Alternaria, covering taxonomy, ecology, pathogenicity, control strategies, and biotechnological relevance. Most of the sections are generally written with conceptual framing rather than critical advancements. Some suggestions are.

I would suggest adding the word “A Review” in the title, it will enhance the clarity for readers.

In the abstract, the phrase “potential pathogens in humans” need clarification to avoid overgeneralization.

Further, the statement regarding “792 species” needed briefly acknowledgment towards ongoing taxonomic uncertainty directly in the abstract to temper expectations of numerical precision.

How this review can be distinguished from other what is the novelty.

Lines 30-33: The description of Alternaria as “aggressive phytopathogens” is somewhat strong. I would suggest phrasing by noting host- and context-dependence of pathogenicity.

Lines 34-36: This information/claim needed proper citation

Lines 40-42: It need to briefly explain the criteria used to define “officially recognized” species.

Lines 43-44: The statement that traditional morphological groupings do not align with molecular data, it need concrete example for clarity.

Lines 50-51: The acronym “AGE” (genome-wide analysis) is introduced without prior definition. Please define it explicitly at first mention and later use abbreviations.

Lines 61-62: I am bit surprised about this, either this refers to localized outbreaks, experimental conditions, or worst-case scenarios?

Lines 68-70: CRISPR/Cas9 is needed brief note, acknowledging applications which remain experimental rather than field-deployed.

Lines 92-95: The manuscript alternates between stating “27” and “29” sections in different places. Please check.

Lines 109-115: please present the list of molecular markers in a more structured manner focusing on core vs. auxiliary markers.

Lines 117-118: The statement that small-spore species are “poorly differentiated” genetically it need clarification as this applies mainly to commonly used loci rather than whole genomes.

Lines 123-126: discussion on chemotaxonomy is limited. I would encourage briefly explaining why secondary metabolite profiles lack sufficient resolution.

Lines 131-132: The claim that whole-genome analysis is the “most promising and reliable” should revised by acknowledge current limitations such as cost, accessibility, and incomplete reference genomes.

Lines 142-143: The inclusion of animals as substrates is underdeveloped. Please clarify whether this refers to colonization, infection, or incidental association.

Lines 147-148: Positive effects of endophytic Alternaria are noted; however, the authors must clearly distinguish between strain-specific effects and general genus-level conclusions.

Lines 152-154: The sentence describing antimicrobial compounds from A. alternata is confusing grammatically. Please rephrase for clarity and specify whether these are endophytic or pathogenic isolates.

Lines 165-166: The transition from endophytic/saprophytic lifestyles to parasitism needed mechanistic explanation.

Lines 171-172: Please rephrase the statement that sexual stages “have not been observed” as “have rarely been observed or are unknown”.

Lines 178-181: The formation of chlamydospores and sclerotia need species-specific evidence for accuracy, as not all Alternaria species form these structures.

Lines 222-230: The detailed toxin descriptions need some clarification and addition of the data with host-specific toxins and non-host-specific toxins.

Lines 234-235: The claim that different species cause “similar infection patterns” should be revised by differences in host specificity and symptom expression.

Lines 242-244: Yield loss percentages should be contextualized geographically or temporally to avoid appearing universally applicable.

I will stop here, specifically for the other section, the information is very general.

Author Response

Dear reviewer. We express our sincere gratitude for your insightful and constructive review of our manuscript. Your comments were extremely valuable and significantly improved the quality of the article. Each comment contributed to important clarifications, improved the precision of wording, and enhanced the scientific rigor of the presentation.

Comments 1: I would suggest adding the word “A Review” in the title, it will enhance the clarity for readers.

Response 1: Thank you for your helpful suggestion to enhance the title's clarity. We agree that explicitly stating the article's format will be beneficial for readers. We revised the title to incorporate your recommendation. Lines 2-3. New version: «An overview of the Alternaria genus: ecology, pathogenicity and importance for agriculture and human health».

Comments 2: In the abstract, the phrase “potential pathogens in humans” need clarification to avoid overgeneralization.

Response 2: We thank for this important clarification. The phrase has been revised to more accurately reflect that the human health impact of Alternaria is primarily associated with opportunistic infections and allergic reactions, rather than implying it is a common primary human pathogen.

Comments 3: Further, the statement regarding “792 species” needed briefly acknowledgment towards ongoing taxonomic uncertainty directly in the abstract to temper expectations of numerical precision.

Response 3: You are right to point out the importance of acknowledging taxonomic uncertainty. Thank you for this suggestion. To accurately reflect the evolving state of Alternaria taxonomy, we will revise the relevant sentence in the abstract to indicate that the figure of “over 792 species” represents the current, but not definitively fixed, state of classification, and that the genus is subject to ongoing revision.

Comments 4: How this review can be distinguished from other what is the novelty.

Response 4: We fully agree with the necessity to clearly articulate the contribution and novelty of our review within the context of the existing literature. In response to your question, we have substantially revised the concluding paragraph of the "Introduction" section (lines 92–105) to explicitly formulate the aim, concept, and unique aspects of our work. The edits made clearly highlight how this article complements previously published reviews by offering an integrated synthesis of fundamental and applied aspects of research on the genus Alternaria. We hope that the specific focus of our work, as well as its value within the current state of research, is now clear to the reader. Of course, no single review article can claim to provide a complete and exhaustive coverage of the entire topic. Therefore, we have consciously concentrated on what we consider to be the key interrelationships between taxonomy, molecular pathogenesis, and contemporary control strategies, including the biotechnological potential of these fungi.

Comments 5: Lines 30-33: The description of Alternaria as “aggressive phytopathogens” is somewhat strong. I would suggest phrasing by noting host- and context-dependence of pathogenicity.

Response 5: Thank you for your important and insightful comment. Your suggestion may more accurately reflect our current understanding of the biology of the genus Alternaria and its complex relationships with its host plants. We have revised the text to reflect your suggestion. Line 35-39.

Comments 6: Lines 34-36: This information/claim needed proper citation

Response 6: Thank you. We've added links to support this statement. Line 42.

Comments 7: Lines 40-42: It need to briefly explain the criteria used to define “officially recognized” species.

Response 7: Noted, thank you for the clarification. The criteria have been clarified in the text. Line 47.

Comments 8: Lines 43-44: The statement that traditional morphological groupings do not align with molecular data, it need concrete example for clarity.

Response 8: Thank you for the important clarification. A clarification has been added to the text explaining the discrepancy between the morphological classification and the molecular phylogenetic data. Linse 50-56.

Comments 9: Lines 50-51: The acronym “AGE” (genome-wide analysis) is introduced without prior definition. Please define it explicitly at first mention and later use abbreviations.

Response 9: Thank you. We used a more logical abbreviation “genome-wide analysis studies (GWAS)” Line 62.

Comments 10: Lines 61-62: I am bit surprised about this, either this refers to localized outbreaks, experimental conditions, or worst-case scenarios?

Response 10: Thank you for your fair comment. You are absolutely right. The loss level indicated does indeed apply to the worst-case scenario (favorable weather conditions for fungal growth). For clarity, a corresponding explanatory note has been added to the text. Lines 73-74.

Comments 11: Lines 68-70: CRISPR/Cas9 is needed brief note, acknowledging applications which remain experimental rather than field-deployed.

Response 11: Thank you. Noted. I agree, it's important to note that the use of CRISPR/Cas9 to combat Alternaria is still in the experimental stage. The text has been updated accordingly. Line 82.

Comments 12: Lines 92-95: The manuscript alternates between stating “27” and “29” sections in different places. Please check.

Response 12: We thank the reviewer for the careful reading of our manuscript and for identifying an important discrepancy in the data regarding the taxonomy of the genus Alternaria. We acknowledge that contradictory information was presented in the text, and we sincerely appreciate the opportunity to correct this. The mention of 27 sections is indeed based on earlier classification schemes. The current taxonomy of the genus Alternaria recognizes 29 sections as the up-to-date and generally accepted structure.

Comments 13: Lines 109-115: please present the list of molecular markers in a more structured manner focusing on core vs. auxiliary markers.

Response 13: Thank you. We've researched the issue and found that there's no clear consensus on the auxiliary markers. So, we simply changed the order without introducing formal categories.

Comments 14: Lines 117-118: The statement that small-spore species are “poorly differentiated” genetically it need clarification as this applies mainly to commonly used loci rather than whole genomes.

Response 14: Thank you for this comment. You are correct. the phrasing should be more precise to specify that the issue of poor differentiation pertains to the conventionally used genetic loci rather than to whole-genome data. The sentence has been revised as follows for clarity. "However, the genetic sequences of the loci commonly used for species identification are poorly differentiated in small-spore species, making their distinction problematic." Lines 144-145.

Comments 15: Lines 123-126: discussion on chemotaxonomy is limited. I would encourage briefly explaining why secondary metabolite profiles lack sufficient resolution.

Response 15: Thank you for this comment. You are absolutely right. We have added an explanation to the text explaining why secondary metabolite profiling, despite its usefulness, has limitations for reliably distinguishing closely related Alternaria species.

"While secondary metabolite profiles are a valuable diagnostic tool and can be used for the identification of some species, their resolving power is often insufficient for reliably distinguishing morphologically similar and phylogenetically close species, such as A. alternata, A. arborescens, and A. tenuissima. This limitation stems from the fact that the synthesis of many secondary metabolites in fungi of the Alternaria genus is conserved within species complexes or can vary depending on environmental conditions and developmental stage, which does not always reflect true phylogenetic boundaries. Therefore, similar to multilocus phylogenetic analysis, chemotaxonomy in this context cannot serve as the sole criterion for species identification." Lines 152-162.

Comments 16: Lines 131-132: The claim that whole-genome analysis is the “most promising and reliable” should revised by acknowledge current limitations such as cost, accessibility, and incomplete reference genomes.

Response 16: This is a very fair point, and we agree that acknowledging the current limitations of whole-genome analysis is crucial for an accurate and balanced perspective. We have modified the text to incorporate this nuance, and we believe the manuscript has been strengthened as a result. Please see the revised lines 169-171.

Comments 17: Lines 142-143: The inclusion of animals as substrates is underdeveloped. Please clarify whether this refers to colonization, infection, or incidental association.

Response 17: We agree that the word "infect" accurately describes the pathogenic interaction and have made this change in the manuscript (lines 179-181).

Comments 18: Lines 147-148: Positive effects of endophytic Alternaria are noted; however, the authors must clearly distinguish between strain-specific effects and general genus-level conclusions.

Response 18: Of course, you're absolutely right. The current wording could create the false impression that the positive effects are characteristic of the entire Alternaria genus, rather than specific strains. Therefore, we've amended the text to provide a more accurate description (lines 184-186).

Comments 19: Lines 152-154: The sentence describing antimicrobial compounds from A. alternata is confusing grammatically. Please rephrase for clarity and specify whether these are endophytic or pathogenic isolates.

Response 19: You are absolutely right. Thank you for catching this inaccuracy. We amend lines 190-193 to state that A. alternata produces these metabolites.

Comments 20: Lines 165-166: The transition from endophytic/saprophytic lifestyles to parasitism needed mechanistic explanation.

Response 20: We have expanded the relevant sentence to clarify that the lifestyle switch is mediated by changes in fungal gene expression and the upregulation of specific virulence factors, thereby providing the requested mechanistic context. (Lines 205-209).

Comments 21: Lines 171-172: Please rephrase the statement that sexual stages “have not been observed” as “have rarely been observed or are unknown”.

Response 21: Thank you for this important and accurate comment. Your edit truly improves the wording, making it more scientifically correct. (Lines 213-215).

Comments 22: Lines 178-181: The formation of chlamydospores and sclerotia need species-specific evidence for accuracy, as not all Alternaria species form these structures.

Response 22: Thanks to the reviewer for the important clarification. The text has been corrected to indicate that the ability to form chlamydospores and sclerotia is characteristic of only some Alternaria species. (Lines 224-225).

Comments 23: Lines 222-230: The detailed toxin descriptions need some clarification and addition of the data with host-specific toxins and non-host-specific toxins.

Response 23: We fully agree with your suggestion. In response to your recommendation, we have prepared a schematic figure that clearly illustrates the mechanisms of action of the key host-specific toxins (AAL, ACR, AF, AM) at the subcellular level (Figure 2. Schematic model of Alternaria toxins action on plant cellular targets).

Comments 24: Lines 234-235: The claim that different species cause “similar infection patterns” should be revised by differences in host specificity and symptom expression.

Response 24: We agree that the original statement was an overgeneralization. We have revised the sentence to acknowledge the shared necrotrophic strategy while explicitly highlighting the key differences in host specificity and symptom expression, as suggested. (Lines 281-283).

Comments 25: Lines 242-244: Yield loss percentages should be contextualized geographically or temporally to avoid appearing universally applicable.

Response 25: Thank you for the important clarification. Indeed, the percentages of crop losses reported are not universally constant, but depend on many factors. We've made the change to clarify the context, clarifying that they refer to losses recorded during disease outbreaks under conditions favorable for their development. This avoids the assumption that they are universally applicable. (Lines 290-293).

Round 2

Reviewer 2 Report

The authors have addressed all my comments and concerns. I have no further comments.

Reviewer 3 Report

I have read the revised version, so far, I can see, it has been significantly improved and the author have properly addressed all concerns. I have not further comment.