The Impact of Different Agricultural Practices on Nematode Biodiversity on Tomato- and Lettuce-Growing Periods Across Two Consecutive Years

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

General comments
I found this manuscript to be both original and well-written, offering novel insights that are highly relevant for nematogists world-wide. The topic is timely, and the authors demonstrate a good knowledge of the literature. However, there are several points that raise concerns and require clarification before the manuscript can be considered for acceptance. I outline these issues in the specific comments below, and I kindly invite the authors to address them in a revised version of the paper. Therefore, my final Recommendation is moderate revisions

Specific comments

1. Statistical analysis:
   As already noted in the annotated PDF, the authors should provide more detailed information regarding the statistical analyses, both in the Materials and Methods section and when reporting the Results. For instance, at present, I cannot understand the number of factors analysed for each faunal parameter (e.g. one way, two-way or three-ways). This weakens the interpretation of the findings.
2. Terminology – "free-living nematodes":
   Throughout the manuscript, the authors refer to “free-living nematodes”, particularly in the context of community analyses. However, the community structure described in the study appears to include taxa such as Tylenchidae and Meloidogynidae, which are not free-living. Therefore, to avoid confusion and improve taxonomic and ecological accuracy, I suggest the authors use the term “soil nematode community structure” and delete the term free-living. I think that this change can better reflects the actual composition of the sampled communities.
3. Conclusions:
   Finally, the conclusions section should be expanded. At present, it is rather concise and does not fully highlight the broader significance and implications of the results. I encourage the authors to provide a more comprehensive synthesis of their findings and to discuss potential applications and future research directions.

Comments for author File: Comments.pdf

Author Response

General comments

I found this manuscript to be both original and well-written, offering novel insights that are highly relevant for nematogists world-wide. The topic is timely, and the authors demonstrate a good knowledge of the literature. However, there are several points that raise concerns and require clarification before the manuscript can be considered for acceptance. I outline these issues in the specific comments below, and I kindly invite the authors to address them in a revised version of the paper. Therefore, my final Recommendation is moderate revisions

Thank you, we greatly appreciate your help in revising this manuscript. We very much hope that the revised manuscript now meets your expectations.

 

Specific comments

 

Statistical analysis:

As already noted in the annotated PDF, the authors should provide more detailed information regarding the statistical analyses, both in the Materials and Methods section and when reporting the Results. For instance, at present, I cannot understand the number of factors analysed for each faunal parameter (e.g. one way, two-way or three-ways). This weakens the interpretation of the findings.

Done. As requested, the Material and Methods section “2.7 Statistical analysis” is implemented

Terminology – "free-living nematodes":

Throughout the manuscript, the authors refer to “free-living nematodes”, particularly in the context of community analyses. However, the community structure described in the study appears to include taxa such as Tylenchidae and Meloidogynidae, which are not free-living. Therefore, to avoid confusion and improve taxonomic and ecological accuracy, I suggest the authors use the term “soil nematode community structure” and delete the term free-living. I think that this change can better reflects the actual composition of the sampled communities.

Done. We have integrated the materials and methods from Section “2.3, Soil Nematode Community Analysis”, and reorganized the results by merging Sections 3.1 and 3.2 (now named as “3.1. Soil Nematode Community Structure and Dynamics”).

Conclusions:

Finally, the conclusions section should be expanded. At present, it is rather concise and does not fully highlight the broader significance and implications of the results. I encourage the authors to provide a more comprehensive synthesis of their findings and to discuss potential applications and future research directions.

Conclusion section is changed according to the requests of reviewer 1 and 2.

Reviewer 2 Report

Comments and Suggestions for Authors

There is a logical inconsistency in paragraph 35–38.

This paragraph lacks internal coherence. It begins by referring to species richness as an indicator of potential interactions within ecosystems, then shifts to describing soil complexity in biological, biochemical and chemical terms, before finally addressing methodological approaches to assessing nematode diversity over the past 30 years. The main message remains unclear: is it an argument for the importance of evaluating nematode diversity, a historical review of methodologies, or an emphasis on the complexity of soil as an environment? It is recommended that the paragraph's structure is clarified and a clear core idea formulated.

 

General information on tomato production (lines 39–46):

Although the data on the global importance of tomatoes, the area under cultivation and the average yield is relevant, it is currently presented in an unstructured way. These facts should be linked more explicitly to the study's central theme, which is the impact of plant-parasitic nematodes and agricultural practices on nematode biodiversity. This will prevent the impression that common knowledge is being cited without analytical integration.

 

Lack of clarity in paragraph structure (lines 47–56):
The paragraph starts by discussing the general effects of stunted plant growth on crop yield, then shifts to greenhouse-related aggravation, then to the synergistic effects of nematodes and phytopathogens, and ends with a brief overview of historical chemical control in Italy. This structure does not guide the reader toward a clear argument. The tone appears emotionally charged, creating a sense of threat rather than grounded scientific reasoning. It is recommended to either narrow the focus to a specific aspect (e.g., challenges of controlling PPNs) or clearly demonstrate how the mentioned elements contribute to a coherent argumentative structure. Scientific writing should appeal to logic and evidence, not impressions.

 

The paragraph (lines 58–85) has an overly broad thematic range.

The passage covers a wide range of topics, from EU regulatory policy and chemical control to microbiota, organic amendments, biofumigation and nematode population dynamics. However, the lack of a clear logical framework complicates comprehension. Generic phrases are frequently used (e.g. 'it is also worth mentioning', 'several studies have demonstrated', 'it is widely recognised'), as are key terms such as 'organic amendments', 'soil biodiversity', and 'PPNs', but these are not sufficiently elaborated on or given conceptual depth. Stylistically, the text appears overly smooth and formulaic, lacking the transitions and variation typical of individual academic expression. Many arguments are based on value-driven claims (e.g. promoting biodiversity and climate adaptation) without analytical substantiation. It is therefore recommended that the focus is narrowed, generalities are reduced, causal connections between statements are strengthened, and analytical substance is prioritised over rhetorical impact.

 

Language-related issues and signs of translation:

Several sections exhibit structural and lexical patterns that are characteristic of translated texts. These patterns often include logical inconsistencies that are likely to result from a literal translation that has not been adapted. It is recommended that a specialist in academic English be engaged for stylistic revision, paying particular attention to logical flow, terminological precision and natural language use.

 

Formulation of study aims (lines 86–91):

The use of the term 'agricultural strategies' suggests an evaluation of systemic or integrated soil management approaches. However, the experimental design only compares one organic amendment with chemical fumigation and a water-treated control. The scope of the study, as stated, does not fully align with the actual design. The authors should either revise the aims to match the scale of the experiment or provide an expanded rationale justifying the strategic relevance of the treatments being compared.

 

There is a lack of discussion of lettuce as an experimental crop.

Although the study includes two vegetable crops, tomato and lettuce, the literature review only addresses tomato. As lettuce is also a focus of the experiment, the introduction should at least briefly justify its inclusion in terms of its agronomic relevance, susceptibility to nematodes or interaction with soil practices. Including this information would make the manuscript more scientifically complete and consistent.

 

Plot labelling and clarity in the experimental design:

Identifying plots only by their area (e.g. 600 m² vs. 300 m²) makes comprehension difficult, particularly in the second year when some plots were subdivided. Assigning clear plot labels (e.g. Plot A, B, C or T1, T2, PE, CTR) and using these consistently throughout the text would improve clarity and avoid confusion.

 

The justification for using CCA is questionable:

Using Canonical Correspondence Analysis (CCA) to assess the relationship between nematode communities and environmental variables is questionable due to a lack of justification. CCA assumes unimodal (bell-shaped) responses of species to environmental gradients, but this may not apply to the experimental design. A preliminary analysis (e.g. detrended correspondence analysis, DCA) is usually employed to determine the length of the gradient and justify the choice of ordination method. No such information is provided in the manuscript. It is therefore recommended that this justification is included, or that Redundancy Analysis (RDA) is considered instead if species responses are linear.

 

Figure 3 shows the scaling of trophic group abundance.

Using a common y-axis scale across nematode trophic groups results in the underrepresentation of groups with lower abundance (e.g. omnivores and fungivores), which makes trends difficult to interpret. It is therefore recommended that the y-axis is rescaled for each trophic group, or that faceted plots with appropriate scaling are used, to enhance the clarity and accuracy of interpretation.

 

Table 1: Overuse of diversity indices:

Given that only seven genera of free-living nematodes were identified, applying nine diversity indices (e.g. Shannon, Simpson, Menhinick, Margalef and Berger–Parker) seems excessive. Many of these indices are highly correlated and reflect similar ecological properties, such as dominance or evenness. The use of this full set should either be justified or reduced to the most ecologically meaningful indices. Alternatively, the full table could be moved to the supplementary materials, as it contains detailed yet non-essential information.

 

Lines 360–361: Ambiguous sentence structure:

The sentence 'SI low values reported a weak capacity to regulate soil nematode populations' is unclear. The Soil Index (SI) cannot 'report' or 'regulate' anything as it is not an active agent. It is also unclear whether this regulatory capacity is supposed to be possessed by the agroecosystem, soil fauna, or specific management practices. This formulation needs to be revised to ensure clarity and scientific accuracy.

 

Conclusions:

The conclusion section is overly declarative and lacks a clear connection to the experimental results or research objectives. Statements such as 'the indicator value of nematodes has been proven' are too broad, particularly given the limited number of taxa and treatment types that were evaluated. It is therefore recommended that the conclusions are aligned more closely with the study’s specific findings.

 

Author Response

There is a logical inconsistency in paragraph 35–38.

 

This paragraph lacks internal coherence. It begins by referring to species richness as an indicator of potential interactions within ecosystems, then shifts to describing soil complexity in biological, biochemical and chemical terms, before finally addressing methodological approaches to assessing nematode diversity over the past 30 years. The main message remains unclear: is it an argument for the importance of evaluating nematode diversity, a historical review of methodologies, or an emphasis on the complexity of soil as an environment? It is recommended that the paragraph's structure is clarified and a clear core idea formulated.

 

As requested, the paragraph's structure is changed. Few concepts in this paragraph are now reassembled in the previous and the following paragraphs. We very much hope that the revised manuscript now meets your expectations.

 

General information on tomato production (lines 39–46):

 

Although the data on the global importance of tomatoes, the area under cultivation and the average yield is relevant, it is currently presented in an unstructured way. These facts should be linked more explicitly to the study's central theme, which is the impact of plant-parasitic nematodes and agricultural practices on nematode biodiversity. This will prevent the impression that common knowledge is being cited without analytical integration.

 

To highlight the focus on the impact of plant-parasitic nematodes and agricultural practices on nematode biodiversity, the following sentence is now added: “Generally, the management of PPNs have inevitable effects on the community of free-living nematodes and on their beneficial effects on the agricultural soils health. Current trends consider the conservation of indigenous soil nematode communities as a fundamental natural resource. In fact, the natural equilibrium in soil as well as co-evolution and co-speciation of soil taxa are basic processes involved in soil ecosystem services such as nematode regulation.”

 

Lack of clarity in paragraph structure (lines 47–56):

The paragraph starts by discussing the general effects of stunted plant growth on crop yield, then shifts to greenhouse-related aggravation, then to the synergistic effects of nematodes and phytopathogens, and ends with a brief overview of historical chemical control in Italy. This structure does not guide the reader toward a clear argument. The tone appears emotionally charged, creating a sense of threat rather than grounded scientific reasoning. It is recommended to either narrow the focus to a specific aspect (e.g.,) or clearly demonstrate how the mentioned elements contribute to a coherent argumentative structure. Scientific writing should appeal to logic and evidence, not impressions.

 

As requested, this paragraph is changed. In particular, to highlight the focus on challenges of controlling PPNs, the following sentence is now added: “In this context, optimizing the approaches used to manage plant pests and pathogens via environmentally friendly practices represents a current pressing challenge for sustainable agricultural systems.”

 

The paragraph (lines 58–85) has an overly broad thematic range.

 

The passage covers a wide range of topics, from EU regulatory policy and chemical control to microbiota, organic amendments, biofumigation and nematode population dynamics. However, the lack of a clear logical framework complicates comprehension. Generic phrases are frequently used (e.g. 'it is also worth mentioning', 'several studies have demonstrated', 'it is widely recognised'), as are key terms such as 'organic amendments', 'soil biodiversity', and 'PPNs', but these are not sufficiently elaborated on or given conceptual depth. Stylistically, the text appears overly smooth and formulaic, lacking the transitions and variation typical of individual academic expression. Many arguments are based on value-driven claims (e.g. promoting biodiversity and climate adaptation) without analytical substantiation. It is therefore recommended that the focus is narrowed, generalities are reduced, causal connections between statements are strengthened, and analytical substance is prioritised over rhetorical impact.

 

As requested, generalities are reduced and statements are better connected.

 

Language-related issues and signs of translation:

 

Several sections exhibit structural and lexical patterns that are characteristic of translated texts. These patterns often include logical inconsistencies that are likely to result from a literal translation that has not been adapted. It is recommended that a specialist in academic English be engaged for stylistic revision, paying particular attention to logical flow, terminological precision and natural language use.

 

English language review has been done.

 

Formulation of study aims (lines 86–91):

 

The use of the term 'agricultural strategies' suggests an evaluation of systemic or integrated soil management approaches. However, the experimental design only compares one organic amendment with chemical fumigation and a water-treated control. The scope of the study, as stated, does not fully align with the actual design. The authors should either revise the aims to match the scale of the experiment or provide an expanded rationale justifying the strategic relevance of the treatments being compared.

 

The scope of the study has been revised.

 

There is a lack of discussion of lettuce as an experimental crop.

 

Although the study includes two vegetable crops, tomato and lettuce, the literature review only addresses tomato. As lettuce is also a focus of the experiment, the introduction should at least briefly justify its inclusion in terms of its agronomic relevance, susceptibility to nematodes or interaction with soil practices. Including this information would make the manuscript more scientifically complete and consistent.

 

The literature review only addresses tomato because this is the main crop. Now this information has been included.

 

Plot labelling and clarity in the experimental design:

 

Identifying plots only by their area (e.g. 600 m² vs. 300 m²) makes comprehension difficult, particularly in the second year when some plots were subdivided. Assigning clear plot labels (e.g. Plot A, B, C or T1, T2, PE, CTR) and using these consistently throughout the text would improve clarity and avoid confusion.

 

As requested, plot labels have been assigned.

 

The justification for using CCA is questionable:

 

Using Canonical Correspondence Analysis (CCA) to assess the relationship between nematode communities and environmental variables is questionable due to a lack of justification. CCA assumes unimodal (bell-shaped) responses of species to environmental gradients, but this may not apply to the experimental design. A preliminary analysis (e.g. detrended correspondence analysis, DCA) is usually employed to determine the length of the gradient and justify the choice of ordination method. No such information is provided in the manuscript. It is therefore recommended that this justification is included, or that Redundancy Analysis (RDA) is considered instead if species responses are linear.

Done. We implemented the section “2.7 Statistical analysis” as requested. Moreover, we reported the DCA plot in the supplementary materials.

 

Figure 3 shows the scaling of trophic group abundance.

 

Using a common y-axis scale across nematode trophic groups results in the underrepresentation of groups with lower abundance (e.g. omnivores and fungivores), which makes trends difficult to interpret. It is therefore recommended that the y-axis is rescaled for each trophic group, or that faceted plots with appropriate scaling are used, to enhance the clarity and accuracy of interpretation.

Done. We rearranged figure 3 as recommended by reviewer.

 

Table 1: Overuse of diversity indices:

 

Given that only seven genera of free-living nematodes were identified, applying nine diversity indices (e.g. Shannon, Simpson, Menhinick, Margalef and Berger–Parker) seems excessive. Many of these indices are highly correlated and reflect similar ecological properties, such as dominance or evenness. The use of this full set should either be justified or reduced to the most ecologically meaningful indices. Alternatively, the full table could be moved to the supplementary materials, as it contains detailed yet non-essential information.

Done. We moved the figure to the supplementary materials.

 

Lines 360–361: Ambiguous sentence structure:

 

The sentence 'SI low values reported a weak capacity to regulate soil nematode populations' is unclear. The Soil Index (SI) cannot 'report' or 'regulate' anything as it is not an active agent. It is also unclear whether this regulatory capacity is supposed to be possessed by the agroecosystem, soil fauna, or specific management practices. This formulation needs to be revised to ensure clarity and scientific accuracy.

Done. We rearranged the sentence.

 

Conclusions:

 

The conclusion section is overly declarative and lacks a clear connection to the experimental results or research objectives. Statements such as 'the indicator value of nematodes has been proven' are too broad, particularly given the limited number of taxa and treatment types that were evaluated. It is therefore recommended that the conclusions are aligned more closely with the study’s specific findings.

Done. We rearranged the conclusion section as indicated by both reviewers.

Round 2

Reviewer 2 Report

Comments and Suggestions for Authors

All comments and suggestions have been thoroughly addressed by the authors. The revisions significantly improved the clarity, structure, and overall quality of the manuscript, bringing it in line with the standards of Diversity. I recommend the article for publication.