Geodiversity as a Driver of Soil Microbial Community Diversity and Adaptation in a Mediterranean Landscape

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

Authors should improve Materials and methods section:

There is no precise information on the soil sampling procedure, sample transport conditions, which soil fraction was analyzed (depth, whether within the rhizosphere?), or how the soil samples were prepared before genomic DNA isolation?

 

Comments on the Quality of English Language

Please improve the English for instance:  instead trees for hectares - Should be per hectare

Author Response

Thank you very much for taking the time to review this manuscript and useful comments and suggestions. We took into account all remarks as far as possible. The changes made with respect to the original manuscript are indicated in red colour in the new submission. The changes made are indicated below.

Comments 1: Authors should improve Materials and methods section: There is no precise information on the soil sampling procedure, sample transport conditions, which soil fraction was analyzed (depth, whether within the rhizosphere?), or how the soil samples were prepared before genomic DNA isolation?

Response 1: L129-132; L211-213 Thank you for pointing this out. We agree with this comment. Therefore, we have improved the manuscript in the Material and Method sections.

Response to Comments on the Quality of English Language

Point 1: Please improve the English for instance:  instead trees for hectares - Should be per hectare

Response 1:  Agree. We have, accordingly, done 

Reviewer 2 Report

Comments and Suggestions for Authors

It is critical to assess the effect of topographic characteristics and soil geochemistry on the spatial distribution of three Actinobacteria genera. Based on field investigation data, the possibility of highlighting some actinobacteria as biomarkers was discussed based on the hydro-geomorphometric factors of the landscape and the geochemical features of soils. The changes in microbial communities can provide valuable information for ecological restoration in the context of long-term climate change. However, the manuscript still needs further improvement in the following aspects:

1. Increase the literature review and background introduction on the specific impacts of climate change on microbial communities.

2. More in-depth discussion of the model optimization and parameter adjustment process, especially how to solve the overfitting problem.

3. Strengthen the discussion of individual results (e.g., Rubrobacter's abnormal behavior in certain soil types) to improve the depth and breadth of conclusions.

4. What was the rationale for selecting actinomyces as biomarkers for the analysis of soil microbial communities in the Mediterranean environment?

5. What specific environmental and geochemical factors were considered in the study, and how were these factors selected as relevant predictors of microbial community composition?

Other modifications:

1. The introduction includes some relevant references. In particular, several studies on Actinobacteria and its adaptability in different environments have been cited (such as Volcanic environments, Antarctic regions, and the Atacama desert, etc.). However, the literature on the effects of climate change and land use change on microbial communities is relatively brief. Further references to specific impacts of climate change on microbiomes, particularly in the Mediterranean region, would add to the context.

2. It is still possible to further strengthen the discussion of the results, especially to explain more unexpected results (such as the low abundance of Rubrobacter in volcanic soils).

 

3. Although the results support the conclusions, they need to be validated on a wider geographical scale, especially in the Mediterranean region under different climatic conditions, to ensure the generalizability of the conclusions.

Author Response

Thank you very much for taking the time to review this manuscript and useful comments and suggestions. We took into account all remarks as far as possible. The changes made with respect to the original manuscript are indicated in red colour in the new submission. The changes made are indicated below.

Comment 1 - Increase the literature review and background introduction on the specific impacts of climate change on microbial communities.

Response 1 - L 63-78 We thank the reviewer for this suggestion. Following your suggestion we added a bibliography relating to the impacts of climate change on microbial communities.

Comment 2 - More in-depth discussion of the model optimization and parameter adjustment process, especially how to solve the overfitting problem.

Response 2 - L 347-366  We appreciate this suggestion and have added a few sentences about the model procedure and its performance.

Comment 3 - Strengthen the discussion of individual results (e.g., Rubrobacter's abnormal behavior in certain soil types) to improve the depth and breadth of conclusions.

Response 3 - L 607-615; 620-632 We thanks for this suggestion. We have improved the discussion section.

Comment 4 - What was the rationale for selecting actinomyces as biomarkers for the analysis of soil microbial communities in the Mediterranean environment?

Response 4 - L519-523 We explained in more detail in the discussion section why we selected actinobacteria as biomarker for the investigate environment.

Comment 5 - What specific environmental and geochemical factors were considered in the study, and how were these factors selected as relevant predictors of microbial community composition?

Response 5 - As illustrated in paragraph 2.5. Geoinformatic analyses we considered geomorphometric, remote sensing (NVI and NDWI) and geochemical parameters, in particular significant ratios of rare earth elements, namely La/Sm and La/Yb. These relationships, in a previous work by the authors, were found to be statistically important in terms of predictability of the spatial variability of the different lithologies of the investigated basin. The relative importance of hydro-geomorphometric and geochemical factors on soil Actinobacteria diversity was determined using machine learning techniques, in particular, random forest for individual genera and multiple regression splines for biomarkers. This information is reported in the results section.

Other modifications:

Comment 1 - The introduction includes some relevant references. In particular, several studies on Actinobacteria and its adaptability in different environments have been cited (such as Volcanic environments, Antarctic regions, and the Atacama desert, etc.). However, the literature on the effects of climate change and land use change on microbial communities is relatively brief. Further references to specific impacts of climate change on microbiomes, particularly in the Mediterranean region, would add to the context.

Response 1 -  We thank the reviewer for this suggestion and agree with him on the need for systematic studies on the impact of climate on microbial composition in the Mediterranean environment. As far as the authors are aware, such studies (with applied research) in the Mediterranean environment are lacking or in particular concern pathogens. The idea of ​​this research was to evaluate the potential of machine learning techniques for the spatial prediction of soil microorganisms, based on: the assumption that a core microbiome signature exists as an indicator of soil status; there are biomarkers of this core microbiome that act as sentinels of the healt state of the soil; that the core microbiome, with its biomarkers, has coevolved together with the physical-chemical aspects of the territory. In a future step of this research the authors would focus on the study  of the climate parameter effects on the composition and distribution of biomarkers.

Comment  2 - It is still possible to further strengthen the discussion of the results, especially to explain more unexpected results (such as the low abundance of Rubrobacter in volcanic soils).

Response 2 - L 607-615 Thanks for this suggestion. What was requested has been implemented.

Comment  3 - Although the results support the conclusions, they need to be validated on a wider geographical scale, especially in the Mediterranean region under different climatic conditions, to ensure the generalizability of the conclusions.

Response 3 - L644-647 We certainly agree, as mentioned before, we want to evaluate in a future step of the research, the effect of some climatic parameters on the spatial distribution of the identified biomarkers and perhaps identify new ones for other Mediterranean areas. 

 

Reviewer 3 Report

Comments and Suggestions for Authors

Land-3455771

Geodiversity as a driver of the soil microbial community diversity and adaptation in a Mediterranean landscape

Pelacani et al. present a detailed analysis of prominent soil microbes in the soils of olive groves in a region of Italy, along with geochemical and geomorphological analyses. I found this manuscript to be written quite clearly, with a few scattered errors or points of confusion; these are detailed below.

Abstract

I suggest you change the list of microbial genera to something like …” spatial distribution models of the genera, Rubrobacter, Gaiella, and Microlunatus and the Fungi to Bacteria ratio in a machine learning-based (ML) framework.” There is a singular/plural grammar mistake in the existing Abstract (LN 16, “a … models”), and the word “genera” is the plural of “genus”, thus it reads very strangely to see individual genus names described as one genera.

This also applies to other sections, such as LN378 and LN381 where “genera” is used when it seems “genus” is a better fit.

1. Introduction

 

LN 40. The plural of phylum is phyla

2. Materials and Methods

I do not see lithium among the listed analytes (LN119-137) but the Abstract (LN20) states that this element is related to Rubrobacter. Should the word in the Abstract change to lithology or a similar term?

3. Results

LN407 – the first appearance of Li, so perhaps I am wrong about that part of the Abstract? But I still do not see any mention of “lithophile” elements in the Materials and Methods section. How were these elements measured?

Also on LN407, the name for Ni is Nickel.

Comments on the Quality of English Language

English, as we all know too well, often has more exceptions than rule-following examples for any grammatical rule. Native English speakers often have trouble with non-standard plurals such as genus (singular) and genera (plural), or phylum (singular) and phyla (plural). Correcting these errors in this manuscript would improve the clarity overall. There are also scattered trivial errors, such as the occasional missing article (a, an, or the) but these do not seriously affect clarity.

Author Response

Thank you very much for taking the time to review this manuscript and useful comments and suggestions. We took into account all remarks as far as possible. The changes made with respect to the original manuscript are indicated in red colour in the new submission. The changes made are indicated below.

Comment 1: Abstract: I suggest you change the list of microbial genera to something like …” spatial distribution models of the genera, Rubrobacter, Gaiella, and Microlunatus and the Fungi to Bacteria ratio in a machine learning-based (ML) framework.” There is a singular/plural grammar mistake in the existing Abstract (LN 16, “a … models”), and the word “genera” is the plural of “genus”, thus it reads very strangely to see individual genus names described as one genera. This also applies to other sections, such as LN378 and LN381 where “genera” is used when it seems “genus” is a better fit.

Response 1: We thank the reviewer and agree with the comment. This was done accordingly to the comment.

 

Comment 2: 1.Introduction: LN 40. The plural of phylum is phyla

Response 2: We thank the reviewer and agree with the comment. This was done accordingly to the comment.

 

Comment 3: Material and Methods: I do not see lithium among the listed analytes (LN119-137) but the Abstract (LN20) states that this element is related to Rubrobacter. Should the word in the Abstract change to lithology or a similar term?

Response 3: L141 We thank the reviewer, we have included the lithium in the Materials and Methods section.

 

Comment 4:  Results LN407 – the first appearance of Li, so perhaps I am wrong about that part of the Abstract? But I still do not see any mention of “lithophile” elements in the Materials and Methods section. How were these elements measured? Also on LN407, the name for Ni is Nickel.

Response 4: L139-L153 We thank the reviewer, as mentioned in the previous comment we have inserted the Li element in materials and methods section. The section "2.1. Soil sampling strategy and geochemical analyses" describes the analytical method.

Response to Comments on the Quality of English Language

Point 1: English, as we all know too well, often has more exceptions than rule-following examples for any grammatical rule. Native English speakers often have trouble with non-standard plurals such as genus (singular) and genera (plural), or phylum (singular) and phyla (plural). Correcting these errors in this manuscript would improve the clarity overall. There are also scattered trivial errors, such as the occasional missing article (a, an, or the) but these do not seriously affect clarity.

Response 1:  Agree. We sincerely thanks and accordingly we corrected the errors.