Rare Earth Elements Distribution and Bacteriome to Assess and Characterize the Soil Landscapes of Old Olive Orchards

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

Dear authors,

your manuscript is original and useful to study ecosystems, especially of agricultural purposes.The study of soil metagenome provides an opportunity to move to a new systemic level of soil ecosystems biodiversity research. Since the structure of soil microbiome reflects the specificity of soil and plant community, it becomes possible to determine the agroecological status of soils based on metagenomic analysis data.

It is desirable the authors to more clearly spell out the use of the new indicators to characterize EVOO soils in Conclusion, to indicate the most important ones.

The manuscript sounds well, is recommended for publication.

Comments on the Quality of English Language

English language of the manuscript is fluent and accurate.

Author Response

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Reviewer 2 Report

Comments and Suggestions for Authors

 

Overall, the work is interesting, relevant and innovative. The authors describe in the introduction the effects of soil components on microbial communities or microbiota. That the soil microbiome and geomorphological characteristics are closely related is no mysterious or any innovation, but bringing specific components forward is very welcome. However, only bacteria are considered in the microorganism studies. They play an important role in soil formation, not to mention its quality parameters, including stability and fertility. When linking REEs with microorganisms and plant communities, the danger they pose must be kept in mind, so their negative effects should also be analyzed when linking them to agrochemical and microbiological soil indicators. Some review papers have investigated the hazards of REEs to human health based on research of REE toxicity both to humans and generally to several biota (Cassee et al., 2011; Pagano et al., 2015; Rim, 2016; Gwenzi et al., 2018; Brouziotis et al., 2022: https://doi.org/10.3389/fenvs.2022.948041). Therefore, it is necessary to assess the condition of the above-ground vegetation (olive groves) in parallel.

Another very important component of the soil microbiome, which characterizes and determines its quality and productivity, is the community of fungi. In this case, fungi may be even more important than bacteria, since with some of them, olive trees form mycorrhizal relationships that determine their long-term survival and prosperity. Therefore, their analysis in this case is no less important than that of bacteria.

Therefore, the main disadvantage of this work, which must be eliminated, is the assessment of the negative effects of REE and the linking of the NGS analysis of fungal communities to the problem under consideration. Perhaps in this case it would be more useful to perform Shotgun metagenomic sequencing instead of NGS. In order to describe the site more comprehensively, as indicated in the title, it is necessary to assess the condition of the vegetation cover. Therefore is recommended to assess the status of the above-ground vegetation and relate it to the soil parameters analyzed.

The references in this manuscript are relevant and pertinent to this study, but the citation on soil fungi is missing.

Also, the authors should rethink and reformulate the general aim of the research, and at the same time clarify the conclusions.

Authors should improve and resubmit the manuscript.

Author Response

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Reviewer 3 Report

Comments and Suggestions for Authors

Dear editor,

 I have carefully reviewed the manuscript entitled "Coupling rare earth elements distribution and bacteriome of centenary olive tree cropped soils to more comprehensively characterize a territory". In my opinion, the paper is interesting; however, it requires substantial improvements for the manuscript to be in an appropriate form for publication in Diversity. I am providing the following suggestions that could contribute to enhancing the work.

 

Abstract

Delve into the justification of the study.

 

Introduction

Please specify how soil mineralogy influences the microbial community.

 

Delve deeper into the justification for the study and the specific problem it aims to address through this type of research. As it stands, the explanation is not clear.

 

Materials and methods

 

Include the agronomic management practices in the sampled soils.

 

Please have the authors justify why they consider only three soil samples to be representative and sufficient to diagnose how REEs influence the microbial community structure, given that soil is a highly heterogeneous resource and can exhibit changes even within a meter's distance between sampling points.

 

Discussion

How can the authors attribute the influence of REEs on the composition of the soil microbial community without considering agronomic management practices in the olive groves or the soil organic matter content, which is one of the main indicators of soil health and a vital substrate for the soil microbial community? Please discuss and explain this in detail.

 

Conclusions

 Please indicate the practical implications of this study for olive producers.

Author Response

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Reviewer 4 Report

Comments and Suggestions for Authors

The manuscript by Roccotelli et al has been reviewed. The manuscript presents an interesting layout aiming to assess the relationships between rare earth elements and associated microbial community. Most of my concerns are positive however, it needs necessary revision before its processed further. 

Title: The current title is misleading and complex, should be simplified

Abstract: should be the accumulation of both quantitative and qualitative results. 

abstract line 5, replace studing with studying, check other places too.  abstract: a brief description of methodological intervention is needed before results summary. Introduction: While, the manuscript is of interest summarizing important data, the rationale flow of information and building a story to tell study importance is lacking in the introduction section. I suggest linking the REEs and their relations with microbial community to build a study problem and effectively highlight the study novelty.  I appreciate manuscripts with added study gap statements and clearly presenting study objectives in bullette points.  M&M: Making sampling points clear in the Figure 1 is needed. How sampling points were selected and did the authors took into account geological formations and microclimatic conditions into account?  Results: currently the results are difficult to understand, maybe they can be arranged in a flow depending on sites and or REEs settings. The authors need to check it by themselves.  If possible a heatmap can better reflect the correlation among sites and relative abundances.  Discussion: Discussion section can be more deeper by taking into account the differences of geology and climatic variables into account.   

Author Response

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Reviewer 5 Report

Comments and Suggestions for Authors

This manuscript integrated findings on soil bacteriome composition, REE distribution, and environmental factors, providing readers with a deeper understanding of the implications of this approach as an effective ecological indicator.

General suggestions,

1.       The acknowledgment of soil bacteriome complexity and the necessity for a multidisciplinary approach is well-founded. However, to strengthen this point scientifically, consider discussing specific methodologies or interdisciplinary frameworks that have been successfully applied in similar studies. For instance, integrating metagenomics with geochemical analyses or machine learning algorithms for community profiling can provide a more robust characterization of bacterial communities in relation to REE distributions.

2.       The assertion that REEs influence microbial metabolic functions aligns with emerging research. To bolster this statement scientifically, it would be beneficial to include mechanistic insights or experimental evidence from studies demonstrating how specific REEs interact with microbial enzymes or metabolic pathways. This could include references to studies investigating the bioavailability of REEs in soil matrices and their impact on microbial community structure and function.

3.       The findings regarding REE distribution in relation to soil types (arenaceous, pyroclastic, shale, limestone) are intriguing. To enhance scientific rigor, consider discussing the geochemical processes that govern REE mobility in these soil types. This might involve references to studies elucidating how soil pH, mineralogy, and organic matter content influence REE speciation and bioavailability. Additionally, provide context on the variability of REE concentrations in different global soil types to broaden the applicability of your findings.

4.       The dominance of Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Verrucomicrobia, and Firmicutes in the bacteriome is consistent with current literature on soil microbiota. To strengthen scientific validity, elaborate on the ecological roles of these phyla in soil ecosystems, particularly in relation to their tolerance to environmental stresses and their contributions to biogeochemical cycling. Discuss how their relative abundance might reflect adaptive strategies to local environmental conditions influenced by REE gradients.

Specific suggestions,

1.       The entire paper lacks line numbers, which complicates the revision process.

2.       Regarding the title, what is the rationale behind characterizing a territory? I am unclear about the aim and significance of this research.

3.       In the abstract, how was the dominance of this bacterium determined?

 

4.       The reference numbers throughout the paper are incorrect.

Author Response

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Reviewer 6 Report

Comments and Suggestions for Authors

I read this manuscript with considerable interest, because I have engaged in REEs research in microbiology, especially in activation of silent bacterial genes in actinomycetes, which may be highly relevant to the present work. I expect the integrated model based on REEs and bacteriome can be a way to characterize a territory.

Author Response

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Round 2

Reviewer 2 Report

Comments and Suggestions for Authors

The authors have completed and corrected the manuscript reasonably well and responded fully to comments. 

Reviewer 3 Report

Comments and Suggestions for Authors

Dear editor

I have carefully reviewed the corrected version of the manuscript titled “Coupling rare earth elements distribution and bacteriome of centenary olive tree cropped soils to more comprehensively characterize a territory”. I believe the manuscript has significantly improved; it is now clearer, and the justification for the study is more evident. The authors have incorporated my suggestions, for which I am grateful. In my opinion, the manuscript is now in an acceptable form for publication in Diversity.

Reviewer 4 Report

Comments and Suggestions for Authors

I am satisfied with the revision and I think manuscript is ready for publicatyion.