Changes in Soil Prokaryotic Diversity in Response to Land-Use Changes in Sub-Saharan Africa

Round 1

Reviewer 1 Report

The manuscript of “Changes in soil microbial diversity in response to land-use changes in sub-Saharan Africa” investigated/compared soil bacterial communities and soil basic characteristics changes under land-use management and natural systems in sub-Saharan Africa. Author showed soil bacterial biomass and soil total carbon significantly decreased after land-use, but bacterial diversity not. In addition, the authors compared and discussed some microbial groups of nitrifiers, Balneimona, Bacillus and Chloroflexi under land-use management compared with natural systems.

After examining the whole manuscript, I have the following issues to propose/discuss:

• Authors showed the relative abundance of nitrifiers was increased in the managed soils, which is interesting results, and might be related with fertilization. It will be interesting to provide some related analysis between soil nitrogen content and relative abundance of nitrifiers. Or provide some analysis based on functional prediction by PICRUSt (https://picrust.github.io/picrust/) to check whether the microbial functions related with nitrogen cycling changed under land-use managements.
• Title: as authors only focused on bacterial communities, “soil microbial diversity” can be changed to “soil bacterial diversity”.
• Line 142, please provide the bioinformatic analysis for raw sequencing data in Method section.
• For NMDS plots and RDA plots, it will be better to indicate site A, B and C separately.
• Please check the statistical analysis in whole manuscript, for example: Figure 1a, “the natural soils at all sites were significantly richer in the total carbon contents than the farm soils (p < 0.01) regardless of the sites (Figure 1a), especially at Site A and Site C” in line 179, how about the Site B, significant or not? It is not clearly from current figure annotation.

Author Response

Thank you for reviewing. We have uploaded the answers for the comments as a PDF. 

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments

Abstract

Line 26-28: I don't really understand the conclusion in the last sentence of the abstract. It does not give a broader view of the results obtained. In the abstract itself, the authors emphasize changes in the diversity and structure of microorganism communities. and the conclusion points to changes in the structure as a result of farming activity.

 

Introduction

Although the third paragraph deals with the effects of soil parameters on bacteria, the papers cited do not specify the direction of these changes, stating only that such changes were recorded.

The introduction is largely devoted to the diversity of microorganisms. It would be useful to formulate a separate hypothesis relating to the community structure of microorganisms and to describe this subject in the introduction.

 

Discussion

The main purpose of this study is to investigate the effect of soil use on bacterial communities, so the discussion needs to be organized. The use of anowa analyses was intended to indicate trends in observed community changes. Therefore, the authors should first focus on the main factors. The influence of sites on the results was also insufficiently addressed. In particular site A stands out very strongly from the rest of the studied sites. In particular, site A stands out very strongly from the other sites studied, indicating how much soil factors influence the data obtained.

In the second part of the discussion, the authors focus on the most important OTUs that change according to land use, which is not entirely consistent with the heatmap (Fig. 4). Are selected, exemplary OTUs included in the Figure?

 

Figure 1 and 2.

There is no information whether the authors used the default settings or another method to compare the variants when using the emmeans package and whether P value was adjusted. In the figures, do the vertical dashes indicate SD or SE.

 

Figure 3 and 5

The figures use the legend from Figs. 1 and 2. It would be better to write in the description that the dark symbols represent natural and the open symbols represent farm land-use.

Author Response

Thank you for reviewing. We have uploaded the answers for the comments as a PDF. 

Author Response File: Author Response.pdf