Impacts of Cropping Systems on Glyphosate and Aminomethylphosphonic Acid Contents and Microbial Community in Field Crop Soils in Quebec (Canada)

Round 1

Reviewer 1 Report

Comments for author File: Comments.pdf

Minor revisions are required.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report

The manuscript is well-written, and the statistical methods are well-executed. Nonetheless, there is some confusion stemming from a lack of clarity in certain sections of the methods, particularly in distinguishing what was applied to specific microbial groups.

The authors have mentioned that the reference databases Greengenes 13.8, SILVA 138, and UNITE v8 were used for taxonomic identification, but they did not specify which one was used for which microbial group. I assume Greengenes was used for bacteria, UNITE for ITS fungi, and SILVA for 18S eukaryotic microbes.  If so, Greengenes isn’t a suitable database for bacterial taxonomy anymore because this database is too old and outdated (last updated more than 10 years ago!). The most suitable database for bacteria taxonomy in this case is also SILVA 138. In addition, details of the Sequence quality control should be specified, and a (supplementary) table with the total number of reads before and after processing should be provided.

The Downstream data analysis also needs better clarity. For example, the authors mention that “for soil prokaryotic, fungal and eukaryotic communities, the number of reads was normalized using the rarefy-even-depth function from the phyloseq R package.” (lines 237-238). It seems the three datasets were normalized altogether. In addition, it is not specified the cutoff. If that’s the case, there are concerns because each dataset, as we all know, is very different in size (number of reads). Each dataset should be normalized to the size of its smallest library.

A discussion on the limitations of the methods used for taxonomic identification of the three groups of microbes should also be provided. For example, because of variability within species in the ITS region, as well as occasional variability within the same genome, clustering of ITS sequences is necessary to achieve reliable resolution in mycobiome studies. As a result, some experts argue that the notion of amplicon sequence variants (ASVs) is not suitable.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Round 2

Reviewer 2 Report

The authors have addressed all my concernes and suggestions and the current version is suitable for publication. Just minor text editing still is necessary.

The authors have addressed all my concernes and suggestions and the current version is suitable for publication. Just minor text editing still is necessary.

Author Response

Thank you very much for your review and comments on our manuscript. We did another check of our manuscript to ensure that we corrected any English errors that we would see. Here is a list of our corrections:

Line 116               Delete the « T » before the word «Nine »

Line 132               A paragraph is inserted between Figure 2 and the text of the Legend of Fig 2. Hence, we changed the position of Figure 2 to fit with the text.

Line 158               Example of missing space between the value and its unit (40 cm)

Line 168               Correct 300rpm pour 300 rpm

Line 177               Delete the space between the value and its temperature unit 280°C and 300°C,

Lines 179-181    Delete the space between the value and its temperature unit in the sentence.

Line 200               Delete the space between the value and its temperature unit 375°C

Line 228               Correct for prokariotic and eukaryotic community

Lines 303, 304, 310         Insert a space between the value and its unit (Ex.: 5400 g.ha^-1)

 Line 319              Figure 3 Title of Y axis correct unit:  ug.g^-1 

Line 414-415      In section Materials & Methods Lines 240-241, the names of enzymes pathway are not in italic while, in the section Results, the same names are in italic in the text of lines 414-415 and 4234-424

Line 481               Insert a space between the value and its unit (1350 g.ha^-1)

Line 500               Insert a space between the value and its unit (Ex.: 5400 g.ha^-1)

Line 546               community

Line 564 Fig. 1    Correct the exponential values of units for ug.g^-1 and g.ha^-1 and insert a space between the value and its unit 0-20 cm and 20-40 cm