Innovative Culturomic Approaches and Predictive Functional Metagenomic Analysis: The Isolation of Hydrocarbonoclastic Bacteria with Plant Growth Promoting Capacity

Round 1

Reviewer 1 Report

Remediation of soils contaminated by oil products is often needed. The remediation can happen if there are microorganisms that have the ability to degrade oil chemicals. There is also a need for microorganisms that stimulates the formation of vegetation.  

In this work, both these aspects have been studied. The soil used for the isolation of microorganisms having the ability to degrade oil, bitumen, and similar compounds have been selected well as well as their identification.

Line 158 you refer to 31 carbon sources. Please, show these!

Line 190.  Something is lacking from the last sentence of this paragraph.

Table 1: what was the origin of humic acid?

The Tables 2, 3, and 4 contain the same data as Table 5. Please, omit Tables 2, 3, and  4 but you can add to the present Table (will be 2) extra heading rows for specialist bacteria, gram-positive bacteria, and bacteria isolated on Eco-plates and add the carbon sources to column 1.

In Table 3 one bacterium is B. thuringiensis. Correct!   

In Table 4 there must be pyruvic (acid).  Correct!

Correct also Actinomycetales!  

The figures 1-11 contain more and less interesting knowledge. More interesting is to know which organism types (in this case amplicon sequence variants) had most often the enzymatic activity presented. Less interesting are those which have only seldom the enzyme activities presented.  In addition, the fonts for the names are now too small. You could solve this problem by presenting only those amplicon sequence variants which include frequencies more than 1 % and inform that the rest x variants present together with the rest y %. Thus, you could increase the font.

Table 2 which dye do you mean? Is it formazan? Which of them and what is the end product after the loss of color?

correct tryptophan!

Arthrobacter line 442.

Correct the italics to those scientific names where it is lacking.

Many of the enzymes, which you study are oxygenase enzymes. Would it mean that their function is to join oxygen to the reactants? If yes, would it mean that the soil which should be remediated should be rich with oxygen – as is possible in the soil after tilling or other soil treatment?  

Author Response

Please see the attachment

 

Author Response File: Author Response.docx

Reviewer 2 Report

Innovative culturomic approaches were adopted to isolate hydrocarburoclastic bacteria capable to degrade diesel oil, bitumen and a selection of polycyclic aromatic hydrocarbons (PAH), from a soil historically contaminated by total petroleum hydrocarbons. In parallel, bacterial community metabarcoding and predictive functional metagenomic analysis was adopted to confirm the potentiality of the isolates in term of functional representativeness in the microbial community of interest. The article contains a lot of work but was not well-organized. Major revisions are required.

 

Major comment

Did the authors evaluate the ability of microbiota in contaminated soil to degrade diesel oil, bitumen and/or PAH. The ability of individual bacteria to degrade does not necessarily mean that they will play the same role as a whole community. I think it is necessary to evaluate the degradation ability and metabolic diversity of the soil microbiota for subsequent discussion.

 

Minor comments

Line 17-19 Here, the authors pointed out that species of Pseudomonas, Arthrobacter, Achromobacter, Bacillus, Lysinibacillus, Microbacterium sps all can utilize diesel oil, bitumen and/or PAH as sole carbon sources. However, in the Results section, there are only three species of bacteria (Table 2). Please check whether there is a problem with the expression.

Line 37-38 Check the quotation.

Line 147-149 Should explain why the pollutant concentrations were selected.

Table 1 “H₂0” should be “H₂O”.

Table 2, 3, and 4 can be combined into one table. Similarly, these results should also be discussed together.

Figure 2, 3, 4, 5, 6, 7, 8, 9, and 10 should also be merged together.

The genus of the isolated strain can be marked in Figure 1.

 

Author Response

Please see the attachment

Author Response File: Author Response.docx

Reviewer 3 Report

The study profiled the bacterial community in hydrocarburoclastic contaminated soil and also isolated some strains to verify their functions for degrading hydrocarburoclastic matters. The study was well performed and the manuscript was also well written.
Genera names in Figures should be italic.

Author Response

Please see the attachment

Author Response File: Author Response.docx

Round 2

Reviewer 1 Report

Still, in line 166 add space after ; (end of the line)!

In references omit [ and ] in each reference!  

Author Response

Still, in line 166 add space after ; (end of the line)!

In references omit [ and ] in each reference!  

Thanks, both errors have been corrected

Reviewer 2 Report

The author has made sufficient modifications.

Author Response

Thanks for your second round of revision