Ascomycetes versus Spent Mushroom Substrate in Mycoremediation of Dredged Sediments Contaminated by Total Petroleum Hydrocarbons: The Involvement of the Bacterial Metabolism

Round 1

Reviewer 1 Report

The study’s goal was to determine the best methodological approach for decontaminating dredged sediments contaminated by petroleum hydrocarbons between bioaugmentation with a strain of  Lambertella sp. and the co-composting with Spent Mushroom Substrate from Pleurotus ostreatus. The former has been confirmed as necessary in order to deplete total petroleum hydrocarbon. The effectiveness of the two methods was determined by comparing the decrease in TPH content, as well as the quantification of ergosterol, and humic and fulvic acids. The bacterial biodiversity involved in the degradation processes was studied by metabarcoding.

Overall, the manus is well organized and clear. I enjoyed reading it with pleasure, and results are consistent and well discussed. I have only reported a few minor comments and noted some minor English changes, even though English is not my mother tongue.

Comments for author File: Comments.pdf

Author Response

First of all thanks for all comments and suggestions that improved the quality of the manuscript.

All changes requested and suggested have been inserted and evidenced in yellow.

More in details:

Line 11: please remove (2964 ±99 mg TPH/kg d.w.) DONE

Line 12 add (SMS) after Substrate DONE

Line 15: please, change as follow: ‘Any total petroleum hydrocarbon (TPH) depletion..’ and use SMS instead of Spent Mushroom Substrate DONE

Lines 82 and 85: the reason why the two types of mesocosms were analysed after different intervals of time (30-60 and 18-28 days) is explained at lines 556-559. I suggest the authors to briefly explain here the reason of this methodological choice ACTUALLY WE DO NOT KNOW HOW TO CLEARLY EXPLAIN THE CONCEPT IN MATERIALS AND METHODS, SECTION THAT IS VERY SCHEMATIC. THE REASON WHY WE REALISED THAT THE LAMBERTELLA SP. BIOAUGMENTED MESOCOSMS WERE PERFORMING BETTER WAS THE ODOUR OF THE SEDIMENTS DURING THE TREATMENT AND THE RESULTS ON SMALL SAMPLES OF THE MATRIX. WE THINKS THAT EXPLAINING WHAT IS HAPPENED IN RESULTS IS MUCH MORE CLEAR

Line 124 Please, change as follow: ‘Humic acid, Fulvic acid, and Ergosterol in Soil Sample’ DONE

Line 145 Specify: Solid Phase Extraction (SPE) DONE

Line 164: How can you state that the granulometry was improved, based on data reported in Table 1? WE CHANGED THE PHRASE. WE THINK THAT THIS VERSION IS MUCH MORE CLEAR

Lines 196-197: Is this increase in the three indexes significative? YES THE DECREASE IN SIGNIFICATIVE AND IT IS ASSESSED/SHOWN IN THE CORRESPONDING FIGURE BY THE SMALL ASTERISKS

Line 218: Actinobacteria instead of Actonibacteria DONE

Lines 217 and 227 sp. not in italic DONE

Line 480: I do not see the second part of the sentence of the line 479. WE DO NOT SEE ANY INTERRUPTION BUT WE REALISED THAT THE LAYOUT THAT WE SEE IS DIFFERENT FROM THE LAYOUT OF THE REVIEWER (LINES NUMBERS ARE DIFFERENT) THUS IT IS NOT CLEAR TO US WHERE THE REVIEWER SEE THE INTERRUPTION. WE HOPE THAT IN THE NEW VERSION THE MISSING SENTENCE WILL DISAPPEAR

Line 603-604: please change ‘saprophytic fungal strain’ with ‘saprotrophic fungal strains’ DONE

Line 607: change leads with lead DONE

Line 610: change hydrocarburoclatics with hydrocarburoclastics DONE

Line 621: I suggest to change as: ‘in humic acids content’ DONE

Line 628: change have with has (‘has been isolated’) DONE

Line 630: Are you referring to bacteria in general, or the genus Orninthinimicrobium in particular ? TO ORNINTHINIMICROBIU, HOWEVER THE SENTENCE HAS BEEN CHANGED BECAUSE IT WAS NOT CLEAR

Line 631: change has with have (‘have been described’) DONE

Author Response File: Author Response.docx

Reviewer 2 Report

The review remark on “Ascomycetes versus spent mushroom substrate in mycoremediation of dredged sediments contaminated by total petroleum hydrocarbons: the involvement of the bacterial metabolism”. The manuscript is well written and organized. The data is well-presented and explained without ambiguity.  However, some of the basic comments worth mentioning regarding the manuscript are as follows:

Reviewer remarks:

• The text in most of the figures are little blurred and faint
• No mention of quartiles in the figures.
• Caption of Figures a and 2 are missing the details of quartile 2
• Fig 4: panel B resolution needs improvement
• Fig 6: resolution needs improvement
• In the discussion, the authors have used term ‘bacterial biodiversity’. A brief explanation about those bacterial species (other than Lambertella sp. MUT 5852) would be an interesting add-on.
• Grammatical and spelling errors in the entire manuscript
• Punctuation errors in the entire manuscript
• Abstract- Ln: 15- incorrect preposition use: ‘of incubation’, instead of ‘on incubation’
• Ln: 118- ‘ggpub version..’; unclear statement
• Ln: 130- spelling error: ‘tetracontane’, instead of ‘tertacontane’
• Ln 155- spelling error: ‘maintained’, instead of ‘mantained’
• Ln 518- spelling error: ‘In this context’, instead of ‘contest’
• Ln 575- incorrect preposition use: ‘dependent on’, instead of ‘dependent by’
• Ln 613: spelling error: ‘the’; instead of ‘tha’
• Difference in font colour in Abstract and Introduction
• References: No uniformity in font size

Author Response

First of all thanks for all comments and suggestions that improved the quality of the manuscript.

All changes requested and suggested have been inserted and evidenced in yellow.

More in details:

• The text in most of the figures are little blurred and faint

We think that it depends on the evidence that in the file sent to teviewers the figures are cut and pasted in a word file while all te figures have been prepared as jpg file at the highest resolution

 

• No mention of quartiles in the figures.

The legends of the corresponding figures have been rephrased

 

• Caption of Figures a and 2 are missing the details of quartile 2

• The legends of the corresponding figures have been rephrased

 

• Fig 4: panel B resolution needs improvement

See the answer at the first bullet point

 

• Fig 6: resolution needs improvement

See the answer at the first bullet point

 

• In the discussion, the authors have used term ‘bacterial biodiversity’. A brief explanation about those bacterial species (other than Lambertella sp. MUT 5852) would be an interesting add-on.

In the Discussion the term bacterial biodiversity was actually associated to the biodiversity indexes reported in numbers and graphs in results, thus the Chao1, the Hill_Shannon and the Hill_Simpson. These are indexes not necessarily associated to the description of a certain taxon. On the other hand, the bacterial genera that determined the changes of the biodiversity index values and were putatively involved in metabolic functions of interest have been discussed later on in the discussion. We are quite convinced that with thousands of information on taxa that derives from the metabarcoding it is necessary to focus in the discussion of the taxon that actually are associated to at least two focal points. In this case the biodiversity indexes and the putative function of the taxon involved

 

• Grammatical and spelling errors in the entire manuscript

The manuscript has been revised for error spelling

 

• Punctuation errors in the entire manuscript

And punctuation

 

• Abstract- Ln: 15- incorrect preposition use: ‘of incubation’, instead of ‘on incubation’

We think that of incubation is more appropriate for describing a time-inteval of incubation

 

• Ln: 118- ‘ggpub version..’; unclear statement

Corrected

 

• Ln: 130- spelling error: ‘tetracontane’, instead of ‘tertacontane’

Corrected

 

• Ln 155- spelling error: ‘maintained’, instead of ‘mantained’

Corrected

 

• Ln 518- spelling error: ‘In this context’, instead of ‘contest’

Corrected

 

• Ln 575- incorrect preposition use: ‘dependent on’, instead of ‘dependent by’

Corrected

• Ln 613: spelling error: ‘the’; instead of ‘tha’

Corrected

 

• Difference in font colour in Abstract and Introduction

Corrected

 

• References: No uniformity in font size

Corrected

 

Author Response File: Author Response.docx