New Xerophilic Species of Penicillium from Soil

Round 1

Reviewer 1 Report

Title: New xerophilic species of Penicillium from soil

Authors: Ernesto Rodríguez-Andrade, Alberto M. Stchigel,and José F. Cano-Lira

Reference:  jof-1086932

Article type: Research

Reviewer Comments:

The manuscript jof-1086932, entitled “New xerophilic species of Penicillium from the soil”, describes four new Penicillium species isolated from soil samples collected from Mexico and Spain.

General comments:

1. English language can be improved in terms of writing style, spelling, and consistency, namely concerning:  

• • English language (please see the Specific comments section)
  • Paragraph length. Each paragraph should have a single topic.
  • Sentence length. Very long sentences, with several ideas incorporated, decrease text readability.
  • Several italics are missing (mainly in the Results section).
  •  

2. Scientific style can be improved in terms of writing style, spelling, and consistency, namely concerning the usage of non-scientific language

• • Line 11: please consider replacing “were unknown for the science.” with “were not previously described”
  • Lines 41: please consider replacing “species names”

Specific comments:

Line 12: please consider replacing “sheath, whereas Penicillium michoacanense” with “sheath. Penicillium michoacanense”

Line 14: please consider replacing “despite all them pertain” with “despite all of them pertain”

Line 26: please consider replacing “ Many of them are responsible for degradation of dead plants” with “ Many of these are responsible for the degradation of dead plants”

Line 28: please consider replacing “soil fertility [1]. The fungi grow” with “soil fertility [1]. Fungi grow”

Lines 33: please consider replacing “ecological niche. Many of these fungi” with “ecological niche. Also, many of these fungi”

Line 36: please consider replacing “erected by Link” with “firstly described by Link”

Line 41: please consider replacing “been described [4, 5]; however, this genus” with “been described [4, 5]. However, this genus”

Line 43: please consider replacing “are ubiquitous geographically” with “are geographically ubiquitous”

Line 44: please consider replacing “are extremophiles, and able” by “are extremophiles, being able”

Line 68: please consider replacing “were poured into 90 mm diam. disposable Petri dishes” with “were poured into Petri dishes”

Line 73: please consider replacing “were transferred to 5 cm diam. Petri dishes containing” with “were transferred to Petri dishes containing”

Line 84: please consider replacing “into 90 mm diam. disposable Petri dishes, being” by “into Petri dishes, being”

Lines 85-88: please consider replacing “Colony diameters were measured after 14 days at 5, 15, 25, 30, 37 and 40 ºC on CYA to determine the minimum, optimum and maximum temperature of growth.” with “To determine the minimum, optimum and maximum temperature of growth, colony diameters were measured after 14 days at 5, 15, 25, 30, 37 and 40 ºC on CYA .”

Line 96: please consider replacing “The DNA were” with “Extracted DNA was”

Line 167: please consider replacing “Because FMR 17424 forms a sister” with “Since FMR 17424 forms a sister”

Line 168: please consider replacing “, and because FMR 17381” with “, and since FMR 17381”

Line 380: please consider replacing “allowed us to recognize four new species of Penicillium from soil in Spain and” with “allowed us to firstly describe four new species of Penicillium isolated from soil samples collected from Spain and”

Line 381: please consider replacing “Mexico: Penicillium melanosporum,” with “Mexico: P. melanosporum,”

Lines 392: please consider replacing “P. cryptum because not forms” with “P. cryptum once it does not form”

Lines 397-398: please consider replacing “Due to our findings, results evident that more studies are needed” with “Our findings evidently reveal that more studies are needed”

Table 1: please consider presenting this table as a Supplementary Table.

Scientific comments:

Lines 54-58 / 58-62: please indicate the Köppen-Geiger climate classification.

Line 62: please clarify how were soil samples collected.

Lines 96-100: please describe the PCR conditions. Please consider inserting a table with the identification of the genomic regions sequenced, the PCR conditions, sequence length, and references.

Lines 100-101: please clarify if agarose or acrylamide gels were used.

Lines 101-102: please clarify about sequencing.

Author Response

General comments:

English language can be improved in terms of writing style, spelling, and consistency, namely concerning:

• English language (please see the Specific comments section). Done.
• Paragraph length. Each paragraph should have a single topic. Done.
• Sentence length. Very long sentences, with several ideas incorporated, decrease text readability. Done.
• Several italics are missing (mainly in the Results section). Done.
• Scientific style can be improved in terms of writing style, spelling, and consistency, namely concerning the usage of non-scientific Language. Done.
• Line 11: please consider replacing “were unknown for the science.” with “were not previously described”. Done.
• Lines 41: please consider replacing “species names”. Done.

Specific comments:

• Line 12: please consider replacing “sheath, whereas Penicillium michoacanense” with “sheath. Penicillium michoacanense”. Done.
• Line 14: please consider replacing “despite all them pertain” with “despite all of them pertain”. Done.
• Line 26: please consider replacing “ Many of them are responsible for degradation of dead plants” with “ Many of these are responsible for the degradation of dead plants”. Done.
• Line 28: please consider replacing “soil fertility [1]. The fungi grow” with “soil fertility [1]. Fungi grow”. Done.
• Lines 33: please consider replacing “ecological niche. Many of these fungi” with “ecological niche. Also, many of these fungi”. Done.
• Line 36: please consider replacing “erected by Link” with “firstly described by Link”. Done.
• Line 41: please consider replacing “been described [4, 5]; however, this genus” with “been described [4, 5]. However, this genus”. Done.
• Line 43: please consider replacing “are ubiquitous geographically” with “are geographically ubiquitous”. Done.
• Line 44: please consider replacing “are extremophiles, and able” by “are extremophiles, being able”. Done.
• Line 68: please consider replacing “were poured into 90 mm diam. disposable Petri dishes” with “were poured into Petri dishes”. Done.
• Line 73: please consider replacing “were transferred to 5 cm diam. Petri dishes containing” with “were transferred to Petri dishes containing”. Done.
• Line 84: please consider replacing “into 90 mm diam. disposable Petri dishes, being” by “into Petri dishes, being”. Done.
• Lines 85-88: please consider replacing “Colony diameters were measured after 14 days at 5, 15, 25, 30, 37 and 40 ºC on CYA to determine the minimum, optimum and maximum temperature of growth.” with “To determine the minimum, optimum and maximum temperature of growth, colony diameters were measured after 14 days at 5, 15, 25, 30, 37 and 40 ºC on CYA .”. Done.
• Line 96 (106): please consider replacing “The DNA were” with “Extracted DNA was”.Done.
• Line 167: please consider replacing “Because FMR 17424 forms a sister” with “Since FMR 17424 forms a sister”. Done.
• Line 168: please consider replacing “, and because FMR 17381” with “, and since FMR 17381”. Done.
• Line 380: please consider replacing “allowed us to recognize four new species of Penicillium from soil in Spain and” with “allowed us to firstly describe four new species of Penicillium isolated from soil samples collected from Spain and”. Done.
• Line 381: please consider replacing “Mexico: Penicillium melanosporum,” with “Mexico: P. melanosporum,”. Done.
• Lines 392: please consider replacing “P. cryptum because not forms” with “P. cryptum once it does not form”. Done.
• Lines 397-398: please consider replacing “Due to our findings, results evident that more studies are needed” with “Our findings evidently reveal that more studies are needed”. Done.
• Table 1: please consider presenting this table as a Supplementary Table. Done.

Scientific comments:

• Lines 54-58 / 58-62: please indicate the Köppen-Geiger climate classification. Done.
• Line 62: please clarify how were soil samples collected. Done.
• Lines 96-100: please describe the PCR conditions. Please consider inserting a table with the identification of the genomic regions sequenced, the PCR conditions, sequence length, and references. Done.
• Lines 100-101: please clarify if agarose or acrylamide gels were used. Done.
• Lines 101-102: please clarify about sequencing. Done.

Reviewer 2 Report

• An interesting and relevant topic is discussed.The aim and topic of the article are well defined and the results provide progress in current knowledge.New well-described species from such large and important genera will always have their justification
• The results are interpreted appropriately, even if some confusing informations are available (see in particular in the materials and methods section).The results are significant, well prepared and carefully documented
• The hole article is written in a suitable way.Data and analyzes are presented clearly.There are several questions (specifically, see the various sections).
• The study is correctly designed.The strictest technical standards have been developed for the analyzes used.The weakness of this work represents a missing of important analyzes of the discussed topic. Well defined species (especially species of the genera Penicillium) are, actually, supported by distinctive features, physiology, production of secondary metabolites (e. g. mycotoxins or toxic compounds) and ecology. Species of the genera Penicillium produce a large number of bioactive extrolites which some of them are unique for one species. Therefore some metabolites represent a very important diagnostic feature. This is a fact that is missing in this paper. I think the impact of the work for the secondary metabolites field would be significantly improved by also including if the tested species produce specific extrolites. The paper will be more stronger and will support new descriped species. Isolates of newly described species may be analyzed using HPLC (e.g).
• The data that are actually represented are sufficient to draw a conclusion, but in fact the authors observed only 4 own data (sequences), that analyzes was performed on a relatively small number of strains. Methods, tools, software and reagents are described in sufficient detail (see some other questions for good understanding).
• Conclusions observed by this work can be very interesting (I miss conclusions in the publication.)
• What is a pity, this type of the article needs some additional data and analyzes which are missing and because of this, the presented work is anfinished and unaccomplished. The aims and the scope are suitable for this journal
• Discussion can be improved
• There is an overall benefit to publishing this work, but with additional analyzes
• English language is appropiate and understandable
• I miss conclusions in the publication.

L53: type of soil? Horizont?

L64: the fungal isolation was done by Stchigel (1998). Which type of plating was used? The question is why you use PCA medium for the isolation? This kind of medium is used for long-term cultivation, for the isolation of microfungi (also from the soil) are used other types of medium depending on which species of microscopic fungi we would like to capture (Czapek, DRBC and many others). Why did you choose like a suitable medium is PCA?

L95: DNA extraction was done through the modified protocol of Marimon (2006). Maybe it will be very useful to complete information what kind of extraction kit was used. Regions of the following nuclear genes were amplified by PCR cycle with which parameters?

L132, 134, 135, 136: names of the species italic

L142: a concatenated dataset from 98 sequences....  Table 1. contains 99 of Penicillium species

L149: names of the sections italic

L154: names of the species italic

L175: section italic

L384, 395: xerophyly= xerophilic species or xerotolerant

Author Response

Comments and Suggestions for Authors

• An interesting and relevant topic is discussed. The aim and topic of the article are well defined and the results provide progress in current knowledge. New well-described species from such large and important genera will always have their justification.
• The results are interpreted appropriately, even if some confusing informations are available (see in particular in the materials and methods section). The results are significant, well prepared and carefully documented.
• The hole article is written in a suitable way. Data and analyzes are presented clearly. There are several questions (specifically, see the various sections).
• The study is correctly designed. The strictest technical standards have been developed for the analyzes used. The weakness of this work represents a missing of important analyzes of the discussed topic. Well defined species (especially species of the genera Penicillium) are, actually, supported by distinctive features, physiology, production of secondary metabolites (e. g. mycotoxins or toxic compounds) and ecology. Species of the genera Penicillium produce a large number of bioactive extrolites which some of them are unique for one species. Therefore some metabolites represent a very important diagnostic feature. This is a fact that is missing in this paper. I think the impact of the work for the secondary metabolites field would be significantly improved by also including if the tested species produce specific extrolites. The paper will be more stronger and will support new descriped species. Isolates of newly described species may be analyzed using HPLC (e.g). We agree with the reviewer that to determine the profile of secondary metabolites of our new species would enrich our article, just as it does in the case of many species of the genus Aspergillus. However, it is not in our power to make such determination at present. However, in order to introduce said information in future works, we are in talks with two international research groups to help us achieve this objective.
• The data that are actually represented are sufficient to draw a conclusion, but in fact the authors observed only 4 own data (sequences), that analyzes was performed on a relatively small number of strains. Methods, tools, software and reagents are described in sufficient detail (see some other questions for good understanding).
• Conclusions observed by this work can be very interesting (I miss conclusions in the publication). Included in the present version of the manuscript.
• What is a pity, this type of the article needs some additional data and analyzes which are missing and because of this, the presented work is an finished and unaccomplished. The aims and the scope are suitable for this journal.
• Discussion can be improved. Done.
• There is an overall benefit to publishing this work, but with additional analyzes.
• English language is appropiate and understandable.
• I miss conclusions in the publication. Included in the new version of the manuscript.
• L53: type of soil? Horizont?. Done.
• L64: the fungal isolation was done by Stchigel (1998). Which type of plating was used? Done. The question is why you use PCA medium for the isolation? This kind of medium is used for long-term cultivation, for the isolation of microfungi (also from the soil) are used other types of medium depending on which species of microscopic fungi we would like to capture (Czapek, DRBC and many others). Why did you choose like a suitable medium is PCA? Potato carrot agar (PCA) is a culture medium employed to recover soil ascomycetes, in which produce more or less easily sexual reproductive structures. In addition, PCA is translucent, allowing detecting such structures still immersed in said culture medium by using a stereoscopic microscope. This information can be easily found in several articles published by us during the last twenty years.
• L95: DNA extraction was done through the modified protocol of Marimon (2006). Maybe it will be very useful to complete information what kind of extraction kit was used. Done. Regions of the following nuclear genes were amplified by PCR cycle with which parameters? Done.
• L132, 134, 135, 136: names of the species italic. Done.
• L142: a concatenated dataset from 98 sequences.... Table 1. contains 99 of Penicillium species. Penicillium echinulonalgiovense was erased from Table 1.
• L149: names of the sections italic. Done.
• L154: names of the species italic. Done.
• L175: section italic. Done.
• L384, 395: xerophyly= xerophilic species or xerotolerant. Done (xerophilic).

Round 2

Reviewer 2 Report

The secondary metabolite profile is still missing. In the future, I think this analysis will be crucial. Nevertheless, the work is very well prepared and bring new and important results for this topic.