Plant Growth-Promoting Microorganisms in Coffee Production: From Isolation to Field Application

Round 1

Reviewer 1 Report

The review is very interesting not only for the economic value of the product, but also for the ecosystem associated to the coffee plantations. Nevertheless, I have some questions and suggestions to the authors

 

1. Introduction

I miss some more information, if there are any, about differences between the PGPR species isolated from coffee plants related to locations and type of culture (traditional, monocultures. forest….), soil, cultivars of coffee plants, etc. Yulatin et al. 2019 mentioned the influence of some of this parameters in PGPR density. The success of inoculants is related to most of this characteristics, and an example of that is mentioned in section 4 for AMF where the species differ depending on soil contions, plants varieties and countries of isolation.

I suggest to include some of this information into the introduction or later on.

2. Diversity of PGPR associated with coffee plantations in different geographical ar-eas

Only in one or two species is indicated the place where the PGPR was isolated (rhizosphere, phyllosphere or endophere). Most of them are from rhizophere, so may be the authors could indicate the ones that are not rhizospheric as B. subtilis AP-3 and 150. I think this information is relevant and more in the case of Gluconacetobacter that as far as I know in this work was isolated from the rhizosphere but usually is an endosymbiont.

 

Table 1.

1-General remarks:

• Columns 2 and 3 “Mode of action and Function in soil or plant” looks quite repetitive. Several times the same information is in both columns, for example in the 1^st line Nitrogen fixation and Nitrogen fixation or the 4^th Phosphates solubilization – Promote plants growth and improve solubilization of phosphorous.
• As properly described by authors in the 1^st paragraph of this section bio-fertiliser promote plant growth, Bio-stimulants produces hormones and Bio-protectors protects from plants diseases, so I suggest to use properly these terms (e.g. Acinetobacter calcoaceticus has a bio-stimulant effect as IAA producer)
• Check edition of the table.
• When known, it is important to include the strain name ( amyloquefaciens is B. amyloquefaciens BT42)
• Some references are not correct, please check it, (for instant reference 21 also previously in this section).

2-Specific remarks.

• 1^st line:The reference for this information is “Jiménez-Salgado et al 1997”. The reference 18 is a review. Please correct it.
• 2^nd line: amyloquefaciens BT42 is an antagonistic bacteria of C. gloeosporioides and F. oxysporum as well as promotes plant growth producing IAA, siderophores and enzyme ACC deaminase and ammonia, and solubilizing phosphate and insoluble zinc oxides. Column 2 and 3 should be revised.
• Lines with Azotobacter: Azotobacter is a well-known nitrogen-fixing bacteria, but this characteristic is not included in the table. Castillo et al. 2011 described the ability of this bacteria literally: “Endosulfan reduced nitrogenase activity but had no impact on indole 3-acetic acid production. Thus, these results suggest that this strain has the potential to act as a biocatalyst in endosulfan degradation.” (Bio-fertilization and Bioremediation).

I suggest to improve and check carefully the information included in table 1.

3. PGPR isolation, multiplication, and inoculum formulation

I suggest to include more bibliography than ref. 57 some in AMF formulation is, paragraph: “ The formulation will depend on the method of application in the plants (i.e., seed inoculation, …….” I think there are AMF commercially available inoculants.

Author Response

Reviewer 1:

Comments and Suggestions for Authors

The review is very interesting not only for the economic value of the product, but also for the ecosystem associated to the coffee plantations. Nevertheless, I have some questions and suggestions to the authors

R: Thank you very much for your positive comments about this review, and the very assertive suggestion. Here, you can see that all the suggested changes and improvements were incorporated in this new version.

1. Introduction

I miss some more information, if there are any, about differences between the PGPR species isolated from coffee plants related to locations and type of culture (traditional, monocultures. forest….), soil, cultivars of coffee plants, etc. Yulatin et al. 2019 mentioned the influence of some of these parameters in PGPR density. The success of inoculants is related to most of this characteristics, and an example of that is mentioned in section 4 for AMF where the species differ depending on soil conditions, plant varieties and countries of isolation. I suggest to include some of this information into the introduction or later on.

R: Thank you. We have clarified this through this information in the introduction: “In the last two decades, modern biotechnologies and plant microbiome engineering have been applied to modify this microbiome towards a specific microbial community, allowing optimized crop growth and thus increasing profitability. Moreover, beneficial plant-microbe interactions can be manipulated to increase crop production in an agricultural field focusing on how microbiome engineering can be incorporated into traditional and emerging techniques that makes on these microbial ecosystem services to additional improve crop yields and resilience [13-15].

2. Diversity of PGPR associated with coffee plantations in different geographical areas

Only in one or two species is indicated the place where the PGPR was isolated (rhizosphere, phyllosphere or endophere). Most of them are from rhizosphere, so maybe the authors could indicate the ones that are not rhizospheric as B. subtilis AP-3 and 150. I think this information is relevant and more in the case of Gluconacetobacter that as far as I know in this work was isolated from the rhizosphere but usually is an endosymbiont.

R: We have included this in the text. Please, see points two and three. Thank you for your comment.

Table 1.

1-General remarks:

• Columns 2 and 3 “Mode of action and Function in soil or plant” looks quite repetitive. Several times the same information is in both columns, for example in the 1^st line Nitrogen fixation and Nitrogen fixation or the 4^th Phosphates solubilization – Promote plants growth and improve solubilization of phosphorous.
• As properly described by authors in the 1^st paragraph of this section bio-fertilizers promote plant growth, Bio-stimulants produces hormones and Bio-protectors protects from plants diseases, so I suggest to use properly these terms (e.g. Acinetobacter calcoaceticus has a bio-stimulant effect as IAA producer)
• Check edition of the table.
• When known, it is important to include the strain name ( amyloquefaciens is amyloquefaciens BT42)
• Some references are not correct, please check it, (for instant reference 21 also previously in this section).

R: Thanks for these suggestions. We have carefully followed all your recommendations to improve the information of this table:

-Columns 2 and 3 have been grouped in one column to avoid redundant information.

-For the bacterial isolates where the strain code is known, it has been added to each species name.

-The references were carefully checked by accessing the source article, and corrections have been done when needed.

2-Specific remarks.

• 1^st line:The reference for this information is “Jiménez-Salgado et al 1997”. The reference 18 is a review. Please correct it

R: You are right, correction changes were made.

• 2^nd line: amyloquefaciens BT42 is an antagonistic bacteria of gloeosporioides and F. oxysporum as well as promotes plant growth producing IAA, siderophores and enzyme ACC deaminase and ammonia, and solubilizing phosphate and insoluble zinc oxides. Column 2 and 3 should be revised.

R: The changes were addressed. Thank you again.

• Lines with Azotobacter: Azotobacter is a well-known nitrogen-fixing bacteria, but this characteristic is not included in the table. Castillo et al. 2011 described the ability of this bacteria literally: “Endosulfan reduced nitrogenase activity but had no impact on indole 3-acetic acid production. Thus, these results suggest that this strain has the potential to act as a biocatalyst in endosulfan degradation.” (Bio-fertilization and Bioremediation).

I suggest to improve and check carefully the information included in table 1.

R: The information was corrected, and the table was rechecked. Please, see the new version of the Table 1.

            PGPR isolation, multiplication, and inoculum formulation

I suggest to include more bibliography than ref. 57 some in AMF formulation is, paragraph: “ The formulation will depend on the method of application in the plants (i.e., seed inoculation, …….” I think there are AMF commercially available inoculants.

R: We have added more information and references to this paragraph. We appreciate your comment.

“The formulation will depend on the method of application in the plants (i.e. bare-root inoculation, bare-root soil inoculation, transplant inoculation, or root inoculation). The most commonly used carriers for AMF inocula produced in beds are sand, perlite, and vermiculite in order to give them a solid consistency (e.g., granular, powder, or pellet form). For high quality AMF propagules produced in vitro for commercial purposes, the formulation can be prepared with solid materials in the form of pellets, tablets or granules [59]. Commercial inoculants containing AMF are also available in the market [63], but a previous analysis to evaluate its efficiency should be carried out”.

Reviewer 2 Report

Dear Authors,

Please find below some minor suggestions/comments in red font that Authors must address before publishing their article in Agronomy.

Title

Delete the ‘and’ between the first and second author names.

Abstract

In the last sentence of the abstract, use “finally” instead of using “in general”.

Introduction

Use the word “occur” instead of “co-occur”

“In the last decade, modern biotechnologies have been applied to modify this microbiome towards a specific microbial community, allowing optimized crop performance and thus increasing profitability”. Please elaborate on this statement and add more references.

Please specify which last decade, i.e. add the numbers.

PGPR inoculated in the soil or seeds improve nutrient absorption, root and shoot formation, seed germination, plant tolerance of environmental stress, nitrogen fixation, and phosphate solubilization. Please indicate under which environmental & agronomic conditions?

Spell out CFU at first mention in the text.

Add a couple of references specific for coffee after this statement “Arbuscular mycorrhizal fungi (AMF) generate mutualistic relationships with plants, where fungi supply plants with nutrients and water and plants provide carbon to fulfil the needs of the fungal partner.”

This sentence seems to be misplaced: Multiple attempts should be made to isolate AMF in pure cultures. Please rewrite it or delete it.

Author Response

Reviewer 2 :

Comments and Suggestions for Authors

Dear Authors,

Please find below some minor suggestions/comments in red font that Authors must address before publishing their article in Agronomy.

Title

Delete the ‘and’ between the first and second author names.

R: Thank you. Sorry for this involuntary mistake.

Abstract

In the last sentence of the abstract, use “finally” instead of using “in general”.

R: Done, the word ¨finally¨ was used, thank you.

Introduction

Use the word “occur” instead of “co-occur”

R: Done, word has been changed.

“In the last decade, modern biotechnologies have been applied to modify this microbiome towards a specific microbial community, allowing optimized crop performance and thus increasing profitability”. Please elaborate on this statement and add more references. Please specify which last decade, i.e. add the numbers.

R: The statement was modified  by:  To date, several studies have demonstrated that when PGPR are inoculated in the soil or seeds using appropriate methods (e.g efficient strains, suitable formulation and inoculation strategies, and suitable agronomic practices, etc.) in addition to control plant pathogens they can improve nutrient absorption, root and shoot formation, seed germination, plant tolerance to environmental stress, nitrogen (N) fixation, and phosphate solubilization [14].

PGPR inoculated in the soil or seeds improve nutrient absorption, root and shoot formation, seed germination, plant tolerance of environmental stress, nitrogen fixation, and phosphate solubilization. Please indicate under which environmental & agronomic conditions?

R: Yes, we have clarified that we ment under agronomic conditions: “To date, several studies have demonstrated that when PGPR are inoculated in the soil or seeds using appropriate methods (e.g efficient strains, suitable formulation and inoculation strategies, and suitable agronomic practices, etc.) in addition to control plant pathogens they can improve nutrient absorption, root and shoot formation, seed germination, plant tolerance of environmental stress, nitrogen (N) fixation, and phosphate solubilization [14].

Spell out CFU at first mention in the text.

R: ¨colony forming units¨ has been included, thank you for your observation.

Add a couple of references specific for coffee after this statement “Arbuscular mycorrhizal fungi (AMF) generate mutualistic relationships with plants, where fungi supply plants with nutrients and water and plants provide carbon to fulfil the needs of the fungal partner.”

R: References were added, thank you very much for your suggestion.

This sentence seems to be misplaced: Multiple attempts should be made to isolate AMF in pure cultures. Please rewrite it or delete it.

R: This statement was rewritten: In order to isolate specific AMF species, multiple attempts should be made to succeed, and then the AMF species effects on coffee plants should be evaluated through physiological, metabolic and biochemical experiments in pots [58].

Reviewer 3 Report

The issue of the effective use of microorganisms in plant production arouses a lot of emotions among scientists. A lot of research has shown that their effectiveness in specific field conditions is very limited. Nevertheless, there are also works (and the peer-reviewed work is an example of this), which indicate the broad positives resulting from the presence of bacteria and fungi in the soil. This one-sidedness is, in a way, a shortcoming of the job. But I think that authors are aware of this. Anyway, in the CONCLUSIONS of the work, there is a sentence about the "needs of further research on microorganisms in the coffee plantations". 

Author Response

REVIEWER 3 :

Comments and Suggestions for Authors

The issue of the effective use of microorganisms in plant production arouses a lot of emotions among scientists. A lot of research has shown that their effectiveness in specific field conditions is very limited. Nevertheless, there are also works (and the peer-reviewed work is an example of this), which indicate the broad positives resulting from the presence of bacteria and fungi in the soil. This one-sidedness is, in a way, a shortcoming of the job. But I think that authors are aware of this. Anyway, in the CONCLUSIONS of the work, there is a sentence about the "needs of further research on microorganisms in the coffee plantations".

R: We deeply appreciate your comments and suggestions and we have included the following in the conclusions section:

Hence, it is important to develop research at the local level in different regions of the world taking into consideration AMF and PGPR inoculation or reinoculation frequency needs to coffee seeds or plantlets, seasonality, type of soil or inoculation substrate in the greenhouse, among many other factors.