The Effects of Plant Health Status on the Community Structure and Metabolic Pathways of Rhizosphere Microbial Communities Associated with Solanum lycopersicum

Round 1

Reviewer 1 Report

The language needs to be improved, pay attention to the sentence fluent and grammatical tenses, for example in the Abstract, material and method…

Abstract: “little is known about how this disease affects the community structure microbial communities associated with tomato plants using shotgun metagenomics.”  The sentence doesn't read smoothly.

“Our results revealed that the rhizosphere microbiome and various functions were more abundant HR followed by DR and bulk soil (BR) in the order HR>DR>BR.” The sentence doesn't read smoothly.

Page1 Line 33-35 “Multiple researchers have explained how the microbiomes interacting with the plant are essential in confirming the plant’s health status and productivity.”  Mind the tense

Page 2 line 55-56 “Among the microbial communities colonizing the plant, environments are pathogenic and prone to cause infections on the plant.”  What ‘s the meaning of this sentence, the environments are pathogenic? Or some microbial are pathogenic?

Page 2 Line 71 The word “much” not appropriate

Page 2 Line 73-74 “such as 16SrRNA, Pyrosequencing, ITS, among others”  Pyrosequencing including 16S rRNA and ITS pyrosequencing

Page 2 Line 74-75 “bacteria and  fungi communities” shoud be “bacterial and fungal communities”

Page 2 Line 76 “no one” not appropriate

Page 4 Line 145-146 “for rhizosphere of tomato and bulk soil samples.” should be “for the microbiome in the rhizosphere”

Page 4 Line 156-157 “Shotgun sequencing and community diversity of tomato rhizosphere and bulk soil analyzed sequences”  can be  “Shotgun sequencing of the microbiome in tomato rhizosphere and bulk soil” , community diversity was not displayed in this part.

Page 5 Line 182-183 “While the fungal and archaeal phyla dominant in the HR site are Ascomycota and Basidiomycota, with a mean abundance of 0.8 and 0.03%, respectively.”   Both Ascomycota and Basidiomycota are not archaeal.

Page 5 Line 191-192 The archaeal phylum is Korarchaeota (0.004%), while no fungi phyla were identified.  Pay attention to the tense of the sentence, “is” and “were”

Page 7 line 204 “3.3 Community structure of the rhizosphere microbiome of tomato plants” The description of this paragraph was similar with those of 3.2.  the authors described the community composition from different classification levels. So the two parts can be combined into one part.

Table 1 and Figure 7 Did the author obtain the same results of diversity indices for bacteria and fungi?

Figure 7 The three replicates of BR, HR and DR samples can be displayed in the plot, from which, we can find the cluster and separation of the samples.

Page 15 Line 340-341  “We observed Streptomyces, Bradyrhizobium, Pseudomonas, and Bacillus in DR, in the rhizo-sphere soil of rusty Panax ginseng” check this sentence

The discussion part should be improved, not only the expression, more description can be focused on the similarity of α diversity, the differences among the soil samples and the associated reasons.

Author Response

The language needs to be improved, pay attention to the sentence fluent and grammatical tenses, for example in the Abstract, material and method…

Abstract: “little is known about how this disease affects the community structure microbial communities associated with tomato plants using shotgun metagenomics.”  The sentence doesn't read smoothly.

 Correction: The sentence has been corrected.

“Our results revealed that the rhizosphere microbiome and various functions were more abundant HR followed by DR and bulk soil (BR) in the order HR>DR>BR.” The sentence doesn't read smoothly.

Correction: Our results showed that the rhizosphere microbiome alongside some specific functions were more abundant in HR followed by DR and bulk soil (BR) in the order HR>DR>BR

Page1 Line 33-35 “Multiple researchers have explained how the microbiomes interacting with the plant are essential in confirming the plant’s health status and productivity.”  Mind the tense

Correction: Several studies have reported how the microbiomes interacting with the plant are essential in observing the plant’s health status and productivity

Page 2 line 55-56 “Among the microbial communities colonizing the plant, environments are pathogenic and prone to cause infections on the plant.”  What ‘s the meaning of this sentence, the environments are pathogenic? Or some microbial are pathogenic?

Correction: Among the microbial communities colonizing the plants, and environments are phytopathogens prone to cause diseases on the plants.

Page 2 Line 71 The word “much” not appropriate

 Correction: the word much has been removed

Page 2 Line 73-74 “such as 16SrRNA, Pyrosequencing, ITS, among others”  Pyrosequencing including 16S rRNA and ITS pyrosequencing

Correction: such as Pyrosequencing including 16SrRNA and ITS

Page 2 Line 74-75 “bacteria and  fungi communities” shoud be “bacterial and fungal communities”

Correction: the correction has been effected

Page 2 Line 76 “no one” not appropriate

 Correction: no study

Page 4 Line 145-146 “for rhizosphere of tomato and bulk soil samples.” should be “for the microbiome in the rhizosphere”

 Correction: the correction has been effected

Page 4 Line 156-157 “Shotgun sequencing and community diversity of tomato rhizosphere and bulk soil analyzed sequences” can be “Shotgun sequencing of the microbiome in tomato rhizosphere and bulk soil”, community diversity was not displayed in this part.

 Correction: the correction has been effected

Page 5 Line 182-183 “While the fungal and archaeal phyla dominant in the HR site are Ascomycota and Basidiomycota, with a mean abundance of 0.8 and 0.03%, respectively.”   Both Ascomycota and Basidiomycota are not archaeal.

Correction: While the fungal phyla dominant in the HR site are Ascomycota and Basidiomycota, with a mean abundance of 0.8 and 0.03%, respectively. The archaeal phylum also abundant in HR includes; Euryarchaeota, Crenarchaeota, Thaumarchaeota (0.3%), and unclassified (Archaea) with a mean abundance of 0.43%, 0.13%, and 0.03%, respectively.

Page 5 Line 191-192 The archaeal phylum is Korarchaeota (0.004%), while no fungi phyla were identified.  Pay attention to the tense of the sentence, “is” and “were”

Correction: The archaeal phylum is Korarchaeota (0.004%), while no fungal phylum was identified.

Page 7 line 204 “3.3 Community structure of the rhizosphere microbiome of tomato plants” The description of this paragraph was similar with those of 3.2.  the authors described the community composition from different classification levels. So the two parts can be combined into one part.

Correction: the parts has been merged

3.2 Distribution of major rhizosphere soil microbiome phyla across the tomato plant sites

Table 1 and Figure 7 Did the author obtain the same results of diversity indices for bacteria and fungi?

Figure 7 The three replicates of BR, HR and DR samples can be displayed in the plot, from which, we can find the cluster and separation of the samples.

Correction: Yes, table 1 explains the diversity indexes while figure 7 explains the Principal coordinate analysis

Page 15 Line 340-341  “We observed Streptomyces, Bradyrhizobium, Pseudomonas, and Bacillus in DR, in the rhizo-sphere soil of rusty Panax ginseng” check this sentence

Correction: We observed Streptomyces, Bradyrhizobium, Pseudomonas, and Bacillus in DR, which was in line with the report of Wei et al., [20] that reported the same genera in the rhizosphere soil of rusty Panax ginseng.

The discussion part should be improved, not only the expression, more description can be focused on the similarity of α diversity, the differences among the soil samples and the associated reasons.

Correction: The discussion has been modified

Author Response File: Author Response.docx

Reviewer 2 Report

The research presented in this manuscript demonstrates differences in microorganism communities in the rhizospheres of healthy versus diseased plants.  The research should be published, but the writing needs work.  Below are a number of specific suggestions and comments. 

Lines 13-14: “microbial communities associated with tomato plants using shotgun

metagenomics”. This phrase doesn’t make much sense.

Lines 18-19; “various functions were more abundant HR followed by DR and bulk soil (BR) in the order HR>DR>BR”.  This phrase doesn’t make much sense.

Line 43: did you mean reduction or inhibition of “harmful organisms”?

Line 46: “caused a considerable loss” instead try ‘caused considerable losses’.

Line 88: delete “South Africa”, you already told us it was South Africa in line 86.

Line 90: delete “work”.

Lines: 92-93: “The average annual rainfall in this region is 300 to 600mm. The temperature ranges from 25 to 38°C, which shows how extreme the temperature is during the summer.” Instead try-- The average annual rainfall is 300 to 600mm and temperatures range from 25 to 38°C.

Lines 94-95: 10C is not extreme cold, that is not even freezing, and tomatoes can survive 10C.  Stop using subjective terms such as “shows how extreme the temperature is”, just say ‘during winter temperatures drop below 10C’ or something similar.

Line 98: delete “only”.

Line 102: “region has an optimum temperature of 28°C”; optimum for whom or what? Is this the average temperature or the maximum temperature?

Line 139: what do you mean by “parasites”? Fungi can be parasitic.

Line 142: I don’t understand what you mean by “unclassified data”.  To me this sounds like unidentified sequences, how do you have Taxonomic values for unidentified sequences?

Lines 158-162: are these means of total numbers of sequences (DNA?) you found in soil samples, then after QC analysis the numbers that were identifiable?

Lines 168 and 169: Archaea or fungi were, not “are”.

Lines 171-173: “relative abundance of microorganisms” are you referring to numbers of microorganisms or taxa?

Sections 3.2 and 3.3: are the percentages associated with each taxon a percentage of that taxon (bacteria, Archaea, or fungus) in the samples, or the percentage of all identified microorganisms?

Lines 264, 266, 267, 271: genera, not “genus”.

Lines 267 and 271: use past tense, were, not “are” or “is”.

Table 2: what are the units for numbers in the HR, DR, and BR columns?

Lines 382-383: “the abundance and diversity of rhizosphere microbial communities are more significant in the healthy rhizosphere”.  How abundance and diversity of rhizosphere microbial communities more significant in the healthy rhizosphere? Abundance and diversity of microbial communities might be greater in the “healthy rhizosphere” but that is not the same as more significant.

Author Response

Lines 13-14: “microbial communities associated with tomato plants using shotgun

metagenomics”. This phrase doesn’t make much sense.

Correction: microbial communities associated with tomato plants employing shotgun metagenomics

Lines 18-19; “various functions were more abundant HR followed by DR and bulk soil (BR) in the order HR>DR>BR”.  This phrase doesn’t make much sense.

Correction: Our results showed that the rhizosphere microbiome and specific functions were more abundant in HR followed by DR and bulk soil (BR) in the order HR>DR>BR

Line 43: did you mean reduction or inhibition of “harmful organisms”?

Correction: phytopathogens

Line 46: “caused a considerable loss” instead try ‘caused considerable losses'.

Correction: the correction has been effected

Line 88: delete “South Africa”, you already told us it was South Africa in line 86.

Correction: the word South Africa has been deleted.

Line 90: delete “work”.

Correction: the word ‘work’ has been deleted.

Lines: 92-93: “The average annual rainfall in this region is 300 to 600mm. The temperature ranges from 25 to 38°C, which shows how extreme the temperature is during the summer.” Instead try-- The average annual rainfall is 300 to 600mm and temperatures range from 25 to 38°C.

Correction: the correction has been effected

Lines 94-95: 10C is not extreme cold, that is not even freezing, and tomatoes can survive 10C.  Stop using subjective terms such as “shows how extreme the temperature is”, just say ‘during winter temperatures drop below 10C’ or something similar.

Correction: the correction has been effected

Line 98: delete “only”.

Correction: the word ‘only’ has been deleted

Line 102: “region has an optimum temperature of 28°C”; optimum for whom or what? Is this the average temperature or the maximum temperature?

Correction: for average temperature

Line 139: what do you mean by “parasites”? Fungi can be parasitic.

Correction: I meant other microorganisms’ sequences not relating to bacteria, fungi and archaea.

Line 142: I don’t understand what you mean by “unclassified data”.  To me this sounds like unidentified sequences, how do you have Taxonomic values for unidentified sequences?

Correction: the word ‘data’ has been changed to ‘sequences’

The taxonomic values of unclassified sequences were obtained after normalization of data was conducted on MG-RAST

Lines 158-162: are these means of total numbers of sequences (DNA?) you found in soil samples, then after QC analysis the numbers that were identifiable?

Correction: Yes

Lines 168 and 169: Archaea or fungi were, not “are”.

Correction: the correction has been effected

Lines 171-173: “relative abundance of microorganisms” are you referring to numbers of microorganisms or taxa?

Correction: relative abundance of the taxa

Sections 3.2 and 3.3: are the percentages associated with each taxon a percentage of that taxon (bacteria, Archaea, or fungus) in the samples, or the percentage of all identified microorganisms?

Correction: Percentage associated with bacteria, fungi, and archaea in the soil samples

Lines 264, 266, 267, 271: genera, not “genus”.

Correction: the correction has been effected

Lines 267 and 271: use past tense, were, not “are” or “is”.

Correction: the correction has been effected

Table 2: what are the units for numbers in the HR, DR, and BR columns?

Correction: the unit is in percentage and it has been input on the table

Lines 382-383: “the abundance and diversity of rhizosphere microbial communities are more significant in the healthy rhizosphere”.  How abundance and diversity of rhizosphere microbial communities more significant in the healthy rhizosphere? Abundance and diversity of microbial communities might be greater in the “healthy rhizosphere” but that is not the same as more significant.

Correction: the words ‘more significant’ have been changed to ‘greater’.

Author Response File: Author Response.docx