A Novel Yeast Genus and Two Novel Species Isolated from Pineapple Leaves in Thailand: Savitreella phatthalungensis gen. nov., sp. nov. and Goffeauzyma siamensis sp. nov.
Round 1
Reviewer 1 Report
The authors deal with the description of two novel yeast species isolated from pineapple leaves in two regions of Thailand.
From my point of view the work looks coherent and after minor revisions it is ready for publication.
Minor revisions:
Line 69-70: This genus shows/has a dimorphic…
Line 84: Melbourne code, would be better if supplemented by a date.
Line 96-97: notation of the species names, not Cryp better C.
Line 130: stored instead of maintained
Line 134 – 143: YM, Corn Meal Agar and V8 were not specified in contrast to the other media
Line 185: … from two pineapple leaf samples…
Line 187: … both located in Patthalung province.
Line 195: …of the sequences of the…
Line 216: wording of “multigene genes”???
Line 234: … type strains of the related species…
Line 243: … but is negative for positive for Protomyces… ???
Line 247: … represent a single novel genes and species of the subphylum… Sense of it???
Line 297: cultivation field
Line 332: Same as before
Line 457: cancel “any”
Author Response
Point-by-point responses to the reviewer’ s comments
Response: Thank you very much for valuable suggestions and comments.
Our responses to the reviewer’s comments are as follows:
Reviewer #1
Comments and Suggestions for Authors
The authors deal with the description of two novel yeast species isolated from pineapple leaves in two regions of Thailand. From my point of view the work looks coherent and after minor revisions it is ready for publication.
Minor revisions:
Line 69-70: This genus shows/has a dimorphic…
Response: We have already corrected (Line 64–65).
Line 84: Melbourne code, would be better if supplemented by a date.
Response: We added “2012” in this sentence (Line 79–80).
Line 96-97: notation of the species names, not Cryp better C.
Response: They were corrected (Line 91–92).
Line 130: stored instead of maintained
Response: It was corrected (Line 126).
Line 134–143: YM, Corn Meal Agar and V8 were not specified in contrast to the other media
Response: The nutrient composition of YM has been provide in Line 122–123, and the composition of Corn Meal Agar and V8 were added (Line 135–140).
Line 185: … from two pineapple leaf samples…
Response: It was corrected (Line 198–199).
Line 187: … both located in Patthalung province.
Response: Done (Line 200).
Line 195: …of the sequences of the…
Response: Done (Line 214).
Line 216: wording of “multigene genes”???
Response: We revised this sentence as “To clarify the placement of the two strains, the phylogenetic analysis of a multilocus dataset (SSU, ITS, LSU, TEF1, ACT1 and RPB2) needs to be conducted.” (Line 239–241).
Line 234: … type strains of the related species…
Response: It was corrected (Line 275).
Line 243: … but is negative for positive for Protomyces…???
Response: It was corrected (Line 284).
Line 247: … represent a single novel genes and species of the subphylum… Sense of it???
Response: We revised this sentence as “we concluded that these two strains, DMKU-PAL186 and DMKU-PAL178, represent a novel genus and species of the subphylum Taphrinomycotina” (Line 287–288).
Line 297: cultivation field
Response: We revised it as “pineapple cultivated field” (Line 370).
Line 332: Same as before
Response: Corrected (Line 405).
Line 457: cancel “any”
Response: Deleted (Line 482).
Reviewer 2 Report
The manuscript contains very interesting, original and useful data. However, several issues should be corrected:
Most of the Keywords are the same as in the title and do not bring any new information.
Line 119: It has been written: "Green and healthy leaves of pineapples leaves" Is this correct?
Line 119: How long were the samples stored until subjected to yeast isolation?
Lines 115-119: The number of samples for each location should be given.
The number of repetitions for each measurement should be given.
Line 186: What did the authors mean by "leaf sample"? One leaf?
Line 285: The description for Savitreella phatthalungensis is less detailed than for other species.
Line 366: Why is there the separate subsection "3.4. Figures, Tables and Schemes"? Moreover, the description of some results is insufficient.
The section Conclusions is missing.
Author Response
Point-by-point responses to the reviewer’ s comments
Response: Thank you very much for valuable suggestions and comments.
Our responses to the reviewer’s comments are as follows:
Reviewer #2
Comments and Suggestions for Authors
The manuscript contains very interesting, original and useful data. However, several issues should be corrected:
Most of the Keywords are the same as in the title and do not bring any new information.
Response: We revised the keywords as “Two new taxa; Yeast taxonomy; Yeast phylogeny; Savitreella phatthalungensis; Goffeauzyma siamensis.; Pineapple; Phyllosphere” (Line 32–33).
Line 115: It has been written: "Green and healthy leaves of pineapples leaves” Is this correct?
Response: We revised this phrase as “Green and healthy leaves of pineapple” (Line 111).
Line 119: How long were the samples stored until subjected to yeast isolation?Response: We specified the time for sample storage as “Leaf samples (five leaves per sample) were put in plastic bags, sealed and kept in icebox for 6–12 h during transfer to the laboratory. The samples were stored at 8⁰C until subjected to yeast isolation, which was no longer than 48 h.” (Line 114–116).
Lines 115-119: The number of samples for each location should be given.
The number of repetitions for each measurement should be given.
Response: We added the numbers of samples for each location and revised this part as “Green and healthy leaves of pineapple (Ananas comosus) were randomly collected from cultivated fields in Chon Buri province (21 samples), eastern region of Thailand, on December 26, 2020, and Phatthalung province (10 samples) southern region of Thailand, on January 13, 2021. Leaf samples (five leaves per sample) were put in plastic bags, sealed and kept in icebox for 6–12 h during transfer to the laboratory. The samples were stored at 8⁰C until subjected to yeast isolation, which was no longer than 48 h.” (Line 111–116).
Line 186: What did the authors mean by "leaf sample"? One leaf?
Response: It means “leaf sample”. We revised this sentence as “Strains DMKU-PAL186 and DMKU-PAL178 were respectively isolated from two pineapple leaf samples, one leaf sample collected at sampling site No. 7 (7°14'5"N/100°10'54"E) and another leaf sample at sampling site No. 9, (7°15'56"N/100°10'23"E), and both located in Phatthalung province,” (L198–204).
Line 285: The description for Savitreella phatthalungensis is less detailed than for other species.
Response: We added additional details in the description for Savitreella gen. nov. as “The genus can be separated from the neighboring genera, Protomyces and Taphrina, by phylogenetic analyses (Figure 1 and 2) and phenotypic characteristics (Table 4).” (Line 357–359).
Line 366: Why is there the separate subsection "3.4. Figures, Tables and Schemes"? Moreover, the description of some results is insufficient.
Response: We deleted this subsection and the Tables and Figures were moved after their first mention of theirs result description (Line 181–348).
The section Conclusions is missing.
Response: We have already added the conclusions section as “A novel yeast genus and two novel species were described and illustrated. Based on the molecular analyses and phenotypic characteristics, the name Savitreella phatthalungensis gen. nov., sp. nov. is proposed in the phylum Ascomycota, and the name Goffeauzyma siamensis sp. nov. is proposed in the phylum Basidiomycota. In the case of Savitreella phatthalungensis, the pathogenicity of this species on pineapple leaves was examined and no damage or disease symptoms were observed on the tested leaves.” (Line 507–512).
Reviewer 3 Report
The proposed manuscript represents novel and original work, that will be of interest for readers working in this area.
I consider the work to be very complete and well written, even though I consider the discussion section still needs improvement. Please see below my minor suggestions.
Minor comments:
- lines 49-54 - this should be in the results section, and not in the introduction
- Line 43 and line 82 - L. was used to abbreviate different species. Correct and please uniformize throughout the manuscript
- Line 96 - Cryp. is not an accepted abbreviation for a genus, according with the rules of nomenclature
- Manuscript is not formatted accordingly to the rules. Tables and Figures should appear after their first mention.
- Discussion section needs to be largely extended. In detail, the number of substitutions in the regions D1/D2 and ITS needs to be compared with the description of other novel yeast species, to validate the need to propose these new species. Some examples of studies that need to be cited and that, due to similar results in these regions, validate the current work:
- Metschnikowia koreensis sp. nov., a novel yeast species isolated from flowers in Korea. https://doi.org/10.1099/00207713-51-5-1927
- Clavispora santaluciae f.a., sp. nov., a novel ascomycetous yeast species isolated from grapes. https://doi.org/10.1099/ijsem.0.004531
- Saccharomyces jurei sp. nov., isolation and genetic identification of a novel yeast species from Quercus robur. doi: 10.1099/ijsem.0.002013
- Starmerella vitis f.a., sp. nov., a yeast species isolated from flowers and grapes. https://doi.org/10.1007/s10482-020-01438-x
- Cryptococcus surugaensis sp. nov., a novel yeast species from sediment collected on the deep-sea floor of Suruga Bay. https://doi.org/10.1099/ijs.0.02712-0 - It would be very interesting to sequence the genome of these new isolates, to evaluate differences in their genome that justify their adaptation to these environments. See for example (https://doi.org/10.3390/jof8010052). Authors should suggest it as future research, to increase the importance of this study.
Author Response
Point-by-point responses to the reviewer’ s comments
Response: Thank you very much for valuable suggestions and comments.
Our responses to the reviewer’s comments are as follows:
Reviewer #3
Comments and Suggestions for Authors
The proposed manuscript represents novel and original work, that will be of interest for readers working in this area. I consider the work to be very complete and well written, even though I consider the discussion section still needs improvement. Please see below my minor suggestions.
Minor comments:
Lines 49-54 - this should be in the results section, and not in the introduction
Response: These sentences in original manuscript was move to the Results section in the revised manuscript (Line 205–211).
Line 43 and line 82 - L. was used to abbreviate different species. Correct and please uniformize throughout the manuscript
Response: We revised L. for Lalaria species as “La. arrabidae, La. inositophila, La. kurtzmanii and La. Veronaerambellii” (Line 77–78).
Line 96 - Cryp. is not an accepted abbreviation for a genus, according with the rules of nomenclature
Response: They were corrected (Line 92–93).
Manuscript is not formatted accordingly to the rules. Tables and Figures should appear after their first mention.
Response: We corrected the formatted of the revised manuscript. The Tables and Figures were moved after their first mention of theirs result description (Line 181–348).
Discussion section needs to be largely extended. In detail, the number of substitutions in the regions D1/D2 and ITS needs to be compared with the description of other novel yeast species, to validate the need to propose these new species. Some examples of studies that need to be cited and that, due to similar results in these regions, validate the current work:
- Metschnikowia koreensis sp. nov., a novel yeast species isolated from flowers in Korea. https://doi.org/10.1099/00207713-51-5-1927
- Clavispora santaluciae f.a., sp. nov., a novel ascomycetous yeast species isolated from grapes. https://doi.org/10.1099/ijsem.0.004531
- Saccharomyces jurei sp. nov., isolation and genetic identification of a novel yeast species from Quercus robur. doi: 10.1099/ijsem.0.002013
- Starmerella vitis f.a., sp. nov., a yeast species isolated from flowers and grapes. https://doi.org/10.1007/s10482-020-01438-x
- Cryptococcus surugaensis sp. nov., a novel yeast species from sediment collected on the deep-sea floor of Suruga Bay. https://doi.org/10.1099/ijs.0.02712-0
Response: We added the details of criteria for yeast identification and mentioned about the number of substitutions in the Discussion section, as per your suggestion. Also, some sentences were revised “In accordance with the guidelines for ascomycetous yeast identification based on nucleotide sequence divergences, the two compared strains with 0–3 nucleotide differences in the D1/D2 domain are designated to be the same species, whereas the strains that differed by greater than 6 nucleotides (1%) are recognized as different species [26]. For basidiomycetous yeasts, the strains that differed by two or more nucleotides in the D1/D2 region represent different taxa [35]. Later, Vu et al. [36] proposed the threshold to consider a strain to belong to a different species from its close relatives is of less than 98.31% similarity (Ascomycota) or 98.61% similarity (Basidiomycota) in terms of ITS region, and less than 99.41% similarity (Ascomycota) or 99.51% similarity (Basidiomycota) when considering the D1/D2 domains. In the present study, the sequences of the D1/D2 of the LSU rRNA gene and ITS regions of the four strains were compared with their closely related species. Two strains (DMKU-PAL186 and DMKU-PAL178) were identical in the D1/D2 and ITS regions, but differed from the type strains of the closely related species by 52-66 nucleotide substitutions in the D1/D2, and by 57-114 nucleotide substitutions in the ITS regions, while two strains (DMKU-PAL39 and DMKU-PAL18) were identical in both rRNA regions, but differed from the type strains of the closely related species by eight nucleotide substitutions in the D1/D2, and by 10 nucleotide substitutions in the ITS regions. According to the criteria mentioned above, these strains are sufficiently separated from known species. Consequently, we were justified in assigning the two strains (DMKU-PAL186 and DMKU-PAL178) as a novel genus and species (namely Savitreella phatthalungensis gen., sp. nov.) of the Taphrinomycetes (phylum Ascomycota), and two strains (DMKU-PAL39 and DMKU-PAL18) as a novel species (namely Goffeauzyma siamensis sp. nov.) of the Tremellomycetes (phylum Basidiomycota). In practice, the two novel species can be distinguished from their closest related species not only by the analysis of nucleotide sequence divergence, but also by phylogenetic analyses and phenotypic characteristics.(Line 440–465).
It would be very interesting to sequence the genome of these new isolates, to evaluate differences in their genome that justify their adaptation to these environments. See for example (https://doi.org/10.3390/jof8010052). Authors should suggest it as future research, to increase the importance of this study.
Response: We added this suggestion as “In order to evaluate differences in their genome that justify their adaptation to these environments, the genome of these new isolates should be sequenced.” (Line 502–503).
Round 2
Reviewer 2 Report
The manuscript has been significantly improved.
lines 84-85: Why did the authors change L. to La.?
Author Response
Reviewer #2
Lines 84-85: Why did the authors change L. to La.?
Response: In this study, we mentioned about the scientific name of the two genera that the genus name initial with “L”, Lactobacillus species (Line 43 of the revised manuscript) and Lalaria species (Line 77–78). According to the general rules for abbreviating the scientific name, if we are discussing two species that belong to different genera that nevertheless start with the same letter. Abbreviations of more than one letter can be used.
For example, the articles proposed by
- Biketova et al. (2022) Reappraisal of the Genus Exsudoporus (Boletaceae) Worldwide Based on Multi-Gene Phylogeny, Morphology and Biogeography, and Insights on Amoenoboletus. Fungi 2022, 8(2), 101; https://doi.org/10.3390/jof8020101. They discussed about Boletus and Butyriboletus species and assigned abbreviation of Boletus species as “B.” (i.e., B. kermesinus, B. pseudofrostii, B. subsplendidus) and as “Bu.” (i.e., Bu. hainanensis).
- Dong et al. (2021). Five Novel Taxa from Freshwater Habitats and New Taxonomic Insights of Pleurotheciales and Savoryellomycetidae . J. Fungi 2021, 7(9), 711; https://doi.org/10.3390/jof7090711. They mentioned about Pleurothecium species (i.e., obovoideum and P. recurvatum) and Phaeoisaria species (i.e., Ph. filiformis).
As mentioned above, we assigned “L.” for abbreviating Lactobacillus species (Line 43) and changed “L.” for Lalaria species to “La.” (Line 77–78) in the revised manuscript.
