Primrose Boynton (boynton_primrose@wheatoncollege.edu), Sonja Blasche (sb2487@mrc-tox.cam.ac.uk), Ignacio Belda (ignaciobelda@ucm.es), Olga Nikoloudaki (Olga.Nikoloudaki@unibz.it), Kate Howell suggested: Thank you for this invitation- however I have significant conflicts of interest with this group and their work. I would suggest Florian Bauer (fb2@sun.ac.za), Miguel de Barros Lopes (miguel.debarroslopes@unisa.edu.au) or Sarah Knight (s.knight@auckland.ac.nz)., Juan Diaz-Colunga suggested: Dr. Ignacio Belda, Universidad Complutense de Madrid (ignaciobelda@ucm.es), Juan Diaz-Colunga suggested: Dr. Javier Ruiz, Universidad Complutense de Madrid (javiru02@ucm.es), Juan Diaz-Colunga suggested: Dr. Jean C. C. Vila, Stanford University (jccvila@stanford.edu), Ignacio Belda suggested: The manuscript by Pourcelot et al. is a nice and valuable contribution to the growing field of applied microbial ecology, particularly focusing on wine fermentations as a model system. This research is notable for offering a refined model system, which utilizes a set of species tagged with fluorescence for precise population monitoring. It also investigates key research questions, such as how taxonomic diversity influences the performance of ecological communities and how varying environmental conditions may impact this performance., Ignacio Belda suggested: Major observations:, Ignacio Belda suggested: - The theoretical background supporting the ecological questions addressed in this work could be better elaborated in the introduction, and more importantly, in the discussion of results. The current discussion primarily focuses on previous observations in wine research rather than drawing connections to other studies in theoretical ecology that have addressed similar questions., Ignacio Belda suggested: - Regarding the two environmental conditions tested (S200 vs. S280), it is unclear whether they genuinely represent contrasting conditions of stress versus non-stress. Does 280 g/L of sugar truly constitute an osmotic stress condition compared to 200 g/L, or does it simply present a more challenging medium for sugar consumption due to cell exhaustion or limited nitrogen availability? While it is evident that osmotic stress persists longer at 280 g/L compared to 200 g/L, it is uncertain if the initial conditions significantly differ in terms of osmotic stress at an ecological or molecular level. If the authors have evidence of stress response induction at 280 g/L versus 200 g/L of sugar, this should be justified in the introduction., Ignacio Belda suggested: - As the authors propose this consortium as a model system, it would be beneficial to conclude the manuscript (at the end of the discussion) with a clear statement of its strengths and weaknesses. Additionally, outlining the oenological and ecological issues that this model system can address, which previous models could not, would provide valuable context and direction for future research., Ignacio Belda suggested: Minor comments:, Ignacio Belda suggested: Abstract, Ignacio Belda suggested: • Lines 33-34: I suggest to rewrite this sentence not to give the impression that this result is a limitation, as this is an actual and important result. Maybe removing the word “Although” is enough, but, please, consider rephrasing., Ignacio Belda suggested: Introduction, Ignacio Belda suggested: • Lines 68-72: It would be interesting to mention here some relevant works that already used wine microbial consortia to explore fundamental ecological questions (see: https://www.cell.com/action/showPdf?pii=S2405-4712%2817%2930390-3; https://www.nature.com/articles/s42003-023-05284-1; https://www.embopress.org/doi/full/10.15252/msb.202311613), Ignacio Belda suggested: Material and methods, Ignacio Belda suggested: • Line 120: While the assays in mock communities effectively demonstrate that the fluorescent tag accurately indicates yeast cell abundance, it would be beneficial to use qPCR to verify that TDH3 expression remains constant during wine fermentation in monocultures of the six species studied. Perhaps another promoter is needed for Mp., Ignacio Belda suggested: • Line 135: Why was pasteurization chosen over filtration? Did you measure the concentration of residual sugars after pasteurization? Could pasteurization be reducing the actual differences between the S280 and S200 trials?, Ignacio Belda suggested: • Line 142: Change "physiological water" to "saline solution.", Ignacio Belda suggested: • Line 145: Is there a rationale for using different scales for different trials, or was this simply due to standard laboratory practices and to reduce the cost of the second batch of experiments? If there is a specific reason, please state it here., Ignacio Belda suggested: • Line 171: There is a typo here: change "functionnality" to "functionality.", Ignacio Belda suggested: • Line 190: Please revise this sentence. There are some unexpected symbols between numbers and units., Ignacio Belda suggested: • Line 204: please, write “1·105 to 5·105”., Ignacio Belda suggested: • Lines 212-213: Are there any data available to support this statement?, Ignacio Belda suggested: • Line 234: When stating “They included four CO2 kinetics…,” isn’t it three?, Ignacio Belda suggested: Results, Ignacio Belda suggested: • Lines 296-298: This sentence is incomplete., Ignacio Belda suggested: • Line 302: How did you measure and adjust the cell concentration from the pre-inoculum to later test theoretical vs. observed cell counts?, Ignacio Belda suggested: • Line 323: If I am interpreting Supplementary Figure S3 correctly, how do the authors explain the detection of cells from other species in monocultures? Are these contaminations or cross-identifications by fluorescence? In addition to the online repository, which is excellent for raw data and scripts, the supplementary material would be better organized in a single file with the corresponding legends to the figures (which have been difficult for this reviewer to find, complicating the interpretation of some results)., Ignacio Belda suggested: • Line 341: When comparing the performance of Sc in monoculture versus as part of consortia, was the concentration of Sc in monoculture 106106? If so, this is 20 times higher than its concentration in the consortia. This should be mentioned to avoid erroneous conclusions about the potential role of the consortia in reducing fermentation kinetics. It is indeed expected that the consortia ferments more slowly compared to S. cerevisiae alone, as the abundance of the primary fermenting agent is reduced., Ignacio Belda suggested: • Lines 373-375: It is interesting that T. delbrueckii does not consume pyruvic acid (a similar observation is made with Sb, but since Sb is much less fermentative, the observation is less relevant). This should be highlighted as a result., Ignacio Belda suggested: • Figure 6: It would be beneficial to include a Supplementary Figure to Fig. 6 that shows absolute cell numbers rather than relative abundance. This would allow for a better understanding of whether changes in the relative abundance of a species are due to direct increases or decreases in its absolute cell count, or if they result from changes in other populations while a species remains unaffected by sugar concentration. In this context, did the higher sugar concentration lead to higher maximum cell concentrations of the total consortium and/or individual species? The results should be discussed accordingly., Ignacio Belda suggested: • Lines 446-447: As mentioned earlier in the "Major comments" section, another possible explanation for this result is that the conditions do not represent significantly different osmotic pressures., Ignacio Belda suggested: • Line 481: Remove the “)” after “value” at the end of the sentence., Ignacio Belda suggested: • Lines 479-481: Why is the system described as low complexity? Please explain this more clearly and establish a reference system for comparison (there are examples of both more complex and simpler model systems).
e.g. John Doe john@doe.com
No need for them to be recommenders of PCIMicrobiol. Please do not suggest reviewers for whom there might be a conflict of interest. Reviewers are not allowed to review preprints written by close colleagues (with whom they have published in the last four years, with whom they have received joint funding in the last four years, or with whom they are currently writing a manuscript, or submitting a grant proposal), or by family members, friends, or anyone for whom bias might affect the nature of the review - see the code of conduct
