Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: BORNEO CORAL REEFS SUBJECT TO HIGH SEDIMENT LOADS SHOW EVIDENCE OF RESILIENCE TO VARIOUS ENVIRONMENTAL STRESSORS
Review round: 2
Reviewer: 1

Output:
Basic reporting: This is a much improved manuscript compared to the first one. However several sentences are still overstated, and there are some typos and other issues throughout. Specific comments written in pdf. Some references not entirely appropriate for the sentence they are inserted into.
Experimental design: Some more information needed in methods. One question about the actual size of quadrats, the size stated doesn't seem right. The discussion mentions non-coral reef builders. Were crustose coralline algae quantified? If so it'd be good to report. If not, explain why. More comments throughout the pdf.
Validity of the findings: look for comments in pdf. Some words/sentences need to be qualified and toned down.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: BORNEO CORAL REEFS SUBJECT TO HIGH SEDIMENT LOADS SHOW EVIDENCE OF RESILIENCE TO VARIOUS ENVIRONMENTAL STRESSORS
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: I suggest the authors state in the manuscript that the reefs studied do not have the typical windward-leeward zonation patterns and are thus more homogenous.  This will help readers better understand the considerations for sampling.
Validity of the findings: I suggest the authors RESTATE in the manuscript that the reefs studied are small and do not have the typical windward-leeward and depth-related zonation patterns. This will help readers better understand when and where the conclusions of the authors most likely apply
Additional comments: Some proof reading of the manuscript and its attachments are still needed.  As examples: the scientific names are not properly formatted in the text e.g., (line 458: "Faviidae" should not be italicized) and in the tables (e.g., Table 1) .  Line 438: "generic" rather than "genetic" diversity; Line 455: "may be" rather than "maybe"


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: COMPREHENSIVE CLASSIFICATION OF THE PLANT NON-SPECIFIC LIPID TRANSFER PROTEIN SUPERFAMILY TOWARDS ITS SEQUENCE–STRUCTURE–FUNCTION ANALYSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: The question posed by the authors is clear and well defined and the methods that have been used are adequate.
Validity of the findings: The findings are sound and good enough.
Discussion and Conclusions are well supported and stated.
Additional comments: The manuscript by Fleury et al. is on the analysis and  classification of the non-specific
lipid transfer protein superfamily in plants. It is the most comprehensive analysis performed so far with regard to the number of sequences taken into consideration.
The question posed by the authors is clear and well defined and the methods that have been used are adequate. The findings are sound and good enough.
I found the web resource developed by the authors an added value to the paper and I wonder and ask them if they intend to update it in the future with additional sequences form other species.
I recommend publication, but also suggest some minor compulsory revisions to improve the overall quality of the manuscript.

Abstract:

The authors stated that “More than 800 different nsLTP sequences have been
characterized so far” but immediately after they claim “we comprehensively investigated 797 nsLTP protein sequences”.  I suggest avoiding this serious inconsistency or at least to explain it.

Introduction:

I would suggest also to briefly and better describe at the beginning of the introduction the efforts made so far for the classification of the members of the superfamily. This is preparatory to a better and understandable reading of the following.

Lines 50-57:  Here I suggest that you improve/expand  with more details the review of recent literature. For example, the recent manuscript by D’Agostino et al, https://doi.org/10.1038/s41598-018-38301-z  (tomato, Solanaceae) should be cited here as well as https://www.frontiersin.org/articles/10.3389/fpls.2018.01285/full and https://www.nature.com/articles/srep38948 (cotton).

Line 58 Please, remove “-“ at the beginning of the paragraph.

Line 78 Please, remove “-“ at the beginning of the paragraph.

Line 82 Please include the reference https://doi.org/10.1038/s41598-018-38301-z

Line 114 Please replace “NsLTPs” with “Non-specific LTPs”

Lines 120-121 this statement is rather risky and does not correspond to reality. There are hundreds of tools out there to analyze  protein gene families. Several of them have been also successfully used by the authors to analyse data for this paper.

I suggest that the authors rephrase the last paragraph of the introduction. As it is , it is not clear enough whether the authors intend to describe the methods they developed for data analysis or whether on the basis of those methods they want to carry out the  analysis of the nsLTP superfamily in plant.

Results:
Line 303 Please replace ”of sequence homology” with “of sequence similarity”.

Conclusions:
Line 717 Please replace “to bioinformatics methods” with “to bioinformatic methods”


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: COMPREHENSIVE CLASSIFICATION OF THE PLANT NON-SPECIFIC LIPID TRANSFER PROTEIN SUPERFAMILY TOWARDS ITS SEQUENCE–STRUCTURE–FUNCTION ANALYSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a very interesting and timely work. The paper is well written, references are appropriate and figures are well prepared.
Experimental design: The paper is clearly within the Aims and Scope of PeerJ. The research question is well defined and the work is performed to high standards. All methods are well described.
Validity of the findings: no comment
Additional comments: There are only two very minor points I would like to raise.
1. The authors very convincingly analyse and define the Type 1 and Type 2 folds of nsLTP. In the text, they frequently refer to the Type 2 fold as a "so called Type 2". This always sounds a bit like the authors do not fully trust their own analyses. I would strongly encourage the authors to remove this "so called" from their paper.
2. The authors should check the use of Roman and Arabien numerals throughout the manuscript. There were some instances where I had the feeling that this was mixed up.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: COMPREHENSIVE CLASSIFICATION OF THE PLANT NON-SPECIFIC LIPID TRANSFER PROTEIN SUPERFAMILY TOWARDS ITS SEQUENCE–STRUCTURE–FUNCTION ANALYSIS
Review round: 1
Reviewer: 3

Output:
Basic reporting: Authors have tried to decipher the functions of nsLTP(s) by collating and analyzing protein sequences, structures and some reported physiological functions. On the basis of homology modelling of different types, they have classified nsLPTs into two main sub-types and developed two bioinformatics tools for analysis of the dataset. It is a good bioinformatics study and I would recommend for publication if the issues raised in general comments are addressed.
Experimental design: The work is carried out using established computational methods.
Validity of the findings: Findings are validated within the limitations of bioinformatics approaches. It would of course be best if they are experimentally validated. However that would not be in the scope of this article.
Additional comments: 1.	Line 116-118: The cited reference for the identification of residues involved in their antifungal activity through SDM has not been carried out in original article Ge et al., 2003.
2.	Line 308 and 311: In many places the authors have written 797 number of sequences was analyzed and at some place 798.
3.	Line 326-335: Explanation for Figure1-A2 and B2, very confusing and not clear.
4.	Line 458-471: The cited reference article Cheng et al., 2008, did not carried out SDM of the residues 54 and 63 in their original article, as claimed by the authors.
5.	Line: 573-578: Without any SDM data available on antifungal activity, it is very unlikely to suggest any potential residues involved in antifungal activity by doing sequence analysis only.
6.	Data for 797/798 sequences extracted, analyzed from different plant sources should also be provided in supplementary file, as mentioned in Boutrot et al., 2008.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: CONSPICUOUS COLOURS REDUCE PREDATION RATES IN FOSSORIAL UROPELTID SNAKES
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is overall well written and addresses an interesting question concerning an unstudied, conspicous color signal found in fossorial snakes. The authors, however, make insufficient use of references and have missed out on important literature from recent years relevant to their publication (examples and suggestions provided in general comments).
What is missing to make this a great manuscript is any information/data/observation on how much longer the handling time really is due to the hardened tail of these snakes. Further, figures should be of the same format and the authors should get rid of some redundancies within the manuscript (see general comments).
Experimental design: The design of the study is sufficient in respect to the hypothesis, however, data on avoidance learning caused by longer handling times (due to the snake’s hard skin shield) as well as data on handling times would significantly improve the overall work.
Validity of the findings: Findings of the study are valid and contribute to a better understanding of unexplained conspicuous coloration in animals.
Additional comments: I do like this manuscript and enjoyed reading about the authors' work. I commend the authors on their study. The study system is very interesting and the authors deliver a good approach to answer their hypothesis. Nonetheless, I have made a number of comments that the authors should consider:
L 37-38	snakes are only (mostly) brightly colored ventrally, correct? If so, please add “ventrally”
L 38-39	the sentence about Batesian mimicry could be discarded here as it might not be necessary in the abstract
L 65 & 67	I think there could be more general (classical) literature added (e.g. Poulton 1870, Cott 1940, Edmunds 1974, etc..)
L 68		give examples
L 69		examples and potentially literature on unexplained or unstudied conspicuous signals. This is extremely interesting and more research is being done on new systems. (for example, and see literature therein: Rößler et al. 2019)
L 70		suggestion: conditions devoid of light
L 71-72	mention examples of snakes (other than your study species)
L 73		“are visual stimuli”… to whom? Only to animals who can perceive this. Make this clearer here.
L 73		…“costly to produce”… This depends strongly on the color. There is a great difference between structural colors and pigments, and between different pigments.
L 79-81	please add information whether these species are diurnal or nocturnal (if information is present). And are they more likely to come to the surface at night or during the day?
L 84		is there any literature on tail morphology of this genus. If so, please cite.
L 84-86	what you describe here is a perfect description of a startle display or deimatic display. I wonder why you have not mentioned this term once in your manuscript. At least there should be a discussion whether this behavior coupled with the coloration could be deimatic (see Umbers et al. 2017, 2015, Umbers & Mappes 2015)
L 88-89	this seems a bit speculative. I imagine a hungry bird still being able to eat the snake, similarly other animals. Why would they keep directing their attack towards the tail?
L 98		main predators: is there information (observation/data/literature) on this? Or do you only assume birds are main predators? What about rodents? In case there is no info, please be more cautious with the phrasing
L 103		again, please use more cautious phrasing, you conclude that they have “evolved as a defense”, but your experiments, even though significant, are just models, you have no information on real predation (see Bateman et al. 2017, Rößler et al. 2018). You also have no information if coloration first evolved with different purposes (thermoregulation, immunobiology..) and later, secondarily, acquired an anti-predator function
L 108		insert space after 34
L 124		how were “representative leaves” chosen? This sounds very subjective
L 128-129	why did you not take measurements from the dorsal surface of the snakes. In the picture of figure 2 (the tail display), clearly the internal contrast, the conspicuous color builds against the dorsal color seems a lot more informative. I don’t disagree about the conspicuousness, but visual models, as nice as they are, really just compare two colors with each other, but detection and conspicuousness in complex environments are more multifaceted than a contrast. Just be cautious about this and the conclusions you draw from visual models
L 141		“contrasts” instead of “colours”
L 145		you mean Weber fraction?
L148		delete bracket
L 132-151	the visual modeling seems very thorough. Well done.
L 154		please clarify: a total of 500 models? Total of 1000 models? (both predation trials?)
L 161		you mention details for the acrylic paint here, why not for the clay product? I know it is in your supplements, but I think it is important to mention the clay product and brand in the main manuscript (again, see Bateman et al. 2017 & Rößler et al. 2018).
L 168		Cite literature and explain how you identified avian attack marks. (e.g. V-shaped or U-shaped marks, Willink et al. 2014)
L 169-170	why two different seasons? Did you check your data for effects? Also predators might be seasonally active, possibly skewing your data..
L 175		“with dough models edible to chickens resembling …” is more or less repeated in the next sentence again. Discard one.
L 178		the yellow and brown paper should be explained. When was which used and why?
L 185		delete bracket
L 196/197	G test & G-test. Please unify throughout the manuscript
L 204-205	please specify in which analyses post-hoc tests for multiple comparisons were conducted. It is not clear from this paragraph
L 219		significantly
L 241		redundancy of “position of first attacks”
L 242		significantly
L 255		may have evolved
L 264		double would
L 278-280	I am not convinced that the handling time would be increased to the extent of stopping an attack. I think deimatic display should be discussed here, including further examples of tail displays in other animals (e.g. Taricha granulosa).
L 280		please add literature on deflection strategies
L 291		I think there is a word missing after “however”.. can be?
L 302-305	split in two sentences. Again, a word missing, after “support”
L 313-328	very nice paragraph, good use of literature!
Literature:	check your literature for genus and species names and use italics (Dendrobates pumilio, Parus major etc…). also check Gans 1986, here you use the journal abbreviation

Figure 4A: why use a different bar chart format here? Be consistent. So, either use the same as in Figure 3 or change Figure 3 to the format of Figure 4A. (use same label of y-axis, grid vs. no grid, p-values vs. asterisk..)

Figure 4B: the snippet of the snake looks a bit sloppy. If possible, either remove the dark background thoroughly, use a different photo, or draw up a simple illustration.
The following bit might be a bit pedantic (feel free to ignore): Use a different illustration of body regions than the curly brackets you used (Even square brackets are okay, either way, please make sure to align them)

You do not mention the supplementary tables S1 and S2 within the text, and I am not entirely sure what they contain (especially S1), as the caption is not really explaining it well. Please explain these supplements and refer to them in the text if needed.

General: check your manuscript for double spaces (“  “), I think I saw some.

References I mentioned in my comments:
Bateman, P.W., Fleming, P.A., Wolfe, A.K., 2017. A different kind of ecological modelling: the use of clay model organisms to explore predator--prey interactions in vertebrates. Journal of Zoology, 301(4), 251–262. https://doi.org/10.1111/jzo.12415

Cott, H.B., 1940. Adaptive coloration in animals, Vol. 540. Oxford, England: Oxford Adaptive coloration in animals.

Edmunds, M., 1974. Defence in animals: a survey of anti-predator defences. Burnt Mill: Longman.

Poulton, E.B., 1870. The colours of animals: their meaning and use, especially considered in the case of insects, p. 400. New York: D. Appleton.

Rößler. D.C., Pröhl, H, Lötters, S. 2018. The future of clay model studies. BMC Zoology 3:6. https://doi.org/10.1186/s40850-018-0033-6

Rößler, D.C., Lötters, S., Mappes, J., Valkonen, J., Menin, M., Lima, A.P., Pröhl, H. 2019. Sole coloration as an unusual aposematic signal in a Neotropical toad. Scientific Reports. https://doi.org/10.1038/s41598-018-37705-1

Umbers, K.D.L., De Bona, S., White, T.E., Lehtonen, J., Mappes, J., Endler, J.A., 2017. Deimatism: a neglected component of antipredator defence. Biology Letters, 13(4). https://doi.org/10.1098/rsbl.2016.0936

Umbers, K.D.L., Lehtonen, J., Mappes, J., 2015. Deimatic displays. Current Biology: CB, 25(2), R58–R59. https://doi.org/10.1016/j.cub.2014.11.011

Umbers, K.D.L., Mappes, J., 2015. Postattack deimatic display in the mountain katydid, Acripeza reticulata. Animal Behaviour, 100, 68–73. https://doi.org/10.1016/j.anbehav.2014.11.009

Willink, B., García-Rodríguez, A., Bolaños, F., Pröhl, H., 2014. The interplay between multiple predators and prey colour divergence. Biological Journal of the Linnean Society. Linnean Society of London, 113(2), 580–589. https://doi.org/10.1111/bij.12355


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: CONSPICUOUS COLOURS REDUCE PREDATION RATES IN FOSSORIAL UROPELTID SNAKES
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Review of Uropeltid snake colors

This is a lovely study with excellent methods and scholarship, but I’m not convinced that the authors have ruled out simpler alternative hypotheses to the one that they present in this manuscript. It needs either to be rewritten, or more data. My detailed comments are below.

63-68: This is actually too broad – could be cut
72-73: Colors aren’t necessarily costly to produce if their structures have some other function. After all, an organism has to have some sort of spectral reflectance distribution
95-104: This hypothesis has strange logic. The cephalized tail is hypothesized to deceive predators, yet the warning coloration is hypothesized to alert predators to this deception.
145: Weber
171-186: It seems that the most appropriate experiment to test whether a cephalic tail increases handling times would be pastry snakes with a distinct head and tail, and pastry snakes with two heads. Birds can certainly learn different handling times in general – there is a mountain of literature to show this. Furthermore, many studies with artificial snakes in the field have shown that attacks are directed towards the heads of snakes rather than the tails. It’s not easy to see what is gained from this experiment.
195: Only a G-test or the GLMM should be used, to present both is redundant. It should really be the GLMM since it reflects the design of the experiment.
229: P-value comes from the Likelihood Ratio Test? Please specify
234 – 238: Isn’t this saying the same thing? Confusing
265: Furthermore
267: Pfennig & Mullen PRSB would be relevant to cite here
284 -290: would be very relevant to have in the Introduction. Also, what were the handling times for snakes that were attacked at the head?
291-301: The major problem that I have with this hypothesis is that to learn that uropeltid coloration signals long handling times, birds would have to encounter multiple snakes, yet encountering multiple snakes makes them more likely to learn to distinguish head from tail. The distinctive colors of uropeltids might then even act as a cue to alert predators to the possibility of the false head. In fact, it is hard to imagine that this is something that the birds wouldn’t learn. To be convinced of the plausibility of this paper’s hypothesis, I would need to see that cephalized tails increase handling times, and that avoidance of colors associated with long handling times is learned more quickly than distinguishing false heads from real heads. Additionally, it would be interesting to see if there is an interaction between tail shape and coloration on attack probability. At present, it is more parsimonious (and equally consistent with the data) to conclude that birds have an innate aversion to uropeltid colors, and that the cephalization of uropeltid’s tails misdirects predator attacks, but that there is not an interaction between the two strategies.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: CONSPICUOUS COLOURS REDUCE PREDATION RATES IN FOSSORIAL UROPELTID SNAKES
Review round: 2
Reviewer: 1

Output:
Basic reporting: I’m happy to see that the authors have significantly increased the use of literature as well as applied the reviewers’ suggestions on several aspects of the discussion, improving the overall manuscript.

Yet, I have a few minor comments (Lines refer to the document including track changes). You can find these under the general comments.
Experimental design: see general comments
Validity of the findings: see general comments
Additional comments: L. 90 		mornings
L. 323-338	I appreciate your inclusion of discussing a deimatic signal function, however, I think that you are too concerned in this paragraph about comparing this function to what you did in your experiment. I do not think this is necessary. Your models were neither moving, nor in the potential startle position, thus, there is no need to compare it, because you simply did not test any deimatic function with your models. I just think, based on the photograph, it is important to mention and discuss the potential presence of deimatism, but be clear that this was not what you tested (or intended to test). I disagree that the avoidance of your static models by birds conveys any information about a potential startle function.
L. 341		be consistent about your use of British English, thus: behaviour
L. 342-344	This sentence is a bit clumsy, can you rephrase?
L. 344		Hence,
L. 344		has
L. 350		shapes
L. 352		be careful about the use of “cue” vs. “signal”. You use “colour cue” here. Be sure to know the difference and use the one you really mean.
L. 355		repetition of predator


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: CONSPICUOUS COLOURS REDUCE PREDATION RATES IN FOSSORIAL UROPELTID SNAKES
Review round: 2
Reviewer: 2

Output:
Basic reporting: see below
Experimental design: see below
Validity of the findings: see below
Additional comments: Review of Uropeltid Snake Colors Revision

The authors have made revisions that greatly improve the manuscript. Still, I am concerned that the hypothesis they advocate for is not the only hypothesis that should be considered to explain the coloration of these fossorial snakes, because given the data available it is not possible to reject simpler alternatives. I think that the presentation needs to be changed to better reflect the information we have gained from the experiments that were done, i.e. which hypotheses were rejected by the data consideration.

1)	I do actually insist that the authors get rid of the G-squared test where the GLMM can be substituted for it; presenting methods used in other studies only makes sense if parameter estimates and their standard errors are going to be extracted and compared. The G-squared test doesn’t provide this information, and is more likely to produce spurious results because it doesn’t account for the structure of the data.
2)	The authors make persuasive arguments in the new Discussion for the plausibility of their hypothesis, but even those these new arguments are very interesting, they don’t add new data that reject other hypotheses. So this doesn’t really address the comments that I made on the earlier draft. It does seem that the data can reject Batesian mimicry, since both yellow and red were protected when local coral snakes are red, but how can one reject the hypotheses that a) tail shape and color operate independently, or that b) tail shape and color interact to misdirect attacks towards the tail (when the tail is flipped upside down, as in Figure 2), but that they aren’t actually signaling longer handling times? The replicas used in the field don’t seem to display the natural defensive positions of these snakes, if Figure 2 is representative, making it even more difficult to conclude exactly what the functional relationship between tail shape and coloration is. I want to be clear that I think the authors have every right to propose the hypothesis that they propose, but I don’t think it is consistent with the scientific method to present it as the hypothesis that is best supported by the data. We trust the hypotheses that we have attempted to reject the most rigorously, and fail to reject after other contenders have been eliminated.
3)	I didn’t catch this on the first read-through, but in the field experiments, are attacks more frequently directed towards the heads, tails, or midsections? Is the pattern consistent with the captive chicken experiment?

261-265: This is a bit odd – if there is no significant difference, it is more accurate to say that the groups were not different.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: CONSPICUOUS COLOURS REDUCE PREDATION RATES IN FOSSORIAL UROPELTID SNAKES
Review round: 3
Reviewer: 1

Output:
Basic reporting: I think the authors sufficiently addressed the concerns raised by the reviewers and revised their work where possible. While there might remain shortcomings in experimental design (which I know are not revisable at this point), I think this study is ready to be published.
Experimental design: see above
Validity of the findings: see above
Additional comments: see above


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: CONSPICUOUS COLOURS REDUCE PREDATION RATES IN FOSSORIAL UROPELTID SNAKES
Review round: 3
Reviewer: 2

Output:
Basic reporting: See Below
Experimental design: See below
Validity of the findings: See Below
Additional comments: The authors have addressed my concerns. I don't see any reason to hold this paper up.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: DYNAMICS OF A METHANOL-FED MARINE DENITRIFYING BIOFILM: 1-IMPACT OF ENVIRONMENTAL CHANGES ON THE DENITRIFICATION AND THE CO-OCCURRENCE OF METHYLOPHAGA NITRATIREDUCENTICRESCENS AND  HYPHOMICROBIUM NITRATIVORANS
Review round: 1
Reviewer: 1

Output:
Basic reporting: This interesting study tests the effect of different levels of various physico-chemical parameters on the denitrification and the co-occurrence of the key taxons, Methylophaga and Hyphomicrobium, in marine methanol-fed denitrification system. It shows the plasticity of the marine methylotrophic biofilm in adapting to different conditions and gives also new insights into the factors controlling the abundance of the key taxons.

The manuscript is written in good English for most parts (see some comments in the general comments part).
Experimental design: The design is quite complex but it is nicely described in the text and in the tables and figures (incl. supplementary).

Research questions and aims are defined but they are mainly very technical. What would be your ultimate aim? Why would make this study? That information is lacking in the introduction. Is it because you want to know how the denitrification and community is controlled in order to benefit the development of optimal denitrifying bioprocess conditions (as stated in abstract)?
Validity of the findings: ANOVA-analysis is done only to test differences in denitrification rates. Why it is not done to test differences in other reported and discussed parameters like protein, growth and qPCR results?

Conclusions should not contain reference to the sister study which has now been also submitted to PeerJ (lines 501-504). Can you move this to discussion or to introduction?

You could also answer your ultimate aim in the conclusions. E.g. if the study is done to benefit the development of optimal denitrifying conditions, then please answer, how this benefits it, or at least if it benefits it? Thus, in general, please answer your ultimate aim in the conclusions.
Additional comments: Abstract

Abstract´s results and conclusions: You report GP59 and NL23 results but not JAM1 results here. Should you include JAM1 here also?

Abstract´s results: Inhibition occurred…. at pH10 or with 1.5% methanol. Should this be reworded in such way that reader understands that HIGH pH and HIGH methanol inhibited the process? Of course, everybody understands that pH 10 is high. But somebody unfamiliar with the subject may not know that 1.5% methanol is high.

Abstract´s conclusions and study´s conclusions: How these results could benefit in the development of optimal denitrifying process?

Introduction

Line 67: Do you mean fluidized-BED?

Line 80: …bioprocess denitrifying activities (Reference lacking here).

Line 87: please correct “reducing NO3- to NO2- “ (not in)

Line 96: strain (not stain)

Results

Line 391: were similar to that reported… (not than)

Discussion

Line 429: stayed (not strayed)

Line 431-432: What factors specifically you suggest make the difference between batch mode system and the original continuous flow system?

Line 479 – 493: This is a matter of taste. However, I think that this part referencing Osaka et al 2008 and Rissanen et al. 2016 could be mentioned in shorter way in the introduction section together with references to your previous works just to show that the Methylophaga and Hyphomicrobium are generally the key taxa in marine/saline methanol-fed denitrification. This could add even more strength to justify your study.

Line 489-490: Please rephrase e.g. “The other denitrification system that is similar to the one that was used at the Biodome is a methanol-fed…”


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: DYNAMICS OF A METHANOL-FED MARINE DENITRIFYING BIOFILM: 1-IMPACT OF ENVIRONMENTAL CHANGES ON THE DENITRIFICATION AND THE CO-OCCURRENCE OF METHYLOPHAGA NITRATIREDUCENTICRESCENS AND  HYPHOMICROBIUM NITRATIVORANS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Payette et al. provide a manuscript in which they assess the influence of diverse physico-chemical parameters on the denitrifying activities in a methanol-fed marine biofilm. The main drivers in this marine denitrifying biofilm are Methylophaga nitratireducenticrescens and Hyphomicrobium nitrativorans. In this study, they are able to show, that this biofilm can adapt to varying conditions, while keeping it’s denitrifying capacity.

Payette et al. provide a clear introduction and background to the topic. However, two questions arise from the introduction:
1)	To what purpose was the marine effluent treated with this biofilm and how was the marine effluent composed?
2)	In line 108 the authors state that the genome of strain GP59 is highly similar to that of strain JAM1. To the authors mean the whole genome or just the genes in respect to denitrification? If the authors mean the whole genome, then a more in depth genome comparison should be provided. If they only mean in respect to certain denitrification genes, then this should clearly be stated and also shown, e.g. with a comparison of the genes, gene arrangement, gene neighbourhood.

Payette et al. provide clear and relevant figures of high-quality.

Following language changes are suggested:

Line 30: change here and elsewhere: ‘the Reference biofilm’ to  ‘the reference biofilm’

Line 45: exposed to pH 10 or to 1.5% methanol

Line 56: development of an optimal denitrifying bioprocess

Line 92: H. nitrativorans NL23 have been sequenced previously

Line 94: ‘during growth of this strain’ or ‘during growth of strain JAM1’

Line 95: Do the authors mean cNor or is this a typo?

Line 96: Change stain to strain

Line 104: batch-mode and anoxic conditions

Line 129: trace elements

Line 131, 133: under ‘various concentrations’ a range should be provided or a reference to a Table indicating the range used

Line 132: Filter-sterilized methanol

Line 149: On average
Line 162: Figure S2 describes the protocol in detail.

Line 164: For the assays that were performed

Line 363: change ‘two-three’ to ‘two to three’

Line 370: ‘which is similar to that found…’

Line 375: ‘at similar level as in the OB’

Line 391: ‘were similar as reported in’

Line 397: ‘were the same as in the…’

Line 398/399: delete ‘important’

Line 403: ‘as in the OB’

Line 415: ‘similar to the ones in the…’
Experimental design: Payette et al. provide here original primary research. In addition, the authors identify how this research could benefit the development of an optimal denitrifying bioprocess.

In line 169 the authors state that “most assays were performed in triplicates”. This is a bit vague. Why have not all assays been carried out in triplicates. Which assays in particular have not been carried out in triplicates and how could that effect the results and conclusions?

Figure 1, Panel B: Was the same concentration of DNA loaded per DGGE lane? If yes this should be stated in Methods and also how much.
Validity of the findings: Payette et al. provide a clear and sound results section.

For the finding  in line 279: ‘Absence of methanol showed very weak denitrifying activities as expected’ more explanation is needed for the reader in order to understand why this is expected.

In lines 435 to 441 the authors could elaborate on the pH optimum of the enzymes, since this might also be a possible explanation for these results.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: DYNAMICS OF A METHANOL-FED MARINE DENITRIFYING BIOFILM: 1-IMPACT OF ENVIRONMENTAL CHANGES ON THE DENITRIFICATION AND THE CO-OCCURRENCE OF METHYLOPHAGA NITRATIREDUCENTICRESCENS AND  HYPHOMICROBIUM NITRATIVORANS
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Just few very minor things.

Lines 62-64. Citations are written twice.

Line 155. I think the correct form to write desimals is 51.2 g/L, not 51,2. (maybe check through the manuscript for this).

Figure 3. “Panel A” and “panel B” are not mentioned in the figure text.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: DYNAMICS OF A METHANOL-FED MARINE DENITRIFYING BIOFILM: 1-IMPACT OF ENVIRONMENTAL CHANGES ON THE DENITRIFICATION AND THE CO-OCCURRENCE OF METHYLOPHAGA NITRATIREDUCENTICRESCENS AND  HYPHOMICROBIUM NITRATIVORANS
Review round: 2
Reviewer: 2

Output:
Basic reporting: All changes were made as suggested and the manuscript was considerably improved.
Experimental design: All changes were made as suggested and the manuscript was considerably improved.
Validity of the findings: All changes were made as suggested and the manuscript was considerably improved.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: GRAZING EFFECTS ON WOODY AND HERBACEOUS PLANT BIODIVERSITY ON A LIMESTONE MOUNTAIN IN NORTHERN TUNISIA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript provide information on maquis vegetation subjected to various intensity of grazing pressure in Tunisia. The authors suggested that grazing can substantially influence the subjected communities and higher grazing pressure cause a homogenisation (expressed in a decrease of beta diversity) but moderate grazing helps to sustain biodiversity. Based on my evaluation the paper has some shortages which should be treated in a revision. Major point of critique subject sampling setup, quantification of grazing and the consciseness of the ms.
Experimental design: (i) Sampling setup – it is not clear how plots/sites were selected for study, which type of livestock grazing subjected the sites (i.e. it is written briefly that goat, sheep and cattle was grazed there – but this type of grazers cannot be treated equally – goats grazing almost everything, sheep are rather selective for forbs, while cattle grazing is directed to community dominants – i.e. in grasslands mostly to the grasses and are selective for patches with high biomass). See respective very recent case study comparing cattle and sheep grazing Tóth et al. (2018).
Tóth et al. (2018):  Livestock type is more crucial than grazing intensity: Traditional cattle and sheep grazing in short-grass steppes. Land Degradation & Development, DOI: 10.1002/ldr.2514
(ii) Quantification of grazing – You mentioned here that the magnitude of grazing pressure was quantified mostly by a the semi-quantitative (ordinal) scale – how high was livestock browsing on trees and shrubs and how high was the presence of other tracks (e.g. fur, droppings). But then you made conclusions on graminoids/forbs of the understory. How could you do that if you haven’t assessed the browsing effects on it at the same scale? It could be that grazing is not subject the trees/shrubs but highly affect the understory. Also it is rather unclear, how you made the assessment that 71% of sites were subjected almost no grazing (group 1). You assessed all schrub and tree species ranking them into the 4 grazing category and finally you made a semi-quantitative mean and if the overall score was below 1.5 than you considered it as not grazed? Some details would be necessary here.
Validity of the findings: No comment. Can be evaluated after the methods section is clear.
Additional comments: (iii) The ms is far too long. I suggested below shortening for the intro, but other sections of the ms also should be shortened by at least 20%. Too wordy and overloaded – but not for the really necessary information.

l59-65 You should also consider rich research in grassland grazing – which has quite similar outcome to your expectations for maquis vegetation. See for example Török et al. (2016) special issue in AGEE for grazing and papers therein.

Török et al. (2016): Grazing in European open landscapes: how to reconcile sustainable land management and biodiversity conservation? Special Issue in Agriculture, Ecosystems and Environment.
https://www.sciencedirect.com/journal/agriculture-ecosystems-and-environment/vol/234

l103-110 Can be omitted.
l111-129 Shorten and move some sections concerning site description to the Materials and methods section
l133 What beta diversity do you refer here (I assume Bray-Curtis similarity)
l136-140 Can be omitted.
l181-192 should be more precise – see general comments – grazing animals, site selection – and maybe a figure on the sampling setup would be fine.
l221-222 Not considered forbs and graminoids in grazing intensity measures. How were grazing effects (i.e. different levels of grazing on subjected species – there is generally preferred and non-preferred species with different levels/magnitude of grazing)
l235 Provide details on altimeter or skip.
l270 which livestock type, was it subjected different type at different site(s).
l400-404 If you do not provide information on vegetation differences, site heterogeneity we cannot assume that the sites were different because of different levels of grazing…


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: GRAZING EFFECTS ON WOODY AND HERBACEOUS PLANT BIODIVERSITY ON A LIMESTONE MOUNTAIN IN NORTHERN TUNISIA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The study examines the effect of grazing and other environmental factor on the vegetation composition of an area in southern Mediterranean region. Given that this region is rather underrepresented in the relevant literature regarding the ecology of Mediterranean ecosystems, the data presented in the manuscript are interesting and worth publishing in an international Journal such us PeerJ. The manuscript reads well and academic English is used throughout. Some spelling and typing errors does not change the proper use of English language. The scopus of the study falls within the interests of the Journal. However, there are several issues that need to be addressed before the manuscript is considered for publication.
The introduction is well written, well structure and well referenced providing all the necessary background information to the reader which allows him to understand the historical role of humans in shaping the Mediterranean landscape, and the need to reconcile anthropogenic activities with nature conservation under the frame of climate and global change. Perhaps it is too extensive and it could be shortened without missing vital information, but I do not consider it an issue for an open access journal.
Experimental design: The sampling design was originally designed for a floristic inventory rather than the study of grazing intensity effect. This resulted in an uneven distribution of the grazing classes within the samples. Furthermore, given the higher sampling intensity of the northern slopes I assume that the most intensively grazed areas were avoided as they probably were too degraded. The uneven representation of the grazing classes within the sample, results in several issues regarding the conclusion that can be drawn based on the multivariate analysis performed in the manuscript. Furthermore, given the high sampling intensity I assume there might be several spatial autocorrelation issues among the samples which the author did not account for. This must be especially true for the low intensity grazing class. Perhaps the authors should run an autocorrelation analysis first and omit some samples which show high spatial autocorrelation. This would result to a smaller number of samples for the further analysis but perhaps more evenly distributed among the grazing intensity classes.
The authors use an indirect method of measuring grazing intensity which relies on the morphological characteristics of shrubs. Although this method does not provide accurate estimation of grazing intensity, compared to other methods such as pellet or animal counts, it is appropriate for such study since it is able to capture the log term effect of grazing on vegetation structure. This is particularly true for woody species which does not respond as quickly as herbaceous species to changes in the grazing regime.
In lines 268-279 the authors describe the way data related to human footprint were collected. It is not clear to me how road data were collected based on OpenStreetMap dating back to 1982. Furthermore, proximity to roads and settlements is often used as a proxy of grazing intensity since in eastern Mediterranean where extensive husbandry is still practiced the herds are mostly kept around settlements. Thus, those two experimental variables when they are accounted for it is expected that the effect of grazing will be minimised. Distance from roads and settlements have only an indirect effect on vegetation through the severity of human activities including wood cutting, grazing and fire. So including them as covariables is likely to obscure the effect of grazing and other anthropogenic activities.
The way environmental variables are treated in order to avoid anomalies in their distribution and collinearity is sound and appropriate and so are the statistical methods employed.
Validity of the findings: The results presented in lines 390-399 are rather confusing. According to the authors the nMDS analysis reveal a clear effect of grazing but at the same time they imply that the grazing has a clear altitudinal pattern. If this is the case how the effect of grazing is separated from this of altitude. In my view perhaps axis 1 represents a grazing intensity gradient, but it is difficult to sai that with certainty because no clear clustering occurs and the high intensity grazing sites fall along the first axis between the no grazing and low intensity grazing sites. Axis 2 seem not to be related to grazing. With that being said I don’t think that the claim made by authors that Ceratonia siliqua is an indicator of unbrowsed sites is justified by this ordination plot. Figure 3 again is not able to give some indication or hypothesis on the potential role of grazing in species composition since again no clear clustering of samples occur. I believe to a great extent that this occurs due to the uneven sample sizes between the 4 grazing regime classes.
In lines 408 to 427 the authors present the results of a modelling approach based on dbRDA. The two ordination plots (4a and b; reference to 4b is missing in the text) and the presented results seem to underestimate the effect of grazing for woody plants (given that it rarely appears in the models). However, I believe that the way geographic location is treated here which according to authors represent a proxy of humidity might confound the effect of other factors including grazing. I am not sure geographic location is an appropriate proxy for humidity and a valid explanatory variable and the results I think they justify my previous comment that an autocorrelation analysis is needed beforehand.
In line 439 why the authors do not accompany their result with a figure as part of figure 5? In lines 450-456 the authors state that there is a significant effect of grazing in the herbaceous species richness and diversity but Supplementary Figure 3 suggests otherwise.  There is a discrepancy there that needs to be clarified. Furthermore I believe Supplementary figure 3 should be included in the main manuscript for the woody plants where significant effects are found.
In lines 460-468 the authors mention in the text tables 4a and b but only one table 4 seem to exist in the tables. Figures 7c and d are not mentioned in the text and the caption is incomlpete.
Overall it seems to me that grazing had a minor effect in determining the vegetation structure and composition in the study area which is rather surprising especially for the beginning of 80s. I also believe, as the authors do, this has to do with the way the grazing intensity classes are represented in the sample and a careful filtering of the samples based on spatial location and autocorrelation issues would reveal a much more informative picture regarding the effect of grazing and other factors.
Apart from the first part of the discussion, in the rest various issues relate to the ecology of Mediterranean ecosystems are discussed which are not directly related to the presented results.  However, it is very well written and interesting and I believe the authors could change the scopus of the study into a more generic investigation of factors affecting vegetation structure and composition in the area, and focus on some specific species and assemblages of conservation and ecological importance much of those discussed in the manuscript would be in accordance to the presented results.
Additional comments: Overall I would like to encourage the authors to elaborate more on their data, alter the aim and objectives of the study and revise the manuscript because I sincerely believe that there is important knowledge that can be generated by this dataset despite its age.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: GRAZING EFFECTS ON WOODY AND HERBACEOUS PLANT BIODIVERSITY ON A LIMESTONE MOUNTAIN IN NORTHERN TUNISIA
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: The manuscript contribute significantly to the scientific literature regarding the ecology and dynamics of Mediterranean ecosystems. This contribution becomes even more significant considering that it regards a geographic region rather underrepresented in the literature and vulnerable to the foreseen climate and other socioeconomic changes.
Additional comments: Dear Editor and Authors.
I am glad to have contributed to the substantial improvement of the manuscript. All my comments have been properly addressed by the authors in the revised version of the manuscript. With that being said I have no hesitation to recommend the publication of the manuscript and I am looking forward to see it published in PeerJ.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: MITOCHONDRIAL DNA IN HUMAN IDENTIFICATION: A REVIEW
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper is an overview of mtDNA typing in forensics and the main topics of the field are illustrated and discussed, though not all of them in exhaustively way. The main issue is to better and clearly explains the fundamental concept concerning the use of mtDNA in forensic identification, that is mtDNA data cannot be applied to the identification of individuals in the same way that nuclear marker can, but it can be used only to make inference about the maternal lineage. This important point should be emphasized.
Other important areas to be improved and updated are nomenclature and sequencing methodology sections.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: There are some points that should be revised:
Introduction
Lines 33, 39: it’s not very clear the difference between “medico-legal purposes” and “forensic purposes”. Please explain why you used both terms.
Line 41: references 1-4 are related to guidelines for mitochondrial DNA typing and they not seem very pertinent in this point of introduction. I suggest to mention other general reviews regarding the use of mtDNA in forensics.
Lines 42-50: This paragraph is identical to the abstract in the previous page. I suggest that you improve the introduction to better explain that mtDNA data cannot be applied to the identification of individuals in the same way that nuclear marker can, but it can be used to make inference about the maternal lineage. I suppose that this review is addressed to not expert users in forensic mtDNA, so this important point should be emphasized.
Survey methodology
Lines, 57-59: If not those cited, what are the selection criteria used?
Mitochondrial DNA biology and genetics
Line 84: Reference number 10 isn’t Andrews et al. Please correct. Moreover the revised mtDNA sequence (rCRS) published by Andrews et al. in 1999 is the reference sequence currently used. Therefore Authors should replace CRS with rCRS throughout the text (e.g lines 161 and 165).
Line 116: The term “haplogroups” need explanation and definition.
Lines 132-141: The sequences comparison issue seems to be not inherent in this paragraph. I suggest to put this issue in another specific paragraph related to forensic interpretation and reporting results of mtDNA typing. Moreover it could be appropriate to mention also the SWGDAM mtDNA interpretation guidelines 2013.
Mitochondrial DNA Nomenclature
Authors describe in this chapter the issue of mtDNA polymorphisms nomenclature, however the topic has not been exhaustively handled, it has poorly precise and it has not updated. For these reasons, this section requires a thorough and wide review. First of all, authors mentioned the nomenclature approach of Wilson et al (ref 37) based of a set of formal rules that was later modified by Budowle et al in 2010, but only the first version of this approach is describe in this review, so it isn’t update. Moreover, the ISFG proposed another kind of nomenclature, based on phylogenetic approach (see guidelines in ref. 4) and it has not even been mentioned. It would be appropriate to mention both and discuss the difference. Otherwise the Authors explain why describe only one approach. Actually, Authors mentioned the phylogenetic approach in Table 2, in the context of ISFG guidelines, but without a discussion. Moreover, the revised mtDNA sequence (rCRS) is the reference sequence used for comparison and notation of polymorphisms and not the CRS. Deletions are annotated as “DEL” or “-“ , and not with a “D”, to avoid confusing with IUB code, where D is considered a mixture of A, G, and T.
Mitochondrial DNA typing guidelines
Line 197: Table 1 is cited after Table 2…it could be better to rename tables in order of appearance in the text.
Mitochondrial DNA sequencing methodology
In this chapter Authors provide an overview of the DNA sequencing methods used in forensic, but I suggest to limit the text only to sequencing methods used for mtDNA typing. The text will appear more fluid and a more detailed description of Sanger sequencing by capillary electrophoresis, which is the most widely used method, would be useful. Moreover, the use of terms like “second generation”, “third generation” seems to be a little confused, please revised to provide more clear definitions. Lastly, the review lacks of information about mtDNA amplification strategies ( e.g complete mtGenome amplification, or entire control region (CR) amplification in a single PCR reaction, or CR region amplification in different overlapping fragments, or HVI-HVII-HVII  in separate amplification) which could improve this chapter.
Lines 236-240: reference 53 could be cited together with other ref at line 246, as it isn’t one of the first study of mtDNA sequencing by MPS and it is relative to heteroplasmy issue.

Mitochondrial DNA population data and databases
The text needs a different organization. I suggest to move the EMPOP section after line 257, as it represent the most important mtDNA haplotypes database for forensic purposes, among those mentioned in the text.
Lines 258-269:  I suggest to eliminate this part, as it seems to be not pertinent in this chapter, and to move it  to another chapter.
Mitochondrial DNA population data and databases
Line 385: reference 97 isn’t relative to Park et al. and it isn’t cited in table 1. Please insert in table 1 reference numbers of cited papers.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: MITOCHONDRIAL DNA IN HUMAN IDENTIFICATION: A REVIEW
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is a review on the role of mitochondrial DNA in medico-legal area. In this regard, the article requires a thorough revision and the following issues should be adressed:
- No reference is made to the last article on the presence of paternal mitochondrial DNA in a group of families, which would have consequences in the field of forensic identification.
- It is mentioned CRS but not rCRS or RSRS., why?
- Reference is made to the nomenclature but the way of transcribing the mutations is not that used in the forensic field (line 162 16,192 C).
- There is some confusion with the reference 93. It is not clear if it refers to an article from 2012. However, in this case mitochondrial DNA is not used. It could be also an article of 2010 but there would be wrong authors, publication data, etc.
- Finally, the conclusions are somewhat surprising. The topic of recombination or paternal mitchondrial DNA is referred to as "challenges", however, this has not been addressed in the review. It also indicates that for years its admissibility or its relation to diseases has been questioned but this aspect are not adressed  in the revision either.
In my opinion these are severe flaws of a wide scope review like this.
Experimental design: No coment
Validity of the findings: No coment
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: MITOCHONDRIAL DNA IN HUMAN IDENTIFICATION: A REVIEW
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors appear to have addressed all the issues raised in review. The only point to solve is that Authors in their rebuttal letter stated that reference to Ambers et al.  was  included in Table 2, but is not so.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: MITOCHONDRIAL DNA IN HUMAN IDENTIFICATION: A REVIEW
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: The authors have reviewed the text with all the corrections that were made to them. But the should check:
line 187. Regarding the nomenclature there are some errors. In the case of deletions, "del" is also accepted in addition to DEL or -. In addition N implies that the 4 bases appear and not that it is unambiguous. In addition, those rules that are literally copied from Parson's article should appear in quotation marks or in italics. The authors should review that paragraph.
line 348. The exclusion rules indicated do not correspond to the article by Parson et al., 2014. Indicate the correct reference.
References. Please change the Rios reference. The corresponding reference to Rios et al. (2010) is:
Identification process in mass graves from the Spanish Civil War I.
Ríos L, Ovejero JI, Prieto JP.
Forensic Sci Int. 2010 Jun 15;199(1-3):e27-36. doi: 10.1016/j.forsciint.2010.02.023.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: DYNAMICS OF A METHANOL-FED MARINE DENITRIFYING BIOFILM: 2—IMPACT OF ENVIRONMENTAL CHANGES ON THE MICROBIAL COMMUNITY
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors conducted meta-transcriptome analysis to compare expressing gene and potentially growing bacteria strain among different conditions of two temperatures, four saline conditions, and four nitrate concentrations. The control experiments were performed and were well summarized as showing high quality figures and tables. Additionally, they also isolated some bacteria strain from the biofilm from denitrification reactor in a national science museum. However, the manuscript includes many ambiguous contexts and was written unclearly. The inconsistence between objectives and conclusion is critical, besides the objectives is unclear in the manuscript. The text format and wording, especially technical terms, should be collected.
Experimental design: Each experiment was designed well and well written. However, the objectives and conclusion were not clearly written.
Validity of the findings: The objectives of this study were stated in abstract (L27–28), ... impact of culture conditions on the dynamics of the overall microbial community.... However, it is not mentioned in the introduction section where "objectives" should be explained logically and clearly. Worse, the answer for the objectives were unclearly mentioned in the conclusion section. It is unclear that what the impact of NaCl, nitrate and temperature on the denitrifying biofilm.

The sections of introduction and results includes inappropriate descriptions.
For introduction section, information of the biofilm from the Biodome is well written but the appropriate explanations for meta-transcriptome analysis (L112–115) and isolation of bacteria strains (L116–177) were lack. Worse, the last paragraph showed the results of the present study that should be in results section.
For results section, some paragraphs include the descriptions of materials and methods, eg. L231–237, L286–296, L304–314, L369–373, and L428–434. Please re-construct the context throughout the manuscript to make descriptions in appropriate section.
Additional comments: Ambiguous and unknown wording should be corrected.
For the bacteria strain of M. Nitratireducenticrescens strain GP59, some different descriptions were seen, eg. M. Nitratireducenticrescens strain GP59, strain GP59, and GP59. Please use appropriate term for them.
In addition, the description of "GP59 gene" is not correct word for indicating "genes of strain GP59".

Unknown/Undefined terms: "concentration". (L92 and L303)

Please correct the format of references in text. (L469–471)


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: DYNAMICS OF A METHANOL-FED MARINE DENITRIFYING BIOFILM: 2—IMPACT OF ENVIRONMENTAL CHANGES ON THE MICROBIAL COMMUNITY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript was clearly written and well structured, however some language errors (spelling and grammar) were found throughout the text. Please proofread the text.

I understand this study is one in a series of studies, however, this paper should be self standing without knowledge of the previous work or even more, work that has has been done but not  published yet. Throughout the paper there are references to a submitted article (Payette et al 2019) which is not accessible to the reviewer at this point. Please provide sufficient information in the text.

Figures and tables are relevant to the article.

Raw sequence data were properly deposited in public repositories.
Experimental design: The article is within the aims and scope of the journal.

In this study, the authors studied the composition of microbial community of a denitrifying biofilm maintained under different growth conditions, studied the transcriptional activity of bacteria in a denitrifying biofilm and in planktonic cultures. The authors also isolated denitrifying bacteria from the biofilms into pure cultures. As stated in lines 599-600, the information from this study should be applicable for development of an an optimal denitrification bioprocess for a marine system.

There was a lot going on in this paper and significant efforts were put in to produce the data. However, I think the study should be framed better, the main goals for this particular paper should be be more clearly stated and the results should be presented so that they form a coherent story and answer the specific research questions. In its present form, different parts seem to be loosely tied together and the results seem more descriptive than answering the specific research questions or proofing/disproofing hypotheses.

One of my major criticisms regards the experimental design. In this study, the authors wanted to test the effect of different environmental conditions on microbial community composition and gene expression patterns. The conditions for the cultures were listed in Table 1. According to this information, in culture 900N-23C two parameters and in 900N-30C three parameters are changed simultaneously compared to the control. How is it possible to to tell apart the effect of a single parameter when multiple parameters are changed at once?

There were also some major shortcomings in describing the methods: The reporting of bioinformatics methods (Lines 146-150) for the 16S reads is not sufficient to replicate the analysis. You should report which programs and which versions were used at each step. Were there any changes to default parameters? Also references to computer programs, such as UCHIME, are missing. Secondly, from line 123 onwards in materials and methods-section: there are some qPCR data in results but the qPCR assay is not described in materials and methods.
Validity of the findings: The conclusions starting from line 580 seem rather general and they didn't really answer all of the specific research questions presented in the beginning of the article.

There was no statistical testing for the microbial community composition data to tell whether the observed changes were significant or not?

Overall, in the light of the results and conclusions, it remained unclear, how do these results help in developing better denitrification systems for salt water systems.
Additional comments: Below are some detailed comments regarding some specific issues in the text.

Lines 23-24: Line "...exposed to a range of physico-chemical parameters" sounds odd as you probably mean environmental conditions. Please reword the sentence.
Line 74: Please add a reference for this estimate.
126-128: the reference here is not accessible and it is not possible for a reviewer to understand the difference in composition of ASW and IO media. They should be described here briefly.
Lines 129, 166 and elsewhere: is "scrapped" correct or should it be "scraped"?
Lines 146-154: I'm afraid thet the use of 16S primers targeting different regions and two different sequencing technologies does not provide data that would allow a valid comparison between samples.
Line 150: how were the samples stored before sending to sequencing? Did they stay frozen the entire time? I'm afraid that the long storage could affect the sequencing outcome as well. Especially if the samples were handled during the storage.
Lines 208-210: how was the statistical analysis performed if there were no replicates?
Lines 244, 246: I think it is confusing to use therm "increased" and "decreased" here as the results came from two separate cultures.
Lines 248-249: According to Table 1 also methanol concentration varied.
Lines 450-460: Considering the goals of the study, why are the overall transcript abundances relevant?
Lines 492-494: I don't understand the relevance of the qPCR data in table 2 and how the qPCR targeting the narG1 gene would solve the issue (as stated on lines 492-494), especially when the reference (marked in the list as submitted) is not accessible at this point. Please clarify.
Lines 595-596: unclear sentence "and (an) uncultured denitrifier(s)...", please revise.

Figure 2. For clarity, you should explain what TPM means (in the figure legend)
Figure 4: The figure legend should express more clearly that the clustering is based on overall gene expression patterns.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: DYNAMICS OF A METHANOL-FED MARINE DENITRIFYING BIOFILM: 2—IMPACT OF ENVIRONMENTAL CHANGES ON THE MICROBIAL COMMUNITY
Review round: 1
Reviewer: 3

Output:
Basic reporting: Villemur et al. provide a manuscript in which they assess the influence of NaCl, nitrate and temperature on the denitrifying community in a methanol-fed marine biofilm. The main drivers in this marine denitrifying biofilm are Methylophaga nitratireducenticrescens and Hyphomicrobium nitrativorans. This study complements two other studies. In this study, they are able to show, that this biofilm can adapt to heterotrophic, non-methylotrophic conditions.

Villemur et al. provide a clear introduction and background to the topic. However, two important concerns came up reading this manuscript:
1)	The authors carried out 16S rRNA gene sequencing, however called it throughout the manuscript “metagenomics” or “metagenomes”. Referring to 16S rRNA gene surveys as "metagenomics" is misleading. Here and elsewhere, do please not confuse or conflate amplicon sequencing and metagenomics. They are not the same.
2)	The authors state e.g. in line 239 and 488 that they used 16S rRNA gene sequencing in order to assess the evolution of the bacterial community. However, throughout the manuscript I could not find any analysis assessing the evolution of the bacterial community, such as e.g. ancestral state reconstruction analysis or others. Maybe, it would be clearer to say that they used 16S rRNA gene sequencing in order to assess the phylogeny of the bacterial community.

Villemur et al. provide clear and relevant figures of high-quality.

In line 41 it is not clear what is meant with “it”. Is it Methylophaga or Hyphomicrobium or both? Please clarify.

Following language changes are suggested:

Lines 26/27: Here, we report the impact of these culture conditions on…

Lines 34/141/230/443/484/489/497/507/521/531/543: Please don’t use metagenomics or metagenomes for 16S rRNA gene sequencing.

Line 36: metatranscriptomes of selected biofilm cultures

Line 40: in the OB, both were absent

Line 43: In these biofilm cultures, emergence of Marinicella sp. occurred.

Line 54: It is suggested to delete “in the biofilm” from this sentence, to allow a better flow of the sentence.

Lines 65/66: of the bioprocesses than a single species biofilm

Line 74: to be composed of

Line 101: under batch mode and anoxic conditions

Line 103: and varying temperatures

Line 108: It is suggested to use “investigated” instead of measured in this sentence.

Lines 115/116: Finally, a culture dependent approach

Line 120: Our results demonstrate

Line 135: change here and elsewhere: “the Reference biofilm” to  “the reference biofilm”

Lines 171/180: start Methylophaga with a capital letter and please in italics (here and elsewhere)

Line 230: Bacterial composition of the biofilm cultures by 16S rRNA gene sequencing

Line 239: It is suggested to use phylogeny instead of evolution

Line 241: Here and elsewhere, please do not use “16S". The correct term is “16S rRNA genes” for DNA or "16S rRNA” for RNA.

Line 244: “ca.” does not need to be in italics

Line 293: To assess the contribution

Lines 357/360: Here and elsewhere, please leave a space between % and NaCl

Lines 422/423: It should be either “ had a lower relative transcript level” or “had lower relative transcript levels”

Line 553: encoding all four denitrification reductases were not found in any of them.

Line 690: Paracoccus should be in italics

Line 719: Mainicella litoralis should be in italics

Line 728: Shewanella should be in italics

Line746: Marinicella sediminis should be in italics
Experimental design: The experimental design of this study is sound and clear.

Could the Electropherogram of the total RNA and the rRNA-depleted mRNA be provided into the Supplementary material?
Validity of the findings: Lines 279/280: “The three isolates affiliated to the Paracoccus spp. have identical 16S rRNA gene sequences” – Are they in fact the same species?

In lines 347/348 the authors state that ‘the strong upregulation of this operon may be related to the increasing need of NADH in the biofilm.” Readers might wonder why there is an increasing need for NADH in the biofilm. I would recommend to include one ot two sentences explaining this.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: DYNAMICS OF A METHANOL-FED MARINE DENITRIFYING BIOFILM: 2—IMPACT OF ENVIRONMENTAL CHANGES ON THE MICROBIAL COMMUNITY
Review round: 2
Reviewer: 1

Output:
Basic reporting: In Figure 1, it seems that the panels A and B have flipped in the pdf-version of the manuscript thet was sent to the reviewers. Please make sure that the panels are in correct order. Also, in the Fig. 1B PCA-plot, it would be good to separate the different conditions (IO, OB and ASW-cultures) with different symbols or at leas label the samples originating from cultures as well. Having a group of unlabeled symbols on the right side of the plot is a bit confusing.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Overall, the authors have improved the manuscript significantly by making revisions suggested by the reviewers. The authors have addressed my comments sufficiently.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: DYNAMICS OF A METHANOL-FED MARINE DENITRIFYING BIOFILM: 2—IMPACT OF ENVIRONMENTAL CHANGES ON THE MICROBIAL COMMUNITY
Review round: 2
Reviewer: 2

Output:
Basic reporting: All changes were made as suggested and the manuscript was considerably improved.
Experimental design: All changes were made as suggested and the manuscript was considerably improved.
Validity of the findings: All changes were made as suggested and the manuscript was considerably improved.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: THE EFFECT OF MANGROVE RESTORATION ON AVIAN ASSEMBLAGES OF A COASTAL LAGOON IN SOUTHERN MEXICO
Review round: 1
Reviewer: 1

Output:
Basic reporting: This article uses sufficient literature that provided adequate background on mangrove ecology and birds. The figures appears sound except for Figure 1 that may benefit some level of modification. Figure 1 The sampling points in three different habitat treatment is not clearly visible.
Experimental design: The research question has been clearly stated in this study. The knowledge gap in this field of study has also been highlighted and this study is probably the first to attempt to provide some light into the restoration ecology on mangrove birds.

However the sampling techniques used may have created bias in bird observation For instance the sampling location were closely located (100m apart), this in turn would result in double counting and inflation in relative abundance. The use of bird observation to indicate abundance can also be misleading, This is should be treated as relative abundance? The sampling saturation from Figure 3 also do not appears to achieve sampling saturation as being cited in the figure caption.
Validity of the findings: The data collected may need to be reviewed carefully. Justification are need from the authors on how potential bias are dealt with.
Additional comments: General Comments

This work should be commended as it reveals the complexity of habitat restoration in relation to avian assemblages. This work will add to the growing literature on restoration ecology and mangrove birds which are lack in many parts of the world. However there are several areas of concern that may need critical justification prior to publication.

Line 48 vertebratesand

180 Additional details on the bird survey is needed. No of observers? How multiple observer bias was overcome? The steps taken to reduce misidentification through mimicry and how birds were identified?

186 sampling point were separated by only 100m- This raises concerns on the possibility of double counting and biases. Please provide details and additional justification. The sampling points are relatively close between treatment habitats which may violate the independence of the point count. Such spatially aggregated placement of sampling point causes the spatial-correlation of abundance of target species and double counting probability.

191 birds that were flying above 15 was also included in the analysis. If the study is comparing the utilization of the different types of mangrove patches by the birds-why would the authors, then consider including transient birds or passing by birds in the analysis. Analysis excluding these species may show a different conclusion?

203 & 215 How was the number of individuals determined for each species? No of observation do not represent number of individuals. This can be misleading as the same individual could be recounted over the sampling period.

223 Please provide justification why RDA was used instead of other widely used multivariate analysis in understanding avian ecology?

243 It is unclear why there are no significant differences on the tree heights between degraded, restored and undisturbed areas.

257 Why was the migratory species included in the analysis? These seasonal birds may have a wide distribution and habitat. Please provide justification why not only Passerines were used in the analysis.

341 de models

In the discussion please provide additional arguments why there are fewer species in the undisturbed forest

The sampling in restored habitat include a wide range of restored period (2-6 years)- Would the heterogeneity between these treatment years have any influence on the avian relative abundance and richness? Please provide some arguments in the discussion.

Figure 1 The sampling points in three different habitat treatment is not clearly visible.
Figure 3 Graphs do not indicate sampling saturation. Please provide details


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: THE EFFECT OF MANGROVE RESTORATION ON AVIAN ASSEMBLAGES OF A COASTAL LAGOON IN SOUTHERN MEXICO
Review round: 1
Reviewer: 2

Output:
Basic reporting: This manuscript was generally well-written, sufficiently referenced, self-contained, and appropriately structured. However, some attention to minor grammatical errors is required throughout the manuscript: e.g. line 156, 341. Also, individual plots in Figures 2 and 3 should be distinguished as a), b), c)...etc.
Experimental design: The research is within the aims and scope of PeerJ, and its contribution to the literature is welcomed at a time when evaluation of restoration success is needed. While the study design is appropriate, some clarification of the research question is required, and the methods used to analyse the data require further description and justification (see general comments below). Furthermore, results of several of the tests used are not adequately reported, and figures/tables are not consistently referred to in the results section.

When justifying the analytical approach used, I would suggest authors consider the following paper, which is more straightforward in its evaluation of bird community structure and identification of indicator species using the ‘IndVal’ method.
J. Mohd-Azlan, R. A. Noske & M.J. Lawes (2012) Avian species-assemblage structure and indicator bird species of mangroves in the Australian monsoon tropics, Emu - Austral Ornithology, 112:4, 287-297, DOI: 10.1071/MU12018
Validity of the findings: Throughout the discussion, care needs to be taken to ensure the claims do not over reach the data collected. For example, lines 387-389 claim that vegetation regrowth due to restoration increases the availability of resources for insectivorous birds. However, insect availability was not measured, and so increases in insectivore resource availability can only be suggested as a speculative statement.
Additional comments: Lines 121-129: The study questions require some clarification. What is ‘natural disturbance’ in the context of this study (line 122)? Does it include mangrove degradation due to cyclone damage and exclude human-caused disturbance, such as harvesting? Results are displayed ‘disturbed’, ‘restored’, and ‘undisturbed’ categories, and these should be referred to in the study questions.

Line 168: What was the distance between the eleven sampling points?

Lines 202-232: It seems that ANOVAs or Kruskal-Wallis tests were used to determine if there were differences between water quality and vegetation parameters between study locations. There needs to be description of these tests and how assumptions were met in the Methods section. Also, there was no mention of any post-hoc analyses for differences between groups following ANOVAs. Was this completed, and if not, why not?

Line 203 to 212: I would suggest providing better explanations of community structure measures used, for example readers may not be familiar with the meanings of ‘dominance’ and ‘evenness’.

Line 240-241: This section is only reporting on water quality and forest structure results, so I suggest removing ‘we did not find a clear effect of these differences on the bird abundances among the sampled areas’

Line 242: Why aren’t measures of mangrove structure also included Figure 2?

Lines 235-246: Figure 2, Table 1, and the reporting of ANOVA results in the results text is somewhat redundant. I would suggest making Figure 2 more comprehensive (to include mangrove structure) or, alternatively, just use Table 1 to report these results.

Lines 245-256: Suggestions should not be included in the results section, only in the discussion.

Line 254: A figure should be referred to with this statement.

Lines 266-267: The results statement requires reference to a table or figure that reports these results.

Lines 278-280: It would be useful to provide a figure of the RDA so that readers can see these trends.

Lines 282-287: To better justify the steps taken during the glm analysis, I would suggest a better description of the ‘mvabund’ glm process and its assumptions in the methods section.

Line 315: It was not clear from reading the results that insectivourous bird abundance was influenced by tidal channel water quality. Foraging guild was not included in the analysis.

Figure 1. An inset map showing the location of the study location in the Gulf Of Mexico would be useful for the reader not familiar with the geographic location of Laguna de Terminos.

Figure 2. Letters should be used to distinguish individual plots, e.g. a, b, c, d…

Figure 3. The two plots should be distinguished as a) and b) and described as such in the figure caption. Furthermore, the caption should not report results (i.e. ‘ most species were recorded….species richness might be higher…’).

Figure 4. Why are only the first six sites ranked?

Figure 5. At the study site? Need to make clear that this pooled over the restored site only, the disturbed and undisturbed sites are excluded.

Table 1. This is repetitive of Figure 2. Suggest including standard error in the table and placing boxplots for all variables in an appendix and/or supplementary materials, or vice versa.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: THE EFFECT OF MANGROVE RESTORATION ON AVIAN ASSEMBLAGES OF A COASTAL LAGOON IN SOUTHERN MEXICO
Review round: 1
Reviewer: 3

Output:
Basic reporting: No comment
Experimental design: Authors used the same methodological approach to detect birds from very different guilds (seabirds, herons, shorebirds, passerines, ...) that are subjected to enormous differences in detectability. While they recognize it (by quoting Bibby et al. 1992) authors should account for it in their models (see e.g. Gibbons & Gregory 2006. Birds IN Ecological census techniques W.J.Sutherland, ed. Cambridge Univ. Press). Without accounting for differences in detectability, both among guilds and between treatments, results of bird abundance (and therefore richness and diversity indexes) between different treatments can be in my opinion strongly biased. One potencial evidence of this bias is that authors had only found 53 bird species troughout the study period in a tropical mangrove area, which overall supports a much higher bird (species) richness. Rarefaction curve is my my opinion a result of potential species detectability with the method used rather than because actual species richness.
Validity of the findings: Based on reported issues of methodological approach used I think that findings are not valid as they are currently stated in the MS. I suggest authors to:

1. Focus response variables (i.e. bird guilds) on the main purpose of the treatment (i..e mangrove restoration). Based on the methodological approach reported, I suggest to focus on waterbirds (i.e. mainly Pelecaniformes, Anseriformes and Charadriiformes) and include the tidal variability in your models. There can be are huge differences in waterbird use of studied areas depending on tidal period (i.e. high and low) and amplitude (see e.g. Basso et al. 2018 Hydrobiologia).

2. If authors would like to include passerine birds, I encourage them to replicate the surveys in the following years increasing the sampling effort to detect least abundant -but important components of the communities- songbirds at mangrove forests. If possible, I woud suggest to develop bird captures using mist nets at each treatment site to account for differences in songbird communities (e.g. Arizaga et al. 2011 Bird Study) at different sites.

Minor comments

Line 254. This result is not in accordance with detailed results (Table 2 and Fig 3).

Line 289. Include the results of model selection based on AIC scores.

Line 296. Remove this sentence.

Lines 296-304. I suggest to move several sentences to the Discussion section

Line 311. Focus your first sentence in the Discussion section to your main findings.

Line 406. Remove this sentence.

Line 426. This is too speculative.

Line 430. Focus your first sentence in the Conclusions section to your own (and not from other quoted studies) findings.

Line 438. This is too speculative.
Additional comments: (While I´m not a native english) In my opinion, the MS is not properly written. Authors used several sentences that appeared basic translations from spanish rather than scientific english writing. With regard to specific terms accounting to (bird) community structure and composition (i.e. abundance -even usied in the title-, richness, diversity), I suggest authors to thoroughly revise the text to homogenize. Specifically about birds, you should properly revise the use of specific terms such as shorebirds, waders, wading birds in order to not confuse the reader (e.g. shorebirds and waders are synonyms, one is used within the Nearctic and Neotropic, and the other is mainly used in the Palearctic). I suggest the same for naming the experimental groups (i.e. disturbed and degraded for the same treatment). There are even some specific words that I can not properly understood (e.g. porewater, litterfall production and gleaning birds...).


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: THE EFFECT OF MANGROVE RESTORATION ON AVIAN ASSEMBLAGES OF A COASTAL LAGOON IN SOUTHERN MEXICO
Review round: 2
Reviewer: 1

Output:
Basic reporting: Although improvement has been made since the first manuscript draft, grammar throughout the manuscript requires a careful edit. Also, please be consistent with terminology throughout the manuscript. For example, in Figure 1 the survey locations are called ‘count points’ but in Figure 2B they are called ‘sampling sites’.

The literature is not sufficiently referenced through-out the introduction, and specific comments highlighting this have been made in the 'General comments for the author'.

The article could be improved by clearly defining the objective of the study and ensuring that analyses used are relevant and not redundant (see specific comments in 'General comments for the author').
Experimental design: There are potential confounding factors that should be addressed given the location of the counting points (Figure 1). For example, could differences in bird species abundance and diversity between undisturbed, restored, and disturbed forests be due to edge effects (i.e. from Figure 1 it looks like most count points for restored forests are located primarily along the forest edge, while disturbed count points are located primarily inside the forest). Additionally, some of the undisturbed count points are very close (<100m) to patches of disturbed forest – is it possible that this could have influenced species recorded in the undisturbed forest?
Validity of the findings: The main conclusion of the paper is not well supported by the results as displayed in figures, please see specific comment #17 in 'General comments for the author'.
Additional comments: 1.	Lines 1-2: Given the study isn’t focused solely on changes in avian abundance, I would suggest a slight title change: ‘The effect of mangrove restoration on avian assemblages of a coastal lagoon in southern Mexico’ or ‘The effect of mangrove restoration on avian diversity and abundance in a coastal lagoon in southern Mexico’.

2.	Lines 21-22: It is perhaps more accurate to say that ‘mangrove forests provide many ecosystem services, including the provision of habitat that supports avian biodiversity’.

3.	Lines 26-29: These two sentences are indicative of a lack of consistency in study objectives throughout the article. Was the study objective to determine the influence of hydrological restoration on biodiversity, or was the objective to use avian diversity and abundance as indicators of restoration success? This needs to be established early on in the article, and be discussed consistently throughout the manuscript.

4.	Line 31: Should ‘relative abundance’ be ‘relative abundance and diversity’?

5.	Lines 34-35: I suggest the following: ‘Furthermore some bird species, such as the Yellow Warbler and Tropical Kingbird, were found to be similarly abundant in both undisturbed and restored sites, but absent or very low in occurrence at the disturbed site.’

6.	Lines 39-40: Since niche availability was not measured directly, it is speculative to say that your results show hydrologic restoration can enhance niche availability.

7.	Lines 47-49: The statement that mangrove forests provide nursery habitat should be referenced.

8.	Lines 69-71: Does the Mohd-Azlan, Noske & Lawes, 2015 paper truly support the statement the most mangrove forests have experienced a loss of connectivity and decrease in heterogeneity? I think that this study was limited to a small region in the northern Australia.

9.	Lines 79-81: These statements should be referenced.

10.	Line 99: Although it may be true that avian assemblages have rarely been used to evaluate restoration success, I would suggest referencing those studies that have, including (but not limited to): Li et al. 2011 ‘Patterns of waterbird community composition across a natural and restored wetland landscape mosaic, Yellow River Delta, China’, Zou et al. 2014 ‘Impact of coastal wetland restoration strategies in the Chongming Dongtan Wetlands, China: Waterbird community composition as an indicator’, Weller 1995, ‘Use of Two Waterbird Guilds as Evaluation Tools for the Kissimmee River Restoration’.

11.	Lines 122-130: Similar to my comment on lines 26-29, I would suggest simplifying the objective to either: 1) determine the influence of hydrological restoration on avian diversity and abundance or 2) use avian diversity and abundance as indicators of restoration success. Once the objective is clear, the paper can be framed accordingly.

12.	Lines 142-144: This is an incomplete sentence.

13.	Lines 213-274: I would also suggest either reducing the number of seemingly redundant analyses i.e. RDAs and GLMs, SIMPER and IndVal, or justify why both are needed.

14.	Lines 268-272: What information did you use to group bird species into foraging groups? The sources for this information should be referenced.

15.	Lines 310-311: Ardeidae and Threskiornithidae are not species.

16.	Lines 318-320: Please justify further why this is a reason for not excluding flying birds.

17.	Lines 370-372: It is not clear from the figures presented that this is the main finding of the study. I would suggest providing a figure that shows the relative abundance of bird guilds in restored, disturbed, and undisturbed forests.

 Figures

18.	Figure 2: I would suggest removing the following results statement from the figure caption: ‘Lack of saturation in the curves indicate that additional effort is required to record the true species richness in the study area.’

19.	Figure 3. In the figure caption, please be more specific as to what is meant by ‘only shown the top six’ – are the ‘top six’ the bird species with the highest abundances?

Tables

20.	Table 1: Please state in the table caption if the mean values being tested are pooled across years, or are following restoration only. Also, what was the sample size in each group, and where are the post-hoc comparisons reported?

21.	Table 3: Please describe in the Table caption what a ‘-‘ indicates in the table.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: IDENTIFICATION AND FUNCTIONAL ANALYSIS OF LECRLK GENES IN TAXODIUM ‘ZHONGSHANSHAN’
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper entitled: Identification and functional analysis of LecRLK genes in Taxodium hybrid ‘Zhongshanshan; in this study, authors performed bioinformatic analysis of ThzLecRLK gene family based on transcriptome data and analyzed the expression of 15 representative LecRLKs in different tissues and under various stresses; however, the data is very speculative, the main of this study was predictions of LecRLK gene family; manuscript need to improve language, figures, etc. For example the figure 7; Expression levels of 15 LecRLK genes in T. hybrid 'Zhongshanshan' tissues, this figure does not corresponds to the tissues. Figures 2 and 3 are illegible.

In Discussion:

“The number of ThzLecRLKs identified here exceeded all the other reported species. Since transcriptome only accounts for small proportions of the whole genome, it is clear that many ThzLecRLKs remained uncharacterized”. It is not clear, please rewrite, What is the relationship between the transcriptome and the uncharacterized genes?

Minor

Hroughout their life cycle: change to: Throughout their life cycle
Experimental design: In results:

Authors concluded that: Subcellular localization prediction found that they were mainly concentrated in the cell membrane system; although I believe that due to the characteristics of the domains of these RLKs, they will be found in membranes, the in silico data to identify them in chloroplast membranes, or other organelles is interesting; However, the authors would have to demonstrate some LecRLKs in plant data with fusions with GFP, etc., because the correlation between the subcellular localization in silico and the in plant has been very low.

Data from RNA-seq-based transcriptomics, these are not clear; In which conditions of salt and waterlogging were carried out, in what times were analyzed?;

Also, data of Unigenes co-expressed with LecRLKs in transcriptome are not clear, for example, how many expression conditions were analyzed to determine which genes are co-expressed.
Validity of the findings: The materials and methods are incomplete.

The manuscript can not be revised, since it is incomplete, the authors do not describe the materials and methods, results, footnotes, concentration of ABA, SA, mannitol, and NaCl, used and how long of treatments, without these data nothing can be concluded.
Additional comments: No additional comments