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: ASSOCIATION OF EPILEPSY AND ASTHMA: A POPULATION-BASED RETROSPECTIVE COHORT STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is well written. The study is based in taiwan however the authors cite prevalence and disease burden rates for the United States. In nature with the international scope of the journal and the nature of this study, it would be better if the author provide some additional background on the global burden of disease as well as some perspective on the prevalence within the study region. The  structure fits well with the scope of the article. The authors provide adequate information within the tables in the manuscript and the supplementary content to infer their results.
Experimental design: The primary research is within the scope of the journal. The research question is well defined and fills a clear knowledge gap.The authors tap into a rich data source to adequately address their research question. Taiwan's NHI program provides a longitudinal dataset that allows a retrospective cohort study to evaluate incidence of asthma and epilepsy in patients with pre-existing epilepsy and asthma respectively.
Validity of the findings: The authors found an increased incidence of epilepsy in all asthmatic patients but an increased incidence of asthma only for age groups of 0-10 years and 31-40 years. The authors provide a discussion of plausible biological pathways that may lead to such findings.
The authors adjust for age, sex , region and income in their findings. They posit that both diagnoses share common biological origins such as presence of susceptible genetic loci, common inflammatory triggers such as viral and injury associated cytokines. However if this was the case the authors would have found significant associations for both outcomes. The fact that asthmatics are more prone to epilepsy but not vice versa suggests that it is the sequelae of an asthma diagnosis that result in epilepsy rather than the causal pathways for asthma itself. This may be due to anoxia due to frequent asthma attacks or due to side-effects of anti-asthma medication. It is not clear to me whether the authors would be able to address this using the current dataset. I would suggest that  this be clarified further in the Discussion and Conclusion sections. I would also suggest that the authors refrain from using the term " bidirectional" in the discussion and conclusion because teh study only provides conclusive evidence for the increased risk of epilepsy in asthmatics.
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: DIAGNOSTIC ACCURACY OF ONEN’S ALTERNATIVE GRADING SYSTEM COMBINED WITH DOPPLER EVALUATION OF URETERAL JETS AS AN ALTERNATIVE IN THE DIAGNOSIS OF OBSTRUCTIVE HYDRONEPHROSIS IN CHILDREN
Review round: 1
Reviewer: 1

Output:
Basic reporting: This article is well written, clear and interesting. This study could have meaningfull influence on clinical care of children with hydronephrosis
Experimental design: The research section is well defined and relevant. The method is correct. Authors should be more carefull with the use of the word obstruction, as its definition is not consensual.

The authors did not tell which statisticall test they used to compare impaired renal function between groups.
Validity of the findings: The findings are interesting and properly exposed.
Additional comments: Thank you for your work. The results of this study suggest that renal scintigraphy could be avoided depending on the US parameters. It is well written and the methodology is appropriate.

Abstract :
Please consider dividing the conclusion in two sentences.

Introduction:
Line 61: I find this sentence somewhat ambigious, as hydronephrosis has a high chance of spontaneous resolution, unlike UPJO. Please specify.
Line 70: Lithiasis and infections should be added as potential indications for surgery.
Line 84: "Older children" is too vague and should be children older than 2 years old. Please precise “unilateral HN” in this sentence.

Material and methods:
Line 89: please update reference 21 with the most recent STARD guidelines (2015)

Statistical analysis:
Statistical test used for calculation of p value should be presented in this section. Which test was used to compare DRF between the groups according to the HN classification ?
Line 152: typos: the left kidney (and not .he left kidney)
Line 158: please add a dot at the end of the sentence.
Line 159: In this sentence, obstruction is used for abnormal excretion curve only, and is different from impaired DRF. This definition of obstruction is not consistent with the same word used in the sentence stating the objective of the study.
Line 164: DRF can be normal despite abnormal excretion curves. Would the author define this as obstruction ? It is convenient that no patient of the study was in this situation.
Line 169 is a repetition of line 161, although referring to another figure.

Discussion:
Line 180: Parameters of US are associated with impaired renal function. It is not proven that US can detect children needing surgery prior to renal function deteriorating.
Line 182: again, older children is too vague and should be precised (> 2 years old)
Line 185: the words “on the other hand” are not needed here.
Line 199: A downside of Onen classification is that discrimination between partial of diffuse renal atrophy is not strictly objective.
Line 209 to 210: The prognosis value of abnormal parenchymal thickness has also been demonstrated before: Scalabre et al. Prognostic Value of Ultrasound Grading Systems in Prenatally Diagnosed Unilateral Urinary Tract Dilatation. J Urol. 2017 Apr;197(4):1144-1149. doi: 10.1016/j.juro.2016.11.103.

Line 223 to 225: The use of both Onen classification and UJF improve overall accuracy in this study. However, the new classification UTD ( Nguyen et al. Multidisciplinary consensus on the classification of prenatal and postnatal urinary tract dilation (UTD classification system) J Pediatr Urol. 2014 Dec;10(6):982-98. doi: 10.1016/j.jpurol.2014.10.002.) and the antero posterior diameter of the renal pelvis have predictive values comparable to Onen classification and are simpler to use. Maybe the authors could precise this point in the discussion, or justify why they choose to use this classification in particular.
Moreover, the Accuracy of Onen score combined with UJF was 90.9% in the present study, which is not superior to the accuracy of the antero-posterior diameter of the renal pelvis or the UTD score in previous studies including younger children. Please comment.
Line 237: A postoperative increase of the UJF score would be another way to confirm the correlation between UJF score and obstruction.


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: DIAGNOSTIC ACCURACY OF ONEN’S ALTERNATIVE GRADING SYSTEM COMBINED WITH DOPPLER EVALUATION OF URETERAL JETS AS AN ALTERNATIVE IN THE DIAGNOSIS OF OBSTRUCTIVE HYDRONEPHROSIS IN CHILDREN
Review round: 1
Reviewer: 2

Output:
Basic reporting: •	The manuscript is clear, unambigious, Professional English language used throughout.
•	The literature is well referenced, and the references are relevant.
•	The structure conforms to PeerJ standards and discipline norm.
•	The three figures, table and raw data are relevant and well described.
Experimental design: •	The data is original primary research within Scope of the journal.
•	The research question has well been defined and meaningful.
•	The method has been described with suffucient detail.
Validity of the findings: •	There are significant meaningful findings benefit to literature, and it has clearly been stated in the text.
•	Data is statistically sound and significant.
•	Conclusions are well stated and linked to original research question. There is no speculation and conclusion is limited to supporting results.
Additional comments: •	Onen et al (Turkish J of Pediatric Surgery – Çocuk Cerrahisi Dergisi, 2016, V30, pp 55) have shown and strongly support your findings regarding the evidence that diffuse cortical atrophy suggest significant obstruction (Onen AGS-4) and renal damage, while Onen AGS-2 units does not develope renal damage (in Lines 167-169 and Lines 207-209 and Lines 213-215). If you read this review in detail, you will find the upgraded Onen’s hydronephrosis grading system is simple, clear and understandable for all specialists including pediatric radiologists and perinatologists. Moreover, the mentioned review has more scientyphic evidens supporting your findings and results. You may find beneficial to add this review as a reference in your present manuscript. It shows clearly the details of anatomic ultrasound findings can suggest many clues on kidney function. Based on detailed and upgraded Onen’s grading system; cortical parenchyme less than 3 mm, disappearance of corticomedullary differantiation, no visual medullary parenchyme and significant hyperechogenecity suggest Onen-4 hydronephrosis which shows significant renal damage.
•	The manuscript is clearly written in professional, unambiguous language. Therefore, the English language is clear enough that an international audience can clearly and easily understand your text.
•	Your most important issue is that your article clearly demonstrate the significant advantages of Onen’s Alternative Grading System on showing significant obstruction that need surgery with high sensitivity, specificity and accuracy (Lines 209-212). The next most important item is that your manuscript has clearly shown the significant differecense between Onen AGS-3 and AGS-4, and thus the importance of dividing these two group in different grade (Line 196-200); all of the AGS-4 units do need surgery, while the majority of AGS-3 units do not. The third most important issue is that when DRF was compared between the Onen AGS units a significant difference was found (Line 166-167). The last most important point is that the majority of hydronephrotic children (Onen AGS-1,2 and 4) actualy do not need an invasive nuclear scans since it has many disadvantages and false results (Lines 233-235). Renal scan indicated only in Onen AGS-3 (Line 215).
•	There is no a significant weakness, therefore the manuscript might be accepted.


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: DIAGNOSTIC ACCURACY OF ONEN’S ALTERNATIVE GRADING SYSTEM COMBINED WITH DOPPLER EVALUATION OF URETERAL JETS AS AN ALTERNATIVE IN THE DIAGNOSIS OF OBSTRUCTIVE HYDRONEPHROSIS IN CHILDREN
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: The use of ANOVA test is only valid when the distributions of the residuals are normal. The authors did not specified if this point was tested before the ANOVA .
Additional comments: The paper was significantly improved, although i would have liked the UTD grading system to be cited in the discussion section (Nguyen 2014).

A few typos remain:

Line 51: in most cases
Line 71: radionucleide
Line 155: between
Line 228: significant

I also understant that ureteral jets were not recorded postoperatively, but this could be an interesting lead for further studies, and could be written at the end of the discussion.

Thank you for your work.


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: DIAGNOSTIC ACCURACY OF ONEN’S ALTERNATIVE GRADING SYSTEM COMBINED WITH DOPPLER EVALUATION OF URETERAL JETS AS AN ALTERNATIVE IN THE DIAGNOSIS OF OBSTRUCTIVE HYDRONEPHROSIS IN CHILDREN
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: This manuscript appears to be appropriate for publication 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: DIAGNOSTIC ACCURACY OF ONEN’S ALTERNATIVE GRADING SYSTEM COMBINED WITH DOPPLER EVALUATION OF URETERAL JETS AS AN ALTERNATIVE IN THE DIAGNOSIS OF OBSTRUCTIVE HYDRONEPHROSIS IN CHILDREN
Review round: 3
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: Thank you for these changes, i indeed think that the Kruskal Wallis test is more appropriate.
Validity of the findings: no comment
Additional comments: I thank the authors for their improvement of the paper. The statisticall analysis is now more valid in my opinion.


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: EFFECTS OF SANDFISH (HOLOTHURIA SCABRA) REMOVAL ON SHALLOW-WATER SEDIMENTS IN FIJI
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper is generally well written. The Introduction provides a clear background to the study and the knowledge gap it addresses. The negative impacts of sea cucumber removal on marine ecosystems are often cited but there is little research to support or identify the mechanisms by which this occurs. This work contributes to our body of knowledge in this area.
Literature was well referenced and relevant, although the reference list was very long for a paper this size.
Lines 93-95: Not all sea cucumbers play an important role in the recycling and remineralization of organic matter or are endangered. Authors should note that it is predominantly the deposit feeding, Aspidochirotid (and a few Dendrochirotid species) sea cucumbers that are commercially exploited and perform this ecological role.
Lines 93-113: There is excessive detail in this paragraph on the issue of stock decline (particularly lines 99-105). It is good to make the point and reference it but so much specific information on individual countries is laboring the point. Please try to reduce the text here.
Lines 121-124: a key statement “The current study aimed to understand how the removal of sea cucumbers affects sedimentary function through in situ experimental manipulations of H. scabra densities, thus providing information on the poorly understood ecological implications of sea cucumber fisheries.” Is currently buried in the Introduction. The authors could consider including this statement in a small paragraph at the end of the Introduction to logically where they can clearly lay out the paper’s rationale, i.e. sea cucumbers are important, they have been overexploited, sandfish in particular are important and this is how we are going to demonstrate it. Paragraph lines 115-141 can focus on the more technical aspects of the study.
Lines 124-125: more suited to the Methods section.
Lines 135-136: “These parameters provide a proxy for the function of sediment as a biocatalytical filter system” would be better placed sooner in the text prior to discussion of the parameters. This would justify why you chose these particular variables to measure.
The referencing is very comprehensive (although as noted above, may be a bit too exhaustive in places, I leave it up to the authors to see if there could be some trimming back of references. Some comments on the references:
Holothuria scabra is not italicized in all references.
Line 498: Gilbert et al. (2014) is not referred to in the ms.
Line 327: Mezali & Soualili, 2013 in ms but not references.
Some references are in wrong order, e.g. Purcell (2004), Uthicke (1999), Huettel et al. (2006), Mercier et al. (1999).
Experimental design: The field design is sound and well designed and executed, often in difficult circumstances by the sound of it. Particularly notable was the use of controls for the fencing which would account for any cage effects that may have occurred. The methods are mostly well described, although could be tightened up and made more clear in parts. I have made some suggestions to this effect but they are not exhaustive.
The primary sediment sampling frequency is not described (despite mentioning twice that stocking density was checked 6 times a week). I had to glean from the Results (and a sentence in the Introduction) that there was monthly sampling with 6 sampling events between September 2015 and February 2016. Furthermore, August 2015 is included in Figure 1, even though Time 0 is September 2015 (Line 170). Please include a clear outline of the sampling schedule early on in the Results section. Thereafter, use T=0, T=1 consistently (including Figure 2).
Lines 175-176: ‘All animals used to restock enclosures were collected from the immediate area around each respective enclosure’ but the results do not mention any restocking. If loss or escape of sandfish was an issue, this should be noted and discussed or not mentioned in the methods.
OPD was only measured from Time 2 onwards (Line 279 in Results). This should be stated in the Methods with an explanation of why.
Lines 218-221: This requires some clarification. Where were the individuals for the sediment turnover experiment monitored? If this was outside the pens in the most common habitats, please clearly say so, also check the n, 17+6+4=27, not 28. Also, it is not clear whether 6 pellets were collected from every hourly sample or just once during the 4-hour faeces monitoring? What is the relevance of a polymerase chain reaction tube given they were then dried in an oven and weighed? Would ‘collected in a vial’ work as well?
The method of analysis is not clearly explained. Also, I question the separate analysis of the two controls (natural vs control) together and the density treatments (high vs exclusion) together. The authors have been prudent in comparing natural vs control to determine whether cage effects occurred before proceeding with the density differences, this is well done. However, there has been a lost opportunity to compare exclusion, natural (i.e. low) and high densities which would have provided further fine-scale information on what density of sandfish might provide the ecosystem benefits that are being investigated. In fact, the abstract implies that this what was done (Lines 34-36). The data analysis is complicated because the storm events interrupt what may have occurred if the treatments had remained in place for the entire 6 months. This needs to be dealt with in the most clear, simple and understandable way. After establishing that there were no cage effects, the control treatment could be dropped and the three density treatments (exclusion, natural or low, and high) analysed. It may help clarify the results later.
Results are only given for Chi-squared analyses and Mann Whitney-Wilcox U Tests. No repeated measures ANOVA results are presented.
Validity of the findings: Overall, the findings are valid and some interesting results emerge from the study. However, the variability in the results and the effects of the two disturbances suggest that more caution is needed in the interpretation (refer also to general comments).
Results on Grain size distribution (Lines 267-276) are slightly confusing and fragmented. This is obviously tricky due to the storm events but the authors could consider moving Lines 272-276 to the start of the paragraph as these tests were done first. The main result for high treatment could follow with emphasis that this is the only significant result (if that is the case). A sentence on the effect of the storm surge between T3 and T4 (if anything) would be informative.
As mentioned above, Line 279 ‘OPD measurements began at T=2 of the experiment’ should be stated earlier in the Methods. If the timing of the storm surge is relevant to this result, please provide more results here on what happened during this period.
I’m afraid I found the OPD results very difficult to reconcile with Figure 2b. The difficulty of differentiating the bars was the main obstacle. I can’t be sure if there is a problem but I would request the authors to carefully check the stated values against the graph and to make sure this is easy to read in a published version.
Results on SOC (Lines 291-299) are also confusing. From Figure 2c, it also appears that cage control SOC also increased substantially from T0-T1, while natural density remained consistent but these are not mentioned. The graph does not seem to support the statement ‘Sediment in exclusion treatment areas generally had a higher O2 uptake than high treatment areas over the course of the study’ (Lines 294-295), except for T1 and T3 and the latter standout value is not mentioned, except in the buffering context. Please keep the terminology consistent (O2 uptake or SOC).
Results on Sediment turnover (Lines 302-311) would be improved if the main result (as dictated by the Methods) is presented first, followed by the supplementary information which allowed estimation of the turnover rate. e.g.
‘On average each H. scabra individual produced 26 sediment pellets h-1 ± 2, which had a mass of 0.36 g ± 0.01. Observations of H. scabra at the study site showed this species actively fed for 10 h day-1 during daylight hours (0600-1800 hrs), and generally remained buried during low tide. During daylight hours H. scabra were found at a density of 31 ind. 100 m-2. Bulk density of sediment at the site was 0.83 g cm-3 ± 0.01. After incorporating…’
This sediment turnover figure is pretty impressive but Line 310 should state that ‘…the estimated population in 1000 m2 at the study site has the potential….’
The abstract includes a statement on turnover that is not included in the ms. ‘Findings revealed that the natural population at the study site can rework ca. 10590 kg dry sediment 1000 m-2 year-1; more than three times the turnover recorded for H. atra and Stichopus chloronotus’. Please check that the entire abstract accurately reflects the ms.
Daylight hours are defined as 0600-1800 hrs in this study. Many studies indicate that sandfish are more active in the afternoon and evening (e.g. Wolkenhauer, 2008. Burying and feeding activity of adult Holothuria scabra (Echinodermata: Holothuroidea) in a controlled environment. SPC Beche-de-mer Information Bulletin, 27, 25-28). The authors state that sandfish numbers were determined by a pilot survey at the study site but should specify whether the survey was carried out at a suitable tide and time of day to optimize counts and hence provide confidence in the population estimates. Or explain if they are sure that sandfish at this site did not exhibit any greater activity at particular times of day.
I found Figure 2 very hard to understand and it must be improved. Suggested Figure 2 modifications:
•	Use T0, T1, T2, etc, not dates as you refer more to times than date in the ms.
•	It would be useful to show significant differences on Figure 2, where relevant.
•	Caption should read something like ‘Plots of results for temperature and rainfall (a), oxygen penetration depth (b), and sediment oxygen consumption (c), at each sampling time’.
•	It might be helpful to note the time of the unusual storm events on the graphs with an arrow or similar.
•	Does the legend in 2b match the order of the bars in the graph? The grey shades don’t seem to.
•	I assume the OPD is presented downwards to represent the direction that this is measured in the sediment but it does not help interpretation of the graph because when we are discussing high and low values we envision the opposite. This is my opinion only, leave it to the authors to decide.
More on Figure 2b. The methods state that cage control and natural treatments were ‘controls’ and analyzed together, as were the exclusion and high treatments. The graph would be more easily interpreted if the two sets were placed side by side in graph 2b. Also note that the bars are insufficiently distinguishable, different shades should be used or dots, hatched bars, etc. Similarly for graph 2c, possibly use same shapes open and closed for the paired analysis sets of data? Graph 2c in particular is very noisy and hard to interpret and I found difficult to reconcile with the Results description in the text. If they can’t be shown more clearly, graph them separately. Alternatively, remove the control treatment if they do not show any difference and are obscuring the results you are trying to highlight.
Line 137 in the Introduction “We hypothesized that high densities of H. scabra would facilitate the efficient degradation of OM.” Why didn’t you measure OM? This is one of the most basic parameters considered in virtually every study of sea cucumbers and their use of and interaction with sediment. There are also suggestions of higher OM concentration in the sediment of the exclusion treatment (Lines344-346), that flooding likely delivered a strong OM-pulse to the reef (Lines 348-349) and so on. Many conclusions are drawn from these ‘potential’ effects which cannot be proven.
Discussion comments:
Line 326 should refer to ‘several sea cucumber species’.
This paragraph should include additional references below noting the complexity of grain size selectivity wrt sandfish. None of the species in the references cited are H. scabra, so sediment selectivity is being assumed. Results would be better described as providing possible indications of grain size selectivity or cautious support to the presence of grain size selectivity. Wiedmeyer (1982) concluded that sandfish select for smaller particle size, especially smaller individuals. However, Tsiresy et al. (2011) did not find evidence for selectivity below 2 mm grain size. He discusses sediment compactness as a factor to be considered in sandfish growth and thus in how they interact with the sediment, potentially affecting the results presented in the ms (for example, storm surges which redistribute sediment may affect compactness even if grain size is unaltered).
Tsiresy et al. (2011) An assessment of Holothuria scabra growth in marine micro-farms in southwestern Madagascar. SPC Beche-de-mer Information Bulletin, 31, 17-22
Wiedmeyer (1982) Feeding behavior of two tropical holothurians Holothuria (Metriatyla) scabra (Jager 1833) and H. (Halodeima) atra (Jager 1833), from Okinawa, Japan. Proceedings of the 7th International Coral Reef Symposium, Guam, 2, 853-860.
Conclusions: lines 448-449, possibly more so for Pacific and other island communities where livelihoods and food security are heavily reliant on these services?
The second half of the Discussion should be reduced and tightened up (from Lines 398-440). The consequences of a malfunctioning sediment biocatalytical filter system in habitats under stress, synergistic effects and how sandfish may or are likely to influence these functions are important. Lines 435-440 are repetitive of, and should be incorporated into, the Conclusion.
Additional comments: The paper is valuable because it involves a high-value commercial species that is believed to be beneficial to the marine environment and has been decimated in most areas where it occurs. The field work has been well done, using novel parameters, and will be of interest to field workers and researchers. I have made some suggestions to make the Methods more readable and clearer. The Results were variable and were affected by other factors which further increased noisiness: a minor sampling issue with the T0 baseline sampling, then storm events affected 2 out of 5 samples, therefore nearly half of the sample times have no significant differences between variables (this is how it appears on the graphs although the written results are presented in a rather piecemeal way). Heavy rain and storms may have had other impacts not considered in the paper and not detected by the analyses, for example, due to freshwater inundation, changes in sediment compactness, etc. The authors mention the numerous factors that they couldn’t control at the start of the Discussion and handle the results of the storm events quite well. There are some good results and they are worth reporting and emphasizing. However, I felt the authors took the sediment function processes scenario too far on fairly limited data. The speculative tone used in lines 418-433 is reasonable but Lines 435-437 draw too strong a conclusion from a six-month study considering the issues noted above. The Discussion should be revised to concentrate on the parameters measured and adopt more cautious conclusions.


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: EFFECTS OF SANDFISH (HOLOTHURIA SCABRA) REMOVAL ON SHALLOW-WATER SEDIMENTS IN FIJI
Review round: 1
Reviewer: 2

Output:
Basic reporting: Abstract:
You say “this fishery” but there are more than 80 fisheries globally. Which one do you refer to?
Are these all “sedimentary functions”? Consider rewording.
If the “natural population at the study site can rework ca. 10590 kg dry sediment 1000 m-2 year-1”, does this mean the population at that site can rework many of these units? The choice of units looks strange. Is there a way to express in kg reworking per animal per year?

Introduction:
Is “biocatalytical” even a word?

Maybe at line 80 put a paragraph break

Line 132: can you add more detail to elaborate on HOW these animals can “alter grain size distribution”?
Experimental design: Line 159:  “plots without mesh” doesn’t sound like a cage control. I encourage the authors to check up on some of the earlier work (decades ago) about cage controls. Rewording is needed here, or extra clarification.

Line 183-184 says that the sediments were placed into containers then dried. Normally for this sort of work, they would be rinsed with freshwater before drying. How might salt have biased the results? Please mention.

Line 225: surely the sediment defecation rate depends on the time of day. Give the range in time that this sampling was done, and give some citations about whether time of day might bias defecation rates. Also, how are these values scaled up to one year, given that this species apparently can bury in sediments for some parts of the day and might be relatively inactive in the cooler time of year?  More consideration needed here.

Line 226: do sea cucumbers have a “caudal end” or is it just a posterior end? Caudal sounds like a fish term.

Line 228: how were length and weight recorded? Give detailed methodology please.

Analyses:

Is Chi-squared test the industry standard for comparing grain size distributions? I believe that this analysis would treat each grain size class as an independent group to compare against the others, which they are not. How did you account for the non-independence of adjacent size classes? A better approach is to use an analysis more suited to the log-normal distribution, and non-independent aspect of how these data are structured. The geological community is quite adept at the proper approach. The data probably need to be reanalysed with a more suitable test.
Validity of the findings: Line 307 states that the “H. scabra population on Natuvu’s reef flat”. But how big is this reef flat and how big is the population?

Line 309 says “Assuming sea cucumbers consume sediment to a depth of 5 mm”. This doesn’t sound very plausible. What have other studies shown? As these are deposit feeders, with peltate tentacles, it is probably more like the first 1-2 mm. Please check and add more references here to back up this statement, as it is not convincing to me.
Additional comments: In running a routine authenticity check, I discovered that part of this study had been published in a couple sources already (one as an abstract in a published report, and the other as a chapter in a published report). Can the authors affirm that the data and results in this manuscript have not been published elsewhere? Also, it might be important to cite the other publications in which these findings or data have also been presented.


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: EFFECT OF ELEVATED TEMPERATURE ON MEMBRANE LIPID SATURATION IN ANTARCTIC NOTOTHENIOID FISH
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article is well-written and the literature review is thorough and informative, especially in the Results and Discussion section.  Raw data are supplied.

The authors might consider using different notation for fatty acids.  Instead of using the format “C16:1c9”, the smaller “c” could be replaced with “Δ”.  In physiological papers, it more common to use “C16:1n9” or C16:1ω9”.
Experimental design: Sample sizes are small and replication of experimental trials was not performed.  However, given the difficulties in working with Antarctic fishes, this is understandable.  The physiology of Antarctic fishes is not well-understood, so a major strength of this paper is providing new information on membrane fatty acid composition, membrane cholesterol, and changes during thermal acclimation.

Inclusion of the non-Antarctic, New Zealand fish species (N. celidotus) in the study needs to be justified.  This species is in a different family (Labridae) than the Antarctic species so it is distantly related, and moreover, this species occurs in habitats that are considerably warmer.  Phylogenetic and environmental effects are confounded, making it difficult to make meaningful comparisons between this species and the Antarctic fishes with respect to membrane fatty acid composition.  I would consider removing it from the analysis.
Validity of the findings: In general, the analysis is appropriate and conclusions are reasonable and well-supported by citing appropriate previous work.  The only significant question I have is the use of the desaturase index.  Although the desaturase index may correlate with membrane saturation state, it does not necessarily reflect a cause and effect relationship.  The decrease in the C16:1/C16:0 index reported by the authors could be due to a decrease in desaturase activity, but it could also be due to changes in mobilization and incorporation rates of specific fatty acids from storage lipids.  If changes in desaturase are involved, then the situation is complex since the response appeared to occur with respect to C16:0 but not C18:0.  Also, changes in C16:0 and C16:1 individually in response to thermal acclimation were not significant in TB according to figure 5, so my confidence in the actual significance of the desaturase index in this case is not particularly strong.  Overall, I do not believe that the desaturase index contributes much to the overall paper since no direct enzymatic data or information regarding storage lipid dynamics are provided, so removing it from the paper should be considered.

A minor point: it is common with fatty acid percentage data to use arcsine transformations to meet assumptions of normality and homogeneity of variances for ANOVA. The authors state that untransformed data were used, so it should be clear that assumptions for the ANOVA were met without transformation of the data.
Additional comments: Overall the paper well-written and is a valuable contribution to our understanding of the physiology of Antarctic fishes.  The two main issues that I would address are:

1. consider removing the data and comparisons involving the non-Antarctic fish since phylogenetic and environmental effects are confounded

2. consider removing the desaturase index since alternate explanations are available and no direct evidence for changes in enzyme activity are provided


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: EFFECT OF ELEVATED TEMPERATURE ON MEMBRANE LIPID SATURATION IN ANTARCTIC NOTOTHENIOID FISH
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper is written in clear English, is relatively easy to follow along, and is organized well.
Experimental design: I would appreciate more information on the housing and experimental setup being added to the manuscript rather than relying on the supplemental information (Expanding lines 116 - 121 to include numbers, time frame of acclimation to water temps, and how water temps were raised).
Validity of the findings: I believe the findings are relatively sound and are analyzed appropriately.
I would suggest removing the information in lines 358-363 trying to explain the day 2 spike in osmolality.  Instead I would just focus on the general decrease in osmolality seen over time post acclimation.
Additional comments: Serveral citations are bit messed up, possibly due to some citation software being used. (lines 124,315).

There is an "unknown MUFA", if you know it is a MUFA then you probably know the carbon chain length but not the location of the double bone. It would be helpful to report this as 18:1 or 20:1 or whatever it is.

I would also remove line 75- 76 and combine lines 76 - 79 into the previous paragraph to wrap up changes that occur to membranes when water temperature rises.

For the PCA, consider using different symbol shapes for the non-antarctic fish, icefish, and antarctic fish to help differentiate them more than the gray scale color alone.


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: DIET BREADTH AND EXPLOITATION OF EXOTIC PLANTS SHIFT THE CORE MICROBIOME OF CEPHALOLEIA, A GROUP OF TROPICAL HERBIVOROUS BEETLES
Review round: 1
Reviewer: 1

Output:
Basic reporting: See comments in: General comments for the author
Experimental design: See comments in: General comments for the author
Validity of the findings: See comments in: General comments for the author
Additional comments: The work of Blankenchip et al. “Diet breadth and exploitation of exotic plants shift the core microbiome of tropical herbivorous beetles“ makes an important contribution because it aims to “to characterize the diversity of bacteria, associated with adults and eggs in species of Cephaloleia beetles: generalist and specialist species”.
Changes in abundance of rare plants may significantly influence the balance between nutritional specificity and dietary breadth of herbivores and may therefore affect the biodiversity of forest-dependent animal species.
Neotropical forests are extremely diverse ecosystems, listed within the biological hotspots of our planet. However, species from these forests are threatened by diverse anthropogenic activities: among them, the replacement of native vegetation by exotic plantations (monocultures), which justifies the accomplishment of this work, although this aspect was little approached in the study of Blankenchip and colleagues.
In general, the Manuscript at hand is well written. Data and analysis performed by authors seems to be the appropriate for this kind of studies to explore the study proposal. The figures and tables are illustrative, well addressed in the text and the captions are adequate and informative.
However, I believe the work needs some improvements, as specified below:

1. Title: This study refers to a specific group of beetles and not to all herbivores. I believe the title should refer to it.

2. Introduction: Why did the authors choose to study only this genus, since there are several other species of herbivores? It should be explained in the introduction.

3. Introduction (lines 67-68): Scientific names, during the first presentation, should have full name + author.

4. Discussion (L 313-324): I think this information gets more interesting in the introduction (see my comment nr 2).

5. Discussion (L 330-331) Which lines?? Mention some literatures that show these lines ..

6. Discussion / Final remarks: (Suggestions to include in the work):
a) What is the implication of the replacement of native plants by exotic plants in the survival of beetles (or other species)? Is it possible to reach these conclusions with your results?
b) In ecological terms, is it possible to use only bacteria to know if the beetles are surviving in native or exotic environments?
c) What are the challenges for the conservation of species of beetles or other groups with the implantation of exotic plants?

7. References: Standardize the formatting of references. Some are complete and others are abbreviated.


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: DIET BREADTH AND EXPLOITATION OF EXOTIC PLANTS SHIFT THE CORE MICROBIOME OF CEPHALOLEIA, A GROUP OF TROPICAL HERBIVOROUS BEETLES
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: In the manuscript entitled “Diet breadth and exploitation  of exotic plants shift the core microbiome of tropical herbivorous beetles” Blankenchip and colleagues describe the microbiome of different beetle species from the Cephaloleia genus. The article presents a very interesting experimental set up where they study the microbiome of 6 different beetles belonging to the same genus, but with different diet breadths. Whereas 4 are specialists, two are generalists.
The authors conclude that all species share a core microbiome consisting of 8 OTUs, and that diversity and community structure is linked to diet breadth, with specialists having higher diversity. They also observe that the microbiome of some beetles feeding on native plants is different than those of the same beetles feeding on invasive plants, and suggest that the latter is a dysbiotic state that could be involved in niche adaptation.

I find this body of work extremely interesting, I really liked the experimental set up and the paper is very well written. The questions asked are central to the field of symbioses. I just have some minor comments that are easily fixable.

First, Blankenchip and colleagues found Wolbachia in the microbiome of all species, but was removed from further analysis arguing “its known prevalence in insects as a reproductive pathogen”.  I believe this may not be a good reason, given that there are instances in the literature where Wolbachia seems to be found in the gut of insects, and also examples where they are not reproductive pathogens, but rather beneficial partners. Since most of the discussion seems focused on gut microbes, are the authors sure that Wolbachia is not located in the gut?

Second, the authors claim that the presence of some OTUs both in the adult beetles as well as on the eggs is suggestive of vertical transmission. However, this is not necessarily the case. The authors do not give enough detail on how the eggs were collected (please include this in the materials and methods section), but it seems that they were obtained from bags were adults had been for a while. The presence of these OTUs on the egg surface may be just contamination after being in the same bag as the adults, where presumably they could have defecated, for instance. If the authors do not want to perform experiments to test the mode of transmission, they should at least mention the possibility of contamination.

Third, the authors suggest the role of the microbiota to be beneficial for the beetles, and put forward various ideas such as degradation of plant complex polymers and secondary metabolites. Cephaloleia beetles belong to the Chrysomelid family. Kirsch and Pauchet have produced a body of work on the degradation of plant polymers in Chrysomelids. They have found that often beetles can degrade pectin and cellulose on their own, without the need of symbionts. Salem et al. 2018 showed that one Chrysomelid species lacks this ability on their own genome, and possesses a highly specialized symbiont that degrades pectin. Either of these cases may, of course, not be the way things work for Cephaloilea, but I feel this literature should be mentioned if the hypothesis is going to be put forward.

Also, the authors suggest detoxification as a possible role for the microbiome, but never mention why these beetles should detoxify. What are the toxic compounds present on the leaves (alkaloids, and polyphenols)? Are these compounds known to be degraded by bacteria? A good reference here would be the work by Ceja Navarro and colleagues showing caffein being degraded by Pseudomonas in the coffee bean borer which leads to fitness benefits for the host beetle.

Minor comments:

Please, check the figure numbers. They should appear in the text in order, Figure 1, Figure 2…etc. Currently, Figure 2 is at the end of the results section. Figure 7 and 6 seem also not to be in order.

L62: the word “exclusively” sounds weird, since the beetles use the plants for almost everything: nutrition, development, reproduction and shelter.

L98: what do the authors mean by “partially dissected beetles”?

L147: how was the representative sequence for each OTU selected: random, longest, most abundant, first picked…(parameter -m in Qiime)?

L248: are these values Shannon indexes, number of OTUs?

L279: where these OTUs that are shared between eggs and adults the exact same OTU (same OTU number), or just same taxonomical binning?

L329: Briones-Roblero and colleagues (reference 34) only show the ability of some members of the microbiota to degrade plant compounds and only put forward the hypothesis that this may be beneficial for the insect. A better example would be that of Ceja Navarro mentioned above.

L332: I am not sure the word “complementary” is the correct one here. It somehow implies that one cannot work without the other because they complement each other. Rather, they are distinct functions of the microbiome, but independent from each other.

Figure 2 and 5: please use the same species name format as in the other figures (C. belti, C. reventazonica etc.)

Figure 4: what does grey and 0.5 mean? Please, explain.

L397: authors observe that microbiome diversity contradicts their previous hypothesis that it should be higher in generalists than specialists. This is a very cool result, but it would be nice to elaborate on why this could be.

L500: Typo in “Degradation”


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 CLIMATE CHANGE ON THE DISTRIBUTION OF A TROPICAL ZOANTHID (PALYTHOA CARIBAEORUM) AND ITS ECOLOGICAL IMPLICATIONS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The work is very well written, clear and concise. The bibliography used is updated and the objectives are well thought out and reached.
Experimental design: The experimental design requires some modifications and clarifications:

The authors said that the sampled areas have only one occurrence per pixel (5 arcminutes = 10 km), but you have several records for the same place (< 10 km2) such as Amaral et al., 2009 and  Edwards & Lubbock, 1983 for the SPSP Archipelago,  the same with Abrolhos bank (Francini filho et al., 2013; Francini filho & Moura, 2010; Segal & Castro, 2011; Villaça & Pitombo, 1997; Bruce et al, 2012).  Several records from the same place may overestimate modeling results. You should leave only one record every 10 km2. Check all used records

It must  to be clear how many variables (of Twenty-seven layers of environmental data) you really used to assemble the model. List all of them in a Table.

Why did you use the variable concentration of calcite?  if the zoanthid P. caribaeorum don't use calcite in your life cycle
Validity of the findings: The article represents an interesting work on a keystone species in the coastal reefs of the Atlantic coast of the Americas. Modeling works on species distributions are important to understand and relate the abiotic parameters that influence the distribution of the same. P. caribaeorum is an excellent organism for this type of studies since it is easy identification and is very abundant in the environments where it inhabits.
As all modeling work is speculative, but the speculations are well based and well discussed, so the scenarios presented have a certain logic within the evaluated parameters. The work was carried out on a global scale and opens the door to work on regional scales in order to better understand the abiotic parameters analyzed in the present study. The results are of great impact for their use in public conservation management policies and establish a baseline for future modeling works with reef benthic communities.
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 CLIMATE CHANGE ON THE DISTRIBUTION OF A TROPICAL ZOANTHID (PALYTHOA CARIBAEORUM) AND ITS ECOLOGICAL IMPLICATIONS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a manuscript on the distribution of the zooanthid Palythoa caribaeorum, both today and as climate change proceeds. I have a few comments:

28	What are coastal processes?  This doesn’t follow from the high salinity and small temperature variation.
31	“would lose one-half of its suitable habitats under (what conditions)?  Temperature, salinity, pH, etc.
39	One of the problems that is not explained in any article on this species is it’s distribution today: it live on the outer reefs, not the onshore reefs. It seems to me that someone needs to figure out why.
297	The habitat is “composed of coastal regions with high chlorophyll-a concenntrations”. This seems odd. Most coral reefs are in areas that have low nutrients, giving rise to crystal clear waters (= low chlorophyll-a) that allows the sunlight to reach the benthic corals with their zooxanthellae. Can you explain why?
258	The discussion-conclusion goes on for 12 pages. I think the authors can cut this in half?
484	The authors do not say what factors this species responds to. “anthropogenic impacts” means what? What will cause the “decrease of suitable habitat” in the southernmost but not the northernmost range?
Experimental design: This is a manuscript on the distribution of the zooanthid Palythoa caribaeorum, both today and as climate change proceeds. I have a few comments:

28	What are coastal processes?  This doesn’t follow from the high salinity and small temperature variation.
31	“would lose one-half of its suitable habitats under (what conditions)?  Temperature, salinity, pH, etc.
39	One of the problems that is not explained in any article on this species is it’s distribution today: it live on the outer reefs, not the onshore reefs. It seems to me that someone needs to figure out why.
297	The habitat is “composed of coastal regions with high chlorophyll-a concenntrations”. This seems odd. Most coral reefs are in areas that have low nutrients, giving rise to crystal clear waters (= low chlorophyll-a) that allows the sunlight to reach the benthic corals with their zooxanthellae. Can you explain why?
258	The discussion-conclusion goes on for 12 pages. I think the authors can cut this in half?
484	The authors do not say what factors this species responds to. “anthropogenic impacts” means what? What will cause the “decrease of suitable habitat” in the southernmost but not the northernmost range?
Validity of the findings: This is a manuscript on the distribution of the zooanthid Palythoa caribaeorum, both today and as climate change proceeds. I have a few comments:

28	What are coastal processes?  This doesn’t follow from the high salinity and small temperature variation.
31	“would lose one-half of its suitable habitats under (what conditions)?  Temperature, salinity, pH, etc.
39	One of the problems that is not explained in any article on this species is it’s distribution today: it live on the outer reefs, not the onshore reefs. It seems to me that someone needs to figure out why.
297	The habitat is “composed of coastal regions with high chlorophyll-a concenntrations”. This seems odd. Most coral reefs are in areas that have low nutrients, giving rise to crystal clear waters (= low chlorophyll-a) that allows the sunlight to reach the benthic corals with their zooxanthellae. Can you explain why?
258	The discussion-conclusion goes on for 12 pages. I think the authors can cut this in half?
484	The authors do not say what factors this species responds to. “anthropogenic impacts” means what? What will cause the “decrease of suitable habitat” in the southernmost but not the northernmost range?
Additional comments: This is a manuscript on the distribution of the zooanthid Palythoa caribaeorum, both today and as climate change proceeds. I have a few comments:

28	What are coastal processes?  This doesn’t follow from the high salinity and small temperature variation.
31	“would lose one-half of its suitable habitats under (what conditions)?  Temperature, salinity, pH, etc.
39	One of the problems that is not explained in any article on this species is it’s distribution today: it live on the outer reefs, not the onshore reefs. It seems to me that someone needs to figure out why.
297	The habitat is “composed of coastal regions with high chlorophyll-a concenntrations”. This seems odd. Most coral reefs are in areas that have low nutrients, giving rise to crystal clear waters (= low chlorophyll-a) that allows the sunlight to reach the benthic corals with their zooxanthellae. Can you explain why?
258	The discussion-conclusion goes on for 12 pages. I think the authors can cut this in half?
484	The authors do not say what factors this species responds to. “anthropogenic impacts” means what? What will cause the “decrease of suitable habitat” in the southernmost but not the northernmost range?


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: COMPARING THE CATCH COMPOSITION, PROFITABILITY AND DISCARD SURVIVAL FROM DIFFERENT TRAMMEL NET DESIGNS TARGETING COMMON SPINY LOBSTER (PALINURUS ELEPHAS) IN A MEDITERRANEAN FISHERY
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscipt “Comparing the catch composition, profitability and discard survival from different trammel net designs targeting common spiny lobster (Palinurus elephas) in the Mediterranean” is, as its title indicates, an attempt to evaluate the common spiny lobster fishery of the Balearic islands regarding its catches and discards, taking into account both the biological and the economic component. It is an interesting contribution providing essential knowledge for fisheries management. The article is within the PeerJ scope. The language is, generally, clear, unambiguous and professional (but see some minor corrections). The Introduction & background provide the context of the study. The literature is generally well referenced & relevant. The structure conforms to PeerJ standards (however the abstract is not a structured abstract according to the instructions). The figures are relevant, high quality, well-labelled & described (but see a comment on Figure 5, listed in detailed comments). Raw data are also supplied. Overall, I believe it will make a good contribution to the journal if accepted.
Experimental design: There is original primary research within the Aims and Scope of the journal. The research question is well defined, relevant & meaningful. It is stated how research fills an identified knowledge gap.

There might be an issue with the sampling design (see my major concern No 1), as I am not sure that the sampling scheme (covering spring and summer) employed is representative of the actual fishery. However, in the Introduction, there I a sentence that hints that this fishery is indeed carried out in these two seasons, but it seems incomplete. See my detailed comments (see Major concerns-comment No 1) below.

The methods are not described with sufficient detail & information to replicate and I believe the readers would need a bit more information (see Significant issues-comment No 3).
Validity of the findings: Generally the statistical methodologies used are adequate. I have a serious reservation about the level at which the data are analyzed (level of “netting panel” or “netting wall”) as I believe that this is problematic (see Major concerns-comment No 2). I would advise analysis at a different level (net type per fishing day/operation) to guarantee independence of observations.
Additional comments: Major concerns:
1) The authors state (Materials & Methods l. 113-114) that sampling was carried out from April to August in 2015-2016. Is this because the specific fishery for lobster is seasonal and occurring only in spring-summer months (it is written in the introduction –l. 71- but the sentence there seems incomplete and there is no further description of the fishery, see my comment No 3…)? If the answer is positive then there is no problem with the temporal aspect of the sampling design (as the sampling is representative of the period of the year of this fishing métier); however this should be clarified in the Introduction. If no, then the design of the study if flawed and I’m afraid that the manuscript should be rejected. This needs to be clarified by the authors.

2) Another important issue regards the analysis at the level of netting walls. As the authors state (l. 118-119) “A trammel net set consisted of several (between 10 and 30) netting walls (or “netting panels”)”. If I understand correctly the analysis (and the presentation of the results) is at the level of netting walls, however –since- a trammel net consists of several netting walls tied together, the observations (the catches per netting wall or the revenues per netting wall) are not independent. So, I believe that the statistical analysis should be instead carried out at the level of net-type per fishing day (the production should again be standardized per 100 m of net/per netting wall, but the catch quantity of all netting walls with similar characteristics for a given fishing day should be pooled before that standardization) and not netting wall per day. I realize that the sampling size is much lower if net types are considered and not netting walls (and it is true that the sampling effort expended is adequate, I realize it is not so easy to carry out this work on many more fishing trips), still I believe the analysis should be carried out on that level. It is OK to present catch abundance standardized per netting wall (i.e. per 100 m of net), but statistical analysis treating netting walls deployed on the same day, by the same vessel at the same location (as one net) is hinting at pseudo-replication.

Significant issues (in order of importance):
3) In general I believe it is essential to see more on the technical characteristics and a description of this fishery. This regards both (a) the Introduction part (to put this fishery into context, e.g. what are the seasons and the depths of the fishery, the common mesh sizes and the fishing effort (net length) used? The authors cite some references, but one or two sentences would be helpful for the reader) and (b) the Methodological part, so that the gears used and the locations fished are adequately described for the reader. Please be reminded that other scientists might, ideally, want to follow your experimental design to ratify your results.

4) What about the differences between the three trammel net types examined on the catches of the target species (common spiny lobster)? Some more information would be necessary to evaluate these gears.

5) Title: I believe the title of the study should be changed. As it stands, “Comparing the catch composition, profitability and discard survival from different trammel net designs targeting common spiny lobster (Palinurus elephas) in the Mediterranean” may mislead the reader to believe it examines the lobster fisheries from the entire Mediterranean. I would change it to either “Comparing the catch composition, profitability and discard survival from different trammel net designs targeting common spiny lobster (Palinurus elephas) in a Mediterranean fishery” or “Comparing the catch composition, profitability and discard survival from different trammel net designs targeting common spiny lobster (Palinurus elephas) in the Balearic islands”

6) l. 139-140: Here the reader can’t help wondering whether it is proper to assign specimens into 10-cm length classes. For some of the species caught a length class of 10 cm is not adequate as it is too broad covering a wide part of the range of between individuals variance. Furthermore, I can’t imagine which length (from this entire range) was used for the weight estimations coming from the length-weight relationships.

7) l. 119: A mesh-size of 160mm seems to be very large, even if this is the diagonal and not the knot-to-knot mesh size (still, clarify which of the two applies). Perhaps this is the size of the two wide-mesh nets (the “further nets on either side” of l. 422) and not the central (main) part? In other areas of the Mediterranean similar fisheries are carried out using old/timeworn trammel nets of various mesh sizes in the main part. Please clarify the actual mesh size of the thin mesh or whether this is the practice followed here, too (see also my general comment on the technical characteristics and description of the fishery).

8) I think that the section “Representativeness of the sampled boats” (first section of Results) would be more adequately placed in the methods and not in the results as it is the means to assure that what you did in terms of sampling was valid and representative of the entire fleet.

9) l. 334-336: The authors write “the differences in the probability of obtaining some commercial catch were relevant: MMF = 0.33 (0.23 to 0.44) versus MMF + greca = 0.44 (0.33 to 0.56)”. In l. 226-228 it was stated that “effects attributable to a given treatment
were labelled statistically not relevant or statistically relevant depending on whether their
corresponding 95% Bayesian credibility intervals overlapped or not.”, so I can’t understand how the difference is relevant since the numbers overlap.

10) l. 468-480: I think the authors should be more reluctant in generalizing their findings as the survival of lobsters didn’t include a very large sample size. The data are valuable, for sure, still the short term survival was assessed only for sixteen lobsters.

11) Figure 5: I am not sure this Figure is very clear (e.g. axis-labels).

12) l. 268: Please correct the Table order and numbers (as the numbering should be according to order of reference in the text). You are referring to Table 2 here, only to refer to Table 1 in l. 378.

13) l. 65-66: Still if you search for works on Mediterranean small-scale fisheries disards, a number of papers pop up. It would be interesting to discuss your findings in comparison to the findings of these works. This would also put the paper into context for a wider international audience in order to attract more interest.

14) Keywords: In my opinion “guarding net (greca)” and “high survival” are not very practical as keywords (especially the first one might never be searched as such). I’d advise to put “guarding net” and “discard survival”.

15) l. 227: as the “statistically relevant/not relevant” is a bit alien as an expression to the readers unfamiliar with Bayesian statistics, perhaps it would be better to intonate that by changing the sentence to “Thereafter, according to a Bayesian framework, effects attributable to a given treatment were labelled statistically not relevant or statistically relevant (contrary to “statistically non-significant”/”statistically significant” of classic inferential statistics), depending on whether their corresponding 95% Bayesian credibility intervals overlapped or not.”.

16) l. 300: Why do you consider the number of commercial individuals low? Is there any reference to compare? As you haven’t provided information on the average number of fishing netting walls for a typical fishing trip in the area in the Introduction, the reader could assume anything, I mean, isn’t it usual to put many fishing walls in a net set?

Elements of minor importance (not enumerated):
Introduction:
l. 54: change to “(Kelleher 2005)”
l. 70-73: Something seems to be missing from these sentences. Please rephrase.
l. 102: Some more information might be useful on this to put it into context. Is this practice a new initiative? Is it a common practice in this fishery?
l. 105: change to: “and to provide a detailed description”
l. 106: change to: “Additionally, we investigate”
l. 106: change to: “estimate the “short-term” (7-day)”

Materials and Methods
l. 148: change to “The quantification of this part of the catch”
l. 165: change “3” to “three”
l. 175: I believe the proper citation style isn’t by giving the website but (R Development Core Team 2008) and in the list of references as: R Development Core Team (2008) R: A language and environment for statistical computing. R Foundation  for  Statistical  Computing,  Vienna.
l. 196-198: I believe this should go before (and not after) the previous sentence.
l. 200: change to: “10-cm length classes (see justification above).”
l. 208: I am not sure this formula displays correctly on my pdf. E.g. I am not familiar with the inverted “?”. Is the formula correct? Perhaps it is the mathematic symbol for integral? Please check it out.
l. 253: change to: “The following taxa” as Raja sp. (referred to in the following line)  is not a species but a genus. Except if you are referring to a specific species (though inidentified), but then this should be indicated in the text.
l. 270: change to “of the seven days”

Results:
l. 305-306 and Figures 3 and 4a: Perhaps the figures could be combined in one showing the fraction of each species that is commercial and discarded (e.g. using different coloured bars for the retained/discarded fraction).

Discussion:
l. 403: change to: “In that case”
l. 407: change to “has not been evaluated here”
l. 424: change to: “when it tries to escape”
l. 447: change to “(Kelleher 2005)”


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: COMPARING THE CATCH COMPOSITION, PROFITABILITY AND DISCARD SURVIVAL FROM DIFFERENT TRAMMEL NET DESIGNS TARGETING COMMON SPINY LOBSTER (PALINURUS ELEPHAS) IN A MEDITERRANEAN FISHERY
Review round: 1
Reviewer: 2

Output:
Basic reporting: •	Writing is generally good, but the manuscript is overly long.  The Methods could be reduced if some of the minute statistical details were placed in supplemental materials and, if as detailed below, the trivial comparison between net materials were omitted.
•	The Introduction lacks a broader setting on the worldwide problem of fishing bycatch and that associated literature.
•	line 86:  awkward sentence structure
•	line 208: the symbol " ¿" in the model is not defined.
•	line 334: awkward sentence structure; do not say that something was statistically "relevant", instead indicate whether significant or not.
•	line 354: missing words; should be: "...mean weight of discards was statistically different..."
•	line 418: awkward sentence
•	Figure 1 could be improved were labeled showing the different mesh sizes and dimensions; this goes for the greca inset figure too.
•	The authors use scientific names of species throughout but many readers may be unfamiliar with these.  I recommend creation of a table that lists scientific names, common names, and broad taxonomic classification of each (i.e., decapods, tunicates, etc.).
•	Figure 7: graphics not described adequately in the legend.
•	Too many figures: Figure 8 & 11 in particular are unnecessary.
•	Table 2 unnecessary
Experimental design: •      The research project is well-designed and implemented, but its relevancy is rather narrow. The great majority of spiny lobster fisheries worldwide are based on the use of traps or artificial structures referred to as "casitas", and are not net fisheries.  Net fisheries for lobsters still persist primarily in developing countries with poorly managed fisheries because they are so destructive.
•      The comparison between the two types of netting materials is trivial.  There is no reason to suspect that nets of similar design but different materials would effect catch or by catch results; the comparison is only relevant with respect to net longevity and cost.  The greta comparison is of a net of a different design, so more reasonable.  The manuscript could be shortened significantly if the trivial comparison between net materials is omitted.
•       The authors focus their statistical analysis on Bayesian statistics, which I am not very familiar with and so can not comment of the validity of their application.
•	The sample size for the juvenile lobster post-catch survival estimation (n = 16) is low.  Why were lobsters held for only 1 week? Is there some prior evidence that this is an appropriate time-frame within which one can determine bycatch discard mortality?
Validity of the findings: •	Though not unusual, it is still disheartening to see that the net bycatch was 2.5 times more speciose than that of the target species and of equal biomass (means = 0.061 - 0.68 kg/net wall).  Moreover, the onboard survival of most species pulled up in the nets was abysmal (0.2-0.6 probability) and probably an underestimate as many more would surely have died after returned to the sea, which was not examined except for the juvenile spiny lobster that are typically hardier than fishes.

•	The authors come across as being a biased in favor of the use of this gear type, which is in appropriate.  Indeed, on line 488 they state: "Based on the results reported here, it is recommended that further research should be conducted in support of an exemption from the Landing Obligation for the spiny lobster ...".  Research needs to be objective and should not be conducted "in support of" one result or another.  Along those same lines, the authors mention (paragraph starting at line 433) an alternative gear type (traps) and cite other studies showing that traps catch less bycatch but also fewer lobsters than nets.  Yet they appear to brush off that alternative because fishers consider them less economically viable.  But the data clearly show that traps cause less environmental harm than nets.
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: COMPARING THE CATCH COMPOSITION, PROFITABILITY AND DISCARD SURVIVAL FROM DIFFERENT TRAMMEL NET DESIGNS TARGETING COMMON SPINY LOBSTER (PALINURUS ELEPHAS) IN A MEDITERRANEAN FISHERY
Review round: 1
Reviewer: 3

Output:
Basic reporting: I am really excited to see a study that address net design and lobster bycatch/discards. Most lobster catch studies focus on trap designs, that, although comprise the bulk of lobster landings around the world, are much more studied than those smaller (but important) lobster fisheries that utilize nets. This is especially true in the Mediterranean where both spiny and slipper lobster fishery data is substantially less known compared with other areas.

This manuscript has two issues that make it difficult to grasp the important points without distractions. First, I believe the length of both the introduction and discussion sections could be shortened to eliminate redundancy and improve clarity. Second, the English grammar, text, word choice, and clarity should be amended to an international audience. I believe these two items would greatly add value, clarity, and comprehension to the science and the associated data that follows.

For both of these suggestions, I have made some example comments that are found in the PDF version of the manuscript.

Most of those graphic outputs in the figures are clear and professionally presented. I have some comments and suggestions with some of the figures:

Fig. 1: Add dimensions to the nets either in the figure caption or on the figure drawing itself. Also, I can’t really discern the difference between the greca and non-greca panel. In your illustration, it’s not entirely clear. Can you improve upon this?

Fig. 4A (and others like it): On your axis, ‘Items/netting wall’, is this given as a proportion? If so, why not a proportion out of 100? In other words, 0 to 1.0.

Fig. 8: Was there a statistically significant difference here? I think a simple 1-way ANOVA would get at this and be helpful to report.

Fig. 10: I am not entirely sure that this figure is needed at all and can be eliminated, especially with the description in your results section and the inclusion of Fig. 11.

Fig. 11: Why would your initial survival not start at 1 or 100%. The authors need to clarify this.

Raw Data: I have taken a look at the raw data files in the supplemental folder and it seems fine. I wonder if the authors ever considered placing their data into a relational database to better examine relationships.

Overall, the structure of this manuscript conforms to the ‘guidelines to authors’ instructions and an appropriate number of references appear to be represented here.
Experimental design: I believe the research is unique and original to the question(s) that are sought in this study. For example, there is a lot of attention to the design of the trammel net design and selection of the netting fiber types (very innovative and detail-oriented). The research question(s) are apparent but again, as mentioned above, could be clarified in the introduction section. There appeared to be many ‘constraints’ as the authors refer to several times. Given this, I am wondering how much confidence we can put into the subsequent results with respect to how robust they might be? With this in-mind, I have summarized some of my concerns below:

Line 208: Your model notation is confusing and difficult to decipher in the current format. I suggest changing this.

Line 165: ‘Due to logistical constrains, only 3 vessels were sampled’ – that is a really small sample size. I am wondering if you had the capacity to port sample? This is a very common practice in fisheries science.

Lines 260-278: lab study and survivorship with lobsters – I appreciate here what the authors are trying to accomplish, but with such a small sample size (n=16), it is very difficult to say anything for sure. Was there opportunities to sample other juvenile lobsters in the survey? Also, were the lobsters kept communally in a tank (this is what seems like the case) or in separate containers or aquaria tanks in the lab. The second design is much more robust and does not contribute to pseudoreplication or artifact effects.
Validity of the findings: I am not sure about the small number of replicate sampling vessels (n=3) as well as the numbers of lobsters that were used in the lab-based survivorship trial (n=16).

Lines 249-250: ‘The time that each animal had been retained in the net was unknown but was less than the maximum soaking time (48 hours)’. This could be a really wide range. Did you do some preliminary work to determine survivorship at incremental times up to 48 hours? Something like 12, 24, 36, and 48? I think this is a real gap in your data.

I appreciate the time and effort the group put into their data syntheses and analyses, especially R-statistics, and PCA outputs.

There is a good and meaningful discussion of impact and linking the original research questions to supporting results and conclusions; however, as stated previously, the Discussion section could be tailored down to remove redundancy and provide more efficient and clarified sentences.
Additional comments: A couple of other things to consider for this manuscript:

1)	The title of the study is lobster specific, however a large amount of data and reporting deals with fish. I am concerned that in this case, the title is a bit misleading and doesn’t fully represent the bulk of the analyses and reporting. Please consider changing the title.
2)	The title of this manuscript also implies an economic assessment (profitability) for targeting lobster, but it is not apparent to me that such an analysis was conducted in this study other than the recommendations of the authors to provide exemption of undersized lobsters from the EU ‘landing obligation’ regulation.


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: COMPARING THE CATCH COMPOSITION, PROFITABILITY AND DISCARD SURVIVAL FROM DIFFERENT TRAMMEL NET DESIGNS TARGETING COMMON SPINY LOBSTER (PALINURUS ELEPHAS) IN A MEDITERRANEAN FISHERY
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors of the manuscript “Comparing the catch composition, profitability and discard survival from different trammel net designs targeting common spiny lobster (Palinurus elephas) in a Mediterranean fishery” have made a serious effort to change the manuscript conforming to the reviewers’ suggestions. As a result, the contribution is significantly improved and can make a good publication in PeerJ. I do not have any major objections or comments. There are still some grammar/syntax mistakes or typos that need correction and overall the English language should be improved in order to ensure that the text is understood by an international audience. Examples of the minor corrections needed are given below.

l. 81: Change “which coincides approximately with the size at first maturity” with “which approximately coincides with the size at first maturity”

l. 86, 89, 91: Change “in the Balearic Island” to “in the Balearic Islands” if you are referring to the Balearic Islands in general or to “in this Balearic Island” in the case you are referring to Majorca in particular.

l. 126: Change “data capture” to “data collection”

l. 135: Change “which is thought to reduce” to “which is considered to reduce”

l. 157: Change “that have entangled” to “that have been entangled”

l. 159: Change “of caught items” to “of entangled individuals”

l. 166: Change ““where dead” animals were observed” to “where “dead” animals were observed”

l. 169-171: Change these two sentences to “During net retrieval, small invertebrates or bed-forming organisms (e.g. Posidonia oceanica) were passively disentangling and falling on the deck in a continuous pattern; therefore, it was not possible to assign this fraction of the catch to a specific netting wall.”

l. 181: Change: “because the fishermen organize fish sales on a single fishing wharf” to “because all sales of fish are carried out in the single fishing wharf of the island”.

l. 217: Change “Due to logistical constraint” to “Due to the logistical constraint”

l. 275: Change “From above analysis,” to “In the analytical setup described above,”

l. 276-277: Change “the data was tested” to “the data were tested”

l. 345: Change “elasmobranches” to “elasmobranchs”

l. 387: Change “Thus, MMF + greca netting walls tend to retain” to “Thus, MMF + greca netting walls tended to retain”.

l. 406: Change “prob. = 0.25” to “p = 0.25”

l. 410: Change “from 8 species” to “from eight species”

l. 435: Change “is probably case specific” to “is probably case-specific”

l.446-448: As the Discussion should refer to the present tense (what you have found in the Results is now a fact and you’re discussing it) change to: “The results reported here for the greca indicate that it affects the capture of some non-commercialized species. It reduces the capture of rays but increases the capture of other smaller elasmobranch species within our study.”

l. 470: Change “our results indicated” to “our results indicate”

l. 512: Change “although base on a” to “although based on a”

l. 515: Change “be indicative for” to “be indicative of”

l. 540: Change “Another trade off” to “Another trade-off”

l. 541-546: Similar to my above suggestion, I’d change these sentences to refer to the present tense.
Experimental design: no comment
Validity of the findings: no comment
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: COMPARING THE CATCH COMPOSITION, PROFITABILITY AND DISCARD SURVIVAL FROM DIFFERENT TRAMMEL NET DESIGNS TARGETING COMMON SPINY LOBSTER (PALINURUS ELEPHAS) IN A MEDITERRANEAN FISHERY
Review round: 2
Reviewer: 2

Output:
Basic reporting: I think sufficient improvements have been made based on my comments and suggested changes.
Experimental design: I think sufficient improvements have been made based on my comments and suggested changes.
Validity of the findings: I think sufficient improvements have been made based on my comments and suggested changes.
Additional comments: I think sufficient improvements have been made based on my comments and suggested changes, and I appreciate the attention to the details rebuttal comments, clear changes in the document using 'Track Changes', and the cautionary approach to interpreting some of the results.

The attached Word document contains some minor corrections, spelling, grammar, etc. that I have made to this document.


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 EXPRESSION ANALYSIS OF CYTOKININ METABOLIC GENES IPTS, CYP735A AND CKXS IN THE BIOFUEL PLANT JATROPHA CURCAS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Please see below general comments to author
Experimental design: Please see below general comments to author
Validity of the findings: Please see below general comments to author
Additional comments: The manuscript entitled "Identification and expression analysis of cytokinin metabolic genes IPTs, CYP735A and CKXs in the biofuel plant Jatropha curcas" is written well. The experiments were executed well and the results described and interpreted properly. The presented work possess novelty and described unambiguously. Potential of this study is related to increase or influence the seed yield in Jatropha. Therefore, I recommend this manuscript as suitable for publication, provided the authors revise the manuscript thoroughly based on points are given below.

Some of my specific comments are as follows:
1.	The statistical analysis performed in this work was not described in the manuscript. So authors should describe the statistical tools used in this study.
2.	Authors didn’t explain the role of LOG gene (cytokinin phosphoribohydrolase ‘Lonely guy’) in cytokinin biosynthesis. It would good to explain their role in cytokinin biosynthesis. Since it also plays a role in the formation of iP, tZ and cZ.
3.	In line no 224, Kaori Miyawaki et al. should be rewritten as Miyawaki et al. (2004).
4.	In Figure no 6 & 7 genes should be written in italics.
5.	The Y- axis in the Figure no:7e should be clarified and mentioned in the figure legends.
6.    Why author did not include LOG genes for expression analysis. ?


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 EXPRESSION ANALYSIS OF CYTOKININ METABOLIC GENES IPTS, CYP735A AND CKXS IN THE BIOFUEL PLANT JATROPHA CURCAS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Please see in general comments.
Experimental design: Please see in general comments.
Validity of the findings: Please see in general comments.
Additional comments: Cai et al report on a number of cytokinin metabolism genes in the potential biofuel plant Jatropha. The paper is generally well written, however the information content is fairly low. The sequence data reported can principally be found in public databases and the construction of exon/intron structures, phylogenetic trees etc. (Fig. 1 to Fig. 5)  is essentially a matter of few mouse clicks.
There is some new information in Fig. 6 which represents gene expression data. However, totally unacceptable is the claim made in line 128: “To deduce the functions of these gene family members … expression pattern were analysed.” Expression pattern are in no way informative about function, this is basic knowledge of biology, the statement needs to be adapted (E.g. “In order to gain more information ….”).
New Fig. 1 is correct with the exception that not only the free bases are degraded by CKX as is indicated in the scheme. In fact, CKX enzymes accept different substrates including the ribosides, ribotides and glucosides (see e.g. Galuszka et al., 2007). Please adapt figure accordingly. In the legend: line 3, In the red frames these are proteins, not genes. cis- and trans should be written italic. The figure misses to show the cytokinin conjugates.
New data concerning knockouts of the only CYP735A gene have been included. This is potentially a valuable and novel contribution but the data are premature. Even if a complete phenotypic analysis of the knockout lines might not be presented, a reasonable level of solid data should be reached. I am opposed to include preliminary data in the abstract and the result section of a manuscript. Either these plants are knockouts of cyp725A or not and either they have the phenotype as shown or not. If this is the case these data should not be described as preliminary but like “First analysis of knockout mutants of CYP735A …”
It is unclear why these data confirm that a single JcCYP725A gene is present in Jatropha (as is claimed in the abstract, line 25/26). One would need to confirm that these knockout plants do not contain trans-zeatin-type cytokinin, which are formed by CYP735A activity. As hormone analysis is straightforward and feasible with a reasonable input these data should be added. This is mandatory to support the claim that is made in the text.
Furthermore, the CRISPR/Cas9 construct used to generate is not completely reported. The complete sequence should be presented in Material and methods.
Why the three lines show the phenotype with different expressivity although all three appear to harbor a knockout mutation of the target gene? Please explain.
Minor points.
Line 18, IPT and CYP725A are collectively named cytokinin synthetase, which is not appropriate (see later in the text). Please check and adapt.
Line 161, “To confirm the activity and distribution of endogenous CKs, we detected …” is not justified. It is rather: “In order to learn more about the distribution of endogenous cytokinins we measured …”
Authors constantly confound genes (italic) and proteins. All text need to be checked carefully and adapted.
It is unclear whether the phenotype of the cyp735a plants is due to accelerated leaf senescence, it could simply be earlier leaf senescence. The phenotype should be compared to the one shown by cyp735a mutants of Arabidopsis and the differences discussed.


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 EXPRESSION ANALYSIS OF CYTOKININ METABOLIC GENES IPTS, CYP735A AND CKXS IN THE BIOFUEL PLANT JATROPHA CURCAS
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comments
Experimental design: no comments
Validity of the findings: no comments
Additional comments: The authors have answered my questions, I recommend acceptance.


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: DIVERSITY AND COMMUNITY STRUCTURE OF MARINE MICROBES AROUND THE BENHAM RISE UNDERWATER PLATEAU, NORTHEASTERN PHILIPPINES
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article is well-written with standard structure and sufficient references.
Experimental design: This article fills a gap by exploring the diversity of microbes in the marine environment near the Philippines. The methods generally followed standards in the field.

I do have some comments:

L142: says SILVA release 102 was used. This database is from 2010 and is only 25% the size of the current release, SILVA 132, with poorer curated alignments. Mismatches and poor alignments to the reference may partially account for the high number of OTUs found.

The mothur-RDP sections and inter-method comparisons could (and I think probably should) be removed because the comparison between pipelines is not completed on enough samples to be broadly useful beyond this publication. The obvious lack of representation of the expected community also argues against the usefulness of the mothur-RDP dataset.
Validity of the findings: The main issue, as mentioned by previous reviewers, is the limited number of samples (N=11 in 3 depth bins). This is useful for a first-pass pilot study but rigorous statistical treatment really isn't feasible with so few samples.

L224: two of these are obligate anaerobes -- how did they get into surface waters?

Figure 3. This comparison between studies is invalid because of the different methods used. The authors might still discuss the general trend of higher diversity with depth, but the surface-only comparisons with other seas aren't meaningful and should be removed. People have found that just about everything affects these diversity measurements, so unless you use identical collection, filtering, DNA extraction methods, primers, PCR conditions, Illumina library kits and methods, demultiplexing, software versions, and database versions, you shouldn't be comparing these numbers (that's why EMP, Tara, OSD, etc. have standardized all of these methods). And *especially* not between metagenomic and amplicon sequencing methods. It's not telling you about the communities, only the methods, and even then it's not telling you very much.
Additional comments: I commend the authors on the extensive metadata they've provided with the manuscript. It is a valuable dataset and I look forward to its eventual publication.


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: DIVERSITY AND COMMUNITY STRUCTURE OF MARINE MICROBES AROUND THE BENHAM RISE UNDERWATER PLATEAU, NORTHEASTERN PHILIPPINES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript meets the criteria required for basic reporting.
Experimental design: The manuscript is a unique primary research study.  There are some issues to resolve regarding experimental design prior to publication. More specifically, the question needs to be better defined given the data presented. The introduction justifies the need to resolve microbial diversity in this part of the ocean.  However, much of the paper and data, figures and supplement are focused more on comparing 16S rDNA community characterization pipelines.  There are several problems with this (see general comments for the author).

The manuscript needs to be reorganized.  It's not clear to me why results from the Mothur MiSeq pipeline were discussed in great detail, and before results from the SILVA pipeline, especially given the clear indication that SILVA produced much better results.

Many of the figures are not discussed in sufficient detail.  Very little information is provided in the results section to help the reader interpret the figures and many of the supplemental figures are not needed. Data in many of the figures and tables are introduced only briefly (a single sentence) and/or presented at different places in the results section.  This makes it very difficult to follow.  Specific example (line 203), the first time Figure 1B is introduced there is no mention of the different 16S rDNA analysis pipelines.  Specific example, Figures S4, S5 and S6 are introduced in only briefly (line 212-217).
Validity of the findings: Much of the supplement is not needed.  It is either presented sufficiently in the text or not discussed in enough detail in the results. Some examples are listed below:

The data in Fig. S2 would be more useful to the community if they were provided in a table.  The plots are OK but not really needed since there is very little difference and the results are expected for this type of system.  Data in a table could be used by others for modeling or other analyses that need the numbers.  Some discussion about the data in the results could help.  For example, what is the range for some of the important variables plotted?  Key features, depths indicating changes in water masses, etc.?

The word contigs is used.  Are these contigs (overlapping sequence reads) or are they individual sequence reads?

Some discussion to help explain Figure 1B line 203 is needed.  What are some of the observed similarities with analysis method and sample type?  What are some of the differences?  This sentence gives the impression that there should only be one bar in the graph for the relative abundance of these groups.  What is the significance of the different bar graphs for these groups? SILVA appears to do a much better job.  Why show differences in the analysis methods? This is mentioned later (line 256) for the SILVA analysis, but by the time I got that far I was already confused about the purpose of the figure.
Additional comments: Reorganize the manuscript using the best data/analysis about diversity in this part of the ocean.  Differences in analysis methods are secondary, if included at all.  If they are included, consider presenting the more accurate data (SILVA) first and discussing the relevance.  Present a methods comparison last.


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: GENETIC INACTIVATION OF ALPHA-SYNUCLEIN AFFECTS EMBRYONIC DEVELOPMENT OF DOPAMINERGIC NEURONS OF THE SUBSTANTIA NIGRA, BUT NOT THE VENTRAL TEGMENTAL AREA, IN MOUSE BRAIN
Review round: 1
Reviewer: 1

Output:
Basic reporting: Tarasova et al., have studied the dynamic change in TH-positive numbers between E10.5 and E13.5 in the SN of asyn KO mice. They report that asyn KO mice display an earlier increase in the number of TH-positive cells than WT cells. Overall, however, number are lower than in WT mice (agreeing with previous reports, Garcia-Reitboeck P et al., 2013). Moreover, they find no changes in the TH-positive cell numbers in VTA region between the two conditions.

The manuscript is clear and unambiguous, language is fine, references are appropriate.
Experimental design: The experimental design is appropriate, methods are described with sufficient detail and ethical standards have been met (got bioethics approval).
Validity of the findings: Data is robust, statistically sound, & controlled. Conclusion are well stated, linked to original research question & limited to supporting 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: GENETIC INACTIVATION OF ALPHA-SYNUCLEIN AFFECTS EMBRYONIC DEVELOPMENT OF DOPAMINERGIC NEURONS OF THE SUBSTANTIA NIGRA, BUT NOT THE VENTRAL TEGMENTAL AREA, IN MOUSE BRAIN
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a very brief report analysing the ontogenesis of dopaminergic neurons in mutant mice for the alpha-synuclein gene, which has been implicated in the pathogenesis of several neurodegenerative diseases including Parkinson's disease (see below for comments on the experimental procedure and validity of findings).
The manuscript is written in a clear and accessible way.
Experimental design: Up to standards
Validity of the findings: These appear valid
Additional comments: Major comment:

The Y-axis scale in Fig. 1B isn't discriminative enough. No need to modify the figure, but the numerical values (mean+/- s.e.m.) should be added in the legend.

Minor corrections:
In general the manuscript is correctly written and the language is fine. A number of typos or minor errors are found, however, throughout the manuscript. These can be easily corrected:

line 48: replace ; by ,

line 49: add comma (,) after "atrophy"

line 53: "...mechanisms that are important for neuronal physiology; including its roles in synaptic vesicle function..." should read: "...mechanisms that are important for neuronal physiology, including synaptic vesicle function..."

line 58: The key mechanism of pathology of PD

line 62: delete EJ

line 64: ventricular shouldn't be in italics

line 74: add comma (,) between populations and the

line 84: spell PFA

line 90: performed instead of reformed

line 103: delete "In contrast" (sentence should begin with: "In WT mice, no substantial increase..")

line 108 "...while in aKO mice this increase..."

line 128: "leads'

line 134: "...leads to an inefficient DA neuron pool formation..."

line 142 : correct deferential to differential

line 147: "...formation of DA neurons..."

Figure 2 legend: correct Substancia to Substantia