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The revisions have been all done as suggested, and this manuscript is ready for publication. I look forward to seeing this in its published form.
Please note a few small corrections (these can be done at the proof stage):
1. line 294 - "analysis" to "analyses".
2. line 338: You say genera but these are family names. Correct, and if you keep family names, remove italics.
I have heard back from two reviewers, both of whom recommend accept. I have also gone over the manuscript in detail, and have added many small corrections here and there (see attached document). These are too many in number to leave to the proof stage, but all are easily corrected. Therefore, my decision is "minor revision" with the emphasis on "minor".
The author addressed all the reviewers' comments and well revised this manuscript. I think this research paper is ready to get published.
I am happy with the changes the authors made and their rebuttal to the points raised by myself and Reviewer 1. I recommend it should be accepted for publication.
Three reviewers have now reported back to me on your manuscript. While one was very positive, two other reviewers raised serious comments on 1) the identification of species of soft coral; 2) the methodology (are 50 points within CPC enough?); and 3) the discussion. As well, the English does need brushing up here and there as indicated by one reviewer. Although the reviews may result in an extensive rewrite of the paper, there are many issues that need your attention as pointed out by the three reviewers, and for this reason my decision is "Major Revision".
The English in some parts of the result and discussion are not clear, need to send for English check. Data in some tables should be rearranged to match with the flow of the article. Also, there are some data mentioned in the text but not in the table or figures. Please see the general comments part for more details.
This work showed a clear define of the research question and have proper approaches. However, there is one question about the experimental design. Author's group used 1x1 m gridded quadrat to investigate the benthic coverage, however just applied 50 random points on CPCe seems low to survey the composition of the benthic group. Can author provide references or evidence to show 50 points is sufficient?
This research is based on the environmental survey, therefore, it is hard to explain some of the correlations between environmental data with biological data. The author's group did found some interesting correlations, however, the discussion seems a bit generalized. It would be better if author could have more discussions on case studies and compared with this study.
Another issue is the discussion of ETS activity. I think as author is the first group tried this method on soft coral, it is better to explain the result with caution. More case studies should be explicated and carefully infer to this study. Other possible reasons causing this ETS result should be discussed. I found contradicted part in this ETS discussion, please see general comments part for more details.
1. Make all the "a" of Chl a and "p" of p-value italic.
2. Line 148
3. Result part
Please cite tables and figures in the begging of the paragraph or when author mentioned the data, it is easier to read. There are some data mentioned in the text but can not found in tables and figures. Also, the information in the table is kind of scatter, from example, in table 3, a lot of data didn’t be mentioned, or it should go with table 5, please remake table result with the flow of the text.
4. “live benthic cover” and table 2
Author mentioned the offshore hard coral and soft coral cover mean, but in table 2., midshore is combined with offshore, please modified author’s table.
5. Line 262
“Bruno et al. (2009) use a cut-off set at more than 50 % cover…”
If author wants to define dominance, they can just use own definition. In this research is not related with phaseshift, no need to brought out this.
6. Line 266
“Soft coral dominance….”
Soft coral cover mean in AB is also higher than hard coral cover, why author don’t consider it is also dominant in AB?
7. Line 302
“…, suggesting that ETS might be lower….”
From figure 4, there are other sites at outer Thousand Islands which have lower ETS than some sites in the bay, please rephrase this sentence.
8. Line 311
Cite table 3 after the (p = 0.004).
9. Line 312 -313
The statement author mentioned can not be seen from table 5, and the p value is from table 3. Also, from table 3, ETS activity of Nephthea sp. also have significant correlation with NH3, meanwhile from table 5 also indicate NH3 as a factor, is there an explanation for that?
10. Line 314 “….(<15% for both species).”
Where is this number from?
11. Line 314 “Similarly….”
Please cite where this data from. And what is it similar to, please rephrase this sentence.
12. Line 316 “For ETS-activity….”
I think author mean table 6? And no significant correlation to what, please rephrase.
13. For result part of “Correlations between water quality, reef condition and ETS activity as well as photosynthetic yield”
How is the correlation of total soft coral cover with water quality? Since some of author’s sites might have other soft corals co-dominate? It might be interesting to discuss this.
14. From line 329 “Both..” to the end of line 333
Please be cautious about these conclusions. There are exceptions in author’s data, please also address them out.
15. Line 364
Sarcophyton sp. has high coverage in Panggang, so I think it might not be proper to say they have similar trend, please rephrase.
16. Line 365 – 372
Again, this research has no evidence on the phase-shift in this area. Therefore besides phase-shift, please discuss more studies on high soft coral cover related with water eutrophication.
17. Line 377 “Dissolved …”
This sentence is not clear, please rephrase it. Also please provide more papers on each factor.
18. Discussion part of “Physiology of Sarcophyton sp. and Nephthea sp.
Please reconstruct this discussion, as this part seem contradicted.
The whole sentence doesn’t make sense. From author’s result photosynthesis and ETS activity decreased as water quality decrease, but the soft coral cover increased while water quality decrease, why it is all negatively correlated with water quality?
Please be cautious to interpret the data of ETS. There is neither case study of ETS on corals, nor other organisms which symbiosis with Symbiodinum. Therefore it is hard to define if ETS is a good bioindicator of energy for organisms that can do hetero-autotrophic. Furthermore, author mentioned in line 436 that ETS is a useful stress biomarker in soft corals, however, there is no direct evidence showing the ETS is related with stress on soft corals. Author also refer to soft corals shown to benefit from extra nutrient input, so is it means they are not under stress? In this sense, how do you define stress?
19. In the discussion, there is no discussion on the benthic topography (rock, rubble?), which is important to determine the distribution patterns of soft coral. In the end of the discussion, author brought out the influence on blast fishing, and implied this might be the reason of high soft coral cover rate in Panggang. Is there any data to characterize this? How about the benthic topography in other locations?
Baum et al, in their work have used all the appropriate methodology to address their question as to whether the physiology of soft corals are linked to water quality in Jakarta Bay. They have used both physiology parameters (photosynthetic yield and ETS activity), chemical oceanography and ecology ecology. Their survey and sampling design has covered; inhabited and non-inhabited islands, strong difference in coral cover and wave exposure and current regime differences.
As expected, although the authors did not comprehensively prove that influence of water quality on the physiology, but due to lack of knowledge on physiological processes and compensating mechanisms of soft corals exposed to stressors, this study is one step towards more future study on this matte and hence findings from this work can be used in future more effective designs to understand the effects of stress on physiology of soft corals in more detail.
I have read the manuscript submitted by Baum et al, which looks at if the abundance and physiology of soft corals are linked to the water quality.
This study makes an important contribution. The effect of pollution and other human disturbance are taking their toll on the coral reefs, their survival and other phenomenon such as phase shifts.
The authors have presented a simple and neat work with all the appropriate methodology and analysis.
I do not have any comments and I would be happy to read it again when it will appear in PeerJ
Basic reporting is good, I however would suggest that the authors try to rely less on "grey literature" when scientific literature is available.
My only worry is the fact that the authors suggest that they worked on two "species", while they clearly worked on two genera and likely included several species per genus in their research. This needs to be address / explained in the paper.
See review for some questions about the interpretation of the results on shift from hard to soft corals.
I enjoyed reading a manuscript which combines water quality parameters with physiology information. An interesting approach and it works well for an area as well-studied as Jakarta Bay.
Major issues [need to be addressed]
1) Lines 107-109 reads: Does water quality affect photosynthesis and ETS activity of two dominant soft corals in the area, Sarcophyton sp. (Family: Alcyoniidae) and Nephthea sp. (Family: Nephtheidae)?
First of all, the genus Nephthea was recently synonymised with Litophyton by Van Ofwegen (2016), see http://www.marinespecies.org/aphia.php?p=taxdetails&id=205891. More importantly, the authors consistently refer to the taxa that they studied as “two species”. In fact, both Sarcophyton and Nephthea/Litophyton are very species rich genera. I know first-hand how problematic soft coral taxonomy and identification can be (did you even try to ID them using sclerites?), but I do not agree with the lumping that the authors do by just calling everything Sarcophyton sp. and then lumping the results for the photosynthetic yield and ETS. And for Sarcophyton there is the added problem that some species can look a lot like Lobophytum and Sinularia! It seems to me that the authors could wrongly be combining the results for many different species that could all have different responses to the tests. In lines 169/170 is mentioned: “At each site, fragments ( ̴ 5 – 10 cm length) of the two soft coral species, Sarcophyton sp. and Nephthea sp., were sampled (n = 5) during SCUBA diving at ̴ 5 m water depth.” If I understand correctly they could have collected 5 different Sarcophyton species and 5 different Nephthea / Litophyton species at each site. This needs to be addressed throughout the manuscript, as it not only impacts the results of the different tests, but also the results of soft coral cover.
2) After reading your manuscript I am left with one main question and I would like to hear your thoughts on it. Would it be possible that the soft corals just didn’t appear from the Bay, whereas the stony corals did? As far as I am aware there is not a lot of data on soft coral cover (maybe in the UNESCO reports?), hence you cannot really know if their abundance increased or decreased over time. In that case the “shift” in coral community comes from the soft corals surviving in an increasingly difficult environment, whereas the hard corals can no longer cope and disappear. If this were the case I am not sure if you can talk about a “shift” and “dominance” (frankly I don’t think that a mean soft coral cover of 12.8% can be considered “dominance”). Jakarta Bay and the Thousands Islands are suffering from long-term decline in coral cover, why would we now (after ca. 100 years decline) be at the turning point of a shift from hard to soft coral?
So my questions is as follows: Is there really a shift (i.e. soft coral cover is increasing) OR did the soft coral cover maintain the same level of cover and the hard corals declined in cover?
Minor issue [optional]
1) This article relies quite heavily on “grey” literature, whereas in some case scientific papers are available with further information. I would prefer to see more references to scientific papers (including older literature) and provided some suggestions in the text.
I’ve made some comments on the annotated manuscript as well.
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