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Excellent work. The manuscript is interesting and well-written. The authors did a great job responding to my comments and have added sufficient information to address all of my prior concerns.
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Your manuscript has now been reviewed and the referee comments are appended below. You will see that, while they find your work of interest, they have raised points that need to be addressed by a revision.
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This paper is well written, clear and concise. The presentation is logical throughout the paper. The introduction and background are thorough with the relevant literature referenced. The Figures are necessary, high quality, and well labelled.
The experimental design is outstanding based on the methods of previous studies of fungal endophytes of woody plants. The research question is interesting and unusual in that little work has been done on fungal endophytes of trees in urban environments. The methods as described are excellent.
The data analysis is rigorous especially important given the many variables. The authors have emphasized the most likely factors that may influence the results namely size of tree and proximity to the bay. In spite of their excellent methods the number of fungal endophytes does not come close to reaching the maximum diversity as shown by the diversity curves. It would take considerably greater sampling to do this. This is an issue with most of the studies dealing with fungal diversity, thus is not unexpected.
A few editorial comments:
In the abstract, ln 12, I suggest inserting “living” before leaves.
Ln 31, insert “of” before the Earth’s…
Under Methods, ln 106, I suggest changing “chose to focus on” to “selected” just for stylistic purposes as you use “focal” later in the sentence.
Lns 108-113, these statements do not belong in the Methods. Perhaps better in Discussion.
Ln 136, delete “until”
Ln 158, 193, and 307, with adverbs ending -ly a hyphen is never needed. This is a great rule to know so one doesn’t have to think about this. Never needed.
Ln 212, change “weren’t” to “were not”
Ln 309, delete “family” as Myrtaceae implies family by the ending “aceae”
Ln 318, delete “quite”
Ln 323, Mycosphaerales??? Mispelled? Not sure, this is not a fungal family with which I am familiar. Is this name correct?
Ln 328, delete “very”
Ln 356, I think you mean “influence” not “influencing”
This paper was clearly written and understandable. The authors describe a survey of fungal endophytes in street trees in San Francisco.
Intro and background are sufficient to show context, however, I think a little more discussion of the types of endophytes would help. Here’s a suggestion for organizing it:
- Introduce classes of endophytes (Rodriguez et al 2009). Talk about what class is likely to inhabit your host species. Talk about why composition could differ among sites or plant species (e.g. ambient environmental differences, environmental filtering). Talk about how those differences may affect your host plant (e.g. disease resistance by preventing pathogen infection)
Figures are very nice looking, relevant to the main points, labeled and described adequately.
All raw data is supplied. This is the most reproducible manuscript I have ever reviewed. Very nice work!
The study objectives were to define the diversity and biogeographic patters of foliar fungal communities in an urban environment. The authors make it clear that little is known about fungal endophyte colonization in urban environments. I would like to see the questions better defined. For instance, What about the urban environment do expect to shape the fungal communities? And how do you plan to measure those things? I give a couple of suggestions for being more quantitative in some areas to improve the explanatory power of your statistical tests and figures.
Very high open research standards. Again, nice work on this. The conclusions are well stated, but I am still curious if some of the environmental variables could be linked to the community data in a more quantitative way. See specific comments for some suggestions.
Abstract:
Line 10: You define the plant microbiome as microbes associated with plant tissues. While I think that is not wrong, it’s not explicitly inclusive of rhizosphere microbes. I suggest changing to “plant tissues and soils” or something like that
Introduction:
Line 33: What do you mean by “can be seen” worldwide? In what way?
Line 78-79: Note that these are specific type of endophyte not likely to be found in tree leaves. You might want to introduce the classes of endophytes from Rodriguez et al 2009. It might be helpful in describing what type of endophytes you expect to be present in your host species.
Line 101-103: Odd to see a summary of results in the introduction. I recommend removing this and ending the section with your expectations.
Methods:
Line 116: what is tall? Was that defined in some way? If so, is there a way to make this quantitative and explore its effect on community composition? Maybe you could create a definition for tall – and count the number of building that meet that standard in some defined radius around each site? Or count all structures in a defined radius around the site and create an “index of urban-ness” (just made that up) by weighting taller buildings more than shorter or houses. With that data, you could see if “urban-ness” was a predictor of variation in your microbial community data.
Line 197: Really impressive reproducibility here! Nice work!
Results:
You mention often that the sampling effort was not sufficient to show the total diversity given species accumulation curves. You might want to report chao1 diversity estimates in that case.
Discussion:
Line 282: check code calls to figures.
Line 283: Wondering if it would make your points clearer if you presented centroids with 95% confidence interval bars on your ordination rather than standard error ellipses. That would make it much easier to tell whether your groups are actually different from one another. Given your permanova results, maybe they would not be different, but it looks like some groups may differ from others.
Line 318-319: Also possible that these fungi are ubiquitously common. If you can find a reference of a study looking at fungal endophytes in other species in CA and/or NZ, it might give the reader insight into whether these fungal groups are just common endophytes everywhere.
Table 2: Check code for the first two Terms.
Figure 5: I wonder what this would look like as a db-RDA. You could then add the DBH into your model and add vectors to your ordination. Table 2 suggests that DBH matters for community composition, adding the vectors to the ordination would help visualize that. Just a suggestion.
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