The authors conducted a comprehensive study that queried whether habitat fragmentation and increasing isolation altered microbial community, and whether this led to a feedback effect on plants. I think this is a neat study and shows clear results.

General comments
In the abstract it isn’t clear to me that matrix refers to urban, and so it is confusing throughout- could this be changed to urban?
Introduction is very well written and reasoned. However, I think a small section on potential for microbial dispersal between fragments etc would be very useful. How does it take place? This would contextualise your work on distance between fragments.
While I understand most of the work is exploratory, I do think a hypothesis for the mesocosm work would be useful around line 150.

Have you also considered fragment size as a reservoir of microbes?

I am concerned about the potential for microbial lysing causing unwanted effects after sterilisation. How did you account for that? Did you check nutrient levels? Also did you get a high number of pathogens moving in to those sterilised mesocosms, or did they remain fairly sterile throughout?

The subheadings of the results and discussion are really clear and informative.

I don’t have any notes for the discussion, it is written very clearly.

Line 57: which soils had these changes?
Line 173-174: I’m having the same problem as with the abstract- the core buffer zone refers to the forest fragment and the matrix refers to the urban? Please make sure this is really clear throughout.
Lines 225-227: which components of diversity (line 225)? How were these measured?
Line 235: cite FUNguild.
Line 243: cite AIC (Akaike 1974)
Lines 248-251: this is for all the species added together?
Line 269: I’m still not sure what your definition of diversity is here- what metric have you used?
Line 304: here you have used urban microbiomes rather than matrix microbiomes- I think this is easier to follow. Please could matrix be changed to urban throughout?
Line 354: is this an observation or actually assessed in the analysis of the mesocosms?

Figure 2- rather difficult to interpret. Could you add ellipses or spiders to help show patterns?
Line 3- I really like this arrangement.