A few comments/questions:
1) are you actually interested in site to site differences?
2) what are these concrete numbers in your covariate class?
3) Gowers log10 seems to be a fairly extreme distance measure when you are only dealing with 0-15 individuals. Why have you selected that one?
4) do you only have one organism? Or are you looking at community data? If it is the former I wonder if you would be better modeeling this by fitting an ANCOVA model - unless you have reason to use a distance based method.