Comparing an ecological subsample to population

I have 2 batches of tree species and abundance data collected for a city. The difference between them is the sampling strategy - one was random unstratified, and the other was stratified and clustered. At a glance the species mixes and relative abundances are fairly similar but i want to test this statistically. I have considered Bray curtis but this test has the assumption that the samples are identical in area, which these arent - the random sample covers a much smaller area of the city.

How can i compare these populations?