When measuring diversity it is good to remember that what we are trying to describe is the relationship of individuals of varying categories within a community. These categories can be species, genera, families, or any other categories that you consider to be important. The categories are well known. In most cases, such as with our biofilm study, this assumption is not violated since the taxonomic classification of organisms that we use is accepted world-wide. This can happen when species are regrouped into new species, genera or families.
All categories are equally different.
Categories are equally different from each other category. This is not always true since two species from the same genera are treated the same as two species from different families. Use a measure of species importance. Usually, one uses the number of individuals, percent coverage, relative density or biomass. The choice usually depends on the ease of measurement.