You can compare presence-absence using beta diversity :)

I found this: https://cran.r-project.org/web/packages/indicspecies/vignettes/IndicatorSpeciesAnalysis.html

However, it seems you will have to perform the analysis for each year separately.

That being said, why would you want to do it because ISA is used to identify important species in a community (typically abundant and widespread) for a specific study site across as many years as possible. Then, the species identified as important (using a certain threshold value) can be monitored consecutive years.

To investigate different indicators for different years seem counterintuitive. Or is it more of a theoretical thing where you want to investigate how the "important" species change over time which will point to changing environmental drivers?