Marine ecosystems are being modified at an alarming rate, and tracking how communities respond to these changes is vital for marine balance and functioning. The status of MPAs' biodiversity can be assessed through long-term monitoring programs, but appropriate protocols containing relevant and an ideal number of indicator species are needed. Benthic communities are a good example of ideal indicators given their role in marine ecosystems, but the MONITORA program in Brazil is including just a few species/groups for their national monitoring program. We aimed to compare protocols of epibenthic and megabenthic targets to assess whether a basic protocol can produce quality information for the MPAs managers in Brazil. The findings show similar core results for the epibenthic targets, but the great reduction of megabenthic indicators substantially changed the results and valuable information got lost. However, too many target species go against the MONITORA program premises, and the Simplified MAArE protocol showed to be the most suitable for megabenthic targets and its application should be considered instead of the MONITORA protocol. We also recommended the inclusion of a filter feeders group among the epibenthic targets and a longer temporal series to better understand variability patterns presented in this work.
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