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  1. Many marine habitats are at risk due to increasing frequency, intensity, and persistence of harmful algal blooms. Repeated cyanobacterial harmful algal blooms (cyanoHABs) in Florida Bay, USA, kill sponges, resulting in reduced filtration and loss of shelter for benthic species. The loss of these key ecosystem functions can impact disease dynamics if fewer pathogens are filtered from the water column (dilution), if shelter loss increases host density in remaining shelters and a directly transmitted disease is present (host regulation), or if shelter loss changes species distributions and foraging patterns (trophic exposure). We show persistent impacts to hard-bottom communities relative to non-impacted communities 2 yr after a significant cyanoHAB. We compared benthic structure, invertebrate epibenthic/infaunal community composition, and parasitism among macroinvertebrates, stone crab Menippe mercenaria , and Caribbean spiny lobster Panulirus argus . On sites degraded by cyanoHABs, we found more, smaller sponges, indicating regrowth. Despite this evidence of recovery, epibenthic/infaunal invertebrate communities were distinct and more diverse on unimpacted sites. Additionally, there were fewer, smaller bivalves on impacted sites. The bivalve Tucetona pectinata , prey for stone crabs, was nearly absent on impacted sites, resulting in decreased prevalence of the apicomplexan gregarine Nematopsis sp., which is trophically transmitted from T. pectinata to M. mercenaria . Panulirus argus virus 1 also appears to be affected by cyanoHABs, as it was absent on impacted sites but present in 26.5% of spiny lobster on unimpacted sites. Impacts remain evident 2 yr after significant cyanoHABs, which does not bode well for these areas considering the frequent reoccurrence of blooms. 
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