Disturbances that result in the mass mortality of reef-building corals are changing the appearance of reefs worldwide. Many reefs are transitioning away from scleractinian-coraldominated assemblages to benthic communities composed primarily of non-scleractinian taxa. This study evaluated recovery patterns of reef communities in the Florida Keys following the mortality associated with the 1997/1998 El Niño. We examined temporal trends among the 5 most spatially abundant reef taxa and stony coral species from 1999 to 2009 at 3 spatial scales, and applied a Principal Coordinate Analysis (PCoA) to determine whether changes in their cover resulted in a shift in community structure. Trends of decreasing stony coral cover were not identified Keys-wide between 1999 and 2009, but 2 of the 3 habitats examined -shallow and deep forereefs -did show a significant decline in cover. Concomitantly, octocoral cover significantly increased Keys-wide and in all 3 habitats. The transition to octocorals was most evident on shallow forereefs, where octocoral cover significantly increased at 9 of 12 reefs and overwhelmingly influenced the PCoA. On deep forereefs, octocoral and sponge cover did significantly increase, but did not impart a clearly defined shift in community structure like that observed on shallow forereefs. Community composition at patch reefs was relatively consistent during the study, but the increase in octocoral cover may accelerate further following a cold-water mortality event in 2010. These results demonstrate that octocorals are emerging as the predominant benthic taxa in the Florida Keys. Although the transition to octocorals may have started long ago, their apparent resilience to present-day stressors will likely allow this shift to continue into the foreseeable future.

Coral reefs worldwide are in a state of decline, but the population status and impacts of stressors for rare species are generally not well documented using broad-scale monitoring protocols. We fate-tracked all known colonies of the pillar coral, Dendrogyra cylindrus, on the Florida Reef Tract (FRT) from 2013 to 2020 to assess population condition and trend, and to document the relative impacts of chronic and acute stressors. Large average colony size, an absence of juveniles, and large geographic distances between genotypes suggest that the Florida D. cylindrus population has been reproductively extinct for decades. During the study period, low-intensity chronic stressors were balanced by regrowth, while back-to-back years of coral bleaching and thermally-exacerbated disease led to declines that the subsequent recovery rates suggest would require 11 uninterrupted years to overcome. The most recent stressor on Florida’s D. cylindrus population is “stony coral tissue loss disease” (SCTLD). Following the appearance of the disease in Florida in 2014, unrecoverable losses occurred within the D. cylindrus population as tissue, colonies, and whole genotypes suffered complete mortality. Losses of 94% of coral tissue, 93% of colonies, and 86% of genotypes between 2014 and the end of 2020 have led to functional extinction of D. cylindrus on the FRT.

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Rare species population dynamics can elucidate the resilience of an ecosystem. On coral reefs, climate change and local anthropogenic stressors are threatening stony coral persistence, increasing the need to assess vulnerable species locally. Here, we monitored the threatened pillar coral, Dendrogyra cylindrus, population in southeast Florida, USA, in relation to consecutive heat stress events in 2014 and 2015. In the fall of each year, D. cylindrus colonies bleached following intense thermal stress and by June 2020 all monitored colonies died from a white-syndrome type disease. This resulted in the ecological extinction of D. cylindrus in the Southeast Florida Coral Reef Ecosystem Conservation Area (ECA). White-syndrome type disease was first seen in February 2014 on four colonies (19% prevalence) near the major international port, Port Everglades and disease prevalence peaked in fall 2015 (58%). Disease prevalence increased with maximum water temperature, while disease related mortality increased with mean water temperature. Our findings suggest that thermal stress exacerbated underlying stony coral disease, resulting in an outbreak contributing to the ecological extirpation of D. cylindrus in the ECA. We suggest that stony coral resilience is severely compromised by chronic environmental disturbance which hinders community recovery.