Citation: Hernández-Delgado, E.A.; Ortiz-Flores, M.F. The Long and Winding Road of Coral Reef Recovery in the Anthropocene: A Case Study from Puerto Rico. Diversity 2022, 14, 804. https:// doi.org/10.3390/d14100804 Academic Editor: Bert W. Hoeksema Received: 5 January 2022 Accepted: 11 August 2022 Published: 27 September 2022 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). diversity Article The Long and Winding Road of Coral Reef Recovery in the Anthropocene: A Case Study from Puerto Rico Edwin A. Hernández-Delgado 1,2,3,4, * and María F. Ortiz-Flores 3 1 Center for Applied Tropical Ecology and Conservation, University of Puerto Rico, San Juan 00925-2537, Puerto Rico 2 Faculty of Natural Sciences Interdisciplinary Program, University of Puerto Rico, San Juan 00925-2537, Puerto Rico 3 Department of Environmental Sciences, University of Puerto Rico, San Juan 00925-2537, Puerto Rico 4 Sociedad Ambiente Marino, San Juan 00931-2158, Puerto Rico * Correspondence: edwin.hernandezdelgado@gmail.com Abstract: The persistence and resilience of marginal shallow coral reefs at their limits of environmen- tal tolerance have declined due to chronic environmental degradation and climate change. However, the consequences for the natural recovery ability of reefs of disturbance remain poorly understood. This study considered the potential for natural recovery through coral recruitment on fringing reefs across different geographic regions under contrasting environmental conditions in Puerto Rico. Reefs in areas with significant water quality degradation and more severe physical impacts of hurricanes were expected to have lower coral recruit density and diversity, and therefore less potential for recovery. Sixteen reefs were assessed across three geographic regions. Degraded reefs sustained a lower percentage of live coral cover and had higher macroalgae and turf algae abundance. Locations affected by high PO 4 , NH 3 + and optical brightness concentrations, high turbidity, and high sea surface temperature anomalies, chlorophyll-a concentration and light attenuation Kd 490 evidenced significantly lower coral recruit density and diversity. Hurricane-decimated reefs also exhibited impoverished coral recruit assemblages. Low coral recruitment could have important long-term implications under projected climate change and sea level rise, particularly in coastal urban habi- tats. There is a need to implement effective environmental conservation, ecological restoration and community participation strategies that facilitate enhanced coral recruitment success and assisted recovery processes. Keywords: benthic community trajectory; coral recruitment; coral reefs; disturbance; hurricanes; recovery; water quality 1. Introduction Coral reefs provide critical resources and ecological services of significant socio- economic value for multiple island nations on a global scale [1–3]. Yet in recent decades, coral reefs have been in continuous decline due to a combination of local human factors and climate change [4–8]. They constitute habitats for multiple species, support important subsistence fisheries and tourism [9], buffer wave energy [10], and capture carbon dioxide (CO 2 ) from the atmosphere, thus helping to reduce the impact of greenhouse gas emis- sions [11]. However, changes in the frequency and severity of disturbance regimes due to combined anthropogenic stressors and climate change are increasingly challenging the natural capacity of coral reefs to absorb impacts and recover from disturbance [6,12,13]. Given the social and ecological importance of coral reef systems, a better understanding of coral reef recovery dynamics following disturbance is required [14]. This is particularly concerning in shallow urban coastal coral reef ecosystems, which are frequently impacted by turbidity, sedimentation, and a combination of anthropogenic stressors, such as eu- trophication, pollution, and fishing [15–17], and that are often characterized by the loss Diversity 2022, 14, 804. https://doi.org/10.3390/d14100804 https://www.mdpi.com/journal/diversity