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1. Persistent coral communities on degraded Caribbean reefs

   https://doi.org/10.3354/meps14999  

   Edmunds, Peter J (November 2025, Marine Ecology Progress Series)

   After decades of coral death, many tropical coral communities consist of populations at low abundances, ensuring that future coral reefs will differ from those of the recent past for decades to come. The large spatial scale of this phenomenon deters further study of the relic communities, yet it is through the study of coral-depauperate reefs that a better understanding of the potential for recovery of coral communities will emerge. Here, 32 yr of annual surveys (1992-2023) of benthic communities at 6 sites on the fringing reefs (7-9 m depth) of St. John, US Virgin Islands, are used to consider the potential future trajectories of change for low-abundance coral communities. On these reefs, the mean cover of macroalgae and of crustose coralline algae, turf, and bare space combined increased at 2.8 and 4.0% decade^-1, respectively, together covering 81% of the reefs by 2023; over the same period, mean coral cover remained at 2-4%. Averaged among years, the sites differed in mean coral cover (range: 1-7%), and while spatial autocorrelation of coral cover (a measure of biotic homogenization) was similar among sites, it increased over time at 2 sites. Coral generic richness trended downward in the third decade of the study in favor of ‘weedy’ corals, but the low-abundance coral communities persisted for 32 yr. With ≤4% mean coral cover, these communities are tropical reefs populated by living corals rather than ‘coral reefs’, yet they retain ecological importance by supporting low-abundance populations of persistent corals. 

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2. Long‐term community dynamics are heterogeneous between fringing‐ and fore‐reef habitats on an Indo‐Pacific coral reef

   https://doi.org/10.1002/ecs2.70398  

   Edmunds, P J; John, C; Leichter, J J; Moritz, C; Scafidi, K C; Speare, K E; Srednick, G; Wyatt, A_S J (October 2025, Ecosphere)

   Abstract Benthic community structure on present‐day coral reefs is often described as rapidly degrading, yet such summative statements do not capture the effects of spatial heterogeneity in communities. We focus on Moorea, French Polynesia, where the fore reef has shown high ecological resilience in recent decades, and ask whether the adjacent fringing reefs show different dynamics as a result of local environmental conditions. Communities on fringing reefs (~4‐m depth) were quantified at six sites from 2005 to 2022, and their community dynamics were tested for association with environmental conditions. Unlike the fore reef, most fringing reefs became degraded with respect to hard coral cover and showed low resilience, and their benthic communities differed more among sites than over time at any one site. The sites were each characterized by different temperature regimes, geomorphology, algal cover, and runoff of rainfall from the land. When pooled among sites and times, variation in coral community structure was most strongly associated with distance from the nearest reef pass and macroalgal cover, while benthic community structure was most strongly associated with the distance from the nearest reef pass and the area of building coverage (i.e., a development index). These findings underscore the strong effects of spatial structuring of anthropogenic disturbances, local‐scale spatial heterogeneity in reef communities, and the limitations of categorical descriptions of reef condition. Together with evidence of resilient fore‐reef communities around Moorea, these results reveal the potential for among‐habitat community asynchrony to mediate island‐scale coral reef community resilience and show that the community dynamics of fringing reefs are important components of holistic summaries of reef condition. While these fringing reefs exhibit degradation and varied resilience, these community trends were more strongly associated with local anthropogenic impacts than climate change. Modifications to local environmental management actions therefore have the potential to alter trajectories of coral community change at the same spatial scale. 

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3. Historical baselines of coral cover on tropical reefs as estimated by expert opinion

   https://doi.org/10.7717/peerj.4308  

   Eddy, Tyler D.; Cheung, William W.L.; Bruno, John F. (January 2018, PeerJ)

   Coral reefs are important habitats that represent global marine biodiversity hotspots and provide important benefits to people in many tropical regions. However, coral reefs are becoming increasingly threatened by climate change, overfishing, habitat destruction, and pollution. Historical baselines of coral cover are important to understand how much coral cover has been lost, e.g., to avoid the ‘shifting baseline syndrome’. There are few quantitative observations of coral reef cover prior to the industrial revolution, and therefore baselines of coral reef cover are difficult to estimate. Here, we use expert and ocean-user opinion surveys to estimate baselines of global coral reef cover. The overall mean estimated baseline coral cover was 59% (±19% standard deviation), compared to an average of 58% (±18% standard deviation) estimated by professional scientists. We did not find evidence of the shifting baseline syndrome, whereby respondents who first observed coral reefs more recently report lower estimates of baseline coral cover. These estimates of historical coral reef baseline cover are important for scientists, policy makers, and managers to understand the extent to which coral reefs have become depleted and to set appropriate recovery targets. 

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4. Coral metabolome quality and contaminant loads track human land use

   https://doi.org/10.1038/s41467-026-74960-7  

   Quinlan, Zachary A; Greene, Austin; Leggat, William; Moriarty, Tess; Ainsworth, Tracy D; Nijagal, Brunda; Falinski, Kim; Sogin, E Maggie; Caldwell, Jamie M; Heron, Scott F; et al (July 2026, Nature Communications)

   Abstract Anthropogenic activities pose a significant risk to vulnerable marine ecosystems like coral reefs, particularly those near human population centers. Despite coral reefs being one of the systems most at risk, the relationship between contaminant exposure and coral health across gradients of ecosystem disturbance remains poorly understood. Our metabolomic analysis of 380 corals from 16 sites spanning an anthropogenic impact gradient reveals that the coral metabolome is predictive of anthropogenic ecosystem disturbance. We found that human activities both within catchments and in the marine ecosystem altered the chemodiversity of coral metabolomes with a direct relationship to historic trends in coral cover: nitrogen reserves and metabolome energetic potential are reduced, while stress metabolites are enriched at more impacted sites. We further identify 25 anthropogenic contaminants from agricultural, cosmetological, industrial, and pharmaceutical sources accumulated in coral metabolomes. Our results suggest that the bioaccumulation of pollutants and compositional changes in the metabolome of corals imposed by anthropogenic activities is correlated with coral benthic cover. Together, our findings suggest a direct relationship between coral health, accumulation of dangerous contaminants within corals, and anthropogenic disturbance that is consistent across species. 

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5. Viral predation pressure on coral reefs

   https://doi.org/10.1186/s12915-023-01571-9  

   Silveira, Cynthia B.; Luque, Antoni; Haas, Andreas F.; Roach, Ty N.; George, Emma E.; Knowles, Ben; Little, Mark; Sullivan, Christopher J.; Varona, Natascha S.; Wegley Kelly, Linda; et al (December 2023, BMC Biology)

   Abstract Background Predation pressure and herbivory exert cascading effects on coral reef health and stability. However, the extent of these cascading effects can vary considerably across space and time. This variability is likely a result of the complex interactions between coral reefs’ biotic and abiotic dimensions. A major biological component that has been poorly integrated into the reefs' trophic studies is the microbial community, despite its role in coral death and bleaching susceptibility. Viruses that infect bacteria can control microbial densities and may positively affect coral health by controlling microbialization. We hypothesize that viral predation of bacteria has analogous effects to the top-down pressure of macroorganisms on the trophic structure and reef health. Results Here, we investigated the relationships between live coral cover and viruses, bacteria, benthic algae, fish biomass, and water chemistry in 110 reefs spanning inhabited and uninhabited islands and atolls across the Pacific Ocean. Statistical learning showed that the abundance of turf algae, viruses, and bacteria, in that order, were the variables best predicting the variance in coral cover. While fish biomass was not a strong predictor of coral cover, the relationship between fish and corals became apparent when analyzed in the context of viral predation: high coral cover (> 50%) occurred on reefs with a combination of high predator fish biomass (sum of sharks and piscivores > 200 g m −2 ) and high virus-to-bacteria ratios (> 10), an indicator of viral predation pressure. However, these relationships were non-linear, with reefs at the higher and lower ends of the coral cover continuum displaying a narrow combination of abiotic and biotic variables, while reefs at intermediate coral cover showed a wider range of parameter combinations. Conclusions The results presented here support the hypothesis that viral predation of bacteria is associated with high coral cover and, thus, coral health and stability. We propose that combined predation pressures from fishes and viruses control energy fluxes, inhibiting the detrimental accumulation of ecosystem energy in the microbial food web. 

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