Microorganisms and dissolved metabolites distinguish Florida's Coral Reef habitats

As coral reef ecosystems experience unprecedented change, effective monitoring of reef features supports management, conservation, and intervention efforts. Omic techniques show promise in quantifying key components of reef ecosystems including dissolved metabolites and microorganisms that may serve as invisible sensors for reef ecosystem dynamics. Dissolved metabolites are released by reef organisms and transferred among microorganisms, acting as chemical currencies and contributing to nutrient cycling and signaling on reefs. Here, we applied four omic techniques (taxonomic microbiome via amplicon sequencing, functional microbiome via shotgun metagenomics, targeted metabolomics, and untargeted metabolomics) to waters overlying Florida's Coral Reef, as well as microbiome profiling on individual coral colonies from these reefs to understand how microbes and dissolved metabolites reflect biogeographical, benthic, and nutrient properties of this 500-km barrier reef. We show that the microbial and metabolite omic approaches each differentiated reef habitats based on geographic zone. Further, seawater microbiome profiling and targeted metabolomics were significantly related to more reef habitat characteristics, such as amount of hard and soft coral, compared to metagenomic sequencing and untargeted metabolomics. Across five coral species, microbiomes were also significantly related to reef zone, followed by species and disease status, suggesting that the geographic water circulation patterns in Florida also impact the microbiomes of reef builders. A combination of differential abundance and indicator species analyses revealed metabolite and microbial signatures of specific reef zones, which demonstrates the utility of these techniques to provide new insights into reef microbial and metabolite features that reflect broader ecosystem processes.

The potential for coral reef restoration to mitigate coastal flooding as sea levels rise

The ability of reefs to protect coastlines from storm-driven flooding hinges on their capacity to keep pace with sea-level rise. Here, we show how and whether coral restoration could achieve the often-cited goal of reversing the impacts of coral-reef degradation to preserve this essential function. We combined coral-growth measurements and carbonate-budget assessments of reef-accretion potential at Buck Island Reef, U.S. Virgin Islands, with hydrodynamic modeling to quantify future coastal flooding under various coral-restoration, sea-level rise, and storm scenarios. Our results provide guidance on how restoration of Acropora palmata, if successful, could mitigate the most extreme impacts of coastal flooding by reversing projected trajectories of reef erosion and allowing reefs to keep pace with the ~0.5 m of sea-level rise expected by 2100 with moderate carbon-emissions reductions. This highlights the potential long-term benefits of pursuing coral-reef restoration alongside climate-change mitigation to support the persistence of essential coral-reef ecosystem services.

Upwelling, climate change, and the shifting geography of coral reef development

The eastern tropical Pacific is oceanographically unfavorable for coral-reef development. Nevertheless, reefs have persisted there for the last 7000 years. Rates of vertical accretion during the Holocene have been similar in the strong-upwelling Gulf of Panamá (GoP) and the adjacent, weak-upwelling Gulf of Chiriquí (GoC); however, seasonal upwelling in the GoP exacerbated a climate-driven hiatus in reef development in the late Holocene. The situation is now reversed and seasonal upwelling in the GoP currently buffers thermal stress, creating a refuge for coral growth. We developed carbonate budget models to project the capacity of reefs in both gulfs to keep up with future sea-level rise. On average, the GoP had significantly higher net carbonate production rates than the GoC. With an estimated contemporary reef-accretion potential (RAP) of 5.5 mm year^-1, reefs in the GoP are projected to be able to keep up with sea-level rise if CO₂ emissions are reduced, but not under current emissions trajectories. With an estimated RAP of just 0.3 mm year^-1, reefs in the GoC are likely already unable to keep up with contemporary sea-level rise in Panamá (1.4 mm year^-1). Whereas the GoP has the potential to support functional reefs in the near-term, our study indicates that their long-term persistence will depend on reduction of greenhouse gases.

The past, present, and future of coral reef growth in the Florida Keys

Coral-reef degradation is driving global-scale reductions in reef-building capacity and the ecological, geological, and socioeconomic functions it supports. The persistence of those essential functions will depend on whether coral-reef management is able to rebalance the competing processes of reef accretion and erosion. Here, we reconstructed census-based carbonate budgets of 46 reefs throughout the Florida Keys from 1996 to 2019. We evaluated the environmental and ecological drivers of changing budget states and compared historical trends in reef-accretion potential to millennial-scale baselines of accretion from reef cores and future projections with coral restoration. We found that historically, most reefs had positive carbonate budgets, and many had reef-accretion potential comparable to the ~3 mm year^-1 average accretion rate during the peak of regional reef building ~7000 years ago; however, declines in reef-building Acropora palmata and Orbicella spp. corals following a series of thermal stress events and coral disease outbreaks resulted in a shift from positive to negative budgets for most reefs in the region. By 2019, only ~15% of reefs had positive net carbonate production. Most of those reefs were in inshore, Lower Keys patch-reef habitats with low water clarity, supporting the hypothesis that environments with naturally low irradiance may provide a refugia from thermal stress. We caution that our estimated carbonate budgets are likely overly optimistic; comparison of reef-accretion potential to measured accretion from reef cores suggests that, by not accounting for the role of nonbiological physical and chemical erosion, census-based carbonate budgets may underestimate total erosion by ~1 mm year^-1 (-1.15 kg CaCO₃ m^-2 year^-1 ). Although the present state of Florida's reefs is dire, we demonstrate that the restoration of reef-building corals has the potential to help mitigate declines in reef accretion in some locations, which could allow some key ecosystem functions to be maintained until the threat of global climate change is addressed.

Comparing management strategies for conserving communities of climate-threatened species with a stochastic metacommunity model

Many species are shifting their ranges to keep pace with climate change, but habitat fragmentation and limited dispersal could impede these range shifts. In the case of climate-vulnerable foundation species such as tropical reef corals and temperate forest trees, such limitations might put entire communities at risk of extinction. Restoring connectivity through corridors, stepping-stones or enhanced quality of existing patches could prevent the extinction of several species, but dispersal-limited species might not benefit if other species block their dispersal. Alternatively, managers might relocate vulnerable species between habitats through assisted migration, but this is generally a species-by-species approach. To evaluate the relative efficacy of these strategies, we simulated the climate-tracking of species in randomized competitive metacommunities with alternative management interventions. We found that corridors and assisted migration were the most effective strategies at reducing extinction. Assisted migration was especially effective at reducing the extinction likelihood for short-dispersing species, but it often required moving several species repeatedly. Assisted migration was more effective at reducing extinction in environments with higher stochasticity, and corridors were more effective at reducing extinction in environments with lower stochasticity. We discuss the application of these approaches to an array of systems ranging from tropical corals to temperate forests.

This article is part of the theme issue ‘Ecological complexity and the biosphere: the next 30 years’.

Ecosystem design as an avenue for improving services provided by carbonate producing marine ecosystems

Ecosystem Design (ED) is an approach for constructing habitats that places human needs for ecosystem services at the center of intervention, with the overarching goal of establishing self-sustaining habitats which require limited management. This concept was originally developed for use in mangrove ecosystems, and is understandably controversial, as it markedly diverges from other protection approaches that assign human use a minor priority or exclude it. However, the advantage of ED lies within the considered implementation of these designed ecosystems, thus preserving human benefits from potential later disturbances. Here, we outline the concept of ED in tropical carbonate depositional systems and discuss potential applications to aid ecosystem services such as beach nourishment and protection of coastlines and reef islands at risk from environmental and climate change, CO₂ sequestration, food production, and tourism. Biological carbonate sediment production is a crucial source of stability of reef islands and reef-rimmed coastlines. Careful implementation of designed carbonate depositional ecosystems could help counterbalance sea-level rise and manage documented erosion effects of coastal constructions. Importantly, adhering to the core ethos of ED, careful dynamic assessments which provide a balanced approach to maximizing ecosystem services (e.g., carbonate production), should identify and avoid any potential damages to existing functioning ecosystems.