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Monitoring coral cover can describe the ecology of reef degradation, but rarely can it reveal the proximal mechanisms of change, or achieve its full potential in informing conservation actions. Describing temporal variation in Symbiodiniaceae within corals can help address these limitations, but this is rarely a research priority. Here, we augmented an ecological time series of the coral reefs of St. John, US Virgin Islands, by describing the genetic complement of symbiotic algae in common corals. Seventy-five corals from nine species were marked and sampled in 2017. Of these colonies, 41% were sampled in 2018, and 72% in 2019; 28% could not be found and were assumed to have died. Symbiodiniaceae ITS2 sequencing identified 525 distinct sequences (comprising 42 ITS2 type profiles), and symbiont diversity differed among host species and individuals, but was in most cases preserved within hosts over 3 yrs that were marked by physical disturbances from major hurricanes (2017) and the regional onset of stony coral tissue loss disease (2019). While changes in symbiont communities were slight and stochastic over time within colonies, variation in the dominant symbionts among colonies was observed for all host species. Together, these results indicate that declining host abundances could lead to the loss of rare algal lineages that are found in a low proportion of few coral colonies left on many reefs, especially if coral declines are symbiont-specific. These findings highlight the importance of identifying Symbiodiniaceae as part of a time series of coral communities to support holistic conservation planning. Repeated sampling of tagged corals is unlikely to be viable for this purpose, because many Caribbean corals are dying before they can be sampled multiple times. Instead, random sampling of large numbers of corals may be more effective in capturing the diversity and temporal dynamics of Symbiodiniaceae metacommunities in reef corals.

 

Some reef-building corals form symbioses with multiple algal partners that differ in ecologically important traits like heat tolerance. Coral bleaching and recovery can drive symbiont community turnover toward more heat-tolerant partners, and this ‘adaptive bleaching’ response can increase future bleaching thresholds by 1–2°C, aiding survival in warming oceans. However, this mechanism of rapid acclimatization only occurs in corals that are compatible with multiple symbionts, and only when the disturbance regime and competitive dynamics among symbionts are sufficient to bring about community turnover. The full scope of coral taxa and ecological scenarios in which symbiont shuffling occurs remains poorly understood, though its prevalence is likely to increase as warming oceans boost the competitive advantage of heat-tolerant symbionts, increase the frequency of bleaching events, and strengthen metacommunity feedbacks. Still, the constraints, limitations, and potential tradeoffs of symbiont shuffling suggest it will not save coral reef ecosystems; however, it may significantly improve the survival trajectories of some, or perhaps many, coral species. Interventions to manipulate coral symbionts and symbiont communities may expand the scope of their adaptive potential, which may boost coral survival until climate change is addressed. 

Once one of the predominant reef-building corals in the region,Acropora cervicornisis now a focal species of coral restoration efforts in Florida and the western Caribbean. Scientists and restoration practitioners have been independently collecting phenotypic data on genets ofA. cervicornisgrown in restoration nurseries. While these data are important for understanding the intraspecific response to varying environmental conditions, and thus the potential genetic contribution to phenotypic variation, in isolation these observations are of limited use for large-scale, multi- institution restoration efforts that are becoming increasingly necessary. Here, we present theAcropora cervicornisData Coordination Hub, a web-accessible relational database to align disparate datasets to compare genet-specific performance. In this data descriptor, we release data for 248 genets evaluated across 38 separate traits. We present a framework to align datasets with the ultimate goal of facilitating informed, data-driven restoration throughout the Caribbean.

 

Dynamic Energy Budget models relate whole organism processes such as growth, reproduction and mortality to suborganismal metabolic processes. Much of their potential derives from extensions of the formalism to describe the exchange of metabolic products between organisms or organs within a single organism, for example the mutualism between corals and their symbionts. Without model simplification, such models are at risk of becoming parameter-rich and hence impractical. One natural simplification is to assume that some metabolic processes act on ‘fast’ timescales relative to others. A common strategy for formulating such models is to assume that ‘fast’ processes equilibrate immediately, while ‘slow’ processes are described by ordinary differential equations. This strategy can bring a subtlety with it. What if there are multiple, interdependent fast processes that have multiple equilibria, so that additional information is needed to unambiguously specify the model dynamics? This situation can easily arise in contexts where an organism or community can persist in a ‘healthy’ or an ‘unhealthy’ state with abrupt transitions between states possible. To approach this issue, we offer the following: (a) a method to unambiguously complete implicitly defined models by adding hypothetical ‘fast’ state variables; (b) an approach for minimizing the number of additional state variables in such models, which can simplify the numerical analysis and give insights into the model dynamics; and (c) some implications of the new approach that are of practical importance for model dynamics, e.g. on the bistability of flux dynamics and the effect of different initialization choices on model outcomes. To demonstrate those principles, we use a simplified model for root-shoot dynamics of plants and a related model for the interactions between corals and endosymbiotic algae that describes coral bleaching and recovery.

 

Abstract Coral reefs are increasingly experiencing stressful conditions, such as high temperatures, that cause corals to undergo bleaching, a process where they lose their photosynthetic algal symbionts. Bleaching threatens both corals’ survival and the health of the reef ecosystems they create. One possible mechanism for corals to resist bleaching is through association with stress-tolerant symbionts, which are resistant to bleaching but may be worse partners in mild conditions. Some corals have been found to associate with multiple symbiont species simultaneously, which potentially gives them access to the benefits of both stress-sensitive and -tolerant symbionts. However, within-host competition between symbionts may lead to competitive exclusion of one partner, and the consequences of associating with multiple partners simultaneously are not well understood. We modify a mechanistic model of coral-algal symbiosis to investigate the effect of environmental conditions on within-host competitive dynamics between stress-sensitive and -tolerant symbionts and the effect of access to a tolerant symbiont on the dynamics of recovery from bleaching. We found that the addition of a tolerant symbiont can increase host survival and recovery from bleaching in high-light conditions. Competitive exclusion of the tolerant symbiont occurred slowly at intermediate light levels. Interestingly, there were some cases of post-bleaching competitive exclusion after the tolerant symbiont had helped the host recover. 

The congruence between phylogenies of tightly associated groups of organisms (cophylogeny) reflects evolutionary links between ecologically important interactions. However, despite being a classic example of an obligate symbiosis, tests of cophylogeny between scleractinian corals and their photosynthetic algal symbionts have been hampered in the past because both corals and algae contain genetically unresolved and morphologically cryptic species. Here, we studied co‐occurring, crypticPocilloporaspecies from Mo′orea, French Polynesia, that differ in their relative abundance across depth. We constructed new phylogenies of the hostPocillopora(using complete mitochondrial genomes, genomic loci, and thousands of single nucleotide polymorphisms) and their Symbiodiniaceae symbionts (using ITS2 and psbA^ncrmarkers) and tested for cophylogeny. The analysis supported the presence of fivePocilloporaspecies on the fore reef at Mo′orea that mostly hosted eitherCladocopium latusorumorC. pacificum.OnlyPocilloporaspecies hostingC. latusorumalso hosted taxa fromSymbiodiniumandDurusdinium. In general, theCladocopiumphylogeny mirrored thePocilloporaphylogeny. WithinCladocopiumspecies, lineages also differed in their associations withPocilloporahaplotypes, except those showing evidence of nuclear introgression, and with depth in the two most commonPocilloporaspecies. We also found evidence for a newPocilloporaspecies (haplotype 10), that has so far only been sampled from French Polynesia, that warrants formal identification. The linked phylogenies of thesePocilloporaandCladocopiumspecies and lineages suggest that symbiont speciation is driven by niche diversification in the host, but there is still evidence for symbiont flexibility in some cases.