Machine-Learning-Based Proteomic Predictive Modeling with Thermally-Challenged Caribbean Reef Corals

Coral health is currently diagnosed retroactively; colonies are deemed “stressed” upon succumbing to bleaching or disease. Ideally, health inferences would instead be made on a pre-death timescale that would enable, for instance, environmental mitigation that could promote coral resilience. To this end, diverse Caribbean coral (Orbicella faveolata) genotypes of varying resilience to high temperatures along the Florida Reef Tract were exposed herein to elevated temperatures in the laboratory, and a proteomic analysis was taken with a subset of 20 samples via iTRAQ labeling followed by nano-liquid chromatography + mass spectrometry; 46 host coral and 40 Symbiodiniaceae dinoflagellate proteins passed all stringent quality control criteria, and the partial proteomes of biopsies of (1) healthy controls, (2) sub-lethally stressed samples, and (3) actively bleaching corals differed significantly from one another. The proteomic data were then used to train predictive models of coral colony bleaching susceptibility, and both generalized regression and machine-learning-based neural networks were capable of accurately forecasting the bleaching susceptibility of coral samples based on their protein signatures. Successful future testing of the predictive power of these models in situ could establish the capacity to proactively monitor coral health.

The Reef Coral Coscinaraea marshae Is Not a High-Latitude Endemic

The ‘temperate’ reef coral Coscinaraea marshae Wells, 1962, is reported from Siberut Island (West Sumatra, Indonesia), a near-equatorial locality, 3375 km away from its northernmost range limit in Western Australia, where it is considered a high-latitude endemic. This tropical record suggests that the latitudinal distributions of poorly recorded reef corals may not yet be fully understood, which might be relevant in the light of progressing seawater warming.

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.

Salpivory by Colonial Reef Corals at Curaçao, Southern Caribbean

Salps (Phylum Tunicata, Family Salpidae) are transparent, gelatinous zooplankton that may occur in large densities (swarms) in the open ocean, where they form a food source for a variety of predators [...]

Linking photoacclimation responses and microbiome shifts between depth-segregated sibling species of reef corals

Metazoans host complex communities of microorganisms that include dinoflagellates, fungi, bacteria, archaea, and viruses. Interactions among members of these complex assemblages allow hosts to adjust their physiology and metabolism to cope with environmental variation and occupy different habitats. Here, using reciprocal transplantation across depths, we studied adaptive divergence in the Caribbean corals Orbicella annularis and O. franksi. When transplanted from deep to shallow, O. franksi experienced fast photoacclimation, low mortality, and maintained a consistent bacterial community. In contrast, O. annularis experienced higher mortality, and limited photoacclimation when transplanted from shallow to deep. The photophysiological collapse of O. annularis in the deep environment was associated with an increased microbiome variability and reduction of some bacterial taxa. Differences in the symbiotic algal community were more pronounced between coral species than between depths. Our study suggests that these sibling species are adapted to distinctive light environments partially driven by the algae photoacclimation capacity and the microbiome robustness, highlighting the importance of niche specialization in symbiotic corals for the maintenance of species diversity. Our findings have implications for the management of these threatened Caribbean corals and the effectiveness of coral reef restoration efforts.

Nutrients attenuate the negative effect of ocean acidification on reef coral calcification in the Arabian Sea upwelling zone (Masirah Island, Oman)

Tropical shallow-water reefs are the most diverse ecosystem in the ocean. Its persistence rests upon adequate calcification rates of the reef building biota, such as reef corals. Optimum calcification rates of reef corals occur in oligotrophic environments with high seawater saturation states of aragonite (Ωsw), which leads to increased vulnerability to anthropogenic ocean acidification and eutrophication. The calcification response of reef corals to this changing environment is largely unknown, however. Here, we present annually and sub-annually resolved records of calcification rates (n = 3) of the coral Porites from the nutrient rich and low Ωsw Arabian Sea upwelling zone (Masirah Island, Oman). Calcification rates were determined from the product of skeletal extension and bulk density derived from X-ray densitometry. Compared to a reference data set of coral skeletons from typical reef environments (Great Barrier Reef, Hawaii), mean annual skeletal bulk density of Porites from Masirah Island is reduced by 28 %. This density deficit prevails over the entire year and probably reflects a year-round low saturation state of aragonite at the site of calcification (Ωcf), independent of seasonal variations in Ωsw (e.g. upwelling). Mean annual extension rate is 20 % higher than for the reference data set. In particular, extension rate is strongly enhanced during the seasons with the lowest water temperatures, presumably due to a high PO43−/NO3−-ratio promoting rapid upward growth of the skeleton. Enhanced annual extension attenuates the negative effect of low density on calcification rate from −25 % to −11 %, while sub-annual calcification rates during the cool seasons even exceed those of the reference corals. We anticipate optimal nutrient environments (e.g. high PO43−/NO3−-ratios) to have significant potential to compensate the negative effect of ocean acidification on reef coral calcification, thereby allowing to maintain adequate rates of carbonate accumulation, which are essential for preserving this unique ecosystem.

Ten Ostreobium (Ulvophyceae) strains from Great Barrier Reef corals as a resource for algal endolith biology and genomics

Ostreobium is a genus of siphonous green algae that lives as an endolith in carbonate substrates under extremely limited light conditions and has recently been gaining attention due to its roles in reef carbonate budgets and its association with reef corals. Knowledge about this genus remains fairly limited due to the scarcity of strains available for physiological studies. Here, we report on 10 strains of Ostreobium isolated from coral skeletons from the Great Barrier Reef. Phenotypic diversity showed differences in the gross morphology and in few structures. Phylogenetic analyses of the tufA and rbcL put the strains in the context of the lineages identified previously through environmental sequencing. The chloroplast genomes of our strains are all around 80k bp in length and show that genome structure is highly conserved, with only a few insertions (some containing putative protein-coding genes) differing between the strains. The addition of these strains from the Great Barrier Reef to our toolkit will help develop Ostreobium as a model species for endolithic growth, low-light photosynthesis and coral-algal associations.

Physiological and ecological consequences of the water optical properties degradation on reef corals

Degradation of water optical properties due to anthropogenic disturbances is a common phenomenon in coastal waters globally. Although this condition is associated with multiple drivers that affect corals health in multiple ways, its effect on light availability and photosynthetic energy acquisition has been largely neglected. Here, we describe how declining the water optical quality in a coastal reef exposed to a turbid plume of water originating from a man-made channel compromises the functionality of the keystone coral species Orbicella faveolata. We found highly variable water optical conditions with significant effects on the light quantity and quality available for corals. Low-light phenotypes close to theoretical limits of photoacclimation were found at shallow depths as a result of reduced light penetration. The estimated photosynthetically fixed energy depletion with increasing depth was associated with patterns of colony mortality and vertical habitat compression. A numerical model illustrates the potential effect of the progressive water quality degradation on coral mortality and population decline along the depth gradient. Collectively, our findings suggest that preserving the water properties seeking to maximize light penetration through the water column is essential for maintaining the coral reef structure and associated ecosystem services.

Mangrove forests mitigate coral bleaching under thermal stress from climate change

Anthropogenic marine heatwaves are progressively degrading coral reef ecosystems worldwide via the process of coral bleaching (the expulsion of photosynthetic endosymbionts which reveals the coral skeleton). Corals from mangrove lagoons are hypothesised to increase resistance and resilience to coral bleaching, highlighting these areas as potential natural refuges for corals. Our study, the first conducted at a global-scale, reveals that coral reefs associated with mangrove forests are less likely to bleach under thermal stress, and thus, under scenarios of climate warming. The onset of severe bleaching occurred after 3.6 Degree Heating Weeks (DHW) in mangrove-associated reefs, compared to 2.23 DHW for non-mangrove associated reefs. These findings highlight the critical role of mangrove forests for coral reef persistence under climate change. Accordingly, conservation actions targeting the protection of mangroves are expected to contribute to the resilience and resistance of reef corals from bleaching as marine heatwaves continue to become more common.

A brief review of the stony coral (Cnidaria: Anthozoa: Scleractinia) papers published by Zootaxa in its first 20 years

In the 20 year history of Zootaxa, thirty-two papers have been published having Scleractinia as its primary focus. Twenty-four of the 32 scleractinian papers deal with Recent taxa, most of which belonging to shallow-water, reef corals. The 8 publications dealing with fossil Scleractinia include 3 monographic works, three papers discussing nomenclatural issues of individual taxa, and 2 papers deal with various aspects of select genera.