Chronic disturbance modulates symbiont (Symbiodiniaceae) beta diversity on a coral reef

Measuring multi-year changes in the Symbiodiniaceae algae in Caribbean corals on coral-depleted reefs

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.

Should I stay or should I go? Coral bleaching from the symbionts' perspective

Coral bleaching, the stress-induced breakdown of coral-algal symbiosis, threatens reefs globally. Paradoxically, despite adverse fitness effects, corals bleach annually, even outside of abnormal temperatures. This generally occurs shortly after the once-per-year mass coral spawning. Here, we propose a hypothesis linking annual coral bleaching and the transmission of symbionts to the next generation of coral hosts. We developed a dynamic model with two symbiont growth strategies, and found that high sexual recruitment and low adult coral survivorship and growth favour bleaching susceptibility, while the reverse promotes bleaching resilience. Otherwise, unexplained trends in the Indo-Pacific align with our hypothesis, where reefs and coral taxa exhibiting higher recruitment are more bleaching susceptible. The results from our model caution against interpreting potential shifts towards more bleaching-resistant symbionts as evidence of climate adaptation-we predict such a shift could also occur in declining systems experiencing low recruitment rates, a common scenario on today's reefs.

Temporal and spatial dynamics of coral symbiont assemblages are affected by local and global impacts

The influence of abiotic variables and anthropogenic pressure on symbiodiniaceans associated with the scleractinian corals Mussismilia hispida and Siderastrea stellata were assessed quarterly at Armação dos Búzios, Brazil, for over 18 months. Thirty-eight Symbiodiniaceae ITS2 rDNA phylotypes were found by metabarcoding, with eight comprising new phylotypes. Both hosts maintained their generalist pattern, with 1-3 dominant lineages. An environmental pressure index and changes in seawater temperature explained the variations in the structure and diversity of Symbiodiniaceae assemblages over time and space. A mild bleaching event affected the photosymbiotic assemblage structure, even in non-bleached colonies. The highly dynamic and diverse photosymbiont assemblages were constantly driven by the influence of environmental variables and human-induced impacts. Furthermore, new strains of Symbiodiniaceae might be associated with lower temperatures caused by upwelling, which is characteristic of this subtropical coral community, highlighting the region's idiosyncrasy and the need for further studies of this coral system.

Dead but not forgotten: complexity of Acropora palmata colonies increases with greater composition of dead coral

Coral reefs are highly biodiverse ecosystems that have declined due to natural and anthropogenic stressors. Researchers often attribute reef ecological processes to corals' complex structure, but effective conservation requires disentangling the contributions of coral versus reef structures. Many studies assessing the relationships between reef structure and ecological dynamics commonly use live coral as a proxy for reef complexity, disregarding the contribution of dead coral skeletons to reef habitat provision or other biogeochemical reef dynamics. This study aimed to assess the contribution of dead coral to reef complexity by examining structural variations in live and dead Acropora palmata colonies. We used photogrammetry to reconstruct digital elevation models (DEMs) and orthomosaics of the benthic region immediately surrounding 10 A. palmata colonies. These reconstructions were used to quantify structural metrics, including surface rugosity, fractal dimension, slope, planform curvature, and profile curvature, as a function of benthic composition (i.e., live A. palmata, dead A. palmata, or non-A. palmata substrate). The results revealed that dead coral maintained more varied profile curvatures and higher fractal dimensions than live or non-coral substrate. Conversely, A. palmata colonies with a higher proportion of live coral displayed more uniform structure, with lower fractal dimensions and less variability in profile curvature measures. Other metrics showed no significant difference among substrate types. These findings provide novel insights into the structural differences between live and dead coral, and an alternative perspective on the mechanisms driving the observed structural complexity on reefs. Overall, our results highlight the overlooked potential contributions of dead coral to reef habitat provision, ecological processes, and other biogeochemical reef dynamics, and could have important implications for coral reef conservation.

Biotic homogenisation and differentiation as directional change in beta diversity: synthesising driver-response relationships to develop conceptual models across ecosystems

Biotic homogenisation is defined as decreasing dissimilarity among ecological assemblages sampled within a given spatial area over time. Biotic differentiation, in turn, is defined as increasing dissimilarity over time. Overall, changes in the spatial dissimilarities among assemblages (termed 'beta diversity') is an increasingly recognised feature of broader biodiversity change in the Anthropocene. Empirical evidence of biotic homogenisation and biotic differentiation remains scattered across different ecosystems. Most meta-analyses quantify the prevalence and direction of change in beta diversity, rather than attempting to identify underlying ecological drivers of such changes. By conceptualising the mechanisms that contribute to decreasing or increasing dissimilarity in the composition of ecological assemblages across space, environmental managers and conservation practitioners can make informed decisions about what interventions may be required to sustain biodiversity and can predict potential biodiversity outcomes of future disturbances. We systematically reviewed and synthesised published empirical evidence for ecological drivers of biotic homogenisation and differentiation across terrestrial, marine, and freshwater realms to derive conceptual models that explain changes in spatial beta diversity. We pursued five key themes in our review: (i) temporal environmental change; (ii) disturbance regime; (iii) connectivity alteration and species redistribution; (iv) habitat change; and (v) biotic and trophic interactions. Our first conceptual model highlights how biotic homogenisation and differentiation can occur as a function of changes in local (alpha) diversity or regional (gamma) diversity, independently of species invasions and losses due to changes in species occurrence among assemblages. Second, the direction and magnitude of change in beta diversity depends on the interaction between spatial variation (patchiness) and temporal variation (synchronicity) of disturbance events. Third, in the context of connectivity and species redistribution, divergent beta diversity outcomes occur as different species have different dispersal characteristics, and the magnitude of beta diversity change associated with species invasions also depends strongly on alpha and gamma diversity prior to species invasion. Fourth, beta diversity is positively linked with spatial environmental variability, such that biotic homogenisation and differentiation occur when environmental heterogeneity decreases or increases, respectively. Fifth, species interactions can influence beta diversity via habitat modification, disease, consumption (trophic dynamics), competition, and by altering ecosystem productivity. Our synthesis highlights the multitude of mechanisms that cause assemblages to be more or less spatially similar in composition (taxonomically, functionally, phylogenetically) through time. We consider that future studies should aim to enhance our collective understanding of ecological systems by clarifying the underlying mechanisms driving homogenisation or differentiation, rather than focusing only on reporting the prevalence and direction of change in beta diversity, per se.

New insights on the role of nitrogen in the resistance to environmental stress in an endosymbiotic dinoflagellate

Endosymbiotic dinoflagellates provide the nutritional basis for marine invertebrates, especially reef-building corals. These dinoflagellates are sensitive to environmental changes, and understanding the factors that can increase the resistance of the symbionts is crucial for the elucidation of the mechanisms involved with coral bleaching. Here, we demonstrate how the endosymbiotic dinoflagellate Durusdinium glynnii is affected by concentration (1760 vs 440 µM) and source (sodium nitrate vs urea) of nitrogen after light and thermal stress exposure. The effectiveness in the use of the two nitrogen forms was proven by the nitrogen isotopic signature. Overall, high nitrogen concentrations, regardless of source, increased D. glynnii growth, chlorophyll-a, and peridinin levels. During the pre-stress period, the use of urea accelerated the growth of D. glynnii compared to cells grown using sodium nitrate. During the luminous stress, high nitrate conditions increased cell growth, but no changes in pigments composition was observed. On the other hand, during thermal stress, a steep and steady decline in cell densities over time was observed, except for high urea condition, where there is cellular division and peridinin accumulation 72 h after the thermal shock. Our findings suggest peridinin has a protective role during the thermal stress, and the uptake of urea by D. glynnii can alleviate thermal stress responses, eventually mitigating coral bleaching events.

Building consensus around the assessment and interpretation of Symbiodiniaceae diversity

Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians (e.g., corals, octocorals, sea anemones, jellyfish), other marine invertebrates (e.g., sponges, molluscs, flatworms), and protists (e.g., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic data has slowed progress in the field and acted as a barrier to reconciling observations. Here, we identify key challenges regarding the assessment and interpretation of Symbiodiniaceae genetic diversity across three levels: species, populations, and communities. We summarize areas of agreement and highlight techniques and approaches that are broadly accepted. In areas where debate remains, we identify unresolved issues and discuss technologies and approaches that can help to fill knowledge gaps related to genetic and phenotypic diversity. We also discuss ways to stimulate progress, in particular by fostering a more inclusive and collaborative research community. We hope that this perspective will inspire and accelerate coral reef science by serving as a resource to those designing experiments, publishing research, and applying for funding related to Symbiodiniaceae and their symbiotic partnerships.

Unlocking the phylogenetic diversity, primary habitats, and abundances of free-living Symbiodiniaceae on a coral reef

Dinoflagellates of the family Symbiodiniaceae form mutualistic symbioses with marine invertebrates such as reef-building corals, but also inhabit reef environments as free-living cells. Most coral species acquire Symbiodiniaceae horizontally from the surrounding environment during the larval and/or recruitment phase, however the phylogenetic diversity and ecology of free-living Symbiodiniaceae on coral reefs is largely unknown. We coupled environmental DNA sequencing and genus-specific qPCR to resolve the community structure and cell abundances of free-living Symbiodiniaceae in the water column, sediment, and macroalgae and compared these to coral symbionts. Sampling was conducted at two time points, one of which coincided with the annual coral spawning event when recombination between hosts and free-living Symbiodiniaceae is assumed to be critical. Amplicons of the internal transcribed spacer (ITS2) region were assigned to 12 of the 15 Symbiodiniaceae genera or genera-equivalent lineages. Community compositions were separated by habitat, with water samples containing a high proportion of sequences corresponding to coral symbionts of the genus Cladocopium, potentially as a result of cell expulsion from in hospite populations. Sediment-associated Symbiodiniaceae communities were distinct, potentially due to the presence of exclusively free-living species. Intriguingly, macroalgal surfaces displayed the highest cell abundances of Symbiodiniaceae, suggesting a key role for macroalgae in ensuring the ecological success of corals through maintenance of a continuum between environmental and symbiotic populations of Symbiodiniaceae.