Marine heatwave hotspots in coral reef environments: physical drivers, ecophysiological outcomes and impact upon structural complexity

A changing climate is driving increasingly common and prolonged marine heatwaves (MHWs) and these extreme events have now been widely documented to severely impact marine ecosystems globally. However MHWs have rarely recently been considered when examining temperature-induced degradation of coral reef ecosystems. Here we consider extreme, localised thermal anomalies, nested within broader increases in sea surface temperature, which fulfil the definitive criteria for MHWs. These acute and intense events, referred to here as MHW hotspots, are not always well represented in the current framework used to describe coral bleaching, but do have distinct ecological outcomes, including widespread bleaching and rapid mass mortality of putatively thermally tolerant coral species. The physical drivers of these localised hotspots are discussed here, and in doing so we present a comprehensive theoretical framework that links the biological responses of the coral photo-endosymbiotic organism to extreme thermal stress and ecological changes on reefs associated after MHW hotspots. We describe how the rapid onset of high temperatures drives immediate heat-stress induced cellular damage, overwhelming mechanisms that would otherwise mitigate the impact of gradually accumulated thermal stress. The warm environment, and increased light penetration of the coral skeleton due to the loss of coral tissues, coupled with coral tissue decay support rapid microbial growth in the skeletal microenvironment, resulting in the widely unrecognised consequence of rapid decay and degeneration of the coral skeletons. This accelerated degeneration of the coral skeletonson a reef scale hinder the recovery of coral populations and increase the likelihood of phase shifts towards algal dominance. We suggest that MHW hotspots, through driving rapid heat-induced mortality, compromise reefs' structural frameworks to the detriment of long term recovery. We propose that MHW hotspots be considered as a distinct class of thermal stress events in coral reefs, and that the current framework used to describe coral bleaching and mass mortality be expanded to include these. We urge further research into how coral mortality affects bioerosion by coral endoliths

A Comparative Analysis of Microbial DNA Preparation Methods for Use With Massive and Branching Coral Growth Forms

In the last two decades, over 100 studies have investigated the structure of the coral microbiome. However, as yet there are no standardized methods applied to sample preservation and preparation, with different studies using distinct methods. There have also been several comparisons made of microbiome data generated across different studies, which have not addressed the influence of the methodology employed over each of the microbiome datasets. Here, we assess three different preservation methods; salt saturated dimethyl sulfoxide (DMSO) – EDTA, snap freezing with liquid nitrogen and 4% paraformaldehyde solution, and two different preparation methodologies; bead beating and crushing, that have been applied to study the coral microbiome. We compare the resultant bacterial assemblage data for two coral growth forms, the massive coral Goniastrea edwardsi and the branching coral Isopora palifera. We show that microbiome datasets generated from differing preservation and processing protocols are comparable in composition (presence/absence). Significant discrepancies between preservation and homogenization methods are observed in structure (relative abundance), and in the occurrence and dominance of taxa, with rare (low abundance and low occurrence) phylotypes being the most variable fraction of the microbial community. Finally, we provide evidence to support chemical preservation with DMSO as effective as snap freezing samples for generating reliable and robust microbiome datasets. In conclusion, we recommend where possible a standardized preservation and extraction method be taken up by the field to provide the best possible practices for detailed assessments of symbiotic and conserved bacterial associations

Differential Responses of the Coral Host and Their Algal Symbiont to Thermal Stress

The success of any symbiosis under stress conditions is dependent upon the responses of both partners to that stress. The coral symbiosis is particularly susceptible to small increases of temperature above the long term summer maxima, which leads to the phenomenon known as coral bleaching, where the intracellular dinoflagellate symbionts are expelled. Here we for the first time used quantitative PCR to simultaneously examine the gene expression response of orthologs of the coral Acropora aspera and their dinoflagellate symbiont Symbiodinium. During an experimental bleaching event significant up-regulation of genes involved in stress response (HSP90 and HSP70) and carbon metabolism (glyceraldehyde-3-phosphate dehydrogenase, α-ketoglutarate dehydrogenase, glycogen synthase and glycogen phosphorylase) from the coral host were observed. In contrast in the symbiont, HSP90 expression decreased, while HSP70 levels were increased on only one day, and only the α-ketoglutarate dehydrogenase expression levels were found to increase. In addition the changes seen in expression patterns of the coral host were much larger, up to 10.5 fold, compared to the symbiont response, which in all cases was less than 2-fold. This targeted study of the expression of key metabolic and stress genes demonstrates that the response of the coral and their symbiont vary significantly, also a response in the host transcriptome was observed prior to what has previously been thought to be the temperatures at which thermal stress events occur

Intestinal Microbiome Richness of Coral Reef Damselfishes (Actinopterygii: Pomacentridae)

Fish gastro-intestinal system harbors diverse microbiomes that affect the host's digestion, nutrition, and immunity. Despite the great taxonomic diversity of fish, little is understood about fish microbiome and the factors that determine its structure and composition. Damselfish are important coral reef species that play pivotal roles in determining algae and coral population structures of reefs. Broadly, damselfish belong to either of two trophic guilds based on whether they are planktivorous or algae-farming. In this study, we used 16S rRNA gene sequencing to investigate the intestinal microbiome of 5 planktivorous and 5 algae-farming damselfish species (Pomacentridae) from the Great Barrier Reef. We detected Gammaproteobacteria ASVs belonging to the genus Actinobacillus in 80% of sampled individuals across the 2 trophic guilds, thus, bacteria in this genus can be considered possible core members of pomacentrid microbiomes. Algae-farming damselfish had greater bacterial alpha-diversity, a more diverse core microbiome and shared 35 ± 22 ASVs, whereas planktivorous species shared 7 ± 3 ASVs. Our data also highlight differences in microbiomes associated with both trophic guilds. For instance, algae-farming damselfish were enriched in Pasteurellaceae, whilst planktivorous damselfish in Vibrionaceae. Finally, we show shifts in bacterial community composition along the intestines. ASVs associated with the classes Bacteroidia, Clostridia, and Mollicutes bacteria were predominant in the anterior intestinal regions while Gammaproteobacteria abundance was higher in the stomach. Our results suggest that the richness of the intestinal bacterial communities of damselfish reflects host species diet and trophic guild

Viral outbreak in corals associated with an in situ bleaching event: atypical herpes-like viruses and a new megavirus infecting Symbiodinium

Previous studies of coral viruses have employed either microscopy or metagenomics, but few have attempted to comprehensively link the presence of a virus-like particle (VLP) to a genomic sequence. We conducted transmission electron microscopy imaging and virome analysis in tandem to characterize the most conspicuous viral types found within the dominant Pacific reef-building coral genus Acropora. Collections for this study inadvertently captured what we interpret as a natural outbreak of viral infection driven by aerial exposure of the reef flat coincident with heavy rainfall and concomitant mass bleaching. All experimental corals in this study had high titers of viral particles. Three of the dominant VLPs identified were observed in all tissue layers and budding out from the epidermis, including viruses that were ∼70, ∼120, and ∼150 nm in diameter; these VLPs all contained electron dense cores. These morphological traits are reminiscent of retroviruses, herpesviruses, and nucleocytoplasmic large DNA viruses (NCLDVs), respectively. Some 300–500 nm megavirus-like VLPs also were observed within and associated with dinoflagellate algal endosymbiont (Symbiodinium) cells. Abundant sequence similarities to a gammaretrovirus, herpesviruses, and members of the NCLDVs, based on a virome generated from five Acropora aspera colonies, corroborated these morphology-based identifications. Additionally sequence similarities to two diagnostic genes, a MutS and (based on re-annotation of sequences from another study) a DNA polymerase B gene, most closely resembled Pyramimonas orientalis virus, demonstrating the association of a cosmopolitan megavirus with Symbiodinium. We also identified several other virus-like particles in host tissues, along with sequences phylogenetically similar to circoviruses, phages, and filamentous viruses. This study suggests that viral outbreaks may be a common but previously undocumented component of natural bleaching events, particularly following repeated episodes of multiple environmental stressors

Characterization of coral-associated microbial aggregates (CAMAs) within tissues of the coral Acropora hyacinthus

Bacterial diversity associated with corals has been studied extensively, however, localization of bacterial associations within the holobiont is still poorly resolved. Here we provide novel insight into the localization of coral-associated microbial aggregates (CAMAs) within tissues of the coral Acropora hyacinthus. In total, 318 and 308 CAMAs were characterized via histological and fluorescent in situ hybridization (FISH) approaches respectively, and shown to be distributed extensively throughout coral tissues collected from five sites in Japan and Australia. The densities of CAMAs within the tissues were negatively correlated with the distance from the coastline (i.e. lowest densities at offshore sites). CAMAs were randomly distributed across the six coral tissue regions investigated. Within each CAMA, bacterial cells had similar morphological characteristics, but bacterial morphologies varied among CAMAs, with at least five distinct types identified. Identifying the location of microorganisms associated with the coral host is a prerequisite for understanding their contributions to fitness. Localization of tissue-specific communities housed within CAMAs is particularly important, as these communities are potentially important contributors to vital metabolic functions of the holobiont

Understanding decay in marine calcifiers: Micro-CT analysis of skeletal structures provides insight into the impacts of a changing climate in marine ecosystems

Calcifying organisms and their exoskeletons support some of the most diverse and economically important ecosystems in our oceans. Under a changing climate, we are beginning to see alterations to the structure and properties of these exoskeletons due to ocean acidification, warming and accelerated rates of bioerosion. Our understanding has grown as a result of using micro‐computed tomography (μCT) but its applications in marine biology have not taken full advantage of the technological development in this methodology. We present a significant advancement in the use of this method to studying decalcification in a marine calcifier. We present a detailed workflow on best practice for μCT image processing and analysis of marine calcifiers, designed using coral skeletons subjected to acute, short‐term microbial bioerosion. This includes estimating subresolution microporosity and describing pore space morphological characteristics of macroporosity, in perforate and imperforate exoskeletons. These metrics are compared between control and bieroded samples, and are correlated with skeletal hardness as measured by nanoindentation. Our results suggest that using subresolution microporosity analysis improves the spatiotemporal resolution of μCT data and can detect changes not seen in macroporosity, in both perforate and imperforate skeletons. In imperforate samples, the mean size and relative number of pores in the macroporous portion of the images changed significantly where total macroporosity did not. The increased number of pores and higher microporosity are both directly related to a physical weakening of the calcareous exoskeletons of imperforate corals only. In perforate corals, increased macroporosity was accompanied by an overall widening of pore spaces though this did not correlate with sample hardness. These novel techniques complement traditional approaches and in combination demonstrate the potential for using μCT scanning to sensitively track the process of decalcification from a structural and morphological perspective. Importantly, these approaches do not necessarily rely on ultra‐high resolution (i.e. single micron) scans and so maintain the accessibility of this technology. The continued optimization of these tools for a variety of marine calcifiers will advance our understanding of the effect of climate change on marine biogenic calcified structures.Australian Research Council, Grant/Award Number: DP180103199; International Coral Reef Societ

Rebuilding relationships on coral reefs: Coral bleaching knowledge-sharing to aid adaptation planning for reef users: Bleaching emergence on reefs demonstrates the need to consider reef scale and accessibility when preparing for, and responding to, coral bleaching

Coral bleaching has impacted reefs worldwide and the predictions of near-annual bleaching from over two decades ago have now been realized. While technology currently provides the means to predict large-scale bleaching, predicting reef-scale and within-reef patterns in real-time for all reef users is limited. In 2020, heat stress across the Great Barrier Reef underpinned the region's third bleaching event in 5 years. Here we review the heterogeneous emergence of bleaching across Heron Island reef habitats and discuss the oceanographic drivers that underpinned variable bleaching emergence. We do so as a case study to highlight how reef end-user groups who engage with coral reefs in different ways require targeted guidance for how, and when, to alter their use of coral reefs in response to bleaching events. Our case study of coral bleaching emergence demonstrates how within-reef scale nowcasting of coral bleaching could aid the development of accessible and equitable bleaching response strategies on coral reefs. Also see the video abstract here: https://youtu.be/N9Tgb8N-vN0

A guide to photosynthetic gas exchange measurements:Fundamental principles, best practice and potential pitfalls

Gas exchange measurements enable mechanistic insights into the processes that underpin carbon and water fluxes in plant leaves which in turn inform understanding of related processes at a range of scales from individual cells to entire ecosytems. Given the importance of photosynthesis for the global climate discussion it is important to (a) foster a basic understanding of the fundamental principles underpinning the experimental methods used by the broad community, and (b) ensure best practice and correct data interpretation within the research community. In this review, we outline the biochemical and biophysical parameters of photosynthesis that can be investigated with gas exchange measurements and we provide step‐by‐step guidance on how to reliably measure them. We advise on best practices for using gas exchange equipment and highlight potential pitfalls in experimental design and data interpretation. The Supporting Information contains exemplary data sets, experimental protocols and data‐modelling routines. This review is a community effort to equip both the experimental researcher and the data modeller with a solid understanding of the theoretical basis of gas‐exchange measurements, the rationale behind different experimental protocols and the approaches to data interpretation