Genomic Data Reveal Diverse Biological Characteristics of Scleractinian Corals and Promote Effective Coral Reef Conservation

Reef-building corals (Scleractinia, Anthozoa, Cnidaria) are the keystone organisms of coral reefs, which constitute the most diverse marine ecosystems. Since the first decoded coral genome reported in 2011, about 40 reference genomes are registered as of 2023. Comparative genomic analyses of coral genomes have revealed genomic characters that may underlie unique biological characteristics and coral diversification. These include existence of genes for biosynthesis of mycosporine-like amino acids, loss of an enzyme necessary for cysteine biosynthesis in family Acroporidae, and lineage-specific gene expansions of DMSP lyase-like genes in the genus Acropora. While symbiosis with endosymbiotic photosynthetic dinoflagellates is a common biological feature among reef-building corals, genes associated with the intricate symbiotic relationship encompass not only those shared by many coral species, but also genes that were uniquely duplicated in each coral lineage, suggesting diversified molecular mechanisms of coral-algal symbiosis. Coral genomic data have also enabled detection of hidden, complex population structures of corals, indicating the need for species-specific, local-scale, carefully considered conservation policies for effective maintenance of corals. Consequently, accumulating coral genomic data from a wide range of taxa and from individuals of a species not only promotes deeper understanding of coral reef biodiversity, but also promotes appropriate and effective coral reef conservation. Considering the diverse biological traits of different coral species and accurately understanding population structure and genetic diversity revealed by coral genomic analyses during coral reef restoration planning could enable us to "archive" coral reef environments that are nearly identical to natural coral reefs.

Simplification, not "tropicalization", of temperate marine ecosystems under ocean warming and acidification

Ocean warming is altering the biogeographical distribution of marine organisms. In the tropics, rising sea surface temperatures are restructuring coral reef communities with sensitive species being lost. At the biogeographical divide between temperate and tropical communities, warming is causing macroalgal forest loss and the spread of tropical corals, fishes and other species, termed "tropicalization". A lack of field research into the combined effects of warming and ocean acidification means there is a gap in our ability to understand and plan for changes in coastal ecosystems. Here, we focus on the tropicalization trajectory of temperate marine ecosystems becoming coral-dominated systems. We conducted field surveys and in situ transplants at natural analogues for present and future conditions under (i) ocean warming and (ii) both ocean warming and acidification at a transition zone between kelp and coral-dominated ecosystems. We show that increased herbivory by warm-water fishes exacerbates kelp forest loss and that ocean acidification negates any benefits of warming for range extending tropical corals growth and physiology at temperate latitudes. Our data show that, as the combined effects of ocean acidification and warming ratchet up, marine coastal ecosystems lose kelp forests but do not gain scleractinian corals. Ocean acidification plus warming leads to overall habitat loss and a shift to simple turf-dominated ecosystems, rather than the complex coral-dominated tropicalized systems often seen with warming alone. Simplification of marine habitats by increased CO₂ levels cascades through the ecosystem and could have severe consequences for the provision of goods and services.

Xarifiid Copepods (Copepoda: Cyclopoida: Xarifiidae) Parasitic in the Coral Psammocora columna Dana, 1846 from Taiwan

A comprehensive knowledge of relationships between coral and coral-associated organisms is essential for the conservation studies of the coral reef community, yet the biodiversity database of coral-inhabiting copepods remains incomplete. Here we surveyed in a widely distributed scleractinian coral, Psammocora columna Dana, 1846, and newly discovered two endoparasitic copepod species, Xarifiayanliaoensis sp. nov. and Xarifia magnifica sp. nov. These two new species are described based on specimens collected in Taiwan, and they share several common morphological characters of Xarifia copepods, i.e., region dorsal to fifth legs having three posteriorly directed processes unequally. However, X. yanliaoensis sp. nov. is distinguishable from other species by the morphology of the endopods of legs, antenna, maxilla, and maxilliped (in both genders). The morphological characters of X. magnifica sp. nov. are the endopods of legs, leg 5, and maxilliped in the male. Including the two new species described in the present work, the genus Xarifia Humes, 1960 belongs to the cyclopoid family Xarifiidae Humes, 1960 currently consists of 94 species, and eight of them live in association with the Psammocora coral. A comparison table and a key to the species of Xarifia from Psammocora corals are given herein.

The history, biological relevance, and potential applications for polyp bailout in corals

Corals have evolved a variety of stress responses to changing conditions, many of which have been the subject of scientific research. However, polyp bailout has not received widespread scientific attention, despite being described more than 80 years ago. Polyp bailout is a drastic response to acute stress in which coral colonies break down, with individual and patches of polyps detaching from the colony and the calcareous skeleton Polyps retain their symbiotic partners, have dispersal ability, and may undergo secondary settlement and calcification. Polyp bailout has been described worldwide in a variety of anthozoan species, especially in Scleractinia. It can be induced by multiple natural stressors, but also artificially. Little is known about the evolutionary and ecological potential and consequences of breaking down modularity, the dispersal ability, and reattachment of polyps resulting from polyp bailout. It has been shown that polyp bailout can be used as a model system, with promise for implementation in various research topics. To date, there has been no compilation of knowledge on polyp bailout, which prompted us to review this interesting stress response and provide a basis to discuss research topics and priorities for the future.

Combined responses of primary coral polyps and their algal endosymbionts to decreasing seawater pH

With coral reefs declining globally, resilience of these ecosystems hinges on successful coral recruitment. However, knowledge of the acclimatory and/or adaptive potential in response to environmental challenges such as ocean acidification (OA) in earliest life stages is limited. Our combination of physiological measurements, microscopy, computed tomography techniques and gene expression analysis allowed us to thoroughly elucidate the mechanisms underlying the response of early-life stages of corals, together with their algal partners, to the projected decline in oceanic pH. We observed extensive physiological, morphological and transcriptional changes in surviving recruits, and the transition to a less-skeleton/more-tissue phenotype. We found that decreased pH conditions stimulate photosynthesis and endosymbiont growth, and gene expression potentially linked to photosynthates translocation. Our unique holistic study discloses the previously unseen intricate net of interacting mechanisms that regulate the performance of these organisms in response to OA.

Eighteen Coral Genomes Reveal the Evolutionary Origin of Acropora Strategies to Accommodate Environmental Changes

The genus Acropora comprises the most diverse and abundant scleractinian corals (Anthozoa, Cnidaria) in coral reefs, the most diverse marine ecosystems on Earth. However, the genetic basis for the success and wide distribution of Acropora are unknown. Here, we sequenced complete genomes of 15 Acropora species and 3 other acroporid taxa belonging to the genera Montipora and Astreopora to examine genomic novelties that explain their evolutionary success. We successfully obtained reasonable draft genomes of all 18 species. Molecular dating indicates that the Acropora ancestor survived warm periods without sea ice from the mid or late Cretaceous to the Early Eocene and that diversification of Acropora may have been enhanced by subsequent cooling periods. In general, the scleractinian gene repertoire is highly conserved; however, coral- or cnidarian-specific possible stress response genes are tandemly duplicated in Acropora. Enzymes that cleave dimethlysulfonioproprionate into dimethyl sulfide, which promotes cloud formation and combats greenhouse gasses, are the most duplicated genes in the Acropora ancestor. These may have been acquired by horizontal gene transfer from algal symbionts belonging to the family Symbiodiniaceae, or from coccolithophores, suggesting that although functions of this enzyme in Acropora are unclear, Acropora may have survived warmer marine environments in the past by enhancing cloud formation. In addition, possible antimicrobial peptides and symbiosis-related genes are under positive selection in Acropora, perhaps enabling adaptation to diverse environments. Our results suggest unique Acropora adaptations to ancient, warm marine environments and provide insights into its capacity to adjust to rising seawater temperatures.

High Diversity of β-Glucosidase-Producing Bacteria and Their Genes Associated with Scleractinian Corals

β-Glucosidase is a microbial cellulose multienzyme that plays an important role in the regulation of the entire cellulose hydrolysis process, which is the rate-limiting step in bacterial carbon cycling in marine environments. Despite its importance in coral reefs, the diversity of β-glucosidase-producing bacteria, their genes, and enzymatic characteristics are poorly understood. In this study, 87 β-glucosidase-producing cultivable bacteria were screened from 6 genera of corals. The isolates were assigned to 21 genera, distributed among three groups: Proteobacteria, Firmicutes, and Actinobacteria. In addition, metagenomics was used to explore the genetic diversity of bacterial β-glucosidase enzymes associated with scleractinian corals, which revealed that these enzymes mainly belong to the glycosidase hydrolase family 3 (GH3). Finally, a novel recombinant β-glucosidase, referred to as Mg9373, encompassing 670 amino acids and a molecular mass of 75.2 kDa, was classified as a member of the GH3 family and successfully expressed and characterized. Mg9373 exhibited excellent tolerance to ethanol, NaCl, and glucose. Collectively, these results suggest that the diversity of β-glucosidase-producing bacteria and genes associated with scleractinian corals is high and novel, indicating great potential for applications in the food industry and agriculture.

A modern scleractinian coral with a two-component calcite-aragonite skeleton

Until now, all of the ca. 1,800 known modern scleractinian coral species were thought to produce skeletons exclusively of aragonite. Asymbiotic Paraconotrochus antarcticus living in the Southern Ocean is the first example of an extant scleractinian that forms a two-component carbonate skeleton, with an inner structure made of high-Mg calcite and an outer structure composed of aragonite. This discovery adds support to the notion that the coral skeletal formation process is strongly biologically controlled. Mitophylogenomic analysis shows that P. antarcticus represents an ancient scleractinian clade, suggesting that skeletal mineralogy/polymorph of a taxon, once established, is a trait conserved throughout the evolution of that clade.

One of the most conserved traits in the evolution of biomineralizing organisms is the taxon-specific selection of skeletal minerals. All modern scleractinian corals are thought to produce skeletons exclusively of the calcium-carbonate polymorph aragonite. Despite strong fluctuations in ocean chemistry (notably the Mg/Ca ratio), this feature is believed to be conserved throughout the coral fossil record, spanning more than 240 million years. Only one example, the Cretaceous scleractinian coral Coelosmilia (ca. 70 to 65 Ma), is thought to have produced a calcitic skeleton. Here, we report that the modern asymbiotic scleractinian coral Paraconotrochus antarcticus living in the Southern Ocean forms a two-component carbonate skeleton, with an inner structure made of high-Mg calcite and an outer structure composed of aragonite. P. antarcticus and Cretaceous Coelosmilia skeletons share a unique microstructure indicating a close phylogenetic relationship, consistent with the early divergence of P. antarcticus within the Vacatina (i.e., Robusta) clade, estimated to have occurred in the Mesozoic (ca. 116 Mya). Scleractinian corals thus join the group of marine organisms capable of forming bimineralic structures, which requires a highly controlled biomineralization mechanism; this capability dates back at least 100 My. Due to its relatively prolonged isolation, the Southern Ocean stands out as a repository for extant marine organisms with ancient traits.

Divergent Capacity of Scleractinian and Soft Corals to Assimilate and Transfer Diazotrophically Derived Nitrogen to the Reef Environment

Corals are associated with dinitrogen (N₂)-fixing bacteria that potentially represent an additional nitrogen (N) source for the coral holobiont in oligotrophic reef environments. Nevertheless, the few studies investigating the assimilation of diazotrophically derived nitrogen (DDN) by tropical corals are limited to a single scleractinian species (i.e., Stylophora pistillata). The present study quantified DDN assimilation rates in four scleractinian and three soft coral species from the shallow waters of the oligotrophic Northern Red Sea using the ¹⁵N₂ tracer technique. All scleractinian species significantly stimulated N₂ fixation in the coral-surrounding seawater (and mucus) and assimilated DDN into their tissue. Interestingly, N₂ fixation was not detected in the tissue and surrounding seawater of soft corals, despite the fact that soft corals were able to take up DDN from a culture of free-living diazotrophs. Soft coral mucus likely represents an unfavorable habitat for the colonization and activity of diazotrophs as it contains a low amount of particulate organic matter, with a relatively high N content, compared to the mucus of scleractinian corals. In addition, it is known to present antimicrobial properties. Overall, this study suggests that DDN assimilation into coral tissues depends on the presence of active diazotrophs in the coral’s mucus layer and/or surrounding seawater. Since N is often a limiting nutrient for primary productivity in oligotrophic reef waters, the divergent capacity of scleractinian and soft corals to promote N₂ fixation may have implications for N availability and reef biogeochemistry in scleractinian versus soft coral-dominated reefs.

Low recruitment due to altered settlement substrata as primary constraint for coral communities under ocean acidification

The future of coral reefs under increasing CO₂ depends on their capacity to recover from disturbances. To predict the recovery potential of coral communities that are fully acclimatized to elevated CO₂, we compared the relative success of coral recruitment and later life stages at two volcanic CO₂ seeps and adjacent control sites in Papua New Guinea. Our field experiments showed that the effects of ocean acidification (OA) on coral recruitment rates were up to an order of magnitude greater than the effects on the survival and growth of established corals. Settlement rates, recruit and juvenile densities were best predicted by the presence of crustose coralline algae, as opposed to the direct effects of seawater CO₂ Offspring from high CO₂ acclimatized parents had similarly impaired settlement rates as offspring from control parents. For most coral taxa, field data showed no evidence of cumulative and compounding detrimental effects of high CO₂ on successive life stages, and three taxa showed improved adult performance at high CO₂ that compensated for their low recruitment rates. Our data suggest that severely declining capacity for reefs to recover, due to altered settlement substrata and reduced coral recruitment, is likely to become a dominant mechanism of how OA will alter coral reefs.

Photosymbiosis and the expansion of shallow-water corals

Roughly 240 million years ago (Ma), scleractinian corals rapidly expanded and diversified across shallow marine environments. The main driver behind this evolution is uncertain, but the ecological success of modern reef-building corals is attributed to their nutritional symbiosis with photosynthesizing dinoflagellate algae. We show that a suite of exceptionally preserved Late Triassic (ca. 212 Ma) coral skeletons from Antalya (Turkey) have microstructures, carbonate ¹³C/¹²C and ¹⁸O/¹⁶O, and intracrystalline skeletal organic matter ¹⁵N/¹⁴N all indicating symbiosis. This includes species with growth forms conventionally considered asymbiotic. The nitrogen isotopes further suggest that their Tethys Sea habitat was a nutrient-poor, low-productivity marine environment in which photosymbiosis would be highly advantageous. Thus, coral-dinoflagellate symbiosis was likely a key driver in the evolution and expansion of shallow-water scleractinians.

A Novel Female-Specific and Sexual Reproduction-Associated Dmrt Gene Discovered in the Stony Coral, Euphyllia ancora

Transcription factors encoded by the Dmrt gene family regulate multiple aspects of animal reproduction. Most studies investigating the Dmrt gene family were conducted in model organisms from bilateral species, with a particular emphasis on gene function in male sex determination. It is still unclear whether the E. ancora Dmrt (EaDmrt) genes found in basal metazoans such as cnidarians share similar characteristics with orthologs in other metazoans. In this study, seven full Dmrt gene transcript sequences for a gonochoric coral, Euphyllia ancora (phylum: Cnidaria; class: Anthozoa), were obtained through transcriptome data mining, RT-PCR analysis, rapid amplification of cDNA ends, and sequencing. These EaDmrts were subjected to quantitative assays measuring temporal and tissue-specific expression. Results demonstrated a unique gene expression pattern for EaDmrtE, which is enriched in female germ cells during the spawning season. Based on the phylogenetic analyses performed across the homologous Dmrt genes in metazoans, we found that the female-specific EaDmrtE gene is not related to the DM1 gene of Acropora spp. coral nor to Dmrt1 of vertebrates, which are involved in sexual reproduction, especially in sex determination (vertebrate Dmrt1). Additionally, high levels of EaDmrtE transcripts detected in unfertilized mature eggs are retained in newly formed zygotes but decrease during embryonic development. We suggest that the newly discovered gene may play a role in oogenesis and early embryogenesis as a maternal factor in corals. Therefore, the sexual reproduction-associated Dmrt gene(s) should have arisen in cnidarians and might have evolved multiple times in metazoans.

The engine of the reef: photobiology of the coral-algal symbiosis

Coral reef ecosystems thrive in tropical oligotrophic oceans because of the relationship between corals and endosymbiotic dinoflagellate algae called Symbiodinium. Symbiodinium convert sunlight and carbon dioxide into organic carbon and oxygen to fuel coral growth and calcification, creating habitat for these diverse and productive ecosystems. Light is thus a key regulating factor shaping the productivity, physiology, and ecology of the coral holobiont. Similar to all oxygenic photoautotrophs, Symbiodinium must safely harvest sunlight for photosynthesis and dissipate excess energy to prevent oxidative stress. Oxidative stress is caused by environmental stressors such as those associated with global climate change, and ultimately leads to breakdown of the coral-algal symbiosis known as coral bleaching. Recently, large-scale coral bleaching events have become pervasive and frequent threatening and endangering coral reefs. Because the coral-algal symbiosis is the biological engine producing the reef, the future of coral reef ecosystems depends on the ecophysiology of the symbiosis. This review examines the photobiology of the coral-algal symbiosis with particular focus on the photophysiological responses and timescales of corals and Symbiodinium. Additionally, this review summarizes the light environment and its dynamics, the vulnerability of the symbiosis to oxidative stress, the abiotic and biotic factors influencing photosynthesis, the diversity of the coral-algal symbiosis, and recent advances in the field. Studies integrating physiology with the developing "omics" fields will provide new insights into the coral-algal symbiosis. Greater physiological and ecological understanding of the coral-algal symbiosis is needed for protection and conservation of coral reefs.

Expression of hsp70, hsp90 and hsf1 in the reef coral Acropora digitifera under prospective acidified conditions over the next several decades

Ocean acidification is an ongoing threat for marine organisms due to the increasing atmospheric CO₂ concentration. Seawater acidification has a serious impact on physiologic processes in marine organisms at all life stages. On the other hand, potential tolerance to external pH changes has been reported in coral larvae. Information about the possible mechanisms underlying such tolerance responses, however, is scarce. In the present study, we examined the effects of acidified seawater on the larvae of Acropora digitifera at the molecular level. We targeted two heat shock proteins, Hsp70 and Hsp90, and a heat shock transcription factor, Hsf1, because of their importance in stress responses and in early life developmental stages. Coral larvae were maintained under the ambient and elevated CO₂ conditions that are expected to occur within next 100 years, and then we evaluated the expression of hsps and hsf1 by quantitative real-time polymerase chain reaction (PCR). Expression levels of these molecules significantly differed among target genes, but they did not change significantly between CO₂ conditions. These findings indicate that the expression of hsps is not changed due to external pH changes, and suggest that tolerance to acidified seawater in coral larvae may not be related to hsp expression.