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Microbes perform critical functions in corals, yet most knowledge is derived from the photic zone. Here, we discover two mollicutes that dominate the microbiome of the deep-sea octocoral, Callogorgia delta, and likely reside in the mesoglea. These symbionts are abundant across the host's range, absent in the water, and appear to be rare in sediments. Unlike other mollicutes, they lack all known fermentative capabilities, including glycolysis, and can only generate energy from arginine provided by the coral host. Their genomes feature several mechanisms to interact with foreign DNA, including extensive CRISPR arrays and restriction-modification systems, which may indicate their role in symbiosis. We propose the novel family Oceanoplasmataceae which includes these symbionts and others associated with five marine invertebrate phyla. Its exceptionally broad host range suggests that the diversity of this enigmatic family remains largely undiscovered. Oceanoplasmataceae genomes are the most highly reduced among mollicutes, providing new insight into their reductive evolution and the roles of coral symbionts. Corals and other marine invertebrates host diverse microbes that remain poorly characterized, especially in the deep sea. Here the authors discover a new clade of bacteria with uniquely streamlined genomes in the tissue of a deep-sea coral that provide insights into the genome reduction of symbionts. [ABSTRACT FROM AUTHOR]

Elevated sea surface temperatures from a severe and prolonged El Niño event (2014–2016) fueled by climate change have resulted in mass coral bleaching (loss of dinoflagellate photosymbionts, Symbiodinium spp., from coral tissues) and subsequent coral mortality, devastating reefs worldwide. Genetic variation within and between Symbiodinium species strongly influences the bleaching tolerance of corals, thus recent papers have called for genetic engineering of Symbiodinium to elucidate the genetic basis of bleaching-relevant Symbiodinium traits. However, while Symbiodinium has been intensively studied for over 50 years, genetic transformation of Symbiodinium has seen little success likely due to the large evolutionary divergence between Symbiodinium and other model eukaryotes rendering standard transformation systems incompatible. Here, we integrate the growing wealth of Symbiodinium next-generation sequencing data to design tailored genetic engineering strategies. Specifically, we develop a testable expression construct model that incorporates endogenous Symbiodinium promoters, terminators, and genes of interest, as well as an internal ribosomal entry site from a Symbiodinium virus. Furthermore, we assess the potential for CRISPR/Cas9 genome editing through new analyses of the three currently available Symbiodinium genomes. Finally, we discuss how genetic engineering could be applied to enhance the stress tolerance of Symbiodinium, and in turn, coral reefs.

Most reef building corals rely on symbiotic microalgae (genus Symbiodinium ) to supply a substantial proportion of their energy requirements. Functional diversity of different Symbiodinium genotypes, endorsing the host with physiological advantages, has been widely reported. Yet, the influence of genotypic specificity on the symbiont's susceptibility to contaminants or cumulative stressors is unknown. Cultured Symbiodinium of presumed thermal-tolerant clade D tested especially vulnerable to the widespread herbicide diuron, suggesting important free-living populations may be at risk in areas subjected to terrestrial runoff. Co-exposure experiments where cultured Symbiodinium were exposed to diuron over a thermal stress gradient demonstrated how fast-growing clade C1 better maintained photosynthetic capability than clade D. The mixture toxicity model of Independent Action, considering combined thermal stress and herbicide contamination, revealed response additivity for inhibition of photosynthetic yield in both tested cultures, emphasizing the need to account for cumulative stressor impacts in ecological risk assessment and resource management. [ABSTRACT FROM AUTHOR]

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Aim Coral reefs rely on the symbiosis between scleractinian corals and intracellular, photosynthetic dinoflagellates of the genus Symbiodinium making the assessment of symbiont diversity critical to our understanding of ecological resilience of these ecosystems. This study characterizes Symbiodinium diversity around the Arabian Peninsula, which contains some of the most thermally diverse and understudied reefs on Earth. Location Shallow water coral reefs throughout the Red Sea ( RS), Sea of Oman ( SO), and Persian/Arabian Gulf ( PAG). Methods Next-generation sequencing of the ITS2 marker gene was used to assess Symbiodinium community composition and diversity comprising 892 samples from 46 hard and soft coral genera. Results Corals were associated with a large diversity of Symbiodinium, which usually consisted of one or two prevalent symbiont types and many types at low abundance. Symbiodinium communities were strongly structured according to geographical region and to a lesser extent by coral host identity. Overall symbiont communities were composed primarily of species from clade A and C in the RS, clade A, C, and D in the SO, and clade C and D in the PAG, representing a gradual shift from C- to D-dominated coral hosts. The analysis of symbiont diversity in an Operational Taxonomic Unit (OTU)-based framework allowed the identification of differences in symbiont taxon richness over geographical regions and host genera. Main conclusions Our study represents a comprehensive overview over biogeography and molecular diversity of Symbiodinium in the Arabian Seas, where coral reefs thrive in one of the most extreme environmental settings on the planet. As such our data will serve as a baseline for further exploration into the effects of environmental change on host-symbiont pairings and the identification and ecological significance of Symbiodinium types from regions already experiencing 'Future Ocean' conditions. [ABSTRACT FROM AUTHOR]

Reef corals harbouring clade D Symbiodinium spp. (endosymbiotic dinoflagellates) appear more tolerant of environmental stress. As sea surface temperatures rise, symbioses involving Symbiodinium D may increase in prevalence. For this reason, eight polymorphic microsatellite loci were developed for clade D Symbiodinium. From the analysis of 132 samples originating from cnidarian hosts in the Atlantic, Pacific and Indian Oceans, 4 to 35 alleles were found at each haploid locus and diversity indices ranged from 0.35 to 0.97. Population genetic analyses of these symbionts should reveal how environmental perturbations affect genetic diversity, geographical distributions, and possible host-range expansions to new coral species. [ABSTRACT FROM AUTHOR]

Modern microbial taxonomy generally relies on the use of single marker genes or sets of concatenated genes to generate a framework for the delineation and classification of organisms at different taxonomic levels. However, given that DNA is the 'blueprint of life', and hence the ultimate arbiter of taxonomy, classification systems should attempt to use as much of the blueprint as possible to capture a comprehensive phylogenetic signal. Recent analysis of whole-genome sequences from coral reef symbionts (dinoflagellates of the family Symbiodiniaceae) and other microalgal groups has uncovered extensive divergence not recognised by current algal taxonomic approaches. In the era of 'sequence everything', we argue that whole-genome data are pivotal to guide informed taxonomic inference, particularly for microbial eukaryotes. Whole-genome sequences are increasingly used as molecular evidence for classifying microbial lineages. Dinoflagellate microalgae of the family Symbiodiniaceae are critical symbionts in coral reefs. Recent studies of symbiodiniacean whole-genome sequences reveal extensive divergence and phylogenetic diversity hidden behind subtly different morphology. Divergence of whole-genome sequences can be used to inform taxonomic classification of microbial eukaryotes. Alignment-free methods capture comprehensive, more-informative phylogenetic signal from whole-genome sequences, compared to phylogenetic analysis using conventional marker genes. [ABSTRACT FROM AUTHOR]

Outbreaks of crown-of-thorn starfish (COTS) have caused dramatic declines in reefs through predation on corals, but the post-bloom effects of COTS may still potentially threaten the environment and living organisms due to massive organic decomposition. This stimulation experiment showed that the decomposition of COTS debris triggered an extra mineralization process and resulted in acidifying, hypoxic, and eutrophic seawater. Consequently, the photosynthetic efficiency of coral symbionts decreased by 83%, and coral bleached after removing the stress within two days, then the coral skeleton dissolved at rates of 0.02–0.05 mg cm−2 day−1. Within two weeks, the photosynthesis and growth of benthic algae were suppressed by 27–86% and 1.5–16%, respectively. The mortality of turf algae and coralline algae indicated compromised primary productivity and limited coral recruitment, respectively. However, macroalgae, as coral competitors, became the only survivors, with increasing chlorophyll content. This study suggests a continuing decline of reefs during the collapse phase of COTS outbreaks and highlights the need for improving control strategies for the COTS population. [ABSTRACT FROM AUTHOR]

Background: Dinoflagellates in the family Symbiodiniaceae are important photosynthetic symbionts in cnidarians (such as corals) and other coral reef organisms. Breakdown of the coral-dinoflagellate symbiosis due to environmental stress (i.e. coral bleaching) can lead to coral death and the potential collapse of reef ecosystems. However, evolution of Symbiodiniaceae genomes, and its implications for the coral, is little understood. Genome sequences of Symbiodiniaceae remain scarce due in part to their large genome sizes (1–5 Gbp) and idiosyncratic genome features. Results: Here, we present de novo genome assemblies of seven members of the genus Symbiodinium, of which two are free-living, one is an opportunistic symbiont, and the remainder are mutualistic symbionts. Integrating other available data, we compare 15 dinoflagellate genomes revealing high sequence and structural divergence. Divergence among some Symbiodinium isolates is comparable to that among distinct genera of Symbiodiniaceae. We also recovered hundreds of gene families specific to each lineage, many of which encode unknown functions. An in-depth comparison between the genomes of the symbiotic Symbiodinium tridacnidorum (isolated from a coral) and the free-living Symbiodinium natans reveals a greater prevalence of transposable elements, genetic duplication, structural rearrangements, and pseudogenisation in the symbiotic species. Conclusions: Our results underscore the potential impact of lifestyle on lineage-specific gene-function innovation, genome divergence, and the diversification of Symbiodinium and Symbiodiniaceae. The divergent features we report, and their putative causes, may also apply to other microbial eukaryotes that have undergone symbiotic phases in their evolutionary history. [ABSTRACT FROM AUTHOR]

Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease. A study part of the Tara Pacific Expedition that surveyed newly sequenced and publicly available metagenomes and genomes revealed pervasive non-retroviral dinoflagellate-infecting endogenous +ssRNA viral elements within coral symbionts. [ABSTRACT FROM AUTHOR]

Context: Primary production on coral reefs varies under changing conditions such as light and nutrient availability. This variation causes changes in basal stable isotopes as photosynthetic and nutrient pathways change. Aims: This study provides a preliminary baseline of nitrogen (δ15N) and carbon (δ13C) stable isotope profiles in Symbiodinium and macroalgae at a spatial scale and along a depth gradient around an island. Methods: Coral fragments and macroalgae were collected at depths from the surface to 26 m. δ15N and δ13C stable isotope values were assessed for Symbiodinium relative to cell density per surface area. Key results: δ15N values showed a uniform nutrient profile across primary producers. However, chlorophyll- a and Symbiodinium density from Montipora stellata had higher concentrations on the southern side of the island. δ15N values of Symbiodinium from Stylophora pistillata and macroalgae did not change with depth. Depth was associated with a significant decrease in Symbiodinium density, and δ13C values in macroalgae. Conclusions: We attribute these findings to Symbiodinium from S. pistillata as depth increases, decreasing cell density but maintaining chlorophyll- a concentration to satisfy the coral-host nutrient requirements. Implications: This study sets the scene for future, more comprehensive research on detecting carbon and nitrogen stable isotope values on primary producers in coral reefs. This study assessed nutrient variations in coral, coral symbionts and algae in relation to depth using nitrogen (δ15N) and carbon (δ13C) stable isotope analysis. Depth was associated with a decrease in symbiont density and δ13C in macroalgae. δ15N did not change with depth for corals, symbionts or macroalgae. We propose that the symbionts may be compensating for nutrient changes associated with depth to satisfy the coral–host requirements. [ABSTRACT FROM AUTHOR]

Global warming increases the temperature of the ocean surface, which can disrupt dinoflagellate‐coral symbioses and result in coral bleaching. Photosynthetic dinoflagellates of the family Symbiodiniaceae include bleaching‐tolerant and bleaching‐sensitive coral symbionts. Therefore, understanding the molecular mechanisms for changing symbiont diversity is potentially useful to assist recovery of coral holobionts (corals and their associated microbes, including multiple species of Symbiodiniaceae), although sexual reproduction has not been observed in the Symbiodiniaceae. Recent molecular phylogenetic analyses estimate that the Symbiodiniaceae appeared 160 million years ago and diversified into 15 groups, five genera of which now have available draft genomes (i.e., Symbiodinium, Durusdinium, Breviolum, Fugacium, and Cladocopium). Comparative genomic analyses have suggested that crown groups have fewer gene families than early‐diverging groups, although many genes that were probably acquired via gene duplications and horizontal gene transfers (HGTs) have been found in each decoded genome. Because UV stress is likely a contributor to coral bleaching, and because the highly conserved gene cluster for mycosporine‐like amino acid (MAA) biosynthesis has been found in thermal‐tolerant symbiont genomes, I reviewed genomic features of the Symbiodiniaceae, focusing on possible acquisition of a biosynthetic gene cluster for MAAs, which absorb UV radiation. On the basis of highly conserved noncoding sequences, I hypothesized that HGTs have occurred among members of the Symbiodiniaceae and have contributed to the diversification of Symbiodiniaceae–host relationships. Finally, I proposed that bleaching tolerance may be strengthened by multiple MAAs from both symbiotic dinoflagellates and corals. [ABSTRACT FROM AUTHOR]

Mesophotic coral ecosystems (30–150 m depth) present a high oceanic biodiversity, but remain one of the most understudied reef habitats, especially below 60 m depth. Here, we have assessed the rates of photosynthesis and dissolved inorganic carbon (DIC) and nitrogen (DIN) assimilation by Symbiodiniaceae associated with four soft coral species of the genus Sinularia and two stony coral species of the genus Leptoseris collected respectively at 65 and 80–90 m depth in the Gulf of Eilat. Our study demonstrates that both Leptoseris and Sinularia species have limited autotrophic capacities at mid‐lower mesophotic depths. DIC and DIN assimilation rates were overall ~ 10 times lower compared to shallow corals from 10 m depth in the same reef. While Leptoseris symbionts transferred at least 50% of the acquired nitrogen to their host after 8‐h incubation, most of the nitrogen was retained in the symbionts of Sinularia. In addition, the host tissue of Sinularia species presented a very high structural carbon to nitrogen ratio (C : N) compared to Leptoseris or to the shallow coral species, suggesting nitrogen limitation in these mesophotic soft corals. The limited capacity of soft coral symbionts to acquire DIN and transfer it to the coral animal, as well as the high C : N ratios, might explain the scarcity of symbiotic soft corals at mid‐lower mesophotic depths compared to their prevalence in the shallower reef. Overall, this study highlights the significance of DIN for the distribution of the Cnidarian‐ Symbiodiniaceae association at mesophotic depth. [ABSTRACT FROM AUTHOR]

We used an integrative genetics approach using sequences of (1) nuclear ribosomal rDNA (internal transcribed spacers and partial large subunit rDNA), (2) single-copy microsatellite nuclear DNA, (3) chloroplast-encoded 23S rDNA, (4) mitochondrial cytochrome b, and (5) repeat variation at eight microsatellite markers, to test the hypothesis that the stress-tolerant, 'morphologically cryptic' Clade D Symbiodinium (Dinophyceae) was composed of more than one species. Concordant phylogenetic and population genetic evidence clearly differentiate separately evolving, reproductively isolated lineages. We describe Symbiodinium boreum sp. nov. and S. eurythalpos sp. nov., two symbionts known to occur in colonies of the zebra coral, Oulastrea crispata (Scleractinia), which lives in turbid, marginal habitats extending from equatorial Southeast Asia to the main islands of Japan in the temperate northwest Pacific Ocean. Symbiodinium boreum was associated with O. crispata in temperate latitudes and S. eurythalpos was common to colonies in the tropics. The geographical ranges of both symbiont species overlapped in the subtropics where they sometimes co-occurred in the same host colony. Symbiodinium trenchii sp. nov. is also described. As a host-generalist symbiont, it often occurs in symbiosis with various species of Scleractinia possessing open (horizontal) modes of symbiont acquisition and is common to reef coral communities thriving in warm turbid reef habitats in the western Pacific Ocean, Indian Ocean, Arabian/Persian Gulf, Red Sea and western Atlantic (Caribbean). As is typical for dinoflagellates, S. boreum and S. eurythalpos were haploid, but microsatellite loci from field-collected and cultured S. trenchii often possessed two alleles, implying that a genome-wide duplication occurred during the evolution of this species. The recognition that Clade D Symbiodinium contains species exhibiting marked differences in host specificity and geographical distribution will yield greater scientific clarity about how stress-tolerant symbionts function in the ecological response of coral-dinoflagellate symbioses to global climate change. [ABSTRACT FROM AUTHOR]

This document is an editorial published in Frontiers in Microbiology titled "Women in microbial symbioses: 2022/2023." The editorial highlights the need to address gender imbalances in STEM fields and focuses on the contributions of women in the study of symbiotic relationships with microorganisms. It discusses various research topics related to microbial symbiosis, including the effects of global warming on coral symbionts, the impact of microbiome disturbance on host gene expression in jellyfish, the presence of viruses in bacterial genomes in the rhizosphere, and the composition of the vaginal microbiota in females. The editorial emphasizes the importance of understanding these relationships for human health and medical treatments. [Extracted from the article]

Photochemical efficiency ( Fv /Fm) was compared between a common symbiotic bioeroding sponge, Cliona cf. orientalis, and a common reef-builder, Acropora palifera using pulse amplitude modulated fluorescence (PAM). The study was conducted on Sesoko Island, Okinawa, where reefs were severely damaged during previous bleaching episodes. Sponge and coral dinoflagellate symbionts were treated with heat and light in a tank experiment, both in hospite (=still within their host) and isolated from their hosts. We found significant differences for photochemical efficiency of holobionts (=host and symbiont together) compared to the isolate symbionts and over time. All symbionts suffered in isolation and displayed stronger reactions to the treatments, and there was evidence for increasing damage despite returning to control conditions. However, because of large variability of the bi-symbiont coral samples and restrictions of the experimental design, our main results remained inconclusive, with no significant differences between sponge and coral samples and between the different stress treatments. Judging the results based on the uniform trends in the subsets of data, the G-clade sponge symbionts appeared to be more stress tolerant than the C- and D-clade coral symbionts, with no treatment effects in hospite and less damage in isolation compared to the coral symbionts, but this is an unconfirmed assumption. Isolated sponge symbionts were very resistant against heat stress, but may have suffered from light stress. In hospite, the latter risk can be countered by the sponge’s 3-dimensional morphology, the endolithic life style that affords shading, and by behavioural adaptation, i.e. the ability to move symbionts away from the source of stress. Overall, C. cf. orientalis symbionts displayed a more stable photochemical efficiency during and after stress than those of A. palifera. Results of this study suggest that with climate change C. cf. orientalis might have a better survival potential than A. palifera, but further investigations are necessary. [ABSTRACT FROM AUTHOR]

Symbiotic microorganisms in reef-building corals, including algae, bacteria, archaea, fungi, and viruses, play critical roles in the adaptation of coral hosts to adverse environmental conditions. However, their adaptation and functional relationships in nutrient-rich environments have yet to be fully explored. This study investigated Duncanopsammia peltata and the surrounding seawater and sediments from protected and non-protected areas in the summer and winter in Dongshan Bay. High-throughput sequencing was used to characterize community changes, co-occurrence patterns, and factors influencing symbiotic coral microorganisms (zooxanthellae, bacteria, and archaea) in different environments. The results showed that nutrient enrichment in the protected and non-protected areas was the greatest in December, followed by the non-protected area in August. In contrast, the August protected area had the lowest nutrient enrichment. Significant differences were found in the composition of the bacterial and archaeal communities in seawater and sediments from different regions. Among the coral symbiotic microorganisms, the main dominant species of zooxanthellae is the C1 subspecies (42.22–56.35%). The dominant phyla of bacteria were Proteobacteria, Cyanobacteria, Firmicutes, and Bacteroidota. Only in the August protected area did a large number (41.98%) of SAR324_cladeMarine_group_B exist. The August protected and non-protected areas and December protected and non-protected areas contained beneficial bacteria as biomarkers. They were Nisaea, Spiroplasma, Endozoicomonas, and Bacillus. No pathogenic bacteria appeared in the protected area in August. The dominant phylum in Archaea was Crenarchaeota. These symbiotic coral microorganisms' relative abundances and compositions vary with environmental changes. The enrichment of dissolved inorganic nitrogen in environmental media is a key factor affecting the composition of coral microbial communities. Co-occurrence analysis showed that nutrient enrichment under anthropogenic disturbances enhanced the interactions between coral symbiotic microorganisms. These findings improve our understanding of the adaptations of coral holobionts to various nutritional environments. [ABSTRACT FROM AUTHOR]

Coral reefs are some of the oldest, most diverse and valuable ecosystems on Earth because they can support one-quarter of all marine life in our oceans. Despite their importance, the world's coral reefs continue to be degraded at unprecedented rates by local and global threats that are warming and creating a more acidic ocean. This paper explores the reproductive challenges of coral for ex situ conservation, using IVF and cryopreservation, and our practical biobanking methods. Coral present challenges for cryopreservation because their reproductive period is often limited to a few nights yearly, they are mostly hermaphrodites with diverse modes of reproduction, including asexual reproduction (i.e. fragmentation and parthenogenesis) and sexual reproduction (i.e. self- and cross-fertilisation) and they express physiological toxins that can inhibit cryopreservation. We have banked spermatozoa from 12 coral species using the same field-hardy methods and have created new coral with thawed spermatozoa. In addition, we describe the cryopreservation of coral symbionts, whose physiology only permits the highest success seasonally. As part of a multidisciplinary conservation strategy, these collections may provide a major hedge against extinction for corals facing the damaging effects of climate change and loss of genetic diversity, and promise to help offset threats to our reefs worldwide. [ABSTRACT FROM AUTHOR]

Background: Dinoflagellates are unicellular marine and freshwater eukaryotes. They possess large nuclear genomes (1.5-245 gigabases) and produce structurally unique and biologically active polyketide secondary metabolites. Although polyketide biosynthesis is well studied in terrestrial and freshwater organisms, only recently have dinoflagellate polyketides been investigated. Transcriptomic analyses have characterized dinoflagellate polyketide synthase genes having single domains. The Genus Symbiodinium, with a comparatively small genome, is a group of major coral symbionts, and the S. minutum nuclear genome has been decoded. Results: The present survey investigated the assembled S. minutum genome and identified 25 candidate polyketide synthase (PKS) genes that encode proteins with mono- and multifunctional domains. Predicted proteins retain functionally important amino acids in the catalytic ketosynthase (KS) domain. Molecular phylogenetic analyses of KS domains form a clade in which S. minutum domains cluster within the protist Type I PKS clade with those of other dinoflagellates and other eukaryotes. Single-domain PKS genes are likely expanded in dinoflagellate lineage. Two PKS genes of bacterial origin are found in the S. minutum genome. Interestingly, the largest enzyme is likely expressed as a hybrid non-ribosomal peptide synthetase-polyketide synthase (NRPS-PKS) assembly of 10,601 amino acids, containing NRPS and PKS modules and a thioesterase (TE) domain. We also found intron-rich genes with the minimal set of catalytic domains needed to produce polyketides. Ketosynthase (KS), acyltransferase (AT), and acyl carrier protein (ACP) along with other optional domains are present. Mapping of transcripts to the genome with the dinoflagellate-specific spliced leader sequence, supports expression of multifunctional PKS genes. Metabolite profiling of cultured S. minutum confirmed production of zooxanthellamide D, a polyhydroxy amide polyketide and other unknown polyketide secondary metabolites. Conclusion: This genomic survey demonstrates that S. minutum contains genes with the minimal set of catalytic domains needed to produce polyketides and provides evidence of the modular nature of Type I PKS, unlike monofunctional Type I PKS from other dinoflagellates. In addition, our study suggests that diversification of dinoflagellate PKS genes comprises dinoflagellate-specific PKS genes with single domains, multifunctional PKS genes with KS domains orthologous to those of other protists, and PKS genes of bacterial origin. [ABSTRACT FROM AUTHOR]

Establishment of the coral–algal symbiosis begins during early ontogeny when juveniles acquire a mix of algae from their environment that often differs from the adults' algal assemblages. Despite the importance of the type of Symbiodiniaceae to this symbiosis, it is largely unknown how coral host identity and environment affect symbiosis establishment and is affected by the genetic composition of the symbionts. Here, we reciprocally transplanted planulae of the octocoral Rhytisma fulvum (Forskål, 1775) across depths and monitored the algal assemblages in the developing juveniles for 11 months. We then compared these to adult assemblages using ITS2 metabarcoding. Juveniles were consistently dominated by Symbiodinium, in addition to multiple Cladocopium species, which shifted in dominance with the juvenile age but maintained high similarity across depths. The type of Symbiodiniaceae environmentally available thus likely contributes to the algal symbionts that are initially acquired, while host identity may play a significant role in selecting for symbionts that are maintained during juvenile development. [ABSTRACT FROM AUTHOR]

Algal symbionts (zooxanthellae, genus Symbiodinium) of scleractinian corals respond strongly to temperature, nutrient and light changes. These factors vary greatly along the north-south gradient in the Red Sea and include conditions, which are outside of those typically considered optimal for coral growth. Nevertheless, coral communities thrive throughout the Red Sea, suggesting that zooxanthellae have successfully acclimatized or adapted to the harsh conditions they experience particularly in the south (high temperatures and high nutrient supply). As such, the Red Sea is a region, which may help to better understand how zooxanthellae and their coral hosts successfully acclimatize or adapt to environmental change (e.g. increased temperatures and localized eutrophication). To gain further insight into the physiology of coral symbionts in the Red Sea, we examined the abundance of dominant Symbiodinium types associated with the coral Pocillopora verrucosa, and measured Symbiodinium physiological characteristics (i.e. photosynthetic processes, cell density, pigmentation, and protein composition) along the latitudinal gradient of the Red Sea in summer and winter. Despite the strong environmental gradients from north to south, our results demonstrate that Symbiodinium microadriaticum (type A1) was the predominant species in P. verrucosa along the latitudinal gradient. Furthermore, measured physiological characteristics were found to vary more with prevailing seasonal environmental conditions than with region-specific differences, although the measured environmental parameters displayed much higher spatial than temporal variability. We conclude that our findings might present the result of long-term acclimatization or adaptation of S. microadriaticum to regionally specific conditions within the Red Sea. Of additional note, high nutrients in the South correlated with high zooxanthellae density indicating a compensation for a temperature-driven loss of photosynthetic performance, which may prove promising for the resilience of these corals under increase of temperature increase and eutrophication. [ABSTRACT FROM AUTHOR]

Although apicomplexans are a widely recognized and important parasitic group, little is known about those associated with invertebrates, such as reef-building scleractinian corals. To resolve the potential impact of apicomplexans on coral health, it is first necessary to further describe this group of putative parasites and determine their prevalence among host species. Here, it was hypothesized that apicomplexan prevalence would vary seasonally, similar to what occurs in other marine apicomplexans as well as some coral symbionts. To test this, Caribbean scleractinian species Porites astreoides, Montastraea (= Orbicella) annularis, M. (= O.) faveolata, and Siderastrea siderea were sampled seasonally from two reefs each in the Florida Keys and the Bahamas for 9- and 5.5-year periods, respectively. Utilizing a PCR-based screening assay, apicomplexan DNA was detected from most Floridian (80.1 %: n = 555/693) and Bahamian (90.7 %: n = 311/343) coral tissue samples collected over these multi-year periods. Furthermore, apicomplexan DNA was detected from nearly all (98.7 %: n = 78/79) single polyps sampled at multiple locations within six M. faveolata colonies, indicating little to no intracolonial variation in the screening assay. Mixed-model logistic regression was utilized to determine the effects of season, host species, and reef on apicomplexan prevalence. The model identified a significant seasonal effect, with the highest apicomplexan prevalence occurring during fall. There also was a large effect of host species, with apicomplexan prevalence significantly lower among S. siderea colonies relative to the other species. While reef did not have a significant effect in the full model, there was a significant difference in apicomplexan prevalence between Floridian and Bahamian reefs for S. siderea, implying regional differences in this host species. Despite seasonal and species-specific differences in prevalence, apicomplexans are ubiquitous constituents of these particular scleractinian coral species from Florida and the Bahamas. [ABSTRACT FROM AUTHOR]

Acoels in the family Convolutidae are commonly found with microalgal symbionts. Convolutids can host green algal Tetraselmis and dinoflagellates within the family Symbiodiniaceae and the genus Amphidinium. The diversity of these microalgae has not been well surveyed. In this study, we used PCR and culture techniques to demonstrate the biodiversity of Tetraselmis and dinoflagellates in symbiosis with meiofaunal acoels. Here, 66 acoels were collected from seven localities around Okinawa, Ishigaki, and Kochi, Japan. While convolutids were heavily represented in this sampling, some acoels formed a clade outside Convolutidae and are potentially a new family of acoels harboring symbiotic microalgae. From the acoels collected, a total of 32 Tetraselmis and 26 Symbiodiniaceae cultures were established. Molecular phylogenies were constructed from cultured material (and from total host DNA) using the 18S rRNA gene (Tetraselmis) and 28S rRNA gene (dinoflagellates). The majority of Tetraselmis sequences grouped within the T. astigmatica clade but strains closely related to T. convolutae, T. marina, and T. gracilis were also observed. This is the first report of Tetraselmis species, other than T. convolutae, naturally associating with acoels. For dinoflagellates, members of Cladocopium and Miliolidium were observed, but most Symbiodiniaceae sequences formed clusters within Symbiodinium, grouping with S. natans, or sister to S. tridacnidorum. Several new Symbiodinium sequences from this study may represent novel species. This is the first molecular record of Miliolidium and Symbiodinium from acoels. Microalgal strains from this study will provide a necessary framework for future taxonomic studies and research on symbiotic relationships between acoels and microalgae. [ABSTRACT FROM AUTHOR]

Coral bleaching is primarily caused by high sea surface temperatures, and nutrient enrichment of reefs is associated with lower resilience to thermal stress and ecological degradation. Excess inorganic nitrogen relative to phosphate has been proposed to sensitize corals to thermal bleaching. We assessed the physiological and proteomic responses of cultures of the dinoflagellate coral symbiont Symbiodinium microadriaticum to elevated temperature under low-nutrient, high-nutrient and phosphate-limited conditions. Elevated temperature induced reductions of many chloroplast proteins, particularly the light-harvesting complexes, and simultaneously increased the abundance of many chaperone proteins. Proteomes were similar when the N:P ratio was near the Redfield ratio, regardless of absolute N and P concentrations, but were strongly affected by phosphate limitation. Very high N:P inhibited Symbiodinium cell division while increasing the abundance of chloroplast proteins. The proteome response to phosphate limitation was greater than that to elevated temperature, as measured by the number of differentially abundant proteins. Increased physiological sensitivity to high temperatures under high nutrients or imbalanced N:P ratios was not apparent; however, oxidative stress response proteins were enriched among proteins responding to thermal stress under imbalanced N:P ratios. These data provide a detailed catalog of the effects of high temperatures and nutrients on a coral symbiont proteome. [ABSTRACT FROM AUTHOR]

For instance, in situ hybridization of coral tissue sections with probes targeting mRNAs showed that certain coral genes were only expressed in gastrodermal cells harbouring Symbiodiniaceae (Traylor-Knowles et al., [35]). Historically, coral research has had a strong microbiological focus because corals engage in symbioses not only with prokaryotes, viruses and fungi - microbes found in association with most animals - but also with unicellular photosymbionts in the family Symbiodiniaceae (Dinophyceae). However, the most common approach to study coral-associated microbes (e.g., genotyping, amplicon sequencing, or various omics techniques) involves the homogenization of coral fragments. [Extracted from the article]

Dinoflagellates are important components of marine ecosystems and essential coral symbionts, yet little is known about their genomes. We report here on the analysis of a high-quality assembly from the 1180-megabase genome of Symbiodinium kawagutii. We annotated protein-coding genes and identified Symbiodinium-specific gene families. No whole-genome duplication was observed, but instead we found active (retro) transposition and gene family expansion, especially in processes important for successful symbiosis with corals. We also documented genes potentially governing sexual reproduction and cyst formation, novel promoter elements, and a microRNA system potentially regulating gene expression in both symbiont and coral. We found biochemical complementarity between genomes of S. kawagutii and the anthozoan Acropora, indicative of host-symbiont coevolution, providing a resource for studying the molecular basis and evolution of coral symbiosis. [ABSTRACT FROM AUTHOR]

Dinoflagellates of the family Symbiodiniaceae are crucial photosymbionts in corals and other marine organisms. Of these, Cladocopium goreaui is one of the most dominant symbiont species in the Indo-Pacific. Here, we present an improved genome assembly of C. goreaui combining new long-read sequence data with previously generated short-read data. Incorporating new full-length transcripts to guide gene prediction, the C. goreaui genome (1.2 Gb) exhibits a high extent of completeness (82.4% based on BUSCO protein recovery) and better resolution of repetitive sequence regions; 45,322 gene models were predicted, and 327 putative, topologically associated domains of the chromosomes were identified. Comparison with other Symbiodiniaceae genomes revealed a prevalence of repeats and duplicated genes in C. goreaui, and lineage-specific genes indicating functional innovation. Incorporating 2,841,408 protein sequences from 96 taxonomically diverse eukaryotes and representative prokaryotes in a phylogenomic approach, we assessed the evolutionary history of C. goreaui genes. Of the 5246 phylogenetic trees inferred from homologous protein sets containing two or more phyla, 35–36% have putatively originated via horizontal gene transfer (HGT), predominantly (19–23%) via an ancestral Archaeplastida lineage implicated in the endosymbiotic origin of plastids: 10–11% are of green algal origin, including genes encoding photosynthetic functions. Our results demonstrate the utility of long-read sequence data in resolving structural features of a dinoflagellate genome, and highlight how genetic transfer has shaped genome evolution of a facultative symbiont, and more broadly of dinoflagellates. [ABSTRACT FROM AUTHOR]

Changing light environments force photoautotroph cells, including coral symbionts, to acclimate to maintain photosynthesis. Photosystem II (PSII) is subjected to photoinactivation at a rate proportional to the incident light, and cells must adjust their rates of protein repair to counter this photoinactivation. We examined PSII function in the coral symbiont Symbiodinium to determine the effect of photoacclimation on their capacity for PSII repair. Colonies of the coral Stylophora pistillata were collected from moderate light environments on the Lizard Island reef (Queensland, Australia) and transported to a local field station, where they were assigned to lower or higher light regimes and allowed to acclimate for 2 weeks. Following this photoacclimation period, the low-light acclimated corals showed greater symbiont density, higher chlorophyll per symbiont cell, and higher photosystem II protein than high-light acclimated corals did. Subsequently, we treated the corals with lincomycin, an inhibitor of chloroplastic protein synthesis, and exposed them to a high-light treatment to separate the effect of de novo protein synthesis in PSII repair from intrinsic susceptibility to photoinactivation. Low-light acclimated corals showed a sharp initial drop in PSII function but inhibition of PSII repair provoked only a modest additional drop in PSII function, compared to uninhibited corals. In high-light acclimated corals inhibition of PSII repair provoked a larger drop in PSII function, compared to uninhibited high-light corals. The greater lincomycin effects in the corals pre-acclimated to high-light show that high-light leads to an increased reliance on the PSII repair cycle. [ABSTRACT FROM AUTHOR]

Parental effects are ubiquitous in nature and in many organisms play a particularly critical role in the transfer of symbionts across generations; however, their influence and relative importance in the marine environment has rarely been considered. Coral reefs are biologically diverse and productive marine ecosystems, whose success is framed by symbiosis between reefbuilding corals and unicellular dinoflagellates in the genus Symbiodinium. Many corals produce aposymbiotic larvae that are infected by Symbiodinium from the environment (horizontal transmission), which allows for the acquisition of new endosymbionts (different from their parents) each generation. In the remaining species, Symbiodinium are transmitted directly from parent to offspring via eggs (vertical transmission), a mechanism that perpetuates the relationship between some or all of the Symbiodinium diversity found in the parent through multiple generations. Here we examine vertical transmission in the Hawaiian coral Montipora capitata by comparing the Symbiodinium ITS2 sequence assemblages in parent colonies and the eggs they produce. Parental effects on sequence assemblages in eggs are explored in the context of the coral genotype, colony morphology, and the environment of parent colonies. Our results indicate that ITS2 sequence assemblages in eggs are generally similar to their parents, and patterns in parental assemblages are different, and reflect environmental conditions, but not colony morphology or coral genotype. We conclude that eggs released by parent colonies during mass spawning events are seeded with different ITS2 sequence assemblages, which encompass phylogenetic variability that may have profound implications for the development, settlement and survival of coral offspring. [ABSTRACT FROM AUTHOR]

Summary: Corals form the framework of the world''s coral reefs and are under threat from increases in disease and bleaching (symbiotic dysfunction), yet the mechanisms of pathogen and symbiont recognition remain largely unknown. Here we describe the isolation and characterisation of an ancient mannose-binding lectin in the coral Acropora millepora, which is likely to be involved in both processes. The lectin (‘Millectin’) was isolated by affinity chromatography and was shown to bind to bacterial pathogens as well as coral symbionts, dinoflagellates of the genus Symbiodinium. cDNA analysis of Millectin indicate extensive sequence variation in the binding region, reflecting its ability to recognise various mannose-like carbohydrate structures on non-self cells, including symbionts and pathogens. This is the first mannose-binding lectin to show extensive sequence variability as observed for pattern recognition proteins in other invertebrate immune systems and, given that invertebrates rely on non-adaptive immunity, is a potential keystone component of coral defence mechanisms. [Copyright &y& Elsevier]

The endosymbionts of Symbiodiniaceae members establish an obligate relationship with most of the reef-building corals. Photosynthates of Symbiodiniaceae symbionts provide the maximum energy requirements of the host coral. Apart from the coral growth benefits, the mutual relationship extends to respond the environmental stress as well. Coral-endosymbiont mutualism is affected by various stress factors such as light, salinity, temperature, and eutrophication. However, the coral-algal symbionts adaptation to these rapid environmental changes is not much studied. Algal endosymbionts are classified into nine clades by genus level (major scleractinian corals – Clade A-D). These clades are named A to I with many subclades being presented in each clade that was identified based on the genetic marker ITS sequences, from which few are found tolerant to adverse conditions. This suggested that coral susceptibility or resistance to stress depends on the type of clade they harbor. Also, the prolonged environmental conditions may bring evolutionarily diverse clade lineages enabling corals to attain stress tolerance to temperature, UV, and high salinity. Thus, the present study may aid in understanding the coral-algal mutualistic adaptations under various stress conditions. [ABSTRACT FROM AUTHOR]

Gorgonian corals form complex interactions with a wide range of microorganisms, which play a key role in maintaining health of the holobiont. To assess the influence that various members of the microbial community exert on the coral lipidome, we analyzed storage (triacylglycerols (TG) and monoalkyldiacylglycerols) and structural (phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol and lyso-phosphatidylcholine) lipid molecular species. A molecular-genetics analysis showed that colonies of Junceella fragilis were associated with Symbiodinium clade C. Sequences of the parasitic dinoflagellate Blastodinium contortum were found in the gorgonian Dichotella sp. Colonies of Astrogorgia rubra were associated with the filiferan hydroid Hydrichthella epigorgia. Fungal sequences were found in Dichotella sp., A. rubra and Menella sp. A molecular species of ether phospholipids with fungal hydroxylated fatty acids (FA), bacterial odd-numbered FAs and alkyl moiety were detected in gorgonian lipids. As both host coral and some bacteria can synthesize ether lipids, a conclusion was drawn that lipids are likely to be transported from members of the microbial community to the coral host, and some molecular species with an odd-numbered alkyl moiety can be derived from anaerobic bacteria. The TG content of the symbiotic gorgonian J. fragilis was 30-fold higher than in asymbiotic gorgonians. TG 18:3/18:4/18:3 can be considered as a marker of zooxanthellae presence in coral. The hydroid H. epigorgia association did not have any evident contribution to the lipid profile of gorgonian A. rubra. Such markers of soft corals as 24:6n-3 and 24:5n-6 PUFAs were found to be distributed in molecular species of lipids of all the studied corals. A high content of these acids was observed as a characteristic feature in corals of the family Plexauridae (Menella sp. and A. rubra). The lipidomic approach allows assessment of the distribution of marker fatty acids in coral lipids, and to tracing the relationships between the microbial community and the coral host. [ABSTRACT FROM AUTHOR]

Summary: Corals are colonized by symbiotic microorganisms that profoundly influence the animal's health. One noted symbiont is a single‐celled alga (in the dinoflagellate family Symbiodiniaceae), which provides the coral with most of its fixed carbon. Thermal stress increases the production of reactive oxygen species (ROS) by Symbiodiniaceae during photosynthesis. ROS can both damage the algal symbiont's photosynthetic machinery and inhibit its repair, causing a positive feedback loop for the toxic accumulation of ROS. If not scavenged by the antioxidant network, excess ROS may trigger a signaling cascade ending with the coral host and algal symbiont disassociating in a process known as bleaching. We use Exaiptasia diaphana as a model for corals and constructed a consortium comprised of E. diaphana–associated bacteria capable of neutralizing ROS. We identified six strains with high free radical scavenging (FRS) ability belonging to the families Alteromonadaceae, Rhodobacteraceae, Flavobacteriaceae and Micrococcaceae. In parallel, we established a consortium of low FRS isolates consisting of genetically related strains. Bacterial whole genome sequences were used to identify key pathways that are known to influence ROS. [ABSTRACT FROM AUTHOR]

Giant clams (Tridacninae) are important members of Indo‐Pacific coral reefs and among the few bivalve groups that live in symbiosis with unicellular algae (Symbiodiniaceae). Despite the importance of these endosymbiotic dinoflagellates for clam ecology, the diversity and specificity of these associations remain relatively poorly studied, especially in the Red Sea. Here, we used the internal transcribed spacer 2 (ITS2) rDNA gene region to investigate Symbiodiniaceae communities associated with Red Sea Tridacna maxima clams. We sampled five sites spanning 1,300 km (10° of latitude, from the Gulf of Aqaba, 29°N, to the Farasan Banks, 18°N) along the Red Sea's North‐South environmental gradient. We detected a diverse and structured assembly of host‐associated algae with communities demonstrating region and site‐specificity. Specimens from the Gulf of Aqaba harbored three genera of Symbiodiniaceae, Cladocopium, Durusdinium, and Symbiodinium, while at all other sites clams associated exclusively with algae from the Symbiodinium genus. Of these exclusively Symbiodinium‐associating sites, the more northern (27° and 22°) and more southern sites (20° and 18°) formed two separate groupings despite site‐specific algal genotypes being resolved at each site. These groupings were congruent with the genetic break seen across multiple marine taxa in the Red Sea at approximately 19°, and along with our documented site‐specificity of algal communities, contrasted the panmictic distribution of the T. maxima host. As such, our findings indicate flexibility in T. maxima‐Symbiodiniaceae associations that may explain its relatively high environmental plasticity and offers a mechanism for environmental niche adaptation. [ABSTRACT FROM AUTHOR]

Environmental change, including global warming and chemical pollution, can compromise cnidarian‐(e.g., coral‐) dinoflagellate symbioses and cause coral bleaching. Understanding the mechanisms that regulate these symbioses will inform strategies for sustaining healthy coral–reef communities. A model system for corals is the symbiosis between the sea anemone Exaiptasia pallida (common name Aiptasia) and its dinoflagellate partners (family Symbiodiniaceae). To complement existing studies of the interactions between these organisms, we examined the impact of menthol, a reagent often used to render cnidarians aposymbiotic, on the dinoflagellate Breviolum minutum, both in culture and in hospite. In both environments, the growth and photosynthesis of this alga were compromised at either 100 or 300 µM menthol. We observed reduction in PSII and PSI functions, the abundances of reaction‐center proteins, and, at 300 µM menthol, of total cellular proteins. Interestingly, for free‐living algae exposed to 100 µM menthol, an initial decline in growth, photosynthetic activities, pigmentation, and protein abundances reversed after 5–15 d, eventually approaching control levels. This behavior was observed in cells maintained in continuous light, but not in cells experiencing a light–dark regimen, suggesting that B. minutum can detoxify menthol or acclimate and repair damaged photosynthetic complexes in a light‐ and/or energy‐dependent manner. Extended exposures of cultured algae to 300 µM menthol ultimately resulted in algal death. Most symbiotic anemones were also unable to survive this menthol concentration for 30 d. Additionally, cells impaired for photosynthesis by pre‐treatment with 300 µM menthol exhibited reduced efficiency in re‐populating the anemone host. [ABSTRACT FROM AUTHOR]

Mutualistic associations with symbiotic dinoflagellates (zooxanthellae) enable invertebrate hosts to thrive in tropical waters that are shallow and oligotrophic. Giant clams can harbor multiple species of symbiotic dinoflagellates (Family: Symbiodiniaceae) from mainly three genera, Symbiodinium, Cladocopium and Durusdinium, but whether they have distinct physiological functions at the genus level in the holobiont remains unclear. As symbiotic dinoflagellates use form II ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) to fix inorganic carbon, we attempted to estimate the phototrophic potentials and thus the relative abundances of Symbiodinium, Cladocopium and Durusdinium in five organs (outer mantle, inner mantle, foot muscle, ctenidium and hepatopancreas) of the fluted giant clam Tridacna squamosa through quantitative real-time PCR (qPCR) with primers that are specific to form II RuBisCO gene sequences (rbcII) of each genus. Based on the transcript levels of rbcII derived from Symbiodinium (Symb-rbcII), Cladocopium (Clad-rbcII) and Durusdinium (Duru-rbcII), we demonstrated that the symbiont population of T. squamosa from Vietnam was dominated by Durusdinium. Furthermore, the proportion of Symb-rbcII, Clad-rbcII and Duru-rbcII, and hence the phototrophic potentials of Symbiodinium, Cladocopium and Durusdinium, varied among five organs of T. squamosa, and along the length of the outer mantle. For dinoflagellates freshly isolated from the outer mantle of T. squamosa, Symb-rbcII, Clad-rbcII and Duru-rbcII exhibited different responses to light at the transcriptional level. Importantly, these results corroborate the proposition that the association with different genera and/or species of dinoflagellates might confer distinct physiological advantages to the host clam, which differs under various environmental conditions. [ABSTRACT FROM AUTHOR]

Awareness of the roles that host‐associated microbes play in host biology has escalated in recent years. However, microbiome studies have focused essentially on bacteria, and overall, we know little about the role of host‐associated eukaryotes outside the field of parasitology. Despite that, eukaryotes and microeukaryotes in particular are known to be common inhabitants of animals. In many cases, and/or for long periods of time, these associations are not associated with clinical signs of disease.Unlike the study of bacterial microbiomes, the study of the microeukaryotes associated with animals has largely been restricted to visual identification or molecular targeting of particular groups. So far, since the publication of the influential Human Microbiome Project Consortium paper in 2012, few studies have been published dealing with the microeukaryotes using a high‐throughput barcoding 'microbiome‐like' approach in animals.Nonetheless, microeukaryotes have an impact on the host physiology and lifestyle and also on the diversity and composition of the wider symbiotic community of bacteria and viruses. Beyond being parasites, microeukaryotes have many different roles in animals. For example, they directly interact with the host immune system in mammals; they have a key role on cellulose degradation, lignocellulose in xylophage termites and cockroaches; and they have an essential role in providing photosynthates to reef‐building corals.Certain microeukaryotic lineages have diversified within hosts more than others. These cases of co‐evolution led to different forms of symbiosis: from mutualism (like Symbiodinium in corals or parabasalians in termites), to commensalism (Blastocystis in humans) or to strict parasitism (apicomplexans or microsporidians in a broad range of hosts). We will review the ecological context and the evolutionary mechanisms that ended up in these different symbiotic scenarios, across the taxonomic range of both symbionts and their metazoan hosts.Host‐associated microeukaryotes have impacts at many levels, from individual animal health to ecosystems and to agroeconomy. Therefore, it is crucial to have a better understanding of their diversity and roles. Novel methodologies are being developed to access the eukaryotic fraction of the microbiome using high‐throughput methods. From ‐omics, to imaging and barcoding approaches biased against metazoans, these novel methodologies and strategies are helping us to increase and improve our knowledge of microeukaryotes in animal‐associated environments. A free Plain Language Summary can be found within the Supporting Information of this article. [ABSTRACT FROM AUTHOR]

Standardized identification of genotypes is necessary in animals that reproduce asexually and form large clonal populations such as coral. We developed a high-resolution hybridization-based genotype array coupled with an analysis workflow and database for the most speciose genus of coral, Acropora, and their symbionts. We designed the array to co-analyze host and symbionts based on bi-allelic single nucleotide polymorphisms (SNP) markers identified from genomic data of the two Caribbean Acropora species as well as their dominant dinoflagellate symbiont, Symbiodinium 'fitti'. SNPs were selected to resolve multi-locus genotypes of host (called genets) and symbionts (called strains), distinguish host populations and determine ancestry of coral hybrids between Caribbean acroporids. Pacific acroporids can also be genotyped using a subset of the SNP loci and additional markers enable the detection of symbionts belonging to the genera Breviolum, Cladocopium, and Durusdinium. Analytic tools to produce multi-locus genotypes of hosts based on these SNP markers were combined in a workflow called the Standard Tools for Acroporid Genotyping (STAG). The STAG workflow and database are contained within a customized Galaxy environment (https://coralsnp.science.psu.edu/galaxy/), which allows for consistent identification of host genet and symbiont strains and serves as a template for the development of arrays for additional coral genera. STAG data can be used to track temporal and spatial changes of sampled genets necessary for restoration planning and can be applied to downstream genomic analyses. Using STAG, we uncover bi-directional hybridization between and population structure within Caribbean acroporids and detect a cryptic Acroporid species in the Pacific. [ABSTRACT FROM AUTHOR]