Thermal regime and host clade, rather than geography, drive Symbiodinium and bacterial assemblages in the scleractinian coral Pocillopora damicornis sensu lato

Frenemies on the reef? Resolving the coral-Endozoicomonas association

Stony corals are poster child holobionts due to their intimate association with diverse microorganisms from all domains of life. We are only beginning to understand the diverse functions of most of these microbial associates, including potential main contributors to holobiont health and resilience. Among these, bacteria of the elusive genus Endozoicomonas are widely perceived as beneficial symbionts based on their genomic potential and their high prevalence and ubiquitous presence in coral tissues. Simultaneously, evidence of pathogenic and parasitic Endozoicomonas lineages in other marine animals is emerging. Synthesizing the current knowledge on the association of Endozoicomonas with marine holobionts, we challenge the perception of a purely mutualistic coral-Endozoicomonas relationship and propose directions to elucidate its role along the symbiotic spectrum.

The microbiome dynamics and interaction of endosymbiotic Symbiodiniaceae and fungi are associated with thermal bleaching susceptibility of coral holobionts

The thermal bleaching percentage of coral holobionts shows interspecific differences under heat-stress conditions, which are closely related to the coral-associated microbiome. However, the ecological effects of community dynamics and interactions between Symbiodiniaceae and fungi on coral thermal bleaching susceptibility remain unclear. In this study, we analyzed the diversity, community structure, functions, and potential interaction of Symbiodiniaceae and fungi among 18 coral species from a high thermal bleaching risk atoll using next-generation sequencing. The results showed that heat-tolerant C3u sub-clade and Durusdinium dominated the Symbiodiniaceae community of corals and that there were no core amplicon sequence variants in the coral-associated fungal community. Fungal richness and the abundance of confirmed functional animal-plant pathogens were significantly positively correlated with the coral thermal bleaching percentage. Fungal indicators, including Didymellaceae, Chaetomiaceae, Schizophyllum, and Colletotrichum, were identified in corals. Each coral species had a complex Symbiodiniaceae-fungi interaction network (SFIN), which was driven by the dominant Symbiodiniaceae sub-clades. The SFINs of coral holobionts with low thermal bleaching susceptibility exhibited low complexity and high betweenness centrality. These results indicate that the extra heat tolerance of coral in Huangyan Island may be linked to the high abundance of heat-tolerant Symbiodiniaceae. Fungal communities have high interspecific flexibility, and the increase of fungal diversity and pathogen abundance was correlated with higher thermal bleaching susceptibility of corals. Moreover, fungal indicators were associated with the degrees of coral thermal bleaching susceptibility, including both high and intermediate levels. The topological properties of SFINs suggest that heat-tolerant coral have limited fungal parasitism and strong microbial network resilience.IMPORTANCEGlobal warming and enhanced marine heatwaves have led to a rapid decline in coral reef ecosystems worldwide. Several studies have focused on the impact of coral-associated microbiomes on thermal bleaching susceptibility in corals; however, the ecological functions and interactions between Symbiodiniaceae and fungi remain unclear. We investigated the microbiome dynamics and potential interactions of Symbiodiniaceae and fungi among 18 coral species in Huangyan Island. Our study found that the Symbiodiniaceae community of corals was mainly composed of heat-tolerant C3u sub-clade and Durusdinium. The increase in fungal diversity and pathogen abundance has close associations with higher coral thermal bleaching susceptibility. We first constructed an interaction network between Symbiodiniaceae and fungi in corals, which indicated that restricting fungal parasitism and strong interaction network resilience would promote heat acclimatization of corals. Accordingly, this study provides insights into the role of microorganisms and their interaction as drivers of interspecific differences in coral thermal bleaching.

Characterization of driving factors for the long-term succession of bloom-forming cyanobacterial genera in Lake Erhai, southwest China

Cyanobacterial blooms pose a global environmental concern, with various genera contributing to their formation. The harmfulness of cyanobacterial blooms varies depending on the specific genus, yet the factors triggering their formation remain incompletely understood. This study conducted qPCR of sediment DNA in Lake Erhai to reconstruct the historical succession of three common bloom-forming cyanobacterial genera (i.e., Microcystis, Dolichospermum, and Aphanizomenon). The driving factors and their corresponding thresholds were identified, and human activities related to driving factors were evaluated. The results revealed two successions in the past century. The first succession transitioned from Aphanizomenon (1902-1978) to Microcystis and Dolichospermum (1978-1999), driven by TN:TP and TP. The second succession shifted from Microcystis and Dolichospermum (1978-1999) to Microcystis (1999-2010), driven by TP, TN:TP, and temperature. The thresholds of TP and TN:TP for the Microcystis bloom were 0.023 mg/L and 17, respectively. TN:TP was significantly influenced by domestic pollution and crop farming in both successions, while TP was significantly impacted by domestic pollution in the first succession and by pollution from crop and dairy farming in the second succession. These results shed light on the underlying mechanism responsible for the blooms of various cyanobacterial genera and could serve as a valuable reference for effectively preventing and controlling nutrient input in the watershed.

Species-specific coral microbiome assemblages support host bleaching resistance during an extreme marine heatwave

Scleractinian assemblages are threatened by marine heat waves with coral survivorship depending on host genetics and microbiome composition. We documented an extreme marine heat wave in Fiji and the response of corals in two thermally stressed reef flats. Through high-throughput amplicon sequencing of 16S and ITS rDNA phylogenetic markers, we assessed coral microbiomes (Symbiodiniaceae, prokaryotes, fungi, and Apicomplexa) of paired bleached and unbleached colonies of four common coral species representative of dominant genera in the South Pacific. While all coral species exhibited one or more pathways to bleaching resistance, harboring assemblages composed primarily of thermally tolerant photosymbionts did not always result in host bleaching resistance. Montipora and Pocillopora species, which associate with diverse Symbiodiniaceae and vertically transmit their photosymbionts, fared better than Acropora, which acquire their photosymbionts from the environment, and Porites, which associate with a narrow photosymbiont assemblage. Prokaryotic and fungal beta diversity did not differ between bleached and unbleached conspecifics, however, the relative abundance of the fungus Malassezia globosa was significantly greater in unbleached colonies of Montipora digitata. Each coral species harbored distinct assemblages of Symbiodiniaceae, prokaryotes, and Apicomplexa, but not fungi, reiterating the importance of host genetics in structuring components of its microbiome. Terrestrial fungal and prokaryotic taxa were detected at low abundance across coral microbiomes, indicating that allochthonous microbial inputs occur, but that coral microbiomes remain dominated by marine microbial taxa. Our study offers valuable insights into the microbiome assemblages associated with coral tolerance to extreme water temperatures.

Lichen holobionts show compositional structure along elevation

Holobionts are dynamic ecosystems that may respond to abiotic drivers with compositional changes. Uncovering elevational diversity patterns within these microecosystems can further our understanding of community-environment interactions. Here, we assess how the major components of lichen holobionts-fungal hosts, green algal symbionts, and the bacterial community-collectively respond to an elevational gradient. We analyse populations of two lichen symbioses, Umbilicaria pustulata and U. hispanica, along an elevational gradient spanning 2100 altitudinal metres and covering three major biomes. Our study shows (i) discontinuous genomic variation in fungal hosts with one abrupt genomic differentiation within each of the two host species, (ii) altitudinally structured bacterial communities with pronounced turnover within and between hosts, and (iii) altitude-specific presence of algal symbionts. Alpha diversity of bacterial communities decreased with increasing elevation. A marked turnover in holobiont diversity occurred across two altitudinal belts: at 11°C-13°C average annual temperature (here: 800-1200 m a.s.l.), and at 7°C-9°C average annual temperature (here: 1500-1800 m a.s.l.). The two observed zones mark a clustering of distribution limits and community shifts. The three ensuing altitudinal classes, that is, the most frequent combinations of species in holobionts, approximately correspond to the Mediterranean, cool-temperate, and alpine climate zones. We conclude that multitrophic microecosystems, such as lichen holobionts, respond with concerted compositional changes to climatic factors that also structure communities of macroorganisms, for example, vascular plants.

Current knowledge of the Southern Hemisphere marine microbiome in eukaryotic hosts and the Strait of Magellan surface microbiome project

Host-microbe interactions are ubiquitous and play important roles in host biology, ecology, and evolution. Yet, host-microbe research has focused on inland species, whereas marine hosts and their associated microbes remain largely unexplored, especially in developing countries in the Southern Hemisphere. Here, we review the current knowledge of marine host microbiomes in the Southern Hemisphere. Our results revealed important biases in marine host species sampling for studies conducted in the Southern Hemisphere, where sponges and marine mammals have received the greatest attention. Sponge-associated microbes vary greatly across geographic regions and species. Nevertheless, besides taxonomic heterogeneity, sponge microbiomes have functional consistency, whereas geography and aging are important drivers of marine mammal microbiomes. Seabird and macroalgal microbiomes in the Southern Hemisphere were also common. Most seabird microbiome has focused on feces, whereas macroalgal microbiome has focused on the epibiotic community. Important drivers of seabird fecal microbiome are aging, sex, and species-specific factors. In contrast, host-derived deterministic factors drive the macroalgal epibiotic microbiome, in a process known as "microbial gardening". In turn, marine invertebrates (especially crustaceans) and fish microbiomes have received less attention in the Southern Hemisphere. In general, the predominant approach to study host marine microbiomes has been the sequencing of the 16S rRNA gene. Interestingly, there are some marine holobiont studies (i.e., studies that simultaneously analyze host (e.g., genomics, transcriptomics) and microbiome (e.g., 16S rRNA gene, metagenome) traits), but only in some marine invertebrates and macroalgae from Africa and Australia. Finally, we introduce an ongoing project on the surface microbiome of key species in the Strait of Magellan. This is an international project that will provide novel microbiome information of several species in the Strait of Magellan. In the short-term, the project will improve our knowledge about microbial diversity in the region, while long-term potential benefits include the use of these data to assess host-microbial responses to the Anthropocene derived climate change.

Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean

Health and resilience of the coral holobiont depend on diverse bacterial communities often dominated by key marine symbionts of the Endozoicomonadaceae family. The factors controlling their distribution and their functional diversity remain, however, poorly known. Here, we study the ecology of Endozoicomonadaceae at an ocean basin-scale by sampling specimens from three coral genera (Pocillopora, Porites, Millepora) on 99 reefs from 32 islands across the Pacific Ocean. The analysis of 2447 metabarcoding and 270 metagenomic samples reveals that each coral genus harbored a distinct new species of Endozoicomonadaceae. These species are composed of nine lineages that have distinct biogeographic patterns. The most common one, found in Pocillopora, appears to be a globally distributed symbiont with distinct metabolic capabilities, including the synthesis of amino acids and vitamins not produced by the host. The other lineages are structured partly by the host genetic lineage in Pocillopora and mainly by the geographic location in Porites. Millepora is more rarely associated to Endozoicomonadaceae. Our results show that different coral genera exhibit distinct strategies of host-Endozoicomonadaceae associations that are defined at the bacteria lineage level.

Response of coral bacterial composition and function to water quality variations under anthropogenic influence

Microbial communities play key roles in the adaptation of corals living in adverse environments, as the microbiome flexibility can enhance environmental plasticity of coral holobiont. However, the ecological association of coral microbiome and related function to locally deteriorating water quality remains underexplored. In this work, we used 16S rRNA gene sequencing and quantitative microbial element cycling (QMEC) to investigate the seasonal changes of bacterial communities, particularly their functional genes related to carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) cycle, of the scleractinian coral Galaxea fascicularis from nearshore reefs exposed anthropogenic influence. We used nutrient concentrations as the indicator of anthropogenic activities in coastal reefs, and found a higher nutrient pressure in spring than summer. The bacterial diversity, community structure and dominant bacteria of coral shifted significantly due to seasonal variations dominated by nutrient concentrations. Additionally, the network structure and nutrient cycling gene profiles in summer under low nutrient stress was distinct from that under poor environmental conditions in spring, with lower network complexity and abundance of CNPS cycling genes in summer compared with spring. We further identified significant correlations between microbial community (taxonomic composition and co-occurrence network) and geochemical functions (abundance of multiple functional genes and functional community). Nutrient enrichment was proved to be the most important environmental fluctuation in controlling the diversity, community structure, interactional network and functional genes of the coral microbiome. These results highlight that seasonal shifts in coral-associated bacteria due to anthropogenic activities alter the functional potentials, and provide novel insight about the mechanisms of coral adaptation to locally deteriorating environments.

From genomics to integrative species delimitation? The case study of the Indo-Pacific Pocillopora corals

With the advent of genomics, sequencing thousands of loci from hundreds of individuals now appears feasible at reasonable costs, allowing complex phylogenies to be resolved. This is particularly relevant for cnidarians, for which insufficient data is available due to the small number of currently available markers and obscures species boundaries. Difficulties in inferring gene trees and morphological incongruences further blur the study and conservation of these organisms. Yet, can genomics alone be used to delimit species? Here, focusing on the coral genus Pocillopora, whose colonies play key roles in Indo-Pacific reef ecosystems but have challenged taxonomists for decades, we explored and discussed the usefulness of multiple criteria (genetics, morphology, biogeography and symbiosis ecology) to delimit species of this genus. Phylogenetic inferences, clustering approaches and species delimitation methods based on genome-wide single-nucleotide polymorphisms (SNP) were first used to resolve Pocillopora phylogeny and propose genomic species hypotheses from 356 colonies sampled across the Indo-Pacific (western Indian Ocean, tropical southwestern Pacific and south-east Polynesia). These species hypotheses were then compared to other lines of evidence based on genetic, morphology, biogeography and symbiont associations. Out of 21 species hypotheses delimited by genomics, 13 were strongly supported by all approaches, while six could represent either undescribed species or nominal species that have been synonymised incorrectly. Altogether, our results support (1) the obsolescence of macromorphology (i.e., overall colony and branches shape) but the relevance of micromorphology (i.e., corallite structures) to refine Pocillopora species boundaries, (2) the relevance of the mtORF (coupled with other markers in some cases) as a diagnostic marker of most species, (3) the requirement of molecular identification when species identity of colonies is absolutely necessary to interpret results, as morphology can blur species identification in the field, and (4) the need for a taxonomic revision of the genus Pocillopora. These results give new insights into the usefulness of multiple criteria for resolving Pocillopora, and more widely, scleractinian species boundaries, and will ultimately contribute to the taxonomic revision of this genus and the conservation of its species.

Viruses may facilitate the cyanobacterial blooming during summer bloom succession in Xiangxi Bay of Three Gorges Reservoir, China

The occurrence of cyanobacterial blooms in summer are frequently accompanied by the succession of phytoplankton communities in freshwater. However, little is known regarding the roles of viruses in the succession, such as in huge reservoirs. Here, we investigated the viral infection characteristics of phytoplankton and bacterioplankton during the summer bloom succession in Xiangxi Bay of Three Gorges Reservoir, China. The results indicated that three distinct bloom stages and two successions were observed. From cyanobacteria and diatom codominance to cyanobacteria dominance, the first succession involved different phyla and led to a Microcystis bloom. From Microcystis dominance to Microcystis and Anabaena codominance, the second succession was different Cyanophyta genera and resulted in the persistence of cyanobacterial bloom. The structural equation model (SEM) showed that the virus had positive influence on the phytoplankton community. Through the Spearman’s correlation and redundancy analysis (RDA), we speculated that both the increase of viral lysis in the eukaryotic community and the increase of lysogeny in cyanobacteria may contributed to the first succession and Microcystis blooms. In addition, the nutrients supplied by the lysis of bacterioplankton might benefit the second succession of different cyanobacterial genera and sustain the dominance of cyanobacteria. Based on hierarchical partitioning method, the viral variables still have a marked effect on the dynamics of phytoplankton community, although the environmental attributes were the major factors. Our findings suggested that viruses played multiple potential roles in summer bloom succession and may help the blooms success of cyanobacteria in Xiangxi Bay. Under the background of increasingly serious cyanobacterial blooms worldwide, our study may have great ecological and environmental significance for understanding the population succession in phytoplankton and controlling the cyanobacterial blooms.

Host-microbiome interaction in fish and shellfish: An overview

The importance of the gut microbiome in the management of various physiological activities including healthy growth and performance of fish and shellfish is now widely considered and being studied in detail for potential applications in aquaculture farming and the future growth of the fish industry. The gut microbiome in all animals including fish is associated with a number of beneficial functions for the host, such as stimulating optimal gastrointestinal development, producing and supplying vitamins to the host, and improving the host's nutrient uptake by providing additional enzymatic activities. Besides nutrient uptake, the gut microbiome is involved in strengthening the immune system and maintaining mucosal tolerance, enhancing the host's resilience against infectious diseases, and the production of anticarcinogenic and anti-inflammatory compounds. Because of its significant role, the gut microbiome is very often considered an "extra organ," as it plays a key role in intestinal development and regulation of other physiological functions. Recent studies suggest that the gut microbiome is involved in energy homeostasis by regulating feeding, digestive and metabolic processes, as well as the immune response. Consequently, deciphering gut microbiome dynamics in cultured fish and shellfish species will play an indispensable role in promoting animal health and aquaculture productivity. It is mentioned that the microbiome community available in the gut tract, particularly in the intestine acts as an innovative source of natural product discovery. The microbial communities that are associated with several marine organisms are the source of natural products with a diverse array of biological activities and as of today, more than 1000 new compounds have been reported from such microbial species. Exploration of such new ingredients from microbial species would create more opportunities for the development of the bio-pharma/aquaculture industries. Considering the important role of the microbiome in the whole life span of fish and shellfish, it is necessary to understand the interaction process between the host and microbial community. However, information pertaining to host-microbiome interaction, particularly at the cellular level, gene expression, metabolic pathways, and immunomodulation mechanisms, the available literature is scanty. It has been reported that there are three ways of interaction involving the host-microbe-environment operates to maintain homeostasis in the fish and shellfish gut i.e. host intrinsic factors, the environment that shapes the gut microbiome composition, and the core microbial community present in the gut system itself has equal influence on the host biology. In the present review, efforts have been made to collect comprehensive information on various aspects of host-microbiome interaction, particularly on the immune system and health maintenance, management of diseases, nutrient uptake, digestion and absorption, gene expression, and metabolism in fish and shellfish.

The bacterial signature offers vision into the machinery of coral fitness across high-latitude coral reef in the South China Sea

Coral-bacterial interaction is a major driver in coral acclimatization to the stressful environment. 16S rRNA High-throughput sequencing was used to classify the role of different coral reef compartments; sediment, water, and tissue; in the South China Sea (SCS), as well as different locations in shaping the microbial community. The majority of OTUs significantly shifted at impacted sites and indicated distinction in the relative abundance of bacteria compartment/site-wise. Richness and diversity were higher, and more taxa were enriched in the sediment communities. Proteobacteria dominated sediment samples, while Cyanobacteria dominated water samples. Coral tissue showed a shift among different sites with Proteobacteria remaining the dominant Phylum. Moreover, we report a dominance of Chlorobium genus in the healthy coral tissue sample collected from the severely damaged Site B, suggesting a contribution to tolerance and adaptation to the disturbing environment. Thus, revealing the complex functionally diverse microbial patterns associated with biotic and abiotic disturbed coral reefs will deliver understanding of the symbiotic connections and competitive benefit inside the hosts niche and can reveal a measurable footprint of the environmental impacts on coral ecosystems. We hence, urge scientists to draw more attention towards using coral microbiome as a self-sustaining tool in coral restoration.

Genotype-environment interactions determine microbiota plasticity in the sea anemone Nematostella vectensis

Most multicellular organisms harbor microbial colonizers that provide various benefits to their hosts. Although these microbial communities may be host species- or even genotype-specific, the associated bacterial communities can respond plastically to environmental changes. In this study, we estimated the relative contribution of environment and host genotype to bacterial community composition in Nematostella vectensis, an estuarine cnidarian. We sampled N. vectensis polyps from 5 different populations along a north-south gradient on the Atlantic coast of the United States and Canada. In addition, we sampled 3 populations at 3 different times of the year. While half of the polyps were immediately analyzed for their bacterial composition by 16S rRNA gene sequencing, the remaining polyps were cultured under laboratory conditions for 1 month. Bacterial community comparison analyses revealed that laboratory maintenance reduced bacterial diversity by 4-fold, but maintained a population-specific bacterial colonization. Interestingly, the differences between bacterial communities correlated strongly with seasonal variations, especially with ambient water temperature. To decipher the contribution of both ambient temperature and host genotype to bacterial colonization, we generated 12 clonal lines from 6 different populations in order to maintain each genotype at 3 different temperatures for 3 months. The bacterial community composition of the same N. vectensis clone differed greatly between the 3 different temperatures, highlighting the contribution of ambient temperature to bacterial community composition. To a lesser extent, bacterial community composition varied between different genotypes under identical conditions, indicating the influence of host genotype. In addition, we identified a significant genotype x environment interaction determining microbiota plasticity in N. vectensis. From our results we can conclude that N. vectensis-associated bacterial communities respond plastically to changes in ambient temperature, with the association of different bacterial taxa depending in part on the host genotype. Future research will reveal how this genotype-specific microbiota plasticity affects the ability to cope with changing environmental conditions.

Learning from the past is not enough to survive present and future bleaching threshold temperatures

In the past decade, the frequency of mass coral bleaching events has increased due to seawater temperature anomalies persisting for longer periods. Coral survival from temperature anomalies has been based on how each species in each location responds to stress, which is unique to individual species and may be due to the way stressful experiences accumulate through time in the form of ecological and physiological memory. A deeper understanding of ecological and physiological memory in corals is necessary to understand their survival strategies into the future. Laboratory experiments can help us simulate seawater temperatures experienced by corals in the past and compare their responses to those of the present and future. In this study, we sampled corals with different life history traits from one location perturbed by seawater temperature incursions (variable site) and from a second, relatively undisturbed location (stable site). We sampled across two seasons to observe the responses to bleaching threshold temperatures in the past (1998-29 °C), present (2018-31 °C), and future (2050-33 °C). Corals were healthy at 29 °C and 31 °C, but a fast-growing, temperature-susceptible coral species experienced high mortality at 33 °C compared to a slow-growing, temperature-resistant coral species. Moreover, corals from the variable site and during the spring season fared better under temperature stress. The results of this study provide insight into the possible role of life-history traits on coral's response to seasons and locations in terms of memory to long-term and short-term thermal anomalies and climate change.

Full-Length Transcriptome Maps of Reef-Building Coral Illuminate the Molecular Basis of Calcification, Symbiosis, and Circa-Dian Genes

Coral transcriptomic data largely rely on short-read sequencing, which severely limits the understanding of coral molecular mechanisms and leaves many important biological questions unresolved. Here, we sequence the full-length transcriptomes of four common and frequently dominant reef-building corals using the PacBio Sequel II platform. We obtain information on reported gene functions, structures, and expression profiles. Among them, a comparative analysis of biomineralization-related genes provides insights into the molecular basis of coral skeletal density. The gene expression profiles of the symbiont Symbiodiniaceae are also isolated and annotated from the holobiont sequence data. Finally, a phylogenetic analysis of key circadian clock genes among 40 evolutionarily representative species indicates that there are four key members in early metazoans, including cry genes; Clock or Npas2; cyc or Arntl; and tim, while per, as the fifth member, occurs in Bilateria. In summary, this work provides a foundation for further work on the manipulation of skeleton production or symbiosis to promote the survival of these important organisms.

Geographically driven differences in microbiomes of Acropora cervicornis originating from different regions of Florida's Coral Reef

Effective coral restoration must include comprehensive investigations of the targeted coral community that consider all aspects of the coral holobiont-the coral host, symbiotic algae, and microbiome. For example, the richness and composition of microorganisms associated with corals may be indicative of the corals' health status and thus help guide restoration activities. Potential differences in microbiomes of restoration corals due to differences in host genetics, environmental condition, or geographic location, may then influence outplant success. The objective of the present study was to characterize and compare the microbiomes of apparently healthy Acropora cervicornis genotypes that were originally collected from environmentally distinct regions of Florida's Coral Reef and sampled after residing within Mote Marine Laboratory's in situ nursery near Looe Key, FL (USA) for multiple years. By using 16S rRNA high-throughput sequencing, we described the microbial communities of 74 A. cervicornis genotypes originating from the Lower Florida Keys (n = 40 genotypes), the Middle Florida Keys (n = 15 genotypes), and the Upper Florida Keys (n = 19 genotypes). Our findings demonstrated that the bacterial communities of A. cervicornis originating from the Lower Keys were significantly different from the bacterial communities of those originating from the Upper and Middle Keys even after these corals were held within the same common garden nursery for an average of 3.4 years. However, the bacterial communities of corals originating in the Upper Keys were not significantly different from those in the Middle Keys. The majority of the genotypes, regardless of collection region, were dominated by Alphaproteobacteria, namely an obligate intracellular parasite of the genus Ca. Aquarickettsia. Genotypes from the Upper and Middle Keys also had high relative abundances of Spirochaeta bacteria. Several genotypes originating from both the Lower and Upper Keys had lower abundances of Aquarickettsia, resulting in significantly higher species richness and diversity. Low abundance of Aquarickettsia has been previously identified as a signature of disease resistance. While the low-Aquarickettsia corals from both the Upper and Lower Keys had high abundances of an unclassified Proteobacteria, the genotypes in the Upper Keys were also dominated by Spirochaeta. The results of this study suggest that the abundance of Aquarickettsia and Spirochaeta may play an important role in distinguishing bacterial communities among A. cervicornis populations and compositional differences of these bacterial communities may be driven by regional processes that are influenced by both the environmental history and genetic relatedness of the host. Additionally, the high microbial diversity of low-Aquarickettsia genotypes may provide resilience to their hosts, and these genotypes may be a potential resource for restoration practices and management.

Transgenerational Effects on the Coral Pocillopora damicornis Microbiome Under Ocean Acidification

Reef-building corals are inhabited by functionally diverse microorganisms which play important roles in coral health and persistence in the Anthropocene. However, our understanding of the complex associations within coral holobionts is largely limited, particularly transgenerational exposure to environmental stress, like ocean acidification. Here we investigated the microbiome development of an ecologically important coral Pocillopora damicornis following transgenerational exposure to moderate and high pCO₂ (partial pressure of CO₂) levels, using amplicon sequencing and analysis. Our results showed that the Symbiodiniaceae community structures in adult and juvenile had similar patterns, all of which were dominated by Durusdinium spp., previously known as clade D. Conversely, prokaryotic communities varied between adults and juveniles, possibly driven by the effect of host development. Surprisingly, there were no significant changes in both Symbiodiniaceae and prokaryotic communities with different pCO₂ treatments, which was independent of the life history stage. This study shows that ocean acidification has no significant effect on P. damicornis microbiome, and warrants further research to test whether transgenerational acclimation exists in coral holobiont to projected future climate change.

Taxonomic profiling of Symbiodiniaceae and bacterial communities associated with Indo-Pacific corals in the Gulf of Thailand using PacBio sequencing of full-length ITS and 16S rRNA genes

Corals live with complex assemblages of microbes including bacteria, the dinoflagellate Symbiodiniaceae, fungi and viruses in a coral holobiont. These coral-associated microorganisms play an important role in their host fitness and survival. Here, we investigated the structure and diversity of algal and bacterial communities associated with five Indo-Pacific coral species, using full-length 16S rRNA and internal transcribed spacer sequences. While the dinoflagellate communities associated with Poriteslutea were dominated with Symbiodiniaceae genus Cladocopium, the other four coral hosts were associated mainly with members of the Durusdinium genus, suggesting that host species was one of the underlying factors influencing the structure and composition of dinoflagellate communities associated with corals in the Gulf of Thailand. Alphaproteobacteria dominated the microbiomes of Pocillopora spp. while Pavonafrondifera and P. lutea were associated primarily with Gammaproteobacteria. Finally, we demonstrated a superior performance of full-length 16S rRNA sequences in achieving species-resolution taxonomic classification of coral-associated microbiota.

Shifting the microbiome of a coral holobiont and improving host physiology by inoculation with a potentially beneficial bacterial consortium

Background

The coral microbiome plays a key role in host health by being involved in energy metabolism, nutrient cycling, and immune system formation. Inoculating coral with beneficial bacterial consortia may enhance the ability of this host to cope with complex and changing marine environments. In this study, the coral Pocillopora damicornis was inoculated with a beneficial microorganisms for corals (BMC) consortium to investigate how the coral host and its associated microbial community would respond.

Results

High-throughput 16S rRNA gene sequencing revealed no significant differences in bacterial community α-diversity. However, the bacterial community structure differed significantly between the BMC and placebo groups at the end of the experiment. Addition of the BMC consortium significantly increased the relative abundance of potentially beneficial bacteria, including the genera Mameliella and Endozoicomonas. Energy reserves and calcification rates of the coral host were also improved by the addition of the BMC consortium. Co-occurrence network analysis indicated that inoculation of coral with the exogenous BMC consortium improved the physiological status of the host by shifting the coral-associated microbial community structure.

Conclusions

Manipulating the coral-associated microbial community may enhance the physiology of coral in normal aquarium conditions (no stress applied), which may hypothetically contribute to resilience and resistance in this host.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02167-5.

Microbiome community and complexity indicate environmental gradient acclimatisation and potential microbial interaction of endemic coral holobionts in the South China Sea

Regional acclimatisation and microbial interactions significantly influence the resilience of reef-building corals facing anthropogenic climate change, allowing them to adapt to environmental stresses. However, the connections between community structure and microbial interactions of the endemic coral microbiome and holobiont acclimatisation remain unclear. Herein, we used generation sequencing of internal transcribed spacer (ITS2) and 16S rRNA genes to investigate the microbiome composition (Symbiodiniaceae and bacteria) and associated potential interactions of endemic dominant coral holobionts (Pocillopora verrucosa and Turbinaria peltata) in the South China Sea (SCS). We found that shifts in Symbiodiniaceae and bacterial communities of P. verrucosa were associated with latitudinal gradient and climate zone changes, respectively. The C1 sub-clade consistently dominated the Symbiodiniaceae community in T. peltata; yet, the bacterial community structure was spatially heterogeneous. The relative abundance of the core microbiome among P. verrucosa holobionts was reduced in the biogeographical transition zone, while bacterial taxa associated with anthropogenic activity (Escherichia coli and Sphingomonas) were identified in the core microbiomes. Symbiodiniaceae and bacteria potentially interact in microbial co-occurrence networks. Further, increased bacterial, and Symbiodiniaceae α-diversity was associated with increased and decreased network complexity, respectively. Hence, Symbiodiniaceae and bacteria demonstrated different flexibility in latitudinal or climatic environmental regimes, which correlated with holobiont acclimatisation. Core microbiome analysis has indicated that the function of core bacterial microbiota might have changed in distinct environmental regimes, implying potential human activity in the coral habitats. Increased bacterial α diversity may lead to a decline in the stability of coral-microorganism symbioses, whereas rare Symbiodiniaceae may help to retain symbioses. Cladocopium, γ-proteobacteria, while α-proteobacteria may have been the primary drivers in the Symbiodiniaceae-bacterial interactions (SBIs). Our study highlights the association between microbiome shift in distinct environmental regimes and holobiont acclimatisation, while providing insights into the impact of SBIs on holobiont health and acclimatisation during climate change.

Response of psychrophilic plant endosymbionts to experimental temperature increase

Countless uncertainties remain regarding the effects of global warming on biodiversity, including the ability of organisms to adapt and how that will affect obligate symbiotic relationships. The present study aimed to determine the consequences of temperature increase in the adaptation of plant endosymbionts (endophytes) that grow better at low temperatures (psychrophilic). We isolated fungal endophytes from a high-elevation (paramo) endemic plant, Chusquea subtessellata. Initial growth curves were constructed at different temperatures (4-25°C). Next, experiments were carried out in which only the psychrophilic isolates were subjected to repeated increments in temperature. After the experiments, the final growth curves showed significantly slower growth than the initial curves, and some isolates even ceased to grow. While most studies suggest that the distribution of microorganisms will expand as temperatures increase because most of these organisms grow better at 25°C, the results from our experiments demonstrate that psychrophilic fungi were negatively affected by temperature increases. These outcomes raise questions concerning the potential adaptation of beneficial endosymbiotic fungi in the already threatened high-elevation ecosystems. Assessing the consequences of global warming at all trophic levels is urgent because many species on Earth depend on their microbial symbionts for survival.

Microbial community and transcriptional responses to increased temperatures in coral Pocillopora damicornis holobiont

A few studies have holistically examined successive changes in coral holobionts in response to increased temperatures. Here, responses of the coral host Pocillopora damicornis, its Symbiodiniaceae symbionts, and associated bacteria to increased water temperatures were investigated. High temperatures induced bleaching, but no coral mortality was observed. Transcriptome analyses showed that P. damicornis responded more quickly to elevated temperatures than its algal symbionts. Numerous genes putatively associated with apoptosis, exocytosis, and autophagy were upregulated in P. damicornis, suggesting that Symbiodiniaceae can be eliminated or expelled through these mechanisms when P. damicornis experiences heat stress. Furthermore, apoptosis in P. damicornis is presumably induced through tumour necrosis factor and p53 signalling and caspase pathways. The relative abundances of several coral disease-associated bacteria increased at 32°C, which may affect immune responses in heat-stressed corals and potentially accelerates the loss of algal symbionts. Additionally, consistency of Symbiodiniaceae community structures under heat stress suggests non-selective loss of Symbiodiniaceae. We propose that heat stress elicits interrelated response mechanisms in all parts of the coral holobiont.

Lipopolysaccharide treatment stimulates Pocillopora coral genotype-specific immune responses but does not alter coral-associated bacteria communities

Corals are comprised of a coral host and associated microbes whose interactions are mediated by the coral innate immune system. The diversity of immune factors identified in the Pocillopora damicornis genome suggests that immunity is linked to maintaining microbial symbioses while also being able to detect pathogens. However, it is unclear which immune factors respond to specific microbe-associated molecular patterns and how these immune reactions simultaneously affect coral-associated bacteria. To investigate this, fragments of P. damicornis and P. acuta colonies from Taiwan were subjected to lipopolysaccharide (LPS) treatment to stimulate immune responses and measure bacteria community shifts. RNA-seq revealed genotype-specific immune responses to LPS involving the upregulation of immune receptors, transcription factors, and pore-forming toxins. Bacteria 16S sequencing revealed significantly different bacteria communities between coral genotypes but no differences in bacteria communities were caused by LPS. Our findings confirm that Pocillopora corals activate conserved immune factors in response to LPS and identify transcription factors coordinating Pocillopora corals' immune responses. Additionally, the strong effect of coral genotype on gene expression and bacteria communities highlights the importance of coral genotype in the investigation of coral host-microbe interactions.

Patterns of environmental variability influence coral-associated bacterial and algal communities on the Mesoamerican Barrier Reef

A coral's capacity to alter its microbial symbionts may enhance its fitness in the face of climate change. Recent work predicts exposure to high environmental variability may increase coral resilience and adaptability to future climate conditions. However, how this heightened environmental variability impacts coral-associated microbial communities remains largely unexplored. Here, we examined the bacterial and algal symbionts associated with two coral species of the genus Siderastrea with distinct life history strategies from three reef sites on the Belize Mesoamerican Barrier Reef System with low or high environmental variability. Our results reveal bacterial community structure, as well as alpha- and beta-diversity patterns, vary by host species. Differences in bacterial communities between host species were partially explained by high abundance of Deltaproteobacteria and Rhodospirillales and high bacterial diversity in Siderastrea radians. Our findings also suggest Siderastrea spp. have dynamic core bacterial communities that likely drive differences observed in the entire bacterial community, which may play a critical role in rapid acclimatization to environmental change. Unlike the bacterial community, Symbiodiniaceae composition was only distinct between host species at high thermal variability sites, suggesting that different factors shape bacterial versus algal communities within the coral holobiont. Our findings shed light on how domain-specific shifts in dynamic microbiomes may allow for unique methods of enhanced host fitness.

The 3D Reconstruction of Pocillopora Colony Sheds Light on the Growth Pattern of This Reef-Building Coral

Coral reefs are formed by living polyps, and understanding the dynamic processes behind the reefs is crucial for marine ecosystem restoration. However, these processes are still unclear because the growth and budding patterns of living polyps are poorly known. Here, we investigate the growth pattern of a widely distributed reef-building coral Pocillopora damicornis from Xisha Islands using high-resolution computed tomography. We examine the corallites in a single corallum of the species in detail, to interpret the budding, growth, and distribution pattern of the polyps, to reconstruct the growth pattern of this important reef-building species. Our results reveal a three-stage growth pattern of P. damicornis, based on different growth bundles that are secreted by polyps along the dichotomous growth axes of the corallites. Our work on the three-dimensional reconstruction of calice and inter-septal space structure of P. damicornis sheds lights on its reef-building processes by reconstructing the budding patterns.

•

We use high-resolution computed tomography to investigate coral forming and polyp budding processes

•

The calice reconstruction shows coral growth patterns and budding information

•

Our work visualizes the growth pattern of Pocillopora damicornis

•

High-resolution computed tomography is a method for future reef-building coral studies

Dispersal, genetic variation, and symbiont interaction network of heat-tolerant endosymbiont Durusdinium trenchii: Insights into the adaptive potential of coral to climate change

Global warming has degraded coral reef ecosystems worldwide. Some corals develop thermal tolerance by associating with heat-tolerant Symbiodiniaceae. Here, we studied the mechanisms surrounding the dispersal, genetic variation and symbionts interaction of heat-tolerant Durusdinium trenchii across 13° latitudes in the South China Sea (SCS), to explore the possible mechanisms underlying these changes. Our results showed that Durusdinium trenchii are widely distributed in the seawater from the SCS. Our analyses of microsatellite loci revealed that D. trenchii has a high genetic diversity in the SCS; STRUCTURE analysis indicated that D. trenchii can be divided into four populations within the SCS; There exist positive correlations between genetic variation and geographic isolation, average sea surface temperature (SST) and variations in SST. Network modelling inferences showed that D. trenchii is a key species in the Symbiodiniaceae communities in the tropical SCS and contributes the greatest number of co-exclusion relationships. These results indicated that D. trenchii can affect the rare Symbiodiniaceae community. The long lifespan and the monsoon-driven ocean currents have shaped the wide distribution of D. trenchii. But low SST limits the ability of D. trenchii to establish stable symbioses with coral in the subtropical habitats. Geographical isolation and SST have shaped significant genetic variation of D.trenchii around the SCS. Our data reveals the biogeography and genetic population characteristics of D. trenchii in the Indo-Pacific region, and suggests that heat-tolerance and high genetic diversity of D. trenchii aid the corals with their adaptation to climate change.

Unraveling Heterogeneity of Coral Microbiome Assemblages in Tropical and Subtropical Corals in the South China Sea

Understanding the coral microbiome is critical for predicting the fidelity of coral symbiosis with growing surface seawater temperature (SST). However, how the coral microbiome will respond to increasing SST is still understudied. Here, we compared the coral microbiome assemblages among 73 samples across six typical South China Sea coral species in two thermal regimes. The results revealed that the composition of microbiome varied across both coral species and thermal regimes, except for Porites lutea. The tropical coral microbiome displayed stronger heterogeneity and had a more un-compacted ecological network than subtropical coral microbiome. The coral microbiome was more strongly determined by environmental factors than host specificity. γ- (32%) and α-proteobacteria (19%), Bacteroidetes (14%), Firmicutes (14%), Actinobacteria (6%) and Cyanobacteria (2%) dominated the coral microbiome. Additionally, bacteria inferred to play potential roles in host nutrients metabolism, several keystone bacteria detected in human and plant rhizospheric microbiome were retrieved in explored corals. This study not only disentangles how different host taxa and microbiome interact and how such an interaction is affected by thermal regimes, but also identifies previously unrecognized keystone bacteria in corals, and also infers the community structure of coral microbiome will be changed from a compacted to an un-compacted network under elevated SST.

Symbiont community diversity is more variable in corals that respond poorly to stress

Coral reefs are declining globally as climate change and local water quality press environmental conditions beyond the physiological tolerances of holobionts-the collective of the host and its microbial symbionts. To assess the relationship between symbiont composition and holobiont stress tolerance, community diversity metrics were quantified for dinoflagellate endosymbionts (Family: Symbiodiniaceae) from eight Acropora millepora genets that thrived under or responded poorly to various stressors. These eight selected genets represent the upper and lower tails of the response distribution of 40 coral genets that were exposed to four stress treatments (and control conditions) in a 10-day experiment. Specifically, four 'best performer' coral genets were analyzed at the end of the experiment because they survived high temperature, high pCO2 , bacterial exposure, or combined stressors, whereas four 'worst performer' genets were characterized because they experienced substantial mortality under these stressors. At the end of the experiment, seven of eight coral genets mainly hosted Cladocopium symbionts, whereas the eighth genet was dominated by both Cladocopium and Durusdinium symbionts. Symbiodiniaceae alpha and beta diversity were higher in worst performing genets than in best performing genets. Symbiont communities in worst performers also differed more after stress exposure relative to their controls (based on normalized proportional differences in beta diversity), than did best performers. A generalized joint attribute model estimated the influence of host genet and treatment on Symbiodiniaceae community composition and identified strong associations among particular symbionts and host genet performance, as well as weaker associations with treatment. Although dominant symbiont physiology and function contribute to host performance, these findings emphasize the importance of symbiont community diversity and stochasticity as components of host performance. Our findings also suggest that symbiont community diversity metrics may function as indicators of resilience and have potential applications in diverse disciplines from climate change adaptation to agriculture and medicine.

Schistosomiasis Vector Snails and Their Microbiota Display a Phylosymbiosis Pattern

Planorbidae snails are the intermediate host for the trematode parasite of the Schistosoma genus, which is responsible for schistosomiasis, a disease that affects both humans and cattle. The microbiota for Schistosoma has already been described as having an effect on host/parasite interactions, specifically through immunological interactions. Here, we sought to characterize the microbiota composition of seven Planorbidae species and strains. Individual snail microbiota was determined using 16S ribosomal DNA amplicon sequencing. The bacterial composition was highly specific to the host strain with limited interindividual variation. In addition, it displayed complete congruence with host phylogeny, revealing a phylosymbiosis pattern. These results were confirmed in a common garden, suggesting that the host highly constrains microbial composition. This study presents the first comparison of bacterial communities between several intermediate snail hosts of Schistosoma parasites, paving the way for further studies on the understanding of this tripartite interaction.

Diversity of Symbiodiniaceae in 15 Coral Species From the Southern South China Sea: Potential Relationship With Coral Thermal Adaptability

It is well-known that the adaptability of coral-Symbiodiniaceae symbiosis to thermal stress varies among coral species, but the cause and/or mechanism behind it are not well-understood. In this study, we aimed to explore this issue based on zooxanthellae density (ZD) and Symbiodiniaceae genus/subclade. Hemocytometry and next-generation sequencing of the internal transcribed spacer region 2 (ITS2) marker gene were used to observe ZDs and Symbiodiniaceae genera/subclades associated with 15 typical coral species in the southern South China Sea (SCS). Average ZDs of all corals were in low levels, ranging from 0.84 to 1.22 × 10⁶ cells cm⁻², with a total of five Symbiodiniaceae genera, Symbiodinium, Cladocopium, Durusdinium, Fugacium, and Gerakladium, as well as 24 dominant subclades, were detected and varied among these coral species. Pocillopora verrucosa was dominated by Durusdinium (subclade D1/D1a), and other colonial corals were dominated by Cladocopium, but the subclades were varied among these species. Porites lutea and Montipora efflorescens were dominated by C15, and Echinopora lamellosa, Hydnophora exesa, and Coscinaraea exesa were dominated by C40. Acropora corymbosa, Merulina ampliata, and five species of Faviidae were mainly associated with Cladocopium types of C3u and Cspc. In contrast to other colonial corals, the dominant subclade of solitary Fungia fungites was C27, with high host specificity. Our study indicates that coral thermal stress adaptability is mainly affected by dominant Symbiodiniaceae type instead of ZD in the southern SCS. Some heat-sensitive corals, such as P. verrucosa corals, have acquired a high abundance of heat-tolerant Durusdinium to adapt to thermal stress. This could be the main reason for these corals becoming the dominant corals in this reef region. Background subclades analyses showed significant differences among coral species in subclade quantity and diversity. These suggest that numbers of coral species may have adapted to high environmental temperature by adopting various symbionts and/or associating with heat-tolerant Symbiodiniaceae.

Searching for phylogenetic patterns of Symbiodiniaceae community structure among Indo-Pacific Merulinidae corals

Over half of all extant stony corals (Cnidaria: Anthozoa: Scleractinia) harbour endosymbiotic dinoflagellates of the family Symbiodiniaceae, forming the foundational species of modern shallow reefs. However, whether these associations are conserved on the coral phylogeny remains unknown. Here we aim to characterise Symbiodiniaceae communities in eight closely-related species in the genera Merulina, Goniastrea and Scapophyllia, and determine if the variation in endosymbiont community structure can be explained by the phylogenetic relatedness among hosts. We perform DNA metabarcoding of the nuclear internal transcribed spacer 2 using Symbiodiniaceae-specific primers on 30 coral colonies to recover three major endosymbiont clades represented by 23 distinct types. In agreement with previous studies on Southeast Asian corals, we find an abundance of Cladocopium and Durusdinium, but also detect Symbiodinium types in three of the eight coral host species. Interestingly, differences in endosymbiont community structure are dominated by host variation at the intraspecific level, rather than interspecific, intergeneric or among-clade levels, indicating a lack of phylogenetic constraint in the coral-endosymbiont association among host species. Furthermore, the limited geographic sampling of four localities spanning the Western and Central Indo-Pacific preliminarily hints at large-scale spatial structuring of Symbiodiniaceae communities. More extensive collections of corals from various regions and environments will help us better understand the specificity of the coral-endosymbiont relationship.

Microbiome of the Black-Lipped Pearl Oyster Pinctada margaritifera, a Multi-Tissue Description With Functional Profiling

Elucidating the role of prokaryotic symbionts in mediating host physiology has emerged as an important area of research. Since oysters are the world’s most heavily cultivated bivalve molluscs, numerous studies have applied molecular techniques to understand the taxonomic and functional diversity of their associated bacteria. Here, we expand on this research by assessing the composition and putative functional profiles of prokaryotic communities from different organs/compartments of the black-lipped pearl oyster Pinctada margaritifera, a commercially important shellfish valued for cultured pearl production in the Pacific region. Seven tissues, in addition to mucous secretions, were targeted from P. margaritifera individuals: the gill, gonad, byssus gland, haemolymph, mantle, adductor muscle, mucus, and gut. Richness of bacterial Operational Taxonomic Units (OTUs) and phylogenetic diversity differed between host tissues, with mucous layers displaying the highest richness and diversity. This multi-tissues approach permitted the identification of consistent microbial members, together constituting the core microbiome of P. margaritifera, including Alpha- and Gammaproteobacteria, Flavobacteriia, and Spirochaetes. We also found a high representation of Endozoicimonaceae symbionts, indicating that they may be of particular importance to oyster health, survival and homeostasis, as in many other coral reef animals. Our study demonstrates that the microbial communities and their associated predicted functional profiles are tissue specific. Inferred physiological functions were supported by current physiological data available for the associated bacterial taxa specific to each tissue. This work provides the first baseline of microbial community composition in P. margaritifera, providing a solid foundation for future research into this commercially important species and emphasises the important effects of tissue differentiation in structuring the oyster microbiome.

Microbiomes of stony and soft deep-sea corals share rare core bacteria

BACKGROUND

Numerous studies have shown that bacteria form stable associations with host corals and have focused on identifying conserved "core microbiomes" of bacterial associates inferred to be serving key roles in the coral holobiont. Because studies tend to focus on only stony corals (order Scleractinia) or soft corals (order Alcyonacea), it is currently unknown if there are conserved bacteria that are shared by both. A meta-analysis was done of 16S rRNA amplicon data from multiple studies generated via identical methodology to allow direct comparisons of bacterial associates across seven deep-sea corals, including both stony and soft species: Anthothela grandiflora, Anthothela sp., Lateothela grandiflora, Lophelia pertusa, Paramuricea placomus, Primnoa pacifica, and Primnoa resedaeformis.

RESULTS

Twenty-three operational taxonomic units (OTUs) were consistently present in greater than 50% of the coral samples. Seven amplicon sequence variants (ASVs), five of which corresponded to a conserved OTU, were consistently present in greater than 30% of the coral samples including five or greater coral species. A majority of the conserved sequences had close matches with previously identified coral-associated bacteria. While known to dominate tropical and temperate coral microbiomes, Endozoicomonas were extremely rare or absent from these deep-sea corals. An Endozoicomonas OTU associated with Lo. pertusa in this study was most similar to those from shallow-water stony corals, while an OTU associated with Anthothela spp. was most similar to those from shallow-water gorgonians.

CONCLUSIONS

Bacterial sequences have been identified that are conserved at the level of class Anthozoa (i.e., found in both stony and soft corals, shallow and deep). These bacterial associates are therefore hypothesized to play important symbiotic roles and are highlighted for targeted future study. These conserved bacterial associates include taxa with the potential for nitrogen and sulfur cycling, detoxification, and hydrocarbon degradation. There is also some overlap with kit contaminants that need to be resolved. Rarely detected Endozoicomonas sequences are partitioned by whether the host is a stony coral or a soft coral, and the finer clustering pattern reflects the hosts' phylogeny.

Disentangling the effect of host-genotype and environment on the microbiome of the coral Acropora tenuis

Genotype-specific contributions to the environmental tolerance and disease susceptibility of corals are widely accepted. Yet our understanding of how host genotype influences the composition and stability of the coral microbiome subjected to environmental fluctuations is limited. To gain insight into the community dynamics and environmental stability of microbiomes associated with distinct coral genotypes, we assessed the microbial community associated with Acropora tenuis under single and cumulative pressure experiments. Experimental treatments comprised either a single pulse of reduced salinity (minimum of 28 psu) or exposure to the cumulative pressures of reduced salinity (minimum of 28 psu), elevated seawater temperature (+2 °C), elevated pCO₂ (900 ppm), and the presence of macroalgae. Analysis of 16S rRNA gene amplicon sequence data revealed that A. tenuis microbiomes were highly host-genotype specific and maintained high compositional stability irrespective of experimental treatment. On average, 48% of the A. tenuis microbiome was dominated by Endozoicomonas. Amplicon sequence variants (ASVs) belonging to this genus were significantly different between host individuals. Although no signs of stress were evident in the coral holobiont and the vast majority of ASVs remained stable across treatments, a microbial indicator approach identified 26 ASVs belonging to Vibrionaceae, Rhodobacteraceae, Hahellaceae, Planctomycetes, Phylobacteriaceae, Flavobacteriaceae, and Cryomorphaceae that were significantly enriched in corals exposed to single and cumulative stressors. While several recent studies have highlighted the efficacy of microbial indicators as sensitive markers for environmental disturbance, the high host-genotype specificity of coral microbiomes may limit their utility and we therefore recommend meticulous control of host-genotype effects in coral microbiome research.

Host-microbiota interactions: from holobiont theory to analysis

In the recent years, the holobiont concept has emerged as a theoretical and experimental framework to study the interactions between hosts and their associated microbial communities in all types of ecosystems. The spread of this concept in many branches of biology results from the fairly recent realization of the ubiquitous nature of host-associated microbes and their central role in host biology, ecology, and evolution. Through this special series "Host-microbiota interactions: from holobiont theory to analysis," we wanted to promote this field of research which has considerable implications for human health, food production, and ecosystem protection. In this preface, we highlight a collection of articles selected for this special issue that show, use, or debate the concept of holobiont to approach taxonomically and ecologically diverse organisms, from humans and plants to sponges and insects. We also identify some theoretical and methodological challenges and propose directions for future research on holobionts.

Evolutionary significance of the microbial assemblages of large benthic Foraminifera

Large benthic Foraminifera (LBF) are major carbonate producers on coral reefs, and are hosts to a diverse symbiotic microbial community. During warm episodes in the geological past, these reef-building organisms expanded their geographical ranges as subtropical and tropical belts moved into higher latitudes. During these range-expansion periods, LBF were the most prolific carbonate producers on reefs, dominating shallow carbonate platforms over reef-building corals. Even though the fossil and modern distributions of groups of species that harbour different types of symbionts are known, the nature, mechanisms, and factors that influence their occurrence remain elusive. Furthermore, the presence of a diverse and persistent bacterial community has only recently gained attention. We examined recent advances in molecular identification of prokaryotic (i.e. bacteria) and eukaryotic (i.e. microalgae) associates, and palaeoecology, and place the partnership with bacteria and algae in the context of climate change. In critically reviewing the available fossil and modern data on symbiosis, we reveal a crucial role of microalgae in the response of LBF to ocean warming, and their capacity to colonise a variety of habitats, across both latitudes and broad depth ranges. Symbiont identity is a key factor enabling LBF to expand their geographic ranges when the sea-surface temperature increases. Our analyses showed that over the past 66 million years (My), diatom-bearing species were dominant in reef environments. The modern record shows that these species display a stable, persistent eukaryotic assemblage across their geographic distribution range, and are less dependent on symbiotic photosynthesis for survival. By contrast, dinoflagellate and chlorophytic species, which show a provincial distribution, tend to have a more flexible eukaryotic community throughout their range. This group is more dependent on their symbionts, and flexibility in their symbiosis is likely to be the driving force behind their evolutionary history, as they form a monophyletic group originating from a rhodophyte-bearing ancestor. The study of bacterial assemblages, while still in its infancy, is a promising field of study. Bacterial communities are likely to be shaped by the local environment, although a core bacterial microbiome is found in species with global distributions. Cryptic speciation is also an important factor that must be taken into consideration. As global warming intensifies, genetic divergence in hosts in addition to the range of flexibility/specificity within host-symbiont associations will be important elements in the continued evolutionary success of LBF species in a wide range of environments. Based on fossil and modern data, we conclude that the microbiome, which includes both algal and bacterial partners, is a key factor influencing the evolution of LBF. As a result, the microbiome assists LBF in colonising a wide range of habitats, and allowed them to become the most important calcifiers on shallow platforms worldwide during periods of ocean warming in the geologic past. Since LBF are crucial ecosystem engineers and prolific carbonate producers, the microbiome is a critical component that will play a central role in the responses of LBF to a changing ocean, and ultimately in shaping the future of coral reefs.

Protists Within Corals: The Hidden Diversity

Previous observations suggested that microbial communities contribute to coral health and the ecological resilience of coral reefs. However, most studies of coral microbiology focused on prokaryotes and the endosymbiotic algae Symbiodinium. In contrast, knowledge concerning diversity of other protists is still lacking, possibly due to methodological constraints. As most eukaryotic DNA in coral samples was derived from hosts, protist diversity was missed in metagenome analyses. To tackle this issue, we designed blocking primers for Scleractinia sequences amplified with two primer sets that targeted variable loops of the 18S rRNA gene (18SV1V2 and 18SV4). These blocking primers were used on environmental colonies of Pocillopora damicornis sensu lato from two regions with contrasting thermal regimes (Djibouti and New Caledonia). In addition to Symbiodinium clades A/C/D, Licnophora and unidentified coccidia genera were found in many samples. In particular, coccidian sequences formed a robust monophyletic clade with other protists identified in Agaricia, Favia, Montastraea, Mycetophyllia, Porites, and Siderastrea coral colonies. Moreover, Licnophora and coccidians had different distributions between the two geographic regions. A similar pattern was observed between Symbiodinium clades C and A/D. Although we were unable to identify factors responsible for this pattern, nor were we able to confirm that these taxa were closely associated with corals, we believe that these primer sets and the associated blocking primers offer new possibilities to describe the hidden diversity of protists within different coral species.