Analysis of composition and abundance of viral communities associated with coral \(\textit{Acropora formosa}\)

Coral reefs harbor the extraordinary biodiversity and not only provide livelihoods for coastal communities but also play a crucial role in economic development generally. Unfortunately, they are in decline in Vietnam and around the world because mass coral bleaching events have become more common worldwide. However, little is discovered, about viruses that infect corals and their symbionts. Herein, we present metagenomic analyses of the viral communities in coral mucus associated with healthy and bleached coral Acropora formosa which was collected at Con Dao Island, Vietnam. Interestingly, the number of viral species in bleached specimens are higher than those in healthy status. Viruses similar to those that infect humans and some marine animals also appeared in the coral viral assemblage. The results indicated that the proportion of shared viruses were quite small, and represented extremely abundance. Among the phage identified, vibriophage and cyanophage were only presented in healthy and bleached coral, respectively. Therefore, coral-associated viruses could prospectively infect all constituents of the holobiont - coral, microalgal and microbial. Thus, we expect viruses to be illustrated prominently in the preservation and breakdown of coral health.

Host-specific epibiomes of distinct Acropora cervicornis genotypes persist after field transplantation

Microbiome studies across taxa have established the influence of host genotype on microbial recruitment and maintenance. However, research exploring host-specific epibionts in scleractinian corals is scant and the influence of intraspecific differences across environments remains unclear. Here, we studied the epibiome of ten Acropora cervicornis genotypes to investigate the relative roles of host genotype and environment in structuring the epibiome. Coral mucus was sampled in a common garden nursery from replicate ramets of distinct genotypes (T0). Coral fragment replicates (n=3) of each genotype were then transplanted to nine different field sites in the Lower Florida Keys and mucus was again sampled one year later from surviving ramets (T12). 16S rRNA amplicon sequencing was used to assess microbial composition, richness, and beta-diversity. The most abundant and consistent amplicon sequencing variants (ASVs) in all samples belonged to Fokiniaceae (MD3-55 genus) and Cyanobacteria (Synechococccus). The abundances of these bacterial taxa varied consistently between genotypes whereas neither the composition nor taxonomic abundance were significantly different among field sites. Interestingly, several high MD3-55 hosting genotypes showed rapid diversification and an increase in MD3-55 following transplantation. Overall, our results indicate healthy A. cervicornis genotypes retain distinct epibiome signatures through time, suggesting a strong host component. Lastly, our results show that differences in MD3-55 abundances can be consistently detected in the epibiome of distinct host-genotypes of A. cervicornis. As this organism (sensu Aquarickettsia rohweri) has been implicated as a marker of disease resistance, this finding reinforces the potential use of microbial indicators in reef restoration efforts via non-invasive surface/mucus sampling.

Coral mucus rapidly induces chemokinesis and genome-wide transcriptional shifts toward early pathogenesis in a bacterial coral pathogen

Elevated seawater temperatures have contributed to the rise of coral disease mediated by bacterial pathogens, such as the globally distributed Vibrio coralliilyticus, which utilizes coral mucus as a chemical cue to locate stressed corals. However, the physiological events in the pathogens that follow their entry into the coral host environment remain unknown. Here, we present simultaneous measurements of the behavioral and transcriptional responses of V. coralliilyticus BAA-450 incubated in coral mucus. Video microscopy revealed a strong and rapid chemokinetic behavioral response by the pathogen, characterized by a two-fold increase in average swimming speed within 6 min of coral mucus exposure. RNA sequencing showed that this bacterial behavior was accompanied by an equally rapid differential expression of 53% of the genes in the V. coralliilyticus genome. Specifically, transcript abundance 10 min after mucus exposure showed upregulation of genes involved in quorum sensing, biofilm formation, and nutrient metabolism, and downregulation of flagella synthesis and chemotaxis genes. After 60 min, we observed upregulation of genes associated with virulence, including zinc metalloproteases responsible for causing coral tissue damage and algal symbiont photoinactivation, and secretion systems that may export toxins. Together, our results suggest that V. coralliilyticus employs a suite of behavioral and transcriptional responses to rapidly shift into a distinct infection mode within minutes of exposure to the coral microenvironment.

Differential Patterns of Microbiota Recovery in Symbiotic and Aposymbiotic Corals following Antibiotic Disturbance

ABSTRACT Microbial relationships are critical to coral health, and changes in microbiomes are often exhibited following environmental disturbance. However, the dynamics of coral-microbial composition and external factors that govern coral microbiome assembly and response to disturbance remain largely uncharacterized. Here, we investigated how antibiotic-induced disturbance affects the coral mucus microbiota in the facultatively symbiotic temperate coral Astrangia poculata, which occurs naturally with high (symbiotic) or low (aposymbiotic) densities of the endosymbiotic dinoflagellate Breviolum psygmophilum. We also explored how differences in the mucus microbiome of natural and disturbed A. poculata colonies affected levels of extracellular superoxide, a reactive oxygen species thought to have both beneficial and detrimental effects on coral health. Using a bacterial and archaeal small-subunit (SSU) rRNA gene sequencing approach, we found that antibiotic exposure significantly altered the composition of the mucus microbiota but that it did not influence superoxide levels, suggesting that superoxide production in A. poculata is not influenced by the mucus microbiota. In antibiotic-treated A. poculata exposed to ambient seawater, mucus microbiota recovered to its initial state within 2 weeks following exposure, and six bacterial taxa played a prominent role in this reassembly. Microbial composition among symbiotic colonies was more similar throughout the 2-week recovery period than that among aposymbiotic colonies, whose microbiota exhibited significantly more interindividual variability after antibiotic treatment and during recovery. This work suggests that the A. poculata mucus microbiome can rapidly reestablish itself and that the presence of B. psygmophilum, perhaps by supplying nutrients, photosynthate, or other signaling molecules, exerts influence on this process. IMPORTANCE Corals are animals whose health is often maintained by symbiotic microalgae and other microorganisms, yet they are highly susceptible to environmental-related disturbances. Here, we used a known disruptor, antibiotics, to understand how the coral mucus microbial community reassembles itself following disturbance. We show that the Astrangia poculata microbiome can recover from this disturbance and that individuals with algal symbionts reestablish their microbiomes in a more consistent manner compared to corals lacking symbionts. This work is important because it suggests that this coral may be able to recover its mucus microbiome following disturbance, it identifies specific microbes that may be important to reassembly, and it demonstrates that algal symbionts may play a previously undocumented role in microbial recovery and resilience to environmental change.

A genomic view of the microbiome of coral reef demosponges

Sponges underpin the productivity of coral reefs, yet few of their microbial symbionts have been functionally characterised. Here we present an analysis of ~1200 metagenome-assembled genomes (MAGs) spanning seven sponge species and 25 microbial phyla. Compared to MAGs derived from reef seawater, sponge-associated MAGs were enriched in glycosyl hydrolases targeting components of sponge tissue, coral mucus and macroalgae, revealing a critical role for sponge symbionts in cycling reef organic matter. Further, visualisation of the distribution of these genes amongst symbiont taxa uncovered functional guilds for reef organic matter degradation. Genes for the utilisation of sialic acids and glycosaminoglycans present in sponge tissue were found in specific microbial lineages that also encoded genes for attachment to sponge-derived fibronectins and cadherins, suggesting these lineages can utilise specific structural elements of sponge tissue. Further, genes encoding CRISPR and restriction-modification systems used in defence against mobile genetic elements were enriched in sponge symbionts, along with eukaryote-like gene motifs thought to be involved in maintaining host association. Finally, we provide evidence that many of these sponge-enriched genes are laterally transferred between microbial taxa, suggesting they confer a selective advantage within the sponge niche and therefore play a critical role in host ecology and evolution.

Chemotactic Response of Vibrio coralliilyticus to mucus from various coral species

<i>Vibrio coralliilyticus</i>, a prominent pathogenic bacteria, is known to cause tissue damage in the coral <i>Pocillopora damicornis</i> and is attracted towards the coral via chemotaxis. However, the potential of <i>V. coralliilyticus</i> to infect most of the other coral hosts via chemotaxis is unknown. The present study used capillary assays to quantify the chemotactic response of <i>V. coralliilyticus</i> to the mucus of four tank-cultivated corals, <i>Cataphyllia jardine</i>, <i>Mussidae</i> sp., <i>Nemenzophyllia turbida </i>and <i>Euphyllia ancora</i> and mucus from three wild corals, <i>Acropora</i> sp., <i>Porites</i> sp. & <i>Montipora</i> sp. The bacteria showed positive chemotactic response to each coral mucus tested, with the highest response recorded to the mucus of <i>Acropora</i> sp and the lowest response to the mucus of <i>Montipora</i> sp. A microfluidic chip was then used to assess the chemotactic preference of <i>V. coralliilyticus </i>to the mucus of the tank cultivated corals. Here too, the bacteria showed positive response with a slightly different ranking order. The strong chemotactic response of <i>V. coralliilyticus</i> towards the mucus tested could indicate a broader host range of <i>V. coralliilyticus</i> and in extension its threat to weakened coral reefs worldwide.

Population Differentiation of Rhodobacteraceae Along Coral Compartments

Coral mucus, tissue and skeleton harbor compositionally different microbiota, but how these coral compartments shape the microbial evolution remains unexplored. Here, we focused on the Rhodobacteraceae, which represents a significant but variable proportion (5-50%) of the coral microbiota. We sequenced 234 genomes constituting two divergent populations inhabiting a prevalent coral species Platygyra acuta. One population diverged into two clades colonizing the mucus and skeleton respectively. We reconstructed the ancestral gene changing events that potentially drove the split, and found that the affected genes matched well with the distinct physicochemical features of the mucus and skeleton. Specifically, the mucus clade acquired functions involved in the utilization of coral osmolytes abundant in the mucus (e.g., methylamines, DMSP, taurine and L-proline), whereas the skeleton clade uniquely harbored traits that may promote adaptation to the low-energy and diurnally anoxic skeleton (e.g., sulfur oxidation and swimming motility). These between-clade genetic differences were largely supported by physiological assays. Expanded analyses by including relatives isolated from various marine environments suggest that the mucus and skeleton clades may have diversified in non-coral habitats, but they also consolidated a key role of distinct coral compartments in diversifying many of the above-mentioned traits. The second population varied only at a few dozen nucleotide sites across the whole genomes, and the Slatkin-Maddison test supported that dispersal limitation between coral compartments is another key mechanism driving microbial population differentiation. Collectively, our results suggest that different coral compartments represent ecologically distinct and microgeographically separate habitats that drive the evolution of the coral microbiota.

The organosulfur compound dimethylsulfoniopropionate (DMSP) is utilized as an osmoprotectant by Vibrio species

Dimethylsulfoniopropionate (DMSP), a key component of the global geochemical sulfur cycle, is a secondary metabolite produced in large quantities by marine phytoplankton and utilized as an osmoprotectant, thermoprotectant and antioxidant. Marine bacteria can use two pathways to degrade and catabolize DMSP, a demethylation pathway and a cleavage pathway that produces the climate active gas dimethylsulfide (DMS). Whether marine bacteria can also accumulate DMSP as an osmoprotectant to maintain the turgor pressure of the cell in response to changes in external osmolarity has received little attention. The marine halophile Vibrio parahaemolyticus, contains at least six osmolyte transporters, four betaine carnitine choline transport (BCCT) carriers BccT1-BccT4 and two ABC-family ProU transporters. In this study, we showed that DMSP is used as an osmoprotectant by V. parahaemolyticus and several other Vibrio species including V. cholerae and V. vulnificus. Using a V. parahaemolyticus proU double mutant, we demonstrated that these ABC transporters are not required for DMSP uptake. However, a bccT null mutant lacking all four BCCTs had a growth defect compared to wild type in high salinity media supplemented with DMSP. Using mutants possessing only one functional BCCT in growth pattern assays, we identified two BCCT-family transporters, BccT1 and BccT2, which are carriers of DMSP. The only V. parahaemolyticus BccT homolog that V. cholerae and V. vulnificus possess is BccT3 and functional complementation in Escherichia coli MKH13 showed V. cholerae VcBccT3 could transport DMSP. In V. vulnificus strains, we identified and characterized an additional BCCT family transporter, which we named BccT5 that was also a carrier for DMSP.Importance DMSP is present in the marine environment, produced in large quantities by marine phytoplankton as an osmoprotectant, and is an important component of the global geochemical sulfur cycle. This algal osmolyte has not been previously investigated for its role in marine heterotrophic bacterial osmotic stress response. Vibrionaceae are marine species, many of which are halophiles exemplified by V. parahaemolyticus, a species that possesses at least six transporters for the uptake of osmolytes. Here, we demonstrated that V. parahaemolyticus and other Vibrio species can accumulate DMSP as an osmoprotectant and show that several BCCT family transporters uptake DMSP. These studies suggest that DMSP is a significant bacterial osmoprotectant, which may be important for understanding the fate of DMSP in the environment. DMSP is produced and present in coral mucus and Vibrio species form part of the microbial communities associated with them. The function of DMSP in these interactions is unclear, but could be an important driver for these associations allowing Vibrio proliferation. This work suggests that DMSP likely has an important role in heterotrophic bacteria ecology than previously appreciated.

Coupled Epidemio-Hydrodynamic Modeling to Understand the Spread of a Deadly Coral Disease in Florida

For the last six years, the Florida Reef Tract (FRT) has been experiencing an outbreak of the Stony Coral Tissue Loss Disease (SCTLD). First reported off the coast of Miami-Dade County in 2014, the SCTLD has since spread throughout the entire FRT with the exception of the Dry Tortugas. However, the causative agent for this outbreak is currently unknown. Here we show how a high-resolution bio-physical model coupled with a modified patch Susceptible-Infectious-Removed epidemic model can characterize the potential causative agent(s) of the disease and its vector. In the present study, the agent is assumed to be transported within composite material (e.g., coral mucus, dying tissues, and/or resuspended sediments) driven by currents and potentially persisting in the water column for extended periods of time. In this framework, our simulations suggest that the SCTLD is likely to be propagated within neutrally buoyant material driven by mean barotropic currents. Calibration of our model parameters with field data shows that corals are diseased within a mean transmission time of 6.45 days, with a basic reproduction number slightly above 1. Furthermore, the propagation speed of the disease through the FRT is shown to occur for a well-defined range of values of a disease threshold, defined as the fraction of diseased corals that causes an exponential growth of the disease in the reef site. Our results present a new connectivity-based approach to understand the spread of the SCTLD through the FRT. Such a method can provide a valuable complement to field observations and lab experiments to support the management of the epidemic as well as the identification of its causative agent.