Coral-associated microorganisms are essential for maintaining the health of the coral holobiont by participating in nutrient cycling and protecting the coral host from pathogens. Under stressful conditions, disruption of the coral prokaryotic microbiome is linked to increased susceptibility to diseases and mortality. Inoculation of corals with beneficial microbes could confer enhanced stress tolerance to the host and may be a powerful tool to help corals thrive under challenging environmental conditions. Here, we explored the feasibility of coral early life stage microbiome manipulation by repeatedly inoculating coral recruits with a bacterial cocktail generated in the laboratory. Co-culturing the two species Acropora tenuis and Platygyra daedalea allowed us to simultaneously investigate the effect of host factors on the coral microbiome. Inoculation cocktails were regularly prepared from freshly grown pure bacterial cultures, which were hence assumed viable, and characterized via the optical density measurement of each individual strain put in suspension. Coral early recruits were inoculated seven times over 3 weeks and sampled once 36 h following the last inoculation event. At this time point, the cumulative inoculations with the bacterial cocktails had a strong effect on the bacterial community composition in recruits of both coral species. While the location of bacterial cells within the coral hosts was not assessed, metabarcoding using the 16S rRNA gene revealed that two and six of the seven bacterial strains administered through the cocktails were significantly enriched in inoculated recruits of A. tenuis and P. daedalea , respectively, compared to control recruits. Despite being reared in the same environment, A. tenuis and P. daedalea established significantly different bacterial communities, both in terms of taxonomic composition and diversity measurements. These findings indicate that coral host factors as well as the environmental bacterial pool play a role in shaping coral-associated bacterial community composition. Host factors may include microbe transmission mode (horizontal versus maternal) and host specificity. While the long-term stability of taxa included in the bacterial inocula as members of the host-associated microbiome remains to be evaluated, our results provide support for the feasibility of coral microbiome manipulation, at least in a laboratory setting.

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Coral reefs are the epitome of species diversity rivaled only by tropical rainforests on land. Yet, the number of described scleractinian coral species, the framework-builders of coral reefs, remains moderate by comparison. DNA sequencing studies are challenging this notion by uncovering a wealth of "cryptic diversity", but the ecological relevance of this diversity remains largely unknown. Here, we present a comprehensive case study of one of the most geographically and environmentally ubiquitous coral species in the Indo-Pacific, Pachyseris speciosa. We provide an annotated draft genome and establish through extensive resequencing that its broad ecological distribution can be explained by the presence of at least three sympatric cryptic lineages. The lineages lack morphologically diagnostic characters yet exhibit genome-wide divergence with demographic modelling indicating an ancient divergence. Targeted genotyping surveys revealed differences in their ecological distributions, as well as in physiological and quantitative skeletal traits. Representatives of the lineages were observed to spawn on different days following the full moon, indicating temporal reproductive isolation that may explain the limited admixture. Fixed differences in genes related to morphogenesis and reproduction are consistent with these data. Overall, these findings highlight that our current taxonomic framework for scleractinian corals may be merely scratching the surface of the ecologically relevant diversity on coral reefs, consequently limiting our ability to protect this diversity effectively.

Marine viruses are the largest, but most poorly explored genetic reservoir on the planet. They occur ubiquitously in the ocean at an average density of 5–15 × 106 viruses per mL of seawater, which represents abundances an order of magnitude higher than those of bacteria. While viruses are known agents of a number of diseases in the marine environment, little is known about their beneficial function to corals. Herein, we briefly introduce the topic of viruses as potential drivers of coral bleaching and disease.