Coral reefs provide habitats for a disproportionate number of marine species relative to the small area of the oceans that they occupy. The mutualism between the cnidarian animal hosts and their intracellular dinoflagellate symbionts provides the nutritional foundation for coral growth and formation of reef structures, because algal photosynthesis can provide >90% of the total energy of the host. Disruption of this symbiosis (“coral bleaching”) is occurring on a large scale due primarily to anthropogenic factors and poses a major threat to the future of coral reefs. Despite the importance of this symbiosis, the cellular mechanisms involved in its establishment, maintenance, and breakdown remain largely unknown. We report our continued development of genomic tools to study these mechanisms in Aiptasia, a small sea anemone with great promise as a model system for studies of cnidarian–dinoflagellate symbiosis. Specifically, we have generated de novo assemblies of the transcriptomes of both a clonal line of symbiotic anemones and their endogenous dinoflagellate symbionts. We then compared transcript abundances in animals with and without dinoflagellates. This analysis identified >900 differentially expressed genes and allowed us to generate testable hypotheses about the cellular functions affected by symbiosis establishment. The differentially regulated transcripts include >60 encoding proteins that may play roles in transporting various nutrients between the symbiotic partners; many more encoding proteins functioning in several metabolic pathways, providing clues regarding how the transported nutrients may be used by the partners; and several encoding proteins that may be involved in host recognition and tolerance of the dinoflagellate.

The importance of associations between microorganisms and their invertebrate hosts is becoming increasingly apparent. An emerging field, driven by the necessity to understand the microbial relationships that both maximize coral health and cause coral disease, is the study of coral-bacteria interactions. In this article, we review our current understanding of the diversity, specificity, development, and functions of coral-associated bacteria. We also summarize what is known regarding the role of coral microbiota in the health and disease of coral. We conduct a meta-analysis to determine whether the presence of unique taxa correlates with the state of coral health (i.e. healthy, diseased or bleached), as well as whether coral reef habitats harbor clusters of distinct taxa. We find that healthy and bleached corals harbor similar dominant taxa, although bleached corals had higher proportions of Vibrio and Acidobacteria. Diseased corals generally had more Rhodobacter, Clostridia, and Cyanobacteria sequences, and fewer Oceanospirillum sequences. We caution, however, that while 16S rRNA is useful for microbial species identification, it is a poor predictor of habitat or lifestyle, and care should be taken in interpretation of 16S rRNA surveys to identify potential pathogens amongst complex coral-microbial assemblages. Finally, we highlight evidence that coral-bacterial assemblages could be sensitive to the effects of climatic change. We suggest that the relationship between coral and their bacterial associates represents a valuable model that can be applied to the broader discipline of invertebrate-microbial interactions.

Coral reef communities are undergoing marked declines due to a variety of stressors including disease. The sea fan coral, Gorgonia ventalina, is a tractable study system to investigate mechanisms of immunity to a naturally occurring pathogen. Functional studies in Gorgonia ventalina immunity indicate that several key pathways and cellular components are involved in response to natural microbial invaders, although to date the functional and regulatory pathways remain largely un-described. This study used short-read sequencing (Illumina GAIIx) to identify genes involved in the response of G. ventalina to a naturally occurring Aplanochytrium spp. parasite. De novo assembly of the G. ventalina transcriptome yielded 90,230 contigs of which 40,142 were annotated. RNA-Seq analysis revealed 210 differentially expressed genes in sea fans exposed to the Aplanochytrium parasite. Differentially expressed genes involved in immunity include pattern recognition molecules, anti-microbial peptides, and genes involved in wound repair and reactive oxygen species formation. Gene enrichment analysis indicated eight biological processes were enriched representing 36 genes, largely involved with protein translation and energy production. This is the first report using high-throughput sequencing to characterize the host response of a coral to a natural pathogen. Furthermore, we have generated the first transcriptome for a soft (octocoral or non-scleractinian) coral species. Expression analysis revealed genes important in invertebrate innate immune pathways, as well as those whose role is previously un-described in cnidarians. This resource will be valuable in characterizing G. ventalina immune response to infection and co-infection of pathogens in the context of environmental change.

Consumer stress models of ecological theory predict that predators are more susceptible to stress than their prey. Intertidal mussels, Mytilus californianus, span a vertical stress gradient from the low zone (lower stress) to the high zone (higher thermal and desiccation stress), while their sea star predators, Pisaster ochraceus, range from the low zone only into the lower edge of the mussel zone. In summer 2003, we tested the responses of sea stars and mussels to environmental stress in an experiment conducted on the Oregon coast. Mussels were transplanted from the middle of the mussel bed to cages in the low and high edges of the mussel bed. Sea star predators were added to half of the mussel cages. Mussels and sea stars were sampled between June and August for indicators of sublethal stress. Mussel growth was measured, and tissues were collected for heat shock protein (Hsp70) analyses and histological analyses of reproduction. Sea stars were weighed, and tissues were sampled for Hsp70 analyses. Mussels in high-edge cages had higher levels of total Hsp70 and exhibited spawning activity earlier in the summer than mussels in the low-edge cages. Sea stars suffered high mortality in the high edge, and low-edge sea stars lost weight but showed no differences in Hsp70 production. These results suggest that stress in the intertidal zone affected the mobile predator more than its sessile prey, which is consistent with predictions of consumer stress models.

The diversity and function of viruses in coral holobionts has only recently received attention. The nonreef building gorgonian octocoral, Gorgonia ventalina, is a major constituent of Caribbean reefs. We investigated viral communities associated with G. ventalina tissues to understand their role in gorgonian ecology. Pyrosequencing was used to prepare a total of 514,632 sequence reads of DNA-and RNA-based mixed-community viral genomes (metaviromes). RNA viral assemblages were comprised of primarily unidentifiable reads, with most matching host transcripts and other RNA metaviromes. DNA metaviromes were similar between healthy and diseased tissues and comprised of contiguous sequences (contigs) that matched primarily metazoan and bacterial proteins. Only *5% of contigs matched viral proteins that were primarily cyanophage and viruses of Chlorella and Ostreococcus. Our results confirm that DNA and RNA viruses comprise a component of the gorgonian holobiont, suggesting that they may play a role in the ecology of G. ventalina.