Table 2.

Questions for future research.

• What are the mechanisms of nutritional and defensive mutualisms between holobiont members?

This is a fundamental question to understand the ecology and physiology of the holobiont. The answers may be of biomedical interest as novel antimicrobial compounds or mechanisms that disrupt pathogen colonization or virulence without bactericidal or bacteriostatic activity (e.g., Krediet et al., 2013) may be involved.

• What is the diversity of vertically-transmitted microorganisms in coral reproduction?

• Do these populations represent obligate or facultative mutualisms?

Novel cultivation-based approaches and genome sequencing or single-cell genomics to recover populations that resist cultivation are necessary. Such improvements will enable testing of hypotheses regarding coevolution and codiversification between corals and their microbiota.

• What is the role of Symbiodinium in shaping microbiota acquisition in gametes, larvae, and adult coral colonies?

• Do algae produce chemical signals that mediate allelopathic recognition or modulate colonization of the microbiota?

• How do chemical signals produced by CCA biofilms promote settlement and/or metamorphosis of coral larvae and how is receipt of these signals coordinated to optimize recruitment?

• What microbial taxa and activities are associated with coral cell-associated microbial aggregates (CAMAs) and what factors mediate their distribution in the coral polyp?

• Do the enclosed microorganisms interact with the coral tissue as mutualists, parasites, or commensals?

• Since several studies have documented lower levels of microbial colonization in Montipora spp. compared to other corals (Marquis et al., 2005; Work and Aeby, 2014), to what extent is antimicrobial activity specific to the coral species or their associated Symbiodinium?

• What role does the endolithic microbial community play in the homeostasis of the coral holobiont?

A potentially transformative avenue for inquiry is exploring the relationship between bacterial activity and skeleton formation in juvenile corals as recently suggested (Sharp et al., 2012).

• What are the molecular mechanisms of the host/holobiont stress response that allow proliferation of pathogen-like bacteria (e.g., Vibrio spp., Alteromonas spp.)?

Emerging coral holobiont transcriptomics studies will shed new light on how the coral holobiont responds to stresses and exists as a robust and resilient system when in a healthy state.