After the Taxonomic Identification Phase: Addressing the Functions of Symbiotic Communities Within Marine Invertebrates

Abstract

Characterizations of the identity and diversity of microbial symbiotic communities (“microbiomes”) within different sponges have advanced considerably over the last two decades. Thousands of microbes, mostly unculturable, operational taxonomic units (OTUs) have been identified through the advances of high-throughput DNA sequencing. However, in spite of compelling data pointing to bona fide symbioses between many microbes and the sponge host, determination of specific microbial symbiont functions remains difficult to pinpoint and equivocal in many cases. In this chapter, I highlight past and present approaches toward addressing the potential functions of microbial symbionts (mostly bacterial) found in marine sponges and invertebrates. In an interesting irony, one barrier to effective definition of some symbiont microbial functions stems from their obligate dependence on their host. Investigations suggest that microbes significantly contribute to fundamental processes such as elemental cycling, anabolism, and catabolism. An additional likely role for symbionts is the biosynthesis of unique secondary metabolites (SMs) and vitamins, exhibited in many sponge species. These can be used as defensive or communication factors increasing fitness and thus benefiting the holobiont, which appears more and more reminiscent of a vibrant community than the traditional notion of an individual sponge. One approach to circumvent the dearth of empirical evidence on specific symbiont functions is to apply modern -omics methods: for example, sequencing the entire sponge holobiont (host and microbiome) as a metagenome and metatranscriptome can reveal potential functional genetic information. Together with computational tools, one can infer function from biological sequence data, although rigorous experimentation is still needed for verifications. Newer combinations of older, sophisticated technologies such as fluorescence in situ hybridization-correlative light and electron microscopy (FISH-CLEM), stable isotope tracking, and nanoscale secondary ion mass spectrometry (NanoSIMS) now promise to reveal more potential symbiont functions. Metaproteomics will also help further advance the understanding of the relationships within the holobiont community, but its wide applicability still remains mostly on the horizon. Other pervasive questions on the origins, coevolution, and fitness of specific symbiont-host partners include relevant microbiome functions within their orbit.