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

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Symbiotic Microbiomes of Coral Reefs Sponges and Corals

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.

“What am I living for and what am I dying for are the same question.”

– Margaret Atwood, The Year of the Flood

A man said to the universe:

“Sir, I exist!”

“However,” replied the universe,

“The fact has not created in me

A sense of obligation.”

– Stephen Crane, War Is Kind and Other Poems

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Acknowledgments

I thank Dr. Susan Sennett, FAU at Harbor Branch Oceanographic Institute, for the archived SEM micrographs. I also thank Dr. Peter Larsen for his PRMT analyses of preliminary RNA-seq data. Part of the preliminary data was also partly supported by a Year 1 BP Gulf of Mexico Research Initiative grant to JVL by the Florida Institute of Oceanography. I thank the following colleagues for feedback on early drafts of the manuscript: Dr. Omar Eldekar, Dr. Cole Easson, and Dr. Hidetoshi Urekawa. I am also grateful to Amy Doyle for final proofreading of the manuscript.

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  1. Halmos College of Natural Sciences and Oceanography, Guy Harvey Oceanographic Center, Nova Southeastern University, Dania Beach, FL, USA

    Jose V. Lopez

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  1. Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China

    Zhiyong Li

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Lopez, J.V. (2019). After the Taxonomic Identification Phase: Addressing the Functions of Symbiotic Communities Within Marine Invertebrates. In: Li, Z. (eds) Symbiotic Microbiomes of Coral Reefs Sponges and Corals. Springer, Dordrecht. https://doi.org/10.1007/978-94-024-1612-1_8

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