Characterization of a sponge microbiome

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Like corals, sponges provide the physical space (a home) for animals to live within the reef and form symbiotic associations with many of them. This picture shows a longlure frogfish (Antennarius multiocellatus) mimicking the purple tube sponge Aplysina archeri to camouflage itself from its prey. Photo credit: Benjamin Mueller, University of Amsterdam


What is the first thing that comes to your mind if someone told you they study sponges? I hope you think of marine sponges, animals that live on beautiful coral reefs and filter litres of seawater a day to obtain their nutrients. Unfortunately, you will see question marks appear in most people’s eyes: Sponges? Like the ones you clean your bathroom with? Others will ask if you have seen SpongeBob SquarePants on any of your dives. Real sponges may not go on fun adventures, but they are still pretty amazing creatures.


Marine sponges are incredibly diverse, colourful, and essential for the existence of coral reefs. Often mistaken for corals, they can occupy up to 50% of the substrate on a reef. Sponges provide food and a place to live for many species (e.g. hiding frogfish, burrowing polychaetes, and adorable nudibranchs), and retain nutrients on coral reefs through the so-called “Sponge Loop” (1, 2). Coral reefs are some of the most productive ecosystems on earth, but are also referred to as marine deserts because nutrient levels in the water are quite low. Because of this, nutrient retention within the reef is critical. That is where marine sponges shine and the so-called “Sponge Loop” comes into play. The Sponge Loop starts with sponges filtering out large amounts of dissolved organic matter that was released into the seawater by organisms living on the reef, which is then converted into sponge biomass. Sponge cells are then released back into the water column (so called “sponge poop”) and eaten by other organisms (detritivores) to complete the loop and keep nutrients locked within the reef (2). Sponges may seem like they are not doing much, but they filter thousands of litres of seawater a day, keeping the recycling of nutrients going. See this video for a demonstration.




Sponges can occupy ~50% of the reef surface. They are often mistaken for corals and come in as many shapes and sizes. A) Ircinia ramosa and foliose (leaf-shaped) sponges on Trunk Reef, Great Barrier Reef. White arrows point towards sponges. B) A spotted moray (Gymnothorax moringa) hiding in the purple tube sponge Aplysina archeri on Bonaire. C-E) A collection of sponges found on Curaçao. Photo credits: A) Heidi Luter, Australian Institute of Marine Science, B-E) Benjamin Mueller, University of Amsterdam









Tropical reef sponges do not live on their own, as millions of microbes (bacteria and archaea) live inside them, collectively termed the sponge microbiome. These microbes can make up 35% of the sponge biomass and exceed 40,000 genetically distinct taxa (3, 4) that are thought to be critical for sponge health. For example, they are thought to provide the host (i.e. the sponge) with nutrients and vitamins, and remove waste products such as ammonia (5). However, these hypotheses are based on 16S rRNA amplicon sequencing, meaning that the microbes’ identities cannot be linked to their functions. Or in other words, we do not know who does what.

To better understand the functional potential of the sponge microbiome and therefore the ecology of sponges, we sequenced 259 microbial genomes from the sponge Ircinia ramosa, inferring their functional roles from their genes and linking them to specific taxonomic groups. Not only did we considerably expand the number and diversity of currently available sponge symbiont genomes, we also identified redundancy in critical functions as well as specific functions carried out by key microbial taxa. For example, the genes that encode multiple autotrophic carbon fixation pathways were spread across diverse microbial phyla. This could mean that multiple microbes are involved in transferring carbon to the sponge host. If so, it might also underlie the resilience of sponges to environmental disturbances (such as increasing seawater temperatures). Furthermore, the Nitrosopumilaceae (a family within the Archaea) were the only group capable of oxidizing ammonia, removing a toxic waste product produced by the sponge. Loss of the Nitrosopumilaceae could therefore have a significant negative effect on the health of the sponge. With this research we are now one step closer to understanding how sponges, critical members of coral reef ecosystems, function as a whole.


You can read more about the work here.

By the way: did you see the frogfish in the cover photo? Photo credit: Benjamin Mueller, University of Amsterdam.

The sponge Ircinia ramosa from John Brewer Reef in the Great Barrier Reef. Photo credit: Heidi Luter, Australian Institute of Marine Science.

References
1. Bell JJ. The functional roles of marine sponges. Estuar Coast Shelf Sci. 2008;79(3):341-53.
2. De Goeij JM, Van Oevelen D, Vermeij MJ, Osinga R, Middelburg JJ, de Goeij AF, et al. Surviving in a marine desert: the sponge loop retains resources within coral reefs. Science. 2013;342(6154):108-10.
3. Thomas T, Moitinho-Silva L, Lurgi M, Björk JR, Easson C, Astudillo-García C, et al. Diversity, structure and convergent evolution of the global sponge microbiome. Nat Commun. 2016;7:11870.
4. Webster NS, Thomas T. The sponge hologenome. MBio. 2016;7(7):e00135-16.
5. Pita L, Rix L, Slaby BM, Franke A, Hentschel U. The sponge holobiont in a changing ocean: from microbes to ecosystems. Microbiome. 2018;6(1):46.

Pamela Engelberts

PhD Student, Australian Centre for Ecogenomics

Pam Engelberts is currently a PhD student at the Australian Centre for Ecogenomics (ACE) at the University of Queensland studying the sponge microbiome.

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