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.
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.
A chosen few, common species are globally widespread. On the other hand, rare bacterial species display high sensitivity to environmental conditions at low relative abundances. Predictable shifts in soil bacterial rarity occur across biomes primarily driven by soil hydration conditions.
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