Low Abundance Taxa Show Diverse Microbial Symbiotic Interactions With the Freshwater Sponge, Radiospongilla crateriformis , Pre and Post Gemmulation

Freshwater sponges, most of which have a dormant stage with gemmules, are well poised for microbiome focused experiments. Here, we leveraged field collections of freshwater sponges pre‐gemmule (Pre) and post‐gemmule (Post) formation to compare the microbial symbiont metatranscriptome at the two developmental stages. There were no broad changes to the microbiome in composition between the two stages; however, there were significant differences in the abundance of several bacterial taxa and functional genes between Pre and Post sponge samples. For example, many Polynucleobacter spp. increased from Pre to Post samples, but no putative symbiosis factors were associated with Polynucleobacter and these may be loosely associated with the sponges. In contrast, we hypothesise that Flavobacterium spp. are facultative symbionts of freshwater sponges that begin to leave when the sponge tissue degrades, or they may decrease their metabolic activity. Functions attributed to Flavobacterium spp. such as type IX secretion system (T9SS) component and ankyrin repeat domains, all decreased in the Post samples and suggests that this group can interact with the sponge host or be free‐living. These results provide a foundation for future hypothesis testing and experimental work with the microbiomes of freshwater sponges.