Microbiome of the freshwater sponge Ephydatia muelleri shares compositional and functional similarities with those of marine sponges

Abstract

Sponges are known for hosting diverse communities of microbial symbionts, but despite persistent interest in the sponge microbiome, most research has targeted marine sponges; freshwater sponges have been the focus of less than a dozen studies. Here, we used 16 S rRNA gene amplicon sequencing and shotgun metagenomics to characterize the microbiome of the freshwater sponge Ephydatia muelleri and identify potential indicators of sponge-microbe mutualism. Using samples collected from the Sooke, Nanaimo, and Cowichan Rivers on Vancouver Island, British Columbia, we show that the E. muelleri microbiome is distinct from the ambient water and adjacent biofilms and is dominated by Sediminibacterium, Comamonas, and unclassified Rhodospirillales. We also observed phylotype-level differences in sponge microbiome taxonomic composition among different rivers. These differences were not reflected in the ambient water, suggesting that other environmental or host-specific factors may drive the observed geographic variation. Shotgun metagenomes and metagenome-assembled genomes further revealed that freshwater sponge-associated bacteria share many genomic similarities with marine sponge microbiota, including an abundance of defense-related proteins (CRISPR, restriction-modification systems, and transposases) and genes for vitamin B12 production. Overall, our results provide foundational information on the composition and function of freshwater sponge-associated microbes, which represent an important yet underappreciated component of the global sponge microbiome.

Dynamics, diversity, and roles of bacterial transmission modes during the first asexual life stages of the freshwater sponge Spongilla lacustris

“…In terms of composition, t 2 to t 4 samples are highlighted by a high abundance of Gammaproteobacteria, with three dominant families: Comamonadaceae, Alteromonadaceae and Pseudomonadaceae. These families are commonly occurring in freshwater sponges [21,31,60] and might be related to chemical defenses [61]. For example, Comamonadaceae were associated with defense mechanisms such as CRISPR and intracellular tra cking within E. muelleri [31], while diverse PKS genes were found within Pseudomonadaceae and Alteromonadaceae (dominant genus: Rheinheimera) associated with the freshwater sponges Rezinkovia echinata (Lake Baikal) and E. uviatilis (Vinkeveense Plassen, the Netherlands), respectively [62,63].…”

“…These families are commonly occurring in freshwater sponges [21,31,60] and might be related to chemical defenses [61]. For example, Comamonadaceae were associated with defense mechanisms such as CRISPR and intracellular tra cking within E. muelleri [31], while diverse PKS genes were found within Pseudomonadaceae and Alteromonadaceae (dominant genus: Rheinheimera) associated with the freshwater sponges Rezinkovia echinata (Lake Baikal) and E. uviatilis (Vinkeveense Plassen, the Netherlands), respectively [62,63]. This speci c bacterial community acquired during the formation of the aquiferous system and the rst lter-feeding activity steps could be linked to the early development of bacterial symbionts acting for the chemical defense of the sponge.…”

“…We hypothesize that the mixed mode transmission occurs, with both VT and HT. First, the VT would be achieved through the transmission of maternal bacteria within the gemmule, but also on its surface, as suggested by Sugden et al [31]. Once the gemmule has hatched and the ltration system is formed, the HT of planktonic bacteria could then constitute an additional factor shaping the S. lacustris microbiome.…”

“…from freshwater or sediment, [21]). Sugden et al showed that bacterial communities of E. muelleri are mainly distinct from those from the surrounding freshwater and bio lms [31]. Geographical differences were also observed between rivers, suggesting that the environment could also shape the host-microbe speci city.…”

Freshwater Sponges as a Neglected Reservoir of Bacterial Biodiversity

“…Sugden et al [2] reported for the first time the comparison between spongeassociated communities and the surrounding environments (e.g., water and biofilm). This latter aspect is of major importance to establish if discrepancies between prokaryotic communities in sponges and water can match the differences that may be observed between benthic and planktonic communities rather than the functional significance of host-microbe specificity [2]. The sponge immune system constitutes a first line of defense against transient microbiota, including the production of biomolecules that recognize conserved microbial structures [24].…”