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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.

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Fig. 1: Locations for sampling the freshwater sponge Ephydatia muelleri.
Fig. 2: Alpha and beta diversity across sponges, water, and biofilms.
Fig. 3: ASV abundance correlations between sponges and water or biofilms.
Fig. 4: Microbial composition of sponge, water, and biofilm samples.
Fig. 5: COGs that were differentially abundant between sponge and water samples.
Fig. 6: Genomic composition of metagenome-assembled genomes.

Data availability

The raw 16 S rRNA gene amplicon sequences, the shotgun metagenome sequences, and the assembled MAG sequences obtained in this study have been deposited as a single project in the NCBI Sequence Read Archive under the accession number PRJNA526747. The assembled E. muelleri mitochondrial genome has been deposited to GenBank under the accession number ON734426. The R codes and workspace required to reproduce all analyses are available from https://github.com/sasugden/Freshwater_sponge_microbiome.

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Acknowledgements

SS would like to thank Sally Leys (Department of Biological Sciences, University of Alberta) for instruction in how to sample and fix sponges and Arlene Oatway (Department of Biological Sciences, University of Alberta) for assistance with microscopy. This work was supported by the BMBF-funded de.NBI Cloud within the German Network for Bioinformatics Infrastructure (de.NBI) (031A532B, 031A533A, 031A533B, 031A534A, 031A535A, 031A537A, 031A537B, 031A537C, 031A537D, 031A538A).

Funding

This study was funded by two Discovery Grants from the Natural Sciences and Engineering Research Council (NSERC) of Canada awarded to LYS and WWM. The funders had no role in study design, data collection, or analysis, or in submission of the work for publication.

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SS and LYS conceived the project idea and designed the study. SS and JH collected the samples. SS processed the 16 S rRNA sequencing data, performed statistical analysis of the metagenome data, and wrote the manuscript. JH performed the bioinformatic analysis of the assembled metagenome data, assembled and characterized the MAGs, assisted with writing, and edited the manuscript. EC performed the bioinformatic analysis of the raw metagenome sequencing data. WWM and LYS funded and supervised the work and edited the manuscript. All authors read and approved the final manuscript.

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Correspondence to Scott Sugden.

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Sugden, S., Holert, J., Cardenas, E. et al. Microbiome of the freshwater sponge Ephydatia muelleri shares compositional and functional similarities with those of marine sponges. ISME J (2022). https://doi.org/10.1038/s41396-022-01296-7

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