Characterization of a sponge microbiome using an integrative genome-centric approach


Marine sponges often host diverse and species-specific communities of microorganisms that are critical for host health. Previous functional genomic investigations of the sponge microbiome have focused primarily on specific symbiont lineages, which frequently make up only a small fraction of the overall community. Here, we undertook genome-centric analysis of the symbiont community in the model species Ircinia ramosa and analyzed 259 unique, high-quality metagenome-assembled genomes (MAGs) that comprised 74% of the I. ramosa microbiome. Addition of these MAGs to genome trees containing all publicly available microbial sponge symbionts increased phylogenetic diversity by 32% within the archaea and 41% within the bacteria. Metabolic reconstruction of the MAGs showed extensive redundancy across taxa for pathways involved in carbon fixation, B-vitamin synthesis, taurine metabolism, sulfite oxidation, and most steps of nitrogen metabolism. Through the acquisition of all major taxa present within the I. ramosa microbiome, we were able to analyze the functional potential of a sponge-associated microbial community in unprecedented detail. Critical functions, such as carbon fixation, which had previously only been assigned to a restricted set of sponge-associated organisms, were actually spread across diverse symbiont taxa, whereas other essential pathways, such as ammonia oxidation, were confined to specific keystone taxa.

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Fig. 1: Combined archaeal and bacterial phylogenetic tree based on single copy marker proteins (inferred with GTDB).
Fig. 2: Metabolic reconstruction and proposed exchange of carbon, nitrogen, sulfur, and vitamins between Ircinia ramosa symbionts and the host.

Data availability

All data for this study can be found under the Bioproject ID PRJNA555144. The metagenomic reads for I. ramosa are available at NCBI under the accession numbers SRR9841427-SRR9841447 and the MAGs can be found under the accession numbers VXLI00000000-VYGU00000000, which are also shown in Table S1.

Change history

  • 05 February 2020

    The supplementary information files were initially linked incorrectly but have since been corrected. All files were available at publication.


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We acknowledge Andrea Severati and other staff at the Australian Institute of Marine Science SeaSim facility who assisted with sample collection and sponge husbandry.

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Correspondence to Nicole S. Webster.

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Engelberts, J.P., Robbins, S.J., de Goeij, J.M. et al. Characterization of a sponge microbiome using an integrative genome-centric approach. ISME J (2020).

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