Viral ecogenomics across the Porifera

Abstract

Background: Viruses directly affect the most important biological processes in the ocean via their regulation of prokaryotic and eukaryotic populations. Marine sponges form stable symbiotic partnerships with a wide diversity of microorganisms and this high symbiont complexity makes them an ideal model for studying viral ecology. Here, we used morphological and molecular approaches to illuminate the diversity and function of viruses inhabiting nine sponge species from the Great Barrier Reef and seven from the Red Sea.

Results: Viromic sequencing revealed host-specific and site-specific patterns in the viral assemblages, with all sponge species dominated by the bacteriophage order Caudovirales but also containing variable representation from the nucleocytoplasmic large DNA virus families Mimiviridae, Marseilleviridae, Phycodnaviridae, Ascoviridae, Iridoviridae, Asfarviridae and Poxviridae. Whilst core viral functions related to replication, infection and structure were largely consistent across the sponge viromes, functional profiles varied significantly between species and sites largely due to differential representation of putative auxiliary metabolic genes (AMGs) and accessory genes, including those associated with herbicide resistance, heavy metal resistance and nylon degradation. Furthermore, putative AMGs varied with the composition and abundance of the sponge-associated microbiome. For instance, genes associated with antimicrobial activity were enriched in low microbial abundance sponges, genes associated with nitrogen metabolism were enriched in high microbial abundance sponges and genes related to cellulose biosynthesis were enriched in species that host photosynthetic symbionts.

Conclusions: Our results highlight the diverse functional roles that viruses can play in marine sponges and are consistent with our current understanding of sponge ecology. Differential representation of putative viral AMGs and accessory genes across sponge species illustrate the diverse suite of beneficial roles viruses can play in the functional ecology of these complex reef holobionts. Video Abstract.

Keywords: AMGs; Coral reef sponges; Functional diversity; Viral ecology; Viromics.

Fig. 1

Sponge species used for viromic analysis. GBR sponges: Callyspongia sp. (a), Echinochalina isaaci (b), Carteriospongia foliascens (c), Ianthella basta (d), Cinachyrella schulzei (e), Cymbastella marshae (f), Lamellodysidea herbacea (g), Pipestela candelabra (h), Sylissa carteri (i); and the Red Sea sponges: Amphimedon ochracea (j), Carteriospongia foliascens (k), Crella cyathophora (l), Hyrtios erectus (m), Mycale sp. (n), Niphates sp. (o), Xestospongia testudinaria (p). Scale bar = 10 cm

Fig. 2

Taxonomic summary of the viral communities associated with coral reef sponges. Column headings display nine sponge species from the Great Barrier Reef and seven from the Red Sea. The top 30 most frequent taxonomic assignments are summarised at the family level based on a normalised comparison (normalised gene count ~ 33,250 per dataset) of viral RefSeq gene assignments in MEGAN6 using parameters defined in Laffy et al. [30]. Abundance for each viral taxa was calculated using contig coverage estimates to identify proportional representation within each dataset. Only viral sequences that underwent taxonomic assignment and datapoints with abundance values of 10 or more were included within this plot. RNA viral taxonomic assignments were filtered from the final dataset

Fig. 3

Endogenous and exogenous determinants of taxonomically assigned viral community composition within marine sponges. Non-metric multidimensional scaling plot based on Bray-Curtis similarity of genus-level taxonomy for predicted genes. Ordination displays similarities in the viral communities of the fifteen sponge species (PERMANOVA, pseudo-F value = 3.9437, df = 14, P value ≤ 0.001) from the Great Barrier Reef and the Red Sea (PERMANOVA, pseudo-F value = 11.354, df = 1, P value ≤ 0.001) (a), and discriminates between species classified as high microbial abundance (HMA) or low microbial abundance (LMA) (PERMANOVA, pseudo-F value = 6.0159, df = 1, P value ≤ 0.001) and host nutritional modes, classified by the presence or absence of photosymbionts (PERMANOVA, pseudo-F value = 3.2176, df = 1, P value = 0.007) (b)

Fig. 4

Transmission electron micrographs depicting representative viral like particles (VLPs) associated with coral reef sponges. Representative tailed VLPs in Stylissa carteri (a, c) and Amphimedon ochracea (b); non-tailed icosahedral VLPs in Pipestela candelabra (d) and Cinachyrella schulzei (e); filamentous VLP from Cinachyrella schulzei (f); Geminate VLPs from Amphimedon ochracea (g); lemon-shaped VLP from Carteriospongia foliascens (h) and brick-shaped VLP from Crella cyathophora (i); using the TEM preparation methods: sponge sections (i) CsCl gradient separation (d, g) and from surface mucus (a-c, e-f, h). Scale bar = 100 nm. Arrow in Fig. 4a denotes the presence of a capsid tail structure

Fig. 5

The top 50 most abundant keywords across all virome datasets associated with coral reef sponges. Swiss-Prot keyword frequency was calculated for each virome by adjusting for contig coverage combined with the overall frequency of each keyword within the Swiss-Prot database and an e value cutoff of 1e⁻¹⁰. Only keywords with a frequency value greater than 2 are displayed within each dataset and keywords are presented sorted by viral functional gene categories, including viral infection, replication, structural formation and putative AMG manual classifications, further sorted by overall frequency values within each category

Fig. 6

Drivers of viral functional variation between sponge species. To identify key functional differences in viromes of each sponge species, the R package mvabund was used to perform univariate tests on Swiss-Prot keyword enrichment frequency values. Heatmap shows all significant differences in Swiss-Prot keyword enrichment frequency data (P value ≤ 0.02), adjusted to account for coverage of the source contig within individual viromes

Fig. 7

Drivers of viral functional variation between sampling sites. To identify key functional differences in sponge viromes between the Great Barrier Reef and Red Sea, the R package mvabund was used to perform univariate tests on Swiss-Prot keyword enrichment frequency values. Heatmap shows all significant differences in Swiss-Prot keyword enrichment frequency data (P value ≤ 0.02), adjusted to account for coverage of the source contig within individual viromes

Fig. 8

Comparison of viral function with sponge nutritional strategy, microbial abundance and geographic location. Comparison of viral functional profiles across 15 coral reef sponge species revealed that viral functions correlate with host nutritional strategy (photosymbionts vs no photosymbionts), microbial abundance (high microbial abundance—HMA, vs low microbial abundance—LMA) and geographic location (Fig. 3). Differential representation of putative AMGs and accessory genes across these ecological traits likely match host ecology. For instance, cellulose biosynthesis genes were enriched in phototrophic sponges, nitrogen metabolism genes were enriched in HMA sponges whilst antibiotic synthesis genes were enriched in LMA sponges. Additionally, heavy metal resistance genes were enriched in Red Sea sponges, whilst herbicide/insecticide resistance genes were enriched in GBR sponge viromes