Viral ecogenomics across the Porifera

BackgroundViruses 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.ResultsViromic 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.ConclusionsOur 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

Metabolic reconstruction of the near complete microbiome of the model sponge Ianthella basta

Many marine sponges host highly diverse microbiomes that contribute to various aspects of host health. Although the putative function of individual groups of sponge symbionts has been increasingly described, the extreme diversity has generally precluded in-depth characterization of entire microbiomes, including identification of syntrophic partnerships. The Indo-Pacific sponge Ianthella basta is emerging as a model organism for symbiosis research, hosting only three dominant symbionts: a Thaumarchaeotum, a Gammaproteobacterium, and an Alphaproteobacterium and a range of other low abundance or transitory taxa. Here, we retrieved metagenome assembled genomes (MAGs) representing &gt;90% of I. basta's microbial community, facilitating the metabolic reconstruction of the sponge's near complete microbiome. Through this analysis, we identified metabolic complementarity between microbes, including vitamin sharing, described the importance of low abundance symbionts, and characterized a novel microbe–host attachment mechanism in the Alphaproteobacterium. We further identified putative viral sequences, highlighting the role viruses can play in maintaining symbioses in I. basta through the horizontal transfer of eukaryotic-like proteins, and complemented this data with metaproteomics to identify active metabolic pathways in bacteria, archaea, and viruses. This data provide the framework to adopt I. basta as a model organism for studying host–microbe interactions and provide a basis for in-depth physiological experiments.</p

Cross‐generational effects of climate change on the microbiome of a photosynthetic sponge

Coral reefs are facing increasing pressure from rising seawater temperatures and ocean acidification. Sponges have been proposed as possible winners in the face of climate change, however little is known about the mechanisms underpinning their predicted tolerance. Here we assessed whether microbiome mediated cross‐generational acclimatisation could enable the photosynthetic sponge\ua0Carteriospongia foliascens\ua0to survive under future climate scenarios. To achieve this, we first established the potential for vertical (cross‐generational) transmission of symbionts. Sixty‐four amplicon sequence variants accounting for >90% of the total\ua0C. foliascens\ua0microbial community were present across adult, larval and juvenile life stages, showing that a large proportion of the microbiome is vertically acquired and maintained. When\ua0C. foliascens\ua0were exposed to climate scenarios projected for 2050 and 2100, the host remained visibly unaffected (i.e. no necrosis/bleaching) and the overall microbiome was not significantly different among treatments in adult tissue, the respective larvae or recruits transplanted amongst climate treatments. However, indicator species analysis revealed that parental exposure to future climate scenarios altered the presence and abundance of a small suite of microbial taxa in the recruits, thereby revealing the potential for microbiome mediated cross‐generational acclimatisation through both symbiont shuffling and symbiont switching within a vertically acquired microbiome

A genomic view of the microbiome of coral reef demosponges

Sponges underpin the productivity of coral reefs, yet few of their microbial symbionts have been functionally characterised. Here we present an analysis of ~1200 metagenome-assembled genomes (MAGs) spanning seven sponge species and 25 microbial phyla. Compared to MAGs derived from reef seawater, sponge-associated MAGs were enriched in glycosyl hydrolases targeting components of sponge tissue, coral mucus and macroalgae, revealing a critical role for sponge symbionts in cycling reef organic matter. Further, visualisation of the distribution of these genes amongst symbiont taxa uncovered functional guilds for reef organic matter degradation. Genes for the utilisation of sialic acids and glycosaminoglycans present in sponge tissue were found in specific microbial lineages that also encoded genes for attachment to sponge-derived fibronectins and cadherins, suggesting these lineages can utilise specific structural elements of sponge tissue. Further, genes encoding CRISPR and restriction-modification systems used in defence against mobile genetic elements were enriched in sponge symbionts, along with eukaryote-like gene motifs thought to be involved in maintaining host association. Finally, we provide evidence that many of these sponge-enriched genes are laterally transferred between microbial taxa, suggesting they confer a selective advantage within the sponge niche and therefore play a critical role in host ecology and evolution

Coral-associated viral communities show high levels of diversity and host auxiliary functions

Stony corals (Scleractinia) are marine invertebrates that form the foundation and framework upon which tropical reefs are built. The coral animal associates with a diverse microbiome comprised of dinoflagellate algae and other protists, bacteria, archaea, fungi and viruses. Using a metagenomics approach, we analysed the DNA and RNA viral assemblages of seven coral species from the central Great Barrier Reef (GBR), demonstrating that tailed bacteriophages of the Caudovirales dominate across all species examined, and ssDNA viruses, notably the Microviridae, are also prevalent. Most sequences with matches to eukaryotic viruses were assigned to six viral families, including four Nucleocytoplasmic Large DNA Viruses (NCLDVs) families: Iridoviridae, Phycodnaviridae, Mimiviridae, and Poxviridae, as well as Retroviridae and Polydnaviridae. Contrary to previous findings, Herpesvirales were rare in these GBR corals. Sequences of a ssRNA virus with similarities to the dinornavirus, Heterocapsa circularisquama ssRNA virus of the Alvernaviridae that infects free-living dinoflagellates, were observed in three coral species. We also detected viruses previously undescribed from the coral holobiont, including a virus that targets fungi associated with the coral species Acropora tenuis. Functional analysis of the assembled contigs indicated a high prevalence of latency-associated genes in the coral-associated viral assemblages, several host-derived auxiliary metabolic genes (AMGs) for photosynthesis (psbA, psbD genes encoding the photosystem II D1 and D2 proteins respectively), as well as potential nematocyst toxins and antioxidants (genes encoding green fluorescent-like chromoprotein). This study expands the currently limited knowledge on coral-associated viruses by characterising viral composition and function across seven GBR coral species

HoloVir: a workflow for investigating the diversity and function of viruses in invertebrate holobionts

Abundant bioinformatics resources are available for the study of complex microbial metagenomes, however their utility in viral metagenomics is limited. HoloVir is a robust and flexible data analysis pipeline that provides an optimized and validated workflow for taxonomic and functional characterization of viral metagenomes derived from invertebrate holobionts. Simulated viral metagenomes comprising varying levels of viral diversity and abundance were used to determine the optimal assembly and gene prediction strategy, and multiple sequence assembly methods and gene prediction tools were tested in order to optimize our analysis workflow. HoloVir performs pairwise comparisons of single read and predicted gene datasets against the viral RefSeq database to assign taxonomy and additional comparison to phage-specific and cellular markers is undertaken to support the taxonomic assignments and identify potential cellular contamination. Broad functional classification of the predicted genes is provided by assignment of COG microbial functional category classifications using EggNOG and higher resolution functional analysis is achieved by searching for enrichment of specific Swiss-Prot keywords within the viral metagenome. Application of HoloVir to viral metagenomes from the coral Pocillopora damicornis and the sponge Rhopaloeides odorabile demonstrated that HoloVir provides a valuable tool to characterize holobiont viral communities across species, environments, or experiments

[PP. 27.24] DIAGNOSTIC ACCURACY AND DIAGNOSTIC GAIN OF CRITERIA TO INTERPRET UNILATERALLY SELECTIVE ADRENAL VEIN SAMPLING (AVS) RESULTS

Objective: 10–20% of AVS performed in Excellence centers for primary aldosteronism (PA) are not bilaterally selective. The ratio of cortisol-corrected aldosterone concentration between adrenal vein and inferior vena cava (unilateral ratio, UR) has been proposed to interpret unilaterally selective AVS [1]:UR&lt;0.5could suggest unilateral PA on the opposite side; UR &gt;5.5 could suggest unilateral PA on the same side, and UR 0.5–5.5 would be inconclusive. Design and method: This retrospective study evaluates the diagnostic value of the UR on AVS data collected over10 years in a referral centre. French AVS-consensus criteria (selectivity index &gt;2, lateralisation ratio &gt;4) were used for AVS interpretation. We first assessed the numbers of cases with left and right UR both &lt;0.5 or both &gt;5.5, because in these cases the interpretation of unilaterally selective AVS will depend only on the side of successful adrenal vein cannulation, not on the side of the disease. We then assessed the sensitivity, specificity and PPV of these criteria for the diagnosis of unilateral PA. Cases with left and right UR both &lt;0.5 or both &gt;5.5 were counted as false positives for these calculations. We finally assessed the diagnostic impact of using the unilateral criteria in case of unilaterally selective AVS. Results: -537AVS were performed from 2001–2010, 64(12%) were not bilaterally selective using the reference criteria (28unilaterally selective and 36 bilaterally non-selective), 287 (53%) were diagnostic of bilateral PA, 99 (18%) of left PA and 87 (16%) of right PA [Table 1]. -Among 473 bilaterally selective AVS, 7 (1.5%) had left and right UR both &lt;0.5 and 32 (7%) had left and right UR both &gt;5.5 [Table 2]. -Sensitivity of UR &lt;0.5 to detect unilateral PA was 55%, specificity 91%, PPV79%. -Sensitivity of UR &gt;5.5 was 51%, specificity71%, PPV53% [Table3]. -Using these criteria to interpret 28 unilaterally selective AVS led to diagnose 2right PA but 0left PA with a contralateral UR &lt;0.5, 10 right PA and 6left PA with an ipsilateral UR &gt;5.5, the remaining 10 cases staying inconclusive. However, among the 16 unilateral PA diagnosed with an ipsilateral UR &gt;5.5, we must expect 8 false positives

Prevalent and persistent viral infection in cultures of the coral algal endosymbiont Symbiodinium

Reef corals are under threat from bleaching and disease outbreaks that target both the host animal and the algal symbionts within the coral holobiont. A viral origin for coral bleaching has been hypothesized, but direct evidence has remained elusive. Using a multifaceted approach incorporating flow cytometry, transmission electron microscopy, DNA and RNA virome sequencing, we show that type C1 Symbiodinium cultures host a nucleocytoplasmic large double-stranded DNA virus (NCLDV) related to Phycodnaviridae and Mimiviridae, a novel filamentous virus of unknown phylogenetic affiliation, and a single-stranded RNA virus related to retroviruses. We discuss implications of these findings for laboratory-based experiments using Symbiodinium cultures

Visual tools for developing student capacity for cross-disciplinary collaboration, innovation and entrepreneurship

This volume identifies and documents pedagogical and practice-based visual approaches to scaffolding and developing capacity for cross-disciplinary collaboration, innovation and entrepreneurship