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

Thermal stress modifies the marine sponge virome

Marine sponges can form stable partnerships with a wide diversity of microbes and viruses, and this high intraspecies symbiont specificity makes them ideal models for exploring how host-associated viromes respond to changing environmental conditions. Here we exposed the abundant Great Barrier Reef sponge Rhopaloeides odorabile to elevated seawater temperature for 48 h and utilised a metaviromic approach to assess the response of the associated viral community. An increase in endogenous retro-transcribing viruses within the Caulimorviridae and Retroviridae families was detected within the first 12 h of exposure to 32 °C, and a 30-fold increase in retro-transcribing viruses was evident after 48 h at 32 °C. Thermally stressed sponges also exhibited a complete loss of ssDNA viruses which were prevalent in field samples and sponges from the control temperature treatment. Despite these viromic changes, functional analysis failed to detect any loss or gain of auxiliary metabolic genes, indicating that viral communities are not providing a direct competitive advantage to their host under thermal stress. In contrast, endogenous sponge retro-transcribing viruses appear to be replicating under thermal stress, and consistent with retroviral infections in other organisms, may be contributing to the previously described rapid decline in host health evident at elevated temperature

Significant differences in physicochemical properties of human immunoglobulin kappa and lambda CDR3 regions

Antibody variable regions are composed of a heavy and a light chain and in humans there are two light chain isotypes: kappa and lambda. Despite their importance in receptor editing, the light chain is often overlooked in the antibody literature, with the focus being on the heavy chain CDR-H3 region. In this paper, we set out to investigate the physicochemical and structural differences between human kappa and lambda light chain CDR regions. We constructed a dataset containing over 29,000 - light chain variable region sequences from IgM-transcribing, newly formed B cells isolated from human bone marrow and peripheral blood. We also used a published human naïve dataset to investigate the CDR-H3 properties of heavy chains paired with kappa and lambda light chains, and probed the Protein Data Bank (PDB) to investigate the structural differences between kappa and lambda antibody CDR regions. We found that kappa and lambda light chains have very different CDR physicochemical and structural properties, whereas the heavy chains with which they are paired do not differ significantly. We also observed that the mean CDR3 N nucleotide addition in the kappa, lambda and heavy chain gene rearrangements are correlated within donors, but can differ between donors. This indicates that TdT may work with differing efficiencies between different people, but the same efficiency in the different classes of immunoglobulin chain within one person. We have observed large differences in the physicochemical and structural properties of kappa and lambda light chain CDR regions. This may reflect different roles in the humoral immune response

Gene correlation networks reveal the transcriptomic response to elevated nitrogen in a photosynthetic sponge

Nutrient levels in coastal environments have been increasing globally due to elevated inputs of sewage and terrigenous sediments carrying fertilizers. Yet, despite their immense filtering capacities, marine sponges appear to be less affected by elevated nutrients than sympatric benthic organisms, such as corals. While the molecular-level stress response of sponges to elevated seawater temperatures and other toxicants has been defined, this study represents the first global gene expression analysis of how sponges respond to elevated nitrogen. Gene correlation network analysis revealed that sponge gene modules, coded by colours, became either highly upregulated (Blue) or downregulated (Turquoise, Black, Brown) as nitrogen treatment levels increased. Gene Ontology enrichment analysis of the different modules revealed genes involved in cell signalling, immune response and flagella motility were affected by increasing nitrogen levels. Notably, a decrease in the regulation of NF-kappaB signalling and an increase in protein degradation was identified, which is comparable to metabolic pathways associated with the sponge thermal stress response. These results highlight that Cymbastela stipitata can rapidly respond to changes in the external environment and identifies pathways that probably contribute to the ability of C. stipitata to tolerate short-term nutrient pulses

Unraveling the microbial processes of black band disease in corals through integrated genomics

Coral disease outbreaks contribute to the ongoing degradation of reef ecosystems, however, microbial mechanisms underlying the onset and progression of most coral diseases are poorly understood. Black band disease (BBD) manifests as a cyanobacterial-dominated microbial mat that destroys coral tissues as it rapidly spreads over coral colonies. To elucidate BBD pathogenesis, we apply a comparative metagenomic and metatranscriptomic approach to identify taxonomic and functional changes within microbial lesions during in-situ development of BBD from a comparatively benign stage termed cyanobacterial patches. Results suggest that photosynthetic CO-fixation in Cyanobacteria substantially enhances productivity of organic matter within the lesion during disease development. Photosynthates appear to subsequently promote sulfide-production by Deltaproteobacteria, facilitating the major virulence factor of BBD. Interestingly, our metagenome-enabled transcriptomic analysis reveals that BBD-Associated cyanobacteria have a putative mechanism that enables them to adapt to higher levels of hydrogen sulfide within lesions, underpinning the pivotal roles of the dominant cyanobacterium within the polymicrobial lesions during the onset of BBD. The current study presents sequence-based evidence derived from whole microbial communities that unravel the mechanism of development and progression of BBD

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

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