Metagenomic analysis of viral communities in diseased Baikal sponge Lubomirskia baikalensis

Butina, Tatyana V.; Bukin, Yu. S.; Ханаев, И. В.; Кравцова, Л. С.; Maikova, O. O.; Tupikin, Alexey E.; Kabilov, Мarsel R.; Беликов, С. И.

doi:10.31951/2658-3518-2019-a-1-155

Cited by 12 publications

(14 citation statements)

References 42 publications

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“…using dsRNA and ssRNA-seq also revealed a diverse RNA viral population, with matches to Totiviridae, Reoviridae and Partitivirdae [32]. Viromic studies have also provided important insights into how the viral community changes in diseased or stressed sponges [33][34][35], with thermal stress leading to an enrichment of endogenous retro-transcribing viruses in Rhopaloeides odorabile [35] and dysbiosis in the virome occurring in diseased Lubomirskia baikalensis [34]. Putative AMGs have also been detected in the viromes of some reef sponges.…”

Section: Introductionmentioning

confidence: 99%

Viral ecogenomics across the Porifera

et al. 2020

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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.

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Section: Introductionmentioning

confidence: 99%

Viral ecogenomics across the Porifera

et al. 2020

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“…Myoviridae , Podoviridae and Siphoviridae ), but had considerable variability in the relative abundance of viruses targeting eukaryotic cells (such as Mimiviridae and Phycodnaviridae ). The role of viruses in host health and environmental stress responses has also been recently started to be explored and demonstrated shifts in viral community profiles ( Butina et al, 2019 ; Laffy et al, 2018 ). Furthermore evidence for genetic exchange through sponge-associated viruses has been given by the discovery of eukaryotic-like genes encoding for ankyrin proteins in bacteriophages that may provide infected bacterial hosts with an increased capacity to avoid eukaryotic phagocytosis ( Jahn et al, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Taxonomic, functional and expression analysis of viral communities associated with marine sponges

Nguyen

Wemheuer

Laffy

et al. 2021

PeerJ

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Viruses play an essential role in shaping the structure and function of ecological communities. Marine sponges have the capacity to filter large volumes of ‘virus-laden’ seawater through their bodies and host dense communities of microbial symbionts, which are likely accessible to viral infection. However, despite the potential of sponges and their symbionts to act as viral reservoirs, little is known about the sponge-associated virome. Here we address this knowledge gap by analysing metagenomic and (meta-) transcriptomic datasets from several sponge species to determine what viruses are present and elucidate their predicted and expressed functionality. Sponges were found to carry diverse, abundant and active bacteriophages as well as eukaryotic viruses belonging to the Megavirales and Phycodnaviridae. These viruses contain and express auxiliary metabolic genes (AMGs) for photosynthesis and vitamin synthesis as well as for the production of antimicrobials and the defence against toxins. These viral AMGs can therefore contribute to the metabolic capacities of their hosts and also potentially enhance the survival of infected cells. This suggest that viruses may play a key role in regulating the abundance and activities of members of the sponge holobiont.

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“…Meanwhile, in Lake Baikal, recent studies have described a phage putatively infecting Polynucleobacter sp. [5], the virome associated with diseased sponges [25], and viromes from the epipelagic zone which suggested that the Baikal virome undergoes changes in composition across seasons [26].…”

Section: Introductionmentioning

confidence: 99%

New viral biogeochemical roles revealed through metagenomic analysis of Lake Baikal

et al. 2020

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Background Lake Baikal is the largest body of liquid freshwater on Earth. Previous studies have described the microbial composition of this habitat, but the viral communities from this ecosystem have not been characterized in detail. Results Here, we describe the viral diversity of this habitat across depth and seasonal gradients. We discovered 19,475 bona fide viral sequences, which are derived from viruses predicted to infect abundant and ecologically important taxa that reside in Lake Baikal, such as Nitrospirota, Methylophilaceae, and Crenarchaeota. Diversity analysis revealed significant changes in viral community composition between epipelagic and bathypelagic zones. Analysis of the gene content of individual viral populations allowed us to describe one of the first bacteriophages that infect Nitrospirota, and their extensive repertoire of auxiliary metabolic genes that might enhance carbon fixation through the reductive TCA cycle. We also described bacteriophages of methylotrophic bacteria with the potential to enhance methanol oxidation and the S-adenosyl-L-methionine cycle. Conclusions These findings unraveled new ways by which viruses influence the carbon cycle in freshwater ecosystems, namely, by using auxiliary metabolic genes that act upon metabolisms of dark carbon fixation and methylotrophy. Therefore, our results shed light on the processes through which viruses can impact biogeochemical cycles of major ecological relevance.

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Metagenomic analysis of viral communities in diseased Baikal sponge Lubomirskia baikalensis

Cited by 12 publications

References 42 publications

Viral ecogenomics across the Porifera

Viral ecogenomics across the Porifera

Taxonomic, functional and expression analysis of viral communities associated with marine sponges

New viral biogeochemical roles revealed through metagenomic analysis of Lake Baikal

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