Expansion of known ssRNA phage genomes: From tens to over a thousand

Callanan, Julie; Stockdale, Stephen R.; Shkoporov, Andrey N.; Draper, Lorraine A.; Ross, R. Paul; Hill, Colin

doi:10.1126/sciadv.aay5981

Cited by 135 publications

(164 citation statements)

References 71 publications

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“…This hints to different factors shaping the mat layers microbial composition, such as bacterial predation by nematodes [122] or seasonal variation in bacterial/archaeal metabolism [123]. While our work shed light on diversity of dsDNA and ssDNA viruses in microbial mats, further work might involve investigation of ssRNA viruses, as these have been found in abundance in other environments [124,125] and could play a role in biofilm formation [54]. We believe that our observations can be expanded to other natural biofilms and contribute to the development of novel microbial dynamics prediction models for biofilms.…”

Section: Discussionmentioning

confidence: 79%

Insights into the dynamics between viruses and their hosts in a hot spring microbial mat

et al. 2020

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Our current knowledge of host–virus interactions in biofilms is limited to computational predictions based on laboratory experiments with a small number of cultured bacteria. However, natural biofilms are diverse and chiefly composed of uncultured bacteria and archaea with no viral infection patterns and lifestyle predictions described to date. Herein, we predict the first DNA sequence-based host–virus interactions in a natural biofilm. Using single-cell genomics and metagenomics applied to a hot spring mat of the Cone Pool in Mono County, California, we provide insights into virus–host range, lifestyle and distribution across different mat layers. Thirty-four out of 130 single cells contained at least one viral contig (26%), which, together with the metagenome-assembled genomes, resulted in detection of 59 viruses linked to 34 host species. Analysis of single-cell amplification kinetics revealed a lack of active viral replication on the single-cell level. These findings were further supported by mapping metagenomic reads from different mat layers to the obtained host–virus pairs, which indicated a low copy number of viral genomes compared to their hosts. Lastly, the metagenomic data revealed high layer specificity of viruses, suggesting limited diffusion to other mat layers. Taken together, these observations indicate that in low mobility environments with high microbial abundance, lysogeny is the predominant viral lifestyle, in line with the previously proposed “Piggyback-the-Winner” theory.

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Section: Discussionmentioning

confidence: 79%

Insights into the dynamics between viruses and their hosts in a hot spring microbial mat

et al. 2020

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“…Environmental studies have indicated that the family Microviridae contains at least five unclassified subfamilies [40][41][42][43][44][45][46][47]. Recently, Callanan et al [48] predicted 331 species and 247 genera among the single-stranded RNA phages, potentially leading to a significant expansion of the family Leviviridae.…”

Section: Future Directionsmentioning

confidence: 99%

Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

et al. 2020

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“…The high diversity of the invertebrate RNA virome suggests that RNA viruses of land plants and vertebrates evolved from viruses infecting invertebrates 2 . The known RNA viromes of plants, fungi, protists and bacteria have also expanded through meta-transcriptome sequencing, albeit not as massively as the invertebrate virome 19,[34][35][36][37][38][39][40][41] .…”

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confidence: 99%

Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome

et al. 2020

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RNA viruses in aquatic environments remain poorly studied. Here, we analysed the RNA virome from approximately 10 l water from Yangshan Deep-Water Harbour near the Yangtze River estuary in China and identified more than 4,500 distinct RNA viruses, doubling the previously known set of viruses. Phylogenomic analysis identified several major lineages, roughly, at the taxonomic ranks of class, order and family. The 719-member-strong Yangshan virus assemblage is the sister clade to the expansive class Alsuviricetes and consists of viruses with simple genomes that typically encode only RNA-dependent RNA polymerase (RdRP), capping enzyme and capsid protein. Several clades within the Yangshan assemblage independently evolved domain permutation in the RdRP. Another previously unknown clade shares ancestry with Potyviridae, the largest known plant virus family. The ‘Aquatic picorna-like viruses/Marnaviridae’ clade was greatly expanded, with more than 800 added viruses. Several RdRP-linked protein domains not previously detected in any RNA viruses were identified, such as the small ubiquitin-like modifier (SUMO) domain, phospholipase A2 and PrsW-family protease domain. Multiple viruses utilize alternative genetic codes implying protist (especially ciliate) hosts. The results reveal a vast RNA virome that includes many previously unknown groups. However, phylogenetic analysis of the RdRPs supports the previously established five-branch structure of the RNA virus evolutionary tree, with no additional phyla.

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Expansion of known ssRNA phage genomes: From tens to over a thousand

Cited by 135 publications

References 71 publications

Insights into the dynamics between viruses and their hosts in a hot spring microbial mat

Insights into the dynamics between viruses and their hosts in a hot spring microbial mat

Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome

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