Diversity and comparative genomics of Microviridae in Sphagnum- dominated peatlands

Abstract

Microviridae, a family of bacteria-infecting ssDNA viruses, is one of the still poorly characterized bacteriophage groups, even though it includes phage PhiX174, one of the main models in virology for genomic and capsid structure studies. Recent studies suggest that they are diverse and well represented in marine and freshwater virioplankton as well as in human microbiomes. However, their diversity, abundance, and ecological role are completely unknown in soil ecosystems. Here we present the comparative analysis of 17 completely assembled Microviridae genomes from 12 viromes of a Sphagnum-dominated peatland. Phylogenetic analysis of the conserved major capsid protein sequences revealed the affiliation to Gokushovirinae and Pichovirinae as well as to two newly defined subfamilies, the Aravirinae and Stokavirinae. Additionally, two new distinct prophages were identified in the genomes of Parabacteroides merdae and Parabacteroides distasonis representing a potential new subfamily of Microviridae. The differentiation of the subfamilies was confirmed by gene order and similarity analysis. Relative abundance analysis using the affiliation of the major capsid protein (VP1) revealed that Gokushovirinae, followed by Aravirinae, are the most abundant Microviridae in 11 out of 12 peat viromes. Sequences matching the Gokushovirinae and Aravirinae VP1 matching sequences, respectively, accounted for up to 4.19 and 0.65% of the total number of sequences in the corresponding virome, respectively. In this study we provide new genome information of Microviridae and pave the way toward quantitative estimations of Microviridae subfamilies.

Towards quantitative viromics for both double-stranded and single-stranded DNA viruses

“…The description of a large unsuspected genetic diversity of ssDNA viruses across multiple ecosystems (Ge et al, 2011; Kim et al, 2011; Rosario, Duffy & Breitbart, 2012; Labonté & Suttle, 2013b; Eaglesham & Hewson, 2013; Quaiser et al, 2015; Dayaram et al, 2016), and unique evolutionary patterns including gene exchanges between RNA and DNA genomes (Krupovic, Ravantti & Bamford, 2009; Diemer & Stedman, 2012), have highlighted ssDNA viruses as one of the most intriguing viral groups in viral ecology. So far, two main types of ssDNA viruses have been frequently detected in viromes: eukaryote-infecting CRESS-DNA viruses and bacteriophages from the Microviridae family.…”

“…While these MDA viromes routinely uncover new viruses (Angly et al, 2006; Angly et al, 2009; Wegley et al, 2007; Kim et al, 2008; Willner et al, 2009; Ng et al, 2009; Rosario et al, 2009; Rosario, Duffy & Breitbart, 2009; López-Bueno et al, 2009; Roux et al, 2012a; Roux et al, 2012b; Labonté & Suttle, 2013a; Labonté & Suttle, 2013b; Zawar-Reza et al, 2014; Quaiser et al, 2015; Dayaram et al, 2016; Male et al, 2016; Steel et al, 2016), the MDA step selects for small circular ssDNA templates, and unevenly amplifies linear genome fragments even when pooling independent reactions (Yilmaz, Allgaier & Hugenholtz, 2010; Kim & Bae, 2011; Marine et al, 2014). The alternative linker amplification (LA) or tagmentation (TAG) methods are quantitative (±1.5-fold) for dsDNA viruses, even from low input samples (100 femtograms, Duhaime et al, 2012) but strongly select against ssDNA templates (Kim & Bae, 2011).…”

Genetic and functional diversity of ubiquitous DNA viruses in selected Chinese agricultural soils

“…Many studies showed majority of viral particles in soils and sediments belonged to single-stranded DNA (ssDNA) viruses, especially Microviridae family26272829. These researches showed that the Microviridae sequences comprised 84.6% of whole virus sequences in the Machair soil sample, 50.3% in the brown earth sample and 74% in Izu-Ogasaware Trench deep-sea sediment.…”

The smallest ssDNA phage infecting a marine bacterium

“…No ssDNA phages with a reduced genome like bacteriophage Mini have been isolated before. The reduced genomes and limited number of genes have also been found in many metagenomic assembled Microviridae phages recovered from soil, human and seawater (Tucker et al ., ; Roux et al ., ; Labonté and Suttle, ; Quaiser et al ., ). A ssDNA phage with a 4.1 kb genome size has been assembled from a metagenome of coastal water (Labonté and Suttle, ).…”

“…Prophages attributed to Microviridae were identified in the Bacteroides genomes (Krupovic and Forterre, ). Microviridae ‐associated prophages were also found in Bacteroides genomes, according to the assembled phage genomes from peatlands metagenomics (Quaiser et al ., ). The finding of both capsid and replication initiator genes in the bacterial genome suggests a common ancestor between vB_RpoMi‐Mini and a prophage or a prophage remnant in the genome of Sphingomonadales , and implies a historical integration of ssDNA phage DNA into Alphaproteobacteria.…”