AUTHOR=Quaiser Achim , Dufresne Alexis , Ballaud Flore , Roux Simon , Zivanovic Yvan , Colombet Jonathan , Sime-Ngando Télesphore , Francez André-Jean 

TITLE=Diversity and comparative genomics of Microviridae in Sphagnum- dominated peatlands

JOURNAL=Frontiers in Microbiology

VOLUME=6

YEAR=2015

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2015.00375

DOI=10.3389/fmicb.2015.00375

ISSN=1664-302X

ABSTRACT=<p><italic>Microviridae</italic>, 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 <italic>Microviridae</italic> genomes from 12 viromes of a <italic>Sphagnum-</italic>dominated peatland. Phylogenetic analysis of the conserved major capsid protein sequences revealed the affiliation to <italic>Gokushovirinae</italic> and <italic>Pichovirinae</italic> as well as to two newly defined subfamilies, the <italic>Aravirinae</italic> and <italic>Stokavirinae</italic>. Additionally, two new distinct prophages were identified in the genomes of <italic>Parabacteroides merdae</italic> and <italic>Parabacteroides distasonis</italic> representing a potential new subfamily of <italic>Microviridae</italic>. 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 <italic>Gokushovirinae,</italic> followed by <italic>Aravirinae,</italic> are the most abundant <italic>Microviridae</italic> in 11 out of 12 peat viromes. Sequences matching the <italic>Gokushovirinae</italic> and <italic>Aravirinae</italic> 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 <italic>Microviridae</italic> and pave the way toward quantitative estimations of <italic>Microviridae</italic> subfamilies.</p>