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=Volume 6 - 2015

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=Microviridae, a family of bacteria-infecting ssDNA viruses, is a member of the still poorly characterized bacteriophages, even though they include 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. Despite previous knowledge, 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. Structural modeling of the Aravirinae major capsid protein showed similarities to Alpavirinae and Pichovirinae but revealed two additional variable regions potentially involved in phage-host recognition. 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 towards quantitative estimations of Microviridae subfamilies.