Structure and diversity of ssDNA Microviridae viruses in two peri-alpine lakes (Annecy and Bourget, France)

Abstract

Microviridae is a subset of single-stranded DNA (ssDNA) viruses infecting bacteria. This group of phages has been previously observed to be very abundant (representing >90% of the total known viral metagenomic sequences) in Lake Bourget. However, this observation was made only during one period (in summer) and from a single sample collected at a single depth (near surface). This result suggests the importance of these viruses, poorly examined thus far, especially in fresh waters. In this study, performed on the two largest natural lakes in France (e.g. Lakes Annecy and Bourget), Microviridae structure was determined each month throughout the year (2011) using PCR-DGGE, with primers that target the major-capsid-protein-encoding gene VP1; cloning/sequencing was used to investigate their diversity. Our results confirm that Microviridae are diverse in peri-alpine lakes and are mainly represented by gokushoviruses. We also found for the first time ssDNA viruses belonging to Alpavirinae, another subfamily within Microviridae recently proposed by Krupovic and Forterre (2011), generally prophages infecting members of the Phylum Bacteroidetes. Our data also support highly variable community composition and dynamics of individual components whose patterns were different between lakes, suggesting distinct host communities and/or abiotic influences between the two ecosystems. We point out that most of the major observed ssDNA Microviridae viruses display boom-bust patterns (with a sharp increase/decline) in their dynamics, with high relative abundances, suggesting brutal control of hosts and rapid regulation of the host community structure.

Seasonal determinations of algal virus decay rates reveal overwintering in a temperate freshwater pond

“…Similar abundance patterns have been observed for viruslike particles and phages in rivers (e.g., Mathias et al, 1995;Farnell-Jackson and Ward, 2003) and lakes (Hofer and Sommaruga, 2001;Bettarel et al, 2004;Hewson et al, 2012;Zhong et al, 2015). Additionally, observations of thousands of viral genomes in metagenomic studies of aquatic environments (Breitbart et al, 2002), and of persistent viruses that exist at low but detectable abundances throughout much of the year (Waterbury and Valois, 1993;Short and Short, 2009;Short et al, 2011a;Zhong et al, 2013), have provided evidence for an environmental 'seed bank.'…”

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

“…Gokushovirionae are constituted by five genes, and one of the genes coding for capsid protein is much conserved37. Therefore, we used the capsid protein gene as a gene marker to investigate the diversity of Microviridae family, and our results confirmed that Microviridae were diverse and mainly represented by gokushoviruses in agricultural soil.…”

The smallest ssDNA phage infecting a marine bacterium

“…Phage vB_RpoMi‐Mini does not cross infect other five marine roseobacterial species tested. Microviridae phages infecting E. coli and Cellulophaga spp., respectively, are known to restrict their infection to a sing host (Bowes and Dowell, ; Holmfeldt et al ., ; Zhong et al ., ). However, several Microviridae phages infecting Chlamydia spp.…”