Abstract
Myocyanophages, a group of viruses infecting cyanobacteria, are abundant and play important roles in elemental cycling. Here we investigated the particle-associated viral communities retained on 0.2 μm filters and in sediment samples (representing ancient cyanophage communities) from four ocean and three lake locations, using high-throughput sequencing and a newly designed primer pair targeting a gene fragment (∼145-bp in length) encoding the cyanophage gp23 major capsid protein (MCP). Diverse viral communities were detected in all samples. The fragments of 142-, 145-, and 148-bp in length were most abundant in the amplicons, and most sequences (>92%) belonged to cyanophages. Additionally, different sequencing depths resulted in different diversity estimates of the viral community. Operational taxonomic units obtained from deep sequencing of the MCP gene covered the majority of those obtained from shallow sequencing, suggesting that deep sequencing exhibited a more complete picture of cyanophage community than shallow sequencing. Our results also revealed a wide geographic distribution of marine myocyanophages, i.e., higher dissimilarities of the myocyanophage communities corresponded with the larger distances between the sampling sites. Collectively, this study suggests that the newly designed primer pair can be effectively used to study the community and diversity of myocyanophage from different environments, and the high-throughput sequencing represents a good method to understand viral diversity.
Highlights
T4virus is a genus of viruses that belongs to the order Caudovirales, the family Myoviridae, and the subfamily Tevenvirinae
These major capsid protein (MCP) gene sequences are from 17 representative genomes, which are assigned to CLUSTER A and CLUSTER B (IgnacioEspinoza and Sullivan, 2012), one freshwater myocyanophage genome, one environmental meta-genome, and one uncultured Mediterranean viral clone sequence
With the newly designed primer, MCP gene was successfully amplified with water and sediment samples
Summary
T4virus is a genus of viruses that belongs to the order Caudovirales, the family Myoviridae, and the subfamily Tevenvirinae. Myocyanophages are highly diverse and abundant in open-ocean, coastal and estuarine environments, fresh water lakes, and paddy soils (Filee et al, 2005; Comeau and Krisch, 2008; Hellweger, 2009; Sullivan et al, 2010; Wang K. et al, 2011; Wang et al, 2016; Chow and Fuhrman, 2012; Ignacio-Espinoza and Sullivan, 2012; Marston et al, 2013) These viruses play a key role in geochemical cycling of carbon and other elements through their interactions with host bacteria. Viruses drive evolution of bacteria by their antagonistic interactions or by introducing new genetic information to bacteria (Lindell et al, 2004; Suttle, 2007; Ignacio-Espinoza and Sullivan, 2012; Marston et al, 2012)
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