Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein.
The small single-stranded DNA (ssDNA) bacteriophages of the subfamily Gokushovirinae were traditionally perceived as narrowly targeted, niche-specific viruses infecting obligate parasitic bacteria, such as Chlamydia. The advent of metagenomics revealed gokushoviruses to be widespread in global environmental samples. This study expands knowledge of gokushovirus diversity in the environment by developing a degenerate PCR assay to amplify a portion of the major capsid protein (MCP) gene of gokushoviruses. Over 500 amplicons were sequenced from 10 environmental samples (sediments, sewage, seawater and freshwater), revealing the ubiquity and high diversity of this understudied phage group. Residue-level conservation data generated from multiple alignments was combined with a predicted 3D structure, revealing a tendency for structurally internal residues to be more highly conserved than surface-presenting protein-protein or viral-host interaction domains. Aggregating this data set into a phylogenetic framework, many gokushovirus MCP clades contained samples from multiple environments, although distinct clades dominated the different samples. Antarctic sediment samples contained the most diverse gokushovirus communities, whereas freshwater springs from Florida were the least diverse. Whether the observed diversity is being driven by environmental factors or host-binding interactions remains an open question. The high environmental diversity of this previously overlooked ssDNA viral group necessitates further research elucidating their natural hosts and exploring their ecological roles.
College of Marine Science, University of South Florida, Saint Petersburg, FL, USA.
Max
M
Hopkins
Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA.
Shweta
S
Kailasan
College of Marine Science, University of South Florida, Saint Petersburg, FL, USA.
Allison
A
Cohen
1] Laboratoire 'Microorganismes: Génome et Environnement', Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France [2] CNRS, UMR 6023, LMGE, Aubière, France.
Simon
S
Roux
Department of Biology, Stevenson University, Stevenson, MD, USA.
Kimberly Pause
KP
Tucker
College of Marine Science, University of South Florida, Saint Petersburg, FL, USA.
Amelia
A
Shevenell
Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA.
Mavis
M
Agbandje-McKenna
College of Marine Science, University of South Florida, Saint Petersburg, FL, USA.
Mya
M
Breitbart
D044822:Biodiversity; D036022:Capsid Proteins / Q000145:classification / Q000235:genetics*; D004277:DNA, Single-Stranded / Q000737:chemistry; D004279:DNA, Viral / Q000737:chemistry; D004783:Environmental Microbiology; D017914:Microviridae / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D016133:Polymerase Chain Reaction
D036022:Capsid Proteins; D004277:DNA, Single-Stranded; D004279:DNA, Viral