title: Distinct circular single-stranded DNA viruses exist in different soil types.
abstract: The potential dependence of virus populations on soil types was examined by electron microscopy, and the total abundance of virus particles in four soil types was similar to that previously observed in soil samples. The four soil types examined differed in the relative abundances of four morphological groups of viruses. Machair, a unique type of coastal soil in western Scotland and Ireland, differed from the others tested in having a higher proportion of tailed bacteriophages. The other soils examined contained predominantly spherical and thin filamentous virus particles, but the Machair soil had a more even distribution of the virus types. As the first step in looking at differences in populations in detail, virus sequences from Machair and brown earth (agricultural pasture) soils were examined by metagenomic sequencing after enriching for circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) virus genomes. Sequences from the family Microviridae (icosahedral viruses mainly infecting bacteria) of CRESS-DNA viruses were predominant in both soils. Phylogenetic analysis of Microviridae major coat protein sequences from the Machair viruses showed that they spanned most of the diversity of the subfamily Gokushovirinae, whose members mainly infect obligate intracellular parasites. The brown earth soil had a higher proportion of sequences that matched the morphologically similar family Circoviridae in BLAST searches. However, analysis of putative replicase proteins that were similar to those of viruses in the Circoviridae showed that they are a novel clade of Circoviridae-related CRESS-DNA viruses distinct from known Circoviridae genera. Different soils have substantially different taxonomic biodiversities even within ssDNA viruses, which may be driven by physicochemical factors.
authors.affiliation: The James Hutton Institute, Dundee, Scotland, United Kingdom Brian.Reavy2@gmail.com Michael.Taliansky@hutton.ac.uk.
authors.forename: Brian
authors.initials: B
authors.lastname: Reavy
authors.affiliation: The James Hutton Institute, Dundee, Scotland, United Kingdom.
authors.forename: Maud M
authors.initials: MM
authors.lastname: Swanson
authors.affiliation: The James Hutton Institute, Dundee, Scotland, United Kingdom.
authors.forename: Peter J A
authors.identifier: http://orcid.org/0000-0001-9513-9993
authors.initials: PJ
authors.lastname: Cock
authors.affiliation: The James Hutton Institute, Craigiebuckler, Aberdeen, Scotland, United Kingdom.
authors.forename: Lorna
authors.initials: L
authors.lastname: Dawson
authors.affiliation: The James Hutton Institute, Craigiebuckler, Aberdeen, Scotland, United Kingdom.
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Freitag
authors.affiliation: University of Western Sydney, Penrith, New South Wales, Australia.
authors.forename: Brajesh K
authors.initials: BK
authors.lastname: Singh
authors.affiliation: The James Hutton Institute, Dundee, Scotland, United Kingdom School of Biology, The University of St Andrews, St Andrews, Scotland, United Kingdom.
authors.forename: Lesley
authors.initials: L
authors.lastname: Torrance
authors.affiliation: National Science Foundation, Arlington, Virginia, USA.
authors.forename: Arcady R
authors.initials: AR
authors.lastname: Mushegian
authors.affiliation: The James Hutton Institute, Dundee, Scotland, United Kingdom Brian.Reavy2@gmail.com Michael.Taliansky@hutton.ac.uk.
authors.forename: Michael
authors.initials: M
authors.lastname: Taliansky
mesh_terms: D001483:Base Sequence; D044822:Biodiversity; D036022:Capsid Proteins / Q000235:genetics; D018136:Circoviridae / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D004267:DNA Viruses / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D004277:DNA, Single-Stranded / Q000235:genetics; D004279:DNA, Viral / Q000235:genetics; D016679:Genome, Viral; D007494:Ireland; D056186:Metagenomics; D017914:Microviridae / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D010802:Phylogeny; D012606:Scotland; D017422:Sequence Analysis, DNA; D012987:Soil / Q000145:classification*; D012988:Soil Microbiology; D014771:Virion / Q000145:classification / Q000302:isolation & purification
chemical_list: D036022:Capsid Proteins; D004277:DNA, Single-Stranded; D004279:DNA, Viral; D012987:Soil
references.citation: BMC Bioinformatics. 2008;9:386
references.pmid: 18803844
references.citation: J Gen Virol. 2013 Aug;94(Pt 8):1827-40
references.pmid: 23596268
references.citation: Science. 2009 Aug 14;325(5942):833
references.pmid: 19679806
references.citation: J Gen Virol. 2009 Oct;90(Pt 10):2418-24
references.pmid: 19570956
references.citation: Science. 2009 Nov 6;326(5954):858-61
references.pmid: 19892985
references.citation: Syst Biol. 2010 May;59(3):307-21
references.pmid: 20525638
references.citation: Science. 2011 Apr 1;332(6025):106-9
references.pmid: 21454789
references.citation: ISME J. 2011 May;5(5):822-30
references.pmid: 21124487
references.citation: PLoS One. 2011;6(5):e19893
references.pmid: 21572966
references.citation: Appl Environ Microbiol. 2011 Nov;77(21):7663-8
references.pmid: 21926223
references.citation: PLoS One. 2012;7(3):e33641
references.pmid: 22432038
references.citation: Science. 2002 May 31;296(5573):1694-7
references.pmid: 12040197
references.citation: Proc Natl Acad Sci U S A. 2002 Aug 6;99(16):10494-9
references.pmid: 12097644
references.citation: Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14250-5
references.pmid: 12384570
references.citation: Appl Environ Microbiol. 2003 Jan;69(1):285-9
references.pmid: 12514006
references.citation: Proc Biol Sci. 2004 Mar 22;271(1539):565-74
references.pmid: 15156913
references.citation: J Bacteriol. 2004 Jun;186(12):3677-86
references.pmid: 15175280
references.citation: Nat Rev Microbiol. 2005 Jun;3(6):504-10
references.pmid: 15886693
references.citation: Appl Environ Microbiol. 2005 Jun;71(6):3119-25
references.pmid: 15933010
references.citation: Trends Microbiol. 2005 Jun;13(6):278-84
references.pmid: 15936660
references.citation: Nucleic Acids Res. 2005;33(17):5691-702
references.pmid: 16214803
references.citation: Proc Natl Acad Sci U S A. 2006 Jan 17;103(3):626-31
references.pmid: 16407148
references.citation: PLoS Biol. 2006 Nov;4(11):e368
references.pmid: 17090214
references.citation: Arch Virol. 2007 Feb;152(2):227-43
references.pmid: 17051420
references.citation: Environ Microbiol. 2007 Oct;9(10):2563-74
references.pmid: 17803780
references.citation: Appl Environ Microbiol. 2007 Nov;73(21):7059-66
references.pmid: 17827313
references.citation: Nature. 2008 Apr 3;452(7187):629-32
references.pmid: 18337718
references.citation: Res Microbiol. 2008 Jun;159(5):349-57
references.pmid: 18565737
references.citation: PLoS One. 2008;3(9):e3263
references.pmid: 18810270
references.citation: Appl Environ Microbiol. 2008 Oct;74(19):5975-85
references.pmid: 18708511
references.citation: Curr Opin Virol. 2011 Oct;1(4):289-97
references.pmid: 22440785
references.citation: Nucleic Acids Res. 2012 Jul;40(Web Server issue):W88-95
references.pmid: 22645318
references.citation: PLoS One. 2012;7(7):e40418
references.pmid: 22808158
references.citation: PLoS One. 2012;7(7):e40683
references.pmid: 22815791
references.citation: Arch Virol. 2012 Oct;157(10):1851-71
references.pmid: 22760663
references.citation: ISME J. 2013 Sep;7(9):1738-51
references.pmid: 23635867
references.citation: Mol Biol Evol. 2013 Dec;30(12):2725-9
references.pmid: 24132122
references.citation: Environ Microbiol. 2014 Feb;16(2):570-85
references.pmid: 23879711
references.citation: ISME J. 2014 Oct;8(10):2093-103
references.pmid: 24694711
references.citation: J Gen Virol. 2012 Dec;93(Pt 12):2668-81
references.pmid: 22915694
references.citation: ISME J. 2013 Feb;7(2):359-69
references.pmid: 23038177
references.citation: PLoS One. 2013;8(2):e57271
references.pmid: 23468952
references.citation: Nat Protoc. 2009;4(4):470-83
references.pmid: 19300441