Genetic and functional diversity of ubiquitous DNA viruses in selected Chinese agricultural soils.
Viral community structures in complex agricultural soils are largely unknown. Electron microscopy and viromic analyses were conducted on six typical Chinese agricultural soil samples. Tailed bacteriophages, spherical and filamentous viral particles were identified by the morphological analysis. Based on the metagenomic analysis, single-stranded DNA viruses represented the largest viral component in most of the soil habitats, while the double-stranded DNA viruses belonging to the Caudovirales order were predominanted in Jiangxi-maize soils. The majority of functional genes belonged to the subsystem "phages, prophages, transposable elements, and plasmids". Non-metric multidimensional analysis of viral community showed that the environment medium type was the most important driving factor for the viral community structure. For the major viral groups detected in all samples (Microviridae and Caudovirales), the two groups gathered viruses from different sites and similar genetic composition, indicating that viral diversity was high on a local point but relatively limited on a global scale. This is a novel report of viral diversity in Chinese agricultural soils, and the abundance, taxonomic, and functional diversity of viruses that were observed in different types of soils will aid future soil virome studies and enhance our understanding of the ecological functions of soil viruses.
State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.|University of the Chinese Academy of Sciences, Beijing 100039, China.
Li-Li
LL
Han
State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.|University of the Chinese Academy of Sciences, Beijing 100039, China.
Dan-Ting
DT
Yu
State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.|University of the Chinese Academy of Sciences, Beijing 100039, China.
Li-Mei
LM
Zhang
State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.|University of the Chinese Academy of Sciences, Beijing 100039, China.
Ju-Pei
JP
Shen
State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.|University of the Chinese Academy of Sciences, Beijing 100039, China.|Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
Ji-Zheng
JZ
He
D000383:Agriculture; D000595:Amino Acid Sequence; D036022:Capsid Proteins / Q000737:chemistry / Q000235:genetics; D002681:China; D004267:DNA Viruses / Q000145:classification* / Q000235:genetics* / Q000648:ultrastructure; D004279:DNA, Viral; D014644:Genetic Variation; D016679:Genome, Viral; D023281:Genomics / Q000379:methods; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology
D036022:Capsid Proteins; D004279:DNA, Viral