Abstract

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.

Highlights

  • Viruses are the most abundant biological entities and major players across all habitats, reaching 1031 virus particles in the Earth[1]

  • In order to study the morphologic diversity of viruses in the six soils, the shape and size of purified virus particles were examined using transmission electron microscopy (TEM) and characterized into three morphological types: tailed bacteriophage-like particles, spherical particles, and filamentous particles (Fig. S1)

  • The alpha diversity, which is based on a species-level annotation, summarizes the diversity of organisms in a sample with a single number, and the annotated species richness indicates the number of distinct species annotations in the combined Metagenomics Rapid Annotation using Subsystem Technology (MG-RAST) dataset

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Summary

Introduction

Viruses are the most abundant biological entities and major players across all habitats, reaching 1031 virus particles in the Earth[1]. The natural viral diversities were deeply studied and found that they were consistently high in local aquatic and soil environments[11,12,13,19,20]. Many studies showed majority of viral particles in soils and sediments belonged to single-stranded DNA (ssDNA) viruses, especially Microviridae family[26,27,28,29]. These researches showed that the Microviridae sequences comprised 84.6% of whole virus sequences in the Machair soil sample, 50.3% in the brown earth sample and 74% in Izu-Ogasaware Trench deep-sea sediment. This study aimed to reveal: (1) the taxonomic and functional diversities of viruses in six typical agricultural soils, (2) the similarities and differences among viromes in this study and other environmental sources, (3) the phylogenetic relationship of major groups existing in these viromes

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