Viruses in soils: morphological diversity and abundance in the rhizosphere

Abstract

Soil viruses are potentially of great importance as they may influence the ecology and evolution of soil biological communities through both an ability to transfer genes from host to host and as a potential cause of microbial mortality. Despite this importance, the area of soil virology is understudied. Here, we report the isolation and preliminary characterisation of viruses from soils in the Dundee area of Scotland. Different virus morphotypes including tailed, polyhedral (spherical), rod shaped, filamentous and bacilliform particles were detected in the soil samples. An apparent predominance of small spherical and filamentous bacteriophages was observed, whereas tailed bacteriophages were significantly less abundant. In this report, we also present observations and characterisation of viruses from different soil functional domains surrounding wheat roots: rhizosheath, rhizosphere and bulk soil. In spite of the differences in abundance of bacterial communities in these domains, no significant variations in viral population structure in terms of morphology and abundance were found. Typically, there were approximately 1.1-1.2 Â 10 9 virions g 21 dry weight, implicating remarkable differences in virus-to-bacteria ratios in domains close to roots, rhizosphere and rhizosheath (approximately 0.27) and in bulk soil (approximately 4.68).

Distinct Circular Single-Stranded DNA Viruses Exist in Different Soil Types

“…Our electron microscopy observations showed that the abundance of virus-like particles in four soil types in this study is of the same order as that found previously in brown earth soil from the Dundee area (10). However, sometimes differences in virus abundances in different soils can be seen, which appear to correlate with soil moisture and organic matter content (4), and this may be due to specific environmental conditions pertinent to those soils.…”

“…A method for the extraction of viruses from 1-g samples of soils was adapted from the method described by Swanson et al (10). One-gram soil samples were divided equally between two 2-ml Eppendorf tubes, and 1 ml of 0.067 M phosphate buffer, pH 7.5, and 250 l of 1-mm-diameter sterile glass beads were added to each tube, which was shaken in a Qiagen Retsch tissue lyser for 5 min at 30 revolutions s Ϫ1 .…”

“…Surveying viruses in soils has started recently, despite the recalcitrant character of many soil samples, and initial estimates of concentrations of viruses in soils are on the order of ϳ1.5 ϫ 10 8 g Ϫ1 (wet weight) to ϳ10 9 virus particles g Ϫ1 (dry weight) (4,9,10). Data on changes to soil virus abundance and diversity caused by environmental factors have recently been reported; for example, it was shown that virus abundance and diversity are greater in wetland forest soil than in drier agricultural soils (4).…”

“…However, the complex morphology of soil debris makes it difficult to distinguish virus particles other than tailed phage (9,10), and improved virus purification techniques showed that while the numbers of tailed bacteriophage (ϳ4.8 ϫ 10 7 g Ϫ1 [dry weight]) were similar to previous reports, they comprised only ϳ4% of the total virus particles present, and the remaining, overwhelming majority of particles consisted of spherical particles of various sizes, along with bacilliform, rod-shaped, and filamentous virus-like entities (10). Recent studies have also shown that 51 to 92% of virus particles in ocean samples are nontailed (13).…”

Introduction: Soils and Their Promotion of Plant Growth

“…However Coleman ( 2011 ) points out that little attention has been given to viruses in soil, despite the understanding that a small but signifi cant amount of C is cycled through viral components in pelagic ecosystems. Small spherical viruses form the major portion of the morphological classes of virus in soil under wheat cultivation (Swanson et al 2011 ) and it is interesting that they show no difference in viral abundance between rhizosheath, rhizosphere and bulk soil despite a signifi cant reduction in bacterial numbers in bulk soil compared to the rhizosphere. This suggests that many viruses in soil are not directly associated with bacterial hosts.…”