Abundance and diversity of viruses in six Delaware soils

Abstract

The importance of viruses in marine microbial ecology has been established over the past decade. Specifically, viruses influence bacterial abundance and community composition through lysis and alter bacterial genetic diversity through transduction and lysogenic conversion. By contrast, the abundance and distribution of viruses in soils are almost completely unknown. This study describes the abundance and diversity of autochthonous viruses in six Delaware soils: two agricultural soils, two coastal plain forest soils, and two piedmont forest soils. Viral abundance was measured using epifluorescence microscopy, while viral diversity was assessed from morphological data obtained through transmission electron microscopy. Extracted soil virus communities were dominated by bacteriophages that demonstrated a wide range of capsid diameters (20 nm to 160 nm) and morphologies, including filamentous forms and phages with elongated capsids. The reciprocal Simpson's index suggests that forest soils harbor more diverse assemblages of viruses, particularly in terms of morphological distribution. Repeated extractions of virus-like particles (VLPs) from soils indicated that the initial round of extraction removes approximately 70% of extractable viruses. Higher VLP abundances were observed in forest soils (1.31 x 10(9) to 4.17 x 10(9) g(-1) dry weight) than in agricultural soils (8.7 x 10(8) to 1.1 x 10(9) g(-1) dry weight). Soil VLP abundance was significantly correlated to moisture content (r = 0.988) but not to soil texture. Land use (agricultural or forested) was significantly correlated to both bacterial (r = 0.885) and viral (r = 0.812) abundances, as were soil organic matter and water content. Thus, land use is a significant factor influencing viral abundance and diversity in soils.

FIG. 1.

Abundance of virus-like particles per gram dry weight (gdw) in six Delaware soils based on single extractions with 1% potassium citrate (white bars) or 10 mM sodium pyrophosphate (black bars). Soils used were Elkton sandy loam (Elk), Woodstown loamy sand (Woods), piedmont wetland soil (PM Wet), piedmont upland soil (PM Upland), Evesboro loamy sand (Eves), and Matapeake silt loam (Mtpk). CP, coastal plain; Ag, agricultural. Bars represent standard errors.

FIG. 2.

Viral abundances in sequential soil extractions. Virus-like particles were extracted from six Delaware soils with 1% potassium citrate. The average percent VLPs extracted, based on triplicate subsamples, is shown; the sum of three extractions equals 100%.

FIG. 3.

Frequency distributions of viral morphologies from six Delaware soils and known phage isolates. Categories include tailless (Tail−), Podoviridae (Podo), Siphoviridae (Sipho), Myoviridae (Myo), filamentous (Fil), and elongate (Elong). The elongate category is a subset of all icosahedral morphologies except filamentous. Histograms are based on measurements of 450 individual viruses per soil. Morphological data for known isolates are from reference .