Prevalence of lysogeny among soil bacteria and presence of 16S rRNA and trzN genes in viral-community DNA

Abstract

Bacteriophages are very abundant in the biosphere, and viral infection is believed to affect the activity and genetic diversity of bacterial communities in aquatic environments. Lysogenic conversion, for example, can improve host fitness and lead to phage-mediated horizontal gene transfer. However, little is known about lysogeny and transduction in the soil environment. In this study we employed atrazine-impregnated Bio-Sep beads (a cell immobilization matrix) to sample active microbiota from soils with prior pesticide exposure history. Once recovered from soil, the bead communities were induced with mitomycin C (MC), and viral and bacterial abundances were determined to evaluate the incidence of inducible prophage in soil bacteria. The inducible fraction calculated within bead communities was high (ca. 85%) relative to other studies in aquatic and sedimentary environments. Moreover, the bacterial genes encoding 16S rRNA and trzN, a chlorohydrolase gene responsible for dehalogenation of atrazine, were detected by PCR in the viral DNA fraction purified from MC-induced bead communities. A diverse collection of actinobacterial 16S rRNA gene sequences occurred within the viral DNA fraction of induced, water-equilibrated beads. Similar results were observed in induced atrazine-equilibrated beads, where 77% of the cloned sequences were derived from actinobacterial lineages. Heterogeneous 16S rRNA gene sequences consisting of fragments from two different taxa were detected in the clone libraries. The results suggest that lysogeny is a prevalent reproductive strategy among soil bacteriophages and that the potential for horizontal gene transfer via transduction is significant in soil microbial communities.

FIG. 1.

Changes in viral and bacterial abundance after induction with MC in Bio-Sep beads that were previously equilibrated with atrazine (A and C) or water (B and D) and buried at the study sites for 4 to 6 weeks prior to induction. BDC, bacterial direct count; VDC, viral direct count.

FIG. 2.

Electron micrographs of viral samples extracted from induced beads. Bars, 200 nm (all panels).

FIG. 3.

Agarose gel (1.75%) electrophoresis of PCR products amplified with trzN primer sets from induced viral DNA (lane 1), uninduced viral DNA (lane 2), and DNA extracted from Arthrobacter aurescens (control for trzN) (lane 3). Lanes 5 and 6 contained PCR products from the same viral samples amplified with atzA primer sets. Lane 7 contains PCR product amplified with atzA primers from Pseudomonas sp. strain ADP. Lane 4, blank; MW, molecular weight markers.

FIG. 4.

Sequence alignment results for the members of the Streptosporangiaceae (species within the green box) and Nocardioidaceae (species within the blue box) in the V7 region of the 16S rRNA gene.