Phylogenetic diversity and assemblage of major capsid genes (g23) of T4-type bacteriophages in paddy field soils during rice growth season in Northeast China

Abstract

Although bacteriophages (phages) are ubiquitous and the most abundant biological entities on Earth, the genetic information on their diversity and community composition in natural environments, particularly in soils, is limited. This study elucidated the diversity and composition of T4-type phages by analyzing partial major capsid gene (g23) sequences in DNA extracts from five paddy field soils in Northeast China during the flooded period of rice (Oryza sativa L.) cultivation. In total, 106 different g23 clones were obtained, among which 88 clones were grouped into Paddy Groups I, III, V, VI, VII, VIII and IX, and the remaining 18 clones were left ungrouped, suggesting the high diversity of g23 clones in paddy field soils in Northeast China. In addition, the distribution of g23 sequences in this study was distinctly different from those in marine and lake freshwater environments. UniFrac analysis of g23 clone assemblages from different environments demonstrated that T4-type phage community compositions varied among marine, lake, paddy field soil and upland soil environments. Within paddy field soils, the T4-type phage community compositions in Northeast China differed from those in Japan.