Survey of major capsid genes (g23) of T4-type bacteriophages in Japanese paddy field soils

Using Signature Genes as Tools To Assess Environmental Viral Ecology and Diversity

“…Phylogenetic analyses revealed distinct clades associated with paddy soil, rice straw, and paddy flood water (paddy groups I to IX), as well as a small number of sequences similar to environmental marine samples from previous studies (36)(37)(38)(39)(40). When comparing manganese nodules in Japanese paddy soil with plow soil and subsoil layers, no differences in phage community structures were found, nor were differences found when comparing soil depth profiles or soils in different regions of Japan or different rice plant parts (40)(41)(42)(43). In an investigation of decomposing straw, a reduction in richness in T4-type phage signatures was found in the late stages of decomposition, the opposite of what was observed for the local bacterial population (44).…”

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

“…In addition, no clone obtained in this study fell into groups of T-evens, PseudoT-evens, SchizoTevens, and ExoT-evens. Figure 2 compared amino acid sequences of g23 clones in this study with 100 representative clones obtained from paddy field soils in Japan (Jia et al 2007;Fujii et al 2008;Wang et al 2009a) and 53 clones from paddy field soils in NE China (Wang et al 2009b). Phylogenetic analysis revealed that 17, 5, 8, 1 and 1 clones in this study belonged to Paddy Groups I, V, VI, VII and IX, respectively.…”

“…The alignments were first compared with T-evens, PseudoT-evens, SchizoT-evens, ExoT-evens and marine clones (Filée et al 2005), and with clones obtained from lake freshwaters (Ló pez-Bueno et al 2009;Butina et al 2010), and then with g23 sequences obtained from paddy fields in Japan (Jia et al 2007;Fujii et al 2008;Wang et al 2009a) and NE China (Wang et al 2009b). The alignment was conducted with ClustalX 1.81 (Thompson et al 1997), a rooted neighbor-joining tree was constructed by Molecular Evolutionary Genetic Analysis software (MEGA 3.0) with 1000-fold bootstrap support (Kumar et al 2004), and an unrooted phylogenetic tree was drawn using the interactive Tree of Life online program (Letunic and Bork 2006) based on the distance matrix data calculated by MEGA 3.0.…”

“…Wide distribution of g23 sequences without en bloc distribution into some specific sub-clusters might be an additional result supporting the conclusion of high diversity. Figure 2 Neighbor-joining phylogenetic tree of g23 sequences showing the relationships of g23 amino acid sequences obtained in this study with those obtained from paddy field soils in Japan (Fujii et al 2008;Wang et al 2009a) and NE China (Wang et al 2009b). The original and reconsidered Paddy Groups (PG) are shown with normal and bold letters, respectively.…”

“…It is necessary to note that the paddy soil samples used for studying g23 sequences in NE China were collected only once before transplanting rice (Oryza sativa L.) seedlings (April 2007), unlike studies conducted in Japan in which sampling time covered all growth stages of rice plants under both flooded and drained conditions (Fujii et al 2008;Wang et al 2009a). Given that soil conditions in paddy fields are remarkably different between the rice growth season under flooded conditions and no growth season under drained conditions, unrevealed g23 sequences were expected in paddy field soils in NE China during the rice growth season under flooded conditions.…”