Comparison of Soil Bacterial Community Structure in Rice Paddy Fields under Different Management Practices using Terminal Restriction Fragment Length Polymorphism (T-RFLP)

To develop a monitoring method for soil microbial communities in rice paddy fields, we usedterminal restriction fragment length polymorphism (T-RFLP) to compare soil bacterial community structure in ricepaddy fields experiencing different management practices: organic practices, conventional practices without awinter barley rotation, and conventional practices with a winter barley rotation. Restriction fragment length profilesfrom soils farmed using organic practices showed very different patterns from those from conventional practiceswith and without barley rotation. In principal component analyses, restriction fragment profiles in organic practicesamples were clearly separated from those in conventional practice samples, while principal component analysisdid not show a clear separation for soils farmed using conventional practices with and without barley rotation.The cluster analysis showed that the bacterial species compositions of soils under organic practices were significantlydifferent from those under conventional practices at the 95% level, but soils under conventional practicewith and without barley rotation did not significantly differ. Although the loadings from principal componentanalyses and the Ribosomal DNA Project II databases suggested candidate species important for soils underorganic farming practices, it was very difficult to get detailed bacterial species information from terminal restrictionfragment length polymorphism. Rank-abundance diagrams and diversity indices showed that restriction fragmentpeaks under organic farming showed high Pielou’s Evenness Index and the reciprocal of Simpson Indexsuggesting high bacterial diversity in organically farmed soils.