Different crop rotation systems as drivers of change in soil bacterial community structure and yield of rice, Oryza sativa

Intensive cropping, especially of rice, is considered to contribute to negative effects not only on soil chemical and biological properties but also on long-term grain yield. Appropriate crop rotation is often practiced as an alternative strategy to overcome the negative side effects of intensive cropping. Although soil microbial diversity and community structure have been shown to respond differently to altered agricultural management practices, little is known about possible links between crop rotation and grain yield on bacterial communities in rice paddy soil. In this study, we investigated the impact of specific rotational crops and compared it with intensive rice cultivation. The main crop rice (Oryza sativa) was rotated with maize (Zea mays) and mungbean (Phaseolus aureus) in different combinations in a system cultivating three crops per year. Soil bacterial communities were studied in two different cropping periods using pyrosequencing of the variable V4 region of the 16S rRNA. Our results showed that rotation with alternative crops increased rice yield by 24–46% depending on rotation structure and that bacterial community structure was altered in the presence of mungbean and/or maize compared to that in rice monoculture. In the crop rotation systems, composition, abundance, and diversity of soil bacterial communities were significantly different and higher than those in rice monoculture. Our results show that effects of crop rotation relate to changes in soil bacterial community structure suggesting that appropriate crop rotations provide a feasible practice to maintain the equilibrium in soil microbial environment for sustainable rice cultivation.