Microbial communities in paddy fields in the Mekong delta of Vietnam

Rice paddy fields are considered to be unique ecosystems. Intensive rice cultivation was developed to increase yield and to meet the need of food security. This practice has many negative effects on the soil ecosystem, such as reduction of soil nutrients, soil and water pollution and increase in soil-borne plant pathogens and a possible reduction of soil microorganism diversity. Alternative management strategies are required to counteract these negative effects to maintain soil fertility. The aims of this thesis are to investigate the microbial community in the rice paddy field to assess the influence of microorganisms on the degree of crop residue degradation and in protecting the next crop against soil-borne plant pathogens, including Rhizoctonia solani, and to understand the relationship between microbial diversity and functional groups involved in straw degradation and the inhibition of R. solani growth. Furthermore, the effect of intensive rice cultivation on the yield, abundance and diversity of the total bacterial community and on the diazotrophic bacterial community compared with the rice crop rotation system is investigated. Bacteria isolated from rice stubble with both cellulolytic and combined cellulolytic and chitinolytic activity were phylogenetically linked to distinct microbial groups. Selected bacterial isolates with these functions inhibited R. solani growth on agar plates; most of these isolates seemed to be neutral with respect to their effect on rice seed germination and radicle length. There was a positive relationship between straw weight loss and the number of isolates and functional groups. Fungal isolates were more important for straw degradation than the bacteria. The growth of R. solani was inhibited when it was inoculated on degraded straw. There was a negative relationship between straw weight loss and the growth of R. solani. Finally, crop management practices had a significant effect on both rice production and bacterial community structure. Rice yield from all the rice crop rotations that included maize and/or mungbean was significantly higher than that from the rice monoculture. Besides the yield effect, the structure and diversity of the total bacterial community and of the potential nitrogen-fixing bacterial community were significantly influenced by crop rotation when compared with that detected in the rice monoculture soil.This thesis highlights that crop rotation systems had a positive impact on rice production and on soil microbial diversity in the rice field ecosystem. Results from this study can be applied in the future development of a sustainable rice management.