Understanding the Interaction of Rice (Oryza Sativa L.) with Soil Nitrification and Microbial Community in Paddy Soil

Paddy rice cultivation is widely practiced under extensive nitrogen fertilizers application,
which in turn causes loss of the applied nitrogen by nitrification process and became a global
concern due to its associated environmental hazards and economic loss. It is therefore
important to understand the driving factors of soil nitrification and find an eco-friendly solution
of it. Thus, this thesis aims to better understand the nitrification variation among different rice
cultivated soils by investigating the plant’s interaction with soil nitrification and functional
microbial community as well as identifying the plant’s genetic factors associated with the
interaction. The study was performed with 56 rice cultivars (Oryza sativa L.), which were
grown in paddy soil microcosms. Soil nitrification was determined using 15N pool dilution and
functional microbial population was assessed by real-time-PCR, along with a genome wide
association study (GWAS) to identify the rice genomic linkage with those factors. First, I
demonstrated that, rice cultivars had significant effect on the soil nitrification with a higher
impact in rhizosphere compared to bulk soil. Secondly, I found that bacterial ammonia oxidizer
population was functionally dominated over archaeal ammonia oxidizer and had positive
relationship with nitrification activity. Next, I revealed that rice genetic markers were
associated with gene loci of the following ontology e.g., nitrogen metabolism, signalling,
photosynthesis, retrotransposon etc., where these genes can drive the root exudation of
biological nitrification inhibitors (BNIs) and hence, be associated with nitrogen use efficiency.
Lastly, in a meta-analysis, I demonstrated that there was variation across different of
nitrification methods (i.e., potential, net and gross nitrification method) and differences within
each method. This thesis reveals the significance of rice cultivar and their interaction in the
nitrification dynamics in molecular and genetic context. It also shed light on the genetic link
of root BNI, which can be useful in future development of improved rice cultivar for sustainable
agriculture.