Microbial Nitrification Paradox: A Paradigm Shift on Nitrogen Uptake by Rice

Nitrogen fertilization is an integral agronomic practice to increasing productivity and profitability in agriculture. But the poor nitrogen use efficiency (NUE, about < 40%) causes many economic and environmental challenges. The microbial oxidative process of converting ammonia to nitrite to nitrate (nitrification) is the rate-limiting step in the N loss. The century-old, conventional theory of nitrification with the involvement of two functionally different bacterial groups as ammonia-oxidizing bacteria and nitrite-oxidizing bacteria has been upturned by the recent discoveries of archaeal members involved in ammonia oxidation (Ammonia-oxidizing archaea, AOA), anaerobic ammonia-oxidizing bacteria (Anammox bacteria) and complete ammonia oxidizing bacteria (Comammox bacteria) in the last two decades, largely due to the advances in molecular and metagenomic methods introduced to study the microbial ecology. What is interesting to know is that nitrate-transporters of host plants, as in rice, are involved in the assembly of the microbiome associated with roots. Besides, rice plants produce the biological nitrification inhibiting (BNI) compounds released through root exudates. Involvement of diverse microbiome members and the plant genome through nitrate transporters on the rice rhizosphere microbiome assembly necessitates the reappraisal of the nitrogen fertilization management options. This paper also highlights the need for gathering new knowledge on the plant-microbe interactions, from the genome to metabolite levels, and conserving these resources for sustainable rice cultivation.