Nitrate has a stronger rhizobacterial-based effect on rice growth and nitrogen use than ammonium in acidic paddy soil

Suitable N source supply is critical to improve plant growth and N uptake, but the importance of nitrate (NO3−) for rice (Oryza sativa L.) and microbiota is often neglected in acidic paddy soils where ammonium (NH4+) is dominant. This study aimed to explore the differential effects of NH4+ and NO3− on rice growth, fertilizer nitrogen recovery efficiency (FNRE), and rhizosphere bacterial community in acid soil. Two rice varieties, Kasalath (Al-sensitive indica) and Koshihikari (Al-tolerant japonica), were exposed to different N sources with or without lime in an acid soil. Liming and NO3− application solely improved the growth and FNRE of the Al-sensitive rice, namely, by increasing soil pH and alleviating Al toxicity. Compared with liming and rice variety, N source had a more pronounced influence on rhizobacterial community composition. Of the two sources, NO3− had a stronger effect on the rhizobacterial community than NH4+. Remarkably, rice plants fed with NH4+ specifically recruited Desulfosporosinus and Desulfitobacterium associated with ferric NH4+ oxidation in the rhizosphere, whereas those exposed to NO3− recruited Alicyclobacillus with NO3−-reducing iron oxidation ability. Three keystone taxa were identified in a rhizobacterial co-occurrence network analysis: Alicyclobacillus, which was positively associated with rice growth and FNRE, and Acidobacteriales and WPS-2, both with negative associations. Compared with NH4+, NO3− enhances the growth and FNRE of Al-sensitive rice and exerts dominant effects on the rhizobacterial community, which indicates the importance of NO3− for rice and has instructive implications for N management in acid soil.