Long-term mineral fertilizer substitution by organic fertilizer and the effect on the abundance and community structure of ammonia-oxidizing archaea and bacteria in paddy soil of south China

Ammonia oxidation in the soil is related to nitrogen (N) availability for plants, nitrate loss, and N fertilizer use efficiency, which is important for studies on the N cycle of paddy field ecosystems. Substitution of partial mineral N fertilizer with organic amendments is commonly considered to optimize fertilization practices and reduce the application of mineral N fertilizer in the paddy fields. However, little is known about the effects of this type of fertilization on the relative contribution of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) to soil nitrification. Therefore, a 34-year field trial including five fertilization regimes (CK, without fertilizer; NPK, mineral NPK fertilizer; NPKM 1, 70% inorganic N + 30% organic N + PK; NPKM 2, 50% inorganic N + 50% organic N + PK; NPKM 3, 30% inorganic N + 70% organic N + PK; P: phosphorus, K: potassium) was conducted. AOA and AOB abundance and community structures were determined by quantitative PCR and high-throughput sequencing analyses. Although the abundance of AOA and AOB increased with the increase in the percentage (30%–70%) of organic N substitution, the abundance ratio of AOA to AOB (133.9–84.7) decreased. Soil potential nitrification rate (PNR) increased dramatically ( p  < 0.05) after replacing chemical N with organic N, and with the increase in the substitution ratio of organic N in paddy soils. AOA and AOB both correlated significantly ( p  < 0.05) with PNR, but the contribution of AOB to PNR exceeded that of AOA. Soil carbon (C) to N ratio was the best predictor (43.0%) for AOA abundance, while total N and NH 4 + -N incorporating models were the best predictors (90.3%) for AOB abundance. Variations in AOA composition correlated strongly with fertilizer-induced changes in soil pH and ammonia concentration, whereas the AOB community was only markedly correlated with pH ( p  = 0.004). The substitution of 30%–70% of mineral N with organic N could increase the soil pH to 5.54–5.87, and that of ammonia concentration to 8.37–24.1 μM, which was the main reason that AOB contributed more to PNR than AOA. These results indicate that the organic substitution fertilizer regime had much stronger effects on the abundance and composition of AOB than AOA, and the potential contribution of AOB to ammonia oxidation in paddy soils should not be ignored after mineral N partial substitution by organic N.