Quantitative analyses of the abundance and composition of ammonia‐oxidizing bacteria and ammonia‐oxidizing archaea of a Chinese upland red soil under long‐term fertilization practices

Abstract

Summary The abundance and composition of soil ammonia‐oxidizing bacteria (AOB) and ammonia‐oxidizing archaea (AOA) were investigated by using quantitative real‐time polymerase chain reaction, cloning and sequencing approaches based on amoA genes. The soil, classified as agri‐udic ferrosols with pH (H2O) ranging from 3.7 to 6.0, was sampled in summer and winter from long‐term field experimental plots which had received 16 years continuous fertilization treatments, including fallow (CK0), control without fertilizers (CK) and those with combinations of fertilizer nitrogen (N), phosphorus (P) and potassium (K): N, NP, NK, PK, NPK and NPK plus organic manure (OM). Population sizes of AOB and AOA changed greatly in response to the different fertilization treatments. The NPK + OM treatment had the highest copy numbers of AOB and AOA amoA genes among the treatments that received mineral fertilizers, whereas the lowest copy numbers were recorded in the N treatment. Ammonia‐oxidizing archaea were more abundant than AOB in all the corresponding treatments, with AOA to AOB ratios ranging from 1.02 to 12.36. Significant positive correlations were observed among the population sizes of AOB and AOA, soil pH and potential nitrification rates, indicating that both AOB and AOA played an important role in ammonia oxidation in the soil. Phylogenetic analyses of the amoA gene fragments showed that all AOB sequences from different treatments were affiliated with Nitrosospira or Nitrosospira‐like species and grouped into cluster 3, and little difference in AOB community composition was recorded among different treatments. All AOA sequences fell within cluster S (soil origin) and cluster M (marine and sediment origin). Cluster M dominated exclusively in the N, NP, NK and PK treatments, indicating a pronounced difference in the community composition of AOA in response to the long‐term fertilization treatments. These findings could be fundamental to improve our understanding of the importance of both AOB and AOA in the cycling of nitrogen and other nutrients in terrestrial ecosystems.

Long-term application of organic manure changes abundance and composition of ammonia-oxidizing archaea in an acidic red soil

“…The archaeal amoA gene copy numbers in our acidic red soil were comparable to those measured with real-time quantitative PCR in other agricultural soils (He et al 2007;Chen et al 2008;Shen et al 2008). The AOA population sizes were observed to be highest in an acidic red soil (pH 3.7-6.0) receiving mineral NPK fertilizer plus organic manure while they were the lowest in the soil receiving mineral N fertilizer only (He et al 2007).…”

“…1). The community structure of AOA was sensitive to different long-term fertilization treatments in the acidic red soils (He et al 2007;Chen et al 2011). Our results show that the application of organic manures, either with or without mineral NPK fertilizer, resulted in a notable shift in the community structure of AOA in comparison with mineral fertilizers only and the nonfertilized control (Fig.…”

“…The AOA population sizes were observed to be highest in an acidic red soil (pH 3.7-6.0) receiving mineral NPK fertilizer plus organic manure while they were the lowest in the soil receiving mineral N fertilizer only (He et al 2007). Moreover, the AOA population sizes were significantly fertilizer; mineral N, phosphorus (P) and potassium (K) fertilizer; organic manure; and organic manure plus mineral NPK fertilizer treatments, respectively.…”

“…These results might suggest that the activity of AOA was significantly increased after the long-term application of organic manures in the acidic red soil. Moreover, the AOB population size may be increased, since soil pH and NH 3 content were significantly increased after the long-term application of organic manures (Table 1), which were key ecological factors determining the AOB population size and activity (Kowalchuk and Stephen 2001;He et al 2007;Shen et al 2008). Hence, both AOA and AOB may contribute to the increased nitrification potential after the long-term application of organic manures.…”

“…Long-term (16-year) application of mineral NPK fertilizer plus organic manure changed the abundance and composition of AOA and nitrification potential in an acidic red soil (He et al 2007). The population size and nitrification potential were greatest after the application of mineral NPK fertilizer plus organic manure, and least after the application of mineral N fertilizer only.…”