Ammonium oxidizing bacteria and archaea vary with season under plastic film mulching and long-term fertilization

Agronomic practices such as long-term use of plastic film mulching (PFM) and application of organic and inorganic fertilizers have profound effect on soil microbial community. However, there is limited information on the abundance and community structure of ammonia-oxidizers where these practices have been employed. In this study, we investigated soil ammonia oxidizers in a long-term application of fertilizer plots with or without PFM in two seasons of a maize-growing period. The fertilization treatments included: non-fertilizer control (CK), nitrogen fertilizer (N), organic manure (M), nitrogen fertilizer plus organic manure combined (MN). Real-time quantitative polymerase chain reaction (qPCR) of ammonia monooxygenase (amoA) genes revealed that the abundances of ammonia-oxidizing archaea (AOA) (1.0 x 107 to 2.0 × 1011 per copies g−1 dry soil weight) significantly (p < 0.05) out-numbered ammonia-oxidizing bacteria (AOB) (5.0 x 105 to 4.0 × 109 copies g−1 dry soil weight) abundances for June, July and October respectively. The phylogenetic analyses of denaturing gradient gel electrophoresis (DGGE) 16S rRNA gene revealed that AOB-uncultured Nitrosospira sp dominated bacterial ammonia oxidizers in fertilized and non-fertilized soils, regardless of PFM treatments for July and October. The non-fertilization treatment significantly increased bacterial richness (15.67 ± 0.33) under PFM treatment relative to fertilized treatments.