Ammonia-oxidizer communities in an agricultural soil treated with contrasting nitrogen sources

Mussie Y Habteselassie,Li Xu,Jeanette M Norton

doi:10.3389/fmicb.2013.00326

Abstract

The community of ammonia-oxidizing prokaryotes was examined in an agricultural soil treated for six seasons with contrasting nitrogen (N) sources. Molecular tools based on the genes encoding ammonia monooxygenase were used to characterize the ammonia oxidizer (AO) communities and their abundance. Soil DNA was extracted from soils sampled from silage corn plots that received no additional N (control), dairy waste compost, liquid dairy waste (LW), and ammonium sulfate (AS) treatments at approximately 100 and 200 kg available N ha-1 over 6 years. The N treatment affected the quantity of AO based on estimates of amoA by real-time PCR. Ammonia oxidizing bacteria (AOB) were higher in soils from the AS200, AS100, and LW200 treatments (2.5 × 107, 2.5 × 107, and 2.1 × 107copies g-1 soil, respectively) than in the control (8.1 × 106 copies g-1 soil) while the abundance of amoA encoding archaea [ammonia oxidizing archaea (AOA)] was not significantly affected by treatment (3.8 × 107 copies g-1 soil, average). The ratio of AOA/AOB was higher in the control and compost treated soils, both treatments have the majority of their ammonium supplied through mineralization of organic nitrogen. Clone libraries of partial amoA sequences indicated AOB related to Nitrosospira multiformis and AOA related to uncultured Nitrososphaera similar to those described by soil fosmid 54d9 were prevalent. Profiles of the amoC-amoA intergenic region indicated that both Nitrosospira- and Nitrosomonas-type AOB were present in all soils examined. In contrast to the intergenic amoC-amoA profile results, Nitrosomonas-like clones were recovered only in the LW200 treated soil-DNA. The impact of 6 years of contrasting nitrogen sources applications caused changes in AO abundance while the community composition remained relatively stable for both AOB and AOA.

Highlights

In soil environments ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) mediate the first, rate-liming step of autotrophic nitrification, which is considered to be a key control point in the nitrogen cycle resulting in increased N mobility and loss of oxidized N forms through leaching and denitrification (Norton, 2008; Schleper, 2010)
Several studies have indicated that AOB and AOA co-exist and play important roles in soils but questions remain concerning their relative importance in agricultural soil environments (Leininger et al, 2006; Jia and Conrad, 2009; Di et al, 2010; Wessen et al, 2010)
Molecular investigations of Ammonia oxidizers (AO) in the environment have mainly focused on methods which can be summarized into three groups: (1) PCR amplification of a target gene followed by either clone assisted or direct sequence analysis, (2) hybridization of whole cell or PCR amplified DNA fragments with specific oligonucleotides probes, and (3) analysis of PCR products with profiling techniques such as denaturing gradient gel electrophoresis (DGGE) or terminal fragment length polymorphism

Summary

Introduction

In soil environments ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) mediate the first, rate-liming step of autotrophic nitrification, which is considered to be a key control point in the nitrogen cycle resulting in increased N mobility and loss of oxidized N forms through leaching and denitrification (Norton, 2008; Schleper, 2010). 39-19, Nitrosospira briensis C128, Nitrosospira tenuis NV-12, Nitrosolobus multiformis 25196, Nitrosomonas europeae 19178, Nitrosomonas eutropha C-91, and Nitrosomonas cryotolerans 49181 were used as references for profiling AOB based on the variable size amo intergenic region and for primer development (Norton et al, 2002).

Results

Conclusion