The influence of synthetic sheep urine on ammonia oxidizing bacterial communities in grassland soil

Abstract In grazed, grassland soils, sheep urine generates heterogeneity in ammonia concentrations, with potential impact on ammonia oxidizer community structure and soil N cycling. The influence of different levels of synthetic sheep urine on ammonia oxidizers was studied in grassland soil microcos...

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Published in:	FEMS microbiology ecology 2006-06, Vol.56 (3), p.444-454
Main Authors:	Mahmood, Shahid, Prosser, James I
Format:	Article
Language:	eng
Subjects:	16S rRNA gene Abundance Accumulation Ammonia Ammonia - metabolism ammonia oxidizing bacteria Amplification Animals Bacteriology Biological and medical sciences Clusters Community structure denaturing gradient gel electrophoresis Deoxyribonucleic acid DNA Ecosystem Electrophoresis Electrophoresis, Gel, Pulsed-Field Fundamental and applied biological sciences. Psychology Gel electrophoresis Gene Amplification Gene sequencing Genes, rRNA - genetics grassland soil Grasslands Heterogeneity Hydrogen-Ion Concentration Level (quantity) Microbiology Microcosms Miscellaneous Nitrates - metabolism Nitrites - metabolism Nucleotide sequence Oxidation Oxidation-Reduction Oxidizing agents Polymerase chain reaction Qualitative analysis Relative abundance Ribonucleic acid RNA rRNA 16S Sequence Analysis, DNA Sheep sheep urine Soil - analysis Soil Microbiology Soil structure Soil treatment Soils Spatial distribution Urine
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Summary:	Abstract In grazed, grassland soils, sheep urine generates heterogeneity in ammonia concentrations, with potential impact on ammonia oxidizer community structure and soil N cycling. The influence of different levels of synthetic sheep urine on ammonia oxidizers was studied in grassland soil microcosms. ‘Total’ and active ammonia oxidizers were distinguished by comparing denaturing gradient gel electrophoresis (DGGE) profiles following PCR and RT-PCR amplification of 16S rRNA gene fragments, targeting DNA and RNA, respectively. The RNA-based approach indicated earlier, more reproducible and finer scale qualitative shifts in ammonia oxidizing communities than DNA-based analysis, but led to amplification of a small number of nonammonia oxidizer sequences. Qualitative changes in RNA-derived DGGE profiles were related to changes in nitrate accumulation. Sequence analysis of excised DGGE bands revealed that ammonia oxidizing communities in synthetic sheep urine-treated soils consisted mainly of Nitrosospira clusters 2, 3 and 4. Nitrosospira cluster 2 increased in relative abundance in microcosms treated with all levels of synthetic sheep urine. Low levels additionally led to increased relative abundance of Nitrosospira cluster 4 and medium and high levels increased relative abundance of cluster 3. Synthetic sheep urine is therefore likely to influence the spatial distribution and composition of ammonia oxidizer communities, with consequent effects on nitrate accumulation.
ISSN:	0168-6496 1574-6941