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

Habteselassie MY, Xu L, Norton JM - Front Microbiol (2013)

Bottom Line: Ammonia oxidizing bacteria (AOB) were higher in soils from the AS200, AS100, and LW200 treatments (2.5 × 10(7), 2.5 × 10(7), and 2.1 × 10(7)copies g(-1) soil, respectively) than in the control (8.1 × 10(6) copies g(-1) soil) while the abundance of amoA encoding archaea [ammonia oxidizing archaea (AOA)] was not significantly affected by treatment (3.8 × 10(7) copies g(-1) soil, average).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.

View Article: PubMed Central - PubMed

Affiliation: Department of Crop and Soil Sciences, The University of Georgia Griffin Campus Griffin, GA, USA.

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 × 10(7), 2.5 × 10(7), and 2.1 × 10(7)copies g(-1) soil, respectively) than in the control (8.1 × 10(6) copies g(-1) soil) while the abundance of amoA encoding archaea [ammonia oxidizing archaea (AOA)] was not significantly affected by treatment (3.8 × 10(7) 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.

No MeSH data available.


Related in: MedlinePlus

AOB and AOA copy # of amoA gene per gram of soil treated with ammonium sulfate (AS), dairy waste compost (DC), and liquid dairy waste (LW) at two rates of application, 100 and 200 kg N ha-1. Bars with same letter superscript are not significantly different at p ≥ 0.05. No significant difference was found between the treatments for AOA copy number.
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Figure 1: AOB and AOA copy # of amoA gene per gram of soil treated with ammonium sulfate (AS), dairy waste compost (DC), and liquid dairy waste (LW) at two rates of application, 100 and 200 kg N ha-1. Bars with same letter superscript are not significantly different at p ≥ 0.05. No significant difference was found between the treatments for AOA copy number.

Mentions: The copy number of amoA genes from AOB and AOA in soils that received different treatments is shown in Figure 1. For AOB amoA copies ranged from 8 × 106 to 3 × 107 g-1 soil equivalent to approximately 106 to 107 cells g-1 soil assuming 2–3 copies of amoA per cell (Norton et al., 2002). These numbers are comparable or slightly higher than the AOB population sizes reported in agricultural soils using competitive and real-time PCR techniques by targeting amoA and 16S rDNA (Phillips et al., 2000b; Mendum and Hirsch, 2002; Okano et al., 2004; Jia and Conrad, 2009; Gubry-Rangin et al., 2010).


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

Habteselassie MY, Xu L, Norton JM - Front Microbiol (2013)

AOB and AOA copy # of amoA gene per gram of soil treated with ammonium sulfate (AS), dairy waste compost (DC), and liquid dairy waste (LW) at two rates of application, 100 and 200 kg N ha-1. Bars with same letter superscript are not significantly different at p ≥ 0.05. No significant difference was found between the treatments for AOA copy number.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3818573&req=5

Figure 1: AOB and AOA copy # of amoA gene per gram of soil treated with ammonium sulfate (AS), dairy waste compost (DC), and liquid dairy waste (LW) at two rates of application, 100 and 200 kg N ha-1. Bars with same letter superscript are not significantly different at p ≥ 0.05. No significant difference was found between the treatments for AOA copy number.
Mentions: The copy number of amoA genes from AOB and AOA in soils that received different treatments is shown in Figure 1. For AOB amoA copies ranged from 8 × 106 to 3 × 107 g-1 soil equivalent to approximately 106 to 107 cells g-1 soil assuming 2–3 copies of amoA per cell (Norton et al., 2002). These numbers are comparable or slightly higher than the AOB population sizes reported in agricultural soils using competitive and real-time PCR techniques by targeting amoA and 16S rDNA (Phillips et al., 2000b; Mendum and Hirsch, 2002; Okano et al., 2004; Jia and Conrad, 2009; Gubry-Rangin et al., 2010).

Bottom Line: Ammonia oxidizing bacteria (AOB) were higher in soils from the AS200, AS100, and LW200 treatments (2.5 × 10(7), 2.5 × 10(7), and 2.1 × 10(7)copies g(-1) soil, respectively) than in the control (8.1 × 10(6) copies g(-1) soil) while the abundance of amoA encoding archaea [ammonia oxidizing archaea (AOA)] was not significantly affected by treatment (3.8 × 10(7) copies g(-1) soil, average).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.

View Article: PubMed Central - PubMed

Affiliation: Department of Crop and Soil Sciences, The University of Georgia Griffin Campus Griffin, GA, USA.

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 × 10(7), 2.5 × 10(7), and 2.1 × 10(7)copies g(-1) soil, respectively) than in the control (8.1 × 10(6) copies g(-1) soil) while the abundance of amoA encoding archaea [ammonia oxidizing archaea (AOA)] was not significantly affected by treatment (3.8 × 10(7) 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.

No MeSH data available.


Related in: MedlinePlus