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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

Ratios of amoA copy # per gram of soil of AOA to AOB. Soil treatments as in Figure 1. *Bars with asterisk indicate that the copy # of amoA of AOA is significantly higher than the copy # of amoA of AOB for that treatment at p ≤ 0.05.
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Figure 2: Ratios of amoA copy # per gram of soil of AOA to AOB. Soil treatments as in Figure 1. *Bars with asterisk indicate that the copy # of amoA of AOA is significantly higher than the copy # of amoA of AOB for that treatment at p ≤ 0.05.

Mentions: During the extent of this field study the role of archaeal prokaryotes containing putative amoA genes in soils became known (Leininger et al., 2006). In our study using archived samples, we were able to quantify the amoA gene copies based on primers targeting archaeal AO (Leininger et al., 2006). The archaeal amoA gene copies were similar or higher than those found for AOB amoA genes with an average value of 3.8 × 107 per gram soil, with no significant differences between soil treatments (Figure 1). The ratio of archaeal to bacterial amoA gene copies is shown in Figure 2. The ratio of AOA/AOB was higher in the control and compost treated soils versus the other treatments. The supply of ammonium via mineralization is higher in the compost treated soils (four year average DC200 treatment is 5.7 mg N kg-1d-1) versus the control (1.4 mg N kg-1 d-1) or the AS200 (1.3 mg N kg-1 d-1) treated soils. However, the DC and Control soils have in common that the majority of their ammonium is supplied through mineralization of organic nitrogen rather than directly through ammonium additions in fertilizers (AS) or LW (Habteselassie et al., 2006a, 2006b). Our findings are consistent with other studies that show AOB are favored by inputs of ammonium. In a wetland soil, AOB abundance was higher in soils with ammonium additions from a septic tank leak compared to unpolluted soils (Hofferle et al., 2010). In fallowed or pasture soils where organic matter was higher than matched cropped fertilized soils, AOA abundance was several fold higher than AOB abundance (Taylor et al., 2010; Zeglin et al., 2011). Under high ammonium concentration, as in situations where ammonium is supplied in a readily available mineral form, AOB abundance was either comparable or higher than the corresponding AOA abundance (Di et al., 2010; Verhamme et al., 2011; Taylor et al., 2012). These studies, along with ours, clearly indicate differential growth response by AOA and AOB to different forms and concentrations of nitrogen sources.


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

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

Ratios of amoA copy # per gram of soil of AOA to AOB. Soil treatments as in Figure 1. *Bars with asterisk indicate that the copy # of amoA of AOA is significantly higher than the copy # of amoA of AOB for that treatment at p ≤ 0.05.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Ratios of amoA copy # per gram of soil of AOA to AOB. Soil treatments as in Figure 1. *Bars with asterisk indicate that the copy # of amoA of AOA is significantly higher than the copy # of amoA of AOB for that treatment at p ≤ 0.05.
Mentions: During the extent of this field study the role of archaeal prokaryotes containing putative amoA genes in soils became known (Leininger et al., 2006). In our study using archived samples, we were able to quantify the amoA gene copies based on primers targeting archaeal AO (Leininger et al., 2006). The archaeal amoA gene copies were similar or higher than those found for AOB amoA genes with an average value of 3.8 × 107 per gram soil, with no significant differences between soil treatments (Figure 1). The ratio of archaeal to bacterial amoA gene copies is shown in Figure 2. The ratio of AOA/AOB was higher in the control and compost treated soils versus the other treatments. The supply of ammonium via mineralization is higher in the compost treated soils (four year average DC200 treatment is 5.7 mg N kg-1d-1) versus the control (1.4 mg N kg-1 d-1) or the AS200 (1.3 mg N kg-1 d-1) treated soils. However, the DC and Control soils have in common that the majority of their ammonium is supplied through mineralization of organic nitrogen rather than directly through ammonium additions in fertilizers (AS) or LW (Habteselassie et al., 2006a, 2006b). Our findings are consistent with other studies that show AOB are favored by inputs of ammonium. In a wetland soil, AOB abundance was higher in soils with ammonium additions from a septic tank leak compared to unpolluted soils (Hofferle et al., 2010). In fallowed or pasture soils where organic matter was higher than matched cropped fertilized soils, AOA abundance was several fold higher than AOB abundance (Taylor et al., 2010; Zeglin et al., 2011). Under high ammonium concentration, as in situations where ammonium is supplied in a readily available mineral form, AOB abundance was either comparable or higher than the corresponding AOA abundance (Di et al., 2010; Verhamme et al., 2011; Taylor et al., 2012). These studies, along with ours, clearly indicate differential growth response by AOA and AOB to different forms and concentrations of nitrogen sources.

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