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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

Analysis of clone library sequences for bacterial amoA gene (534 bp). Neighbor joining tree for bacterial partial amoA sequences from soils from the various treatments (see Figure 1) and reference sequences from GenBank. Scale represents number of changes per 100 bp. Clone sequences from this study are in bold and designated with the treatment (see Figure 1) and are followed with the number of clones with sequences with >99% identity.
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Figure 4: Analysis of clone library sequences for bacterial amoA gene (534 bp). Neighbor joining tree for bacterial partial amoA sequences from soils from the various treatments (see Figure 1) and reference sequences from GenBank. Scale represents number of changes per 100 bp. Clone sequences from this study are in bold and designated with the treatment (see Figure 1) and are followed with the number of clones with sequences with >99% identity.

Mentions: The nucleic acid based comparison of the clone sequences and selected pure culture AOB and AOA strains is shown in Figures 4 and 5. The corresponding amino acid based phylogenetic trees (not shown) were also constructed resulting in similar topology but with differences in branch lengths separating two sequences due to the occurrences of neutral mutations in amino acids (Rotthauwe et al., 1997). The superiority of nucleotide sequence over amino acids for analyzing phylogenetic relationship between closely related strains of bacteria has been previously noted (Yamamoto and Harayama, 1996; Rotthauwe et al., 1997).


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

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

Analysis of clone library sequences for bacterial amoA gene (534 bp). Neighbor joining tree for bacterial partial amoA sequences from soils from the various treatments (see Figure 1) and reference sequences from GenBank. Scale represents number of changes per 100 bp. Clone sequences from this study are in bold and designated with the treatment (see Figure 1) and are followed with the number of clones with sequences with >99% identity.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Analysis of clone library sequences for bacterial amoA gene (534 bp). Neighbor joining tree for bacterial partial amoA sequences from soils from the various treatments (see Figure 1) and reference sequences from GenBank. Scale represents number of changes per 100 bp. Clone sequences from this study are in bold and designated with the treatment (see Figure 1) and are followed with the number of clones with sequences with >99% identity.
Mentions: The nucleic acid based comparison of the clone sequences and selected pure culture AOB and AOA strains is shown in Figures 4 and 5. The corresponding amino acid based phylogenetic trees (not shown) were also constructed resulting in similar topology but with differences in branch lengths separating two sequences due to the occurrences of neutral mutations in amino acids (Rotthauwe et al., 1997). The superiority of nucleotide sequence over amino acids for analyzing phylogenetic relationship between closely related strains of bacteria has been previously noted (Yamamoto and Harayama, 1996; Rotthauwe et al., 1997).

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