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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

(A–C) PCR amplicons of the intergenic region between amoC and amoA with amoC305F-amoA310R primer set from soil samples that received control, AS100, AS200, DC100, DC200, LW100, and LW200 treatments from three replicate field blocks (A–C). Lanes NC, PC, and Marker correspond to negative control (NC), positive controls (PC) (from top to bottom, Nitrosospira multiformis 25196, Nitrosospira sp. NpAV, and Nitrosomonas europaea 19178) and molecular weight markers (marker), respectively. (D) Cluster analysis for intergenic profiles from four blocks and all seven treatments (see above).
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Figure 3: (A–C) PCR amplicons of the intergenic region between amoC and amoA with amoC305F-amoA310R primer set from soil samples that received control, AS100, AS200, DC100, DC200, LW100, and LW200 treatments from three replicate field blocks (A–C). Lanes NC, PC, and Marker correspond to negative control (NC), positive controls (PC) (from top to bottom, Nitrosospira multiformis 25196, Nitrosospira sp. NpAV, and Nitrosomonas europaea 19178) and molecular weight markers (marker), respectively. (D) Cluster analysis for intergenic profiles from four blocks and all seven treatments (see above).

Mentions: Visible products of the amo intergenic region from soil DNA extracts (Figure 3) were obtained through semi-nested PCR reactions. Several primer sets were assessed through use with pure cultures of AOB, soil DNA and in silico and the use of amoC305/amoA310 resulted in the most reproducible banding patterns. The predicted and observed sizes of the amplicons of amoC305F/amoA310R from some pure culture AOB strains are shown in Table 2. DNA extracts from soils that received the AS, DC, and LW treatments were first amplified with amoC305F/amoA302R primer sets and subsequently semi-nested with amoC305F/amoA310R. PCR amplification of the genomic DNA of the pure culture strains indicated that amoC305F/amoA302R gave a single band amplicon for all the pure cultures as predicted. Although direct amoC305F/amoA310R amplification with genomic DNA gave multiple bands for some of the strains, we did not observe this in semi-nested PCR (data not shown). The profiles of the amoC305F/amoA310R amplicons (Figure 3) show differences in AOB community composition between the different treatments. The amoC305/amoA310 gave visible bands (5–10 total) for all the treatments from all of the field block replicates, three of which are shown in Figure 3. The band patterns of each treatment from the field block replicates were not exactly identical indicating the inherent variability among the replicates.


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

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

(A–C) PCR amplicons of the intergenic region between amoC and amoA with amoC305F-amoA310R primer set from soil samples that received control, AS100, AS200, DC100, DC200, LW100, and LW200 treatments from three replicate field blocks (A–C). Lanes NC, PC, and Marker correspond to negative control (NC), positive controls (PC) (from top to bottom, Nitrosospira multiformis 25196, Nitrosospira sp. NpAV, and Nitrosomonas europaea 19178) and molecular weight markers (marker), respectively. (D) Cluster analysis for intergenic profiles from four blocks and all seven treatments (see above).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: (A–C) PCR amplicons of the intergenic region between amoC and amoA with amoC305F-amoA310R primer set from soil samples that received control, AS100, AS200, DC100, DC200, LW100, and LW200 treatments from three replicate field blocks (A–C). Lanes NC, PC, and Marker correspond to negative control (NC), positive controls (PC) (from top to bottom, Nitrosospira multiformis 25196, Nitrosospira sp. NpAV, and Nitrosomonas europaea 19178) and molecular weight markers (marker), respectively. (D) Cluster analysis for intergenic profiles from four blocks and all seven treatments (see above).
Mentions: Visible products of the amo intergenic region from soil DNA extracts (Figure 3) were obtained through semi-nested PCR reactions. Several primer sets were assessed through use with pure cultures of AOB, soil DNA and in silico and the use of amoC305/amoA310 resulted in the most reproducible banding patterns. The predicted and observed sizes of the amplicons of amoC305F/amoA310R from some pure culture AOB strains are shown in Table 2. DNA extracts from soils that received the AS, DC, and LW treatments were first amplified with amoC305F/amoA302R primer sets and subsequently semi-nested with amoC305F/amoA310R. PCR amplification of the genomic DNA of the pure culture strains indicated that amoC305F/amoA302R gave a single band amplicon for all the pure cultures as predicted. Although direct amoC305F/amoA310R amplification with genomic DNA gave multiple bands for some of the strains, we did not observe this in semi-nested PCR (data not shown). The profiles of the amoC305F/amoA310R amplicons (Figure 3) show differences in AOB community composition between the different treatments. The amoC305/amoA310 gave visible bands (5–10 total) for all the treatments from all of the field block replicates, three of which are shown in Figure 3. The band patterns of each treatment from the field block replicates were not exactly identical indicating the inherent variability among the replicates.

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