Dataset Information

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

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.

SUBMITTER: Habteselassie MY

PROVIDER: S-EPMC3818573 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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

Habteselassie Mussie Y MY Xu Li L Norton Jeanette M JM

Frontiers in microbiology 20131106

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 approximat ...[more]

PMID: 24223575

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Project description:The milieu in soil in which microorganisms dwell is never constant. Conditions such as temperature, water availability, pH and nutrients frequently change, impacting the overall functioning of the soil system. To understand the effects of such factors on soil functioning, proxies (indicators) of soil function are needed that, in a sensitive manner, reveal normal amplitude of variation. Thus, the so-called normal operating range (NOR) of soil can be defined. In this study we determined different components of nitrification by analyzing, in eight agricultural soils, how the community structures and sizes of ammonia oxidizing bacteria and archaea (AOB and AOA, respectively), and their activity, fluctuate over spatial and temporal scales. The results indicated that soil pH and soil type are the main factors that influence the size and structure of the AOA and AOB, as well as their function. The nitrification rates varied between 0.11 ± 0.03 μgN h(-1) gdw(-1) and 1.68 ± 0.11 μgN h(-1) gdw(-1), being higher in soils with higher clay content (1.09 ± 0.12 μgN h(-1) gdw(-1)) and lower in soils with lower clay percentages (0.27 ± 0.04 μgN h(-1) gdw(-1)). Nitrifying activity was driven by soil pH, mostly related to its effect on AOA but not on AOB abundance. Regarding the influence of soil parameters, clay content was the main soil factor shaping the structure of both the AOA and AOB communities. Overall, the potential nitrifying activities were higher and more variable over time in the clayey than in the sandy soils. Whereas the structure of AOB fluctuated more (62.7 ± 2.10%) the structure of AOA communities showed lower amplitude of variation (53.65 ± 3.37%). Similar trends were observed for the sizes of these communities. The present work represents a first step toward defining a NOR for soil nitrification. The sensitivity of the process and organisms to impacts from the milieu support their use as proxies in the NOR of agricultural soils. Moreover, the clear effect of soil texture established here suggests that the NOR should be defined in a soil type-specific manner.

Project description:The Baltic Sea is one of the largest brackish water bodies in the world. Redoxclines that form between oxic and anoxic layers in the deepest sub-basins are a semi-permanent character of the pelagic Baltic Sea. The microbially mediated nitrogen removal processes in these redoxclines have been recognized as important ecosystem service that removes large proportion of the nitrogen load originating from the drainage basin. However, nitrification, which links mineralization of organic nitrogen and nitrogen removal processes, has remained poorly understood. To gain better understanding of the nitrogen cycling in the Baltic Sea, we analyzed the assemblage of ammonia oxidizing bacteria and archaea in the central Baltic Sea using functional gene microarrays and measured the biogeochemical properties along with potential nitrification rates. Overall, the ammonia oxidizer communities in the Baltic Sea redoxcline were very evenly distributed. However, the communities were clearly different between the eastern and western Gotland Basin and the correlations between different components of the ammonia oxidizer assemblages and environmental variables suggest ecological basis for the community composition. The more even community ammonia oxidizer composition in the eastern Gotland Basin may be related to the constantly oscillating redoxcline that does not allow domination of single archetype. The oscillating redoxcline also creates long depth range of optimal nitrification conditions. The rate measurements suggest that nitrification in the central Baltic Sea is able to produce all nitrate required by denitrification occurring below the nitrification zone. Two color array (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype). Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array. Signal is the ratio of Cy3 to Cy5. Three replicate probes were printed for each archetype. Two replicate arrays were run on duplicate targets.

Dataset Information

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

Publications

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

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