No abstract

In agricultural cropping systems, crop residues are sources of organic carbon (C), an important factor influencing denitrification. The effects of red clover, soybean, and barley plant residues and of glucose on denitrifier abundance, denitrification gene mRNA levels, nitrous oxide (N 2 O) emissions, and denitrification rates were quantified in anoxic soil microcosms for 72 h. nosZ gene abundances and mRNA levels significantly increased in response to all organic carbon treatments over time. In contrast, the abundance and mRNA levels of Pseudomonas mandelii and closely related species (nirS P ) increased only in glucose-amended soil: the nirS P guild abundance increased 5-fold over the 72-h incubation period (P < 0.001), while the mRNA level significantly increased more than 15-fold at 12 h (P < 0.001) and then subsequently decreased. The nosZ gene abundance was greater in plant residue-amended soil than in glucose-amended soil. Although plant residue carbon-to-nitrogen (C:N) ratios varied from 15:1 to 30:1, nosZ gene and mRNA levels were not significantly different among plant residue treatments, with an average of 3.5 ؋ 10 7 gene copies and 6.9 ؋ 10 7 transcripts g ؊1 dry soil. Cumulative N 2 O emissions and denitrification rates increased over 72 h in both glucose-and plant-tissue-C-treated soil. The nirS P and nosZ communities responded differently to glucose and plant residue amendments. However, the targeted denitrifier communities responded similarly to the different plant residues under the conditions tested despite changes in the quality of organic C and different C:N ratios.

This study measured total bacterial and denitrifier community abundances over time in an agricultural soil cropped to potatoes (Solanum tuberosum L.) by using quantitative PCR. Samples were collected on 10 dates from spring to autumn and from three spatial locations: in the potato "hill" between plants (H), close to the plant (H p ), and in the "furrow" (F). The denitrification rates, N 2 O emissions, and environmental parameters were also measured. Changes in denitrifier abundance over time and spatial location were small (1.7-to 2.7-fold for the nirK, nosZ, and cnorB B guilds), whereas the cnorB P community (Pseudomonas mandelii and closely related spp.) showed an ϳ4.6-fold change. The seasonal patterns of denitrifier gene numbers varied with the specific community: lower nosZ gene numbers in April and May than in June and July, higher cnorB P gene numbers in May and June than in March and April and September and November, higher nirK gene numbers in early spring than in late autumn, and no change in cnorB B gene numbers. Gene numbers were higher for the H p than the H location for the nosZ and nirK communities and for the cnorB P community on individual dates, presumably indicating an effect of the plant on denitrifier abundance. Higher cnorB P gene numbers for the H location than the F location and for nosZ and cnorB B on individual dates reflect the effect of spatial location on abundance. Denitrifier abundance changes were not related to any environmental parameter, although a weak relationship exists between cnorB P gene numbers, extractable organic carbon values, and temperature. Denitrification and N 2 O emissions were mostly regulated by inorganic nitrogen availability and water-filled pore space but were uncoupled from denitrifier community abundances measured in this system.

Lands under riparian and agricultural management differ in soil properties, water content, plant species and nutrient content and are therefore expected to influence denitrifier communities, denitrification and nitrous oxide (N 2 O) emissions. Denitrifier community abundance, denitrifier community structure, denitrification gene expression and activity were quantified on three dates in a maize field and adjacent riparian zone. N 2 O emissions were greater in the agricultural zone, whereas complete denitrification to N 2 was greater in the riparian zone. In general, the targeted denitrifier community abundance did not change between agricultural and riparian zones. However, nosZ gene expression was greater in the riparian zone than the agricultural zone. The community structure of nirS-gene-bearing denitrifiers differed in June only, whereas the nirK-gene-bearing community structure differed significantly between the riparian and the agricultural zones at all dates. The nirKgene-bearing community structure was correlated with soil pH, while no significant correlations were found between nirS-gene-bearing community structure and soil environmental variables or N 2 O emissions, denitrification or denitrifier enzyme activity. The results suggested for the nirK and nirS-gene-bearing communities different factors control abundance vs. community structure. The nirK-gene-bearing community structure was also more responsive than the nirS-gene-bearing community structure to change between the two ecosystems.

No abstract

The influence of liquid dairy and swine manure, soil water‐extractable C (WEC) and glucose on the amount of denitrification, the N2O molar ratio [N2O/(N2O + N2)], and the abundance of soil denitrifiers was investigated using repacked soil cores. Quantitative polymerase chain reaction was used to measure the abundance of the total bacteria (16S rRNA gene), two denitrifier guilds bearing the cnorB gene, and nosZ gene communities. The availability of both C and N oxides influenced the amount of denitrification and the N2O molar ratio for simple (glucose) and complex (liquid manure and WEC) C sources. A positive relationship (R2 = 0.77) was measured between respiration (cumulative CO2 emissions) and total denitrification. A negative relationship (R2 = 0.70) was found between respiration and the N2O molar ratio, demonstrating that C availability in soil promotes the reduction of N2O to N2 The abundance of the 16S rRNA and cnorBB (Bosea/Bradyrhizobium/Ensifer spp.) gene bearing bacteria was not significantly affected by the addition of C. The abundance of cnorBP (Pseudomonas mandelii and related species) gene bearing bacteria increased in response to glucose and manure addition, but only when also amended with NO3− Significant positive correlations were found between the abundance of the cnorBP gene bearing bacteria and respiration. The nosZ gene bearing bacteria significantly increased only in soil amended with liquid manures. No significant relationships were found between the abundance of denitrifiers and total denitrification, N2O emissions, or the N2O molar ratio. Changes in denitrifier community abundance appeared to reflect changes in C substrate availability and were uncoupled to denitrification activity.

The quantification of denitrifying bacteria is a component in the further understanding of denitrification processes in the environment. Real-time PCR primers were designed to target two segments of the denitrifier population (cnorB P [Pseudomonas mandelii and closely related strains] and cnorB B [Bosea, Bradyrhizobium, and Ensifer spp.]) in agricultural soils based on functional cnorB (nitric oxide reductase) gene sequences. Total population numbers were measured using 16S rRNA gene real-time PCR. Two soil microcosm experiments were conducted. Experiment 1 examined the response of the indigenous soil microbial population to the addition of 500 mg/kg glucose-C daily over 7 days in soil microcosms. Changes in the total population were correlated (r ‫؍‬ 0.83) between 16S rRNA gene copy numbers and microbial biomass carbon estimates. Members of the cnorB P population of denitrifiers showed typical r-strategy by being able to increase their proportion in the total population from starting levels of <0.1% to around 2.4% after a daily addition of 500 mg/kg glucose-C. The cnorB B guild was not able to increase its relative percentage of the total population in response to the addition of glucose-C, instead increasing copy numbers only in proportion with the total population measured by 16S rRNA genes. Experiment 2 measured population dynamics in soil after the addition of various amounts of glucose-C (0 to 500 mg/kg) and incubation under denitrifying conditions. cnorB P populations increased proportionally with the amount of glucose-C added (from 0 to 500 mg/kg). In soil microcosms, denitrification rates, respiration, and cnorB P population densities increased significantly with increasing rates of glucose addition. cnorB B guild densities did not increase significantly under denitrifying conditions in response to increasing C additions.

Environmental conditions can change dramatically over a crop season and among locations in an agricultural field and can increase denitrification and emissions of the potent greenhouse gas nitrous oxide. In a previous study, changes in the overall size of the denitrifier community in a potato crop field were relatively small and did not correlate with variations in environmental conditions or denitrification rates. However, denitrifying bacteria are taxonomically diverse, and different members of the community may respond differently to environmental changes. The objective of this research was to understand which portion of the nirK denitrifying community is active and contributes to denitrification under conditions in a potato crop field. Denaturing gradient gel electrophoresis (DGGE) of nirK genes in soil-extracted DNA showed changes in the composition of the nirK denitrifier community over the growing season and among spatial locations in the field. By contrast, the composition of the active nirK denitrifier community, as determined by DGGE analysis of nirK transcripts derived from soil-extracted mRNA, changed very little over time, although differences in the relative abundance of some specific transcripts were observed between locations. Our results indicate that the soil denitrifier populations bearing nirK genes are not all contributing to denitrification and that the denitrifying populations that are active are among the most abundant and ubiquitous nirK-bearing denitrifiers. Changes in the community composition of the total and active nirK denitrifiers were not strongly correlated with changes in environmental factors and denitrification activity.Conditions in an agricultural field can vary dramatically over a crop growing season due to natural phenomena, such as cool, wet springs and hot, dry summers, and agronomic practices, such as application of fertilizers. Environmental changes have the potential to influence the metabolic activity of soil microbes that can lead to undesirable effects, including the emission of nitrous oxide (N 2 O), an important greenhouse gas and ozone-depleting substance, through microbial denitrification. Denitrification is an alternative respiratory process in which nitrogen oxides such as nitrate (NO 3 Ϫ ) and nitrite (NO 2 Ϫ ) are used as electron acceptors and reduced to N 2 O and dinitrogen (N 2 ) gases under oxygen-limited conditions (37). The capacity to use nitrogen oxides as final electron acceptors is widespread among bacteria (43). Denitrification not only yields a potent greenhouse gas but is also responsible for nitrogen loss from agricultural soils (3,7,15).Denitrification in soil is influenced by numerous interacting physical, chemical, and biological factors (26, 37). Soil aeration, temperature, and carbon and nitrate availability fluctuate over time and are major parameters regulating denitrification in agricultural soils (15,30,34,35). Conditions known to be conducive to denitrification activity include low soil aeration (influenced by soil structure, texture...