Bernie J. Zebarth

Changes in denitrifier abundance, denitrification gene mRNA levels, nitrous oxide emissions and denitrification in anoxic soil microcosms amended with glucose and plant residues.

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 (N2O) 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 (nirSP) increased only in glucose-amended soil: the nirSP 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 × 107 gene copies and 6.9 × 107 transcripts g−1 dry soil. Cumulative N2O emissions and denitrification rates increased over 72 h in both glucose- and plant-tissue-C-treated soil. The nirSP 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.

Changes in bacterial denitrifier community abundance over time in an agricultural field and their relationship with denitrification activity

ABSTRACT 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 (Hp), and in the “furrow” (F). The denitrification rates, N2O 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 cnorBB guilds), whereas the cnorBP community (Pseudomonas mandelii and closely related spp.) showed an ∼4.6-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 cnorBP 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 cnorBB gene numbers. Gene numbers were higher for the Hp than the H location for the nosZ and nirK communities and for the cnorBP community on individual dates, presumably indicating an effect of the plant on denitrifier abundance. Higher cnorBP gene numbers for the H location than the F location and for nosZ and cnorBB 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 cnorBP gene numbers, extractable organic carbon values, and temperature. Denitrification and N2O emissions were mostly regulated by inorganic nitrogen availability and water-filled pore space but were uncoupled from denitrifier community abundances measured in this system.

Abundance, diversity and functional gene expression of denitrifier communities in adjacent riparian and agricultural zones

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 nirK-gene-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.

Opportunities for improved fertilizer nitrogen management in production of arable crops in eastern Canada: a review.

There is increasing public pressure to reduce the environmental impacts of agricultural production. Therefore, one key challenge to producers is to manage their crop production systems in order to minimize losses of nitrogen to air or water, while achieving crop yield and quality goals. Many strategies have been developed in recent years to meet this challenge. These include: development of new tools to measure crop N status in order to refine in-season fertilizer N management, development of new soil N tests to improve prediction of soil N supply, development of new fertilizer N products with release patterns more closely matched to crop N uptake patterns, and development of site-specific N management strategies. We review the opportunities and limitations to these new strategies within different arable crop production systems under the humid and sub-humid soil moisture regimes present in eastern Canada. Future research opportunities to improve the efficiency of fertilizer N utilization include developme...

Research perspective on nitrogen bmp development for potato

Nutrient best management practices (BMPs) are developed to optimize tuber yield and quality, and also to reduce environmental losses of nutrients. Nitrogen (N) management is important both in controlling potato growth and development and in minimizing the risks of groundwater contamination by nitrate and emissions of nitrous oxide, a greenhouse gas. Development of BMPs for N management must consider variation in the magnitude and timing of both N supply and crop N demand. Consequently, these BMPs must reflect differences among potato cultivars, soil properties, cropping systems, water management, and climatic conditions. Despite decades of research, selection of the appropriate rate and timing of fertilizer N application remains a challenging task. A greater understanding of soil N cycling, the development of test-based N recommendation systems, improvements in controlled-release fertilizer technology, and opportunities for spatially variable N management may provide new answers to the old question of “How much N do I apply to my potato crop, at what growth stage, and in what form?”ResumenSe desarrollaron las mejores prácticas de manejo (BMPs) para mejorar el rendimiento y calidad de los tubérculos y también para reducir la pérdida de nutrientes. El manejo del nitrógeno (N) es importante para controlar el crecimiento y desarrollo de la planta y reduce la contaminación del agua del suelo por nitratos y emisiones de ácido nitroso o gas de invernadero. El desarrollo de BMPs para el manejo del N debe considerar la variacián en magnitud y tiempo, tanto del suministro de N como de la demanda de N por el cultivo. Por consiguiente, estos BMPs deben reflejar diferencias entre cultivares de papa, propiedades del suelo, sistemas de cultivo, manejo del agua y condiciones climáticas. A pesar de décadas de investigatión, la selectión de un grado apropiado y momento de aplicación de fertilizante nitrogenado permanecen como tarea discutible. Un mejor entendimiento del ciclo del N, desarrollo de sistemas de recomendación basados en pruebas de N, mejoras en la tecnología de liberatión de fertilizantes controlados y oportunidades para el manejo espacialmente variable del N, puede proporcionar nuevas respuestas a preguntas viejas de “¿Cuanto N debo aplicar a mi cultivo de papa, en que estado de desarrollo y en que forma?”

Effect of split application of fertilizer nitrogen on N2O emissions from potatoes

The timing of fertilizer nitrogen (N) application influences the availability of NO3− as a substrate for denitrification. This study examined the effect of split application of fertilizer N on N2O emissions and denitrification rate in potato (Solanum tuberosumL.) production over 2 yr. Three treatments were used: 0 or 200 kg N ha-1 at planting, and 120 kg N ha-1 at planting plus 80 kg N ha-1 at final hilling. Fertilizer N application increased cumulative N2O emissions. Split fertilizer N application decreased cumulative N2O emissions in 2003, but not in 2002, compared with all fertilizer N applied at planting. A greater proportion of N2O emissions occurred between planting and hilling in 2003 (67%) compared with 2002 (17%). In 2003, the higher emissions during this period resulted from the coincidence of high soil NO3− availability and increased rainfall resulting in reduced aeration. Split N application was effective in reducing N2O emissions by minimizing the supply of NO3− when demand for terminal elect...

Nitrogen Dynamics and Indices to Predict Soil Nitrogen Supply in Humid Temperate Soils

Abstract Knowledge of the nitrogen (N) available to crops during the growing season is essential for improving fertilizer-use efficiency and minimizing the adverse impacts of N losses on the environment. In humid temperate regions, soil N supply is dominated by in-season N mineralization because plant-available N (NH 4 –N and NO 3 –N) is transformed to nonlabile forms or lost from the soil–plant system during fall and winter. The microbially mediated reactions that generate the soil N supply in agroecosystems are affected by system-specific conditions, including soil properties, agricultural management (crop rotation, tillage system, organic amendments), and most importantly, climate. Potentially mineralizable N ( N 0 ) determined from long-term soil incubation is regarded as the standard measure of soil N mineralization potential and may provide a good approximation of the soil N supply. However, this method is time consuming and not practical for routine use. Several chemical methods to estimate the N mineralization potential of soils are discussed in this chapter. The major limitation of chemical methods is that they cannot simulate the microbial-mediated release of plant-available N under field conditions. Consequently, any single chemical method may not be a good predictor of soil N supply. Thus, we suggest a holistic approach to estimate soil N supply in humid temperate regions, which involves (1) the use of a combination of N indices together with weather data and (2) identification and quantification of a specific fraction (s) of organic N that is the dominant contributor (s) to N supply in a particular system.

N2O emissions from spring barley production as influenced by fertilizer nitrogen rate

Usage of mineral nitrogen (N) fertilizers for agricultural crop production systems is a major contributor to anthropogenic nitrous oxide (N2O) emissions. As part of a national study to quantify N2O emissions under different cropping systems and in different eco-regions, this study quantified the effect of fertilizer N rate on spring barley (Hordeum vulgare L.) on N2O emissions in 3 yr in a cool maritime climate with humid soil moisture regimes. Treatments were 0, 75 and 150 kg N ha-1 as ammonium nitrate applied as a pre-plant broadcast. N2O emissions were increased by fertilizer N application in each year. In 2003 and 2005, elevated N2O emissions occurred in the 6-wk period following fertilizer application when soil NO3-N concentrations were high. However, in 2004 and 2005, peak N2O emissions occurred near crop harvest. Elevated N2O emissions at this time were attributed to increased carbon availability due to re-wetting of dry soil. Therefore, the effect of fertilizer N management on N2O emissions may no...

Effect of pH and temperature on denitrification gene expression and activity in Pseudomonas mandelii.

ABSTRACT Pseudomonas mandelii liquid cultures were studied to determine the effect of pH and temperature on denitrification gene expression, which was quantified by quantitative reverse transcription-PCR. Denitrification was measured by the accumulation of nitrous oxide (N2O) in the headspace in the presence of acetylene. Levels of gene expression of nirS and cnorB at pH 5 were 539-fold and 6,190-fold lower, respectively, than the levels of gene expression for cells grown at pH 6, 7, and 8 between 4 h and 8 h. Cumulative denitrification levels were 28 μmol, 63 μmol, and 22 μmol at pH 6, 7, and 8, respectively, at 8 h, whereas negligible denitrification was measured at pH 5. P. mandelii cells grown at 20°C and 30°C exhibited 9-fold and 94-fold increases in levels of cnorB expression between 0 h and 2 h, respectively, and an average 17-fold increase in levels of nirS gene expression. In contrast, induction of cnorB and nirS gene expression for P. mandelii cells grown at 10°C did not occur in the first 4 h. Levels of cumulative denitrification at 10 h were 6.6 μmol for P. mandelii cells grown at 10°C and 20°C and 30 μmol for cells grown at 30°C. Overall, levels of cnorB and nirS expression were relatively insensitive to pH values over the range of pH 6 to 8 but were substantially reduced at pH 5, whereas gene expression was sensitive to temperature, with induction and time to achieve maximum gene expression delayed as the temperature decreased from 30°C. Low pH and temperature negatively affected denitrification activity.

Soil inorganic nitrogen content in commercial potato fields in New Brunswick

Information on inorganic N content in commercial potato fields in Atlantic Canada is limited. Soil inorganic N measurements were collected from 228 commercial potato fields from 1999 to 2001. Soil NO3 content to 30 cm depth at planting ranged from 2 to 124 kg N ha-1, and was generally higher for preceding potato, red clover, or hay crops compared to preceding cereal or other crops. Soil NH4 content to 30 cm depth measured at planting ranged from 3 to 64 kg N ha-1, indicating that both soil NO3 and NH4 need to be measured to assess plant-available soil N content in spring. Soil NO3 content to 30-cm depth at tuber harvest ranged from 3 to 250 kg N ha-1, generally increased with increasing fertilizer N application rate, and differed among different potato cultivars. Soil NO3 content measured to 30-cm depth in spring ranged from 3 to 100% of soil NO3 at harvest in the preceding fall, indicating that highly variable losses of soil NO3 from the root zone occur between growing seasons. Key words: Nitrate, ammoni...