Crop residue influence on denitrification, N2O emissions and denitrifier community abundance in soil
Introduction
Biological denitrification is central to the global nitrogen cycle. It is a dissimilatory process whereby nitrate (NO3−) and nitrite (NO2−), are used as alternative electron acceptors and reduced to gaseous nitric oxide (NO), nitrous oxide (N2O) and molecular nitrogen (N2). N2O is an intermediate in the denitrification process, and consequently both the amount of denitrification and the N2O molar ratio (N2O:(N2 + N2O)) are important in understanding and predicting N2O emissions. The N2O molar ratio is variable in space and time and this is of concern because N2O is a greenhouse gas and a catalyst of stratospheric ozone degradation (Crutzen, 1981).
Both the rate of denitrification and the N2O molar ratio in soil are regulated by various environmental factors including soil water content, temperature, soil pH, redox potential, nitrogen oxide concentrations and availability of carbon (C) (Firestone and Davidson, 1989, Hutchinson and Davidson, 1993). Denitrification is generally promoted under high soil moisture conditions where oxygen is limited, and NO3− and organic C are available for denitrifying microorganisms (Luo et al., 1999).
Carbon availability is one of the most important factors controlling denitrification rates (Beauchamp et al., 1989). It is of interest because it generally increases the amount of denitrification while either decreasing (Weier et al., 1993, Mathieu et al., 2006) or increasing (Dendooven et al., 1996, Mathieu et al., 2006) the N2O molar ratio. This influence of C on denitrification is both through the provision of C directly to the denitrifiers, and/or stimulation of microbial metabolism, which increases the consumption of O2 and creates conditions favorable for denitrification (Beauchamp et al., 1989). Laboratory studies have been conducted using simple C substrates (Weier et al., 1993, Jarvis and Hatch, 1994); however, fewer studies have used complex C sources that are common inputs in agricultural systems, such as crop residues (Dendooven et al., 1996). This is primarily due to the difficulty in assessing C availability in these more complex C sources (Beauchamp et al., 1989).
Microbial denitrification is believed to be a primary source of N2O (Wrage et al., 2004); however, few studies have examined the denitrifier community and their influence on N2O emissions. Denitrifier bacteria belong to a variety of physiological and taxonomic groups (Zumft, 1997) and have commonly been characterized by using most probable number (MPN) counts (Jacobson and Alexander, 1980, Lensi et al., 1995) and the denitrifier enzyme activity (DEA) assay (Martin et al., 1988). Using a modified DEA, Cavigelli and Robertson (2000) reported that under identical environmental conditions there was an increase in the N2O molar ratio in soil from an agricultural field compared with a successional field, and suggested there was a significant functional role of the denitrifier community. More recently, molecular methods have been used to examine the denitrifying community composition and diversity (Rich and Myrold, 2004, Boyle et al., 2006), as well as the abundance of denitrifiers (Henry et al., 2004, Henry et al., 2006, Kandeler et al., 2006, Dandie et al., 2007a) by focusing on the amplification of functional genes involved in denitrification. The genes include nitrate reductase (napA and narG), nitrite reductase (nirS and nirK), nitric oxide reductase (qnorB and cnorB), and nitrous oxide reductase (nosZ). However, not all denitrifying bacteria produce the complete suite of enzymes required to complete the denitrification process (Zumft, 1997).
Literature reviews have suggested that the composition and density of soil denitrifier communities may be factors affecting denitrification (Philippot and Hallin, 2005, Wallenstein et al., 2006), with studies reporting that the denitrifier community differs in response to environmental conditions that indirectly control the rate of denitrification (Cavigelli and Robertson, 2000, Holtan-Hartwig et al., 2000). Therefore, there is a need to understand the community dynamics of denitrifiers and the environmental factors influencing the abundance of the denitrifiers in soil to determine if the denitrifying community may play a role in controlling denitrification. For example, few studies have evaluated how C sources will affect the denitrifier community, and more specifically, the abundance of bacteria possessing these functional genes. Studies using quantitative real-time PCR revealed that soil amended with a mixed C substrate resulted in a four-fold increase in the number of nirK gene copies as compared with the same soil amended with water (Henry et al., 2004). Although quantification of soil denitrifier gene copy numbers has been reported previously in ecological studies, few studies have analyzed the response of denitrifier community abundance in agricultural soils to C amendment treatments, and none of these studies have evaluated the influence of crop residues on the denitrifier community abundance while comparing it with denitrification activity measured using biochemical assays. The objective of this study was to determine the influence of crop residue amendments on: (i) the amount and N2O molar ratio of gaseous denitrification losses; and (ii) total bacterial and denitrifier community abundance. Bacterial abundance was measured using quantitative PCR and targeting the 16S rRNA gene for the total bacterial community, the Pseudomonas mandelii and related species cnorBP, Bosea/Bradyrhizobium/Ensifer spp. cnorBB and nosZ functional genes for the denitrifier communities.
Section snippets
Soil
In January 2006, frozen soil (0–15 cm) was collected from a field previously cropped to spring wheat (Triticum aestivum L.) in Fredericton, New Brunswick, Canada (45°52′ N, 66°31′ W). In order to maintain a low soil NO3− concentration, the soil was kept frozen at −20 °C. Three days prior to experimentation, the soil was thawed, air-dried to a gravimetric water content of 0.30 g g−1 dry weight, homogenized and passed though a 2 mm sieve and stored in the dark at 4 °C. Soil texture (pipette method with
Experiment 1
The objective was to determine the influence of C and NO3− availability on the amount and N2O molar ratio of gaseous denitrification losses. The soil NO3− concentration prior to receiving NO3− and C additions was 3 mg NO3−-N kg−1 soil. At the end of the incubation, soil NO3− concentrations decreased to <1 mg NO3−-N kg−1 soil for all treatments except for the G250N50 treatment, and the three treatments which did not receive glucose but were amended with NO3− (Table 1). Soil NH4+ concentrations
Denitrification and N2O emissions
Microbial denitrification and nitrification are responsible for the majority of N2O emissions in many soil environments (Firestone and Davidson, 1989). N2O resulting from denitrification generally occurs in soil when the WFPS is >60% (Davidson, 1991). In the present study, decreasing soil NO3− concentrations were accompanied by an increase in N2O emissions in the presence of C2H2 in soil cores with a WFPS of 70%. This suggests that the N2O emissions were primarily a result of denitrification.
Acknowledgements
Funding for this research was supplied by the GAPS Program of Agriculture and Agri-Food Canada (AAFC) and a Natural Sciences and Engineering Research Council of Canada (NSERC) Strategic grant. Technical support was provided by Ginette Decker, Jason Dalziel, Drucie Janes, Mona Levesque, and Karen Terry.
References (58)
- et al.
Inhibitory effect of nitrate on reduction of N2O to N2 by soil microorganisms
Soil Biology & Biochemistry
(1978) - et al.
Reciprocal transfer effects on denitrifying community composition and activity at forest and meadow sites in the Cascade Mountains of Oregon
Soil Biology & Biochemistry
(2006) - et al.
Relationships between the denitrification capacities of soils and total, water-soluble and readily decomposable soil organic matter
Soil Biology & Biochemistry
(1975) - et al.
16S rDNA analysis for characterization of denitrifying bacteria isolated from three agricultural soils
FEMS Microbial Ecology
(2000) - et al.
Analysis of denitrification genes and comparison of nosZ, cnorB and 16S rDNA from culturable denitrifying bacteria in potato cropping systems
Systematic & Applied Microbiology
(2007) - et al.
Denitrification in permanent pasture soil as affected by different forms of C substrate
Soil Biology & Biochemistry
(1996) - et al.
Dynamics of trace gas production following compost and NO3 amendments to soil at different initial TOC/NO3 ratios
Soil Biology & Biochemistry
(2002) - et al.
Quantification of denitrifying bacteria in soils by nirK gene targeted real-time PCR
Journal of Microbiological Methods
(2004) - et al.
Comparison of denitrifying communities in organic soils: kinetics of NO3− and N2O reduction
Soil Biology and Biochemistry
(2000) - et al.
Nitrate loss from soil in relation to temperature, carbon source and denitrifier populations
Soil Biology & Biochemistry
(1980)
Potential for denitrification at depth below long-term grass swards
Soil Biology & Biochemistry
Denitrifiers and denitrifying activity in size fractions of a mollisol under permanent pasture and continuous cultivation
Soil Biology & Biochemistry
Factors regulating denitrification in a soil under pasture
Soil Biology & Biochemistry
Emissions and spatial variability of N2O, N2 and nitrous oxide mole fraction at the field scale, revealed with 15N isotopic techniques
Soil Biology & Biochemistry
Denitrification potential in a grassland subsoil: effect of carbon substrates
Soil Biology & Biochemistry
Finding the missing link between diversity and activity using denitrifying bacteria as a model functional community
Current Opinion in Microbiology
Community composition and activities of denitrifying bacteria from adjacent agricultural soil, riparian soil, and creek sediment in Oregon, USA
Soil Biology & Biochemistry
Quantification of functional genes from prokaryotes in soil by PCR
Journal of Microbiological Methods
Phases of denitrification following oxygen depletion in soils
Soil Biology & Biochemistry
Measuring the mole fraction and source of nitrous oxide in the field
Soil Biology & Biochemistry
Mineralization and denitrification in upland nearly saturated and flooded subtropical soil. II. Effect of organic manures varying in N content and C:N ratio
Biology & Fertility of Soils
Nitrification and denitrification as sources of atmospheric nitrous oxide—role of oxidizable carbon and applied nitrogen
Biology & Fertility of Soils
Nitrous oxide emission from soils after incorporating crop residues
Soil Use & Management
Contributions of nitrification and denitrification to N2O emissions from soils at different water-filled pore space
Biology & Fertility of Soils
Denitrification
Carbon sources for bacterial denitrification
Advances in Soil Science
Acetylene blockage technique leads to underestimation of denitrification in oxic soils due to scavenging on intermediate nitric oxide
Soil Biology & Biochemistry
Denitrification in soil. II. Factors affecting denitrification
Journal of Agricultural Science
The functional significance of denitrifier community composition in a terrestrial ecosystem
Ecology
Cited by (286)
Amendment of straw with decomposing inoculants benefits the ecosystem carbon budget and carbon footprint in a subtropical wheat cropping field
2024, Science of the Total EnvironmentEnhanced nitrogen fertilizer combined with straw incorporation can reduce global warming potential with higher carbon sequestration in a summer maize-winter wheat rotation system
2024, Agriculture, Ecosystems and EnvironmentMitigation of soil N<inf>2</inf>O emissions by decomposed straw based on changes in dissolved organic matter and denitrifying bacteria
2023, Science of the Total EnvironmentEffect of co-application of straw and various nitrogen fertilizers on N<inf>2</inf>O emission in acid soil
2023, Journal of Environmental ManagementHigher N<inf>2</inf>O emissions from organic compared to synthetic N fertilisers on sandy soils in a cool temperate climate
2023, Agriculture, Ecosystems and Environment
- 1
Present address: Centre for Environmental Risk Assessment and Remediation, University of South Australia, Mawson Lakes, SA 5095, Australia.