Balancing Nitrogen Sinks and Sources Using Cover Crops On Manured Fields

Final Report for GNE10-005

Project Type: Graduate Student
Funds awarded in 2010: $10,179.00
Projected End Date: 12/31/2011
Grant Recipient: Cornell University
Region: Northeast
State: New York
Graduate Student:
Faculty Advisor:
Dr. Harold van Es
Cornell University
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Project Information

Spring nitrogen dynamics, nitrous oxide emissions and leaching losses under winter cover crops on heavily manured fields

Increased animal production and concomitant land application of manure create conditions conducive for significant environmental losses of manure-N. Scavenger cover crops have shown some promise in mitigating off-field losses. In this study, we tested the effects of oat (Avena sativa) and winter rye (Secale cereal) cover crops on N losses in soils with a history of manure management during the volatile spring season. Undisturbed cores were taken from replicated plots planted to oats, winter rye or fallow at three points during the spring season. After a simulated rainfall, emissions were collected for a subsequent 96-hour incubation period. Nitrous oxide emissions in cover crop treatments showed no significant difference over a control plot during the early spring season. However, as temperatures warmed, winter rye was found to decrease average N2O emissions by approximately 70% when compared to either the oat or fallow treatment. Furthermore, nitrate concentrations found in leachate at 55 cm were dramatically lower in rye plots, while the winter-killed oat showed no decrease in nitrate leaching when compared to a control. These stark contrasts in oat and rye treatments were likely the result of the re-growth of the rye during the sampling period. Stimulation of N losses in manured fields could in fact be hastened during the spring season with the use of oats as a fall cover crop, while rye appears to have a positive effect on N-cycling during the same period.


Manure and N Losses

Approximately 140 Tg. of manure-N is applied to arable lands each year, which has roughly doubled since World War II (Davidson, 2009). Application of manure often includes applying nutrients in incompatible ratios with those for crop uptake (Edmeades, 2003). Due to the simple issue of disposal, accumulation of macronutrients (particularly N and P) is a likely result. Furthermore, manured agricultural systems often combine low N-use efficiency with readily available carbon for high N losses (Oenema et al., 2010).

With the high variability of manure composition, the extent of available N and C is dynamic in these systems. In a study of manure mineralization dynamics, van Kessel et al. (2000) found that compounds such as urea, simple peptides and amino acids, protein supplements, ruminal bacteria and colonic cells stimulated faster mineralization while other, more recalcitrant compounds, such as ADF, NDF and lignin resist decomposition and mobilization. Additionally, as nutrients are mobilized, they are subject to rapid adsorption by the soil matrix (Angers et al., 2006). In a study on fall-applied manure, Eghball (2000) found that 11% of composted manure and 21% of non-composted manure N was mineralized during the following year. Consequently, the temporal component of this system will have a large effect on nutrient losses.

Spring thaw in temperate climates is a period of potential heavy N losses. Christensen and Tiedje (1990) found N2O production to be far higher during the thaw period than in any other period tested throughout the year. Further research has produced similar results from cores subjected to freeze/thaw cycles, which suggests a possible mechanism for physical disruption of aggregates to promote the production of N2O (Christensen and Tiedje, 1990, Christensen and Christensen, 1991, van Bochove et al., 2000, Muller et al., 2002). Using 15N techniques, Wagner-Riddle et al. (2008) found that high emissions were due to newly produced gas as opposed to older N2O that might have been trapped deeper in the soil profile. Using frozen and unfrozen cores with a straw amendment, Christensen and Christensen (1991) found that extractable carbon increased after a thaw period and then returned to levels similar to the unfrozen treatment on subsequent freezing while maintaining significantly higher denitrification levels. This suggests that while freezing and thawing may produce available carbon through dead microbial biomass, additional carbon is liberated from previously sequestered fractions in the soil. Thus N2O production in the spring is greatly facilitated by the amount and quality of carbon present in the soil before the winter freeze period.

Nitrogen losses in the spring are especially acute in manured systems. In the denitrification process, high levels of organic carbon in manure correlate with increased N2O emissions (Beauchamp and Paul, 1989, Clemens and Huschka, 2001, Miller et al., 2009). The incorporation of manure in the fall promotes N2O emissions with as much as 65% of yearly emissions occurring in the spring thaw period (Wagner-Riddle et al, 1997). Additionally, leaching losses of NO3-N are susceptible, particularly when fall-applied early and in warm, wet autumns (van Es et al., 2006).

Beckwith et al. (1998) found that applications of various manures applied between September and November significantly increased leaching losses over a control with as much as 20% leaching loss as a percentage of total applied. Similarly, Smith et al. (2002) found average leaching losses of approximately 15% of applied manure-N with high CV values ranging from 2-53%. Furthermore, nitrate leached into groundwater is subject to rapid degassing as N2O when exposed to the atmosphere (Reay et al., 2003). The current emissions factor for this indirect pathway under IPCC guidelines is 0.0075 kg N2O-N kg-1 per kg N leaching/runoff with a considerable range of uncertainty (IPCC, 2006).

Cover Crops

Winter cover crops are increasingly adopted for both N-fixing and N-foraging properties, as well as their ability to suppress weeds, reduce erosion and improve water-holding capacity (Fageria, 2007, Kaspar et al., 2007, Meisinger et al., 1991). Cover crops may interact with soil nitrogen cycle dynamics, potentially serving as an additional C source to fuel nitrate reduction or, conversely, by immobilizing residual N making it unavailable for chemical and physical soil processes. Cover crop utilization of N, like any other link in the nitrogen cycle, is highly variable and subject to prevailing environmental conditions and indigenous soil properties (Thorup-Kristensen et al., 2003).

Various cover crops can take up and release N at different times and rates, which makes effects difficult to study and sometimes contradicting. Jarecki et al. (2009) found contrasting results in laboratory and field experiments on denitrification. Their research concluded that a rye cover crop reduced N2O emissions in a microcosm experiment with swine manure additions. However, in field studies, rye and oat cover crops had no effect on emissions. On the other hand, Sauer et al. (2009) investigated the interacting effects of a rye cover crop with poultry manure in a bermudagrass pasture and found that rye reduced denitrification losses in the spring, which they attributed to a reduced soil NO3 -N pool. Moreover, N uptake by the succeeding crop may be erratic. Ball et al. (2005) found residue-derived-N content in grain to vary according to climatic factors. In wet years N was a limiting factor and cover crops improved yields. This uptake is likely to be variable even within a growing season, which would likely contribute to field-scale variability in subsequent trial periods.

The objective of this study was to determine the impact of two catch (cover) crops -rye and oat- on nitrogen flows in a manured agroecosystem during the volatile spring season. Rye and oats were selected as treatments due to their popularity in the northeastern US and also for their physiological disparity in winter tolerance and how this affects carbon and nitrogen cycling.

Project Objectives:

- Assess the nitrogen dynamics associated with the addition of winter forage cover crops (winter rye and oats) on manured soils. This study will assess the effect of these cover crops with respect to leaching losses and denitrification as compared to a control factor.

- Through the use of 15N isotope enrichment as labelled biomass, the study allows for the partitioning of residue N. Isotope enrichment allows one to trace its movement within a given system, which then allows for an analysis of the interactions between treatments. This step assesses the management aspect of this study. Under the use of different cover crops, this step measures the effectiveness of applying cover crops.

- Demonstrate the potential for winter rye and oats as forage cover crops in the temperate Northeast while investigating the associated tradeoffs between N sinks and losses.


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  • Chris Graham
  • Dr. Harold van Es


Materials and methods:


This study was conducted on a working dairy farm located in Lansing, NY, USA (42°35’ N, 76°31’W; 264 m a.s.l.) using soils with a history of manure application. The soil at the research site is a silt-loam with average surface soil texture measured as 330 g kg-1 sand, 550 g kg-1 silt and 120 g kg-1 clay determined using procedures described by Kettler et al. (2001). Average organic matter content was 40 g kg-1 soil, determined gravimetrically by loss on ignition and pH 7.1, determined in a 1:1 water slurry. During the past three years, manure was applied on 4/10/2008, 10/05/2009 and 4/15/2010 (final application before study commencement) at rates of 7,800 gal/acre, 8,700 gal/acre and 5,000 gal/acre, respectively.

Field sampling was conducted during three separate events in April and May of 2011 when the average temperature ranges from 1 – 13 °C and 6 – 20°C respectively. Normal total precipitation for these months is typically 84 mm in April and 82 mm in May. Over the experimentation period, however, April rainfall was more than twice the average with 188 mm of precipitation and May had a total of 157 mm.

Cover Crops

Winter rye (Secale cereale) and oat (Avena sativa) were broadcast seeded on September 24th, 2010 in a 3x4 spatially-balanced, complete block design (van Es et al., 2007) at a rate of 112 kg ha-1 (Figure 1). Along with control plots, each cover crop treatment was replicated four times for a total of twelve blocks. Quadrats of rye and oats were subsequently harvested on December 3rd, 2010 and analyzed for N uptake by dry combustion using a Europa ANCA-GSL CN auto-analyzer (PDZ Europa Ltd., Sandbach, UK). The rye plots were harvested two additional times in the Spring on April 22nd and May 26th.

Soil and Water Sampling

Soil samples were taken periodically throughout the spring season. On day of year (DOY) 77, 97, 118 and 146 soil was sampled from the 0-15 and 15-30 cm soil layers for mineral N analysis. Additional cores were taken for bulk density and N2O analysis (DOY – 97, 123 and 144). Tension lysimeters (Soil Moisture Equipment Corp., Santa Barbara, CA) were installed on September 24th, 2010 at a depth of 55 cm. At DOY 97, 118 and 146, a sample was obtained by after applying a 70-80 kPa tension through a battery-operated pump and maintained for 24 hours. The pore water was then collected and analyzed for NO3 concentration.

Soil and Water Analysis

Soils collected from the field were placed in a drying oven at 60°C for 24 hours and then sieved through a 2 mm mesh screen. The procedure to determine ammonium and nitrate concentrations was based on that of Keeney and Nelson (1982) with minor modifications. An 8-gram subsample was extracted from both soil layers with 40 ml of 2M KCl from each replication and shaken on a reciprocal shaker for 30 minutes, then filtered through ashless filter paper (Whatman no. 42). Ammonium and nitrate concentrations from soil extracts and water samples were determined using a segmented-flow autoanalyzer (Seal Analytical, Mequon, WI).

Additional samples from the 0-15 cm soil layer were taken for determining potentially mineralizable N (PMN) and active carbon. PMN measures a soil’s capacity to mineralize organic nitrogen. Soil materials were prepared in the same manner as previously described for NH4 and NO3 analysis, based on an anaerobic incubation method described by Drinkwater et al. (1996). Briefly, NH4 from paired soil samples is extracted before and after a 7-day incubation period at 37°C. The first sample serves as the initial NH4 present, which is then subtracted from the final NH4 concentration at t=7 days for the total mineralized N. Ten ml of DDI water was added to the sample and the sample container was purged with N2 to ensure anoxic conditions during incubation. The method of extraction for NH4 in the final sample was the same as the initial sample, however, 2.67 M KCl was substituted for 2M KCl.

Biologically active carbon was determined according to Weil et al. (2003). Briefly, a 2.5 g soil sample was reacted with 20 ml of .02 M potassium permanganate (KMnO4) solution over a two-minute shaking period. The solution was centrifuged and the resultant supernatant was measured for absorbance at 550 nm using a hand-held colorimeter (Hach, Loveland, CO).

N2O Procedures and Analysis

Three undisturbed soil cores, 13.6 cm x 5.2 cm, were taken from each plot using PVC pipe for a total of 12 cores per treatment. For destructive analysis, 9 additional cores were collected for sampling during the incubation period. To equilibrate, the cores were placed in an incubator simulating the average air temperature for that time of year (10°C for DOY 97, 15°C for DOY 123 and 20°C for DOY 144) for 24 hours prior to the first sampling (t=0). At this time, the headspace from the sealed cores was sampled followed by a 5-minute simulated rainfall of 150 mm hr-1 (12.5 mm total) using a drip-type rainfall simulator (Ogden et al., 1997). Additional samples were taken at hour 6, 12, 24, 48, 72 and 96.

For each sampling, three blanks and all cores were placed in 1-L Mason jars fitted with an airtight seal for one hour (Millar and Baggs, 2004). Because the gas flux was found to be linear over this time period, flux can be calculated as the difference between the sample and the blank over the 1-hour period. A 20 ml sample was taken from the headspace of each jar with a syringe and injected for storage in 12 ml evacuated glass vials (Labco, UK). All samples were analyzed within ten days using a Shimadzu GC-14A gas chromatograph fitted with an electron capture detector operating at 325°C (Shimadzu, Tokyo, Japan). Denitrification rates were calculated using the formula similar to Hernandez-Ramirez et al. (2009) where

N2O production rate = ?(Vhs +Vlp?)/S

and ? is the measured N2O production rate (?g L-1), Vhs is the headspace volume (L), Vlp is the liquid phase (L), ? is the Bunsen absorption coefficient in water (Tiedje, 1982; Christensen and Tiedje, 1988), and S is the incubated soil mass (kg).

Statistical Analysis

Statistical analysis was done using a combination of SAS (PROC MIXED) and R Statistical software programs. Nitrous oxide emissions were analyzed using a mixed model to test both main effects and interactions over time using log-transformed data. Results were subsequently back-transformed for illustrative purposes with averages presented as geometric means. With one exception, all other data were tested for normality and heteroscedasticity and analyzed using two-way ANOVA. Nitrate leachate was found to be severely, negatively skewed, which did not allow for transformation. Welch’s t-test was used to analyze treatment effects on these data.

Research results and discussion:

Cover Crop Biomass Accumulation and N Contents
The rye cover crop produced much higher levels of biomass than the oat cover crop (Table 1). Aboveground biomass was nearly 300 kg ha-1 greater in the rye plots. In total, rye produced 3.02 times more biomass. Similarly, rye N uptake was 16.27 kg ha-1 or 269% greater than the oat cover crop.

Nitrate Leaching

Treatment effects on nitrate leaching losses were found to vary considerably (Fig. 2). Rye significantly and markedly decreased NO3-N losses over the control and oat treatments. Losses among the other two treatments remained high throughout the spring season with an increasing trend through the early part of the spring season and then a gradual decrease with the oats generally maintaining higher average losses throughout the sample period. Throughout the spring season, average measured nitrate levels were 43.36, 51.96 and 0.82 mg NO3-N L-1 for the control, oat and rye plots, respectively.

N2O emissions

While variability was high, both spatially and temporally, significant results were found in nitrous oxide emissions. Clear trends emerged particularly when replications are averaged over treatments. Treatment effects changed as the spring season progressed (Table 2). The oat treatment produced similar results to the control throughout the sample period while rye decreased N2O emissions after a high initial flux. Average emissions from the rye treatment were roughly half of the control and oat treatments during the final two samplings. Emissions in the rye were reduced by 57% and 49% over the oat plots and 71% and 46% over the control plots during the final two samplings respectively.

The majority of emissions occurred during the first 48 hours of each incubation (Fig. 3). Particularly between the oats and control treatments, variability was extremely high with an average CV of 55% and 67% of the mean respectively. In contrast, emissions for the rye treatment were far more stable and varied by less than half of that of the other treatments.

Soil Characteristics and Mechanisms for N2O emissions

N2O production in this experiment represents a simulated heavy-rainfall event during the spring season, and the trends offer insight into the dynamics of N2O production during this volatile period with the onset of a heavy rainfall. Compared to a control-fallow treatment, both rye and oats produced much more N2O on average during the early spring yet, statistically significant differences were not detected. As the season progressed, however, N2O emissions decreased significantly in the rye treatment while emissions from both the control and oat treatments increased.

Wagner-Riddle et al. (2008) demonstrated that high N2O production during spring-thaw events was a result of newly liberated carbon and available nitrate through freeze-thaw processes in surface soil layers. Based on linear regressions, active carbon was positively correlated (p = 0.004) with nitrous oxide production during the early spring sample period. However, active carbon did not correlate well with emissions later in the season (Fig. 4). Furthermore, nitrate, sampled from the top 30 cm was found to be a significant predictor variable only in the mid-spring sample (Fig. 5). These results, combined with the trends shown in Table 2, suggest that throughout the spring season, N2O emissions rely on a complex interaction between variables with relative importance shifting depending on the sample date.

Additionally, nitrate appears to be the primary limiting factor in N2O production. Within the rye plots, soil NO3 contents were significantly reduced during the mid-spring period, which corresponds to the period of high N-uptake by the rye crop (Table 1). N2O emissions were reduced correspondingly (Fig. 2). In the late spring, however, NO3 rebounded in the rye plots with higher levels of active C, yet N2O production remained lower on average. While the latter differences were not statistically significant, the lower emissions are difficult to interpret and perhaps indicate that physical differences affecting oxygen diffusivity should be examined further to help explain these results.

The emissions of the mid-Spring period corroborate work from previous lab studies. Parkin et al (2006) found that a rye cover crop reduced N2O emissions after the addition of swine manure, particularly at high rates of application. Similarly, McSwiney et al. (2010) noted that N2O production was decreased in maize plots following winter rye cover when fertilization rates were applied in excess of crop physiological need.

In the rye plots, N-uptake regulates the nitrate pool size, a proximal driver of N2O, by outcompeting bacteria for available nutrients (Smith and Tiedje, 1979). Another indirect or distal factor controlling emissions among the treatments is the combined effects of mineralization and immobilization. Parkin et al. (2006) speculated that recent manure additions may in fact increase mineralization, which could lead to increased N2O emissions. Biomass incorporation stimulates these processes and its effect on N2O emissions has been an area of study.

In a rice-wheat cropping system, Aulakh et al. (2001) found that initial N2O emissions after rice transplanting were higher in plots receiving a narrow C:N green manure over plots amended with a higher C:N ratio wheat residue. Over a longer time scale, however, the trend was reversed, which the authors theorized was the result of mineralization and long-term availability of carbon. This could explain the sustained emissions in the oat plots in this study, which remained high throughout the entire spring period with soil nitrate levels remaining fairly stable (Table 3). At the time of winter-kill, the oat plots had accumulated an average of 8.62 kg ha-1 of N in the aboveground biomass and another 1 kg ha-1 of N in root biomass. Oats die with the onset of frost and the biomass is returned to the soil. Additionally, the coefficient of variation (sigma/mu) in emissions from oat plots varied much more as the season progressed. Dispersion increased from approximately 15% in the early spring to 32% in the late spring.

The increasing coefficient of variation and sustainment of higher average emissions is possibly the result of increased rates of oat residue decomposition as temperatures increase throughout the spring thus mobilizing N. High nitrate levels in lysimeters beneath oat plots toward the end of the spring season corroborate this hypothesis, particularly in comparison with fallow plot leachate.

Increased decomposition may also explain the high variability and occurrence of “hotspots” within these plots (Parkin, 1987, McClain et al., 2003). Heterogeneous decomposition patterns would likely produce localized areas of relatively high NO3 and/or labile carbon contents. Denitrification variability decreased within the rye plots later in the spring season (Fig. 3), which, perhaps due to more uniform coverage, resulted in labile nitrate being consumed in a homogenous fashion and decreasing the possibility for localized denitrification zones. Additionally, PMN did not vary significantly among treatments and mineralization potential remained fairly stable throughout the sample period (Fig. 6), which supports the notion that deposited carbon and nitrate from the oat biomass increased the likelihood of denitrification microsites due to fresh biomass additions as opposed to more complicated microbial interactions(mineralization/nitrification) among treatments. Increased tillage, manure inputs and living plants can raise mineralization rates (Wander et al. 1994). The oats were not incorporated and that which was cycling through SOM may actually have a neutralizing effect through increased activity by fresh inputs offsetting immobilized nutrients due to its high C:N ratio.

Research conclusions:

During the volatile spring period when field N losses can be high, rye cover crops show potential to mitigate negative environmental effects. In this treatment, emissions resulting from a heavy rainfall event were highest in the early spring, averaging nearly 24 g N ha-1 day-1 with a 70% decrease during later portions of the spring when the rye was actively taking up N and producing biomass. Oats on the other hand averaged consistently higher emissions throughout the spring period with a range of 24 to 33 g N ha-1 day-1.

In the control/fallow plots emissions and variability increased as the spring progressed averaging 14 g N ha-1 day-1 and increasing to over 26 g N ha-1 day-1 by the end of the spring. Rye had an even greater impact on reducing leaching losses. Nitrate losses in rye were extremely low throughout the sampling period and decreased throughout the spring. Oats, when compared to the control treatment, showed no improvements in decreasing nitrate losses. Further nitrous oxide losses may be expected from leached nitrates at the terrestrial-aquatic interface (Clough et al., 2007), thereby amplifying the treatment effects.

This trial investigated nitrate losses under winter cover crops from fields with a history of manure management during the spring season. To remove the effects of seasonal climatic variation, nitrous oxide emissions were measured by simulating a heavy rainfall at the average ambient temperature at a given sample date. Due to the inherent physiological differences, notably its ability to survive cold temperatures, rye had a much more significant and positive effect on N leaching and denitrification potential than oats. Therefore, winter hardy cereal cover crops should be given strong consideration over winter-killed cover crops when environmental N losses are a concern.

Participation Summary

Education & Outreach Activities and Participation Summary

Participation Summary:

Education/outreach description:
A history of manure management affects nitrous oxide emission potential and the denitrification molar ratio

This funding allowed further investigation into the ratio of N2 and N2O from emissions of heavily manured soils using isotopically labelled KNO3. Attached is the final report.

Project Outcomes

Project outcomes:

Farmer Adoption

Farmer adoption was not reported. However, future consideration should be given to the effectiveness of an oat catch crop versus rye with respect to environmental N losses. The results herein suggest little benefit of the oat catch crop in reducing N losses during the spring season.

Assessment of Project Approach and Areas of Further Study:

Areas needing additional study

This study addresses the use of cover crops on heavily manured fields and the subsequent effects on nitrous oxide and nitrate leaching during the volatile spring season. Additional study is necessary to address N dynamics during the primary growing season (e.g. maize, soybean) as affected by the preceding cover crop. This study focused on the environmental impacts and the economic benefits should also be accounted for for a more complete analysis.

Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture or SARE.