U.S. Department of Energy, Office of Science

Program for Ecosystem Research

Research Project   Can soil genomics predict the impact of precipitation on nitrous oxide (N2O) fluxes from soil?

Principal investigator:   Egbert Schwartz

Project goal

Understand and predict how changes in precipitation will impact nitrous oxide efflux from soil using analyses of DNA extracted from soil and traditional N-cycle measurements.

Ecosystem being studied

Desert grassland and grass components of pinyon-juniper, ponderosa pine, and mixed conifer forests. These ecosystems cover large areas of the western United States. The specific research sites are located on an elevational gradient close to Flagstaff, AZ.

N2O flux versus elevation by precipitation treatment

Increased precipitation caused significantly increased N2O flux in the high elevation (i.e., ponderosa pine and mixed conifer forest) ecosystems.


Experimental changes in precipitation had different effects on N2O flux from soils in different ecosystems. Increased precipitation (150% of ambient amount) caused large releases of N2O release from soils at higher elevations relative to the same ecosystems receiving ambient precipitation (see figure). The soils at higher elevation have more carbon per unit ground area, and this can drive a microbial process that produces nitrous oxide called denitrification. Nitrous oxide flux from soil did correlate significantly with denitrification rates.

To link soil genomics with these observations from the field experiments, genes involved in the nitrogen cycle are being characterized and quantified. Measurements of the abundance of archaeal and bacterial amoA sequences from soil DNA extracts have been optimized, using a realtime PCR approach. In addition, the nos Z and nirK genes in soil samples are being studied.

A new method was developed to extract DNA from large (50 grams) soil samples. Commercial soil DNA extraction kits extract DNA from only 0.5 grams of soil but ecosystem measurements are taken on much larger samples. The new DNA extraction method will allow direct comparison of genomic and ecosystem data. The new extraction method also yielded enough product to measure the natural abundance delta15N of DNA extracted from soil. In measurements so far, DNA is depleted in 15N relative to the microbial biomass from which the DNA is extracted. The delta15N of both the microbial biomass and the extracted DNA showed a strong linear relationship to the C/N ratio of the soil extract. This indicates that the delta15N of bio-molecules in soil can be used as a integrated measure of C and N availability to microorganisms. Because C and N availability control denitrification and nitrification rates, both processes that may produce nitrous oxide, the delta15N of DNA may be a powerful tool to study nitrous oxide flux from soil.

Why this is important

Nitrous oxide is a potent greenhouse gas. Presently it is not understand what controls the emission of nitrous oxide from soils. For instance, when precipitation increases, idiosyncratic responses in the amount of nitrous oxide emitted from soil have been observed.

The project intends to find a genetic signature in the DNA extracted from soil microorganisms that can provide insight into the control of nitrous oxide release. Genes that are important in metabolic pathways producing nitrous oxide are being targeted. By understanding the mechanisms that control nitrous oxide flux from soil, reliable predictions of how changes in precipitation might affect atmospheric nitrous oxide concentration will be possible.


One of the experimental sites (desert grassland) on the Arizona transect.


Lysimeters were installed in the field in May of 2002 and since then have been subjected to three different precipitation treatments: ambient, increased (+50%), and decreased (-30%), affected by redirecting rainfall into the lysimeters that receive extra precipitation, and by diverting rain from those in the low rainfall treatments. Several processes within the nitrogen cycle are being measured in these lysimeters including nitrous oxide efflux from soil, denitrification, nitrification, net N mineralization, nitrogen fixation, and microbial biomass N. Genes encoding enzymes that catalyze important processes within the nitrogen cycle are being characterized and quantified.

The genes being targeting are nifH (involved in nitrogen fixation), amoA (a subunit of ammonia oxygenase, an important enzyme in nitrification), and norB (which encodes the enzyme that reduces nitric oxide to nitrous oxide).


Egbert Schwartz, Northern Arizona University

Bruce Hungate, Northern Arizona University

Paul Keim, Northern Arizona University

Michael Cummings, University of Maryland (subaward)

Funding period:   August 2004 to present