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Assessing Nitrogen Transformations in a Flooded Agroecosystem Using the Isotope Pairing Technique and Nitrogen Functional Gene Abundances

Penton, C. Ryan1; Deenik, Jonathan L.2; Popp, Brian N.3; Bruland, Gregory L.4; Engstrom, Pia5; Mueller, Jaclyn6; Worden, Andrew1; Tiedje, James M.1

Soil Science:
doi: 10.1097/SS.0000000000000038
Technical Article

Abstract: Predicting N losses in flooded agricultural systems is complex because of the large number of potential N transformation pathways. Although coupled nitrification/denitrification at the flooded sediment near-surface oxic/anoxic interface is a recognized pathway of fertilizer N loss, the role of the newly discovered anaerobic ammonium oxidation (anammox) pathway in agricultural systems is poorly understood. A survey study was implemented to characterize sediment denitrification rates, anammox activity, and fluxes of ammonium and nitrate, and the vertical distribution of N functional genes were measured in Hawaiian taro (Colocasia esculenta) fields under three fertilizer management regimens (conventional, organic, and hybrid) as a model for flooded agroecosystems. Potential denitrification rates and anammox activity were measured using a slurry-based isotope pairing technique, and fluxes were determined by porewater modeling. Although significant numbers of anammox 16S rRNA genes were detected, only negligible anammox activity was found, illustrating the need to quantify not only the presence but also the activity of these bacteria. Quantitative polymerase chain reaction was performed for bacterial amoA, nirS, nosZ, and the 16S rRNA gene at 1-cm soil depth increments. Slurry isotope pairing technique–based potential denitrification rates (4.3–12.3 mmol N2 m−2 day−1) were on the high end of previous anaerobic incubation studies. Flux-derived denitrification rates were up to three orders of magnitude lower than slurry isotope pairing technique rates, suggesting strong nitrification regulation. Organically managed fields exhibited significantly lower slurry and flux-based denitrification rates than conventional and hybrid systems. This study supports the use of alternative fertilizer management techniques in flooded agroecosystems by the mitigation of N losses through denitrification and decreased overall N flux rates.

Author Information

1Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USA.

2Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, Hawaii, USA.

3Department of Geology and Geophysics, University of Hawaii at Manoa, SOEST, Honolulu, Hawaii, USA.

4Principia College, Biology and Natural Resources Department, Elsah, Illinois, USA.

5Sven Lovén Center for Marine Sciences, Fiskebäckskil, Sweden.

6School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, Honolulu, Hawaii, USA.

Address for correspondence: Dr. Christopher R. Penton, Center for Microbial Ecology, Michigan State University, 540 Plant and Soil Science Bldg, East Lansing, MI 48824, USA. E-mail:

Received November 12, 2013.

Accepted for publication February 21, 2014.

Financial Disclosures/Conflicts of Interest: This study was funded by the US Department of Agriculture National Institute of Food and Agriculture (award 2008-35107-04526). This is SOEST Contribution No. 9102.

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