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Use of aliphatic n-alkynes to discriminate soil nitrification activities of ammonia-oxidizing thaumarchaea and bacteria Public Deposited

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  • Ammonia (NH₃)-oxidizing bacteria (AOB) and thaumarchaea (AOA) co-occupy most soils, yet no short-term growth-independent method exists to determine their relative contributions to nitrification in situ. Microbial monooxygenases differ in their vulnerability to inactivation by aliphatic n-alkynes, and we found that NH₃ oxidation by the marine thaumarchaeon Nitrosopumilus maritimus was unaffected during a 24-h exposure to ≤20 μM concentrations of 1-alkynes C₈ and C₉. In contrast, NH₃ oxidation by two AOB (Nitrosomonas europaea and Nitrosospira multiformis) was quickly and irreversibly inactivated by 1 μM C₈ (octyne). Evidence that nitrification carried out by soilborne AOA was also insensitive to octyne was obtained. In incubations (21 or 28 days) of two different whole soils, both acetylene and octyne effectively prevented NH₄⁺-stimulated increases in AOB population densities, but octyne did not prevent increases in AOA population densities that were prevented by acetylene. Furthermore, octyne-resistant, NH₄⁺-stimulated net nitrification rates of 2 and 7 μg N/g soil/day persisted throughout the incubation of the two soils. Other evidence that octyne-resistant nitrification was due to AOA included (i) a positive correlation of octyne-resistant nitrification in soil slurries of cropped and noncropped soils with allylthiourea-resistant activity (100 μM) and (ii) the finding that the fraction of octyne-resistant nitrification in soil slurries correlated with the fraction of nitrification that recovered from irreversible acetylene inactivation in the presence of bacterial protein synthesis inhibitors and with the octyne-resistant fraction of NH₄⁺-saturated net nitrification measured in whole soils. Octyne can be useful in short-term assays to discriminate AOA and AOB contributions to soil nitrification.
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  • Taylor, A. E., Vajrala, N., Giguere, A. T., Gitelman, A. I., Arp, D. J., Myrold, D. D., ... & Bottomley, P. J. (2013). Use of aliphatic n-alkynes to discriminate soil nitrification activities of ammonia-oxidizing thaumarchaea and bacteria. Applied and Environmental Microbiology, 79(21), 6544-6551. doi:10.1128/AEM.01928-13
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  • 79
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  • 21
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  • This research was supported by USDA NIFA Award No. 2012-67019-3028, US Department of Agriculture (Grant 2005-35319), an Oregon Agricultural Research Foundation competitive grant, the Oregon Agricultural Experiment Station, and the Oregon State University Provost Distinguished Graduate Fellowship. Additional support obtained from the Oregon State University community included: QPCR facilities at the Center for Genome Research and Biocomputing, field sites maintained by the Hyslop Field Research Laboratory, Columbia Basin Agricultural Research Center, Klamath Basin Research and Extension Center, and the Central Oregon Agricultural Research Center. N. maritimus was generously provided by David Stahl, University of Washington.
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