Ammonia (NH 3 )-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 NH 3 oxidation by the marine thaumarchaeon Nitrosopumilus maritimus was unaffected during a 24-h exposure to <20 M concentrations of 1-alkynes C 8 and C 9 . In contrast, NH 3 oxidation by two AOB (Nitrosomonas europaea and Nitrosospira multiformis) was quickly and irreversibly inactivated by 1 M C 8 (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 NH 4 ؉ -stimulated increases in AOB population densities, but octyne did not prevent increases in AOA population densities that were prevented by acetylene. Furthermore, octyne-resistant, NH 4 ؉ -stimulated net nitrification rates of 2 and 7 g 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 M) 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 octyneresistant fraction of NH 4 ؉ -saturated net nitrification measured in whole soils. Octyne can be useful in short-term assays to discriminate AOA and AOB contributions to soil nitrification.
For about a century, most ammonia (NH 3 ) oxidation in soils was thought to be carried out by chemolithoautotrophic ammonia-oxidizing bacteria (AOB). In 2005, the nitrification paradigm changed with the discovery of another type of microorganism from the phylum Thaumarchaeota that performs NH 3 oxidation (1). Molecular techniques have shown that ammoniaoxidizing Thaumarchaeota (AOA) are widely distributed in soils throughout the world (2, 3). AOA are usually more numerous in soil than AOB, and in some soils, AOB are present at levels below the detection limit of quantitative PCR (qPCR) (4, 5). This has led to speculation about the extent to which AOA contribute to soil nitrification (6, 7). AOA may be more metabolically versatile than AOB, with some cultured AOA growing at acid pH (8), scavenging NH 4 ϩ at low concentrations (9), and showing mixotrophic growth on a combination of pyruvate and NH 4 ϩ (10), and an AOA soil population has been shown to convert organic N sources to NO 3 Ϫ (11). The evidence for AOA contributing to soil nitrification has arisen from enrichment approaches involving long incubations (4 to 6 weeks) of soil in the laboratory, where NH 3 oxidation was accompanied either by the incorp...