Ammonia-Oxidizing Bacteria along Meadow-to-Forest Transects in the Oregon Cascade Mountains

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Abstract
Although nitrification has been well studied in coniferous forests of Western North America, communities of NH3-oxidizing bacteria in these forests have not been characterized. Studies were conducted along meadow-to-forest transects at two sites (Lookout and Carpenter) in the H. J. Andrews Experimental Forest, located in the Cascade Mountains of Oregon. Soil samples taken at 10- or 20-m intervals along the transects showed that several soil properties, including net nitrogen mineralization and nitrification potential rates changed significantly between vegetation zones. Nonetheless, terminal restriction fragment length polymorphism (T-RFLP) analysis of the PCR-amplified NH3monooxygenase subunit A gene (amoA) showed the same DNA fragments (TaqI [283 bp],CfoI [66 bp], andAluI [392 bp]) to dominate ≥45 of 47 soil samples recovered from both sites. Two fragments (491-bpAluI [AluI491] andCfoI135) were found more frequently in meadow and transition zone soil samples than in forest samples at both sites. At the Lookout site the combinationAluI491-CfoI135 was found primarily in meadow samples expressing the highest N mineralization rates. Four uniqueamoAsequences were identified among 15 isolates recovered into pure culture from various transect locations. Six isolates possessed the most common T-RFLPamoAfingerprint of the soil samples (TaqI283-AluI392-CfoI66), and theiramoAsequences shared 99.8% similarity with a cultured species,Nitrosospirasp.strain Ka4 (cluster 4). The other threeamoAsequences were most similar to sequences ofNitrosospirasp.strain Nsp1 andNitrosospira briensis(cluster 3). 16S ribosomal DNA sequence analysis confirmed the affiliation of these isolates withNitrosospiraclusters 3 and 4. TwoamoAclone sequences matched T-RFLP fingerprints found in soil, but they were not found among the isolates.