Nitrification is an important component of the global nitrogen cycle and the end-product is nitrate and the rate of nitrate production is very different among soil types. Nitrification can lead to different effects ranging from too much nitrate, causing environmental problems, or too little nitrate can lead to reduced crop yields. Differences in physical and chemical properties of soils are often well documented, but much less is known about the soil nitrifying bacterial communities. We studied three soils of China to determine their soil nitrification activities, numbers of nitrifying bacteria, and the ammonia-oxidizing bacterial community. Maximum nitrification potential was found in Fluvoaquic soil with almost 100% of ammonium-N being transformed into nitrate-N after 28 days. Minimum nitrification potential was measured in the Red Earth soil with only a 4.9% conversion rate during the same time period. Numbers of ammonia-oxidizing bacteria, determined by the MPN-Griess method, were significantly different among the three soils. However, numbers of nitrite-oxidizing bacteria determined by the MPN-PCR method were similar. A PCR technique using the ammonia monooxygenase gene (amoA) combined with the new DNA fingerprinting technique, denaturing gradient gel electrophoresis (DGGE), were used to analyze the composition of ammonia oxidizing bacteria in soils. DGGE analysis of the three soils were different from each other; there were 2 similar bands present in DGGE columns from the Fluvo-aquic soil and the Permeable paddy soil, but no similar bands were found in columns from Red Earth soil. Further study of the sequence of amoA indicated that there were differences of ammonia-oxidizing bacteria communities among the three soils. A phylogenetic tree including the amoA studied in this paper and amoA from other environments the database was established.
There were four species of AOB found in Red Earth, both were different from the other two soils studied. Further comparison showed that these two species were closely related to Nitrosospira cluster 3b Z97838 and Nitrosospira cluster 3a AF353263, respectively. There were five species of AOB found in Fluvo-aquic soil and two of these were similar to those found in the Permeable paddy soil. Fluvo-aquic soil and Permeable paddy soil had a specific species which was closely related to Nitrosospira cluster 3b Z97849. There were four species of AOB found in Permeable paddy soil, and one of them was specific species for Permeable paddy soil and this was closely related to Nitrosospira cluster 3a AF353263. The nitrification activities of nitrifiers selected from these three soils were different. All the results obtained from this experiment implied that PCR-DGGE based on the amoA gene was a useful method to study AOB communities in soils. Each soil contained specific AOB species different from the others. Furthermore, the AOB of the Red Earth were particularly different from the other two soils, which might be related to the low pH of this soil. There was no relationship between the nitrification potential and nitrifying bacteria numbers of soils and this might be explained by the different physical properties of the soils.