Purpose

Microbial nitrification plays an important role in nitrogen cycling in ecosystems. Nitrification is performed by ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB) including complete ammonia oxidizers. However, the relative importance of nitrifiers in autotrophic nitrification in relation to soil pH is still unclear.

Materials and methods

Combining DNA-based stable isotope probing (SIP) and molecular biological techniques, we investigated the abundance, structure, and activity of AOA, AOB, and NOB along a pH-gradient (3.97–7.04) in a vegetable cropped soil.

Results and discussion

We found that AOA abundance outnumbered AOB abundance and had a significantly negative relationship with soil pH. The abundances of NOB Nitrospira 16S rRNA, nxrB gene, and Nitrobacter nxrA gene were affected by soil pH. Incubation of soil with ¹³CO₂ and DNA-SIP analysis demonstrated that significant ¹³CO₂ assimilation by AOA rather than by AOB occurred in the acidic soils, whereas the labeled ¹³C level of AOA was much less in the neutral soil than in the acidic soils. There was no evidence of ¹³CO₂ assimilation by NOB except for Nitrobacter with NxrB gene at pH 3.97. Phylogenetic analysis of AOA amoA gene in the ¹³C- and ¹²C-labeled treatments showed that the active AOA mainly belonged to Nitrososphaera in the acidic soils.

Conclusions

These results suggested that the main performer of nitrification was AOA in the acidic soils, but both AOA and AOB participated in nitrification in the neutral soil with low nitrification activity. NOB Nitrospira and Nitrobacter did not grow in the soils with pH 4.82–7.04 and other populations of NOB were probably involved in nitrite oxidation in the vegetable cropped soil.