Fig. S1. Agarose gel electrophoresis of putative archaeal ureC genes (with an expected size of ∼ 1260 bp) amplified from ultracentrifuged DNA over the entire density range of the SIP gradient from the microcosms of forest soil (A) and tea orchard soil (B) after incubation for 56 days. The ultracentrifuged DNA gradient diagram shows buoyant density fractions (from light to heavy, from top to bottom respectively). 13CO2 and 13CO2 + C2H2 indicate that the soil microcosms were incubated with 13CO2 as labelled treatment and 13CO2 + C2H2 as control treatment. Day-56-H2O and Day-56-Urea indicate that the soil microcosms were amended with water and urea, respectively, over an incubation course of 56 days. The marker denotes the DNA ladder. PCR amplicons, indicated by the blue-box, were excised from the labelled treatment for the construction of the target ureC gene clone library (indicated by arrows) and for sequencing analysis.

Fig. S2. Relationship between archaeal amoA gene copies and soil NO3-N concentrations in soil microcosms amended with urea and water for incubation. The sampling volume for linear regression was 60 from triplicate microcosms of forest and tea orchard soils. Significant correlation was observed at P < 0.001.

Table S1. The rates of net nitrification and mineralization in SIP microcosms incubated with urea or water for 56 days.

Table S2. Pyrosequencing results of the total 16S rRNA genes in the fractionated DNA isolated from SIP microcosms of forest soil.

Table S3. Pyrosequencing results of the total 16S rRNA genes in the fractionated DNA isolated from SIP microcosms of tea orchard soil.

Table S4. Summary of the dominant OTUs of archaeal 16S rRNA genes in 13C-DNA isolated from forest soil and tea orchard soil.

Table S5. The estimated cell number of AOA and cell-specific rate of soil archaeal nitrification.

Table S6. Primers and conditions used in this study.

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