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Fig. S1. Boxplot representations of logarithm-transformed data from Fig. 3 describing (a) abundance and (b) transcript copy numbers of amoA of AOB, (c) abundance and (d) transcript copy numbers of amoA of AOA affected by ‘nitrogen’ or ‘time points’.

Fig. S2. Boxplot representations of logarithm-transformed data from Fig. 3 describing (a) abundance and (b) transcript copy numbers of nxrA of Nitrobacter, (c) abundance of 16S rRNA of Nitrospira affected by ‘nitrogen’ or ‘time points’.

Fig. S3. Principal component analysis of AOA T-RFLP profiles determined in flooded soils. Each circle indicates an individual T-RFLP profile. Different colours denote for different soil and root compartments. The relative abundance of each of the TRF can be estimated from the perpendicular projection of each sample to the individual arrow while the length of each arrow indicates the variance (range of relative abundance values) of its respective TRF.

Fig. S4. Neighbour-joining phylogenetic tree based on partial bacterial amoA sequences (150 amino acids). The clone sequences from this study were retrieved from the d50 surface soil and roots. In silico TRF sizes are shown after the clone names. The scale bar represents 5% sequence divergence and the GenBank accession numbers of reference sequences are indicated. Bootstrap values are given at nodes when greater than 60%.

Fig. S5. Neighbour-joining phylogenetic tree based on partial archaeal amoA sequences (197 amino acids). The clone sequences from this study were retrieved from the d50 surface soil and roots. In silico TRF sizes are shown after the clone names. The scale bar represents 5% sequence divergence and the GenBank accession numbers of reference sequences are indicated. Bootstrap values are given at nodes when greater than 60%.

Fig. S6. Neighbour-joining phylogenetic tree based on partial Nitrospira 16S rRNA sequences. The clone sequences from this study were retrieved from the d50 surface soil and roots. The scale bar represents 5% sequence divergence and the GenBank accession numbers of reference sequences are indicated. Bootstrap values are given at nodes when greater than 70%.

Fig. S7. Phylogenetic tree of nxrA sequences (282 bp) derived from soil and roots samples. The scale bar represents 5% sequence divergence and the GenBank accession numbers of reference sequences are indicated. Bootstrap values are given at nodes when greater than 60%.

Fig. S8. Photographs of the set-up of rice-planted microcosms.

Table S1. Primers and PCR conditions used in this study.

Table S2.anova analysis for gene abundance and transcript copy numbers of amoA of AOB, amoA of AOA, nxrA of Nitrobacter, and abundance of Nitrospira-like 16 s rRNA gene. Significant effects (P-value < 0.05) are highlighted in bold.

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