Table 3.

ANOVA for gene and transcript copies in all treatments and times (see Supplementary Figs. 4 and 5). Time had a significant effect on most genes, whilst fertilizer treatment did not, affecting only the AOB which were significantly more abundant and active where urea was applied without NI

Gene copies g−1 soil	d.f.	16S Bacteria	16S Archaea	ITS	AOA amoA	AOB amoA	ureC	nxr-bacter	nxr-spira	Comammox
Time	F 2, 51	5.13, P = 0.010	NS	4.96, P = 0.011	NS	19.96, P < 0.001	4.10, P = 0.023	18.49, P < 0.001	NS	NS
Treatment	F4, 51	NS	NS	NS	NS	8.71, P < 0.001	NS	NS	NS	NS
Time × treat	F8, 51	NS	NS	NS	NS	NS	NS	NS	NS	NS
Transcripts g−1 soil	d.f.	16S bacteria	16S archaea	ITS	AOA amoA	AOB amoA
Time	F 2, 51	21.58, P < 0.001	27.83 P < 0.001	13.29, P < 0.001	28.50, P < 0.001	23.68, P = 0.006
Treatment	F4, 51	NS	NS	NS	NS	33.97, P = 0.003
Time × treat	F8, 51	NS	NS	NS	NS	NS

NS not statistically significant