Table 4. Summary of qPCR analysis across all years and sample dates for all genes and nucleic acid types.

	qPCR average copy numbers for nifH RNA data set (mean ± SE)	qPCR average copy numbers fornifH DNA data set (mean ± SE)	qPCR average copy numbers for 16SrRNA gene data set (mean ± SE)
year (Y)
2007	9.29×106±2.85×106b	5.69×105±6.81×104b	8.05×107±1.17×107a
2008		3.89×106±2.62×105c	5.26×107±2.30×107a
2009	3.92×104±5.37×103a	1.77×105±6.34×104a	2.96×108±1.29×108a
sample date (SD)
March	8.46×105±4.99×105b	1.45×106±2.65×105a	2.99×108±1.29×108
June	6.62×105±2.33×105b	1.42×106±2.51×105a	4.31×107±7.29×106a
September	1.25×107±4.16×106a	1.76×106±3.45×105a	8.66×107±2.41×107a
Crop protection (CP)
org	6.25×106±2.72×105a	1.74×106±2.44×105a	1.06×107±5.20×107a
con	3.07×106±1.18×106a	1.35×106±2.27×105b	1.81×108±8.13×107a
fertility management
org	4.97×106±2.59×106a	1.64×106±2.31×105a	1.23×108±3.92×107a
con	4.35×106±1.53×106a	1.45×106±2.42×105	1.63×108±7.99×107a
ANOVA P values
Y	<0.001	<0.001
SD	<0.001		0.032
CP		0.013
Y*SD	0.005		<0.001
Y*FM	0.001	0.032
CP*FM	0.037
Y*SD*FM		0.022

P-values are only shown for terms with P<0.05; all data were log-transformed before analysis. Means followed by the same letter for a given factor are not significantly different (P<0.05; Tukey’s HSD test where there are more than two treatment levels).