Table 2. Determining drivers of bacterial community assembly using CAP.

	Constrained factor	Bray–Curtis			Weighted Unifrac			Unweighted Unifrac
		%	P-value	CI	%	P-value	CI	%	P-value	CI
Soil type+environment	Compartmenta	31	***	21, 48	33	***	20, 52	36	***	23, 64
	Environmenta	11	***	8, 16	8.2	***	5, 13	9.8	***	7, 14
	Compartmentb	25	***	15, 47	24	***	13, 46	37	***	19, 78
	Genotypeb	9.1	***	7.3, 11	12	***	8.5, 16	4.8	*	4.2, 5.5
	Compartmentc	31	***	20, 50	39	***	22, 67	33	***	21, 53
	Soil typec	15	***	9, 26	11	***	6, 20	15	***	10, 25
Time course	Compartment	19	***	14, 27	25	***	17, 39	18	***	14, 26
	Time point	9.9	***	7.8, 13	12	***	8.5, 18	6.6	***	5.7, 7.8
	Soil batch	6.6	***	4.9, 9.1	5.3	***	3.6, 8	8.4	***	6.6, 11
	Flowering stage	1.5	NS	1.2, 1.9	1.3	NS	1.0, 1.9	1.8	*	1.3, 2.5
	Mutant background	0.6	NS	0.4, 0.8	0.8	NS	0.5, 1.2	0.7	NS	0.5, 1.1
Diversification	Compartment	21	***	12, 37	26	***	12, 51	18	***	12, 31
	Soil batch	19	***	14, 28	20	***	12, 32	18	***	14, 24
	Plant species	10	***	8, 14	10	***	7, 15	7.3	***	6, 9

Abbreviations: CAP, constrained analysis of principal coordinates; CI, confidence interval; NS, non-significant; PERMANOVA, permutation-based analysis of variance.

Variation (in %) between samples in the ‘soil type and environment', ‘time course' and ‘diversification' experiments based on Bray–Curtis, weighted and unweighted UniFrac distances, constraining for the indicated factors. P-value based on PERMANOVA (999 permutations). *P<0.05, **P<0.01, ***P<0.001. Samples were analyzed separately according to the three different experimental setups as stated in Table 1. In addition, the ‘soil type and environment' samples were separated as follows:

^aGal60 grown at the natural site and the greenhouse.

^bGal60, Gal5 and Paj grown in French soil in the greenhouse.

^cPaj grown in the French and Cologne soil in the greenhouse.