Table 2. Experimental factors predicting β-diversity of leaf- and root- associated bacterial communities.

	Leaf			Root
	PCo1	PCo2	PCo3	PCo1	PCo2	PCo3
R2	0.84	0.63	0.64	0.89	0.76	0.44
Site	F2,55=232	F2,48=39	F2,46=73.3	F2,35=457	F2,32=70.9	F2,38=20.9
	P<3e−16	P=8.8e−11	P=1.1e−14	P<3e−16	P=4.9e−12	P=8.6e−07
Geno.	F4,12=7.65	F4,261=3.82	F4,13=4.08	F4,25=0.224	F4,17=0.234	F4,28=0.118
	P=0.0088	P=0.0098	P=0.026	P=1	P=1	P=1
Geno. × Site	F8,257=4.53	F8,259=1.89	F8,258=1.27	F8,255=1.04	F8,255=0.312	F8,260=0.857
	P=0.00011	P=0.12	P=0.26	P=1	P=1	P=1
Age	F2,65=0.789	F2,63=3.34	F2,63=0.734	F2,55=0.43	F2,49=61.2	F2,64=13.4
	P=0.92	P=0.13	P=0.92	P=0.65	P=1.5e−13	P=2.8e−05
Age × Site	F4,62=1.55	F4,61=0.229	F4,61=1.26	F4,55=2.31	F4,48=10.8	F4,62=2.87
	P=0.6	P=0.92	P=0.6	P=0.07	P=7.7e−06	P=0.06
Year	F1,59=5.88	F1,69=0.009	F1,41=3.88	F1,61=18.4	F1,60=7.65	F1,61=25.2
	P=0.055	P=0.93	P=0.11	P=0.00013	P=0.0076	P=1.4e−05
Year × Site	F2,97=0.511	F2,73=1.27	F2,68=0.975	F2,65=2.54	F2,66=6.94	F2,93=0.178
	P=0.86	P=0.86	P=0.86	P=0.17	P=0.0055	P=0.84
Block	χ21=0.06	χ21=4.54	χ21=3.59	χ21=5.49	χ21=1.26	χ21=0.09
	P=0.81	P=0.099	P=0.12	P=0.057	P=0.52	P=0.76
Line	χ21=0.16	χ21=0	χ21=1.3e−05	χ21=1.00	χ21=0.28	χ21=1.53
	P=1	P=1	P=1	P=0.65	P=0.65	P=0.65
Obs	F1,279=17.3	F1,273=156	F1,239=24.7	F1,177=8.84	F1,205=3.2	F1,127=19.1
	P=4.2e−05	P<3e−16	P=2.6e−06	P=0.0067	P=0.075	P=7.5e−05
MiSeq run	χ21=4.62	χ21=1.41	χ21=0.001	χ21=1.2	χ21=2.94	χ21=0.28
	P=0.095	P=0.47	P=0.97	P=0.55	P=0.26	P=0.59

ANOVA, analysis of variance.

Statistics describe linear random-intercept models of weighted UniFrac principal coordinates in leaves and roots. ‘Geno', plant genotype; and ‘Obs', total number of observations (log-transformed). All P values were adjusted for multiple comparisons using the sequential Bonferroni correction. Significance was assessed using type III ANOVA with F tests for fixed effects and likelihood ratio tests for random effects. Bold values indicate statistically significant results after correction for multiple comparisons, P<0.05.