Table 1.

Respective effects of habitat, bedrock, and elevation on microbial beta-diversity, as assessed by variation partitioning on Bray–Curtis dissimilarity matrices obtained from CE-SSCP profiles.

Taxa	Factors	Df	SS	MS	FR	R2	Pr(>F)
Bacteria	Habitat	1	0.046	0.046	5.902	0.028	0.001
	Bedrock	1	0.142	0.142	18.262	0.088	0.001
	Elevation	1	0.026	0.026	3.302	0.016	0.004
	Habitat: bedrock	1	0.068	0.068	8.747	0.042	0.001
	Habitat: elevation	1	0.005	0.005	0.697	0.003	0.666
	Bedrock: elevation	1	0.015	0.015	1.876	0.009	0.070
	Habitat: bedrock: elevation	1	0.012	0.012	1.563	0.008	0.126
	Residuals	168	1.304	0.008	NA	0.806	NA
	Total	175	1.617	NA	NA	1.000	NA
Fungi	Habitat	1	0.552	0.552	5.004	0.026	0.001
	Bedrock	1	0.644	0.644	5.843	0.030	0.001
	Elevation	1	0.663	0.663	6.014	0.031	0.001
	Habitat: bedrock	1	0.259	0.259	2.353	0.012	0.002
	Habitat: elevation	1	0.137	0.137	1.244	0.006	0.199
	Bedrock: elevation	1	0.232	0.232	2.102	0.011	0.010
	Habitat: bedrock: elevation	1	0.182	0.182	1.654	0.009	0.041
	Residuals	168	18.522	0.110	NA	0.874	NA
	Total	175	21.191	NA	NA	1.000	NA

The models also include the interaction effects on the microbial assemblages. Df, degrees of freedom; SS, sum of square; MS, mean square; FR, pseudo F-ratio; R², partial variance explained by the factor, Pr(>F), P-value. Colons in factors indicate interactions. The effect of habitat type was significant regardless of the permutation strategy adopted, i.e., when samples were permuted within each Population, Transect, Massif or without strata (Table A3).