Table 3. Pairwise comparisons between RAS and AS systems based on DGGE and 454 pyrosequencing data sets.

Statistical test	Analytical Method		RAS vs. AS
			D00	D07	D14	D28	D42
Perm. ANOVA	GUT	DGGE	P:0.0710	P:0.0022	P:0.0202	P:0.0063	P:0.0099
		454	NA	P:0.0152	NA	NA	P:0.0056
ANOSIM		DGGE	R:0.244 P:0.0020	R:0.731 P:0.0001	R:0.496 P:0.0001	R:0.881 P:0.0001	R:0.872 P:0.0001
		454	NA	R:1 P:0.0001	NA	NA	R:1 P:0.0001
Perm. ANOVA	WATER	DGGE	P:0.0983	P:0.008	P:0.0187	P:0.0136	P:0.0062
ANOSIM			R:0.820 P:0.0010	R:0.944 P:0.0010	R:0.940 P:0.0003	R:1 P:0.0020	R:0.990 P:0.0020

Tests were performed by sample type per sampling day, with P values for each comparison from two different statistical tests (PERMANOVA and ANOSIM). ANOSIM analysis is complementary to PERMANOVA as it provides information on the degree of separation between groups, suggested by R statistic. N.A.: No pyrosequencing data available for that day. D00, 07, 14, 28, 42: sampling day 0,7,14,28 & 42 respectively, AS1-5: replicate active suspension system 1 till 5, Ra & Rb: replicate recirculating system a & b. P values are based on 9999 Monte Carlo permutations.