Table 3.

Results from PERMANOVA analyses. Compilation of relevant p-values, for all statistical analyses of three univariate community metrics (number of species, organism abundance, and total biomass) and the multivariate benthic community structure. Significant p-values are shown in bold numbers, α = 0.05. Df degrees of freedom, num numerator, den denominator, PsF pseudo-F value, t t-value, P(perm) p-value by permutation, P(MC) p-value from Monte Carlo sampling

a. Two-factor PERMANOVA analyses
Depth	Factor		Df (num, den)	Number of species		Abundance		Biomass		Community structure
				PsF	P(perm)	PsF	P(perm)	PsF	P(perm)	PsF	P(perm)
30 m	Month (n = 2)		1, 24	6.45	0.019	0.10	0.748	1.11	0.305	3.24	0.001
	Treatment (n = 4)		3, 24	14.5	0.001	27.5	0.001	3.78	0.023	3.46	0.001
	Month × Treatment		3, 24	7.80	0.002	5.69	0.005	3.64	0.028	2.16	0.001
80–95 m	Month (n = 2)		1, 16	1.42	0.245	2.49	0.130	1.54	0.875	4.75	0.001
	Treatment (n = 3)		2, 16	31.8	0.001	5.99	0.011	8.88	0.003	4.03	0.001
	Month × Treatment		1, 16	0.44	0.515	0.09	0.759	1.54	0.229	2.43	0.010
b. Pairwise comparisonsb
Depth	Pairwise comparison		Df (num, den)	Number of species		Abundance		Biomass		Community structure
				t	P(perm)	t	P(perm)	t	P(perm)	t	P(perm)
30 m	Lime-30 vs Ref-30		1, 12	1.13	0.303	2.03	0.173	1.97	0.190	4.11	0.001
	Clay-30 vs Ref-30		1, 12	2.10	0.168	11.2	0.007	2.03	0.180	2.12	0,231
	AC+clay-30 vs Clay-30		1, 12	34.4	0.001	150	0.001	7.97	0.018	3.74	0.001
	AC+clay-30 vs Ref-30		1, 12	38.6	0.001	48.2	0.001	2.69	0.123	3.66	0.001
80–95 m	AC+clay-95 vs Ref-80		1, 12	56.1	0.001	8.46	0.015	22.1	0.001	2.31	0.001
	AC+clay-95 vs Ref-95		1, 10	6.37	0.034	7.15	0.028	0.41	0.532	1.51	0.046
	Ref-80 vs Ref-95		1, 10	3.64	0.005	0.04	0.838	3.00	0.116	2.05	0.006
c. Post hoc pairwise tests (one-factorial)
Depth	Pairwise comparison		Df (num, den)	Number of species		Abundance		Biomass		Community structure
				t	P(MC)	t	P(MC)	t	P(MC)	t	P(MC)
30 m	Lime-30 vs Ref-30	1 month	1, 4	0.86	0.444	0.32	0.767	2.84	0.046	1.89	0.040
	Lime-30 vs Ref-30	14 months	1, 8	0.60	0.562	2.05	0.077	0.34	0.742	1.90	0.013
	Clay-30 vs Ref-30	1 month	1, 4	1.93	0.119	4.53	0.010	1.02	0.362	1.23	0.243
	Clay-30 vs Ref-30	14 months	1, 8	0.06	0.952	1.55	0.159	1.25	0.247	1.69	0.025
	AC+clay-30 vs Ref-30	1 month	1, 4	0.20	0.843	2.82	0.047	0.06	0.959	2.24	0.020
	AC+clay-30 vs Ref-30	14 months	1, 8	9.65	0.001	7.78	0.001	2.34	0.048	1.86	0.018
	AC+clay-30 vs Clay-30	1 month	1, 4	1.72	0.160	7.62	0.002	0.89	0.426	2.41	0.016
	AC+clay-30 vs Clay-30	14 months	1, 8	7.26	0.001	11.5	0.001	3.40	0.009	1.64	0.043
	1 vs 14 months	AC+clay-30	1, 6	5.59	0.002	4.17	0.007	2.70	0.035	1.55	0.079
	1 vs 14 months	Clay-30	1, 6	0.84	0.434	0.75	0.485	0.27	0.802	1.38	0.113
	1 vs 14 months	Lime-30	1, 6	0.20	0.848	1.46	0.197	1.82	0.121	1.34	0.129
	1 vs 14 months	Ref-30	1, 6	1.94	0.099	0.94	0.382	0.78	0.458	2.10	0.011
80–95 m	AC+clay-95 vs Ref-80	1 month	1, 4	3.98	0.018	5.01	0.007	7.32	0.002	1.51	0.102
	AC+clay-95 vs Ref-80	14 months	1, 8	6.85	0.001	2.17	0.064	2.31	0.046	2.46	0.002
	AC+clay-95 vs Ref-95	14 months	1, 8	3.19	0.011	2.39	0.044	0.58	0.575	1.62	0.034
	Ref-80 vs Ref-95	14 months	1, 8	3.94	0.004	0.19	0.853	1.58	0.149	2.22	0.002
	1 vs 14 months	AC+clay-95	1, 6	0.36	0.734	0.78	0.471	0.94	0.380	1.86	0.022
	1 vs 14 months	Ref-80	1, 6	1.20	0.282	1.53	0.181	1.13	0.301	1.82	0.022

^aRef-95 not included in the interaction analysis since this field was introduced after 14 months

^bPairwise results derived from a planned contrast design