Hatchery type influences the gill microbiome of Atlantic farmed salmon (Salmo salar) after transfer to sea

Table 2 PERMANOVA for sources of variation between mucosal gill microbiomes for beta diversity measures Bray–Curtis and Unweighted Unifrac

Group	Sources of Variance	Bray–Curtis Dissimilarity R² p < 0.001 (***)	Unweighted Unifrac R² p < 0.001 (***)
All Atlantic salmon	Sites (n = 13)	0.580 (***)	0.316 (***)
Freshwater salmon	Hatchery sites (n = 6)	0.539 (***)	0.307 (***)
Seawater salmon	Farm sites (n = 7)	0.528 (***)	0.244 (***)
All Atlantic salmon n = 112	Season of Input (S0 vs S1)	0.098 (***)	0.057 (***)
All Atlantic salmon n = 112	Water type (Freshwater vs. Seawater)	0.046 (***)	0.022 (***)
Freshwater hatchery salmon (n = 56)	Season of Input (S0 vs S1)	0.080 (***)	0.043 (***)
Freshwater hatchery salmon (n = 56)	Hatchery water system (Loch vs. RAS vs. FT)	0.226 (***)	0.131 (***)
Seawater farm salmon (n = 56)	Season of Input (S0 vs S1)	0.093 (***)	0.047 (***)
	Prev. hatchery water system (Loch vs. RAS vs. FT)	0.164 (***)	0.070 (***)
	Input weight (g)	0.078 (***)	0.036 (***)
	Days at Sea	0.096 (***)	0.038 (***)

R² represents the variability explained between microbial communities. p < 0.1 (n.s), p < 0.05 (*), p < 0.01 (**), p < 0.001 (***). Each of the six titles in the Groups column represents a different PERMANOVA test

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