Table S5. Constrained PCoA (Bray-Curtis ~ Type) and PERMDISP				
"The retained primary block uses Bray-Curtis dissimilarities calculated after rarefaction to 88,397 reads per sample, followed by square root of the dissimilarity values (not square-root transformation of ASV counts). Physicochemical variables are not constraints. The exploratory Type-constrained CPCoA model returned R?? = 0.503, adjusted R?? = 0.254, pseudo-F(2,4) = 2.02, and P = 0.025 after vegan::anova.cca enumerated 5,039 nonidentity unrestricted sample permutations. The default median-centre PERMDISP result was F(2,4) = 4.62 and P = 0.001 with 999 requested permutations. Small, unbalanced Type sizes, incomplete Type ?? Group crossing, and heterogeneous dispersion limit interpretation to exploratory description; the legacy raw/untransformed block is retained only as a sensitivity record."				
				
Metric	"Value (recorded primary: sqrt Bray?€?Curtis distance, rarefied 88,397)"			
R2	0.502968187			
adj_R2	0.25445228			
F	2.023887297			
df_model	2			
df_residual	4			
p_value_model	0.025			
PERMDISP_F	4.6195			
PERMDISP_p	0.001			
Type mean distance-to-median (PRIMARY)	"precipitate=0.3365, wall=0.4395, water=0.2194"			
				
"LEGACY / sensitivity value (2026-09-09 original: untransformed, non-rarefied Bray-Curtis)"				
Metric	Value (LEGACY)			
R2	0.582039983			
adj_R2	0.373059974			
F	2.752602654			
df_model	2			
df_residual	4			
p_value_model	0.01			
PERMDISP_F	3.199794618			
PERMDISP_p	0.001			
Type mean distance-to-median (LEGACY)	"wall=0.34 (largest), water=0.09 (smallest); precipitate not separately reported in the original 2026-09-09 note"			
"Note: the two blocks are the SAME underlying ASV table and Type assignment, differing only in the distance transform / rarefaction step; treat differences here as a methodological sensitivity check, not as evidence one pipeline is wrong. Full 6-way input x transform sensitivity grid: results/cpcoa_distance_sensitivity_sonnet_own_data.csv (scripts/08_cpcoa_sensitivity.R)."				
				
				
"Site (sample) CAP scores - LEGACY (untransformed, non-rarefied Bray-Curtis)"				
Sample	Type	Group	CAP1	CAP2
1st_BFP	AMD precipitate-associated biofilm	1st	-0.210182508	0.514816482
1st_BFW1	wall-attached biofilm	1st	-0.701402141	-0.249375571
1st_BFW2	wall-attached biofilm	1st	-0.387379314	-0.224493332
2nd_BFP	AMD precipitate-associated biofilm	2nd	-0.271778474	1.386618971
2nd_BFW	wall-attached biofilm	2nd	-0.364736335	-1.108716904
2nd_wt	water	2nd	0.942613769	-0.310762391
3rd_wt	water	3rd	0.992865001	-0.008087254
				
"Site (sample) CAP scores - PRIMARY (sqrt Bray-Curtis, rarefied to 88,397)"				
Sample	Type	Group	CAP1	CAP2
1st_BFP	AMD precipitate-associated biofilm	1st	-0.352011191	0.757088134
1st_BFW1	wall-attached biofilm	1st	-0.632161317	-0.529506016
1st_BFW2	wall-attached biofilm	1st	-0.479741765	-0.37509144
2nd_BFP	AMD precipitate-associated biofilm	2nd	-0.347284625	1.306522713
2nd_BFW	wall-attached biofilm	2nd	-0.35985001	-0.974484253
2nd_wt	water	2nd	1.070482921	-0.165841658
3rd_wt	water	3rd	1.100565987	-0.018687479