Table 3.

Overview of the average relative abundance (%) and standard deviation of the major bacterial phyla and major families, discussed in this study. Sampling days 73 and 162 for the activated sludge samples and 185 and/or 227 for the biotrickling filter samples were taken into account. A zero means that in none of those samples, OTUs of this phylum or family were found

Taxonomy	Activated sludge	Biotrickling filter 1 – non‐inoculated						Biotrickling filter 2 – inoculated
		Stage1		Stage 2		Stage 3		Stage 1		Stage 2
		Biofilm	Water	Biofilm	Water	Biofilm	Water	Biofilm	Water	Biofilm	Water
Sampling day	73 + 162	185	185	185 + 227	185 + 227	185 + 227	185 + 227	185	185	185 + 227	185 + 227
Proteobacteria	40.1 ± 1.1	39.7 ± 0.5	50.8 ± 2.8	45.2 ± 2.8	51.2 ± 7.4	57.7 ± 8.8	38.0 ± 3.9	42.5 ± 0.4	24.7 ± 0.1	51.6 ± 2.2	26.3 ± 15.3
Comamonadaceae	11.2 ± 5.1	17.0 ± 0.9	43.6 ± 4.3	22.8 ± 10.1	39.5 ± 3.5	27.9 ± 4.6	34.3 ± 4.6	14.4 ± 0.1	6.3 ± 0.5	14.8 ± 2.4	4.6 ± 1.0
Xanthomonadaceae	3.4 ± 0.8	5.5 ± 0.02	1.4 ± 0.3	6.7 ± 4.3	0.4 ± 0.2	14.2 ± 2.0	0.5 ± 0.2	14.0 ± 0.7	2.8 ± 0.2	17.9 ± 3.6	2.8 ± 2.8
Alcaligenaceae	0.4 ± 0.2	6.4 ± 1.4	2.4 ± 0.1	4.7 ± 2.9	2.2 ± 0.6	0.9 ± 0.3	0.5 ± 0.3	4.6 ± 0.2	6.8 ± 0.2	6.2 ± 3.3	8.7 ± 6.8
Rhodocyclaceae	5.0 ± 1.7	< 0.1	< 0.1	< 0.1	0	< 0.1	< 0.1	< 0.1	< 0.1	< 0.1	< 0.1
Nitrosomonadaceae	4.1 ± 0.1	0.8 ± 0.009	0.1 ± 0.02	1.5 ± 0.9	0.1 ± 0.1	10.7 ± 5.5	1.6 ± 1.1	0.6 ± 0.1	0.1 ± 0.04	1.2 ± 0.1	0.3 ± 0.3
Piscirickettsiaceae	< 0.1	2.7 ± 0.7	1.4 ± 0.8	2.4 ± 3.2	3.7 ± 4.0	0.5 ± 0.3	0.1 ± 0.1	4.0 ± 0.5	3.6 ± 0.9	5.1 ± 1.5	4.5 ± 2.6
Methylophilaceae	< 0.1	1.8 ± 0.3	0.4 ± 0.03	2.5 ± 1.6	2.0 ± 2.2	0.3 ± 0.2	< 0.1	0.1 ± 0.01	0.1 ± 0.05	< 0.1	< 0.1
Bradyrhizobiaceae	0.6 ± 0.3	< 0.1	< 0.1	< 0.1	< 0.1	< 0.1	< 0.1	< 0.1	< 0.1	1.2 ± 0.5	< 0.1
Legionellaceae	< 0.1	0.1 ± 0.002	0.2 ± 0.02	< 0.1	0.2 ± 0.2	0.3 ± 0.2	0.2 ± 0.1	0.3 ± 0.1	< 0.1	0.3 ± 0.3	0.1 ± 0.1
Bacteriodetes	29.1 ± 0.5	45.0 ± 0.2	27.5 ± 1.1	38.4 ± 2.6	30.0 ± 3.7	21.6 ± 5.7	44.7 ± 2.4	33.0 ± 2.4	35.9 ± 0.5	29.0 ± 3.6	35.7 ± 10.1
Flavobacteriaceae	0.6 ± 0.5	30.6 ± 0.2	16.2 ± 0.1	28.5 ± 2.5	20.2 ± 5.4	6.8 ± 4.8	32.9 ± 4.2	17.7 ± 1.9	7.5 ± 0.2	13.4 ± 5	8.9 ± 5.3
Cytophagaceae	0.2 ± 0.1	1.7 ± 0.1	6.6 ± 1.7	0.9 ± 0.9	6.1 ± 3.8	0.6 ± 0.3	10.4 ± 2.7	1.7 ± 0.5	20.9 ± 0.1	0.7 ± 0.5	15.6 ± 18.2
Chitinophagaceae	10.4 ± 4.1	9.2 ± 0.3	3.2 ± 0.3	5.4 ± 1.3	2.7 ± 0.3	7.8 ± 1.2	0.6 ± 0.2	9.3 ± 1.2	3.5 ± 0.5	9.5 ± 1.8	6.6 ± 3.3
Cryomorphaceae	0.1 ± 0.1	1.5 ± 0.05	0.5 ± 0.02	1.6 ± 0.6	0.6 ± 0.2	1.7 ± 0.9	0.4 ± 0.1	1.2 ± 0.3	3 ± 0.2	0.9 ± 0.7	3.4 ± 2.0
Saprospiraceae	11.2 ± 4.0	0.7 ± 0.2	0.1 ± 0.001	0.6 ± 0.2	0.1 ± 0.1	0.4 ± 0.2	< 0.1	0.2 ± 0.03	0.1 ± 0.01	0.7 ± 0.5	0.1 ± 0.1
Actinobacteria	5.7 ± 2.4	4.9 ± 0.01	12.2 ± 4.0	5.6 ± 2.1	8.4 ± 7.1	8.4 ± 2.1	6.9 ± 4.4	8.6 ± 1.8	22.8 ± 0.9	6.8 ± 3.4	20.6 ± 14.3
Intrasporangiaceae	0.2 ± 0.1	1.4 ± 0.1	11.5 ± 3.8	1.8 ± 0.8	7.9 ± 7.4	2.5 ± 1.0	6.7 ± 4.4	3.2 ± 1.7	20.5 ± 1.3	3.5 ± 3.1	19.1 ± 14.5
Saccharibacteria	4.5 ± 0.5	2.5 ± 0.2	6.9 ± 0.5	2.3 ± 0.9	6.5 ± 4.7	4.0 ± 1.1	7.9 ± 3.8	2.3 ± 0.1	8.8 ± 0.2	2.1 ± 0.4	10.3 ± 2.5
Deinococcus–Thermus	< 0.1	2.4 ± 0.4	0.4 ± 0.2	4.1 ± 1.2	0.1 ± 0.1	1.2 ± 0.4	< 0.1	5.4 ± 0.2	0.3 ± 0.1	2.9 ± 0.8	0.1 ± 0.2
Trueperaceae	< 0.1	2.4 ± 0.4	0.4 ± 0.3	4.1 ± 1.9	<0.1	1.2 ± 0.4	< 0.1	5.7 ± 0.2	0.3 ± 0.1	2.9 ± 0.8	0.1 ± 0.2
Chloroflexi	5.0 ± 0.7	0.1 ± 0.02	< 0.1	0.1 ± 0.04	< 0.1	0.1 ± 0.05	< 0.1	0.2 ± 0.006	< 0.1	0.2 ± 0.08	< 0.1
Acidobacteria	3.6 ± 1.8	0	< 0.1	< 0.1	< 0.1	0	0	< 0.1	0	0.1 ± 0.1	< 0.1
Nitrospirae
Nitrospiraceae	0.8 ± 0.3	0	0	0	0	0	0	< 0.1	0	< 0.1	0
Unassigned	1.1 ± 0.3	1.9 ± 0.3	0.5 ± 0.03	1.3 ± 0.5	1.0 ± 0.8	1.8 ± 1.0	0.4 ± 0.3	1.8 ± 0.2	1.9 ± 0.2	1.7 ± 0.2	0.8 ± 0.2