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Supplementary Materials Supplementary materials Scheme 1. Taxonomy analysis of 16S and ITS amplicon sequencing. Table S1. A. Taxonomy of 16S amplicon sequencing. Six sub-groups of three bees each were analysed. Table presents relative abundance of each of the listed bacterium (numbers as percentages) in relation to the entire amplicon. Sample PL1 PL1 PL1 PL2 PL2 PL2 PL3 PL3 PL3 PL4 PL4 PL4 PL5 PL5 PL5 PL6 PL6 PL6 Bacteria (%) (1) (2) (3) (1) (2) (3) (1) (2) (3) (1) (2) (3) (1) (2) (3) (1) (2) (3) Firmicutes 21,20 21,43 21,39 44,22 41,81 9,48 10,61 19,91 18,45 19,60 42,83 44,36 45,74 66,04 64,59 65,48 Lactobacillus γ-proteobacteria 6,99 6,95 7,33 26,97 27,15 55,68 52,38 34,91 35,42 35,63 28,51 28,31 28,55 6,21 5,54 5,02 Orbales Gilliamella α-proteobacteria Acetobacterales 4,36 4,31 4,24 15,18 15,40 0,44 0,48 1,23 1,09 1,15 7,81 6,80 7,09 6,05 6,48 6,64 Commensalibacter α-proteobacteria Rhizobiales 59,70 59,62 59,40 5,19 6,16 2,40 2,87 27,36 27,40 26,41 12,04 12,03 11,14 12,43 12,82 12,49 Bartonella γ-proteobacteria Neisseriaceae 7,36 7,29 7,24 4,53 4,97 23,69 24,48 15,44 16,37 15,90 2,37 2,33 2,02 1,10 1,18 1,27 Snodgrassella ND ND Actinobacteria Bifidobacterium 0,38 0,34 0,36 1,89 2,25 0,23 0,23 0,98 1,13 1,17 0,85 0,92 0,95 8,00 9,21 8,84 γ-proteobacteria Orbales 0,00 0,00 0,00 0,94 0,89 2,48 2,30 0,00 0,00 0,00 0,00 0,00 0,00 0,13 0,14 0,10 Frischella Bacteroidetes Dysgonomonas 0,00 0,00 0,00 0,59 0,81 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 Bacteroidetes Apibacter 0,00 0,00 0,00 0,45 0,55 5,36 6,51 0,00 0,01 0,01 5,05 4,87 4,08 0,00 0,00 0,00 γ-proteobacteria Enterobacteriales 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,09 0,04 0,03 0,38 0,25 0,28 0,00 0,00 0,00 Serratia Other 0,01 0,06 0,04 0,04 0,01 0,24 0,14 0,08 0,09 0,1 0,16 0,13 0,15 0,04 0,04 0,16 ND – no data. Table S1. B. Taxonomy of ITS2 amplicon sequencing. Six subgroups of three bees each were analysed. Hits for plants and fungi were grouped into separate fractions. % for either Plant or Fungi is a sum of all counts for each fraction (high- lighted in grey). PL1 PL1 PL1 PL2 PL2 PL2 PL3 PL3 PL3 PL4 PL4 PL4 PL5 PL PL5 PL6 PL6 PL6 Sample (1) (2) (3) (1) (2) (3) (1) (2) (3) (1) (2) (3) (1) 5(2) (3) (1) (2) (3) Plant (%) 1,32 2,34 1,76 93,49 85,25 92,46 89,38 90,19 86,67 12,06 13,8 10,53 42,08 37,91 41,77 87,91 89,41 88,78 Brassicaceae 0,01 0,01 0,01 66,23 60,61 57,97 16,13 14,76 11,07 0,19 0,15 0,07 0,00 0,00 0,00 0,01 0,06 0,06 unassigned Brassicaceae 0,00 0,00 0,00 24,34 22,35 26,97 2,06 2,26 1,51 0,04 0,00 0,00 0,00 0,00 0,00 0,01 0,05 0,09 Raphanus Brassicaceae 0,00 0,00 0,00 0,18 0,13 0,00 1,43 1,34 1,29 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 Brassica Brassicaceae 0,00 0,00 0,00 0,01 0,04 0,00 0,13 0,04 0,07 1,28 2,02 1,86 0,08 0,04 0,10 0,00 0,00 0,00 Berteroa Brassicaceae 0,00 0,00 0,00 0,06 0,12 3,62 0,00 0,00 0,04 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 Erysimum Asteraceae 0,00 0,00 0,01 0,74 0,53 3,21 61,40 61,42 61,08 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 Scorzoneroides Ericaceae 0,07 0,21 0,17 0,00 0,01 0,01 0,00 0,00 0,01 0,06 0,00 0,01 0,01 0,00 0,01 87,68 88,85 88,26 Calluna Asteraceae 0,00 0,02 0,00 0,01 0,01 0,00 0,00 0,00 0,00 0,00 0,00 0,00 36,01 33,12 35,82 0,00 0,00 0,00 Helianthus Polygonaceae 0,00 0,00 0,00 0,19 0,17 0,00 4,61 5,60 6,26 0,01 0,16 0,04 0,02 0,00 0,00 0,01 0,04 0,06 Rumex Fabaceae 0,13 0,46 0,21 0,11 0,12 0,00 0,10 0,22 0,16 4,65 5,87 3,80 1,50 1,22 0,95 0,10 0,12 0,05 Ornithopus Hypericaceae 0,00 0,00 0,00 0,00 0,00 0,00 1,88 2,75 3,17 0,00 0,00 0,00 0,03 0,05 0,11 0,00 0,00 0,00 Hypericum Plantaginaceae 0,00 0,00 0,00 0,21 0,10 0,00 0,00 0,01 0,01 2,08 2,29 2,38 0,00 0,00 0,00 0,00 0,00 0,00 Plantago other 1,11 1,64 1,36 1,41 1,06 0,68 1,64 1,79 2 3,75 3,31 2,37 4,43 3,48 4,78 0,1 0,29 0,26 Fungi (%) 94,14 93,19 94,16 6,5 14,72 7,54 10,62 9,8 13,33 87,61 85,5 88,82 57,61 61,93 57,95 12,01 10,58 11,18 Cladosporiaceae 2,20 2,50 4,55 2,37 4,44 0,01 1,31 1,12 1,19 11,88 9,80 11,06 9,74 13,79 10,17 0,20 0,30 0,43 Cladosporium Capnodiales 16,37 14,72 11,51 0,00 0,00 0,00 0,00 0,00 0,00 0,42 0,33 0,31 0,12 0,09 0,57 0,00 0,00 0,00 unassigned Pseudeurotiaceae 4,78 4,50 3,33 0,01 0,10 0,00 0,14 0,27 0,19 9,80 10,90 12,90 0,28 0,10 0,18 0,10 0,05 0,04 Bettsia Saccharomycetaceae 33,28 34,99 39,49 0,06 0,04 0,00 0,85 1,05 1,72 2,87 2,84 2,59 0,70 0,80 2,50 0,04 0,14 0,12 Zygosaccharomyces Aspergillaceae 2,30 2,59 1,29 0,23 0,66 0,00 2,65 2,62 6,01 16,55 15,60 15,79 0,24 0,84 0,38 0,02 0,11 0,00 Aspergillus Sclerotiniaceae 0,00 0,14 0,00 0,19 1,05 0,00 0,30 0,33 0,16 0,57 0,75 1,04 0,01 0,00 0,00 0,53 0,53 0,45 unassigned Mycosphaerellaceae 2,46 1,99 3,79 0,89 2,12 0,00 1,52 0,58 0,34 4,51 3,81 4,80 5,19 7,03 7,84 0,55 0,96 0,67 Mycosphaerella Pleosporaceae 2,77 4,32 3,12 0,26 0,56 7,47 0,89 1,09 0,91 0,67 0,47 1,06 3,19 3,40 1,98 0,59 0,46 0,42 Alternaria Aspergillaceae 5,04 3,53 3,05 0,14 0,47 0,00 0,26 0,15 0,16 9,66 9,95 13,59 0,56 1,05 0,74 0,89 1,08 0,91 Penicillium Myxotrichaceae 2,37 3,13 3,54 0,00 0,04 0,00 0,33 0,36 0,33 2,70 2,57 2,74 0,05 0,00 0,12 1,14 0,74 0,52 unassigned Sporidiobolaceae 0,00 0,04 0,10 0,25 0,50 0,00 0,26 0,17 0,34 0,06 0,08 0,56 5,31 5,35 3,71 0,00 0,00 0,15 Rhodotorula Leotiomycetes 0,01 0,00 0,03 0,03 0,06 0,00 0,00 0,08 0,03 0,21 0,26 0,27 3,00 4,25 3,38 0,09 0,03 0,08 unassigned other 22,56 20,74 20,36 2,07 4,68 0,06 2,11 1,98 1,95 27,71 28,14 22,11 29,22 25,23 26,38 7,86 6,18 7,39 Unassigned (%) 4,54 4,47 4,08 0,01 0,03 0,00 0,00 0,01 0,00 0,33 0,70 0,65 0,31 0,16 0,28 0,08 0,01 0,04 Table S2.
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