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Supplemen a y File 2: Suppo ing ables and igu es
Table S1 To al numbe o eads, mean eads pe sample, o al unique OTUs/ axa iden i ied pe sample ype, and mean unique axa pe sample iden i ied pos
cleaning o each subs a e and ma ke . Values in pa en heses ep esen s anda d de ia ions, and means a e calcula ed ac oss all indi idual samples.
Bac e ia (16S)
Animal (COI)
Fungi (ITS1)
Plan (ITS2)
Subs a e
To al
eads
Mean
eads
To al
unique
axa
Mean
unique
axa
To al
eads
Mean
eads
To al
unique
axa
Mean
unique
axa
To al
eads
Mean
eads
To al
unique
axa
Mean
unique
axa
To al
eads
Mean
eads
To al
unique
axa
Mean
Unique
axa
Hi e
Deb is
22761
843
(901.46)
33
22.04
(4.91)
43502
1611.19
(2249.56)
4
2.59
(0.84)
329247
12194.33
(7281.02)
195
42.59
(12.54)
510953
18924.19
(10149.67)
56
18.74
(4.6)
Hi e
En ance
20685
795.58
(598.58)
32
21.85
(3.73)
52906
2300.26
(3999.39)
4
2.83
(0.83)
347253
13355.88
(6983.56)
232
56.58
(12.33)
512808
19723.38
(8964.55)
55
20.88
(4.71)
Honey
5310
295
(202.87)
33
17.89
(4.56)
9815
613.44
(559.74)
4
1.81
(0.75)
42990
2528.82
(1537.82)
160
36.41
(13.19)
187170
11010
(9130.55)
51
23.76
(8.4)
In e nal
Pollen
2969
70.69
(111.05)
27
5.4
(3.11)
937
58.56
(120)
4
1.5
(0.73)
280580
6680.48
(4605.41)
180
21.36
(8.12)
1038153
24717.93
(12286.53)
42
12.9
(3.16)
Pollen
T ap
2016
118.59
(62.37)
23
8.24
(2.97)
4629
420.82
(697.35)
4
1.64
(0.67)
178499
9916.61
(4110.64)
151
26.78
(7.46)
378011
21000.61
(14444.85)
43
15.33
(3.12)
Re u n
Fo age Bees
105116
5839.78
(2378.66)
28
18.72
(1.93)
13140
730
(619.34)
4
2.56
(0.7)
168269
9348.28
(4433.22)
137
26.89
(6.92)
525715
29206.39
(13987.88)
33
13
(3.53)
Top Box Bees
133221
7401.17
(3788.68)
27
18.5
(1.1)
13574
754.11
(573.6)
4
2.5
(0.51)
55944
3108
(2741.13)
90
13.33
(4.81)
286861
15936.72
(7693.5)
41
14.11
(3.76)
To al
292078
1759.51
(3010.24)
35
15.19
(7.69)
138503
1073.67
(2121.86)
4
2.3
(0.87)
1402782
8450.49
(6301.94)
309
32.19
(16.8)
3439671
20720.91
(12107.32)
62
16.62
(5.87)
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Table S2 Signi icance compa isons be ween numbe o axa obse ed be ween each sample ype o
ma ke s ITS ( ungi) and ITS2 (plan s). HD = hi e deb is; HE = hi e en ance; Ho = honey; IP = in e nal
pollen; PT = pollen ap; RFB = e u n o age bees; TBB = op box bees. Signi ican di e ences be ween
numbe o axa obse ed based on - es a e shown in bold.
ITS2
ITS
HD
HE
Ho
IP
PT
RFB
TBB
HD
1
1
0.168
0.098
0.026
0.061
HE
0.013
1
0.017
0.009
0.002
0.005
Ho
0.311
0.004
0.281
0.276
0.137
0.19
IP
0.0002
4.73E-06
0.238
1
1
1
PT
0.0004
5.83E-06
0.68
0.68
1
1
RFB
0.0002
7.85E-06
0.68
0.444
0.785
1
TBB
7.56E-08
1.63E-07
0.011
0.08
0.002
0.0002
Table S3 Signi icance compa isons be ween numbe o axa obse ed be ween each sample ype o
ma ke s 16S (bac e ia) and COI (animal). HD = hi e deb is; HE = hi e en ance; Ho = honey; IP = in e nal
pollen; PT = pollen ap; RFB = e u n o age bees; TBB = op box bees. Signi ican di e ences be ween
numbe o axa obse ed based on - es a e shown in bold.
COI
16S
HD
HE
Ho
IP
PT
RFB
TBB
HD
1
0.657
0.038
0.323
1
1
HE
1
0.56
0.032
0.261
1
1
Ho
0.088
0.038
0.53
1
0.56
0.536
IP
2.11E-06
7.43E-09
4.71E-07
1
0.029
0.053
PT
6.04E-06
9.38E-08
1.01E-05
0.088
0.232
0.207
RFB
0.018
0.001
0.693
4.71E-07
2.76E-05
1
TBB
0.011
0.0002
0.296
2.69E-06
6.59E-05
1
Table S4 To al numbe o eads assigned o con igs and unique i uses iden i ied pos - il e ing o each
subs a e.
Subs a e
To al eads
Con ig
leng h ange
A e age con ig leng h
Numbe o axa
Hi e En ance
4,243,239
535-7806
2833.81
29
Honey
130,845
503-5337
1298.83
42
In e nal Pollen
11,846,161
573-9343
3865.82
10
Top Box Bees
1,099,671
594-8460
3544.36
24
To al
17,319,916
503-9343
3519.49
67
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Fig.S1 Shannon di e si y indices ac oss each sample ype o bac e ia (16S), animal (COI), ungi (ITS) and
plan (ITS2) me aba coding ma ke s.
Hi e Deb is Swabs
Hi e En ance Swabs
Honey
In e nal Pollen
Pollen T ap
Re u n Fo age Bees
Top Box Bees
1
2
Alpha Di e si y Measu e
Bac e ia (16S)
Hi e Deb is Swabs
Hi e En ance Swabs
Honey
In e nal Pollen
Pollen T ap
Re u n Fo age Bees
Top Box Bees
0.00
0.25
0.50
0.75
1.00
Alpha Di e si y Measu e
Animal (COI)
Hi e Deb is Swabs
Hi e En ance Swabs
Honey
In e nal Pollen
Pollen T ap
Re u n Fo age Bees
Top Box Bees
1.0
1.5
2.0
2.5
3.0
Alpha Di e si y Measu e
Fungi (ITS1)
Hi e Deb is Swabs
Hi e En ance Swabs
Honey
In e nal Pollen
Pollen T ap
Re u n Fo age Bees
Top Box Bees
0.5
1.0
1.5
2.0
Alpha Di e si y Measu e
Plan s (ITS2)
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Fig.S2 Species accumula ion cu es o bac e ia (16S), ungi (ITS) and plan (ITS2) me aba coding
ma ke s.
2 4 6 8
0 5 10 15 20 25 30
Bac e ia (16S)
Cumula i e numbe o samples
Numbe o axa de ec ed
Hi e En ance Swabs
Hi e Deb is Swabs
Pollen T ap
In e nal Pollen
Honey
Re u n Fo age Bees
Top Box Bees
2 4 6 8
1 2 3 4 5
Animal (COI)
Cumula i e numbe o samples
Numbe o axa de ec ed
Hi e En ance Swabs
Hi e Deb is Swabs
Pollen T ap
In e nal Pollen
Honey
Re u n Fo age Bees
Top Box Bees
2 4 6 8
0 50 100 150 200
Fungi (ITS1)
Cumula i e numbe o samples
Numbe o axa de ec ed
Hi e En ance Swabs
Hi e Deb is Swabs
Pollen T ap
In e nal Pollen
Honey
Re u n Fo age Bees
Top Box Bees
2 4 6 8
0 10 20 30 40 50
Plan s (ITS2)
Cumula i e numbe o samples
Numbe o axa de ec ed
Hi e En ance Swabs
Hi e Deb is Swabs
Pollen T ap
In e nal Pollen
Honey
Re u n Fo age Bees
Top Box Bees
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Fig.S3 Top 10 euka yo e species (excluding A. melli e a) iden i ied in aw RNA sequencing ou pu s o
each sample ype. All species a e plan s excep A. melanogenum which is a ungus.
0.00
0.25
0.50
0.75
1.00
Hi e En ance Swabs
Honey
In e nal Pollen
Top Box Bees
P opo ion o eads
Au eobasidium melanogenum
Camellia lanceoleosa
Camellia sinensis
Escallonia he e ae
Escallonia ub a
Eucalyp us g andis
He acleum sosnowskyi
Macadamia in eg i olia
Telopea speciosissima
Top 10 Euka yo e Species
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Fig.S4 Shannon di e si y indices ac oss each sample ype o RNA i uses.
Hi e En ance Swabs
Honey
In e nal Pollen
Top Box Bees
0.5
1.0
1.5
2.0
Alpha Di e si y Measu e
Shannon di e si y index o RNA da a
