Supplementary Table 1. Abundance of taxa from Phylum to Order for the
three methods used. The number of OTUs is shown for Phylochip, the number
of total sequences for 454 pyrotags, and the number of sequences for each
separate clone library (Bacteria and Archaea). Abundance was determined as
the % of the total for each strategy. In bold are the subtotals for each group.
Microarray
Phylum
Class
454 pyrotags
Clone Library
Order
No.
(%)
No.
(%)
No.
(%)
Archaea
Unclassified
Unclassified
Unclassified
0
10
(0.21)
161
(65.19)
Crenarchaeota
Thermoprotei
Unclassified
0
10
(0.21)
13
(5.26)
Methanobacteria
Methanobacteriales
0
0
2
(0.82)
Methanomicrobia
Methanosarcinales
0
0
1
(0.41)
Thermoplasmata
Thermoplasmatales
0
4
9
(3.64)
Unclassified
Unclassified
0
0
61
(24.69)
0
4
(0.08)
73
(29.56)
0
24
(0.5)
247
(100)
(46.02)
11
(6.40)
(1.16)
Euryarchaeota
Total Euryarchaeota
Total Archaea
(0.08)
Bacteria
Bacteria - Unclassified
Unclassified
Unclassified
16
(4.32)
2,209
Acidobacteria_Gp1
Unclassified
2
(0.33)
0
2
Acidobacteria_Gp2
Unclassified
2
(0.49)
0
0
Acidobacteria_Gp3
Unclassified
2
(0.46)
0
0
Acidobacteria_Gp5
Unclassified
1
(0.79)
0
0
Acidobacteria_Gp6
Unclassified
3
(1.29)
0
0
Acidobacteria_Gp18
Unclassified
2
(0.72)
0
0
Acidobacteria_Gp22
Unclassified
2
(0.73)
0
0
14
(4.81)
0
2
(1.16)
Acidimicrobiales
5
(0.99)
0
14
(8.14)
Actinomycetales
23
(7.62)
13
Coriobacteriales
1
(0.22)
0
0
Nitriliruptorales
1
(0.36)
0
0
Acidobacteria
Total Acidobacteria
Actinobacteria
(0.27)
0
Actinobacteria
Rubrobacterales
0
Solirubrobacterales
1
(0.19)
0
Unclassified
1
(0.47)
43
(0.9)
0
32
(9.85)
64
(1.33)
14
Aquificales
1
(0.48)
0
0
Ktedonobacterales
0
0
1
Bacteroidia
Bacteroidales
5
(1.32)
0
0
Sphingobacteria
Sphingobacteriales
5
(0.95)
1
Unclassified
Unclassified
2
(0.61)
0
12
(2.88)
1
Total Actinobacteria
Aquificae
Aquificae
Bacteria_incertae_sedis Ktedonobacteria
8
(0.17)
0
0
(0.02)
(8.14)
(0.58)
0
Bacteroidetes
Total Bacteroidetes
(0.02)
1
(0.58)
1
(0.58)
BRC1
Unclassified
Unclassified
1
(0.34)
0
Chlamydiae
Chlamydiae
Chlamydiales
1
(0.14)
18
Chlorobi
Chlorobia
Chlorobiales
1
(0.25)
0
0
Caldilineae
Caldilineales
1
(0.36)
0
0
Chloroflexi
Chloroflexales
0
Dehalococcoidetes
Unclassified
1
(0.27)
0
0
Thermomicrobia
Sphaerobacterales
1
(0.24)
0
0
Unclassified
Unclassified
2
(0.53)
0
0
5
(1.4)
1
(0.02)
0
(0.04)
0
1
0
(0.38)
(0.02)
0
0
Chloroflexi
Total Chloroflexi
Cyanobacteria
Cyanobacteria
Unclassified
4
(0.95)
2
Deinococcus-Thermus
Deinococci
Thermales
1
(0.17)
0
Bacillales
2
(1.03)
2
Lactobacillales
1
(0.41)
0
Clostridiales
22
(7.2)
23
Natranaerobiales
1
(0.29)
0
Unclassified
3
(0.94)
9
Thermolithobacteria
Thermolithobacterales
1
(0.54)
0
Unclassified
Unclassified
0
0
(0.04)
0
Bacilli
Clostridia
0
(0.48)
1
(0.58)
0
Firmicutes
Total Firmicutes
(0.19)
2
0
5
(0.1)
0
(0.81)
3
30
(10.41)
39
Gemmatimonadetes
Gemmatimonadetes
Gemmatimonadales
6
(1.43)
0
0
Lentisphaerae
Lentisphaeria
Unclassified
1
(0.26)
0
0
Nitrospira
Nitrospira
Nitrospirales
2
(1.18)
10
(0.21)
13
OD1
Unclassified
Unclassified
0
6
(0.13)
0
OP10
Unclassified
Unclassified
2
(0.71)
0
(1.16)
0
(1.74)
(7.56)
Planctomycetes
Planctomycetacia
Planctomycetales
7
Caulobacterales
0
Rhizobiales
20
Rhodobacterales
(1.62)
116
(2.42)
6
(3.49)
1
(0.02)
0
(5.37)
9
(0.19)
0
3
(0.73)
0
Rhodospirillales
4
(1.25)
131
(2.73)
13
(7.56)
Rickettsiales
0
9
(0.19)
2
(1.16)
Sphingomonadales
2
(0.74)
0
Unclassified
22
(0.76)
55
(1.15)
1
(0.58)
Total Alphaproteobacteria
51
(8.85)
205
(4.27)
16
(9.30)
Burkholderiales
38
(13.8)
249
(5.19)
44
(25.58)
Methylophilales
2
(0.49)
0
Nitrosomonadales
2
(0.23)
8
(0.17)
0
Rhodocyclales
4
(1.3)
2
(0.04)
1
(0.58)
Unclassified
3
(0.89)
1122
(23.38)
33
(19.19)
Total Betaproteobacteria
49
(16.71) 1,381
(28.77)
78
(45.35)
Acidithiobacillales
0
(0.27)
3
(1.74)
Alteromonadales
2
(0.71)
0
Chromatiales
3
(0.76)
1
Enterobacteriales
1
(0.52)
0
Legionellales
1
(0.56)
131
Methylococcales
2
(1.08)
0
Pseudomonadales
2
(0.83)
1
Thiotrichales
2
(0.78)
0
Xanthomonadales
7
(2.36)
18
(0.38)
1
(0.58)
Unclassified
5
(2.18)
104
(2.17)
8
(4.65)
Total Gammaproteobacteria
25
(9.78)
268
(5.58)
24
(13.95)
Desulfobacterales
1
(0.4)
0
0
Desulfovibrionales
7
(2.5)
0
0
Myxococcales
5
(1.04)
2
Syntrophobacterales
5
(2.33)
0
0
Unclassified
12
(4.22)
0
0
Total Deltaproteobacteria
30
(10.49)
2
Epsilonproteobacteria
Campylobacterales
23
(9.15)
0
Unclassified
Unclassified
0
0
Alphaproteobacteria
0
0
Betaproteobacteria
Proteobacteria
Gammaproteobacteria
13
0
(0.02)
0
0
(2.73)
12
(6.98)
0
(0.02)
0
0
(0.04)
0
Deltaproteobacteria
183
(0.04)
0
0
(3.81)
1
(0.58)
Total Proteobacteria
178
(54.98) 2,039
(42.48)
119
(69.19)
0
2
(1.16)
Spirochaetes
Spirochaetes
Spirochaetales
0
Synergistetes
Synergistia
Synergistales
5
(1.76)
0
0
Tenericutes
Mollicutes
Acholeplasmatales
1
(0.08)
0
0
Thermodesulfobacteria
Thermodesulfobacteria
Thermodesulfobacteriales
1
(0.21)
0
0
TM7
Unclassified
Unclassified
2
(0.79)
262
(5.46)
0
Verrucomicrobiae
Verrucomicrobiales
2
(0.37)
9
(0.19)
0
Spartobacteria
Unclassified
1
(0.09)
0
0
Unclassified
Unclassified
2
(0.56)
0
0
5
(1.02)
9
(0.19)
0
328
100
4,800
100
172
Verrucomicrobia
Total Verrucomicrobia
Total Bacteria
100