ELECTRONIC SUPPLEMENTARY MATERIAL
SOILS, SEC 5 • SOIL AND LANDSCAPE ECOLOGY • RESEARCH ARTICLE
Bacterial communities estimated by pyrosequencing in the soils of Chinampa, a
traditional sustainable agro-ecosystem in Mexico
Salvador Embarcadero-Jiménez1 • Flor N. Rivera-Orduña1 • En Tao Wang1
Received: 13 May 2015 / Accepted: 24 September 2015
© Springer-Verlag Berlin Heidelberg 2015
Responsible editor: Jizheng He
1
Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto
Politécnico Nacional, Mexico D. F., C.P. 11340, Mexico
 En Tao Wang
entaowang@yahoo.com.mx
Table S1 Taxonomic distribution of the 140,790 pyrosequencing reads at Phylum level from the six samples
of Chinampa soils
No.
Phylum*
1
Candidate Division AC1
2
SBCh1 DBCh1
SBCh2 DBCh2
SRCh1
SBCh1- 2
Total reads
%#
0
0
3
0
0
0
3
0.002
Acidobacteria
2775
913
2579
1175
903
2990
11335
8.051
3
Actinobacteria
428
658
1544
1305
200
466
4601
3.268
4
Candidate Division AncK6
0
0
0
0
2
0
2
0.001
5
Armatimonadetes
143
13
76
18
57
170
477
0.339
6
Candidate Division BHI80-139
0
0
1
0
0
1
2
0.001
7
Candidate Division BRC1
8
Bacteroidetes
9
15
5
170
4
6
18
218
0.155
2575
1695
2511
1386
153
2354
10694
7.596
Caldithrix
7
8
78
1
10
2
106
0.075
10
Chlamydiae
0
0
2
0
0
0
2
0.001
11
Chlorobi
12
Chloroflexi
13
791
187
1722
139
374
687
3900
2.770
2012
4256
5276
5499
1774
1919
20736
14.72
Cyanobacteria
25
21
39
15
6
21
127
0.090
14
Elusimicrobia
87
6
54
9
5
72
233
0.165
15
Candidate Division FBP
5
0
0
0
0
6
11
0.008
16
Candidate Division FCPU426
3
0
7
0
0
4
14
0.010
17
Fibrobacteres
3
0
44
3
0
2
52
0.037
18
Firmicutes
1054
6631
390
3044
543
981
12643
8.980
19
Candidate Division GAL15
0
0
0
0
3
0
3
0.002
20
Candidate Division GN02
33
3
126
4
8
29
203
0.144
21
Candidate Division GN04
32
5
101
3
18
37
196
0.139
22
Candidate Division GOUTA4
2
0
5
0
0
1
8
0.005
23
Gemmatimonadetes
Candidate Division Kazan-3B28
608
156
745
283
116
605
2513
1.785
0
0
43
4
1
4
52
0.037
0
0
6
0.004
24
25
Lentisphaerae
0
0
6
0
26
Candidate Division MVP-21
1
0
6
5
0
2
14
0.010
27
Candidate Division NC10
0
1
2
0
56
0
59
0.042
28
Candidate Division NKB19
49
16
151
29
32
64
341
0.242
29
Nitrospirae
633
413
649
522
355
562
3134
2.226
30
Candidate Division OD1
219
77
1207
61
126
207
1897
1.347
31
Candidate Division OP11
70
52
106
21
51
49
349
0.248
32
Candidate Division OP3
14
5
38
5
1
19
82
0.058
33
Candidate Division PAUC34f
0
0
1
0
0
0
1
0.001
34
Planctomycetes
835
718
2257
1139
281
954
6184
4.392
35
Proteobacteria
5486
3295
22694
5318
4190
6209
47192
33.51
36
Candidate Division SAR406
0
0
2
0
0
0
2
0.001
37
Candidate Division SBR1093
7
59
28
48
50
9
201
0.143
38
Spirochaetes
2
0
635
0
17
2
656
0.466
39
Candidate Division TM6
36
49
300
43
29
22
479
0.340
40
Candidate Division TM7
41
Tenericutes
42
Verrucomicrobia
43
143
225
290
177
21
102
958
0.680
1
16
79
10
0
1
107
0.076
228
36
620
47
17
425
1373
0.975
Candidate Division WPS-2
1
0
1
0
0
1
3
0.002
44
Candidate Division WS1
0
0
6
0
0
0
6
0.004
45
Candidate Division WS2
15
3
17
2
3
16
56
0.039
46
Candidate Division WS3
45
1
79
3
47
53
228
0.162
47
Candidate Division WS4
0
0
2
0
1
0
3
0.002
48
Candidate Division WS5
0
0
2
0
0
0
2
0.001
49
Candidate Division WS6
1
0
1
0
0
0
1
0.001
50
Candidate Division ZB3
0
0
5
0
0
0
5
0.003
51
Caldithrix
5
2
10
0
7
4
28
0.019
52
Deinococcus-Thermus
8
4
31
8
6
9
66
0.046
53
Insertae sedis
340
523
735
774
290
510
3172
2.253
54
Unclassified
754
1150
1741
1040
532
856
6073
4.313
19491
21202
47217
22144
10291
20445
140790
100.00
Total reads
*. The phyla in boldface were the maim groups with more than 1% relative abundance
#. % Refers the relative abundance of the taxa
Table S2 Relative abundance of the main bacterial phyla in the Chinampa soils
Bacterial Phylla
Relative abundance (%)
SBCh1 SBCh1-2
DBCh1
SBCh2 DBCh2 SRCh1
Average
Acidobacteria
14.24
14.62
4.31
5.46
5.31
8.77
8.785
Actinobacteria
2.20
2.28
3.10
3.27
5.89
1.94
3.113
Bacteroidetes
13.21
11.51
7.99
5.32
6.26
1.49
7.630
4.06
3.36
0.88
3.65
0.63
3.63
2.702
Chloroflexi
10.32
9.39
20.07
11.17
24.83
17.24
15.503
Firmicutes
5.41
4.80
31.28
0.83
13.75
5.28
10.225
Gemmatimonadetes
3.21
2.96
0.74
1.58
1.28
1.13
1.817
Nitrospirae
3.25
2.75
1.95
1.37
2.36
3.45
2.523
OD1
1.12
1.01
0.36
2.56
0.28
1.22
1.092
Planctomycetes
4.28
4.67
3.39
4.78
5.14
2.73
4.165
Proteobacteria
27.66
29.80
15.27
46.46
23.37
40.85
30.568
Alphaproteobacteria
8.78
11.30
6.50
10.47
9.98
10.38
9.568
Betaproteobacteria
4.42
4.57
1.20
12.12
2.13
9.14
5.597
Gammaproteobacteria
8.43
8.49
3.01
13.60
4.78
4.65
7.160
Chlorobi
6.03
5.44
4.56
10.27
6.48
16.68
8.317
Other
Deltaproteobacteria
5.43
6.17
2.77
8.31
2.70
4.31
4.948
Insertae sedis
1.74
2.49
2.47
1.55
3.50
2.79
2.423
Unclassified
3.87
4.19
5.42
3.69
4.70
5.17
4.507
100.00
100.00
100.00
100.00
100.00
100.00
100.00
Total
Table S3 Taxonomic distribution of the most abundant bacterial taxa at Class level (Relative abundance
>0.5 %)
Classes
SBCh1
DBCh1
SBCh2
DBCh2
SRCh1
SBCh1- 2
Total reads*
Phylum Acidobacteria
Chloracidobacteria
788
496
312
395
105
597
2693
Acidobacteria-5 (Gp-5)
200
55
134
112
50
160
711
Acidobacteria-6 (Gp-6)
1281
161
1131
369
420
1643
5005
Solibacteres
186
59
362
110
96
250
1063
“Sva0725”
85
25
223
29
26
86
474
Acidimicrobiia
216
446
1029
1042
96
221
3050
Actinobacteria
107
135
127
152
21
113
655
82
33
266
58
50
104
593
Rhodothermi
68
85
246
100
21
61
581
Saprospirae
522
10
390
5
25
477
1429
Phylum Actinobacteria
Thermoleophilia
Phylum Bacteroidetes
Bacteroidia
3
6
674
2
23
7
715
Cytophagia
1676
1545
691
1235
64
1526
6737
147
19
273
13
8
146
606
533
148
1509
99
287
491
3067
1431
3804
3569
4450
1147
1246
15647
302
253
716
564
374
363
2572
“SAR202”
58
51
236
114
73
68
600
“TK17”
88
57
272
154
50
96
717
Bacilli
689
6114
267
2713
536
621
10940
Clostridia
360
485
115
313
7
358
1638
Flavobacteria
Phylum Chlorobi
Ignavibacteria
Phylum Chloroflexi
Anaerolineae
“S085”
Phylum Firmicutes
Phylum Gemmatimonadetes
“Gemm-1”
201
7
99
16
45
197
565
“Gemm-5”
142
50
199
115
18
130
654
Gemmatimonadetes
187
29
131
61
31
178
617
633
413
649
522
355
562
3134
78
33
356
19
36
77
599
Phycisphaerae
308
74
925
135
57
389
1888
Planctomycetia
468
629
1173
981
214
525
3990
Alphaproteobacteria
1712
1379
4944
2210
1068
2311
13624
Betaproteobacteria
861
255
5722
471
941
934
9184
Phylum Nitrospirae
Nitrospira
Candidate Division OD1
“ZB2”
Phylum Planctomycetes
Phylum Proteobacteria
Deltaproteobacteria
1175
966
4850
1434
1717
1113
11255
Gammaproteobacteria
1644
639
6420
1058
417
1735
11913
0
0
463
0
9
1
473
93
103
89
103
13
69
470
268
753
Phylum Spirochaetes
Leptospirae
Candidate Division TM7
“TM7-1”
Phylum Verrucomicrobia
Pedosphaerae
131
11
319
15
9
*. The Classes listened in this table represent 84.24 % of the total reads obtained by pyrosequencing
Table S4 Taxonomic distribution of the most abundant bacterial taxa at Order level (Relative abundance
>0.5 %)
Order names
SBCh1-2
Total
reads*
SBCh1
DBCh1
SBCh2
DBCh2
SRCh1
1198
150
1053
321
320
1520
4562
“RB41” (Class Chloracidobacteria)
778
480
311
372
87
591
2619
Solibacterales (Class Solibacteres)
186
59
362
110
96
250
1063
216
446
1029
1042
96
221
3050
1676
1545
691
1235
64
1526
6737
Phylum Acidobacteria
“iii1-15” (Class Acidobacteria-6)
Phylum Actinobacteria
Acidimicrobiales (Class Acidimicrobiia)
Phylum Bacteroidetes
Cytophagales (Class Cytophagia)
Bacteroidales (Class Bacteroidia)
3
6
674
2
23
7
715
Saprospirales (Class Saprospirae)
522
10
388
5
25
475
1425
533
148
1509
99
287
491
3067
“DRC31” (Class Anaerolineae)
299
2023
1222
2544
153
254
6495
“GCA004” (Class Anaerolineae)
38
88
400
121
293
52
992
“envOPS12” (Class Anaerolineae)
148
125
377
129
79
115
973
“S0208” (Class Anaerolineae)
105
131
266
167
206
84
959
Caldilineales (Class Anaerolineae)
180
967
405
879
36
161
2628
“SBR1031” (Class Anaerolineae)
469
380
453
483
102
396
2283
Bacillales (Class Bacilli)
460
6061
240
2680
535
399
10375
Clostridiales (Class Clostridia)
347
426
79
290
6
352
1500
633
413
649
522
355
562
3134
Pirellulales (Class Planctomycetia)
232
422
792
545
123
244
2358
Planctomycetales (Class Planctomycetia)
209
153
312
324
55
239
1292
Phycisphaerales (Class Phycisphaerae)
154
38
332
67
29
185
805
Rhizobiales (Class Alphaproteobacteria)
719
885
1774
1377
467
743
5965
Rhodospirillales (Class Alphaproteobacteria)
322
210
1212
373
366
345
2828
Rhodobacterales (Class Alphaproteobacteria)
162
99
637
128
35
324
1385
Sphingomonadales (Class Alphaproteobacteria)
232
41
436
55
21
614
1399
Burkholderiales (Class Betaproteobacteria)
151
30
181
38
272
130
802
0
8
2966
11
162
1
3148
Phylum Chlorobi
Ignavibacteriales (Class Ignavibacteria)
Phylum Chloroflexi
Phylum Firmicutes
Phylum Nitrospirae
Nitrospirales (Class Nitrospira)
Phylum Planctomycetes
Phylum Proteobacteria
Hydrogenophilales (Class Betaproteobacteria)
“MND1” (Class Betaproteobacteria)
190
102
1123
160
71
227
1873
Desulfobacterales (Class Deltaproteobacteria)
1
28
1527
28
145
0
1729
Desulfuromonadales (Class Deltaproteobacteria)
0
48
975
27
133
2
1185
Myxococcales (Class Deltaproteobacteria)
232
68
388
80
82
217
1067
Syntrophobacterales (Class Deltaproteobacteria)
697
670
1168
1048
1027
635
5245
Chromatiales (Class Gammaproteobacteria)
47
23
1193
23
40
37
1363
Pseudomonadales (Class Gammaproteobacteria)
236
37
298
52
94
222
939
Thiotrichales (Class Gammaproteobacteria)
436
146
1899
252
55
474
3262
Xanthomonadales (Class Gammaproteobacteria)
577
69
365
87
119
633
1850
131
11
318
15
9
268
752
Phylum Verrucomicrobia
Pedosphaerales (Class Pedosphaerae)
* The Orders listed in this table represent 65.22 % of the total reads obtained by pyrosequencing
SBCh1-2
SRCh1
DBCh2
SBCh2
DBCh1
Family name (Class/Order)*
SBCh1
Table S5. Taxonomic distribution of the most abundant bacterial taxa at Family level (Relative abundance
>0.25 %)
Total
reads
Phylum Acidobacteria
“Mb2424” (Acidobacteria-6/“iii1-15”)
128
56
118
94
30
157
583
83
11
161
27
43
103
428
703
298
279
191
15
516
2002
78
28
237
41
46
98
528
1582
1313
315
1082
43
1434
5769
Flammeovirgaceae (Cytophagia/Cytophagales)
61
177
317
105
17
53
730
Flavobacteriaceae (Flavobacteriia/Flavobacteriales)
93
18
152
13
7
94
377
Rhodothermaceae (Rhodothermi/Rhodothermales)
61
55
183
67
11
51
428
425
8
67
3
7
383
893
530
141
1451
99
283
490
2994
2
29
291
35
2
2
361
Caldilineaceae (Anaerolineae/Caldilineales)
180
955
402
867
36
159
2599
“A4b” (Anaerolineae/“SBR1031”)
427
306
355
341
73
365
1867
225
5304
174
2415
148
199
8465
46
141
17
65
64
37
370
Turicibacteraceae (Bacilli/Turicibacterales)
214
31
0
19
1
205
470
Clostridiaceae (Clostridia/Clostridiales)
270
152
32
92
0
278
824
“0319-6A21” (Nitrospira/Nitrospirales)
41
33
139
47
131
47
438
Nitrospiraceae (Nitrospira/Nitrospirales)
576
376
489
467
185
501
2594
Pirellulaceae (Planctomycetia/Pirellulales)
232
422
792
545
123
244
2358
Planctomycetaceae (Planctomycetia/Planctomycetales)
209
153
312
324
55
239
1292
342
486
625
840
233
349
2875
65
11
254
11
9
224
574
“RB40” (Acidobacteria-6/“iii1-15”)
“Ellin6075” (Chloracidobacteria/“RB41”)
Phylum Actinobacteria
Gaiellaceae (Thermoleophilia/Gaiellales)
Phylum Bacteroidetes
Cytophagaceae (Cytophagia/Cytophagales)
Chitinophagaceae (Saprospirae/Saprospirales)
Phylum Chlorobi
Ignavibacteriaceae (Ignavibacteria/Ignavibacteriales)
Phylum Chloroflexi
Anaerolinaceae (Anaerolineae/Anaerolineales)
Phylum Firmicutes
Bacillaceae (Bacilli/Bacillales)
Planococcaceae (Bacilli/Bacillales)
Phylum Nitrospirae
Phylum Planctomycetes
Phylum Proteobacteria
Hyphomicrobiaceae (Alphaproteobacteria/Rhizobiales)
Hyphomonadaceae (Alphaproteobacteria/Rhodobacterales)
Rhodobacteraceae (Alphaproteobacteria/Rhodobacterales)
97
88
382
117
25
95
804
Rhodospirillaceae (Alphaproteobacteria/Rhodospirillales)
283
179
1104
298
341
298
2503
Sphingomonadaceae (Alphaproteobacteria/Sphingomonadales)
184
39
368
49
19
579
1238
Comamonadaceae (Betaproteobacteria/Burkholderiales)
107
18
160
16
17
99
417
Hydrogenophilaceae (Betaproteobacteria/Hydrogenophilales)
0
8
2966
11
162
1
3148
Desulfobulbaceae (Deltaproteobacteria/Desulfobacterales)
1
17
938
14
94
0
1064
Desulfobacteraceae (Deltaproteobacteria/Desulfobacterales)
0
11
556
14
50
0
631
696
669
1088
1047
995
634
5129
0
32
787
19
109
2
949
232
21
287
26
59
220
845
49
1
353
8
23
50
484
Halomonadaceae (Gammaproteobacteria/Oceanospirillales)
0
87
9
304
0
1
401
Thiotrichaceae (Gammaproteobacteria/Thiotrichales)
0
0
648
1
11
0
660
Piscirickettsiaceae (Gammaproteobacteria/Thiotrichales)
435
146
989
251
43
472
2336
Sinobacteraceae (Gammaproteobacteria/Xanthomonadales)
334
51
266
77
76
371
1175
Xanthomonadaceae (Gammaproteobacteria/Xanthomonadales)
242
18
98
9
43
261
671
0
0
460
0
9
1
470
Syntrophobacteraceae (Deltaproteobacteria/Syntrophobacterales)
Pelobacteraceae (Deltaproteobacteria/Desulfuromonadales)
Pseudomonadaceae (Gammaproteobacteria/Pseudomonadales)
Marinicellaceae (Gammaproteobacteria/Marinicellales)
Phylum Spirochaetes
Leptospiraceae (Leptospirae/Leptospirales)
+ The
Families listed in this table represent 44.56 % of the total reads obtained by pyrosequencing
Table S6 Distribution of the main bacterial genera in the Chinampa soils
Sequence number
Phylum (Class)
Genus
Total
SBCH1
SBCH1-2
DBCH1
SBCH2
DBCH2
SRCH1
Rhodoplanes
131
112
90
233
213
89
868
Kaistobacter*
121
434
10
212
11
4
792
Afifella
Proteobacteria
(-proteobacteria) Ochrobactrum
26
23
35
112
70
39
305
2
0
12
255
18
0
287
Pedomicrobium
27
40
110
92
248
58
575
Devosia
67
59
24
63
29
8
250
Gallionella
0
1
1
177
0
34
216
Thiobacillus
0
0
8
2662
10
149
2829
Variovorax
39
53
0
0
0
0
92
Lysobacter
91
102
0
7
0
1
201
Acinetobacter
2
2
16
8
25
35
88
Thermomonas
45
35
0
0
0
0
80
Halomonas
0
0
87
9
301
0
397
Pseudomonas
206
191
20
248
24
54
743
Steroidobacter
91
87
11
32
25
2
248
Thioalkalimicrobium
0
1
0
127
0
0
128
Aquicella
19
10
22
24
17
3
95
Desulfurivibrio
0
0
0
101
0
1
102
Bdellovibrio
30
23
2
34
6
1
91
Desulfococcus
0
0
9
192
6
27
234
Desulfosarcina
0
0
0
169
0
15
184
Peredibacter
7
3
0
64
0
1
75
Acidobacteria
Candidatus Solibacter
16
26
4
29
10
13
98
Actinobacteria
Salinispora
0
0
0
1
0
189
190
Pontibacter
144
118
95
17
65
10
449
Flavobacterium
32
34
1
80
1
1
149
Rubricoccus
37
31
3
61
7
0
139
Adhaeribacter
52
36
0
18
0
0
106
Flavisolibacter
46
43
0
0
0
0
89
Salinimicrobium
24
37
3
8
2
1
75
Ardenscatena
45
37
4
16
3
1
116
Ignavibacterium
0
0
2
136
1
7
146
Anaerolinea
1
1
28
138
30
2
200
Bacillus
140
121
4756
126
2164
128
7435
Turicibacter
214
205
31
0
19
1
470
Marinibacillus
2
0
102
11
38
8
171
Paenisporosarcina
5
3
44
5
18
62
137
Solibacillus
13
11
63
4
27
0
118
Proteobacteria
(-proteobacteria)
Proteobacteria
(-proteobacteria)
Proteobacteria
(-proteobacteria)
Bacteroidetes
Chloroflexi
Firmicutes
Nitrospirae
Planctomycetes
Paenibacillus
17
14
27
2
17
15
92
Clostridium
17
12
23
11
16
0
79
Anaerobacillus
1
0
46
0
31
0
78
Alkaliphilus
0
0
50
5
23
0
78
Nitrospira
406
369
57
273
91
108
1307
Planctomyces
209
239
153
312
324
55
1292
Pirellula
20
28
13
17
24
2
104
Gemmata
5
10
16
20
21
3
75
Leptospira
0
0
0
270
0
1
271
Turneriella
0
1
0
188
0
8
197
Acholeplasma
0
0
0
78
0
0
78
Luteolibacter
9
15
0
71
0
0
95
Opitutus
19
19
0
40
1
0
79
Spirochaetes
Tenericutes
Verrucomicrobia
*. Also similar to Sphingomonas
Table S7 Potential functions of the main bacterial genera in the Chnampa soils
Phylum (Class)
Proteobacteria
(-roteobacteria)
Genus
Potential function
Anoxic photolitotrophic y aerobic chemicoheterotrophic aquatic
868
Kaistobacter
Anoxic photosynthetic, soil surface, degradation of pads
792
Devosia
Aerobic heterotrophic Soil bacteria
250
Afifella
Anoxygenic photoheterotrophic
305
Ochrobactrum
Aerobic heterotrophic soil bacteria
287
Pedomicrobium
Aquatic photoheterotrophic bacteria
575
Subtotal
Gallionella
Proteobacteria
Thiobacillus
(-proteobacteria)
Variovorax
3077
Microaerophilic and chemolithotrophic, iron-oxidizing, aquatic
216
Chemolithotrophic, sulfur-oxidizing, sediments
2829
Aerobic soil bacterium in many important biodegradative processes
Subtotal
Proteobacteria
(-proteobacteria)
Abundance
Rhodoplanes
92
3137
Lysobacter
Use complex compounds, Inhibit other microbes, in soil and water
201
Acinetobacter
Soil bacteria with multiple bioactivities
88
Thermomonas
Hot spring and water-treatment procedure
80
Halomonas
Halophylic bacteria, consuming the submerged metal
397
Pseudomonas
Universal in various hábitats
743
Steroidobacter
Anaerobic testosterone degradation
248
Thioalkalimicrobium Haloalkaliphilic, obligately autotrophic, sulfur-oxidizing, water
Aquicella
Water bacteria, aerobic heterotroph
Subtotal
Desulfurivibrio
Bdellovibrio
Proteobacteria
Desulfococcus
(-proteobacteria)
Desulfosarcina
Peredibacter
128
95
1980
Thiosulfate/polysulfide as electron acceptor at pH 10, sea sediment
102
Soil bacteria, Diverse sulfate-reducing bacteria
91
Sulfate-reducing bacteria, lake, marine seep
234
Diverse sulfate-reducing bacteria
184
Bdellovibrio-like bacteria, soil, water
75
Subtotal
686
Acidobacteria
Candidatus
Solibacter
Soil bacteria
98
Actinobacteria
Salinispora
Degrading complex compounds, not cellulose and chitins, marine sediments
190
Pontibacter
Soil, rhizosphere
449
Flavobacterium
Soil, water
149
Rubricoccus
Aerobic, heterotrophic, Sea water
139
Adhaeribacter
Aerobic, in water and soil
106
Flavisolibacter
Aerobic, in soil
89
Salinimicrobium
Heterotrophic, facultatively anaerobic, marine environments
75
Bacteroidetes
Subtotal
Chloroflexi
1007
Ardenscatena
Ferric iron- and nitrate-reducing, iron-rich coastal hydrothermal field
116
Ignavibacterium
Anaerobic, in hot spring
146
Anaerolinea
Anaerobic sludge
200
Subtotal
462
Firmicutes
Bacillus
Very diverse function, like degradation, N2-fixation, denitrification, etc.
7435
Turicibacter
Anaerobic, febrile patient with acute appendicitis
470
Marinibacillus
Moderate halophile in marine water
171
Paenisporosarcina
Similar to Bacillus
137
Solibacillus
Similar to Bacillus
118
Paenibacillus
Similar to Bacillus
92
Clostridium
Similar to Bacillus, but anaerobic
79
Anaerobacillus
Anaerobic diazotrophic bacillus
78
Alkaliphilus
Anaerobic alkaliphilic bacterium in water
78
Subtotal
Nitrospirae
Planctomycetes
8658
Nitrospira
Nitrite-oxidizing in water and wetland
1307
Planctomyces
Aerobic ammonia-oxidizers, in water and wetland (rice paddies)
1292
Pirellula
Similar to Planctomyces
104
Gemmata
Chemoheterotrophs, in acid bogs, swamps, and the soil
75
Subtotal
1471
Leptospira
Saprophytic or pathogens, various habitats, fresh water
271
Turneriella
Similar to Leptospira
197
Spirochaetes
468
Subtotal
Tenericutes
Acholeplasma
Saprotrophic or pathogenic
78
Luteolibacter
Degrader of algae compounds in water, soil, active sluge
95
Opitutus
Anaerobic, wetland
79
Verrucomicrobia
Subtotal
174
TOTAL
22793
Fig. S1 Rarefaction curve analysis calculated at 97 % similarity, using the pyrosequencing data from the six
samples
DBCh2
SBCh2
DBCh1
SRh1
OTU ID
denovo218
denovo1914
denovo4103
denovo4362
denovo4863
denovo5049
denovo6361
denovo7310
denovo9124
denovo11483
denovo12775
denovo13048
denovo13733
denovo13975
denovo14042
denovo14955
denovo16045
denovo17055
denovo17341
denovo17702
denovo20844
denovo21900
denovo21936
denovo22249
denovo26674
SBCh1-2
Taxonomy of each OTU
Proteobacteria;c__Betaproteobacteria;o__MND1
Chloroflexi;c__Anaerolineae;o__DRC31
Actinobacteria;c__Acidimicrobiia;o__Acidimicrobiales
Chloroflexi;c__Anaerolineae;o__DRC31
Bacteroidetes;c__Cytophagia;o__Cytophagales;f__Cytophagaceae
Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae
Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus
Proteobacteria;c__Deltaproteobacteria;o__Desulfuromonadales;f__Pelobacteraceae
Proteobacteria;c__Deltaproteobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae
Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae
Chloroflexi;c__Anaerolineae;o__DRC31
Nitrospirae;c__Nitrospira;o__Nitrospirales;f__Nitrospiraceae
Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus
Proteobacteria;c__Gammaproteobacteria;o__Chromatiales
Chloroflexi;c_Anaerolineae;o__envOPS12
Chloroflexi;c__Anaerolineae;o__envOPS12
Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Pedomicrobium
Proteobacteria;c__Gammaproteobacteria
Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus
Chloroflexi;c__S085
Proteobacteria;c__Betaproteobacteria;o__Hydrogenophilales;f__Hydrogenophilaceae;g__Thiobacillus
Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Kaistobacter
Proteobacteria;c__Betaproteobacteria;o__Hydrogenophilales;f__Hydrogenophilaceae;g__Thiobacillus
Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Piscirickettsiaceae
Proteobacteria;c__Betaproteobacteria;o__Hydrogenophilales;f__Hydrogenophilaceae;g__Thiobacillus
SHCh1
file:///Users/EMBARCADERO/Desktop/Soil/otus/OTU_Heatmap/otu_...
083 97 35 400 56 38
0
00 3 69 431 343
31
20 9 290 437 169
32
35 27 90 341 246
436 392 1 17 598 722
34
35 39 372 121 87
3
2 15 28 730 1548
0 89 562 4
5
0
266 235 261 174 128 86
0
0 11 608 1
0
1
2 15 77 439 299
59
51 37 115 133 100
7
7
44 45 234 442
0
0 19 553
2
1
85
72 15 107 97
88
0
0
213 187 79 58
27
0
709
843
956
771
2166
688
2326
660
1150
620
833
495
779
575
464
537
523
30 86 235 106
767
22 741
1
3
0
0 139 317 456
506
40 14 160 179 73
919
0 43 871
3
2
616
92 355 3 148 10
8
0
0 32 665
699
1
1
243 238 21 462 36
36 1036
0 39 517 3
0
562
3
0
40
0
39
0
0
TOTAL READS
TOTAL: 20656
Fig. S2 Heat map of the 25 most abundant OTUs in soil samples from Chinampas. Their sequences represent
14.67 % of total reads
1 de 1
28/03/15 22:20
Fig. S3 Core microbiome of the analysed Chinampa soils. The cladogram was produced with MEGAN
Software version 5.1.5
Fig. S4 Functional profiles of microbial communities from Chinampa soils, annotated using
METAGENassist server