From bacterial finches to bactivorous
meiofauna:
Microbial biogeography of the deep crustal
biosphere
T.C. Onstott1, C. Chehoud1, E. van Heerden2, D. Litthauer2,
A. Jugdave2, K. Albertyn2, T. Kieft3, G. Borgonie4, A. GarcíaMoyano5 and D. Chivian6
1.
2.
3.
4.
5.
6.
Princeton University,
University of the Free State, South Africa,
New Mexico Institute of Mining and Technology,
University of Ghent, Belgium,
University of Bergen, Bergen, Norway,
Lawrence Berkeley National Lab, USA (DCChivian@lbl.gov)
Evander
How long can deep, sequestered
microbial communities survive?
Northam Platinum Mine –
Bushveld Igneous Complex
Age: 2054 Ma
Cr, PGE, V
Temp: 42°C – 53°C
pH: 8 – 11
Barnes et al., 2004; Scoates et al., 2008; Wanger et al., 2008
16S rRNA gene sequence analysis
1.
2.
3.
4.
5.
6.
7.
1,916 sequences deposited in NCBI from 58 sites and 84 sites+time
points.
983 OTUs identified at 97% identity
718 OTUs occur only once
16S rRNA gene sequences classified as contaminants because
a. Present in 10 sites of mining water, mine air and acid mine
water
b. Present in same OTU as found in mining water, mine air and acid
mine water
c. Guilt by association – closely associated with contaminant OTUs
on phylogenetic tree.
279 OTUs labeled as contaminants
%contaminated sequences varied from 0 to 97% with 8 sites+time
points with ≥50% contaminants were removed from canonical
analysis.
Taxonomic identification to the family level with 80% confidence.
279 Contaminant OTUs out of 982
total OTUs.
140
128
120
100
Guilt by
association
80
73
59
60
40
19
20
0
service water
predicted
acid mine water
mine air
Family Richness in 8 Mines
1
80
Mining Water from Kloof,
Driefontein, Mponeng
and Evander
70
Observed OTU’s
60
Beatrix (Lin et al. 2006)
50
40
Evander 2 and 8 shaft combined
30
Kloof, Mponeng and Driefontein combined
20
10
0
0
100
200
300
400
Sampled Sequences
500
600
700
Mine Archaeal Family Compositions
Mine Bacterial Family Composition
Mine Bacterial Family Composition
140
biofilms
Species number
120
rock cartridges
borehole water
100
80
60
40
20
0
0.0
0.5
1.0
1.5
2.0
2.5
Depth (kmbls.)
3.0
3.5
4.0
1.0
Eveness
0.8
0.6
0.4
0.2
0.0
0.0
0.5
1.0
1.5
2.0
2.5
Depth (kmbls.)
3.0
3.5
4.0
Sorensen Similarity Index
1.00
Only 50 OTUs occur at more than one site
and only 3 OTUs are distributed across the
y = -0.00034x + 0.16568
basin.
R² = 0.09706
0.10
Y = -3.4x10-4 x+ 0.165
R2 = 0.01
0.01
0
50
100
150
200
250
Horizontal Distance (km)
300
350
400
105
Tree Showing the Distances between the OTUs
99
603690
976
7
432
56 58
60
1
2
6
9
13
15
4
7
5
5
1
94
6
3
10
3
0
8
7
5
5
7
8
7
6
4
5
7
9
0
6
7
3
4
25
39
40
5
2
2
6
53
7
5
6
8
8
2
8
7
5
8
0
3
3
3
4
5
5
6
1
8
1
1
0
3
5
6
32
7
5
47
5
64
4
3
74
47
8
59
73 205437
3883
78
1586
8
3
3
5
4
6
632556
5
63
64
9
3
1
4
24
8
29
67
9
4
3
8908
3
21641 7
3 1
4773382 1743 6
864481 457 448
7200 7 3560
8 34 3009008
88 2 415
2
3
36
670
33
30
21
671
33
569
404
35710
18
490
3 401
717
587
6466103
48646837888798872 4917
698 87
69
36
771153
86787579
78
764767407997098 6963
0850628315476477120907
5
370505778061 691
46766
94248687425
276818
53172474 90 861640828637864629683981341765
8035
41988345310
93454347
268
9363689
8 0
5614
5
27
41
29
8
709
857 718
738
100
739
885
687889
25 577940
30
87
68
8886
88
7221 49410
82780276
3327
92 35
8275875284
66487267848 8475
6982725 8210
11 71298 6 53794272348
447671618765371336 7170974 29 7
1 7
9
32639
388
330
91
421
428
37
5480
81
7
62
93 1
838470
1
8 128
640
2713739
72 62 563833
634
564
7 2
6 15335
9516
344
6833 9243 63
5
66
5015
88
48
6 3
8
00
120
756
65
2813
70
1561
5 439
69
63
70 85 9 396 4
81
53 20
17
76829559
6346216733106735
18692424462854767414
480363 9665956213346262381
213667912 4736718 4
33650 67462 3
6341958 4 21802046736
40943933
6731313
3
3965
3
41 6
54
84
9
602
361554
268
4 29
1
10
6
61
21
3
909
420 4
843
43
603
99
716
4250
57
4
3
0
8
4654
3
50
3 11
9
6
6
53
36
1
98
8
1
85
4
2
6
3
44
0
66
9
0051
67
4
4
1
5
3
7
43
8
8
0
3
4
276
5
5
6
73
7
6
3
4
77
9
2
4
3
3
517
8
8
3
8
2
6
9
6
0
8
5
4
8
8
6
3 3
8
4136
50
6
30
8
4
4
4
3
6
2
3
4
7
12
22
1
5
3
36
8
5
6
1
8
6
7
3
9
3
5
7
9
8
8
2
6
7
0 712
35
3
75
50
9
47
1
38
71
9
273
9
3
67
364
40
87
73
744
682
745
746
180
181
748
747
414
679
743
5
65
27
6
2654
6
6
48
06
784
7
6
7
51
5
3
1
5
46
842
6544560
6524
8
75
1
8275
599
3543
653
652
655
656
588
844
645 843
199
86
6
7
9
5
23
72
84
7
57
93
59
22
91
79
1
37
94
089
5
55
65
79
961
459
433
822
190
204
507
196
11
00548 598819697 869
139
8429 7
892
128903747703786863192190257178700735 80
0
809 76 89
55
46
39042226
2 800
819 274
933
826
846
85
7325
93
93
360
285
19
51258 821
212 820
6
9844 75 2
95 6 26 64
065 27164
0081 87916248
641 822847248 795
1
79
8609912 504
9817134347905 27093
6709871210352366
9
8245 3757251497493917895
434 41 4
186
94
94
2
854
94
54
98
22
25
221
53 3
432
29 91 2
47
64407
76
80134
04
2766
192
855
851
301
847
649
428
70929
816
10
5
17
22
8 96
8
46
5
3
7
21
5
0
2
5
040
2
889
2
6
7
0
9
74
4
9
162
4
0
9
4
81
5
81
2
3
5
9
509
82
2
2
6
99
4
4
93
9
782
4
2
0
0710
0
9
1
19
1
5
668
9
4
774
971
1
2
9
92
4
2
0
97
6
77
271
93
79036
78
5
6
2
4
8
8
2
4
1
7
1
8
4
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9
7
1
9 2
48 1
38
511 87
7
7
5
0
4
9
7
5
92
5
4
1
16
32 33
578
821
90
436214639
4
94
9
6
8
31
5
44
65
52
62 48
09
2
326
278
81
21
03
58
7
14
317
9
6
20 665
7
1
4
6
2
2
8
5
7
2
54
61
520
925226
7071268272
72387730
130
78
7
28412
7921 613230
916431
4187721507 791919 497069862851700 945348656
49791386538127183
9785771086528795 7495
89041 345250
559109297364984 456
869791 9418315
297
3 75306260
6 3
29 766 6741 17695317
96 803442
468
802 807
808
806
924
927
931
40
503
5
804
92
0
8
40
399
805
39
926
97
59
1
1
1
16
45
5
91
5
1560
8
1
15
2
21
8
5
2
07
9
0
98
8
1
4
5
705
57
1
8
3
1
29 2
2
8
8
2
543 7
578 149 26
6
57
5 38
94
9
50
3
5
9
9
5
1
9
1
6
24
6
9
3
0
1
5
2
28
0 69
5
1
5
225
2
85
5
5
2
8
9
5
9
7
3
5
1
2
5
5
2
3
7
2
60
2
2
5
2
5
2
7
9
3
2
3
9
8
4
2
6
2
6
4
2
1
9
1
5
7
5
52
8
2
2
25
5
2
90
3
4
0
51
242
741
874
5347832
2205996
92
23
563321
99756 9 505350
37 0 7
153246 4245162942542595474
957982 9813456716515180492628312
269 52 5316229526626
925 229024 11
31965
55
3
94
6
57333
54
8
13
51
4472
67 55
39
3
456
813530
9
36456915717584
3
7
9955
49
158
22 7
1
50
16
3.3 km
2.0 km
3.2 km
1.7 km
2.8 km
2.7 km
1 km
1.5 km
Conclusion
• The lack of overlap in OTUs between 37 fractures
sampled to date suggests an “desert oases”
biogeographical pattern that could encompass
~8,000 OTUs within the Witwatersrand Basin.
• A combination of pyrosequencing and rock filters
may reveal a greater diversity – hopefully with
the help of the CoDL.
• Singe cell genomes of the “finches” will enable a
more direct correlation of genome structure,
environment and geographic dispersion.
Esta vanHeerden
Tom Kieft
Derek Litthauer
Duane Moser
Gaetan Borgonie
Acknowledgements
• NSF - Geobiology and Low-Temperature
Geochemistry Program
• Sloan Foundation through the Deep
Carbon Observatory