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. García-

Moyano5 and D. Chivian6

1. Princeton University, 2. University of the Free State, South Africa, 3. New Mexico Institute of Mining and Technology, 4. University of Ghent, Belgium, 5. University of Bergen, Bergen, Norway, 6. Lawrence Berkeley National Lab, USA (DCChivian@lbl.gov)

South Africa

WitwatersrandBasin

How long can deep, sequestered microbial communities survive?

Evander

Northam Platinum Mine – Bushveld Igneous Complex

Barnes et al., 2004; Scoates et al., 2008; Wanger et al., 2008

Cr, PGE, V

Age: 2054 Ma

Temp: 42°C – 53°CpH: 8 – 11

16S rRNA gene sequence analysis1. 1,916 sequences deposited in NCBI from 58 sites and 84 sites+time

points.2. 983 OTUs identified at 97% identity3. 718 OTUs occur only once4. 16S rRNA gene sequences classified as contaminants because

a. Present in 10 sites of mining water, mine air and acid mine waterb. Present in same OTU as found in mining water, mine air and acid

mine waterc. Guilt by association – closely associated with contaminant OTUs

on phylogenetic tree. 5. 279 OTUs labeled as contaminants6. %contaminated sequences varied from 0 to 97% with 8 sites+time

points with ≥50% contaminants were removed from canonical analysis.

7. Taxonomic identification to the family level with 80% confidence.

279 Contaminant OTUs out of 982 total OTUs.

Guilt by association

Family Richness in 8 Mines

1

0 100 200 300 400 500 600 7000

10

20

30

40

50

60

70

80

Sampled Sequences

Obs

erve

d O

TU’s

Beatrix (Lin et al. 2006)

Kloof, Mponeng and Driefontein combined

Mining Water from Kloof, Driefontein, Mponeng and Evander

Evander 2 and 8 shaft combined

Mine Archaeal Family Compositions

Mine Bacterial Family Composition

Mine Bacterial Family Composition

0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.00

2

4

6

8

10

12

Depth (kmbls.)

Spec

ies n

umbe

rbiofilms

borehole water

rock cartridges

0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.00.00.61.21.82.43.03.64.24.85.46.06.67.27.88.49.09.6

10.2

Depth (kmbls.)

Even

ess

0 50 100 150 200 250 300 350 4000.01

0.10

1.00

f(x) = − 0.000341073359824178 x + 0.165683090788688R² = 0.0970561867914718

Y = -3.4x10-4 x+ 0.165R2 = 0.01

Horizontal Distance (km)

Sor

ense

n Si

mila

rity

Inde

x

Only 50 OTUs occur at more than one site and only 3 OTUs are distributed across the basin.

Tree Showing the Distances between the OTUs

1 km

1.5 km

1.7 km

2.0 km

2.7 km

2.8 km

3.2 km

3.3 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.

Tom Kieft

Duane Moser

Esta vanHeerden

Derek Litthauer

Gaetan Borgonie

Acknowledgements

• NSF - Geobiology and Low-Temperature Geochemistry Program

• Sloan Foundation through the Deep Carbon Observatory