Collaborative Research: ETBC: Deep Crustal Biosphere: Microbial Cycling of Carbon

Recent studies of the continental subsurface microbial ecosystem present in the Witwatersrand Basin, South Africa have shown that with increasing depth and fracture water age and salinity, biogenic methane diminishes and abiogenic hydrocarbons and H2 increase (7, 10) and the concentration of planktonic cells slowly declines (6) . Similarly studies of the 16S rRNA gene of the planktonic community revealed a decrease in the relative abundance of methanogens and an increase in the relative abundance of low G+C Firmicutes with increasing depth (4) .   Metagenome analyses of one member of this Firmicutes community, D. Audaxviator, indicated that it was capable of both heterotrophic and chemoautotrophic activity (1) . An in situ incubation experiment suggests that some of the Firmicutes are acetogens that may support the aceticlastic methanogens (8) . Geochemical and isotopic analyses appear to indicate that the abiogenic hydrocarbons are not being utilized by the microbial community, but that a chemoautotrophic ecosystem is being sustained by radiolytic generation of H2 and oxidants (5) . Abiogenic hydrocarbon gases and elevated H2 have also been reported from the Canadian and Fennoscandian Precambrian shields (7) and from ocean floor vents. The subsurface ecosystem present in the Witwatersrand Basin, therefore, is potentially wide spread in both the continental and marine crust, yet quite distinct from continental sedimentary basins or coastal margin sea floor sediments where degradation of photosynthetically produced organic matter deposited within the strata is believed to limit the extent of the subsurface microbial ecosystem (2, 3) . Alternatively, organic acids, thermogenically produced ~2 by ago from the thin shale layers present in the Witwatersrand Basin, could be sustaining the microbial community observed today.

The proposed project will determine whether the subsurface microbial community in the Witwatersrand Basin (Fig. 1) and in the Bushveld Igneous Complex (BIC) (Fig. 2) is deriving its organic substrates from chemolithoautrophy, i.e the SLiMeS hypothesis of Stevens and McKinley (9), or from the abiogenic hydrocarbons either by syntrophic consortia or SRB capable of hydrocarbon degradation, or from thermogenic degradation of the organic matter deposited in the 2.9 Ga shale or of the abiogenic hydrocarbons. In the case of the BIC, thermogenic degradation of organic matter is not an option since by its igneous nature photosentate is not present and abiogenic hydrocarbons have yet to be detected. To distinguish between these alternative we will utilize a combination of C and H stable isotope and 14C analyses of dissolved hydrocarbons, inorganic carbon and organic acids, C and H stable isotope and 14C analyses of lipids, stable isotope probes, SIP, of the 16S rDNA and 16S rRNA genes, functional gene analyses and GCMS characterization of the TOC/DOC of fracture water. These analyses will be performed on fracture water and planktonic cells collected from boreholes in South African mines. Sites will be selected to represent a range of ages from millions of years to modern and differing biogeochemical processes (sulfate reduction and methanogenesis). Groundwater age will be quantified by noble gas analysis. Cells will be quantified by total cell counts, LIVE/DEAD BacLight (dead cells) and CARD-FISH (metabolically active cells). Microorganisms involved in the production of organic acids and in the degradation of hydrocarbons will be identified by SIP analyses. 

Broader Impacts.   A broad scientific impact of this study will to develop techniques that can be applied to other environments, e.g., deep-sea sediment and ocean crust. The project will engage undergraduate and graduate students in hands-on interdisciplinary research, with the aim of recruiting underrepresented minority students. Undergrads will contribute through molecular biology approaches and thus will have ownership of a significant project component. The grad student ‘s project will integrate geochemistry and modeling. Students will participate in fieldwork. The project will build upon ongoing collaborations with South African scientists and students.   A publicly accessible web site will archive SEM photographs of subsurface microorganisms, photos and videos of the underground safaris.

Geological map of the Witwatersrand

Fig. 1. Geological map of the Witwatersrand Basin showing the locations of the principal gold mining districts that will be the target of this research. Diamond mines in this region will also be examined as opportunities present themselves. The deepest mine to be studied, Tau Tona, is located in the Carletonville region.

Geological map of the Bushveld

Fig. 2. Geological map of the 2.0 Ga Bushveld Igneous Complex showing the locations of the principal Pt mining districts that will be the target of this research. The deepest mine is Northam located on the northern edge of the Western Limb.




Related publications

2015  Cara Magnabosco*, Kathleen Ryan*, Maggie C.Y. Lau*, Olukayode Kuloyo, Barbara Sherwood Lollar, Thomas L. Kieft, Esta van Heerden, and T.C. Onstott, A Metagenomic Window into Carbon Metabolism at 3 km Depth in Precambrian Continental Crust. The ISME Journal, doi:10.1038/ismej.2015.150.

2015  Simkus, D. N., G. F. Slater, B. Sherwood Lollar, K. Wilkie, T. L. Kieft, C. Magnabosco, M.C.Y. Lau, M. J. Pullin, S. B. Hendrickson, K. E. Wommack, E. G. Sakowski, E. van Heerden, O. Kuloyo, B. Linage, G. Borgonie, T. C. Onstott, Variations in microbial carbon sources and cycling in the deep continental subsurface. Geochim. Cosmochim. Acta, 173:264–283.doi:10.1016/j.gca.2015.10.003.

2015  Borgonie G, Linage-Alvarez B, Ojo A, Shivambu S, Kuloyo O, Cason E, Maphanga S, Vermeulen J, Litthauer D, Ralston C, Onstott TC, Sherwood-Lollar B, van Heerden E, Deep subsurface mine stalactites trap endemic fissure fluid Archaea, Bacteria, and Nematoda possibly originating from ancient seas. Frontiers in Microbiology, 6:833.doi: 10.3389/fmicb.2015.00833.

2014  Sherwood Lollar, B., TC Onstott, G. Lacrampe-Couloume, C. J. Ballentine.  The contribution of the Precambrian continental lithosphere to global H2 production.  Nature, 516, 379-382. doi: 10.1038/nature14017

2014  Lau, C. Y. M*, C. Cameron, C. Magnabosco*, C. T. Brown, F., Schilkey, S. Grim, S. Hendrickson, M. Pullin, G. Lacrampe-Couloume, B. Sherwood Lollar, Esta van Heerden, T.L. Kieft and T.C. Onstott, Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships. Frontiers in Microbiology, doi: 10.3389/fmicb.2014.00531.

2008  Chivian, D., E. Alm, E. Brodie, D. Culley, P. Dehal, T. DeSantis, T. Gihring, A. Lapidus, L.-H. Lin, S. Lowry, D. Moser, P. Richardson, G. Southam, G. Wanger, L. Pratt, G. Andersen, T. Hazen, F. Brockman, A. Arkin, and T. Onstott.  Environmental genomics reveals a single species ecosystem deep within the Earth. Science 322:275-278. doi: 10.1126/science.1155495

2008  Silver, B. J. The Nutritional and Energetic Constraints on Life in the Deep Biosphere of South Africa. Princeton University, Princeton.

2006  Gihring, T. M., D. P. Moser, L.-H. Lin, M. M. Davidson, T. C. Onstott, L. Morgan, M. Milleson, T. Kieft, E. Trimarco, D. L. Balkwill, and M. Dollhopf. The distribution of microbial taxa in the subsurface water of the Kalahari Shield, South Africa. Geomicrobiology Journal 23:415-430. doi: 10.1080/01490450600875696

2006  Lin, L. H., P.-L. Wang, D. Rumble, J. Lippmann-Pipke, E. Boice, L. M. Pratt, B. Sherwood Lollar, E. Brodie, T. Hazen, G. Andersen, T. DeSantis, D. P. Moser, D. Kershaw, and T. C. Onstott.  Long term biosustainability in a high energy, low diversity crustal biome. Science 314:479-482. doi: 10.1126/science.1127376

2006  Pfiffner, S. M., J. M. Cantu, A. Smithgall, A. D. Peacock, D. C. White, D. P. Moser, T. C. Onstott, and E. van Heerden.  Deep subsurface microbial biomass and community structure in Witwatersrand Basin mines. Geomicrobiology Journal 23:431-442. doi: 10.1080/01490450600875712

2006  Sherwood Lollar, B., G. Lacrampe-Couloume, G. F. Slater, J. Ward, D. P. Moser, T. M. Gihring, L.-H. Lin, and T. C. Onstott. Unravelling abiogenic and biogenic sources of methane in the Earth’s deep subsurface. Chemical Geology 226:328-339.doi: 10.1016/j.chemgeo.2005.09.027

2004  Ward, J. A., G. F. Slater, D. P. Moser, L.-H. Lin, G. Lacrampe-Couloume, A. P. Bonin, M. Davidson, J. A. Hall, B. Mislowack, R. E. S. Bellamy, T. C. Onstott, and B. Sherwood Lollar.  Microbial Hydrocarbon Gases in the Witwatersrand Basin, South Africa: Implications for the Deep Biosphere. Geochim. Cosmochim. Acta. 68:3239-3250. doi:10.1016/j.gca.2004.02.020

2004 D'Hondt, S., B. B. Jorgensen, D. J. Miller, A. Batzke, R. Blake, B. A. Cragg, H. Cypionka, G. R. Dickens, T. Ferdelman, K. U. Hinrichs, N. G. Holm, R. Mitterer, A. Spivack, G. Z. Wang, B. Bekins, B. Engelen, K. Ford, G. Gettemy, S. D. Rutherford, H. Sass, C. G. Skilbeck, I. W. Aiello, G. Guerin, C. H. House, F. Inagaki, P. Meister, T. Naehr, S. Niitsuma, R. J. Parkes, A. Schippers, D. C. Smith, A. Teske, J. Wiegel, C. N. Padilla, and J. L. S. Acosta. Distributions of microbial activities in deep subseafloor sediments. Science 306:2216-2221. doi: 10.1126/science.1101155

2002  D'Hondt, S., S. Rutherford, and A. J. Spivack. Metabolic activity of subsurface life in deep-sea sediments. Science 295:2067-2070. doi: 10.1126/science.1064878

1995  Stevens, T. O., and J. P. McKinley.  Lithoautotrophic microbial ecosystems in deep basalt aquifers. Science 270:450-454.doi: 10.1126/science.270.5235.450