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Tullis Onstott - Research

Research Statement

The principle focus of my research projects are the activity and survival of bacteria and other microorganisms in the deep subsurface (> 0.5 km) and their impact on the geochemistry and mineralogy of their environment. Among the questions we attempt to address are: 1) How do subsurface microorganisms evolve by adaptation or selection or horizontal gene transfer? 2) What constrains the diversity and density of microorganisms? 3) What role does radiation play as an energy source for life? 4) Could life have originated in the subsurface? 5) What methods can be adapted to test for life in the Martian subsurface?
These projects have been and continue to be field-based and require a multi-disciplinary, multi-institutional approach. Field measurements, sample acquisition, laboratory analyses and publication of results by geochemists, microbiologists and molecular biologists have to be highly coordinated in order for the questions above to be addressed.
Currently we are involved in two field projects, the first situated in the Canadian Arctic and the second sited in the world’s deepest mines in South Africa. Both projects seek to address fundamental scientific question regarding bacteria/rock interactions while at the same time developing applications of this information that will benefit mankind. We are also involved with educational outreach efforts for the South African project focusing on previously disadvantaged, postgraduate students in South Africa and black American students in the U.S. 

Indiana-Princeton-Tennessee Astrobiology Institute (IPTAI)

During the past two years IPTAI has established a Mars analog site in the Canadian arctic where we can access through mines and boreholes deep permafrost. This region of Canada is unique in that it provides ready access to rock/permafrost in Archean metavolcanic and metasedimentary strata, permafrost that extends to a depth of 400-500 meters, much like is anticipated on Mars. Currently we are working with the Finish Geological Survey, the Univ. of Toronto and the Univ. of Waterloo to profile the microbial diversity, density and activity and the permafrost and subpermafrost saline water transition and we are learning how to successfully drill down to this region and install downhole instrumentation. Graduate student Dan McGown has been developing approaches to extract large DNA fragments for metagenome sequencing from these sites. The entire genome for an uncultured sulfate reducing bacteria that dominates the South African sites below 2.5 km has just been completed. All three of these aspects are vital to any planned mission to Mars that will attempt to search for life in the subsurface. Postdoc John Kessler has been developing instrumentation for analyses of CH4 isotopic composition using field portable laser spectrometers that we hope will eventually be flown to Mars to identify the source of the CH4 that has been detected there by telescopic searches. This gas may be a signature of martian subsurface life and characterization of its isotopic composition is essential to the future of the Mars exploration program. On Earth such devices will revolutionize our understanding of global carbon cycles and greenhouse gas inputs. 

The NELSAM Project

This project builds upon the data gathered in the Witwatersrand Deep Microbiology Project that ran from 1998 to 2006 and described in more detail below. The NELSAM project funded by the Tectonics and Geodynamics Program at NSF has enabled us to establish an under ground laboratory (URL) for investigating the relationship between tectonic processes and microbial activity. The URL is located at a depth of 3.8 km in quartzite within the seismically active Pretorious fault zone. Four boreholes have been cored across this fault zone, two for the installation of geophysical instruments to record fault displacements, one for the analyses of gases released during seismic events and the fourth (known as DAFBIO) to record changes in the fluid chemistry and microbiology associated with seismic events. Installing these boreholes at this depth and remote from the access shafts and into rock with an ambient temperature of 60oC has not been easy and has required 2 years of concerted. The cores collected during drilling of the 40 m long DAFBIO hole are currently being processed for DNA and 35SO4 activity. The borehole has been imaged and fracture zones identified and soon a specially designed packer will be installed to isolate water weeping fractures. Using this packer we will be able to conduct in situ microbial activity experiments to test the long term activity of the indigenous thermophilic microorganisms. Grad student, Mark Davidson has been designing and performing experiments using thermophilic sulfate reducing bacteria that are similar to the dominant microorganism in the South African deep subsurface and these experiments are being used to design the experiments that will be performed at the URL.

The Witwatersrand Deep Microbiology Project

Due to the expense and contamination associated with coring from the surface, few microbial rock and water samples have been collected from depths greater than 0.5 kilometers. These few samples, nevertheless have demonstrated that microbial communities do exist in a variety of subsurface rocks and sediments down to 2.8 kilometers below the surface (kmbls.). Conditions in the deep subsurface approach the limits for life and novel "extremophiles" have been isolated from these environments. Investigations of deep, terrestrial environments also offer great potential for gaining insights into potential exobiological niches and into how microorganisms can adapt to and survive in relatively harsh environments. The extreme conditions encountered in the subsurface include excesses in temperature, pressure, salinity, and ambient radiation, and the low availability of energy sources and liquid H2O. The paucity of high quality samples, however, has greatly hindered efforts to determine the size, structure, and metabolic activities of the deep subsurface microbial communities and the biogeochemical processes that support them.
Many fundamental questions remain to be answered regarding the relationship between subsurface microbial community dynamics and biogeochemical and hydrological processes.
  • Does primary production of organic substrates by autotrophic microorganisms dominate in certain subsurface terrestrial environments over heterotrophic utilization of organic substrates originally produced by surface-based photosynthesis? This question has been hotly contested in the recent literature.
  • What are the abiotic mechanisms and rates for H2 and C1-4 production in the subsurface and are they sufficient to support chemolithotrophic microbial communities? Radiolytic reactions have been proposed as a source of H2 and abiotic redox reactions involving water, inorganic C and mineral-bound Fe(II) have been proposed as sources of H2, CH4 and light hydrocarbons.
  • Are in situ microbial activities so low as to only support average doubling times on the order of centuries? Phelps et al. (1994) proposed this on the basis of geochemical modeling, which yielded rates that were 103-106 lower than laboratory measurements. In situ measurements at high temperature and pressure analogous to those performed at deep-sea vents have not been undertaken. If true, have subsurface microorganisms evolved special agents to guard against the deleterious environmental effects, such as ambient radiation?
  • A fracture flow hydrogeological regime dominates most terrestrial deep subsurface settings. Are the deep subsurface microbial communities present in fluid-filled fractures distinct from those embedded in the rock strata? Are they responsible for the precipitation of fracture-filling minerals? Because coring such environments from the surface utilizes high pressure drilling fluids, which invariably contaminates the fracture surfaces and adjacent rock matrix these questions have not been appropriately addressed. Expensive packer systems are also required to isolate discrete fracture zones for fluid sampling to avoid mixing and contamination. Microbial colonization of the deep subsurface occurs primarily by microbial transport through fractures, particularly when topographically or hydrothermally-driven meteoric water flow and fracture-generated permeability is enhanced by tectonics. Consequently, difference between fracture and rock matrix microbial communities may reflect differences in their residence time.
These questions will never be resolved with the collection of one core from a single site or a set of rock or water samples from one mine. Rather, the distribution, diversity and activity of microbial communities in a subsurface environment must be examined in terms of a hydrogeologically and geochemically well-characterized location by a sustained effort over several years.
To overcome this deficiency, we investigated the potential for the ultradeep Au mines of South Africa to provide unique "windows" into the deep, continental biosphere through which a detailed analysis of microbial communities as a function of various environmental parameters could be performed. The depths and pressures of these mines approach those at ocean ridges and the temperatures of the mined formations lie within the zone for microbial thermophilicity (45-70oC). The microbial communities encountered in these mines are composed of a mixture of contaminating (allochthonous) and indigenous (autochthonous) microorganisms. To distinguish autochthonous from allochthonous microorganisms we developed sample collection and processing techniques that quantified and minimized the allochthonous bacterial contaminants in the mine samples. This permits evaluation of the relationship between the indigenous microbial communities and large-scale hydrogeochemical facies as well as small scale geochemical heterogeneity.
Thanks to the support from the NSF LExEn (Life in Extreme Environments) Program, we are developing the ultradeep mines in South Africa into a Long-term Site for Interdisciplinary Studies into subsurface microbiology. This facility will be comprised of an on-site laboratory with access to multiple mines in S. Africa. With the collaboration of South Africa’s mining industry and academic institutions this site will be able to offer the following attributes.  
  1. The rock formations encountered by the deep Au mines are representative of most terrestrial cratonic environments and include dolomite, mafic to siliceous lava, quartzite and shale. The deep Pt mines occur in a 2.05 Ga basic to ultramafic, hypabyssal intrusive providing an environment similar to the ocean crust and the Martian subsurface.
  1. The hydrogeological environment is a fracture flow regime similar to most deep, hard rock settings. Rock cores from fracture zones bearing " fracture " water at high temperature and pressure can be obtained by side-wall coring. This type of sampling permits for the first time to study the microbial communities and biomineralization processes occurring in the low permeability rock matrix versus those of the fluid-filled fracture.
  1. These mines are sufficiently deep (>3.0 kmbls.) to yield thermophiles having enormous biotechnological potential from rock samples and "fracture" water with temperatures ranging up to 75oC. These mines are the deepest on earth and plans for still deeper mining are underway.