astrobiology: the search for life on earth and...
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Astrobiology: The Search for Life on Earth and
Beyond
Susan Pfiffner and Kim DavisUniversity of Tennessee
Jane Skinner, Amy Arnold, John Smithand a host of contributors
The Study of the Living Universe
Planet X
MultidisciplinaryCross-cutting ResearchState-of-the–art Science Beyond...
The Deep Underground Science and Engineering
Laboratory (DUSEL): An Opportunity for Multidisciplinary Deep Subsurface
Geomicrobiology Research
A National Science Foundation initiative to establish a national underground laboratory for research in physics, Earth and environmental sciences, civil and Mining engineering, and the biosciences.
What is DUSEL?
“The science cuts across disciplines and Directorates(ENG, GEO, and MPS) and provides opportunitiesfor transformational breakthroughs and to educatethe scientists & engineers of the 21st century”Michael S. Turner, Assist, Dir. for MPS (NSF)
NSF Solicitations
• Solicitation 3: Planning grant to develop full proposal including suite of initial experiments, MREFC and Presidential Budget for 2008.
• Solicitation 1: Planning grant to define science and infrastructure requirements for science modules will result in a glossy publication and a NSF report (December 2005).
• Solicitation 2: Site development grants has been award to Henderson, CO and Homestake, SD (July 2005).
Earth’s Subsurface Microbial Ecology
• The biosphere extends deep into the subsurface• Limited by geothermal gradient and nutrient flux• Biomass generally low relative to the surface• Distribution is very patchy and heterogeneous• Rates of community metabolism are very low• Volumetrically largest
part of the biosphere
Todd Stevens
Subsurface Microbiology 1986-present• Drilling and tracer technologies• Extended known biosphere
greater than 3 km• Revealed biomass &
biodiversity• Isolates in culture collections• Linked microbial activity with
geological interfaces• Slow rates of subsurface
microbial activity• Indications of autotrophic
ecosystems
CHRONOLOGY OF SUBSURFACE MICROBIAL INVESTIGATIONS
SALT MINES
OIL&GAS FIELDS
DEEP-SEA VENTS
SUBSURFACE
POLAR-ENDOLITHS
1930 1950 1970 1990
1 9 8 7 1 9 9 0 1 9 9 5
HanfordINEEL
Taylorsville Bas inCerro Negro
Piceance Bas in
Marine Sediment s
Coas t al Plain
Oys t e r
Nevada Test Sit e
MolSt ripa Äspö
WIPP
Savannah R.
2.0 Ga
2.9 Ga2.7 Ga
2.0 Ga 300 Ma
2.3 Ga
Transvaaldolomiticsediments
10 kmbls
Basement 3.4 Ga
120oC
9-15oC/km25oC/km 20oC/km
Introduction
• The terrestrial and oceanic deep subsurface biosphere is spatially expansive and is a large component of the global biomass.
• The structure, distribution and function of subsurface microbial communities remain poorly understood due to the difficulty of access
• The ultradeep gold mines of the South African Witwatersrand provide an excellent opportunity for direct exploration of the deep subsurface biosphere
• Why do we want to look at extreme environments in the deep subsurface?– To gain a better understanding of the
types of microbial communities existing in the subsurface• Abundance and Diversity
• Activities and the geobiochemical processes that support them
• Potential for in-situ or ex-situ processes
How do we look for microorganisms?• Direct microscopic counts (acridine orange)
– Estimate of total microbial abundance• Cultivation methods - bacteria, fungi, and protozoa
– Plate counts and most probable number– Selective and differential media
• Activity assays - metabolic and respiratory capabilities– Utilization and formation of metabolic end-products– Radiolabeled electron donors or acceptors– Utilization of methane and hydrogen– Enzyme screening
How do we look for microorganisms?• Analytical Chemistry
– Quantifying cellular macromolecules• Phospholipid fatty acids and DNA
– Petrology, chemical and isotopic analyses
• Statistical Analyses– Correlations– Artificial neural networks– Modeling software
Major Questions in Geoscience Fundamental Energy Exchange Processes at Depth• How do the coupled Hydro-Thermal-Mechanical-
Chemical-Biological (HTMCB) processes in fractured rock masses vary as function of the physical and time scales involved?
• Relative influences of these processes on – groundwater flow; contaminant transport; ore forming processes
– long-term isolation of hazardous and toxic wastes, carbon sequestration and hydrocarbon storage underground
– energetic slip on faults and fractures; stability of undergroundexcavations
Scientific Case for DUSEL: Isolation
• Longtime sequestered• Old water• Old sediments/rocks• Multiple interfaces• Varied T, P, lithology,
stress
Major Questions in Geomicrobiology1. How deeply does life extend into the Earth?
What are the lower limits of life in the biosphere? What is the temperature barrier, the influence of pressure, the interplay of energy restrictions with the above?
0.0E+00
1.0E+03
2.0E+03
3.0E+03
4.0E+03
5.0E+03
1.E+01 1.E+03 1.E+05 1.E+07 1.E+09
Cells/ml or Cells/g
De
pth
(m
)
Weeping BoreholeWeeping BoreholeOpen to mine airOpen to mine airDevelopment of Development of metalliferousmetalliferous and and microbiallymicrobially rich rich biofilmsbiofilms
16S rDNA & DSR Desulfotomaculumgeothermicum
SRB’s grown at 60oC
34S of sulfate &sulfide indicate 90% conversion
FeS drip with108 cells/g
Sampling Fracture Waters
• CH4 (30-80%)• C2+ (3-4%) • H2 (up to 30%)• He (up to 10%)• balance N2
• some NH3?
SubsurfaceSubsurfaceMicrobialMicrobial
BiogeochemicalBiogeochemicalCyclingCycling
SamplingSampling
MicroscopyMicroscopy& Mineral & Mineral
GeochemistryGeochemistryAqueousAqueous
GeochemistryGeochemistry
EnvironmentEnvironmentDissolved Gases, Dissolved Gases,
Cosmogenic Cosmogenic & Stable Isotopes& Stable Isotopes
PLFAPLFA--cell membranecell membrane
Isolates &Isolates &ArchivesArchives
FunctionFunction
16SrDNA16SrDNA
Community StructureCommunity Structure EnrichmentsEnrichmentsgenes, & genes, & enzymesenzymes
S. African Au Mine Bacterial Isolates
Vesicles
PHB’s
Thermusscotoductus
Geobacillus thermoleovoransAlkaliphilus
transvaalensis
Culture-Independent Microbial Characterization
• Extract all DNA• Amplify rRNA genes (rDNA)
using polymerase chain reaction (PCR) and universalArchaeal or Bacterial primers
• Clone genes into Escherichia coli• Screen clones by restriction
fragment length polymorphism (rflp) analysis
• Sequence rDNA of unique clones• Compare sequences to databases• Construct phylogenetic trees
Dec-98
Feb-99
Nov- 2001
Nov-2002
Isolate DR504
Clone 24
Clone 24
Clone 24
Clone 24
DR546BH1 T-RFLP 16S DNA extracted and amplified
Isolate DR 520
Isolate DR 520
from: Gihring, Moser, et al., in prep
Major Questions in Geomicrobiology
2. What fuels the deep biosphere? – Do deep microbial ecosystems exist that are
dependent upon geochemically generated energy sources ("geogas": H2, CH4, etc.) and independent from photosynthesis. How do such systems function, their members interact to sustain the livelihood?
3. Does the interplay between biology and geology shape the subsurface? Role of microbes in Hydro-Thermal-Mechanical-Chemical-Biological (HTMCB)
Major Questions in Geomicrobiology
Drilling forDrilling forsubsurfacesubsurfacelife on Mars?life on Mars?
5. Did life on the earth's surface come from underground?– Does the deep subsurface
harbor primitive life processes today?
– Has the subsurface acted as refuge during extinctions.
– What "signs of subsurface life" should we search for on Mars?
Major Questions in Geomicrobiology
4. What are subsurface genomes telling us?
– Microbes may have been isolated from the surface gene pool for very long periods of time. How different are they from microbes on the surface?
– How do they evolve with very low population density, extremely low metabolism rate and high longevity?
* SASFiG-1
SASFiG-2
SASFiG-3SASFiG-4
SASFiG-5
SASFiG-6
SASFiG-7SASFiG-9
SASFiG-8
*
*SASFiG-9 (isolated)
Detected within a water-bearing dyke/fracture at 3.2 Km depth.
strictly anaerobic; iron-reducer
optimal growth temperature = 60 oC
virgin rock temp = ~ 45 oC
Novel Bacterial lineages unique to the SA deep-subsurface:South Africa Subsurface Firmicutes Groups (SASFiG)
1 µm
Novel and unusual microbes and sequences, deep branching indicative of ancestral linkages, less evolved sequences (early life?), biomed and biotech applications
image courtesy of Gordon Southam
Major Questions in Geomicrobiology
6. Is there life as we don't know it?– Does unique biochemistry, e.g. non-nucleic acid
based, and molecular signatures exist in isolated subsurface niches?
– Is the subsurface a reservoir for unexpected and biotechnologically useful enzymes?
Exciting Science and Engineering• Compelling questions: • National resource for research in physics, life sciences,
chemistry, geosciences and engineering• Multidisciplinary
– Not just a juxtaposition for political convenience– Overlap of questions: between fields and between
fundamental and applied – Multidisciplinary approaches: e.g. geo-micro-biologists– New Synergies
• Instrumentation of the rock prior to construction of physics cavities
• Low radioactivity methods, instrumentation, data acquisition
Exciting Science and Engineering• Marvelous education and outreach
opportunity– Training of a new generation of multidiciplinary
scientists and engineers
– Exciting the imagination of K-12 students (Bio+Earth+Physics+Astronomy)
– Involvement of local population (Native Americans, Southern Appalachia)
Education and Public Outreach
Discover Underground!
A national resource for research in physics, life sciences, chemistry, geosciences and engineering
Undergraduate students extract DNA from underground rocks to search for life.
Young children in hard hats quiz an engineer about where that underground water comes from and where it goes.
High schools students deliver a detector component they built for testing.
Summary •Research to be conducted at DUSEL will address fundamental questions in physics, biology, earth sciences and engineering. The results will help us to address wide ranging practical issues of societal interest, including:
• Development of advanced detectors for use in medicine, seismology and for national security
• Development of improved techniques to search for fresh water and to clean up contaminated aquifers
• Development of new techniques to explore for and extract valuable resources needed by modern societies, such as copper, gold, silver, oil, coal, etc.
• Identification and testing of novel bioengineering techniques that lead to development of new drugs
•DUSEL is unique: located in the U.S., dedicated, controlled access, isolated environment, multiple scales, many disciplines, education and outreach
AcknowledgementNational Science Foundation
S-1 planning grantwith special thanks
Bernard Sadoulet, Hamish Robertson, Eugene Beier, Charles Fairhurst, Tullis Onstott, James Tiedje, and
S-1 working group leaders
ReferencesEarthLab 2003, A Subterranean Laboratory and
Observatory to Study Microbial Life, Fluid Flow, and Rock Deformation, Geosciences Professional Services, Inc.
NeSS02 Final Report, International Workshop on Neutrino and Subterranean Science, September 19–21, 2002, Washington D.C.
Proc. Intern’l Symp. ROCKSTORE 77; 80 (Stockholm)
Spatial scale, x,y,z
Depth, z -> ∆σ; ∆Τ
Time, t