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2009 Annual Science Report

Pennsylvania State University Reporting  |  JUL 2008 – AUG 2009

Executive Summary

The Penn State Astrobiology Research Center (PSARC) has charted a new direction focused on the recognition and characterization of microbial life, past and present. At the core of Astrobiology and at the forefront of NASA goals is the construction of a fundamental scientific knowledge base that enables the recognition of signatures of life on the early Earth, in extreme environments, and in extraterrestrial settings. Our new work focuses on four major projects: (1) Developing New Biosignatures, (2) Biosignatures in relevant microbial ecosystems, (3) Biosignatures in ancient rocks, and (4) Biosignatures in extraterrestrial settings.

Developing New Biosignatures
The development and experimental testing of potential indicators of life is essential for providing a critical scientific basis for the exploration of life in the cosmos. In microbial cultures, potential new biosignatures can be found among isotopic ratios, elemental compositions, and chemical changes to the growth media. Additionally, life ... Continue reading.

Field Sites
32 Institutions
4 Project Reports
65 Publications
11 Field Sites
Roadmap
Objectives

Project Reports

  • Biosignatures in Extraterrestrial Settings

    This project looks at the evolution of the composition of gases in the cold disk from which planets form; the evolution of the atmosphere after planet formation, in particular, the role of trace gases in the early greenhouse effect; and, some aspects of the the formation and later dynamical evolution of extrasolar planets.

    ROADMAP OBJECTIVES: 1.1 1.2 2.1 4.1
  • Biosignatures in Ancient Rocks

    The Earth’s Archean and Proterozoic eons offer the best opportunity for investigating a microbial world, such as might be found elsewhere in the cosmos. The ancient record on Earth provides an opportunity to see what geochemical signatures are produced by microbial life and how these signatures are preserved for geological time. Researchers have recognized a variety of mineralogical and geochemical characteristics in ancient rocks (sedimentary and igneous rocks; paleosols) that may be used as indicators of: (i) specific types of organisms that lived in the oceans, lakes and on land; and (ii) their environmental conditions (e.g., climate; atmospheric and oceanic chemistry). Our project addresses the following questions: Are some or all of these characteristics true or false signatures of organisms and/or indicators of specific environmental conditions? Do a “biosignature” in a specific geologic formation represent a local or global phenomenon? How are the biosignatures on Mars and other planets expected to be similar to (or different from) those in ancient terrestrial rocks?

    ROADMAP OBJECTIVES: 1.1 3.2 4.1 4.2 4.3 5.1 5.2 5.3 6.1 6.2 7.1 7.2
  • Biosignatures in Relevant Microbial Ecosystems

    In this project, PSARC team members explore the isotope ratios, gene sequences, minerals, organic biomarkers, and other biosignatures in modern ecosystems that function as analogs for early earth ecosystems, or for life that may be present elsewhere in the solar system and beyond. Many of these environments are “extreme” by human standards and/or have conditions that are at the limit for microbial life on Earth.

    ROADMAP OBJECTIVES: 4.1 4.3 5.1 5.2 5.3 6.1 7.1 7.2
  • Developing New Biosignatures

    The development and experimental testing of potential indicators of life is essential for providing a critical scientific basis for the exploration of life in the cosmos. In microbial cultures, potential new biosignatures can be found among isotopic ratios, elemental compositions, and chemical changes to the growth media. Additionally, life can be detected and investigated in natural systems by directing cutting-edge instrumentation towards the investigation of microbial cells, microbial fossils, and microbial geochemical products. Over the next five years, we will combine our geomicrobiological expertise and on-going field-based environmental investigations with a new generation of instruments capable of revealing diagnostic biosignatures. Our efforts will focus on creating innovative approaches for the analyses of cells and other organic material, finding ways in which metal abundances and isotope systems reflect life, and developing creative approaches for using environmental DNA to study present and past life.

    ROADMAP OBJECTIVES: 2.1 2.2 3.1 3.4 4.1 5.2 5.3 7.1 7.2

Education & Public Outreach

Publications

  • Battistuzzi, F. U., & Hedges, S. B. (2008). A Major Clade of Prokaryotes with Ancient Adaptations to Life on Land. Molecular Biology and Evolution, 26(2), 335–343. doi:10.1093/molbev/msn247

  • Beal, E. J., House, C. H., & Orphan, V. J. (2009). Manganese- and Iron-Dependent Marine Methane Oxidation. Science, 325(5937), 184–187. doi:10.1126/science.1169984

  • Cameron, V., Vance, D., Archer, C., & House, C. H. (2009). A biomarker based on the stable isotopes of nickel. Proceedings of the National Academy of Sciences, 106(27), 10944–10948. doi:10.1073/pnas.0900726106

  • Collins, M. J., Penkman, K. E. H., Rohland, N., Shapiro, B., Dobberstein, R. C., Ritz-Timme, S., & Hofreiter, M. (2009). Is amino acid racemization a useful tool for screening for ancient DNA in bone?. Proceedings of the Royal Society B: Biological Sciences, 276(1669), 2971–2977. doi:10.1098/rspb.2009.0563

  • Czaja, A. D., Kudryavtsev, A. B., Cody, G. D., & William Schopf, J. (2009). Characterization of permineralized kerogen from an Eocene fossil fern. Organic Geochemistry, 40(3), 353–364. doi:10.1016/j.orggeochem.2008.12.002

  • Hausrath, E. M., Neaman, A., & Brantley, S. L. (2009). Elemental release rates from dissolving basalt and granite with and without organic ligands. American Journal of Science, 309(8), 633–660. doi:10.2475/08.2009.01

  • Hausrath, E. M., Treiman, A. H., Vicenzi, E., Bish, D. L., Blake, D., Sarrazin, P., … Brantley, S. L. (2008). Short- and Long-Term Olivine Weathering in Svalbard: Implications for Mars. Astrobiology, 8(6), 1079–1092. doi:10.1089/ast.2007.0195

  • Hedges, S. B., Marin, J., Suleski, M., Paymer, M., & Kumar, S. (2015). Tree of Life Reveals Clock-Like Speciation and Diversification. Molecular Biology and Evolution, 32(4), 835–845. doi:10.1093/molbev/msv037

  • Hoashi, M., Bevacqua, D. C., Otake, T., Watanabe, Y., Hickman, A. H., Utsunomiya, S., & Ohmoto, H. (2009). Primary haematite formation in an oxygenated sea 3.46 billion years ago. Nature Geosci, 2(4), 301–306. doi:10.1038/ngeo465

  • House, C. H. (2009). The Tree of Life Viewed Through the Contents of Genomes. Methods in Molecular Biology, None, 141–161. doi:10.1007/978-1-60327-853-9_8

  • House, C. H., Orphan, V. J., Turk, K. A., Thomas, B., Pernthaler, A., Vrentas, J. M., & Joye, S. B. (2009). Extensive carbon isotopic heterogeneity among methane seep microbiota. Environmental Microbiology, 11(9), 2207–2215. doi:10.1111/j.1462-2920.2009.01934.x

  • Jones, D. S., Tobler, D. J., Schaperdoth, I., Mainiero, M., & MacAlady, J. L. (2010). Community Structure of Subsurface Biofilms in the Thermal Sulfidic Caves of Acquasanta Terme, Italy. Applied and Environmental Microbiology, 76(17), 5902–5910. doi:10.1128/aem.00647-10

  • Loveland-Curtze, J., Miteva, V. I., & Brenchley, J. E. (2009). Herminiimonas glaciei sp. nov., a novel ultramicrobacterium from 3042 m deep Greenland glacial ice. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 59(6), 1272–1277. doi:10.1099/ijs.0.001685-0

  • Loveland-Curtze, J., Miteva, V., & Brenchley, J. (2009). Novel ultramicrobacterial isolates from a deep Greenland ice core represent a proposed new species, Chryseobacterium greenlandense sp. nov.. Extremophiles, 14(1), 61–69. doi:10.1007/s00792-009-0287-6

  • Luo, G., Kump, L. R., Wang, Y., Tong, J., Arthur, M. A., Yang, H., … Xie, S. (2010). Isotopic evidence for an anomalously low oceanic sulfate concentration following end-Permian mass extinction. Earth and Planetary Science Letters, 300(1-2), 101–111. doi:10.1016/j.epsl.2010.09.041

  • Lyons, J. R. (2009). Atmospherically-derived mass-independent sulfur isotope signatures, and incorporation into sediments. Chemical Geology, 267(3-4), 164–174. doi:10.1016/j.chemgeo.2009.03.027

  • Lyons, J. R., Bergin, E. A., Ciesla, F. J., Davis, A. M., Desch, S. J., Hashizume, K., & Lee, J-E. (2009). Timescales for the evolution of oxygen isotope compositions in the solar nebula. Geochimica et Cosmochimica Acta, 73(17), 4998–5017. doi:10.1016/j.gca.2009.01.041

  • Lyons, J. R., Lewis, R. S., & Clayton, R. N. (2009). Comment on “Experimental Test of Self-Shielding in Vacuum Ultraviolet Photodissociation of CO”. Science, 324(5934), 1516–1516. doi:10.1126/science.1167717

  • Miteva, V., Teacher, C., Sowers, T., & Brenchley, J. (2009). Comparison of the microbial diversity at different depths of the GISP2 Greenland ice core in relationship to deposition climates. Environmental Microbiology, 11(3), 640–656. doi:10.1111/j.1462-2920.2008.01835.x

  • Morrow, A. L., Luhman, K. L., Espaillat, C., d’Alessio, P., Adame, L., Calvet, N., … Bohac, C. J. (2008). Observations of Disks around Brown Dwarfs in the TW Hydra Association with the Spitzer Infrared Spectrograph. The Astrophysical Journal, 676(2), L143–L146. doi:10.1086/587462

  • Orphan, V. J., & House, C. H. (2009). Geobiological investigations using secondary ion mass spectrometry: microanalysis of extant and paleo-microbial processes. Geobiology, 7(3), 360–372. doi:10.1111/j.1472-4669.2009.00201.x

  • Orphan, V. J., Turk, K. A., Green, A. M., & House, C. H. (2009). Patterns of 15 N assimilation and growth of methanotrophic ANME-2 archaea and sulfate-reducing bacteria within structured syntrophic consortia revealed by FISH-SIMS. Environmental Microbiology, 11(7), 1777–1791. doi:10.1111/j.1462-2920.2009.01903.x

  • Rambaut, A., Ho, S. Y. W., Drummond, A. J., & Shapiro, B. (2008). Accommodating the Effect of Ancient DNA Damage on Inferences of Demographic Histories. Molecular Biology and Evolution, 26(2), 245–248. doi:10.1093/molbev/msn256

  • Rhodes, M. E., Fitz-Gibbon, S. T., Oren, A., & House, C. H. (2010). Amino acid signatures of salinity on an environmental scale with a focus on the Dead Sea. Environmental Microbiology, 12(9), 2613–2623. doi:10.1111/j.1462-2920.2010.02232.x

  • Schopf, J. W. (2009). The hunt for Precambrian fossils: An abbreviated genealogy of the science. Precambrian Research, 173(1-4), 4–9. doi:10.1016/j.precamres.2009.01.003

  • Schopf, J. W., & Bottjer, D. J. (2009). World summit on ancient microscopic fossils. Precambrian Research, 173(1-4), 1–3. doi:10.1016/j.precamres.2009.06.001

  • Schopf, J. W., & Kudryavtsev, A. B. (2009). Confocal laser scanning microscopy and Raman imagery of ancient microscopic fossils. Precambrian Research, 173(1-4), 39–49. doi:10.1016/j.precamres.2009.02.007

  • Tian, F., Kasting, J. F., & Solomon, S. C. (2009). Thermal escape of carbon from the early Martian atmosphere. Geophysical Research Letters, 36(2), n/a–n/a. doi:10.1029/2008gl036513

  • Wander, M. C. F., & Schoonen, M. A. A. (2008). Reduction of N2 by Fe2+ via Homogeneous and Heterogeneous Reactions. Orig Life Evol Biosph, 38(2), 127–137. doi:10.1007/s11084-008-9122-9

  • Wander, M. C. F., Kubicki, J. D., & Schoonen, M. A. A. (2008). Reduction of N2 by Fe2+ via Homogeneous and Heterogeneous Reactions Part 2: The Role of Metal Binding in Activating N2 for Reduction; a Requirement for Both Pre-biotic and Biological Mechanisms. Orig Life Evol Biosph, 38(3), 195–209. doi:10.1007/s11084-008-9133-6

  • Young, S. A., Saltzman, M. R., Foland, K. A., Linder, J. S., & Kump, L. R. (2009). A major drop in seawater 87Sr/86Sr during the Middle Ordovician (Darriwilian): Links to volcanism and climate?. Geology, 37(10), 951–954. doi:10.1130/g30152a.1

  • Battistuzzi, F.U. & Hedges, S.B.  (2009).  Archaebacteria.  In: Hedges, S.B. & Kumar, S. (Eds.).  The Timetree of Life.  New York: Oxford University Press.
  • Battistuzzi, F.U. & Hedges, S.B.  (2009).  Eubacteria.  In: Hedges, S.B. & Kumar, S. (Eds.).  The Timetree of Life.  New York: Oxford University press.
  • Beal, E.J.  (2009).  Geochemical Requirements of the Anaerobic Oxidation of Methane in the Eel River Basin.  Geosciences.  The Pennsylvannia State University.
  • Bhattacharya, D., Yoon, H-S., Hedges, S.B. & Hackett, J.D.  (2009).  Eukaryotes (Eukaryota).  In: Hedges, S.B. & Kumar, S. (Eds.).  The Timetree of Life.  New York: Oxford University Press.
  • Hedges, S.B. & Kumar, S.  (2009).  Timetree (www.timetree.org) [Online].  Website: www.timetree.org.
  • Hedges, S.B. & Vidal, N.  (2009).  Lizards, snakes, and amphisbaenians (Squamata).  In: Hedges, S.B. & Kumar, S. (Eds.).  The Timetree of Life.  New York: Oxford University Press.
  • Hedges, S.B.  (2009).  Life.  In: Hedges, S.B. & Kumar, S. (Eds.).  The Timetree of Life.  New York: Oxford University Press.
  • Hedges, S.B.  (2009).  Vertebrates (Vertebrata).  In: Hedges, S.B. & Kumar, S. (Eds.).  The Timetree of Life.  New York: Oxford University Press.
  • Heinicke, M.P.  (2009).  A molecular phylogenetic perspective on the evolutionary history of terraranan frogs, a vertebrate mega-radiation.  Department of Biology.  University Park: The Pennsylvania State University.
  • Heinicke, M.P., Naylor, J.P. & Hedges, S.B.  (2009).  Cartilaginous fishes (Chondrichthyes).  In: Hedges, S.B. & Kumar, S. (Eds.).  The Timetree of Life.  New York: Oxford University Press.
  • Heinicke, M.P., Sander, J.M. & Hedges, S.B.  (2009).  Lungfishes (Dipnoi).  In: Hedges, S.B. & Kumar, S. (Eds.).  The Timetree of Life.  New York: Oxford University Press.
  • Hoashi, M., Watanabe, Y. & Ohmoto, H.  (2009).  Primary hematite formation in an oxygenated deep sea 3.46 billion years ago.  Goldschmidt conference.  Davos, Switzerland.
  • Horodyskyj, L.  (2009).  Soil formation and terrestrial biosignatures in the Middle Cambrian [electronic resource].  Geosciences.  University Park: The Pennsylvania State University.
  • Johnson, I.  (2009).  The Earth’s oldest (~3.4 GA) paleosol at Trendall Ridge in the North Pole Dome region of the Eastern Pilbara Craton, Western Australia.  Geosciences.  University Park: The Pennsylvania State University.
  • Johnson, I., Watanabe, Y., Stewart, B. & Ohmoto, H.  (2009).  Earth’s oldest (~3.4 Ga) lateritic paleosol in he Pilbara Craton, Western Australia.  Goldschmidt conference.  Davos, Switzerland.
  • Jones, D.S., Schaperdoth, I. & MacAlady, J.L.  (2010).  Microbial communities from extremely acidic sulfidic cave biofilms.  Environmental Microbiology, submitted.
  • Kimball, B.  (2009).  Biogeochemical Cycling of Copper in Acid Mine Drainage.  Geosciences.  University Park: The Pennsylvania State University.
  • Kump, L.R., Condie, K.C. & Arthur, M.A.  (2009).  Co-evolutionary implications of alternative models of plate tectonics in Earth history.  Geol. Soc. America Ann. Meeting.  Portland, OR.
  • Kump, L.R., Meyer, K.M., Ridgwell, A. & Payne, J.L.  (2009).  Biosphere response to volcanic CO 2 release: Siberian Traps and End-Permian Mass Extinction.  Geol. Soc. America Ann. Meeting.  Portland, OR.
  • Lal, A.K.  (2008).  Origin of life.  Astrophysics and Space Sceince, 317: 267-278.
  • Meyer, K.M., Kump, L.R., MacAlady, J., Schaperdoth, I. & Freeman, K.  (in review).  Benthic production of a putative planktonic biomarker.  Geobiology.
  • Miteva, V.  (2009).  Microorganisms associated with glaciers.  In: V. P. Singh, P.S.a.U.K.H. (Eds.).  Encyclopedia of Snow, Ice and Glaciers.  Springer (submitted).
  • Moody, K.  (2009).  Three Body Dynamics in Dense Gravitational Systems.  Department of Astronomy.  University Park: The Pennsylvania State University.
  • Ohmoto, H.  (2009).  Redox evolution of volcanic gas through geologic time.  Goldschmidt conference.  Davos, Switzerland.
  • Ohmoto, H., Bevacqua, D.C. & Watanabe, Y.  (2009).  Alteration of submarine volcanic rocks in oxygenated Archean oceans.  American Geophysical Union Annual Meeting.  San Francisco, CA.
  • Saltzman, M.R., Young, S.A., Kump, L.R., Foland, K.A. & Leslie, S.  (2009).  The Late Ordovician glaciation and mass extenction: Relation to basaltic weathering and volcanic degassing.  Geol. Soc. America Ann. Meeting.  Portland, OR.
  • Schopf, J.W. & Bottjer, D.J.  (2009).  World Summit on Ancient Microscopic Fossils, Special Issue.  Vol. 173.  Precambrian Research.
  • Schopf, J.W.  (2009).  Emergence of Precambrian paleobiology: a new field of science.  In: Sepkoski, D. & Ruse, M. (Eds.).  The Paleobiological Revolution, Essays on the Growth of Modern Paleontology.  Chicago: University of Chicago Press.
  • Schopf, J.W.  (2009).  Organismal evolution and radiation before the Cambrian.  In: Ruse, M., Travis, J. & Zinser, J. (Eds.).  Evolution: The First 4 Billion Years.  Cambridge: Harvard University Press.
  • Schopf, J.W.  (2009).  Paleontology, Microbial.  In: Lederberg, J. & Schaechter, M. (Eds.).  Encyclopedia of Microbiology, 3rd Edition.  Amsterdam: Elsevier.
  • Urban, N., Bralower, T., Keller, K. & Kump, L.R.  (2009).  Statistical interpretation of the rate of carbon isotope changes at the onset of the Paleocene-Eocene Thermal Maximum.  American Geophysical Union Fall Meeting.  San Francisco, CA.
  • Vidal, N., Rage, J-C., Coulous, A. & Hedges, S.B.  (2009).  Snakes (Serpentes).  In: Hedges, S.B. & Kumar, S. (Eds.).  The Timetree of Life.  New York: Oxford University Press.
  • Yamaguchi, K.E., Kato, Y., Nakamura, K., Suzuki, K., Watanabe, Y., Nedachi, M. & Ohmoto, H.  (2009).  REE+Y geochemistry of the 3.46 Ga Marble Bar Chert recovered by the Archean Biosphere Drilling Project.  Goldschmidt Conference.  Davos, Switzerland.
  • Zerkle, A.L., Junium, C.K., Canfield, D.E. & House, C.H.  (2008).  Production of 15 N-depleted biomass during cyanobacterial N 2 -fixation at high Fe concentrations.  J. Geophys. Res, 113(G03024).

2009 Teams