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2012 Annual Science Report

Pennsylvania State University Reporting  |  SEP 2011 – AUG 2012

Executive Summary

Through an integration of education and research, the Penn State Astrobiology Research Center (PSARC) is dedicated to developing the conceptual, analytical, and technical tools to detect life, extant or extinct. This past year has been a great one for PSARC researchers. Each of our four major research projects had splendid results, novel directions, and new important papers.

Developing New Biosignatures

The Developing New Biosignatures project is aimed at 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. This past year saw significant progress on several areas of research for this project. In particular, The detection of diverse microscopic fossils preserved in gypsum is of significance for the potential discovery of fossils in Mars sulfates and should influence ... Continue reading.

Field Sites
44 Institutions
4 Project Reports
44 Publications
14 Field Sites
Roadmap
Objectives

Project Reports

  • Developing New Biosignatures

    The Developing New Biosignatures project is aimed at 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: 4.1 5.1 7.1
  • Biosignatures in Relevant Microbial Ecosystems

    PSARC is investigating microbial life in some of Earth’s most mission-relevant modern ecosystems. These environments include the extremely salty Dead Sea, the impact-fractured crust of the Chesapeake Bay impact structure, methane seeps on the ocean floor, deep ice in the Greenland ice sheet, and oxygen-free waters including deep subsurface groundwater. We target environments that, when studied, provide fundamental information that can serve as the basis for future solar system exploration. Combining our expertise in molecular biology, geochemistry, microbiology, and metagenomics, and in collaboration with some of the planet’s most extreme explorers, we are deciphering the microbiology, fossilization processes, and recoverable biosignatures from these mission-relevant environments.

    ROADMAP OBJECTIVES: 4.1 4.3 5.1 5.2 5.3 6.1 7.1 7.2
  • Biosignatures in Extraterrestrial Settings

    Exploring the prospects for biosignatures in extraterrestrial settings is a multi

    ROADMAP OBJECTIVES: 1.1 1.2 2.1 2.2 3.1 4.1 4.3 6.2 7.1 7.2
  • Biosignatures in Ancient Rocks

    The Biosignatures in Ancient Rocks group investigates the co-evolution of life and environment on early Earth using a combination of geological field work, geochemical analysis, genomics, and numerical simulation.

    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

Education & Public Outreach

Publications

  • Cui, Y., & Kump, L. R. (2015). Global warming and the end-Permian extinction event: Proxy and modeling perspectives. Earth-Science Reviews, 149, 5–22. doi:10.1016/j.earscirev.2014.04.007

  • Dawson, K. S., Freeman, K. H., & MacAlady, J. L. (2012). Molecular characterization of core lipids from halophilic archaea grown under different salinity conditions. Organic Geochemistry, 48, 1–8. doi:10.1016/j.orggeochem.2012.04.003

  • Fulton, J. M., Arthur, M. A., & Freeman, K. H. (2012). Subboreal aridity and scytonemin in the Holocene Black Sea. Organic Geochemistry, 49, 47–55. doi:10.1016/j.orggeochem.2012.05.008

  • Fulton, T. L., Wagner, S. M., Fisher, C., & Shapiro, B. (2012). Nuclear DNA from the extinct Passenger Pigeon (Ectopistes migratorius) confirms a single origin of New World pigeons. Annals of Anatomy – Anatomischer Anzeiger, 194(1), 52–57. doi:10.1016/j.aanat.2011.02.017

  • Ginolhac, A., Vilstrup, J., Stenderup, J., Rasmussen, M., Stiller, M., Shapiro, B., … Orlando, L. (2012). Improving the performance of True Single Molecule Sequencing for ancient DNA. BMC Genomics, 13(1), 177. doi:10.1186/1471-2164-13-177

  • Hedges, S. B. (2012). Amniote phylogeny and the position of turtles. BMC Biol, 10(1), 64. doi:10.1186/1741-7007-10-64

  • Higham, T., Compton, T., Stringer, C., Jacobi, R., Shapiro, B., Trinkaus, E., … Fagan, M. (2011). The earliest evidence for anatomically modern humans in northwestern Europe. Nature, 479(7374), 521–524. doi:10.1038/nature10484

  • Horodyskyj, L. B., White, T. S., & Kump, L. R. (2012). Substantial biologically mediated phosphorus depletion from the surface of a Middle Cambrian paleosol. Geology, 40(6), 503–506. doi:10.1130/g32761.1

  • House, C. H., Beal, E. J., & Orphan, V. J. (2011). The Apparent Involvement of ANMEs in Mineral Dependent Methane Oxidation, as an Analog for Possible Martian Methanotrophy. Life, 1(1), 19–33. doi:10.3390/life1010019

  • House, C. H., Oehler, D. Z., Sugitani, K., & Mimura, K. (2013). Carbon isotopic analyses of ca. 3.0 Ga microstructures imply planktonic autotrophs inhabited Earth’s early oceans. Geology, 41(6), 651–654. doi:10.1130/g34055.1

  • Kasting, J. F. (2013). What caused the rise of atmospheric O2?. Chemical Geology, 362, 13–25. doi:10.1016/j.chemgeo.2013.05.039

  • Kasting, J. F. (2014). Modeling the Archean Atmosphere and Climate. Treatise on Geochemistry, None, 157–175. doi:10.1016/b978-0-08-095975-7.01306-1

  • Kasting, J. F., & Canfield, D. E. (2012). The Global Oxygen Cycle. Fundamentals of Geobiology, None, 93–104. doi:10.1002/9781118280874.ch7

  • Kistler, L., & Shapiro, B. (2011). Ancient DNA confirms a local origin of domesticated chenopod in eastern North America. Journal of Archaeological Science, 38(12), 3549–3554. doi:10.1016/j.jas.2011.08.023

  • Kumar, S., & Hedges, S. B. (2011). TimeTree2: species divergence times on the iPhone. Bioinformatics, 27(14), 2023–2024. doi:10.1093/bioinformatics/btr315

  • Letts, B., & Shapiro, B. (2011). Case Study: Ancient DNA Recovered from Pleistocene-Age Remains of a Florida Armadillo. Ancient DNA, None, 87–92. doi:10.1007/978-1-61779-516-9_12

  • Loope, G. R., Kump, L. R., & Arthur, M. A. (2013). Shallow water redox conditions from the Permian–Triassic boundary microbialite: The rare earth element and iodine geochemistry of carbonates from Turkey and South China. Chemical Geology, 351, 195–208. doi:10.1016/j.chemgeo.2013.05.014

  • Lorenzen, E. D., Nogués-Bravo, D., Orlando, L., Weinstock, J., Binladen, J., Marske, K. A., … Willerslev, E. (2011). Species-specific responses of Late Quaternary megafauna to climate and humans. Nature, 479(7373), 359–364. doi:10.1038/nature10574

  • Maresca, J. A., Crowe, S. A., & MacAlady, J. L. (2012). Anaerobic photosynthetic ecosystems. Geobiology, 10(3), 193–195. doi:10.1111/j.1472-4669.2012.00327.x

  • Martino, A. J., Rhodes, M. E., Biddle, J. F., Brandt, L. D., Tomsho, L. P., & House, C. H. (2012). Novel Degenerate PCR Method for Whole-Genome Amplification Applied to Peru Margin (ODP Leg 201) Subsurface Samples. Frontiers in Microbiology, 3. doi:10.3389/fmicb.2012.00017

  • Ming, R., VanBuren, R., Liu, Y., Yang, M., Han, Y., Li, L-T., … Shen-Miller, J. (2013). Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biology, 14(5), R41. doi:10.1186/gb-2013-14-5-r41

  • Minyard, M. L., Bruns, M. A., Liermann, L. J., Buss, H. L., & Brantley, S. L. (2012). Bacterial Associations with Weathering Minerals at the Regolith-Bedrock Interface, Luquillo Experimental Forest, Puerto Rico. Geomicrobiology Journal, 29(9), 792–803. doi:10.1080/01490451.2011.619640

  • Molak, M., Lorenzen, E. D., Shapiro, B., & Ho, S. Y. W. (2012). Phylogenetic Estimation of Timescales Using Ancient DNA: The Effects of Temporal Sampling Scheme and Uncertainty in Sample Ages. Molecular Biology and Evolution, 30(2), 253–262. doi:10.1093/molbev/mss232

  • Ohmoto, H., Watanabe, Y., Lasaga, A. C., Naraoka, H., Johnson, I., Brainard, J., & Chorney, A. (2014). Oxygen, iron, and sulfur geochemical cycles on early Earth: Paradigms and contradictions. Earth’s Early Atmosphere and Surface Environment, None, 55–95. doi:10.1130/2014.2504(09)

  • Rhodes, M. E., Oren, A., & House, C. H. (2012). Dynamics and Persistence of Dead Sea Microbial Populations as Shown by High-Throughput Sequencing of rRNA. Applied and Environmental Microbiology, 78(7), 2489–2492. doi:10.1128/aem.06393-11

  • Schopf, J. W., & Kudryavtsev, A. B. (2012). Biogenicity of Earth’s earliest fossils: A resolution of the controversy. Gondwana Research, 22(3-4), 761–771. doi:10.1016/j.gr.2012.07.003

  • Schopf, J. W., Farmer, J. D., Foster, I. S., Kudryavtsev, A. B., Gallardo, V. A., & Espinoza, C. (2012). Gypsum-Permineralized Microfossils and Their Relevance to the Search for Life on Mars. Astrobiology, 12(7), 619–633. doi:10.1089/ast.2012.0827

  • Shi, C. S., Schopf, J. W., & Kudryavtsev, A. B. (2013). Characterization of the stem anatomy of the Eocene fern Dennstaedtiopsis aerenchymata (Dennstaedtiaceae) by use of confocal laser scanning microscopy. American Journal of Botany, 100(8), 1626–1640. doi:10.3732/ajb.1300027

  • Vidal, N., Marin, J., Sassi, J., Battistuzzi, F. U., Donnellan, S., Fitch, A. J., … Hedges, S. B. (2012). Molecular evidence for an Asian origin of monitor lizards followed by Tertiary dispersals to Africa and Australasia. Biology Letters, 8(5), 853–855. doi:10.1098/rsbl.2012.0460

  • Williford, K. H., Ushikubo, T., Schopf, J. W., Lepot, K., Kitajima, K., & Valley, J. W. (2013). Preservation and detection of microstructural and taxonomic correlations in the carbon isotopic compositions of individual Precambrian microfossils. Geochimica et Cosmochimica Acta, 104, 165–182. doi:10.1016/j.gca.2012.11.005

  • Hedges, S.  (2011).  On the use of high-level taxonomic names.  Zootaxa, 2867: 67-68.
  • Letts, B., Fulton, T.L., Stiller, M., Andrews, T., MacKay, G., Popkp, R. & Shapiro, B.  (2012).  Ancient DNA Reveals Genetic Continuity in Mountain Woodland Caribou of the Mackenzie and Selwyn Mountains, Northwest Territories, Canada.  Arctic Institute of North America, 65(5).
  • Marlow et al.  (2012, In Review).  Carbonate Hosted Methanotrophy: An Unrecognized Methane Sink in the Deep Sea.  Nature Geosciences.
  • Melezhik, V., Kump, L., Fallick, A., Strauss, H., Hanski, E., Prave, A. & Lepland, A.  (2012).  Reading the Archive of Earth’s Oxygenation. Volume 3: Global Events and the Fennoscandian Arctic Russia – Drilling Earth Project.  Springer, Heidelberg.
  • Melezhik, V., Prave, A., Fallick, A., Hanski, E., Lepland, A., Kump, L. & Strauss, H.  (2012).  Reading the Archive of Earth’s Oxygenation. Volume 2: The Core Archive of the Fennoscandian Arctic Russia – Drilling Early Earth Project.  Springer, Heidelberg.
  • Melezhik, V., Prave, A., Hanski, E., Fallick, A., Lepland, A., Kump, L. & Strauss, H.  (2012).  Reading the Archive of Earth’s Oxygenation. Volume 1: The Palaeoproterozoic of Fennoscandia as Context for the Fennoscandian Arctic Russia – Drilling Earth Project.  Springer, Heidelberg.
  • Nasdala, L., Beyssac, O., Schopf, J.W. & Bleisteiner, B.  (2012).  Application of Raman-based images in the Earth sciences.  In: Zoubir, A. (Eds.).  Optical Sciences.  Vol. 168.  Raman Imaging.
  • Nasdala, L., Beyssac, O., Schopf, J.W. & Bleisteiner, B.  (2012).  Application of Raman-based images in the Earth sciences.  In: Zoubir, A. (Eds.).  Raman Imaging, Springer Series in Optical Sciences.  Vol. 168.  Amsterdam: Springer.
  • Ohmoto, H. & House, C.H.  (2012, Sbmitted).  Did continental growth end the anaerobic world.  Nature Geosciences.
  • Orlando, L., Ginolhac, A., Froese, D., Vilstrup, J., Raghavan, M., Stiller, M., Cappelini, E., Rasmussen, M., Zazula, G., Weinstock, J., Hofreiter, M., Gilbert, M.T.P., Zhang, G., Olsen, J.V., Nielsen, R., Shapiro, B., Jun, W. & Willerslev, E.  (2012, Submitted).  Horse evolutionary genomics as revealed by a 700,000 year old genome.
  • Otake, T. & Watanabe, Y.  (2011).  Using multiple sulfur isotopes to understand the Earth’s surface environments during the Archean era.  Geochemical Journal, 45: 251-264.
  • Schopf, J.W. & Kudryavtsev, A.B.  (2012, Submitted).  Biogenicity of Earth’s earliest fossils.  In: Dilek, L. & Furnes, H. (Eds.).  Archean Earth and Early Life.  Springer.
  • Schopf, J.W.  (2012).  The fossil record of cyanobacteria.  In: Whitton, B.A. (Eds.).  Ecology of Cyanobacteria II. Their Diversity in Space and Time.  Berlin Heidelberg New York: Springer.
  • Schopf, J.W.  (2012, In Prss).  Forward [Book Chapter].  The Flyer: Boris Sokolov: Natural History and 21st Century Russia Sokolov.  Indiana University Press.

2012 Teams