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 the selection of sites for Mars surface sample collection. This discovery, coupled with that of Schopf and his colleagues of a previously unreported Precambrian sulfur-dependent ecosystem — sulfuretums essentially identical to that living today and now known from their work to be preserved in 1,800- and 2,300-Ma-old geological units — hold promise for the discovery of ancient and perhaps even extant life on Mars. Our work on DNA as a biosignature also say significant progress with papers on DNA preservation in Pleistocene-aged fossils (e.g., Letts and Shapiro, 2012), as well as progress on new methods for amplifying trace amounts of DNA. We also reported the use of Scytonemin as an interesting biomarker showing cyanobacterial populations.
Biosignatures in Relevant Microbial Ecosystems
The Biosignatures in Relevant Microbial Ecosystems project explores the isotope ratios, gene sequences, minerals, organic molecules, and other signatures of life in modern environments that have important similarities with early earth conditions, or with 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. During the last year, the team made great progress with work on the Dead Sea, the Chesapeake Bay impact structure, Eel River Basin methane seeps, Greenland glacier ice, and redox-stratified precambrian ocean analog sites.
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. Our team made great progress this last year with a high number of papers submitted to peer-reviewed journals. Also, during the reporting period, the team published a manuscript reporting evidence for a large depletion of phosphorous from the surface of a Cambrian paleosol, as well as a three volume book of the extensive results of the NAI co-funded FAR-DEEP continental drilling project that investigated the record of Earth’s oxygenation during the Palaeoproterozoic.
Biosignatures in Extraterrestrial Settings
The Biosignatures in Extraterrestrial Settings explores indicators of life outside of Earth, both within the Solar System and on extrasolar planets. The work includes studies of the chemistry and composition of the Solar System, and the past history of conceivable sites for life in the Solar System. We also look for habitable planets outside the Solar System; work on developing new techniques to find and observe potentially habitable planets; and model the dynamics, evolution and current status of a variety of extrasolar planets. This past year saw the “habitable zone planet finder near-infrared spectrograph” funded by a National Science Foundation Major Research Instrumentation grant, leveraging off the pathfinder instrument which was funded in part by NAI. Also of particular interest, Graduate student Matthew Route published results of a radio search for sub-stellar companions to nearby stars, and graduate student Sara Gettel published results of the search for exoplanets around K2-giant stars. This past year also saw the continuation of and initiation of a high number of collaborations and projects related to various topics including impact panspermia, exoplanet abundance, and the prospects for mid-infrared detection of habitable worlds.
Publications
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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
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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
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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
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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
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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
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Hedges, S. B. (2012). Amniote phylogeny and the position of turtles. BMC Biol, 10(1), 64. doi:10.1186/1741-7007-10-64
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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
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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
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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
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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
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Kasting, J. F. (2013). What caused the rise of atmospheric O2?. Chemical Geology, 362, 13–25. doi:10.1016/j.chemgeo.2013.05.039
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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
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Kasting, J. F., & Canfield, D. E. (2012). The Global Oxygen Cycle. Fundamentals of Geobiology, None, 93–104. doi:10.1002/9781118280874.ch7
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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
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Kumar, S., & Hedges, S. B. (2011). TimeTree2: species divergence times on the iPhone. Bioinformatics, 27(14), 2023–2024. doi:10.1093/bioinformatics/btr315
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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
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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
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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
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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
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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
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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
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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
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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
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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)
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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
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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
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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
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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
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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
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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.