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2003 Annual Science Report

Pennsylvania State University Reporting  |  JUL 2002 – JUN 2003

Executive Summary

The Penn State Astrobiology Research Center (PSARC), created five years ago as part of the NASA Astrobiology Institute, is composed of 16 (Co)-PIs and their research teams from The Pennsylvania State University (13), The University of Pittsburgh (2), and SUNY Stony Brook (1). The investigators represent a wide range of disciplines: geochemistry (Michael Arthur, Susan Brantley, Rosemary Capo, Lee Kump, Hiroshi Ohmoto, Martin Schoonen, and Brian Stewart), paleontology (Mark Patzkowski), atmospheric chemistry (Jim Kasting and Robert Minard), geomicrobiology (Kate Freeman and Chris House), evolutionary genomics (Blair Hedges and Masatoshi Nei), and biochemistry and microbiology (Jean Brenchley and Greg Ferry). The proximity of all members has enabled close interaction and a variety of collaborative research, teaching, and public outreach programs. During the fifth year, PSARC has supported all or part of the research/education/PO activities carried out by 142 persons (16 (Co-)PIs, 22 research associates and postdoctoral fellows, five research assistants, two technicians, 49 graduate students, 37 undergraduate students, and five staff in administration/IT/EPO).

The primary research goal of PSARC over the past five years (under the theme Coevolution of the Earth and Life) has been to increase understanding of the connections between the rise of major life forms during the early history of Earth (between ~3.8 and 0.5 billion years ago) and the evolution of the environment (especially atmospheric O2, CO2, and CH4). This goal has been pursued primarily from multidisciplinary and multidimensional research focused on the following seven topics (Tasks):

  1. Environment of prebiotic Earth and the origin of life
    1. Experimental approach (Schoonen)
    2. Prebiotic chemistry of hydrogen cyanide (Minard)
  2. Biochemistry of Archea and Bacteria
    1. Enzymes of ancient metabolic pathways (Ferry)
    2. Biochemistry of psychrophilic organisms (Brenchley)
    3. Microbe-mineral interactions (Brantley)
  3. GEOPULSE: Gene Expressions Observations for Planetary Life Study (House, Ferry, Freeman, Brantley)
  4. Timescale for the evolution of life on Earth: Molecular evolutionary approach (Hedges and Nei)
  5. Evolution of atmospheric O2, climate, and biosphere (Kump, Kasting, Freeman, Capo, Stewart, and Ohmoto)
  6. Neoproterozoic variations in carbon and sulfur cycling (Arthur)
  7. Causes and consequences of the diversification and extinction of metazoans (Patzkowsky)

Progress in each of the above topics is reported separately in the following pages. Excellent progress has been made in all phases of our research projects. The new discoveries made and the new theories developed from these investigations during the fifth year have been presented in 34 published papers (including those in press) and 20 papers (submitted, in review, or in revision) in refereed journals and book chapters, and 71 abstracts presented at international and national meetings.


Topic 1: Prebiotic Environment

Martin Schoonen’s group has conducted a series of photochemical experiments using pyrite, and suggests pyrite-induced OH radical formation may have placed an important constraint on the stability of biomolecules, such as ribonucleic acid (RNA), on early Earth. Protective mechanisms, such as encapsulation of biomolecules by lipids, may have been a prerequisite to escape decomposition via OH radical attack.

Robert Minard has synthesized H13C15N polymers under a variety of conditions, and analyzed their structures using solid-state nuclear magnetic resonance (NMR). Based on these data, Minard suggests the HCN polymer structural model provides a mechanism for the formation of heteropolypeptides on the primitive Earth.

Topic 2: Biochemistry of Archea and Bacteria

Greg Ferry has discovered a novel flavoprotein family (archaeoflavoprotein) that is unique to the Archaea domain of life.

Jean Brenchley’s group has demonstrated that a wide, and perhaps surprising, diversity of organisms have survived entrapment in a Greenland glacier for over 120,000 years. They have analyzed nearly 800 isolates, grouping them into taxonomic and phylogenetic categories.

Susan Brantley’s group has found that Fe (II) released from goethite by siderophore-producing soil bacteria has a δ56Fe value -1.6‰ relative to goethite. They have also found that nitrogen-fixing bacteria may secrete molybdenum-complexing ligands to solution in order to extract Mo for nitrogenase: for example, Azotobacter vinelandii secretes aminochelin when grown in Mo-deficient but Fe-replete conditions.

Topic 3. Gene Expression for Planetary Life Study

Using whole genomic analysis, Chris House’s group has deduced that sulfur reduction is the most geologically plausible for the base of the Archaea. They have also found that: (a) Methanosarcina acetevorans have surprisingly high oxygen tolerance, allowing them to grow even at about 1% oxygen; (b) Archaeoglobus does not oxidize methane in spite of the similarity of Archaeoglobus to ANME-1 and ANME-2; and© there are conditions that increase trace methane oxidation by methanogens, providing some insight into how anaerobic methane oxidation occurs.

Topic 4. Evolutionary genomics

Blair Hedges’s group has found, using molecular clock studies of large numbers of genes (50-200), that plants, animals, and fungi diverged about 1.5 billion years ago, with living groups in each kingdom diverging relatively soon thereafter. This is as much as one billion years earlier than indicated by the fossil record.

Masatoshi Nei, a member of the National Academy of Science, was awarded the 2002 International Prize for Biology in the field of “Biology of Evolution” for his contributions in evolutionary genomics.

Topic 5. Evolution of atmospheric O2, climate, and biosphere

Lee Kump’s group has found from numerical modeling of microbial mats that O2 levels in Archean cyanobacterial mats may have exceeded modern atmospheric saturation values by a factor of 2-3, as modern mats do during afternoon hours. This conclusion is independent of the oxygen or sulfide content of the overlying water. From carbon isotope analyses of Paleoproterozoic carbonate, Kump also suggests that pelagic marine organisms in the Paleoproterozoic (1.8 billion years ago) apparently were modifying the nutrient and carbon chemistry of the ocean in much the same way and to a similar extent as modern organisms do. Kump also suggests the banded iron formations in the Neoproterozoic “Snowball Earth” period may have been the result of high iron fluxes from mid-ocean ridges, which were enhanced by a sea-level change and the low-sulfate oceans.

Jim Kasting’s group, based on photochemical modeling, suggests that: (a) enhanced methane concentrations could provide a plausible explanation for the extended warmth of the Mid-Proterozoic Era, 2.2-0.8 Ga; and (b) ozone and methane might be observed simultaneously in a Mid-Proterozoic-type terrestrial planet atmosphere. The simultaneous presence of O2 (or O3) and reduced gases is considered the firmest remote evidence for extraterrestrial life.

Based on molecular analyses of organic matter from sedimentary rocks of late Archean age, Kate Freeman’s group suggests diverse life already existed in the Late Archean. There is evidence for all three domains existing at that time. Isotopic and stratigraphic data reveal ecological differences associated with lithofacies. Shallower facies were more oxygenated, a phenomenon that is reflected in the recorded microbial processes. Deeper waters were largely anoxic, although there is evidence for redox cycling between elemental sulfur and sulfide. Isotopically enriched tetramethyl- and trimethylbenzene released via pyrolysis can be linked to inputs from green sulfur bacteria in ancient (Cretaceous) lake deposits. This may extend the available biomarkers for this source of organic matter.

Rosemary Capo and Brian Stewart’s group has found that the Sm-Nd isotope system can be used to evaluate the pedogenic mobilization and possible later remobilization of geochemical tracers in ancient soil profiles. Soil carbonate is a significant repository for rare Earth elements (REE), an important paleoatmospheric tracer, and must be considered in working out the REE budgets of ancient soil profiles formed under arid conditions. They further suggest the REE patterns of the ~3 Ga Steep Rock paleosol, Canada, reflect pedogenic processes.

Hiroshi Ohmoto has organized the Archean Biosphere Drilling Project (ABDP), an international collaborative research project under the Astrobiology Drilling Program (ADP). The drilling, which began in the Pilbara district, Western Australia, in June 2003, has already revealed unequivocal evidence that the hematite (ferric oxide) crystals in the 3.46 Ga Marble Bar chert/jasper sequence were not formed by the modern oxidation of ferrous-rich carbonate (siderite) as postulated by many previous investigators, but instead formed by the mixing of Fe2+-bearing submarine hydrothermal fluids and oxygenated local seawater when the rocks accumulated on the ocean floor. This is important evidence suggesting the oceans and atmosphere were already oxygenated 3.46 Ga ago. The ABDP has also recovered a large amount of black shales, containing remnants of microbes that lived in the Archean oceans. The mineralogical and geochemical investigations (e.g., C, N, and S isotopes; rare Earth elements) by Ohmoto’s group on Archean shales and banded iron formations from the Abitibi district, Canada, the Pilbara-Hamersley district, Australia, and other places have also revealed that the redox structure of the Archean oceans was probably identical to that of modern oceans: globally oxic oceans with locally developed anoxic basins that sustained complexed ecosystems. Based on analyses of thermodynamic data and carbon isotope data on siderite (FeCO3), which is abundant in banded iron formations older than ~1.8 Ga, Ohmoto and Watanabe suggest the CO2 level of the Archean atmosphere was at least 100 times greater than today, implying CO2, rather than methane, was the major green-house gas in Archean, as well as in the later geologic time.

Figure 1 The first drilling site of the ABDP.

Figure 2 Hiroshi Ohmoto examines the first core with Bruce Runnegar (incoming NAI Director) at the site.

Topic 6. Neoproterozoic carbon and sulfur cycles

Based on sulfur isotope analyses of trace sulfate in carbonates, Mike Arthur’s group suggests the seawater sulfate concentrations in the mid- to late-Proterozoic were perhaps 10% of those at present. These low concentrations led to profound changes in ocean and atmospheric chemistry, ultimately producing near-global glaciations.

Topic 7. The Ordovician extinction of metazoans

Mark Patzkowski’s group has made significant progress in understanding the environmental causes of the Late Ordovician glaciation and the evolutionary consequences of the Late Ordovician mass extinction. Based on numerical modeling, they suggest the pCO2 level was < 8 times the present atmospheric level (PAL) when the glaciation began and > 10 PAL when it ended.