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Project Reports

• Life Underground

  Our multi-disciplinary team from USC, Caltech, JPL, DRI, RPI, and now also Northwestern is developing and employing field, laboratory, and modeling approaches aimed at detecting and characterizing microbial life in the subsurface—the intraterrestrials. We posit that if life exists, or ever existed, on Mars or other planetary body in our solar system, evidence thereof would most likely be found in the subsurface. This study takes advantage of unique opportunities to explore the subsurface ecosystems on Earth through boreholes, mine shafts, sediment coring, marine vents and seeps, and deeply-sourced springs. Access to the subsurface—both continental and marine—and broad characterization of the rocks, fluids, and microbial inhabitants is central to this study. Our focused research themes require subsurface samples for laboratory and in situ experiments. Specifically, we are carrying out in situ life detection, culturing and isolation of heretofore unknown intraterrestrial archaea and bacteria using numerous novel and traditional techniques, and incorporating new and existing data into regional and global metabolic energy models.

  ROADMAP OBJECTIVES: 2.1 2.2 3.1 3.3 4.1 5.1 5.2 5.3 6.1 6.2 7.2

• Biogenic Gases From Anoxygenic Photosynthesis in Microbial Mats

  This lab and field project aims to measure biogenic gas fluxes in engineered and natural microbial mats composed of anoxygenic phototrophs and anaerobic chemotrophs, such as may have existed on the early Earth prior to the advent of oxygenic photosynthesis. The goal is to characterize the biogeochemical cycling of S, H, and C in an effort to constrain the sources and sinks of gaseous biosignatures that may be relevant to the detection of life in anoxic biospheres on habitable exoplanets.

  ROADMAP OBJECTIVES: 4.1 5.2 5.3 6.1 6.2 7.2

• Biosphere-Geosphere Stability and the Evolution of Complex Life

  Both the rise of complex life and the Phanerozoic mass extinctions are accompanied by significant perturbations of the carbon cycle. Attention is usually focused on causality, and environmental change is almost always considered the driver. Yet the co-evolution of life and the environment suggests that the fundamental issue is not causality but rather stability. This project seeks to develop a theory of biosphere-geosphere stability and to test it using the geochemical and fossil records.

  ROADMAP OBJECTIVES: 4.2 4.3 5.2 6.1

• Biosignatures in Ancient Rocks – Kump Group

  We are analyzing FAR-DEEP cores that span the putative “oxygen overshoot” associated with the termination of the Great Oxidation Event, 2.0 billion years ago. The volcanic rocks in question are highly oxidized. Our hypothesis is that oxygen-enriched groundwaters altered these rocks during a time interval when atmospheric oxygen concentrations approached modern levels, falling subsequently to lower values characteristic of the ensuing billion years. Kump has also proposed a new explanation for the “second rise of atmospheric oxygen” in the Neoproterozoic (ca. 850 Ma).

  ROADMAP OBJECTIVES: 1.1 4.1 4.2 4.3 5.2 6.1

• Biosignatures in Ancient Rocks – Ohmoto Group

  This project has been aimed at understanding the chemical and biological natures of the ocean-atmosphere-lithosphere systems during the Archean. A second objective is testing a hypothesis that the MIF-S isotope signatures, which characterize some Archean and younger sedimentary rocks, were generated during reactions between hydrothermal fluids and organic-rich sediments, rather than through atmospheric reactions.

  ROADMAP OBJECTIVES: 1.1 4.1 6.1

• Coupled Energy Balance Ecosystem-Atmosphere Modeling of Thermodynamically-Constrained Biogenic Gas Fluxes Project

  The thermodynamically-constrained fluxes of gases to and from a biosphere has profound, planet-wide consequences. These fluxes can directly control the redox state of the surface environment, the atmospheric composition, and the concentration of nutrients and metals in the oceans. Through these direct effects, they also create strong forcings on the climate, the redox state of the interior of the planet, and the detectability of the biosphere by remote observations. This is a theoretical modeling study to constrain biomass, productivity, and biogenic gas fluxes given a range of geologic parameters.

  ROADMAP OBJECTIVES: 1.1 1.2 5.2 5.3 6.1 7.2

• Project 1C: Studies of Early-Evolved Enzymes in Modern Organisms May Reveal the History of Earth’s Ambient Temperature Over Geological Time

  By addressing a focused question — “Does the thermal stability of the reconstructed ancient enzymes of modern organisms provide evidence of the temperature of the environment in which the enzymes originated?” — this study asks a much broader question, namely, “can the biochemistry of extant life provide evidence of ancient environments?” In the geological record, there is virtually no mineralogical evidence to determine ambient surface temperature and data from other sources are ambiguous and contradictory. By analyzing the thermal stability of ancient reconstructed enzymes we hope that this work will pave the way to solve this fundamental problem and, by doing so, demonstrate a new way to understand the co-evolution of life and its planetary environment.

  ROADMAP OBJECTIVES: 4.1 5.1 6.1

• Early Animals: Modeling the Biotic-Abiotic Interface in the Early Evolution of Multicellular Form

  The size of early multicellular organisms was sufficint to modify their local environment. Our initial work modeling of Neoproterozoic frond-like forms in the earliest-known communities of multicellular organisms demonstrates they were of sufficient scale and density to generate a distinctive canopy flow-regime. This modified environment yielded a selective advantage towards large eukaryotic forms that evolved at this time. This result is a function of limits imposed by diffusion at the surface of organisms, and how height and attendant velocity exposure escape these limits. Building on these results, we are now developing additional models of abiotic/biotic interactions at organismal surfaces, which are implicit in the morphology, development and orientation of other Neoproterozoic fossils. Ultimately, this work will help illuminate how forms initialy dependent on passive diffusion became more trophically complex, yielding a transition to the animal radiation.

  ROADMAP OBJECTIVES: 4.1 4.2 5.2 6.1

• Project 4: Rapid Evolution in Stressed Populations: Theory

  Evolution is typically thought of as occurring over millions of years. But recently it has become clear that we have grossly over-estimated this time scale. Perhaps the most famous example of this is the rapid evolution of resistance of bacteria, worldwide, to modern antibiotics. Similarly, early life has an evolution time scale problem: given the age of the Earth and the known age of the Last Universal Common Ancestor, life must have arisen and evolved the majority of the complexity of the modern cell in less than a billion years. This project is a theoretical attempt to understand how a fluctuating environment can accelerate evolution rate, and lead to evolution on ecosystem time scales. Eventually, this work will join up with the experimental work being done by our team, using the GeoBioCell, in Project 8.

  ROADMAP OBJECTIVES: 4.1 4.2 5.1 5.2 5.3 6.1

• Project 5: The Origins of Life’s Diversity

  The huge diversity of life poses a major challenge to ecological theory and a major source of optimism for astrobiology. Ecological theory argues that a single environmental niche should be colonized by a single species of organism, or perhaps a small community, and so the diversity of life should be essentially a measure of the number of niches present. The huge diversity of life does suggest, however, that the ability of life to explore, colonize and especially create environmental niches has been drastically underestimated. Accordingly, the likelihood of extraterrestrial life arising is also underestimated, or at least inadequately estimated, by our present understanding of biological evolution. This project attempts to solve this problem by developing a new theory for niche diversity.

  ROADMAP OBJECTIVES: 3.4 4.1 4.2 5.1 5.2 5.3 6.1 6.2

• Project 6. Mining Archaeal Genomes for Signatures of Early Life: Comparison of Metabolic Genes in Methanogens

  Methanogenic archaea derive energy from simple starting materials, producing methane and carbon dioxide in the process. The chemical simplicity of the growth substrates and versatility of the organisms in extreme environments provide for a possibility that they could exist on other planets. By characterizing the evolution of methanogens from the most simple to most complex organism as well as their growth characteristics under controlled environments, we hope to address the question as to whether they could exist on planets such as Mars, where bursts of methane have been seen, yet no source has yet been identified.

  ROADMAP OBJECTIVES: 1.1 2.1 3.1 3.2 3.3 3.4 4.1 4.2 5.1 5.2 5.3 6.1 6.2 7.1 7.2

• Biosignatures of Life in Ancient Stratified Ocean Analogs

  Instigated by Macalady and Kump in 2010, this project investigates biosignatures of life in modern analogs for stratified ancient and/or extraterrestrial oceans. The primary field site is a sinkhole in Florida. Other field site include stratified ocean analogs in the Bahamas, New York State, and the Dominican Republic. A website monitoring the activities of an informal working group on Early Earth Photosynthesis is maintained by Macalady (http://www.geosc.psu.edu/~jlm80/EEP.html).

  ROADMAP OBJECTIVES: 2.1 3.3 3.4 4.1 5.2 5.3 6.1 7.1 7.2

• Project 8 Culturing Microbial Communities in Controlled Stress Micro-Environments

  This project explores the adaptation and evolution of organisms under controlled environmental conditions, and compares the behavior across two Domains of Life in order to identify and quantify universal aspects of evolutionary response.

  ROADMAP OBJECTIVES: 6.1 6.2

• Planetary Surface and Interior Models and SuperEarths

  We use computer models to simulate the evolution of the interior and the surface of real and hypothetical planets around other stars. Our goal is to determine the initial characteristics that are most likely to contribute to making a planet habitable in the long run. Observations in our own Solar System show us that water and other essential materials are continuously consumed via weathering (and other processes: e.g., subduction, sediment burial) and must be replenished from the planet’s interior via volcanic activity to maintain a biosphere. The surface models we are developing will be used to predict how gases and other materials will be trapped through weathering and biological processes over time. Our interior models are designed to predict tidal effects, heat flow, and how much and what sort of materials will come to a planet’s surface through resurfacing and volcanic activity throughout its history.

  ROADMAP OBJECTIVES: 1.1 1.2 4.1 5.2 6.1

• Project 2C: Developing the 13C-18O Clumped Isotope Thermometer

  One of the critical parameters in understanding the evolution of the Earth is the temperature of the oceans. Proposals, for example, that early life was hyperthermophilic would be supported if there was evidence for a “hot early ocean”, which some stable isotope data support. However, arguments against a “hot early ocean” include lower solar luminosity early in Earth history, and evidence for widespread glaciations. A new geothermometer is based on the enhanced thermodynamic stability of “clumped isotopes” (e.g., ¹³C-¹⁸O bonds) in carbonate minerals, which exhibits a temperature dependence. However, attempts to calibrate this temperature dependence have identified kinetic isotope effects that can give apparently anomalous results. In this project, experiments were designed to systematically probe formation rate effects on ¹³C-¹⁸O bonding during calcite mineral lattice assembly from aqueous solutions. Preliminary results do not show a correlation between precipitation rate and ¹³C-¹⁸O bonding over the range investigated but do provide evidence that is being used to deconvolute and identify physiochemical conditions and processes that lead to disequilibrium in ¹³C-¹⁸O bonding during carbonate mineral formation.

  ROADMAP OBJECTIVES: 4.1 6.1 7.1 7.2

• Stoichiometry of Life – Task 1 – Laboratory Studies in Biological Stoichiometry

  This project component involves a set of studies of microorganisms with which we are trying to better understand how living things use chemical elements (nitrogen, phosphorus, iron, etc.) and how they cope, in a physiological sense, with shortages of such elements. For example, how does the “elemental recipe of life” change when an organism is starved for phosphorus or nitrogen or iron? Is this change similar for different species of microorganisms? Are the changes the same if the organism is limited by a different key nutrient? Furthermore, how does an organism shift its patterns of gene expression when it is starved by various nutrients? This will help in interpreting studies of gene expression in natural environments.

  ROADMAP OBJECTIVES: 5.2 5.3 6.1 6.2

• Project 10: Identifying Key Innovations in the Origin of the Cell

  Identifying essential functions of conserved hypothetical genes holds the key to understanding the origins of key innovations in the origin of the cell. Our goal is to take a comparative genomic approach to define the molecular machinery that differentiate the Bacterial from its sister lineage that later diverged to became the Archaea and Eukaryotes. One of the obstacles clouding our view of these early cells from a comparative approach is the large number of conserved hypothetical genes present in Archaeal and Eukaryote genomes whose cellular functions are unknown. Our approach is to identify which conserved hypothetical genes are essential to the function of the model crenarchaeon Sulfolobus islandicus. The Crenarchaea are one of the major lineages with in the Archaeal domain with close ties in function to the cellular biology of Eukaryotes. The essential gene profile has not been identified within any organism in this lineage and holds the key to understanding the origin of cellular features in central processing of genomic information through replication, recombination, repair and the shaping of the chromosome.

  ROADMAP OBJECTIVES: 3.4 4.2 5.1 6.1 6.2

• Project 2E: Carbonate-Associated Sulfate (CAS) as a Tracer of Ancient Microbial Ecosystems

  The chemical compound sulfate is present in ocean water and ratios of its stable isotopes of sulfur and oxygen have varied over geological time and are indicators of global geochemical processes. Other researchers have extracted trace amounts of sulfate from carbonate minerals of various ages as a glimpse into the Earth’s geological past. We are, however, applying this approach to carbonate minerals formed by microbial processes during burial of sedimentary rocks, which we hoped would give information on the microbial ecosystems. We needed to modify and develop existing methods for extracting the trace amounts of sulfate because our samples would be mineralogically much more complex. Initially, just to test the method we tried it on material from the local Monterey Formation rocks, which are of Miocene age (approx. 13 My old) and were delighted to find that the results enabled us to see the workings of a very complex microbial ecosystem with at least three different sorts of metabolism operating.

  ROADMAP OBJECTIVES: 5.2 6.1 7.1

• Stoichiometry of Life, Task 2a: Field Studies – Yellowstone National Park

  Yellowstone National Park harbors an array of hydrothermal ecosystems with widely varying geochemical characteristics and microbial communities. Our research aimed to understand how the geochemistry of these hot springs shapes their constituent microbial communities including their composition and function. To accomplish this aim, we measured (1) physical and geochemical properties of hot spring fluids and sediments, (2) the rates of biogeochemical processes (i.e., methane oxidation, nitrogen fixation, microbial Fe cycling, photosynthesis, de-nitrification, etc.), and (3) markers for microbial community diversity (i.e., SSU rRNA, metabolic genes, lipids, proteins).

  ROADMAP OBJECTIVES: 5.1 5.2 5.3 6.1 6.2 7.2

• Stoichiometry of Life – Task 2b – Field Studies in Cuatro Cienegas

  We performed two studies to evaluate ecological impacts of nitrogen and/or phosphorus fertilization in a P-deficient and hyperdiverse shallow pond in the valley of Cuatro Cienegas, Mexico.

  ROADMAP OBJECTIVES: 5.1 5.2 5.3 6.1 6.2

• Understanding Past Earth Environments

  This year, this interdisciplinary effort continued on two major fronts. First, we furthered the development and use of new techniques that help us characterize environmental conditions on ancient Earth. This included progress on our development of a technique for estimating the atmospheric pressure on Archean Earth, and the development and use other techniques for analyzing the chemistry of Archean lakes. We also used our existing models of ancient Earth to simulate other conditions consistent with the conclusions reached from these laboratory analyses.

  ROADMAP OBJECTIVES: 1.1 1.2 4.1 4.2 5.1 5.2 6.1

• Stoichiometry of Life – Task 2c – Field Studies – Other

  We performed biogeochemical and microbiological studies of novel aquatic habitats, floating pumice in lakes of northern Patagonia that were derived from the 2011 eruption of the Puyehue / Cordon Caulle volcano in Chile.

  ROADMAP OBJECTIVES: 4.1 5.2 5.3 6.1

• Taphonomy, Curiosity and Missions to Mars

  Members of our team continue to be involved in both the MER and MSL missions on Mars. On the latter mission, team members have recently documented a long-lived, habitable environment in Gale Crater dominated by rivers and lakes. Research on the mineralogy and geochemistry of rocks at the base of Mt Sharp has improved our understanding of their complex diagenetic history. Progress has also been made in linking orbital observations with those made by the rovers; this has been advanced particularly by field research at Rio Tinto and detailed laboratory experiments that constrain the relationship between mineral combinations and their signatures in infrared reflectance spectroscopy—and their effect on our ability to detect organics.

  ROADMAP OBJECTIVES: 2.1 4.1 4.2 6.1 7.1

• Education and Public Outreach

  Our ongoing Education and Public Outreach activities include: (1) a Massively Open Online Course (MOOC) in which over 36,000 students have participated worldwide; (2) workshops for middle school and high school teachers; (3) formal in person and online for-credit courses at the University of Illinois Urbana-Champaign in which 240 students have participated; informal courses in Yellowstone in collaboration with the Yellowstone Association Institute; and (4) ongoing development and writing of a new book.

  ROADMAP OBJECTIVES: 6.1 6.2

• Project 3C: The Role of Early Continental Weathering in Providing a Habitable Planet

  Recent studies of biogeochemical cycles recorded in Archean sedimentary rocks suggest an early diverse microbial ecology that may have required extensive continentally-sourced nutrients (i.e., phosphorus) early in Earth history. Widespread continental weathering is at odds, however, with studies that suggest a majority of continental crust was submerged and seawater chemistry was largely controlled by oceanic hydrothermal fluids. Here, we present new Sr and O isotope results from stratiform barite deposits from the 3.23 Ga Fig Tree Group, South Africa. The Sr and O isotope data indicate the barite was formed from a mixture of hydrothermal fluids and seawater, and that seawater was more radiogenic then previously predicted. The only appreciable source of radiogenic Sr is from continental weathering, and thus we propose that continental weathering was more extensive throughout the Archean than previously thought. This in turn has important implications for the availability of continentally-sourced nutrients to early marine environments on Earth.

  ROADMAP OBJECTIVES: 1.1 4.1 6.1 7.1 7.2

• Project 3D: A Microbial Iron Shuttle in Early Earth Marine Basins

  Iron-based metabolisms are deeply rooted in the tree of life, and yet comparatively little attention has been paid to searching for Fe-based biosignatures as compared, for example, photosynthetically-based metabolisms. Dissimilatory Iron Reduction (DIR) is found in both Archaea and Bacteria domains of life, its electron acceptors and donors are widespread in the solar system. This project focuses on determining the basin-scale footprint of DIR in well preserved samples of Mesoarchean age (~3 Ga) in the Witwatersrand Supergroup of South Africa. Preliminary results show a trend of iron enrichment that correlates with δ⁵⁶Fe depletion from the proximal shelf to the deep distal basin, which is interpreted to indicate a DIR-driven “iron pump” or “shuttle”, where microbially-produced aqueous Fe(II) on continental shelves was pumped to the deep basin and trapped as Fe-bearing sulfides or oxides. These results not only confirm that Fe-based metabolisms were important on the early Earth ~3 b.y. ago, but that it had a substantial “footprint” in the biosphere on a basin-wide scale.

  ROADMAP OBJECTIVES: 4.1 5.2 6.1 7.1 7.2

• Task 4: Biogeochemical Impacts on Planetary Atmospheres

  Oxygenation of Earth’s early atmosphere must have involved an efficient mode of carbon burial. In the modern ocean, carbon export of primary production is dominated by fecal pellets and aggregates produced by the animal grazer community. But during most of Earth’s history the oceans were dominated by unicellular, bacteria-like organisms (prokaryotes) causing a substantially altered biogeochemistry. In this task we experiment with the marine cyanobacterium Synechococcus sp. as a model organism and test its aggregation and sinking speed as a function of nutrient (nitrogen, phosphorus, iron) limitation. We have found that these minute cyanobacteria form aggregates in conditions that mimic the open ocean and can sink gravitationally in the water column. Experiments with added clay minerals (bentonite and kaolinite) that might have been present in the Proterozoic ocean, show that these can accelerate aggregate sinking. In addition we find that Synechococcus could potentially export carbon 2–3 times of that contained in their cells via aggregation, likely due to the scavenging of transparent exopolymer particles and dissolved organic matter. Thus, aggregation and sinking by these small cyanobacteria could have constituted an important mode of carbon export in the Proterozoic ocean.

  ROADMAP OBJECTIVES: 4.1 4.2 5.2 6.1 7.2

• Project 3E: Sulfur-Cycling Fossil Bacteria From the 1.8 Ga Duck Creek Formation Provide Promising Evidence of Evolution’s Null Hypothesis

  In the absence of change in the physical-biological environment, evolution of the fundamental aspects of a well-adapted ecosystem — “the form, function and metabolic requirements” of its components — should not occur. Indeed, documentation of evolution in the absence of such changes would show that current understanding of Darwinian evolution is seriously flawed. The mid-Precambrian 2.3 and 1.8 Ga microbial sulfur-cycling assemblages here studied, the first two fossil communities described from quiescent, deep sea, anoxic subsurface mud, are indistinguishable from their modern counterpart. We regard it likely that other essentially identical ancient sub-seafloor microbial biocoenoses will be discovered and think it probable that this initial work will be regarded as having confirmed the linchpin of Darwinian evolution, its logically required null hypothesis.

  ROADMAP OBJECTIVES: 4.1 5.1 6.1

• Project 3F — Apatitic Latest Precambrian and Early Cambrian Fossils Provide Direct Evidence of Concentrations of Environmental Oxygen

  Means are not currently available to asses either quantitatively or semi-quantitatively the concentration of oxygen in Earth’s atmosphere over geological time. Despite this, the environmental availability of O₂ has been repeatedly postulated to be a cause of major changes in Earth’s biota, most particularly at the Precambrian-Cambrian boundary-defining “Cambrian Explosion of Life,” a time in Earth history when large deposits of phosphate-rich apatite were deposited in shallow basins worldwide. This study shows that substitution of Sm⁺³ in the Ca I and Ca II sites of fossil-permineralizing, -infilling, and -encrusting apatite can differentiate between oxic, dysoxic, an anoxic settings of apatite formation. Further studies are to be undertaken to establish such REE-substitution as a quantitative O₂ paleobarometer.

  ROADMAP OBJECTIVES: 4.1 4.2 6.1 6.2 7.2