nai

Project Reports

• Investigation 1: Habitability of Icy Worlds

  Habitability of Icy Worlds investigates the habitability of liquid water environments in icy worlds, with a focus on what processes may give rise to life, what processes may sustain life, and what processes may deliver that life to the surface. Habitability of Icy Worlds investigation has three major objectives. Objective 1, Seafloor Processes, explores conditions that might be conducive to originating and supporting life in icy world interiors. Objective 2, Ocean Processes, investigates the formation of prebiotic cell membranes under simulated deep-ocean conditions, and Objective 3, Ice Shell Processes, investigates astrobiological aspects of ice shell evolution.

  ROADMAP OBJECTIVES: 2.1 2.2 3.2 4.1 5.1 5.2 5.3 6.2 7.1 7.2

• Biosignatures in Ancient Rocks – Kasting Group

  The work by Ramirez concerned updating the absorption coefficients in our 1-D climate model. Harman’s work consisted of developing a 1-D code for modeling hydrodynamic escape of hydrogen from rocky planets.

  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

• Life Underground

  Our multidisciplinary team from USC, Caltech, JPL, DRI, and RPI 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, 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 seek to carry out in situ life detection and characterization experiments, employ numerous novel and traditional techniques to culture heretofore unknown intraterrestrial archaea and bacteria, and incorporate 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

• Culturing Microbial Communities in Controlled Stress Micro-Environments

  In NAI Theme 4B, our goal in Year 1 has been to initiate our understanding of how cells structure their genomes in response to specific environmental stresses and to determine whether or not such mechanisms have been a major force in directing the evolution of cells in natural environments over evolutionary time. Natural environments are typically rather heterogeneous at small scales, as established by sampling from geothermal hot spring communities, and so it is important to understand the generic impact on the evolution and structure of microbial communities. Our first step towards probing this phenomenon has been to culture living bacterial populations within a small specially constructed microfluidic device (called the GeoBioCell), where strong physical, chemical and biological gradients can be imposed under carefully controlled conditions.

  ROADMAP OBJECTIVES: 3.2 3.4 4.1 4.2 5.1 5.2 5.3 6.1

• Experimental Evolution and Genomic Analysis of an E. Coli Containing a Resurrected Ancestral Gene

  In order to study the historical pathways and modern mechanisms of protein evolution in a complex cellular environment, we combined ancestral sequence reconstruction with experimental evolution. Our first goal was to identify how ancestral states of a protein effect cellular behavior by directly engineering an ancient gene inside a modern genome. We could then identify the evolutionary steps of this organism harboring the ancient gene by subjecting it to laboratory evolution, and directly monitoring the resulting changes within the integrated ancient gene as well as the rest of the host genome.

  ROADMAP OBJECTIVES: 3.4 4.1 5.1 5.2 6.1 6.2

• Biosignatures in Relevant Microbial Ecosystems

  PSARC is investigating microbial life in some of Earth’s most mission-relevant modern ecosystems. These environments include the Dead Sea, the Chesapeake Bay impact structure, methane seeps, ice sheets, and redox-stratified Precambrian ocean analogs. 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.

  PSARC Ph.D. (now postdoctoral researcher at Caltech) Katherine Dawson published a new paper documenting the anaerobic biodegradation of organic biosignature compounds pristane and phytane. PSARC Ph.D. Daniel Jones (now postdoctoral researcher at U. Minnesota) published a new paper that uses metagenomic data to show how sulfur oxidation in the deep subsurface environments may contribute to the formation of caves and the maintenence of deep subsurface microbial ecosystems. PSARC Ph.D. student Khadouja Harouaka published a new paper that represents some of the first available information about possible Ca isotope biosignatures. Lastly, the Macalady group published a paper showing how ecological models based on available energy resources can be used to predict the distribution of microbial populations in space and time.

  ROADMAP OBJECTIVES: 4.1 4.3 5.1 5.2 5.3 6.1 7.1 7.2

• Early Animals: What Made “fronds” Grow in Neoproterozoic Deep Seas?

  Rangeomorph fossils look superficially like plants, however, some lived in aphotic deep water and their nutrition is inferred to involve direct uptake of dissolved resources. We employ models of flow in the rangeomorph community and uptake at the organismal surface to demonstrate how these larger organisms had an advantage over bacteria, despite sharing a similar ecological niche. Through these reconstructions we demonstrate that height provides access to higher velocities in these communities, and under these low-flow conditions, velocity dictates nutrient uptake. Thus we demonstrate the nature of adaptive advantage for larger eukaryotic life forms in the first communities of large organisms in the late Precambrian, just prior to the radiation of animals.

  ROADMAP OBJECTIVES: 4.1 4.2 5.2 6.1

• The Nature of the Last Archaeal and Eukaryal Ancestor

  The evolutionary history of the eukaryotic cell is intimately linked evolution of atmospheric oxygen and with the endosymbiosis of bacterial symbionts to become the mitochondrial organelles. This project seeks to understand the evolutionary history of the eukaryotic cell using contemporary analogs of ancestral anaerobic eukaryotes (rumen ciliates), which are often associated with endosymbiotic archaea and bacteria in tightly associated communities. We study the evolution of this association using state-of-the-art metagenomic and ecological methods to gain a better understanding of the evolution of these types of associations and thus of eukaryotic evolutionary history.

  ROADMAP OBJECTIVES: 3.4 4.1 4.2 5.2 6.1

• Thermodynamics of Life

  Although thermodynamics dictates that all spontaneous processes must be purely dissipative and “destructive” (the notoriously ungenerous face of the “2nd law”), under particular circumstances a spontaneous process can be a compound of two mechanistically coupled sub-processes only one of which (necessarily the larger one), is dissipative while its coupled, lesser partner is literally “driven” to be creative and generative – that is, a process that can “do work”, “build stuff”, and “make things happen”. A system functioning in this way is technically an engine and all living systems are necessarily, examples of such thermodynamically compound and creative “engine” systems – while at the same time operating internally via a complex, interlinked clockwork of such engines.
  Moreover, living systems inherently belong to a special thermodynamic subclass of such engines, namely those that are “autocatalytic” (self-growing and self-stabilizing) in their operation. Arguably, in fact, it is the property of being autocatalytic thermodynamic engines which at root underlies the potency and magic of living systems and which at the same time constitutes life’s most assuredly universal, fundamental, and primitive property. However, as of yet, we understand the implications of these thermodynamic facts quite poorly – notwithstanding that they seem certain to materially impact questions regarding the origin of life, evolutionary dynamics, and community, trophic, and ecology-level organization.
  The present project undertakes to redress this situation to some extent by investigating the formal dynamical behavior of model systems made up of interacting, thermodynamically driven, autocatalytic engines.

  ROADMAP OBJECTIVES: 3.3 3.4 4.2 5.1 5.2

• Genetic Evolution and the Origin of Life

  In this task biologists and chemists use field and laboratory work to better understand the environmental effects on growth rates for freshwater stromatolites and the mechanisms that govern their adaptation to their environment. Stromatolites are microbial mat communities that have the ability to calcify under certain conditions. They are believed to be an ancient form of life, that may have dominated the planet’s biosphere more than 2 billion years ago. Our work focuses on understanding these communities as a means of understanding environmental impacts on evolution, and characterizing their metabolisms and gas outputs, for use in planetary models of ancient environments. This year we also started a new project looking at the chemical affinities of the building blocks of life, as a way to understand how life might have initially formed from these chemical precursors.

  ROADMAP OBJECTIVES: 3.2 3.4 4.1 4.2 5.2 5.3 6.1 6.2

• Subsurface Exploration for Astrobiology: Oceanic Basaltic Basement Biosphere

  While extraterrestrial life is likely to exist within the subsurface of water-occupied objects such as Enceladus and Europa, the continued investigation of the subsurface biosphere on the earth provides important insight and implications for astrobiology. This research investigates a deep sub-seafloor basement biosphere. At the ocean floor, lying underneath an often times thick layer of sediment is hard basaltic rock, or basement. Seawater enters the basement and circulates within. It is now known that low temperature hydrothermal fluids (<100oC) circulate everywhere within the porous and permeable volcanic rocks of the upper ocean basement, providing temperature and chemical gradients that host extensive alteration of basement rocks and fluids and form plausible habitats for microbial life. While microbial activity has been observed in deeply buried sediments and exposed basement rock, few direct tests have been carried out in deep subseafloor basement rocks or fluids. A majority of the crustal hydrothermal flow and seawater-crustal fluid exchange, and the corresponding advective heat and mass output, occurs on the flanks of the mid-ocean ridge with basement ages of >1 million years old. This low-temperature ridge flank flow rivals the discharge of all rivers to the ocean and is about three orders of magnitude greater than the high temperature discharge at mid-ocean ridges. The resulting ridge flank chemical flux impacts ocean biogeochemical cycles and may sustain deep basement microbial communities. Access to uncontaminated fluids from subseafloor basement is problematic, especially where ridge flanks and ocean basins are buried under thick, impermeable layers of sediment (i.e., thick enough to act as a barrier to rapid exchange of fluids). We rely on custom designed instrumentation to collect large volume high integrity basement fluids, where the concentrations of microorganisms are often very low (e.g. about 1/10 of bottom seawater concentrations). By studying the chemical composition of crustal fluids, we have learned that several important energy sources, such as dissolved methane and hydrogen, are available. In addition, the isotopic signature of dissolved methane suggests that microbial production and consumption occurs in the basement environment. By filtering microbial biomass from the fluids and investigating their nucleic acids, we are investigating the evolutionary and functional characteristics of the diverse bacterial, archaeal, and viral communities that inhabit the deep subsurface of Earth. Our on-going research includes the investigation of temporal (at hourly-resolution) and spatial (at a few hundred meter scale) biogeochemical and biological variability in order to more effectively constrain our measured parameters. We are also characterizing the dissolved organic carbon pool in basement fluids to investigate the role that basement environment plays in the global carbon cycle.

  ROADMAP OBJECTIVES: 4.1 5.1 5.2 5.3 6.1 6.2

• Life and Environments: Geochemistry of Late Precambrian Oxygenation

  The first year of work marked a successful transition from the goals and projects defining our last NAI node and the initiation of new, exciting research lines. Recently, our work on the Ediacaran transition in the Earth system culminated in an integrated geochemical study that both covers the state of the late Precambrian world, but also serves as a critical tie point for our upcoming work on Cryogenian ocean and atmospheric chemistry. This entails the extension of similar tools to those we applied in the Ediacaran, as well as the development of a new ¹⁷O system in the Johnston Lab that will serve as a central measurement for the upcoming projects.

  ROADMAP OBJECTIVES: 4.1 4.2 5.2 6.1

• 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 work out what sorts of initial characteristics 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 2E: Carbonate-Associated Sulfate (CAS) as a Tracer of Ancient Microbial Ecosystems

  The iron carbonate mineral, siderite, in sedimentary rocks is usually formed by microbial processes. The presence of small amounts of metals other than iron, and the stable isotope compositions of carbon and oxygen, give information on the details of the microbial ecosystem that produced it and its environment of formation. In particular, if associated with iron sulfide (pyrite), it indicates the former presence of at least two different microbial metabolic processes. In addition, carbonate minerals can contain trace amounts of the chemical compound sulfate, in which the isotopic compositions of sulfur and oxygen reveal further details of the microbial process if that sulfate can be released unaltered from the minerals. Our first challenge in this project has been to develop a method for releasing the original, preserved sulfate without contaminating it with somewhat similar material produced from oxidation of pyrite as an artifact of the preparation method.

  ROADMAP OBJECTIVES: 5.2 6.1 7.1

• Molecular Biosignatures: Reconstructing Events by Comparative Genomics

  Reconstructing ancient events in genome evolution provides a valuable narrative for planetary history. Phylogenetic analysis of protein families within microbial lineages can be used to detect horizontal gene transfers and the evolution of new metabolic pathways and physiologies, many of which are significant in reconstructing ancient ecologies and biogeochemical events. These gene transfers can also be used to constrain molecular clock models for early life evolution, applying principles of stratigraphy and date calibration. A better understanding of gene evolution, including partial horizontal gene transfer, is needed to improve these inferences and avoid systematic errors.

  ROADMAP OBJECTIVES: 3.2 3.4 4.1 4.2 4.3 5.1 5.2 6.1

• Understanding Past Earth Environments

  For much of the history Earth, life on the planet existed in an environment very different than that of modern-day Earth. Thus, the ancient Earth represents a planet with a biosphere that is both dramatically different than the one in which we live, but that is also accessible to detailed study. As such, it serves as a model for what types of biospheres we may find on other planets. A particular focus of our work was on the “Early Earth” (formation through to about 500 million years ago), a timeframe poorly represented in the geological and fossil records but comprises the majority of Earth’s history. We have studied the composition, pressure and climate of the ancient atmosphere; the delivery of biologically available phosphorus; studied the sulfur, oxygen and nitrogen cycles; and explored atmospheric formation of molecules that were likely important to the origins of life on Earth.

  ROADMAP OBJECTIVES: 1.1 1.2 4.1 4.2 5.1 5.2 6.1

• Project 3A: Banded Iron Formation Deposition Across the Archean-Proterozoic Boundary

  Prior to widespread oxygenic photosynthesis, reduced iron, Fe(II), was the dominant form of soluble iron in surface environments on the early Earth, and likely Mars. On Earth, extensive iron deposits, Banded Iron Formations (BIFs), which currently supply the majority of the iron used in our society, largely formed prior to the Great Oxidation Event of ~2.4 Ga age, and yet contain substantial quantities of oxidized iron, Fe(III). The pathways by which these different oxidation states arose remains unclear. In addition, the chemical and isotopic compositions of BIFs have been used as proxies for ancient seawater or paleoenvironments. In competition with this proposal, however, has been use of BIFs as a tracer of microbial iron cycling. To test the use of BIFs as ambient paleoenvironmental proxies or proxies of microbial process, BIFs from South Africa and Australia were examined from the micron scale to the 100’s of meter scales. We find that BIFs tend to record specific pathways of oxidation of Fe(II), as well as reduction of Fe(III), and extensive post-depositional changes, and it may be quite difficult to infer ambient paleoenvironmental conditions form such deposits.

  ROADMAP OBJECTIVES: 2.1 4.1 5.2 6.1 7.1 7.2

• Project 3B: Carbon Isotope Analysis of Archean Microfossils

  We have completed a study of petrography, Raman microspectroscopy, and in situ analyses of carbon isotope and H/C ratios using secondary ion mass spectrometry (SIMS) of diverse organic microstructures, including possible microfossils. This work has focussed on two localities of the 3.4-billion-year-old Strelley Pool Formation (Western Australia). For the first time, we show that the wide range of carbon isotope ratios recorded at the micrometer scale correlates with specific types of texture for organic matter (OM), arguing against abiotic processes to produce the textural and isotopic relations. These results support the biogenicity of OM in the Strelley Pool Formation.

  ROADMAP OBJECTIVES: 1.1 2.1 4.1 4.2 5.2 6.2 7.2

• Neoproterozoic Aerobic Transition

  The Proterozoic carbon isotopic record contains evidence of a series of large perturbations to the global carbon cycle, some or all of which may be associated with changes in atmospheric O₂. Our team is formulating a theoretical model to explain not only these disruptions but also the permanent increase in O₂ levels that occurred by the end of the Proterozoic.

  ROADMAP OBJECTIVES: 1.1 4.1 4.2 5.2 6.1

• 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 3C: Carbon Isotope Analysis of Proterozoic Microfossils

  We have developed procedures for accurate in situ analysis of carbon isotope ratios by SIMS for individual Precambrian microfossils of unquestioned biogenicity. Data for three Proterozoic localities show a consistent fractionation of 19 per mil between organic matter and coexisting carbonates, in spite of over 6 per mil variability from rock to rock, consistent with fractionations seen for modern cyanobacteria. In one sample, a phytoplanktonic protistan acritarch, found within the same mm-scale domains, are 6 per mil more fractionated, consistent with photosynthetic eukaryotes. These findings show for the first time the possibility of using in situ isotopic microanalysis of fossil microbial mats and ancient sediments in order to distinguish metabolic fingerprints within complex microbial ecosystems and consortia.

  ROADMAP OBJECTIVES: 2.1 4.1 4.2 5.2 7.2

• 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

• Project 3D: Microfossil Insights Into Proterozoic Microbial Ecology

  In a study of the chert-permineralized 1.8 Ga Duck Creek Dolomite, and underlying units, Western Australia, Schopf found that in sequences of 2.3 to 1.8 Ga age that indicate little environmental change, there has been no evolution of the form, function, or metabolic requirements of its biotic components. In a second study of sulfur-cycling bacteria from the 775 Ma chert-permineralized Bambui Group of Brazil, Schopf showed that pyritized microbes of this age were anaerobic sulfur-cyclers. This work, in addition to previous studies, forms the basis for ongoing studies of the biotic response to the Great Oxidation Event.

  ROADMAP OBJECTIVES: 4.1 5.1 5.2 6.1 7.2

• Stoichiometry of Life – 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 cyano-bacterium Synechococcus sp. as a model organism and test its aggregation and sinking speed as a function of nutrient (nitrogen, phosphorus, iron) limitation. So far, 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.

  ROADMAP OBJECTIVES: 4.1 4.2 5.2 6.1 7.2

• 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 aims to understand how the geochemistry of these hot springs shapes their constituent microbial communities including their composition and function. To accomplish this aim, we measure (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 – Cuatro Cienegas

  Cuatro Cienegas is a unique biological preserve in México (state of Coahuila) in which there is striking microbial diversity, potentially related to extreme scarcity of phosphorus. We aim to understand this relationship via field sampling of biological and chemical characteristics and a series of enclosure and whole-pond fertilization experiments. 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

• Stoichiometry of Life, Task 3b: Ancient Records – Genomic

  Task 3b team members are involved in deciphering genomic records of modern organisms as a way to understand how life on Earth evolved. At its core, this couples the integrated measurement and modeling of evolutionary mechanisms that drove the differences between extant genomes (and metagenomes), with experimental data on how environmental dynamics might have shaped these differences across geological timescales. This goal draws from team members’ expertise encompassing theoretical and computational biology, microbial evolution, and studying life in both extreme and dynamic environments across the planet.

  ROADMAP OBJECTIVES: 5.1 5.2 5.3