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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

• 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

• 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

• 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

• Project 1A: Detection of Biosignatures in Extreme Environments and Analogs for Mars

  Sulfate, a chemical form containing sulfur and oxygen, is present in ocean water and is a component of minerals on Earth and on Mars, created by evaporation of such water. We have been measuring variations in the relative abundances of naturally-occurring, non-radioactive oxygen isotopes in sulfate to indicate what processes were involved in sulfate formation: for example microbes gaining energy from sulfide or via a non-biological route. A precursor chemical in the formation of sulfate is sulfite, containing sulfur and just a little less oxygen. We have shown recently that the oxidation of sulfite (adding more oxygen), governs the oxygen isotope composition of sulfate. This work will be of significant importance in helping us to understand conditions of formation of ancient minerals.

  ROADMAP OBJECTIVES: 5.3 7.1

• 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

• Investigation 2: Survivability on Icy Worlds

  Investigation 2 focuses on survivability. As part of our survivability investigation, we examine the similarities and differences between the abiotic chemistry of planetary ices irradiated with ultraviolet photons (UV), electrons, and ions, and the chemistry of biomolecules exposed to similar conditions. Can the chemical products resulting from these two scenarios be distinguished? Can viable microbes persist after exposure to such conditions? These are motivating questions for our investigation.

  ROADMAP OBJECTIVES: 1.1 2.2 3.2 5.1 5.3 6.1 6.2

• Investigation 3: Detectability of Icy Worlds

  Detectability of Icy Worlds investigates the detectability of life and biological materials on the surface of icy worlds, with a focus on spectroscopic techniques, and on spectral bands that are not in some way connected to photosynthesis.The primary component of Investigation 3 is the field campaign in Barrow, AK to characterize and quantify methane release from the Alaskan North Slope region and to understand the origin and fate of the methane.

  ROADMAP OBJECTIVES: 1.1 2.2 5.3 6.1 6.2

• Mineralogical Traces of Early Habitable Environments

  The goal of our work is to understand how habitability (potential to support life) varies across a range of physical and chemical parameters, in order to support a long term goal of characterizing habitability of environments on Mars.
  The project consists of two main components:
  1. We are examining the interplay between physicochemical environment and associated microbial communities in a subsurface environment dominated by serpentinization (a reaction involving water and crustal rocks, which indicated by surface mineralogy to have occurred on ancient Mars).
  2. We are working to understand how mineral assemblages can serve as a lasting record of prior environmental conditions, and therefore as indicators of prior habitability. This component directly supports the interpretation of mineralogy data obtained by the CheMin instrument on the Mars Science Laboratory.

  ROADMAP OBJECTIVES: 2.1 5.3

• Dynamics of Self-Programming Systems

  Living systems are unique in that they have the capacity to evolve. Evolving systems can reprogram themselves and so they are able to respond to perturbations by creating new functionality. This feature is something very different from physical systems, which obey a fixed or predetermined equation of motion. This project is a theoretical attempt to describe this state of affairs mathematically, and to construct computer programs that have the capacity to evolve and thus become more complex without this being “built in” by the original programmer.

  ROADMAP OBJECTIVES: 3.2 4.1 4.2 5.3 6.2

• Extremophile Ribosomes

  Many animals share a common response to environmental stresses. The responses include reorganization of cellular organelles and proteins. Similar stress responses between divergent species suggest that these protective mechanisms may have evolved early and been retained from the earliest eukaryotic ancestors. Many eukaryotic cells have the capacity to sequester proteins and mRNAs into transient stress granules (SGs) that protect most cellular mRNAs. Our observations extend the phylogenetic range of SGs from trypanosomatids, insects, yeast and mammalian cells, where they were first described, to a species of the lophotrochozoan animal phylum Rotifera. We focus on the distribution of three proteins known to be associated with both ribosomes and SG formation: eukaryotic initiation factors eIF3B, eIF4E and T-cell-restricted intracellular antigen 1. We found that these three proteins co-localize to SGs in rotifers in response to temperature stress, osmotic stress and nutrient deprivation as has been described in other eukaryotes. We have also found that the large ribosomal subunit fails to localize to the SGs in rotifers. Furthermore, the SGs in rotifers disperse once the environmental stress is removed as demonstrated in yeast and mammalian cells. These results are consistent with SG formation in trypanosomatids, insects, yeast and mammalian cells, further supporting the presence of this protective mechanism early in the evolution of eukaryotes.

  ROADMAP OBJECTIVES: 3.2 4.2 5.3

• Project 1E: Metagenomic Analysis of Novel Chemolithoautotrophic Bacterial Cultures

  Metagenomic sequence information was obtained from two chemolithoautotrophic bacterial cultures: (1) an iron-oxidizing, nitrate-reducing culture that is capable of growth with either soluble or insoluble, mineral-bound (biotite, smectite) Fe(II) as the sole energy source; and (2) an aerobic iron/sulfur-oxidizing culture that grows with insoluble framboidal pyrite as the sole energy source. Both of these cultures carry-out novel neutral-pH lithotrophic microbial pathways, the discovery of which broadens our view of potential Fe/S based life on Earth (past and present) and other rocky planets. We hypothesize that genetic components of Fe/S oxidation identified in the metagenome of the cultures will bear resemblance to analogous components to be identified in other iron-oxidizing pure cultures being sequenced at JGI, together with existing published and unpublished information from other chemolithoautotrophic microorganisms. Identification of such genetic systems will enable comparative genomic analysis of mechanisms of extracellular phyllosilicate Fe/S redox metabolism, and facilitate development of techniques to detect the presence and expression of genes associated with chemolithotrophic Fe/S metabolism in various terrestrial environments.

  ROADMAP OBJECTIVES: 3.2 5.1 5.3 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

• Project 1F: Organics Exposure in Orbit (OREOcube): A Next-Generation Space Exposure Platform

  The OREOcube (ORganics Exposure in Orbit cube satellite) experiment on the International Space Station (ISS) investigates the effects of solar and cosmic radiation on organic thin films. By depositing organic samples onto inorganic substrates, structural changes and photo-modulated organic-inorganic interactions are examined to study the role that solid mineral surfaces play in the photo-chemical evolution, transport, and distribution of organics. The results of these experiments in low Earth orbit (LEO) allow extrapolation to different solar system and interstellar/interplanetary environments. Organic molecules appropriate for study in thin-film form include biomarkers such as amino acids and nucleobases, as well as polyaromatic hydrocarbons (PAHs), redox molecules, and organosulfur compounds. Inorganic substrates include silicates, metal oxides, iron sulfides, nano-phase iron, and iron-nickel alloys. By measuring changes in the UV-vis-NIR spectra of samples as a function of time in situ on the ISS, OREOcube will provide data sets that capture critical kinetic and mechanistic details of sample reactions that cannot be obtained with current exposure facilities in LEO. Combining in situ, real-time kinetic measurements with post-flight sample analysis will provide time-course studies, as well as in-depth chemical analysis, enabling us to characterize and model the chemistry of organic species associated with mineral surfaces in the astrobiological context.

  ROADMAP OBJECTIVES: 3.1 5.3 7.1

• 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

• Water and Habitability of Mars and the Moon and Antarctica

  Water plays an important role in shaping the crusts of the Earth and Mars, and now we know it is present inside the Moon and on its surface. We are assessing the water budgets and total inventories on the Moon and Mars by analyzing samples from these bodies.

  We also study local concentrations of water ice on the Moon, Mars, and at terrestrial analogue sites such as Antarctica and Mauna Kea, Hawaii. We are particularly interested in how local phenomena or microclimates enable ice to form and persist in areas that are otherwise free of ice, such as cold traps on the Moon, tropical craters with permafrost, and ice caves in tropical latitudes. We approach these problems with field studies, modeling, and data analysis. We also develop new instruments and exploration methods to characterize these sites. Several of the terrestrial field sites have only recently become available for scientific exploration.

  HI-SEAS (Hawaii Space Exploration Analog and Simulation, hi-seas.org) is a small habitat at a Mars analog site in the saddle area of the Island of Hawaii. It is a venue for conducting research relevant to long-duration human space exploration. We have just completed our first four-month long mission, and are preparing for three more, of four, eight and twelve months in length. The habitat is a 36’ geodesic dome, with about 1000 square feet of floor space over two stories. It is a low-impact temporary structure that can accommodate six crewmembers, and has a kitchen, a laboratory, and a flexible workspace. Although it is not airtight, the habitat does have simulated airlock, and crew-members don mockup EVA suits before going outside. The site is a disused quarry on the side of a cinder/splatter cone, surrounded by young lava fields. There is almost no human activity or plant life visible from the habitat, making it ideal for ICE (isolated/confined/extreme) research.

  ROADMAP OBJECTIVES: 1.1 2.1 3.1 5.3 6.1 6.2 7.1

• Molecular Biosignatures: Hopanoid Sources in Modern Systems

  Molecular fossils preserved in sedimentary rocks provide a record of Earth’s early biosphere and its associated carbon cycle. Among the earliest and most abundant molecular fossils are the hopanoids. Derived primarily from bacteria, their diagenetic products, the hopanes, are detectable over timescales of billions of years and have been proposed to be among the most abundantly preserved molecules on Earth. However, an overall picture of their environmental, physiological, and taxonomic origins remains elusive. Are they primarily remnants of primary producers or of heterotrophic consumers? Do they primarily come from free-living marine communities, or from shallow mats, tidal zone communities, or even terrigenous runoff? Here we aim to obtain compound-specific carbon isotope data for hopanoids to infer their sources in modern systems, as proxies for understanding ancient environments.

  ROADMAP OBJECTIVES: 3.2 5.1 5.3 6.1

• The Long Wavelength Limit of Oxygenic Photosynthesis

  Oxygenic photosynthesis (OP) produces the strongest biosignatures at the planetary scale on Earth: atmospheric oxygen and the spectral reflectance of vegetation. Both are controlled by the properties of Chlorophyll a, its ability to perform the water-splitting to produce oxygen, and its spectral absorbance that is limited to red and shorter wavelength photons. We seek to answer what is the long wavelength limit at which OP might remain viable, and how. This would clarify whether and how to look for OP adapted to the light from red dwarfs or M stars, which emit little visible light but abundant far-red and near-infrared. Very recently discovered cyanobacteria have been found to harbor alternative chlorophylls adapted to spectral light environments very much like that of M stars. This projects uses field, lab, and modeling studies to study these far-red adapted cyanobacteria as analogues for extrasolar oxygenic photosynthesis pushing the long wavelength limit.

  ROADMAP OBJECTIVES: 3.2 4.2 5.1 5.3 6.2 7.2

• Molecular Biosignatures: Preservation in Mineral-Forming Ecosystems

  Molecular biosignatures are an important and informative means to reconstruct ancient ecosys-tems, especially, in the case of those dominated by microbes. Most microbes leave only fragmentary chemical records and fossilized hard-parts confined to those taxa with mineralized tests. Preservation can be significantly enhanced when these molecular biosignatures are encapsulated in minerals which are actively forming where the microbes are living and where they may be sequestered from the deleterious effects of oxygen and radiation. We studied several such organo-mineral associations comprising carbonate, silica and gypsum and document a diverse range of molecular biosignatures some of which would be preservable over long timescales. These results are relevant for the study of sediments on the ancient earth, but are also useful in predictive sense for the study of minerals on other planets.

  ROADMAP OBJECTIVES: 5.1 5.3 7.1

• 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

• Task 3.5.1: Titan as a Prebiotic Chemical System

  Six years ago, NASA sponsored a National Academies report that asked whether life might exist in environments outside of the traditional habitable zone, where “weird” genetic molecules, metabolic processes, and bio‐structures might avoid the water‐based biochemistry that is found across the terran biosphere. In pursuit of this “big picture” question, we turned to Titan, which has exotic solvents both on its surface (methane‐hydrocarbon) and sub‐surface (perhaps super‐cooled ammonia‐rich water). This work sought genetic molecules that might support Darwinian evolution in both environments, including non‐ionic polyether molecules in the first and biopolymers linked by exotic oxyanions (such as phosphite, arsenate, arsenite, germanate) in the second. Further, we asked about the possibility that Titan might inform our understanding of prebiotic chemical processes, including those on “warm Titans”. Our experimental activities found few possibilities for non‐phosphate-based genetics in subsurface aqueous environments, even if they are rich in ammonia at very low temperatures. Further, we showed that polyethers are insufficiently soluble in hydrocarbons at very low temperatures, such as the 90‐100 K found on Titan’s surface. However, we did show that “warm Titans” could exploit propane as a biosolvent for certain of these “weird” alternative genetic biopolymers; propane has a huge liquid range (far larger than water). Further, we integrated this work with other work that allows reduced molecules to appear as precursors for more standard genetic biomolecules, especially through interaction with various mineral species.

  ROADMAP OBJECTIVES: 1.1 1.2 2.2 3.1 3.2 4.1 4.2 5.3 6.2 7.1 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

• 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