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Project Reports

• Life Underground

  Our multi-disciplinary team from the University of Southern California, California Institute of Technology, Jet Propulsion Lab, Desert Research Institute, Rensselaer Polytechnic Institute, and Northwestern University 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 3.2 3.3 4.1 5.1 5.2 5.3 6.1 6.2 7.2

• Project 1: From Generalist to Specialists (Or Not): A Case Study in Enzyme Evolution

  Metabolic enzymes, although prodigious catalysts, are not perfectly specific for their physiological substrates. They typically possess secondary activities as a consequence of the assemblage of highly reactive functional groups, metal ions and cofactors in their active sites. Secondary activities that are physiologically irrelevant, either because they are too inefficient to contribute to fitness or because the enzyme never encounters the substrate, are termed promiscuous activities.

  Promiscuous activities are important from an evolutionary standpoint because they provide a reservoir of catalytic potential within a proteome that can be drawn upon when the environment changes. A promiscuous activity may become important for fitness when a new source of carbon, nitrogen or phosphorous appears in the environment, or when a previously available compound, such as an amino acid or cofactor, becomes unavailable. A promiscuous activity may also become critical when the organism is exposed to a novel toxin, such as an antibiotic or pesticide.

  A newly recruited promiscuous activity is unlikely to be the optimal solution to an environmental challenge or opportunity. In this project, we are using a model system in E. coli to characterize the genetic changes by which a gene encoding an enzyme whose promiscuous activity has become essential for growth duplicates and diverges to encode a pair of genes encoding efficient specialist enzymes. This work will provide a better understanding of the process by which large superfamilies of enzymes have diverged from generalist enzymes in the last universal common ancestor.

  ROADMAP OBJECTIVES: 5.1 5.3 6.2

• Field Activities at the Coast Range Ophiolite Microbial Observatory (CROMO)

  CROMO provides ongoing excellent exposure to samples of ophiolite-hosted serpentinites and associated rocks, access to monitoring wells important for observing serpentinization-related groundwater flow regimes, and serves as a community-building platform that fosters new scientific collaboration. CROMO has served as a test-bed for refining new experimental approaches, and progressing from basic observations to more complex, multi-disciplinary science.

  Within the past year, studies at CROMO have focused on the subsurface hydrogeochemical dynamics, by monitoring groundwater hydrology, measuring the concentrations and composition dissolved iron, sulfur, dissolved inorganic carbon, major inorganic anions and cations, dissolved hydrogen, carbon monoxide and methane gases, and organic compounds, in addition to time-series analyses.

  CROMO datasets are being incorporated into an exploratory database project aimed at addressing NASA’s public data requirements. Once developed, this database will help to address data sharing plans for collaborators and serve as a valuable tool for CROMO data management across collaborating labs.

  In 2015, project members Dawn Cardace, Masako Tominaga, Michael Kubo, Lauren Seyler, Mary Sabuda, Abigail Johnson, Ken Wilkinson, & Cameron Hearne participated in a field trip to CROMO from August 21-27, to continue seasonal bio/geo/chemical monitoring of the wells, as well as assessing the site for future geophysical measurements.

  ROADMAP OBJECTIVES: 5.1 5.2 5.3 6.1 6.2 7.1 7.2

• Project 2: Function by Reduction: Do Extant Symbiont Enzymes Recapitulate Ancient Metabolic Generalists

  The origins of mitochondria and chloroplasts are two of the great unsolved mysteries in biology. It is now clear that these organelles used to be bacteria, but the evolutionary paths taken as they transitioned from bacteria to organelle are not well understood because they happened more than 1.5 billion years ago. Some insect endosymbionts have symbioses with bacteria which resemble organelles in many ways. We use these more recent symbioses as models to better understand the origins of organelles, one of the most critical events in the evolution of complex life.

  ROADMAP OBJECTIVES: 4.2 5.2 6.2

• Inv 3 – Planetary Disequilibria: Characterizing Ocean Worlds and Implications for Habitability

  INV 3 looks at how, where, and for how long might
disequilibria exist in icy worlds, and what that may imply in terms of
habitability. A major interest for this work is how ocean composition affects habitability. We are investigating chemistry behaves under conditions of pressure, temperature, and composition not found on Earth. Our simulations of deep ocean world chemistry couple with models for ocean dynamics, ocean ice interaction, and tectonics within the ice. We are examining each of these, how they interact, and how they relate to what future missions may discover. Members of our team are involved in missions to Mars, Jupiter’s moon Europa, Saturn, and Pluto. We are also involved in studies of exoplanets, and are working to understand how ocean worlds like Ganymede and Europa might provide analogues for more distant watery super-earths.

  ROADMAP OBJECTIVES: 1.1 1.2 2.2 3.1 4.2 6.2 7.1 7.2

• Project 3: Theory for the Darwinian Transition

  One of the key puzzles of astrobiology concerns the precision, uniqueness and rapidity of early evolution. In order for life to have evolved the main components of the modern cell as early 3.8 billion years ago, with a unique genetic code that is virtually optimal in terms of minimizing translational errors, the mode of evolution would have had to be different from the current vertical transmission of genes. We had shown in 2006 that the collective mechanism of horizontal gene transfer (HGT) is the only one capable of solving the puzzle of early evolution. The HGT means that the evolutionary process before LUCA can be thought of as a network of interactions rather than a tree, as would be the case in vertical gene transfer. The multiple connectivity of the network accelerates the evolution and allows rapid convergence to a unique, near-optimal genetic code. With all these advantages of HGT, why would it ever stop? Our project uses computer simulation of digital organisms in order to address these generic questions about the exit of life from the collective, progenote phase to the current era of vertically dominated evolution.

  This project is potentially important for understanding biosignatures of life. Even on Earth, we are familiar with the tree-like structure of individual organismal lineages. If life were a network, as we believe that it once was, the usual phylogenetic pattern of individuality and species would not apply. If we encounter life on other planets, we cannot be sure if it will be in the collective (progenote) phase or the vertical-dominated phase. Thus it is interesting to understand better the inexorability and timing of the Darwinian Transition.

  ROADMAP OBJECTIVES: 3.2 3.4 4.1 4.2 5.1 6.2

• Project 3: Consequences of recA Duplication for Recombination, Genome Stability and Fitness

  Homologous recombination (HR) – the exchange of genetic information between similar DNA molecules – is an ancient process that is central to the emergence of biological complexity, diversity and stability. Yet, it must be tightly regulated, as it is likewise an important source of destabilizing genomic rearrangements. Despite the importance of HR, we still have a poor understanding of the balance of these creative, stabilizing and destabilizing contributions to organismal fitness, complexity and genome evolution. We are using the extraordinary genome evolutionary dynamics and duplicated copies of the HR gene recA in the cyanobacterium Acaryochloris as a model to gain novel insights on the fitness consequences that emerge from the interplay between HR-mediated maintenance of genome stability, selectively favored gene duplications and non-adaptive genomic rearrangements.

  ROADMAP OBJECTIVES: 4.2 5.1 5.3 6.1 6.2

• Project 4: Co-Evolution of Escherichia Coli and Its Parasite Bdellovibrio Bacteriovorus: An Experimental Model for Eukaryogenesis

  This project seeks to address a long-standing question in the early evolution of life on Earth: how and why did simpler cell types (prokaryotes) transition into more complex (eukaryotic) cells (i.e. eukaryogeneis)? Because this conversion happened millions of years ago and left scant fossil evidence, we have been attempting to “re-create” a similar transformation in the lab that can be easily manipulated and studied in detail. A greater understanding of the events that ocurred both before and after eukaryogenesis will not only help NASA scientists predict what extraterrestrial life might look like, it will also help us understand how modern eukaryotic cells function and evolve.

  ROADMAP OBJECTIVES: 3.3 3.4 5.1 6.2

• Mars Analogs: Habitability and Biosignatures in the Atacama Deser

  This project focuses on the study of habitability in the Atacama Desert of northern Chile, one of the driest regions on Earth. We want to understand how life adapts and survives in an environment where liquid water is exceedingly rare, and how biosignatures are preserved in that environment after microorganisms die. These studies can become a very useful guide for future robotic missions to Mars. This year we focused on microbial communities that inhabit the interior of salt nodules in evaporitic lake deposits. These are the only known active microbial comunities in the driest parts of the Atacama. We wanted to understand how these microbial communities survive in an environment that excludes every other form of life. We suspected that the salt communities use atmospheric water vapor as a source of water to run their metabolic processes. We showed that this is indeed the case with a combination of field and laboratory tools. Our results suggest that the salt substrate could be one of the last possible habitats for life in extremely dry environments.

  ROADMAP OBJECTIVES: 2.1 5.1 5.3 6.1 6.2 7.1 7.2

• Project 5: Adaptation, Mutation Supply, and Evolution of Synergy in Biofilm Communities

  We will quantify the dynamics of adaptation and identify the mutational causes in evolving biofilms with high precision, and therefore illustrate how microbes colonizing a new surface can transform their environment and set the stage for primitive multicellularity. Biofilms resemble tissues in their subdivided labor, varied physical structure and shared metabolism. We predict that the stability of this ecological cooperation rests on population-genetic controls on selfish lineages associated with mutators, much as tissues are liable to selfish invasion by cancers.

  ROADMAP OBJECTIVES: 4.2 5.1 5.2 6.1 6.2

• Project 6: Life’s Diversity

  This project is on the theoretical modeling of life’s complexity and diversity, where we are modeling evolvability, diversity, and complexity in mathematical terms. Since these models are of high complexity, we are employing asymptotic and other approximate methods for their solution.

  ROADMAP OBJECTIVES: 4.2 6.2

• Project 6: The Evolution of Complexity via Multicellularity and Cellular Differentiation

  The evolution of multicellular organisms from single-celled ancestors set the stage for unprecedented increases in complexity, especially in land plants and animals. We have used the unicellular green alga Chlamydomonas reinhardtii to generate de novo origins of simple (undifferentiated) multicellularity in two separate experiments. Using these experimentally evolved algae, we will ascertain the genetic bases underlying the evolution of multicellularity, evaluate the role of genetic assimilation in the evolution of multicellularity, and observe the evolutionary origin of multicellular development in real time.

  ROADMAP OBJECTIVES: 4.2 5.1 6.2

• Subglacial Environments as Water‐Rock Hosted Microbial Ecosystems

  Glaciers, ice sheets and ice caps cover ~11% of the earth’s surface, and likely covered up to 100% during Neoproterozoic glaciations. The beds of these ice masses can have significant sectors at the pressure melting point. The resulting water lubricates ice sliding and accelerates erosion, provides habitat for subglacial microbial ecosystems, and may have acted as refugia during past global glaciations on Earth. Such environments may also act as habitats for life on other planetary bodies.

  Grinding of bedrock by glaciers exposes fresh mineral surfaces capable of sustaining microbial metabolism. The foci of RPL investigations on subglacial environments are categorized into two key areas of relevance to habitability studies: i) determine the extent to which minerals support chemotrophic metabolism and the production of biosignatures (e.g., weathering products), and ii) quantifying the influence of water-rock interactions in supplying substrates to support energy metabolism. Through these interdisciplinary and collaborative studies, we aim to characterize the active microbial processes in subglacial environments and to define the sources of energy that sustains this microbial life.

  ROADMAP OBJECTIVES: 2.1 5.1 5.2 5.3 6.1 6.2 7.2

• Project 7: Mining Archaeal Genomes for Signatures of Early Life: Comparison of Metabolic Genes in Methanogens

  Methanogens represent the largest diversity among the archaea and have the unique ability to generate methane from simple compounds such as carbon dioxide, acetate and methylamines which were common in the anaerobic environments of early Earth and perhaps Mars. Methane biosynthesis also requires the presence/uptake of important ions such as sulfates, sulfides, carbonates, phosphates, and various light metal ions. In this project, we are attempting to analyze the evolution of the methanogens’ central cellular functions of translation, transcription, replication, and metabolism. To accomplish this, we are constructing the metabolic and regulatory networks of Methanosarcina acetivorans, the most complex methanogen known, and using these models to establish a framework for studying the evolution of methanogens. Results will be tested through microfluidic studies using varying carbon and ion sources.

  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

• Project 7: Error Rate and the Origin and Early Evolution of Life

  Our project investigates the evolutionary relationship between rates of genetic mutation and genetic recombination. It addresses very general questions about the stability of heredity and the implications of that stability for adaptation and persistence of organisms. Such questions are likely to apply wherever and whenever life evolves. In prior theory work we have shown that the mutation rate of a population will tend towards ever-higher values in the absence of genetic recombination. Because mutation is the ultimate source of the variation required for the evolution of a population, it might be thought that a high mutation rate would enable more rapid evolutionary adaptation. We and others have shown, however, that too high a mutation rate can cause extinction of a population. Because early life probably had very high mutation rates, early life would have been at considerable risk of evolving a lethal mutation rate. This should have produced strong pressure for genetic recombination to evolve. In our project we are using experimental evolution, analytical theory, and computer simulations to test the effect that recombination has on mutation rate evolution, the effect that high mutation rates have on population adaptation and persistence, and the effect of mutation on the evolution of cooperation among life forms.

  ROADMAP OBJECTIVES: 4.2 5.2 6.2

• Project 8: Limits to Optimality in Adaptive Evolution

  The goal of this project is to determine how the genetic makeup of an organism influences its future evolution. We have developed a tracking system that allows us to track the emergence of mutations that make an organism more fit in a certain environment – we will be deploying this system to track such emergences in yeast strains with slightly different genetic makeup. This will allow us to see how the genetic makeup influences the evolutionary process.

  ROADMAP OBJECTIVES: 5.1 6.2

• Project 8: The Evolution of the Eukaryote-Archaea Common Ancestor

  The goals of our lab with respect to the NAI project are to describe early evolutionary via genomic and cellular comparisons of diverse eukaryotes to diverse archaea. We are interested in comparing genomes from diverse free-living eukaryotes to investigate the origins and evolution of eukaryotic complexity. Evolutionary reconstructions of early eukaryotes are challenged by a lack of sufficient taxonomic sampling. Few genomes of free-living microbial eukaryotes are sequenced, despite their critical importance in ecology, evolution, and basic cellular biology. The real challenge to protistan genomics is actually quite mundane; it concerns the lack of available and cultivatable free-living protists (mainly heterotrophs) in the laboratory. Yet, a better understanding of the genomic content diverse eukaryotes facilitates the evolutionary analysis of archaeal genomes. To address these issues of poor taxonomic sampling of eukaryotic genomes, my lab has developed a molecular method to separate eukaryotic DNA from bacterial DNA. We have demonstrated conclusively that we can separate eukaryotic chromatin from a mixture of eukaryotic and bacterial genomic DNA. This method will be widely applicable to the study of protistan genomics. Currently, our lab is in the process of assembling and annotating ten eukaryotic genomes from my lab’s culture collection of over 100 amoeboid protists from diverse phylogenetic groups. Many of these amoeba represent novel phyla-level lineages of eukaryotes.

  One amoebal genome is form is Nuclearia sp., which is an amoeboid protist closely and a member of a primary “supergroup” of eukaryotes – the Optisthokonts. This supergroup includes all animals, fungi, and several types of unicellular or colonial protists including choanoflagllates. Thus, genomic analyses of Nuclearia will inform the evolution of complexity and multicelllularity in both Fungi and Animals.

  ROADMAP OBJECTIVES: 3.2 3.4 4.2 6.2

• Rock Powered Life: Education and Communications

  The central theme of the Rock Powered Life research effort is to define how, where and when water/rock interactions release energy and how this energy is harvested to support microbial communities. These studies are of fundamental importance for improving understanding of how microbial life was supported on early Earth. Moreover, since similar reactions can be expected on any rocky planet with liquid water, these studies provide new constraints for predicting the distribution of life on other planetary bodies.

  The focus of our team – rock-hosted microbial ecosystems that are dependent on chemical rather than light energy – provides novel avenues to engage the next generation of astrobiologists and to disseminate knowledge to the broader public. Here we describe current and ongoing efforts by members of Rock Powered Life that are aimed at improving engagement and training in astrobiology. Of particular relevance are efforts to provide opportunities to provide underrepresented high school and undergraduate students hands on training opportnities in astrobiology-focused studies. We also describe advancements in Rock Powered Life’s digital-based information sharing technologies. Through these integrated team efforts we aim to attract and train future generations of astrobiologists and to provide greater access to the current knowledge base with which to understand the potential for life elsewhere on other planetary bodies.

  ROADMAP OBJECTIVES: 3.2 4.1 4.2 5.1 5.2 5.3 6.1 6.2

• Project 9: Metapopulation Structure

  Although often modeled as a single well mixed populations, microbes in terrestrial systems likely exist as metapopulations, isolated but connected by infrequent migration. This can change the evolution of complexity, increasing the effect of genetic drift and decreasing the effect of selection. It can increase diversity and the rate at which complexity evolves. We have argued that metapopulation structure may have existed in early life and been responsible for the rapid evolution of LUCA and diversification across the tree of life. We investigate microbial genome evolution in metapopulations in Yellowstone National Park. We find that indeed they represent evidence for both natural selection and genetic drift shaping these populations.

  ROADMAP OBJECTIVES: 3.2 3.4 4.2 6.2

• The Long Wavelength Limit of Oxygenic Photosynthesis

  Oxygenic photosynthesis (OP) produces the strongest known biosignatures at the planetary scale on Earth: atmospheric oxygen and the spectral reflectance of vegetation. The pigment chlorophyll a was long considered the unique controller of both of these biosignatures, in its capability to enable water splitting to obtain electrons and thus produce oxygen as a biogenic gas, through spectral absorbance of light from the blue to 680 nm in the red. Then the discovery in 1996 of the cyanobacterium Acaryochloris marina shattered this conventional wisdom. A. marina was found to have replaced 93-97% of Chl a with Chl d, which enables it to perform oxygenic photosynthesis with much lower energy photons in the far-red/near-infrared. Since that first discovery in 1996, more far-red oxygenic phototrophs have been discovered, revealing a previously unsuspected diversity in the photosystems of oxygenic phototrophs. We seek to determine the long wavelength limit at which OP might remain viable and what factors affect the selection of that wavelength limit. This would clarify whether and how to look for OP adapted to the light from stars with a difference radiance spectrum from our Sun.

  Under this project in previous years and with other co-investigators, we spectrally quantified the thermodynamic efficiency of photon energy use in Acaryochloris marina str. MBIC11017, determined that its water-splitting wavelength is in the range 710-723 nm, and that it is more efficient than a Chl a cyanobacterium. The current focus of the project is to understand the adaptations of far-red/near-infrared (NIR) oxygenic photosynthetic organisms in general: in which environments they are competitive against chlorophyll a organisms, and what energetic shifts have been made in their photosynthetic reactions centers to enable their use of far-red/NIR photons. We are conducting field sampling and measurements to isolate new strains of far-red-utilizing oxygenic photosynthetic organisms, to quantify the spectral and temporal light regime in which they (and previously discovered strains) live in nature, and to use these light measurements to drive kinetic models of photon energy use to determine efficiency thresholds of survival.

  ROADMAP OBJECTIVES: 3.2 4.2 5.1 5.3 6.2 7.2

• Project 11: 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

• Undergraduate Research Associates in Astrobiology (URAA)

  2015 saw the twelfth session of our summer program for talented science students (Under-graduate Research Associates in Astrobiology), a ten-week residential research program tenured at Goddard Space Flight Center and the University of Maryland, College Park (http://astrobiology.gsfc.nasa.gov/education.html). Competition was again very keen, with an over-subscription ratio of 4.7. Students applied from over 19 Colleges and Universities in the United States, and 4 Interns from 4 institutions were selected. Each Intern carried out a defined research project working directly with a GCA scientist at Goddard Space Flight Center or the University of Maryland. As a group, the Associates met with a different GCA scientist each week, learning about his/her respective area of research, visiting diverse laboratories and gaining a broader view of astrobiology as a whole. At summer’s end, each Associate reported his/her research in a power point presentation projected nation-wide to member Teams in NASA’s Astrobiology Institute, as part of the NAI Forum for Astrobiology Research (FAR) Series.

  ROADMAP OBJECTIVES: 1.1 1.2 2.1 2.2 3.1 6.2 7.1

• Project 3G: A 3,400 Ma-Old Shallow Water Anaerobic Sulfuretum Evidences the Anoxic Archean Atmosphere

  Carbonaceous cherts of the ~3430 Ma Strelley Pool Formation contain innumerable “swirls” of fossilized sulfuretum bacteria encompassing quartz-replaced anhydrite nodules intermixed with layered assemblages of phototrophic filamentous fossil microbes. The geologic setting of the fossil-hosting unit, the preservation of the sulfuretum swirls adpressed to quartz pseudomorphs of precipitated anhydrite or gypsum, and the lack of physical disruption of the assemblage document its near-surface quiescent marine environment. The anaerobic physiology of the sulfuretum microbes indicates that Earth’s surface was anoxic. This exceedingly ancient biota is therefore interpreted to be composed of anaerobic H2S-producing sulfuretum microbes and H₂S-using anoxygenic phototrophic bacteria. As such, this first-identified fossil microbial consortium provides firm evidence of the anoxia of Earth’s early environment.

  ROADMAP OBJECTIVES: 4.1 5.2 6.2 7.2