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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

• Astrobiology of Icy Worlds

  Our goal in the Astrobiology of the Icy Worlds Investigation is to advance our understanding of the role of ice in the broad context of astrobiology through a combined laboratory, numerical, analytical, and field investigations. Icy Worlds team pursues this goal through four major investigations namely, the habitability, survivability, and detectability of life of icy worlds coupled with “Path to Flight” Technology demonstrations. A search for life linked to the search for water should naturally “follow the ice”. Can life emerge and thrive in a cold, lightless world beneath hundreds of kilometers of ice? And if so, do the icy shells hold clues to life in the subsurface? These questions are the primary motivation of our science investigations

  ROADMAP OBJECTIVES: 1.1 2.1 2.2 3.1 3.2 4.1 5.1 5.2 5.3 6.2 7.1

• 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

• Project 3: The Origin of Homochirality

  A universal aspect of living systems on Earth is their homochirality: Life uses dextrorotary sugars and levorotary amino acids. The reasons for this are hotly debated and not close to being settled. However, the leading idea is that autocatalytic reactions grew exponentially fast at the origin of life, and whatever chiral symmetry breaking was accidentally present became amplified subsequently. We are calculating the way in which this can take place using statistical mechanics, and also trying to see how a uniform homochirality could be stable to spatial fluctuations.

  ROADMAP OBJECTIVES: 3.2 3.4 4.1 4.2 5.1 5.2 7.1 7.2

• 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 1E: Microbial Communities in Chocolate Pots Hot Spring, Yellowstone National Park

  DNA was extracted from samples obtained from cores collected at six locations along a transect following the main fluid flow path at at Chocolate Pots (CP) hot spring, Yellowstone National Park. 454 pyrosequencing of 16S rRNA gene amplicons was performed on the extracts, resulting in the generation more than 70 amplicon libraries, each containing a between ca. 2500 and 7500 ca. 300 base pair-long reads. The raw reads were processed and analyzed for their phylogenetic affiliation and other comparisons using the QIIME pipeline. The results indicate that microbial communities in the upper few cm of the Fe/Si-rich CP deposits varied significantly along the sampling transect. Communities at two sites most proximal to the vent source differed substantially from one another and from communities at downstream sites. Although communities at downstream sites were not identical, they were more similar to one another than to the vent-proximal sites. A wide diversity of prokaryotic taxa, including both Bacteria and Archaea, were identified in the libraries, many of which are only distantly (e.g. <90% similarity in 16S rRNA gene sequence) related to known taxa. Communities in cores close to the vent were dominated by anaerobic taxa, many of which have the potential to function as Fe(III) reducers. This result is consistent with the relatively high abundance of reduced (ferrous) iron [Fe(II)] and the rapid rate of Fe(II) production observed in in vitro Fe(III) reduction experiments with material from sites near the vent. Abundant taxa at downstream sites included organisms related to the known Fe(II)-oxidizing organism Sideroxydans paludicola. These results are consistent with Fe geochemical data, which indicate that Fe(II) oxidation is likely the dominant Fe redox cycling pathway in deposits more than 1-2 meters from the vent source. A detailed metagenomic analysis of communities in the upper 1 cm at three sites is underway, with the goal of confirming the function of recognized taxa, and revealing the identity and function of potentially novel Fe redox cycling taxa.

  ROADMAP OBJECTIVES: 2.1 4.1 5.1 5.3 7.1

• 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 Extremely Energy-Limited Environments

  The terrestrial subsurface is the least explored habitat on earth and is characterized by darkness and reducing conditions that limit how fast microbes can obtain energy (low energy fluxes). The diversity and metabolic strategies of microbes in this environment are the subject of our investigation.

  ROADMAP OBJECTIVES: 4.1 4.3 5.1 5.3 7.1

• Project 7 Control of Evolvability and Chromosomal Rearrangement by Stress

  Evolution of the genome happens predominantly by gross chromosomal rearrangements (GCR), usually involving non-homologous recombination, and point mutation or single nucleotide variation (SNV). GCR re-assorts domains and regulatory functions, and frequently changes gene copy number, allowing further evolution. SNV changes coding sequences, modifying the properties of encoded macromolecules and their regulation. We are able to measure both SNV and GCR in the same assay in Escherichia coli, and have established that both are dramatically up-regulated in response to stress. Through many year’s work, we have learnt many details of these mechanisms, but some of the outstanding questions are crucial to understanding the significance of stress in evolution, notably the signaling and execution of the pathway from stress to mutation, and how the decision is made between SNV and GCR. This project aims to answer these questions.

  ROADMAP OBJECTIVES: 5.1

• Project 9: Evolution Through the Lens of Codon Usage

  The sequences of protein encoding genes are subject to multiple levels of selection. First, amino acid changes that adversely alter protein function are unlikely to survive. In addition, the genetic code of organisms is degenerate; it includes alternative (synonymous) codons for most of the amino acids. Codon usages in a genome are generally viewed as a balance between drift and selection for rapid and accurate translation of mRNAs into proteins. This balance defines the native codon usage of the organism. Later, it was recognized that many horizontally transferred genes have distinctive codon usages. It was assumed that these reflected the codon usages of the organisms that contributed the genes. We viewed this as an opportunity to identify those sources.

  These studies of this have led us to discover that: (i) most of the recently acquired genes come from such closely related organisms that their distinctive codon usages cannot be attributed to a phylogenetically distant source; (ii) the transfers commonly exceed recognized boundaries of microbial species; (iii) after their acquisition, some of the genes do not drift to match the native codon usage of the recipient; (iv) many of the genes that are most up-regulated under starvation conditions have this same codon usage; and (v) a distinctive stress/starvation-associated codon usage is a recurring theme that is observed in diverse Bacteria and Archaea.

  These studies entailed the development of a variety of new codon usage analysis tools. We are making these tools available, and are integrating them into the RAST genome annotation and analysis server at Argonne National Laboratory.

  ROADMAP OBJECTIVES: 5.1 5.2 5.3

• 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

• Molecular Biosignatures of Redox-Sensitive Bacteria and Hyperthermophiles

  The Summons lab has been researching a range of molecular and isotopic phenomena aimed at shedding light on what controls Neoproterozoic ocean redox, evolutionary trends in the abundances of molecular fossils (biomarkers) and the enigmatic natural variability carbon isotopic compositions of organic and inorganic carbon at this time. Our studies of carotenoid pigment biomarkers for green and purple sulfur bacteria have revealed that they are ubiquitous in rock extracts of Proterozoic to Paleozoic age—implying that the shallow oceans became sulfidic more frequently than previously thought. Other projects focused on the biosynthesis of another important biomaker, the hopanoids, vesicles released from marine bacteria for interaction between cells and their environment, and the molecular signatures of microbial communities in hot springs in Yellowstone National Park.

  ROADMAP OBJECTIVES: 4.1 4.2 5.1 5.2 7.1

• 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 (Chl 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 stars redder than our Sun.

  Previously under this project, with other co-investigators we spectrally quantified the thermodynamic efficiency of photon energy use in the chlorophyll d utilizing cyanobacterium, Acaryochloris marina str. MBIC11017, determining that it is more efficient than a Chl a cyanobacterium. The current focus of the project is aimed at understanding the adaptations of far-red/near-infrared (NIR) oxygenic photosynthetic organisms in general: what is their ecological niche where they are competitive against chlorophyll a organisms in nature, and what energetic shifts have been made in their photosynthetic reactions centers to enable their use of far-red/NIR photons. Field sampling and measurements are being conducted 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 use these light measurements to drive kinetic models of photon energy use to ascertain light thresholds of survival.

  ROADMAP OBJECTIVES: 3.2 4.2 5.1 5.3 6.2 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 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

• 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

• 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