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2006 Annual Science Report

University of Washington Reporting  |  JUL 2005 – JUN 2006

Executive Summary

In this, our fifth (and final?) year, our group continues its Year 4 drive at full productivity. It was also the year of Stardust, the highly successful comet return mission with co-I Don Brownlee serving as Mission PI. As in past years, our NAI sponsored research at the University of Washington has concentrated on the following important astrobiological questions:

  1. What are the characteristics of planets that can evolve complex organisms?
  2. Where might such planets occur?
  3. How does biological complexity evolve on a planet, and how might it end?
  4. What are the limits and permissible chemistries of life and how might they arise?

During the 2005-2006 period significant progress into these problems was made. Below, our results and progress is summarized based on specific research problems defined in our original proposal.

How often, where, and under which conditions do habitable planets form and persist?

Assessing the habitability potential of extrasolar planets remains one of the most fruitful areas of Astrobiology. As one approach to understanding the evolution of habitability, Co-I Tom Quinn and his team have studied solar system formation with computer models.

In collaboration with Mayer, Quinn is exploring the viability of the gravitational instability model for the formation of gas giant planets. With Mejia and Lufkin, they have conducted the first 3D SPH radiative transfer simulations of a massive protoplanetary disk. They have also used high-resolution 3D SPH simulations to study the evolution of self-gravitating binary protoplanetary disks. They find that massive disks that fragment if considered in isolation develop only transient overdensities when part of a binary system with a separation of 60 AU.
Kaib along with Barnes and Raymond have simulated the formation of terrestrial planets in four systems with known giant planets under the assumption that the giant planet inventory is complete. If the giant planets formed and migrated quickly to their current orbits, then terrestrial planets may form from a second generation of planetesimals. They find that only the 55 Cancri system can form terrestrial planets in the habitable zone with substantial water in this scenario.
Kaib has also been exploring the evolution of the Oort cloud, and the intensity of resulting comet showers under the assumption that the Solar System formed in a dense stellar environment. The stellar environment has a significant effect on the number of comets that end up in the Oort cloud, and therefore the intensity of comet showers. This work has application to other team members of the UW group, especially those looking at mass extinctions.

What caused the delivery and retention of organics and volatiles through Earth History?

The enormous success of the Stardust Mission colored so much of not only this area, but the entire UW team. In addition to this, however, Brownlee and his post doc G. Matrajt have continued their study of interplanetary dust particles, and have made significant breakthrough: they continue their important work on the identification of amino acids from these interplanetary dust particles. They built a special furnace that duplicates the ~5 second heat pulse and atmosperic environment that entering particles are exposed to. They have made 10µm thin films of nano-porous alumina particles impregnated, in different runs, with lysine, coronene, and 2 pentadecanone (a ketone) and exposed them to the simulated atmospheric entry heating environment. By measuring pre and post-heating concentrations with GC/MS and electrospray/MS, they have been able to determine survival curves with temperature. Remarkably, all three of these relatively volatile compounds survive at the several percent level for the dynamic pulse heating to 600 C, a common maximum temperature during atmospheric entry. Lesser amounts survive even a >800C!

How do mass extinctions and impacts affect the evolution and survival of complex organisms, i.e., the long-term habitability of planets?

Large impacts are the norm for all bodies, habitable or not. Project leader Ward and his team consisting of Ken Farley, Roger Buick, Joe Kirschvink and David Kring have been concentrating on impacts.

Impacts can have major effects on the evolution of macroscopic life (e.g., ocean sterilizing events, dinosaur extinctions). However, we don’t understand the details of these effects and how they might affect in different ways various environments and types of organisms and survivability. If we are to seek existing or past life elsewhere, we should understand how those planets’ history of impacts might have affected the evolution of those organisms. We also want to know what predictions can be made about fossil and current life at different time periods, environments, and locations on other habitable bodies. These areas were examined in the 2005-2006-time interval.

Laboratory work continues on samples from the Permian-Triassic boundary in Africa and Canada, and the Triassic-Jurassic boundary in the Queen Charlotte Islands, Nevada, Italy, and the Newark Basin. We made new collecting trips to New Zealand and South Africa. During the year we continued to analyze samples from previous fieldwork for evidence of shocked quartz, Helium3, Iridium, and carbon isotopes.
One of our most significant accomplishments was the attainment of a drilled core from Permian/Triassic boundary beds in South Africa. Long experience in isotopic geochemistry and paleomagnetism has demonstrated that results from studies based on properly collected drill core are vastly superior to surface samples (see the surface vs. drill core comparisons for the P/T boundary work on the GK-1 core from the Alps by Holser et al (1989), and the Triassic/Jurassic Newark Basin drilling project by Olsen et al (1996). In September of 2005 we conducted a pilot operation at Carlton Heights in the Karoo basin of South Africa, aimed at getting continuous core across the terrestrial P/T extinction 'event beds’ reported by Ward et al. (2000). The operation was an incredible success, with nearly 40 meters of intact, oriented core being obtained in only 5 working days. Work also continued on the search for extraterrestrial material at extinction boundaries.

In the summer of 2005 Frank Kyte and several others (including Luann Becker) undertook a very detailed resampling of the best-studied Permian/Triassic boundary in the world, at Meishan, China. Care was taken to sample every single bed in the vicinity of the boundary. In addition all unusual bedding planes (thin clay seams) were also sampled. Very large samples were acquired, carefully homogenized, and distributed blindly to about 15 different investigators. Co-I Farley analyzed all 19 of the consortium samples for He concentration and isotopic composition. He detected no extraterrestrial 3He in any of the samples. These results are consistent with our earlier work (Farley et al. 2001) but again are contrary to the published results of Becker et al. (Becker et al. 2001).

Previous evidence for an impact at the Triassic/Jurassic Boundary includes shocked quartz (Bice et al. 1992) and a small iridium anomaly (Olsen et al. 2002). To further investigate the possible role of impact at this time we (Ward and Farley) undertook a detailed study of He concentration and isotopic composition across the T/J boundary in Muller Canyon, in the New York Mountains of Nevada. No evidence of extraterrestrial material was discovered.

What can we learn from the geological and fossil record about the evolution of eukaryotes and metazoans?

During the 2005-2006 interval co-I Buick’s research continued in the following 6 areas: late Archean — early Paleoproterozoic hydrocarbon biomarker molecules, Archean sulfur isotopes and sulfur cycling, metamorphism of early Archean biosignatures, nutrient availability (N, P) in Precambrian oceans, paleobarometry of the Archean atmosphere and diamond drilling of astrobiologically significant Archean and early Proterozoic sedimentary horizons in the Pilbara Craton of Australia. Field-work was conducted on early Archean supracrustal rocks of the Fortescue, Warrawoona and Coonterunah Groups in the Pilbara Craton, Australia and the Isua Supracrustal Belt, Greenland. Principal outcomes were:

  • publication of the discovery of hydrocarbon biomarker molecules in early Paleoproterozoic fluid inclusions showing that ancient cyanobacterial and eukaryotic geolipids are not contaminants, that these organisms existed before the first of the “Snowball Earth” events and the rise in atmospheric oxygen, and that molecular fossils can survive for much longer under high temperature regimes than previously expected;
  • construction of a working computer box-model of the Archean sulfur biogeochemical cycle, which will lead to a better understanding of the role of sulfur in the regulation of redox states on the early Earth;
  • equipping the NAI Finnegan 253 IRMS mass-spectrometer for the analysis of sulfur isotopes;
  • analysis of carbon isotopes and total organic carbon contents of 2.6-2.4 billion year old sedimentary rocks from the NAI ADP drill-cores showing that mass-independent fractionations of sulfur isotopes are not correlated with either, ruling out the possibility that they are induced by organic diagenesis;
  • detailed mapping of 3.8 billion year old metasedimentary rocks from Isua, Greenland, showing that interpretations of a turbidite depositional environment are most consistent with field evidence;
  • collection and analysis of samples for Archean paleobarometry, indicating that atmospheric pressure was different to modern levels early in Earth’s history.

What can the study of life in ice tell us about the potential for life beyond the Earth?

Co-I Jody Deming continued to study life in saline ice formations, guided by the importance of attachment to surfaces and including work on Bacteria, Archaea, viruses, exopolymers and enzymes. Accomplishments this year stem primarily from work with our model cold-adapted bacterium, Colwellia psychrerythraea 34H, and cold-active bacteriophage 9A that infects 34H. A whole-genomic and proteomic analysis of our Colwellia strain was published (Methé et al., 2005), including distinction of the psychrophilic proteome from proteomes of other thermal classes, an apparent record number of encoded products destined for export from the cell, and evidence of lateral gene transfer (presence of Archaeal genes and two viral genomes). She and her team published evidence that live C. psychrerythraea 34H cells incorporate more leucine into protein down to —20°C when coated with exopolymers (an attachment mechanism) and continue to do so at detectable rates when dropped to sub-eutectic temperatures (≤ —80°C). They verified over-production of exopolymers at subzero temperatures, under elevated pressures, and in high salt solutions (manuscript in preparation) as a stress response, reinforcing the importance of exopolymers to microbial survival in extreme habitats. Our hypotheses and data on exopolymer effects on protease activity down to —18°C are in press; a manuscript with evidence for the persistence of Archaea in Arctic winter sea ice down to —28°C is in preparation. Several papers on cold-active viruses have been published or submitted, including on viral lysis of bacteria at —12°C in sea-ice brine and viral stability under these conditions. They initiated experimental work, based on the 9A-34H phage-host system, to test for lateral gene transfer in the cold. Underway are microbial analyses of samples from previously unexplored sites in the Arctic, called Smoking Hills, which experience continuous heating beneath the extreme cold of winter ice cover, a potential extraterrestrial analog of interest.

Evolutionary pathways by which microbes and their communities evolve, and by which complex organisms originate

Three separate groups carried out our team’s investigations into specific microbes and microbial communities that are not in ice: the Staley lab, the Leigh lab, and the Stahl lab.

The Staley lab has continued to study the evolution of the tubulin-containing bacteria in the bacterial phylum, Verrucomicrobia. Recent research indicates Prosthecobacter, which contains homologs for alpha- and beta- tubulin, BtubA and BtubB, are unlikely to be the progenitors of the eukaryotic cell. Evidence for this comes from a comparative genomic study of their other proteins, only 10 of which produced high-scoring matches against a database of 347 eukaryotic signature proteins (Staley et al., 2005). The source of these genes in Prosthecobacter species is unknown but they likely came from an ancient horizontal gene transfer event. The genes have been cloned and expressed in E. coli and the resultant proteins produced protofilaments that, like eukaryotic microtubules have GTPase activity (Sontag et al., 2005). Our recent report indicates that Verrucomicrobium spinosum, a close relative of Prosthecobacter, which does not have tubulin genes, produces a unique bacterial FtsZ a divergent homolog of tubulins (Yee et al., submitted).
Other lab research has focused on the Black Sea’s suboxic zone which is a model for early Earth environments as well as Europa. We reported that several other groups of the Planctomycetes phylum, in addition to the anammox bacteria, reside at different redox positions in the suboxic zone (Kirkpatrick et al., 2006). Furthermore the Black Sea has unique bacteria involved in denitrification based upon their nirS and nirK genes (Oakley et al., in press).

The Staley lab has also worked on cold life. This year the Staley lab discovered that Psychromonas ingrahami grows at —12°C, the lowest temperature reported for a bacterium with an authenticated growth curve. Staley is now comparing this organism with its south polar counterpart, which is a member of this same species.

The John Leigh lab is also looking at anaerobic microbes, in their case methanogens. This past year, Leigh and his colleagues studied the response of M. maripaludis to hydrogen limitation, as well as studying electron flow in the process of methanogenesis. To do this, Leigh made mutations in genes involved in the various steps in methanogenesis to determine the roles of these enzymes. Hydrogenotrophic methanogenesis occurs in a variety of anaerobic habitats, may have played an important role on early earth, and could be a dominant metabolism on other planetary bodies. In previous years we published our genome sequence of Methanoccoccus maripaludis, a model species of hydrogenotrophic methanogen and a member of the domain Archaea. In the past year we have made considerable progress in the post-genomics of M. maripaludis. Thus, we used chemostat-grown cultures and expression arrays to learn how M. maripaludis responds to conditions in which growth is limited by the supply of hydrogen, an important electron donor in methanogenesis. A manuscript describing this work is currently in preparation. In a related project, we published two papers in the past year on the transcriptomics and proteomics of a mutant deficient in a specific hydrogenase. Our studies have also given us insight into nitrogen regulation in the Archaea. Not surprisingly, the components of the regulatory apparatus are different in this branch of life, and we have published two papers describing this apparatus in detail.

The third co-I in this project is Dave Stahl. The primary research objective of Stahl’s lab is to better understand the origins and adaptive radiation of an ancient and biogeochemically significant assemblage of microorganisms, the sulfate-reducing prokaryotes (SRP). Research activities addressing this objective included field studies of SRP in habitats possibly similar to those that existed on early earth (microbial mats and hot springs) and comparative sequence analysis of genes encoding the pathway for sulfate respiration.

The Stahl group continued studies that examined the importance of alternative electron donors to sulfate respiration in hot springs within Yellowstone National Park by measuring the stimulation of sulfate reduction by exogenous substrate addition (lactate, acetate, hydrogen). These studies refined preliminary analyses showing that only hydrogen significantly stimulates sulfate respiration, confirming the presence of sulfate respiring microbiota that might have been sustained within geothermal systems of an early Earth (Köenneke, de la Torre et al. 2004; Köenneke, de la Torre et al. in preparation).

The Stahl group currently has three papers in preparation from Astrobiology funded work on the microbial mat communities in Guerrero Negro, MX and Yellowstone National Park, WY. This research was performed during Dr. Dillon’s post-doctoral fellowship in Dr. Stahl’s lab at the University of Washington, in collaboration with members of the EMERG group coordinated by Drs. David DesMarais, Tori Hoehler, Brad Bebout and others at NASA Ames Research Center. These three manuscripts all relate to work investigating the diversity and biogeochemical activity of microbial mats. These modern mats are currently found in extreme environments such as the hypersaline ponds and hot spring that we have studied. From an astrobiological perspective, these mats also serve as modern analogs of some of the earliest complex communities on Earth. By improving understanding of the spatial and temporal dynamics of the sulfate-respiring bacteria in relationship to other populations (Dillon, Miller et al. In preparation; Dillon, Fishbain et al. In preparation; Dillon, Miller et al. Revision in preparation), we have contributed to a better understanding of the relationship between population structure and biogeochemistry of these analogs of early earth communities.