USC Wrigley Institute | Geobiology Course

10.00 Benner and Ellington
Introduction to Symposium

Session 1. Chemistry Behind Life-I:Andy Ellington, Chair
10.30 Steven Benner (University of Florida)
Genomes to Life
Steven Benner kicked off the first course symposium with examples linking the genetic record of gene duplications to the fossil record. He described the difficulty of aligning both records, but gave some examples where there was a strong correlation between the fossil and genetic records. He showed a graph of duplications through time in yeast, depicting significant duplication events approximately 80 million years ago that correlated with the noted origin in the fossil record of angiosperms and fermentable fruits. His talk set the tone for the symposium and the course, combining elements of fascination, powerful intellectual diversity and the blend of geo-bio-chem that had symposium guests buzzing.

11.20 Yohei Yokobayashi (CalTech)
Catalytic and Autocatalytic Peptide Networks
For his Ph.D. and postdoctoral work, Yohei has studied peptides that are self-replicating. Sometimes by themselves, and sometimes in the presence of another molecule or under certain conditions, they serve as a "template" that catalyzes amino acid synthesis of an identical protein or else one that is symmetric, or antisymmetric to the original protein, in some predictable and organized way. These proteins "evolve" in the respect that they can "compete" with each other and "select" individual structures with specific properties most favorable to fast self-replication in experimental conditions.

Session 2.Chemistry Behind Life-II: Steven Benner, Chair
13.50 Chris Switzer (University of California, Riverside)
Molecular Recognition in Nucleic Acids
What kind of nucleic acids were the first to form in early Earth history? This question became one of the themes of Chris Switzer's talk. He described the ease of making 2'5' bonds versus making 3'5' bonds in nucleic acids and compared the relative stability of these forms as well as other similar polymers involving trioses instead of pentoses. Each of these different structures was postulated as a possible experimental step taken on the road from prebiotic chemistry to the modern DNA world.

14.40 Jack Szostak (Harvard Medical School)
Towards Darwinian Systems in the Laboratory
Jack presented the work that he and his graduate students have done trying to synthesize liposomes, fatty-acid micelles, lipid-bilayer membranes, and artificial cells that will self-replicate and "evolve" on a laboratory bench. In particular he described a method for getting liposomes, approximately 100 nanometers in size, to "divide" by forcing them to extrude through pores in filters. He also showed examples of liposomes forming with particles of clay inside them leading to the question of what role clay might have played in the origin of life.

15.30 Andy Ellington (University of Texas)
The RNA World Hypothesis
Andy introduced the concept of the RNA world, midway down the path between early Earth's prebiotic soup and the modern DNA world. In the RNA world, organisms exist without DNA or proteins, instead encoding all their genetic information in RNA and rely on RNA molecules to catalyze reactions. The basis for this hypothesis lies partly in the conceptual improbability of the modern DNA-RNA-protein world having evolved in a single step, and partly in the evidence of certain molecules (such as ribozymes and molecules making up the ribosome) in which the catalytic centers are predominantly RNA controlled, despite the presence of proteins (believed to be later additions) in other areas of the molecules.

"STROMATOLITES:
LINKING THE PAST AND PRESENT"

Saturday, July 20, 2002

A Mini-Symposium Organized by the
Agouron Geobiology Course

Instructors: John Grotzinger (MIT), Andy Knoll (Harvard),
David Des Marais (NASA-Ames), Brad Bebout (NASA-Ames),
Jim Kasting (Penn State)

Stromatolites are among the earliest fossilized life-forms reflecting microbially mediated mineral precipitation-true or false? How can geobiologists differentiate organized mineral deposits which are microbially influenced from mineral deposits which are otherwise self-organized? Under what conditions will microbes live within harsh sedimentary environments, what is their relationship to the mineral environment and how do microbial communities impact atmospheric evolution?

Program

10.00 Grotzinger, Knoll, Des Marais, Bebout, and Kasting
Introduction to Symposium

Session 1. Ancient and Modern Mat-Communities-I: John Grotzinger, Chair

10.30 Jack Farmer (Arizona State)
Microbialite Morphogenesis and Fossil Biosignature Preservation in Hydrothermal Environments
Jack stressed the importance of morphology in the search for fossil biosignatures, particularly in hydrothermal environments in which organics are rapidly degraded and undergo mineral replacement. Despite the recent debate on morphological identification (e.g., the Schopf-Brasier debate on the Apex chert microfossils), Jack noted that due to the environmental conditions in hydrothermal areas, morphology is likely to be the only biosignature to survive diagenesis. Various morphotypes were related to physico-chemical conditions within the hot spring.

11.20 Don Canfield (Odense, Denmark)
Salt Encrusted Microbial Communities from Eliat, Israel
Don Canfield reviewed layered microbial communities, especially those found in hypersaline environments such as Baja, California tidal flats and in Eliat, Israel. Communities displaying differently pigmented microorganisms (colour banded microbial mats) are characterized by typical geochemical profiles reflecting the metabolisms of the predominant prokaryotic organisms in each layer. The "fossil record" of these communities may be complex since, as more sediment accumulates, the photic zone moves upward through the areas colonized by previous communities.

Session 2. Ancient and Modern Mat-Communities-II: Brad Bebout, Chair

13.50 Pieter Visscher (University of Connecticut)
Modern Stromatolites and Microbial Mat Systems: Key to Understanding Lithification Mechanisms?
Pieter Visscher reviewed inorganic pH-Eh chemistry of calcium carbonate in light of a variety of typical metabolic oxidation-reduction reactions, linking various metabolic pathways to the precipitation and dissolution of calcium carbonate. Although metabolically-induced changes in pH were not included in the kinetics of these reactions, this analysis provided the foundation for the chemical quantification of metabolic processes through the observation of calcium carbonate precipitation/dissolution. Specific metabolisms associated with the precipitation of calcium carbonate are oxygenic photosynthesis, sulfate reduction, anaerobic denitrification, and methanogenesis, whereas aerobic respiration, ammonium oxidation, and aerobic sulfide oxidation are associated with the dissolution of calcium carbonate.

14.40 Steve Golubic (Boston University)
Microbial Architects of Sedimentary Structures
Steve Golubic gave us a review of various microbial mat structures in the environment, highlighting the difference between stromatolites and microbial mats, and between stratified structures and laminated structures. He focused on the interactions between different constituents of mat communities with each other and the exterior environment. Finally, Steve gave us a walking tour through desert microbial crusts and illustrated the prevalence of microbial mats in all parts of the globe and their importance in understanding the capabilities of life and its effect upon the Earth's geochemistry.

15.30 Lee Prufert-Bebout (NASA-AMES)
Cyanobacterial Distribution in Experimental Benthic Ecosystems
Along with her co-workers at NASA-AMES Lee Prufert-Bebout studies the types of cyanobacterial communities that exist in modern stromatolite environments. In this talk she discussed the diversity of cyanobacteria she isolated from stromatolites at Highborne-Cay in the Bahamas. In addition to her fieldwork, Lee also presented experimental data modeling the growth of microbial mats, using the cyanobacteria she had isolated from modern stromatolites. In her experiments she examined several different parameters that are influential for the growth and morphology of modern stromatolites, particularly flow velocity, sediment size, and sedimentation rate.

"CURRENT ASPECTS of MICROBES, COMMUNITIES and METALS"

Saturday, August 3, 2002

A Mini-Symposium Organized by the
Agouron Geobiology Course

Course Instructors: Kurt Hanselmann (U. Zurich),
Dianne Newman (Caltech), Ken Nealson (USC),
Gary Olsen (U. IL.), Tom Schmidt (MSU)

Ever since the late 1600's when Anthony van Leeuwenhoek observed samples from the scurf of his teeth under the microscope, it has been obvious to microbiologists that solid surfaces are a welcome home for bacteria. If a sterile glass slide is left in any water body, it becomes entirely covered by microorganisms within a few days. For geobiologists, this intimate association between bacteria and surfaces is particularly important when microbes attach to and transform minerals. Indeed, microbes are known to play an important role in the weathering of rocks near the surface and perhaps even at depth. This symposium will feature presentations by speakers whose research pertains to how microbial communities operate, ranging from the molecular details of how they interact with one another and/or with mineral surfaces, to how they affect the chemistry of their environment(s).

Program

10.00 Hanselmann, Newman, Nealson, Olsen, and Schmidt
Introduction to Symposium

Session 1: Microbial Communities: Interactions with other cells: Ken Nealson, Chair

10.30 Bonnie Bassler (Princeton)
Small Talk: Cell-to-Cell Communication in Bacteria
Bonnie summarized work done in her lab to study the mechanisms behind the quorum sensing signals leading to bioluminescence in the free living bacterium Vibrio harveyi. She described two distinct pathways that lead to bioluminescence in V. harveyi, each of which alone or in concert can induce bioluminescence. She demonstrated that one pathway is activated by a quorum sensing molecule produced solely by V. harveyi, while the other pathway responds to a quorum sensing molecule that is widely produced by microbes. Investigation of this latter pathway revealed that the key component to this molecule was a boron atom, raising the possibility that boron may play an important and hitherto unappreciated role in metabolic processes.

11.20 Roberto Kolter (Harvard Medical School)
Biofilms: Microbes on a Surface
Roberto Kolter described biofilm formation by Bacillus subtilis. This process involves the initial interaction of the bacteria with the surface, and its subsequent colonization as the bacteria form a coherent biofilm. After reaching structural maturity, the bacteria cluster to form fruiting bodies above the biofilm surface. These bodies then sporulate and seed the next generation of biofilm formation. Roberto demonstrated these various stages by showing videos of biofilm formation. Particularly interesting were videos showing bacteria that were mutated to limit their motility, inhibiting their ability to form biofilms.

Session 2: Microbial Communities: Interactions with minerals: Tom Schmidt, Chair

13.50 Terry Beveridge (U. Guelph)
Surfaces, Metals, and Minerals
Terry discussed the process of metal reduction in aqueous environments, particularly addressing the bioavailability of Fe(III), the insoluble form of iron needed for iron reduction. Three primary means have been observed to provide microbes with Fe(III). If microbes attach to particulate Fe(III) in the water column, they can reduce the iron with which they are in direct contact. If, however, microbes are unable to attach to particulate iron, they need to use more indirect methods. One such method is the microbial production of iron chelators which bind to iron particles and are subsequently absorbed into microbial cells. Another method used by microbes involves the production of an intermediate compound which is oxidized by coming into contact with Fe(III), in the process reducing the iron to Fe(II). When the microbes come into contact with the oxidized intermediary, the reduction of the compound is used to power the microbial metabolism. He also discussed atomic force microscope measurements of cell wall strength.

14.40 Derek Lovley (U. Mass)
Microbial Metal Reduction
Derek Lovley's talk described his work with Geobacter at sites of uranium contamination. He explained Geobacter's use for oxidizing uranium(VI) to uranium(IV) in soils and therefore precipitating the uranium, preventing it from spreading further. This has tremendous applications for bioremediation of areas contaminated by uranium mining. He also summarized Geobacter's wide range of other metabolic capabilities, and briefed us on the state of Geobacter's genome.

15.30 Jill Banfield (UC Berkeley)
Microbes and Metal Cycling
Jill described her fieldwork at the acid mine drainage site at Iron Mountain, a former pyrite-containing mine in northern California. Approximately 11 tons of pyrite are oxidized every day, an exergonic process which consumes 8,000 m3/day of oxygen and generates enough warmth to heat the environment interior to the mine over 50°C. In the process, protons released by the oxidation of pyrite drive the pH to extremely low levels, in places frequently reaching pH values less than 0.5. Despite these harsh conditions, an established microbial community exists. Prominent in this community are iron oxidizers which catalyze these reactions, and iron reducers which convert Fe(III) back into Fe(II). Jill discussed methods to decrease the toxicity of the site by either inhibiting microbial iron oxidation or encouraging microbial iron reduction, both of which would increase the pH of the water flowing through the mine, ameliorating the environmental damage caused by the mine drainage.