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2013 Annual Science Report

Arizona State University Reporting  |  SEP 2012 – AUG 2013

Stoichiometry of Life, Task 3b: Ancient Records - Genomic

Project Summary

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.

4 Institutions
3 Teams
3 Publications
0 Field Sites
Field Sites

Project Progress

Team members for Task 3b have been involved in several noteworthy accomplishments. DuPont was a co-author on two recent publications, one in Nature Geoscience, on the role of zinc in the early biosphere (this publication bridges with Task 3a). Eukaryotic metallomes in particular may have been particularly dependent on zinc, and its bio-availability may have constrained (or driven) the evolution of early eukaryotes. Team members Boyd and Raymond continue to make advances in studying the genomic record of how life adapts to environmental extremes, with Yellowstone National Park as a focus for field studies. Several manuscripts are now in preparation, and this work was the foundation for a paper by Raymond on using signatures derived from metagenomes to better understand microbial evolution. These projects substantially advanced the doctoral progress of ASU students Alsop and Kellom. Though the project will draw to a close in the near future, collaborations between team members will continue to drive new ways to integrate their interests and expertise into a stronger understanding of how the availability of key elements drove biological innovation and evolution.

Figure 1: Phylogeny of 1,424 sequenced microbes, colored based on how well taxonomic assignments based on short oligonucleotide fragments (derived, for instance, from metagenomic data) agree with those derived from 16S rRNA phylogeny (red-to-blue=better-to-worse taxonomic assignments). This advance in methods illustrated new approaches for using the ever-increasing availability of environmental DNA sequencing as a tool for understanding diversity in natural environments (from Alsop and Raymond 2013).
Figure 2: Zn–Fe cross-plot revealing paleomarine Zn partitioning recorded by the authigenic iron oxide record. Lines represent conservative models of Zn–Fe co-precipitation behavior for hypothetical paleomarine Zn and Fe reservoirs, including those previously predicted by chemical equilibrium modeling. Near-modern paleomarine Zn concentrations are clearly indicated regardless of sample age (from Robbins et al. 2013).

    Jason Raymond Jason Raymond
    Project Investigator
    Christopher Dupont

    Janet Siefert

    Eric Alsop

    Eric Boyd

    Matthew Kellom

    Objective 5.1
    Environment-dependent, molecular evolution in microorganisms

    Objective 5.2
    Co-evolution of microbial communities

    Objective 5.3
    Biochemical adaptation to extreme environments