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2002 Annual Science Report

Michigan State University Reporting  |  JUL 2001 – JUN 2002

Genomic and Proteomic Analysis of Permafrost Bacteria

4 Institutions
3 Teams
0 Publications
0 Field Sites
Field Sites

Project Progress

The overall objective of this project is to identify genes and proteins that enable bacteria to inhabit the permafrost environment. An initial goal is to determine the complete genome sequence – the “informational content” – of two permafrost isolates. Toward this end, we completed a phenotypic survey of 20 permafrost bacterial isolates and used this information to choose the two isolates: these are Exiguobacterium 255-15 and Psychrobacter 273-4. These strains, which were isolated from 2-3 million and 20-40 thousand year old permafrost soils, respectively, have genomes of about 2.5 Mb (determined by pulse field gel electrophoresis) and are capable of growing at low temperature (-2.5ºC) and at low water activity (5 osmolar salt), distinctive characteristics that one would anticipate for microbes inhabiting the permafrost. Within the past month, DNA sequence representing a 10-fold coverage of the Exiguobacterium isolate has been obtained in collaboration with the Department of Energy (DOE) Joint Genome Institute. Similar sequencing coverage for the Psychrobacter strain should soon be available.

An integral component of this project is to determine how expression of the Exiguobacterium 255-15 and Psychrobacter 273-4 genomes is affected by low temperature and other conditions associated with the permafrost environment. Results from the phenotypic survey provide evidence that both of the isolates can sense and respond to low temperature: both strains showed differences in the utilization patterns of 96 carbon sources at 24ºC and 4ºC; the Exiguobacterium strain was more difficult to lyse when grown at 24ºC as compared to 4ºC; and exposure of the Psychrobacter strain to low temperature resulted in an increase in ice nucleation activity and an increase in freezing tolerance. To monitor gene expression at the proteome level, a 2-dimensional liquid phase protein separation method was developed to fractionate soluble and membrane proteins expressed by the Exiguobacterium strain. Finally, we have demonstrated transfer of a wide host range plasmid from Escherichia coli to the Psychrobacter strain, a critical first step in the development of a transposon mutagenesis procedure to identify genes that are responsive to changes in the environment and are required for life at low temperature.

    Michael Thomashow
    Project Investigator

    James Tiedje
    Project Investigator

    James Cole

    Richard Goldstein

    Sophie Kathariou

    David Lubman

    John McGrath

    Susan Lucas

    Sarah Gilmour

    Peter Bergholz
    Doctoral Student

    Robert North
    Doctoral Student

    Kimberly O'Neil
    Doctoral Student

    Monica Ponder
    Doctoral Student

    Tatiana Vishnivetskaya
    Doctoral Student

    Suping Zheng
    Doctoral Student

    Objective 4.0
    Expand and interpret the genomic database of a select group of key microorganisms in order to reveal the history and dynamics of evolution.

    Objective 7.0
    Identify the environmental limits for life by examining biological adaptations to extremes in environmental conditions.

    Objective 15.0
    Model the future habitability of Earth by examining the interactions between the biosphere and the chemistry and radiation balance of the atmosphere.

    Objective 16.0
    Understand the human-directed processes by which life can migrate from one world to another.