Faculty

Jo Handelsman
(608) 263-8783

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Department of Plant Pathology
University of Wisconsin - Madison
1630 Linden Dr.
Madison, WI 53706

rev. January 15, 2004

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Complex Cross-talk:  Functional Genomics of Uncultured Microorganisms

 This project is designed to understand the phylogeny, function, and modes of communication of the microbial life in soil that cannot be cultured by standard techniques.  The soil likely contains the most complex and rapidly changing microbial community on Earth.  The challenge in studying this community is in defining it in space and time and then describing its changing structure and accompanying functions.  Although soil microbiology is one of the oldest branches of microbiology, the definition of the community has eluded us because we have looked at the soil through the petri plate, a prism that refracts, distorts, and limits the vision of its subject. 

 For a long time, microbiologists have known that fewer than 1% (and perhaps as few as 0.1%) of the viable bacteria in soil can be cultured on known media.  Collaborative work between my lab and and others, as well as numerous studies by other groups have demonstrated through an analysis of the 16S rRNA genes of soil organisms that the uncultured Bacteria and Archaea diverged deeply from the cultured organisms.  This work tantalized scientists around the world because of the predicted vast metabolic diversity that would likely be associated with such phylogenetic diversity.  However, for years it was not clear how to tap into this genetic potential without attempting to culture every organism, which seemed unwieldy given the size of the soil community.  To address this challenge, in a multi-lab collaboration involving the labs of Bob Goodman (http://www.plantpath.wisc.edu/fac/rmg.htm) and Jon Clardy (http://www.chem.cornell.edu/department/Faculty/Clardy/clardy.html), we developed the approach that we designated ‘metagenomics’, which is the analysis of the collective genomes of the microorganisms in the soil community.  Our approach is to clone DNA in large fragments directly from soil into a culturable host and conduct a sequence-based and functional genomic analysis on it.  The intended outcomes of this project are diverse and ambitious, including the isolation of new chemical signals, new secondary metabolites that might have utility to humans, and the reconstruction of an entire genome of an uncultured organism.

 Although the metagenomic analysis of the soil is in its infancy, a number of exciting discoveries have been made that indicate that a cornucopia of chemistry and biology is waiting to be unearthed.  In a collaborative effort, we constructed a number of libraries that collectively contain more than 1 Gigabase of anonymous soil DNA in E. coli.  We have found two structurally related, novel antibiotics, designated turbomycin A and turbomycin B, a multigene pathway for a previously described antibiotic, and numerous 16S rRNA genes that indicate that a vast diversity of organisms, including many that diverge deeply from cultured microbes, contributed DNA to the library.  The 16S rRNA genes or other phylogenetic indicators, sequence analysis, and functional screening provide the opportunity to link phylogeny and function.  Ultimately, this information may provide the basis for strategies to culture the organisms from which the DNA was derived or may provide the basis for in situ probing to determine when, where, and with whom the genes are expressed.

 While elucidating a comprehensive picture of the soil microbial community may not be feasible, we believe that we will be able to capture a full view of one microbial function in soil that confers a selectable phenotype using traditional and molecular approaches.  To test this possibility, the Handelsman lab has recently initiated a new project to understand the mechanism by which bacteria acquire phosphorous from P-limited soils.  We will use traditional culture-based methods as well as metagenomics to identify genes responsible for acquisition of phosphorous from highly reduced forms, such as phosphonite, and mineral forms such as apatite and the highly insoluble lanthanide phosphates.  The site of interest is the soil in a boreal forest in Alaska, including soils that are under permafrost and others that undergo rapid and frequent freeze-thaw cycles.  In collaboration with a geologist, a microbial physiologist, and an ecosystem ecologist, we are hoping to determine the microbial contribution to phosphorous availability in a system that is dependent on P for productivity.

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