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Martin Polz, Ph.D.

Department of Civil and Environmental Engineering
Associate Professor

Room 48-417
617-253-7128 (phone)


M.S. Zoology, University of Vienna, 1991
Ph.D. Harvard University, 1997
Assistant Professor, Department of Civil and Environmental Engineering, 1998
Associate Professor, Department of Civil and Environmental Engineering, 2004

Research Summary

The main focus of the Polz lab is the exploration of structure-function relationships in microbial communities. Environmental microbiology is at an important cross roads. We have learnt during the last 20 years that microbes are the most ubiquitous organisms on Earth. Yet what governs the interactions and evolution of microorganisms within the complex communities present in the environment remains almost completely unknown. What environmental factors control the diversity and dynamics of microbial populations? What is the functional role and redundancy of individual populations within the community? What is the range of genome similarity that defines a functional unit? What mechanisms govern diversification of microbial populations in the environment? We seek to address these questions by a combination of in situ molecular approaches, environmental genomics, traditional physiological techniques and qualitative modeling using primarily the coastal Ocean as a model system. The ultimate goal of these studies is to gain better understanding and predictability of environmental processes involving microorganisms, including successful bioremediation to avoidance of pathogen outbreaks in the environment.

The main focus of the Polz lab is the investigation of environmental genomics � understanding how native genomes interact with each other and with the environment. As microbial ecologists, we are interested in quantifying microbial populations in complex environmental settings, estimating diversity, isolating and studying large genomic fragments, and examining interactions within and among microbial populations. One of our model systems is oceanic bacterioplankton, which represent the largest microbial ecosystem on Earth.

Enumerating the organisms in the ocean
We are using molecular genomics methods to estimate the microbial diversity in a natural ecosystem. One ml of seawater contains about one million bacterial cells. Yet, more than 99% of marine microbes are difficult or impossible to culture and cannot be studied in the laboratory, including most of the dominant species. To estimate their diversity and relationships to one another, we study a subset of genes that are common to all microbial species, such as 16S rRNA. These model genes turn out to exhibit enormous genetic diversity even within a single sample of seawater, suggesting that a great number of genomes co-exist in the ocean. Our observation that many species have closely related sequences suggests that these communities undergo continuous creation of diversity by sequence mutation, but lack a strong mechanism to remove that diversity.

Genomic structures of closely related organisms
We have isolated a large strain collection of oceanic bacterioplankton for studies of genomic diversity. This collection, like other native species, exhibits a range of relationships -- from closely related to more distantly related. Analysis of genome structure shows that the closely related strains undergo extremely high levels of exchange of genetic material leading to co-existence of polymorphism within populations. Because such exchange of genetic material does not happen with equal frequency between more distantly related strains, we currently hypothesize that these mechanisms may delineate closely related strains as an "ecological/evolutionary unit." This unit may function in the marine bacterioplankton ecosystem in an analogous way that species function among eukaryotes.

Ecology of the mouse gut
The mammalian intestine is host to a large and diverse bacterial community -- up to 400 different species -- in which bacteria interact among themselves, with the host and with invading pathogens. One result of bacteria-pathogen interactions is the development of resistance to infection. In order to investigate the role of natural microflora in pathogen infections, we are collaborating with bioengineering investigators Jim Fox and David Schauer to study germfree mice that have been colonized with a standardized set of eight common anaerobic bacterial species (the so-called Altered Schaedler Flora set, or ASF) to protect them against common infections. We have developed quantitative assays for each of species, and we are now deploying these assays to study the spatial and temporal dynamics of these species throughout the mouse gut during pathogen infection. Ultimately, this model may lend important insights to studies of human intestinal pathogenesis.

Selected Publications

  • Acinas, S.G., Marcelino, L., Klepac-Ceraj, V., Polz, M.F. (2004) Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J. Bacteriol. 186(9):2629-2635.
  • Sarma-Rupavtarm, R.B., Ge, Z., Schauer, D.B., Fox, J.G., Polz, M.F. (2004) Spatial distribution and stability of the eight microbial species of the Altered Schaedler Flora in the gastrointestinal tract of mice. Appl. Environ. Microbiol. 70(5):2791-2800.
  • Klepac-Ceraj, V. Bahr, M., Crumb, B., Teske, A., Hobbie, J., Polz, M.F. (2004) High overall diversity and dominance of microdiverse relationships in salt marsh sulfate-reducing bacteria. Environ. Microbiol. 6(7):686-698.
  • Thompson, J.R., Randa, M.A., Marcelino, L..A., Tomita, A., Lim, E., Polz, M.F. (2004) Diversity and dynamics of a North Atlantic coastal vibrio community. Appl. Environ. Microbiol. 70(7):4103-4110.
  • Acinas, S.G., Klepac-Ceraj, V., Hunt, D.E., Pharino, C., Ceraj, I., Distel, D.L., Polz, M.F. (2004) Fine-scale phylogenetic architecture of a complex bacterial community. Nature. 430:551-554.

Last Updated: April 16, 2008