Fiscal Year 2002 Awards

Division of Biological Infrastructure

Postdoctoral Research Fellowships in Microbial Biology


Fellow’s Name Host Institution       Research Area/Training Plan           NSF Award #


Title of Research & Training Plan



Anne E. Arnold         Duke University           Systematic Biology                       0200413


"Diversity of fungi within living leaves: molecular insights into ecology and evolution of endophytic fungi in leaves of tropical trees."


Fungal endophytes, fungi inhabiting plants without causing disease, are highly diverse in tropical trees, yet are poorly known. This research assesses tropical endophyte diversity using (a) traditional isolations and multilocus sequencing and (b) direct amplification of endophyte DNA from leaves. Its overall goal is to integrate endophytes into the broader fungal phylogeny and explore the evolution of fungus-photobiont associations.

Anne E. Bernhard       University of Washington    Metabolic Biochemistry          0200512


"Measuring activity and diversity of ammonia-oxidizing bacteria in estuarine sediments."


This research focuses on ammonia-oxidizing bacteria as a model system to study the     relationship between microbial diversity and community processes in estuarine sediments. It employs real-time reverse transcription polymerase chain reaction (PCR) to measure changes in the expression of the enzyme responsible for ammonia oxidation, that is, ammonia monooxygenase (AMO).

Jennifer A. Bieszke           Michigan State University           Cell Biology                  0200228


"Role of histone deacetylases in the virulence of a plant pathogenic fungus."


Histone deacetylases (HDACs) are important regulators of many cellular processes. Four HDAC genes have been identified in the maize pathogen, Cochliobolus carbonum, and one of them has been shown to be important for virulence. Biochemical, immunological, and genetic techniques are being used to study the role of these HDACs in development and pathogenicity.




Alison Buchan             Yale University        Metabolic Biochemistry         0200164


"Retrieving novel bacterial genes involved in aromatic compound degradation from natural environments using Acinetobacter as a host."


Many naturally occurring aromatic compounds are broken down by microbes via the beta-ketoadipate pathway. This research manipulates the genetic system of a naturally transformable soil bacterium and uses it as a vehicle for understanding the versatility and diversity of this ecologically important pathway in uncultivated natural bacterial assemblages.

Sherry L. Dollhopf        Florida State University         Ecology        0200203


"The microbiology of iron reduction in the salt marsh."


This research is investigating the importance of microorganisms that use iron to obtain energy for growth in the salt marsh ecosystem. Comprehensive geochemical and microbiological laboratory techniques are being used to quantify the contribution of microbial iron respiration to total organic matter decomposition in different salt marsh environments to estimate the importance of iron respiration to carbon cycling on a marsh-wide scale. The diversity and community structure of iron-reducing microorganisms is being investigated using serial dilution cultures, 16S rRNA based techniques, fluorescent in situ hybridization, and microscopy. This research could lead to the discovery of new iron-reducing organisms that are important in coastal marine environments.

Melinda Duplessis    University of Washington   Evol & Ecol Physiology    0200104


"Chloroplast gene experssion studies on the toxic bloom-forming organism Heterosigma akashiwo during resting cell formation and activation."


Massive blooms of the toxic golden-brown alga Heterosigma akashiwo negatively impact all levels of the food web. It can form a resting stage that allows it to withstand stressful environmental conditions. This research examines chloroplast genes involved in environmental recognition and the regulatory processes that enable Heterosigma to enter and escape dormancy.

Katherine E. Gibson          Stanford University                Cell Biology                   0200482


"Symbiotic regulation and function of proteins in Sinorhizobium melilota Outer Membrane."


Sinorhizobium melilota, a gram negative bacterium, and the legume Medicago truncatula are partners in a symbiosis that requires coordinated differentiation for productive nodulation. This research seeks to identify bacterial outer membrane proteins (OMPs) differentially expressed in plant-associated bacteroids compared to free-living bacteria, to be followed by a genetic and physiological analyses of the role these proteins play at the interface of the bacterium and plant. This will enhance our understanding of the complex metabolic coupling between bacteria and plant required for nitrogen fixation.


David E. Graham           Virginia Tech University           Biochemistry            0200122


"Biosynthesis of two coenzymes in methanogenic microorganisms."


The methanogenic microorganism Methanococcus jannaschii grows in hydrothermal vents, using hydrogen and carbon dioxide to make methane gas. This project seeks to identify how M. jannaschii produces two coenzymes, Coenzyme M and Coenzyme B, which cooperate in the final steps of methanogenesis to release methane and conserve energy for the cell.

Christine V. Hawkes    University of California-Berkeley      Ecology      0200720


"Effects of plant roots, mycorrhizal fungi, and rhizosphere bacteria on soil carbon cycling."


The aim of this research is to elucidate how interactions among plants, arbuscular mycorrhizae, and rhizosphere bacteria affect carbon cycling both locally and at the ecosystem level. This requires a combination of DNA-based microbial community characterization, engineered bacterial reporter gene systems to detect specific carbon compounds, traditional isotope techniques and 13C PLFA for following the flow and fate of carbon, and an experimental design incorporating different rhizosphere communities from congeneric native and introduced plant species in CA and the UK. The results of this work will add to our understanding of microbial interactions in the rhizosphere and their consequences, improve our ability to predict system-level responses to global change, and add to our capacity to manage biological invasions.

Jason D. Hoeksema   U California-Santa Cruz    Ecol & Evol Physiology          0200129


"Does coniferous forest plant community composition influence the evolution of host specificity in mycorrhizal fungi?


We have little understanding of spatio-temporal variation in the interactions of mycorrhizal fungi with their host plants. This research investigates the impact of large-scale variation in plant community composition in the Pacific Northwest on the evolution of host specificity of ectomycorrhizal fungi in the genus Rhizopogon.

Nicole T. Liberati-Moore    Massachusetts General Hospital       Cell Biology       0200718


"Pseudomonas aeruginosa Multi-Host Virulence."


Using a novel system of invertebrate hosts to rapidly identify Pseudomonas aeruginosa genes that confer virulence, significant overlap in the genes required for pathogenesis in both invertebrate and mammalian hosts has been discovered, suggesting that the mechanisms that direct pathogenesis are common among the many hosts of P. aeruginosa. To dissect the molecular events of pathogenesis the role of the fatty acid biosynthesis gene, fabF, a gene isolated by multi-host screening, is being examined. Novel virulence factors are also being identified using a library of non-redundant mutants with a disruption in every non-essential open reading frame in the P. aeruginosa genome. The defined nature of this library allows exhaustive screening for all genes required for P. aeruginosa pathogenesis. Such analyses will provide a comprehensive view of the universal mechanisms employed by P. aeruginosa to infect its many hosts.

Timothy I. McLean        University of Southern California     Genetics       0200212


"Molecular analysis to identify genes that contribute to the establishment and maintenance of a protistan symbiosis."


Little is known at the molecular level about the mechanisms underlying symbiotic associations. This project seeks to identify the genes involved in the symbiosis between two protistan species. Biological screens for symbiosis using mutagenized symbionts and 2D gel electrophoresis will yield mutants or proteins, respectively, which can be used ultimately to derive DNA sequence. The sequence data will allow for the identification of the involved genes.

Charles E. Mitchell           Cornell University    Population Biology            0200469


"Effects of environmental change on a generalist microbial pathogen: barley yellow dwarf virus in wild grass communities."


A major challenge for microbial biology is to understand how environmental change affects microbes. Pathogenic microbes infecting multiple host species are influenced by altered host community composition. This research is testing how three other components of environmental change - nitrogen deposition, decreased species diversity, and land-use change - interact with host community composition to affect barley yellow dwarf virus, a generalist viral pathogen of grasses.

Karyn Lynn Newman     Univ California-Berkeley     Integrated Plant Biology      0200493


"Investigating the Role of Cell-to-Cell Communication by the Endophytic Bacterium Xylella fastidiosa in the Colonization of Grapevines."


Bacterial cells can communicate using signaling molecules, allowing them to monitor population size and to coordinate behavior as a group. Xylella fastidiosa colonizes the xylem vessels of plants, causing blockage and water-stress symptoms in some hosts. The role of cell-cell signaling and community behavior in successful colonization of the xylem is being investigated.

Jean J. Pan          University of Minnesota         Population Biology                0200378


"The fungal community on corn (Zea mays) resistant and susceptible to smut (Ustilago maydis)."


The effects of selective breeding and changing host genetic environment on non-target, potentially beneficial microorganisms are often overlooked. This research investigates these effects by studying the fungal microbial community on corn plants resistant or susceptible to one its major pathogens, smut. It will have important implications for understanding how altering the host plant genetic environment can affect species diversity and genetic structure of non-target microorganisms.

Jennifer A. Rudgers      Indiana University      Population Biology     0200485


"Do fungal endosymbionts of grasses structure community diversity and modify food web dynamics?"


Endophytic fungi form symbioses with grasses and produce toxic alkaloids that reduce herbivory to their hosts. This research evaluates how grass endophytes modify the diversity and dynamics of plant, pathogen, and arthropod assemblages and asks how fungal alkaloid chemistry influences these effects. This investigation will expand our understanding of how plant-microbe mutualisms influence community dynamics and biodiversity.

Chad W. Saltikov   Calif Institute of Technology     Metabolic Biochemistry    0200145


"Molecular characterization of microbial respiratory arsenate reduction: diversity and environmental expression of metalloid reductase genes."


Microbial respiratory arsenate reduction can significantly alter the mobility and toxicity of arsenic in the environment. Little is known about the molecular mechanisms for arsenic respiration. The research goals of this research are to identify genes involved in arsenate respiration in a variety of species, including Sulfurospirillum and Shewanella strains, and measure arsenate respiratory activity in contaminated sites.

Emily L. Stowe-Evans    Indiana University   Biochemistry of Gene Expression      0204235


"Microarray analysis to discover light-quality regulated genes in the cyanobacteria Fremyella diplosiphon."


Microarrays allow researchers to analyze global gene expression. Fremyella diplosiphon has an adaptive response to light color called complementary chromatic adaptatio(CCA). However, only three operons have been identified as regulated by light color. This research uses microarrays of PCR amplified genomic fragments to discover novel genes that are light color regulated and then uses gene-specific microarrays to examine the expression kinetics of these genes.

Paul D. Straight           Harvard University               Genetics                 0200307


"Bacterial-fungal interactions: novel signals and response mechanisms that influence development of bacterial communities in the presence of fungi."


In the natural environment, many microorganisms construct complex communities known as biofilms. This research focuses on signaling interactions between bacteria and fungi in the context of biofilms through characterization of multiple bacterial-fungal pairs. Genetic techniques and microarray analyses are being used to identify genes involved in dual-species interactions to define signaling mechanisms important to bacterial-fungal communities.

Alexis S. Templeton    Scripps Inst Oceanography    Metabolic Biochemistry     0200505


"Molecular and biogeochemical investigations of microbial communities associated with ocean-ridge basalts."


The proposed research is directed towards identifying which microorganisms are involved in the initial stages of basalt weathering reactions, their phylogeny and modes of metabolic activity, and how transient these microbial communities may be. The research combines sampling of marine, ocean-ridge environments with laboratory enrichment culturing techniques and molecular biology methods.

John C. Wertz           Yale University                  Ecol & Evol Physiology             0200631


"Have colicin type antibiotic genes evolved to increase their host bacteria

competitiveness, or are they selfish addictive genes?"


Colicin type bacteriocins are believed to have evolved as allelopathic agents that confer a competitive advantage to bacterial strains that harbor them. This research investigates an alternative hypothesis that colicin plasmids are selfish elements and utilize a form of post   segregational killing to insure their maintenance by host bacteria.



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