Fiscal Year 2001 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 and Training Plan

Douglas Abbot University of Texas Austin Ecological & Evolutionary Physiology 0102094
Evolutionary patterns and processes in symbiotic fungi associated with fungus-growing ants
Many microbes form close associations ("symbioses") with plants and animals. Symbiosis involves a dramatic change for microbial species, permitting us to understand how differences in life styles and environments shape microbial biodiversity and evolution. Fungus-growing ants in the Neotropical tribe Attini (Formicidae) comprise a group of about 200 described species which are all dependent on the cultivation of fungus for food. Some ants repeatedly domesticated fungi from free-living stock, while other associations are ancient and highly specialized. This study explores how symbiotic associations have shaped the evolutionary processes and patterns in the fungal symbionts of attine ants. It further seeks to determine if symbiosis with ants involves a switch from sexual reproduction to reproduction without sex. The proposed work will provide valuable insights into how intimate associations with ants have shaped the patterns and processes of evolution in symbiotic fungi.

Laura Broughton Marine Biological Laboratory Ecosystem Studies 0102108
Understanding the role of the soil microbial community in the arctic tundra: integrating microorganisms with climate change theory
Soil microorganisms control the flow of nitrogen, carbon, and phosphorus through ecosystems. Soil samples are being taken from established sites which have undergone existing long-term manipulations of temperature and nutrient and light availability. The sample microbial communities in these samples are being studied to determine whether treatments known to affect plant communities also affect soil microbial biomass, activity, and community composition as measured by terminal restriction fragment length polymorphisms (tRFLP).

Christina Burch University of Idaho Population Biology 0102079
Can selection to minimize the effects of translational and/or mutational errors explain codon usage patterns in microbes despite their diversity?
The investigation of error minimization mediated by biased codon usage will be extended from bacteria to their bacteriophage parasites, using both comparative genome analyses of natural isolates and laboratory evolution experiments. Primarily, the research pursues the preliminary observations that patterns of codon usage bias in bacteria appear to reflect selection for error minimization, and phage genome type (e.g. dsDNA vs. ssDNA) appears to influence the degree of error minimization, but not the degree to which phage codon usage reflects host codon usage.

Mary Connolly University of Dayton Ecological & Evolutionary Physiology 0102085

Effects of bacterial signal mimic compounds produced by pea plants on the nitrogen-fixing symbiont Rhizobium leguminosarum
Cell-to-cell signaling within a bacterial population, "quorum sensing," plays a major role in bacterial growth, survival, and host-microbe interactions. The sponsoring scientists have shown that peas secrete "signal mimics," compounds which interact specifically with bacterial quorum-sensing receptors. This is a comprehensive study of quorum-sensing-regulated gene expression in Rhizobium leguminosarum, by determining the effects of pea signal mimics on gene expression, behavior, diversity, and viability in the rhizosphere.

Cindy DeLoney Loyola Univesity Chicago Microbial Genetics 0102114
Conversations between bacterium and squid: Studying the genetics behind V. fischeri's response to its symbiotic host, E. scolopes
Colonization of the squid, E. scolopes, by its bacterial symbiont, V. fischeri, requires the bacterial sensor kinase RscS. This research tests the hypothesis that RscS regulates other genes essential to the symbiosis by identifying these genes using a variety of molecular methods. Further, laser-scanning confocal microscopy is being used to identify where in the symbiosis process RscS is required.

Christopher Francis Princeton University Ecology 0102106
Molecular characterization of microbial nitrite reductase genes from a permanently ice covered Antarctic lake
Lake Bonney is a permanently ice-covered, chemically-stratified Antarctic lake that is unusual in that denitrification occurs in the deep anoxic waters of the east but not the west lobe. The goal of this project is to compare the distribution, diversity, and expression of denitrification genes (nitrite reductase) from microorganisms in the two lobes in an attempt to explain this mystery.

Eric Johnson University of California Berekely Metabolic Biochemistry 0102092
Producing hydrogen gas from sunlight and water using green algae
The photosynthesis pathway in green algae can be altered to produce hydrogen instead of oxygen. This research tests if the algae's need for metabolic energy is the driving force behind this solar-powered hydrogen production. An understanding of this phenomenon will aid in the development of green algae as an alternative-energy fuel source.

Brian Leander University of British Columbia Systematic Biology 0102097
The Origin and Early Evolution of Apicomplexans
Apicomplexans are microbial parasites that appear to have descended from phototrophic dinoflagellates. "Aseptate gregarines" are apicomplexans that inhabit marine worms and possess many ancestral features. Moreover, many taxa of uncertain phylogenetic position possess apicomplexan-like characteristics. Morphological and molecular phylogenetics of these "enigmatic taxa" are being investigated and are expected to throw light on apicomplexan origins and the evolution of novel characters.

Anthea Lee California Institute of Technology Microbial Genetics 0102080
Development of a two-species biofilm to study bacteria-bacteria interactions
This project applies the power of bacterial genetics to an environmental biofilm to determine the intricate associations between 2 different species of bacteria. Shewanella and Desulfovibrio species are ubiquitous environmental bacteria that form natural biofilms and promote steel corrosion. This ecological system is genetically and chemically tractable and is being used to develop a model for a 2-species biofilm to examine the structural impact of each species on the biofilm, identify and characterize genes that are induced or expressed during biofilm development, and identify parameters essential for maintaining the 2-species biofilm.

Scott Miller North Carolina State University Population Biology 0102100

Evolutionary genetics of ecological diversification in cyanobacterial populations from hot spring habitats differing in nitrogen availability
Understanding how ecological differences evolve in microbial populations is essential for explaining the magnitude and distribution of microbial diversity. This research uses a combination of quantitative, population and developmental genetic approaches to: test for ecological divergence between populations of the cyanobacterium Mastigocladus laminosus from habitats differing in nitrogen availability; evaluate the evolutionary processes shaping ecological structure in these populations; and link molecular genetic variation to variation in the ability to assimilate different nitrogen sources.

Beronda Montgomery Indiana University Molecular Biochemistry 0102084
Utilizing biochemical and genetic methods to dissect how a cyanobacterium senses and responds to changing light conditions
The test organism is Fremyella diplosiphon. A detailed biochemical analysis is being made of RcaE, a putative phytochrome-like photoreceptor that controls the process of complementary chromatic adaptation (CCA). Specifically, the experiments address the phosphorelay model which holds that RcaE is the photoreceptor that differentially controls the phosphorylation state of the response regulator RcaF in different light qualities, which in turn regulates the phosphorylation levels of RcaC.

David Reed University of Utah Ecological & Evolutionary Physiology 0102112
Molecular studies of microbial coevolution and endosymbiosis in a complex assemblage of hosts
Chewing lice that infect birds harbor endosymbiotic bacteria (putatively Rickettsia) in specialized cells. Lice probably require these bacteria for digestion of the feathers on which they live. Selected nucleic acids are being sequenced to correctly place these bacteria in a phylogeny. Rates of evolution are being compared and cophylogeny with their hosts is being tested. Finally, the effect of endosymbiosis on nucleotide sequence evolution is being evaluated.

Tara Sirvent Boyce Thompson Institute Metabolic Biochemisty 0102090
Using the Tools of Molecular Biology and Chemistry to Characterize Pigment Biosynthesis in the Chestnut Blight Fungus
The goal of this research is to analyze the pathway for production of polyketide pigments in the fungus Cryphonectria parasitica. Genes required for biosynthesis of emodin and other related anthraquinone compounds are being cloned, sequenced, and characterized from an ordered cosmid library and by PCR amplification of PKS genes. These approaches will permit analysis of genetic diversity within a conserved pathway present in numerous fungi and plants.

Bongkeun Song Princeton University Biochemistry of Gene Expression 0102078
Genetic Diversity in Benzoate Degrading Denitrifying Bacteria and Environmental Samples
Genetic diversity of 16S rRNA, nitrite reductase, and benzoyl-CoA reductase in bacteria capable of degrading benzoate under denitrifying conditions are being investigated with bacterial pure cultures isolated from estuarine sediments of a contaminated landfill site. In addition, DNAs will be extracted directly from the same sediment and environmental DNA clonal libraries (metagenome library) will be constructed to link the different kind of genetic information obtained from 16S rRNA genes and functional genes involved in benzoate degradation and denitrification in the environment.

John Spear University of Colorado, Boulder Systematic Biology 0102111
Microbial Diversity and Hydrogen in the Yellowstone Ecosystem
The goal of this work is to describe the microbial composition and metabolic underpinnings of the Yellowstone geothermal ecosystem, with the hypothesis that hydrogen is the primary biological energy source. First, hydrogen concentration in waters are being measured. Then, the associated biomass, consisting of hydrogen-metabolizing microorganisms, is being characterized using a molecular phylogenetic approach.

Christopher Steiner Rutgers University Ecology 0102105
Effects of energy, environmental variation, and dynamic constraints on the structure of experimental microbial food webs

A lab-based microbial system, comprised of bacteria, autotrophic algae, heterotrophic protozoa, and rotifers, is being used to determine the effects of environmental variability and energy on the emergent structure of food webs. Webs of varying complexity are experimentally perturbed and changes in web structure are compared to stability measures to assess how perturbations and stability-complexity interact to generate community organization.

Jennifer Wilcox University of Arizona Ecological & Evolutionary Physiology 0102096
Coevolution at the genomic level of aphids and their bacterial endosymbionts
An ancient association between the aphid, Melaphis rhois, and its bacterial endosymbiont, Buchnera aphidicola, has produced an obligate mutualism in which symbionts provide essential amino acids to their hosts. Buchnera gene expression patterns over the course of the host complex life cycle are being characterized using microarray technology.

Charles Wolgemuth University of California Berkeley Cellular Organization 0102095
Can Bacteria Move by Slime Extrusion? The physics of A-type motility in Mxyococcus xanthus
Myxococcus xanthus moves by gliding utilizing two distinct genetic mechanisms: social (S) and adventurous (A) motility. This is a study of A-type motility using a slime extrusion model based on a nozzle-like organelle discovered in cyanobacteria. A theoretical model is being explored and experiments performed to determine if this type of mechanism can drive A-motility.

Erik Zinser Massachusetts Institute of Technology Ecological & Evolutionary Physiology 0102109
Developing gene expression tools to identify the physiological states of natural populations of a marine cyanobacterium
The important physiological activities of microorganisms that facilitate their survival and define their roles within an ecosystem are largely unknown. This research focuses on adapting new gene expression technologies (DNA microarrays, in situ RT-PCR, and proteomics) to identify the environmentally-significant physiological activities of the highly-abundant, globally-significant marine cyanobacterium, Prochlorococcus spp.