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May. 19, 2019

Research Experiences for Undergraduates

Microbiology in the Post Genome Era


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REU Speakers


Dr. Brian Hedlund

Invited Speaker (2013)

Dr. Brian Hedlund
Greg Fullmer Associate Professor of Life Sciences, University of Nevada, Las Vegas
Hedlund Lab

Title: Nitrogen Cycling in Terrestrial Geothermal Systems and Genomic Exploration of “Microbial Dark Matter”

Abstract: Thermophiles have been studied by microbiologists for decades; however, only a few studies have measured microbial activities in natural geothermal systems. As a result, our knowledge of the ecology of high-temperature ecosystems remains limited. We have studied the nitrogen biogeochemical cycle in geothermal springs by using a combination of approaches and have defined apparent upper temperature limits for ammonia oxidation (~82-85°C) and nitrite oxidation (~65°C). These limitations regulate the supply of oxidized nitrogen for denitrifiers.

We have also found that many springs in lower-temperature geothermal areas (e.g. away from Yellowstone) host abundant novel lineages that have never been cultivated in the lab – so-called “microbial dark matter”. Currently less than 50% of phylum-level lineages of Bacteria and Archaea have been cultivated and studied in the laboratory. The biology of these organisms is a major frontier in microbiology. We have combined single-cell genomics and metagenomics synergistically to reconstruct near-complete genomes from several “microbial dark matter” groups, allowing development of models on their evolution, cell architecture, physiology, and ecology. Our work on candidate phylum OP9, now called “Atribacteria”, will be discussed as an example.


Dr. William Adney

Invited Speaker (2012)

Dr. William Adney
Senior Microbiologist, Center for Agricultural and Environmental Biotechnology, Discovery and Analytical Sciences, Research Triangle Institute (RTI) International

Title: Microbial Production of Advanced Fuels

Abstract: The Department of Energy has invested in the microbial production of transportation fuels for a number of years. Although significant progress has been made there are still fundamental questions that must eventually be answered. In the area of enzymatic conversion of biomass to sugars the National Renewable Energy Laboratory (NREL) has contributed a wealth of information about the complex relationship between biomass composition, pretreatment, and the process of breaking the complex carbohydrates into their monosaccharide components. I will discuss some of the past work performed at NREL, current efforts being taken at RTI International, and challenges and barriers to the microbial production of advanced fuels from lignocellulosic biomass.


Dr. Mary Ann Moran

Invited Speaker (2011)

Dr. Mary Ann Moran
Professor, Department of Marine Sciences, University of Georgia
Moran Research Group

Title: Cloud Formation in a Genomic Era: Marine Bacteria and DMSP

Abstract: Marine bacteria play a crucial role in determining the fate of dimethylsufoniopropionate (DMSP), an abundant organic sulfur compound in ocean waters involved in ocean-atmosphere sulfur flux and cloud formation. Research using cultured bacteria in the marine Roseobacter lineage has allowed us to identify key bacterial genes that mediate DMSP degradation, including a homolog of the glycine cleavage T-family gene and two previously unknown genes related to fatty acid β-oxidation. One-third of surface ocean bacteria harbor homologs to these DMSP genes and thereby route a substantial fraction of global organic sulfur production into the marine microbial food web


Dr. David E. Graham

Invited Speaker (2011)

Dr. David E. Graham
Group Leader, BioSciences Division, Microbial Ecology & Physiology Group, Oak Ridge National Laboratory
Microbial Ecology & Physiology Group

Title: Enzymology and metabolic engineering of cellulose-degrading bacteria for renewable biofuel production

Abstract: Liquid transportation biofuels, such as biodiesel or bioethanol, can address future energy needs using renewable feedstocks. However, the economic feasibility and sustainability of cellulosic biofuels are limited by the inefficient breakdown of recalcitrant cellulose fibers into sugars and their microbial fermentation into biofuels and by-products. This process can be achieved in separate steps, or potentially combined into a single step, termed consolidated bioprocessing (CBP), which could reduce costs significantly. An efficient CBP scheme could either exploit a consortium of cellulolytic and ethanologenic microorganisms, or it could use a single, fully integrated microorganism. No natural microorganisms have been identified that possess all the characteristics necessary for the ideal CBP strain, therefore genetic engineering will likely be required to construct an efficient CBP microorganism. Three microbial systems will be discussed as prototypes for CBP, focusing on their biomass degredation and fermentation capabilities. We have developed defined growth conditions for the thermophilic cellulose-degrading bacterium Clostridium thermocellum, emphasizing nitrogen and sulfur assimilation to understand its physiology. Genetic engineering of the mesophilic Clostridium cellulolyticum bacterium has dramatically altered the mixture of fermentation products from cellulosic feedstocks, favoring alcohol production. Quantitative proteomic analysis of the extremely thermophilic Caldicellulosiruptor obsidiansis and Caldicellulosiruptor bescii has identified key strategies that these bacteria use to degrade plant material. Insights from these natural systems are informing new experiments to design improved CBP organisms by expanding substrate utilization and altering metabolic flux to produce more valuable bioproducts.


Dr. Bob B. Buchanan

Invited Speaker (2011)

Dr. Bob B. Buchanan
Professor, Executive Associate Dean, College of Natural Resources, University of California Berkeley
Plant and Molecular Biology at UC-Berkeley

Title: A 50-year Journey – from Anaerobes (Bacteria) to Aerobes (Plants) and Back to Anaerobes (Archaea)

Abstract: Abstract: The presentation summarizes my career as a scientist: college, graduate school, postdoctoral study and professional career. There are several lessons to be gained from my experience:

  • Microbiology provides an excellent foundation to launch a career in science
  • Follow your scientific interests irrespective of field
  • Collaborations may be key to achieving your goals
  • Although extremely useful, genome sequences may not be the final answer
  • Your findings may go against firmly held dogma. If so, believe in yourself and your data. Don't give up. In the end, truth will win the day


Dr. Lori Maggio-Hall

Invited Speaker (2010)

Dr. Lori Maggio-Hall,
Senior Research Microbiologist, DuPont Central Research and Development.
How DuPont developed a superior polymer.

Title: Metabolic Engineering of E. coli for the Commercial Production of 1,3-propanediol

Abstract: DuPont has established itself at the forefront of metabolic engineering through the successful development and commercial-scale implementation of a bioprocess to convert corn sugar to 1,3-propanediol (BioPDO). BioPDO is now widely available in a number of consumer products, from carpets to shampoo. This talk will highlight construction of the E. coli biocatalyst, including optimization of the BioPDO pathway and significant modification of the host's native metabolism to maximize carbon flux from glucose into the product pathway.



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Research Experience For Undergraduates (REU) Microbiology is funded by the National Science Foundation Award Number 1156954.