Research

Microbial Cell Metabolism in Bacteria and Archaea

Our lab research focuses on understanding the physiology and molecular biology of anaerobic metabolism and associated gene control in model syntrophic and associated methanogenic microorganisms. We also study the structure and function of their associated cell envelopes using a variety of genetic, molecular and biochemical approaches:

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1) Genomics and Proteomics of the Syntrophic Bacteria  The Syntrophic Bacteria along with their Methanogenic Partners are experts in the anaerobic recycling of carbon materials in most marine and fresh water environments.  However, we know little about their metabolism, cell structure or ability to adapt to changing conditions. Using genomic, transcriptomic and proteomic tools we are elucidating core metabolic pathways for carbon utilization and energy harvesting in several model syntrophic microorganisms and suitable methanogenic partners. The longer term goal of these projects is to generate predictive metabolic models that describe the co-operative microbial partnerships that occur between the methanogenic hydrogen consumer and the syntrophic bacterium.

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2) Structure and Function of Microbial Cell Envelopes We are studying the composition and function of representative archaeal and bacterial cell envelopes. These structures often include a protein coat or surface layer that surrounds and protect the cell membrane from environmental challenges. As the archaea and bacteria colonize a wide range of habitats on Earth, they provide interesting views of how cell types adapt to environmental conditions of temperature, pH, salinity, pressure and light. For example, we recently isolated and identified the major cell envelope proteins of the archaeal srain Methanosarcina mazei where most were previously annotated as hypothetical proteins. One of these forms the primary outermost cell layer (termed an S-layer). The protein is post-translationally modified, exported and assembled into a semipermeable layer that surrounds and protects the cytoplasmic membrane. Recent studies have also revealed the first high resolution three-dimensional S-layer structure.

Other model organisms include several mesophilic methanogens Methanospirillum hungatei, Methanosarcina acetivorans and Methanosarcina barkeri in addition to the thermophilic sulfate and sulfur reducing microbes, Archaeoglobus fulgidus and Thermococcus kodakarensis.

3) Gene Regulation in Methanogenic Archaea Our research focuses on understanding the physiology and molecular biology of gene regulation in model bacteria and archaea. Emphasis is on the central pathways for cell respiration and carbon flow in pure as well as in co-cultures

The molecular basis of gene expression in the methanogenic archaea remains poorly understood relative to the bacteria. To address this we are studying how cells adapt to changing environmental conditions of nutrient and substrate availability in several model species. These highly evolved modern day microbes are believed to be derived from the most ancient microbes on Earth and thus provide interesting clues about the biochemical and molecular events that occurred early in evolutionary time.

4) Web-Assisted Undergraduate Microbiology Education We are authoring a series of web-based educational materials in support of undergraduate learning of basic microbiology principles. These topics include aspects of bacterial catabolic and anabolic metabolism, gene regulation, cell structure and cell biogenesis. The educational materials are available at the open-access web portal ecolistudentportal.org and are intended to complement traditional classroom experiences and build on the rich resources of the Escherichia coli model organism database located at EcoCyc.org.