My research

Click this link for the most up-to-date list of Dr. Noll’s peer-reviewed publications in PubMed: Noll publications

The nature of the earliest ancestors of bacteria and the impact of horizontal gene transfer from Archaea to bacteria

Examinations of molecular sequences have provided pictures of the evolutionary history of microbial groups. One of the first and most comprehensive of these analyses, using sequences of genes encoding small subunit ribosomal RNAs, indicated that many of the most thermophilic extant microbes are the closest descendants of the common ancestor of all life. This hypothesis has been highly controversial and other measures of microbial evolution and the evolution of individual genes have not supported this concept. Extremely thermophilic or hyperthermophilic organisms are found largely in the archaeal group of microbes. Only two bacterial groups, the Aquificales and Thermotogales, have members that grow at temperatures high enough to consider them hyperthermophiles. Consequently the evolution of these bacterial groups is of interest in addressing the larger question of the nature of the common ancestor of archaea and bacteria. Recently members of the Thermotogales have been shown to be non-thermophilic, i.e. mesophiles. This raises the possibility that the extant Thermotogales species are actually descendants of mesophilic ancestors. Our laboratory, in collaboration with the lab of Peter Gogarten, is examining this question using newly available genome sequence data from several species of Thermotogales. We are doing so using sophisticated bioinformatics tools, synthesis of hypothetical ancestral genes, and examinations of the functions of putative ancestral proteins. Our studies will reveal features of the ancestors of this lineage of bacteria and will provide important information about how life evolves to adapt to different temperature environments.

(Work currently funded by the NASA Astrobiology: Exobiology and Evolutionary Biology program.)

The roles of horizontal gene transfer in the evolution of bacteria

The Thermotogales provide an interesting illustration of the potential impact of horizontal gene transfer on phylogenetic reconstruction and microbial adaptation. When the first genome sequenced of a species of Thermotogales, Thermotoga maritima , was determined , it was reported that over 20% of its genes (or "open reading frames") are most similar to those from the Archaea. Subsequent analyses that attempted to minimize the influence of these horizontally acquired genes so as to find the "true" ancestral position of the Thermotogales indicated that Thermotoga maritima is most closely related to the gram-positive bacteria, the Firmicutes. Two hypotheses were proposed to explain this finding. First, the Thermotogales are indeed a deep branching lineage as reflected in several single gene phylogenies or second that in genome based trees, the Thermotogales appear deep branching because the many genes they acquired from the archaea provide a signal that moves them away from their true relatives, the thermophilic Firmicutes. Our laboratory, in collaboration with Peter Gogarten's group, will attempt to differentiate between these hypotheses by examining phylogenies derived from the sequences of all the open reading frames in several Thermotogales genomes in an effort to discern the "true" phylogenetic position of this clade.

(Work currently funded by the National Science Foundation's Assembling the Tree of Life program.)

Hydrogen production from sugars by Thermotogales species

Recent interest in renewable fuels has spurred research concerning microbes capable of fuel production from biomass including wastes or cultivated plants. Many anaerobic microbes produce hydrogen gas during fermentation of sugars derived from these materials. Microbes that do so at high temperatures may provide benefits including increased yields of hydrogen or rates of hydrogen production. Our laboratory is conducting studies of species of the Thermotogales that are capable of hydrogen production from sugars in an effort to better understand how they carry out this process. We work in collaboration with Drs. Robert Kelly (North Carolina State University) and Paul Blum (University of Nebraska-Lincoln). Our portion of the project includes an effort to develop genetic tools in a newly isolated member of the Thermotogales, Kosmotoga olearia . This organism is unusual for this group because it can grow very well at moderate temperatures as well as high temperatures. It can also tolerate oxygen better than many members of this group. These and other features make it a promising candidate for genetic manipulation so that we can better dissect the hydrogen generation process in the laboratory. In addition, we are investigating the nature of the "toga" that surrounds the cells of these organisms. This outer layer of these cells contains two major proteins along with enzymes that allow cells to break down complex carbohydrates. We do not know if these enzymes are produced only when those carbohydrates are available or if the enzymes are arranged in the toga in a particular pattern that might allow them to work in concert with one another. These possibilities are being examined in our lab.

(Work currently funded by the US Dept. of Energy's Genomic Science program.