My research

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

To understand some of my research, I need to explain first how we go about studying the evolutionary history of microbes. The best way to find out the evolutionary relationships among different groups of microorganisms is to extract a kind of molecule from representatives of all the different groups that all the microbes possess.  One of the best molecules for this purpose is a ribonucleic acid (RNA) called the 16S ribosomal RNA. All bacteria and archaea have this. We can find out the composition of each 16S rRNA by determining the sequence of the four nucleotides that make up RNA. There are about 1500 nucleotides in each 16S rRNA and each group of microbes has a unique sequence of nucleotides. By comparing these sequences with one another one finds that close relatives have more similar sequences than distant relatives. Examinations of these sequences have provided a picture of the evolutionary history of all known microbial groups.

Currently funded research

Interspecies sharing of chromosomal genes among extremely thermophilic bacteria

The selective forces that dictate where horizontally acquired genes recombine and how they change in their new hosts has only been examined using sequence comparisons. In this project we are investigating the mechanisms behind these processes of horizontal gene transfer using laboratory adaptive evolution experiments. Those experiments involve growing different strains or species of bacteria together in the lab and measuring when genes are shared between them. We are examining chromosomal gene transfers between different species under different levels of selection to determine where genes recombine and how they are expressed in their new host. Our first experiments are using DNA extracted from different thermophilic hosts to transform mutants of Thermus thermophilus as the host species. Later we plan to grow these T. thermophilus mutants with living cells of two of those DNA donors in co-cultures to then determine if the host strains can acquire traits from the donor cells.

(This work is funded by the NASA Astrobiology: Exobiology and Evolutionary Biology program.)

Previously funded research

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

Many analyses of 16S rRNA sequences indicated that the most thermophilic (high temperature-loving) microbes are the closest descendants of the common ancestor of all life. Extremely thermophilic or “hyperthermophilic" organisms mostly belong to the Archaea, a group of microbes that look like Bacteria, but are not closely related to them. Only two bacterial groups, the Aquificae and Thermotogae, 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. Some members of the Thermotogae were shown to be non-thermophilic, so-called mesophiles. This raises the possibility that today’s Thermotogae species are actually descendants of mesophilic ancestors. Our laboratory, in collaboration with the lab of Dr. Peter Gogarten, examined whether a group of Thermotogae species, those of the Thermotoga genus, evolved from a thermophilic or a mesophilic ancestor. To do so we recreated proteins from ancestors of living Thermotoga species. By comparing the amino acid sequences of a protein common to the living species, we were able to surmise the sequences of the same protein in their ancestors. The gene encoding this protein was inherited by a Thermotoga ancestor from a member of the Archaea and we could determine the sequence of that ancestral protein, too. By examining the protein sequences from several living archaea, we could surmise the sequences of archaeal versions of this protein. We constructed genes encoding these extinct proteins and had E. coli synthesize them. We studied the properties of these proteins and found all of them were stable to much higher temperatures than those of their living descendants. This supports the hypothesis that the ancestor of the Thermotoga lineage was much more thermophilic and also that the ancestors of the archaea, some of which currently grow at 100°C, also lived at higher temperatures. This suggests that these lineages did descend from much more thermophilic ancestors.

(This work was funded by the NASA Astrobiology: Exobiology and Evolutionary Biology program.)

The roles of horizontal gene transfer in the evolution of bacteria

The Thermotogae provide an interesting illustration of the potential impact of horizontal gene transfer on phylogenetic reconstruction and microbial adaptation. When the first genome of a species of Thermotogae, from Thermotoga maritima, was sequenced, it was reported that over 20% of its genes 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 Thermotogae indicated that T. maritima is most closely related to the Gram-positive bacteria, the Firmicutes. Two hypotheses were proposed to explain this finding. First, the Thermotogae are indeed a deep branching lineage as reflected in several single gene phylogenies or second that in genome based trees, the Thermotogae 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, attempted to differentiate between these hypotheses by examining phylogenies derived from the sequences of all the open reading frames in several Thermotogae genomes in an effort to discern the "true" phylogenetic position of this clade. We found that the Thermotogae are a lineage that diverged early from the other bacteria and have exchanged many genes with Firmicutes. Many of those genes encode functions allowing them to use a variety of different kinds of sugars, so perhaps acquiring these genes has allowed them to live in new environments where those sugars are abundant.

(This work was funded by the National Science Foundation's Assembling the Tree of Life program.)

Hydrogen production from sugars by Thermotogales species

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 was part of a collaboration of labs that conducted studies of species of the Thermotogae that are capable of hydrogen production from sugars in an effort to better understand how they carry out this process. We worked in collaboration with Drs. Robert Kelly (North Carolina State University) and Paul Blum (University of Nebraska-Lincoln). Our portion of the project investigated the nature of the "toga" that surrounds the cells of these organisms. This outer layer contains two major structural proteins along with enzymes that allow cells to break down complex carbohydrates. We were able to identify the genes that encode the major structural protein as well as identify new genes that encode the varieties of the second structural protein. We also found an unusual pattern of evolution of this secondary protein among other members of the Thermotogae.

(This work was funded by the US Dept. of Energy's Genomic Science program.

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