Browsing by Subject "Archaea"

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    Cataloging Essential Genes for Natural Transformation and Expanding Genetic Tools for Study of Archaea
    (2023-04) Fonseca, Dallas
    Horizontal gene transfer is a near ubiquitous way for organisms to acquire new geneticinformation. One mechanism of horizontal gene transfer is natural transformation, the uptake/incorporation of DNA from the environment into the genome. In Bacteria, DNA uptake has been well documented in numerous phylogenetically diverse species. Across all of these organisms, four operational steps have to occur. First, the pathway must be induced, entering cells into a state known as competence. Extracellular appendages on the cell then reach out from the cell surface and adsorb DNA. DNA is subsequently translocated through a transporter ComEC and bound by intracellular single-strand binding proteins for integration into the genome. In Archaea, no mechanism of natural transformation has been previously identifiedand homologs of bacterial competence genes are sparse. Presented here is the identification of the process of natural transformation in two distinct members of the Archaea. Using a variety of genetic techniques, I identify several components that are essential to the natural transformation pathway. This includes Type IV-like pili, putative membrane-bound substrate transporters, proteins predicted to bind DNA, as well as several hypothetical proteins. While this thesis provides the first catalog of genes essential to natural transformation, the exact mechanism that underlies this process is still elusive. The later chapters of this thesis will discuss preliminary approaches to determine the mechanisms of natural transformation mediated DNA uptake.
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    Planktonic archaeal diversity and ammonia-oxidizer abundance change with depth in Lakes Malawi, Kivu and Superior
    (2014-05) Munoz Ucros, Juana
    Planktonic Archaea may play a key role in the nitrogen cycle by oxidizing ammonia, but little is known about these microbes in large lakes of the world. Differences in the abundance of total Archaea, marine group I Archaea (MG-1), and ammonia-oxidizing Archaea (AOA) measured in 2010, 2011, and 2012 were compared during stratified conditions in Lake Malawi, a tropical African great lake, to previous work completed in Lake Superior and Lake Kivu. Total Archaea, MG-1, and AOA abundances increased by more than two orders of magnitude in Lake Malawi from the warm epilimnion to the oxic upper hypolimnion during thermally stratified conditions from November to January, but remained abundant in the deeper anoxic hypolimnion. 16S rRNA clones related to the Thaumarchaeota, possible ammonia oxidizers, and archaeal clones from previous work in Lake Victoria were present in both Lake Malawi and Kivu, and euryarchaeal clones were common in the deeper anoxic waters. The distribution and diversity of planktonic Archaea in this tropical great lake was similar to that in Lake Superior, a temperate great lake of comparable trophic status.While more detailed seasonal work about archaeal abundance and community diversty has been completed in the western basin of Lake Superior, spatial patterns of archaeal distribution have not been evaluated across this lake. Here, I compared the abundance of these 3 archaeal gene markers in the epilimnion and hypolimnion from seven sites across Lake Superior during the stratified period in 2009 and 2010. The abundance of the total Archaea, MG-1, and AOA was consistently lower in the epilimnion, and at least an order of magnitude higher in the hypolimnion at all sites. Although my aim was not to elucidate the causes of such distribution in Lake Superior, this study does provide additional evidence that planktonic Archaea are more abundant in colder waters of the hypolimnion and their abundance is restricted in the surface waters of thermally stratified lakes.
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    Supporting data for The fluorescence-activating and absorption-shifting tag (FAST) enables live-cell fluorescence imaging of Methanococcus maripaludis
    (2022-05-06) Hernandez, Eric; Costa, Kyle; kcosta@umn.edu; Costa, Kyle; University of Minnesota Costa Lab
    Microscopy images of Methanococcus maripaludis cells expressing FAST1 tagged to different genes involved in methanogenesis. Images were used for quantification of protein expression in live cells.