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School of Biological Sciences

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College of Sciences

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Center for the Study of Systems Biology

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Publication Search Results

Now showing 1 - 9 of 9

Genetic elements and molecular mechanisms driving the evolution of the pathogenic marine bacterium Vibrio parahaemolyticus

(Georgia Institute of Technology, 2009-07-06) Hazen, Tracy Heather

Vibrio parahaemolyticus is an opportunistic human pathogen that occurs naturally in a non-pathogenic form in coastal estuarine and marine environments worldwide. Following the acquisition of virulence-associated genes, V. parahaemolyticus has emerged as a significant pathogen causing seafood-borne illnesses. The mechanisms and conditions that promote the emergence of disease causing V. parahaemolyticus strains are not well understood. In addition, V. parahaemolyticus clinical strains isolated from disease-associated samples and environmental strains from sediment, water, and marine organisms have been identified with considerable diversity; however, the evolutionary relationships of disease-causing strains and environmental strains are not known. In the following research, the evolutionary relationships of V. parahaemolyticus clinical and environmental strains are examined. In addition, the contribution of genetic elements and molecular mechanisms such as deficiency of DNA repair to the evolution of V. parahaemolyticus clinical and environmental strains is shown. Molecular analysis of the evolutionary relationships of V. parahaemolyticus clinical and environmental strains demonstrated separate lineages of pathogenic and non-pathogenic strains with the exception of several environmental strains that may represent a reservoir of disease-causing strains in the environment. Sequence characterization of plasmids isolated from diverse environmental Vibrios indicated a role of plasmids in strain evolution by horizontal transfer of housekeeping genes. In addition, analysis of plasmids from V. parahaemolyticus clinical and environmental strains indicated the existence of a plasmid family distributed among V. parahaemolyticus, V. campbellii, and V. harveyi environmental strains. Sequence characterization of a plasmid of this family from a V. parahaemolyticus environmental strain indicated the contribution of these plasmids to the emergence of the clonal pandemic strains. Investigation of the role of molecular mechanisms to the evolution of V. parahaemolyticus strains showed that inactivation of the DNA repair pathway methyl-directed mismatch repair (MMR) increased the accumulation of spontaneous mutations leading to increased nucleotide diversity in select genes. The research findings in the following chapters demonstrate a considerable contribution of genetic elements and molecular mechanisms to the evolution of genetic and phenotypic diversity.
Molecular Characterization of Microbial Communities Fouling Concrete Infrastructures

(Georgia Institute of Technology, 2008-07-10) Giannantonio, David John

The objective of this study was to identify and characterize naturally-occurring communities of Bacteria and Fungi fouling the surfaces of concrete structures in Georgia, USA, through the use of culture-independent and culture-dependent approaches. Genomic DNA was extracted and ribosomal RNA genes were PCR amplified from 4 biofouled sites located in or around the cities of Atlanta, Gainesville, LaGrange, and Savannah. Bacterial and fungal community composition was determined by phylogenetic analysis. Molecular analysis revealed five bacterial phyla, and representatives of the phylum Cyanobacteria and the classes Betaproteobacteria and Gammaproteobacteria dominated the bacterial clone libraries. Fungal clone libraries showed the dominant phylotypes to be most closely related to Alternaria, Cladosporium, Epicoccum and Udeniomyces. Phylogenetically distinct microbial populations were present at each of the biofouled sites. In addition, cultured isolates were obtained from sites and tested for their ability to foul concrete of varied compositions under laboratory-controlled conditions. Biofouling tests revealed that fungal isolates obtained from the field were able to colonize concrete surfaces when supplied with moisture (95-100% relative humidity) and a nutrient source, and that fouling was affected by concrete water/cement ratio, surface roughness, and the presence of photocatalytically-activated cement added to inhibit microbial growth.
Multiscale analyses of microbial populations in extreme environments

(Georgia Institute of Technology, 2008-06-23) Martinez, Robert J.

Extreme environments created through natural and anthropogenic processes harbor microbes with diverse physiologies capable of catalyzing chemical reactions which are environmentally beneficial on local and global scales. This work focused on two unique environments, the Gulf of Mexico (GoM) submarine mud volcano systems and the subsurface soils at the Department of Energy s (DOE) Field Research Center (FRC) located in the Oak Ridge National Laboratory Reservation (Oak Ridge, TN). In addition to the physical and chemical extremes present within mud volcano sediments and FRC subsurface soils, these environments are sources of greenhouse gases as well as metal/radionuclide contaminants, respectively. Within the previously uncharacterized mud volcano cold seep sediments, culture-independent analyses of microbial community structure via DNA and RNA clone libraries indicated Gammaproteobacteria and anaerobic methane oxidizing Archaea as the dominant methane oxidizing taxa. Culture-dependent studies of FRC subsurface Arthrobacter and Bacillus isolates demonstrated extensive lateral gene transfer of the PIB-type ATPase metal resistance genes. Additionally, FRC Bacillus and Rahnella isolates demonstrated U(VI) sequestration capabilities as up to 95% soluble U(VI) was immobilization via biogenic phosphate mineral production resulting from constitutive nonspecific phosphohydrolase activity. Findings from these studies identify the prokaryotic diversity within aquatic and terrestrial sediments that contribute to the geochemical cycling of carbon, metals, and radionuclides.
Microbial diversity in sediments and gas hydrates associated with cold seeps in the Gulf of Mexico

(Georgia Institute of Technology, 2004-07-08) Mills, Heath Jordan

A molecular phylogenetic approach was used to characterize the composition of microbial communities from two gas hydrate sedimentary systems in the Gulf of Mexico. Nucleic acids were extracted from three distinct locales on surface breaching gas hydrate mounds, i.e., sediment overlaying gas hydrate, sediment/hydrate interface and sediment-free hydrate, and from three sediment depths, i.e., 0-2, 6-8 and 10-12 cm, in Beggiatoa sp. mat-associated sediments located several meters from exposed gas hydrate. Samples were collected from a research submersible (water depth 550-575 m) during two research cruises aboard the R/V Seward Johnson I and II funded by the NSF Life in Extreme Environments program. The 16S rRNA gene and 16S rRNA were amplified using PCR and reverse transcription-PCR, respectively, from DNA and RNA extracted from the total microbial community. The primers targeted microorganisms at the domain-specific, i.e., Bacteria and Archaea, and group-specific, i.e., sulfate-reducing bacteria (SRB) and putative anaerobic methane-oxidizing (ANME) archaea, level. Sequence analysis of the Bacteria clones revealed that the microbial communities were primarily dominated by Deltaproteobacteria. Other Proteobacteria classes, including Epsilon- and Gammaproteobacteria, represented a large fraction of the total microbial community isolated from the sediment overlying hydrate sample and the metabolically active fraction of the 0-2 cm sediment depth sampled from the Beggiatoa sp. mat-associated sediments. Sequence analysis indicated the majority of the archaeal clones were most closely related to Methanosarcinales, Methanomicrobiales and distinct lineages within the ANME groups. Several novel lineages were identified including a fourth ANME-2 clade, i.e., ANME-2D, and three clades with no closely related previously sequenced 16S rRNA gene clones or isolates, i.e., Unclassified Bacteria groups 1 and 2 and Unclassified Euryarchaeota. These studies represent the first 16S rRNA gene and 16S rRNA phylogenetic-based description of microbial communities extant in sediment-free gas hydrate and in methane-rich hydrate-associated and Beggiatoa sp.-associated sediments from a hydrocarbon seep region in the Gulf of Mexico.
A genetic system for studying uranium reduction by Shewanella putrefaciens

(Georgia Institute of Technology, 2002-08) Wade, Roy, Jr.
Differentiation of plasmids in marine diazotroph assemblages determined by randomly amplified polymorphic DNA analysis

(Georgia Institute of Technology, 2001-08) Beeson, Keri Elizabeth
Replicons derived from endogenously isolated plasmids used to classify plasmids occurring in marine sediment bacteria

(Georgia Institute of Technology, 2001-05) Cook, Marisa Anne
Practical applications of plasmids : overexpression of a bacterial alkaline phosphatase as a mechanism for heavy metal and radionuclide sequestration

(Georgia Institute of Technology, 2000-05) Powers, Leigh Gayle
Marine bacterial isolates utilize unique mercury resistance mechanisms

(Georgia Institute of Technology, 1999-08) Reyes, Nikolle Susanne