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UBC Theses and Dissertations

The biology of deep soil microbacteria Li, Ka Chi Jarvis


The use of antibiotics to treat bacterial infections has been one of the most significant breakthroughs in modern medicine. However, drug resistance is increasingly threatening the efficacy of the current repertoire of antimicrobials. The search for novel classes of antimicrobials from microbes in varied natural environments has become a useful approach to this issue. The topic of my thesis is to study the resistome and the microbial composition of deep soil samples collected from the Vancouver campus of UBC, and to use these soils in the isolation of Actinobacteria with the potential of producing new antimicrobials. The detection of antibiotic resistance genes in these soils was carried out by a PCR approach. I found a spatial relationship between the presence of genes aac(3), erm, vanX and tetM/otrA and the different microbial populations in various layers of soil. The bacterial community compositions of these soils were determined by metagenomic sequencing of the small subunit 16S rRNA gene. The results of these analyses prompted a search in the Actinobacteria-rich soil samples as the sources for isolation of novel antibiotic-producing bacteria. Twenty-two bacterial isolates were isolated and screened for the production of inhibitory compounds against a panel of bacterial pathogens. The principal focus of this thesis is the study of Microbacterium strains isolated from soil. Microbacterium is a genus of Actinobacteria first discovered in 1919 by Dr. Sigurd Orla-Jensen. To date, there have been 97 distinct species of microbacteria identified from a wide variety of natural, clinical and manmade environments. Representatives of the genus have been implicated as plant commensals and for the bioremediation of environmental contaminants. The microbacteria have not been studied for the production of antimicrobials. Microbacterium sp. D3N3, isolated from a deep soil sample, produces phenylacetic acid which displays broad-spectrum antimicrobial activity and other bioactivities such as gene activation in Staphylococcus aureus as well as weak additive interactions with the antibiotics tetracycline, colistin, ampicillin and novobiocin. Four microbacteriophages that infect two Microbacterium strains from this work were isolated from the UBC wastewater treatment plant, sea water and a soil sample from UBC Wreck beach.

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