Novel Means for Manipulating Bacterial Communities with Applications in Plant Growth Enhancement and Pathogen Reduction

Prokaryotes participate in every ecosystem on Earth and have tremendous impacts on the oceans, soil, plants, animals, and human bodies. While infections from these microorganisms continue to cause a large public health burden, they are also indispensable to many industries such as agriculture, food and pharmaceutical production, wastewater treatment, and bioremediation. It is therefore crucial to continuously develop new means to harness their beneficial impacts and reduce their harm. Nanobubble (NB) technology has attracted increasing attention due to its unique properties such as high aeration efficiency and ability to produce reactive oxygen species. NBs have proven suitable for diverse applications including algal bloom mitigation, wastewater treatment, and intracellular drug delivery. NBs can also promote the growth and health of various plants and animals, which might be mediated by interactions between NBs and microorganisms in soil, plant rhizosphere, and animal gut. Other studies have investigated the use of NBs as an environmentally friendly disinfectant to remove bacteria from water pipes and other surfaces with encouraging results. In this dissertation, I evaluated the potential of NB as a new means to manipulate microbial communities in two contexts: sustainable agricultural production and bacterial decontamination. For Aim 1, I examined the effects of different NB types on bacteria and archaea in soil and tomato rhizosphere using 16S rRNA gene sequencing. Soil samples treated with hydrogen NBs and oxygen NBs for 4 weeks had similar microbiome structures, which were distinct from the control. In addition, tomato plants irrigated with water containing nitrogen NBs and oxygen NBs for 32 days had significantly different rhizosphere microbiome than plants irrigated with tap water. Furthermore, NB treatment was associated with the enrichment of many beneficial bacterial taxa that contributed to soil nutrient turnover, metal resistance, and pathogen suppression. Network analysis also suggests that NBs facilitated microbial interactions and reduced niche formation. For Aim 2, I evaluated the potential of NBs to prevent and remove bacterial biofilms when used alone or in combination with other anti-biofilm agents. NBs significantly enhanced the effectiveness of sodium hypochlorite against planktonic Enterococcus faecalis and reduced biofilm formation by Escherichia coli and E. faecalis. The impacts of NBs on mature biofilms were also examined in a flow system with E. coli and a static system with E. faecalis. NBs achieved a 1.7-log reduction on E. coli cell count compared to control in the flow system, but did not have a significant effect on E. faecalis biofilms in the static system. While NB is a promising anti-biofilm agent, it is not easily applied in contexts such as routine surface disinfection in high-traffic facilities. Therefore, for Aim 3, I adapted one of the biofilm models in Aim 2 to assess the efficacy of an organosilicon-based disinfection product against surface contamination by Staphylococcus aureus. A field test was also conducted over 6 weeks at a university athletic facility. The test product persisted on surfaces and prevented S. aureus colonization for up to 30 days. In addition, weekly applications of the test product were more effective at reducing surface bacterial load in the field test than daily applications of a control product. Overall, this dissertation contributes to our understanding of how novel agents such as NBs interact with complex microbial communities, as well as highlights ways that existing antimicrobials may be combined or modified to enhance their effectiveness.