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- All Subjects: Microbiology
- Creators: Abbaszadegan, Morteza
Description
This thesis research focuses on phylogenetic and functional studies of microbial communities in deep-sea water, an untapped reservoir of high metabolic and genetic diversity of microorganisms. The presence of photosynthetic cyanobacteria and diatoms is an interesting and unexpected discovery during a 16S ribosomal rRNA-based community structure analyses for microbial communities in the deep-sea water of the Pacific Ocean. Both RT-PCR and qRT-PCR approaches were employed to detect expression of the genes involved in photosynthesis of photoautotrophic organisms. Positive results were obtained and further proved the functional activity of these detected photosynthetic microbes in the deep-sea. Metagenomic and metatranscriptomic data was obtained, integrated, and analyzed from deep-sea microbial communities, including both prokaryotes and eukaryotes, from four different deep-sea sites ranging from the mesopelagic to the pelagic ocean. The RNA/DNA ratio was employed as an index to show the strength of metabolic activity of deep-sea microbes. These taxonomic and functional analyses of deep-sea microbial communities revealed a `defensive' life style of microbial communities living in the deep-sea water. Pseudoalteromonas sp.WG07 was subjected to transcriptomic analysis by application of RNA-Seq technology through the transcriptomic annotation using the genomes of closely related surface-water strain Pseudoalteromonas haloplanktis TAC125 and sediment strain Pseudoalteromonas sp. SM9913. The transcriptome survey and related functional analysis of WG07 revealed unique features different from TAC125 and SM9913 and provided clues as to how it adapted to its environmental niche. Also, a comparative transcriptomic analysis of WG07 revealed transcriptome changes between its exponential and stationary growing phases.
ContributorsWu, Jieying (Author) / Meldrum, Deirdre R. (Thesis advisor) / Zhang, Weiwen (Committee member) / Abbaszadegan, Morteza (Committee member) / Neuer, Susanne (Committee member) / Arizona State University (Publisher)
Created2013
Description
Water quality in surface water is frequently degraded by fecal contamination from human and animal sources, imposing negative implications for recreational water use and public safety. For this reason it is critical to identify the source of fecal contamination in bodies of water in order to take proper corrective actions for controlling fecal pollution. Bacteroides genetic markers have been widely used to differentiate human from other sources of fecal bacteria in water. The results of this study indicate that many assays currently used to detect human-specific Bacteroides produce false positive results in the presence of freshwater fish. To further characterize Bacteroides from fish and human, the fecal samples were cultured, speciated, and identified. As a result, forty six new Bacteroides 16S rRNA gene sequences have been deposited to the NCBI database. These sequences, along with selected animal fecal sample Bacteroides, were aligned against human B. volgatus, B. fragilis, and B. dorei to identify multi-segmented variable regions within the 16S rRNA gene sequence. The collected sequences were truncated and used to construct a cladogram, showing a clear separation between human B. dorei and Bacteroides from other sources. A proposed strategy for source tracking was field tested by collecting water samples from central AZ source water and three different recreational ponds. PCR using HF134 and HF183 primer sets were performed and sequences for positive reactions were then aligned against human Bacteroides to identify the source of contamination. For the samples testing positive using the HF183 primer set (8/13), fecal contamination was determined to be from human sources. To confirm the results, PCR products were sequenced and aligned against the four variable regions and incorporated within the truncated cladogram. As expected, the sequences from water samples with human fecal contamination grouped within the human clade. As an outcome of this study, a tool box strategy for Bacteroides source identification relying on PCR amplification, variable region analysis, human-specific Bacteroides PCR assays, and subsequent truncated cladogram grouping analysis has been developed. The proposed strategy offers a new method for microbial source tracking and provides step-wise methodology essential for identifying sources of fecal pollution.
ContributorsKabiri-Badr, Leila (Author) / Abbaszadegan, Morteza (Thesis advisor) / Bingham, Scott (Committee member) / Rock, Channah (Committee member) / Fox, Peter (Committee member) / Mclain, Jean (Committee member) / Arizona State University (Publisher)
Created2012
Description
Nanotechnology is a scientific field that has recently expanded due to its applications in pharmaceutical and personal care products, industry and agriculture. As result of this unprecedented growth, nanoparticles (NPs) have become a significant environmental contaminant, with potential to impact various forms of life in environment. Metal nanoparticles (mNPs) exhibit unique properties such as increased chemical reactivity due to high specific surface area to volume ratios. Bacteria play a major role in many natural and engineered biogeochemical reactions in wastewater treatment plants and other environmental compartments. I have evaluated the laboratory isolates of E. coli, Bacillus, Alcaligenes, Pseudomonas; wastewater isolates of E. coli and Bacillus; and pathogenic isolate of E. coli for their response to 50 & 100 nm sized Cu nanoparticles (CuNPs). Bactericidal tests, scanning electron microscopy (SEM) analyses, and probable toxicity pathways assays were performed. The results indicate that under continuous mixing conditions, CuNPs are effective in inactivation of the selected bacterial isolates. In general, exposure to CuNPs resulted in 4 to >6 log reduction in bacterial population within 2 hours. Based on the GR, LDH and MTT assays, bacterial cells showed different toxicity elicitation pathways after exposure to CuNPs. Therefore, it can be concluded that the laboratory isolates are good candidates for predicting the behavior of environmental isolates exposed to CuNPs. Also, high inactivation values recorded in this study suggest that the presence of CuNPs in different environmental compartments may have an impact on pollutants attenuation and wastewater biological treatment processes. These results point towards the need for an in depth investigation of the impact of NPs on the biological processes; and long-term effect of high load of NPs on the stability of aquatic and terrestrial ecologies.
ContributorsAlboloushi, Ali (Author) / Abbaszadegan, Morteza (Thesis advisor) / Alum, Absar (Committee member) / Fox, Peter (Committee member) / Olson, Larry (Committee member) / Arizona State University (Publisher)
Created2012
Description
Megapolitan cities have emerged due to unprecedented urban migration. These changes strain urban resources, especially water distribution and treatment systems. The recent rise of Legionella cases linked to water distribution systems highlights this issue.Bacterial growth and biofilm formation are influenced by factors, such as type and concentration of residual disinfectant, pipe material, water temperature. Experiments were conducted in identical model water distribution systems (WDSs) constructed of three different pipe materials: galvanized steel, copper, and cross-linked polyethylene (PEX) operated under a continuous flow rate of 15 L/min. Each model WDS includes 11 steel coupons screwed to the water distribution pipes. City of Tempe (Arizona) municipal water was used in the experimentation, with no nutrients added. Following biofilm growth, coupons were removed and processed by scrubbing biofilm into
phosphate-buffered saline (PBS). Reasoner's 2A (R2A), Trypticase Soy Agar (TSA), Brilliant, and buffered charcoal yeast extract (BCYE) agar media were used to examine biofilm samples for heterotrophic plate counts (HPC), metabolically active bacteria, E coli,
and Legionella. Simultaneously, water samples from the reservoirs of model WDSs were also collected and examined for the same bacteria.Next, an electrochlorination cell maintained free chlorine residuals in unheated PEX and copper model WDSs. These two systems maintained free chlorine residuals for one week and evaluated biofilm and bacterial kinetics. Higher water temperature increased biofilm development. Bacterial counts in biofilms were higher on new (fresh) coupons compared to the old coupons. Heterotrophic and metabolically active bacteria behaved similarly. Only control and heating systems in copper water reservoirs have Legionella spp. Biofilms
formed less on copper systems than steel and PEX systems. Initially, PEX had more HPC than copper. After electrochlorination, HPC concentration in the PEX system rapidly declined to non-detect, whereas in the copper system dropped to 0.54 log CFU/mL.
Thus, higher temperature increases biofilm growth on all pipe materials and reservoirs bacterial concentration. Electrochlorination is a potential biofilm and microbial disinfection method. This thesis topic investigated how these parameters affect the model distribution system bacterial populations and biofilm growth.
ContributorsKolahi Kouchaki, Bita (Author) / Abbaszadegan, Morteza (Thesis advisor) / Alum, Absar (Committee member) / Perreault, Francois (Committee member) / Arizona State University (Publisher)
Created2022
Description
Water quality assessment is essential for maintaining healthy ecosystems and protecting human health. Data interrogation and exploratory data analysis techniques are used to analyze the spatial and temporal variability of water quality parameters, identifying correlations, and to better understand the factors that impacts microbial and chemical quality of water. The seasonal dynamics of microbiome in surface waters were investigated to identify the factors driving these dynamics. Initial investigation analyzed two decades of regional water quality data from 20 various locations in Central Arizona, USA. Leveraging advanced data science techniques, the study uncovered correlations between crucial parameters, including dissolved organic carbon (DOC), ultraviolet absorbance (UVA), and specific ultraviolet absorbance (SUVA). These findings provide foundational insights into the dynamic of overall water quality. A comprehensive 12-month surface water sample collection and study was conducted to investigate potential bias in bacterial detection using EPA approved Membrane Filtration (MF) technique. The results underscore that while MF excels in recovering bacteria of public health significance, it exhibits biases, particularly against small and spore-forming bacteria and Archaea, such as Bacilli, Mollicutes, Methylacidiphilae, and Parvarchaea. This emphasizes the importance of complementing standard microbiology approaches to mitigate technological biases and enhance the accuracy of microbial water quality testing, especially for emerging pathogens. Furthermore, a complementary study of microbial dynamics within a model drinking water distribution systems (DWDSs) using treated water from the same source water as the above study. The influence of pipe material and water temperature on the microbiome and trace element composition was investigated. The research unveiled a preferential link between pipe material and trace elements, with water temperature significantly impacting the microbiome to a higher degree than the chemical composition of water. Notably, Legionellaceae and Mycobacteriaceae were found to be prevalent in warmer waters, highlighting the substantial influence of water temperature on the microbiome, surpassing that of pipe material. These studies provide comprehensive insights into the spatial and temporal variability of water quality parameters. Analyzing microbial data in depth is crucial in detecting bacterial species within a monitoring program for adjusting operational conditions to reduce the presence of microbial pathogens and enhance the quality of drinking water.
ContributorsAloraini, Saleh (Author) / Abbaszadegan, Morteza (Thesis advisor) / Fox, Peter (Committee member) / Perreault, Francois (Committee member) / Alum, Absar (Committee member) / Arizona State University (Publisher)
Created2023
Description
This dissertation focused on studying risks associated with emerging drinking water contaminants and tradeoffs related to water management interventions. The built environment impacts health, as humans on average spend ~90% of their time indoors. Federal regulations generally focus on drinking water at the water treatment plant and within the distribution system as opposed to when it enters buildings after crossing the property line. If drinking water is not properly managed in buildings, it can be a source or amplifier of microbial and chemical contaminants. Unlike regulations for chemical contaminants that are risk-based, for pathogens, regulations are either based on recommended treatment technologies or designated as zero, which is not achievable in practice. Practice-based judgments are typically made at the building level to maintain water quality. This research focuses on two drinking water opportunistic pathogens of public health concern, Legionella pneumophila and Mycobacterium avium complex (MAC). Multiple aspects of drinking water quality in two green buildings were monitored in tandem with water management interventions. Additionally, a quantitative microbial risk assessment framework was used to predict risk-based critical concentrations of MAC for drinking water-related exposures in the indoor environment corresponding to a 1 in 10,000 annual infection target risk benchmark. The overall goal of this work was to inform the development of water management plans and guidelines for buildings that will improve water quality in the built environment and promote better public health. It was determined that a whole building water softening system with ion exchange softening resin and expansion tanks were unexplored reservoirs for the colonization of L. pneumophila. Furthermore, it was observed that typical water management interventions such as flushing and thermal disinfection did not always mitigate water quality issues. Thus, there was a need to implement several atypical interventions such as equipment replacement to improve the building water quality. This work has contributed comprehensive field studies and models that have highlighted the need for additional niches, facility management challenges, and risk tradeoffs for focus in water safety plans. The work also informs additional risk-based water quality policy approaches for reducing drinking water risks.
ContributorsJoshi, Sayalee (Author) / Hamilton, Kerry A (Thesis advisor) / Abbaszadegan, Morteza (Committee member) / Conroy-Ben, Otakuye (Committee member) / Halden, Rolf (Committee member) / Arizona State University (Publisher)
Created2023
Description
This dissertation studies the larger issue of antibiotic resistance with respect to how antibiotics are being introduced into the environment, focusing on two major anthropogenic pathways: animal husbandry for human consumption, and the recycling of wastewater and municipal sludge generated during conventional biological sewage treatment.
For animal production on land (agriculture) antibiotics are often used for growth enhancement and increased feed efficiency. For animal production in water (aquaculture) antibiotics are often used as a prophylactic. I found that the same antibiotics are being used in both industries and that the same strains of human pathogens have also been isolated from both sources, expressing identical resistance mechanisms. In U.S. seafood, five out of 47 antibiotics screened for were detected at levels of 0.3 to 7.7 ng/g fresh weight. Although compliant with FDA regulations, the risk for resistance still exists, as even low antibiotic concentrations have been shown to exert selective pressure on bacteria.
Similarly low concentrations of antibiotics were found in U.S. biosolids at levels of 0.6 to 19.1 ng/g dry weight. Of the five antibiotics detected, two have never been reported before in biosolids. Three have never been reported before in U.S. biosolids. Using the raw numbers obtained from antibiotic screenings in biosolids, I assessed the impact of employing four different LC-MS/MS methods, concluding that analysts should experimentally determine the most appropriate quantitation method based on the analyte targeted, matrix investigated, and research goals pursued. Preferred quantitation approaches included the isotope dilution method with use of an analogous standard and, although time and resource demanding, the method of standard addition.
In conclusion, antibiotics introduced into the environment via agriculture, aquaculture, and wastewater recycling pose a combination of chemical and biological threats. Aside from exerting outright chemical toxicity to non-target organisms, antibiotic residues can promote the development of multi-drug resistance in human pathogens. Public health protection approaches to stem the risks posed by animal husbandry may include reserving drugs for exclusive, human use, decreasing their usage altogether, improving reporting efforts, reevaluating existing regulations on agricultural and aquacultural antibiotic usage, and improved risk assessment for biosolids application on land.
For animal production on land (agriculture) antibiotics are often used for growth enhancement and increased feed efficiency. For animal production in water (aquaculture) antibiotics are often used as a prophylactic. I found that the same antibiotics are being used in both industries and that the same strains of human pathogens have also been isolated from both sources, expressing identical resistance mechanisms. In U.S. seafood, five out of 47 antibiotics screened for were detected at levels of 0.3 to 7.7 ng/g fresh weight. Although compliant with FDA regulations, the risk for resistance still exists, as even low antibiotic concentrations have been shown to exert selective pressure on bacteria.
Similarly low concentrations of antibiotics were found in U.S. biosolids at levels of 0.6 to 19.1 ng/g dry weight. Of the five antibiotics detected, two have never been reported before in biosolids. Three have never been reported before in U.S. biosolids. Using the raw numbers obtained from antibiotic screenings in biosolids, I assessed the impact of employing four different LC-MS/MS methods, concluding that analysts should experimentally determine the most appropriate quantitation method based on the analyte targeted, matrix investigated, and research goals pursued. Preferred quantitation approaches included the isotope dilution method with use of an analogous standard and, although time and resource demanding, the method of standard addition.
In conclusion, antibiotics introduced into the environment via agriculture, aquaculture, and wastewater recycling pose a combination of chemical and biological threats. Aside from exerting outright chemical toxicity to non-target organisms, antibiotic residues can promote the development of multi-drug resistance in human pathogens. Public health protection approaches to stem the risks posed by animal husbandry may include reserving drugs for exclusive, human use, decreasing their usage altogether, improving reporting efforts, reevaluating existing regulations on agricultural and aquacultural antibiotic usage, and improved risk assessment for biosolids application on land.
ContributorsDone, Hansa Yi-Yun (Author) / Halden, Rolf U. (Thesis advisor) / Haydel, Shelley E (Committee member) / Abbaszadegan, Morteza (Committee member) / Arizona State University (Publisher)
Created2015
Description
Bacteria of the Legionella genus are a water-borne pathogen of increasing concern due to being responsible for more annual drinking water related disease outbreaks in the United States than all other microbes combined. Unfortunately, the development of public health policies concerning Legionella has impeded by several key factors, including a paucity of data on their interactions and growth requirements in water distribution networks, a poor understanding of potential transmission sources for legionellosis, and limitations in current methodology for the characterization of these pathogens. To address these issues, a variety of research approaches were taken. By measuring Legionella survival in tap water, association in pipe material biofilms, population dynamics in a model distribution system, and occurrence in drinking water distribution system biofilms, key aspects of Legionella ecology in drinking water systems were revealed. Through a series of experiments qualitatively and quantitatively examining the growth of Legionella via nutrients obtained from several water sources, environmental nutritional requirements and capability for growth in the absence of host organisms were demonstrated. An examination of automobile windshield washer fluid as a possible source of legionellosis transmission revealed Legionella survival in certain windshield washer fluids, growth within washer fluid reservoirs, high levels and frequency of contamination in washer fluid reservoirs, and the presence of viable cells in washer fluid spray, suggesting the potential for exposure to Legionella from this novel source. After performing a systematic and quantitative analysis of methodology optimization for the analysis of Legionella cells via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, several strains of this microbe isolated from separated and varied environmental water sampling sites were distinctly typed, demonstrating a potential application of this technology for the characterization of Legionella. The results from this study provide novel insight and methodology relevant to the development of programs for the monitoring and treatment of Legionella in drinking water systems.
ContributorsSchwake, David Otto (Author) / Abbaszadegan, Morteza (Thesis advisor) / Alum, Absar (Committee member) / Fox, Peter (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2014
Description
Since its first report in 1976, many outbreaks of Legionella have been reported in the world. These outbreaks are a public health concern because of legionellosis, which cause Pontiac fever and Legionnaires disease. Legionnaires disease is a type of pneumonia responsible for the majority of the illness in the reported outbreaks. This study consists of an extensive literature review and experimental work on the aerosolization of Legionella and a bacterial surrogate under laboratory conditions. The literature review summarizes Legionella characteristics, legionellosis, potential sources of Legionella, disease outbreaks, collection and detection methodologies, environmental conditions for growth and survival of Legionella, Gaussian plume dispersion modeling, and recommendations for reducing potential Legionella outbreaks. The aerosolization and airborne dispersion of Legionella and E. coli was conducted separately inside of a closed environment. First, the bacterial cells were sprayed inside of an airtight box and then samples were collected using a microbial air sampler to measure the number of bacterial cells aerosolized and transported in air. Furthermore, a Gaussian plume dispersion model was used to estimate the dispersion under the experimental conditions and parameters. The concentration of Legionella was estimated for a person inhaling the air at three different distances away from the spray. The concentration of Legionella at distances of 0.1 km, 1 km, and 10 km away from the source was predicted to be 1.7x10-1, 2.2x10-3, and 2.6x10-5 CFU/m3, respectively.
ContributorsTaghdiri, Sepideh (Author) / Abbaszadegan, Morteza (Thesis advisor) / Fox, Peter (Committee member) / Estes, Robert (Committee member) / Arizona State University (Publisher)
Created2014
Description
This study was devised to elucidate key information concerning the potential risk posed by Legionella in reclaimed water. A series of biological experiments and a recharge basin soil column study were conducted to examine the survival, growth, and transport of L. pneumophila through engineered reclaimed water systems. A pilot-scale, column study was set up to measure Legionella transport in the columns under Arizona recharge basin conditions. Two columns, A and B, were packed to a depth of 122 cm with a loamy sand media collected from a recharge basin in Mesa, Arizona. The grain size distribution of Column A differed from that of Column B by the removal of fines passing the #200 sieve. The different soil profiles represented by column A and B allowed for further investigation of soil attributes which influence the microbial transport mechanism. Both clear PVC columns stand at a height of 1.83 m with an inner diameter of 6.35 cm. Sampling ports were drilled into the column at the soil depths 15, 30, 60, 92, 122 cm. Both columns were acclimated with tertiary treated waste water and set to a flow rate of approximately 1.5 m/d. The columns were used to assess the transport of a bacterial indicator, E. coli, in addition to assessing the study's primary pathogen of concern, Legionella. Approximately, 〖10〗^7 to 〖10〗^9 E. coli cells or 〖10〗^6 to 〖10〗^7Legionella cells were spiked into the columns' head waters for each experiment. Periodically, samples were collected from each column's sampling ports, until a minimum of three pore volume passed through the columns.
The pilot-scale, column study produced novel results which demonstrated the mechanism for Legionella to be transported through recharge basin soil. E. coli was transported, through 122 cm of the media in under 6 hours, whereas, Legionella was transported, through the same distance, in under 30 hours. Legionella has been shown to survive in low nutrient conditions for over a year. Given the novel results of this proof of concept study, a claim can be made for the transport of Legionella into groundwater aquifers through engineering recharge basin conditions, in Central Arizona.
The pilot-scale, column study produced novel results which demonstrated the mechanism for Legionella to be transported through recharge basin soil. E. coli was transported, through 122 cm of the media in under 6 hours, whereas, Legionella was transported, through the same distance, in under 30 hours. Legionella has been shown to survive in low nutrient conditions for over a year. Given the novel results of this proof of concept study, a claim can be made for the transport of Legionella into groundwater aquifers through engineering recharge basin conditions, in Central Arizona.
ContributorsMcBurnett, Lauren Rae (Author) / Abbaszadegan, Morteza (Thesis advisor) / Alum, Absar (Committee member) / Fox, Peter (Committee member) / Arizona State University (Publisher)
Created2014