Application of Advanced Molecular Techniques in Applied Environmental Microbiology

Persistent Link:
http://hdl.handle.net/10150/301699
Title:
Application of Advanced Molecular Techniques in Applied Environmental Microbiology
Author:
Iker, Brandon Charles
Issue Date:
2013
Publisher:
The University of Arizona.
Rights:
Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author.
Abstract:
Recent advancements in molecular biology such as next generation sequencing and more sensitive and rapid molecular detection methods like qPCR, have historically been developed for clinical applications in human genetics and for health care diagnostic purposes. The high demand for faster and more accurate molecular assays in the health care field has driven rapid development of inexpensive molecular techniques that when applied to the science of environmental microbiology, provides an unprecedented level of understanding of the microbial world around us. The goal of this dissertation is to begin to apply more advanced molecular technologies to problems in applied environmental microbiology. Appendix A is a brief literature review of next generation sequencing technologies for applications in environmental microbiology. Appendix B focuses on the development of a more robust virus nucleic extraction kit for the detection of viral genomes from environmental samples found to contain high concentrations of qPCR inhibitors, such as humic acids or heavy metals. Appendix C summarizes one of the largest virus surveys done in the US, using state of the art qPCR technologies in both wastewater influent and effluent from two wastewater treatment plants in the Southwest. Data suggests that traditional virus indicators may not be a viable tool to evaluate fecally impacted source water or virus removal during water treatment. The third study summarized in Appendix D, provides one of the first insights into the microbial ecology of biofilms utilized as biological treatment media using Roche 454 amplicon sequencing of the 16S rRNA gene.
Type:
text; Electronic Dissertation
Keywords:
nucleic acid extraction; pathogens; P.O.U.; virus; water filtration; Soil, Water & Environmental Science; next generation sequencing
Degree Name:
Ph.D.
Degree Level:
doctoral
Degree Program:
Graduate College; Soil, Water & Environmental Science
Degree Grantor:
University of Arizona
Advisor:
Pepper, Ian L.; Gerba, Chuck P.

Full metadata record

DC FieldValue Language
dc.language.isoenen_US
dc.titleApplication of Advanced Molecular Techniques in Applied Environmental Microbiologyen_US
dc.creatorIker, Brandon Charlesen_US
dc.contributor.authorIker, Brandon Charlesen_US
dc.date.issued2013-
dc.publisherThe University of Arizona.en_US
dc.rightsCopyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author.en_US
dc.description.abstractRecent advancements in molecular biology such as next generation sequencing and more sensitive and rapid molecular detection methods like qPCR, have historically been developed for clinical applications in human genetics and for health care diagnostic purposes. The high demand for faster and more accurate molecular assays in the health care field has driven rapid development of inexpensive molecular techniques that when applied to the science of environmental microbiology, provides an unprecedented level of understanding of the microbial world around us. The goal of this dissertation is to begin to apply more advanced molecular technologies to problems in applied environmental microbiology. Appendix A is a brief literature review of next generation sequencing technologies for applications in environmental microbiology. Appendix B focuses on the development of a more robust virus nucleic extraction kit for the detection of viral genomes from environmental samples found to contain high concentrations of qPCR inhibitors, such as humic acids or heavy metals. Appendix C summarizes one of the largest virus surveys done in the US, using state of the art qPCR technologies in both wastewater influent and effluent from two wastewater treatment plants in the Southwest. Data suggests that traditional virus indicators may not be a viable tool to evaluate fecally impacted source water or virus removal during water treatment. The third study summarized in Appendix D, provides one of the first insights into the microbial ecology of biofilms utilized as biological treatment media using Roche 454 amplicon sequencing of the 16S rRNA gene.en_US
dc.typetexten_US
dc.typeElectronic Dissertationen_US
dc.subjectnucleic acid extractionen_US
dc.subjectpathogensen_US
dc.subjectP.O.U.en_US
dc.subjectvirusen_US
dc.subjectwater filtrationen_US
dc.subjectSoil, Water & Environmental Scienceen_US
dc.subjectnext generation sequencingen_US
thesis.degree.namePh.D.en_US
thesis.degree.leveldoctoralen_US
thesis.degree.disciplineGraduate Collegeen_US
thesis.degree.disciplineSoil, Water & Environmental Scienceen_US
thesis.degree.grantorUniversity of Arizonaen_US
dc.contributor.advisorPepper, Ian L.en_US
dc.contributor.advisorGerba, Chuck P.en_US
dc.contributor.committeememberRock, Channahen_US
dc.contributor.committeememberBright, Kellyen_US
dc.contributor.committeememberPepper, Ian L.en_US
dc.contributor.committeememberGerba, Chuck P.en_US
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