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INVESTIGATING MICROBIAL BIOFILM COMMUNITY MEDIATED PROCESSES ON SURFACES: FROM SINGLE CELL GENOMICS TO COMMUNITY META-OMICS
by
Jeffrey Scott McLean
A Dissertation Presented to the
FACULTY OF THE USC GRADUATE SCHOOL
UNIVERSITY OF SOUTHERN CALIFORNIA
In Partial Fulfillment of the
Requirements for the Degree
DOCTOR OF PHILOSOPHY
(GEOLOGICAL SCIENCES)
August 2013
Copyright 2013 Jeffrey Scott McLean
Object Description
| Title | Investigating microbial biofilm community mediated processes on surfaces: from single cell genomics to community meta-omics |
| Author | McLean, Jeffrey Scott |
| Author email | jsmclean@usc.edu;jsm_is@msn.com |
| Degree | Doctor of Philosophy |
| Document type | Dissertation |
| Degree program | Geological Sciences |
| School | College of Letters, Arts And Sciences |
| Date defended/completed | 2013-06-06 |
| Date submitted | 2013-08-01 |
| Date approved | 2013-08-01 |
| Restricted until | 2013-08-01 |
| Date published | 2013-08-01 |
| Advisor (committee chair) | Nealson, Kenneth H. |
| Advisor (committee member) |
Amend, Jan Berelson, William M. Finkel, Steven E. |
| Abstract | The study of microbial biofilms on reactive surfaces integrates many disciplines including biogeochemistry, engineering, physics and microbiology and has benefited greatly from recent approaches based in genomics and bioinformatics. Experimental biofilm studies have been predominately conducted on model systems containing single species. Most processes in nature and many in human disease however are driven by reactions occurring within complex microbial biofilm communities in contrast to a few processes that are the result of a single species. Many hurdles still remain and overcoming these will rely on technological and experimental advances that disentangle the immense complexity of a multispecies biofilm. This dissertation deals with complex microbial biofilm communities involved in the degradation of minerals: hydroxyapatite-based biominerals in the oral cavity. This work is inherently and extensively interdisciplinary, involving microbiology, molecular biology, genomics and metagenomics, as well as microbial physiology and geology. This work has involved the development and use of methods for the study of the structure and function of biofilms on one hand, and for the genomic characterization of interacting community members with single cell genomics on the other. Both top-down and bottom up approaches are clearly needed to more fully understand the abiotic and biotic processes that contribute to the fundamental process of mineral dissolution. The goals of the work are focused on using this interdisciplinary approach to gain insight into how microbial biofilm communities interact with surfaces such as human biominerals (teeth enamel made of hydroxyapatite mineral). However, the approaches and techniques developed here involving sampling a complex biofilm for single cell genomic reconstruction are widely applicable to the study of biofilms involved with geobiological activities everywhere. |
| Keyword | biofilms; metagenomics; single cell genomics; geobiology; biogeochemistry; dental caries; microbial communities; microbiome |
| Language | English |
| Format (imt) | application/pdf |
| Part of collection | University of Southern California dissertations and theses |
| Publisher (of the original version) | University of Southern California |
| Place of publication (of the original version) | Los Angeles, California |
| Publisher (of the digital version) | University of Southern California. Libraries |
| Provenance | Electronically uploaded by the author |
| Type | texts |
| Legacy record ID | usctheses-m |
| Contributing entity | University of Southern California |
| Rights | McLean, Jeffrey Scott |
| Physical access | The author retains rights to his/her dissertation, thesis or other graduate work according to U.S. copyright law. Electronic access is being provided by the USC Libraries in agreement with the author, as the original true and official version of the work, but does not grant the reader permission to use the work if the desired use is covered by copyright. It is the author, as rights holder, who must provide use permission if such use is covered by copyright. The original signature page accompanying the original submission of the work to the USC Libraries is retained by the USC Libraries and a copy of it may be obtained by authorized requesters contacting the repository e-mail address given. |
| Repository name | University of Southern California Digital Library |
| Repository address | USC Digital Library, University of Southern California, University Park Campus MC 7002, 106 University Village, Los Angeles, California 90089-7002, USA |
| Repository email | cisadmin@dots.usc.edu |
| Filename | etd-McLeanJeff-1930.pdf |
| Archival file | uscthesesreloadpub_Volume7/etd-McLeanJeff-1930.pdf |
Description
| Title | Page 1 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@dots.usc.edu |
| Full text | INVESTIGATING MICROBIAL BIOFILM COMMUNITY MEDIATED PROCESSES ON SURFACES: FROM SINGLE CELL GENOMICS TO COMMUNITY META-OMICS by Jeffrey Scott McLean A Dissertation Presented to the FACULTY OF THE USC GRADUATE SCHOOL UNIVERSITY OF SOUTHERN CALIFORNIA In Partial Fulfillment of the Requirements for the Degree DOCTOR OF PHILOSOPHY (GEOLOGICAL SCIENCES) August 2013 Copyright 2013 Jeffrey Scott McLean |
