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Composition and Stability of Single-Stranded DNA Viral Populations in Wastewater Treatment Plants

Title: Composition and Stability of Single-Stranded DNA Viral Populations in Wastewater Treatment Plants.
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Name(s): Pearson, Victoria M., author
Rokyta, Darin, professor directing dissertation
Beerli, Peter, university representative
Dennis, Jonathan Hancock, committee member
Hughes, Kimberly A., 1960-, committee member
Tang, Hengli, committee member
Florida State University, degree granting institution
College of Arts and Sciences, degree granting college
Department of Biological Science, degree granting department
Type of Resource: text
Genre: Text
Doctoral Thesis
Issuance: monographic
Date Issued: 2017
Publisher: Florida State University
Place of Publication: Tallahassee, Florida
Physical Form: computer
online resource
Extent: 1 online resource (90 pages)
Language(s): English
Abstract/Description: Regular emergence and re-emergence of viral pathogens emphasizes the importance of understanding viral biogeography and migration. Single-stranded DNA (ssDNA) viruses are among the least understood groups of microbial pathogens, yet the group contains known agricultural pathogens, which infect both livestock and crops (Circoviridae and Geminiviridae), and model organisms (Microviridae). Wastewater treatment plants (WWTPs) receive water from multiple sources, becoming reservoirs for the collection of many viral families that infect a large range of hosts. Investigations utilizing high-throughput sequencing have determined that local viral diversity is extremely high but does not scale to produce an exponentially higher global diversity. It follows that similar genotypes can be found great distances apart, although they may not be permanent constituents of any single population. Transient genotypes have been observed in temporal surveys of closed systems, where genotypes migrate between individual populations. This study focused on the geographic and temporal population stability of single-stranded DNA (ssDNA) viruses in open systems. Sampling from WWTPs in three neighboring cities in Northwest Florida, which receive constant inflow and potentially receive the same viruses from the local environment, was conducted across a nine-month time span. A combination of polyethylene glycol (PEG) precipitation and filter concentration was used to isolate whole viral particles from the complex wastewater samples. The ssDNA viruses were isolated from larger viruses using a sucrose gradient for size selection and rolling circle amplification was performed to both bias the sample towards ssDNA and prepare the samples for high-throughput sequencing. Amplified genomes were sequenced using Illumina platforms and de novo assembled. Given the increased potential for migration, we expected the populations would be mostly homogenous with relatively few viruses that are unique to individual WWTPs. Viral genotypes with genetic similarity to Circoviridae, Geminiviridae, and Microviridae were recovered from all three WWTPs, however <25% of recovered genes match genotypes (>80% amino acid identity) recovered from neighboring sample sites. We determined that <10% of the genotypes were present in all three plants and the majority of genotypes were specific to one WWTP. Unexpectedly, the WWTPs that were closest to each other geographically were the least similar, and the plants geographically distant from each other had the most observed genetic overlap. These results highlight the high level of diversity within each population, while the high observed heterogeneity indicates localized genetic success and limited migration opportunities between the WWTPs. Throughout time the communities experienced a large degree of genetic turnover. Only 30% of the genotypes were present in more than one time point, 5% were recovered in three of more samplings and <1% were present in all five time points. This thesis concludes that viral genomes are continually moving through the environment and their presence in any given area may be temporary. Therefore, viruses are a continual selective force on their host species through the sheer volume of genetic potential in an area at any given time.
Identifier: FSU_FALL2017_Pearson_fsu_0071E_14170 (IID)
Submitted Note: A Dissertation submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy.
Degree Awarded: Fall Semester 2017.
Date of Defense: October 23, 2017.
Keywords: Bacteriophage, Environmental Microbiology, Genomics, Metagenomics, Virus
Bibliography Note: Includes bibliographical references.
Advisory Committee: Darin Rokyta, Professor Directing Dissertation; Peter Beerli, University Representative; Jonathan Dennis, Committee Member; Kimberly Hughes, Committee Member; Hengli Tang, Committee Member.
Subject(s): Virology
Biology
Genetics
Persistent Link to This Record: http://purl.flvc.org/fsu/fd/FSU_FALL2017_Pearson_fsu_0071E_14170
Owner Institution: FSU

Choose the citation style.
Pearson, V. M. (2017). Composition and Stability of Single-Stranded DNA Viral Populations in Wastewater Treatment Plants. Retrieved from http://purl.flvc.org/fsu/fd/FSU_FALL2017_Pearson_fsu_0071E_14170