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Diversity, Relative Abundance, and Functional Potential of Viral and Bacterial Communities.

Record Type:	Electronic resources : Monograph/item
Title/Author:	Diversity, Relative Abundance, and Functional Potential of Viral and Bacterial Communities./
Author:	Palermo, Christine Natalie.
Published:	Ann Arbor : ProQuest Dissertations & Theses, : 2022,
Description:	189 p.
Notes:	Source: Dissertations Abstracts International, Volume: 84-01, Section: B.
Contained By:	Dissertations Abstracts International84-01B.
Subject:	Microbiology. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=28969882
ISBN:	9798834059042

Diversity, Relative Abundance, and Functional Potential of Viral and Bacterial Communities.
Palermo, Christine Natalie.

Diversity, Relative Abundance, and Functional Potential of Viral and Bacterial Communities. - Ann Arbor : ProQuest Dissertations & Theses, 2022 - 189 p.

Source: Dissertations Abstracts International, Volume: 84-01, Section: B.

Thesis (Ph.D.)--University of Toronto (Canada), 2022.

This item must not be sold to any third party vendors.

Viral and bacterial communities in Hamilton Harbour were explored to discern seasonal and spatial changes in diversity, relative abundance, and functional potentials. The following chapters describe findings derived from metagenomic sequencing and analysis of environmental DNA using a variety of techniques. In the study outlined in Chapter 2, virus diversity and relative abundances were found to be highly variable over small spatial scales. Virophages were often the most abundant group, and discrete virophage taxa were stable despite fluctuations in Mimiviridae community composition. Diverse and distinct Mimiviridae populations were detected, suggesting that Mimiviridae are important algal viruses. The results from Chapter 3 demonstrated that several insights into virus diversity, relative abundances, and host inferences are lost by the common practice of filtering water samples to separate viruses from cells prior to DNA extraction and sequencing. Many viruses of eukaryotes, such as Mimiviridae, Phycodnaviridae, Iridoviridae and Poxviridae, were detected exclusively in the often-disregarded larger size fractions, while higher Caudovirales diversity was captured by the smaller size fractions. Cyanophages were more abundant in the larger size fractions, which may indicate replication within cells during ongoing infections. Analysis of either size fraction alone provides only a partial perspective of dsDNA viruses in the environment, highlighting the need for more comprehensive approaches for metagenomic analyses of aquatic viruses. Unlike the virus communities, the results from Chapter 4 revealed that bacterial communities were similar at different sites within the harbour and demonstrated strong seasonality regarding taxonomy and functional potentials. Some functional categories were highly variable while others were stable, suggesting the presence of generalist gene categories that are always essential versus specialist gene categories that fluctuate based on selective pressures. The results presented in this thesis expand the documented diversity of freshwater viruses and abundant Cyanobacteria in Hamilton Harbour, providing the first observations of highly abundant and potentially ecological important virophage, Mimiviridae, and Limnoraphis robusta populations. Ultimately, this work revealed seasonal and spatial dynamics in microbial community diversity, relative abundances, and functional potentials that can be used to inform ongoing monitoring and remediation efforts in Hamilton Harbour and likely apply broadly to other temperate freshwater lakes.

ISBN: 9798834059042Subjects--Topical Terms:

536250
Microbiology.
Subjects--Index Terms:

Algal viruses

Diversity, Relative Abundance, and Functional Potential of Viral and Bacterial Communities.
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245 1 0 $a Diversity, Relative Abundance, and Functional Potential of Viral and Bacterial Communities.
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300 $a 189 p.
500 $a Source: Dissertations Abstracts International, Volume: 84-01, Section: B.
500 $a Advisor: Short, Steven M.
502 $a Thesis (Ph.D.)--University of Toronto (Canada), 2022.
506 $a This item must not be sold to any third party vendors.
520 $a Viral and bacterial communities in Hamilton Harbour were explored to discern seasonal and spatial changes in diversity, relative abundance, and functional potentials. The following chapters describe findings derived from metagenomic sequencing and analysis of environmental DNA using a variety of techniques. In the study outlined in Chapter 2, virus diversity and relative abundances were found to be highly variable over small spatial scales. Virophages were often the most abundant group, and discrete virophage taxa were stable despite fluctuations in Mimiviridae community composition. Diverse and distinct Mimiviridae populations were detected, suggesting that Mimiviridae are important algal viruses. The results from Chapter 3 demonstrated that several insights into virus diversity, relative abundances, and host inferences are lost by the common practice of filtering water samples to separate viruses from cells prior to DNA extraction and sequencing. Many viruses of eukaryotes, such as Mimiviridae, Phycodnaviridae, Iridoviridae and Poxviridae, were detected exclusively in the often-disregarded larger size fractions, while higher Caudovirales diversity was captured by the smaller size fractions. Cyanophages were more abundant in the larger size fractions, which may indicate replication within cells during ongoing infections. Analysis of either size fraction alone provides only a partial perspective of dsDNA viruses in the environment, highlighting the need for more comprehensive approaches for metagenomic analyses of aquatic viruses. Unlike the virus communities, the results from Chapter 4 revealed that bacterial communities were similar at different sites within the harbour and demonstrated strong seasonality regarding taxonomy and functional potentials. Some functional categories were highly variable while others were stable, suggesting the presence of generalist gene categories that are always essential versus specialist gene categories that fluctuate based on selective pressures. The results presented in this thesis expand the documented diversity of freshwater viruses and abundant Cyanobacteria in Hamilton Harbour, providing the first observations of highly abundant and potentially ecological important virophage, Mimiviridae, and Limnoraphis robusta populations. Ultimately, this work revealed seasonal and spatial dynamics in microbial community diversity, relative abundances, and functional potentials that can be used to inform ongoing monitoring and remediation efforts in Hamilton Harbour and likely apply broadly to other temperate freshwater lakes.
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650 4 $a Bioinformatics. $3 553671
650 4 $a Aquatic sciences. $3 3174300
653 $a Algal viruses
653 $a Cyanobacteria
653 $a Great Lakes
653 $a Hamilton Harbour
653 $a Metagenomics
653 $a Nutrient metabolism
690 $a 0410
690 $a 0715
690 $a 0792
710 2 $a University of Toronto (Canada). $b Physical and Environmental Sciences. $3 3346298
773 0 $t Dissertations Abstracts International $g 84-01B.
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791 $a Ph.D.
792 $a 2022
793 $a English
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=28969882