Viral Community Dynamics and Functional Specialization in the Pacific Ocean

Persistent Link:
http://hdl.handle.net/10150/265369
Title:
Viral Community Dynamics and Functional Specialization in the Pacific Ocean
Author:
Hurwitz, Bonnie Louise
Issue Date:
2012
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:
Viruses are the most abundant biological entity on Earth and outnumber their hosts ten-to-one. Ocean viruses (phages) impact bacterial-driven global biogeochemical cycles through lysis, manipulating host metabolism, and horizontal gene transfer. However, knowledge of virus-host interactions and viral roles in ecosystems remains limited due to few cultured marine phage genomes and non-quantitative culture-independent metagenomes. Here, I develop and apply novel and well-tested bioinformatic techniques to explore Pacific Ocean viral communities using quantitative datasets derived from rigorously-tested preparation methods. To evaluate concentration and purification methods, I examined triplicate metagenomes from a single ocean sample using four protocols. Concentration protocols showed statistical differences in taxonomy whereas purification protocols did not. Specifically, TFF-concentrated metagenomes contained trace bacterial contamination and had fewer abundant taxa as compared to FeCl₃-precipitated metagenomes. K-mer analysis using the complete dataset revealed polymerase choice defined access to "rare" sequences.To explore unknown viral sequences, I organized known and unknown sequence space into 27K high-confidence protein clusters (PCs) from 32 diverse Pacific Ocean Virus (POV) metagenomes, which doubled available PCs and included the first pelagic deep-sea viral metagenomes. Using PCs as a whole-viral-community diversity metric revealed decreases from coastal to open ocean, winter to summer, and deep to surface, that correlate with data from microbial genetic diversity markers (no parallel viral markers exist).Biologically, POV metagenomes showed that viruses likely reprogram central metabolic pathways in microbial communities far beyond the "photosynthesis viruses" paradigm. Gene distribution patterns from 35 viral gene families (31 new) revealed niche-specific (photic vs aphotic zone) altered pathway carbon flux presumably optimized to best locally generate energy and drive viral replication. Further, these PCs define the first "core" (180 genes) and "flexible" (423K genes total) viral community genome. Functionally, core genes again suggest niche-differentation with extensive Fe-S cluster-related genes for electron transport and metabolic enzyme catalysis in photic samples, and manipulation of host pressure-sensitive genes in aphotic samples. Taxonomically, these data deconstruct the culture-based paradigm that tailed viruses dominate in the wild - instead they appear ubiquitous, but not abundant.
Type:
text; Electronic Dissertation
Keywords:
metagenomics; ocean; phage; viruses; Ecology & Evolutionary Biology; co-evolution; marine biology
Degree Name:
Ph.D.
Degree Level:
doctoral
Degree Program:
Graduate College; Ecology & Evolutionary Biology
Degree Grantor:
University of Arizona
Advisor:
Sullivan, Matthew B.

Full metadata record

DC FieldValue Language
dc.language.isoenen_US
dc.titleViral Community Dynamics and Functional Specialization in the Pacific Oceanen_US
dc.creatorHurwitz, Bonnie Louiseen_US
dc.contributor.authorHurwitz, Bonnie Louiseen_US
dc.date.issued2012-
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.abstractViruses are the most abundant biological entity on Earth and outnumber their hosts ten-to-one. Ocean viruses (phages) impact bacterial-driven global biogeochemical cycles through lysis, manipulating host metabolism, and horizontal gene transfer. However, knowledge of virus-host interactions and viral roles in ecosystems remains limited due to few cultured marine phage genomes and non-quantitative culture-independent metagenomes. Here, I develop and apply novel and well-tested bioinformatic techniques to explore Pacific Ocean viral communities using quantitative datasets derived from rigorously-tested preparation methods. To evaluate concentration and purification methods, I examined triplicate metagenomes from a single ocean sample using four protocols. Concentration protocols showed statistical differences in taxonomy whereas purification protocols did not. Specifically, TFF-concentrated metagenomes contained trace bacterial contamination and had fewer abundant taxa as compared to FeCl₃-precipitated metagenomes. K-mer analysis using the complete dataset revealed polymerase choice defined access to "rare" sequences.To explore unknown viral sequences, I organized known and unknown sequence space into 27K high-confidence protein clusters (PCs) from 32 diverse Pacific Ocean Virus (POV) metagenomes, which doubled available PCs and included the first pelagic deep-sea viral metagenomes. Using PCs as a whole-viral-community diversity metric revealed decreases from coastal to open ocean, winter to summer, and deep to surface, that correlate with data from microbial genetic diversity markers (no parallel viral markers exist).Biologically, POV metagenomes showed that viruses likely reprogram central metabolic pathways in microbial communities far beyond the "photosynthesis viruses" paradigm. Gene distribution patterns from 35 viral gene families (31 new) revealed niche-specific (photic vs aphotic zone) altered pathway carbon flux presumably optimized to best locally generate energy and drive viral replication. Further, these PCs define the first "core" (180 genes) and "flexible" (423K genes total) viral community genome. Functionally, core genes again suggest niche-differentation with extensive Fe-S cluster-related genes for electron transport and metabolic enzyme catalysis in photic samples, and manipulation of host pressure-sensitive genes in aphotic samples. Taxonomically, these data deconstruct the culture-based paradigm that tailed viruses dominate in the wild - instead they appear ubiquitous, but not abundant.en_US
dc.typetexten_US
dc.typeElectronic Dissertationen_US
dc.subjectmetagenomicsen_US
dc.subjectoceanen_US
dc.subjectphageen_US
dc.subjectvirusesen_US
dc.subjectEcology & Evolutionary Biologyen_US
dc.subjectco-evolutionen_US
dc.subjectmarine biologyen_US
thesis.degree.namePh.D.en_US
thesis.degree.leveldoctoralen_US
thesis.degree.disciplineGraduate Collegeen_US
thesis.degree.disciplineEcology & Evolutionary Biologyen_US
thesis.degree.grantorUniversity of Arizonaen_US
dc.contributor.advisorSullivan, Matthew B.en_US
dc.contributor.committeememberRam, Sudhaen_US
dc.contributor.committeememberHackett, Jeremiahen_US
dc.contributor.committeememberSanderson, Michaelen_US
dc.contributor.committeememberSullivan, Matthew B.en_US
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