RNA Viral Diversity and Dynamics Along the Antarctic Peninsula
Ph.D. University of Hawaii at Manoa 2015. Includes bibliographical references. Marine viruses are capable of driving species succession during plankton blooms and greatly influencing biogeochemical cycling and food web dynamics through cell lysis. Most of our knowledge has come from studies in tempe...
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ftunivhawaiimano:oai:scholarspace.manoa.hawaii.edu:10125/51000 2023-05-15T13:59:06+02:00 RNA Viral Diversity and Dynamics Along the Antarctic Peninsula Miranda, Jaclyn 2015-05 application/pdf http://hdl.handle.net/10125/51000 eng eng [Honolulu] : [University of Hawaii at Manoa], [May 2015] Theses for the degree of Doctor of Philosophy (University of Hawaii at Manoa). Oceanography http://hdl.handle.net/10125/51000 marine RNA viruses viral ecology metagenomes viromes nucleic acid extraction reverse transcription quantitative PCR (RT-qPCR) Antarctica Thesis Text 2015 ftunivhawaiimano 2022-07-17T13:05:13Z Ph.D. University of Hawaii at Manoa 2015. Includes bibliographical references. Marine viruses are capable of driving species succession during plankton blooms and greatly influencing biogeochemical cycling and food web dynamics through cell lysis. Most of our knowledge has come from studies in temperate and sub-tropical waters, but whether they play a major role in eukaryotic phytoplankton blooms in polar waters has not been investigated. RNA viruses in particular have been shown to contribute up to half of the total virioplankton and are known to predominantly infect eukaryotes. The goals of this dissertation were to provide the first description of RNA viruses in the Antarctic, determine their relative and absolute abundances, and investigate the diversity and dynamics of these viruses to better understand how they contribute to the ecology of eukaryotic plankton. A temporal analysis of RNA viral metagenomes collected throughout the summer bloom in the Western Antarctic Peninsula (WAP) revealed an abundant and diverse community of positive-sense, single-stranded (+ss) RNA viruses within the order Picornavirales. RNA viral metagenomes from the Eastern Antarctic Peninsula were analyzed to investigate spatial diversity, and revealed a similar dominance of +ssRNA viruses in the order Picornavirales, but a much lower diversity than the WAP metagenomes. Novel RNA virus genomes were assembled and primers were designed to target the RNA-dependent RNA polymerase gene to track individual phylotypes throughout the season in the WAP. In order to determine the absolute abundance of these RNA viruses, two methods were evaluated and optimized. First, a method for extraction of viral nucleic acids from plankton harvested on nanoporous anodic aluminum oxide filters was improved and validated. Second, a reverse transcription quantitative PCR (RT-qPCR) assay was developed to accurately quantify specific RNA viruses in nucleic acid extracts. Both methods were applied to provide the first estimates of abundance of specific RNA ... Thesis Antarc* Antarctic Antarctic Peninsula Antarctica ScholarSpace at University of Hawaii at Manoa Antarctic Antarctic Peninsula The Antarctic |
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collection |
ScholarSpace at University of Hawaii at Manoa |
op_collection_id |
ftunivhawaiimano |
language |
English |
topic |
marine RNA viruses viral ecology metagenomes viromes nucleic acid extraction reverse transcription quantitative PCR (RT-qPCR) Antarctica |
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marine RNA viruses viral ecology metagenomes viromes nucleic acid extraction reverse transcription quantitative PCR (RT-qPCR) Antarctica Miranda, Jaclyn RNA Viral Diversity and Dynamics Along the Antarctic Peninsula |
topic_facet |
marine RNA viruses viral ecology metagenomes viromes nucleic acid extraction reverse transcription quantitative PCR (RT-qPCR) Antarctica |
description |
Ph.D. University of Hawaii at Manoa 2015. Includes bibliographical references. Marine viruses are capable of driving species succession during plankton blooms and greatly influencing biogeochemical cycling and food web dynamics through cell lysis. Most of our knowledge has come from studies in temperate and sub-tropical waters, but whether they play a major role in eukaryotic phytoplankton blooms in polar waters has not been investigated. RNA viruses in particular have been shown to contribute up to half of the total virioplankton and are known to predominantly infect eukaryotes. The goals of this dissertation were to provide the first description of RNA viruses in the Antarctic, determine their relative and absolute abundances, and investigate the diversity and dynamics of these viruses to better understand how they contribute to the ecology of eukaryotic plankton. A temporal analysis of RNA viral metagenomes collected throughout the summer bloom in the Western Antarctic Peninsula (WAP) revealed an abundant and diverse community of positive-sense, single-stranded (+ss) RNA viruses within the order Picornavirales. RNA viral metagenomes from the Eastern Antarctic Peninsula were analyzed to investigate spatial diversity, and revealed a similar dominance of +ssRNA viruses in the order Picornavirales, but a much lower diversity than the WAP metagenomes. Novel RNA virus genomes were assembled and primers were designed to target the RNA-dependent RNA polymerase gene to track individual phylotypes throughout the season in the WAP. In order to determine the absolute abundance of these RNA viruses, two methods were evaluated and optimized. First, a method for extraction of viral nucleic acids from plankton harvested on nanoporous anodic aluminum oxide filters was improved and validated. Second, a reverse transcription quantitative PCR (RT-qPCR) assay was developed to accurately quantify specific RNA viruses in nucleic acid extracts. Both methods were applied to provide the first estimates of abundance of specific RNA ... |
format |
Thesis |
author |
Miranda, Jaclyn |
author_facet |
Miranda, Jaclyn |
author_sort |
Miranda, Jaclyn |
title |
RNA Viral Diversity and Dynamics Along the Antarctic Peninsula |
title_short |
RNA Viral Diversity and Dynamics Along the Antarctic Peninsula |
title_full |
RNA Viral Diversity and Dynamics Along the Antarctic Peninsula |
title_fullStr |
RNA Viral Diversity and Dynamics Along the Antarctic Peninsula |
title_full_unstemmed |
RNA Viral Diversity and Dynamics Along the Antarctic Peninsula |
title_sort |
rna viral diversity and dynamics along the antarctic peninsula |
publisher |
[Honolulu] : [University of Hawaii at Manoa], [May 2015] |
publishDate |
2015 |
url |
http://hdl.handle.net/10125/51000 |
geographic |
Antarctic Antarctic Peninsula The Antarctic |
geographic_facet |
Antarctic Antarctic Peninsula The Antarctic |
genre |
Antarc* Antarctic Antarctic Peninsula Antarctica |
genre_facet |
Antarc* Antarctic Antarctic Peninsula Antarctica |
op_relation |
Theses for the degree of Doctor of Philosophy (University of Hawaii at Manoa). Oceanography http://hdl.handle.net/10125/51000 |
_version_ |
1766267477882306560 |