MICROBIAL DIVERSITY AND COMMUNITY COMPOSITION IN THE OPEN OCEAN AND MARINE SEDIMENT
Over the last fifteen years, there has been a large increase in the literature on microbial community composition in marine sediment (Inagaki et al., 2006, 2015; Biddle et al., 2012; Briggs et al., 2012; Breucker et al., 2013; Lloyd, 2014; Teske et al., 2014; Nunoura et al., 2016; Walsh et al., 2016...
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ftunivrhodeislan:oai:digitalcommons.uri.edu:oa_diss-2308 2023-07-30T04:02:08+02:00 MICROBIAL DIVERSITY AND COMMUNITY COMPOSITION IN THE OPEN OCEAN AND MARINE SEDIMENT Kerrigan, Zak 2021-01-01T08:00:00Z application/pdf https://digitalcommons.uri.edu/oa_diss/1288 https://doi.org/10.23860/diss-kerrigan-zak-2021 https://digitalcommons.uri.edu/context/oa_diss/article/2308/viewcontent/Kerrigan_uri_0186A_12679.pdf unknown DigitalCommons@URI https://digitalcommons.uri.edu/oa_diss/1288 doi:10.23860/diss-kerrigan-zak-2021 https://digitalcommons.uri.edu/context/oa_diss/article/2308/viewcontent/Kerrigan_uri_0186A_12679.pdf Open Access Dissertations text 2021 ftunivrhodeislan https://doi.org/10.23860/diss-kerrigan-zak-2021 2023-07-17T19:03:52Z Over the last fifteen years, there has been a large increase in the literature on microbial community composition in marine sediment (Inagaki et al., 2006, 2015; Biddle et al., 2012; Briggs et al., 2012; Breucker et al., 2013; Lloyd, 2014; Teske et al., 2014; Nunoura et al., 2016; Walsh et al., 2016; Petro et al., 2017; Harrison et al., 2018; Hoshino et al., 2020), and seawater (Quaiser et al., 2011; Hamdan et al., 2013; Walsh et al., 2016; Medina-Silva et al., 2018; Mestre et al., 2018; Quero et al., 2019). As molecular study of these biomes progresses, and the tools available for detailed analyses expand, it has become important to evaluate those tools for their effectiveness and limitations. By combining environmental microbial investigations with evaluation of some of the most common genetic protocols, I have characterized microbial diversity and community composition in (i) Pacific, Atlantic, and Arctic seawater and (ii) Pacific and Atlantic sediment, and I have identified the common results obtainable using (i) two different 16S ribosomal RNA gene (rRNA) hypervariable regions of interest, and (ii) the two amplicon analysis pipelines most commonly used to determine microbial diversity and community composition. My first manuscript, “Influence of 16S rRNA Hypervariable Region on Estimates of Bacterial Diversity and Community Composition in Seawater and Marine Sediment”, looks at the bacterial diversity and community composition of deep-ocean sediment and overlying seawater from one site in the Central North Atlantic and one site in the Equatorial Pacific. In each case, we amplified both the V4 and V6 hypervariable regions of the 16S rRNA gene of each sample and clustered the sequences into operational taxonomic units (OTUs) of 97% similarity. In doing so, we determined that while OTU-level diversity metrics and community composition are quite different between the two tags, (i) vertical patterns of relative diversity are broadly the same, (ii) community composition is very similar for both tags at the class ... Text Arctic North Atlantic University of Rhode Island: DigitalCommons@URI Arctic Briggs ENVELOPE(-63.017,-63.017,-64.517,-64.517) Medina ENVELOPE(-66.233,-66.233,-68.453,-68.453) Pacific |
institution |
Open Polar |
collection |
University of Rhode Island: DigitalCommons@URI |
op_collection_id |
ftunivrhodeislan |
language |
unknown |
description |
Over the last fifteen years, there has been a large increase in the literature on microbial community composition in marine sediment (Inagaki et al., 2006, 2015; Biddle et al., 2012; Briggs et al., 2012; Breucker et al., 2013; Lloyd, 2014; Teske et al., 2014; Nunoura et al., 2016; Walsh et al., 2016; Petro et al., 2017; Harrison et al., 2018; Hoshino et al., 2020), and seawater (Quaiser et al., 2011; Hamdan et al., 2013; Walsh et al., 2016; Medina-Silva et al., 2018; Mestre et al., 2018; Quero et al., 2019). As molecular study of these biomes progresses, and the tools available for detailed analyses expand, it has become important to evaluate those tools for their effectiveness and limitations. By combining environmental microbial investigations with evaluation of some of the most common genetic protocols, I have characterized microbial diversity and community composition in (i) Pacific, Atlantic, and Arctic seawater and (ii) Pacific and Atlantic sediment, and I have identified the common results obtainable using (i) two different 16S ribosomal RNA gene (rRNA) hypervariable regions of interest, and (ii) the two amplicon analysis pipelines most commonly used to determine microbial diversity and community composition. My first manuscript, “Influence of 16S rRNA Hypervariable Region on Estimates of Bacterial Diversity and Community Composition in Seawater and Marine Sediment”, looks at the bacterial diversity and community composition of deep-ocean sediment and overlying seawater from one site in the Central North Atlantic and one site in the Equatorial Pacific. In each case, we amplified both the V4 and V6 hypervariable regions of the 16S rRNA gene of each sample and clustered the sequences into operational taxonomic units (OTUs) of 97% similarity. In doing so, we determined that while OTU-level diversity metrics and community composition are quite different between the two tags, (i) vertical patterns of relative diversity are broadly the same, (ii) community composition is very similar for both tags at the class ... |
format |
Text |
author |
Kerrigan, Zak |
spellingShingle |
Kerrigan, Zak MICROBIAL DIVERSITY AND COMMUNITY COMPOSITION IN THE OPEN OCEAN AND MARINE SEDIMENT |
author_facet |
Kerrigan, Zak |
author_sort |
Kerrigan, Zak |
title |
MICROBIAL DIVERSITY AND COMMUNITY COMPOSITION IN THE OPEN OCEAN AND MARINE SEDIMENT |
title_short |
MICROBIAL DIVERSITY AND COMMUNITY COMPOSITION IN THE OPEN OCEAN AND MARINE SEDIMENT |
title_full |
MICROBIAL DIVERSITY AND COMMUNITY COMPOSITION IN THE OPEN OCEAN AND MARINE SEDIMENT |
title_fullStr |
MICROBIAL DIVERSITY AND COMMUNITY COMPOSITION IN THE OPEN OCEAN AND MARINE SEDIMENT |
title_full_unstemmed |
MICROBIAL DIVERSITY AND COMMUNITY COMPOSITION IN THE OPEN OCEAN AND MARINE SEDIMENT |
title_sort |
microbial diversity and community composition in the open ocean and marine sediment |
publisher |
DigitalCommons@URI |
publishDate |
2021 |
url |
https://digitalcommons.uri.edu/oa_diss/1288 https://doi.org/10.23860/diss-kerrigan-zak-2021 https://digitalcommons.uri.edu/context/oa_diss/article/2308/viewcontent/Kerrigan_uri_0186A_12679.pdf |
long_lat |
ENVELOPE(-63.017,-63.017,-64.517,-64.517) ENVELOPE(-66.233,-66.233,-68.453,-68.453) |
geographic |
Arctic Briggs Medina Pacific |
geographic_facet |
Arctic Briggs Medina Pacific |
genre |
Arctic North Atlantic |
genre_facet |
Arctic North Atlantic |
op_source |
Open Access Dissertations |
op_relation |
https://digitalcommons.uri.edu/oa_diss/1288 doi:10.23860/diss-kerrigan-zak-2021 https://digitalcommons.uri.edu/context/oa_diss/article/2308/viewcontent/Kerrigan_uri_0186A_12679.pdf |
op_doi |
https://doi.org/10.23860/diss-kerrigan-zak-2021 |
_version_ |
1772812857402982400 |