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43
lorenzianus (94.1% ID and 90% coverage) and C. constrictus (93% ID and 94.3% coverage) from
Las Cruces, Chile.
Environmental Amplicon Data
Before using this 18S rRNA sequence to look for this isolate in the available amplicon
sequencing data for the Narragansett Bay Times Series site, we first confirmed that there was
enough diversity within the V4 hypervariable region across the genus Chaetoceros to
distinguish this isolate from other members of the same genus. Using aligned V4 regions of the
same species and sequences shown in Supplementary Table 1, we constructed a tree with the
same branching pattern as Figure 4 (shown in Figure S2). This means that using primers that
amplify the V4 region is an acceptable means of searching for this isolate in environmental
sequencing datasets that rely on this hypervariable region of the 18S rRNA gene.
Processing the publicly-available diatom sequences from Narragansett Bay resulted in
5170 distinct amplicon sequence variants (ASVs); however only 20 of these ASVs had an
average relative abundance greater than one percent of recovered amplicons across the data
set, suggesting there are a large number of relatively rare diatom ASVs in this environment.
When BLASTed, the most common diatom genera were Thalassiosira (eight), Skeletonema
(four), and Minidiscus (two)( Table S2). These are consistent with previous observations at
Narragansett Bay, where Thalassiosira and Skeletonema often dominate the diatom community
(Canesi and Rynearson 2016; Rynearson et al. 2020b). Of these 20 most abundant recovered
ASVs, one was a perfect match (100% ID and 100% coverage across the V4 hypervariable
region) to the 18S rRNA gene sequence we recovered from WGS data.
Object Description
| Title | Thermal diversity within marine phytoplankton communities |
| Author | Kling, Joshua David |
| Author email | Joshuakl@usc.edu;Joshuakl@berkeley.edu |
| Degree | Doctor of Philosophy |
| Document type | Dissertation |
| Degree program | Biology (Marine Biology and Biological Oceanography) |
| School | College of Letters, Arts and Sciences |
| Date defended/completed | 2020-08-11 |
| Date submitted | 2020-08-11 |
| Date approved | 2020-08-11 |
| Restricted until | 2020-08-11 |
| Date published | 2020-08-11 |
| Advisor (committee chair) | Hutchins, David |
| Advisor (committee member) |
Levine, Naomi Heidelberg, John Ehrenreich, Ian |
| Abstract | Marine photosynthetic carbon fixation in the sunlit upper reaches of the ocean is almost entirely carried out by chlorophyll-containing, single-celled microorganisms, and is responsible for half of the net primary production on the planet. Because of this connection to the marine carbon cycle, it is essential to assess the responses of marine phytoplankton to global change. However, this work is challenged by the dazzling diversity of both eukaryotic and prokaryotic lineages which coexist in complex phytoplankton assemblages. My dissertation contributes to this effort by investigating how the diversity of phytoplankton influences their resilience to rising temperatures. In my first study, I used natural California coastal communities collected across three seasons to show that the phytoplankton assemblage as a whole was able to maintain growth well above typical temperature ranges. However, either steady or fluctuating temperatures exceeding the maximum threshold recorded in a decade-long observational dataset caused drastic rearrangements in the phytoplankton community, including the appearance of novel dominant species. My dissertation work also highlights that there are still unrecognized but environmentally-important taxa with bizarre and unexpected life histories and thermal responses, even in the most well-studied environments. In my second study, I characterized a recently isolated nanoplanktonic diatom from the Narragansett Bay Time Series that occupies a distinct low-light, low-temperature niche. This isolate demonstrated an unusual sensitivity to light, whereby its ability to respond to what should be favorable increases in temperature is constrained by light intensity. Six years of amplicon sequencing data from the time series site suggest that this diatom is a temperate wintertime/early spring specialist, and will likely not fare well in a warmer and more stratified future ocean. In addition to expanding knowledge of functional diversity at the species level, my work also examines the potential of intra-specific diversity to house hidden adaptations to rising temperatures. Natural microbial populations are composed of distinct individual strains, whose relative abilities to contribute to the success of the whole population in a changing environment have not been well-studied. In my third study, I compared the thermal responses of 11 strains of the marine unicellular cyanobacterium Synechococcus simultaneously isolated from a single estuarine water sample to explore this cryptic intra-specific diversity. Surprisingly, these nearly genetically-identical strains showed distinct low and high temperature phenotypes. This study indicates that strain-level variation could be a key yet understudied element in the responses of phytoplankton to global change. Together, these studies highlight that the diversity of marine phytoplankton at the species and individual level includes both functional variability and redundancy relative to temperature. We can expect community composition to change over time in a warming ocean, reflecting the increasing abundance of preadapted groups or individual strains; however, wherever there are winners there are also losers. Besides providing new insights into the contribution of diversity to climate resilience, this dissertation also highlights the need to expand our knowledge of functional thermal traits, especially for typically under-studied pico- and nanoplankton which are often only known from sequence data. |
| Keyword | thermal response; phytoplankton; community ecology |
| Language | English |
| Part of collection | University of Southern California dissertations and theses |
| Publisher (of the original version) | University of Southern California |
| Place of publication (of the original version) | Los Angeles, California |
| Publisher (of the digital version) | University of Southern California. Libraries |
| Provenance | Electronically uploaded by the author |
| Type | texts |
| Legacy record ID | usctheses-m |
| Contributing entity | University of Southern California |
| Rights | Kling, Joshua David |
| Physical access | The author retains rights to his/her dissertation, thesis or other graduate work according to U.S. copyright law. Electronic access is being provided by the USC Libraries in agreement with the author, as the original true and official version of the work, but does not grant the reader permission to use the work if the desired use is covered by copyright. It is the author, as rights holder, who must provide use permission if such use is covered by copyright. The original signature page accompanying the original submission of the work to the USC Libraries is retained by the USC Libraries and a copy of it may be obtained by authorized requesters contacting the repository e-mail address given. |
| Repository name | University of Southern California Digital Library |
| Repository address | USC Digital Library, University of Southern California, University Park Campus MC 7002, 106 University Village, Los Angeles, California 90089-7002, USA |
| Repository email | cisadmin@lib.usc.edu |
| Filename | etd-KlingJoshu-8915.pdf |
| Archival file | Volume13/etd-KlingJoshu-8915.pdf |
Description
| Title | Page 48 |
| Full text | 43 lorenzianus (94.1% ID and 90% coverage) and C. constrictus (93% ID and 94.3% coverage) from Las Cruces, Chile. Environmental Amplicon Data Before using this 18S rRNA sequence to look for this isolate in the available amplicon sequencing data for the Narragansett Bay Times Series site, we first confirmed that there was enough diversity within the V4 hypervariable region across the genus Chaetoceros to distinguish this isolate from other members of the same genus. Using aligned V4 regions of the same species and sequences shown in Supplementary Table 1, we constructed a tree with the same branching pattern as Figure 4 (shown in Figure S2). This means that using primers that amplify the V4 region is an acceptable means of searching for this isolate in environmental sequencing datasets that rely on this hypervariable region of the 18S rRNA gene. Processing the publicly-available diatom sequences from Narragansett Bay resulted in 5170 distinct amplicon sequence variants (ASVs); however only 20 of these ASVs had an average relative abundance greater than one percent of recovered amplicons across the data set, suggesting there are a large number of relatively rare diatom ASVs in this environment. When BLASTed, the most common diatom genera were Thalassiosira (eight), Skeletonema (four), and Minidiscus (two)( Table S2). These are consistent with previous observations at Narragansett Bay, where Thalassiosira and Skeletonema often dominate the diatom community (Canesi and Rynearson 2016; Rynearson et al. 2020b). Of these 20 most abundant recovered ASVs, one was a perfect match (100% ID and 100% coverage across the V4 hypervariable region) to the 18S rRNA gene sequence we recovered from WGS data. |
