Molecular ecology and transcriptomics of marine photosynthetic picoeukaryotes
Pearman, John K. (2012) Molecular ecology and transcriptomics of marine photosynthetic picoeukaryotes. PhD thesis, University of Warwick.
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Photosynthetic picoeukaroytes (PPEs), defined here as single celled organisms <3
μm in diameter, are significant contributors to primary production. Until recently,
marine PPEs had received relatively little research attention in contrast to the more
numerous picocyanobacteria. Molecular studies have now started to reveal the
diversity of this group, using both the nuclear 18S rRNA gene and the plastidtargeted
16S rRNA gene as taxonomic markers. The latter marker has the advantage
of directly targeting the PPE community, counteracting the problem of heterotrophic
sequences dominating clone libraries. As well as PCR based molecular approaches,
genomic studies of PPEs are starting to reveal the metabolic capabilities of these
In this thesis, taxonomic information obtained on two flow-sorted PPE populations
(Euk-A and Euk-B) showed that pico-prymnesiophytes, largely representing lineages
with no close cultured counterpart, dominated the Euk-A and Euk-B libraries (54 and
58%, respectively) in tropical and sub-tropical waters of the Atlantic Ocean.
Radiotracer work performed elsewhere had shown these PPE groups contribute up to
19% and 38% (Euk-A and Euk-B, respectively) to total CO2 fixation, demonstrating
the importance of these PPE groups in marine carbon cycling.
To further assess the taxonomic composition and distribution of these Euk-A and
Euk-B PPE populations at the ocean-basin scale, clone libraries were constructed
along an Atlantic Meridional Transect (AMT18). Major components of these flow
cytometry sorted PPE populations were Prymnesiophyceae and Chrysophyceae
using plastid markers, or Prasinophyceae and Dinophyceae (nuclear markers)
including several lineages with no cultured counterparts. In surface waters a
latitudinal diversity gradient was observed with a peak in PPE diversity found in the
equatorial region. Distribution patterns of specific PPE groups and OTUs were
subsequently correlated with measured environmental parameters, although most of
the variation in PPE diversity was not explained by the measured variables.
Attempts were undertaken to obtain into culture novel PPEs, especially those
representative of oligotropic regions. However, the majority of isolates obtained
were related to Prasinoderma or Chlorella which are cosmopolitan, fast-growing
genera. Even so, some isolates more relevant of open ocean environments were
obtained, including a clade VIIA prasinophyte and a Pelagomonas sp.
Trancriptomics was used to further assess the functional potential of specific PPE
populations, firstly in cultures using both an Ochromonas sp. and a prasinophyte as
being representative of organisms present along AMT18. This approach revealed a
C4 carbon concentrating mechanism in the clade VIIA prasinophyte and enzymes
required for a functioning urea cycle in the Ochromonas sp. A pipeline was also
developed to undertake a metatranscriptomic approach on a flow cytometrically
sorted PPE population from the south Atlantic gyre. This approach revealed a
diatom-like C4 carbon concentrating system in the metatranscriptome.
Overall, this thesis has given new insights into the diversity of specific PPE groups
at the ocean basin-scale, developed a new pipeline for the transcriptomic analysis of
PPEs both in culture and in the environment, and in so doing has provided new
information on the functional potential of these important photosynthetic organisms.
|Item Type:||Thesis or Dissertation (PhD)|
|Subjects:||Q Science > QR Microbiology|
|Library of Congress Subject Headings (LCSH):||Protista -- Genetics, Marine organisms -- Genetics|
|Official Date:||January 2012|
|Institution:||University of Warwick|
|Theses Department:||School of Life Sciences|
|Supervisor(s)/Advisor:||Scanlan, David J., 1963- ; Zubkov, Mikhail|
|Extent:||xix, 283 leaves : ill., charts|
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