Biogeography, Cultivation and Genomic Characterization of Prochlorococcus in the Red Sea

Handle URI:
http://hdl.handle.net/10754/584234
Title:
Biogeography, Cultivation and Genomic Characterization of Prochlorococcus in the Red Sea
Authors:
Shibl, Ahmed A. ( 0000-0002-8147-8406 )
Abstract:
Aquatic primary productivity mainly depends on pelagic phytoplankton. The globally abundant marine picocyanobacteria Prochlorococcus comprises a significant fraction of the photosynthetic biomass in most tropical, oligotrophic oceans. The Red Sea is an enclosed narrow body of water characterized by continuous solar irradiance, and negligible annual rainfall, in addition to elevated temperatures and salinity levels, which mimics a global warming scenario. Analysis of 16S rRNA sequences of bacterioplankton communities indicated the predominance of a high-light adapted ecotype (HL II) of Prochlorococcus at the surface of the Northern and Central Red Sea. To this end, we analyzed the distribution of Prochlorococcus at multiple depths within and below the euphotic zone in different regions of the Red Sea, using clone libraries of the 16S–23S rRNA internal transcribed spacer (ITS) region. Results indicated a high diversity of Prochlorococcus ecotypes at the 100 m depth in the water column and an unusual dominance of HL II-related sequences in deeper waters of the Red Sea. To further investigate the microdiversity of Prochlorococcus over a wider biogeographical scope, we used a 454-pyrosequencing approach to analyze rpoC1 gene pyrotags. Samples were collected from the surface of the water column to up to 500 m at 45 stations that span the Red Sea’s main basin from 4 north to south. Phylogenetic analysis of abundant rpoC1 OTUs revealed genotypes of recently discovered strains that belong to the high-light and lowlight clades. In addition, we used a rapid community-profiling tool (GraftM) and quantitatively analyzed rpoC1 gene abundance from 45 metagenomes to assess the Prochlorococcus community structure across vertical and horizontal physicochemical gradients. Results revealed the clustering of samples according to their depth and a strong influence on ecotypic distribution by temperature and oxygen levels. In efforts to better understand how the cells survive the unusual features of the Red Sea, a Prochlorococcus strain of the HL II adapted clade from the euphotic zone was cultured, enabling morphological analyses and growth rates measurements for the strain. In addition, we successfully sequenced and annotated the genome of the strain, which was then used for genomic comparison with other ecotypes. Interestingly, the set of unique genes identified in the draft genome included genes encoding proteins involved in salt tolerance mechanisms. The expression level and pattern of these genes in the Red Sea water column was explored through metatranscriptomic mapping and revealed their occurrence throughout, independent of the diel cycle. This led to the hypothesis that Prochlorococcus populations in the highly saline Red Sea are able to biosynthesize additional compatible solutes via several pathways to counterbalance the effects of salt stress. The results presented in this dissertation provide the first glimpse on how the environmental parameters of the Red Sea can affect the evolution, diversity and distribution patterns of Prochlorococcus ecotypes.
Advisors:
Stingl, Ulrich ( 0000-0002-0684-2597 )
Committee Member:
Moran, Xose Anxelu G. ( 0000-0002-9823-5339 ) ; Pain, Arnab ( 0000-0002-1755-2819 ) ; Siam, Rania
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Marine Science Program
Program:
Marine Science
Issue Date:
16-Dec-2015
Type:
Dissertation
Appears in Collections:
Marine Science Program; Dissertations; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.advisorStingl, Ulrichen
dc.contributor.authorShibl, Ahmed A.en
dc.date.accessioned2016-01-12T09:23:05Zen
dc.date.available2015-12-20T07:05:11Zen
dc.date.available2016-01-12T09:23:05Zen
dc.date.issued2015-12-16en
dc.identifier.urihttp://hdl.handle.net/10754/584234en
dc.description.abstractAquatic primary productivity mainly depends on pelagic phytoplankton. The globally abundant marine picocyanobacteria Prochlorococcus comprises a significant fraction of the photosynthetic biomass in most tropical, oligotrophic oceans. The Red Sea is an enclosed narrow body of water characterized by continuous solar irradiance, and negligible annual rainfall, in addition to elevated temperatures and salinity levels, which mimics a global warming scenario. Analysis of 16S rRNA sequences of bacterioplankton communities indicated the predominance of a high-light adapted ecotype (HL II) of Prochlorococcus at the surface of the Northern and Central Red Sea. To this end, we analyzed the distribution of Prochlorococcus at multiple depths within and below the euphotic zone in different regions of the Red Sea, using clone libraries of the 16S–23S rRNA internal transcribed spacer (ITS) region. Results indicated a high diversity of Prochlorococcus ecotypes at the 100 m depth in the water column and an unusual dominance of HL II-related sequences in deeper waters of the Red Sea. To further investigate the microdiversity of Prochlorococcus over a wider biogeographical scope, we used a 454-pyrosequencing approach to analyze rpoC1 gene pyrotags. Samples were collected from the surface of the water column to up to 500 m at 45 stations that span the Red Sea’s main basin from 4 north to south. Phylogenetic analysis of abundant rpoC1 OTUs revealed genotypes of recently discovered strains that belong to the high-light and lowlight clades. In addition, we used a rapid community-profiling tool (GraftM) and quantitatively analyzed rpoC1 gene abundance from 45 metagenomes to assess the Prochlorococcus community structure across vertical and horizontal physicochemical gradients. Results revealed the clustering of samples according to their depth and a strong influence on ecotypic distribution by temperature and oxygen levels. In efforts to better understand how the cells survive the unusual features of the Red Sea, a Prochlorococcus strain of the HL II adapted clade from the euphotic zone was cultured, enabling morphological analyses and growth rates measurements for the strain. In addition, we successfully sequenced and annotated the genome of the strain, which was then used for genomic comparison with other ecotypes. Interestingly, the set of unique genes identified in the draft genome included genes encoding proteins involved in salt tolerance mechanisms. The expression level and pattern of these genes in the Red Sea water column was explored through metatranscriptomic mapping and revealed their occurrence throughout, independent of the diel cycle. This led to the hypothesis that Prochlorococcus populations in the highly saline Red Sea are able to biosynthesize additional compatible solutes via several pathways to counterbalance the effects of salt stress. The results presented in this dissertation provide the first glimpse on how the environmental parameters of the Red Sea can affect the evolution, diversity and distribution patterns of Prochlorococcus ecotypes.en
dc.language.isoenen
dc.subjectProchlorococcusen
dc.subjectRed Seaen
dc.subjectGenomicsen
dc.subjectDiversityen
dc.subjectrpoC1en
dc.subjectmetatranscriptomicen
dc.titleBiogeography, Cultivation and Genomic Characterization of Prochlorococcus in the Red Seaen
dc.typeDissertationen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentMarine Science Programen
thesis.degree.grantorKing Abdullah University of Science and Technologyen_GB
dc.contributor.committeememberMoran, Xose Anxelu G.en
dc.contributor.committeememberPain, Arnaben
dc.contributor.committeememberSiam, Raniaen
thesis.degree.disciplineMarine Scienceen
thesis.degree.nameDoctor of Philosophyen
dc.person.id116457en

Version History

VersionItem Editor Date Summary
2 10754/584234grenzdm2016-01-12 09:19:02.0Student submitted updated dissertation file.
1 10754/584234.1Ameen Ghawanmeh2015-12-20 07:05:11.0null
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