Distribution of Prochlorococcus Ecotypes in the Red Sea Basin Based on Analyses of rpoC1 Sequences

Handle URI:
http://hdl.handle.net/10754/623248
Title:
Distribution of Prochlorococcus Ecotypes in the Red Sea Basin Based on Analyses of rpoC1 Sequences
Authors:
Shibl, Ahmed A. ( 0000-0002-8147-8406 ) ; Haroon, Mohamed; Ngugi, David K.; Thompson, Luke R.; Stingl, Ulrich ( 0000-0002-0684-2597 )
Abstract:
The marine picocyanobacteria Prochlorococcus represent a significant fraction of the global pelagic bacterioplankton community. Specifically, in the surface waters of the Red Sea, they account for around 91% of the phylum Cyanobacteria. Previous work suggested a widespread presence of high-light (HL)-adapted ecotypes in the Red Sea with the occurrence of low-light (LL)-adapted ecotypes at intermediate depths in the water column. To obtain a more comprehensive dataset over a wider biogeographical scope, we used a 454-pyrosequencing approach to analyze the diversity of the Prochlorococcus rpoC1 gene from a total of 113 samples at various depths (up to 500 m) from 45 stations spanning the Red Sea basin from north to south. In addition, we analyzed 45 metagenomes from eight stations using hidden Markov models based on a set of reference Prochlorococcus genomes to (1) estimate the relative abundance of Prochlorococcus based on 16S rRNA gene sequences, and (2) identify and classify rpoC1 sequences as an assessment of the community structure of Prochlorococcus in the northern, central and southern regions of the basin without amplification bias. Analyses of metagenomic data indicated that Prochlorococcus occurs at a relative abundance of around 9% in samples from surface waters (25, 50, 75 m), 3% in intermediate waters (100 m) and around 0.5% in deep-water samples (200–500 m). Results based on rpoC1 sequences using both methods showed that HL II cells dominate surface waters and were also present in deep-water samples. Prochlorococcus communities in intermediate waters (100 m) showed a higher diversity and co-occurrence of low-light and high-light ecotypes. Prochlorococcus communities at each depth range (surface, intermediate, deep sea) did not change significantly over the sampled transects spanning most of the Saudi waters in the Red Sea. Statistical analyses of rpoC1 sequences from metagenomes indicated that the vertical distribution of Prochlorococcus in the water column is correlated with physicochemical gradients: temperature and oxygen are positively correlated with HL II (R2 = 0.71, p ≤ 0.05) while Chl a concentration, nutrient concentrations and salinity correlate with the prevalence of LL clades.
KAUST Department:
Marine Microbial Ecology Research Group; Red Sea Research Center (RSRC)
Citation:
Shibl AA, Haroon MF, Ngugi DK, Thompson LR, Stingl U (2016) Distribution of Prochlorococcus Ecotypes in the Red Sea Basin Based on Analyses of rpoC1 Sequences. Frontiers in Marine Science 3. Available: http://dx.doi.org/10.3389/fmars.2016.00104.
Publisher:
Frontiers Media SA
Journal:
Frontiers in Marine Science
Issue Date:
25-Jun-2016
DOI:
10.3389/fmars.2016.00104
Type:
Article
ISSN:
2296-7745
Sponsors:
We thank AbdulAziz Al-Suwailem and the scientists, captain and crew of the R/V Aegaeo from the KAUST Red Sea Expedition 2011, the Coastal and Marine Resources Core Lab (CMRC) and the Biosciences Core Laboratory (BCL) at KAUST for their logistical and technical support. We also thank Benjamin Woodcroft and Joel Boyd for their help with GraftM. This study was supported by the SABIC Career Development Chair from KAUST to US.
Additional Links:
http://journal.frontiersin.org/article/10.3389/fmars.2016.00104/full
Appears in Collections:
Articles; Red Sea Research Center (RSRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorShibl, Ahmed A.en
dc.contributor.authorHaroon, Mohameden
dc.contributor.authorNgugi, David K.en
dc.contributor.authorThompson, Luke R.en
dc.contributor.authorStingl, Ulrichen
dc.date.accessioned2017-04-17T11:33:46Z-
dc.date.available2017-04-17T11:33:46Z-
dc.date.issued2016-06-25en
dc.identifier.citationShibl AA, Haroon MF, Ngugi DK, Thompson LR, Stingl U (2016) Distribution of Prochlorococcus Ecotypes in the Red Sea Basin Based on Analyses of rpoC1 Sequences. Frontiers in Marine Science 3. Available: http://dx.doi.org/10.3389/fmars.2016.00104.en
dc.identifier.issn2296-7745en
dc.identifier.doi10.3389/fmars.2016.00104en
dc.identifier.urihttp://hdl.handle.net/10754/623248-
dc.description.abstractThe marine picocyanobacteria Prochlorococcus represent a significant fraction of the global pelagic bacterioplankton community. Specifically, in the surface waters of the Red Sea, they account for around 91% of the phylum Cyanobacteria. Previous work suggested a widespread presence of high-light (HL)-adapted ecotypes in the Red Sea with the occurrence of low-light (LL)-adapted ecotypes at intermediate depths in the water column. To obtain a more comprehensive dataset over a wider biogeographical scope, we used a 454-pyrosequencing approach to analyze the diversity of the Prochlorococcus rpoC1 gene from a total of 113 samples at various depths (up to 500 m) from 45 stations spanning the Red Sea basin from north to south. In addition, we analyzed 45 metagenomes from eight stations using hidden Markov models based on a set of reference Prochlorococcus genomes to (1) estimate the relative abundance of Prochlorococcus based on 16S rRNA gene sequences, and (2) identify and classify rpoC1 sequences as an assessment of the community structure of Prochlorococcus in the northern, central and southern regions of the basin without amplification bias. Analyses of metagenomic data indicated that Prochlorococcus occurs at a relative abundance of around 9% in samples from surface waters (25, 50, 75 m), 3% in intermediate waters (100 m) and around 0.5% in deep-water samples (200–500 m). Results based on rpoC1 sequences using both methods showed that HL II cells dominate surface waters and were also present in deep-water samples. Prochlorococcus communities in intermediate waters (100 m) showed a higher diversity and co-occurrence of low-light and high-light ecotypes. Prochlorococcus communities at each depth range (surface, intermediate, deep sea) did not change significantly over the sampled transects spanning most of the Saudi waters in the Red Sea. Statistical analyses of rpoC1 sequences from metagenomes indicated that the vertical distribution of Prochlorococcus in the water column is correlated with physicochemical gradients: temperature and oxygen are positively correlated with HL II (R2 = 0.71, p ≤ 0.05) while Chl a concentration, nutrient concentrations and salinity correlate with the prevalence of LL clades.en
dc.description.sponsorshipWe thank AbdulAziz Al-Suwailem and the scientists, captain and crew of the R/V Aegaeo from the KAUST Red Sea Expedition 2011, the Coastal and Marine Resources Core Lab (CMRC) and the Biosciences Core Laboratory (BCL) at KAUST for their logistical and technical support. We also thank Benjamin Woodcroft and Joel Boyd for their help with GraftM. This study was supported by the SABIC Career Development Chair from KAUST to US.en
dc.publisherFrontiers Media SAen
dc.relation.urlhttp://journal.frontiersin.org/article/10.3389/fmars.2016.00104/fullen
dc.rightsThis is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.titleDistribution of Prochlorococcus Ecotypes in the Red Sea Basin Based on Analyses of rpoC1 Sequencesen
dc.typeArticleen
dc.contributor.departmentMarine Microbial Ecology Research Groupen
dc.contributor.departmentRed Sea Research Center (RSRC)en
dc.identifier.journalFrontiers in Marine Scienceen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionDepartment of Pediatrics, University of California, San Diego, CA, USAen
kaust.authorShibl, Ahmed A.en
kaust.authorHaroon, Mohameden
kaust.authorNgugi, David K.en
kaust.authorThompson, Luke R.en
kaust.authorStingl, Ulrichen
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