Revealing microbial functional activities in the Red Sea sponge S tylissa carteri by metatranscriptomics

Handle URI:
http://hdl.handle.net/10754/550163
Title:
Revealing microbial functional activities in the Red Sea sponge S tylissa carteri by metatranscriptomics
Authors:
Moitinho-Silva, Lucas; Seridi, Loqmane; Ryu, Tae Woo; Voolstra, Christian R. ( 0000-0003-4555-3795 ) ; Ravasi, Timothy ( 0000-0002-9950-465X ) ; Hentschel, Ute
Abstract:
The persistence of coral reef ecosystems relies on the symbiotic relationship between scleractinian corals and intracellular, photosynthetic dinoflagellates in the genus Symbiodinium. Genetic evidence indicates that these symbionts are biologically diverse and exhibit discrete patterns of environmental and host distribution. This makes the assessment of Symbiodinium diversity critical to understanding the symbiosis ecology of corals. Here, we applied pyrosequencing to the elucidation of Symbiodinium diversity via analysis of the internal transcribed spacer 2 (ITS2) region, a multicopy genetic marker commonly used to analyse Symbiodinium diversity. Replicated data generated from isoclonal Symbiodinium cultures showed that all genomes contained numerous, yet mostly rare, ITS2 sequence variants. Pyrosequencing data were consistent with more traditional denaturing gradient gel electrophoresis (DGGE) approaches to the screening of ITS2 PCR amplifications, where the most common sequences appeared as the most intense bands. Further, we developed an operational taxonomic unit (OTU)-based pipeline for Symbiodinium ITS2 diversity typing to provisionally resolve ecologically discrete entities from intragenomic variation. A genetic distance cut-off of 0.03 collapsed intragenomic ITS2 variants of isoclonal cultures into single OTUs. When applied to the analysis of field-collected coral samples, our analyses confirm that much of the commonly observed Symbiodinium ITS2 diversity can be attributed to intragenomic variation. We conclude that by analysing Symbiodinium populations in an OTU-based framework, we can improve objectivity, comparability and simplicity when assessing ITS2 diversity in field-based studies.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division; Red Sea Research Center (RSRC)
Citation:
Revealing microbial functional activities in the Red Sea sponge S tylissa carteri by metatranscriptomics 2014, 16 (12):3683 Environmental Microbiology
Publisher:
Wiley-Blackwell
Journal:
Environmental Microbiology
Issue Date:
9-Jul-2014
DOI:
10.1111/1462-2920.12533
Type:
Article
ISSN:
14622912
Additional Links:
http://doi.wiley.com/10.1111/1462-2920.12533
Appears in Collections:
Articles; Red Sea Research Center (RSRC); Biological and Environmental Sciences and Engineering (BESE) Division; Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorMoitinho-Silva, Lucasen
dc.contributor.authorSeridi, Loqmaneen
dc.contributor.authorRyu, Tae Wooen
dc.contributor.authorVoolstra, Christian R.en
dc.contributor.authorRavasi, Timothyen
dc.contributor.authorHentschel, Uteen
dc.date.accessioned2015-04-15T14:07:04Zen
dc.date.available2015-04-15T14:07:04Zen
dc.date.issued2014-07-09en
dc.identifier.citationRevealing microbial functional activities in the Red Sea sponge S tylissa carteri by metatranscriptomics 2014, 16 (12):3683 Environmental Microbiologyen
dc.identifier.issn14622912en
dc.identifier.doi10.1111/1462-2920.12533en
dc.identifier.urihttp://hdl.handle.net/10754/550163en
dc.description.abstractThe persistence of coral reef ecosystems relies on the symbiotic relationship between scleractinian corals and intracellular, photosynthetic dinoflagellates in the genus Symbiodinium. Genetic evidence indicates that these symbionts are biologically diverse and exhibit discrete patterns of environmental and host distribution. This makes the assessment of Symbiodinium diversity critical to understanding the symbiosis ecology of corals. Here, we applied pyrosequencing to the elucidation of Symbiodinium diversity via analysis of the internal transcribed spacer 2 (ITS2) region, a multicopy genetic marker commonly used to analyse Symbiodinium diversity. Replicated data generated from isoclonal Symbiodinium cultures showed that all genomes contained numerous, yet mostly rare, ITS2 sequence variants. Pyrosequencing data were consistent with more traditional denaturing gradient gel electrophoresis (DGGE) approaches to the screening of ITS2 PCR amplifications, where the most common sequences appeared as the most intense bands. Further, we developed an operational taxonomic unit (OTU)-based pipeline for Symbiodinium ITS2 diversity typing to provisionally resolve ecologically discrete entities from intragenomic variation. A genetic distance cut-off of 0.03 collapsed intragenomic ITS2 variants of isoclonal cultures into single OTUs. When applied to the analysis of field-collected coral samples, our analyses confirm that much of the commonly observed Symbiodinium ITS2 diversity can be attributed to intragenomic variation. We conclude that by analysing Symbiodinium populations in an OTU-based framework, we can improve objectivity, comparability and simplicity when assessing ITS2 diversity in field-based studies.en
dc.publisherWiley-Blackwellen
dc.relation.urlhttp://doi.wiley.com/10.1111/1462-2920.12533en
dc.rightsThis is the peer reviewed version of the following article: Arif, C., Daniels, C., Bayer, T., Banguera-Hinestroza, E., Barbrook, A., Howe, C. J., LaJeunesse, T. C. and Voolstra, C. R. (2014), Assessing Symbiodinium diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region. Molecular Ecology, 23: 4418–4433, which has been published in final form at http://doi.wiley.com/10.1111/1462-2920.12533. This article may be used for non-commercial purposes in accordance With Wiley Terms and Conditions for self-archiving.en
dc.subjectmicrobe:higher organism interactionsen
dc.subjectmicrobial communitiesen
dc.subjectmicrobial ecologyen
dc.subjectsymbiontsen
dc.subjectmetatranscriptomicsen
dc.titleRevealing microbial functional activities in the Red Sea sponge S tylissa carteri by metatranscriptomicsen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Divisionen
dc.contributor.departmentRed Sea Research Center (RSRC)en
dc.identifier.journalEnvironmental Microbiologyen
dc.eprint.versionPost-printen
dc.contributor.institutionDepartment of Botany II; Julius-von-Sachs Institute for Biological Sciences; University of Wuerzburg; Julius-von-Sachs Platz 3 97082 Wuerzburg Germanyen
dc.contributor.institutionDepartment of Botany II; Julius-von-Sachs Institute for Biological Sciences; University of Wuerzburg; Julius-von-Sachs Platz 3 97082 Wuerzburg Germanyen
kaust.authorSeridi, Loqmaneen
kaust.authorRyu, Tae Wooen
kaust.authorVoolstra, Christian R.en
kaust.authorRavasi, Timothyen
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