Extracellular DNA amplicon sequencing reveals high levels of benthic eukaryotic diversity in the central Red Sea

Handle URI:
http://hdl.handle.net/10754/594059
Title:
Extracellular DNA amplicon sequencing reveals high levels of benthic eukaryotic diversity in the central Red Sea
Authors:
Pearman, John K. ( 0000-0002-2237-9723 ) ; Irigoien, Xabier ( 0000-0002-5411-6741 ) ; Carvalho, Susana ( 0000-0003-1300-1953 )
Abstract:
The present study aims to characterize the benthic eukaryotic biodiversity patterns at a coarse taxonomic level in three areas of the central Red Sea (a lagoon, an offshore area in Thuwal and a shallow coastal area near Jeddah) based on extracellular DNA. High-throughput amplicon sequencing targeting the V9 region of the 18S rRNA gene was undertaken for 32 sediment samples. High levels of alpha-diversity were detected with 16,089 operational taxonomic units (OTUs) being identified. The majority of the OTUs were assigned to Metazoa (29.2%), Alveolata (22.4%) and Stramenopiles (17.8%). Stramenopiles (Diatomea) and Alveolata (Ciliophora) were frequent in a lagoon and in shallower coastal stations, whereas metazoans (Arthropoda: Maxillopoda) were dominant in deeper offshore stations. Only 24.6% of total OTUs were shared among all areas. Beta-diversity was generally lower between the lagoon and Jeddah (nearshore) than between either of those and the offshore area, suggesting a nearshore–offshore biodiversity gradient. The current approach allowed for a broad-range of benthic eukaryotic biodiversity to be analysed with significantly less labour than would be required by other traditional taxonomic approaches. Our findings suggest that next generation sequencing techniques have the potential to provide a fast and standardised screening of benthic biodiversity at large spatial and temporal scales.
KAUST Department:
Red Sea Research Center (RSRC)
Citation:
Pearman JK, Irigoien X, Carvalho S (2015) Extracellular DNA amplicon sequencing reveals high levels of benthic eukaryotic diversity in the central Red Sea. Marine Genomics. Available: http://dx.doi.org/10.1016/j.margen.2015.10.008.
Publisher:
Elsevier BV
Journal:
Marine Genomics
Issue Date:
Nov-2015
DOI:
10.1016/j.margen.2015.10.008
PubMed ID:
26525270
Type:
Article
ISSN:
1874-7787
Sponsors:
King Abdullah University of Science and Technology
Appears in Collections:
Articles; Red Sea Research Center (RSRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorPearman, John K.en
dc.contributor.authorIrigoien, Xabieren
dc.contributor.authorCarvalho, Susanaen
dc.date.accessioned2016-01-19T13:20:18Zen
dc.date.available2016-01-19T13:20:18Zen
dc.date.issued2015-11en
dc.identifier.citationPearman JK, Irigoien X, Carvalho S (2015) Extracellular DNA amplicon sequencing reveals high levels of benthic eukaryotic diversity in the central Red Sea. Marine Genomics. Available: http://dx.doi.org/10.1016/j.margen.2015.10.008.en
dc.identifier.issn1874-7787en
dc.identifier.pmid26525270en
dc.identifier.doi10.1016/j.margen.2015.10.008en
dc.identifier.urihttp://hdl.handle.net/10754/594059en
dc.description.abstractThe present study aims to characterize the benthic eukaryotic biodiversity patterns at a coarse taxonomic level in three areas of the central Red Sea (a lagoon, an offshore area in Thuwal and a shallow coastal area near Jeddah) based on extracellular DNA. High-throughput amplicon sequencing targeting the V9 region of the 18S rRNA gene was undertaken for 32 sediment samples. High levels of alpha-diversity were detected with 16,089 operational taxonomic units (OTUs) being identified. The majority of the OTUs were assigned to Metazoa (29.2%), Alveolata (22.4%) and Stramenopiles (17.8%). Stramenopiles (Diatomea) and Alveolata (Ciliophora) were frequent in a lagoon and in shallower coastal stations, whereas metazoans (Arthropoda: Maxillopoda) were dominant in deeper offshore stations. Only 24.6% of total OTUs were shared among all areas. Beta-diversity was generally lower between the lagoon and Jeddah (nearshore) than between either of those and the offshore area, suggesting a nearshore–offshore biodiversity gradient. The current approach allowed for a broad-range of benthic eukaryotic biodiversity to be analysed with significantly less labour than would be required by other traditional taxonomic approaches. Our findings suggest that next generation sequencing techniques have the potential to provide a fast and standardised screening of benthic biodiversity at large spatial and temporal scales.en
dc.description.sponsorshipKing Abdullah University of Science and Technologyen
dc.publisherElsevier BVen
dc.subjectMarine sedimenten
dc.subjectExtracellular DNAen
dc.subjectBiodiversityen
dc.subjectAmplicon sequencingen
dc.subjectEukaryotaen
dc.subjectRed Seaen
dc.titleExtracellular DNA amplicon sequencing reveals high levels of benthic eukaryotic diversity in the central Red Seaen
dc.typeArticleen
dc.contributor.departmentRed Sea Research Center (RSRC)en
dc.identifier.journalMarine Genomicsen
kaust.authorPearman, John K.en
kaust.authorIrigoien, Xabieren
kaust.authorCarvalho, Susanaen

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