Cob gene pyrosequencing enables characterization of benthic dinoflagellate diversity and biogeography

Kohli, GS; Neilan, BA; Brown, MV; Hoppenrath, M; Murray, SA

Cob gene pyrosequencing enables characterization of benthic dinoflagellate diversity and biogeography

Kohli, GS

Neilan, BA Brown, MV Hoppenrath, M Murray, SA

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Publication Type:: Journal Article
Citation:: Environmental Microbiology, 2014, 16 (2), pp. 467 - 485
Issue Date:: 2014-02-01

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Field	Value	Language
dc.contributor.author	Kohli, GS https://orcid.org/0000-0002-4578-2355	en_US
dc.contributor.author	Neilan, BA	en_US
dc.contributor.author	Brown, MV	en_US
dc.contributor.author	Hoppenrath, M	en_US
dc.contributor.author	Murray, SA https://orcid.org/0000-0001-7096-1307	en_US
dc.date.available	2013-09-01	en_US
dc.date.issued	2014-02-01	en_US
dc.identifier.citation	Environmental Microbiology, 2014, 16 (2), pp. 467 - 485	en_US
dc.identifier.issn	1462-2912	en_US
dc.identifier.uri	http://hdl.handle.net/10453/36176
dc.description.abstract	Dinoflagellates in marine benthic habitats living epiphytically on macroalgae are an important but highly understudied group of protists. Many produce toxins that can have severe economic impacts on marine-based economies, and improved monitoring tools are required to enhance the management of toxin-related hazards. We analysed the distribution and diversity of epibenthic dinoflagellates inhabiting eight sites in Cocos (Keeling) Islands, Papua New Guinea, and Broome and Exmouth, Western Australia. We used pyrosequencing approaches based on two DNA barcoding marker genes - 18S ribosomal RNA (rRNA) and mitochondrial cytochrome b (cob) - and compared these to an approach based on clone libraries (197 sequences) using the cob gene. Dinoflagellate sequences accounted for 133 [64 unique operational taxonomic units (OTU)] out of 10529 18S rRNA gene sequences obtained from all samples. However, using the dinoflagellate specific assay targeting the cob gene marker, we obtained 9748 (1217 unique OTU) dinoflagellate sequences from the same environmental samples, providing the largest, to date, set of dinoflagellate cob gene sequences and reliable estimates of total dinoflagellate richness within the samples and biogeographic comparisons between samples. This study also reports the presence of potentially toxic species of the genera Gambierdiscus, Ostreopsis, Coolia, Prorocentrum and Amphidinium from the above-mentioned geographical regions. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.	en_US
dc.relation.ispartof	Environmental Microbiology	en_US
dc.relation.isbasedon	10.1111/1462-2920.12275	en_US
dc.subject.classification	Microbiology	en_US
dc.subject.mesh	Dinoflagellida	en_US
dc.subject.mesh	Cytochromes b	en_US
dc.subject.mesh	DNA, Protozoan	en_US
dc.subject.mesh	RNA, Ribosomal, 18S	en_US
dc.subject.mesh	Likelihood Functions	en_US
dc.subject.mesh	Sequence Analysis, DNA	en_US
dc.subject.mesh	Biodiversity	en_US
dc.subject.mesh	Phylogeny	en_US
dc.subject.mesh	Western Australia	en_US
dc.subject.mesh	Papua New Guinea	en_US
dc.title	Cob gene pyrosequencing enables characterization of benthic dinoflagellate diversity and biogeography	en_US
dc.type	Journal Article
utslib.citation.volume	2	en_US
utslib.citation.volume	16	en_US
utslib.for	0607 Plant Biology	en_US
utslib.for	0605 Microbiology	en_US
utslib.for	0603 Evolutionary Biology	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - C3 - Climate Change Cluster
utslib.copyright.status	closed_access
pubs.issue	2	en_US
pubs.publication-status	Published	en_US
pubs.volume	16	en_US

Abstract:

Dinoflagellates in marine benthic habitats living epiphytically on macroalgae are an important but highly understudied group of protists. Many produce toxins that can have severe economic impacts on marine-based economies, and improved monitoring tools are required to enhance the management of toxin-related hazards. We analysed the distribution and diversity of epibenthic dinoflagellates inhabiting eight sites in Cocos (Keeling) Islands, Papua New Guinea, and Broome and Exmouth, Western Australia. We used pyrosequencing approaches based on two DNA barcoding marker genes - 18S ribosomal RNA (rRNA) and mitochondrial cytochrome b (cob) - and compared these to an approach based on clone libraries (197 sequences) using the cob gene. Dinoflagellate sequences accounted for 133 [64 unique operational taxonomic units (OTU)] out of 10529 18S rRNA gene sequences obtained from all samples. However, using the dinoflagellate specific assay targeting the cob gene marker, we obtained 9748 (1217 unique OTU) dinoflagellate sequences from the same environmental samples, providing the largest, to date, set of dinoflagellate cob gene sequences and reliable estimates of total dinoflagellate richness within the samples and biogeographic comparisons between samples. This study also reports the presence of potentially toxic species of the genera Gambierdiscus, Ostreopsis, Coolia, Prorocentrum and Amphidinium from the above-mentioned geographical regions. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

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http://hdl.handle.net/10453/36176