Using high-throughput sequencing of ITS2 to describe Symbiodinium metacommunities in St. John, US Virgin Islands
Symbiotic microalgae (Symbiodinium spp.) strongly influence the performance and stress-tolerance of their coral hosts, making the analysis of Symbiodinium communities in corals (and metacommunities on reefs) advantageous for many aspects of coral reef research. High-throughput sequencing of ITS2 nrD...
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2017-06-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/3472.pdf |
| _version_ | 1797424412527427584 |
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| author | Ross Cunning Ruth D. Gates Peter J. Edmunds |
| author_facet | Ross Cunning Ruth D. Gates Peter J. Edmunds |
| author_sort | Ross Cunning |
| collection | DOAJ |
| description | Symbiotic microalgae (Symbiodinium spp.) strongly influence the performance and stress-tolerance of their coral hosts, making the analysis of Symbiodinium communities in corals (and metacommunities on reefs) advantageous for many aspects of coral reef research. High-throughput sequencing of ITS2 nrDNA offers unprecedented scale in describing these communities, yet high intragenomic variability at this locus complicates the resolution of biologically meaningful diversity. Here, we demonstrate that generating operational taxonomic units by clustering ITS2 sequences at 97% similarity within, but not across, samples collapses sequence diversity that is more likely to be intragenomic, while preserving diversity that is more likely interspecific. We utilize this ‘within-sample clustering’ to analyze Symbiodinium from ten host taxa on shallow reefs on the north and south shores of St. John, US Virgin Islands. While Symbiodinium communities did not differ between shores, metacommunity network analysis of host-symbiont associations revealed Symbiodinium lineages occupying ‘dominant’ and ‘background’ niches, and coral hosts that are more ‘flexible’ or ‘specific’ in their associations with Symbiodinium. These methods shed new light on important questions in coral symbiosis ecology, and demonstrate how application-specific bioinformatic pipelines can improve the analysis of metabarcoding data in microbial metacommunity studies. |
| first_indexed | 2024-03-09T08:01:52Z |
| format | Article |
| id | doaj.art-b05d35d2dd6c4cc2bd2051326d212bc0 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T08:01:52Z |
| publishDate | 2017-06-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-b05d35d2dd6c4cc2bd2051326d212bc02023-12-03T00:40:43ZengPeerJ Inc.PeerJ2167-83592017-06-015e347210.7717/peerj.3472Using high-throughput sequencing of ITS2 to describe Symbiodinium metacommunities in St. John, US Virgin IslandsRoss Cunning0Ruth D. Gates1Peter J. Edmunds2Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Kāne‘ohe, HI, United States of AmericaHawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Kāne‘ohe, HI, United States of AmericaDepartment of Biology, California State University, Northridge, CA, United States of AmericaSymbiotic microalgae (Symbiodinium spp.) strongly influence the performance and stress-tolerance of their coral hosts, making the analysis of Symbiodinium communities in corals (and metacommunities on reefs) advantageous for many aspects of coral reef research. High-throughput sequencing of ITS2 nrDNA offers unprecedented scale in describing these communities, yet high intragenomic variability at this locus complicates the resolution of biologically meaningful diversity. Here, we demonstrate that generating operational taxonomic units by clustering ITS2 sequences at 97% similarity within, but not across, samples collapses sequence diversity that is more likely to be intragenomic, while preserving diversity that is more likely interspecific. We utilize this ‘within-sample clustering’ to analyze Symbiodinium from ten host taxa on shallow reefs on the north and south shores of St. John, US Virgin Islands. While Symbiodinium communities did not differ between shores, metacommunity network analysis of host-symbiont associations revealed Symbiodinium lineages occupying ‘dominant’ and ‘background’ niches, and coral hosts that are more ‘flexible’ or ‘specific’ in their associations with Symbiodinium. These methods shed new light on important questions in coral symbiosis ecology, and demonstrate how application-specific bioinformatic pipelines can improve the analysis of metabarcoding data in microbial metacommunity studies.https://peerj.com/articles/3472.pdfSymbiodiniumMetabarcodingCoral reefsITS2SymbiosisMetacommunity |
| spellingShingle | Ross Cunning Ruth D. Gates Peter J. Edmunds Using high-throughput sequencing of ITS2 to describe Symbiodinium metacommunities in St. John, US Virgin Islands PeerJ Symbiodinium Metabarcoding Coral reefs ITS2 Symbiosis Metacommunity |
| title | Using high-throughput sequencing of ITS2 to describe Symbiodinium metacommunities in St. John, US Virgin Islands |
| title_full | Using high-throughput sequencing of ITS2 to describe Symbiodinium metacommunities in St. John, US Virgin Islands |
| title_fullStr | Using high-throughput sequencing of ITS2 to describe Symbiodinium metacommunities in St. John, US Virgin Islands |
| title_full_unstemmed | Using high-throughput sequencing of ITS2 to describe Symbiodinium metacommunities in St. John, US Virgin Islands |
| title_short | Using high-throughput sequencing of ITS2 to describe Symbiodinium metacommunities in St. John, US Virgin Islands |
| title_sort | using high throughput sequencing of its2 to describe symbiodinium metacommunities in st john us virgin islands |
| topic | Symbiodinium Metabarcoding Coral reefs ITS2 Symbiosis Metacommunity |
| url | https://peerj.com/articles/3472.pdf |
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