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| Status |
Public on Sep 30, 2014 |
| Title |
Comparing bacterial community composition of healthy and dark-spot-affected Siderastrea siderea in Florida and the Caribbean. |
| Platform organisms |
Bacteria; Archaea |
| Sample organism |
mixed sample |
| Experiment type |
Other
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| Summary |
Coral disease is one of the major causes of reef degradation and therefore of concern to management and conservation efforts. Dark Spot Syndrome (DSS) was described in the early 1990’s as brown or purple amorphous areas of tissue on a coral and has since become one of the most prevalent diseases reported on Caribbean reefs. It has been identified in a number of coral species, but there is debate as to whether it is in fact the same disease in different corals. Further, it is questioned whether these macroscopic signs are in fact diagnostic of an infectious disease, since they can also be caused by physical injury in some species. The most commonly affected species in the Caribbean is the massive starlet coral Siderastrea siderea. We sampled this species in two geographic locations, Dry Tortugas National Park and Virgin Islands National Park. Tissue biopsies were collected from both healthy colonies with normal pigmentation and those with dark spot lesions. Microbial-community DNA was extracted from coral samples (mucus, tissue, and skeleton), amplified using bacterial-specific primers, and applied to PhyloChip™ G3 microarrays to examine the bacterial diversity associated with this coral. Samples were also screened for the presence of a fungal ribotype that has recently been implicated as a causative agent of DSS in another coral species, however the amplicon pools were overwhelmed by coral 18S rRNA genes from S. siderea. Unlike a similar study on a white-plague-like disease, S. siderea samples did not cluster consistently based on health state (i.e., normal versus dark spot). Various bacteria, including Cyanobacteria and Vibrios, were observed to have increased relative abundance in the discolored tissue, but the patterns were not consistent across all DSS samples. Overall, our findings do not support the hypothesis that DSS in S. siderea is linked to a bacterial pathogen or pathogens. This dataset provides the most comprehensive overview to date of the bacterial community associated with the healthy scleractinian coral S. siderea.
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| Overall design |
17 samples, coral tissue punches from healthy and also from dark-spot-affected Siderastrea Siderea coral in the Virgin Islands and the Dry Tortugas National Parks was collected for comparison of associated bacterial communities
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| Contributor(s) |
Kellogg CA, Piceno YM, Tom LM, DeSantis TZ, Gray MA, Andersen GL |
| Citation(s) |
25289937 |
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| Submission date |
Aug 21, 2014 |
| Last update date |
Dec 24, 2014 |
| Contact name |
Yvette M Piceno |
| Organization name |
LBNL
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| Department |
Ecology
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| Lab |
Andersen
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| Street address |
1 Cyclotron Rd., MS 70A-3317
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| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
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| Platforms (1) |
| GPL16546 |
[PhyloChip] Affymetrix G3 PhyloChip |
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| Samples (17)
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| Relations |
| BioProject |
PRJNA258662 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE60622_MIAME_GEO-format_PhyloChip-data_Siderastrea.xlsx |
6.2 Mb |
(ftp)(http) |
XLSX |
| GSE60622_RAW.tar |
94.2 Mb |
(http)(custom) |
TAR (of CEL) |
| GSE60622_README_PhyloChip_Siderastrea_Kellogg.txt |
4.0 Kb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
| Processed data are available on Series record |
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