19:I[42426,["/_next/static/immutable/chunks/1xctgzqre-wsy.js","/_next/static/immutable/chunks/06_-wz6pdtp2b.js","/_next/static/immutable/chunks/30e52g49hg40p.js","/_next/static/immutable/chunks/02yq6tul2z-oh.js","/_next/static/immutable/chunks/10bx_ec2vj7n_.js","/_next/static/immutable/chunks/33bfn03fo8xnt.js","/_next/static/immutable/chunks/0tfjf78scu61b.js","/_next/static/immutable/chunks/31xnvej4n1bi9.js"],"default"] 1a:T4e2,

Cycle threshold (CT) data were imported into R v3.6.0 using the steponeR package (Cunning 2018). Symbiont to host cell ratios for each algal symbiont genus were calculated adjusting for differences in target locus copy number, DNA extraction efficiency, and probe fluorescence intensity following Cunning & Baker (2013) and converted to relative abundance within each sample.

This dataset was generated using code available at Zenodo DOI 10.5281/zenodo.3827500, which contains code for amplicon sequencing data QA/QC, dada2 ASV generation and taxonomic assignment, phyloseq analysis and removal of chloroplast and mitochondrial ASVs, visualization of taxonomic data, and diversity estimates using breakaway and divnet.

BCO-DMO Processing:
- Adjusted field/parameter names to comply with BCO-DMO naming conventions;
- Missing data identifiers "NA" and "NAN" replaced with 'nd' (BCO-DMO's default missing data identifier);
- Changed dates incorrectly entered as "2019-01-21" to "2019-01-24";
- Added columns for Latitude and Longitude;
- Added a conventional header with dataset name, PI names, version date.

1b:Tcf7,NSF Award Abstract: Climate change represents an existential threat to coral reef ecosystems worldwide, with coral bleaching driven by continued ocean warming presenting the most pressing challenge to the persistence of these ecosystems over the next few decades. Given the severity and urgency of this threat it is critical to investigate mechanisms by which some corals might survive warming, assess the degree to which this is happening on reefs, and apply these discoveries to inform conservation interventions that might improve survival trajectories wherever possible. This project aims to fulfill these objectives by testing whether reef corals in the Caribbean are undergoing shifts in their algal symbionts in favor of more heat-tolerant types, what the consequences of these shifts might be for coral reef ecosystems, and the way in which we might use this information to help conserve them. Scientific objectives will be leveraged to improve the effectiveness of reef restoration efforts in the Caribbean by applying findings to ongoing intervention trials which aim to seed outplanted corals (both adult fragments raised in nurseries, and sexually derived coral recruits) with heat tolerant algae that are climate-resistant. It also takes advantage of emerging opportunities at two major public aquariums to highlight the plight of coral reefs to engaged public audiences primed to receive this message and learn about the role of science in both understanding and mitigating the problem. Finally, numerous high school, undergraduate, and graduate students will receive mentorship during this project, helping to train the next generation of marine scientists. This project tests whether continued climate warming is causing heat-tolerant algal symbionts (such as Durusdinium trenchii) to become increasingly common on coral reefs in the Caribbean. Understanding the changing symbiotic "milieu" in the region, the processes underlying the spread of D. trenchii, and the consequences of this spread, are very timely questions that have the potential to help us understand future reef states. This project will: (1) Manipulate coral symbioses in the laboratory, including a number of Caribbean coral species never before attempted, to assess in a standardized way their relative ability to acquire heat-tolerant symbionts; (2) Outplant corals with manipulated symbiont communities to reefs to assess real-world ecophysiological tradeoffs to heat tolerance, such as reduced growth rate; (3) Introduce heat-tolerant symbionts to coral colonies in the field using tissue implants in order to understand environmental controls on the persistence or loss of introduced symbionts; (4) Evaluate transgenerational feedbacks in the symbiotic milieu by investigating the roles of temperature and D. trenchii availability on the acquisition and establishment of these symbionts in newly settled coral larvae; and (5) Quantify changes in the incidence and relative abundance of heat-tolerant symbionts in the Caribbean over the last ~20 years using unique archived samples dating back to 1995-2002 from Florida, Bahamas, Belize, and Bermuda. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.6:["$","$L19",null,{"dataset":{"_id":"855439","description":"","problem":"","acquisition":"

Tissue samples from colonies of O. faveolata were collected from Mermaid Reef and sensitive Sandy Cay Reef between 21 and 24 January 2019. Genomic DNA from each coral sample was extracted and assayed using qPCR targeting loci specific to O. faveolata and each of four symbiont genera (Symbiodinium, Breviolum, Cladocopium, and Durusdinium). All reactions were performed on a QuantStudio 3 Real-Time PCR system (Life Technologies, Foster City, CA, USA). The resulting cycle threshold (CT) values at a set threshold of delta Rn = 0.01 were used for data analysis.

\n","processing":"$1a","bcodmoProcessing":"","title":"Symbiont community structure in Orbicella faveolata from Mermaid Reef and Sandy Cay Reef in Abaco, The Bahamas in January 2019","nickname":"Symbiont community structure in Orbicella faveolata","dataUrl":"","currentState":"Final no updates expected","currentStateId":"7","validated":true,"restricted":false,"version":"1","version_date":"2021-11-12T05:00:00.000Z","abstract":"This dataset contains results from genus-specific qPCR assays to quantify the abundance of Symbiodinium, Breviolum, Cladocopium, and Durusdinium symbionts relative to coral cells in Orbicella faveolata from Abaco, The Bahamas in January 2019. Bulk genomic DNA was extracted from tissue scrapings collected by SCUBA divers, and used as a template for qPCR assays. Resulting CT values were used to calculate symbiont to host cell ratios for each symbiont genus within each coral. The publication based on these data can be found here: http://dx.doi.org/10.1007/s00338-020-01948-0.","citation":"Parker, K., Cunning, R. (2021) Symbiont community structure in Orbicella faveolata from Mermaid Reef and Sandy Cay Reef in Abaco, The Bahamas in January 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-11-12 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.855439.1 [access date]","citationParts":{"identifier":"doi:10.26008/1912/bco-dmo.855439.1","versionDate":"2021-11-12","versionId":"1","year":"2021","title":"Symbiont community structure in Orbicella faveolata from Mermaid Reef and Sandy Cay Reef in Abaco, The Bahamas in January 2019","authors":"Parker, K., Cunning, R.","publisher":"Biological and Chemical Oceanography Data Management Office (BCO-DMO)."},"doi":"10.26008/1912/bco-dmo.855439.1","release_date":null,"field_dataset_location":"","temporal_extent":{"start":"2019-01-24T05:00:00.000Z","end":"2019-01-24T05:00:00.000Z"},"temporal":{"resolution":"time:unitDay","type":"time:Instant","start":{"value":"","label":""},"end":{"value":"","label":""}},"spatial_extent":{"shape":"polygon","center":{"latitude":26.476249999654,"longitude":-77.021249998986},"wkt":"POLYGON ((-77.0535 26.3989, -76.989 26.3989, -76.989 26.5536, -77.0535 26.5536, -77.0535 26.3989))","north":26.5536,"east":-76.989,"south":26.3989,"west":-77.0535},"dataset_type":["Other Field Results"],"keywords":["oceans"],"data_files":[{"id":"903403","title":"qpcr.csv","url":"https://datadocs.bco-dmo.org/dataset/855439/file/8XXgnK4uQZnXq4/qpcr.csv","showTableUrl":"https://www.bco-dmo.org/dataset/855439/data/view/903403","description":"Primary data file for dataset ID 855439","filename":"qpcr.csv","bytesize":13502,"checksum":{"value":"cfbc2c62e978dc1b03369e4d3a33c129","Algorithm":{"_id":"190","name":"MD5"}},"mimetype":"text/csv","fileType":{"_id":"192","name":"Comma Separated Values (.csv)"},"isErddap":"","date":"","isPublicDuringEmbargo":false,"primaryDataFile":true,"showTable":true,"restricted":false}],"supplemental_files":[],"roles":[{"role":{"_id":"138","name":"Principal Investigator"},"performedBy":{"_id":"817979","name":"Ross Cunning"},"performedAtOrganization":{"_id":"683480","name":"Shedd Aquarium"}},{"role":{"_id":"140","name":"Co-Principal Investigator"},"performedBy":{"_id":"855447","name":"Katie Parker"},"performedAtOrganization":{"_id":"683480","name":"Shedd Aquarium"}},{"role":{"_id":"133","name":"Contact"},"performedBy":{"_id":"817979","name":"Ross Cunning"},"performedAtOrganization":{"_id":"683480","name":"Shedd Aquarium"}},{"role":{"_id":"145","name":"BCO-DMO Data Manager"},"performedBy":{"_id":"835206","name":"Taylor Heyl"},"performedAtOrganization":{"_id":"191","name":"Woods Hole Oceanographic Institution"}},{"role":{"_id":"145","name":"BCO-DMO Data Manager"},"performedBy":{"_id":"51498","name":"Shannon Rauch"},"performedAtOrganization":{"_id":"191","name":"Woods Hole Oceanographic Institution"}}],"deployments":[],"funding":[{"_id":"817977","name":"OCE-1851305","fundingSource":{"_id":"355","name":"NSF Division of Ocean Sciences"},"url":"https://www.nsf.gov/awardsearch/show-award?AWD_ID=1851305"}],"instruments":[{"_id":"856671","name":"","description":"","type_id":"707569","type_name":"qPCR Thermal Cycler","type_desc":"An instrument for quantitative polymerase chain reaction (qPCR), also known as real-time polymerase chain reaction (Real-Time PCR).","type_acronym":"qPCR"}],"parameters":[{"_id":"864752","name":"sample_id","format":"","frictionlessType":"string","description":"

unique identifier for samples of each coral colony

","units":{"_id":"","name":"unitless"},"type":{"_id":"960","name":"sample","description":"

unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent

"}},{"_id":"864753","name":"site","format":"","frictionlessType":"string","description":"

reef site location of coral colony

","units":{"_id":"","name":"unitless"},"type":{"_id":"1124","name":"site","description":"

Sampling site identification.

"}},{"_id":"864754","name":"Latitude","format":"","frictionlessType":"number","description":"

location of sample site

","units":{"_id":"","name":"decimal degrees"},"type":{"_id":"730","name":"latitude","description":"

latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes

"}},{"_id":"864755","name":"Longitude","format":"","frictionlessType":"number","description":"

location of sample site

","units":{"_id":"","name":"decimal degrees"},"type":{"_id":"731","name":"longitude","description":"

longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datasets as degrees, minutes

"}},{"_id":"864756","name":"genus","format":"","frictionlessType":"string","description":"

coral colony genus

","units":{"_id":"","name":"unitless"},"type":{"_id":"2009","name":"genus","description":"

taxonomic genus of organism

"}},{"_id":"864757","name":"species","format":"","frictionlessType":"string","description":"

coral colony species

","units":{"_id":"","name":"unitless"},"type":{"_id":"976","name":"species","description":"

a taxonomic binomial that consists of a genus name followed by the species name of an organism

"}},{"_id":"864758","name":"colony_tag","format":"","frictionlessType":"integer","description":"

number on tag affixed to coral colony in the field

","units":{"_id":"","name":"unitless"},"type":{"_id":"903","name":"number","description":"

number of organisms counted/observed, a generic term, specific to the data set in which it appears

"}},{"_id":"864759","name":"colony_depth","format":"","frictionlessType":"number","description":"

depth of sampled coral colony on the reef

","units":{"_id":"","name":"meters"},"type":{"_id":"808","name":"depth","description":"

Observation/sample depth below the sea surface. Units often reported as: meters, feet.

\nWhen used in a JGOFS/GLOBEC dataset the depth is a best estimate; usually but not always calculated from pressure; calculated either from CTD pressure using Fofonoff and Millard (1982; UNESCO Tech Paper #44) algorithm adjusted for 1980 equation of state for seawater (EOS80) or simply equivalent to nominal depth as recorded during sampling if CTD pressure was unavailable.

"}},{"_id":"864760","name":"date_sampled","format":"%Y-%m-%d","frictionlessType":"date","description":"

date that the coral sample was collected

","units":{"_id":"","name":"unitless"},"type":{"_id":"1070","name":"date","description":"

date; generally reported in GMT as YYYYMMDD (year; month; day); also as MMDD (month; day); EqPac dates are local Hawaii time. ISO_Date format is YYYY-MM-DD (http://www.iso.org/iso/home/standards/iso8601.htm)

"}},{"_id":"864761","name":"A_CT_mean","format":"","frictionlessType":"string","description":"

qPCR cycle threshold value for Symbiodinium (clade A) assay, mean of technical replicates

","units":{"_id":"","name":"cycles"},"type":{"_id":"491108","name":"mean","description":"