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Microbial orders comprising the core microbiome across all samples as measured by taxa prevalence, 2009-2012 (HERBVRE project) (NCEI Accession 0277281)

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This dataset contains biological data collected at Florida Keys National Marine Sanctuary during deployment Burkepile_FL_Keys on 2017-01-10. These data include taxon. These data were collected by Deron Burkepile and Rebecca Vega Thurber of Florida International University as part of the "Cascading interactions of herbivore loss and nutrient enrichment on coral reef macroalgae, corals, and microbial dynamics (HERBVRE)" project. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) submitted these data to NCEI on 2023-01-23.

The following is the text of the dataset description provided by BCO-DMO:

Core microbiome

Dataset Description:
This dataset contains microbial orders comprising the core microbiome across all samples as measured by taxa prevalence, from Florida Keys National Marine Sanctuary. Cyanobacteria, Bacteroidetes and Actinobacteria were most abundant in all coral genera, with a core set of 13 bacterial orders in ≥95% of all samples. Published in Nature Communications (2016) https://doi.org/10.1038/ncomms11833, Supplementary Data 3a.

Natural history of the study site:
This experiment was conducted in the area of Pickles Reef (24.99430, -80.40650), located east of Key Largo, Florida in the United States. The Florida Keys reef tract consists of a large bank reef system located approximately 8 km offshore of the Florida Keys, USA, and paralleling the island chain. Our study reef is a 5-6 m deep spur and groove reef system within this reef tract. The reefs of the Florida Keys have robust herbivorous fish populations and are relatively oligotrophic. Coral cover on most reefs in the Florida Keys, including our site, is 5-10%, while macroalgal cover averages ~15%, but ranges from 0-70% depending on location and season. Parrotfishes ( Scaridae ) and surgeonfishes ( Acanthuridae ) are the dominant herbivores on these reefs as fishing for them was banned in 1981. The other important herbivore on Caribbean reefs, the urchin Diadema antillarum , remains at low densities across the Florida Keys following the mass mortality event in 1982-3.

Related Reference:
Zaneveld, J.R., D.E. Burkepile, A.A. Shantz, C. Pritchard, R. McMinds, J. Payet, R. Welsh, A.M.S. Correa, N.P. Lemoine, S. Rosales, C.E. Fuchs, and R. Vega Thurber (2016) Overfishing, nutrient pollution, and temperature interact to disrupt coral reefs down to microbial scales. Nature Communications 7:11833 https://doi.org/10.1038/ncomms11833 Supplementary Information
  • Cite as: Burkepile, Deron; Vega Thurber, Rebecca (2023). Microbial orders comprising the core microbiome across all samples as measured by taxa prevalence, 2009-2012 (HERBVRE project) (NCEI Accession 0277281). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0277281. Accessed [date].
gov.noaa.nodc:0277281
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Distributor NOAA National Centers for Environmental Information
+1-301-713-3277
NCEI.Info@noaa.gov
Dataset Point of Contact NOAA National Centers for Environmental Information
ncei.info@noaa.gov
Time Period 2017-01-10 to 2017-01-10
Spatial Bounding Box Coordinates
West: -80.4065
East: -80.4065
South: 24.9943
North: 24.9943
Spatial Coverage Map
General Documentation
Associated Resources
  • Biological, chemical, physical, biogeochemical, ecological, environmental and other data collected from around the world during historical and contemporary periods of biological and chemical oceanographic exploration and research managed and submitted by the Biological and Chemical Oceanography Data Management Office (BCO-DMO)
    • NCEI Collection
      Navigate directly to the URL for data access and direct download.
  • Burkepile, D., Vega Thurber, R. (2017) Microbial orders comprising the core microbiome across all samples as measured by taxa prevalence, 2009-2012 (HERBVRE project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2017-01-10. https://doi.org/10.26008/1912/bco-dmo.674398.1
    • Parent ID (indicates this dataset is related to other data):
    • gov.noaa.nodc:BCO-DMO
Publication Dates
  • publication: 2023-03-30
Data Presentation Form Digital table - digital representation of facts or figures systematically displayed, especially in columns
Dataset Progress Status Complete - production of the data has been completed
Historical archive - data has been stored in an offline storage facility
Data Update Frequency As needed
Supplemental Information
Acquisition Description:
To identify how algal communities and nutrient pollution affected the coral microbiome, we collected DNA samples from the surface mucus layer of 80 coral colonies (genera Porites, Siderastrea and Agaricia) at approximately monthly intervals. From these samples, 478 were used for 16S ribosomal RNA (rRNA) gene amplicon analyses following quality control ( Supplementary Data 2 sheets a–d ). (Zaneveld, 2016)

Analysis of microbial β-diversity: Microbial community β-diversity was calculated based on the weighted UniFrac distance matrix67. This is a phylogenetic measure of community similarity that takes into account organismal abundance and phylogeny67. Phylogenetic trees used to calculate this metric were constructed in QIIME 1.8 (ref. 65) through alignment of representative sequences of each OTU with PyNAST against the greengenes core set alignment66, and approximate maximum likelihood phylogenetic inference with FastTree. We considered the pool of distances between samples within each metadata category of interest (for example, algal competition or categories of temperature) using QIIME’s make_distance_boxplots.py. Significance was assessed by non-parametric t-tests, each with 1,000 Monte Carlo permutations (permutation is important in this instance to account for the non-independence of distances). The effect of this procedure is to ask whether different factors increase the dispersion of communities. PCoA plots of β-diversity were visualized in the Emperor software. When multiple categories (for example, different algal types) were tested for effects on β-diversity, the false discovery rate (FDR) for multiple comparisons was controlled at a threshold of q=0.05 using the Bejamini–Hochberg method. (Zaneveld, 2016)
Purpose This dataset is available to the public for a wide variety of uses including scientific research and analysis.
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  • accessLevel: Public
  • Distribution liability: NOAA and NCEI make no warranty, expressed or implied, regarding these data, nor does the fact of distribution constitute such a warranty. NOAA and NCEI cannot assume liability for any damages caused by any errors or omissions in these data. If appropriate, NCEI can only certify that the data it distributes are an authentic copy of the records that were accepted for inclusion in the NCEI archives.
Dataset Citation
  • Cite as: Burkepile, Deron; Vega Thurber, Rebecca (2023). Microbial orders comprising the core microbiome across all samples as measured by taxa prevalence, 2009-2012 (HERBVRE project) (NCEI Accession 0277281). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0277281. Accessed [date].
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Theme keywords NODC DATA TYPES THESAURUS NODC OBSERVATION TYPES THESAURUS WMO_CategoryCode
  • oceanography
BCO-DMO Standard Parameters Originator Parameter Names
Data Center keywords NODC COLLECTING INSTITUTION NAMES THESAURUS NODC SUBMITTING INSTITUTION NAMES THESAURUS Global Change Master Directory (GCMD) Data Center Keywords
Platform keywords BCO-DMO Platform Names
Place keywords Provider Place Names
Project keywords BCO-DMO Standard Projects Provider Deployment IDs Provider Funding Award Information
Keywords NCEI ACCESSION NUMBER
Use Constraints
  • Cite as: Burkepile, Deron; Vega Thurber, Rebecca (2023). Microbial orders comprising the core microbiome across all samples as measured by taxa prevalence, 2009-2012 (HERBVRE project) (NCEI Accession 0277281). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0277281. Accessed [date].
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  • Use liability: NOAA and NCEI cannot provide any warranty as to the accuracy, reliability, or completeness of furnished data. Users assume responsibility to determine the usability of these data. The user is responsible for the results of any application of this data for other than its intended purpose.
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  • In most cases, electronic downloads of the data are free. However, fees may apply for custom orders, data certifications, copies of analog materials, and data distribution on physical media.
Lineage information for: dataset
Processing Steps
  • 2023-03-30T20:26:28Z - NCEI Accession 0277281 v1.1 was published.
Output Datasets
Last Modified: 2024-05-31T15:15:28Z
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