Dataset: Suppl 3a: core microbiome

Name: Microbial orders comprising the core microbiome across all samples as measured by taxa prevalence, 2009-2012 (HERBVRE project)
Published: 2017-01-10
Keywords: biota, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.674398.1

Spatial Extent: N:24.9943 E:-80.4065 S:24.9943 W:-80.4065

Project:

Cascading interactions of herbivore loss and nutrient enrichment on coral reef macroalgae, corals, and microbial dynamics (HERBVRE)

Principal Investigator:

Deron Burkepile (Florida International University, FIU)

Co-Principal Investigator:

Rebecca Vega Thurber (Florida International University, FIU)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2017-01-10

Restricted:

Validated:

Yes

Current State:

Final no updates expected

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

Abstract:

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) doi:10.1038/ncomms11833, Supplementary Data 3a.

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2017-01-10	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.674398.1	2021-08-05

Description

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 doi:10.1038/ncomms11833 Supplementary Information

Methods & Sampling

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)

Data Processing Description

BCO-DMO Processing:
- added conventional header with dataset name, PI name, version date, reference information
- renamed parameters to BCO-DMO standard

Data Files

File
S3a_core_microbes.csv (Comma Separated Values (.csv), 4.40 KB) MD5:697a771612a3dc35ffada583b62cb828 Primary data file for dataset ID 674398

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1130786

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
Burkepile_FL_Keys		2009-06-01	Florida Keys National Marine Sanctuary		data info

Instruments

None available yet

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
taxonomy	microbe taxonomic identification from QIIME Greengenes 13_8	unitless	taxon
all_tmt_95pcent	95% carriage of the microbial order in coral mucus samples across all treatments	unitless	flag
all_tmt_75pcent	75% carriage of the microbial order in coral mucus samples across all treatments	unitless	flag
all_tmt_50pcent	50% carriage of the microbial order in coral mucus samples across all treatments	unitless	flag
core_only_95pcent	95% carriage of the microbial order in coral mucus samples for Greengenes core set only	unitless	flag
core_only_75pcent	75% carriage of the microbial order in coral mucus samples for Greengenes core set only	unitless	flag
core_only_50pcent	50% carriage of the microbial order in coral mucus samples for Greengenes core set only	unitless	flag

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Database

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Dataset: Suppl 3a: core microbiome