Microbial sample metadata for water samples used in SourceTracker analysis, 2009-2012

Website: https://www.bco-dmo.org/dataset/674390
Data Type: Other Field Results
Version: 1
Version Date: 2016-12-19

Project
» Cascading interactions of herbivore loss and nutrient enrichment on coral reef macroalgae, corals, and microbial dynamics (HERBVRE)
ContributorsAffiliationRole
Burkepile, DeronFlorida International University (FIU)Principal Investigator
Vega Thurber, RebeccaFlorida International University (FIU)Co-Principal Investigator
Copley, NancyWoods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager

Abstract
This dataset contains microbial sample metadata for water samples used in SourceTracker analysis, from Pickles Reef, Florida Keys National Marine Sanctuary from August of 2011 and 2012. Published in Nature Communications (2016) doi:10.1038/ncomms11833, Supplementary Data 2d.


Coverage

Spatial Extent: Lat:24.9943 Lon:-80.4065

Dataset Description

This dataset contains microbial sample metadata for water samples used in SourceTracker analysis, from Pickles Reef, Florida Keys National Marine Sanctuary from August of 2011 and 2012. Published in Nature Communications (2016) doi:10.1038/ncomms11833, Supplementary Data 2d.

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


Processing Description

BCO-DMO Processing:
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions
- reduced decimal places of HCOM temperature and salinity columns from 4 or 8 to 3 in consideration of sampling precision; reduced lat and lon from 6 to 5 places
- reformatted date from m/d/yyyy to ISO_Date: yyyy-mm-dd
- removed the following columns from display: project, concatenated_date, year, month, day, plot_code_month_year; SequencingCenter, OldSampleID; altitude, country, assigned_from_geo, elevation, env_biome, env_feature, HCOM_temp_0m_degrees; HCOM_temp_5m_degrees; HCOM_avg_0m_degrees; HCOM_avg_temp_5m_degrees; temp_and_salinity_source, SourceSink, Description, ANONYMIZED_NAME, degrees_above_28, degrees_below_28.


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Related Publications

Zaneveld, J. R., Burkepile, D. E., Shantz, A. A., Pritchard, C. E., McMinds, R., Payet, J. P., … Thurber, R. V. (2016). Overfishing and nutrient pollution interact with temperature to disrupt coral reefs down to microbial scales. Nature Communications, 7(1). doi:10.1038/ncomms11833
Results

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Parameters

ParameterDescriptionUnits
sample_location_namename of sampling location unitless
latitudelatitude; north is positive decimal degrees
longitudelongitude; east is positive decimal degrees
depthsample collection depth meters
primer_nameprimer identifier unitless
SampleIDsample identifier unitless
BarcodeSequencegenetic sequence of barcode for this sample unitless
LinkerPrimerSequencelinker primer sequence unitless
Replicatereplicate number unitless
SampleID_no_replicateSampleID without replicate number appended unitless
McMindsSampleIDMcMinds Sample identifier unitless
Individualidentifier for individual organism unitless
barcode_numberbarcode identifier number unitless
run_prefixrun name prefix unitless
analysis_nameanalysis identifer; same as project unitless
sequencing_runsequencing run identifier unitless
sample_site_idsampling site identifier unitless
date_collecteddate sample was collected formatted as yyyy-mm-dd unitless
HCOM_temp_0mtemperature at surface from Hybrid Coordinates Ocean Model HCOM_31_0 degrees Celsius
HCOM_temp_5mtemperature at 5 meters depth from Hybrid Coordinates Ocean Model HCOM_31_0 degrees Celsius
HCOM_avg_temp_0maverage temperature at surface from Hybrid Coordinates Ocean Model HCOM_31_0 degrees Celsius
HCOM_avg_temp_5maverage temperature at 5 meters depth from Hybrid Coordinates Ocean Model HCOM_31_0 degrees Celsius
HCOM_salt_0msalinity at surface from Hybrid Coordinates Ocean Model HCOM_31_0 PSU
HCOM_salt_5msalinity at 5 meters depth from Hybrid Coordinates Ocean Model HCOM_31_0 PSU
HCOM_salt_avg_0maverage salinity at surface from Hybrid Coordinates Ocean Model HCOM_31_0 PSU
HCOM_salt_avg_5maverage salinity at 5 meters depth from Hybrid Coordinates Ocean Model HCOM_31_0 PSU
plot_codeplot code unitless
Projectproject identifier; same as analysis_name unitless
EnvMarine unitless
temp_cattemperature category: high (>30 C) mid (24-30 C) or low (unitless

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Deployments

Burkepile_FL_Keys

Website
Platform
Florida Keys National Marine Sanctuary
Start Date
2009-06-01
End Date
2012-08-31
Description
Herbivore effects on reef algae


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Project Information

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

Coverage: Key Largo, Florida Keys, USA; N 24.99430, W 080.40650


Description from NSF award abstract:
Coral reefs in the Caribbean Sea are undergoing unprecedented declines in coral cover due in large part to climate change, pollution, and reductions in fish biodiversity and abundance. Macroalgae have become abundant on reefs, probably due to decreases in herbivory (e.g., through overfishing) and increases in anthropogenic inputs of nutrients. The spread of macroalgae has negative feedbacks on reef recovery because algae are often superior competitors and suppress growth of both adult and juvenile corals. A majority of reef studies to date have focused on how stressors affect macroorganisms, while relatively few have investigated how these stressors and the resultant algal-dominated states affect microorganisms. Yet, coral reef-associated microbes play significant roles in coral reef ecosystems through biogeochemical cycling and disease. Since microbes are important mutualists of corals as well as potential pathogens, it is important to understand the mechanisms that control their taxonomic and functional diversity.

The goal of this proposal is to quantify how alterations of top-down (removal of herbivorous fish) and bottom-up (inorganic nutrient addition) forces alter macrobial as well as microbial dynamics on coral reefs in order to understand the mechanisms that reinforce coral-depauperate reef systems. This work asks two main questions:

Q1. How do nutrient enrichment and herbivore removal interact to affect benthic algal abundance, coral-algal interactions, and coral survivorship and growth?

Q2. How do nutrient enrichment and herbivore removal affect bacterial abundance, taxonomic diversity, and functional diversity on and within corals?

The proposed research will directly and empirically address many of the current hypotheses about how bottom-up and top-down forces alter reef dynamics. The PIs will investigate: (1) the impact of multiple stressors over several years; (2) impacts on multiple levels of biological organization (from fishes to algae to microbes); and (3) the mechanisms underlying changes in algal-coral microbe interactions. Significantly, the approach will provide the statistical power necessary to distinguish between seasonal- and stress-induced changes in macro- and microbial diversity.

Resulting Publication:
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.
Access to data via Supplementary Information.



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Funding

Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)

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