Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Related Publications
• Related Datasets
• Parameters
• Deployments
• Project Information
• Funding

This dataset contains benthic community composition data for the study plots at Pickles Reef, Florida Keys National Marine Sanctuary from 2009-2013. Published in Nature Communications (2016) doi:10.1038/ncomms11833, Supplementary Data 2c.

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

Quantification of benthic cover:
At least once every season (for example, spring, summer, fall, winter at 12–14 week intervals), we visually quantified benthic cover within four, 50 × 50 cm quadrats in each of the 1 m2 treatment areas. These quadrats were divided into 49 points, and benthic organisms under each point were identified to species or genus. Algae that are challenging to identify taxonomically under field conditions (for example, crustose coralline algae and filamentous algae) were classified into algal functional groups. Filamentous algae were classified into short algal turf (<0.5 cm in height) or algal turf (>0.5 cm in height) given that taller, thicker algal turf can often be deleterious to coral health and growth10.

Benthic cover was quantified in June 2009 1 week before treatments were initiated to provide a baseline from which to assess changes in algal abundance and community structure. No significant differences among treatments in algal abundance could be detected at the beginning of the experiment (see initial time points in Fig. 1a,b), as expected given random assignment of subplots to treatment conditions. Further, during the summer of each year (2009–2012) when algal cover was often at its highest, we also surveyed open areas of reef (areas that did not have three-sided exclosure controls) within the 9-m2 plots to assess whether the exclosure controls had any effect on algal abundance or community composition. We did not detect any differences in algal abundance or community composition between the open unmanipulated areas and exclosure controls (Supplementary Data 1).

BCO-DMO Processing:
- extracted the benthic community columns from the full table, plus the sample id, site, latitude, and longitude columns;
- added conventional header with dataset name, PI name, version date, reference information;
- renamed parameters to comply with BCO-DMO naming conventions;
- replaced 'unknown' with 'nd' ('no data').

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.