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Title: PHOTO IDENTIFICATION GUIDE OF THE BENTHIC TAXA INHABITING THE MESOPHOTIC REEFS OF THE FLORIDA KEYS NATIONAL MARINE SANCTUARY.
Creator: Reed, John K., Farrington, Stephanie, Pomponi, Shirley A., Diaz, Maria Cristina, Harbor Branch Oceanographic Institute, Hanisak, M. Dennis
Abstract/Description: A 17-day research cruise was conducted to the Florida Keys National Marine Sanctuary (FKNMS), August 12-29, 2019 by the Cooperative Institute for Ocean Exploration, Research, and Technology (CIOERT) at Harbor Branch Oceanographic Institute, Florida Atlantic University (HBOI-FAU) aboard the University of Miami ship R/V F.G. Walton Smith. Harbor Branch Oceanographic Institute Technical Report Number 197.
Date Issued: 2021
PURL: http://purl.flvc.org/fau/fd/FAUIR000419
Format: Document (PDF)

Title: Characterization of the Mesophotic Coral Reefs in the Florida Keys National Marine Sanctuary.
Creator: Reed, John K., Farrington, Stephanie, Harbor Branch Oceanographic Institute, Hanisak, M. Dennis, Pomponi, Shirley M.
Abstract/Description: A 17-day research cruise was conducted to the Florida Keys National Marine Sanctuary (FKNMS), August 12-29, 2019 by the Cooperative Institute for Ocean Exploration, Research, and Technology (CIOERT) at Harbor Branch Oceanographic Institute, Florida Atlantic University (HBOI-FAU) aboard the University of Miami ship R/V F.G. Walton Smith. Harbor Branch Oceanographic Institute Technical Report Number 198.
Date Issued: 2021
PURL: http://purl.flvc.org/fau/fd/FAUIR000420
Format: Document (PDF)

Title: SOUTH ATLANTIC MPAS AND OCULINA HAPC: Characterization of Fish Communities, Benthic Habitat, and Benthic Macrobiota Final Report for 2018-2019 NOAA Ship Pisces Cruises (18-02, 19-02).
Creator: Harter, Stacey, Reed, John K., Farrington, Stephanie
Abstract/Description: The South Atlantic Fishery Management Council (SAFMC) and Department of Commerce through the Magnuson-Stevens Fishery Management Act have established eight deepwater Marine Protected Areas (MPAs), five deepwater Coral Habitat Areas of Particular Concern (CHAPCs), and the Oculina Coral HAPC along the outer continental shelf off the southeastern U.S. This project proposed to document and characterize the benthic habitat, benthic sessile biota, and fish populations within some of these protected...
Show moreThe South Atlantic Fishery Management Council (SAFMC) and Department of Commerce through the Magnuson-Stevens Fishery Management Act have established eight deepwater Marine Protected Areas (MPAs), five deepwater Coral Habitat Areas of Particular Concern (CHAPCs), and the Oculina Coral HAPC along the outer continental shelf off the southeastern U.S. This project proposed to document and characterize the benthic habitat, benthic sessile biota, and fish populations within some of these protected areas and within the jurisdiction of the SAFMC. In February 2009, the SAFMC implemented eight Type II MPAs between Cape Hatteras, NC and the Florida Keys to protect seven species of the deepwater snapper-grouper complex. The closures, however, will provide ecosystem-level benefits to the entire complex as well as protect the shelfedge reef habitat they utilize. These consist of five species of grouper: snowy grouper (Hyporthodus niveatus), yellowedge grouper (H. flavolimbatus), warsaw grouper (H. nigritus), misty grouper (H. mystacinus) and speckled hind (Epinephelus. drummondhayi), and two species of tilefish: golden tilefish (Lopholatilus chamaeleonticeps) and blueline tilefish (Caulolatilus microps). The shelf-edge MPAs are known to contain reef habitat exploited by these five species of grouper as well as deepwater soft bottom habitat used by the two tilefish species. These species are considered to be at risk due to currently low stock densities and to life history characteristics which subject them to substantial fishing mortality. This monitoring program for the MPAs will ensure the Council remains well informed of changes within reef fish populations and coral habitats associated with these MPAs. NOAA NMFS conducted preliminary examinations of five of these potential MPA sites in 2004, 2006, 2007 and 2008. Post-closure data were also collected in 2009, 2010, and 2012 – 2019. The MPAs afforded the opportunity to obviate the criticisms of comparing MPAs with adjacent open-to fishing areas by examining the MPAs for four years prior to the closures. Since monitoring began in 2004, this project has produced population density estimates of targeted reef fish species within the boundaries of five of the eight MPAs and adjacent control areas, before and after closure.
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Date Issued: 2020
PURL: http://purl.flvc.org/fau/fd/FAUIR000409
Format: Document (PDF)

Title: CUBA’S MESOPHOTIC CORAL REEFS Sponge Photo Identification Guide 1st Edition.
Creator: Diaz, Maria Cristina, Pomponi, Shirley A., Reed, John K., Busutil, Linnet, Garcia-Hernandez, Maria Rosa
Abstract/Description: Mesophotic coral reef ecosystems (MCEs) are light-dependent benthic communities that occur deeper than shallow reefs and typically range from depths of 30 m to the bottom of the photic zone, which may extend to >150 m in some regions. MCEs represent in part an extension of shallow-water coral reef ecosystems and support a diverse assemblages of habitat-building taxa, including corals, sponges and algae, and associated fish (Reed et al., 2018). Many MCEs worldwide appear to be thriving...
Show moreMesophotic coral reef ecosystems (MCEs) are light-dependent benthic communities that occur deeper than shallow reefs and typically range from depths of 30 m to the bottom of the photic zone, which may extend to >150 m in some regions. MCEs represent in part an extension of shallow-water coral reef ecosystems and support a diverse assemblages of habitat-building taxa, including corals, sponges and algae, and associated fish (Reed et al., 2018). Many MCEs worldwide appear to be thriving compared to shallow reefs. The deep reef refugia hypothesis suggests that MCEs may be less impacted from natural and anthropogenic impacts than shallow coral reefs, and may be more stable and resilient than shallow reefs. MCEs may also act as refugia for shallow reef species through the export of fish and coral larvae. However, it is now apparent that MCEs are also vulnerable to disturbances from all facets of perturbations including climate change, bottom trawling, invasive species, and pollution. Whereas considerable data have been reported regarding the distribution, ecology, and health of Cuba’s shallow reefs, relatively little is known about the distribution, community structure and health of Cuba’s deep mesophotic reefs. Cuba’s strong marine policies and legislation has already resulted in 105 MPAs, covering nearly 25% of its insular shelf, yet overfishing, poaching, pollution and global warming are threats to these vulnerable ecosystems, as reefs worldwide are threatened.
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Date Issued: 2019
PURL: http://purl.flvc.org/fau/fd/FAUIR000405
Format: Document (PDF)

Title: Cuba's Mesophotic Coral Reefs Macroalgae Photo Identification Guide.
Creator: Martinez-Daranas, Beatriz, González-Sanchez, Patricia M., Ramos, Amanda, Gomez, Emma E., Alfonso, Yusimi, Suarez, Ana M., Hanisak, M. Dennis, Reed, John K., Farrington, Stephanie
Date Issued: 2018
PURL: http://purl.flvc.org/fau/fd/FAUIR000357
Format: Citation

Title: Morphological Diagnoses of Sponges Collected at Shelf-edge MPAs from Eastern Florida to North Carolina, between depths of 51 and 150 m, during CIOERT Expeditions (2018-2019).
Creator: Diaz Ronda, Maria Cristina, Farrington, Stephanie, Reed, John K., Pomponi, Shirley A.
Abstract/Description: This paper is a result of the taxonomic analyses of the sponges collected during the NOAA Ship Pisces expeditions in 2018 and 2019 with the University of North Carolina, Wilmington (UNCW) Mohawk ROV. This is part of a 9-year project conducted by NOAA National Marine Fisheries (NMF) in collaboration with the Cooperative Institute for Ocean Exploration, Research, and Technology (CIOERT) at Harbor Branch Oceanographic Institute, Florida Atlantic University (HBOI-FAU) to document and monitor the...
Show moreThis paper is a result of the taxonomic analyses of the sponges collected during the NOAA Ship Pisces expeditions in 2018 and 2019 with the University of North Carolina, Wilmington (UNCW) Mohawk ROV. This is part of a 9-year project conducted by NOAA National Marine Fisheries (NMF) in collaboration with the Cooperative Institute for Ocean Exploration, Research, and Technology (CIOERT) at Harbor Branch Oceanographic Institute, Florida Atlantic University (HBOI-FAU) to document and monitor the Marine Protected Areas (MPAs) of the southeastern U.S. continental shelf (eastern Florida to North Carolina, 50-165 m deep). The most prominent and conspicuous sponges were collected with the intention of evaluating the biodiversity of this important benthic group in these mesophotic habitats. Eleven sponge samples were collected, and taxonomic evaluation, studying the internal and external morphology, resulted in: 1) three well recognized species from the Tropical Western Atlantic (Leiodermatium lynceus, Neofibularia nolitangere, Clathria foliacea), 2) four species with sibling recognized species but with major morphological differences that might require the description of new species (Epipolasis cf. profunda, Cliona cf. tumula, Cliona aff. celata), and 3) three species that only could receive generic assignations (Penares sp.1, Clathria sp.1, and Aaptos sp.1). These results show that more than half of the species collected represent unknown species to science, or unknown variations of recognized species. Careful comparison with species types and observations of spicules under SEM would allow the necessary evidence to characterize and classify these new species or varieties. We suggest further characterization of these novel fauna considering their level of abundance and distribution in the MPAs studied. A synoptic description of each species studied, with live, deck and microscopy photographs is here presented.
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Date Issued: 2018 - 2019
PURL: http://purl.flvc.org/fau/fd/FAUIR000407
Format: Document (PDF)

Title: A Well-Kept Treasure at Depth: Precious Red Coral Rediscovered in Atlantic Deep Coral Gardens (SW Portugal) after 300 Years.
Creator: Boavida, Joana, Paulo, Diogo, Aurelle, Didier, Arnaud-Haond, Sophie, Marschal, Christian, Reed, John K., Gonçalves, Jorge M. S., Serrao, Ester A., Pronzato, Roberto
Abstract/Description: Background The highly valuable red coral Corallium rubrum is listed in several Mediterranean Conventions for species protection and management since the 1980s. Yet, the lack of data about its Atlantic distribution has hindered its protection there. This culminated in the recent discovery of poaching activities harvesting tens of kg of coral per day from deep rocky reefs off SW Portugal. Red coral was irregularly exploited in Portugal between the 1200s and 1700s, until the fishery collapsed....
Show moreBackground The highly valuable red coral Corallium rubrum is listed in several Mediterranean Conventions for species protection and management since the 1980s. Yet, the lack of data about its Atlantic distribution has hindered its protection there. This culminated in the recent discovery of poaching activities harvesting tens of kg of coral per day from deep rocky reefs off SW Portugal. Red coral was irregularly exploited in Portugal between the 1200s and 1700s, until the fishery collapsed. Its occurrence has not been reported for the last 300 years. Results Here we provide the first description of an Atlantic red coral assemblage, recently rediscovered dwelling at 60–100 m depth in southern Portugal.We report a very slow growth rate (0.23 mm year-1), comparable to Mediterranean specimens. In comparison with most of the Mediterranean reports, the population reaches much larger sizes, estimated to be over one century old, and has a more complex coral branch architecture that promotes a rich assemblage of associated species, with boreal and Mediterranean affinities. Atlantic red coral is genetically distinct, yet mitochondrial analyses suggest that red corals from the Atlantic may have introgressed the Mediterranean ones after migration via the Algeria current. Our underwater surveys, using advanced mixed-gas diving, retrieved lost fishing gear in all coral sites. Besides illegal harvesting, the use and loss of fishing gears, particularly nets, by local fisheries are likely sources of direct impacts on these benthic assemblages. Conclusions We extended the knowledge on the distribution of C. rubrum in the Atlantic, discovered its genetic distinctiveness, and reveal a rich deep-dwelling fauna associated to these coral assemblages. These findings support a barrier role of the Atlantic-Mediterranean transition zone, but reveal also hints of connectivity along its southern margin. The results highlight the genetic and demographic uniqueness of red coral populations from SW Iberia. However, we also report threats to these vulnerable populations by direct and indirect fishing activities and argue that its protection from any mechanically destructive activities is urgent as a precautionary approach. This study advances our understanding of phylogeographic barriers and range edge genetic diversity, and serves as a baseline against which to monitor future human and environmental disturbances to Atlantic C. rubrum.
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Date Issued: 2016-01-22
PURL: http://purl.flvc.org/fau/fd/FAUIR000048
Format: Citation

Title: South Atlantic MPAs and deepwater coral HAPCs: Characterization of benthic habitat, benthic macrobiota, and fish communities; NOAA Ship Nancy Foster 2014 cruise. NOAA CIOERT Report.
Creator: Reed, John K., Farrington, Stephanie, Harter, Stacey, Harbor Branch Oceanographic Institute
Date Issued: 2015
PURL: http://purl.flvc.org/fau/fd/FA00007515
Subject Headings: Marine parks and reserves, Deep sea corals, Benthos Habitat, Fish communities
Format: Document (PDF)

Title: Preliminary Cruise Report. 2015 HBOI-FAU Cruise. Mesophotic and deepwater reef ecosystems- ROV/AUV surveys of SW Florida Shelf including Northern Pulley Ridge and Howell Hook regions. May 7-20, 2015.
Creator: Reed, John K., Farrington, Stephanie, Pomponi, Shirley A., Price, Melissa, Harbor Branch Oceanographic Institute
Date Issued: 2015
PURL: http://purl.flvc.org/fau/fd/FA00007518
Subject Headings: Deep sea corals, Corals--Ecology, Pulley Ridge, Continental shelf--Florida
Format: Document (PDF)

Title: Photo album and taxonomy of benthic macrobiota and fish from 2011-2013 ROV dives on shelf-edge MPAs off southeastern U.S.
Creator: Reed, John K., Farrington, Stephanie, Harbor Branch Oceanographic Institute
Date Issued: 2014
PURL: http://purl.flvc.org/fau/fd/FA00007512
Subject Headings: Marine parks and reserves, Southeastern United States, Taxonomy (Biology), Benthos
Format: Document (PDF)

Title: Photo album and taxonomy of benthic macrobiota from 2012-2013 ROV dives on Pulley Ridge mesophotic reefs.
Creator: Farrington, Stephanie, Reed, John K., Hanisak, M. Dennis, Harbor Branch Oceanographic Institute
Date Issued: 2014
PURL: http://purl.flvc.org/fau/fd/FA00007510
Subject Headings: Pulley Ridge, Benthos, Cnidaria--Classification, Coral reefs
Format: Document (PDF)

Title: Photo album and taxonomy of benthic macrobiota from 2012-2013 ROV dives on Tortugas mesophotic reefs.
Creator: Reed, John K., Farrington, Stephanie, Harbor Branch Oceanographic Institute
Date Issued: 2014
PURL: http://purl.flvc.org/fau/fd/FA00007511
Subject Headings: Dry Tortugas (Fla.), Benthos, Cnidaria--Classification, Coral reefs
Format: Document (PDF)

Title: Proposal to Gulf of Mexico Fishery Management Council: Proposed Pulley Ridge HAPC Extension. Presented to GOMFC- Coral Group Meeting Webinar, Dec. 4, 2014.
Creator: Reed, John K., Farrington, Stephanie, Harbor Branch Oceanographic Institute
Date Issued: 2014
PURL: http://purl.flvc.org/fau/fd/FA00007520
Subject Headings: Pulley Ridge, Gulf of Mexico Fishery Management Council, Marine habitat conservation
Format: Document (PDF)

Title: Proposed HAPCs/MPAs for mesophotic and deepwater coral/sponge habitat and essential fish habitat in the eastern Gulf of Mexico. A proposal to the Gulf of Mexico Fishery Management Council. GOMFMC Webinar, September 22, 2014.
Creator: Reed, John K., Farrington, Stephanie, Harbor Branch Oceanographic Institute
Date Issued: 2014
PURL: http://purl.flvc.org/fau/fd/FA00007513
Subject Headings: Marine parks and reserves Mexico, Sponges--Mexico, Gulf of, Deep sea corals, Fishes--Habitat
Format: Document (PDF)

Title: Proposal to Gulf of Mexico Fishery Management Council and FKNMS: Mesophotic reefs outside of the Tortugas Ecological Reserves.
Creator: Reed, John K., Farrington, Stephanie, Harbor Branch Oceanographic Institute
Date Issued: 2014
PURL: http://purl.flvc.org/fau/fd/FA00007521
Subject Headings: Dry Tortugas (Fla.), Coral reefs
Format: Document (PDF)

Title: Connectivity of the Pulley Ridge - South Florida Coral Reef Ecosystem:Processes to Decision-Support Tools.
Creator: Farrington, Stephanie, Reed, John K., Hanisak, M. Dennis, Harbor Branch Oceanographic Institute
Date Issued: 2014
PURL: http://purl.flvc.org/fau/fd/FA00007509
Subject Headings: Pulley Ridge, Coral reef ecology--Florida, Underwater exploration
Format: Document (PDF)

Title: Proposed HAPC/MPA for deepwater Lophelia coral habitat and essential fish habitat in the eastern Gulf of Mexico. Presented to GOMFC- Coral Group Meeting Webinar, Dec. 4, 2014.
Creator: Brooke, S. D., Etnoyer, P., Reed, John K., Harbor Branch Oceanographic Institute
Date Issued: 2014
PURL: http://purl.flvc.org/fau/fd/FA00007519
Subject Headings: Marine habitat conservation, Lophelia, Marine parks and reserves Mexico
Format: Document (PDF)

Title: Deep-water benthic habitat characterization and cable impact assessment for the South Florida ocean measurement facility (SFOMF).
Creator: Messing, Charles G., Walker, Brian K., Reed, John K.
Date Issued: 2012-07
PURL: http://purl.flvc.org/fcla/dt/3360206
Subject Headings: Benthos--Habitat, Fishes--Habitat
Format: Document (PDF)

Title: NOAA CIOERT cruise report: Survey of the pulley ridge mesophotic reef ecosystem.
Creator: Reed, John K., Farrington, Stephanie, Pomponi, Shirley A., Hanisak, M. Dennis, Voss, Joshua
Date Issued: 2012-02-15
PURL: http://purl.flvc.org/fcla/dt/3360202
Subject Headings: Ocean exploration, Oceanography--Research, Corals Ecology, Deep sea corals
Format: Document (PDF)

Title: Final Report: Siting study for a hydrokinetic energy project located offshore southeastern Florida: protocols for survey methodology for offshore marine hydrokinetic energy projects.
Creator: Vinick, C., Riccobono, A., Messing, Charles G., Walker, Brian K., Reed, John K., Rogers, S.
Date Issued: 2012
PURL: http://purl.flvc.org/FCLA/DT/3340533
Subject Headings: Ocean energy resources, Renewable energy, Geophysical surveys
Format: Document (PDF)

HBOI Faculty Contributions (61)	+ -
HBOI Technical Reports (23)	+ -
Mesophotic Coral Reefs of Cuba (2)	+ -
FAU College Collections (1)	+ -

Oculinidae (14)	+ -
Deep sea corals (11)	+ -
Marine natural products (10)	+ -
Sponges (7)	+ -
Scleractinia (5)	+ -

Benthos (4)	+ -
Bioactive compounds (4)	+ -
Biodiversity--Research (4)	+ -
Biomedical Research (4)	+ -
Pulley Ridge (4)	+ -
Biomedical research (3)	+ -
Coral reef ecology (3)	+ -
Coral reef ecology --Florida (3)	+ -
Coral reefs (3)	+ -
Corals (3)	+ -
Corals Ecology (3)	+ -
Marine habitat conservation (3)	+ -
Marine metabolites (3)	+ -
Oceanographic submersibles (3)	+ -
Octocorallia (3)	+ -
Porifera (3)	+ -
Southeastern United States (3)	+ -
Submersibles (3)	+ -
Benthos Habitat (2)	+ -
Benthos--Sampling (2)	+ -
Bioherms (2)	+ -
Cnidaria--Classification (2)	+ -
Coral reef ecology --Research --Florida (2)	+ -
Coral reefs and islands (2)	+ -
Corals--Ecology (2)	+ -

article (60)	+ -
technical report (23)	+ -
Technical report (1)	+ -
report (1)	+ -

Reed, John K. (85)	+ -
Pomponi, Shirley A. (23)	+ -
Farrington, Stephanie (17)	+ -
Wright, Amy E. (16)	+ -
Harbor Branch Oceanographic Institute (15)	+ -

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