Comparative Thermal Performance of the Reef-Building Coral Orbicella
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UC Merced UC Merced Electronic Theses and Dissertations
UC Merced UC Merced Electronic Theses and Dissertations Title Deep Amplicon Sequencing Quantitatively Detected Mixed Community Assemblages of Symbiodinium in Orbicella faveolata and Orbicella franksi Permalink https://escholarship.org/uc/item/31n4975j Author Green, Elizabeth Publication Date 2014 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, MERCED Deep Amplicon Sequencing Quantitatively Detected Mixed Community Assemblages of Symbiodinium in Orbicella faveolata and Orbicella franksi THESIS submitted in partial satisfaction of the requirements for the degree of MASTER OF SCIENCE in Quantitative and Systems Biology by Elizabeth A. Green Committee in charge: David Ardell, chair Miriam Barlow Mónica Medina Michele Weber 2014 © Elizabeth A. Green, 2014 All rights reserved The thesis of Elizabeth A. Green is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Miriam Barlow Mónica Medina Michele Weber David Ardell Chair University of California, Merced 2014 iii Dedication This thesis is dedicated to my loving and supportive husband, Colten Green. iv Table of Contents Page SIGNATURE PAGE ……………………….…………………………………… iii LIST OF FIGURES ……………………………………………………………... vi LIST OF TABLES ………………………………………………………………. vii ACKNOWLEDGEMENTS ……………………………………………………… viii ABSTRACT ……………………………………………………………………… ix INTRODUCTION ………………………………………………………………… 1 METHODS ………………………………………………………………………… 6 RESULTS …………………………………………………………………………. -
Marine Ecology Progress Series 506:129
Vol. 506: 129–144, 2014 MARINE ECOLOGY PROGRESS SERIES Published June 23 doi: 10.3354/meps10808 Mar Ecol Prog Ser FREEREE ACCESSCCESS Long-term changes in Symbiodinium communities in Orbicella annularis in St. John, US Virgin Islands Peter J. Edmunds1,*, Xavier Pochon2,3, Don R. Levitan4, Denise M. Yost2, Mahdi Belcaid2, Hollie M. Putnam2, Ruth D. Gates2 1Department of Biology, California State University, 18111 Nordhoff Street, Northridge, CA 91330-8303, USA 2Hawaii Institute of Marine Biology, University of Hawaii, PO Box 1346, Kaneohe, HI 96744, USA 3Environmental Technologies, Cawthron Institute, 98 Halifax Street East, Private Bag 2, Nelson 7042, New Zealand 4Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA ABSTRACT: Efforts to monitor coral reefs rarely combine ecological and genetic tools to provide insight into the processes driving patterns of change. We focused on a coral reef at 14 m depth in St. John, US Virgin Islands, and used both sets of tools to examine 12 colonies of Orbicella (for- merly Montastraea) annularis in 2 photoquadrats that were monitored for 16 yr and sampled genetically at the start and end of the study. Coral cover and colony growth were assessed annu- ally, microsatellites were used to genetically identify coral hosts in 2010, and their Symbiodinium were genotyped using chloroplastic 23S (cloning) and nuclear ITS2 (cloning and pyrosequencing) in 1994 and 2010. Coral cover declined from 40 to 28% between 1994 and 2010, and 3 of the 12 sampled colonies increased in size, while 9 decreased in size. The relative abundance of Symbio- dinium clades varied among corals over time, and patterns of change differed between photo- quadrats but not among host genotypes. -
Bacterial Profiling of White Plague Disease Across Corals and Oceans
Molecular Ecology (2014) 23, 965–974 doi: 10.1111/mec.12638 Bacterial profiling of White Plague Disease across corals and oceans indicates a conserved and distinct disease microbiome CORNELIA RODER,* CHATCHANIT ARIF,* CAMILLE DANIELS,* ERNESTO WEIL† and CHRISTIAN R. VOOLSTRA* *Red Sea Research Center, King Abdullah University of Science and Technology, 23955 Thuwal, Saudi Arabia, †Department of Marine Sciences, University of Puerto Rico, PO BOX 9000, Mayaguez, Puerto Rico 00680, USA Abstract Coral diseases are characterized by microbial community shifts in coral mucus and tissue, but causes and consequences of these changes are vaguely understood due to the complexity and dynamics of coral-associated bacteria. We used 16S rRNA gene microarrays to assay differences in bacterial assemblages of healthy and diseased colo- nies displaying White Plague Disease (WPD) signs from two closely related Caribbean coral species, Orbicella faveolata and Orbicella franksi. Analysis of differentially abun- dant operational taxonomic units (OTUs) revealed strong differences between healthy and diseased specimens, but not between coral species. A subsequent comparison to data from two Indo-Pacific coral species (Pavona duerdeni and Porites lutea) revealed distinct microbial community patterns associated with ocean basin, coral species and health state. Coral species were clearly separated by site, but also, the relatedness of the underlying bacterial community structures resembled the phylogenetic relationship of the coral hosts. In diseased samples, bacterial richness increased and putatively opportunistic bacteria were consistently more abundant highlighting the role of oppor- tunistic conditions in structuring microbial community patterns during disease. Our comparative analysis shows that it is possible to derive conserved bacterial footprints of diseased coral holobionts that might help in identifying key bacterial species related to the underlying etiopathology. -
Coral-Associated Bacteria Demonstrate Phylosymbiosis and Cophylogeny
ARTICLE DOI: 10.1038/s41467-018-07275-x OPEN Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny F. Joseph Pollock1, Ryan McMinds 2, Styles Smith1, David G. Bourne3,4, Bette L. Willis3,5, Mónica Medina 1,6, Rebecca Vega Thurber2 & Jesse R. Zaneveld7 Scleractinian corals’ microbial symbionts influence host health, yet how coral microbiomes assembled over evolution is not well understood. We survey bacterial and archaeal 1234567890():,; communities in phylogenetically diverse Australian corals representing more than 425 million years of diversification. We show that coral microbiomes are anatomically compartmenta- lized in both modern microbial ecology and evolutionary assembly. Coral mucus, tissue, and skeleton microbiomes differ in microbial community composition, richness, and response to host vs. environmental drivers. We also find evidence of coral-microbe phylosymbiosis, in which coral microbiome composition and richness reflect coral phylogeny. Surprisingly, the coral skeleton represents the most biodiverse coral microbiome, and also shows the stron- gest evidence of phylosymbiosis. Interactions between bacterial and coral phylogeny sig- nificantly influence the abundance of four groups of bacteria–including Endozoicomonas-like bacteria, which divide into host-generalist and host-specific subclades. Together these results trace microbial symbiosis across anatomy during the evolution of a basal animal lineage. 1 Department of Biology, Pennsylvania State University, 208 Mueller Lab, University Park, State College, PA 16802, USA. 2 Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR 97331, USA. 3 College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia. 4 Australian Institute of Marine Science, Townsville, QLD 4810, Australia. 5 ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia. -
Protected Species Order 2015
Protected Species Order 2015 August 2015 GOVERNMENT OF BERMUDA MINISTRY OF HEALTH, SENIORS AND ENVIRONMENT Department of Conservation Services Protected Species Order 2015 – Protected Species Act 2003 2015 Bermuda and the surrounding reef platform, 1998 Bermuda and the surrounding reef platform, 1998 Protected Species Order 2015 – Protected Species Act 2003 Table of Contents 1.0. Introduction ................................................................................................................................................................................................ 1 Purpose of legislation ...................................................................................................................................................................................... 2 Goal ................................................................................................................................................................................................................. 2 Objectives ........................................................................................................................................................................................................ 2 How species are nominated ............................................................................................................................................................................. 2 Levels of protection for protected species ...................................................................................................................................................... -
Growth Rates of Porites Astreoides and Orbicella Franksi in Mesophotic Habitats Surrounding St
Growth rates of Porites astreoides and Orbicella franksi in mesophotic habitats surrounding St. Thomas Sarah H. Groves1,5,*, Daniel M. Holstein2, Ian C. Enochs3,4, Graham Kolodzeij3, Derek P. Manzello3, Marilyn E. Brandt5, Tyler B. Smith5 1. National Centers for Coastal Ocean Science Marine Spatial Ecology Division, National Oceanic and Atmospheric Administration, 101 Pivers Island Rd., Beaufort, NC 28516, USA 2. Duke University Marine Laboratory, Nicholas School of the Environment, Duke University, 135 Duke Marine Lab Rd., Beaufort, NC 28516 3.Atlantic Oceanographic and Meteorological Laboratories (AOML), NOAA, 4301 Rickenbacker Cswy., Miami, FL 33149, USA 4. Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Cswy., Miami, FL 33149, USA 5. Center for Marine and Environmental Studies, University of the Virgin Islands, 2 John Brewer’s Bay, St. Thomas, Virgin Islands 00802, USA *Communicating author: [email protected] Keywords Mesophotic coral ecosystems, Sclerochronology, Refugia, Shelf edge reefs, Orbicella spp. Abstract Mesophotic coral ecosystems (MCEs) are deep (>30 m), light-dependent communities that are abundant in many parts of the global ocean. MCEs are potentially connected to shallow reefs via larval exchange and may act as refuges for reef organisms. However, MCE coral community recovery after disturbance, and thus, community resilience, are poorly understood components of their capacity as refuges. To assess the potential for disturbance and growth to drive community structure on MCEs with differential biophysical conditions and coral communities, we collected colonies of Orbicella franksi and Porites astreoides and used computerized tomography to quantify calcification. The divergence of coral growth rates in MCEs with different environmental conditions may be species specific; habitat-forming O. -
Comparative Thermal Performance of Orbicella Franksi at Its Latitudinal Range Limits 2 Running Title: Comparative Thermal Performance of O
bioRxiv preprint doi: https://doi.org/10.1101/583294; this version posted March 20, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Title: Comparative thermal performance of Orbicella franksi at its latitudinal range limits 2 Running title: Comparative thermal performance of O. franksi 3 4 Nyssa J. Silbiger*1, Gretchen Goodbody-Gringley2, John F. Bruno3, Hollie M. Putnam4 5 6 7 1Department of Biology, California State University, 18111 Nordhoff Street, Northridge, CA 8 91330-8303, USA 9 2Bermuda Institute of Ocean Sciences, 17 Biological Station, Ferry Reach, St.George's GE 01 10 Bermuda 11 3Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599- 12 3280 USA 13 4University of Rhode Island, Department of Biological Sciences, 120 Flagg Rd. Kingston, RI 14 02881 USA 15 16 17 18 * Corresponding Author 19 [email protected] 20 21 Keywords: Thermal performance curve, gross photosynthesis, dark respiration, calcification, 22 coral, climate change 23 24 25 Summary statement: We apply a thermal performance curve approach to a variety of fitness 26 related parameters in a reef building coral across its geographic range and various functions to 27 improve our understanding of the inherent variability in thermal tolerance. 28 29 30 31 1 bioRxiv preprint doi: https://doi.org/10.1101/583294; this version posted March 20, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. -
A Trillion Coral Reef Colors: Deeply Annotated Underwater Hyperspectral Images for Automated Classification and Habitat Mapping
data Data Descriptor A Trillion Coral Reef Colors: Deeply Annotated Underwater Hyperspectral Images for Automated Classification and Habitat Mapping Ahmad Rafiuddin Rashid and Arjun Chennu * Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany; [email protected] * Correspondence: [email protected] Received: 28 January 2020; Accepted: 17 February 2020; Published: 18 February 2020 Abstract: This paper describes a large dataset of underwater hyperspectral imagery that can be used by researchers in the domains of computer vision, machine learning, remote sensing, and coral reef ecology. We present the details of underwater data acquisition, processing and curation to create this large dataset of coral reef imagery annotated for habitat mapping. A diver-operated hyperspectral imaging system (HyperDiver) was used to survey 147 transects at 8 coral reef sites around the Caribbean island of Curaçao. The underwater proximal sensing approach produced fine-scale images of the seafloor, with more than 2.2 billion points of detailed optical spectra. Of these, more than 10 million data points have been annotated for habitat descriptors or taxonomic identity with a total of 47 class labels up to genus- and species-levels. In addition to HyperDiver survey data, we also include images and annotations from traditional (color photo) quadrat surveys conducted along 23 of the 147 transects, which enables comparative reef description between two types of reef survey methods. This dataset promises benefits for efforts in classification algorithms, hyperspectral image segmentation and automated habitat mapping. Dataset: https://doi.org/10.1594/PANGAEA.911300 Dataset License: CC-BY-NC Keywords: hyperspectral imaging; proximal sensing; machine learning; hierarchical learning; coral reef; biodiversity; classification; habitat mapping; image segmentation 1. -
Boulder Star Coral & Mountainous Star Coral Orbicella Annularis
Boulder star coral & Mountainous star coral Orbicella annularis & Orbicella faveolata Venezuela Compiler: Ana Yranzo Duque Contributors: Estrella Villamizar, Ana Teresa Herrera, Jeannette Pérez, Hazael Boadas, Carlos Pereira, Gregorio Rodríguez, Samuel Narciso, Freddy Bustillos, Francoise Cavada-Blanco Suggested citation: Yranzo, A. et al (2019). A survival blueprint for the Boulder star coral, Orbicella annularis and the Mountainous star coral, Orbicella faveolata, an output from the Institute of Tropical Ecology and Zoology, Venezuela and EDGE of Existence fellowship, Zoological Society of London, London, UK. 1. STATUS REVIEW 1.1 Taxonomy: The genus Orbicella was classified before as Montastraea and three species within the genus, Orbicella annularis, Orbicella faveolata and Orbicella franksi were classified as the Montastraea annularis complex until 1994 (Weil & Knowlton, 1994). This fact makes temporal comparisons for each species difficult. The genus changed to Orbicella in 2012 after Budd et al. (2012). Currently, taxonomy is as follows: Class: Anthozoa; Subclass: Hexacorallia; Order: Scleractinia; Family: Merulinidae; Genus: Orbicella; Species: Orbicella annularis and Orbicella faveolata; species name author: Ellis & Solander, 1786; common names: boulder star coral and mountainous star coral, taxonomic sources: Ellis, J.; Solander, D. (1786); Hoeksema, B. W.; Cairns, S. (2019). 1.2 Distribution and population status: Orbicella annularis and O. faveolata are distributed throughout over 30 countries in the Caribbean, Southern Florida, Bahamas, Bermuda and the Gulf of Mexico. After the decline of Acropora palmata species in the in the early 1980s (Aronson and Precht, 2001), Orbicella has been considered the most important genus of shallow reef building corals in the Caribbean region. Nevertheless, their populations have been suffering a drastic decline caused by bleaching events, disease episodes and negative impacts caused by anthropic activities. -
Coral Life History Differences Determine the Refugium Potential of a Remote Caribbean Reef
bioRxiv preprint doi: https://doi.org/10.1101/062869; this version posted July 8, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Coral life history differences determine the refugium potential of a remote Caribbean reef 2 3 Sarah W. Davies12,*, +, Marie E. Strader1*, ++, Johnathan T. Kool3, Carly D. Kenkel14 and 4 Mikhail V. Matz1 5 6 1. Department of Integrative Biology, The University of Texas at Austin, 1 University 7 Station C0990, Austin, TX 78712, USA 8 9 2. Department of Marine Sciences, The University of North Carolina at Chapel Hill, 123 10 South Road, Chapel Hill, NC 27599, USA 11 12 3. Geoscience Australia, Cnr Jerrabomberra Ave and Hindmarsh Drive, Symonston, 13 ACT, 2609, Australia 14 15 4. Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, QLD, 16 4810, Australia 17 18 * These authors contributed equally to this work 19 + Address correspondence regarding experiments to [email protected] 20 ++ Address correspondence regarding modeling to [email protected] 21 +++ Address general correspondence to [email protected] bioRxiv preprint doi: https://doi.org/10.1101/062869; this version posted July 8, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 22 Abstract 23 Remote populations can influence connectivity and may serve as refugia from climate 24 change. -
Elkhor Coral Is One of the Most Impor Ant Corals in the Gulf Wide Reef
Elkhorn Coral (Acropora Palmata) Elkhor coral is one of the most imporant corals in the Gulf wide reef ecosystem. Along with other coral species they built coral reefs in the region over last 5000 years. Elkhor coral can for dense goups called “thickets” in ver shallow water. These provide imporant habitat for other reef animals, especially fi sh. Elkhor coral is found tically in clear, shallow water (1 to 15 feet) on coral reefs throughout the Bahamas, Florida, and the Caribbean. Elkhor coral lives in high-energ zones, with a lot of wave action. However, high wave action that occurs during major stors can cause this species of branching coral to break. Elkhor coral have both male and female reproductive organs, they release eggs and sper into the water col- The geatest threat to elkhor coral is ocean war- umn once a year, generally a few days aſt er a fll moon in July/Augst. Baby corals (larae) remain fl oating in ing, which cause the corals to become stssed and the water about 5 to 20 days before they se le on substates. Most elkhor larae prefer to se le on red algae. release the sybiotic algae called zooxanthellae. This Coralline (red) algae is thought to sere as a se lement indicator that aids in surival. Once coral larae se le sybiotic algae lives in the tissue of coral and pro- they are reff ered as “spat”. Elkhor coral prefer to se le on upward facing sides of substate. vides them food via photosythesis. If corals becomes stessed for too long they can exel a high volume Due to their tee-like gowth foration, elkhor corals provide complex habitat for fi sh and other coral reef of this algae making them more susceptible that organisms. -
Introduction to Coral Reefs
AGRRA: Introduction to Coral Reefs Found on “healthy” coral reefs stony corals stony corals crustose coralline reef algae fishes sparse turf algae Revision: 2016-05-24 Judith Lang Images in this presentation are Copyright © by New World Publications and by other photographers as noted. Copyright © Ocean Research & Education Foundation Permission is granted to use this Powerpoint presentation for educational purposes with the AGRRA Program and, with attribution, for other valid educational purposes. All other uses are strictly prohibited. For permission to use their images, special thanks to: L. Benvenuti, A. Bruckner, J. Bruno, K. Desai, P. Dustan, P. Edmunds, M. Gerber, E. Hickerson, H. Hudson, P. Humann, L. Ilyes, B. Kakuk, J.-P. Maréchal, R. McCall, M. Moe, H. Moody, A. Moulding, M. Nugues, J. Reichman, C. Rogers, A. St. Gelais, G. Schmahl, R. Steneck, C. van Dongen, E. Weil, L. Williams What are Coral reefs? © H. Moody “wave-resistant limestone structures built dominantly by the vertical accumulation of coral skeletons” + capped by live corals & lots of other organisms! Stony corals are the major framework constructors of coral reefs. Their soft polyps overlie stony (calcareous) skeletons. The polyps expand to feed on plankton, usually at night. © R. McCall Meandrina jacksoni Colonies are formed when the polyps divide asexually. Tentacle Mouth Skeleton Colony Single Polyp Diagram from P. Humann Diverse patterns of asexual division and growth create corals of many different shapes and sizes. © K. Marks © M.McField © R. Steneck © K. Marks fast growing acroporids slower growing massives Reef corals need flowing water, food, space on the substratum, warm temperatures–and light.