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RNA Detection Technology for Applications in Marine Science: Microbes to Fish Robert Michael Ulrich University of South Florida, [email protected]
University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School 6-25-2014 RNA Detection Technology for Applications in Marine Science: Microbes to Fish Robert Michael Ulrich University of South Florida, [email protected] Follow this and additional works at: https://scholarcommons.usf.edu/etd Part of the Biology Commons, and the Molecular Biology Commons Scholar Commons Citation Ulrich, Robert Michael, "RNA Detection Technology for Applications in Marine Science: Microbes to Fish" (2014). Graduate Theses and Dissertations. https://scholarcommons.usf.edu/etd/5321 This Dissertation is brought to you for free and open access by the Graduate School at Scholar Commons. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. RNA Detection Technology for Applications in Marine Science: Microbes to Fish by Robert M. Ulrich A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy College of Marine Science University of South Florida Major Professor: John H. Paul, Ph.D. Valerie J. Harwood, Ph.D. Mya Breitbart, Ph.D. Christopher D. Stallings, Ph.D. David E. John, Ph.D. Date of Approval June 25, 2014 Keywords: NASBA, grouper, Karenia mikimotoi, Enterococcus Copyright © 2014, Robert M. Ulrich DEDICATION This dissertation is dedicated to my fiancée, Dr. Shannon McQuaig for inspiring my return to graduate school and her continued support over the last four years. On no other porch in our little town have there been more impactful scientific discussions, nor more words of encouragement. ACKNOWLEDGMENTS I gratefully acknowledge the many people who have encouraged and advised me throughout my graduate studies. -
Evidence of Sexual Transition in Leopard Grouper (Mycteroperca Rosacea )
Ovarian development of M. rosacea in captivity Hidrobiológica 2010, 20 (3): 213-221213 Evidence of sexual transition in Leopard Grouper (Mycteroperca rosacea) individuals held in captivity Evidencia de transición sexual en individuos de cabrilla sardinera (Mycteroperca rosacea) mantenidos en cautiverio Margarita Kiewek-Martínez, Vicente Gracia-López and Carmen Rodríguez-Jaramillo Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Mar Bermejo 195, Col. Playa Palo Sta. Rita, La Paz B.C.S. 23090, México e-mail: [email protected] Kiewek-Martínez, M., V. Gracia-López and C. Rodríguez-Jaramillo. 2010. Evidence of sexual transition in Leopard Grouper (Mycteroperca rosacea) individuals held in captivity. Hidrobiológica 20 (3): 213-221. ABSTRACT This study describes histological observations of the gonads of 12 captive leopard grouper, M. rosacea maintained in captivity. Monthly gonad samples during February to April 2003, were obtained by catheterization and analyzed to determine sex and degree of ovarian development. Oocytes were classified into 5 stages of development and the fre- quencies were obtained to describe the oocyte distribution in the ovary. Two fish that were females in February were in a bisexual stage in March and functional males in April. The transitional stage was observed during the reproductive season and included degeneration of primary oocytes and proliferation of spermatogonia. Key words: Gonad development, leopard grouper, captivity. RESUMEN Este estudio describe las observaciones histológicas del desarrollo gonadal de 12 individuos de la cabrilla sardinera, en condiciones de cautiverio. De febrero a abril del 2003 se obtuvieron muestras mensuales de la gónada mediante un catéter flexible, las cuales fueron analizadas para determinar el sexo del organismo y el estadio de desarrollo gonadal. -
Parasites of Coral Reef Fish: How Much Do We Know? with a Bibliography of Fish Parasites in New Caledonia
Belg. J. Zool., 140 (Suppl.): 155-190 July 2010 Parasites of coral reef fish: how much do we know? With a bibliography of fish parasites in New Caledonia Jean-Lou Justine (1) UMR 7138 Systématique, Adaptation, Évolution, Muséum National d’Histoire Naturelle, 57, rue Cuvier, F-75321 Paris Cedex 05, France (2) Aquarium des lagons, B.P. 8185, 98807 Nouméa, Nouvelle-Calédonie Corresponding author: Jean-Lou Justine; e-mail: [email protected] ABSTRACT. A compilation of 107 references dealing with fish parasites in New Caledonia permitted the production of a parasite-host list and a host-parasite list. The lists include Turbellaria, Monopisthocotylea, Polyopisthocotylea, Digenea, Cestoda, Nematoda, Copepoda, Isopoda, Acanthocephala and Hirudinea, with 580 host-parasite combinations, corresponding with more than 370 species of parasites. Protozoa are not included. Platyhelminthes are the major group, with 239 species, including 98 monopisthocotylean monogeneans and 105 digeneans. Copepods include 61 records, and nematodes include 41 records. The list of fish recorded with parasites includes 195 species, in which most (ca. 170 species) are coral reef associated, the rest being a few deep-sea, pelagic or freshwater fishes. The serranids, lethrinids and lutjanids are the most commonly represented fish families. Although a list of published records does not provide a reliable estimate of biodiversity because of the important bias in publications being mainly in the domain of interest of the authors, it provides a basis to compare parasite biodiversity with other localities, and especially with other coral reefs. The present list is probably the most complete published account of parasite biodiversity of coral reef fishes. -
Updated Checklist of Marine Fishes (Chordata: Craniata) from Portugal and the Proposed Extension of the Portuguese Continental Shelf
European Journal of Taxonomy 73: 1-73 ISSN 2118-9773 http://dx.doi.org/10.5852/ejt.2014.73 www.europeanjournaloftaxonomy.eu 2014 · Carneiro M. et al. This work is licensed under a Creative Commons Attribution 3.0 License. Monograph urn:lsid:zoobank.org:pub:9A5F217D-8E7B-448A-9CAB-2CCC9CC6F857 Updated checklist of marine fishes (Chordata: Craniata) from Portugal and the proposed extension of the Portuguese continental shelf Miguel CARNEIRO1,5, Rogélia MARTINS2,6, Monica LANDI*,3,7 & Filipe O. COSTA4,8 1,2 DIV-RP (Modelling and Management Fishery Resources Division), Instituto Português do Mar e da Atmosfera, Av. Brasilia 1449-006 Lisboa, Portugal. E-mail: [email protected], [email protected] 3,4 CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal. E-mail: [email protected], [email protected] * corresponding author: [email protected] 5 urn:lsid:zoobank.org:author:90A98A50-327E-4648-9DCE-75709C7A2472 6 urn:lsid:zoobank.org:author:1EB6DE00-9E91-407C-B7C4-34F31F29FD88 7 urn:lsid:zoobank.org:author:6D3AC760-77F2-4CFA-B5C7-665CB07F4CEB 8 urn:lsid:zoobank.org:author:48E53CF3-71C8-403C-BECD-10B20B3C15B4 Abstract. The study of the Portuguese marine ichthyofauna has a long historical tradition, rooted back in the 18th Century. Here we present an annotated checklist of the marine fishes from Portuguese waters, including the area encompassed by the proposed extension of the Portuguese continental shelf and the Economic Exclusive Zone (EEZ). The list is based on historical literature records and taxon occurrence data obtained from natural history collections, together with new revisions and occurrences. -
Xchel G. MORENO-SÁNCHEZ1, Pilar PEREZ-ROJO1, Marina S
ACTA ICHTHYOLOGICA ET PISCATORIA (2019) 49 (1): 9–22 DOI: 10.3750/AIEP/02321 FEEDING HABITS OF THE LEOPARD GROUPER, MYCTEROPERCA ROSACEA (ACTINOPTERYGII: PERCIFORMES: EPINEPHELIDAE), IN THE CENTRAL GULF OF CALIFORNIA, BCS, MEXICO Xchel G. MORENO-SÁNCHEZ1, Pilar PEREZ-ROJO1, Marina S. IRIGOYEN-ARREDONDO1, Emigdio MARIN- ENRÍQUEZ2, Leonardo A. ABITIA-CÁRDENAS1*, and Ofelia ESCOBAR-SANCHEZ2 1Instituto Politecnico Nacional, Centro Interdisciplinario de Ciencias Marinas (CICIMAR-IPN), Departamento de Pesquerías y Biología Marina La Paz, BCS, Mexico 2CONACYT-Universidad Autónoma de Sinaloa-Facultad de Ciencias del Mar (CONACYT UAS-FACIMAR) Mazatlán, SIN, Mexico Moreno-Sánchez X.G., Perez-Rojo P., Irigoyen-Arredondo M.S., Marin- Enríquez E., Abitia-Cárdenas L.A., Escobar-Sanchez O. 2019. Feeding habits of the leopard grouper, Mycteroperca rosacea (Actinopterygii: Perciformes: Epinephelidae), in the central Gulf of California, BCS, Mexico. Acta Ichthyol. Piscat. 49 (1): 9–22. Background. The leopard grouper, Mycteroperca rosacea (Streets, 1877), is endemic to north-western Mexico and has high commercial value. Although facts of its basic biology are known, information on its trophic ecology, in particular, is scarce. The objective of the presently reported study was to characterize the feeding habits of M. rosacea through the analysis of stomach contents, and to determine possible variations linked to sex (male or female), size (small, medium, or large), or season (spring, summer, autumn, or winter), in order to understand the trophic role that this species plays in the ecosystem where it is found. Materials and methods. Fish were captured monthly, from March 2014 to May 2015 by spearfishing in Santa Rosalía, BCS, Mexico. Percentages by the number, by weight, and frequency of appearance of each food category, the index of relative importance (%IRI), and prey-specific index of relative importance (%PSIRI) were used to determine the importance of each prey item in the leopard grouper diet. -
Serranidae), in the Southeastern Adriatic Sea by Branko GLAMUZINA, Pero TUTMAN, Valter KO∏UL, Nik≈A GLAVI¶ & Bo≈Ko SKARAMUCA (1
NOTE ICHTYOLOGIQUE - ICHTHYOLOGICAL NOTE THE FIRST RECORDED OCCURRENCE OF THE MOTTLED GROUPER, MYCTEROPERCA RUBRA (SERRANIDAE), IN THE SOUTHEASTERN ADRIATIC SEA by Branko GLAMUZINA, Pero TUTMAN, Valter KO∏UL, Nik≈a GLAVI¶ & Bo≈ko SKARAMUCA (1) RÉSUMÉ. - Premier spécimen de badèche rouge, Mycteroperca The specimen in question, examined at the Biological Institute, rubra (Serranidae), signalé en mer Adriatique du sud-est. had a total length of 327 mm; a wet mass of 381.5 g; and was Le premier exemplaire de badèche rouge, Mycteroperca rubra, estimated to be 3 years old by scale reading under binocular micro- (poids = 381,5 g ; LT = 327 mm) a été capturé en mer Adriatique scope (Fig. 2). du sud-est, au large de Dubrovnik, Croatie (42,5°N), en septembre The main feature that distinguishes M. rubra from groupers of 2001. La présence de la badèche rouge dans les eaux de la mer the genus Epinephelus, especially the very similar E. caninus, is Adriatique conforte l’hypothèse du réchauffement actuel des eaux the number of soft anal fin rays: from 10 to 13, usually 11-12, for de la Méditerranée septentrionale. M. rubra; 7 to 10 for Epinephelus and 8 for E. caninus (Heemstra and Randall, 1993). Key words. - Serranidae - Mycteroperca rubra - MED - Adriatic All other important morphological characteristics of the cap- Sea - First record. tured specimen fit well with the species description provided by Heemstra and Randall (1993) (Table I). For example, the caudal- The proposition of Francour et al. (1994) that the Mediterranean fin margin is truncated, as is typical in this genus for fish from Sea is warming is supported, at least circumstantially, by the accu- 20-50 cm SL. -
Species of Pseudorhabdosynochus (Monogenea, Diplectanidae) From
RESEARCH ARTICLE Species of Pseudorhabdosynochus (Monogenea, Diplectanidae) from Groupers (Mycteroperca spp., Epinephelidae) in the Mediterranean and Eastern Atlantic Ocean, with Special Reference to the ‘ ’ a11111 Beverleyburtonae Group and Description of Two New Species Amira Chaabane1*, Lassad Neifar1, Delphine Gey2, Jean-Lou Justine3 1 Laboratoire de Biodiversité et Écosystèmes Aquatiques, Faculté des Sciences de Sfax, Université de Sfax, Sfax, Tunisia, 2 UMS 2700 Service de Systématique moléculaire, Muséum National d'Histoire Naturelle, OPEN ACCESS Sorbonne Universités, Paris, France, 3 ISYEB, Institut Systématique, Évolution, Biodiversité, UMR7205 (CNRS, EPHE, MNHN, UPMC), Muséum National d’Histoire Naturelle, Sorbonne Universités, Paris, France Citation: Chaabane A, Neifar L, Gey D, Justine J-L (2016) Species of Pseudorhabdosynochus * [email protected] (Monogenea, Diplectanidae) from Groupers (Mycteroperca spp., Epinephelidae) in the Mediterranean and Eastern Atlantic Ocean, with Special Reference to the ‘Beverleyburtonae Group’ Abstract and Description of Two New Species. PLoS ONE 11 (8): e0159886. doi:10.1371/journal.pone.0159886 Pseudorhabdosynochus Yamaguti, 1958 is a species-rich diplectanid genus, mainly restricted to the gills of groupers (Epinephelidae) and especially abundant in warm seas. Editor: Gordon Langsley, Institut national de la santé et de la recherche médicale - Institut Cochin, Species from the Mediterranean are not fully documented. Two new and two previously FRANCE known species from the gills of Mycteroperca spp. (M. costae, M. rubra, and M. marginata) Received: April 28, 2016 in the Mediterranean and Eastern Atlantic Ocean are described here from new material and slides kept in collections. Identifications of newly collected fish were ascertained by barcod- Accepted: July 8, 2016 ing of cytochrome c oxidase subunit I (COI) sequences. -
A Parasite of Deep-Sea Groupers (Serranidae) Occurs Transatlantic
Pseudorhabdosynochus sulamericanus (Monogenea, Diplectanidae), a parasite of deep-sea groupers (Serranidae) occurs transatlantically on three congeneric hosts ( Hyporthodus spp.), one from the Mediterranean Sea and two from the western Atlantic Amira Chaabane, Jean-Lou Justine, Delphine Gey, Micah Bakenhaster, Lassad Neifar To cite this version: Amira Chaabane, Jean-Lou Justine, Delphine Gey, Micah Bakenhaster, Lassad Neifar. Pseudorhab- dosynochus sulamericanus (Monogenea, Diplectanidae), a parasite of deep-sea groupers (Serranidae) occurs transatlantically on three congeneric hosts ( Hyporthodus spp.), one from the Mediterranean Sea and two from the western Atlantic. PeerJ, PeerJ, 2016, 4, pp.e2233. 10.7717/peerj.2233. hal- 02557717 HAL Id: hal-02557717 https://hal.archives-ouvertes.fr/hal-02557717 Submitted on 16 Aug 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Pseudorhabdosynochus sulamericanus (Monogenea, Diplectanidae), a parasite of deep-sea groupers (Serranidae) occurs transatlantically on three congeneric hosts (Hyporthodus spp.), -
Islnad Grouper Status Review 2015
Island Grouper (Mycteroperca fusca) Status Review Report Photo Credit: Philippe Burnel © July 2015 Ronald J. Salz Fishery Biologist National Marine Fisheries Service National Oceanic and Atmospheric Administration Silver Spring, MD Acknowledgements I thank João Pedro Barreiros, Claudia Ribeiro, and Fernando Tuya for providing their time, expertise, and insights as external peer reviewers of this report. I also thank the following NMFS co-workers who provided valuable information and feedback as internal reviewers: Dwayne Meadows, Maggie Miller, Marta Nammack, Angela Somma, and Chelsea Young. Other helpful sources of information were George Sedberry, Carlos Ferreira Santos, Albertino Martins, Rui Freitas, and the Portugal National Institute of Statistics. I also thank NOAA librarian Caroline Woods for quickly responding to article requests, and Philippe Burnel for allowing me to use his island grouper photograph on the cover page. This document should be cited as: Salz, R. J. 2015. Island Grouper (Mycteroperca fusca) Draft Status Review Report. Report to National Marine Fisheries Service, Office of Protected Resources. July 2015, 69 pp. 2 Executive Summary On July 15, 2013, NMFS received a petition to list 81 species of marine organisms as endangered or threatened species under the Endangered Species Act (ESA). If an ESA petition is found to present substantial scientific or commercial information that the petitioned action may be warranted, a status review shall be promptly commenced (16 U.S.C. 1533(b)(3)(A)). NMFS determined that for 27 of the 81 species, including the island grouper (Mycteroperca fusca), the petition had sufficient merit for consideration and that a status review was warranted (79 FR 10104, February 24, 2014). -
Activity, Habitat Use, Feeding Behavior, and Diet of Four Sympatric Species of Serranidae (Actinopterygii: Perciformes) in Southeastern Brazil
Neotropical Ichthyology, 5(3):387-398, 2007 Copyright © 2007 Sociedade Brasileira de Ictiologia Activity, habitat use, feeding behavior, and diet of four sympatric species of Serranidae (Actinopterygii: Perciformes) in southeastern Brazil Fernando Zaniolo Gibran Diplectrum formosum (the sand perch), Diplectrum radiale (the aquavina), Epinephelus marginatus (the dusky grouper) and Mycteroperca acutirostris (the comb grouper) are four sympatric serranid of remarkable ecological and commercial importance. This study investigated the feeding of these four species in the São Sebastião Channel, São Paulo State (southeastern Brazil), comparing their diet, habitat utilization and morphological features related to foraging. These four serranids are opportunistic visual predators that use a total of nine different tactics to capture their preys, feed mostly on crustaceans during the day and twilight, and keep stationary and quiescent at night. The ecomorphological study was conducted to test its predictive value to infer lifestyles. It was verified that such analysis should be used carefully and must be complemented by field observations. Although morphologically and behaviorally very similar, D. formosum and D. radiale showed different preferences to the substratum type used by large individuals, which are exclusively sit-and-wait predators. On the other hand, E. marginatus displayed more sedentary habits than M. acutirostris, the most versatile predator from the studied species. The studied species of Diplectrum and E. marginatus can be regarded as benthic serranids, while M. acutirostris could be viewed as a nektobenthic species. Diplectrum formosum, Diplectrum radiale (micholes-da-areia), Epinephelus marginatus (garoupa-verdadeira) e Mycteroperca acutirostris (badejo-mira) são quatro espécies simpátricas que pertencem à família Serranidae, de reconhecida importância ecológica e comercial. -
Using Fishers' Anecdotes, Naturalists' Observations and Grey
F I S H and F I S H E R I E S , 2005, 6, 121–133 Using fishers’ anecdotes, naturalists’ observations and grey literature to reassess marine species at risk: the case of the Gulf grouper in the Gulf of California, Mexico Andrea Sa´enz–Arroyo1,2, Callum M. Roberts2, Jorge Torre1 & Micheline Carin˜o-Olvera3 1Comunidad y Biodiversidad A.C., Bahı´a de Bacochibampo, S/N Colonia Lomas de Corte´s, Guaymas, 85450 Sonora, Me´xico; 2Environment Department, University of York, York YO10 5DD, UK; 3Universidad Auto´noma de Baja California Sur, A´ rea Interdisciplinaria de Ciencias Sociales, Apartado Postal 19 -B, La Paz, 23080 Baja California Sur, Me´xico Abstract Correspondence: Designing fishing policies without knowledge of past levels of target species Andrea Sa´enz– Arroyo, Comunidad y abundance is a dangerous omission for fisheries management. However, as fisheries Biodiversidad A.C., monitoring started long after exploitation of many species began, this is a difficult Bahı´a de Bacochib- issue to address. Here we show how the ‘shifting baseline’ syndrome can affect the ampo, S/N Colonia stock assessment of a vulnerable species by masking real population trends and Lomas de Corte´s, thereby put marine animals at serious risk. Current fishery data suggest that landings Guaymas, 85450 Sonora, Me´xico of the large Gulf grouper (Mycteroperca jordani, Serranidae) are increasing in the Gulf Tel.: +52622-2212670 of California. However, reviews of historical evidence, naturalists’ observations and a Fax: +52622-2212671 systematic documentation of fishers’ perceptions of trends in the abundance of this E-mail: asaenz@ species indicate that it has dramatically declined. -
Mucosal Health in Aquaculture Page Left Intentionally Blank Mucosal Health in Aquaculture
Mucosal Health in Aquaculture Page left intentionally blank Mucosal Health in Aquaculture Edited by Benjamin H. Beck Stuttgart National Aquaculture Research Center, Stuttgart, Arkansas, USA Eric Peatman School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Alabama, USA AMSTERDAM • BOSTON • HEIDELBERG • LONDON • NEW YORK OXFORD • PARIS • SAN DIEGO • SAN FRANCISCO • SINGAPORE SYDNEY • TOKYO Academic Press is an Imprint of Elsevier Academic Press is an imprint of Elsevier 125, London Wall, EC2Y 5AS, UK 525 B Street, Suite 1800, San Diego, CA 92101-4495, USA 225 Wyman Street, Waltham, MA 02451, USA The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, UK Copyright © 2015 Elsevier Inc. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means electronic, mechanical, photocopying, recording or otherwise without the prior written permission of the publisher. Permissions may be sought directly from Elsevier’s Science & Technology Rights Department in Oxford, UK: phone (+44) (0) 1865 843830; fax (+44) (0) 1865 853333; email: [email protected]. Alternatively, visit the Science and Technology Books website at www.elsevierdirect.com/rights for further information. Notice No responsibility is assumed by the publisher for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions or ideas contained in the material herein.