Variation in Righting Times of Holothuria Atra, Stichopus Chloronotus, And
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Parameterisation and Application of Dynamic Energy Budget Model to Sea Cucumber Apostichopus Japonicus
Vol. 9: 1–8, 2017 AQUACULTURE ENVIRONMENT INTERACTIONS Published January 10 doi: 10.3354/aei00210 Aquacult Environ Interact OPENPEN ACCESSCCESS Parameterisation and application of dynamic energy budget model to sea cucumber Apostichopus japonicus Jeffrey S. Ren1, Jeanie Stenton-Dozey1, Jihong Zhang2,3,* 1National Institute of Water and Atmospheric Research, 10 Kyle Street, PO Box 8602, Christchurch 8440, New Zealand 2Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao 266071, PR China 3Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Aoshanwei, Jimo, Qingdao 266200, PR China ABSTRACT: The sea cucumber Apostichopus japonicus is an important aquaculture species in China. As global interest in sustainable aquaculture grows, the species has increasingly been used for co-culture in integrated multitrophic aquaculture (IMTA). To provide a basis for opti - mising stocking density in IMTA systems, we parameterised and validated a standard dynamic energy budget (DEB) model for the sea cucumber. The covariation method was used to estimate parameters of the model with the DEBtool package. The method is based on minimisation of the weighted sum of squared deviation for datasets and model predictions in one single-step pro- cedure. Implementation of the package requires meaningful initial values of parameters, which were estimated using non-linear regression. Parameterisation of the model suggested that the accuracy of the lower (TL) and upper (TH) boundaries of tolerance temperatures are particularly important, as these would trigger the unique behaviour of the sea cucumber for hibernation and aestivation. After parameterisation, the model was validated with datasets from a shellfish aqua- culture environment in which sea cucumbers were co-cultured with the scallop Chlamys farreri and Pacific oyster Crassostrea gigas at various combinations of density. -
Genomic Insights of Body Plan Transitions from Bilateral to Pentameral Symmetry in Echinoderms
ARTICLE https://doi.org/10.1038/s42003-020-1091-1 OPEN Genomic insights of body plan transitions from bilateral to pentameral symmetry in Echinoderms Yongxin Li1, Akihito Omori 2, Rachel L. Flores3, Sheri Satterfield3, Christine Nguyen3, Tatsuya Ota 4, Toko Tsurugaya5, Tetsuro Ikuta6,7, Kazuho Ikeo4, Mani Kikuchi8, Jason C. K. Leong9, Adrian Reich 10, Meng Hao1, Wenting Wan1, Yang Dong 11, Yaondong Ren1, Si Zhang12, Tao Zeng 12, Masahiro Uesaka13, 1234567890():,; Yui Uchida9,14, Xueyan Li 1, Tomoko F. Shibata9, Takahiro Bino15, Kota Ogawa16, Shuji Shigenobu 15, Mariko Kondo 9, Fayou Wang12, Luonan Chen 12,17, Gary Wessel10, Hidetoshi Saiga7,9,18, ✉ ✉ R. Andrew Cameron 19, Brian Livingston3, Cynthia Bradham20, Wen Wang 1,21,22 & Naoki Irie 9,14,22 Echinoderms are an exceptional group of bilaterians that develop pentameral adult symmetry from a bilaterally symmetric larva. However, the genetic basis in evolution and development of this unique transformation remains to be clarified. Here we report newly sequenced genomes, developmental transcriptomes, and proteomes of diverse echinoderms including the green sea urchin (L. variegatus), a sea cucumber (A. japonicus), and with particular emphasis on a sister group of the earliest-diverged echinoderms, the feather star (A. japo- nica). We learned that the last common ancestor of echinoderms retained a well-organized Hox cluster reminiscent of the hemichordate, and had gene sets involved in endoskeleton development. Further, unlike in other animal groups, the most conserved developmental stages were not at the body plan establishing phase, and genes normally involved in bila- terality appear to function in pentameric axis development. These results enhance our understanding of the divergence of protostomes and deuterostomes almost 500 Mya. -
SPC Beche-De-Mer Information Bulletin #39 – March 2019
ISSN 1025-4943 Issue 39 – March 2019 BECHE-DE-MER information bulletin v Inside this issue Editorial Towards producing a standard grade identification guide for bêche-de-mer in This issue of the Beche-de-mer Information Bulletin is well supplied with Solomon Islands 15 articles that address various aspects of the biology, fisheries and S. Lee et al. p. 3 aquaculture of sea cucumbers from three major oceans. An assessment of commercial sea cu- cumber populations in French Polynesia Lee and colleagues propose a procedure for writing guidelines for just after the 2012 moratorium the standard identification of beche-de-mer in Solomon Islands. S. Andréfouët et al. p. 8 Andréfouët and colleagues assess commercial sea cucumber Size at sexual maturity of the flower populations in French Polynesia and discuss several recommendations teatfish Holothuria (Microthele) sp. in the specific to the different archipelagos and islands, in the view of new Seychelles management decisions. Cahuzac and others studied the reproductive S. Cahuzac et al. p. 19 biology of Holothuria species on the Mahé and Amirantes plateaux Contribution to the knowledge of holo- in the Seychelles during the 2018 northwest monsoon season. thurian biodiversity at Reunion Island: Two previously unrecorded dendrochi- Bourjon and Quod provide a new contribution to the knowledge of rotid sea cucumbers species (Echinoder- holothurian biodiversity on La Réunion, with observations on two mata: Holothuroidea). species that are previously undescribed. Eeckhaut and colleagues P. Bourjon and J.-P. Quod p. 27 show that skin ulcerations of sea cucumbers in Madagascar are one Skin ulcerations in Holothuria scabra can symptom of different diseases induced by various abiotic or biotic be induced by various types of food agents. -
Morphology of an Endosymbiotic Bivalve, Entovalva Nhatrangensis (Bristow, Berland, Schander & Vo, 2010) (Galeommatoidea)
Molluscan Research 31(2): 114–124 ISSN 1323-5818 http://www.mapress.com/mr/ Magnolia Press Morphology of an endosymbiotic bivalve, Entovalva nhatrangensis (Bristow, Berland, Schander & Vo, 2010) (Galeommatoidea) J. LÜTZEN1, B. BERLAND2, & G.A.BRISTOW2* 1Biological Institute, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark 2Department of Biology, University of Bergen, N-5020 Bergen, Norway *Corresponding author, Email: [email protected] Abstract We describe the morphology of Entovalva nhatrangensis Bristow, Berland, Schander & Vo, 2010, an endosymbiontic bivalve living in the oesophagus of Holothuria spinifera and H. leucospilota in Vietnam. The delicate shells are entirely internalized. The body is very small compared to the foot, which is dorso-ventrally flattened and contains the digestive diverticula and the fertile parts of the gonads. Even though the gills are small, they probably serve in collecting suspended matter, and in addition, the species clearly feeds on benthic diatoms, which it probably sorts out from the contents of the host’s gut. The species is a protandric hermaphrodite. Most males have a total length of 1.5–3.0 mm and above that size start changing sex to become females, which may attain a total length of nearly nine mm. Sperm is transferred in spermatophores with a solid wall produced by glands within the male siphon. One to three spermatophores are placed on the gills of females and the ova become fertilized as they pass from the genital pores to the siphon, where they are brooded until released as D-larvae. Key words: functional anatomy, hermaphroditism, protandry, spermatophore, Holothuria spinifera, Holothuria leucospilota, Bivalvia, Heterodonta Introduction following morning. -
Sexual Reproduction in a Fissiparous Holothurian Species, Holothuria
SPC Beche-de-mer Information Bulletin #18 – May 2003 33 D’Silva, D. 2001. The Torres Strait beche-de-mer Skewes, T.D. Dennis, D.M. and Burridge, C. 2000. (sea cucumber) fishery. SPC Beche-de-Mer Survey of Holothuria scabra (sandfish) on Information Bulletin 15:2–4. Warrior Reef, Torres Strait, January 2000. CSIRO Division of Marine Research. Jaquemet, S. and Conand, C. 1999. The Beche-de- Mer trade in 1995/1996 and an assessment of TRAFFIC South America. 2000. Evaluation of the exchanges between main world markets. SPC trade of sea cucumber Isostichopus fuscus Beche-de-Mer Information Bulletin 12:11–14. (Echinodermata: Holothuroidea) in the Galapagos during 1999. Quito. 19 p. Lokani, P. 1990. Beche-de-mer research and devel- opment in Papua New Guinea. SPC Beche-de- Uthicke, S. and Benzie, J.A.H. 2001. Effect of beche- Mer Information Bulletin 2:1–18. de-mer fishing on densities and size structure of Holothuria nobilis (Echinodermata: Secretariat of the Pacific Community. 1994. Sea cu- Holothuridae) populations on the Great cumbers and beche-de-mer of the tropical Barrier Reef. Coral Reefs 19:271–276. Pacific. A handbook for fishers. Handbook no. 18. SPC, Noumea New Caledonia. 51 p. Sexual reproduction in a fissiparous holothurian species, Holothuria leucospilota Clark 1920 (Echinodermata: Holothuroidea) Pradina Purwati1,2 and Jim Thinh Luong-van2 Abstract Holothuria leucospilota Clark 1920 inhabiting tropical Darwin waters primarily undergo asexual reproduc- tion by fission throughout the year (Purwati 2001). However, there is also evidence of sexual reproduction. Monthly sampling from August 1998 to January 2000 revealed that the gonadal tubules within each indi- vidual of H. -
Seychelles: a Hotspot of Sea Cucumber Fisheries in Africa and the Indian Ocean Region
195 Seychelles: a hotspot of sea cucumber fisheries in Africa and the Indian Ocean region Riaz Aumeeruddy Island Conservation Society Victoria, Seychelles E-mail: [email protected] Chantal Conand Université de la Réunion Saint-Denis, France E-mail: [email protected] Aumeeruddy, R.; Conand, C. 2008. Seychelles: a hotspot of sea cucumber fisheries in Africa and the Indian Ocean region. In V. Toral-Granda, A. Lovatelli and M. Vasconcellos (eds). Sea cucumbers. A global review of fisheries and trade. FAO Fisheries and Aquaculture Technical Paper. No. 516. Rome, FAO. pp. 195–209. SUMMARY The Seychelles Archipelago, comprising 115 islands, is located in the middle of the Western Indian Ocean and has a large Exclusive Economic Zone (EEZ 1.4 millions km2). Sea cucumbers in Seychelles have been fished for more than a hundred years, but the fishery has recently seen a rapid development. Sea cucumbers are mostly collected by divers using SCUBA gear. They are processed for the export market. The population status is presented for the five main species caught (“pentard”, white teatfish, black teatfish, prickly redfish and sandfish) from the estimated stock and the overall density (ind./ha). Catch and effort data have been collected since 1999 by Seychelles Fishing Authority (SFA). The data are provided by the fishers as per the requirements of their fishing license conditions. The catch per unit effort (CPUE), expressed in numbers of sea cucumbers collected per diver per day, shows mostly a downward trend. The sea cucumber fishery in Seychelles was open-access until 1999. As part of a recent FAO- funded project, a management plan for the fishery has been prepared, based on the results of the resource assessment. -
Apostichopus Japonicus
Acta Oceanol. Sin., 2018, Vol. 37, No. 5, P. 54–66 DOI: 10.1007/s13131-017-1101-4 http://www.hyxb.org.cn E-mail: [email protected] Differential gene expression in the body wall of the sea cucumber (Apostichopus japonicus) under strong lighting and dark conditions ZHANG Libin1, 2, FENG Qiming1, 3, SUN Lina1, 2, FANG Yan4, XU Dongxue5, ZHANG Tao1, 2, YANG Hongsheng1, 2* 1 CAS Key laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China 2 Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China 3 University of Chinese Academy of Sciences, Beijing 100049, China 4 School of Agriculture, Ludong University, Yantai 264025, China 5 College of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China Received 25 January 2017; accepted 9 March 2017 © Chinese Society for Oceanography and Springer-Verlag GmbH Germany, part of Springer Nature 2018 Abstract Sea cucumber, Apostichopus japonicus is very sensitive to light changes. It is important to study the influence of light on the molecular response of A. japonicus. In this study, RNA-seq provided a general overview of the gene expression profiles of the body walls of A. japonicus exposed to strong light (“light”), normal light (“control”) and fully dark (“dark”) environment. In the comparisons of “control” vs. “dark”, ”control” vs. “light” and “dark” vs. “light”, 1 161, 113 and 1 705 differentially expressed genes (DEGs) were identified following the criteria of |log2ratio|≥1 and FDR≤0.001, respectively. Gene ontology analysis showed that “cellular process” and “binding” enriched the most DEGs in the category of “biological process” and “molecular function”, while “cell” and “cell part” enriched the most DEGs in the category of “cellular component”. -
SPC Beche-De-Mer Infomation Bulletin
SPC Beche-de-mer Information Bulletin #23 – February 2006 39 AbstractsAbstracts && publicationspublications beche-de-merbeche-de-mer SPC translates two chapters of Chantal Conand’s 1989 thesis1:“Aspidochirote holothurians of the New Caledonia lagoon: Biology, ecology and exploitation” SPC's Reef Fisheries Observatory has organised the translation of two chapters of Chantal Conand's semi- nal thesis on the ecology and biology of sea cucumbers. Although this thesis was published in French in 1989, a long time ago, many results were never made available to the wider audience of non-French speak- ers. Since the initial publication of this work, interest on holothurian resources and their management has only increased, and SPC hopes this translation will be of use to fishers, researchers and managers alike. Chantal Conand is now Professor Emeritus at La Reunion University. Her PhD was undertaken at the ORSTOM (now IRD) Center in New Caledonia, and the Laboratory Océanographie Biologique of the University of Bretagne Occidentale in France. She is still involved in sea cucumber research, as the sci- entific editor of this Beche-de-mer Bulletin published by SPC and several programmes of regional and international interest. The translated parts of the PhD thesis are listed below: Part of Chapter two: Ecology of the aspidochirote holothurians 4. Autoecology 4.1 Analytical methods 4.2 General results on distribution, density and biomass 4.3 Ecology of main species 4.4 Discussion of results 5. Taxocoenoses 5.1 Methods 5.2 Richness of the various biotopes 5.3 Main taxocoenosess 5.4 Discussion 5.5 Factors of the distribution 6. -
Stichopodidae 1185
click for previous page Order Aspidochirotida - Stichopodidae 1185 Order Aspidochirotida - Stichopodidae STICHOPODIDAE iagnostic characters: Body square-shaped or trapezoidal in cross-section. Cuvierian organs absent. DGonads forming 2 tufts appended on each side of the dorsal mesentery. Dominant spicules in form of branched rods and C-and S-shaped rods. Key to the genera of Stichopodidae occurring in the area (after Clark and Rowe, 1971) 1a. Bivium covered with large papillae, leaf-shaped, simple or branched, and without podia regularly arranged longitudinally; spicules never developod as tables, but numerous grains, dichotomously branched rods ............................Thelenota 1b. Bivium covered with tubercules and papillae, at least on sides; trivium more or less covered by podia; spicules developod as tables, branched rods, and C-and S-shaped rods ..............................................Stichopus List of species of interest to fisheries occurring in the area The symbol * is given when species accounts are included. * Stichopus chloronotus Brandt, 1835 * Stichopus horrens Selenka, 1867 * Stichopus variegatus Semper, 1868 * Thelenota ananas (Jaeger, 1833) * Thelenota anax Clark, 1921 1186 Holothurians Stichopus chloronotus Brandt, 1835 Frequent synonyms / misidentifications: None / None. FAO names: En - Greenfish; Fr - Trépang vert. row of large papillae anus terminal calcareous ring mouth ventral, with papillae and 20 tentacles spicules of podia spicules of tentacles spicules of tegument (after Féral and Cherbonnier, 1986) Diagnostic characters: Body firm, rigid with quadrangular section, flattened ventrally (trivium); body wall easily disintegrates outside sea water. Radii of bivium with characteristic double row of large papillae, each radius ending in a small red or orange papilla. Trivium delimited by characteristic double row of large papillae; stout podia arranged regularly on 3 radial bands, with 10 rows in the medio-ventral band and 5 in the lateral. -
Predator Defense Mechanisms in Shallow Water Sea Cucumbers (Holothuroidea)
PREDATOR DEFENSE MECHANISMS IN SHALLOW WATER SEA CUCUMBERS (HOLOTHUROIDEA) JESSICA A. CASTILLO Environmental Science Policy and Management, University of California, Berkeley, California 94720 USA Abstract. The various predator defense mechanisms possessed by shallow water sea cucumbers were surveyed in twelve different species and morphs. While many defense mechanisms such as the presence of Cuverian tubules, toxic secretions, and unpalatability have been identified in holothurians, I hypothesized that the possession of these traits as well as the degree to which they are utilized varies from species to species. The observed defense mechanisms were compared against a previously-derived phylogeny of the sea cucumbers of Moorea. Furthermore, I hypothesized that while the presence of such structures is most likely a result of the species’ placement on a phylogenetic tree, the degree to which they utilize such structures and their physical behavior are influenced by their individual ecologies. The presence of a red liquid secretion was restricted to individuals of the genus Holothuria (Linnaeus 1767) however not all members of the genus exhibited this trait. With the exception of H. leucospilota, which possessed both Cuverian tubules and a red secretion, Cuverian tubules were observed in members of the genus Bohadschia (Ostergren 1896). In accordance with the hypothesis, both the phylogenetics and individual ecology appear to influence predator defense mechanisms. However, even closely related species of similar ecology may differ considerably. Key words: holothurians; defense; toxicity; Cuverian tubules; Moorea, French Polynesia INTRODUCTION (Sakthivel et. Al, 1994). Approximately 20 species in two families and five genera, Sea cucumbers belong to the phylum including Holothuria, Bohadschia, and Thenelota, Echinodermata and the class Holothuroidea. -
Population Genetics and Phylogeography of Hawaiian Coral Reef Echinoderms
ISLANDS, ARCHIPELAGOS, AND BEYOND: POPULATION GENETICS AND PHYLOGEOGRAPHY OF HAWAIIAN CORAL REEF ECHINODERMS A DISSERTATION SUBMITTED TO THE GRADUATE DIVISION OF THE UNIVERSITY OF HAWAI‘I AT MĀNOA IN PARTIAL FULFILLMENT OF THE REQUIREMENT FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN ZOOLOGY AUGUST 2012 By Derek J. Skillings Dissertation Committee: Robert Toonen, Chairperson Brian Bowen Charles Birkeland Andrew Taylor Ronald Bontekoe i DEDICATION This dissertation is dedicated to my wife, Melissa Kay Skillings. ii ACKNOWLEDGEMENTS First, I would like to thank my committee members who provided essential guidance and encouragement throughout my graduate career. Foremost, I would like to thank my advisor and committee chair Rob Toonen. He has generously offered me a near endless supply of advice and guidance, as he does for anyone who knocks on his door. He also gave me the flexibility and encouragement needed to make getting two simultaneous graduate degrees possible. My graduate career has been very unconventional, and Rob has supported me every step of the way. I would like to thank Brian Bowen for giving me the structure I needed to succeed. Given my tendency to get lost in an always increasing number of projects, I would have never finished in a reasonable amount of time without his firm hand at setting deadlines and his enthusiastic encouragement to meet those deadlines. Rob and Brian gave me the perfect balance of freedom and focus that I needed to succeed. I would like to thank Chuck Birkeland for helping me to put my work in the larger perspective of coral reef ecosystems. Chuck also encouraged my philosophical and historical investigations into biology through insightful conversation; every time I saw he seemed to have a valuable and important text that he wanted to give me for my collection, many from his personal library. -
Yellow Coloured Mats from Lava Tubes of La Palma (Canary Islands, Spain
www.nature.com/scientificreports OPEN Yellow coloured mats from lava tubes of La Palma (Canary Islands, Spain) are dominated by Received: 27 July 2017 Accepted: 16 January 2018 metabolically active Actinobacteria Published: xx xx xxxx Jose L. Gonzalez-Pimentel1, Ana Z. Miller 1, Valme Jurado1, Leonila Laiz1, Manuel F. C. Pereira2 & Cesareo Saiz-Jimenez1 Microbial diversity in lava tubes from Canary Islands (Spain) has never been explored thus far ofering a unique opportunity to study subsurface microbiology. Abundant yellow coloured mats developing on coralloid speleothems in a lava tube from La Palma Islands were studied by next-generation sequencing and DNA/RNA clone library analyses for investigating both total and metabolically active bacteria. In addition, morphological and mineralogical characterization was performed by feld emission scanning electron microscopy (FESEM), micro-computed tomography, X-ray difraction and infrared spectroscopy to contextualize sequence data. This approach showed that the coralloid speleothems consist of banded siliceous stalactites composed of opal-A and hydrated halloysite. Analytical pyrolysis was also conducted to infer the possible origin of cave wall pigmentation, revealing that lignin degradation compounds can contribute to speleothem colour. Our RNA-based study showed for the frst time that members of the phylum Actinobacteria, with 55% of the clones belonging to Euzebyales order, were metabolically active components of yellow mats. In contrast, the DNA clone library revealed that around 45% of clones were afliated to Proteobacteria. Composition of microbial phyla obtained by NGS reinforced the DNA clone library data at the phylum level, in which Proteobacteria was the most abundant phylum followed by Actinobacteria. Microbial mats frequently coat extensive areas of walls and ceilings of karstic caves and lava tubes, usually devel- oping yellow, tan, orange, grey, pink and white-coloured bioflms1–6.