Scleractinian corals increasingly are studied as geochemical archives of modern- and palaeoclimate, but microsampling for geochemical data is complicated by: 1) the microstructural complexity and spatial variability in skeletal growth in different coral genera; and 2) the rapidity and scale of diagenetic alteration that occurs in living coralla. Geochemical sampling techniques now have spatial resolution into the sub-micrometer to tens of micrometers range, and it is hoped that the spatial resolution can be translated to temporal resolution. This study investigated the effects on geochemical analyses imposed by microstructure and diagenesis in different live-collected coral genera representing somewhat different depositional environments. Suites of samples of four reef-building genera (Acropora, Pocillopora, Goniastrea and Porites) were collected from three adjacent environments in intertidal and subtidal positions near the reef edge at Heron Reef, Great Barrier Reef and studied by means of optical and scanning electron microscopy, combined with vibrational and energy dispersive spectroscopy. The first section of this study compares and documents the microstructure of the four coral genera. Each genus was found to have very different three-dimensional arrangements of microstructural elements, and a new general growth model was proposed for Acropora, to take into account differences in the timing of precipitation of trabeculae and thickening deposits. The results highlight the complexity and spatial variability of skeletal growth in different coral genera. Because microstructural patterns vary in different genera, direct observation of microstructural elements and growth lines are necessary to allow geochemical microsamples to be placed into series that represent temporal sequences with known degrees of time averaging. Coral growth rates (i.e., rates of extension) are discussed to determine the range of temporal relationships that exist between closely spaced skeletal microstructural elements. Such data are necessary in order for coral skeletogenesis to be understood and are critical for constraining microsampling strategies aimed at developing true time series geochemical data at very fine spatial and temporal scales. The second part of the study focused on early diagenetic alteration of the corals, which is an equally important concern for geochemical analysis. Early marine diagenesis was documented in the same live-collected samples of the four common reef-building coral genera. Samples show extensive early marine diagenesis where parts of the coralla less than three years old contain abundant macro- and microborings (sponges, algae, cyanobacteria and fungi) and significant amounts of aragonite, high-Mg calcite, low-Mg calcite and brucite [Mg(OH)2] cements. Many of the cements are associated with microendoliths and endobionts that inhabit recently abandoned parts of the skeleton. The cements are problematic for palaeoclimate reconstruction because geochemical proxies used for paleoclimate studies are meant to reflect ambient seawater chemistry and conditions, but the occurrence of brucite and low-Mg calcite demonstrates how far fluid chemistry in microenvironments within the corals has evolved from ambient seawater. Some Porites lobata specimens have had as much as 60% of the most recently deposited skeletal aragonite (i.e., the part of the skeleton that projects into the layer of living polyps) bored and replaced by low-Mg calcite cement. The low-Mg calcite cement has significantly different trace element ratios (Sr/Ca(mmol/mol) = 6.3 ± 1.4; Mg/Ca(mmol/mol) = 12.0 ± 5.1) than the host coral skeletal aragonite (Sr/Ca(mmol/mol) = 9.9 ± 1.3; Mg/Ca(mmol/mol) = 4.5 ± 2.3), thus providing a serious challenge for Sr/Ca or Mg/Ca based sea surface temperature calculations. This study illustrates that many diagenetic changes that can radically alter important geochemical characteristics of coral skeleton occur very early on the sea floor (i.e., while corals are still alive). Documented cements altered trace element inventories (e.g., Sr and Mg), thus, interfering with the use of those elements in palaeotemperature calculations. Hence, significant diagenetic changes that jeopardise palaeoclimate data do not require long-term diagenesis or meteoric exposure. Some of the diagenetic changes (e.g., calcite filled borings) occur at scales that are very difficult to detect short of visual inspection using SEM. Hence, vetting of coral samples with SEM is required before any sample is subjected to geochemical analysis.

Sexual reproduction in Porites divaricata (Le Sueur, 1820) was studied over a one year period (August, 2012 to August, 2013) in a shallow water (~2m depth) carbonate bank (also described as marginal) habitat at Rodriguez Key, a small island located 1.44 km off the east coast of Key Largo. Porites divaricata is a brooding, gonochoric species with peak reproductive output (planula release) occurring in March and at least a smaller event in May. This species showed an overall female to male sex ratio of 3.5:1. However, during peak reproduction, the sex ratio was 1.2:1. Spawning (sperm release) most likely occurred in late February when 78% of all oocytes and 84% of all spermaries were in stage IV of development. The largest output of stage IV eggs (n=164) occurred at this time, and these oocytes also had the second largest average individual oocyte volume (3.34x10-3 mm3, n = 79) compared to those from other sample dates. The largest average egg volume (3.79x10-3 mm3, n = 8) occurred in May, but with fewer eggs present (n=13). Population surveys showed P. divaricata densities of 7.4 and 17.7 colonies m-² at Site 1 and 2, respectively. Temperature data documented that SSTs were highly variable in the seagrass/coral habitat at site 2 (primary collection site), ranging from 13.1 to 34.9°C, with an average temperature of 25.9°C. Corals at Rodriquez Key are exposed to temperatures much higher (+3.8°C) during the summer and much lower (-8.2°C) in winter compared to corals living at a nearby bank reef (Molasses Reef). This is the first comprehensive reproductive study performed on Porites divaricata and may provide valuable information to the ongoing debate concerning the taxonomic relationships among P. divaricata, P. porites, and P. furcata.

Animal and plant genomes produce numerous small RNAs (smRNAs) that regulate gene expression post-transcriptionally affecting metabolism, development, and epigenetic inheritance. In order to characterize the repertoire of endogenous microRNAs and potential gene targets, we conducted smRNA and mRNA expression profiling over nine experimental treatments of cultures from the dinoflagellate Symbiodinium sp. A1, a photosynthetic symbiont of scleractinian corals. We identified a total of 75 novel smRNAs in Symbiodinum sp. A1 that share stringent key features with functional microRNAs from other model organisms. A subset of 38 smRNAs was predicted independently over all nine treatments and their putative gene targets were identified. We found 3,187 animal-like target sites in the 3’UTRs of 12,858 mRNAs and 53 plantlike target sites in 51,917 genes. Furthermore, we identified the core RNAi protein machinery in Symbiodinium. Integration of smRNA and mRNA expression profiling identified a variety of processes that could be under microRNA control, e.g. regulation of translation, DNA modification, and chromatin silencing. Given that Symbiodinium seems to have a paucity of transcription factors and differentially expressed genes, identification and characterization of its smRNA repertoire establishes the possibility of a range of gene regulatory mechanisms in dinoflagellates acting post-transcriptionally.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第18102号 / 理博第3980号 / 新制||理||1574(附属図書館) / 30960 / 京都大学大学院理学研究科生物科学専攻 / (主査)講師 宮崎 勝己, 教授 朝倉 彰, 教授 疋田 努 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

Les coraux Scléractiniaires se développent généralement dans la zone photique peu profonde, exposée au rayonnement ultraviolet (UVs), la composante la plus dangereuse du rayonnement solaire. Le rayonnement UVs augmente avec le réchauffement climatique et s’ajoute à l’ensemble des pressions auxquelles sont soumis les coraux. Les enjeux de cette thèse ont été 1) de mieux comprendre les effets des UVs sur la réponse physiologique des coraux, les flux de matière organique et les bactéries associées au mucus et au corail; et 2) de caractériser l’effet combiné des UVs et d’une augmentation de température, et/ou d’un changement de disponibilité en sels nutritifs. Les résultats obtenus montrent tout d’abord que l’exposition des coraux aux UVs amplifie l’effet négatif de la température sur leur physiologie. Il en est de même pour l’absence en sels nutritifs, essentiels pour la physiologie corallienne. Nos résultats indiquent également que la sensibilité des coraux à un stress UV dépend de l’espèce étudiée et de la densité de symbiontes présents dans les tissus. L’effet négatif des UVs augmente avec la densité de symbiontes, vraisemblablement dû à la formation d’espèces réactives de l’oxygène (ROS) qui provoquent des dommages à l’organisme. Dans cette thèse, nous avons montré que la voie de signalisation JNK (c-Jun N-terminal kinase), hautement conservée au sein des êtres vivants, est impliquée dans la gestion de ces espèces réactives et que son inhibition entraine un blanchissement très rapide des coraux sous UVs et forte température. Finalement, l’excrétion de matière organique ainsi que les bactéries associées sont également impactés par les UVs ce qui pourrait contribuer à d’importants changements biochimiques dans l’eau des récifs coralliens. Les travaux de cette thèse apportent de nouvelles connaissances sur les effets des UVs sur les coraux et soulignent l’importance de les prendre en considération lors de nos prédictions sur le devenir des récifs coralliens face au réchauffement climatique. / Scleractinian corals mainly grow in the shallow euphotic zone, exposed to ultraviolet radiation (UVR), the most harmful part of the solar radiation. UVR increases with climate change and adds to the different environmental pressures that corals are facing. The aims of this thesis were to 1) better understand the effects of UVR on coral physiology, organic matter fluxes and associated bacteria; 2) assess the combined effects of UVR and thermal stress and/or nutrient level. Results show that UVR worsens the negative effect of temperature on coral physiology, similarly to nutrient depletion. Our results also indicate that the sensitivity to UVR stress (i.e. an increase in UVR) is species dependent and function of the symbiont density. The negative effects of UVR increase with the number of symbionts, likely due to the formation of reactive oxygen species (ROS) which cause cellular damages. In the thesis, we showed that the JNK signalling pathway (c-Jun N-terminal kinase), highly conserved in living organisms, is involved in the early response of corals to UVR and its activation is required to repress stress-induced ROS accumulation. Finally, organic matter release and mucus and coral-associated bacteria are also significantly impacted by UVR, which could contribute to important biochemical changes in reef waters. The work conducted in this thesis brings new insights into the effects of UVR on corals and highlights the importance of taking this environmental factor into account when predicting the future of coral reefs under climate change.

Submitted by Johnsson Rodrigo (r.johnsson@gmail.com) on 2013-09-02T12:08:06Z No. of bitstreams: 1 ROBERTA.pdf: 21017159 bytes, checksum: 41e6a847bf3ae9866b8f2160a17c81bf (MD5) / Approved for entry into archive by Alda Lima da Silva(sivalda@ufba.br) on 2013-09-26T18:00:23Z (GMT) No. of bitstreams: 1 ROBERTA.pdf: 21017159 bytes, checksum: 41e6a847bf3ae9866b8f2160a17c81bf (MD5) / Made available in DSpace on 2013-09-26T18:00:23Z (GMT). No. of bitstreams: 1 ROBERTA.pdf: 21017159 bytes, checksum: 41e6a847bf3ae9866b8f2160a17c81bf (MD5) / CNPq, FAPESB / O gênero Mussismilia (M. hispida, M. harttii e M. braziliensis) é endêmico do litoral brasileiro e inclui as principais espécies de corais construtores. Estudos com a carcinofauna associada à Mussismilia são escassos e restritos a M. hispida no setor sudeste. Dentre os organismos registrados em associação com M. hispida, destacam-se os caranguejos-de-galha e copépodes sifonostomatóides. Para todo Atlântico, são registrados apenas cinco gêneros de Cryptochiridae (Decapoda, Brachyura) (Detocarcinus, Cecidocarcinus, Opecarcinus, Troglocarcinus e Kroppcarcinus – o último, recentemente descrito). Para o Brasil, considerando os dados da literatura, três espécies são registradas para a costa brasileira: Opecarcinus hypostegus, Troglocarcinus corallicola e Kroppcarcinus siderastreicola. Uma nova espécie de Troglocarcinus, gênero até então monoespecífico, foi encontrada em associação às espécies de Mussismilia no litoral da Bahia. Troglocarcinus n. sp. difere de sua congênere por (1) possuir numerosos espinhos bem desenvolvidos na carapaça (delimitando as regiões protogástrica e mesogástrica), pelo (2) segmento basal da antênula (que não se estende até o pedúnculo ocular), pela (3) presença de cerdas no esternito do primeiro pereópodo e, finalmente, pelo (4) terceiro pleópodo da fêmea unirreme ou birreme. Para a inclusão da nova espécie, foi necessária a elaboração de uma emenda na diagnose do gênero. No Atlântico Sul, a família Entomolepididae (Copepoda, Siphonostomatoida) está representada apenas por Spongiopsyllus. Uma nova espécie de Spongiopsyllus foi encontrada em amostras de Mussismilia hispida provenientes da Praia da Boa Viagem, na Baía de Todos-os-Santos. Spongiopsyllus n. sp. se distingue de S. adventicius pela redução no número de segmentos da antênula, ornamentação do endópodo da antena e pela cerdação do maxilípede e da P1. Spongiopsyllus n. sp. é o segundo registro do gênero para o Atlântico Sul e a primeira ocorrência da família associada com Scleractinia. Adicionalmente, foi elaborada uma chave de identificação para todas as espécies de Entomolepididae. O inventário da biodiversidade marinha na Província Brasileira ainda é incipiente. Deste modo, os resultados obtidos no presente estudo contribuem ao conhecimento da carcinofauna, com ênfase às formas associadas de hábito críptico, revelando que novas espécies e ocorrências geográficas permanecem amplamente desconhecidas pela comunidade acadêmica e científica. / Salvador

Reproductive characters of the elliptical star coral Dichocoenia stokesi (Cnidaria: Scleractinia) were investigated based in histological examination of tissues collected in southeastern Florida between September 1999 and September 2000. The study population was predominantly gonochoric with a small incidence of hermaphroditism. Dichocoenia stokesi exhibits intermediate egg size (312.2 ± 40.4μm; mean ± SD) compared with other scleractinian species, suggesting a moderately lecithotrophic larval stage. Although spawning was not directly observed in this study, two separate spawning events per year are inferred from histological slide analyses; the first in late August or early September, and the second in early October. Sea water temperature was significantly positively correlated with female gonadal development in D. stokesi, whereas insolation was significantly inversely correlated with gonadal development. A recent epizootic of White Plague Type II in south Florida appears to be skewing local D. stokesi populations toward smaller - and potentially less fecund - colony sizes, although colony size and fecundity were not correlated in this study. The mean fecundity of the study population is estimated as 1138.1 eggs cm-2 yr-1.

The health of coral reefs has been decreasing globally due to acute and diffuse anthropogenic impacts. Historically corals have persisted through periods of adverse conditions for coral growth via evolutionary selective processes, making successful sexual reproduction paramount to the future of coral reefs. Little is known about sexual reproduction of Caribbean corals at high latitude, specifically in southeast Florida on the northern most extension of the Florida reef tract. Here, a comprehensive histological analysis of gametogenesis, spawning, and size of sexual maturity is provided for Siderastrea siderea at 26°N (Broward County, Florida, USA), with accompanying analysis of fecundity variation from the upper Florida Keys (25"N) through Martin County Florida (27°N). Histological analysis of tissue samples in combination with lunar, tidal, and temperature cues suggest primary spawning occurs following the new moon of October. Massive and rapid post-spawning oocyte resorption was observed and characterized across both years indicating that spawning is generally incomplete in the study area. Histological observations suggest that size at sexual maturity in a nearshore, high sediment environment may be >20cm2 which is considerably smaller than previously reported. Fecundity decreased by 85% from 25°N to 27°N. Changes in fecundity were not attributed to significant differences in oocyte quantity between regions but to differences in oocyte volume which decreased by 65% from 25°N to 27°N. Drastic decreases in fecundity observed over a relatively small geospatial scale have important implications for regional population structure and connectivity and should prompt a further, multi-species, investigation.

Coral recruitment in Southeast Florida is being outpaced by mortality, resulting in population declines in many species. Identifying the coral species most likely to recruit and survive on Southeast Florida reefs and evaluating spatial variation in recruitment and survivorship is crucial for managing decreasing coral populations. This study focuses on 12 sites in Broward and Miami-Dade counties that have served as long-term stations for monitoring adult coral cover and demographics. At each site, thirty-two 225cm2 grooved terracotta settlement tiles were attached to the substrate in winter of 2015 and retrieved in winter of 2016 to evaluate scleractinian and octocoral recruitment rates. Thirty-two corresponding 0.25 m2 quadrats were surveyed in situ for coralsconditions, such as Poritidae, Siderastreidae, and Octocorallia, exhibit signs of recruitment success and/or juvenile survivorship. Scleractinian recruitment was not variable spatially, but juvenile densities varied on site-level spatial scales, suggesting that differential survivorship structures adult scleractinian communities. This study will inform reef management and restoration efforts within Southeast Florida by identifying sites and species with potential to recover from disturbance through natural recruitment processes.

Image analysis was used to measure basal areas of selected colonies of Montastraea annularis and Porites astreoides, following the colonies over a three-year period from 2002 to 2004. Existing digital images of permanently-marked quadrats in the Caye Caulker Marine Reserve, Belize, were selected based on image quality and availability of images of selected quadrats for all three years. Annual growth rates were calculated from the basal-area measurements. Mean growth rates (radial skeletal extension) for M. annularis and P. astreoides were 0.02 cm yr-1 and -0.20 cm yr-1, respectively. Basal area measurements demonstrated a large degree of variability. Increases were approximately balanced by declines giving the impression of stasis. By removing negative values and correcting by 25% to allow for comparison with vertical growth rates, mean values increased to ~0.5 cm yr-1 for M. annularis and ~0.8 cm yr-1 for P. astreoides. Basal area as a growth measure was compared to methods used in earlier studies. A new growth index based on basal area and perimeter was proposed and modeled. This growth index can be useful for reporting growth measured from basal areas and comparable other methods. The index also measures negative growth, or mortality, which conventional methods cannot do.