This thesis aims to initially define the present knowledge of pathogens which infect algae, highlighting the potential economic significance of such pathogens, given the recent rise in algaculture. Focus is given to the oomycetes, a group of organisms which already contain several significant genera of plant (Phytophthora) and animal (Saprolegnia) pathogens, as well as Olpidiopsis; a genus reported to significantly impact algaculture in Asia. Subsequent chapters aim to genetically characterise stramenopiles (specifically oomycetes and hyphochytrids) associated with algae in two ways. Firstly known pathogens of algae, Olpidiopsis feldmanni and Anisolpidium rosenvingei are morphologically diagnosed by microscopy and genetically surveyed at phylogenetically significant loci. Further morphological information on these two pathogens is reported here expanding the current knowledge of these rarely reported organisms. Surprisingly, genetic evidence indicates that Anisolpidium, a uniflagellate genus, belongs to the biflagellate class Oomycota and not the closely related uniflagellate class Hyphochytriomycota, as previously suspected. Morphological and genetic features of these classes are contrasted to justify this molecular interpretation. These first two studies, along with the publically available sequences of algal pathogens are then used to design primers, which enable an oomycete-directed metagenomic survey of brown algae, allowing the investigation of what organisms are associated with these. At present the results of this survey are unreported. Finally a Eurychasma dicksonii transcriptome as well as genomic sequences of other stramenopiles are investigated for the presence of cadherin protein models. At present such models are automatically annotated and reported. This study is the first manual curation of the protein and defines a unique protein family which is presented by the oomycete genera Eurychasma, Pythium, Phytophthora and Albugo as well as the labyrinthulomycete Aurantiochytrium limanicum. The protein model is not reported from other sequenced oomycete genera or photosynthetic stramenopiles.

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published_or_final_version / Botany / Doctoral / Doctor of Philosophy

Three species of higher algicolous fungi were examined at the autecologica1, cultural, light microscope, and scanning and transmission electron microscope levels. Fungal development and the host-parasite relationship are described for each association. The seasonal occurrence of marine fungi from intertidal populations of Dilsea carnosa, Ascophyllum nodosum and Chondrus crispus was examined at Bembridge, Isle of Wight, UK. A basidiomycete pathogen, Mycaureola dilseae, was found on D. carnosa, and two ascomycetes, Mycosphaerella ascophylli and Lautitia danica, on A. nodosum and C. crispus, respectively. Mycaureola dilseae is host specific and exhibited a limited reproductive cycle with green necrotic lesions and basidiomata observed only during September and October. Mycosphaerella ascophylli is an obligate endophyte of A. nodosum, an association in which the fungal and algal reproductive cycles were found to be synchronous with sporocarps confmed to host receptacles. This fungus is also found in Pelvetia canaliculata. Sporocarps of L. danica were recorded on cystocarpic C. crispus throughout the year, with a higher incidence of the fungus on older fronds. Tetrasporic C. crispus was also infected and in both cases the fungus was confmed to algal reproductive tissues. Mycosphaerella ascophylli was isolated from A. nodosum and P. canaliculata tissues and the anamorph, Septoria ascophylli was induced to sporulate. Growth of M. di/seae from D. carnosa lesions was limited and Lautitia danica could not be isolated from infected C. crispus tissues. Ascospore (L. danica and M. ascophylli) and basidiospore (M. di/seae) cultures did not grow beyond the germ tube phase. Hyphae of M. dilseae grew both inter- and intra-cellularly in D. carnosa. Penetration of algal cells was initially achieved by fme bifurcated penetration hyphae and there is evidence of mechanical pressure and localized enzyme action. The fungus caused a progressive breakdown of algal cell walls and cell contents; particularly evident was the damage to chloroplasts and dissolution of Floridean starch grains. Infection fmally resulted in the formation on necrotic lesions, each surrounded by a ring of basidiomata. Transmission electron microscopy showed the ascus of M. ascophylli to be bitunicate with a thick endoascus and thin ectoascus. Intra-membranous haustoria were occasionally observed in the outer cell wall of A. nodosum and P. canaliculata. Lautitia danica asci were bitunicate and ascospores were covered with a mucilagenous layer. Penetration of host cells caused extensive damage and blackening of host reproductive tissues. The relevance of these results are discussed in relation to algal pathology and marine fungal ultrastructure.

Le modèle biogéochimique de résolution complexe MIRO a été développé pour étudier la dynamique des efflorescences de Phaeocystis en zone côtière belge (BCZ) en réponse aux apports de nutriments anthropiques délivrés directement par l’Escaut et indirectement par la Seine via les eaux atlantiques entrantes. Le modèle MIRO décrit les cycles du carbone (C), de l’azote (N), du phosphore (P) et de la silice (Si) au travers de 38 compartiments chimiques, planctoniques et benthiques clés de l’écosystème côtier dominé par Phaeocystis. Il a été validé dans une configuration multi boite simple en utilisant des forçages climatologiques pour la période 1989-1999 et sur base d’une comparaison visuelle des simulations de nutriments et des variables planctoniques avec les données récoltées durant cette même période. Le modèle validé a ensuite été utilisé pour étudier le fonctionnement de l’écosystème et les cycles biogéochimiques associés. Plus précisément, les bilans de carbone et de nutriments réalisés sur base des flux biologiques modélisés ont montré que l’écosystème de la BCZ, dominé par les efflorescences de Phaeocystis, se caractérise par une faible efficience trophique, une faible capacité de rétention/élimination des apports de nutriments d’origine anthropique et une faible capacité d’absorption du CO2 atmosphérique. Des scénarios annulant tour à tour l’activité biologique et les apports de carbone par les rivières ont permis de déterminer les rôles respectifs de la température, des processus biologiques et des apports de nutriments et de carbone par les rivières dans l’évolution saisonnière de la pCO2 des eaux de surface. L’effet combiné des apports anthropiques de nutriments et des conditions météorologiques locales (débit, vent, température) a été étudié sur base d’une simulation effectuée pour la période contemporaine (1989-2003) en utilisant les forçages réels mesurés. La comparaison visuelle des simulations et des observations montre que, si le modèle est parfaitement capable de reproduire les successions phytoplanctoniques, il est par contre moins performant en ce qui concerne la reproduction des signaux extrêmes. Il apparaît donc que l’échelle de temps (mensuelle) utilisée pour décrire la variabilité des forçages est trop longue et ne permet pas de capter les variations hydrologiques à court terme résultant du vent et de la marée. De manière à mieux comprendre le lien entre les activités humaines sur le bassin versant et l’eutrophisation des zones côtières, le modèle MIRO a été couplé aux sorties du modèle de rivière RIVERSTRAHLER appliqué à la Seine et à l’Escaut sur une période de 50 ans (1950-1998). Les résultats obtenus montrent que l’importance des efflorescences de diatomées est conditionnée par les apports de PO4, alors que l’importance des Phaeocystis est directement liée à l’importance des apports de NO3. Un bilan établi pour la BCZ montre que plus de 50% des apports annuels de N et 60% des apports annuels de P proviennent des eaux Atlantiques et pointe l‘importance des apports de la Seine pour l’enrichissement de la BCZ. Différents scénarios de réduction des apports de nutriments provenant des rivières ont été réalisés afin de cibler le ou les nutriments à diminuer prioritairement pour réduire les efflorescences de Phaeocystis. Les résultats montrent que, dans les conditions actuelles, seule une réduction des apports de NO3 prédit une diminution des efflorescences de Phaeocystis. De plus, pour avoir un abattement significatif de ces efflorescences, il est nécessaire d’agir de manière conjointe sur les apports de la Seine et de l’Escaut. En vue de l’implémentation du code MIRO dans un modèle 3D hydrodynamique et pour tenir compte de la variabilité spatiale des sédiments dans la zone étudiée, une paramétrisation des flux de nutriments à l’interface eau-sédiment a été recherchée sur base des résultats obtenus avec un modèle diagénétique analytique décrivant la dégradation de la matière organique et les cycles de l’azote et du phosphore dans les sédiments.

Major and trace element analyses were made on biogenic carbonate, silica, and fish debris and on authigenic philhipsite, micronodules, and yellow and brown aggregates recovered from Bauer and Roggeveen Basin metalliferous sediments. Phase components and the bulk samples were analyzed by INAA and MS methods. Leachates and residues from ammonium oxalate and mild HC1 leaches of bulk and fine sediment fractions were also analyzed. The mild acid leach removed fish debris and carbonate, and the oxalate leach dissolved the micronodule phase. Sediments of the Bauer and Roggeveen Basins differ in bulk composition, yet respond to various chemical treatments in similar manner. I interpret this as indicative of a close similarity in the mineralogy of these two areas. An iron-rich smectite, manganese micronodules, and fish debris dominate the sediment compositions of both basins. The smectite phase concentrates Fe, Si, and Al. Manganese, Co, Ni, Ce, and W are concentrated in the micronodule phase and Ca, Sc, and the lanthanides predominantly in the fish debris component. The trace elements Cu, Zn, As, and Sb are distributed in a complex manner among the three principal phases. Barium, and some Al and Fe, may be present in small quantities of barite, feldspars, and goethite, respectively. Silica, carbonate, and phillipsite phases exist in. such low concentrations that they do not contribute significantly to the bulk composition of the sediments. The response of the various size fractions leached indicates a uniformity of distribution of sediment components from the coarse to the fine fractions. / Graduation date: 1978

New Zealand is a continental island surrounded by deep-ocean, with a complex system of currents and oceanographic anomalies that may serve to isolate populations of coastal marine organisms. In particular Cook Strait is a 26 km wide body of water separating the North and South Islands which is characterised by complex interactions of tides and converging water masses. Cook Strait is a geologically recent formation that may also impart an historical influence on the biogeographic distribution of coastal marine taxa. In order to investigate the phylogeographic structure of coastal marine taxa around New Zealand's coastline and to investigate the processes that may contribute toward this genetic structure, I analysed mitochondrial DNA genes from limpet species of the Cellana genus. Phylogenetic analyses of the ribosomal 12S and 16S DNA genes showed that C. ornata may approximate the founding lineage to New Zealand, but these genes were unable to resolve between contrasting biogeographic hypotheses about the origin of Cellana in New Zealand. Intraspecific analyses of the mitochondrial cytochrome b gene from populations throughout the biogeographic range of Cellana ornata, C. radians and C. flava showed concordant genetic discontinuity at Cook Strait. Further analyses suggest that allopatric fragmentation and restricted gene flow have caused significant genetic differentiation between populations of the North and South Island. Demographic expansion was also identified for C. radians. The influence of contemporary nearshore currents and sea surface temperature was assessed using the mitochondrial cytochrome b gene for C. radians and C. ornata. Low levels of genetic differentiation between populations corresponding to 'current-zones' suggests that contemporary oceanic processes may be contributing to the genetic pattern observed for these species. However, the shallow divergence between haplotypes and populations restricted thorough investigation of contemporary gene flow. Genealogical concordance across co-distributed marine taxa of New Zealand also lends support to the historic association of genetic and species discontinuities with recent geological changes, such as sea level fluctuations.

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