Dissertations / Theses on the topic 'Symbiotic associations'

Les associations d'espèces sont définies comme la culture simultanée d'au moins deux espèces sur la même parcelle pendant une période significative de leur croissance. Ce système permettrait d'améliorer l'utilisation des ressources du milieu (eau, azote, lumière…) et ainsi d'augmenter le rendement et la qualité des grains par rapport aux cultures monospécifiques. L'objectif de notre travail était d'analyser le fonctionnement et d'évaluer la performance des associations blé dur - pois d'hiver et blé dur - féverole d'hiver pour aider à la conception d'itinéraires techniques adaptés à différents objectifs de production. Pour cela nous avons testé, au cours de trois années d'expérimentations, différentes combinaisons de variétés de blé dur, disponibilités en azote, structures de couverts et densités de plantes. Nos résultats ont confirmé l'intérêt de ces systèmes pour améliorer le rendement et la teneur en protéines du blé dur comparativement aux cultures monospécifiques mais également pour la réduction des ravageurs, maladies et de l'enherbement dans certaines conditions. Ces systèmes sont ainsi particulièrement bien adaptés aux situations à faible disponibilité en azote en raison de la complémentarité entre céréale et légumineuse pour l'utilisation de l'azote (minéral du sol et fixation symbiotique) mais aussi pour la captation de l'énergie lumineuse. In fine, ce travail a permis de proposer des prototypes d'itinéraires techniques d'associations adaptés à différents objectifs de production, grâce notamment à l'analyse dynamique des compétitions et complémentarités entre espèces au sein du couvert et en particulier de l'élaboration du rendement du blé dur en association.

The colonial marine bryozoan, Bugula neritina, harbors an uncultured endosymbiont, “Candidatus Endobugula sertula” throughout its life stages. The bacterial symbiont has been proposed to be a source of complex polyketide metabolites, the bryostatins, that chemically defend B. neritina larvae from predation. Within a bryozoan colony, significantly higher amounts of bryostatins are found in ovicell-bearing zooids where the developing larvae are brooded, as compared to ovicell-free zooids. It is hypothesized that signaling between B. neritina and “Ca. Endobugula sertula” may be involved in the regulation of bryostatin production in different zooids, as well as in maintenance of the symbiosis. In this study, suppression subtractive hybridization (SSH) was used to identify differentially expressed host genes during this association. The identified genes suggest that the host plays a role in the distribution and localization of bacterial symbionts in different host zooids, possibly to regulate levels of bryostatin production in the zooids.

This thesis focuses on the genomic study of symbionts of two different groups of hymenopterans: bees and ants. Both groups of insects have major ecological impact, and investigating their microbiomes increases our understanding of their health, diversity and evolution. The study of the bee gut microbiome, including members of Lactobacillus and Bifidobacterium, revealed genomic processes related to the adaptation to the gut environment, such as the expansion of genes for carbohydrate metabolism and the acquisition of genes for interaction with the host. A broader genomic study of these genera demonstrated that some lineages evolve under strong and opposite substitution biases, leading to extreme GC content values. A comparison of codon usage patterns in these groups revealed ongoing shifts of optimal codons. In a separate study we analysed the genomes of several strains of Lactobacillus kunkeei, which inhabits the honey stomach of bees but is not found in their gut. We observed signatures of genome reduction and suggested candidate genes for host-interaction processes. We discovered a novel type of genome architecture where genes for metabolic functions are located in one half of the genome, whereas genes for information processes are located in the other half. This genome organization was also found in other Lactobacillus species, indicating that it was an ancestral feature that has since been retained. We suggest mechanisms and selective forces that may cause the observed organization, and describe processes leading to its loss in several lineages independently. We also studied the genome of a species of Rhizobiales bacteria found in ants. We discuss its metabolic capabilities and suggest scenarios for how it may affect the ants’ lifestyle. This genome contained a region with homology to the Bartonella gene transfer agent (GTA), which is a domesticated bacteriophage used to transfer bacterial DNA between cells. We propose that its unique behaviour as a specialist GTA, preferentially transferring host-interaction factors, originated from a generalist GTA that transferred random segments of chromosomal DNA. These bioinformatic analyses of previously uncharacterized bacterial lineages have increased our understanding of their physiology and evolution and provided answers to old and new questions in fundamental microbiology.

Fungi with dark-coloured mycelia - also known as black fungi - form a ubiquitous fraction of microbial communities on rock surfaces all over the world. These organisms show a high capacity to adapt to a wide range of ecological conditions, including those peculiar of extreme environments. Their high tolerance to multiple abiotic stresses, such as solar radiation and osmotic stress is assured by the production of melanin pigments and osmoprotective compounds. The cosmopolitan genera Lichenothelia and Saxomyces were taken as iconic representatives of polyextremotolerant rock-inhabiting black fungi. I investigated their phylogenetic relationships with an extended taxon sampling within the class Dothideomycetes, the most diverse and life-style rich fungal class in Ascomycota. The three loci phylogenetic inference I set up, considering both environmental samples and culture isolates, highlighted the paraphyly of the two genera. The integrative taxonomy approach based on morphological as well as phylogenetic evidences allowed the taxonomical revision of the genera and the description of three new taxa. Rock inhabiting fungi often share substrata with green algae and cyanobacteria and some of them are associated with lichen thalli. Lichenothelia is of a particular interest because it includes lichen parasites and species which are loosely associated with algae or which grow independently on rock. Given their life style plasticity, we chose it for an in vitro culture experiment, studying the development of three Lichenothelia species when co-cultured with two different subaerial algae isolated from lichens (i.e., lichen photobionts). The results showed that the presence of algae neither influence the growth rate of fungi nor the formation of any lichen-like structure. However, this standardized approach proved suitable for future investigations on fungal-algal interactions in other systems. Previous multi-locus phylogenies of Dothideomycetes have investigated evolutionary relationships at order and family level within the class but they often failed to resolve the early diverging nodes, which were generating inconsistent placements of some clades. Here, I applied a phylogenomic approach to resolve relationships in Dothideomycetes, adding the newly sequenced Lichenothelia and Saxomyces genomes, to a wide dataset comprised of 238 individuals. I explored the influence of tree inference methods, supermatrix vs. coalescent-based species tree, and the impact of varying amounts of genomic data. The phylogenomic reconstructions, based on up to three thousand genes, provide well-supported topologies for Dothideomycetes, recovering Lichenothelia and Saxomyces among the earliest diverging lineages in the class together with other rock inhabiting fungi and lichens and thus, suggesting the rock-inhabiting life style as ancestral in the class. Further studies will be necessary to shed light on the molecular bases of stress tolerance and latent capacity of establishing symbiosis of these fungi.

The biology of the sub-aquatic lichen, Dermatocarpon luridum, was investigated. This lichen is sparsely distributed within the temperate climatic zones around the world, colonizing rock along watercourses that regularly experience water level fluctuations. Specimens collected from Canada and Austria were cultured using standard growth media. Brightfield microscopy was used for algal species identification, while fungal ITS, algal ITS and algal actin gene sequences were used for phylogenetic and population genetic evaluation. Results were: 1) axenic cultures of the photobiont were successful, while those of the mycobiont were not successful; 2) Diplosphaera chodatii is the photobiont associated with D. luridum var. luridum and allies, suggesting algal sharing between mycobiont species; 3) genetic diversity is high, and gene flow was high within local populations, but low between continental populations. Diplosphaera chodatii may be a keystone species contributing to the survival of D. luridum var. luridum along with other sub-aquatic, aquatic and terrestrial lichens.

La grande dépendance de G. Lutea vis-à-vis des associations mycorhiziennes VA est mise en évidence ainsi que le rôle positif de ces associations sur la nutrition phosphatée de la plante. Une analyse ultrastructurale permet de définir les différents stades de la progression de l'infection. Une analyse ultracytochimique indique la présence de composés protéiques et polyosiques au niveau de l'interface cellule-hôte / champignon VA. On montre que l'établissement d'une association mycorhizienne est le résultat d'une compatibilité cellulaire entre les deux partenaires

Thesis (MSc)--University of Stellenbosch, 2005.<br>ENGLISH ABSTRACT: The Mountain Fynbos biome, a division of the Cape Floristic Region (CFR), is home to round-leafed Buchu [Agathosma betulina (Berg.) Pillans], one of South Africa’s best-known endangered herbal medicinal plants. Agathosma betulina is renowned as a traditional additive to brandy or tea, which is used for the treatment of a myriad of ailments. In its natural habitat, A. betulina thrives on mountain slopes in acid and highly leached gravelly soils, with a low base saturation and low concentrations of organic matter. To adapt to such adverse conditions, these plants have formed mutualistic symbioses with arbuscular mycorrhizal (AM) fungi. In this study, the effect of indigenous AM taxa on the physiology of A. betulina is investigated. In addition, the AM taxa responsible for these physiological responses in the plant were identified using morphological and molecular techniques. Agathosma betulina was grown under glasshouse conditions in its native rhizosphere soil containing a mixed population of AM fungi. Control plants, grown in the absence of AM fungi, were included in the experimentation. In a time-course study, relative growth rate (RGR), phosphorus (P)-uptake, P utilization cost, and carbon (C)-economy of the AM symbiosis were calculated. The data showed that the initial stages of growth were characterized by a progressive increase in AM colonization. This resulted in an enhanced P-uptake in relation to non-AM plants once the symbiosis was established. Consequently, the lower P utilization cost in AM plants indicated that these plants were more efficient in acquiring P than non-AM plants. When colonization levels peaked, AM plants had consistently higher growth respiration. This indicated that the symbiosis was resulting in a C-cost to the host plant, characterized by a lower RGR in AM plants compared to non-AM plants. Arbuscular mycorrhizal colonization decreased with increasing plant age that coincided with a decline in P-uptake and growth respiration, along with increases in RGR to a level equal to non-AM plants. Consequently, the AM benefit was only observed during the initial stages of growth. In order to identify the AM fungi in planta, morphological and molecular techniques were employed, which indicated colonization by AM fungi belonging to the genera Acaulospora and Glomus. Phylogenetic analyses of a dataset containing aligned 5.8S ribosomal RNA gene sequences from all families within the Glomeromycota, including sequences obtained during the study, supported the above mentioned identification.<br>AFRIKAANSE OPSOMMING: Die Fynbos bergbioom, ‘n onderafdeling van die Kaapse Floristiese Streek, huisves rondeblaar Boegoe [Agathosma betulina (Berg.) Pillans], een van Suid Afrika se bekendste bedreigde medisinale plante. Agathosma betulina is bekend vir sy gebruik as tinktuur vir die behandeling van verskeie kwale. Die plant kom voor in bergagtige streke, in suur en mineraal-arm grond, met ‘n lae organiese inhoud. Gevolglik, om aan te pas by hierdie ongunstige kondisies, vorm die plante simbiotiese assosiasies met blaasagtige, struikvormige mikorrisa (BSM). In die huidige studie is die effek van hierdie BSM op die fisiologie van A. betulina ondersoek. Die identiteit van die BSM is ook gevolglik met morfologiese en molekulêre identifikasie tegnieke bepaal. Agathosma betulina plante is onder glashuis kondisies in hul natuurlike grond gekweek, wat ‘n natuurlike populasie van BSM bevat het. Kontroles is ook in die eksperiment ingesluit en hierdie stel plante is met geen BSM geïnokuleer nie. Gevolglik is die relatiewe groeitempo, fosfor opname, fosfor verbuikerskoste asook die koolstof ekonomie van die plante bereken. Die data het getoon dat die eerste groeifase gekarakteriseer is deur toenames in BSM kolonisasie vlakke. Dit het tot ‘n hoër fosfor opname in BSM geïnokuleerde plante gelei. Die laer fosfor verbuikerskoste gedurende hierdie fase het aangedui dat die plante wat geïnokuleer is met BSM oor beter meganismes beskik het om fosfor uit die grond te bekom. Toe BSM kolonisasie vlakke gepiek het, was groei respirasie hoër in BSM geïnokuleerde plante as in die kontroles. Dit het aangedui dat die BSM kolonisasie van plante tot hoër koolstof kostes vir hierdie plante gelei het, wat weerspieël is in die laer groeitempo van die BSM geïnokuleerde plante. Die BSM kolonisasie vlakke het gedaal met toenemende ouderdom van hul gasheer plante, wat gekarakteriseer is deur ‘n laer opname van fosfor en laer groei respirasie, tesame met ‘n toename in relatiewe groeitempo tot vlakke soortgelyk aan die van die kontrole plante. Die BSM voordele vir die plant is dus net gedurende die eerste groeifase waargeneem. Die BSM wat verantwoordelik is vir hierdie fisiologiese veranderinge is gevolglik geïdentifiseer met behulp van morfologiese en molekulêre tegnieke en dit is gevind dat BSM wat behoort tot die genera Acaulospora en Glomus binne hierdie plante voorkom. Filogenetiese analise gegrond op opgelynde 5.8S ribosomale RNA geen volgordes afkomstig van al die families binne Glomeromycota asook volgordes gevind in die studie, het die bogenoemde identifikasie gestaaf.

Abstract Most plants form symbiotic associations with various fungi in natural ecosystems. Traditionally, many of these associations are viewed as mutually beneficial, but recent studies show that symbiotic interactions can be complex and labile. I studied the variability of interactions between grasses and fungi, using root-associated fungi and foliar endophytes in grasses as study systems. First, I studied experimentally how root-associated fungi colonize their host grasses in different natural and artificial conditions. I then investigated experimentally how foliar endophytes affect their host grasses, and whether the endophyte contributes to the host’s adaptation to local and/or foreign habitats. Finally, I reviewed the current use of foliar endophytes in agriculture, with a particular focus on Europe, and critically considered their potential for practices beyond agriculture. I found root fungi to be common, but different types of root fungi had contrasting colonization patterns in natural environments. However, I found that grasses lose almost all of their root fungi in controlled and more favourable conditions, indicating that the associations are fairly loose and conditional to environmental context. My results also showed that foliar endophytes affected the host’s performance in varying ways, depending on plant origin and experimental country, indicating that the associations were context dependent and could represent conditional mutualism. I also found that endophytes contribute to plant adaptation only weakly, but that the grasses were clearly locally adapted to their sites of origin, especially in regard to reproduction. However, the grasses of subalpine origin performed well vegetatively also in Northern Finland, suggesting that they may have high adaptive potential under changing climates. The literary review showed that foliar endophytes are successfully used in agriculture, e.g. in the USA and New Zealand, and that they possess the potential for several practical applications. However, the intentional use of endophyte-enhanced grasses is non-existent in Europe, although many European grass cultivars have great potential for improvement via endophytes. Taken together, these results show that plant–fungal interactions are highly variable along sites, environmental contexts and origins of the symbiotum, making predictions for these interactions difficult<br>Tiivistelmä Luonnollisissa ekosysteemeissä melkein kaikilla kasveilla on symbionttisia sienikumppaneita. Perinteisesti monien näiden vuorovaikutusten on oletettu olevan molemmille hyödyllisiä, mutta viimeaikaiset tutkimukset osoittavat symbionttisten yhteyksien olevan vaihtelevia. Väitöskirjassani tutkin tätä heinien ja sienien välisten yhteyksien vaihtelevuutta, käyttäen heinissä esiintyviä juurisieniä ja lehtiendofyyttejä tutkimuskohteinani. Ensiksi tutkin kokeellisesti, kuinka juurisienet kolonisoivat heiniä erilaisissa luonnon- ja kasvihuoneolosuhteissa. Seuraavaksi tutkin kokeellisesti, kuinka lehtiendofyytit vaikuttivat heinien menestymiseen ja edesauttoivatko endofyytit heinien sopeutumista paikallisiin ja/tai vieraisiin elinympäristöihin. Viimeiseksi selvitin kirjallisuuskatsauksen avulla, kuinka lehtiendofyyttejä hyödynnetään maataloudessa ja arvioin endofyyttien potentiaalista käyttöarvoa maatalouden ulkopuolella, erityisesti keskittyen niiden hyödyntämiseen Euroopassa. Tutkimukseni osoitti, että heinien juurisienet ovat yleisiä, mutta niiden keskinäiset runsaussuhteet vaihtelivat luonnollisissa ympäristöissä. Kasvihuoneolosuhteissa heinät kuitenkin menettivät juurisienensä, viitaten siihen, että kyseinen yhteys on melko löyhä ja riippuvainen ympäristöstä. Tutkimukseni osoitti myös, että lehtiendofyytit vaikuttivat heinien menestykseen vaihtelevasti riippuen heinien alkuperästä sekä koemaasta, viitaten siihen, että nämä yhteydet ovat niin ikään olosuhteista riippuvaisia. Endofyytti vaikutti vain heikosti heinien sopeutumiseen, mutta heinät olivat selkeästi paikallisesti sopeutuneita niiden alkuperäisiin elinympäristöihin, erityisesti heinien lisääntymisen suhteen. Alppien heinät kuitenkin menestyivät vegetatiivisesti myös Pohjois-Lapissa, mikä viittaa siihen, että näillä heinillä saattaa olla korkea sopeutumispotentiaali muuttuvissa olosuhteissa. Kirjallisuuskatsaukseni osoitti, että lehtiendofyyttejä käytetään menestyksekkäästi mm. USA:n ja Uudessa-Seelannin maataloudessa. Euroopassa niiden käyttö on kuitenkin lähes olematonta, vaikka endofyyteillä voisi olla monia käyttömahdollisuuksia, sekä maataloudessa että ympäristön hoidossa. Kaiken kaikkiaan tutkimukseni osoittavat, että heinien ja sienten väliset vuorovaikutukset ovat hyvin vaihtelevia riippuen ympäristöstä ja heinien alkuperästä, minkä vuoksi näiden sienien vaikutuksia heiniin on vaikea ennustaa

Certains symbiotes intracellulaires résident dans le cytoplasme des cellules et manipulent le système reproductif de leurs hôtes. Du fait de leur transmission maternelle, ces parasites sont sélectionnés pour optimiser la survie et la reproduction de leurs hôtes femelles. Chez les arthropodes, la bactérie Wolbachia infecte au moins 66% des espèces d’insectes mais peuvent aussi infecter des nématodes. Cette large distribution dans les populations hôtes confère à Wolbachia un potentiel important en tant que moteur d’évolution. En particulier, elle pourrait être utilisée comme vecteur transgène dans les espèces nuisibles. Mais la dynamique évolutive des infections à l’échelle des communautés est mal connue, en particulier la fréquence des transferts de parasites entre hôtes de différentes espèces et la stabilité évolutive des associations. Mon travail de thèse a porté sur la détection et dynamique des infections de Wolbachia à une échelle micro-évolutive, c’est-à-dire, dans des communautés d’arthropodes avec moins de 5 My. L’objectif de ce travail était à la fois la caractérisation des communautés géographiques d’arthropodes et celle des infections par Wolbachia de ces communautés. Nous avons également examiné l’existence de transferts horizontaux récents de ces symbiotes entre des taxa distantes ainsi que les routes écologiques potentielles pour ces transmissions<br>Sexual parasites are intracellular symbionts capable of manipulating the reproduction of their hosts. They are widespread in Arthropods where they display a wide range of reproductive manipulations; these can be potentially involved in the evolution of mating systems, speciation, gene acquisition and sex determination. In particular, Wolbachia is thought to infect more than 66% of insect species and is also found in nematodes. However, little is known about the dynamics of Wolbachia infections at the community level. Although at the intra-population level, invasion dynamics have been extensively studied, the same is not true at the community level where the turnover of infections remains largely uncharacterised. The question of how often are new infections acquired through horizontal transfers between distantly related hosts remains also open. Moreover, as Wolbachia is seen as a good candidate for a transgenic vector against pests, understanding its dynamic at the community level is crucial. We proposed to address them by performing an exhaustive characterisation of sexual parasites in simplified systems, using the opportunity offered by small arthropod communities in isolated islands

In this thesis, we presented three main types of analyses of metabolism, most of which involved symbiosis: metabolic dialogue between a trypanosomatid and its symbiont, comparative analyses of metabolic networks and exploration of metabolomics data. All of them were essentially based on genomics data where metabolic capabilities were predicted from the annotated genes of the target organism, and were further refined with other types of data depending on the aim and scope of each investigation. The metabolic dialogue between a trypanosomatid and its symbiont was explored with functional and evolutionary goals which included analysing the classically defined pathways for the synthesis of essential amino acids and vitamins, exploring the genome-scale metabolic networks and searching for potential horizontal gene transfers from bacteria to the trypanosomatids. The comparative analyses performed focused on the common metabolic capabilities of different lifestyle groups of bacteria and we proposed a method to automatically establish the common and the group-specific activities. The application of our method on metabolic stories enumeration to the yeast response to cadmium exposure was a validation of this approach on a well-studied biological response to stress. We showed that the method captured well the underlying knowledge as it extracted stories allowing for further interpretations of the metabolomics data mapped into the genome-scale metabolic model of yeast

L'expression du phénotype des organismes dépend en partie d'organismes symbiotiques avec qui ils sont en interaction étroite. Selon le mode de transmission du symbiote, ce dernier va être en conflit d'intérêt plus ou moins intense avec l'hôte pour l'expression du phénotype, conduisant parfois le symbiote à évoluer vers la manipulation du phénotype de l'hôte. Nous avons tenté d'identifier différents facteurs génétiques et environnementaux influençant l'expression et l'évolution de la manipulation chez l'insecte parasitoïde de larves de drosophiles, Leptopilina boulardi, et son virus manipulateur du comportement, LbFV. Ce virus bénéficie d'une transmission mixte, verticale et horizontale, cette dernière étant favorisée par l'induction de superparasitisme induite par le virus. L'étude de la contribution du génotype du parasitoïde dans l'expression de la manipulation a révélé la présence de gènes de résistance partielle à la manipulation. Le potentiel évolutif de cette résistance a ensuite été évalué par des expériences d'évolution expérimentale. Nous avons également montré que LbFV augmente la virulence du parasitoïde envers les larves de drosophiles, révélant ainsi une évolution vers une forme de mutualisme sur ce trait. Par ailleurs, le travail montre qu'un même parasitoïde peut être non seulement infecté par plusieurs souches du virus LbFV mais également infecté par un virus à ARN, décrit pour la première fois dans cette thèse. La transmission verticale, la prévalence élevée et les forts effets phénotypiques de ce virus soulignent de nouveau l'importance des virus dans l'expression du phénotype en population naturelle.

Positive biotic interactions such as mutualism, commensalism and facilitation are ubiquitous in nature, but historically have received considerably less research attention than negative interactions such as competition, predation and parasitism. The paucity of research on positive interactions is particularly evident in stream ecosystems and in vertebrate communities. Stream fishes clearly provide an ideal system for advancing research on positive interactions. Many minnows (Cyprinidae) of eastern North America engage in a potentially mutualistic reproductive interaction known as nest association, in which individuals of one species (nest associates) spawn in nests constructed by host species. In nest association, hosts provide unsilted gravel substrate for spawning nest associates, and increased parental care to associate broods. High associate: host egg ratios can create a dilution effect, reducing the probability that host eggs will be preyed upon by egg predators. Nest associative interactions are common, but are relatively understudied compared to other interactions among stream fishes. The goals of this study were to apply general ecological models to this novel system to (a) gain new insight into the mechanisms structuring nest associative stream fish communities, and (b) to use inference from stream fish communities to potentially expand and improve the general ecological models. These goals required completion of three objectives, including (1) examining the influence of abiotic and biotic contexts on reproductive behavior and fitness outcomes between a cyprinid host and associate, using the biological markets model to generate predictions; (2) examining the utility of the nest web framework (previously only used for cavity nesting vertebrate communities) and the stress gradient hypothesis (previously applied almost exclusively to plant communities) for predicting which associate species spawn on nests built by various nest building species, and the consequences of these choices, respectively; and (3) using two-species occupancy modeling to determine the relative influence of biotic interactions and habitat covariates on the co-occurrence of a host and two nest associates. To accomplish these goals, I conducted a large-scale experiment to manipulate presence of mutualists (Nocomis leptocephalus, host; Chrosomus oreas, associate), egg predators (biotic context) and habitat quality (abiotic context). I conducted behavioral nest observations and conducted repeated stream fish stream fish community surveys to collect demographic data. I constructed a nest web from observational data, and implemented structural equation modeling through an information-theoretic framework to identify nest web plausibility across a large spatial extent. I tested some predictions of the stress gradient hypothesis by regressing juveniles-per-nest and a metric of cyprinid community structure on a composite measure of physical stress (scaled gradients of catchment-scale agricultural land use and catchment area). I used two-species occupancy modeling to model co-occurrence of N. leptocephalus hosts and two associates, C. oreas and Clinostomus funduloides, and used an information-theoretic framework to compare hypotheses representing the importance of biotic interactions, habitat covariates or both at determining species co-occurrence. Results corroborated some (but not all) model predictions, and identified room for improvement in each of the general models. Nest associative spawning by C. oreas was not context dependent; C. oreas did not spawn in the absence of a reproductively active male N. leptocephalus at any treatment level. However, the net fitness outcome of host and associate species was mutualistic, and the interaction outcome switched from commensalistic to mutualistic with abiotic context. N. leptocephalus reproductive success was improved by C. oreas presence in less-silted habitats, but not in heavily-silted habitats. This is most likely because broods were subject to predation in both habitat types, but were also negatively affected by siltation in silted habitats. Accordingly, egg dilution by associates was not sufficient to support a mutualistic relationship in less favorable habitats. Results suggest that the biological markets model may be a useful tool for predicting fitness outcomes of nest associative mutualism, but may not be as useful for predicting the behavioral outcomes of obligate mutualisms. Future applications of the biological markets model should carefully consider species traits, specifically the degree to which trading behavior is obligate for participants. Future work with this model will yield more insight by considering highly facultative associates. Nest webs constructed from nest observational data suggested an interaction topology in which strong (nearly-obligate) associates relied most frequently on N. leptocephalus nests, and less frequently on nests constructed by Campostoma anomalum. Weak (facultative) associates were seldom associated with nests constructed by either species, and probably spawned before hosts began nesting activity. Structural equation models corroborated this topology throughout the New River basin, although some less-supported model evidence specified some nest association by weak associates. Juveniles-per-nest of strong associates responded positively to physical stress, while this metric for other cyprinid reproductive groups showed no relationship. Proportional representation of Nocomis and strong associates also increased predictably with physical stress. This study suggests that the nest web framework can be informative to systems outside the ones for which it was developed; future studies may be able to use this framework to better understand the role of habitat-modifying species in communities other than cavity nesting terrestrial vertebrates and nest associative stream fishes. This work extended the nest web framework by (a) modeling the outcomes of interactions instead of the interactions themselves, and (b) by using structural equation modeling to test nest web predictions with an information-theoretic framework. This study also suggests that the stress gradient hypothesis can be useful for understanding interaction dynamics in vertebrate communities; this represents the first direct evidence that this model can be used in vertebrate communities. Further, I demonstrate that the stress gradient hypothesis may be extended to predict community structure. However, more research in a diversity of systems will be needed to determine the extent to which this can be applied. This study provides some of the first evidence of large-scale positive co-occurrence patterns in vertebrates. However, the precise roles of habitat covariates and biotic interactions were species-specific. Occupancy results suggest that co-occurrence between N. leptocephalus and nest associate C. funduloides is driven only by reproductive behavioral interactions. Alternatively, evidence suggests that co-occurrence between N. leptocephalus and C. oreas is driven by both nest association and habitat covariates. That two-species occupancy modeling can be a useful tool for comparing difficult-to-test hypotheses involving biotic interactions at large spatial scales. This study represents the first quantitative, multi-scale treatment of positive interactions in stream ecosystems. This study demonstrates that applying general ecological models to stream fish communities can yield new insights about both the study system and the models themselves. While models of negative interactions, food webs and dispersal have been applied to stream fishes, we stand to gain much ground by also considering positive biotic interactions. In doing so, stream fish ecologists will also be able to contribute to the advancement of general ecology, and thus raise awareness for these understudied ecosystems and taxa.<br>Ph. D.

博士<br>國立臺灣海洋大學<br>海洋生物研究所<br>104<br>Coral reefs are one of the most complex marine ecosystems. At least 310 species of decapods crustaceans can be found living in the spaces of coral structures, particularly with the branching corals. Many of these fauna provide considerable benefits to their host corals. A comprehensive understanding of the association between these decapods and their hosts could help clarify the relationship, interaction, and importance of symbionts with reef fauna as hosts. In this thesis, symbiotic decapods in coral reefs were studied using two approaches; the field studies and the laboratory studies. In the field studies, the symbiotic caridean shrimps, anomuran and brachyuran crabs, were identified from areas of northeastern Taiwan; western Fanzaiao Bay near Badouzi, Keelung Island, Longdong, Yenliao Bay, Doufu Cape, and Guishan Island. Eighty-six species of symbiotic decapods, which comprised of 41 caridean shrimps, 8 anomuran crabs and 37 brachyuran crabs, were discovered. Among these, 14 species were reported for the first time in Taiwan. More than half of the decapods associated with branching corals of the Acropora and Pocilloporidae. In Acropora, symbiotic decapod species richness and carapace width of Tetralia crabs showed linear regression relationships with inter-branch volume of coral colonies. These may imply that the abundance of the branching corals strongly influence the biodiversity of symbiotic decapods. It also indicates that corals were healthy in the area investigated because some of these symbiotic fauna are considered to increase the persistence and resilience for their host. Cluster analysis of symbiotic decapods in Taiwan revealed that climate and oceanic current mainly influenced the decapod fauna and separated them into 2 groups. The first group which located in the area south of Tropic of Cancer was affected by sub-tropical climate, South China Sea water and Kuroshio Current. The second group was from the study areas in northeastern Taiwan, north of Tropic of Cancer, which is influenced by sub-temperate climate, complex hydrographic system of the China Coastal Current and Kuroshio branch water. Distributions of the three coral symbiotic decapod taxon; Pontoniinae, Tetraliidae, and Trapeziinae, in the Coral Triangle did not exhibit the clear pattern of species decline in the same way with scleractinian corals and other marine fauna, suggesting that the more intensive collection of decapods in Taiwan may reveal hidden species and definitely bridge the distributional gaps. The laboratory studies were conducted focusing on the most abundance coral crab in the coastal area of Badouzi, namely Tetralia rubridactyla. This crab inhabits branching corals of the genus Acropora, which are considered to be an index species of coral reef, and shows some host species discrimination in the field. The crab was examined with respect to its host preference and fidelity underlying host selection and detection. Five oceanic objects were provided to the crabs in the selection experimental series; 2 species of common host coral (Acropora hyacinthus and A. digitifera), 2 species of reported uncommon host coral (Pocillopora damicornis and Stylophora pistillata), and dead coral skeleton. The results demonstrated T. rubridactyla host selection conditioning as follows; (1) Under the no-choice condition, inhabit any choice object for shelter, (2) under the choice condition, if without a common host, randomly inhabit any uncommon choice object as a host, and (3) under the choice condition, if a common host is available, selecting the common host is the first priority because it could provide food and space. During the selection experiment, the crabs in the treatments with no Acropora corals as choice object showed rather high position changing percentage throughout the experimental period. On the other hands, the crabs in the treatments contained at least one Acropora coral as a choice object seldom changed position after found Acropora host. The host detecting experiment demonstrated that the crabs distinguish and trace the coral hosts primarily by detecting chemical cues from Acropora. The present studies also revealed that T. rubridactyla expresses neither fidelity nor preference between A. hyacinthus and A. digitifera and within the Acropora species. Thus the distribution of T. rubridactyla on Acropora corals in the reef may be affected by an abundance of corals, rather than on the preference for specific coral species. Currently, coral reefs are facing the threat of various anthropogenic pressures. To effectively maintain and manage the reef ecosystem, it will be essential to increase the knowledge of reef biodiversity and fauna. Intensive studies on the diverse marine fauna of Taiwan and the ecological functions of them will be of immense interest in furthering the understanding of marine environments. Moreover, this information could be applied to monitoring of possible changes in reef ecosystems in the future.

Thesis (M.S.)--University of Wisconsin--Madison, 1994.<br>Typescript. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references (leaves 88-92).

Die Familie der Physciaceen (lichenisierte Ascomyceten) und deren kompatible Photobionten wurden mit Hilfe von nrITS-Sequenzierungen untersucht. Es wurde Frisch- oder Herbarmaterial bearbeitet, das weltweit gesammelt worden war und 23 der 27 Physciaceengattngen repräsentierte. Die Sequenzdaten erlaubten eine differenzierte taxonomische Bearbeitung beider Biontengruppen. Basale Linien der Physciaceenphylogenie waren eng korreliert mit der Verteilung mehrerer phänotypischer Merkmale. Es konnte gezeigt werden, daß die Caliciaceen, eine andere Flechtenfamilie, die Schwestergruppe zu einer der vier Hauptlinien der Physciaceen bilden. Alle Proben der Physciaceen waren mit Algen aus der Gattung Trebouxia assoziiert. Ein Datensatz von über 300 Trebouxia nrITS-Sequenzen wurde zusammengestellt, der eine zuvor ungekannte Diversität innerhalb der Gattung Trebouxia repräsentiert. Die Taxonomie dieser Gattung wurde revidiert und ein System zur Abgrenzung und Zuordnung von nrITS-Varianten vorgeschlagen, das eine Strukturierung der gefundenen Diversität erlaubt. Viele der untersuchten Physciaceenarten erschienen hoch selektiv in Bezug auf ihre kompatiblen Photobionten. Im Gegensatz dazu konnte bei keinem der Photobionten eine Beschränkung auf nur eine Mycobiontenlinie gezeigt werden. Die Beschränkung vieler Mycobionten auf einen bestimmten Photobionten wurde als eine ökologische Abhängigkeit des Mycobionten von seinem kompatiblen Photobionten interpretiert. Daher wurde untersucht, ob Artbildungsereignisse in Trebouxia, Artbildungsereignisse in den assoziierten Physciaceen auslösen können. In einem Vergleich der Trebouxia- mit der Physciaceenphylogenie konnten jedoch keine korrelierten Verzweigungsmuster festgestellt werden. Hauptlinien der Trebouxien waren allerdings mit Umweltparametern, wie z.B. Substrat-pH und Makroklima korreliert. Die Evolution der Physciaceen war von diesen Faktoren offensichtlich deutlich weniger abhängig.Die nrSSU-Gene der Physciaceen enthielten mehr Introns als die aller anderen bekannter Organismengruppen. Der einzigartige Datensatz konnte genutzt werden, um konservierte Regionen innerhalb dieser Introns zu identifizieren. Auf diese konservierten Regionen konnten Primer konstruiert werden, die mit allen Introns einer Insertionsstelle kompatibel waren. Mit Hilfe dieser Primer konnten Introns detektiert werden, die bei der nrSSU-Sequenzierung unerkannt geblieben waren.

碩士<br>國立交通大學<br>電控工程研究所<br>99<br>In artificial immune system, antibodies represent the solutions. With the cooperative concept in genetic algorithm, the symbiotic artificial immune system has been developed, and partially specified antibodies are defined as the partial solutions. When the partially specified antibodies are not linear independent; have correlation with the others, or face the high-dimensional problem, put all partially specified antibodies in the same swarm which result in low efficiency in the algorithm. Frequent pattern growth algorithm is adopted in this thesis to find the correlation between each dimension, in which the strength of the connectivity determines whether the classification rules are valid or not. Generally, reasonable classification rules cause the algorithm work more effectively. Hence, for the algorithm, the partially specified antibody classification plays a very important role in the evolutionary process. The classification rules defined in this thesis are determined according to the correlation between each dimension, and they are adjustable under different problem, which greatly enhance the applicability of many kinds of problems.

Το βακτήριο Wolbachia είναι ένα ενδοκυττάριο και μητρικά κληρονομούμενο συμβιωτικό βακτήριο. Ανήκει στην ομοταξία των Alphaproteobacteria και την τάξη των Rickettsiales. Αποτελεί ίσως τον πιο διαδεδομένο ενδοκυττάριο συμβιωτικό οργανισμό στον πλανήτη, καθώς έχει εντοπιστεί μέχρι στιγμής σε πληθώρα αρθροπόδων και νηματωδών της φιλαρίασης. Πρόσφατες μελέτες εκτιμούν ότι πάνω από το 40% των ειδών αρθροπόδων είναι μολυσμένα με το βακτήριο Wolbachia. Το συμβιωτικό αυτό βακτήριο επηρεάζει τις βιολογικές λειτουργίες και ιδιότητες των ξενιστών του και είναι υπεύθυνο για μια σειρά αναπαραγωγικών ανωμαλιών, όπως η κυτταροπλασματική ασυμβατότητα, η παρθενογένεση, η θανάτωση των αρσενικών εμβρύων και η θηλυκοποίηση. Τα μοναδικά αυτά βιολογικά χαρακτηριστικά του βακτηρίου Wolbachia προσελκύουν όλο και περισσότερο το ενδιαφέρον διαφόρων ερευνητών τόσο για το ρόλο του βακτηρίου σε εξελικτικές διαδικασίες (κυρίως ειδογένεση) όσο και για τη χρησιμοποίησή του σε περιβαλλοντικά φιλικές εφαρμογές καταπολέμησης οργανισμών που είναι επιβλαβείς στους τομείς του γεωργικού και δασικού περιβάλλοντος, και της υγείας. Τα είδη του γένους Glossina (Diptera: Glossinidae), γνωστά και ως μύγες τσε-τσε, αποτελούν ξενιστές του βακτηρίου Wolbachia. Η μύγα τσε-τσε είναι ο σημαντικότερος φορέας των παθογόνων τρυπανοσωμάτων στην τροπική Αφρική, τα οποία προκαλούν την ασθένεια του ύπνου (sleeping sickness) στον άνθρωπο και την αντίστοιχη τρυπανοσωμίαση, γνωστή ως nagana, στα ζώα. Η χρησιμοποίηση του βακτηρίου Wolbachia σε μεθόδους βιολογικής καταπολέμησης της μύγας τσε-τσε προαπαιτεί την πλήρη γνώση της γενετικής του ταυτότητας και των αλληλεπιδράσεων του με το ξενιστή. Προς την κατεύθυνση αυτή, και στα πλαίσια της παρούσας διατριβής, πραγματοποιήθηκε η ανίχνευση του συμβιωτικού βακτηρίου Wolbachia σε περισσότερα από 5300 άτομα από φυσικούς και εργαστηριακούς πληθυσμούς 11 διαφορετικών ειδών μύγας τσε-τσε από 13 Αφρικανικές χώρες. Τα αποτελέσματα έδειξαν τεράστια απόκλιση της παρουσίας του βακτηρίου τόσο μεταξύ ειδών όσο και μεταξύ πληθυσμών του ίδιου είδους. Επίσης, πραγματοποιήθηκε ο γενετικός χαρακτηρισμός των στελεχών Wolbachia από συνολικά 29 αντιπροσωπευτικά δείγματα διαφόρων πληθυσμών και ειδών μύγας τσε-τσε, ενώ σε αρκετά από αυτά παρατηρήθηκαν πολλαπλά στελέχη του βακτηρίου. Διαπιστώθηκε εντυπωσιακή γενετική ποικιλότητα στελεχών Wolbachia που απαντούν στα διάφορα είδη μύγας τσε-τσε καθώς και ασυμφωνία μεταξύ των φυλογενειών των στελεχών Wolbachia και των μυγών τσε-τσε ξενιστών της, γεγονός που σημαίνει οριζόντια μετακίνηση του συμβιωτικού βακτηρίου κατά την εξέλιξη. Επιπρόσθετα, εντοπίστηκαν για πρώτη φορά εκτεταμένα γεγονότα οριζόντιας μεταφοράς βακτηριακών γονιδίων στο γονιδίωμα τριών ειδών μύγας τσε-τσε: στο Glossina morsitans morsitans, Glossina pallidipes και Glossina austeni. Από εξελικτικής σκοπιάς, κρίσιμα ερωτήματα προκύπτουν από τα παραπάνω ευρήματα, και πιο συγκεκριμένα σχετικά με: την προέλευση-μηχανισμό αυτών των γεγονότων οριζόντιας μεταφοράς, τον χρονικό προσδιορισμό τους, τον πιθανό ρόλο τους σε διαδικασίες ειδογένεσης και την επιλεκτική εμφάνισή τους σε ορισμένα μόνο είδη Glossina π.χ. στo υποείδos Glossina morsitans centralis που είναι πολύ συγγενικό του Glossina morsitans morsitans δεν παρατηρήθηκε το φαινόμενο. Εξίσου σημαντική και επιβεβλημένη κρίνεται η διεξοδική διερεύνηση του ενδεχομένου τα βακτηριακά γονίδια που ενσωματώθηκαν στο ευκαρυωτικό γονιδίωμα της μύγας τσε-τσε να ευθύνονται για την έκφραση νέων λειτουργιών-ιδιοτήτων (ή να μεταβάλλουν τις ήδη υπάρχουσες), ιδίως μάλιστα εάν αυτές συνδέονται με την αποδοτικότητα μετάδοσης της νόσου της τρυπανοσωμίασης μέσω του φορέα της, δηλαδή της μύγας τσε-τσε. Τέλος, διαπιστώθηκε πιθανή αρνητική συσχέτιση της παρουσίας του βακτηρίου Wolbachia με τον παθογόνο ιό Salivary Gland hypertrophy Virus (SGHV), γεγονός που συζητείται στα πλαίσια βιολογικών εφαρμογών καταπολέμησης του εντόμου-φορέα και της τρυπανοσωμίασης. Παράλληλα, μεγάλο ενδιαφέρον παρουσιάζει η προοπτική χρησιμοποίησης του βακτηρίου Wolbachia για τη βιολογική καταπολέμηση εντόμων αγροτικής ή /και περιβαλλοντικής σημασίας, όπως είναι οι αφίδες και η καρπόκαψα καστανιάς. Το γεγονός αυτό προϋποθέτει την ανίχνευση και τη γενετική ταυτοποίηση του βακτηρίου σε φυσικούς πληθυσμούς εντόμων. Στα πλαίσια της παρούσας διατριβής πραγματοποιήθηκε ανίχνευση και χαρακτηρισμός του βακτηρίου Wolbachia σε 78 συνολικά άτομα από 22 είδη αφίδων, από 26 φυσικούς πληθυσμούς από την Ελλάδα. Από αυτούς τους 26 πληθυσμούς, μόλις οι 4 βρέθηκαν να είναι μολυσμένοι με το βακτήριο Wolbachia και συγκεκριμένα πληθυσμοί των ειδών: Aphis fabae, Aphis hederae, Metopolophium dirhodum και Baizongia pistaciae. Τα αποτελέσματα αυτά δείχνουν για πρώτη φορά ότι η παρουσία του βακτηρίου Wolbachia στις αφίδες είναι πιθανά πιο διαδεδομένη από ότι προέκυπτε από προηγούμενες μελέτες. Επίσης, μελετήθηκε η ανίχνευση και ο χαρακτηρισμός του βακτηρίου Wolbachia στα είδη Cydia splendana, Cydia fagiglandana και Pammene fasciana. Το βακτήριο Wolbachia ανιχνεύθηκε για πρώτη φορά στα συγκεκριμένα είδη και μάλιστα διαπιστώθηκε ότι η συχνότητα εμφάνισής του ποικίλει τόσο μεταξύ των δύο ειδών Cydia όσο και μεταξύ των πληθυσμών του κάθε είδους. Στο είδος Pammene fasciana, το βακτήριο ανιχνεύθηκε σε όλα τα άτομα που μελετήθηκαν. Τα αποτελέσματα της παρούσας διατριβής συζητούνται από τη σκοπιά τόσο της οικολογικής και εξελικτικής σημασίας τους όσο και της προοπτικής χρησιμοποίησης του συμβιωτικού βακτηρίου Wolbachia για τον πληθυσμιακό έλεγχο επιβλαβών εντόμων όπως οι μύγες τσε-τσε, οι αφίδες και η καρπόκαψα καστανιάς.<br>Wolbachia is an intracellular and maternally inherited symbiotic bacterium that belongs to the class of Alphaproteobacteria and the order of Rickettsiales. It is the most ubiquitous intracellular symbiotic organism of the planet, since it has been estimated that over 40% of insect species, in addition to filarial nematodes, crustaceans, and arachnids are infected with Wolbachia. In arthropods Wolbachia affects the biological functions and properties of its hosts and it is responsible for a number of reproductive abnormalities, such as cytoplasmic incompatibility (CI), thelytokous parthenogenesis, feminization of genetic males and male killing. These unique biological characteristics of Wolbachia are attracting the interest of various researchers for: (a) decyphering the role of Wolbachia in evolutionary processes (mainly speciation), and (b) for its use in environmentally friendly applications for the control of agricultural pests and disease vectors. The species of genus Glossina (Diptera: Glossinidae) known as tsetse flies, have been found to be infected with Wolbachia. Tsetse flies are the sole vectors of pathogenic trypanosomes in tropical Africa, causing the “sleeping sickness” in humans and the “nagana” in animals. The potential use of Wolbachia for the control of tsetse flies, prerequisite a thorough knowledge of its genetic identity and the interactions with the host. To further characterize the prevalence of Wolbachia in tsetse flies an extensive screen of more than 5300 specimens from natural and laboratory populations of 11 different Glossina species originating from 13 African countries was carried out. Our results indicated a huge divergence in the prevalence of Wolbachia, both among the species and among populations of the same species. Further characterization by MLST and wsp genotyping was carried out for the Wolbachia strains of 29 representative populations and species of tsetse flies. An impressive genetic diversity of Wolbachia strains in tsetse flies was revealed. Interestingly, disconcordance between the phylogeny of Wolbachia and that of the tsetse flies was observed, suggesting horizontal transmission of Wolbachia during the evolution. Moreover, extended horizontal gene transfer events were detected for first time in Glossina morsitans morsitans, Glossina pallidipes και Glossina austeni. These results raise critical questions concerning: (a) the origin/mechanism of these horizontal gene transfer events, (b) their temporal determination, (c) their potential role as agents of speciation and (d) their selective appearance in only some Glossina species e.g in the subspecies Glossina morsitans centralis which is closely related with Glossina morsitans morsitans the phenomenon was not observed. Equally important will be to examine if genes from the chromosomal insertions were potentially expressed and examine if these genes are associated with the vectorial capacity of tsetse flies for the trypanosoma transmission. Finally, a negative correlation between the presence of Wolbachia with the Salivary Gland Hypertrophy Virus (SGHV) was identified. This is further discussed in the context of biological applications for control of tsetse fly-vector and trypanosomiasis. Finally in this thesis, the detection and characterization of Wolbachia in 78 specimens of 22 aphids species, from 26 natural populations, from Greece was examined. Only 4 out of 26 populations were found to be infected with Wolbachia, and specifically the species: Aphis fabae, Aphis hederae, Metopolophium dirhodum και Baizongia pistaciae. These results indicated that the presence of Wolbachia in aphids is probably more prevalent than it was derived from previous studies. Also, detection and characterization of Wolbachia in the Cydia splendana, Cydia fagiglandana and Pammene fasciana was carried out. Wolbachia was detected for first time in these species, and it was found that the prevalence of Wolbachia varies between the two species of Cydia and among populations of each species, with the infection in Pammene fasciana being fixed. At the end the ecological and evolutionary importance of Wolbachia, together with the use of the bacterium for the population control of harmful insects like tsetse flies, aphids and moths is further discussed.