Phytophthora cinnamomi is an important pathogen of many plant species in natural ecosystems and horticulture industries around the world. In Western Australia, a high proportion of native plant species are susceptible to P. cinnamomi attack. Acacia pulchella, a resistant legume species native to Western Australia has been considered as a potential biological control tool against P. cinnamomi. To develop effective control methods, it is important to understand the interactions between the control agent and the different life forms of the pathogen. In this thesis the interactions are investigated between P. cinnamomi and varieties of A. pulchella which occur in jarrah (Eucalyptus marginata) forest and sand plain ecosystems. The soil inoculum of P. cinnamomi was compared under the potted plants of the three common varieties of A. pulchella, var. pulchella, var. glaberrima and var. goadbyi. These were grown in infected jarrah forest soil in the glasshouse and in vitro in a sterilised soil-less mix aseptically. Acacia urophylla (a species non suppressive towards P. cinnamomi) was also included as a control. An isolate of the most commonly found clonal lineage of P. cinnamomi in the jarrah forest, A2 type 1 was selected for use in experiments after testing showed it reliably produced zoospores and chlamydospores both axenically and in non-sterile conditions, in comparison to several other isolates. The lowest survival of P. cinnamomi inoculum was found under A. pulchella var. goadbyi plants grown both in non sterile soil and in aseptic soil-less mix. All the life forms of P. cinnamomi were affected by A. pulchella (Chapters 2, 3, 4 and 5). The soil leachates from potted plants of A. pulchella var. goadbyi reduced sporangial production (Chapter 2) and caused cytoplasm collapse of chlamydospores (Chapter 3). The confirmation was obtained that soil under A. pulchella was inhibitory to sporangial stage of P. cinnamomi and new evidence was obtained on chlamydospore inactivation. Cytoplasm collapse in the chlamydospores was observed both for chlamydospores on mycelial discs on Mira cloth exposed to the soil leachate and within infected roots buried in soils under the three varieties of A. pulchella plants. The effect was strongest under the plants of A. pulchella var. goadbyi and indicated that the chlamydospores of P. cinnamomi are unlikely to act as persistent structures under A. pulchella var. goadbyi plants. In Chapter 4, bioassays were conducted with axenically produced mycelia, chlamydospores and zoospores to test the inhibitory effect of the root exudates collected from aseptically grown A. pulchella var. goadbyi plants. The zoospores of the same isolate used in the soil leachate tests were immobilised (became sluggish and encysted) within one to two minutes. When incubated for 24 h, zoospores predominantly clumped and germ tubes were observed only from the clumped ones. Chlamydospores produced by four isolates of the common A2 type 1 strain and the only one A2 type 2 strain available at the time were tested. A higher percentage of chlamydospores collapsed and a very low percentage germinated after 24 h. Chlamydospores of all the A2 type 1 isolates were inhibited by the root exudates whilst the A2 type 2 isolate remained viable. The findings showed that the suppressive effect must be due at least in part to substances exuded by the A. pulchella plants. However, it appeared that the A2 type 1 isolates were more vulnerable to this effect than the single A2 type 2 isolate. In Chapter 5, the effect of season on sporangial suppression of P. cinnamomi was shown using field soils collected from three jarrah forest soil vegetation types and a Banksia woodland on Bassendean sand, collected in winter and summer. The effect of age of A. pulchella plants was demonstrated using the soils collected from rehabilitated bauxite mine pits. In all the locations soils were collected under A. pulchella plants and 5 m away from the nearest A. pulchella. An effect of soil type was evident as whilst the soil leachates made from the three lateritic jarrah forest soil types where A. pulchella is common in the understorey were suppressive to the sporangial stage of P. cinnamomi, this effect was not evident in the Bassendean sand under A. pulchella. A. pulchella soils collected in winter were less suppressive towards sporangial production than soils collected in summer. An effect of plant age was demonstrated as soil leachates from four year-old A. pulchella stands in rehabilitated bauxite mine sites were more suppressive for sporangia than leachates from one year-old stands. Further information on the behaviour of the pathogen in soil and in potting mix with and without A. pulchella was obtained by infecting lupin radicles with an isolate of each A2 type, 1 and 2 strains of P. cinnamomi and burying them in the soil under the three varieties of A. pulchella plants. After a week, the chlamydospores were mostly collapsed and hyphae deteriorated. Oospores were observed and in significant numbers under the potted plants of A. pulchella var. glaberrima. Isolates of all three clonal lineages of P. cinnamomi found in Australian soil were tested for the ability to produce oospores. Two isolates of the A1 and A2 type 2 and three isolates of the common A2 type 1 were screened. The two isozyme types of the A2 clonal lineage isolated in Australia varied in ability to self and produce oospores in planta in several soils from the jarrah forest. The isozyme type 2 of the A2 clonal lineage of P. cinnamomi produced oospores under these experimental conditions. This stimulation was not effective for most of the tested isolates of the A2 type 1 and the A1 clonal lineage. The in planta oospores were viable but dormant and the oogonial-antheridial associations were amphigynous both in vitro and in vivo. For the first time it was established that, the stimulus for selfing and oospore formation in the A2 type 2 of P. cinnamomi is available in some jarrah forest soils, with and without A. pulchella and also in the potting mix used. This raises important questions for the management of the pathogen. Several factors were identified as potential stimuli for selfing. Among them, soil nutrient levels and essentially enhanced sulphur presence were found important. Temperature also played a key role. Oospores were produced abundantly at 21 – 25 ºC but not over 28 ºC. The biology of P. cinnamomi has been studied for several decades but some important aspects remain un-researched. This thesis pioneers research into the in planta selfing aspect of the pathogen in soil. It also improved the understanding of the interactions between P. cinnamomi and A. pulchella which to some extent supports use of A. pulchella as a biological control tool against P. cinnamomi. However, attention is drawn to the natural mechanisms of this complex pathogen to survive in planta by producing oospores, the most persistent form of its life cycle.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniversitet, 2005. / Härtill 5 uppsatser.

Thesis (M.S.)--Virginia Polytechnic Institute and State University, 1993. / Includes bibliographical references (leaves 84-91). Also available via the Internet.

The aim of this thesis was to assess the effect of root exudates on the biodegradability of dissolved organic matter. The experiment was done in laboratory conditions, using the dissolved organic matter sampled in a spruce swamp forest located in Šumava National Park and an artificial mixture of root exudates prepared according to known composition of root exudates released by peatland plants. Main hypothesis was that the input of root exudates into the peatland pore water will affect decomposition of less-degradable dissolved organic matter, with the resulting effect dependent on the quantity and quality (C:N ratio) of the input.

nÃo hà / Imagens de fundo de olho constituem um valioso recurso para o diagnÃstico mÃdico, pois muitas vezes apresentam indicaÃÃes de doenÃas oftÃlmicas como as da retina e atà mesmo doenÃas sistÃmicas como diabetes, hipertensÃo e arteriosclerose. Esta tese trata de algoritmos de detecÃÃo de estruturas como a fÃvea, mÃcula, exsudatos e disco Ãptico (DO) em imagens de retina. Em se tratando de algoritmos de detecÃÃo da fÃvea em imagens coloridas de retina, propomos um algoritmo assim como conjunto de regras para avaliaÃÃo dos mesmos. A detecÃÃo automÃtica desta estrutura anatÃmica à um prÃ-requisito para o diagnÃstico auxiliado por computador de vÃrias doenÃas da retina, como a degeneraÃÃo macular. Entretanto, as pequenas dimensÃes e baixo contraste da fÃvea dificultam a execuÃÃo desta tarefa de detecÃÃo. O algoritmo proposto determina a regiÃo de interesse levando em consideraÃÃo as coordenadas do DO e o fato da fÃvea ser uma Ãrea escura, homogÃnea e sem presenÃa de vasos sanguÃneos. Em seguida, o mÃtodo realiza a etapa de segmentaÃÃo dos vasos e pesquisa pela janela com menor mÃdia de intensidade de cor na imagem resultante da fusÃo entre os canais vermelho e verde. Os testes do algoritmo de detecÃÃo da fÃvea foram realizados em trÃs bases de imagens pÃblicas de referÃncia ARIA, DRIVE e MESSIDOR. Neste trabalho, propomos ainda um algoritmo de detecÃÃo de exsudatos em imagens de retina. A metodologia proposta combina agrupamento nebuloso e tÃcnicas de morfologia matemÃtica. Os resultados confirmam a melhoria no desempenho do mÃtodo de detecÃÃo quando comparado aos mÃtodos disponÃveis na literatura. Portanto, comparamos os resultados de seis algoritmos automÃticos de detecÃÃo do DO disponÃveis na literatura, utilizando dados de referÃncia das bases pÃblicas ARIA, STARE, DRIVE e MESSIDOR. O objetivo era determinar a robustez dos mesmos em detectar o DO em imagens de retina saudÃveis e com a presenÃa de patologias. Observamos que em geral os mÃtodos de detecÃÃo de DO que apresentam melhor desempenho o fazem em bases menos desafiadoras como as duas Ãltimas, ou seja, eles alcanÃam as maiores taxas de acerto. / Fundus images are valuable resource in diagnosis because they often present indications about retinal, ophthalmic, and even systemic diseases such as diabetes, hypertension, and arteriosclerosis. This thesis focuses on algorithms to detect fovea, exudates and optic disk (OD) in retina images. Regarding fovea detection algorithms in colored retina images, we propose an algorithm and furthermore a set of rules to assess them. Automatic detection of this anatomical structure is a prerequisite for computer-aided diagnosis of several retinal diseases, such as macular degeneration. However, the small dimension and weak contrast of the fovea area on retina images make difficult this task detection, directly. The proposed algorithm determines a region of interest taking into account OD coordinates and the fact that the fovea is a homogeneous dark area without blood vessels. Then, the method performs the vessel segmentation step and searches for the lowest mean color intensity window in the image that results from the fusion between the red and green channels. Tests were carried out on three public benchmark databases. In addition, this thesis proposes an algorithm for exudate detection in retina images. The proposed methodology combines fuzzy clustering and mathematical morphology techniques. The results confirm the performance improvement provided by the proposed methodology, when comparing it to other methods available in the literature. In this work, we compare the results of six different automatic algorithms for OD detection, using the public benchmark image database named ARIA, STARE, DRIVE and MESSIDOR. We aimed to test the robustness of the algorithms in detecting the OD in healthy and pathological retina images. In general, we observed that these methods performed better in less challenging databases as the two last ones, i.e. they achieved the highest success rates in DRIVE and MESSIDOR.

Orientador: Marcia Regina Braga / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-12T18:52:46Z (GMT). No. of bitstreams: 1 Simoes_Kelly_D.pdf: 3512548 bytes, checksum: 21ccb89a97ae81d965d0171998569c9e (MD5) Previous issue date: 2008 / Resumo: Sesbania virgata (Cav.) Pers. e Hymenaea courbaril L. var. stilbocarpa (Fabaceae) são duas espécies tropicais que acumulam, respectivamente, galactomanano e xiloglucano como polissacarídeos de reserva nas sementes, os quais são mobilizados logo após protrusão da radícula, gerando grande quantidade de monossacarídeos e oligossacarídeos. Parte desses açúcares é liberada para o meio, sem que haja, contudo, contaminações por microrganismos. Estudos prévios indicaram que exsudatos dessas sementes apresentam substâncias com atividade antifúngica e fitotóxica e sugeriram também que oligossacarídeos oriundos da degradação do galactomanano agem como moléculas sinalizadoras de mecanismos de defesa em plantas. Entretanto, a liberação, natureza química e atividade biológica desses compostos ainda não haviam sido estudadas. Dessa forma, este trabalho teve por objetivos elucidar as estruturas químicas e estudar a exsudação de substâncias fitotóxicas e antifúngicas por sementes de S. virgata e H. courbaril, assim como, verificar a possível influência de oligossacarídeos derivados de galactomanano na produção desses metabólitos ativos em S. virgata. As sementes de S. virgata e H. courbaril foram germinadas em câmaras climatizadas à 25º C e fotoperíodo de 12 h e seus exsudatos foram coletados em diferentes períodos do processo de embebição, sendo posteriormente submetidos à bioensaios de fitotoxicidade com sementes de alface (Lactuca sativa L.) e de tomate (Solanum lycopersicum L.). Para o isolamento de compostos ativos, extratos dos exsudatos e extratos das sementes foram obtidos em larga escala através de extrações com solventes orgânicos, sendo, posteriormente, fracionados em colunas de gel de sílica utilizando gradientes de diclorometano e MeOH. As frações coletadas foram ensaiadas quanto a sua atividade fitotóxica em plântulas de Arabidopsis thaliana L. e de arroz (Oryza sativa L.) cultivadas in vitro. A atividade antifúngica dos extratos e frações foi determinada por métodos de bioautografia e microdiluição in vitro com fungos filamentosos e leveduras. As substâncias isoladas foram identificadas e caracterizadas por técnicas de 13C RMN e 1H RMN (1-D e 2-D). Quantificação e detecção de compostos também foram realizadas por análises em HPLC, HPLCMS e GC-MS. Os resultados obtidos demonstraram que ambas as sementes exsudam metabólitos secundários antifúngicos e fitotóxicos logo no início do processo de embebição. O flavonóide (+)-catequina é a principal fitotoxina dos exsudatos das sementes de S. virgata, sendo encontrada no tegumento das sementes e liberada em altas concentrações no primeiro dia de embebição. Quercetina também foi encontrada no tegumento das sementes de S. virgata, mas não é exsudada durante a germinação. Análises cromatográficas sugeriram a presença do alcalóide sesbanimida A nos extratos do embrião e nos exsudatos de S. virgata, como a principal substância antifúngica presente. Sementes de S. virgata embebidas em soluções contendo oligossacarídeos de galactomanano exsudaram maior quantidade de (+)-catequina do que aquelas embebidas apenas em água destilada, sugerindo que esses oligossacarídeos possam atuar como oligossacarinas sinalizadoras. Duas bicumarinas, a ipomopsina, anteriormente extraída de outra espécie vegetal e a himenaína, uma bicumarina inédita, foram isoladas de extratos do embrião das sementes de H. courbaril. Esses metabólitos também são exsudados durante a germinação e apresentam toxicidade às raízes de plântulas de A. thaliana quando co-aplicados e não apresentam atividade antifúngica, com exceção da escopoletina, também detectada nestes extratos. Entretanto, essas substâncias apresentaram atividade antioxidante, sendo himenaína a que apresentou maior capacidade seqüestradora do radical livre DPPH, sugerindo o envolvimento desses compostos na proteção a danos causados por radicais livres. Os dados obtidos neste trabalho sobre a atividade fitotóxica, antifúngica e antioxidante dos metabólitos isolados das sementes de S. virgata e H. courbaril sugerem que eles podem funcionar como estratégias adaptativas que contribuem para o sucesso do estabelecimento inicial dessas espécies. / Abstract: Sesbania virgata (Cav.) Pers. and Hymenaea courbaril L. var. stilbocarpa (Fabaceae) are two tropical legume species with seeds that contain galactomannan and xyloglucan, respectively, as seed storage polysaccharides, which are broken down after germination, generating large amounts of monosaccharides and oligosaccharides. Part of these sugars is released to the environment, but no contamination is observed. Previous studies demonstrated that these seed leachates have antifungal and phytotoxic activity and also suggested that oligosaccharides derived from galactomannan can act as signaling molecules in plant defense mechanisms. However, exudation, chemical structure and biological activities of the compounds have not been studied. Therefore, the aims of this work were to study the release of the bioactive compounds from seeds of S. virgata and H. courbaril, to elucidate their chemical structure and to analyze the influence of galactomannan oligosaccharides on the production of these substances in S. virgata. Seeds of S. virgata and H. courbaril were germinated at 25º C and photoperiod of 12 h, and the leachates were collected at different periods of the imbibition process, and submitted to phytotoxic bioassays with seeds of lettuce (Lactuca sativa L.) and tomato (Solanum ycopersicum L.). For compound isolation, extracts of seeds and leachates were obtained in large amounts and fractionated in silica gel columns with different gradient of dichloromethane and methanol. The fractions collected were assayed in vitro with seedlings of Arabidopsis thaliana L. and rice (Oryza sativa L.). The antifungal activity of the extracts and fractions were determined by bioautography and microdilution tests. The compounds were identified and characterized by 13C NMR and 1H NMR (1-D and 2-D) techniques. Compounds were also detected and quantified by HPLC, HPLC-MS and GC-MS. Our results showed that both seeds exude antifungal and phytotoxic metabolites at the beginning of imbibition process. The flavonoid (+)-catechin is the major phytotoxin in the S. virgata seed exudates, being found in the seed coat and leached in high amounts at the first day of imbibition. Quercetin was also found in the seed coat of S. virgata seeds, but it is not released during germination. The alkaloid sesbanimide A was detected in the embryo and exudates extracts of S. virgata, being the most important antifungal compound found in the extracts. Seeds of S. virgata imbibed with a galactomannan oligosaccharide solution leached more (+)-catechin than those imbibed in distilled water, suggesting that these molecules can act as oligosaccharins. Two biscoumarin, ipomopsin, previously reported in other plant species, and hymenain, a novel one, were identified in embryo extracts of H. courbaril. These compounds are also released by the seeds during germination, and showed a phytotoxic effect on roots of A. thaliana seedlings when co-applied, but they have not antifungal activity. Escopoletin were also detected in the embryo extracts, and showed antifungal activity to Cladosporium sphaerospermum Pemzig. Additionally, the biscoumarin and scopoletin, showed antioxidant activity, hymenain being the substance with higher scavenger activity to DPPH free radical, suggesting its involvement in the protection of the cells against free radical damages. Our findings related to the phytotoxic, antifungal, and antioxidant activities of metabolites isolated from seeds of S. virgata and H. courbaril suggest that they could act as adaptive strategies that contribute to the success of the initial establishment of these species. / Doutorado / Biologia Celular / Doutor em Biologia Celular e Estrutural

Copper oxide nanoparticles (NPs) are used in an expanding range of industries including a potential for agricultural applications as a fungicide. Accidental spills or misapplication of CuO NPs may lead to soil contamination. Plant roots exude a wide range of organic chemicals for bioprotection and to enhance bioavailability of nutrients. Many of these chemicals are metal chelators that may increase the solubility of CuO NPs, thus enhancing the impact of these NPs on plants. This work was directed towards understanding which plant exudates force increased solubility of CuO NPs and to determine if the level of NP in the growth matrix drives a feedback effect, regarding composition and quantity of exudates. Wheat seedlings (Triticum aestivum cv Deloris) were grown in a sand matrix for 10 days after 3 days of germination. The sand was amended with sublethal doses of CuO NPs from 0 to 300 mg Cu/kg dry sand. Sand was selected as the solid growth matrix as a proxy for soil in terms of plant root morphology, mechanical impedance and water stress, while providing a low background of dissolved organic carbon for the isolation of root exudates. After plant growth, the pore water was collected from the sand by vacuum filtration and analyzed. By coupling analytic techniques including Triple Quad Mass Spectroscopy and ion chromatography with geochemical modeling, we have identified citrate and the phytosiderophore, deoxymugineic acid (DMA) as chelators that drove the majority of dissolution of CuO NPs, especially DMA at higher CuO NP doses. Altered biogeochemistry within the rhizosphere was correlated with increased plant uptake of Cu and bio-response via exudate type, quantity and metal uptake. Exposure of wheat to CuO NPs lead to dose-dependent reduction in Fe, Ca, Mg, Mn and K in roots and shoots. This work is relevant to growth of commercially important crop wheat in the presence of CuO NPs as a fertilizer, fungicide or a pollutant.

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第21150号 / 農博第2276号 / 新制||農||1059(附属図書館) / 学位論文||H30||N5124(農学部図書室) / 京都大学大学院農学研究科地域環境科学専攻 / (主査)教授 北山 兼弘, 教授 小杉 緑子, 教授 本田 与一 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

Wheat (Triticum aestivum) is a crop that dominates the diets of about 35% of the world's human population. But wheat yields can be severely affected by drought. Therefore, in this experiment, root exudation of winter wheat was compared to find out how exudation changes during drought stress. This was done by using control plants that were compared to plants that experienced 8 days of drought and subsequently, 3 days of rewetting. Moreover, it was explored which one of two wheat genotypes, Capo or Aristaro, is better adapted to drought by measuring plant physiology and if beneficial rhizosphere microorganisms could help alleviate drought in wheat. Exudations were analysed using a photometer. It was found that drought and rewetting treatment influenced shoot dry weight, shoot water content, relative chlorophyll, as well as exuded phenols, sugars and amino acids. Aristaro was found to be more drought tolerant, because Aristaro plants had higher and more stable shoot water content, lower non-photochemical quenching (NPQ(T)), and exuded more phenols and amino acids, which could help recruit plant-growth promoting rhizobacteria. However, Capo might be able to avoid drought through early maturity and can therefore be used in regions where drought occurs later in the year. The implications of this experiment are therefore useful for improving wheats resilience to drought and food security with use of microorganisms.

Monospecific stands of invasive plant species are found in nearly all known ecosystems and can cause permanent lasting ecosystem damage via deleterious effects in soils. These deleterious soil effects are a proposed mechanism which drives invasions by plants and are known to be influenced by kin recognition in plants. Uncovering whether invasive species utilize kin recognition to facilitate their own ecological persistence via soil conditioning will allow us to better understand the drivers of plant invasions and help combat them. In my master’s thesis, I examined the role of kin recognition and kin selection on soil effects. I grew groups of Potentilla recta in groups of maternal half-sibs or strangers to condition the soil. I then grew a second generation of plants in that conditioned soil to determine the impacts of soil conditioning effects on plant performance. I found soil conditioning by groups of plants affected the performance of a second generation of plants based on the relatedness of the conditioning plants. Further, these soil effects of conditioning selectively benefit future individuals of a subsequent generation based on their relatedness. Moreover, these soil effects only existed in soil that has not been sterilized, indicating these soil effects depended on soil microbes. / Thesis / Master of Biological Science (MBioSci) / Invasive plants form dense stands of same-species individuals that can cause lasting deleterious effects to the soil. These deleterious soil effects have been proposed as a mechanism driving plant invasions. In my master’s thesis, I examined the role of kin recognition and kin selection on soil effects. I first grew groups of Potentilla recta in groups of maternal half-sibs or strangers to condition the soil, and then grew a second generation of plants in that conditioned soil to determine the impacts on plant performance. I found that soil influenced by groups of related plants affect increased the performance of a second generation of plants, particularly if the second generation was related to the first. Moreover, these soil effects only existed in soil that has not been sterilized, indicating these soil effects depended on soil microbes. I found that these soil effects of conditioning selectively benefited future individuals of a subsequent generation based on their relatedness.