Letteratura scientifica selezionata sul tema "Sols suppressifs"

Abstract To understand the role of Los1p in pre-tRNA splicing, we sought los1 multicopy suppressors. We found SOLl that suppresses both point and null LOS1 mutations. Since, when fused to the Gal4p DNA-binding domain, Los1p activates transcription, we tested whether Los1p regulates SOL1. We found that los1 mutants have depleted levels of SOL1 mRNA and Sollp. Thus, LOS1 appears to positively regulate SOL1. SOL1 belongs to a multigene family with at least two additional members, SOL2 and SOL3. Sol proteins have extensive similarity to an unusual group of glucose-6phosphate dehydrogenases. As the similarities are restricted to areas separate from the catalytic domain, these G6PDs may have more than one function. The SOL family appears to be unessential since cells with a triple disruption of all three SOL genes are viable. SOL gene disruptions negatively affect tRNA-mediated nonsense suppression and the severity increases with the number of mutant SOL genes. However, tRNA levels do not vary with either multicopy SOL genes or with SOL disruptions. Therefore, the Sol proteins affect tRNA expression/function at steps other than transcription or splicing. We propose that LOS1 regulates gene products involved in tRNA expression/function as well as pre-tRNA splicing.

Previous studies have shown that various Eucalyptus species can yield allelopathic chemicals which may be effective in suppressing understorey vegetation. However, the techniques employed in many studies do not resemble natural ecological processes. This study used germination of Lolium and growth of Lolium, Lemna, Eucalyptus and Acacia to test for allelopathy. Extraction techniques mimicked typical daily rainfall rates upon quantities of foliage, leaf litter and bark litter that are typically encountered in forests; root leachates were obtained hydroponically; stemflow was obtained following rainfall; soils were leached with water; and volatiles from leaves were studied in an enclosed chamber. Fresh intact leaves caused little growth suppression, in contrast to coarsely chopped leaves and extracted leaf essential oils which were both highly suppressive. Whole leaf litter, shed bark and, especially, stemflow yielded suppressive leachates. Evaporative concentration of leachates in soils was demonstrated, which increased their inhibitory effect. It is apparent that allelopathy must be considered in relation to rainfall and the soil water balance. Decay was shown to reduce the allelopathic effects of leaf and bark litter leachates but some inhibitory chemicals remained after 5 months. It was concluded that allelopathy is likely to be a cause of understorey suppression by Eucalyptus species especially in drier climates.

Diseases remain a yield-limiting factor for crops despite the availability of control measures for many pathogens. Indigenous soil microorganisms can suppress some plant pathogens, yet there is little systematic information on the effects of cropping systems on disease-suppressive populations in soil. Streptomyces have been associated with suppression of plant diseases in several naturally occurring disease-suppressive soils. Pathogen-suppressive activity of Streptomyces communities is correlated with higher bacterial densities and with inhibitory phenotypes, driven by competition among indigenous soil bacteria. We sought to characterize relationships between cropping practices and pathogen suppression among soil Streptomyces. We evaluated bacterial and Streptomyces densities and inhibitory activities in soils from a long-term crop rotation experiment. Signaling interactions that altered inhibitory phenotypes among sympatric populations were also evaluated for a subset of samples. Soils from longer rotations, which had a higher number of plant species over time, had larger bacterial and Streptomyces densities, and more inhibitors than soils from shorter rotations. In addition, signaling occurred more frequently among isolates from higher-density communities. Our work shows that bacterial density, pathogen suppression and signaling are interrelated and are affected by crop rotation, suggesting the potential for management to optimize suppressive populations.

Soils suppressive to soilborne pathogens have been identified worldwide for almost 60 years and attributed mainly to suppressive or antagonistic microorganisms. Rather than identifying, testing and applying potential biocontrol agents in an inundative fashion, research into suppressive soils has attempted to understand how indigenous microbiomes can reduce disease, even in the presence of the pathogen, susceptible host, and favorable environment. Recent advances in next-generation sequencing of microbiomes have provided new tools to reexamine and further characterize the nature of these soils. Two general types of suppression have been described: specific and general suppression, and theories have been developed around these two models. In this review, we will present three examples of currently-studied model systems with features representative of specific and general suppressiveness: suppression to take-all (Gaeumannomyces graminis var. tritici), Rhizoctonia bare patch of wheat (Rhizoctonia solani AG-8), and Streptomyces. To compare and contrast the two models of general versus specific suppression, we propose a number of hypotheses about the nature and ecology of microbial populations and communities of suppressive soils. We outline the potential and limitations of new molecular techniques that can provide novel ways of testing these hypotheses. Finally, we consider how this greater understanding of the phytobiome can facilitate sustainable disease management in agriculture by harnessing the potential of indigenous soil microbes.

Cover crops are an important component of integrated weed management programs in annual and perennial cropping systems because of their weed suppressive abilities. They influence weed populations using different mechanisms of plant interaction which can be facilitative or suppressive. However, the question often arises if cover crops can be solely relied upon for weed management or not. In this review we have tried to provide examples to answer this question. The most common methods of weed suppression by an actively growing cover crop include competition for limited plant growth resources that result in reduced weed biomass, seed production, and hence reductions in the addition of seeds to the soil seedbank. Cover crop mulches suppress weeds by reducing weed seedling emergence through allelopathic effects or physical effects of shading. However, there is a great degree of variability in the success or failure of cover crops in suppressing weeds that are influenced by the cover crop species, time of planting, cover crop densities and biomass, time of cover crop termination, the cash crop following in the rotation, and the season associated with several climatic variables. Several studies demonstrated that planting date was important to achieve maximum cover crop biomass, and a mixture of cover crop species was better than single cover crop species to achieve good weed suppression. Most of the studies that have demonstrated success in weed suppression have only shown partial success and not total success in weed suppression. Therefore, cover crops as a sole tool may not be sufficient to reduce weeds and need to be supplemented with other weed management tools. Nevertheless, cover crops are an important component of the toolbox for integrated weed management.

In disease-suppressive soils, microbiota protect plants from root infections. Bacterial members of this microbiota have been shown to produce specific molecules that mediate this phenotype. To date, however, studies have focused on individual suppressive soils and the degree of natural variability of soil suppressiveness remains unclear. Here, we screened a large collection of field soils for suppressiveness to Fusarium culmorum using wheat ( Triticum aestivum ) as a model host plant. A high variation of disease suppressiveness was observed, with 14% showing a clear suppressive phenotype. The microbiological basis of suppressiveness to F. culmorum was confirmed by gamma sterilization and soil transplantation. Amplicon sequencing revealed diverse bacterial taxonomic compositions and no specific taxa were found exclusively enriched in all suppressive soils. Nonetheless, co-occurrence network analysis revealed that two suppressive soils shared an overrepresented bacterial guild dominated by various Acidobacteria. In addition, our study revealed that volatile emission may contribute to suppression, but not for all suppressive soils. Our study raises new questions regarding the possible mechanistic variability of disease-suppressive phenotypes across physico-chemically different soils. Accordingly, we anticipate that larger-scale soil profiling, along with functional studies, will enable a deeper understanding of disease-suppressive microbiomes.

Soils in which disease fails to develop despite pathogen presence are considered disease-suppressive. They offer sustainable, effective protection to plants against infection by soil-borne pathogens. Naturally disease-suppressive soils have been reported for diseases of a diverse range of agricultural crops worldwide yet the underlying mechanisms of disease suppression are still not completely understood. Two large greenhouse experiments, conducted during 2017/18 (Year 1) and 2018/19 (Year 2), determined that soils naturally suppressive to stem canker and black scurf of potato (caused by Rhizoctonia solani) are present in vegetable-arable cropping soils of the Auckland and Waikato regions of New Zealand. Soil was pre-treated with heat prior to inoculation with R. solani and compared with untreated and uninoculated controls to ascertain if stem canker and black scurf suppression was ‘general’, or ‘specific’ (i.e. transferable; possibly involving specific microorganisms). Rhizoctonia solani inoculation was also combined with transfer of one part test soil to nine parts of a known disease-conducive soil. Abiotic factors such as soil texture and organic matter content influenced black scurf incidence and severity. Soil microorganisms were also involved in disease suppression since black scurf incidence and severity markedly increased when they were eliminated or reduced by soil heat pre-treatment. Microbial profiling of the soils through sequencing revealed that taxa of geographically close soils of the same type had similar fungal and bacterial community structure and diversity even though they differed in their capacity to suppress black scurf. These results suggest that although the soil microbiome as a whole, was mainly responsible for soil disease suppressiveness, certain bacterial genera or species may play a role in black scurf suppression.

Abstract We have previously reported that IL-4 suppresses the response of murine myeloid dendritic cells (mDCs) to Type I interferons (IFN). We are now investigating the molecular mechanisms of this inhibition in myeloid bone marrow-derived DCs (BMDCs). We have found that sub-optimal doses of IL-4 (down to 0.25ng/mL) can still suppress IFN-a induced gene expression and phosphorylation of STAT1 and STAT2, suggesting that IL-4 acts at the level or upstream of STAT molecules in the Type I IFN signaling pathway. IL-4 suppresses when administered before and also after Type I IFN stimulation and it inhibits the response of DCs to the autocrine IFN-b that is induced upon IFN-a stimulation, acting on its positive feedback loop. The inhibition of protein synthesis by Cyclohexamide (CHX) abrogated the suppressive effects of IL-4 indicating that IL-4 represses Type I IFN signaling through the upregulation of a protein. We then tested the expression of the SOCS molecules as immediate candidates that negatively regulate Type I IFN signaling and are regulated at the transcription level. The gene expression of SOCS-1was highly induced by IL-4 treatment and was synergistically upregulated in the presence of IL-4 and IFN-a; the levels drastically went down when DCs were pretreated with CHX, suggesting that SOCS-1 maybe one of the key players in suppressing the IFN responses. We are currently testing this hypothesis by silencing SOCS-1 expression in DCs.

A soil acidified by ammonium sulphate following annual application of the fertilizer for 9 years was suppressive of the saprophytic growth of Gaeumannomyces graminis var. tritici in soil (pathogen suppressive). The same soil amended with lime was pathogen conducive. In natural field soil microbial respiration and the 'total' number of aerobic microorganisms were greater in the conducive than in the suppressive soil. In a soil-sandwich bioassay of the transferable suppression of saprophytic growth of the pathogen there were higher numbers of 'total' aerobic microorganisms, fluorescent pseudomonads, and Gram-negative organisms, but lower numbers of filamentous fungi and yeasts in the conducive than in the suppressive soil. It was estimated that Trichoderma spp. made up 71 and 34% of the total numbers of fungi counted in the suppressive and conducive soils, respectively. It is proposed that Trichoderma spp. played a major role in the transferable pathogen suppression in the suppressive soil.

The induction of disease-suppressive soils in response to specific cropping sequences has been demonstrated for numerous plant-pathogen systems. The role of host genotype in elicitation of the essential transformations in soil microbial community structure that lead to disease suppression has not been fully recognized. Apple orchard soils were planted with three successive 28-day cycles of specific wheat cultivars in the greenhouse prior to infestation with Rhizoctonia solani anastomosis group (AG)-5 or AG-8. Suppressiveness to Rhizoctonia root rot of apple caused by the introduced isolate of R. solani AG-5 was induced in a wheat cultivar-specific manner. Pasteurization of soils after wheat cultivation and prior to pathogen introduction eliminated the disease suppressive potential of the soil. Wheat cultivars that induced disease suppression enhanced populations of specific fluorescent pseudomonad genotypes with antagonistic activity toward R. solani AG-5 and AG-8, but cultivars that did not elicit a disease suppressive soil did not modify the antagonistic capacity of this bacterial community. When soils were infested prior to the initial wheat planting, all cultivars were uniformly susceptible to R. solani AG-8. However, when pathogen inoculum was added after three growth-cycles, wheat root infection during the fourth growth-cycle varied in a cultivar specific manner. The same wheat cultivar-specific response in terms of transformation of the fluorescent pseudomonad community and subsequent suppression of Rhizoctonia root rot of apple was observed in three different orchard soils. These results demonstrate the importance of host genotype in modification of indigenous saprophytic microbial communities and suggest an important role for host genotype in the success of biological control.

La réduction de l'utilisation des produits phytosanitaires constitue l'un des axes majeurs de la transition agroécologique. Dans ce contexte, il est urgent de développer des stratégies assurant une gestion efficace et durable de la pression parasitaire, tout en préservant l'environnement. La mobilisation du microbiome du sol, et notamment des communautés de bactéries qui le composent, représente une de ces solutions. S'il a été démontré qu'une partie de ces communautés était capable de limiter l'impact de pathogènes des cultures, les relations entre l'environnement de ce microbiome et sa capacité à réguler les maladies des plantes restent encore largement méconnus. L'ambition de ce projet de thèse était d'évaluer l'impact de facteurs, telles que les conditions pédologiques et les pratiques agricoles, sur la structure et le fonctionnement du microbiome du sol et d'analyser la relation entre ces modifications et la capacité du microbiome à participer à la régulation de la fusariose de l'épi. Ce projet s'articule autour de deux axes de recherche, visant à (1) déterminer quels facteurs expliquent le caractère suppressif des sols vis-à-vis de l'agent pathogène Fusarium graminearum, et (2) évaluer l'influence de l'environnement sur l'assemblage du microbiome du sol et du blé. Pour répondre à ces objectifs, un réseau de 103 parcelles d'agriculteurs de la plaine de Limagne (Puy-de-Dôme, France) a été mobilisé. Les parcelles représentaient une diversité de types de sols et de pratiques agricoles, et se répartissaient soit en agriculture conventionnelle, soit en agriculture biologique, soit en agriculture de conservation. Des échantillons de sol ont été prélevés dans chaque parcelle et caractérisés par (1) les pratiques agricoles (2) des analyses physico-chimiques, (3) leur communauté bactérienne par metabarcoding du gène ADNr 16S et (4) des tests d'inhibition in vitro (fongistase) du champignon pathogène Fusarium graminearum. Parmi ces 103 parcelles, 98 ont servi au prélèvement d'échantillons de rhizosphère et de racines de blé (Triticum aestivum) dont la communauté bactérienne a également été recensée. Enfin, neuf sols parmi les 103 ont été sélectionnés pour la culture et l'infection du blé par F. graminearum en conditions contrôlées. Le test de fongistase a révélé une grande variabilité au sein de l'échantillon ainsi que la capacité de certains sols à inhiber complètement la germination du champignon. Les caractéristiques pérennes du sol et la diversité bactérienne étaient liées à la fongistase des sols. Il existait aussi une corrélation entre l'abondance de Burkholderia spp. et la fongistase. La comparaison des microbiomes bactériens du sol, de la rhizosphère et des racines du blé a révélé des compositions différentes entre les trois compartiments. La composition microbienne dans les sols influençait celles de la rhizosphère et des racines dans une même parcelle. Les caractéristiques physico chimiques et le système de culture influençaient la composition de la communauté bactérienne dans les trois compartiments. L'expérimentation en conditions contrôlées n'a pas révélé de lien entre microbiome (diversité et composition) et symptômes de la fusariose, ni de lien entre fongistase et symptômes in planta sur un même sol. Dans l'ensemble, ces travaux contribuent à évaluer les possibilités d'utilisation des pratiques agricoles comme levier de contrôle agroécologique de la fusariose du blé, à travers la modulation des communautés microbiennes naturelles
Reducing the use of phytosanitary products constitutes one of the major axes of the agroecological transition. In this context, it is urgent to develop strategies ensuring effective and sustainable management of parasitic pressure, while preserving the environment. Mobilization of the soil microbiome, and particularly the bacterial community, represents one of these solutions. Although it has been demonstrated that part of these communities is capable of limiting the impact of crop pathogens, the relationships between the environment of the microbiome and its capacity to regulate plant diseases still remain largely unknown. The ambition of this thesis project was to evaluate the impact of factors, such as soil conditions and agricultural practices, on the structure and functioning of the soil microbiome and to analyze the relationship between these modifications and the capacity of the microbiome to participate in the regulation of Fusarium head blight. This project is structured around two axes of research, aiming to (1) determine which factors explain the suppressive nature of soils with respect to the pathogen Fusarium graminearum, and (2) evaluate the influence of the environment on the assembly of the soil and wheat microbiome. To meet these objectives, a network of 103 plots in the Limagne plain (Puy-de-Dôme, France) was mobilized. The plots represented a diversity of soil types and agricultural practices, and were divided into either intensive agriculture, organic agriculture, or soil conservation agriculture. Soil samples were taken from each plot and characterized by (1) agricultural practices (2) physicochemical analyses, (3) their bacterial community by metabarcoding of the 16S rDNA gene and (4) in vitro inhibition tests (fungistasis) of the pathogenic fungus Fusarium graminearum. Among these 103 plots, 98 were used to collect samples of wheat (Triticum aestivum) rhizosphere and roots, that were also described through their bacterial community. Finally, nine soils among the 103 were selected for the cultivation and infection of wheat by F. graminearum under controlled conditions. The fungistasis test revealed great variability within the sample as well as the ability of certain soils to completely inhibit the germination of the fungus. Perennial soil characteristics and bacterial diversity were related to soil fungistasis. There was also a correlation between the abundance of Burkholderia spp. and fungistasis. Comparison of bacterial microbiomes from soil, wheat rhizosphere and roots revealed different compositions between the three compartments. The microbial composition in the soil influenced those of the rhizosphere and roots of the same plot. The physicochemical characteristics and the management system influenced the composition of the bacterial community in the three compartments. Experimentation under controlled conditions did not reveal a link between microbiome (diversity and composition) and symptoms of Fusarium head blight, nor a link between fungistasis and in planta symptoms on the same soil. Overall, this work contributes to evaluating the possibilities of using agricultural practices as a lever for agroecological control of Fusarium head blight in wheat, through the modulation of natural microbial communities

Les bactéries du sol produisant des antifongiques comme le 2,4-diacétylphloroglucinol(DAPG) protègent les racines des plantes vis-à-vis des champignons phytopathogènes. Néanmoins, les conditions de fonctionnement de ces populations bactériennes dans le sol restent très mal connues. Dans certains sols, dits résistants aux maladies, ces bactéries phytoprotectrices sont présentes à des effectifs importants et leur activité est suffisante pour protéger la plante malgré la présence du pathogène. L'objectif de cette thèse a été de comprendre la relation entre la résistance des sols à la maladie de la pourriture noire des racines de tabac, et la fonction de synthèse du DAPG chez les bactéries du genre Pseudomonas. Dans la situation de référence de Morens (Suisse), les sols résistants diffèrent des sols sensibles par la présence de vermiculite, argile capable de relarguer du fer. On sait que la présence de vermiculite améliore la phytoprotection assurée par les Pseudomonas producteurs de DAPG, mais les mécanismes moléculaires sous-jacents restent inconnus. Dans un premier temps, la quantification de ces bactéries par une nouvelle méthode de PCR quantitative développée ici, a confirmé que leurs effectifs sont élevés dans les sols résistants, mais aussi dans les sols sensibles, suggérant que la résistance puise plutôt dépendre d'une plus forte expression de la fonction de synthèse du DAPG. Dans un second temps, l'étude de l'expression des gènes de synthèse du DAPG en système de sol artificiel, à l'aide de la souche rapportrice P. protegens phlA-gfp, a montré que la présence de vermiculite dans le sol se traduit par une plus forte biodisponibilité du fer pour les Pseudomonas, induisant une plus forte expression des gènes de synthèse du DAPG et la protection du tabac. En conclusion, la résistance des sols de Morens à la maladie de la pourriture noire des racines est conditionnée par plusieurs facteurs abiotiques et biotiques, dont la biodisponibilité du fer qui régule l'expression des gènes de synthèse du DAPG chez Pseudomonas
Soil bacteria producing antimicrobial compounds like 2,4-diacetylphloroglucinol (DAPG) protect plants from soil-borne phytopathogens. Nevertheless, the functioning of these bacterial populations in the soil is largely unknown. In certain soils, termed disease- suppressive soils, these bacteria are present at high numbers and their activity is sufficient to assure effective plant protection in the presence of the pathogen. The aim of this thesis was to understand the relation between soil suppressiveness towards black root rot of tobacco, and the 2,4-diacetylphloroglucinol synthesis ability of certain Pseudomonas. In Morens region (Switzerland), suppressive soils differ from conducive soil by the presence of vermiculite, an iron-releasing clay. It is known that DAPG-producing Pseudomonas provide better plant protection in the presence of vermiculite, but the molecular basis of this interaction is still unknown. First, the quantification of these bacteria, through a new real-time PCR method developed here, confirmed that high numbers of DAPG-producing Pseudomonas occur in suppressive soils, as well as in conducive ones, raising the possibility that suppressiveness depends rather on a higher expression of DAPG synthetic genes. Second, expression studies of DAPG synthetic genes using a P. protegens ph/A- gfp reporter strain and artificial soil systems, confirmed that the presence of vermiculite in the soil can translate into higher iron bioavailability for Pseudomonas, triggering higher expression of DAPG synthetic genes and effective plant protection. In conclusion, black root rot suppressiveness of Morens soils is determined by several abiotic and biotic factors, among which iron bioavailability regulating the expression of DAPG synthetic genes in plant-protecting Pseudomonas

Root-knot nematodes (RKN), Meloidogyne spp., are the most economically important genus of plant parasitic nematodes that cause considerable damage and yield losses of horticultural crops worldwide. RKN management strategies tend to reduce chemical nematicides by encouraging alternative control methods like the use of plants bearing resistance genes (R-genes) and/or by microbe-inducing plant resistance, and the antagonistic potential of soils. In the thesis, two biological control approaches of Meloidogyne spp. were evaluated: 1) the application of selected nematode antagonists, the fungus Pochonia chlamydosporia and the bacteria Bacillus firmus I-1582 (Bf I-1582), to know its ability to induce plant resistance, and 2) the level of soil suppressiveness of vegetable production sites conducted under organic or integrated standards. Regarding the ability of P. chlamydosporia and Bf I-1582 to induce plant resistance, the results of this thesis provide evidence that two out of five P. chlamydosporia isolates (M10.43.21 and M10.55.6) and Bf I-1582 are able to induce systemic resistance against M. incognita in the susceptible tomato (Solanum lycopersicum) cv. Durinta but not in the cucumber (Cucumis sativus) cv. Dasher II in split-root experiments. In addition, the cardinal temperatures for the Bf I-1582 growth and biofilm formation were determined in order to improve its use in field conditions. Moreover, Bf I-1582 was transformed with GFP to study its effect on nematode eggs and on tomato and cucumber root colonization. In tomato, the number of egg masses and the number of eggs per plant were reduced by M10.43.21 and M10.55.6 P. chlamydosporia isolates and by Bf I-1582. P. chlamydosporia isolates colonized both tomato and cucumber roots, being the M10.43.21 and the M10.55.6 isolates the best root colonizers in tomato and cucumber, respectively. In the case of Bf I-1582, the bacteria colonized endophytically roots of both plants, but highest values were recorded in tomato. The dynamic regulation of genes related to jasmonic acid (JA) and salicylic acid (SA) was determined by RT-qPCR at three different times after nematode inoculation (dani). Bf I-1582 primed tomato plants by both SA and JA at all the times in tomato, but only SA at 7 dani in cucumber. Regarding P. chlamydosporia, isolate M10.43.21, induced the expression of the SA pathway in tomato at 0, 7 and 42 dani. The JA pathway was also up regulated at 7 dani. These results show the similar model of dynamic regulation of these plant hormone pathways related to plant defense mechanisms against the nematode. Also, Bf I-1582 grew and formed biofilm between 15 and 45 ºC, being 35 ºC the optimal temperature. Bf I-1582GFP was adhered to the egg shell and inside the eggs. Also, Bf I-1582GFP colonized root hairs and epidermal cells and some bacteria were found inside the tomato root. In cucumber, few bacteria were observed on epidermal cells and the bacteria were no found inside the root. In relation to the level of soil suppressiveness of vegetable production it was carried out a study in four organic and two integrated vegetables production standards sites located in north-eastern Spain. The fluctuation both of Meloidogyne population density and fungal egg parasitism were determined during the rotation sequences in two years (2015-2016). Five out of six of these sites were suppressive soils to Meloidogyne spp. The percentage of fungal egg parasitism ranged from 11.2 to 55 % and P. chlamydosporia was the only fungal species isolated from the eggs. In parallel, two tomato pots experiments were carried out using sterilized and non-sterilized soils from each site and inoculated with second-stage juveniles (J2) to achieve a rate of 1 J2 cm-3 of soil. In both, in five of them the number of nematode eggs per plant was reduced in all nonsterilized soils compared to the sterilizes ones. Also, P. chlamydosporia was the only fungal species isolated from parasitized nematode eggs.
Meloidogyne spp. (RKN) es el género de nematodos fitopatógenos que causan las mayores pérdidas económicas y que más afectan al rendimiento de cultivos hortícolas a nivel mundial. Las estrategias de manejo de RKN tienden a sustituir la utilización de nematicidas químicos por medidas de control alternativas como son el uso de plantas con genes de resistencia (genes R) y/o mediante la utilización de microorganismos inductores de resistencia, y el potencial antagónico del suelo. En esta tesis, se han evaluado dos enfoques de control biológico: 1) la aplicación de microorganismos antagónicos, el hongo Pochonia chlamydosporia (Pc) y la bacteria Bacillus firmus I-1582 (Bf I-1582) para evaluar su capacidad de inducir mecanismos de resistencia, y 2) el nivel de supresividad del suelo de diferentes lugares bajo estándares de producción orgánica e integrada. Con respecto a la capacidad de Pc y Bf I-1582 para inducir resistencia, los resultados de esta tesis muestran que dos (M10.43.21 y M10.55.6) de los cinco aislados de Pc utilizados y la bacteria Bf I-1582 inducen resistencia sistémica frente a M. incognita en el tomate susceptible (Solanum lycopersicum) cv. Durinta pero no en el pepino (Cucumis sativus) cv. Dasher II usando el modelo split-root. En el caso de Bf I-1582, se determinaron las temperaturas cardinales para el crecimiento y la formación de biofilms de Bf I-1582 con el fin de mejorar su utilización en condiciones de campo y se transformó con la GFP para estudiar su efecto sobre los huevos de RKN y sobre la colonización radicular. Los aislados M10.43.21 y M10.55.6 de Pc y Bf I-1582 redujeron el número de masas de huevos y el número de huevos por planta en tomate. Todos los aislados de Pc colonizaron raíces de tomate y pepino, siendo los aislados M10.43.21 y M10.55.6 los mejores colonizadores en tomate y pepino, respectivamente. En el caso de Bf I-1582, la bacteria colonizó endofíticamente las raíces de ambas plantas, pero los valores más altos se registraron en tomate. La expresión de los genes relacionados con el ácido jasmónico (JA) y el ácido salicílico (SA) se determinó a tres tiempos tras la inoculación de nematodos (dani). En plantas de tomate inoculadas con Bf I-1582 la expresión de los genes relacionados con SA y JA aumentaron en los tres puntos, pero en pepino solo se observó un incremento de expresión en el gen relacionado con la ruta de SA a los 7 dani. Con respecto a Pc, el aislado M10.43.21, indujo la expresión de la vía SA en tomate a los 0, 7 y 42 dani. La vía JA también aumentó su expresión a los 7 dani. Además, Bf I-1582 creció y formó biofilms entre 15 y 45 ºC, siendo 35 ºC la temperatura óptima. Bf I-1582GFP se adhirió a la cubierta y al interior de los huevo de M. incognita. Además, Bf I-1582GFP en tomate colonizó los pelos radiculares, así como las células epidérmicas y se encontraron algunas bacterias en el interior radicular. En el pepino, se observó un menor número de bacterias en las células epidérmicas y no se encontraron bacterias en el interior radicular. En relación con el nivel de supresión del suelo, se realizó un estudio en cuatro lugares de producción hortícola orgánica y dos de producción integrada en el noreste de España. Durante la secuencias de rotación en 2015-2016 se determinó la fluctuación tanto de la densidad de población de Meloidogyne en suelo como del parasitismo de huevos de nematodos. Cinco de estos sitios resultaron ser supresivos a Meloidogyne spp. Paralelamente, se llevaron a cabo dos experimentos en macetas con suelo esterilizado y no esterilizado de cada sitio donde las plantas de tomate se inocularon con juveniles (J2) para lograr una tasa de 1 J2 cm-3 de suelo. En cinco de ellos, el número de huevos de nematodos por planta se redujo en todos los suelos no esterilizados en comparación con los esterilizados. Respecto al parasitismo, Pc fue la única especie aislada de los huevos de Meloidogyne spp. p
Els nematodes formadors de gal·les, Meloidogyne spp., és el gènere més important nematodes fitoparàsits que causen danys considerables i generen pèrdues econòmiques en cultius hortícoles arreu del món. Les estratègies actuals de gestió de Meloidogyne solen reduir l’ús dels nematicides químics fomentant mètodes de control alternatius com l’ús de plantes amb gens de resistència (gens R) i/o l’ús de la resistència vegetal induïda per microorganismes, i el potencial antagonista dels sòls. En la present tesis, dos aproximacions al control biològic de Meloidogyne spp. van ser estudiades: 1) l’aplicació d’antagonistes dels nematodes: el fong Pochonia chlamydosporia i el bacteri Bacillus firmus aïllat I-1582 i es a avaluar la seva capacitat per induir resistència vegetal, i 2) el nivell de supressivitat de sòls de producció vegetal orgànica o integrada. Respecte a la capacitat de P. chlamydosporia i B. firmus I-1582 (Bf I-1582) a induir resistència vegetal, els resultats d’aquesta tesis van donar evidències que dos de cinc aïllats de P. chlamydosporia (M10.43.21 i M10.55.6) i Bf I-1582 induien resistència sistèmica enfront M. incognita en tomàquet susceptible (Solanum lycopersicum) cv. Durinta però no en cogombre (Cucumis sativus) cv. Dasher II en experiments “split-root”. A més, les temperatures cardinals de creixement i de formació de biofilm de Bf I-1582 van ser determinades per tal de millorar el seu ús en condicions de camp. A més, el bacteri va ser transformat amb GFP per estudiar el seu efecte sobre els ous del nematode i la seva colonització sobre les arrels de tomàquet i cogombre per microscopia de rastreig làser confocal. En tomàquet, tant el nombre de masses d'ou com el nombre d'ous per planta es va veure reduït quan s’aplicaven tant els aïllats fúngics com el bacteri. Els aïllats de P. chlamydosporia colonitzaven les arrels de tomàquet i cogombre, però diferien en el nivell de colonització. L’aïllat M10.43.21 va ser el millor colonitzador de les arrels de tomàquet mentre que l’aïllat M10.55.6 ho va ser per cogombre. En el cas de Bf I-1582, el bacteri va ser capaç de colonitzar endofíticament les arrels de les dues plantes, però es va trobar un 61% més de densitat d’ADN de bacteri en arrels de tomàquet. La regulació dinàmica dels gens relacionats amb l’àcid jasmònic (JA) i l’àcid salicílic (SA) a tres temps diferents van ser avaluats: 7 dies després de la inoculació de l’antagonista i just després de la inoculació del nematode (0 dani), 7 dies desprès de la inoculació del nematode (7 dani) i 40 dies desprès de la inoculació del nematode (40 dani). Les dues vies SA (gen PR-1) i JA (gen Lox D) van ser sobre-expressades plantes de tomàquet a 0 dani, reduint el nombre de masses d’ou al final de l’experiment “split-root” quan es va inocular amb Bf I-1582. No obstant, no hi va haver diferencies en l’expressió dels gens relacionats SA (PR 1) i JA (Lox D) en cogombre inoculat amb el bacteri com tampoc en el nombre de masses d’ou produïdes en les arrels de cogombre. A 7 dani, el gen relacionat amb el JA (Lox D) estava sobre-expressat en tomàquet i podria afectar el desenvolupament del nematode i la seva reproducció. En cogombre, la via del SA (Pal I) estava sobre-expressada tant en les plantes inoculades amb M. incognita com en les co-inoculades amb el bacteri i el nematode. A 40 dani, quan va començar l’eclosió dels ous i es van produir noves infeccions a l’arrel, les plantes de tomàquet co-inoculades amb els nematode 2 i Bf I-1582 tenia reprimit el gen relacionat amb el JA (Lox D), mentre que el gen relacionat amb la via del SA (PR 1) estava sobre-expressat en plantes co-inoculades i també amb només Bf I-1582, però va ser reprimit en plantes inoculades només amb el nematode. En cogombre, les dues vies, JA i SA, van ser reprimides en plantes inoculades amb M. incognita però només la JA en plantes co-inoculades. Respecte l’aïllat de P. chlamydosporia M10.43.21, va induir l’expressió de la via del SA en arrels de tomàquet a 0, 7 i 42 dani. La via del JA va ser també sobre-expressada a 7 dani. Per tant, alguns aïllats de P. chlamydosporia i l’aïllat Bf I-1582 poden induir resistència sistèmica envers al nematode, encara que depèn de l’espècie vegetal. Aquests resultats han demostrat el model similar de regulació dinàmica d’aquestes vies d’hormones vegetals relacionades amb mecanismes de defensa de les plantes contra el nematode. El bacteri Bf I-1582 va créixer en el rang de temperatures des de 15 ºC a 45 ºC, sent 35 ºC la temperatura òptima de creixement tant en medi sòlid com en líquid, però no a 10 ºC i 50 ºC. Igualment, es va observar la formació de biofilm entre 15 ºC i 45 ºC però tampoc a 10 ºC ni a 50 ºC, sent més gruixut i uniforme a 35 ºC. La degradació de la closca del nematode i la colonització dels ous per Bf I-1582 GFP va mostrar que a 3 dies desprès de la seva inoculació (dai) el bacteri estava envoltant i degradant l'ou del nematode; a 5 dai, colònies de bacteri es van adherir a la closca de l’ou i es van trobar alguns bacteris dins de l’ou; a 10 dai, el bacteri era completament adherit a la closca de l’ou i dins de l’ou. A més, Bf I-1582GFP va colonitzar les pèls radiculars i cèl·lules epidèrmiques a 5 dai; es van observar colònies de bacteris en pèls radiculars de tomàquet i alguns bacteris dins de l’arrel a 10 dai. En cogombre, es van observar pocs bacteris a les cèl·lules epidèrmiques a 5 dai i no es va trobar el bacteri dins de l’arrel a 10 dai. En relació al nivell de supressivitat del sòl, es va realitzar un estudi a sis parcel·les de producció d’hortalisses localitzades al nord-est d’Espanya. Quatre realitzaven producció orgànica (M10. 16, M10.41, M10.55, i M10.56) i dues (M10.43 i M10.45) producció integrada. La fluctuació de la densitat de població de Meloidogyne i el parasitisme d’ous per part de fongs van ser determinats durant la seqüència de rotació de cultius durant dos anys (2015-2016). Cinc dels sols estudiats eren sòls supressius a Meloidogyne spp. El percentatge de parasitisme d’ous va variar de 11.2 a 55 % i P. chlamydosporia va ser l'única espècie fúngica aïllada dels ous. En paral·lel, dos experiments es van dur a terme utilitzant sòl de cada parcel·la. Una part de cada sòl es va esterilitzar i es va barrejar amb sorra estèril, i una altre part no es va esterilitzar i es va barrejar també amb sorra estèril amb una relació 1:1 i es va col·locar en testos de 3-l. El cultivar susceptible de tomàquet Durinta es va trasplantar en cada test i es va inocular amb juvenils de segon estadi (J2) amb un nivell de 1 J2 cm-3 de sòl. En els dos experiments en testos, els nombre d’ous per planta es va reduir (P<0.05) en tots els sòls no esterilitzats comparats amb els estèrils, excepte en el M10.45. També, P. chlamydosporia va la única espècie fúngica aïllada d’ous parasitats de nematodes. P. chlamydosporia és el fong més freqüent i més prevalent amb una alta plasticitat capaç d’adaptar-se a les pràctiques agronòmiques en un sistema de producció vegetal molt pertorbat.

A number of growth factors and cytokines involved in the local regulation of bone remodelling are either synthesised by osteoblasts or have osteoblasts as their target. These include the RANK-L/OPG system, the gp130 cytokine family, including IL-6, and insulin like growth factors. In addition, aberrant cytokine signalling is strongly linked with pathological states characterised by increased bone resorption, including osteoporosis and renal osteodystrophy. The range of action and potency of these osteotropic cytokines requires that their actions are tightly regulated. Amongst such potential control mechanisms are the suppressors of cytokine signalling (SOCS), the presence and role of which in bone has not been studied in detail. The aim of this thesis was (i) to examine the direct effect of uraemia on cytokine release in human osteoblastic cells; (ii) to determine if the regulatory SOCS genes are expressed in these cells and, if so, (iii) to characterise their functional significance. In initial studies, osteoblastic cells were cultured in media containing sera from either healthy volunteers or haemodialysis treated chronic kidney disease patients. Concentrations of OPG and IL-6 were then measured in harvested supernatants. Additionally, individual serum samples collected prior to, and during, a haemodialysis (HD) session were assayed for IL-6, IL-1β and soluble IL-6 receptor (sIL-6R). HD patients had significantly higher concentrations of IL-6 than normal subjects, but there were no significant differences in either IL-1β or sIL-6R. These concentrations did not change significantly during HD. There were no differences in OPG production by osteoblastic cells after exposure to either normal or uraemic serum. Incubation with untreated sera from normal subjects increased IL-6 production by ~6-fold above control, whereas sera from uraemic subjects increased it only ~2-3-fold. HD did not restore the capacity of uraemic serum to augment IL-6 release to the same degree as normal serum. Further work examined a variety of osteotropic stimuli for their ability to induce SOCS1- 3 and CIS expression in human osteoblastic cells. The utility of both conventional RTPCR and fluorescence-based kinetic real time PCR for this purpose are compared. These SOCS were found to be expressed constitutively and could be induced to a variable degree by relevant growth factors. In general, the temporal pattern of SOCS expression was consistent with a negative feedback function. Potential functionality was explored following transfection with SOCS1 and SOCS3 plasmid DNA. Significantly enhanced IL-6 secretion was found in both the basal and stimulated state, whilst OPG production was enhanced only in the latter. Function was also studied in the context of osteoblastic apoptosis, the regulation of which is highly relevant to skeletal disease. Initial experiments developed a framework for subsequent studies: serum starvation for 24h produced reproducible cell death that could be attenuated in a dose dependent manner by IGF-I. SOCS1 and SOCS3 overexpression had limited influence on osteoblast survival, whereas gene knock down experiments using siRNA indicated that IL-1β-induced cell death is mediated differentially, depending on the type of cell death involved. SOCS1 and SOCS3 are involved in the apoptotic cascade, while IL-1β-induced necrosis appears to be independent of SOCS3. Collectively these studies demonstrate that the augmentation of IL-6 production by osteoblastic cells after exposure to normal serum is greater than after uraemic serum. HD does not correct this disparity; perhaps indicating a non-dialysable inhibitor of IL-6 release is involved in the dysregulated bone turnover of uraemic patients. Further work establishes the constitutive presence of the SOCS family in human osteoblastic cells, as well as their transient inducibility by key osteotropic stimuli. Several novel aspects of SOCS function, including influence on IL-6 and OPG production and involvement within apoptotic pathways are demonstrated.

Orientador: Gustavo Luiz Chagas Manhães de Abreu
Resumo: O presente trabalho propõe uma nova estratégia para supressão ativa robusta do fenômeno Ground Resonance (GR) em Helicópteros. O modelo clássico de análise deste fenômeno é desenvolvido para um rotor isotrópico e a análise de estabilidade é feita no domínio de Coleman, para encontrar as fronteiras de instabilidade. Também é proposta uma nova estratégia para lidar com essas fronteiras de instabilidade e suprimir o GR usando controladores com formulação descrita por conjuntos politópicos convexos. Controladores são projetados via desigualdades lineares matriciais (LMIs, Linear Matrix Inequalities), formulados de acordo com a Teoria de Estabilidade de Lyapunov. Adicionalmente, incertezas paramétricas na frequência de lead-lag das pás e a apresentação de uma falha estrutural nos atuadores são consideradas e, assim, novos controladores robustos são projetados a fim de expandir o envelope operacional da aeronave. Ainda, são considerados diferentes tipos de não-linearidades estruturais na rigidez e amortecimento do trem de pouso do helicóptero e a caracterização da estabilidade não-linear do sistema exibe oscilações em ciclo limite (LCO, Limit Cycle Oscillation), que são determinadas a partir da construção de Diagramas de Bifurcação. Utiliza-se a modelagem Fuzzy-TS do sistema para cada caso de estudo e, com base nas fronteiras de estabilidade não-linear do GR, definidas a partir dos Diagramas de Bifurcação, têm-se o projeto de controladores para supressão das LCOs do sistema. Os res... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: The present work proposes a new strategy for robust active suppression of Ground Resonance (GR) phenomenon in Helicopters. The classical model to analysis of this phenomenon is developed for an isotropic rotor and stability analysis is done in Coleman domain, to nd the boundaries of instability. It is also proposed a new strategy for dealing with these boundaries of instability and suppressing GR using controllers with polytopic convex hulls formulation. Controllers are designed via Linear Matrix Inequalities (LMIs), formulated according to the Lyapunov Stability Theory. Additionally, parametric uncertainties in the lead-lag frequency of the blades and actuators faults are considered and thus new robust controllers are designed to expand the aircraft operating envelope. Also, di erent types of structural nonlinearities in the landing gear sti ness and damping of the helicopter are considered, and the characterization of the nonlinear stability of the system exhibits Limit Cycle Oscillation (LCO), which are determined from the construction of Bifurcation Diagrams. Fuzzy-TS modeling is used for each case study and, based on the nonlinear stability boundaries of the GR, de ned from the Bifurcation Diagrams, the controllers to suppress the LCO are designed. The results of numerical simulations, discussions and conclusions are presented and show that the control strategy proposed is an attractive solution to suppress the linear and nonlinear GR problem, being able to expand the o... (Complete abstract click electronic access below)
Doutor

La thèse est dédiée au problème de la stéréophotométrie non-Lambertienne sans connaissance a priori sur les conditions d'illumination et son application aux images de boîte de Pétri. Pour obtenir une bonne reconstruction de surfaces non-Lambertiennes, il est proposé de traiter une séquence d'entrée en deux étapes: premièrement il faut supprimer les effets spéculaires et obtenir ainsi des images de surface 'pseudo-Lambertienne'. Ensuite dans une deuxième étape à partir de ces images une reconstruction stéréophotométrique Lambertienne sans aucune information préalable sur les directions d'illumination est effectuée. Dans ce travail nous proposons deux méthodes originales respectivement pour la suppression de spécularités et la reconstruction de surface sans information a priori. Les méthodes proposées sont appliquées pour la caractérisation des colonies microbiennes.La spécularités est un effet optique lié à la nature physique complexe des objets. Il est utile pour la perception humaine des objets 3D mais il gêne le processus de traitement automatique d'images. Pour pouvoir appliquer le modèle Lambertien à la stéréophotométrie, les spécularités doivent être supprimées des images d'entrée. Nous proposons donc une méthode originale pour la correction des zones spéculaires adaptée pour une reconstruction ultérieure. L'algorithme proposé est capable de détecter les spécularités comme des valeurs anormalement élevées d'intensité dans une image de la séquence d'entrée, et de les corriger en utilisant les informations des autres images de la séquence et une fonction de correction continue. Cette méthode permet de faire la suppression des spécularités en préservant toutes les autres particularités de distribution de lumière qui sont importantes pour la reconstruction de surface.Après nous proposons une technique de reconstruction stéréophotométrique de surface Lambertienne sans connaissance a priori sur l'illumination. Le modèle mis en œuvre consiste en quatre composantes, deux composantes (albédo et normales) permettent de d'écrire des propriétés de surface et deux autres (intensités des sources de lumière et leurs directions) décrivent illumination. L'algorithme proposé de reconstruction utilise le principe de l'optimisation alternée. Chaque composante du modèle est trouvée itérativement en fixant toutes les variables sauf une et en appliquant des contraintes de structures, valeurs et qualité pour la fonction d'optimisation. Un schéma original de résolution permet de séparer les différents types d'information inclus dans les images d'entrée. Grâce à cette factorisation de matrices, la reconstruction de surface est faite sans connaissance préalable sur les directions de lumière et les propriétés de l'objet reconstruit. L'applicabilité de l'algorithme est prouvée pour des donnés artificielles et des images de bases publiques pour lesquelles la vérité terrain sur les surfaces des objets est disponible.La dernière partie de la thèse est dédiée à l'application de la chaine complète proposée pour le traitement d'images de boîte de Pétri. Ces images sont obtenues en utilisant les sources de lumières complexes qui sont supposées être inconnues pour le processus de reconstruction. L'évaluation de surfaces de colonies microbiennes s'est révélée être une étape importante pour l'analyse visuelle et automatique des colonies. La chaine proposée est efficace pour ce type de données et permet de compléter les informations d'images par de la surface 3D.

Take-all, caused by the soilborne fungus, Gaeumannomyces graminis var. tritici (Ggt), is an important root disease of wheat that can be reduced by take-all decline (TAD) in successive wheat crops, due to general and/or specific suppression. A study of 112 New Zealand wheat soils in 2003 had shown that Ggt DNA concentrations (analysed using real-time PCR) increased with successive years of wheat crops (1-3 y) and generally reflected take-all severity in subsequent crops. However, some wheat soils with high Ggt DNA concentrations had low take-all, suggesting presence of TAD. This study investigated 26 such soils for presence of TAD and possible suppressive mechanisms, and characterised the microorganisms from wheat roots and rhizosphere using polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE). A preliminary pot trial of 29 soils (including three from ryegrass fields) amended with 12.5% w/w Ggt inoculum, screened their suppressiveness against take-all in a growth chamber. Results indicated that the inoculum level was too high to detect the differences between soils and that the environmental conditions used were unsuitable. Comparison between the Ggt DNA concentrations of the same soils collected in 2003 and in 2004 (collected for the pot trial), showed that most soils cropped with 2, 3 and 4 y of successive wheat had reduced Ggt DNA concentrations (by 195-2911 pg g-1 soil), and their disease incidences revealed 11 of the 29 test soils with potential take-all suppressiveness. Further pot trials improved the protocols, such that they were able to differentiate the magnitudes of suppressiveness among the soils. The first of the subsequent trials, using 4% w/w Ggt inoculum level, controlled conditions at 16°C, 80% RH with alternate 12 h light/dark conditions, and watering the plants twice weekly to field capacity (FC), screened 13 soils for their suppressiveness against take-all. The 13 soils consisted of 11 from the preliminary trial, one wheat soil that had been cropped with 9 y of wheat (considered likely to be suppressive), and a conducive ryegrass soil. The results revealed that 10 of these soils were suppressive to take-all. However, in only four of them were the effects related to high levels of microbial/biological involvement in the suppression, which were assessed in an experiment that first sterilised the soils. In a repeat trial using five of the soils H1, H3, M2, P7 (previously cropped with 3, 3, 4 and 9 y successive wheat, respectively) and H15 (previously cropped with 5 y of ryegrass), three of them (H1, H3 and M2) had reduced Ggt DNA concentrations (>1000 pg g-1 soil reductions), and were confirmed to be suppressive to take-all. A pot trial, in which 1% of each soil was transferred into a γ-irradiated base soil amended with 0.1% Ggt inoculum, indicated that soils H1 and H3 (3 y wheat) were specific in their suppressiveness, and M2 (4 y wheat) was general in its suppressiveness. The microbial communities within the rhizosphere and roots of plants grown in the soils, which demonstrated conduciveness, specific or general suppressiveness to take-all, were characterised using PCR-DGGE, and identities of the distinguishing microorganisms (which differentiated the soils) identified by sequence analysis. Results showed similar clusters of microorganisms associated with conducive and suppressive soils, both for specific and general suppression. Further excision, re-amplification, cloning and sequencing of the distinguishing bands showed that some actinomycetes (Streptomyces bingchengensis, Terrabacter sp. and Nocardioides sp.), ascomycetes (Fusarium lateritium and Microdochium bolleyi) and an unidentified fungus, were associated with the suppressive soils (specific and general). Others, such as the proteobacteria (Pseudomonas putida and P. fluorescens), an actinomycete (Nocardioides oleivorans), ascomycete (Gibberella zeae), and basidiomycete (Penicillium allii), were unique in the specific suppressiveness. This indicated commonality of some microorganisms in the take-all suppressive soils, with a selected distinguishing group responsible for specific suppressiveness. General suppressiveness was considered to be due to no specific microorganisms, as seen in soil M2. An attempt to induce TAD by growing successive wheat crops in pots of Ggt-infested soils was unsuccessful with no TAD effects shown, possibly due to variable Ggt DNA concentrations in the soils and addition of nutrients during the experiment. Increasing numbers of Pseudomonas fluorescens CFU in the rhizosphere of plants, during successive wheat crops was independent of the Ggt DNA concentrations and disease incidence, suggesting that increases in P. fluorescens numbers were associated with wheat monoculture. This study has demonstrated that TAD in New Zealand was due to both specific and general suppressiveness, and has identified the distinguishing microorganisms associated with the suppression. Since most of these distinguishing microorganisms are known to show antagonistic activities against Ggt or other soilborne pathogens, they are likely to act as antagonists of Ggt in the field. Future work should focus on validating their effects either individually, or interactively, on Ggt in plate and pot assays and under field conditions.

This study focuses on the soil- and water-borne plant pathogen Phytophthora cinnamomi Rands and the phenomenon of P. cinnamomi suppressive soil. In particular, this thesis reports on the outcome of field surveys and glasshouse assays undertaken to locate P. cinnamomi suppressive soils and to confirm the involvement of biological processes in suppression. The potential role of cellulase and laminarinase in suppression was investigated and a molecular technique known as length heterogeneity PCR (LH-PCR) was used to analyse the structure and diversity of bacterial and fungal communities in avocado orchard soils that were suppressive and conducive to P. cinnamomi. Four avocado orchards with P. cinnamomi suppressive soils were identified and soils were ã-irradiated to destroy their suppressive capacity, thus confirming biological suppression. Suppression was also partially transferred to ã-irradiated and conducive soils by mixing with 10% suppressive avocado soils. Cellulase and laminarinase activities measured in avocado orchard soils inoculated with P. cinnamomi were not associated with disease severity in lupin seedlings during glasshouse assays involving the same soil samples. Minor shifts in bacterial and fungal community structure were observed in response to mixing conducive and irradiated soils with suppressive soils. This was associated with decreased disease severity in avocado seedlings in these treatments. The shift in bacterial community structure was partially determined by the appearance and increased abundance of several bacterial 16S rDNA sequences, which were unique to the suppressive soils, in the mixed soil treatments. It is suggested that the bacteria and fungi from which these sequences originated may be involved in suppression and further work should be undertaken to determine their identity and confirm their potential role in the development and maintenance of P. cinnamomi suppressive soils.
Doctor of Philosophy (PhD)

Our capacity to maintain world food production depends heavily on the thin layer of soil covering the Earth's surface. The health of this soil determines whether crops can grow successfully, whether a farm business is profitable and whether an enterprise is sustainable in the long term. Farmers are generally aware of the physical and chemical factors that limit the productivity of their soils but often do not recognise that soil microbes and the soil fauna play a major role in achieving healthy soils and healthy crops. Soil Health, Soil Biology, Soilborne Diseases and Sustainable Agriculture provides readily understandable information about the bacteria, fungi, nematodes and other soil organisms that not only harm food crops but also help them take up water and nutrients and protect them from root diseases. Complete with illustrations and practical case studies, it provides growers and their consultants with holistic solutions for building an active and diverse soil biological community capable of improving soil structure, enhancing plant nutrient uptake and suppressing root pests and pathogens. The book is written by scientists with many years' experience developing sustainable crop production practices in the grains, vegetable, sugarcane, grazing and horticultural industries. This book will be useful for: growers, consultants, agronomists and soil chemists, extension personnel working in the grains, livestock, sugarcane and horticultural industries, professionals running courses in soil health/biological farming, and students taking university courses in soil science, ecology, microbiology, plant pathology and other biological sciences.

Abstract Management of plant diseases relies on two general strategies: avoidance and control. Avoidance tactics involve evasion of pathogens by not planting susceptible crops in areas where virulent pathogens are present, and exclusion of pathogens through phytosanitary practices. Control tactics rely on planting crop cultivars with genetic and physiological resistance to pathogens, enhancing diversity in cropping systems through intercropping or crop rotation, and cultural practices such as increased plant spacing, sanitation of crop debris, and careful management of irrigation. Breeding for resistant cultivars through traditional backcross breeding has focused mostly on incorporating one or more major genes for resistance into elite cultivars with superior horticultural traits. Increasingly, genetic transformation is used to move genes for resistance or other useful traits directly into the crop genome, using either biolistics or transformation with Agrobacterium. Other useful approaches in agricultural biotechnology include gene editing with CRISPR-Cas nucleases and RNA interference. Major gene resistance is vulnerable to boom-and-bust cycles as pathogens evolve to overcome resistance. To increase the durability of resistance, crop breeders are exploring the use of gene pyramiding, multilines, and quantitative (polygenic) resistance traits. Active management can either disinfect soils of pathogen populations or promote active microbial communities in suppressive soils. Suppressive soils are less conducive to disease development, and can show either general or specific soil suppression. Chemical and biological control applications can supplement these strategies to help reduce infection or spread of pathogens.

The unique features of Brazilian State capitalism include (a) a combination of governmental control of traditional SOEs, with the same SOEs being minority shareholders in a large number of supposedly private corporations, and (b) the noticeable exercise of shareholder activism by State-controlled institutional investors both in private and public companies. SOEs experience a clear conflict between the social and political objectives of the government as a controlling shareholder, on one hand, and the interests of minority investors, on the other. Government control over banks has also led to a significant influence of political considerations over firms’ decisions. The creeping influence of the State and public officials has been responsible for the main public corruption scandals of the last decade. The quasi-fiscal activities of these SOEs have had various side effects, including imposing significant costs on the SOEs themselves, suppressing demand for alternative competing products, reducing incentives for improving efficiency, and increasing environmental costs.

Membrane SOAs are integrated inside the interferometer arms of Si-MZM, in which the SOAs have on-chip gain of 11-5.3 dB at 25-80℃. In this configuration, SOAs can be used in saturated region suppressing pattern effect.

The production of oil mist in machinery processing workshop is harmful. To control concentration of oil mist, the TiO2 which can treat with manifold organic pollutants is used to purify oil mist. At first, the nanometer TiO2 is prepared using the sol-gel method on the optimum formulation that showed a higher activity. Then it is treated by dip-coating technique using the non-woven fabric as composite support. The efficiency of suppression of oil mist is compared with ordinary materials. With the increase of time, the purification of the nanometer TiO2 photocatalyst sieve against oil mist of non-woven fabric is investigated in solar radiation at room temperature. It oxidizes pollutants of oil mist to CO2 and H2O. The experiments demonstrat oil mist is oxidized on the TiO2 sol at the 22nd minute with a maximum capacity of 0.3219g. It infers from the experiments the photodegradation effect is high and the reaction is fast. It also concludes that the nanometer TiO2 photocatalysis material is an ideal material for suppressing oil mist in air. At last, a status the application of technology in air purification as well as its problems and trends are presented. The technique has a promising prospect to solve the increasing air problem of the workshop.

An experimental investigation was carried out to examine the effects on stall margin of flow injection into, and flow removal out of, the endwall region of an axial compressor blade row. A primary objective of the investigation was clarification of the mechanism by which casing treatment (which involves both removal and injection) suppresses stall in turbomachines. To simulate the relative motion between blade and treatment, the injection and removal took place through a slotted hub rotating beneath a cantilevered stator row. Overall performance data and detailed (time-averaged) flowfield measurements were obtained. Flow injection and removal both increased the stalling pressure rise, but neither was as effective as the wall treatment. Removal of high blockage flow is thus not the sole reason for the observed stall margin improvement in casing or hub treatment, as injection can also contribute significantly to stall suppression. The results also indicate that the increase in stall pressure rise with injection is linked to the streamwise momentum of the injected flow, and it is suggested that this should be the focus of further studies.

We demonstrate unprecedented 2nm broadband ASE source-enabled digital-analog radio-over-fiber mobile fronthaul system with joint force of SOAs for intensity noise suppression and multicore fiber for self-homodyne detection. We achieve 35GHz(=7core×5GHz) aggregated bandwidth with 2Tb/s CPRI-equivalent data rate sup-porting 1024-QAM signal.

With the invention of the stereoscope, loci of retinal stimulation became the focus of investigation for understanding single and double vision. From the first stereoscope experiment Wheatstone (1838) concluded that (a) slightly different pictures can lead to single vision, and (b) “similar pictures falling on corresponding points of the two retinas may appear double and in different places.” Wheatstone’s first claim was immediately accepted. The mechanism responsible for single vision, however, remained unclear; there has been disagreement as to whether suppression or fusion is involved. Our first set of experiments showed that single vision is achieved by suppression in some conditions and by fusion in others. Wheatstone’s second claim, on the other hand, was challenged. Our second set of experiments with a stereogram in which markers were embedded in the crossed or uncrossed areas of the two halffields supports Wheatstone's second claim. The results from our two sets of experiments can be understood in terms of loci of retinal stimulation interacting with other variables, such as extent of disparity and compatibility with other information, rather than being the sole determinant of visual direction.

Original objectives: Our initial project objectives were to 1) Determine and compare the composition of seed-colonizing microbial communities on seeds, 2) Determine the dynamics of development of microbial communities on seeds, and 3) Determine and compare the composition of seed-colonizing microbial communities with the composition of those in the soil and rhizosphere of the plants. Revisions to objectives: Our initial work on this project was hampered by the presence of native Pythium species in the soils we were using (in the US), preventing us from getting accurate assessments of spermosphere microbial communities. In our initial work, we tried to get around this problem by focusing on water potentials that might reduce damage from native Pythium species. This also prompted some initial investigation of the oomycete communities associated seedlings in this soil. However, for this work to proceed in a way that would allow us to examine seed-colonizing communities on healthy plants, we needed to either physically treat soils or amend soils with composts to suppress damage from Pythium. In the end, we followed the compost amendment line of investigation, which took us away from our initial objectives, but led to interesting work focusing on seed-associated microbial communities and their functional significance to seed-infecting pathogens. Work done in Israel was using suppressive compost amended potting mix throughout the study and did not have such problems. Our work focused on the following objectives: 1) to determine whether different plant species support a microbial induced suppression of Pythium damping-off, 2) to determine whether compost microbes that colonize seeds during early stages of seed germination can adequately explain levels of damping-off suppression observed, 3) to characterize cucumber seed-colonizing microbial communities that give rise to the disease suppressive properties, 4) assess carbon competition between seed-colonizing microbes and Pythium sporangia as a means of explaining Pythium damping-off suppression. Background: Earlier work demonstrated that seed-colonizing microbes might explain Pythium suppression. Yet these seed-colonizing microbial communities have never been characterized and their functional significance to Pythium damping-off suppression is not known. Our work set out to confirm the disease suppressive properties of seed-colonizing microbes, to characterize communities, and begin to determine the mechanisms by which Pythium suppression occurs. Major Conclusions: Compost-induced suppression of Pythium damping-off of cucumber and wheat can be explained by the bacterial consortia colonizing seeds within 8 h of sowing. Suppression on pea was highly variable. Fungi and archaea play no role in disease suppression. Potentially significant bacterial taxa are those with affinities to Firmicutes, Actinobacteria, and Bacteroidetes. Current sequencing efforts are trying to resolve these taxa. Seed colonizing bacteria suppress Pythium by carbon competition, allowing sporangium germination by preventing the development of germ tubes. Presence of Pythium had a strong effect on microbial community on the seed.

Fusarium oxysporum spp. causes Panama disease in bananas and crown and root rot in an array of vegetables and field crops, but increased regulations have restricted the use of many conventional chemical pesticides, and there are a limited number of commercially available products effective against them. The soil microbiome represents a largely untapped reservoir of secondary metabolites that can potentially antagonize fungal pathogens. However, most soil bacteria cannot be cultivated using conventional techniques and therefore most of these compounds remain unexplored. The overall goal of this two-year project was to extract and characterize novel secondary metabolites from "unculturable" soil microbiomes that antagonize Fusarium and other fungal plant pathogens. Initially, the Cytryn lab at the Volcani Institute (ARO) identified candidate biosynthetic gene clusters (BGCs) encoding for potentially novel antifungal compounds (specifically non-ribosomal peptides and polyketides) in soil and plant root microbiomes using cutting-edge metagenomic platforms. Next, the Brady lab at Rockefeller University (RU) screened archived soil metagenomic cosmid libraries for these BGCs, and heterologously expressed them in suitable hosts. Finally, the Frenkel and Cytryn labs at ARO assessed the capacity of these heterologous expressed strains to antagonize Fusarium and other fungal plant pathogens. Initially tomato and lettuce were analyzed, and subsequently roots of cucumbers grown in suppressive (biochar amended) soils were targeted. We found that the composition of tomato and lettuce root BGCs are similar to each other, but significantly different from adjacent bulk soil, indicating that root bacteria possess specific secondary metabolites that are potentially associated with rhizosphere competence. BGC linked to known metabolites included various antimicrobial, (e.g., streptazone E, sessilin), antifungal (heat-stable antifungal factor- HSAF, II and ECO-02301), and insecticidal (melingmycin, orfamide A) compounds. However, over 90% of the identified BGCs were moderately to significantly different from those encoding for characterized secondary metabolites, highlighting the profusion of potentially novel secondary metabolites in both root and soil environments. Novel BGCs that were abundant in roots and remotely resembled those of antifungal compounds were transferred to RU for subsequent screening and five were identified in RU soil metagenomic cosmid libraries. Two of these clusters (BARD-1711 BARD-B481) were heterologously-expressed in a Streptomyces albus J1074 strain, and transferred to ARO. The strain harboring BARAD-B481 was found to antagonize Fusarium significantly more than the host strain, indicating that this BGCs product has antifungal activity. Future studies will need to work on chemically characterizing the BARAD-B481 BGC and progress with the above described pipeline for other interesting BGCs.

Concentrated flow erosion in rills, pipes, ephermal gullies, and gullies is a major contributor of downstream sedimentation. When rill or gullies form in a landscape, a 3- to 5-fold increase in soil loss commonly occurs. The balance between the erosive power of the flow and the erosion resistance of the bed material determines the rate of concentrated flow erosion. The resistance of the bed material to detachment depends primarily on the magnitude of the interparticle forces or cohesion holding the particles and aggregates together. The effect of soil properties on bed material resistance and concentrated flow erosion was evaluated both in the laboratory and field. Both rill erodibility and critical hydraulic shear were greater when measured in 9.0 m long rills under field conditions compared with laboratory mini-flumes. A greater hydraulic shear was required to initiate erosion in the field compared to the mini-flume because of the greater aggregate and clod size and stability. Once erosion was initiated, however, the rate of erosion as a function of hydraulic shear was greater under field conditions because of the greater potential for slaking upon wetting and the greater soil surface area exposed to hydraulic shear. Erosion tests under controlled laboratory conditions with the mini-flume allowed individual soil variables to be studied. Attempts to relate rill erosion to a group soil properties had limited success. When individual soil properties were isolated and studied separately or grouped separately, some trends were identified. For example, the effect of organic carbon on rill erodibility was high in kaolinitic soils, low in smectitic soils, and intermediate in the soils dominated by illite. Slow prewetting and aging increased the cohesion forces between soil particles and decreased rill erodibility. Quick prewetting increased aggregate slaking and increased erodibility. The magnitude of the effect of aging depended upon soil type. The effect of clay mineralogy was evaluated on sand/clay mixtures with montmorillonite (M), Illite (I), and kaolinite (K) clays. Montmorillonite/sand mixtures were much less erodible than either illite or kaolonite sand mixtures. Na-I and Na-K sand mixtures were more erodible than Ca-I and Ca-K due to increased strength from ionic bonding and suppression of repulsive charges by Ca. Na-M was less erodiblethan Ca-M due to increased surface resulting from the accessibility of internal surfaces due to Na saturation. Erodibility decreased when salt concentration was high enough to cause flocculation. This occurred between 0.001 mole L-1 and 0.01 mole L-1. Measuring rill erodibility in mini-flumes enables the measurement of cohesive forces between particles and enhances our ability to learn more about cohesive forces resisting soil detachment under concentrated water flow.