<p>Eastern black walnut (<i>Juglans nigra</i> L.) ranks among the most highly valued timber species in the central hardwood forest and across the world. This valuable tree fills a critical role in native ecosystems as a mast bearing pioneer on mesic sites. Along with other <i>Juglans</i> spp. (Juglandaceae), <i>J. nigra</i> is threatened by thousand cankers disease (TCD), an insect-vectored disease first described in 2009. TCD is caused by the bark beetle <i>Pityophthorus juglandis</i> Blackman (Corthylini) and the phytopathogenic fungus <i>Geosmithia morbida</i> Kol. Free. Ut. & Tiss. (Bionectriaceae). Together, the <i>P. juglandis</i>-<i>G. morbida</i> complex has expanded from its historical range in southwest North America throughout the western United States (U.S.) and Europe. This range expansion has led to widespread mortality among naïve hosts <i>J. nigra</i> and <i>J. regia</i> planted outside their native distributions.</p> <p> The severity of TCD was previously observed to be highest in urban and plantation environments and outside of the host native range. Therefore, the objective of this work was to provide information on biotic and abiotic environmental factors that influence the severity and impact of TCD across the native and non-native range of <i>J. nigra</i> and across different climatic and management regimes. This knowledge would enable a better assessment of the risk posed by TCD and a basis for developing management activities that impart resilience to natural systems. Through a series of greenhouse-, laboratory- and field-based experiments, environmental factors that affect the pathogenicity and/or survival of <i>G. morbida</i> in <i>J. nigra</i> were identified, with a focus on the microbiome, climate, and opportunistic pathogens. A number of potentially important interactions among host, vector, pathogen and the rest of the holobiont of TCD were characterized. The <i>holobiont</i> is defined as the whole multitrophic community of organisms—including <i>J. nigra</i>, microinvertebrates, fungi and bacteria—that interact with one another and with the host.</p> <p>Our findings indicate that interactions among host, vector, pathogen, secondary pathogens, novel microbial communities, and novel abiotic environments modulate the severity of TCD in native, non-native, and managed and unmanaged contexts. Prevailing climatic conditions favor reproduction and spread of <i>G. morbida</i> in the western United States due to the effect of wood moisture content on fungal competition. The microbiome of soils, roots, and stems of trees and seedlings grown outside the host native range harbor distinct, lower-diversity communities of bacteria and fungi compared to the native range, including different communities of beneficial or pathogenic functional groups of fungi. The pathogen <i>G. morbida</i> was also associated with a distinct community of microbes in stems compared to <i>G. morbida</i>-negative trees. The soil microbiome from intensively-managed plantations facilitated positive feedback between <i>G. morbida</i> and a disease-promomting endophytic <i>Fusarium solani</i> species complex sp. in roots of <i>J. nigra</i> seedlings. Finally, the nematode species <i>Bursaphelenchus juglandis</i> associated with <i>P. juglandis</i> synergizes with <i>G. morbida</i> to cause foliar symptoms in seedlings in a shadehouse; conversely, experiments and observations indicated that the nematode species <i>Panagrolaimus</i> sp. and cf. <i>Ektaphelenchus</i> sp. could suppress WTB populations and/or TCD outbreaks.</p> <p>In conclusion, the composition, function, and interactions within the <i>P. juglandis</i> and <i>J. nigra</i> holobiont play important roles in the TCD pathosystem. Managers and conservationists should be aware that novel associations outside the host native range, or in monocultures, intensive nursery production, and urban and low-humidity environments may favor progression of the disease through the effects of associated phytobiomes, nematodes, and climatic conditions on disease etiology. Trees in higher diversity, less intensively managed growing environments within their native range may be more resilient to disease. Moreover, expatriated, susceptible host species (<i>i.e.</i>, <i>J. nigra</i>) growing in environments that are favorable to novel pests or pest complexes (<i>i.e.</i>, the western U.S.) may provide connectivity between emergent forest health threats (<i>i.e.</i>, TCD) and native host populations (<i>i.e.</i>, <i>J. nigra</i> in its native range).</p>

Tesis por compendio / [ES] La acuicultura se proyecta como un medio vital para alimentar de manera sostenible a la creciente población mundial. Sin embargo, para lograrlo, la producción de peces debe abordarse con sostenibilidad y adaptabilidad en mente, especialmente frente a desafíos como el cambio climático y la disminución de recursos. Esto requiere innovaciones en genética y nutrición para garantizar la resiliencia de las poblaciones de peces cultivados. Comprender las interacciones entre organismos, microbiota y el medio ambiente es crucial, y las tecnologías ómicas ofrecen una manera de profundizar en estas dinámicas. Se ha secuenciado el genoma del dorado, una especie significativa de acuicultura europea, lo que ha llevado a conocer la expansión génica y la plasticidad fenotípica. Esta tesis tuvo como objetivo aprovechar este conocimiento integrando diversas aproximaciones ómicas para anotar el genoma y la microbiota intestinal de esta importante especie mediterránea. El enfoque se centró en acciones para hacer más sostenibles las prácticas futuras de acuicultura. Un aspecto crítico abordado fue la gestión de los niveles de oxígeno, dada su disminución debido al cambio climático. Comprender las respuestas de los peces al oxígeno reducido es vital para la acuicultura sostenible. La investigación sobre el dorado reveló adaptaciones a la hipoxia leve, incluida una disminución general de la respuesta metabólica y variaciones a nivel de expresión génica. La selección genética y los avances en piensos acuícolas también son esenciales para la acuicultura sostenible. La tesis monitoreó la evolución de los peces y la dieta junto con un programa de cría para el crecimiento, revelando respuestas diferenciales en peces alimentados con recursos marinos reducidos. La selección genética por un crecimiento rápido es capaz de influir en la composición y la actividad de la microbiota intestinal. La caracterización de esta comunidad también reveló su importancia en la salud y el crecimiento de los peces. Los factores genéticos parecían jugar un papel más importante que la dieta en la formación de la composición de la microbiota intestinal, pero las interacciones entre genética y dieta influenciaron tanto las respuestas del huésped como las microbianas. En resumen, la tesis presenta resultados prometedores para mejorar el crecimiento, la salud y la adaptación ambiental en especies de acuicultura, contribuyendo también a la sostenibilidad del sector acuícola. / [CA] L'aqüicultura es projecta com un mitjà vital per a alimentar de manera sostenible la creixent població mundial. No obstant això, per a aconseguir-ho, la producció de peixos ha d'abordar-se amb sostenibilitat i adaptabilitat en ment, especialment front a desafiaments com el canvi climàtic i la disminució de recursos. Això requereix innovacions en genètica i nutrició per a garantir la resiliència de les poblacions de peixos cultivats. Comprendre les interaccions entre organismes, microbiota i el medi ambient és crucial, i les tecnologies òmiques oferixen una manera de profunditzar en aquestes dinàmiques. S'ha sequenciat el genoma de l'orada, una espècie significativa d'aqüicultura europea, la qual cosa ha portat a conèixer l'expansió gènica i la plasticitat fenotípica de l'espècie. Aquesta tesi té com a objectiu aprofitar aquest coneixement integrant diverses aproximacions òmiques per a anotar el genoma i la microbiota intestinal d'aquesta important espècie mediterrània. L'enfocament es va centrar en accions per a fer més sostenibles les pràctiques futures d'aqüicultura. Un aspecte crític abordat va ser la gestió dels nivells d'oxigen, donada la seua disminució a causa del canvi climàtic. Comprendre les respostes dels peixos a l'oxigen reduït és vital per a l'aqüicultura sostenible. La investigació va revelar adaptacions a la hipòxia lleu, inclosa una disminució general de la resposta metabòlica i variacions a nivell d'expressió gènica. La selecció genètica i els avanços en pinso per a l'aqüicultura també són essencials per a la sostenibilitat del sector. La tesi va monitorar l'evolució dels peixos i la dieta juntament amb un programa de sel·lecció genètica per creixement, revelant respostes diferencials en peixos alimentats amb recursos marins reduïts. La selecció genètica per a un creixement ràpid és capaç d'influir en la composició i l'activitat de la microbiota intestinal. La caracterització d'aquesta comunitat també va revelar la seua importància en la salut i el creixement dels peixos. Els factors genètics semblaven jugar un paper més important que la dieta en la formació de la composició de la microbiota intestinal, però les interaccions entre genètica i dieta van influir tant en les respostes de l'organisme com en les microbianes. En resum, la tesi presenta resultats prometedors per a millorar el creixement, la salut i l'adaptació ambiental en espècies d'aqüicultura, contribuint també a la sostenibilitat del sector aqüícola. / [EN] Aquaculture is projected as a vital means to feed the growing global population sustainably. However, to achieve this, fish production must be approached with sustainability and adaptability in mind, especially in the face of challenges like climate change and resource depletion. This requires innovations in genetics and nutrition to ensure the resilience of farmed fish populations. Understanding the interactions between organisms, microbiota, and the environment is crucial, and omics technologies offer a way to delve deeper into these dynamics. The genome of the gilthead sea bream, a significant European aquaculture species, has been sequenced, leading to insights into gene expansion and phenotypic plasticity. This thesis aimed to leverage this knowledge by integrating various omics approaches to annotate the genome and gut microbiome of this important Mediterranean species. The focus was on actions to conserve and "green" future aquaculture practices. One critical aspect addressed was the management of oxygen levels, given their declining availability due to climate change. Understanding fish responses to reduced oxygen is vital for sustainable aquaculture. Research on gilthead sea bream revealed adaptations to mild hypoxia, including a hypo-metabolic general response and changes in metabolic processes and gene expression profiling. Selective breeding and advancements in aquafeeds are also essential for sustainable aquaculture. The thesis monitored fish and diet evolution alongside a breeding program for growth, revealing differential responses in fish fed with reduced marine resources. Genetic selection for fast growth influenced the gut microbiota, highlighting the interconnectedness of genetics, diet, and microbial communities. Characterization of the gut microbiota revealed its importance in fish health and growth. Genetic factors appeared to play a more significant role than diet in shaping the gut microbiota composition, but interactions between genetics and diet influenced both host and microbial responses. Overall, the thesis presents promising outcomes for enhancing growth, health, and environmental adaptation in aquaculture species. By understanding the interconnectedness of genetics, nutrition, and microbiota, it aims to contribute to the sustainability of the aquaculture sector. / This PhD thesis has been elaborated by the PhD candidate thanks to two research contracts appointed to the framework of two H2020 European projects: AQUAEXCEL2020 “AQUAculture infrastructures for EXCELlence in European fish research towards 2020” (2015-2020; grant agreement nº 652831), and AquaIMPACT “Genomic and nutritional innovations for genetically superior farmed fish to improve efficiency in European aquaculture” (2019-2023; grant agreement nº 818367). During the thesis, the candidate completed a 3-months (91 days) stay in the Centre for Integrative Genetics (CIGENE), belonging to the Norwegian University of Life Sciences (NMBU) in Ås, Norway. This stay was financed by an EMBO Scientific Exchange Grant (grant agreement nº 10168). A grant from the iMOVE program from CSIC (grant agreement nº IMOVE23080) was also awarded, but not financially executed. Core publications of this thesis were funded by: AQUAEXCEL2020 H2020 EU Project (652831); PerformFISH H2020 EU Project (H2020-SFS-2016-2017; 727610); AquaIMPACT H2020 EU Project (818367); ThinkInAzul (THINKINAZUL/2021/024, PRTR-C17.I1); Bream-AquaINTECH (RTI2018–094128-B-I00); The rest of publications in which the candidate was involved received extra funding from: GAIN H2020 EU Project (773330) y AQUAEXCEL3.0 H2020 EU Project (871108) / Naya Català, F. (2024). The Two Genomes of Gilthead Sea Bream (Sparus aurata): a Multi-Omics and Holobiont Approach [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/205692 / Compendio