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BEATRIZ JORRIN RUBIO.Pdf Universidad Politécnica de Madrid Escuela Técnica Superior de Ingenieros Agrónomos Genomics of Specificity in the Symbiotic Interaction between Rhizobium leguminosarum and Legumes Ph.D Thesis Beatriz Jorrín Rubio Licenciada en Biología 2016 Universidad Politécnica de Madrid Escuela Técnica Superior de Ingenieros Agrónomos Departamento de Biotecnología Ph.D Thesis: Genomics of Specificity in the Symbiotic Interaction between Rhizobium leguminosarum and Legumes Author: Beatriz Jorrín Rubio Licenciada en Biología Director: Juan Imperial Ródenas Licenciado en Biología Doctor en Biología Madrid, 2016 A mis padres A Sofía A mis hermanos “There’s the story, then there’s the real story, then there’s the story of how the story came to be told. Then there’s what you leave out of the story. Which is part of the story too.” Maddaddam Margaret Atwood RECONOCIMIENTOS Esta Tesis se ha desarrollado en el laboratorio de Genómica y Biotecnología de Bacterias Diazotróficas Asociadas con Plantas del Centro de Biotecnología y Genómica de Plantas (UPM-INIA). Para el desarrollo de esta Tesis he contado con una beca UPM homologada financiada por el proyecto MICROGEN: Genómica Comparada Microbiana (Programa Consolider), que ha sido también el proyecto financiador del trabajo experimental. Quisiera reconocer la labor de aquellas personas que han contribuido al desarrollo y consecución de esta Tesis. Dr. Juan Imperial, por la dirección y supervisión de esta Tesis. Por ser un gran mentor y por enseñarme todo lo que sé. Dr. Manuel González Guerrero, por enseñarme los entresijos de la Ciencia y del trabajo en el laboratorio. Dra. Gisèle Laguerre, por su participación en el inicio de este proyecto y por facilitarnos el suelo P1 de Dijon. Dr. Paulo Arruda, por la formación que obtuve durante mi estancia en el laboratorio de Estudio de la Regulación y de la Expresión génica de la Universidad Estatal de Campinas. Dra. Belén Brito, por su gran ayuda en la primera fase de este proyecto y por recomendarme, sin ella nunca hubiera empezado esta Tesis. Rosabel Prieto, por su inestimable ayuda para la obtención de los Pool-Seqs y por enseñarme muchas de las técnicas que he necesitado durante la Tesis. Santiago de la Peña, por su valiosa ayuda en el análisis bioinformático de los genomas individuales. Dra. Julia Quintana, por enseñarme los conceptos de genética de poblaciones y por las largas discusiones científicas que tanto me han aportado. Dra. Viviana Escudero, por enseñarme a cuidar las plantas y valorar las cosas realmente importantes. Dra. Carmen Sánchez, por enseñarme las técnicas básicas de microbiología y genética molecular durante mi periodo como estudiante de máster. Dr. David Durán, por enseñarme los conceptos básicos de filogenia. XI AGRADECIMIENTOS Escribir los agradecimientos es la parte más difícil de una tesis, no porque sea complicado, si no porque es la única parte que se lee todo el mundo y supone una gran presión añadida. Siempre me imaginaba escribir esta parte como algo extremadamente emotivo, pero después de escribir más de 200 páginas me he quedado sin palabras. La ciencia siempre fue lo que quise hacer, pero nunca pensé que pudiera hacerlo, pero… here I am! Ha sido un camino largo y duro, pero no lo cambiaría por nada, me he convertido en lo que quería y he conocido a los mejores. Desde que tengo 13 años sabía que quería estudiar esto, gracias a la inspiración de mi profesora de biología Marisa Alonso. Cuando llegué a la carrera, las cosas no fueron como esperaba, pero aún así descubrí mi pasión por la micro, la genética y las plantas… Y sobre todo conocí a grandes personas. Desde luego la mejor decisión que tomé fue hacer el máster, este fue el punto de inflexión, descubrí que era hacer ciencia… y eso me enganchó. Quiero agradecer a Pepe Palacios por acogerme en su laboratorio durante este periodo, ya que sin duda, mi paso por allí marcó mi vuelta. Por ello también quiero agradecer a todos los Rizobios y Levaduros, y en especial a Carmen Sánchez, por ser mi supervisora en los inicios y enseñarme muchas de las técnicas básicas de micro y genética molecular que he aprendido. No me puedo olvidar de dar las gracias a Tomás Ruíz Argüeso, siempre ha estado ahí cuando lo he necesitado, incluso acompañándome a fumar un cigarro. Indudablemente gracias a Belén Brito, por recomendarme y por ver lo mejor en mí. Y a los que hablaron con Belén, ¡gracias! Empezar la Tesis ha sido lo mejor que me ha pasado en mi carrera profesional. Sin duda tengo el mejor director de Tesis posible, Juan. ¡Muchas gracias! Gracias por el conocimiento, la experiencia y la libertad para desarrollarme como científica, por ser un gran mentor y mejor persona, ¡GRACIAS! Yo soy yo y mi circunstancia, y en mi circunstancia científica está Manuel González Guerrero, gracias por dejarme acompañarte en tu punto de inflexión, por enseñarme el alma de la ciencia, por no dejarme nunca bajar los brazos y por ser mi amigo. Gracias a Rosabel, sin su ayuda, no solo como técnico, si no también como persona, este proyecto hubiera sido muchísimo más difícil. Gracias a todos mis compañeros: Rosario, Marta, Amalia, Javier, Nuria, Manolo, Vivi, Isidro, Patricia y Rosabel; siempre habéis hecho del laboratorio un lugar fantástico donde trabajar. Gracias a todos los estudiantes que han estado a mi cargo: Adriana, Amalia, Miguel y Merce. Es más difícil enseñar que aprender, pero con vosotros como conejillos de indias ha sido más fácil. Gracias a XIII todas las personas que han pasado por el laboratorio, y en especial a Benja, ¡qué grande eres! El CBGP ha sido mi casa durante estos cinco años, sin el personal de SEL (María y Carmen), del Invernadero (Mar y Chendo), de administración (Sonia, Jesús y Alejandro) de informática (Gonzalo) o de conserjería (Antonio), nada hubiera sido igual, muchas gracias a todos. A demás he conocido a grandes personas que se han convertido en buenos amigos: gracias a Lucía, Sara, Carlos, Balta, Manuel Guillermo, Marce y Rafa. Gracias a los Diazotroopers de Luis Rubio, por los grandes momentos en los congresos. Gracias a Rocío, Alonso, Aurora, Mónica y a mis colegas de cigarro. Gracias a Julia, por creer en mi, por entenderme, por grandes momentos que se han convertido en recuerdos inolvidables y por todo lo que nos queda por compartir, ¡Gracias!. Gracias a Vivi, por ser como eres, tan suave… Por tu sinceridad, por tus jarros de realidad y por tu cariño. Sin vosotras también tendría una tesis, pero hubiera sido mucho más aburrido y mucho menos enriquecedor. A mis amigas con las que empecé la carrera, Lore, Rocío, Gonzalo (una más) y Alba. Because we’re worth it! Ya son más de trece años… ¡por muchos más! A mis cookies, Sandra y Elena. Gracias por confiar en mi. Por las tardes de bolos, las habitaciones rojas, los paseos en bici hasta el infinito y por el Pad Thai. A mis amiguinxis con las que acabé la carrera, Ana, Elisa, Yvonne, Bea, Gloria, Raquel, Yolanda, Lidia y Cristina. Como dijo Miss Tegucigalpa del mismo modo en sentido contrario: “no cambiéis, ¡Grasias!” A mis festivaleras, Paula, Patri y Gema. Por el xamón, los furaños, la buena música, los gintonics, los jägers y la playa; ya sabéis, venimos del mismo lugar… A mis amigas del colegio, Ana, Mónica y Laura. Porque aunque pasen los años y evolucionemos, parece que aún seguimos teniendo quince años jugando a “Celeste” en tecnología. Y por último, pero no por ello menos importante, gracias a mi familia. Gracias a mis padres, han sido, son y siguen siendo el mayor apoyo que he tenido nunca. Sin ellos no estaría hoy aquí y no sería quien soy. Gracias Mamá, Gracias Papá. A mi hermano Gonzalo, no se puede tener un hermano mejor y no me has podido hacer mejor regalo. Gracias a “my sister-in-law” Ximena, por regalarme a Sofía y por las conversaciones en la cocina. A mi sobri, por alegrarme cada día desde que existes, espero que siempre puedas estar orgullosa de tu tía. A toda mi familia, que siempre se ha preocupado por mi Tesis; a mi abuelo que siempre me dice “esto que haces tú sale mucho en los periódicos, es importante”. A mis tíos, mis padrinos, mi padrina, mis primos, mis enanos, los que llegan y los que se han ido. ¡Gracias! A todos ¡mil gracias! Abstract ABSTRACT For centuries legumes have been used in crop rotations to incorporate nitrogen into agricultural systems, thus avoiding the need for fertilization. This is possible because of their symbiotic interaction with specific diazotrophic soil bacteria, collectively known as rhizobia, that infect legume roots, form root nodules and fix atmospheric nitrogen into ammonia using the nitrogenase enzyme. The establishment and maintenance of this symbiotic partnership results from a molecular conversation that guarantees specificity and guides the co-development of both organisms during root nodule formation. Rhizobium leguminosarum bv. viciae is a member of the α-Proteobacteria that can establish effective symbioses with members of the Fabeae legume tribe (Pisum, Lathryrus, Lens and Vicia). Previous studies have suggested that, although all R. leguminosarum bv. viciae isolates can effectively nodulate all Fabeae, different Fabeae select specific genotypes of rhizobia from those available in soil. The aim of this Thesis was to characterize the genomic, genetic and molecular bases of the selection of specific R. leguminosarum bv. viciae genotypes by different host legumes (Pisum sativum, Lens culinaris, Vicia faba and V. sativa) from a well- characterized agricultural soil. We established a population genomics methodology based on pooled DNA samples (Pool-Seq) from R. leguminosarum isolates obtained from different sources: legume plant hosts used as rhizobial traps (P. sativum, L.
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