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Taxogenómica En Rhodobacteraceae

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Departamento de Microbiología y Ecología Colección Española de Cultivos Tipo Programa de Doctorado en Biomedicina y Biotecnología TAXOGENÓMICA EN RHODOBACTERACEAE Directores de Tesis David Ruiz Arahal Mª Jesús Pujalte Domarco Alexandra La Mura Arroyo Tesis Doctoral Valencia, Noviembre, 2019 Dr. David Ruiz Arahal, Profesor Titular del Departamento de Microbiología y Ecología de la Universidad de Valencia, y Dra. María Jesús Pujalte Domarco, Catedrática del Departamento de Microbiología y Ecología de la Universidad de Valencia, INFORMAN : Que Alexandra La Mura Arroyo, Graduada en Biología por la Universidad de Valencia, ha realizado bajo su dirección el trabajo titulado Taxogenómica en Rhodobacteraceae, y que hallándose concluida, reúne todos los requisitos para su juicio y calificación. Por tanto, autorizan su depósito, a fin de que pueda ser juzgado por el tribunal correspondiente para la obtención del grado de Doctor por la Universidad de Valencia. Y para que conste, en el cumplimiento de la legislación, firman el presente informe en Valencia, a 13 de noviembre de 2019. David Ruiz Arahal Mª Jesús Pujalte Domarco Relación de publicaciones derivadas de la presente Tesis Doctoral Esta Tesis Doctoral ha sido financiada por la Subvención para la contratación de personal investigador de carácter predoctoral (ACIF/2016/343) de la Generalitat Valenciana y el Fondo Social Europeo. Los resultados obtenidos a lo largo de la realización de la Tesis Doctoral se han presentado a través de publicaciones y comunicaciones científicas en el ámbito de la taxonomía, y son los siguientes: • Artículos: La Mura A, Arahal DR, Pujalte MJ. (2018). Roseivivax atlanticus (Li, Lai, Liu, Sun and Shao, 2015) is a later heterotypic synonym of Roseivivax marinus (Dai, Shi, Gao, Liu and Zhang, 2014). Int J Syst Evol Microbiol. 68, 2650-2652. Arahal DR, La Mura A, Lucena T, Rodrigo-Torres L, Aznar R, Pujalte MJ. (2019). Shimia thalassica sp. nov., and reclassification of Pseudopelagicola gijangensis as Shimia gijangensis comb. nov. and Thalassobius activus as Cognatishimia activa comb. nov. Int J Syst Evol Microbiol. doi: 10.1099/ijsem.0.003629. • Congresos Comunicación póster: La Mura A, Pujalte MJ, Arahal DR. Taxogenomic study of marine bacteria belonging to the family Rhodobacteraceae. Presentada en el 7th Congress of European Microbiologist (FEMS) realizado en Valencia en 2017. Comunicación oral: La Mura A, Arahal DR, Aznar R, Pujalte MJ. Reclasificación y sinonimias en la era taxogenómica: Estudio de la familia Rhodobacteraceae. Presentada en la Reunión de los Grupos Especializados en Taxonomía, Filogenia y Diversidad Microbiana y de Microbiología del Medio Acuático de la Sociedad Española de Microbiología realizada en Sitges (Barcelona) en 2018. Comunicación oral: La Mura A, Arahal DR, Lucena T, Rodrigo-Torres L, Aznar R, Pujalte MJ. Shimia thalassica sp. nov., y reclasificación de Pseudopelagicola gijangensis como Shimia gijangensis comb. nov. y Thalassobius activus como Cognatishimia activa comb. nov. Presentada en el XXVII Congreso SEM realizado en Málaga en 2019. AGRADECIMIENTOS En primer lugar quiero agradecer a mis directores de tesis, David Ruiz Arahal y María Jesús Pujalte, el apoyo recibido tanto a nivel profesional como personal. Gracias por confiar en mí a pesar de mi inexperiencia, por vuestra paciencia, por ayudarme a convertirme en la científica que soy ahora y sobre todo por inculcarme la pasión por la Microbiología desde el primer momento... yo que años atrás decía que jamás de los jamases me dedicaría a esta área de conocimiento... y voilà aquí estoy. ¡Gracias de corazón! A mis compañeros de la CECT: MariCarmen, Laura, Bea, Rosa, Nuria, Jordi, MJou, Ana, Aurora, Teresa, Amparo, Patri y Chemi, sin vuestra ayuda esto no habría sido posible. En especial, quiero agradecer a Rosa Aznar por darme la oportunidad de formarme en la Colección. Sin olvidarme de mis chicas del 0.27, Lidia, María Nicolás y María Piñar creo que tras estos tres años solo os puedo decir una cosa con total seguridad: Os quiero. Lidia gracias por contestarme a las eternas dudas (... pero para eso eres nuestra Reina y la piedra angular de ya sabes donde), y por tener la paciencia de enseñarme a utilizar los programas bioinformáticos. Esta tesis es mía y un poco tuya. Chicas, gracias por estar ahí en los momentos de agobio, por permitirme ensayar con vosotras todas las presentaciones una y otra vez, por ser mi diccionario particular de sinónimos, por las risas en el despacho, por los viajes, los miércoles de cine, el coffee break, por Rupert y Helen y por convertir a Ramona en toda una influencer... En general gracias por todos los momentos de felicidad vividos y los que nos quedan. No tengo ninguna duda que sin vosotras esto no habría salido adelante! Espero en un futuro poder volver a trabajar junto a vosotras. ¡Sois geniales! A toda la gente del EAM Lab. Especialmente a Martina y Stefàno por aceptarme en vuestro laboratorio y hacerme sentir una más. Paolo, Dani (o mejor dicho ‘el loco Danielito’) gracias por compartir vuestro despacho conmigo, por enseñarme y ayudarme cuando algo salía mal, por enseñarme el italiano y que nunca se puede añadir mayonesa a la pasta! A ti Priscilla, gracias por hacerme sentir como en casa aunque estuviera lejos, por ser mi amiga, por compartir los momentos de desgracias en el laboratorio, por explorar juntas Italia y por descubrirme el Pão de queijo (delicioso! Aunque no pueda decir lo mismo del mate...) ¡Muchas gracias por hacer que los tres meses pasaran volando! Te deseo todo lo mejor. Espero verte pronto. Y no olvides que tú molas mucho! Gracias de verdad! Por último, agradecer eternamente a mi familia y amigos el apoyo constante recibido y a todos aquellos que de una forma u otra habéis hecho posible esta tesis. ÍNDICE INTRODUCCIÓN .................................................................................................................. 1 1. Taxonomía de procariotas ....................................................................................... 1 1.1. Definición y concepto .............................................................................................. 1 1.2. Historia de la taxonomía de procariotas ................................................................. 2 1.3. Técnicas y metodologías empleadas en la taxonomía polifásica de procariotas .... 4 1.4. Introducción de la taxonomía de procariotas en la era genómica .......................... 9 1.5. Aplicación del enfoque taxogenómico en la delimitación de taxones bacterianos 10 1.6. Aplicación del enfoque taxogenómico en la reconstrucción filogenética ............ 12 1.7. Limitaciones del enfoque taxogenómico en la taxonomía de procariotas ........... 16 2. Generalidades de la familia Rhodobacteraceae ..................................................... 17 OBJETIVOS Y PLAN DE TRABAJO ....................................................................................... 23 MATERIAL Y MÉTODOS .................................................................................................... 27 1. Material: Cepas bacterianas ................................................................................. 27 2. Metodología ........................................................................................................ 28 RESULTADOS Y DISCUSIÓN ............................................................................................... 41 1. Secuenciación genómica de novo ......................................................................... 41 1.1. Cultivo celular y obtención de DNA genómico ...................................................... 41 1.2. Secuenciación ........................................................................................................ 41 1.3. Evaluación de los datos brutos obtenidos en la secuenciación ............................. 42 1.4. Evaluación de la calidad de los ensamblados ........................................................ 42 1.5. Confirmación de la identidad específica de los genomas secuenciados ................ 44 2. Análisis genómico e inferencia fenotípica ............................................................. 46 2.1. Organización y contenido del genoma .................................................................. 46 2.2. Metabolismo central de carbohidratos ................................................................. 53 2.3. Metabolismo del nitrógeno ................................................................................... 59 2.4. Metabolismo del hierro ......................................................................................... 73 2.5. Metabolismo del fósforo ....................................................................................... 78 2.6. Metabolismo de compuestos C1 ........................................................................... 83 2.7. Degradación de compuestos aromáticos .............................................................. 94 2.8. Movilidad bacteriana ........................................................................................... 100 2.9. Adherencia y producción de biopelículas ............................................................ 107 2.10. Mecanismos de defensa frente a diferentes condiciones de estrés .............. 110 2.11. Producción de metabolitos secundarios ........................................................ 119 2.12. Resistencia a metales y otros elementos tóxicos ........................................... 125 3. Validación de la inferencia fenotípica .................................................................
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  • Artificial Neural Network Analysis of Microbial Diversity in the Central and Southern Adriatic

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    www.nature.com/scientificreports OPEN Artifcial neural network analysis of microbial diversity in the central and southern Adriatic Sea Danijela Šantić1*, Kasia Piwosz2, Frano Matić1, Ana Vrdoljak Tomaš1, Jasna Arapov1, Jason Lawrence Dean3, Mladen Šolić1, Michal Koblížek3,4, Grozdan Kušpilić1 & Stefanija Šestanović1 Bacteria are an active and diverse component of pelagic communities. The identifcation of main factors governing microbial diversity and spatial distribution requires advanced mathematical analyses. Here, the bacterial community composition was analysed, along with a depth profle, in the open Adriatic Sea using amplicon sequencing of bacterial 16S rRNA and the Neural gas algorithm. The performed analysis classifed the sample into four best matching units representing heterogenic patterns of the bacterial community composition. The observed parameters were more diferentiated by depth than by area, with temperature and identifed salinity as important environmental variables. The highest diversity was observed at the deep chlorophyll maximum, while bacterial abundance and production peaked in the upper layers. The most of the identifed genera belonged to Proteobacteria, with uncultured AEGEAN-169 and SAR116 lineages being dominant Alphaproteobacteria, and OM60 (NOR5) and SAR86 being dominant Gammaproteobacteria. Marine Synechococcus and Cyanobium- related species were predominant in the shallow layer, while Prochlorococcus MIT 9313 formed a higher portion below 50 m depth. Bacteroidota were represented mostly by uncultured lineages (NS4, NS5 and NS9 marine lineages). In contrast, Actinobacteriota were dominated by a candidatus genus Ca. Actinomarina. A large contribution of Nitrospinae was evident at the deepest investigated layer. Our results document that neural network analysis of environmental data may provide a novel insight into factors afecting picoplankton in the open sea environment.