11 PHD POSITIONS (FPI PROGRAM) IN DIFFERENT RESEARCH AREAS (# of pos: 11)

The Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA/CSIC), a Centre of Excellence Severo Ochoa, offers 11 PhD student positions for young, motivated scientists. These 11 PhD student positions are funded by the FPI program from the Spanish Research Agency and aim to incorporate talented doctoral students that will be supported by a 4-year contract.

WHAT DO WE OFFER:

CBGP offers modern and fully equipped facilities to carry out state of the art research in plant molecular biology and agronomic science and a unique, stimulating work environment. Researchers enrolled under the frame of this FPI Program will be hired as PhD student’s researchers at the CBGP and if they complete their Ph.D. in three years, they will be funded for a period of 1 year as Postdoctoral researchers.

Please send your CV and a motivation letter with an indication of the chosen research topic and the corresponding code in the title of the email to [email protected] .

THE DEADLINE FOR APPLICATION SUBMISSION IS OCTOBER 21ST, 2022.

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BACTERIAL CHEMOSENSING IN THE ADAPTATION TO PLANT ENVIRONMENT AND ITS FUNCTION IN PATHOGENESIS - PID2021-125673OB-I00

Project summary: the outcome of the interaction between phytopathogenic bacteria and their host plants is determined by the ability of bacteria to survive and adapt to the plant surface environment, to eventually enter the plant and cause disease. During these initial stages, bacterial perception of environmental cues constitutes an important mechanism that will determine the success of infection. Bacterial ability to sense and respond to chemical gradients (chemotaxis) is mediated by specialized signal transduction systems known as chemosensory systems, which rely on chemoreceptor proteins (CRs) able to bind diverse chemical ligands. Phytopathogenic bacteria, in particular, encode a high number of CRs in their genomes. To gain more information on the role of chemosensory functions in phytopathogenic bacteria, in this project selected CRs potentially relevant for the pathogenic interaction with host plants will be characterized in two model phytopathogens (Pseudomonas syringae pv. tomato and Dickeya dadantii). The role of certain CRs potentially involved in the perception of changes in the intracellular energy status (via energy taxis) will also be analyzed. In addition, we are also interested in unveiling the distribution of chemosensory domains in bacteria from crop-associated habitats, that is, from the phyllosphere, rhizosphere and soil microbiomes of two model crops, tomato and potato. Ultimately, this project intends to lay the foundations for the development of alternative sustainable solutions in the field of crop protection. The selected student will use very different approaches (from the fields of microbiology, biochemistry, molecular biology, phytopathology, bioinformatics, genomics and metagenomics) to address project challenges.

Profile: candidate should have a bachelor’s and master’s degree in biology, biotechnology, biochemistry or related disciplines. Experience in molecular biology, microbiology, and biochemistry will be valued.

Principal Investigators: Emilia López Solanilla , José J. Rodríguez Herva .

Web: Phytopathogenic bacteria

NEW PERCEPTION AND SIGNALING MECHANISMS OF PLANT IMMUNITY ACTIVATED BY MOLECULAR PATTERNS ASSOCIATED WITH PLANT CELL DAMAGE (DAMPS) (DAMPSENSE) - PID2021-126006OB-I00

Project summary: There is an urgent need to replace current chemical-based technologies by biological-based solutions, such as the generation of natural bioproducts triggering physiological/disease resistance responses in crops (biostimulants). The use of MAMPs/DAMPs represent a powerful technology for the development of biological products in agriculture. Therefore, the general objective of DAMPSENSE is to understand the perception and signaling mechanisms of new DAMPs identified in the laboratory in order to apply this knowledge to the design of effective strategies to deal with biotic stresses. To do this, the selected researcher will identify new DAMPs derived from the wall using chromatographic techniques and will characterize the immune responses activated by them. Also, will work in the characterization of new mutants impaired in the perception and/or signalling of novel DAMPs, and the search for Pattern-Recognition Receptor (PRR) interactors, by using in silico molecular dynamics, multiple -omics, and protein-protein or glycan-protein interaction methodologies and molecular biology approaches to characterize this layer in plant innate immunity that links with cell wall.

Profile: We are looking for Graduates and Master in Biotechnology / Biochemistry / Biology or related areas. Experience in Molecular Biology, Biochemistry or Plant Pathology will be highly valued.

Principal investigators: Antonio Molina Fernández , Lucía Jordá Miró

Web: Plant Innate Immunity and resistance to necrotrophic fungi

FORMATION OF THE IRON-SULFUR CORE OF NITROGENASE CATALYTIC COFACTOR - PID2021-128802OB-I00

Project summary: This project aims to understand the biochemical mechanism for the assembly and transformations of NifB-co, the unique iron-sulfur precursor of the nitrogenase active-site iron-molybdenum cofactor. This knowledge is essential to bioengineer plant nitrogenases and implement biological nitrogen fixation in cereal crops. Because these metal cluster rearrangements are unprecedented and unique to nitrogenase, they lie at the frontier of knowledge. The subject of study defies current paradigms in metalloprotein assembly and has broad implications in inorganic biochemistry. The selected candidate will work at the Biochemistry of Nitrogen Fixation group of the Center for Plant Biotechnology and Genomics of Madrid, will be integrated in a highly internationalized group, with extensive network of international collaborators, and will receive further training in Molecular Biology, anaerobic protein purification, and biochemical characterization of nitrogenase related iron-sulfur proteins. This FPI contract is associated to the project PID2021-128802OB-I00 of MICINN.

Profile: Candidate should hold a bachelor’s and master’s degree in biology, biotechnology, biochemistry, or related disciplines that allows them to be admitted to the PhD program.

Principal Investigator: Luis Manuel Rubio Herrero

Web: Biochemistry of Nitrogen Fixation

CYTOSOLIC IRON TRAFFICKING FOR BIOLOGICAL NITROGEN FIXATION PID2021-124060OB-I00

Project summary: Iron is an essential, growth-limiting nutrient for all life forms. This metal is required for energy transduction, free radical control, and nitrogen metabolism among many other processes. However, “free”, hydrated, iron in the cytosol is highly toxic for the cell. It is alway bound to a plethora of small molecules and proteins that keep iron soluble, prevent toxicity, and avoid mis-metallation of metalloproteins. Therefore, iron delivery in the cytosol is the result of a “bucket-brigade” in which protein-protein interactions, their docking surfaces, and their relative iron affinities determine the specific allocation of this essential nutrient. In this project we intend to identify the proteins, iron-chaperones, that specifically target iron for nitrogen-fixing enzymes using as a model legume root nodules. These organs host endosymbiotic bacteria capable of converting N2 into ammonia, a critical reaction in natural environments and sustainable agriculture. Previous research in our group has shown that nodules are excellent systems to study iron homeostasis, as they have high iron requirements, have little functional redundancy, and nitrogen fixation is an unique iron-dependent reaction in nodules that is relatively easy to dissect. The selected candidate will be trained in classical plant physiology methods, metalloprotein biochemistry, confocal microscopy, and metal visualization at synchrotron facilities. As a result, we should have characterized the first plant iron-chaperones that will be instrumental toward iron-fortification of crops, improving nitrogen fixation in legumes, and developing nitrogen-fixing cereals.

Profile: Candidates should hold an undergraduate and a MSc degree in Biochemistry, Biotechnology, Biology, or related areas. Previous experience in plant-microbe interactions, protein purification, and/or plant nutrition will be valued.

Principal Investigator: Manuel Gonzalez-Guerrero

Web: Metalsym

GENETIC RESOURCES OF VICIA SATIVA FOR A SUSTAINABLE AGRICULTURE- PID2021-122138OR-I00

Project summary: General losses in production due to climate change and associated drought is one of the main problems faced by current crops, including legumes. Legumes are the main source of vegetable protein for human food and livestock feed but are also relevant for their nitrogen fixation capacity. Symbiotic systems in legumes reduce nitrogen fertilization in crops, thus diminishing the inputs of chemical fertilizers into the environment, making these crops relevant in sustainable agriculture. This project proposes the use of natural variation of genetic resources from genebanks to improve agriculture production by selecting and characterizing local varieties (V. sativa, as model and other legumes) more tolerant to drought, and more efficient in nitrogen fixation with increased crop production. For this achievement we will use transcriptomic methods to identify new genes involved in response to drought, dissect the impact of nodulation on drought tolerance and analyze the role of root architecture on nodulation ability, nitrogen fixation and water deficit.

Profile: Candidate should hold a bachelor’s and master’s degree in biology, biotechnology, microbiology, or related disciplines that allows them to be admitted to the PhD program.

Principal Investigator: Elena Ramírez Parra

Web: Phenotypic and molecular analysis of crop natural variation in legumes

EVALUATION OF BENEFICIAL MICROORGANISM (PGPRS) ON GRAPEVINE PERFORMANCES UNDER DROUGHT IN CONTROLLED AND FIELD CONDITIONS PID2021-125575OR-C21

Project summary: Maintenance of plant physiological functions under drought stress is normally considered a positive feature as it indicates sustained plant health and growth. In literature, there is some evidence that PGPRs (Plant Growth-Promoting Rhizobacteria) have the potential to maintain plant growth and yield under drought stress. The project will be devoted to test the effectiveness of the selected PGPRs under drought conditions. Activities will include vines treated with PGPR under drought conditions, in both controlled and field conditions, using rootstocks showing divergent behaviour in response to the water scarcity. In order to identify and validate biomarkers of PGPR plant interaction under drought conditions, vine subjected to limited conditions will be characterized from the point of view of phenotype, transcriptome and metabolome in both controlled (using untargeted methods) and field (using targeted methods) conditions. The final purpose of the project is to find strategies for the development of a commercial product to be used as a biological stimulant/fertilizer in viticulture. Therefore, we will characterize the impact of the PGPR on the bacterial and fungal microbiota associated with grapevine in controlled and field conditions. In this contex, the holistic approach proposed in the project is particularly powerful in that it allows to understand the different biosynthetic pathways activated by the plant-bacteria interaction at both laboratory and field level, in order to understand the best way to transfer these techniques to the field.

Profile: Candidate should hold a bachelor’s and master’s degree in biology, biotechnology, microbiology, or related disciplines that allows them to be admitted to the PhD program.

Principal Investigator: Rosa A Arroyo García

Web: Phenotypic and molecular analysis of crop natural variation

STUDY OF FUNCTIONAL AND PHYLOGENETIC BIODIVERSITY OF LOW ABUNDANCE UNCULTIVATED MICROORGANISMS AND THEIR DYNAMICS UNDER ENVIRONMENTAL CHANGE - PID2021-127210NB-I00

Project summary: Microbial biodiversity is dominated by low-abundant organisms that we have barely started to understand: the rare biosphere. Although low abundant species are known to modulate nutrients cycling, determine the resilience of ecosystems to pollutants, and impact the tolerance of natural habitats to climate change, we profoundly ignore the mechanisms governing these processes.

This project will investigate how the rare microbial biosphere relates to ecological functioning. For this, we will employ a combination of experimental and computational approaches to study the dynamics of low abundance organisms in various habitats, covering more than 300 soil and extreme environment samples from around the globe. Special emphasis will be put on investigating the genetic variability and biodiversity of specific molecular functions, such as the ones related with the nutrients cycling, biodegradation.

Profile: Skills and clear motivation for a bioinformatics project. Previous knowledge and motivation for evolutionary and ecological questions. Aptitudes for big data statistical analysis, programming, use of bioinformatic software and large scale computations. Candidates must apply via FPI program, but are encouraged to discuss the details of the project prior to the application deadline by contacting to [email protected]

Principal Investigator: Jaime Huerta Cepas

Web: Comparative genomics and metagenomics

ENGINEERING MULTI-FUNCTIONAL MICROBES FOR PLANT-RELATED APPLICATIONS WITH SYNTHETIC BIOLOGY - CEX2020-000999-S-20-1

Project summary: The rational design and implementation of novel functions in microbes using synthetic biology approaches helps us reach new application domains. We are seeking a candidate who is passionate about understanding and engineering genetic circuits in bacterial cells for novel plant-microbe interaction strategies. Within the project, you will optimize existing genetic parts to work on different bacterial hosts; that is, to shape their context dependency behaviour. You will be using directed evolution methods to find robust and efficient parts and setting up modular cloning techniques for the high-throughput assembly of genetic circuits. You will also characterise constructs using flow cytometry to analyse gene expression noise. The project aims at engineering the bacterium Pseudomonas protegens to provide beneficial functions to plants and crops. The candidate will join a team of people that are already working on this direction.

Profile: Candidate should hold a bachelor’s and master’s degree in biology, biotechnology, microbiology, or related disciplines that allows them to be admitted to the PhD program.

Principal Investigator: Ángel Goñi-Moreno

Web: Biocomputation Lab

DECIPHERING NOVEL PLANT RESPONSES AND PLANT-MICROBIOME INTERACTIONS UNDER HEAT STRESS AND NUTRITION SCARCITY (ΜNUTRI-HEAT) - CEX2020-000999-S-20-2

Project summary: Climate change is already affecting plant growth and productivity. Different models predict that the impact of these changes will get worse, having a strong negative effect on food security. In addition, crop production will be further threated by the simultaneous concurrence of several stresses. The μNUTRI-HEAT project aims at analyzing the effects of heat stress and phosphate nutritional deficiency on plants. We will employ different genomics, transcriptomic and metabolomics tools to understand how plant adapt their growth and production under these two stresses. We will also screen for novel fungi that will enhances plant growth and productivity in tomato plants challenged to high temperatures and nutritional deficiencies. These fungi will be used as bioproducts to enhance plant resilience to adverse conditions. For this project, we will use a novel device that simulate the natural soil, TGRooZ. Using this approach, we will identify new genes involved in the response to heat and Pi starvation as well as microorganisms that might enhance plant growth and production under adverse conditions.

Profile: Candidate should hold a bachelor’s and master’s degree in biology, biotechnology, microbiology, or related disciplines that allows them to be admitted to the PhD program.

Principal Investigator: Juan Carlos del Pozo

Web: Regulation of lateral root development during nutrient deficiencies

UNLOCKING THE HIDDEN BIODIVERSITY OF PLANT-ASSOCIATED MICROBIOTA: FUNCTIONAL AND COMMUNITY STRUCTURE DYNAMICS OF LOW-ABUNDANCE ORGANISMS ACROSS TIME AND CROP CONDITIONS - CEX2020-000999-S-20-3

Project description: Microorganisms have a profound impact on plant health and growth. Many studies have focused on the analysis of abundant plant-associated microbes. However, it is currently acknowledged that microbial biodiversity is dominated by a large number of neglected low-abundance organisms that we have barely started to understand. Recent work suggests that this enormous fraction of elusive organisms might play a role in the plant-microbiome dynamics, affecting plant biomass production and resistance against environmental changes. It has also been postulated that low-abundance organisms could respond to niche adaptations, modulating the community structure of the plant microbiome. Nevertheless, our current understanding of the dynamics of low- versus high-abundance plant-microbiota remains largely anecdotal. Reasons for such a knowledge gap are twofold. Firstly, we lack genomic approaches that allow for phylogenetically-broad and high-throughput exploration of low-abundance plant-associated microbes. Secondly, very few studies have addressed the comparative study of plant microbiota at the large scale, investigating the effect of time, crop type and environmental conditions under the same controlled framework. Here, we aim at modelling the dynamics of the rare microbial biosphere associated with the phyllo- and rhizosphere, over time, under pathogen infection and at different nutritional conditions on three common crop types: tomato, pea and lentil. To do so, we will use a novel set of customly designed capture enrichment panels targeting the high-depth sequencing of several microbial gene families particularly informative for the evolutionary and functional characterization of plant-associated microorganisms and their interactions.

Profile: Candidates should have a clear motivation for a bioinformatics project, but wet lab experience will be valued (i.e. DNA extractions and metagenomic library preparation). Desired skills include: big data statistical analysis, programming, use of bioinformatic software and computing clusters and basic knowledge on microbiology and molecular biology techniques. Candidates must apply via FPI program, but are encouraged to discuss the details of the project prior to the application deadline by contacting to [email protected]

Principal Investigator: Jaime Huerta Cepas , Emilia López Solanilla

Web: Comparative genomics and metagenomics , Phytopathogenic bacteria

CSPINT-CBGP: INTERNATIONAL COLLABORATIVE SCIENTIFIC PROGRAMMES - CEX2020-000999-S-20-4

Project challenges: Agricultural soils and terrestrial ecosystems are essential for all life-sustaining processes on our planet. Healthy soils are essential for plant growth, development as well as for crop nutrition, yield, and long-term agriculture sustainability. However, current agricultural practices are rapidly depleting macro/micronutrients and altering soil microbial communities. In addition, climate changes, associated with adverse climatic conditions (drought, flooding, heat, ect.) are rapidly alerting and degrading soils ecosystems. We will lunch international collaborative projects with CEPLAS (Germany) to contribute to the recently approved EU Mission “Caring for soil is caring for life” and aims at understanding crops edaphic adaptation to develop a sustainable agriculture for the future. To achieve these challenges, we propose to develop additional tools from synthetic/cell biology, genomic, transcriptomic or epigenetic analyses, plant physiology, metabolomics, microbiome-associated plant improvement and integrative theoretical models, including gene regulatory/metabolic networks.

Profile: Candidate should hold a bachelor’s and master’s degree in biology, biotechnology, microbiology, or related disciplines that allows them to be admitted to the PhD program.

Principal investigators: Antonio Molina Fernández

Web: Plant Innate Immunity and resistance to necrotrophic fungi

ABOUT CENTRO DE BIOTECNOLOGÍA Y GENÓMICA DE PLANTAS (CBGP, UPM-INIA/CSIC)

The Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA/CSIC) is a joint research centre of the Universidad Politécnica de Madrid (UPM) and the Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), recently integrated as National Centre in the Consejo Superior de Investigaciones Científicas (CSIC). Since 2017 CBGP is a Severo Ochoa Center of Excellence and has been recently awarded a new SO accreditation for the period 2022-2025. The strategic objectives of CBGP are the generation of fundamental knowledge on the genetic and molecular bases of key biological and physiological processes in plants and plant-interacting organisms, and on genomics of plants and plant-interacting organisms. The Centre also aims to develop new Computational Biology technologies for the functional analysis of plants/microorganisms. CBGP has attracted many talented scientists since its foundation, including tenure-track positions, ERC Starting Grants, as well as CM Atracción de Talento, Beatriz Galindo and Ramon y Cajal researchers.