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RESEARCH TOPICS FOR XLI CYCLE

Second Selection procedure (published on May 30, 2025): 4 positions with grant

1 (one) position with grant to be carried out mainly at the University of Modena and Reggio Emilia (Italy) on the following Research topic:

Title: Microbes and microbial products impacting on health, environment, food, and sustainability
Scientific tutor: Alberto Amaretti
Hosting Institution: University of Modena and Reggio Emilia (Italy)

Microbial diversity represents an inexhaustible reservoir of biochemical and metabolic capabilities that remains largely unexplored. Microorganisms and their communities exhibit remarkable adaptability to various environments and possess the ability to produce and modify a vast array of molecules, compounds, enzymes, and other substances of great potential for health, environment, and industry.
The proposed research topic aims to explore fungal and bacterial biodiversity in order to identify metabolites and/or metabolic activities that may be relevant to human health and sustainable bioproductions.
The project will include characterization of complex microbial communities, including the human microbiome, and microbial isolates through culturomics, genomics and metagenomics. Bioreactor cultures of pure strains or consortia will be utilized to study the microbial metabolism, the interactions, and to develop fermentative processes yielding valuable chemicals or health-promoting nutraceutical products.

 

1 (one) position with grant to be carried out mainly at the University of Modena and Reggio Emilia (Italy) on the following Research topic:

Title: Polymicrobial fermentation by synthetic consortia to unravel microbe-to-microbe interactions in natural whey starter metacommunities for hard-cooked cheese production (MICROSOCIAL)
Scientific Tutor: Lisa Solieri
Hosting Institution: University of Modena and Reggio Emilia (Italy)

Polymicrobial fermentation using synthetic consortia mimics back-slopped fermentation carried out by natural microbial communities to improve food quality, while overcoming key limitations such as low predictability and poor standardization of the final product. This approach is emerging in various fermented foods, particularly in dairy products, thanks to significant advances in metagenomics that have enabled the definition of core microbial communities involved in fermentation.

Building on our previous project involving a biobank of natural whey starter (NWS) cultures used in the production of Parmigiano Reggiano PDO cheese, this PhD project aims to design synthetic consortia composed of core lactic acid bacteria species from NWS. The goal is to map species-to-species interactions and elucidate the specific metabolic contributions of each member in determining NWS acidification and cheesemaking performance.

This study will provide insights into the ecological forces shaping NWS communities, ensuring their resilience and effective acidification activity. To achieve these objectives, metagenomic and metatranscriptomic approaches will be employed.

A research period of at least six months will be carried out at a foreign research institution.

 

1 (one) position with grant to be carried out mainly at the University of Modena and Reggio Emilia (Italy) on the following Research topic:

Title: Integrated phenomics and genomics for cereal predictive breeding
Scientific Tutor: Nicola Pecchioni
Hosting Institution: University of Modena and Reggio Emilia (Italy)

The project aims at advancing cereal breeding, in particular wheat, for improving quantitative relevant traits as yield-related and quality-related one, for sustainable farming.

To reach the goal, the PhD candidate will search for improvements of genomic selection given by a number of approaches, in particular the use of digitally phenotyped traits, coupled with extensive use of machine learning and its bioinformatic developments.

In parallel, a set of standard phenomic tools will be used to study the diversity of germplasm collections for association genomics and for introduction into novel breeding programmes.

For the success of the project, the candidate will spend a period of at least 6 months at one or more foreign research institutes, where she/he will be able to develop further knowledge in the field of genomic selection and innovative plant breeding.

 

1 (one) position with grant to be carried out mainly at the University of Modena and Reggio Emilia (Italy) on the following Research topic:

Title: Assessing canopy microclimate and wetness conditions to improve growth and phytopathological status of fruit trees towards sustainable crop productions
Scientific Tutor: Francesco Reyes
Hosting Institution: University of Modena and Reggio Emilia (Italy)

The terrestrial hydrological cycle is by a large extent regulated by specific dynamics such as evapotranspiration, interception of precipitations and condensation at the canopy-atmosphere interface, and is affected by the microclimate conditions as well as by the micromorphology and distribution of canopies and the soil. The influence of these dynamics on crop productions is paramount, determining the availability of green (sustainable) water for the crops, as well as influencing the crop phytosanitary status and the need for phytosanitary treatments.

The PhD project aims at increasing our knowledge and ability to predict the dynamics of the hydrological cycle at the tree canopy-atmosphere interface, to enhance the management of commercial tree crops. The methods that will be used entail microclimate monitoring, analysis of canopy micro-morphology, process based and empirical modeling of canopy-atmosphere interactions, ecophysiological and plant growth measurements. Modeling will include both conceptual and numerical approaches, and will cover processes such as radiation propagation, interception of precipitation, translocation of water within canopies and the liquid to vapor change of water status. The knowledge, methods and models developed during the PhD course will be beneficial not only for the management of tree crops, but also for understanding aspects of the canopy-atmosphere hydrological cycle on herbaceous crops and non crop plants.

The candidate will spend a period of at least 6 months in a foreign university, where enhancing her/his skills on topics related to the study and start to develop her/his international scientific network

 

 

First selection procedure (published on March 12, closed on May 9th, 2025).

1 (one) position with grant to be carried out mainly at the University of Modena and Reggio Emilia (Italy) on the following Research topic:

Title: Multivariate analysis of spectral and image data for smart and sustainable applications in the agri-food sector
Scientific tutor: Alessandro Ulrici; Co-Tutors: Giorgia Foca, Rosalba Calvini
Hosting Institution: University of Modena and Reggio Emilia (Italy)

The agri-food sector is undergoing a transformation towards more efficient, sustainable, and data-driven decision-making processes. A key challenge in this transition is the need for rapid, non-destructive, and cost-effective analytical techniques that can be implemented in portable and real-time monitoring systems. This PhD research project will focus on the development and optimization of innovative chemometric methods for the analysis of multivariate data originating from different sensing technologies, including Near-Infrared (NIR) spectroscopy, RGB imaging and NIR hyperspectral imaging. These techniques provide valuable information regarding the chemical and physical properties of agricultural and food products. However, the large volume and complexity of the collected data require advanced multivariate statistical approaches to efficiently extract the relevant information. The research will aim to develop and apply state-of-the-art chemometric strategies to improve the predictive performance of spectral and image-based models, while reducing the computational effort. This will facilitate the implementation of real-time monitoring systems in various agri-food applications, such as enabling smart quality control, optimizing food processing, detecting defects or adulterants, and improving waste valorization in a circular economy framework.

Required skills: solid background in chemometrics, hands-on experience with spectroscopic and imaging data, strong problem-solving skills in an interdisciplinary environment, proficiency in MATLAB, and good communication skills in English. The PhD student is required to spend at least 6 months (not necessarily consecutive) at one or more foreign research institutions.

 

1 (one) position with grant to be carried out mainly at the University of Modena and Reggio Emilia (Italy) on the following Research topic:

Title: Acetic acid bacteria diversity: a challenge in the UMCC biobank
Scientific Tutor: Maria Gullo
Hosting Institution: University of Modena and Reggio Emilia (Italy)

The Unimore Microbial Culture Collection (UMCC) has started to collect and study acetic acid bacteria from different sources more than 20 years ago. During years, characterization and preservation methods of strains allowed to obtain several outputs on their metabolic abilities, the cultivation constraints, as well as on their potential role in the bioindustry.

This PhD project aims at providing a further advance in the knowledge of acetic acid bacteria. Main objectives are: 1) to obtain the whole genome sequencing and analysis of strains which are already known for their phenotypical traits of industrial interest; 2) to set-up new co-culture strategies using acetic acid bacteria in combination with members of other microbial groups for studying and evaluating improved strategies of co-cultivation, aimed at producing biomolecules of industrial interest. The information released from point 1) and 2) will be the basis for evaluating co-culturing as a new strategy for obtaining added value molecules from agro-wastes. 

To guarantee the scheduled timeline, the whole activities will be organized in a work-package system.  

Within this PhD, a period of research to conduct in a foreign research institute (minimum 6 months, not necessarily consecutive), is planned.

Required skills: High motivation to build up and conduct research activity at the home institution and in international research teams. Critical view of drawbacks and results analysis, high capacity to communicate results orally and in preparing scientific reports.

 

1 (one) position with grant to be carried out mainly at the University of Almeria (Spain) on the following Research topic:

Title: Sustainable strategies for the determination of microplastics and plasticizer in foods.
Scientific Tutors: Roberto Romero Gonzįlez, Antonia Garrido Frenich
Hosting Institution: University of Almeria (Spain)

Plastic contamination in the food chain has become a growing environmental and public health concern. In addition to microplastics (MPs) and microbioplastics (MBPs), plasticizers, particularly non-phthalate plasticizers, have gained attention due to their potential migration into food and possible health risks. For instance, non-phthalate plasticizers are increasingly used as alternatives to traditional phthalate-based plasticizers in food packaging and processing materials.

This PhD project aims to develop and implement sustainable analytical strategies for the determination of microplastics and emerging plasticizers in food matrices, focusing on minimizing the environmental impact of analytical methodologies, which will be based on chromatographic techniques coupled to mass spectrometry.

The research will integrate:

- Development and validation of green analytical methods for detecting MPs, MBPs, and emerging plasticizers in food samples.

- Investigation of plastic contamination sources, including food packaging, processing, and environmental exposure.

- Evaluation of toxicological implications and regulatory perspectives on microplastics and plasticizers in food.

This project will contribute to a more eco-friendly and efficient approach to monitoring plastic-related contaminants in food, integrating the principles of green analytical chemistry. The findings will provide valuable insights for food safety assessments, regulatory policies, and the transition towards sustainable materials in the food industry.

 

1 (one) position with grant to be carried out mainly at the Agricultural University of Iceland (Iceland) on the following Research topic:

Title: Enhancing Agroecological Transitions in the EU: Policy, Resource Efficiency, and Scaling of Innovations in Agricultural Living Labs (AELLs)
Scientific Tutors: Friederike Dima Danneil, Utra Mankasingh
Hosting Institution: Agricultural University of Iceland (Iceland)

Sustainable food production systems are urgently needed to protect our environment and ensure food security. This has driven the EU to promote agroecological transitions, yet policy gaps, resource inefficiencies, and scalability challenges remain significant barriers. Agricultural Experimental Living Labs (AELLs) provide an innovative framework to test and implement agroecological principles, but their success depends on well-designed policies, efficient resource use, and effective scaling strategies. This research is timely and relevant as it aligns with EU Green Deal objectives, Farm to Fork Strategy, and circular economy initiatives.

This PhD focuses on resource reuse in AELLs as a means of circular resource management by optimizing closed-loop systems to optimize resource flows (CO2 reuse) in circular farming and to identify key factors for scaling agroecological innovations. It will also examine current EU agricultural policy to offer insights into sustainable agroecological transitions. The project is suited for candidates in Environmental Sciences, Agricultural Sciences, Biogeochemistry, Agroeconomy, Public Policy, Environmental Economics, and other related disciplines.

A period of research will be conducted in a foreign research institute.

Required skills: 1) highly motivated to plan and conduct research, both at the home institute and with international partners; 2) critical thinking and problem-solving skills; 3) good knowledge of statistics and statistical software (e.g., R) or willingness to learn; 4) excellent oral and written communication skills and the ability to work effectively in teams; 5) circular economy concepts, or willingness to learn.

 

1 (one) position with grant to be carried out mainly at the Polytechnic University of Coimbra (Portugal)

Title: Alternative Proteins for a Sustainable Food System
Scientific Tutors: Marta Henriques, Carlos Dias Pereira, Davide Tagliazucchi
Hosting Institution: Polytechnic University of Coimbra (Portugal)

The project aims to explore and develop novel alternative protein sources that can help reduce the environmental footprint of traditional livestock production while meeting the growing demand for protein. These alternative proteins not only offer nutritional benefits comparable to conventional sources, but also provide opportunities for novel food formulations to meet diverse dietary preferences. Through advances in production technologies and evaluation of their environmental and socio-economic impacts, sustainable foods from alternative proteins promise to play a crucial role in shaping a more resilient and resource-efficient food system for the future.

This PhD proposal will focus on: 1) Identification, Production/Evaluation of the potential of innovative alternative protein sources for different food applications (e.g., algae, insects, fungi, cultured meat or others); 2) Characterization and nutritional quality assessment (purity and aminoacids profile, chemical composition, bioaccessibility, bioavailability, nutritional adequacy, techno-functional properties relevant for food formulation and human nutrition); 3) Allergenicity and Safety Assessment (determination of allergenic polypeptides, antinutritional factors, safety data for commercialization, possible contaminants); 4) Exploration of Emerging Technologies (investigation of emerging technologies to improve protein extraction, purification processes, and functional properties of protein concentrates/isolates from alternative sources); 5) Development of Food Prototypes (preparation and optimization of food prototypes incorporating selected alternative proteins (e.g. fortified foods, meat substitutes, hybrid products) and evaluate consumer acceptance through sensory analysis and assess market readiness.

By leveraging scientific innovation and international collaboration, the project aims to contribute to the development of environmentally friendly food products that meet global dietary needs while promoting sustainable practices in agriculture and food technology.

Include a research period in a foreign institution (e.g., Italy) to broaden perspectives and achieve European PhD certification.

Required Skills: High motivation for interdisciplinary research in sustainable food systems. Open-minded approach to innovative solutions and critical analysis of research outcomes. Strong communication skills for collaborating in international research teams and presenting findings effectively.

 

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