PhD Programme in Agriculture, Food and Environment

State of the art

Compared to a few decades ago, agricultural sciences have taken important steps towards the principles of sustainability. The limits of industrial agriculture – based on high consumption of fossil energy and extreme specialization – are now widely recognized, as is the positive value of ecosystem services related to agriculture. Nevertheless, agricultural sciences will face new and important challenges over the next decade. A large part of food in Europe is still produced with unsustainable techniques that involve a strong dependence on external inputs (feed, fertilizers, pesticides), high consumption of natural resources such as water and land, high levels of carbon and nutrient emissions in the environment and a simplification of production processes, which severely limits the natural cycle of nutrients and the conservation of biodiversity. However, population growth and the need to ensure safe access to food for the greatest number of people in the world are putting pressure on agricultural systems, which are also subjected to the challenges related to climate change. This scenario, on the whole, raises concerns about the resilience of agri-food systems and calls for adaptation and mitigation strategies that have also been mentioned in the recent COP21 agreements.

FAO, in defining the Sustainable Development Goals, has clearly indicated that agriculture in the coming decades will have to constantly reduce its environmental impact, improve access to food and strategic nutrients for a constantly growing world population, while guaranteeing a decent income to agricultural producers and helping to keep rural areas alive. It is therefore a question of guaranteeing the three cornerstones of sustainability: environmental, social, and economic. The use of a wide range of new emerging technologies – based on omics sciences, information technologies, robotics, artificial intelligence – will contribute to the achievement of these goals. At the same time there is an emerging need – already recognized by international organizations – for the innovation paths based on these technologies to integrate with agroecological principles, so that production systems are redesigned taking into account the specificities of rural communities and territories in which they develop. In this context of growing demand for enabling technologies capable of improving the efficiency of agricultural systems by reducing their environmental impact, there is the need to fully seize the opportunities offered by the so-called “bioeconomic revolution”, based on strong progress in the transformation processes of biomass in bioproducts.

The PhD program

The PhD program of Agriculture, Food and Environment is a three-year post-graduate research course at the homonymous department (DAFE) of the University of Pisa. The University of Pisa (UNIPI) is one of the most important universities in Italy and has a long tradition of excellence in terms of education and scientific research. The Department of Agriculture, Food and Environment is dedicated to research at the frontiers of agricultural, food and agro-environmental sciences. The Director of DAFE is currently Prof. Marcello Mele ( and the teaching staff consists of 69 professors and researchers.

The PhD program moves from the awareness that food sustainability is a goal to be achieved through a set of activities that range from production to consumption, involves a myriad of actors and mobilizes natural and human-made resources. Focus on sustainability implies that specialization of agricultural science, necessary to deal with increasing complexity, is accompanied by a strong commitment to take into account systemic implications, including unintended consequences of given technological solutions.

Sustainability is also a multidimensional concept, and its assessment can be carried out against a multeplicity of criteria, namely environmental, social, economic, and health-related, so that the choice between technological trajectories may face trade-offs, contradictions, different perspectives and interests. For this reason, a large involvement of stakeholders in the definition of sustainability goals, research goals and methods is needed.

Aims and scope

The PhD course in Agricultural, Food and Agro-environmental Sciences aims to train researchers (also through agreements with external public and private bodies and with the business world) who have the necessary skills to face the challenges of sustainability in the agri-food sector and the need to ensure the greatest efficiency of production systems, food high nutritional quality, and safe access to food. To this end, the main research topics developed within the PhD program concern: the study of sustainable and resilient agricultural systems with respect to the challenges of climate change; the application of plant, animal and microbial biotechnologies; the application of the principles of agroecology to production systems; the study of ecology, physiology, genomics, proteomics and metabolomics of animals and plants for food use; the development of sustainable food technologies; the study of the quality of plant and animal foods and of the main genetic and environmental factors that determine their variability; the application of enabling technologies for the development of precision farming systems in the context of plant and animal production processes; technologies for plant and soil protection and environmental remediation, even in urban environments; the development of technologies for the application of the principles of the bioeconomy, with particular reference to the use of by-products of the agri-food supply chains for the production of feed, fertilizers, soil improvers, biostimulants and as sources of substances with a nutraceutical effect.

Given these premises, the Phd course has as central theme ‘Food sustainability’ and can be ascribed to the EC “Food 2030” strategy. It refers to different ERC areas as LS9 (Applied Life Sciences), LS2 (Genetics, Genomics, Bioinformatics and Systems Biology), SH3 (Environment, Space and Population), SH1 (Individuals, Institutions and Markets). The course aims at training researchers with an up-to-date, excellent disciplinary ground and with a deep understanding of the systemic implications of their specific field of activity and awareness of the importance of mutual learning with enterprises, administrations and civil society.

To this purpose, we have built an interdisciplinary program combining agricultural sciences with a selected range of biological disciplines. Its scope is articulated around three main areas:

  • biological basis of food sustainability
  • sustainability of food production systems
  • food quality and safety

The Phd program encourages the development of a common systemic approach through its training program, which is centered upon the principles of sustainability science, and through its partnership strategy. In this sense, specific agreements with external institutions (Italian National Research Council, F.A.O.) and also with some firms (as for example ABOCA s.r.l.) are established for specific research themes, with double (university and external institution) supervision.

The PhD program and the National Recovery and Resilience Plan

Some PhD scholarships will be funded or co-financed by the Ministry of University and Research (MUR) through the National Recovery and Resilience Plan (NRRP). In fact, the educational objectives of the PhD course are consistent with the issues of the NRRP relating to the green and ecological transition of the economy and the society and with the digital transition and the technological innovation needs of companies and public administrations. In particular, in the first case, various scientific disciplinary sectors relating to the doctorate have active research lines in the field of agroecology, the protection and conservation of agricultural biodiversity, the circular economy, the reduction of chemical inputs, the reduction of gas emissions. greenhouse effect and the release of nutrients into the environment, with reference to both agricultural processes and those of food processing and conservation.

In the wake of the tradition that has seen the agricultural school of Pisa engaged since its foundation in the development of sustainable agriculture models, the research lines of the department that are expressed in the PhD program pay particular attention to the ecological transition of agriculture through the introduction of innovations that make agricultural systems more sustainable. The experimental facilities of the “Enrico Avanzi” Agro-environmental Research Center of the University of Pisa (to which almost all the teachers of the college belong) also guarantees the possibility for PhD students to carry out research on different scales and to obtain results readily transferable to agri-food companies. In the second case, there are just as many research initiatives related to the development of enabling and intelligent technologies to improve production efficiency and the sustainability of agricultural and transformation processes and to make more effective the certification and quality control systems of products and processes. The research lines on precision agriculture cover all areas of agricultural production, from crops to livestock and provide for applications both at the level of primary production companies and at the level of food companies. The models and tools dedicated to fostering the digital transition do not neglect the need to involve the public administration as well, envisaging digitization approaches that are also useful in those sectors of the public administration dedicated to the development and implementation of European policies in the agri-food sector, consistent with plans of rural development. These lines of research are active on both European and national projects. The activity of the scientists of the PhD board in technology transfer is also very significant, an aspect that guarantees a broad applicability of the results of these lines of research to the world of agri-food companies and a higher probability for PhDs to achieve important work positions. In fact, the disciplinary areas and the issues addressed are consistent with the needs of the country, as well as of the regional territories interested in the PhD program, in terms of highly qualified figures oriented to meet the innovation needs of the companies referred to in the PNRR.

PhD Program overview

The Doctorate Board includes 21 professors and researchers at the University of Pisa and four senior scientists at research institutes and universities in Italy or abroad. Currently, more than 50 PhD students are attending the course or are waiting for the final examination; ten students come from overseas universities.

The Doctorate Board for the academic year 2022-2023 is composed as follows:

Faculty members: Monica Agnolucci, Luciana Angelini, Daniele Antichi, Iduna Arduini, Gianluca Brunori, Angelo Canale; Andrea Cavallini, Riccardo Gucci, Lorenzo Guglielminetti, Lucia Guidi, Andrea Lucchi, Rossano Massai, Marcello Mele, Cristina Nali, Lucia Natali, Alberto Pardossi, Elisa Pellegrini, Laura Pistelli, Michele Raffaelli, Andrea Serra, Angela Zinnai.

External experts: Allison Marie Loconto (INRA, France), Beatrice Pezzarossa (CNR, Pisa), Barbara Ruffoni (CREA, Sanremo), Andrea Scartazza (CNR, Pisa).

The PhD program essentially consists in conducting an original research work under supervision and writing a dissertation (thesis) concerning the following topics:

  • food science and technology;
  • genomics, proteomics and metabolomics of species of agricultural interest;
  • multifunctional agriculture;
  • plant and animal production systems, even in urban environment;
  • plant physiology, ecology and biochemistry;
  • plant, animal and microbial biotechnologies;
  • technologies for plant and soil protection and environmental bioremediation.

Each PhD student is supported by a supervisor and a co-supervisor, of which at least one belongs to DAFE. The official language of the PhD course is English.

Activities planned during the PhD course (2022/2025, XXXVIII cycle)

The PhD students participate in educational activities such as courses, seminars, summer schools and congresses organized by the University of Pisa or other institutions in Italy or abroad, following a tailor-made training plan aimed at achieving in-depth knowledge of specific scientific issues and improving general skills.

In particular, during the first and the second year, the PhD students will attend courses and seminars organized in part by the University of Pisa for all its PhD students and in part by the PhD itself, which will offer specific courses for its students.

The so-called “transversal” activity, organized by the University of Pisa for all its PhD students, will include a “Scientific English” course (mandatory), an “Open Science and Research Data Management” course, a “Statistics for research” course, a “Computer Tools for Research” course, a “Research Promotion” course, and a “Responsible Research and Innovation” course. These courses will be held in the period January-June 2023.

PhD students in Agricultural, Food and Agro-environmental Sciences will also attend some ad hoc organized courses, such as “Fundamentals of Statistics for Agricultural Research” (1st year, 20 hrs – held by Prof. G. Conte, in March-April 2023), “Publishing in International Scientific Journals” (1st year, 10 hrs – held by Prof. G. Benelli, in June 2023), and “Innovative methodologies in Agricultural Sciences” (2nd year, 12 hrs – held by a teacher yet to be established, in may 2023).

All the PhD students will be invited to spend at least six months in renowned research institutes abroad during the second and/or third year of the course.

At the end of each year, each PhD student prepares a report on his/her academic and research activities and holds a public seminar, which will be evaluated and approved by the Doctorate Board.

To achieve the title, the candidate must have published at least one article in an indexed scientific journal. At the end of the course, the thesis (in English) will be preliminary evaluated by two external referees belonging to other Universities in Italy or abroad. Finally, the PhD degree will be awarded after a public examination in the form of defense of the dissertation in front of a committee, which is appointed by the Doctorate Board.

From 2020 to 2022, PhD students at DAFE have published more than 300 articles, including research or review papers in peer-reviewed journals or in conference proceedings. In total, these papers were cited nearly 800 times.


The admission call for 2022 will be open in June and the selection will take place in early September. The candidates should check the website  regularly for additional information on application, in particular on the date and the venue of interview.

Candidates are required to have a Master’s degree and have to demonstrate good knowledge of the research themes reported above. The Doctorate Board establishes a number of research lines available each year for PhD students, which are listed below.

The number of graduates students admitted to the course varies from year to year depending on the number of grants available and the results of the selection process.

The last year (cycle XXXVII, 2021-2024) thirteen grants were available, one of which was reserved for candidates who completed their Master’s Degree abroad.

The scholarship consists of a salary of approx. € 13,600 per year (in addition to the social security contribution) for the whole duration of the PhD program (3 years maximum). The grant is increased by 50% if the student does an internship (at least 15 days) abroad in a foreign academic or research institution. Each year, each candidate receives an annual research contribution of approximately € 1,600.

The selection of PhD candidates will be based on their educational (f.i., average exam grade, final numerical grade for the entire degree, honor etc.) and scientific (publications, positions as young scientist, stage abroad etc.) curriculum and on an interview conducted on their master thesis and in one of the research lines available each year for PhD students, which will be reported on this webpage as soon as delivered by the Doctorate Board.

Candidates may also be admitted, at any time, under the supernumerary category if they hold a grant funded by the European Union or, in the case of non-EU citizens, by their country of origin.

2022 Research Lines

The research lines available for the 2022 PhD program are as follows:

  • Mechanization in digital agriculture for sustainable farming systems
  • Biofertilizer and biostimulant microorganisms for the improvement of use efficiency of soil natural resource and water by plants
  • Precision farming and agroecology for sustainable management of cropping systems
  • Enhancement of the sustainability of Tuscan viticulture and grape quality in the context of climate change through innovative canopy management techniques
  • Molecular technologies for analysis, conservation and valorization of crop plant biodiversity
  • Dissecting the halophytes role in the context of climate change: molecular, physiological, and biochemical strategies behind their adaptation to saline soil and potential exploitation as cash crop
  • Application of smart technologies in livestock farms aimed to improve animal welfare and efficiency
  • Recycling of cigarette butts as growth substrate for ornamental plants: a circular economy example
  • Sustainable management of invasive alien species (IAS) to support biodiversity and ecosystem resilience: Comparative analysis of morpho-functional traits and adaptation to climate change of alien and native plant species

Other PhD grants will be specifically dedicated to these research lines (see Application):

  • Design and implementation of a local food policy (funded by MUR/NRRP)
  • Costs and benefits of digital technologies in agriculture
  • Food policies and social innovation
  • Measuring the sustainability of livestock production (funded by MUR-NRRP “National Centers”)

Other PhD grants are co-funded by MUR/NRRP and by companies (see Application):

  • New sources of fertilisers from industrial wastes and innovative agronomic
    solutions to improve soil fertility and plant nutrient use efficiency for sustainable and high-
    quality agricultural production (co-funded by Ferro Duo Italia s.r.l.)
  • Turf management aimed at maximizing net carbon sequestration using new technologies (co-funded by Euroambiente s.r.l.)
  • Investigation of the mechanisms of action of natural bioactive compounds: antifungal activity and induction of plant defence responses (co-funded by KWIZDA Agro GmbH)
  • Ingredients with high nutraceutical value obtained by food byproducts and environmental friendly packaging systems to increase the shelf life and reduce the waste of bakery products (co-funded by Barilla G&R Flli)
  • Intelligent sensors and laser spectroscopy for improving quality and prolonging the shelf life of food without chemical additives (co-funded by Antares Vision S.p.A.)


  • Coordinator: Prof. Andrea Cavallini, DAFE,
    via Del Borghetto 80, 56124 Pisa (Italy)Tel. +39 050 2216 663; email:
  • Secretariat: Dr. Stefano Fanti, DAFE,
    via Del Borghetto 80, 56124 Pisa (Italy)Tel. +39 050 2216 083; email: