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PROTINUS Report Summary

Project ID: 645717
Funded under: H2020-EU.1.3.3.

Periodic Reporting for period 1 - PROTINUS (PROviding new insighT into INteractions between soil fUnctions and Structure)

Reporting period: 2015-01-01 to 2016-12-31

Summary of the context and overall objectives of the project

The PROTINUS project assembles a multi-disciplinary team from the EU and three associated countries, viz. France, Italy, Denmark, New Zealand, Mexico and Japan These teams combine advanced, experimental and theoretical research expertise in soil physics and chemistry, microbiology, image analysis, computer sciences, and systems modelling to develop a new standard in modelling the interactions between soil structure and soil functions. This project proposes an interdisciplinary integrated methodology based on imaging and analysis of soil structure to allow modelling and predicting soil functions. Soil structure impacts a range of services that soil renders to humans, including for example, contaminant filtering, gas regulation, and nutrient cycling. Quantifying dynamics of the microstructure of soils will allow evaluating the impact of soil management on these ecosystem services, and thereby, will assist in developing ways to reduce the environmental footprint of anthropogenic activities. The development of an integrated methodology is only possible by bringing together experts in soil science, hydrology, microbiology, reactive transfer modelling, imaging and image processing.

Our project aims to answer the following questions:

• Can trans-disciplinary understanding and sharing of standards developed separately in different research areas provide a way to foster synergies between disciplines?
• Can synergies be found between the four pillars to develop a new trans-disciplinary approach?
• Can a trans-disciplinary approach to the understanding of the interaction between soil structure and functions improve current theoretical understanding?
• Can each of the four pillars benefit from a new trans-disciplinary approach?

Our specific objectives are to:
• Put together best and up-to-date best practices in soil science, image processing, and soil functions modelling;
• Confront, adapt or improve these practices in the framework of an integrated multidisciplinary methodology;
• Use this integrated methodology to challenge nowadays theory on mathematical description of soil functions;
• Develop new strategies and approaches to build transversal paradigms.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

"Since the beginning of the project, part of work package 1 was achieved, and work packages 2 and 3 were finished.
Within work package 1 ""Coordination, management and dissemination"", the Partnership Agreement was implemented, a kick-off meeting and an international conference and summer school were organsised. Regular communication among partners and with the public was organised through the emails, meetings and a website. Conferences, lectures, reports and scientific articles allowed the dissemination of the project results.

The work package 2 is the first scientific work package, entitled: “Understanding today’s best practice across discipline”. The objectives were to gather knowledges on all disciplines involving all project participants and identify potential improvements in each research area. Supplementary funding was also gathered to support our experiments (for example from JSPS Japan/France, University of Grenoble Alpes (France) and The University of Auckland (New Zealand)).
This work package allowed our multi-disciplinary team to set the pace of our research project by first gathering all our knowledge in the respective field of interests, explore the most promising approaches currently developed, and propose improvements using shared experimental material. Each partner has compelling expertise in different areas of soil science, going from soil physics, soil chemistry and soil microbiology to image processing. By reviewing our expertise and the current state-of-the-art through extensive literature search, we could develop adequate experimental protocols, modified CT scanning methods, image processing practices and modelling approaches. The biggest events during this work package was the organisation of our 1st international workshop in Grenoble (20-22 July 2015), the 2nd one being held in Auckland, New Zealand (20-22 January 2016), and the generation of a technical report on best practices in CT scanning, image analysis, soil experiments and modelling. These best practices were further tested on the same material in France, Japan, Mexico and Italy at their respective institute’s imaging facilities.

The work package 3 entitles “Implement multi/trans-disciplinary protocols”. The objectives were to confront restrictions, limitations and requirements in each discipline. When necessary, we developed new or improved existing protocols for experiments, image acquisition and analysis, and modelling, and explore their limitations and advantages. We especially confronted each discipline by coupling Imaging and Analysis, Modelling and Theory, Analysis and modelling, and Theory and Modelling. To complete the 4 tasks listed in Work Package 3, the following key experiments were selected to test these protocols:
- Imaging of printed porous network from CT scanned soil core
- Multiphase behaviour of sandy soils and multiphase segmentation
- Correlation between simulated flow with the SPH method and key parameters describing the pore network typology of an Andosol
- Development of variation on the kriging segmentation techniques using a image J java based programming platform

This work package was also a strong year for lectures and training. The largest event was the organisation of our first summer school in Grenoble-France (18-20 July). This three days summer school aimed at presenting up to date practices and methodologies used for 3D or 3+1D (3 spaces and 1 temporal dimensions) observations of porous media. We invited one keynote speaker (Steffen Schlüter, UFZ Germany) and we had 10 speakers, all participants to the project. 10 students attended the school, 8 of them were PhD students and 2 engineers. 6 of them were French and 4 from all over Europe. We also organised lectures for postgraduate students of the Computer Science Department at The University of Auckland (New Zealand) in January 2016, at the Geology Institute at la UNAM, Mexico, and at Kumamoto University (Japan)."

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The PROTINUS project offers a unique opportunity for all the academic participants to consolidate their knowledge in their specific field. It has been the case during the different workshops and schools the participants organised during these two first years. By selecting key experiments, it allowed PROTINUS participants to investigate new topics related to soil experiments, tomography image acquisition, image analysis and modelling. The project also created a new theoretical perspective for our industrial partner Novitom (spin-off from University of Grenoble) with the development of new post-processing interface. The collaboration between soil scientists and image specialists gave way to the development of soil analysis algorithms capable of providing information of the morphological properties of different types of soils datasets obtained through micro tomography. Using the methods and algorithms developed during the PROTINUS project, three scientific papers have been published. The algorithm is also been tested in the “Laboratorio Nacional De Manufactura Aditiva, Digitalización 3D y Tomografía Computarizada (MADiT)- UNAM” in order to develop an industrial implementation of the system.

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