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PROviding new insighT into INteractions between soil fUnctions and Structure

Periodic Reporting for period 2 - PROTINUS (PROviding new insighT into INteractions between soil fUnctions and Structure)

Reporting period: 2017-01-01 to 2018-12-31

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 aimed 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?

The main results of PROTINUS project were:
• 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.
"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”. 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 ( July 2015), the 2nd one being held in Auckland, New Zealand ( January 2016), and the generation of a technical report on best practices in CT scanning, image analysis, soil experiments and modelling.

The work package 3 entitles “Implement multi/trans-disciplinary protocols”. The objectives were to confront restrictions, limitations and requirements in each discipline. 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, following key experiments were selected to test these protocols=.
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 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).

The work package 4 entitles ""Create a unified trans-disciplinary approach "". A detailed protocol for acquiring and analysing images was proposed for void and soil organic matter localization. New data analysis algorithms (segmentation, characterisation) integrating a priori knowledge (structure, heterogeneity) were tested. Two-dimensional pore-scale numerical model was developed to investigate the main mechanisms governing biofilm growth in porous media and results of the numerical simulation were presented. An emphasis was put on applying fundamental concepts of fluid mechanics, thermic and contaminant transport to simulate transport phenomenon in the pore volume of soils.
During WP4, series of master and PhD courses in Grenoble, Kumamoto, Mexico and Auckland, were organised on image analysis techniques, multiscale approaches and upscaling and soil physics, mechanistic and stochastic modelling approaches for transfer in porous media. In July 2017, an international workshop in Kumamoto was co-organised between PROTINUS and IROAST which allowed all PROTINUS partners to present their work.

In the last work package (WP5), we tested and validated our unified protocols investigated in WP #3 and developed in WP#4 and new computational models using outcomes of experiments completed in WP#2 and #4, with analysis techniques discussed in WP #2 and improved in WP#3. The different steps were presented during our spring school in Bologna in march 2018 and is also being published in a special issue on PROTINUS in Soil Research special issue which is going to be published mid
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The breakthrough of PROTINUS project is the publication of an integrated methodology coupling up-to-date soil experiments and imaging protocols and modelling techniques at the pore scale. The project also created a new theoretical perspective for our industrial partner Novitom with the development of new post-processing interface. Examples of the application of this methodology were published in 12 scientific papers and a special issue in Soil Research will be released mid 2019. Another potential breakthrough is the release of segmentation tool that couple expert vision and up-to-date techniques that are adapted to soils.

The scientific community of soil and agricultural science can benefit from research advances and the trans-disciplinary approach that was developed within PROTINUS. For instance, the advancements in the mutual collaboration of scientists from different disciplines (engineers, soil and agricultural scientists, computer scientists) has provided new approaches for understanding, gas movement in differently managed agricultural soils with implications for the crop productivity and sustainability of agricultural practices. This impact is illustrated by the workshop conjointly organised by PROTINUS and the Italian Association of Agronomy in March 2018. Similarly, the understanding soil organic matter dynamics with a trans-disciplinary approach in PROTINUS is strategic: soil organic matter has been recently adopted by the UN for implementation of Sustainable Development Goals.
Reconstructed porous network of a soil cube
water flow as simulated by SPH method in a soil pore
worm cavities as seen by CT scan in a soil sample
Roots seen by CT scan at different resolutions