Biotechnology develops and applies microorganisms for the production of bioproducts with industrial interest. Next-generation-sequencing (NGS) plays an increasingly important role in improving and accelerating microbial strain development for existing and novel bioproducts via screening, gene and pathway discovery, metabolic engineering and additional optimization and understanding of large-scale manufacturing. NGS technologies have become main stream due to an important reduction in costs and an increase in sequence quality. However, data analysis still requires substantial bioinformatics expertise and adaptation to specific purposes due to the large datasets, data management and infrastructure supporting an NGS research facility. These challenges are particularly relevant in the research centers of the widening countries such as the case of the Centre of Biotechnology of Sfax (CBS) in Tunisia. In line with EU orientations and twinning requirements, NGS-4-ECOPROD aims to: (i) improve creativity, excellence capacity, and resources, (ii) raise the reputation, research profile, and attractiveness, and (iii) strength research management capacities and administrative skills in the CBS, through addressing the existing gaps in the field of NGS. NGS-4-ECOPROD project will allow CBS to exploit its NGS platform to develop original biotechnology products (extremozymes, sporeless biopesticides, antioxidant-ergothioneine, and bioplastics) useful as eco-friendly alternative to chemicals ones. This will be achieved thanks to the tight collaboration and networking activities (staff exchanges, workshops, conferences, training young researchers, and summer school activities) between the CBS and two leading well renowned research EU Partners in the field of NGS namely the University Claude Bernard Lyon 1 in France and the Georg August University of Göttingen in Germany. The NGS-4-ECOPROD will ultimately adopt an integrated communication and dissemination strategy with openness on the socio-economic sectors.

Insect pests can damage agricultural crops, consume and/or damage harvested food, in addition to diseases transition to humans and animals. Chemical insecticides and pesticides can affect human health directly or indirectly by disrupting ecological systems (air, rivers, lakes, oceans, streams, wetlands, forests and fields). At national and European levels, there is no regulation on the presence of pesticides in the air as it is the case for other pollutants typically. Since the early 1900s, Bacillus thuringiensis (Bt) bacterium group has received great attention, alternative to chemical products, for its use as an insect pest control agent, due to the parasporal inclusion production. The morphology of these inclusions may vary among Bt strains as bipyramidal, cuboidal, amorphous, spherical and irregular crystal morphologies can be observed. Previously it was believed to be important to end up with high spore counts. It was later shown that the spore count can give a good estimate of the growth of Bt in fermentation, but it does not always reflect the fermentation yield in terms of insecticide production since the amount of crystal protein, the main active compound, per bacterial cell can vary. Evaluation of these Bt products can be performed classically using several types of analysis ranging from bioassays to diverse biochemical methods. The main disadvantages of these methods are their expensiveness and their time-consuming character. Hence, an alternative physical method based on light scattering has been developed in order to quantify inclusion body formation and growth in recombinant cells. We recently showed that polarized speckle imaging method can be used to distinguish between Bt spherical crystal size and concentration within different fermentation products. In this project, we intend to extend our optical characterization, towards a real-time monitoring of the chemical fermentation reaction. Instead of embedding crystals into agarose gel to get rid of the Brownian motion, aqueous suspensions of crystals and/or spores will be studied; the reference Bt strains (HD1 and HD133) as well as isolated strains from Lebanese and Tunisian soil samples will be used. This project paves the way for potentially using laser polarized speckle at an industrial scale as a low-cost and non-invasive technique in order to characterize crystal geometry and to evaluate the yield of crystal production within fermentation. To achieve the objectives, the project gathers together experts in physics, chemistry and biology from three Mediterranean countries: France (UBO), Lebanon (USJ) and Tunisia (CBS).

In the Mediterranean region, crop production and food security are closely linked to the adaptation of cropping systems to multiple abiotic stresses, i.e. drought and salinity. Traditionally, monoculture practices are widespread in this area resulting in impaired the soil fertility and productivity. Furthermore, crop production is facing many challenges, such as climate change and population increase, particularly severe in the Mediterranean dry lands. Τhe strategic goal of BIOACT is to provide solutions for improving agroecosystem resilience to climate change, for decreasing GHG emissions and increasing carbon storage, and for reducing chemical inputs and waste production in the Mediterranean area. In this context, regenerative agriculture practices are considered as an efficient agronomic approach to improve soil and water conservation, to restore soil biodiversity, through the exploitation of wild crop relatives and the application of microorganisms-enriched composted organic waste, and to promote food security The proposed approach aims to improve wheat-based agroecosystem by developing a set of regenerative farming practices exploiting the biodiversity of wheat germplasm. This will be achieved by harnessing the selected drought tolerant durum wheat genotype from PRIMA EXPLOWHEAT project. Climate and stress-resilient wheat lines will be incorporated in intercropped wheat-legume systems in arid and marginal lands thriving in the Med region, to improve crop yield and quality and soil fertility. In addition, the functional indigenous microbial diversity will be explored to empower the wheat-legume intercropped system. BIOACT proposes a concept based on two main aspects: 1-introducing the cultivation of high-performance durum wheat cultivars in arid and marginal land of Mediterranean area; 2- developing agroecological practices exploiting the microbiome of the soil-wheat system. BIOACT will develop regenerative agricultural practices based on durum wheat plants intercropped with legume. Wheat and legume residues will be composted with wheat associated microbiome and enriched with Trichoderma to obtain an enriched compost to be incorporated before the successive wheat crop. Application of endophytic fungi as Trichoderma spp. could mitigate the harmful impact of abiotic and biotic stress and stimulate plant growth mainly enhancing the macronutrient availability from the organic substrate, while reducing in particular the potential lack of N, increasing NutUE and minimizing agro-chemical inputs decrease of losses due to Fusarium culmorum and associated mycotoxins negative impacts.

In Mediterranean countries, the olive industry represents a major agricultural sector, generating liquid and solid wastes (cake, stalks and wood residues) with detrimental environmental impacts (salinity, acidity and high polyphenol load). The PYRODIGEST project aims to render the olive oil industry more sustainable through a new integrated waste treatment system for the olive industry based on the principle of “industrial symbiosis”, associated with the production of high-value products. For this purpose, a hybrid energy system integrating anaerobic digestion, and pyrolysis processes will be tested and optimized, combining the production of multi-purpose energy carriers, fertilizer/amending, soil improver, and high-value products. The project provides an integrated approach for the treatment of both solid and liquid wastes from the oil industry in a circular economy concept. Solid wastes (wood, leaves, stone, pomace…) are treated through pyrolysis process, converting organic matter in syngas and bio-oil used as energy carriers, and biochar that can be used both as soil improver, or activated carbon precursor (high-value product). Liquid wastes (OMEs: Olive Mill Effluents) are treated through anaerobic digestion (AD), producing biogas as an energy carrier, and digested (stabilized) organic matter as fertilizer and soil improver. OMEs are rich in polyphenols, a strong inhibitor of AD processes, also causing environmental pollution due to its toxicity. To tackle this issue, polyphenols will be extracted prior to AD process in view of their recovery as marketable high-value product by adsorption on Activated Carbons using biochar from solid wastes pyrolysis as precursor. Subsequently, detoxified OMEs effluents will be degraded through advanced UASB (Upflow Anaerobic Sludge Blanket) technology, further optimized by the application of various biofilm supports (ceramic balls; plastics carriers and granular activated carbon). Finally, digestate and biochar generated in the hybrid system can be applied as high-value fertilizer and soil improver, reducing the industrial fertilizers use and answering the main concern of soil preservation. The synergistic application of biochar together with digestate can increase the retention of nutrients applied to the soil, thus improving plant uptake and reducing the leaching of nutrients, heavy metals and organic contaminants. Furthermore, due to its physico-chemical properties, biochar can also improve the water retention capacity and reduce soil acidity, which is of high interest for the Mediterranean agricultural soils. The main objective of the PYRODIGEST project is to develop a hybrid energy system providing fertilizer and soil improver for the preservation soil quality, fertility and organic matter, along with high-value products for local self-sufficiency and local economic development. The PYRODIGEST project will include seven partners in five countries (France, Turkey, Tunisia, Algeria and Morocco). Project partners will comprise universities (University of Mohammed VI; University of ORAN,Ege University), research institutes (General Directorate of Agricultural Research-Olive Research Center; Agropolymer Engineering and Emerging Technologies; Biotechnology Center of Sfax) and a private association (Association pour l'Environnement et la sécurité en Aquitaine).