Increasing productivity while using responsible practices is essential in the prospects of modern agriculture. In a context of increasingly demanding economic, societal and regulatory pressure, farmers are aware that they must change their farming practices by limiting the impact of their activity on the environment while maintaining their productivity.
In the case of field crops, the main limit of productivity is abiotic stress. To cope with these stresses and biotic stresses, farmers have no choice but to use more and more inputs. Among these inputs, plant protection products are mainly targeted with the prohibition of the use of a number of them, such as néonicotinoїdes. The alternatives are to select new resistant plant varieties, or even to develop GMOs with the time and regulatory constraints we know. With scientific advances, trends in new farming practices are integrating the plant into its environment (tryptic: plant, microorganisms, soil structure) to promote its intrinsic ability to defend itself. Bio-inputs are the first actors in these new practices.
The function of bioinputs, when applied to the plant or rhizosphere, is to stimulate natural processes to improve nutrient absorption and efficiency, tolerance to biotic and abiotic stresses, and increase crop quality. Identifying the actors of these associations remains an important challenge that Biointrant addresses by using the most efficient technologies.
Among the bacteria in the plant rhizosphere (rhizobacteria) that play an important role in the water supply of plants, those that modify the structure of the soil adhering to the roots have been studied in particular by the Biointrant scientific team. These bacteria derive their carbon and energy source from the plant's root exudates, which can represent 8 to 12% of the plant's photosyntheses (Nguyen, 2003; Haichar et al., 2014; Haichar et al., 2016).
Biointrant scientists have described a wide diversity of exopolysaccharide-producing bacteria (EPS) in a wide variety of soils (1) ranging from soils with very high clay contents (Amellal et al., 1998; Achouak et al., 1999) to very sandy ones (Heulin et al., 2003; Kaci et al, 2005), through saline soils (Ashraf et al., 1999) and (2) in the rhizosphere of several cultivated plants such as wheat (Gouzou et al., 1993; Amellal et al., 1998; Guemouri-Athmani et al., 2000; Kaci et al., 2005) and sunflower (Alami et al., 2000) or in that of a wild brassicas, Arabidopsis thaliana (Berge et al., 2009).
Biointrant scientists have also helped to highlight that the EPS produced by these bacteria, from root exudates, are very diversified in terms of their biochemical structure and physico-chemical properties (Hebbar et al, 1992; Falk et al., 1996; Alami et al., 1998; Villain-Simonnet et al., 1999; Villain-Simonnet et al., 2000; Vanhaverbeke et al., 2001; Vanhaverbeke et al., 2003; Rinaudo, 2004; Lodhi-Hassan et al., 2008; Crapart et al., 2012).
The microbial ecology of plants is a science at the frontier of many expertises, requiring the analysis of many data to understand phenomena. Advances in bioinformatics provide solutions to meet these analytical needs (In silico research strategy, see diagram).
Biointrant has developed tools to integrate bioinformatics into its optimized screening process. Genome annotation (Ortet et al., 2011, De Luca et al., 2011, Achouak et al., 2003) highlights bacterial properties of agronomic interest. Metadata analysis associated with genome exploration for database creation (Ortet et al., 2012; Barakat et al., 2013; Ortet et al., 2015) are combinatorial elements for selecting and understanding the most relevant associations.
The stimulation of plants by the use of bacteria is a 100% biological approach for which no solvents, treatment or purification are used. This technology has already proven itself on many crops. The positive effect of PSE on rhizospheric soil aggregation and/or plant growth has been demonstrated in laboratory conditions in wheat (Gouzou et al. 1993; Amellal et al., 1999, Bezzate et al., 2000; Alami et al., 2000), sunflower (Alami et al., 2000) and rapeseed (Santaella et al., 2008). Inoculation of a proprietary strain of Biointrant at sunflower crop planting (shown at right, after Allami et al., 2000) improved both the structure of the adhering soil and the structure of the plant itself.
Achouak, W., Christen, R., Barakat, M., Martel, M.-H., and Heulin, T. (1999). Burkholderia caribensis sp. nov., an exopolysaccharide-producing bacterium isolated from vertisol microaggregates in Martinique. International Journal of Systematic and Evolutionary Microbiology 49, 787–794.
Achouak, W., Conrod, S., Cohen, V., and Heulin, T. (2004). Phenotypic variation of Pseudomonas brassicacearum as a plant root-colonization strategy. Molecular Plant-Microbe Interactions 17, 872–879.
Alami, Y., Achouak, W., Marol, C., and Heulin, T. (2000). Rhizosphere soil aggregation and plant growth promotion of sunflowers by an exopolysaccharide-producing Rhizobiumsp. Strain isolated from sunflower roots. Applied and Environmental Microbiology 66, 3393–3398.
Amellal, N., Bartoli, F., Villemin, G., Talouizte, A., and Heulin, T. (1999). Effects of inoculation of EPS-producing Pantoea agglomerans on wheat rhizosphere aggregation. Plant and Soil 211, 93–101.
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Bezzate, S., Aymerich, S., Chambert, R., Czarnes, S., Berge, O., and Heulin, T. (2000). Disruption of the Paenibacillus polymyxa levansucrase gene impairs its ability to aggregate soil in the wheat rhizosphere. Environmental Microbiology 2, 333–342.
De Luca, G., Barakat, M., Ortet, P., Fochesato, S., Jourlin-Castelli, C., Ansaldi, M., Py, B., Fichant, G., Coutinho, P.M., and Voulhoux, R. (2011). The cyst-dividing bacterium Ramlibacter tataouinensis TTB310 genome reveals a well-stocked toolbox for adaptation to a desert environment. PLoS One 6, e23784.
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Gouzou, L., Cheneby, D., Nicolardot, B., and Heulin, T. (1995). Dynamics of the diazotroph Bacillus polymyxa in the rhizosphere of wheat (Triticum aestivum L.) after inoculation and its effect on uptake of 15N-labelled fertilizer. European Journal of Agronomy 4, 47–54.
Hebbar, K.P., Gueniot, B., Heyraud, A., Colin-Morel, P., Heulin, T., Balandreau, J., and Rinaudo, M. (1992). Characterization of exopolysaccharides produced by rhizobacteria. Applied Microbiology and Biotechnology 38, 248–253.
Kaci, Y., Heyraud, A., Barakat, M., and Heulin, T. (2005). Isolation and identification of an EPS-producing Rhizobium strain from arid soil (Algeria): characterization of its EPS and the effect of inoculation on wheat rhizosphere soil structure☆☆The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of Rhizobium sp. KYGT207 is AY675940. Research in Microbiology 156, 522–531.
Ndour, P.M.S., Gueye, M., Barakat, M., Ortet, P., Bertrand-Huleux, M., Pablo, A.-L., Dezette, D., Chapuis-Lardy, L., Assigbetsé, K., Kane, N.A., et al. (2017). Pearl Millet Genetic Traits Shape Rhizobacterial Diversity and Modulate Rhizosphere Aggregation. Front. Plant Sci. 8.
Ortet, P., Barakat, M., Lalaouna, D., Fochesato, S., Barbe, V., Vacherie, B., Santaella, C., Heulin, T., and Achouak, W. (2011). Complete genome sequence of a beneficial plant root-associated bacterium Pseudomonas brassicacearum. Journal of Bacteriology JB–00411.
Ortet, P., De Luca, G., Whitworth, D.E., and Barakat, M. (2012). P2TF: a comprehensive resource for analysis of prokaryotic transcription factors. BMC Genomics 13, 628.
Ortet, P., Whitworth, D.E., Santaella, C., Achouak, W., and Barakat, M. (2014). P2CS: updates of the prokaryotic two-component systems database. Nucleic Acids Research 43, D536–D541.
Santaella, C., Schue, M., Berge, O., Heulin, T., and Achouak, W. (2008). The exopolysaccharide of Rhizobium sp. YAS34 is not necessary for biofilm formation on Arabidopsis thaliana and Brassica napus roots but contributes to root colonization. Environmental Microbiology 10, 2150–2163.