Abdelrahman ALAHMAD

Doctorant
Equipe: AEB
abed_ahmd@outlook.com

Sujet de la thèse

« Study of the interaction plant-rhizosphere-microorganisms in a framework of ecologically intensive agriculture ».

Mots-clés

Agricultural Practices, Ecology, Plant-Soil Interaction, Ecological Intensive Agriculture, Tillage, Cover crops, Soil biodiversity, Bacteria, Fungi, Metagenomics, Sequencing

Résumé

According to demographic projections, world population will reach 9 billion people by 2050 (FAO, 2009). This increase will be associated with higher demand of agricultural products. Although intensive agriculture using high agricultural inputs and tillage has allowed sufficient food production to meet the global demand (Odegard and van der Voet, 2014), an important ecological cost and the degradation of ecosystem services was observed in return (Tilman et al., 2001; Fawcett and Towery, 2002). Therefore, alternative / innovative approaches are envisaged to meet global demand (Rosenzweig, 2003; Fedoroff et al., 2010). From them the ecologically intensive agriculture is strongly supported due to the fact that based on three principles: (i) minimum soil disturbance, (2) presence of a permanent soil cover and (3) diversification of crops cultivated (crop rotation) and / or associations (intercroping). These approaches should help to reduce soil degradation, to increase soil organic matter, soil biodiversity, infiltration rate, water storage, carbon sequestration capacity and the profitability of the crop production (Vanlauwe et al., 2010: Corbeels, 2012; Brouder and Gomez-Macpherson, 2014 ; Derpsch et al., 2014 ; Pittelkow et al., 2015). These new agricultural practices will therefore influence the properties of the soil; however plants and physico-chemical properties of soil are environmental filters which are highly involved in the microbial soil (Zhao et al., 2014). Therefore moving from intensive to ecologically intensive agriculture should lead to modifications in soil biodiversity (Schipanski et al., 2014). Using an experimental system allowing comparison between conventional tillage practices and no-till associated with direct seeding with or without permanent cover, studies of the taxonomic and functional soil microbial diversity (bacteria, fungi and micro-eukaryotes) will be undertaken. This will be achieved by high-throughput sequencing of the hypervariable regions of the genes encoding RNA16S (bacteria) and 18S (fungus and micro-micro-eukaryotes), but also by sequencing of specific genes such as nif, nosZ, amoA which are involved in nitrogen cycle. Sequencing will be performed using an Illumina platform (MiSeq, Illumina 2013) and the sequences obtained will be analyzed using various bioinformatic tools (MG-RAST, mothur).

In addition, there is a strong relationship between the plant genome and the composition of the microbial soil biodiversity (Gaba et al., 2014; Lakshmanan et al., 2014 ; Schlatter et al., 2014) constituting a crucial asset for the plants adaptation (Liebig et al., 2012). Metagenomic approaches will also be undertaken to assess the role of plant genome (crop and covered) in microbial community structure.

Références

Brouder, S.M. and Gomez-Macpherson, H. (2014) The impact of conservation agriculture on smallholder agricultural yields: A scoping review of the evidence. Agric. Ecosyst. Environ., 187, 11–32.
Corbeels, M. (2012) Agro-ecological attributes of Conservation Agriculture for sustainable land use. Agro Env. 2012.
Derpsch, R., Franzluebbers, A.J., Duiker, S.W., Reicosky, D.C., Koeller, K., Friedrich, T., Sturny, W.G., Sá, J.C.M. and Weiss, K. (2014) Why do we need to standardize no-tillage research? Soil Tillage Res., 137, 16–22.
FAO (2009) How to feed the World in 2050, FAO, Food and Agriculture Organization of the United Nations.
Fawcett, R. and Towery, D. (2002) Conservation tillage and plant biotechnology: how new technologies can improve the environment by reducing the need to plow.
Fedoroff, N.V., Battisti, D.S., Beachy, R.N., et al. (2010) Radically Rethinking Agriculture for the 21st Century. Science, 327, 833–834.
Gaba, S., Bretagnolle, F., Rigaud, T. and Philippot, L. (2014) Managing biotic interactions for ecological intensification of agroecosystems. Agroecol. Land Use Syst., 2, 29.
Illumina. (2013) MiSeq Reporter Metagenomics Workflow.
Lakshmanan, V., Selvaraj, G. and Bais, H.P. (2014) Functional Soil Microbiome: Belowground Solutions to an Aboveground Problem. Plant Physiol., 166, 689–700.
Liebig, M.A., Franzluebbers, A.J. and Follett, R.F. (2012) Managing Agricultural Greenhouse Gases: Coordinated Agricultural Research Through GRACEnet to Address Our Changing Climate, Academic Press.
Odegard, I.Y.R. and Voet, E. van der (2014) The future of food — Scenarios and the effect on natural resource use in agriculture in 2050. Ecol. Econ., 97, 51–59.
Pittelkow, C.M., Liang, X., Linquist, B.A., et al. (2015) Productivity limits and potentials of the principles of conservation agriculture. Nature, 517, 365-368.
Rosenzweig, M. (2003) Win-win ecology : how the earth’s species can survive in the midst of human enterprise, Oxford University Press.
Schlatter, D.C., Bakker, M.G., Bradeen, J.M. and Kinkel, L.L. (2014) Plant community richness and microbial interactions structure bacterial communities in soil. Ecology.
Tilman, D., Fargione, J., Wolff, B., et al. (2001) Forecasting Agriculturally Driven Global Environmental Change. Science, 292, 281–284.
Vanlauwe, B., Bationo, A., Chianu, J., et al. (2010) Integrated soil fertility management Operational definition and consequences for implementation and dissemination. Outlook Agric., 39, 17–24.
Zhao, J., Ni, T., Li, Y., Xiong, W., Ran, W., Shen, B., Shen, Q. and Zhang, R. (2014) Responses of Bacterial Communities in Arable Soils in a Rice-Wheat Cropping System to Different Fertilizer Regimes and Sampling Times. PLoS ONE, 9.

Publications

Conference Paper: Relations entre diversité microbienne et contamination métallique dans des sols industriels. (Oct 2015)

Conference Poster: Dynamique des paramètres physico-chimiques et microbiologiques des luvisols loessiques après défrichement. (Les Journées Condorcet July 2015, At Compiègne)

Conference presentation: Impact d’un couvert végétal permanent sur la biodiversité microbienne du sol. ((Les Journées Condorcet January 2016, At Reims)