Metagenomic for a better understanding of cultivated soil health

Soil health is defined as the ability of a soil to function as a vital, living ecosystem, supporting the growth of plant, animal and humain This capacity is highly dependent on the microorganisms living in the soil due to their role in biochemical cycles linked to the recycling and availability of nutrients such as carbon (C), nitrogen (N), and phosphorus (P). Due to their disruption of the soil microbiome, conventional farming practices negatively affect the long-term health of cultivated soils (Montgomery & Biklé, 2021). The establishment of soil’s health indices is a complex matter due to the grand variability of existing soil’s type, texture, soil physicochemicalcharacteristics, and the variation in crop’s needs. Those three cycle where chosen for their importance in the context of agricultural’s plants needs and those critical process include the fixation of atmospheric nitrogen and the recycling of nitrogen compound from organic matter and the production of acid and alkaline phosphatase by soil’s archeae, bacteria and fungy. Those process are deemed critical by the introduction in a usable form of critical nutriment to plant’s grow that are other wise in a unusable form for the plant. To this end, we observed the impact of 4 different kind of mulches, all with reduced tillage, and a standard treatment with conventional farming practice over a 3 years period, with two sampling per year, one in May and one in August. The obtention of the soil’s microbiome composition was done with the shotgun metagenomic technique using the AVITI plateform. The metagenomic shotgun technique was chosen for its capacity to obtain an overall picture of the population of fungi, bacteria, and archaea composing the soil microbiome in a single sequencing run, thus avoiding PCR bias due to multiple amplicon sequencing on the microbiome's proportions. In this presentation, the observed variation in the soil’s microbiome population du to the treatments and their impacts on the soil critical process will be explored. We hypothesize that the soil under the conventional treatment will have a lower redundancy level compare to the soil under the other treatment.

Lehmann, J., Bossio, D. A., Kögel-Knabner, I., & Rillig, M. C. (2020). The concept and future prospects of soil health. Nature Reviews Earth & Environment, 1(10), 544-553. https://doi.org/10.1038/s43017-020-0080-8

Montgomery, D. R., & Biklé, A. (2021). Soil Health and Nutrient Density: Beyond Organic vs. Conventional Farming [Review]. Frontiers in Sustainable Food Systems, 5. https://doi.org/10.3389/fsufs.2021.699147