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Before the Industrial Revolution, the concentration of CO2 in the atmosphere was 280 ppm and in time increasing fossil fuels use increased CO2 concentration up to 416 ppm in a preset time. Meanwhile, increasing population growth (around 8 billion) has also started to put serious pressure on soil ecosystem for more food production demand. With the demand for more food production, intensive chemical inputs and soil cultivation practices applied to the soil has increased the amount of CO2 released to the atmosphere. Increasing CO2 concentration in the atmosphere triggers global warming and climate change which is negatively affect plant growth and consequently food security. In order to ensure food security under climate change conditions, it seems that the need to re-enact nature’s own mechanisms has arisen. In this context, it is aimed to reduce the effect of climate changes by keeping more carbon as a sink by operating the effects of plant root mechanisms on the soil health according to ecological principles. Under long term filed conditions the effects of different soil-plant managements, especially mycorrhiza fungi, were investigated. Since 1996, several researches have been carried out under long-term field studies to see the effect of mycorrhizal fungi and other microorganisms on carbon sequestration, as well as the emission of CO2 from the greenhouse gases to the atmosphere. Regularly CO2 flux, emissions, photosynthesis rate, C, N sequestration and yield parameters are measured. Data are yearly evaluated. Results revealed that under long-term field conditions, organic fertilizers application and mycorrhizal inoculation sequestered more carbon in soil profile. It has been shown that, using animal manure, compost, biochar, nitrogen-fixing bacteria and mycorrhizal fungi significantly kept more carbon in plant tissue and soil. It is determined that there is an increase of 1.5 ppm CO2 concentration in atmosphere per year. It has been determined that especially long-term addition of organic matter and management of natural mycorrhizae increase soil organic carbon and accordingly soil quality and productivity increase. As the effect of climate change and population growth have significant negative impact on food security, definitely a new agriculture revelation is needed to overcome of climate and food security problem. Soil and plant management must be managed according to low-input ecological principles.