The atmospheric carbon dioxide (CO2) concentration has increased by 31 % since the onset of industrial revolution around 1850, from 280 ppm/year to 400 ppm/year in 2013. Chemical fertilizers, pesticides, tillage, irrigation and seed use improvements have increased agricultural production. Moreover, agricultural mismanagement may have affected atmospheric CO2 through the intensified degradation of soil organic matter (SOM). Water deficiency, high temperatures and land degradation could be the result of increasing atmospheric CO2 concentrations, particularly in semi-arid Mediterranean regions. High temperatures, decreased water availability and post-harvest straw burning in preparation for the next crop reduce the soil organic carbon (SOC). Note that soil quality and productivity are also declining. In addition, the intensity of climate change is expected to increase. Soil provides a sink for atmospheric CO2 and therefore reduces net CO2 emissions associated with agricultural ecosystems, mitigating the 'greenhouse effect'. There are several techniques to mitigate atmospheric CO2. One approach involves fixing atmospheric CO2 via the natural process of photosynthesis in terrestrial ecosystems (soil and biota). Plants fix atmospheric CO2 in soil and biota because plant roots and mycorrhizal fungi require carbon (C) and contribute to C sequestration (CSQ). Therefore, small changes in the soil C cycle could have large impacts on atmospheric CO2 concentrations. Arbuscular mycorrhizal fungi (AMF) are obligate symbionts of most plant species, and they are important for soil aggregation and stabilization. Mycorrhizae fungi are the major component of soil microbial biomass. AMF hyphae produce glomalin that contains C and that is an important part of the terrestrial C pool. The effects of mycorrhizal colonization on nutrient uptake and root growth have been extensively studied. CSQ and aggregate C storage have become priority topics in soil science since 1990s. Interest in the effects of mycorrhizal hyphae (glomalin as the by-product) and humic substances that enhance aggregate stability is increasing. AMF play a key role in soil aggregate formation and stabilization. This long-term experiment was established in 1996 to assess crop and soil management effects on mycorrhizal development and SOC accumulation. The principal objective was to determine how soil management affects indigenous mycorrhizae and SOC dynamics. Results show that mycorrhizal colonization and sporulation depend on soil and crop management and that soil aggregate development is affected by SOC content and mycorrhizal presence.