In the analysis of the environmental impact of bioethanol (and other biofuels too), some of the key factors concern the impact of the increasing quantities of dedicated crops on soil carbon levels and subsequent photosynthesis: these changes will also influence the atmospheric concentrations of GHG such as CO2 and CH4.

The main problem concerns the fact that, when a system in equilibrium experiences persistent changes, it can take decades before a new equilibrium with a constant carbon level is reached. Taking the current situation in Europe as concerns wheat and sugar beet crops, there is an estimated depletion of approximately 0.84 t of C or 3.1 t CO2 equivalent ha-1 years-1 from the ground. If no crops were grown on the soil, this depletion would be even greater, i. e. 6.5 t of C each year for sugar beet and 4.9 t of C for wheat. Apart from the effects on ground carbon levels, there are also signs of other adverse effects indirectly linked to crops grown for energy purposes, such as the increase in the amount of C in the atmospheric levels of GHG. Irrigation with good-quality water also exacerbates carbon sequestering: the water used for irrigation contains dissolved calcium and carbon dioxide (in the form of HCO3-); Ca and HCO3- react together, giving rise to the precipitation of CaCO3 and the consequent release of CO2 into the atmosphere. In the typical dry conditions of the USA, further reactions take place and irrigation is responsible for the transfer of CO2 from the ground into the atmosphere (Rees et al., 2005). An important type of crop that can be used to reduce soil carbon sequestering is defined as "zero tillage", which means that it can be grown year after year without disturbing the soil. Seed crops (such as wheat) may be zero tillage, but not root crops (such as Panicum virgatum). Zero tillage has variable effects, and in some cases carbon sequestering in the soil may even increase, but this phenomenon can be completely overturned by a one-off application of conventional tillage. If only the carbon in the soil is considered, zero tillage leads in the long term to less global warming than growing conventional crops in damp climates, but in areas with dry climates, there is no certainty of any such beneficial effect (Six et al., 2004). Using straw from cereals can increase the carbon levels in the soil. Such residue is useful in maintaining soil carbon levels (Blair et al., 1998; Blair and Crocker, 2000) because it has a low rate of breakdown, so it is important for the residue to go back into the ground in order to keep the farming system sustainable. Since removing the residue from the ground has other negative effects too, such as an increased soil erosion and a lesser availability of macro — and micronutrients, some have suggested in the United States (Lal, 2005) that it would be advisable to remove only 20­40% of the residue for the purposes of bioethanol production, whereas it was claimed (Sheehan et al., 2004) that if up to 70% of the residue were removed to produce bioethanol, the carbon levels would initially decline and then remain stable for about 90 years. Increasing the land used to grow energy crops would have a substantial impact on the concentrations of carbon-containing gases in the atmosphere. If areas covered with forest were converted into arable land, the carbon sequestering would go from values of around 50-145 t-ha-1 to approximately 50-200 t-ha-1, assuming a 60-year rotation (Reijinders & Huijbregts, 2007).