An asset of organic farming systems with diversified crop rotations, next to a cut in pesticide and mineral fertilizer application, is the built-up of organic carbon stocks in the long-term. In addition, the inclusion of deep-rooting legumes like alfalfa is known to improve soil structure and increase particulate organic matter contents in the subsoil. These views have been challenged recently ascribing limited potential for legume-based crop rotations to increase carbon stocks in Chernozems (Mollisols) due to limited accrual of mineral-associated organic carbon. Likewise, the direct impact of these legumes on soil structure and associated soil properties like water retention and transport has been questioned and linked to indirect effects instead.

The objective of this study was to investigate the impact of legume-based crop rotations on carbon stocks and soil structure properties in the Flurweg II long-term farming systems trial (26 years) established on a Chernozem soil in Germany. We compared one conventional (INT) and two organic farming systems, with (O + M) and without (O - M) integrated livestock management. The three farming systems differ in biomass return via plant residues or farmyard manure as well as share and type of legumes in the eight-year crop rotation (INT: pea, O - M: faba bean and pea, O + M: biannual alfalfa). The comparison included yields, carbon stocks, soil physical properties and microstructure properties based on X-ray computed tomography of soil within and beneath the plow horizon. All farming systems underwent conventional plowing. In addition, we compared carbon stocks and microstructure properties with those from the nearby Westerfeld tillage trial with conventional and reduced tillage in a legume-free crop rotation.

The carbon stocks in the plowed topsoil of the Flurweg II systems trial increased significantly with organic farming including livestock (INT: 53 ± 2 vs. O + M: 61 ± 2 t ha⁻¹), but not without (O - M: 53 ± 4 t ha⁻¹), likely because of farmyard manure application in the O + M system. This increase in topsoil carbon stocks is only moderate compared to the increase in topsoil carbon stocks in the Westerfeld tillage trial by switching from conventional to reduced tillage (53 vs. 70 t ha⁻¹). The carbon stocks of the whole soil profile (down to 48 cm) in the Flurweg II systems trial tended to increase with organic farming irrespective of livestock integration (INT: 72 ± 5 t ha⁻¹ vs. O ± M: 82–83 ± 7 t ha⁻¹). Particulate organic matter (POM) contents and biopore diameter below the plow layer tended to increase with alfalfa in the crop rotation of the O + M farming system. However, the legacy effect four years after the presence or absence of alfalfa was only in the range of natural, spatial variability. As a result of similar soil microstructure there was also hardly any difference in hydraulic conductivity and no difference in soil mechanical properties between farming systems.

This study shows that Chernozems in this region still have the capacity to increase POM contents and carbon stocks with climate-smart, regenerative agricultural management, but also demonstrate that this has limited effects on structural properties.