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Organic and conventional farming practices differ in the use of several management strategies, including use of catch crops, green manure, and fertilization, which may influence soil properties, greenhouse gas emissions and productivity of agroecosystems. An 11-yr-old field experiment on a sandy loam soil in Denmark was used to compare several crop rotations with respect to a range of physical, chemical and biological characteristics related to carbon (C) and nitrogen (N) flows. Four organic rotations and an inorganic fertilizer-based system were selected to evaluate effects of fertilizer type, catch crops, of grass-clover used as green manure, and of animal manure application. Soil was sampled from winter wheat and spring barley plots on 19 September 2007, 14 April 2008 and 22 September 2008, i.e. before, during, and after the growth season. The soils were analyzed for multiple attributes: total soil organic carbon (SOC), total N, microbial biomass N (MBN), potentially mineralizable N (PMN), and levels of potential ammonium oxidation (PAO) and denitrifying enzyme activity (DEA). In situ measurements of soil heterotrophic carbon dioxide (CO₂) respiration and nitrous oxide emissions were conducted in plots with winter wheat. In April 2008, prior to field operations, intact soil cores were collected at two depths (0-5 and 5-10cm) in plots under winter wheat. Water retention characteristics of each core were determined and used to calculate relative gas diffusivity (D P/D o). Finally, crop growth was monitored and grain yields measured at harvest maturity. The different management strategies between 1997 and 2007 led to soil carbon inputs that were on average 18-68% and 32-91% higher in the organic than inorganic fertilizer-based rotations for the sampled winter wheat and spring barley crops, respectively. Nevertheless, SOC levels in 2008 were similar across systems. The cumulative soil respiration for the period February to August 2008 ranged between 2 and 3t CO₂-C ha⁻¹ and was correlated (r =0.95) with average C inputs. In the organic cropping systems, pig slurry application and inclusion of catch crops generally increased soil respiration, PMN and PAO. At field capacity, relative gas diffusivity at 0-5cm depth was >50% higher in the organic than the inorganic fertilizer-based system (P
