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There is considerable interest in using straw for industrial fibre or biofuel (ethanol) production. Removing straw from farm fields could have detrimental effects on soil quality. The objective of this work was to evaluate the role of above-ground vs. below-ground crop residues on soil organic C content, soil microbiological and physical properties, and crop yields. In a barley (Hordeum vulgare L), field pea (Pisum sativa L.), wheat (Triticum aestivum L.), canola (Brassica napus L) crop rotation from 2007 to 2010, we varied straw inputs by removing or retaining straw, with or without N fertilization, and also by fallowing some treatments in some years. Grain yields were unaffected by straw management or crop residue input, probably due to soil moisture deficits in three of the four years. Soil nitrate accumulation was consistently higher in fallow and N-fertilizer treatments, and grain N uptake was reduced after three years of retaining straw on the surface, indicating probable net N immobilization. The coarse (>0.5 mm) light fraction of soil organic matter was reduced by fallowing the preceding year or disking in the straw, and was significantly correlated with the most recent input amounts of straw or total residue (root plus straw) dry matter (DM). The fine light fraction did not correlate with those residue inputs. Soil aggregation was indicated by mean weight diameter and was not affected by straw management. Non-rhizosphere soil microbial biomass C and P-glucosidase enzyme activity were consistently lowest in the control (no cropping) treatment and the treatment with straw incorporated by disking, but the amounts of C and N mineralized were not affected by straw treatments. Non-rhizosphere soil MBC was strongly correlated with cumulative total residue DM input. However, because crop yields did not vary much with straw management, they did not correlate with soil quality parameters. Therefore, varying above- and below-ground crop residue inputs, as well as tillage (disking in straw), over four years affected some early indicators of soil quality but not crop yields. Crown Copyright (C) 2012 Published by Elsevier B.V. All rights reserved.