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The densely populated, intensively cropped subtropical highlands of the world have agricultural sustainability problems from soil erosion and fertility decline. In 1991, the International Maize and Wheat Improvement Center (CIMMYT) initiated a long-term field experiment at its semi-arid highland experiment station in Mexico (2240 masl; 19.31 degrees N, 98.50 degrees W; Cumulic Phaeozem) to investigate the long-term effects of tillage/seeding practices, crop rotations, and crop residue management on maize and wheat grown under rainfed conditions. Soil ecology status contributes to agricultural system sustainability, and evaluations were made to determine the effect of different management practices on soil microbial biomass (SMB) (substrate-induced respiration (SIR) and chloroform fumigation incubation (CFI)) and micro-flora physiological and catabolic diversity (BIOLOG (TM) ecoplate well system). SMB-C (CFI, SIR) was significantly and respectively 1.2 and 1.3 times higher for residue retention (average 387 mg C kg(dry soil)(-1) and 515 mg C kg(dry soil)(-1), respectively) compared to residue removal. SMB-C (CFI) was significantly higher for wheat (369 mg C kg(dry soil)(-1)) compared to maize (319 mg C kg(dry soil)(-1)). SMB-N (CFI) was significantly 1.3 times higher for residue retention (average 28 mg N kg(dry soil)(-1)) compared to residue removal. The average well color development (AWCD) obtained by the BIOLOG (TM) ecoplate essay indicated there were large differences in the catabolic capability of soil microbial communities after 15 years of contrasting management practices. While maize and wheat rotation under conventional tillage with residue retention showed a significantly higher overall AWCD value compared to the other treatments, AWCD of maize with zero tillage and residue removal was significantly lower than in the other treatments. AWCD was significantly higher for residue retention compared to residue removal and for wheat as compared to maize. For maize, the management practices were divided into two groups; zero tillage with residue removal was separate from all other treatments. For wheat, conventional tillage was separate from all zero tillage treatments. This study suggests that in the target area, a cropping system that includes zero tillage, crop rotation, and crop residue retention can increase overall biomass and micro-flora activity and diversity compared with common farming practices. in the long term, zero tillage combined with residue retention creates conditions favourable for the development of antagonists and predators, and fosters a new ecological stability. Zero tillage without residue retention is an unsustainable practice that leads to poor soil health in the long run. (c) 2007 Elsevier B.V. All rights reserved.