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Tropical and subtropical highlands of the world have been densely populated and intensively cropped. Agricultural sustainability problems resulting from soil erosion and fertility decline have arisen throughout this agro-ecological zone. We assessed practices that would sustain higher and stable yields for wheat (Tritictan aestivum L.) and maize (Zea mays L.) in this region. A long-term experiment (randomized complete block) was started in 1991 under rainfed conditions in the volcanic highlands of central Mexico (2240 in a.s.l.; 19.31 degrees N, 98.50 degrees W; Phaeozem). Our objective was to determine infiltration, soil moisture content, root diseases and nematode populations at the end of 12 years of 16 management treatments front a factorial arrangement of: (1) four rotations (monocropping and rotation of maize and wheat), (2) two tillage (conventional tillage [CT] and zero tillage [ZT]) and (3) two crop residue management practices (residue retention and removal). Water infiltration and soil moisture levels were greater under ZT when residue was left in the field then when residue was removed. Higher infiltration rates and favourable moisture dynamics supported up to 30% yield increase. A significantly higher incidence of root rot was found in monoculture of maize under ZT than CT. Residue retention significantly increased maize root rot incidence compared to residue removal. Rotation of maize and wheat decreased the incidence of maize root rot up to 30%. In general, the incidence of root disease was lower in wheat (up to 3 on a scale of 7) than in maize (up to 3.93 on a scale of 4) for all treatment. In maize, both non-parasitic and parasitic nematodes increased under ZT; however, in wheat no effect of tillage was seen. Incidence of root rot and parasitic nematode populations were not correlated with yield. Although root diseases may have affected crop performance, they affected yield less than other critical plant growth factors Such as infiltration and water availability. Both environmental conditions and microflora played a key role in the biology and expression of soil pathogens. In the semi-arid and rainfed subtropical highlands of central Mexico, positive effects were observed with zero tillage, crop rotations and crop residue retention, compared with common farming practices. (c) 2006 Elsevier B.V. All rights reserved.