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Multi-strain biofertilizer consisting of three indigenous cyanobacterial isolates was applied to an organically poor semi-arid clay-loam soil (pH 7; electrical conductivity, EC, 0.8 dSm(-1); total organic carbon, TOC, 0.34%; total Kjeldahl Nitrogen, TKN, 0.06%) in pot-house experiment. During the 240 d experiment under conditions of limited water regime (6-12% soil moisture), there was a significant (p < 0.05) increase in TOC, TKN and PO43-P during the middle, which, however, diminished at later stages of the experiment. The biofertilizer (BF) improved carbon and nitrogen mineralization by promoting soil microbial activities and narrowed down C:N ratio. Effect of BF on cation exchange capacity of the soil became evident with time. Physical structure of the soil was influenced due to BF as indicated by significant (p < 0.01) decline in bulk density and increase in water holding capacity, hydraulic conductivity and mean weight diameter at the end of both pearl millet and wheat crop. Plant growth and yield of pearl millet-wheat sequence in the soil increased in response to cyanobacterial biofertilizer. Response of pearl millet to BF was more pronounced for certain parameters at the lower water level, W-2 (6% moisture). The native strains showed remarkable potential for improving structural stability, nutrient status and productivity of the soil under limited water regime. (c) 2006 Published by Elsevier B.V.