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The ability of organic biodynamic fertilizers to improve soil quality was evaluated in arid loamy sand soils in farmers’ fields in Rajasthan, India in cowpea cropping and citrus orchards. Water holding capacity, organic carbon and ammoniacal nitrogen improved significantly in organic farming. Microbial community was evaluated using both a culture dependent and independent approach. Actinomycetes increased significantly in organic cropping and orchard by 92 and 100%, respectively, compared to conventional management. Bacterial populations increased significantly on nutritionally diverse media in organic farm soils over conventional, both copiotrophs (+52-119%) as well as oligotrophs (+25-79%). The arbuscular mycorrhizal protein, glomalin increased by 56-82% in organic farms. Nitrogen fixers, ammonifiers, nitrifiers and sulfur oxidizers did not show significant differences. There was a consistent increase in soil enzymatic activities in organic farms-acid phosphatase (1.5x in cropping; 3x in orchard), flourescein diacetate hydrolysis (1.8x; 3.3x), dehydrogenase (2.4x; 3.5x) and beta-glucosidase ( 2.2x; 6.3x). Quantification of 16S rDNA abundances in soil using qPCR showed a clear 1.8 fold increase in both organic cropping and organic orchard soils. The abundance of amoA gene decreased by 22 and 11 folds in organic cropping and orchards. The culture independent analysis of eubacterial 16S rRNA gene showed that organically cropped farms and orchards had more diverse bacterial community compared to the conventional. The distribution of bacterial species observed in organic cropping is more even. Representation of Proteobacteria among the eubacterial species was 20% lesser in organic as compared to conventional cropping whereas Actinobacteria were higher by 10% in organic cropping. Overall, the results demonstrated unequivocally that organic amendments improved the biological quality through an alteration of the microbial community structure and function. We conclude that organic manures may thus be appropriately included in the group of ’Ecosystem Engineers’ that selectively modify the environment and make soil ecosystems more sustainable. (C) 2014 Elsevier B.V. All rights reserved.