The effects on bacterial, yeast and fungal communities present within an agricultural soil treated with a pig slurry-derived digestate were studied using a multidisciplinary (biochemical and 454 pyrose-quencing platform) approach. Biochemical analyses showed a significant increase of CO2 emissions from soil 5 days after the amendment with digestate, whereas soil microbial biomass (C-biomass) increased significantly only after 12 and 30 days. PLFAs analysis revealed a significant increase in Gram-negative bacteria 90 days after the amendment. Results from 454 pyrosequencing revealed the presence of OTUs attributed to bacteria, yeasts and filamentous fungi. Proteobacteria, Bacteroidetes and Firmicutes exhibited a significant predominance in the first 5 days, whereas Ascomycota became predominant 90 days after the amendment. Overall, both bacterial and yeast + fungal richness exhibited a decreasing trend from 0 to 90 days after the amendment. Canonical analysis of principal coordinates showed that the cumulative effect of amendment and incubation time explained approximately 45% and 36% of the total variance observed in the bacterial and yeast fungal communities, respectively. The correlation among some bacterial and fungal OTUs suggested the probable existence of specific biological interactions among different phyla. The results reported represent a picture of the changes of soil microbial diversity in relation with some agronomic practices, such as organic amendments. (c) 2014 Elsevier Ltd. All rights reserved.