DNA fingerprinting reveals links among agricultural crops, soil properties, and the composition of soil microbial communities

Rapid methods for characterizing soil microbial communities are essential to assess responses to perturbations and to improved management practices. This study compared the composition of microbial communities in 47 agricultural soil and adjacent land use samples collected in the San Joaquin Valley, CA. Microbial communities were characterized by DNA fingerprinting of the Intergenic Transcribed Spacer (ITS) region, using primers universal for bacteria or eucarya. Bacterial DNA fingerprints were more complex (containing 25-30 bands) than were eucaryotic fingerprints (8-15 bands). Field replicates from within an agricultural field were more similar to one another than samples collected in different fields under the same crop type or in close proximity to one another. Microbial communities in almond, grape, and tomato soils across different locations were more similar to one another than communities in cotton and safflower soils. Bacterial DNA fingerprints were significantly correlated with soil electrical conductivity, soil texture, inorganic carbon, and nitrogen content but not with pH and organic carbon content. The grouping of soil samples based on their soil reflectance properties was similar to the grouping based on the bacterial ITS analysis. Despite similarities among communities under some crops and at some locations, there is tremendous unexplained diversity within agricultural soil microbial communities. More extensive sampling is needed to better understand the driving forces underlying microbial community composition. (C) 2003 Published by Elsevier Science B.V.