New quality of assessment of microbial diversity in arable soils using molecular and biochemical methods

New molecular and biomarker approaches allow now a better understanding of the microbial diversity in soils. Examples are presented to demonstrate the new performance of these approaches and the quality of results. Investigations of the diversity of a bacterial indicator genus as well as studies of the whole microbial community structure are presented. Genotypes of Ochrobactrum were isolated by immunotrapping and characterized by PCR - fingerprinting. On a fallow land no significant changes in the intragenus diversity of this indicator bacterium was observed over a period of one year. In contrast, crop rotation was accompanied by a shift in the dominant genotypes of Ochrobactrum, while the genetic potential was not affected. Phospholipid fatty acid (PLFA)-pattern revealed significant shifts in the structure of the whole microbial community in a soil of a hop plantation as compared to a similar soil with crop rotation. The quantity of anaerobic bacteria, represented by the non-ester linked fatty acids were lower in soil samples derived from crop rotation as compared to a former hop plantation soil, which was contaminated with copper. In contrast, the ester linked fatty acids which are present in a wide range of Gram-negative and Gram-positive bacteria, exhibited a reverse relation. Soil samples of the hop plantation contained low amounts of saturated ester linked fatty acids branching on the 10th C atom. This indicates that actinomycetes are present in relative small proportions in the hop plantation soil.