Assessing soil biological characteristics: a comparison of bulk soil community DNA-, PLFA-, and Biolog™-analyses

Soil microbiological analyses may serve as a means for assessing soil characteristics. Standard microbiological culture-techniques, however, leave over 90% of the microorganisms in the environment unaccounted for. Several more recently developed analytical techniques such as DNA, phospholipid fatty acid (PLFA), and community level substrate utilization (CLSU) fingerprints allow for more detailed analyses of soil microbial communities. We applied analyses of (1) community DNA with PCR and restriction fragment length polymorphism (RFLP), (2) community PLFAs with gas chromatography and mass spectrometry, and (3) CLSU with Biolog™ gram-negative-plates, to evaluate the biological characteristics of three soils used in pesticide degradation studies. Each of these methods analyzes a different aspect of soil microbial characteristics. A protocol was developed for the statistical comparison and combination of the data from all the analyses, thus allowing for a polyphasic approach to biological soil characterization. We found that all three methods yielded highly reproducible results for each soil and allowed to distinguish the soils based on the structures of specific gene- and PLFA-pools as well as on CLSU fingerprints. Not all methods, however, revealed the same relative similarities of the three soils based on cluster analysis of the biological characteristics. These results demonstrate the value of comparative data analyses and indicate that biological soil characterization needs to be interpreted with caution if it is performed with one method only.