Structural diversity of microbial communities in arable soils of a heavily industrialised area determined by PCR-DGGE fingerprinting and FAME profiling

Microbial community structure in soil sampled from sites contaminated with different levels of heavy metals was assessed by PCR-DGGE analysis of 16S rDNA fragments and MIDI-FAME profiling of total cell fatty acids. Total community DNA was extracted from these soils by three methods to compare their usefulness for generation of reprrsentative pools of bacterial community 16S rRNA genes. Crude DNA extracts were purified and then amplified using eubacterial primers. PCR products were analysed by DGGE to obtain bacterial community patterns. Culturable fractions of fast growing bacteria separated from soil colloids by blending and differential centrifugation were also analysed by profiling of cellular fatty acids. PCR-DGGE analysis showed significant differences in microbial community structure between the soils studied, which were related to the contamination levels. Polluted soils could be characterised by a community differing in 'richness' and structure of dominating bacterial populations from those of a pristine soil. The differences in the bacterial community structure were still visible after 10-fold dilution of the target DNA, indicating that even less dominant populations were affected by heavy metals. However. organic matter content, soil type and crop cultivation could also affect the bacterial populations that established in these soils. The direct methods for DNA extraction from soil generated information about the microbial community composition different from that of the indirect method. The latter method was less efficient than both direct methods with respect to the generation of representative pools of bacterial community 16S rRNA genes. The structure of the culturable bacterial community was not dependent on the concentrations of heavy metals in soil, as determined by MIDI-FAME profiling. It is possible that this fraction of soil bacteria was less diverse (dominated by gram-positive bacteria) than the total community analysed at the DNA level without prior cultivation. (C) 2001 Elsevier Science B.V. All rights reserved.