Structural diversity of microbial communities in arable soils of a heavilyindustrialised 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 r DNA fragments and MIDI-FAME profiling of total cell fatty acids. Total comm unity DNA was extracted from these soils by three methods to compare their usefulness for generation of reprrsentative pools of bacterial community 16 S rRNA genes. Crude DNA extracts were purified and then amplified using eub acterial primers. PCR products were analysed by DGGE to obtain bacterial co mmunity patterns. Culturable fractions of fast growing bacteria separated f rom soil colloids by blending and differential centrifugation were also ana lysed by profiling of cellular fatty acids. PCR-DGGE analysis showed signif icant differences in microbial community structure between the soils studie d, which were related to the contamination levels. Polluted soils could be characterised by a community differing in 'richness' and structure of domin ating bacterial populations from those of a pristine soil. The differences in the bacterial community structure were still visible after 10-fold dilut ion of the target DNA, indicating that even less dominant populations were affected by heavy metals. However. organic matter content, soil type and cr op 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 o f the indirect method. The latter method was less efficient than both direc t methods with respect to the generation of representative pools of bacteri al community 16S rRNA genes. The structure of the culturable bacterial comm unity was not dependent on the concentrations of heavy metals in soil, as d etermined by MIDI-FAME profiling. It is possible that this fraction of soil bacteria was less diverse (dominated by gram-positive bacteria) than the t otal community analysed at the DNA level without prior cultivation. (C) 200 1 Elsevier Science B.V. All rights reserved.