Polyphasic examination of microbial communities in soils contaminated with organic pollutants

A polyphasic approach was used to examine the impact of contamination on soil microbial community structure. Two systems were examined using a combined biochemical and molecular biological approach. Petroleum hydrocarbon contaminated soils from two Northern Canadian sites, representing long-term contamination, were examined using Biolog GN plates and PCR-denaturing gradient gel electrophoresis (DGGE) analysis of total community 16S rDNA. Results obtained using both methods demonstrated a positive correlation between samples that was based on the geographical origin of the samples, not on contamination level. In the second system, non-contaminated soil was contaminated with the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) to monitor the effect of short- to medium-term contamination. Changes in the soil microbial community were examined using PCR-DGGE of total community 16S rDNA combined with RDX mineralization and chemical analysis of intermediates. The non-contaminated loam soil had an inherent RDX degradative capability and contamination of soil columns with 1000 mg RDX/kg soil did not significantly change the 16S rDNA bacterial community profile. The bacterial diversity remained high as estimated by the number of bands present in the DGGE and by NQ-78704 statistical rarefaction analysis of 16S rDNA clone RFLPs. The same soil, used in 10% soil slurries (w/v), demonstrated two apparently different RDX degradation mechanisms based on mineralization and chemical analysis. The differences were based on aerobic versus anaerobic conditions and the presence/absence of Na₃ citrate. PCR-DGGE performed on 16S rDNA from aerobic slurries amended with Na₃-citrate detected the stimulation of 3 operational taxonomic units, identified as Stenotrophomonas sp., Sphingomonas sp. and a member of the Alcaligenaceae. The results from the two systems examined (short- to medium-term and long-term contamination) demonstrated the utility of a polyphasic approach in the examination of bacterial communities impacted by anthropogenic organic contamination. Significant information about the effect of contamination on soil microbial communities was obtained which can be used to correlate in situ observations and contribute to an environmental effects monitoring strategy for regulatory bodies entrusted with environmental protection and conservation.