Response of the bacterial community to root exudates in soil polluted with heavy metals assessed by molecular and cultural approaches

We have used PCR based on 16S rDNA sequences followed by denaturing gradient gel electrophoresis (PCR-DGGE) in conjunction with cultivation-based methods to describe the effect of artificial root exudates (ARE), of which the composition simulated maize root exudates, on the structural diversity of bacterial communities in various soils differing in the level of contamination with heavy metals. The aim of this study was to evaluate the effects of organic compounds of a root exudates as a potential mechanism for selectively enhancing specific bacterial populations in contaminated soils, leading to the development of shifted communities differing in qualitative and quantitative composition. Soil microcosms were either just enriched with ARE or enriched and, additionally, flooded. To characterise the response of the soil microflora to the enrichment, PCR-DGGE was applied for assessment of the total bacterial community structure. Cultivation techniques were used to determine the numbers of total heterotrophic bacteria as well as of pseudomonads (which are considered to be stimulated by components of root exudates). The community structure of culturable bacteria was studied using the concept of r- and K-strategists, and isolates from dominant colonies growing on King’s B agar were identified by MIDI-FAME profiling. The results obtained showed a significant effect of root exudates on the development of bacterial populations in soil contaminated with heavy metals. Depending on their availability and conditions prevailing in the habitat (e.g. stronger enrichment by flooding) different bacterial populations were stimulated, resulting in generation of different community patterns by DGGE. The most significant response to root exudates occurred among the culturable fraction of the soil bacteria. Distribution of bacterial classes (i.e. majority of colonies appeared after 24 h), values of EP (from 0.220 to 0.533) and CD (from 43 to 88) indices directly showed that the culturable fraction of bacteria was highly affected by the organic mixture simulating root exudates. These exudates reduced the bacterial diversity towards domination of r-strategists and the reduction of diversity was greater in soil with a higher contamination level. Furthermore, flooding of the soils enhanced the dominance of fast growing bacteria (over 70% formed visible colonies after 24 h even on day 6) and reduced the community diversity (EP and CD indices were from about 0.291 to 0.425 and from 66 to 87, respectively).