Centimeter scale analysis of soil heterogeneities within a long-term, heavy-metal contaminated site

Heterogeneities within soil are evident on several spatial scales and control key soil parameters including the amount and distribution of organic carbon, O2, metals, and nutrients. Traditionally researchers have sieved and mixed soil samples in order to reduce sample heterogeneity and generate an overall estimate for these parameters. As a result the spatial relationships are lost and this possibly obscures the real impact of pollution on key soil processes. In order to improve our understanding of how the spatial arrangements within a soil affects microbial communities a heavy-metal contaminated soil was assessed using care not to disturb the soil\u27s spatial structure. Using soil aggregations (150 mg) collected from across a soil surface as our sampling unit we conducted a sequential analysis that included an assessment of metabolic activity (using 14C-glucose), community structure (using denaturing gradient gel electrophoresis (DGGE) of PCR products of the 16S rRNA gene), and total metal content determination (using inductively coupled plasma-atomic emission spectroscopy (ICP-AES)). A detailed geostatistical analysis revealed a strong spatial dependence (at up to 30 cm) for metabolic activity, Pb, and Cr levels. In general, within spatial kriging maps, zones of high metal content corresponded to areas of low metabolic activity suggesting that metals negatively impacted the microbial community. However, PCR-DGGE analysis revealed that diverse communities were present and also revealed a random distribution of phylotypes throughout the sampling zones. These data suggest that distance has spatially isolated the microbial communities within the contaminated site. To determine the frequency of locations with a high content of culturable metal resistant microbes (specifically CrR microbes), a soil incubation chamber using low nutrient fluxes was developed and utilized. This soil incubation chamber system was first tested with agricultural soil where the proportion of bacteria recovered using the soil incubation chamber was 400-fold higher than that using traditional bacteriological media alone. Furthermore, microcolonies of difficult to culture bacterial phyla (specifically the Acidobacteria and Verrucomicrobia) were able to be cultured using this system. Thus, the chamber was utilized to detect locations within two different soils (one contaminated with metals, the other pristine) where high proportions of CrR microbes were cultivated. Exposure to metals resulted in a lower percentage of recovered colony forming units for the pristine soil compared to the metal contaminated site. This was reflected in the DGGE analysis which revealed that the community from the contaminated site was more diverse than that from the forested soil. In sum, a more thorough understanding of the complexities of soil ecosystems can be garnered using small scale analyses such as those utilized here