Print PageWe extensively characterized three terrestrial subsurface bacterial assemblages from Hanford, WA; Rifle, CO; and Oak Ridge, TN. This characterization is part of a larger experiment designed to assess the relative importance of assemblage structure, composition, functional potential, and the geochemical environment as factors influencing realized assemblage functions and trajectories during uranium bioremediation. The experimental design is a reciprocal-transplant of assemblages between sediments and requires a small mass of inoculum to be used.
We conducted a taxa sampling effort relationship experiment using sieved, homogenized sediment from each site. DNA was extracted from five sediment masses ranging from 1.0–3.0 g, in triplicate for each sediment (15 total samples per sediment). The assemblages were analyzed using high-density microarrays to determine assemblage composition (16S rRNA gene analysis by PhyloChip) and functional potential (whole-genome DNA by GeoChip) in order to determine an inoculum mass and characterize the assemblages.
Results/Conclusions
The three sediments differed markedly in geochemical parameters such as particle size distribution, mineralogy, extractable Fe, cation exchange capacity, and porewater composition and ionic strength. However the porewater pH and sediment pH (in 0.01 M CaCl2) were within narrow ranges (pH 8.0-8.3 and 7.5-7.6 respectively). Cell counts ranged from 2.3 x 107 to 1.7 x 108 cells/g dry sediment. We found no significant differences in detected richness at the operational taxonomic unit (OTU) or sub-family level by sample mass within a sediment type; although mean detected OTU richness differed consistently by site, ranging from 5,145 in the Hanford sediment to 11,508 in Rifle. The degree of compositional overlap was low between the three sediments, with 44.4% of 16,584 detected OTUs common to all three sediments. Anosim analysis of presence/absence data at different taxonomic ranks shows that the assemblages in each sediment are significantly different and distinguishable at the phylum-level.
