The effects of physical and geochemical perturbation on small bacterial communities at a contaminated site with a focus on the model phylum Patescibacteria

Small bacteria are often identified as abundant in terrestrial and aquatic environments with many of the small cells identified as members of the diverse candidate phyla radiation (CPR) condensed to the phylum Patescibacteria. This phylum maintains a small cell volume and is highly abundant among the 0.1 µm [micrometer] microcell/ultra-micro cell size fraction in groundwater systems. While the abundance of this group has been documented, the dispersal of the population under reducing conditions and in contaminated solid subsurface material remains largely uncharacterized. Therefore, this dissertation assessed the composition of small filterable bacteria including Patescibacteria during stimulated reducing conditions in-situ and in solid media adjacent to uranium-waste disposal ponds. The results support a functional group of Patescibacteria orders associated with reducing conditions and with potentially syntrophic relationships among sulfate reducers and archaea. The abundance of Patescibacteria order Wolfebacteria was highly correlated with acetate production and sulfate reduction with a high differential enrichment under reducing conditions. The abundance of Patescibacteria is highly stochastic across the solid media at the site, but are positively associated with coarse material. In a comparison of wells at the site, the coarse material and fractured saprolite produced the highest proportion of small cell counts. Suggesting that the preferential mobility for this phylum is associated with the presence of macropores and fractures. These data further support the importance of improved subsurface characterization in the interpretation of groundwater communities where local differences in flow and sediment composition can result in differences in community composition. This work also suggests that the presence of small bacteria particularly Patesciabcteria may serve as a natural tracer for transport mechanisms in the subsurface.