Identification and Isolation of a Castellaniella Species Important during Biostimulation of an Acidic Nitrate- and Uranium-Contaminated Aquifer

Abstract

Immobilization of uranium in groundwater can be achieved through microbial reduction of U(VI) to U(IV) upon electron donor addition. Microbial community structure was analyzed in ethanol-biostimulated and control sediments from a high-nitrate (>130 mM), low-pH, uranium-contaminated site in Oak Ridge, TN. Analysis of small subunit (SSU) rRNA gene clone libraries and polar lipid fatty acids from sediments revealed that biostimulation resulted in a general decrease in bacterial diversity. Specifically, biostimulation resulted in an increase in the proportion of Betaproteobacteria (10% of total clones in the control sediment versus 50 and 79% in biostimulated sediments) and a decrease in the proportion of Gammaproteobacteria and Acidobacteria. Clone libraries derived from dissimilatory nitrite reductase genes (nirK and nirS) were also dominated by clones related to Betaproteobacteria (98% and 85% of total nirK and nirS clones, respectively). Within the nirK libraries, one clone sequence made up 59 and 76% of sequences from biostimulated sediments but only made up 10% of the control nirK library. Phylogenetic analysis of SSU rRNA and nirK gene sequences from denitrifying pure cultures isolated from the site indicate that all belong to a Castellaniella species; nearly identical sequences also constituted the majority of biostimulated SSU rRNA and nirK clone libraries. Thus, by combining culture-independent with culture-dependent techniques, we were able to link SSU rRNA clone library information with nirK sequence data and conclude that a potentially novel Castellaniella species is important for in situ nitrate removal at this site.

Distribution of typical denitrifying functional genes and diversity of the <i>nirS</i>-encoding bacterial community related to environmental characteristics of river sediments

“…Therefore, we used the nirS gene to characterize the diversity of denitrifier communities in the Pearl River sediment. Most of the nirS sequences in this sediment had a close match with those originally detected in estuarine and marine sediments as well as sludge (Nogales et al, 2002;Tsuneda et al, 2005;Osaka et al, 2006;Ruiz-Rueda et al, 2007;Spain et al, 2007;Bulow et al, 2008), suggesting that this river has both tidal and urban characteristics. When the river is affected by both domestic pollutions and irregularly tides, diversity and distributions of denitrifying bacteria should become more complicated.…”

“…One OTU was closely related to the family Comamonadaceae. Both these families were usually found in aquatic sediment habitats, constructed wetland, and activated sludge (RuizRueda et al, 2007;Spain et al, 2007). Sequences of Cluster-B were similar to species Ralstonia eutropha strain (78-90 % indentify),belonging to the family Burkholderiaceae.…”

Functional Diversity and Electron Donor Dependence of Microbial Populations Capable of U(VI) Reduction in Radionuclide-Contaminated Subsurface Sediments

“…grow with nitrate as an electron acceptor and enzymatically catalyze the reduction of U(VI) to U(IV) (18,66). The Betaproteobacteria genera Dechloromonas, Diaphorobacter, Acidovorax, and Castellaniella were abundant during the time points of shifting TEAPs in our microcosms, and these groups were detected previously in ORFRC subsurface sediments (2,15,48,61). Taxa within the Dechloromonas and Diaphorobacter genera reduce nitrate (22,28,29) and are likely responsible for mediating nitrate reduction in the carbon-amended microcosms.…”

Functional Gene Array-Based Analysis of Microbial Community Structure in Groundwaters with a Gradient of Contaminant Levels

“…The contaminants alter local bacterial populations by exerting selective pressure (Akob et al, 2007), but leave other populations intact (Bagwell et al, 2006). Many studies of this site have used culturing techniques (M. Fields et al, 2005;Spain et al 2007) and molecular biomarker analysis (Palumbo et al, 2004;Bagwell et al, 2006;Yan et al, 2003;Akob et al, 2007, Spain et al 2007 to examine the bacterial diversity and functional capabilities of bacteria present in the area, but none of these studies have been able to simultaneously examine the 4 diversity of multiple functional genes. The objective of this study is to examine the bacterial community structure in wells of varying contamination and to determine which contaminants have the greatest effects on bacterial diversity.…”