Biology subjects

Paradis, C. J.

Publications and source records attributed to Paradis, C. J..

3 recordsLinked to original sources

bioRxiv2021

Sustained ability of a natural microbial community to remove nitrate from groundwater

Microbial-mediated nitrate removal from groundwater is widely recognized as the predominant mechanism for nitrate attenuation in contaminated aquifers and is largely dependent on the presence of a carbon-bearing electron donor. The repeated exposure of a natural microbial community to an electron donor can result in the sustained ability of the community to remove nitrate; this phenomenon has been clearly demonstrated at the laboratory scale. However, in situ demonstrations of this ability are lacking. For this study, ethanol (electron donor) was repeatedly injected into a groundwater well (treatment) for six consecutive weeks to establish the sustained ability of a microbial community to remove nitrate. A second well (control) located up-gradient was not injected with ethanol during this time. The treatment well demonstrated strong evidence of sustained ability as evident by concomitant ethanol and nitrate removal and subsequent sulfate removal upon consecutive exposures. Both wells were then monitored for six additional weeks under natural (no injection) conditions. During the final week, ethanol was injected into both treatment and control wells. The treatment well demonstrated sustained ability as evident by concomitant ethanol and nitrate removal whereas the control did not. Surprisingly, the treatment well did not indicate a sustained and selective enrichment of a microbial community. These results suggested that the predominant mechanism(s) of sustained ability likely exist at the enzymatic- and/or genetic-levels. The results of this study demonstrated that the in situ ability of a microbial community to remove nitrate can be sustained in the prolonged absence of an electron donor. Moreover, these results implied that the electron-donor exposure history of nitrate-contaminated groundwater can play an important role nitrate attenuation. Article Impact StatementGroundwater microbes sustain ability to remove nitrate in absence of carbon and energy source.

ecology↗

bioRxiv2019

Integrated characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer

The processing of sediment to accurately characterize the spatially-resolved depth profiles of geophysical and geochemical properties along with signatures of microbial density and activity remains a challenge especially in complex contaminated environments. To provide site assessment for a larger study, we processed cores from two sediment boreholes from background and contaminated core sediments and surrounding groundwater from the ENIGMA Field Research Site at the United States Department of Energy (DOE) Oak Ridge Reservation (ORR). We compared fresh core sediments by depth to capture the changes in sediment structure, sediment minerals, biomass, and pore water geochemistry in terms of major and trace elements including contaminants, cations, anions, and organic acids. Soil porewater samples were matched to groundwater level, flow rate, and preferential flows and compared to homogenized groundwater-only samples from neighboring monitoring wells. This environmental systems approach provided detailed site-specific biogeochemical information from the various properties of subsurface media to reveal the influences of solid, liquid, and gas phases. Groundwater analysis of nearby wells only revealed high sulfate and nitrate concentrations while the same analysis using sediment pore water samples with depth was able to suggest areas high in sulfate- and nitrate- reducing bacteria based on their decreased concentration and production of reduced by-products that could not be seen in the groundwater samples. Positive correlations among porewater content, total organic carbon, trace metals and clay minerals revealed a more complicated relationship among contaminant, sediment texture, groundwater table, and biomass. This suggested that groundwater predominantly flowed through preferential paths with high flux and little mixing with water in the interstices of sediment particles, which could impact microbial activity. The abundant clay minerals with high surface area and high water-holding capacity of micro-pores of the fine clay rich layer suggest suppression of nutrient supply to microbes from the surface. The fluctuating capillary interface had high concentrations of Fe and Mn-oxides combined with trace elements including U, Th, Sr, Ba, Cu, and Co. This suggests the mobility of highly toxic elements, sediment structure, and biogeochemical factors are all linked together to impact microbial communities, emphasizing that solid interfaces play an important role in determining the abundance of bacteria in the sediments.

systems biology↗

bioRxiv2017

Plasmid DNA analysis of pristine groundwater microbial communities reveal extensive presence of metal resistance genes

Native plasmids constitute a major category of extrachromosomal DNA elements responsible for harboring and transferring genes important in survival and fitness. A focused evaluation of plasmidomes can reveal unique adaptations required by microbial communities. We examined the plasmid DNA from two pristine wells at the Oak Ridge Field Research Center. Using a cultivation-free method that targets plasmid DNA, a total of 42,440 and 32,232 (including 67 and 548 complete circular units) scaffolds > 2 kb were obtained from the two wells. The taxonomic distribution of bacteria in the two wells showed greater similarity based on their plasmidome sequence, relative to 16S rRNA sequence comparison. This similarity is also evident in the plasmid encoded functional genes. Among functionally annotated genes, candidates providing resistance to copper, zinc, cadmium, arsenic, and mercury were particularly abundant and common to the plasmidome of both wells. The primary function encoded by the most abundant circularized plasmid, common to both wells, was mercury resistance, even though the current ground water does not contain detectable levels of mercury. This study reveals that the plasmidome can have a unique ecological role in maintaining the latent capacity of a microbiome enabling rapid adaptation to environmental stresses.

microbiology↗