Microorganisms play important roles in complex and dynamic environments such as agricultural soils and contaminated site sediments. Molecular methods have greatly advanced the understanding of microbial processes, such as nitrogen cycling, carbon cycling and contaminant biodegradation, by providing insights into the structure, function and dynamics of microbial communities. The first project evaluated the impact of four agricultural management practices (no tillage, conventional tillage, reduced input, biologically based) on the abundance and diversity of microbial communities regulating nitrogen cycling using shotgun sequencing. The relative abundance values, diversity and richness indices, taxonomic classification and genes associated with nitrogen metabolism were examined. The microbial communities involved in nitrogen metabolism are sensitive to varying soil conditions, which in turn, likely has important implications for N2O emissions. This work was conducted virtually during the COVID pandemic. The second project examined the impact of plant diversity, soil pore size, and incubation time on soil microbial communities in responses to new carbon inputs (glucose). Soil cores from three plant systems (no plants, monoculture switchgrass, and high diversity prairie) were incubated with labeled and unlabeled glucose. The phylotypes responsible for the carbon uptake from glucose were identified using stable isotope probing (SIP). The microbial communities were influenced by plan diversity but not by pore size or incubation time. The differentiated carbon assimilators may be linked to different carbon assimilation strategies (r- vs. K-strategists) depending on pore size. The third and fourth projects focused on the biodegradation of the common groundwater contaminant, 1,4-dioxane. 1,4-Dioxane was commonly used as a stabilizer in 1,1,1-trichloroethane formulations and is now frequently detected at sites where the chlorinated solvents are present. A major challenge in addressing 1,4-dioxane contamination concerns chemical characteristics that result in migration and persistence. Given the limitations associated with traditional remediation methods, interest has turned to bioremediation to address 1,4-dioxane contamination. The third project examined the impact of yeast extract and basal salts medium (BSM) on 1,4-dioxane biodegradation rates and the microorganisms involved in carbon uptake from 1,4-dioxane. For this, laboratory sample microcoms and abiotic controls were inoculated with three soils and amended with media (water or BSM and yeast) and 2 mg/L 1,4-dioxane. SIP was then utilized to identify the active phylotypes involved in the 1,4-dioxane biodegradation. The amendment of BSM and yeast enhanced the 1,4-dioxane degradation in all three soil types. Gemmatimonas, unclassified Solirubacteraceae and Solirubrobacter were associated with carbon uptake from 1,4-dioxane and may represent novel degraders. Solirubrobacter and Pseudonocardia were associated with propane monooxygenases genes which potentially function in 1,4-dioxane biodegradation. The fourth project further explored the impact of yeast extract on 1,4-dioxane degradation at low concentrations (< 500 g/L) using sediment from three impacted sites and four agricultural soils. 1,4-Dioxane biodegradation trends differed between inocula sources and treatments. For two of the impacted sites, no 1,4-dioxane biodegradation was observed for any treatment, indicating a lack of 1,4-dioxane degraders. In contrast, 1,4-dioxane degradation occurred in all treatments in microcosms inoculated with the agricultural soil or the other impacted site sediments. Bioaugmentation with agricultural soils initiated 1,4-dioxane biodegradation in the sediments with no intrinsic degradation capacities. Overall, yeast extract enhances 1,4-dioxane biodegradation in specific sediments. Bioaugmenting site sediments with agricultural soils may represent a promising approach for the remediation of 1,4-dioxane contaminated sites.
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