Document Type

Dissertation - Open Access

Award Date


Degree Name

Doctor of Philosophy (PhD)


Agricultural and Biosystems Engineering

First Advisor

Rachel McDaniel


Agriculture, Antimicrobial Resistance, Microbes, Nutrient Filter Materials, Subsurface Drainage Systems, Woodchip Bioreactor


Many in-field and edge-of-field management practices have been used to reduce nutrient loads from agricultural fields. The denitrification woodchip bioreactor (WB) is one edgeof- field management practice that has proven to be effective in removing nitrate from subsurface drainage water. The success in nitrate removal achieved with WBs has raised interest in expanding their capabilities for removing other agricultural pollutants, including phosphorus, by using other types of media like phosphorus-sorbing filters or combining these filters with woodchips to remove both nitrate and phosphorus as dual-nutrient removal systems. Despite the extensive research done on WBs and nutrient filter materials, little consideration has been given to the potential effect of these removal systems on other contaminants, including microbes. Therefore, the main goal of this study was to quantify the potential effect of WBs and nutrient filter materials on altering drainage water microbes, including the potential for these systems to decrease unwanted microbes (e.g., E. coli), change the general microbial population, and alter antimicrobial resistance (AMR) microbe concentrations in subsurface drainage waters. To achieve this goal, two laboratory-studies and one field-scale study were conducted. The results of this research demonstrated the potential for WBs to alter microbial concentrations in subsurface drainage waters. The results of the laboratory study revealed that WBs are capable of significantly reducing E. coli concentrations (49% - 77%) and increasing culturable microbial concentrations (250% - 573%) from synthetic tile drainage water. Additionally, the recovered isolates from the general microbial populations from the influents and effluents had similar ratios of AMR. The similar ratio of AMR combined with the increased culturable microbial population detected in the effluents of laboratory WBs indicates the potential for increased concentrations of AMR microbes in tile drainage water when these waters pass through WBs. However, the results from monitoring an in-situ WB varied. Thirteen out of 19 samples resulted in an increase in E. coli concentrations (2% - 1700%) and the majority of sample pairs processed for culturable microbes (five out of six) had an increase in general microbial concentrations (53% - 902%); however, neither increases were significant. In addition, the estimated AMR concentrations did not significantly increase in the tile drainage water from the inlet to the outlet due to the lack of significant change in AMR ratios as well as culturable microbial population; however, the sample size was limited (n = 6) and the p-value was at the edge of significance (p = 0.063). In addition, the results showed the capability of systems with steel turnings, woodchips, woodchips followed by steel turnings, and woodchips combined with biochar to remove E. coli (43% - 97%) from water passing through these systems. Higher concentrations of E. coli in the influent decreased the efficiency of nutrient removal systems to remove the E. coli. Additional laboratory and future in-field studies are warranted to support the development of an effective design for microbial contaminant removal from waters passing through these nutrient removal systems.

Library of Congress Subject Headings

Subsurface drainage.
Escherichia coli.
Microbial populations.
Nutrient pollution of water.
Water quality management.
Drug resistance in microorganisms.



Number of Pages



South Dakota State University


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Available for download on Saturday, December 18, 2021