Faculty Mentors: Gerrad Jones, Tala Navab-Daneshmand
Mentor Departments: Biological & Ecological Engineering; Chemical, Biological, and Environmental Engineering
Worldwide, water shortages are becoming an ever-present threat to crop production systems. To compensate for these shortages, growers increasingly rely on alternative water sources for irrigation, including wastewater effluent, which is rich in essential nutrients. In addition to wastewater effluent, growers increasingly utilize the high volumes of sludge biosolids produced by wastewater treatment facilities. These biosolids are used as fertilizers due to their high nitrogen and phosphorous content. Despite the many benefits to both the agricultural and wastewater treatment communities, an unintended consequence of biosolids and wastewater use in agricultural systems has been the emergence of antibiotic-resistant bacteria in agricultural soils. This increase in resistance is driven by elevated societal use of antibiotics and antimicrobial products and has become one of the largest public health concerns worldwide. Currently, no effective and well-tested management practices are available for reducing the health risks associated with these resources in agricultural soils. Therefore, our objective is to track the movement of both antibiotics and antibiotic-resistant genes in agricultural soils at the Biocycle Farm near Eugene, Oregon. The Biocycle Farm is a poplar plantation that was created to actively manage land-applied biosolids generated from the Eugene-Springfield Regional Wastewater Treatment Facilities. The Biocycle Farm provides a highly unique opportunity to 1) comprehensively study the movement of antibiotics and antibiotic-resistant genes in a full-scale agricultural setting, and 2) investigate how different aged stands of popular trees affect these concentrations in the soil and groundwater.
The selected student will spend approximately equal portions of time performing field work, lab work, and data analysis. Field work will consist of digging shallow groundwater wells and collecting samples. The Biocycle Farm is a 600 acre poplar plantation with 23 shallow groundwater wells; however, within the treed portion of the property, only 4 groundwater monitoring wells are present. In order to augment the sampling locations, the student will use a soil auger to dig additional wells within each of the 3 stands of trees. At monthly intervals, water and soil samples will be collected and taken to the lab for analysis.
Laboratory work will consist of analyzing soil samples for antibiotics and antibiotic resistant genes. Organic chemicals including antibiotics will be processed in Dr. Jonesâ€™ lab. Organics will be stripped from soils and water using solid phase extraction. The student will then run the samples at OSUâ€™s Mass Spectrometry Center for quantification. In addition, the student will quantify the prevalence and abundance of antibiotic-resistant genes using quantitative polymerase chain reactions (qPCR) in Dr. Navab-Daneshmandâ€™s lab.
This analysis will contribute significantly to ongoing research within both labs, so it is expected that the student will contribute to manuscripts that will be submitted for publication and presented at regional and national conferences.
Description of Student Responsibilities
Field work will be conducted off campus at Springfield/Eugene's Biocycle farm. This facility produces class B biosolids, so the student will be required to follow safety procedures outlined by the facility. The student will help identify locations and drill wells on site. The student will collect samples from 10-12 different wells using a geo-pump, and will bring the samples back to the lab immediately. For chemical analysis, samples will be filtered immediately to remove sediments, extracted using solid phase extraction cartridges, and then frozen. Chemical processing takes ~1 week. The student will analyze samples at OSU's mass spectrometer center to quantify the presence of several antibiotics within the water and soil. For microbial analyses, the student will fix and store collected samples for further molecular analyses. The student will also use DNA extraction kits to extract cellular DNA from stored samples for further gene quantification. With both chemical and microbial data sets, the student will import data from excel into Python or R. The student will develop simple scripts for statistical analysis (e.g., checking for outliers, regression, ANOVA) to identify differences in chemical/microbial composition among the different sites. This analysis will generate results and figures that will be presented in a poster at the end of the project.
Required Skills- students must be creative, excited, and willing to fail. Research is ~80% problem solving. Most ideas donâ€™t work as originally planned, but with creative out-of-the-box thinking, we can overcome any problem we encounter. It is important for students to be able to take control of the project and think of new ways to tackle a problem. Otherwise, students will not be able to find creative solutions to overcome obstacles.
Learned Skills- at the end of this research experience, students will be familiar with general environmental chemistry concepts (e.g., chemical fate and transport) as well as biochemistry laboratory techniques. In addition, students will get exposure to data analysis tools that are easy to code in Python or R. The ultimate goal is to reduce the risk of antibiotic resistance in agricultural systems, so students will use these skills to make sustainable management recommendations that improve human health and safety.
Our primary aim is to determine how the management strategies of the BIocycle Farm affect the abundance of antibiotics and antibiotic-resistant genes in soils and groundwater. With the data that is collected, we anticipate that the student will be able to address this goal. Secondary outcomes include 1) identifying the likely mechanisms triggering antibiotic resistance based on the spatial and temporal patterns of antibiotics and antibiotic resistant genes, and 2) identifying the chemical fingerprints that are indicative of antibiotic resistance within the environment. Finally, the results from this pilot study will serve as the preliminary data for a USDA grant that is to be submitted late in summer 2019.
There are several student outcomes as well. The student will become proficient in water quality sampling and laboratory analysis in both labs. The student is expected to participate in data analysis and will learn basic statistical analysis tools in either Python or R. Finally, the student is expected to develop presentation skills, and will have the opportunity to present at local-national conferences.
For the project, our primary aim is to determine how the management strategies of the Biocycle Farm affect the abundance of antibiotics and antibiotic-resistant genes in soils and groundwater. Secondary outcomes include testing three different hypotheses proposed for triggering antibiotic resistance based on the spatial and temporal patterns of antibiotics and antibiotic resistant genes, and identifying the chemical fingerprints that are indicative of antibiotic resistance within the environment.