Location: Agricultural Water Efficiency and Salinity Research Unit
2018 Annual Report
Objectives
The overall goal of the project is to develop improved understandings and new tools for the protection of food and water supplies from contamination by ARBs and ARGs associated with fecal indicator bacteria (FIB), and ARGs from CAFOs, WWTPs effluent, and urban runoff.
Research Tasks – Three tasks crosscut the research objectives creating a subtask matrix. The subtasks are listed under each corresponding objective.
Task I: Mechanistic studies of conjugation - Mechanistically study and model the transport, retention, and release of NRB, ARB containing ARGs in the presence of various environmental stressors under different physicochemical conditions at the laboratory scale.
Task II: Runoff Studies with sediment from the SAR Watershed - Investigate factors that influence the development, spread, and mitigation of ARB, ARGs, and pathogenic E. coli and Salmonella in sediment/runoff water from the SAR watershed.
Task III: Root zone transport and uptake studies - Investigate the influence of environmental stressors on the development, spread, and mitigation of ARB and ARGs in the root zone and in food crops.
Objective 1: Identify and quantify microbial contaminants, antibiotics and antibiotic resistance genes, and develop methods and tools for tracking their transport and fate.
Subtask Ia. Identification of environmental conditions and stressors concentrations that promote HGT and the transport of ARB in idealized systems.
Subtask Ib. Create models to simulate the transport and fate of ARB and HGT.
Subtask IIa. Identification of environmental conditions and stressors concentrations that promote HGT and the transport of ARB in runoff water.
Subtask IIb. Apply models to simulate the transport and fate of ARB and HGT.
Subtask IIIa. Identification of environmental conditions and stressors concentrations that promote HGT and the transport of ARB in the root zone and in food crops.
Subtask IIIb. Apply models to simulate the transport and fate of aRB and HGT.
Objective 2: Evaluation of metagenomics and culture methods to identify specific pathogens, antibiotics, ARGs and their mechanisms of transfer (e.g., horizontal gene transfer (HGT)) in the environment from contamination sources to water, food, and humans.
Subtask Ic. Development of procedures to quantitatively study HGR under idealized systems.
Subtask IIc. Isolation, identification, and quantification of ARGs in indicator microbes, pathogens, and the microbial community in runoff water and natural sediment.
Subtask IIIc. Isolation, identification, and quantification of aRGs in the root zone and food crops.
Objective 3: Evaluation of effective methods and practices to protect crops often eaten raw from antibiotics, antibiotic resistance genes, and pathogen contamination.
Subtask Id. Models developed in Task I will be used in Task II and II to simulate HGT and ARB in runoff water and the root zone.
Subtask IId. Develop strategies to manage ARB and HGT in runoff water and sediment that is used to irrigate crops.
Subtask IIId. Develop strategies to manage ARB and HGT in the root zone.
Approach
Mechanistical studies (batch and column, runoff chamber, and lysimeter scales) will be conducted to investigate the influence of environmental factors and stressors (heavy metals and biocidal organics) on the development and migration of ARB, ARGs, and gene transfer between indicator microorganisms and pathogenic bacteria in soils, recharge water, sediments, runoff water, the root zone, and food crops. New mathematical modeling tools to better understand and simulate the transport, fate, and transfer of ARBs/ARGs will be developed. Furthermore, state-of-the-art detection protocols will be implemented to quantify the types, amounts and distribution of ARB and ARGs.
Progress Report
Objective 1: The type of bacteria from the intestinal track of different animals and the environment with resistance to multiple antibiotics was investigated. In particular, Escherichia Coli (E. coli) isolates collected from different animal sources and the environment were sequenced for markers known to carry antibiotic resistance and virulence genes from bacteria to bacteria.
Objective 2: Additional sequencing in combination with different analytical tools proved successful in detecting antibiotics resistance and virulence genes from E. coli isolates to determine the animal source(s) with the highest potential for gene transfer to the environment and humans. Preliminary results from this study suggest that one of the E. coli isolates from swine is resistant to more than ten antibiotics and belongs to an international high-risk clone which should be monitored closely.
Batch experiments were conducted to examine the influence of physical (temperature, shaking and non-shaking), chemical (solution ionic strength, and absence and presence of antibiotics), and microbiological (growing and non-growing cultures of E. coli actors on horizontal gene transfer (HGT). HGT increased with temperature, for shaken conditions, and under immediate ionic strength conditions, presumably due to differences in cell-cell interactions. The presence of antibiotics either increased, decreased, or did not change HGT depending on the antibiotic type, the growth condition, and the solution chemistry. The greatest amount of HGT occurred in the presence of an antibiotic under non-growing conditions at immediate ionic strength, suggesting that greater research attention should be given to these conditions. Results also indicate considerable complexity in the HGT process that presently is not accurately described in existing mathematical models. Ongoing experiments are being conducted to test various hypotheses to explain this behavior.
Objective 3: A greenhouse study is being conducted to examine the absorption and transfer of spiked antibiotics and antibiotic resistance gene from soil to plant roots and to the edible portion of the plants using spinach as a model plant. Quantification of antibiotics from soil, roots, and leaf as well as antibiotic resistance genes in bacteria is in progress.
Accomplishments
1. Design of surfaces to minimize microorganism retention. An ARS researcher from Riverside, California, and collaborators from the China Agricultural University in China and Chonbuk National University in South Korea, developed approaches to improve the prediction of microbial interactions on surfaces. Results reveal that the surface roughness properties controlled the interaction between a microbe and solid surface for a given solution chemistry. Design of surfaces with specific roughness properties can now be used to enhance or diminish microbial retention. In addition, microbes were found to have diminished retention on very thin surfaces compared to thick solid surfaces. Diminished microbe retention on natural and engineered surfaces is to be applied in healthcare environments, commercial production facilities, and homes to obtain clean surfaces that minimize the risks of infection and the overuse of antibiotics.
2. Assessment of antibiotics resistance genes in manure to environment. An understanding of factors that influence the fate and transport of antibiotic resistance genes and antibiotic resistant bacteria in manure and other water systems are needed to develop focused antibiotics resistant management practices. An ARS researcher from Riverside, California, and collaborators from California State Polytechnic University, performed experiments to determine the concentrations of antibiotic resistance genes and their co-occurrence with associated genetic elements in different animal manure and in the environment. Some of the genetic elements found in manure samples included mobile genetic elements and metal resistance genes. Further examination of host resistance genes indicated that high levels of tetracycline, multidrug, macrolide, and aminoglycoside were more abundant in swine and cattle manure than other animal sources. This assessment will lead to the development of management practices that will reduce the transfer of antibiotics resistance genes and antibiotics resistant bacteria from swine or cattle manure to the environment.
Review Publications
Ibekwe, A.M., Gonzalez-Rubio, A., Suarez, D.L. 2017. Impact of treated wastewater for irrigation on soil microbial communities. Science of the Total Environment. 622:1603-1610. https://doi.org/10.1016/j.scitotenv.2017.10.039.
Silva, R.A., Borja, D., Hwang, G., Hong, G., Gupta, V., Bradford, S.A., Zhang, Y., Kim, H. 2017. Analysis of the effects of natural organic matter in zinc beneficiation. Journal of Cleaner Production. 168:814-822. https://doi.org/10.1016/j.jclepro.2017.09.011.
Shen, C., Bradford, S.A., Wang, Z., Huang, Y., Zhang, Y., Li, B. 2017. DLVO interaction energies between hollow spherical particles and collector surfaces. Langmuir. 33:10455-10467. http://pubs.acs.org/doi/abs/10.1021/acs.langmuir.7b02383.
Bradford, S.A., Kim, H., Shen, C., Sasidharan, S., Shang, J. 2017. Contributions of nanoscale roughness to anomalous colloid retention and stability behavior. Langmuir. 33:10094-10105. http://pubs.acs.org/doi/abs/10.1021/acs.langmuir.7b02445.
Shen, C., Bradford, S.A., Li, T., Li, B., Huang, Y. 2018. Can nanoscale surface charge heterogeneity really explain colloid detachment from primary minima upon reduction of solution ionic strength? Journal of Nanoparticle Research. 20:165. https://doi.org/10.1007/s11051-018-4265-8.
Bradford, S.A., Sasidharan, S., Kim, H., Hwang, G. 2018. Comparison of types and amounts of nanoscale heterogeneity on bacteria retention. Frontiers in Environmental Science. 6:56. https://doi.org/10.3389/fenvs.2018.00056.
Hwang, G., Gomez-Florez, A., Bradford, S.A., Choi, S., Jo, E., Kim, S.B., Tong, M., Kim, H. 2018. Analysis of stability behavior of carbon black nanoparticles in ecotoxicological media: Hydrophobic and steric effects. Colloids and Surfaces A: Physicochemical and Engineering Aspects. 554:306-316. https://doi.org/10.1016/j.colsurfa.2018.06.049.
Li, L., Ma, J., Ibekwe, A.M., Wang, Q., Yang, C. 2018. Influence of Bacillus subtilis B068150 on cucumber rhizosphere microbial composition as a plant protective agent. Plant and Soil. 429(1):519-531. https://doi.org/10.1007/s11104-018-3709-3.
Obayiuwana, A., Ogunjobi, A., Yang, M., Ibekwe, A.M. 2018. Characterization of bacterial communities and their antibiotic resistance profiles in wastewaters obtained from pharmaceutical facilities in Lagos and Ogun States, Nigeria. International Journal of Environmental Research and Public Health. 15(7):1365. https://doi.org/10.3390/ijerph15071365.
Ibekwe, A.M., Murinda, S.E. 2018. Continuous flow-constructed wetlands for the treatment of swine waste water. International Journal of Environmental Research and Public Health. 15(7):1369. https://doi.org/10.3390/ijerph15071369.
