Monitoring antibiotic resistance in agroecosystems

dc.contributor.advisor Adina Howe
dc.contributor.author Colgan, Phil
dc.contributor.department Department of Agricultural and Biosystems Engineering (ENG)
dc.date 2021-01-16T18:19:49.000
dc.date.accessioned 2021-02-25T21:38:01Z
dc.date.available 2021-02-25T21:38:01Z
dc.date.copyright Tue Dec 01 00:00:00 UTC 2020
dc.date.embargo 2020-11-30
dc.date.issued 2020-01-01
dc.description.abstract <p>The livestock industry is the largest consumer of antibiotics worldwide. Antimicrobial resistant bacteria generated by this industry are introduced directly into the soil where we grow much of our food. Agricultural best management practices must be examined closely to identify those that may be improved upon in order to minimize impact on the evolution and spread of antimicrobial resistance. Monitoring for antibiotic resistance genes in the soil and water associated with agroecosystems can provide information regarding the impact these practices have on the spread of antibiotic resistance. The various methods of detection used for monitoring ARGs involve tradeoffs in sensitivity, diversity of targets, and throughput. The appropriate method used for monitoring ARGs in the environment is dependent on the scope of the experiment, and often multiple approaches are necessary to develop a comprehensive understanding of the complex processes involved in ARG dissemination in the environment. The experiments described in this dissertation leverage model systems simulating artificially drained crop soil along with a combination of methods used to monitor ARGs including shotgun metagenomic sequencing, MF-qPCR, and culture-based methods to assess the impact of various agricultural practices on the resistomes of agricultural soil and water. We found that the majority of the ARGs resulting from fertilization of crop soil with swine or beef cattle manure was not distinguishable from background by the end of our simulated growing seasons. However, those that did persist through the end of our studies were associated with mobile genetic elements that enhance the potential for those ARGs to transfer between members of a bacterial community. Additionally, we determined that swine and beef manure associated ARGs are transferred through the soil and into drainage water very differently.</p>
dc.format.mimetype application/pdf
dc.identifier archive/lib.dr.iastate.edu/etd/18296/
dc.identifier.articleid 9303
dc.identifier.contextkey 21104714
dc.identifier.doi https://doi.org/10.31274/etd-20210114-31
dc.identifier.s3bucket isulib-bepress-aws-west
dc.identifier.submissionpath etd/18296
dc.identifier.uri https://dr.lib.iastate.edu/handle/20.500.12876/94448
dc.language.iso en
dc.source.bitstream archive/lib.dr.iastate.edu/etd/18296/Colgan_Revised_July_19_2021.pdf|||Fri Jan 14 21:39:46 UTC 2022
dc.source.bitstream archive/lib.dr.iastate.edu/etd/18296/Colgan_iastate_0097E_19206.pdf|||Sat Jan 16 18:19:49 UTC 2021
dc.subject.keywords Agriculture
dc.subject.keywords antibiotic
dc.subject.keywords Manure
dc.subject.keywords resistance
dc.subject.keywords Soil
dc.subject.keywords Water
dc.title Monitoring antibiotic resistance in agroecosystems
dc.type thesis en_US
dc.type.genre thesis en_US
dspace.entity.type Publication
relation.isOrgUnitOfPublication 8eb24241-0d92-4baf-ae75-08f716d30801
thesis.degree.discipline Agricultural and Biosystems Engineering
thesis.degree.level thesis
thesis.degree.name Doctor of Philosophy
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