Author ORCID Identifier
https://orcid.org/0000-0001-9785-0359
Date Available
8-1-2026
Year of Publication
2025
Document Type
Doctoral Dissertation
Degree Name
Doctor of Philosophy (PhD)
College
Agriculture, Food and Environment
Department/School/Program
Plant and Soil Sciences
Faculty
Dr. Luke A. Moe
Faculty
Dr. Rebecca L. McCulley
Abstract
The implementation of crop rotation on a farm can have many benefits for agroecosystem health and production. This practice can potentially reduce nutrient amendments, disrupt pest and disease cycles, and increase crop yields. In Kentucky, one common rotation consists of either corn or soybean grown the first year, followed by the other crop, repeated every two years. Industrial hemp, grown for fiber or grain, is an emerging crop that has shown promise as a rotation alternative, although not much is known about its effects on soil health, agroecosystem functioning, and microbial communities. To better characterize hemp’s role within American agriculture, the aims of this work are: 1) to determine influences on soil bacterial communities driven by the substitution of hemp into crop rotations, 2) to quantify and compare hemp’s soil-to-atmosphere greenhouse gas fluxes to another common crop, 3) and to identify transformations within the retting microbial community.
To elucidate hemp’s influence on soil microbial communities when substituted into a rotation, three rotations split into six treatments were established at University of Kentucky Spindletop farm (UK) and Kentucky State University Benson farm (KS). The treatments were as follows: corn-soybean-corn, soybean-corn-soybean; hemp fiber-soybean-hemp fiber, soybean-hemp fiber-soybean; hemp grain-corn-hemp grain, corn-hemp grain-corn; with winter wheat as a cover crop for all. 16s rRNA gene amplicon sequencing of the winter wheat rhizosphere was performed, detecting no significant differences between alpha diversity indices or bacterial community compositions of the rotations. Significant changes in the abundances of bacterial phyla and genera were more likely attributed to field conditions or management history, rather than the substitution of hemp. Additionally, field productivity measured via crop yield was unaffected by the rotation type.
Using a subset of plots from the rotation, soil-to-atmosphere gas fluxes and root biomasses of hemp and corn plots under the same management were quantified. Carbon dioxide (CO2), nitrous oxide (N2O), and methane (CH4) fluxes were collected throughout the 2022 and 2023 summer growing seasons, alongside monthly POxC measurements, and root biomass at the end of the growing season. CO2 fluxes were similar between both crops and the conversion of N2O and CH4 fluxes to CO2 warming equivalents did not have an impact on total greenhouse gas emissions despite N2O and CH4 fluxes being significantly different in 2022. Corn root biomass was 3.7 times greater than that of hemp plots at the time of harvest and permanganate oxidizable carbon stocks were equivalent between crops, indicating that microbial respiration was unlikely to be distinct between plots and that hemp roots emitted greater amounts of CO2 than corn roots.
A metagenomic analysis of hemp’s microbial community throughout retting, a microbially controlled degradation used to separate fibers, generated 3.3 billion microbial reads collected over seven weeks (T0-T7). These reads were assembled into 1.1 million contigs, annotated, and binned into 817 genomes, eight of which are near-complete metagenome assembled genomes (MAGs). The retting microbial community was initially heavily dominated by the bacterial phylum Proteobacteria (T0: 77%, T7: 57%), but evened out over time, with increases to the bacterial phylum Actinobacteria (T0: 13%, T7: 23%) and the fungal phylum Ascomycota (T0: 1.5%, T7: 6%). Twenty-two carbohydrate active enzymes related to plant polysaccharide degradation were identified to have significantly changed in gene abundance over the time points. Eight metagenome assembled genomes (MAGs) were constructed from high quality bins, three of which were identified to have saprotrophic lifestyles linked to carbohydrate linkage decay.
Collectively, the findings of this work identified characteristics of hemp pertinent to discussions of its potential in agriculture. From the first project, hemp rotations did not differentially impact soil bacterial populations, which were instead more driven by yearly conditions. While hemp’s inclusion in a crop rotation system showed promise for diversifying cropping systems, its potential as a climate friendly alternative may not be realized under this system’s conditions as it released similar levels of greenhouse gases as corn. The metagenomic analysis of retting hemp offered new insights into a crucial step of fiber processing, moving past microbial taxonomy and detailing microbial function related to retting. The assessment of hemp is far from complete; however, the results held within this dissertation contribute to a deeper comprehension of industrial hemp within American agriculture.
Digital Object Identifier (DOI)
https://doi.org/10.13023/etd.2025.296
Funding Information
This research was supported by a United States Department of Agriculture National Institute of Food and Agriculture Grant (No. 2020-67013-30863) awarded in 2020
Student funding was provided by a National Science Foundation Graduate Research Fellowship Grant (No. 1839289) from 2022 to 2025
Recommended Citation
Pham, Kent D., "Characterizing Agroecosystem Effects of Industrial Hemp on a Rotational Row Cropping System and Microbial Communities" (2025). Theses and Dissertations--Plant and Soil Sciences. 191.
https://uknowledge.uky.edu/pss_etds/191
Included in
Agricultural Science Commons, Agriculture Commons, Environmental Microbiology and Microbial Ecology Commons
