Theses and Dissertations

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Open Access
A comprehensive microbiome analysis of wheat and its wild relatives
(Colorado State University. Libraries, 2018) Cantor, Heather, author; Byrne, Patrick F., advisor; Broders, Kirk, committee member; Stromberger, Mary, committee member
Microbiomes are diverse assemblages of endophytic and free-living microorganisms that can confer competitive advantages to their plant hosts such as water acquisition, nutrient mobilization, drought tolerance, salt tolerance, and disease resistance (Chaparro et al., 2012; Sherameti et al., 2008; Zolla et al., 2013). Plant domestication and selective breeding have altered the composition of these plant-microbe interactions in several crops. It is thought that the progenitors of the A, B, and D genomes in modern hexaploid wheat (Triticum aestivum) manage environmental stress in their native environment by establishing symbioses with a consortium of beneficial microbes (Iannucci et al., 2017). However, these microbial communities are not well understood. The goal of this study is to better understand the core community of microbes in wild wheat relatives and how they differ from the microbiome of cultivated wheat. This study compares the bacterial and fungal taxa found in and on the leaves, roots, and rhizosphere of three accessions of hard winter wheat and 14 accessions of eight wild relative species grown in a common soil. These plants and the agricultural soil they inhabit were sampled from a randomized complete block design with two replications, grown in well-watered and water-limited treatments in Fort Collins, Colorado. DNA was extracted and barcoded amplicon sequencing of the 16S-V4 (bacteria/archaea) and ITS2 (fungi) small subunit ribosomal RNA (rRNA) genes was used to describe the diversity of the microbial community associated with the root, rhizosphere and leaves of each accession. The results indicate that while there were limited differences in microbial communities among plant species, plant tissue type appears to be a strong predictor of microbial community structure. Across all plant genotypes, the rhizosphere consistently contained the most diverse and abundant microbiomes, followed by roots, and lastly leaves, which were the least diverse tissue type. When these three tissue types were analyzed independently (PERMANOVA), there was a significant difference in rhizosphere communities between the wet and dry treatments. Wet treatments contained a greater number of facultative anaerobes and bacteria common to cold, saturated soils. The wet treatment received an additional 13 mm of water, applied five days prior to collection. Overall, while plant host genotypes did not differ significantly in their microbiomes, some unique symbioses among different plant accessions indicate evolutionary adaptation. An initial look at the core microbiome shared among representatives of the five plant genomes in this study showed few shared sequence variants (<2% of total microbial SV's). However, this was largely explained by the use of high-resolution SV's that do not necessarily equate to different taxonomic assignment, suggesting an inflated number of actual microbial taxa. Coarser taxonomic overviews depicted a more realistic, and narrow, number of participating taxonomic groups in the phytobiome. Plant tissue type remained a chief driver of microbiome composition. Soil moisture and fertility may have also played a role in determining microbial community structure, but since they were not measured in this study, claims cannot as yet be made. The close genetic relationships among plant species in this study may have reduced the observable differences in microbial community structure. Additionally, common garden experiments limit the pool of potential plant-microbe interactions. Despite the advancement and evolution of modern wheat, the microbiome remains essentially the same as the microbiomes of wild relatives, when grown in the same soil. This indicates that modern winter wheat retains the same ability to recruit and sustain its microbiome as its wild relatives. In the future, microbiome consensus studies in these hosts' centers of origin could broaden our understanding of long-evolved microbial symbioses.
Open Access
A mechanistic approach to modeling saturation and protection mechanisms of soil organic matter
(Colorado State University. Libraries, 2009) Olchin, Gabriel Peter, author; Paustian, Keith, advisor
Simulation models have been used extensively as a research tool in the field of soil organic matter (SOM) dynamics and should embody our best understandings of the processes and mechanisms controlling these dynamics. Our objective was to develop and evaluate a SOM model based upon measureable soil organic carbon (SOC) fractions and optimize it against long-term tillage experiments in North America. This model will include (1) soil aggregate dynamics, with direct influence from tillage events; (2); and the mechanisms of SOM stabilization; and (3) explicitly address the concept of potential SOC saturation. The major proposed mechanisms for SOM stabilization-physical occlusion, organic recalcitrance, and organo-mineral interactions-have limited explicit inclusion in current SOM models.
Open Access
A study of long-term soil moisture dynamics: assessing biologically available water as a function of soil development
(Colorado State University. Libraries, 2015) Salley, Shawn William, author; Kelly, Eugene F., advisor; Martin, Patrick H., advisor; Knapp, Alan, committee member; Kahosla, Raj, committee member
Forecasting ecosystem responses to global change is highly uncertain in light of the alarming rates of climate change predicted by the scientific community. Rising CO₂ concentrations not only cause increased warming, but may also influence the amount and distribution of rainfall in terrestrial ecosystems. This in turn affects plant growth and the ability of ecosystems to perform important functions including nutrient cycling and decomposition. Soil moisture is considered the major control of ecosystem structure and function, and it is considered the most limiting resource to biological activity in semi-arid grassland ecosystems. Total soil moisture potentials are controlled by edaphic properties such as texture, structure, micro-porosity, bulk density, soil depth, clay mineralogy, and organic matter content. Physical and chemical properties interact with hydrologic inflows and outflows to control soil moisture causing the soil to act as a store and regulator in the water flow system of the overall ecosystem. Thus, the soil acts as both temporary storage of precipitation inputs and as a regulator controlling the partition between inputs and the major outflows: evapotranspiration, runoff, leaching, and flow between organisms. Understanding the pedologic controls of water retention is critical in considering the long-term dynamics of ecosystems and projecting the consequence of global change. The focus of my dissertation is twofold: to elucidate the change in water holding characteristics of soils through pedogenesis and to quantify how global change will impact soil moisture in the U.S. Great Plains. In order to best address my research questions, I began by studying two established soil-chronosequences in northeast Colorado and central Wyoming to assess the characteristics of soil's physical and chemical properties. I examined how they control the biologically available water holding capacities that change predictably as a function of soil age. Next, I examined other notable soil chronosequences across the western United States to test the millennial evolution of soil water holding capacities through various climates and soil parent materials. Finally, I used a soil moisture simulation to spatially model the historical, contemporary, and future projections of soil moisture on the Great Plains. I found in semi-arid ecosystems that three broad stages of soil development exist and are linked to landscape ages that are ecologically and biogeochemically significant: aggrading, equilibrium, and retrogressive stages. Soils in the aggrading stage are typically weakly developed, have genetically simple horizon differentiation, and minimal water retention. Prominent clay and carbonate features are expressed in the equilibrium stage soils which show more complex soil horizonation, structure, aggregation, and porosity. Within these intermediate soils, the capacity to store water reaches a maximum. Declining or retrogressive stage soils show losses of clays and carbonates, have undergone extensive leaching, and the soil's capacity to store water is at a minimum compared to the aggrading and equilibrium stages. Furthermore, I confirmed when modeling soil moisture in the Great Plains that course-textured landscapes store less soil water and when accompanied with disturbance are more vulnerable to climate change. Overall, my dissertation focuses on understanding the role pedogenesis has on soil water holding characteristics and how global change impacts semiarid landscapes. My results have helped improve understanding of long-term ecosystem biophysical feedbacks through quantifying soil moisture retention characteristics across soil age and climatic processes by linking soil water properties to climatic and pedogenic variables.
Open Access
Active sensing: an innovative tool for evaluating grain yield and nitrogen use efficiency of multiple wheat genotypes
(Colorado State University. Libraries, 2012) Naser, Mohammed Abdulridha, author; Khosla, Rajiv, advisor; Haley, Scott, committee member; Reich, Robin, committee member
Precision agricultural practices have significantly contributed to the improvement of crop productivity and profitability. Remote sensing based indices, such as Normalized Difference Vegetative Index (NDVI) have been used to obtain crop information. It is used to monitor crop development and to provide rapid and nondestructive estimates of plant biomass, nitrogen (N) content and grain yield. Remote sensing tools are helping improve nitrogen use efficiency (NUE) through nitrogen management and could also be useful for high NUE genotype selection. The objectives of this study were: (i) to determine if active sensor based NDVI readings can differentiate wheat genotypes, (ii) to determine if NDVI readings can be used to classify wheat genotypes into grain yield productivity classes, (iii) to identify and quantify the main sources of variation in NUE across wheat genotypes, and (iv) to determine if normalized difference vegetation index (NDVI) could characterize variability in NUE across wheat genotypes. This study was conducted in north eastern Colorado for two years, 2010 and 2011. The NDVI readings were taken weekly during the winter wheat growing season from March to late June, in 2010 and 2011 and NUE were calculated as partial factor productivity and as partial nitrogen balance at the end of the season. For objectives i and ii, the correlation between NDVI and grain yield was determined using Pearson's product-moment correlation coefficient (r) and linear regression analysis was used to explain the relationship between NDVI and grain yield. The K-means clustering algorithm was used to classify mean NDVI and mean grain yield into three classes. For objectives iii and iv, the parameters related to NUE were also calculated to measure their relative importance in genotypic variation of NUE and power regression analysis between NDVI and NUE was used to characterize the relationship between NDVI and NUE. The results indicate more consistent association between grain yield and NDVI and between NDVI and NUE later in the season, after anthesis and during mid-grain filling stage under dryland and a poor association in wheat grown in irrigated conditions. The results suggest that below saturation of NDVI values (about 0.9), (i.e. prior to full canopy closure and after the beginning of senescence or most of the season under dryland conditions) NDVI could assess grain yield and NUE. The results also indicate that nitrogen uptake efficiency was the main source of variation of NUE among genotypes grown in site-years with lower yield. Overall, results from this study demonstrate that NDVI readings successfully classified wheat genotypes into grain yield classes across dryland and irrigated conditions and characterized variability in NUE across wheat genotypes.
Open Access
Adaptability of oilseed species at high altitudes of Colorado and technology transfer to Afghanistan
(Colorado State University. Libraries, 2012) Sediqi, Mohammad Navid, author; Johnson, Jerry J., advisor; Byrne, Patrick F., committee member; Jha, Ajay K., committee member
To view the abstract, please see the full text of the document.
Open Access
Adsorption, leaching, and dissipation of pyroxasulfone and two chloroacetamide herbicides
(Colorado State University. Libraries, 2012) Westra, Eric P., author; Barbarick, Ken, advisor; Shaner, Dale, committee member; Khosla, Raj, committee member; Schwartz, Howard, committee member
Pyroxasulfone is a new pyrazole herbicide that controls weeds by inhibiting very long chain fatty acid synthesis. This mechanism of action places pyroxasulfone in the Weed Science Society of America (WSSA) group 15 or Herbicide Resistant Action Committee (HRAC) group K3 herbicides that include s-metolachlor and dimethenamid-p. Dimethenamid-p and s-metolachlor are referred to in literature as acetamide, acetanilide, chloroacetamide, or chloroacetanilide herbicides. In this thesis, these two herbicides are referred to as chloroacetamide herbicides based on the HRAC classification. The soil interactions of pyroxasulfone were evaluated and compared to s-metolachlor and dimethenamid-p to better understand how pyroxasulfone will behave under various field conditions Pyroxasulfone was compared with these two standard herbicides because of their similar mechanisms of action, use patterns, potential for use in similar cropping systems, and similar weed control spectrums. Sorption coefficients were determined for 25 different soils to evaluate relative differences in binding among pyroxasulfone, dimethenamid-p, and s-metolachlor. Across all soil types, the relative order of binding was pyroxasulfone=dimethenamid-p < s-metolachlor. Pyroxasulfone and dimethenamid-p were not statistically different in terms of their binding; however, s-metolachlor binding was statistically greater than both dimethenamid-p and pyroxasulfone. For all three herbicide, organic matter was the only soil property which was highly and significantly correlated to herbicide adsorption; all other soil properties correlated with herbicide adsorption could be explained by the correlation of OM and those soil properties. Based on the water solubility of these three herbicides, we expected the order of binding to be dimethenamid-p < s-metolachlor < pyroxasulfone. This study displayed the unique characteristics of pyroxasulfone in that it has the lowest water solubility of the three herbicides, yet sorption coefficient values indicate that pyroxasulfone is only loosely adsorbed by soil. Reduced soil binding along with a higher unit of activity makes pyroxasulfone a potent herbicide that provides comparable weed control when applied as low as one-eighth of typical application rates for other chloroacetamide herbicides. Field studies were conducted in 2009 and 2010 at two contrasting field sites to evaluate the dissipation and movement of pyroxasulfone and s-metolachlor in the top 30 cm of the soil profile. The site at the horticultural farm (HORT) has a Nunn clay loam soil (Argiustoll), whereas the site at the Limited Irrigation Farm (LIRF) has an Olney fine sandy loam soil (Haplargid). Dissipation half-lives (DT50) were the shortest at the Hort farm site with the heavier textured clay loam soil and increased moisture content. The LIRF site with lighter textured sandy loam soil and decreased moisture resulted in extended DT50 values and more variation between replicates for both herbicides. Across both years and field sites, pyroxasulfone DT50s were approximately twice as long as for s-metolachlor. The extended half-life of pyroxasulfone suggests that it would provide longer weed control compared to s-metolachlor. Herbicide movement in the top 30 cm of the soil profile was greater at the LIRF site which suggests that movement was influenced by soil type to a greater extent than irrigation amount, since the LIRF site received much less total irrigation yet had the most movement downward in the profile. In general, pyroxasulfone moved downward in the profile to a greater extent than s-metolachlor. Observed herbicide movement confirmed sorption coefficient data that shows that pyroxasulfone is bound less to the soil compared to metolachlor and, hence, is more available in the soil solution where the herbicide movement is influenced by mass flow. Extended observed half-lives, reduced soil binding, and increased unit activity indicate that pyroxasulfone is a potent inhibitor of very long chain fatty acid (VLCFA) biosynthesis that can provide comparable weed control for longer periods of time at reduced use rates when compared to commonly used chloroacetamide herbicides.
Open Access
Agronomic factors affecting dryland grain sorghum maturity and production in northeast Colorado
(Colorado State University. Libraries, 2012) Sauer, Sally M., author; Johnson, Jerry J., advisor; Hansen, Neil C., committee member; Jha, Ajay K., committee member; McMaster, Gregory S., committee member; Vigil, Merle F., committee member
To view the abstract, please see the full text of the document.
Open Access
Agronomic responses of grass and alfalfa hayfields to no and partial season irrigation as part of a Western Slope water bank
(Colorado State University. Libraries, 2015) Jones, Lyndsay P., author; Brummer, Joe, advisor; Cabot, Perry, committee member; Davis, Jessica, committee member
Prolonged drought and increasing demand for water resources has caused growing concern over Colorado's ability to fulfill legal water obligations as identified in the Colorado River Compact. A Western Slope Water Bank, which would entail agricultural water users entering into short-term leases and temporarily withholding or reducing irrigation, could be a partial solution to free up water to fulfill these obligations. Grass and alfalfa (Medicago sativa L.) hayfields may be ideal for inclusion in a water bank as they are the primary users of agricultural water in this region and may have a greater ability to withstand water stress in comparison to other crops. This study was conducted to determine effects of withholding irrigation for a full season from high elevation grass hayfields and implementing partial season irrigation on lower elevation alfalfa hayfields on forage yield, nutritional quality, and associated recovery period to confirm if this approach is worth pursuing. In Year 1, five established grass hayfields on the Colorado Western Slope were split into side-by-side plots, one of which was irrigated according to the manager’s normal practices as the control while the other was subjected to total cessation of irrigation. Both plots were irrigated in Year 2. In Year 1, average dry matter yields in non-irrigated plots were reduced to 39% (2497 kg ha-1) of the control (6377 kg ha-1). Neutral detergent fiber (aNDF) concentration in non-irrigated plots was 5% lower while crude protein (CP) content was 30% greater than the control. In-vitro true digestibility (IVTD) was unaffected by irrigation treatment. Yields of non-irrigated plots did not fully recover when returned to irrigation in Year 2 producing 49% (3623 kg ha-1) of the control (7442 kg ha-1). When returned to irrigation, aNDF concentrations were still reduced by 8% and CP contents were similar to that of the control. In the single site sampled after returning to full irrigation for 2 years, yields had fully recovered. It is probable that participation by producers in a water bank would be largely influenced by compensation for reduced yields the season of withholding irrigation as well as the following year when irrigation is returned to grass hayfields. Three established alfalfa fields were subjected to irrigation treatments including irrigation according to the manager’s normal practices (control), irrigation stopped after the 1st cutting (SA1), and irrigation stopped after the 2nd cutting (SA2) for 2 consecutive years. Averaged over both years, SA2 plots maintained production similar to the control in the 1st and 2nd cutting while SA1 plots were reduced to 61% (2089 kg ha-1) of the control (3430 kg ha-1) by the 2nd cutting. By the 3rd cutting, SA2 and SA1 yields decreased to 53% (1804 kg ha-1) and 30% (1013 kg ha-1) of the control, respectively. On a total season basis, both plots receiving partial season irrigation were reduced with SA2 plots producing 72% (7880 kg ha-1) and SA1 plots producing 33% (3650 kg ha-1) of the control (11040 kg ha-1). aNDF concentrations were greatest in the control at 34.6% and lowest in SA1 plots at 28.2%. By the 2nd cutting, SA1 plots had the highest IVTD (80%), and by the 3rd cutting, SA2 and SA1 plots were equally greater (80%) than the control (75%). Effects on CP content were inconsistent. These results suggest that reduced irrigation may improve forage quality slightly, but will significantly reduce yields. When irrigation is returned the following year, forages may have increased quality due to reduced fiber content, but grass yields will likely not fully recover while alfalfa yields may recover depending on length and severity of reduced irrigation. Due to its ability to recover, using partial season irrigation similar to that of the SA2 treatment on alfalfa hayfields may be the most practical approach to make water available to a Western Slope water bank.
Open Access
Alfalfa reference crop evapotranspiration in Colorado and its use for irrigation scheduling
(Colorado State University. Libraries, 2015) Aljrbi, Abdulkariem Mukhtar, author; Davis, Jessica G., advisor; Andales, Allan A., advisor; Qian, Yaling, committee member; Hansen, Neil, committee member
The goal of irrigation scheduling is efficient use of water such that water is applied to the field for optimal crop production. Previous studies have optimized irrigation scheduling using different models to manage sprinkler irrigation. This research evaluated approaches for obtaining alfalfa reference evapotranspiration (ETr) and its use in a new irrigation scheduling model for a furrow irrigation system. The objectives of this research were to: 1) Compare seasonal trends of daily ETr from the American Society of Civil Engineers Standardized Penman-Monteith (ASCE-SPM) equation and the Penman-Kimberly (PK) equation along a climatic gradient in Colorado, 2) Verify the agreement between calculated ETr from the ASCE-SPM equation and measured ETr from a lysimeter during the 2010 season for the Arkansas Valley of Colorado and correct the lysimeter ETr for alfalfa overgrowth, and 3) Test the ASCE-SPM ETr along with a locally adapted Kcr curve for corn in an irrigation scheduling spreadsheet tool for simulating the daily soil water deficit of furrow irrigated corn in northeast Colorado. The two reference ET equations were compared using R2, Root-Mean-Square Error (RMSE), Relative Error (RE), and index of agreement (d). The R2 values ranged from 0.93 to 0.99; d ranged from 0.98 to 0.99, RMSE ranged from 0.29 to 0.75 mm/d, and RE ranged from -6.35 to 1.91 %. In a comparison of the ASCE-SPM and PK equations at the Fort Collins and Rogers Mesa sites in 2011, differences were observed between the energy balance and aerodynamic terms of each equation. The energy budget calculated by the ASCE-SPM was generally 28% lower than the energy budget calculated by the PK equation at both locations for 2011. On the other hand, the aerodynamic term calculated by the ASCE-SPM equation was from 27 - 28 % higher than the aerodynamic term calculated from PK during most of 2011 at both locations. The second objective of this research compared alfalfa ET measured with a lysimeter in the center of a 4.06 ha furrow irrigated field at the Colorado State University Arkansas Valley Research Center in Rocky Ford, CO to the calculated values from the ASCE-SPM equation in periods of reference conditions in 2010. Four days were selected when alfalfa in the lysimeter was 50 - 55 cm tall, unstressed, completely covering the ground, but with its canopy extending beyond the outer walls of the lysimeter. On these dates, hourly lysimeter ETr was 0.08 to 0.11 mm/h higher than ASCE-SPM ETr. The theoretical surface area of the lysimeter was 9.181 m², while the observed effective canopy area was up to 12.461 m² due to overgrowth. Surface area corrections for the overgrowth increased the index of agreement (d) between hourly lysimeter ETr and ASCE-SPM ETr from the 0.96 - 0.98 range to the 0.99 - 1.0 range. These results showed that it is important to use the correct effective canopy area when computing ETr from a weighing lysimeter. The CIS model for calculating water deficit under a furrow irrigation system with the addition of some data from field measurements such as soil moisture content, gross irrigation, climate data, and plant height and leaf area index generated good results. The water deficit under corn was simulated at the Limited Irrigation Research Farm (LIRF) located near Greeley, Colorado during the years 2010, 2011 and 2012. Daily corn crop ET (ETc) calculated from daily ASCE-SPM ETr and a locally-derived crop coefficient curve (Kcr) were used by the CIS for daily soil water deficit calculations via water balance. This data was used to test a furrow irrigation system via the CIS model and to simulate the field irrigation by predicting the time and the amount of water for the next irrigation. The results showed good agreement between calculated and measured deficits where index of agreement (d) ranged from 0.5 to 0.99 for most years of this study, specifically when measurements of soil water content (SWC) were inserted bi-weekly or monthly. The RMSE did not exceed 2.54 mm when using SWC once per season in 2011, while bi-weekly measurements recorded d to be 0.96 in 2010, 0.99 in 2011 and 0.70 in 2012. Also, the CIS showed that irrigation water usage could be reduced by 30 to 50% through use of CIS.
Open Access
Alfalfa water use under deficit irrigation for farm savings
(Colorado State University. Libraries, 2022) Sitterson, Jan, author; Andales, Allan A., advisor; Mooney, Daniel F., committee member; Brummer, Joe E., committee member
Colorado water law allows for water rights to be leased between agriculture and municipality users. Decreasing the consumptive use (CU) of agricultural land while maintaining profits and yields will allow farmers to lease their water rights for revenue. Deficit irrigation is a water-saving approach to avoid the complete dry up of irrigated farmland while providing profitable yields and monetary gains from water transfers. To maximize water savings, efficient irrigation systems such as subsurface drip irrigation (SDI) are used to prevent water losses from soil evaporation. This study evaluated the feasibility of using SDI with deficit irrigation practices to grow alfalfa (Medicago Sativa L.) at production scale in northeast Colorado (2018 – 2022). Alfalfa was found to have good potential for decreasing CU due to its drought tolerance, multiple harvests per season, and improved quality of hay with less irrigation water. The Water Irrigation Scheduler for Efficient Application (WISE) model was also found to be a useful tool for estimating CU of deficit irrigated alfalfa and the regrowth phases after multiple harvests in a growing season. Mid-season corrections of the soil water deficit in WISE improved the accuracy of modeled CU. Overall the water savings from deficit irrigation at low, medium, and high irrigation levels with an SDI system can be profitable when prices for leasing water exceed hay prices per unit area of production.
Open Access
Amendment effects on soil physical properties and restoration of decommissioned forest roads
(Colorado State University. Libraries, 2017) Berlejung, John Michael, author; Fonte, Steven, advisor; Rhoades, Charles, committee member; Paschke, Mark, committee member
Unsealed forest roads, including logging roads and unauthorized roads created by hunters, miners, and recreational users, generate significant harmful effects to local ecosystems and waterways. Rapid restoration of these roads is necessary to prevent erosion, downstream implications for water quality, and a variety of other deleterious ecosystem impacts. Soil amendments, including mulches, composts, and other materials, offer promise to improve soil health, restore soil structure, and support revegetation of these sites. I tested the viability of three locally-sourced soil amendments wood straw mulch, Biosol fertilizer, and biochar alone and in paired combinations to restore soil physical properties important for improved hydrologic function and plant growth. I found that amendment combinations of biochar + mulch and biochar + Biosol significantly reduced soil bulk density when compared to unamended controls. Other factors (aggregate stability, infiltration, sediment production) suggested potential for improvement relative to unamended control plots, but no significant differences between treatments were observed due to high variability within and between sites. Regression analyses revealed that soil physical properties, particularly wet aggregate stability, was significantly correlated with key soil erosion parameters such as infiltration and runoff, suggesting aggregate stability could provide a useful measure of soil restoration success.
Open Access
An integrated approach to local based biofuel development
(Colorado State University. Libraries, 2011) Enjalbert, Jean-Nicolas, author; Johnson, Jerry J., advisor; Peterson, Gary, 1940-, committee member; Olsen, Daniel B., committee member; McKay, John K., committee member; Byrne, Patrick F., 1948-, committee member
Oilseed crops have potential to replace a portion of the on-farm energy demand currently satisfied by fossil fuel. This dissertation allies mechanical engineering, field testing, and molecular breeding research into an integrated approach to solve problems associated with straight vegetable oil (SVO) production and use on Colorado farms. Four related topics of investigation and activity are reported. To identify an adapted, short-season oilseed crop that could fit into the current High Plains dryland cropping system, a genetic diversity study was conducted on three potential oilseed species: Brassica juncea, Brassica carinata, and Camelina sativa. To illuminate the genetic basis of camelina response to drought stress, a two-year study of quantitative trait loci (QTLs) was implemented under dry and irrigated conditions using 181 recombinant inbred lines (RILS) developed from European cultivars. To understand and eventually manage camelina production, a multi-environmental regional trial of camelina seed yield, oil content, and oil quality was conducted with eight American and European varieties. Extension activities introduced SVO information and technology to farmers in Colorado. Camelina sativa showed better adaptation to semi-arid environments than B. juncea and B. carinata, outyielding them due to camelina's shorter stature, higher harvest index, and greater resistance to flea beetle. Camelina yield, oil content, and linolenic fatty acid (FA) content were higher in cool, wet environments than in warm, dry environments. Linolenic FA content and seed size were negatively correlated (p<0.05) with early flowering time. Earlier flowering was associated with increased seed yield (p<0.01) under dry and hot environments, but with decreased seed yield under irrigation. Environment was a larger source of variation than genotype for all the traits measured in this study. Twenty-nine QTLs were found in camelina for seed yield, oil quality, and drought-tolerance-related traits such as leaf water content and leaf nitrogen content, which could lead to breeding for improvement of camelina performance in semi-arid environments. Some QTLs were shared by multiple traits, suggesting either pleiotropic effects or proximity of genes. The cumulative effect of stable, favorable alleles for seed yield was a 16% increase in yield. Trait responses to moisture varied widely, both in the multi-environmental regional trial using cultivars and in the single-location trial using RILs. The range of trait response reflects variation in plasticity in camelina germplasm. Two analysis methods, namely, additive main effects and multiplicative interaction (AMMI) and the moisture difference value method, were used to detect false positive QTLs and to predict QTL effect in specific environments. AMMI was used successfully to delineate mega-environments within the study region and to identify the best-adapted varieties for these mega-environments. With the QTL data developed in this study, marker-assisted selection could be used to identify camelina varieties adapted to specific environments or to a broad range of environments. Five lines possessing three favorable yield QTLs expressed under drought conditions are undergoing seed increase and additional multi-locational testing for potential release. Oilseed-for-biofuel workshops, crusher demonstrations, and oilseed field days were conducted to demonstrate the feasibility of potential advantages of SVO for farmers wanting an alternative energy source to reduce their use of fossil fuel. A limited number of early adopters are beginning to integrate camelina into their crop rotation. Three small oilseed crushing and processing facilities have been established from collaboration with farmers and other agencies, and another is in the design stage. Two extension fact sheets will be published on camelina production and on biofuel production at a farm scale.
Open Access
An NLR gene likely underlying RMES1 provides global sorghum resistance bolstered by RMES2
(Colorado State University. Libraries, 2023) VanGessel, Carl, author; Morris, Geoffrey, advisor; Nalam, Vamsi, committee member; Roberts, Robyn, committee member; Mason, Esten, committee member
Breeding for aphid host plant resistance in sorghum has been an area of interest since the emergence of Melanaphis sorghi in North America a decade ago. In order to develop durable sorghum aphid resistance, breeders must be equipped with tools (trait package) and knowledge (molecular mechanisms) of host plant resistance. In this dissertation, I characterize the current state of sorghum aphid breeding and propose a genotype to phenotype map for the major source of global resistance, Resistance to Melanaphis sorghi 1. Relying on near-isogenic lines, I demonstrate that RMES1 is applying selection pressure to sorghum aphid through reduction in fecundity that discriminates among aphid species. In global sorghum lines, RMES1 is rare whereas a second resistance source, RMES2, is common and present in historic breeding germplasm. I mapped RMES2 in Haitian breeding populations where it contributes fitness increases while lacking antagonistic pleiotropy and is selected for alongside RMES1. These results suggest breeding programs may unknowingly be deploying both sources of resistance which in combination are reducing the likelihood of M. sorghi biotype shifts to overcome RMES1. As aphid resistance may rely on phytochemical and/or induction with extended phenotypes regarding aphid populations, I used pan-genomic, transcriptomic, and metabolomic resources to describe the molecular mechanism of RMES1. Structural variation at the Chr06 locus underlies presence/absence variation of several nucleotide-binding leucine-rich repeat receptor (NLR) genes. Two of these candidate genes, SbPI276837.06G016400 and SbPI276837.06G016600, are representatives of two orthologous NLR groups which have genomic and transcriptomic evidence of underlying RMES1 resistance. The PAL branch of the salicylic acid pathway is the primary phytohormone pathway responsible for RMES1-induced resistance. Finally, metabolome reorganization mirroring transcriptome changes suggest RMES1 is inducing multiple downstream mechanisms responsible for reducing aphid fecundity. While the causal gene underlying RMES1 remains to be cloned and the eliciting aphid factor is unknown, this research suggests that gene-for-gene dynamics could lead to resistance-breaking biotype shifts and combining RMES1 with additional resistance genes e.g. RMES2, will help achieve durability.
Open Access
Analysis of land use change and greenhouse gas emissions in Kalasin Province, Thailand
(Colorado State University. Libraries, 2018) Chailangka, Preeyarat, author; Paustian, Keith, advisor; Fonte, Steven, committee member; Leisz, Stephen, committee member
Growing global population causes many stresses on the environment, perhaps the most serious is global warming due to Greenhouse Gas (GHG) emissions. Major contributors to GHG emissions include agricultural production and land use change. Southeast Asia is one of the world's fastest growing regions and provides many crops for export, so the land use changes are rapid and not always made in an environmentally conscious manner. The province chosen for this study, Kalasin, is located in a major economic development region with the multi-country East-West Economic Corridor (EWEC) running through it. The EWEC has brought many changes to this province such as expansion of the manufacturing sector, more urban growth to support new factories, and new roads to reach areas which were previously not developed. The largest single land use in Thailand and the Kalasin province is cropland. There have been many changes in farming practices in the province as well, from the types of crops grown to the increasing numbers of commercial farms. These shifts in land use are leading to changes in the amount of GHG emissions and are also leading to land degradation in parts of the province as well. The largest GHGs emissions in agricultural sector come from rice cultivation (45%), followed by biomass carbon stock losses (40%). Some government policies have led to crops being grown on unsuitable lands, which is often associated with greater use of fertilizers and intensive tillage practices applied. Other practices involve draining wetlands, creating rice paddies on unsuitable soils, or clearing forests to farm the area. In this study we look at land use and land use changes throughout the province and use that data to estimate a GHG emissions inventory in the agricultural sector in order to better understand the effects that growth, land use and land use changes in the Kalasin province have on the environment.
Open Access
Analysis of wheat spike characteristics using image analysis, machine learning, and genomics
(Colorado State University. Libraries, 2022) Hammers, Mikayla, author; Mason, Esten, advisor; Ben-Hur, Asa, committee member; Mueller, Nathan, committee member; Rhodes, Davina, committee member
Understanding genetics regulating yield component and spike traits can contribute to the development of new wheat cultivars. The flowering pathway in wheat is not entirely known, but spike architecture and its relationship with yield component traits could provide valuable information for crop improvement. Spikelets spike-1 (SPS) has previously been positively associated with kernel number spike (KNS) and negatively correlated with thousand kernel weight, meaning a further understanding of SPS could help unlock full yield potential. While genomics research has improved efficiency over time with the development of techniques such as genotyping by sequencing (GBS), phenotyping remains a labor and time intensive process, limiting the amount of phenomic data available for research. Recently, there has been more interest in generating high-throughput methods for collecting and analyzing phenotypic data. Imaging is a cheap and easily reproducible way to collect data at a specific maturity point or over time, and is a promising candidate for implementing deep learning algorithms to extract traits of interest. For this study, a population of 594 soft red winter wheat (SRWW) inbred lines were evaluated for wheat spike characteristics over two years. Images of wheat spikes were taken in a controlled environment and used to train deep learning algorithms to count SPS. A total of 12,717 images were prepared for analysis and used to train, test, and validate a basic classification and regression convolutional neural network (CNN), as well as a VGG16 and VGG19 regression model. Classification had a low accuracy and did not allow for an assessment of error margins. Regression models were more accurate. Of the regression models, VGG16 had the lowest mean absolute error (MAE) (MAE = 1.09) and mean squared error (MSE) (MSE = 2.08), and the highest coefficient of determination (R2) (R2 = 0.53) meaning it had the best fit of all models. The basic CNN was the next well fit model (MAE = 1.27, MSE = 2.61, r = 0.48) followed by the VGG19 (MAE = 1.32, MSE = 2.98, r = 0.45). With an average error of just above one spikelet, it is possible that counting methods could provide enough data with an accuracy high enough for use in statistical analyses such as genome wide association studies (GWAS), or genomic selection (GS). A GWAS was used to identify markers associated with SPS and yield component traits, while demonstrating the use of genomic selection (GS) for prediction and screening of individuals across multiple breeding programs. The GWAS results indicated similar markers and genotypic regions underpinning both KNS and SPS on chromosome 6A and spike length and SPS on chromosome 7A. It was observed that favorable alleles at each locus were associated with higher KNS and SPS on chromosome 6A and longer wheat spikes with higher SPS on chromosome 7A. Significant markers on 7A were observed in the region near WAPO1, the causal gene for SPS on the long arm of chromosome 7A, indicating they could be associated with that gene. GS results showed promise for whole genome selection, with the lowest prediction accuracy observed for heading date (rgs = 0.30) and the highest for spike area (rgs = 0.62). SPS showed prediction accuracies ranging from 0.33 to 0.42, high enough to aid in the selection process. These results indicate that knowledge of the flowering pathway and wheat spike architecture and how it relates to yield components could be beneficial for making selections and increasing grain yield.
Open Access
Annual cool-season forage systems for fall grazing by cattle
(Colorado State University. Libraries, 2015) Villalobos, Luis Alonso, author; Brummer, Joe E., advisor; Davis, Jessica G., committee member; Whittier, Jack C., committee member; Meiman, Paul, committee member
Extending the grazing season is one method that beef producers can use to reduce the need for preserved forages and supplements as these are the major inputs influencing profitability of their operations. Annual forages planted during mid- to late-summer have great potential for extending the grazing season into the fall and early winter in northern Colorado and similar environments. The development of forage systems for livestock operations must start with selection of forage species/cultivars that can yield enough biomass and have a high enough nutritive value to meet the requirements of the livestock to be fed. Accordingly, the research in this dissertation started with an evaluation of nine forage brassica cultivars from which four were chosen based on their unique traits. Barnapoli rape (Brassica napus L. var. napus) had the highest yields and stood up under a snow load; Groundhog radish (Raphanus sativus var.oleifer Strokes) and Barkant turnip (Brassicas rapa L. var. rapa) had fast growth and their bulbs provided extra feed and penetrated the soil, potentially reducing compaction; and Pasja hybrid (Chinese cabbage [Brassica rapa L. chinensis] x Turnip hybrid) had a high leaf-to-stem ratio which provided high quality forage for beef cattle. These were combined in a four-way mixture and evaluated in subsequent studies. In addition, the above study evaluated the impact of planting date on resulting yields of the brassicas and determined that they need to be planted by mid- to late-July to yield high amounts of biomass that can be stockpiled for fall grazing. The nutritive value of the brassicas was high and did not decline over time, but they were very low in fiber which can create rumen upset for beef cattle grazing them in monocultures or in brassica only mixtures. To develop a more balanced diet for beef cattle, the brassica mixture was seeded with cool-season grasses (triticale [×Triticosecale Wittm ex A. Camus {Secale x Triticum}], winter wheat [Triticum aestivum L.], and barley [Hordeum vulgare L.]) following a warm-season hay crop (pearl millet [Pennisetum glaucum L.]) that was either controlled or allowed to regrow. When the latter was controlled by spraying, brassicas dominated the mixtures to the detriment of the cool-season grasses which contributed little to available dry matter. The seed proportions of the cool-season grasses within the mixture were much lower than those used when grown in monocultures. When the proportions of cool-season grasses within mixtures were increased, their contribution to yield increased. Oats (Avena sativa) were particularly competitive when grown with the brassica mix. When the millet was allowed to regrow, it dominated the available dry matter, which influenced overall yield and nutritive value of the mixtures. Mixtures of cool-season forages and millet regrowth had lower quality than the same mixtures grown where the millet was controlled. This resulted from the brassicas dominating the mixtures where the millet regrowth was controlled, which resulted in higher quality that will likely require fiber supplements for grazing cattle. Mixtures grown with millet had higher fiber content, which negates the need for fiber supplementation. Cool-season forages and mixtures were also interseeded into corn at the V6 growth stage, which resulted in higher quality biomass on offer to beef cattle grazing cornstalks during fall and winter months. Their higher quality negates the need for supplementation, especially of protein, that is usually required to offset the low nutritive value of cornstalks. Of the forages evaluated, the brassica mix and annual ryegrass (Lolium perenne L. ssp. multiflorum [Lam.] Husnot) had the highest yields which was the determining factor for interseeded cool-season forages to compete with the costs of preserved forages that are normally used as supplements for beef cattle grazing cornstalks. Thus, the forage systems described in this dissertation provide insight into how annual forages can extend the grazing season into the fall and early-winter months, reducing the need for preserved forages to be fed in beef cattle operations. Sustainability of production systems can be enhanced when producers integrate current knowledge into their operations. Planting annual forages has the potential to benefit production of livestock and crops.
Open Access
Association mapping for yield, yield components and drought tolerance-related traits in spring wheat grown under rainfed and irrigated conditions
(Colorado State University. Libraries, 2013) Edae, Erena Aka, author; Byrne, Patrick, advisor; Haley, Scott, advisor; Black, William, committee member; Storlie, Eric, committee member
Genome-wide association mapping shows promise for identifying quantitative trait loci (QTL) for many traits including drought stress tolerance. Candidate gene analysis also has been used to identify functional single nucleotide polymorphisms (SNPs) that can be associated with important traits. In 2010 and 2011, we evaluated an International maize and wheat improvement center (CIMMYT) spring wheat association mapping panel under rainfed and full irrigation conditions in Greeley, CO, and Melkassa, Ethiopia (total of five environments) for grain yield and its components, canopy spectral reflectance, and several other phenological or drought-related traits. A total of 287 lines were genotyped with Diversity Array Technology (DArT) markers to identify associations with measured traits under different moisture regimes. Significant differences among lines were observed for most traits within each environment and across environments. Best linear unbiased predictors (BLUPs) of each line were used to calculate marker-trait associations using 1863 markers with a mixed linear model with population structure and a kinship-matrix included as covariates. Three drought responsive candidate genes (Dehydration-Responsive Element Binding 1A, DREB1A; Enhanced Response to abscisic acid (ABA), ERA1; and Fructan 1-exohydrolase, 1-FEH), were amplified using genome-specific primers and sequenced from 126 lines to identify single nucleotide polymorphisms (SNPs) within the candidate genes and determine their association with measured traits. For genome wide association mapping, the highest number of stable associations was obtained for kernel hardness followed by grain volume weight (test weight), an important trait under drought stress conditions. The most stable marker-trait association was obtained for grain yield on chromosome 2DS. All marker-trait associations for above-ground biomass were environment-specific. Multi-trait marker-trait association for grain yield and other traits such as harvest index, final biomass, thousand kernel weight, plant height and flag leaf length were detected on chromosome 5B. A grain yield QTL was again co-localized with harvest index QTL on chromosome 1BS. Normalized difference vegetation index (NDVI) shared QTL region with a harvest index QTL on chromosome 1AL, while green leaf area shared a QTL with harvest index on chromosomes 5A. For drought tolerance candidate genes, SNPs within DREB1A gene were associated with final biomass, spikelets per spike, days to heading and NDVI. The 1-FEH gene amplified from the A genome showed associations with grain yield, final biomass, NDVI, green leaf area, kernel number per spike and spike length. However, 1-FEH from the B genome was associated with traits such as days to heading, days to maturity, thousand kernel weight and test weight. The ERA1 gene from the B genome was associated with spike m-2, harvest index, grain filling duration, leaf senescence, flag leaf width, plant height and spike length, whereas ERA1 from the D genome was associated with kernel weight per spike, flag leaf width, leaf senescence, kernel number per spike and harvest index. In general, each candidate gene had effects on multiple traits under both rainfed and irrigated conditions. Both genome wide and candidate gene approaches showed that most of the measured traits are controlled by several QTL/genes with minor effects. QTL/genes with pleotropic effects were also detected. Therefore, the information generated by this study might be used in marker-assisted selection to improve drought tolerance of wheat.
Open Access
Azolla biofertilizer growth and utilization for vegetable production
(Colorado State University. Libraries, 2017) Widiastuti, Dwi P., author; Davis, Jessica G., advisor; Stromberger, Mary E., committee member; Bartolo, Michael E., committee member; Storteboom, Heather, committee member; Gafur, Sutarman, committee member
To view the abstract, please see the full text of the document.
Open Access
Bi-parental mapping and genome-wide association studies for grain quality traits in winter wheat under contrasting soil moisture conditions
(Colorado State University. Libraries, 2015) Dao, Hung Quoc, author; Byrne, Patrick F., advisor; Brick, Mark A., committee member; Haley, Scott D., committee member; Jahn, Courtney E., committee member
Wheat grain quality is characterized by parameters such as grain protein concentration (Gpc), grain ash concentration (Gac), kernel weight (Kw), kernel diameter (Kd), and kernel hardness (Kh). Grain protein determines dough strength and loaf volume, while kernel hardness and size impact milling efficiency. Drought stress at flowering time can cause floral organ necrosis, thus, decreasing the number of grains per spike and filled grain percentage, while drought stress during grain filling reduces kernel weight and size, but increases grain protein concentration. A previous study reported three chromosomal regions (1B, 6B, and 7B) associated with many quantitative trait loci (QTL) co-located for grain quality traits in a doubled haploid (DH) population derived from the cross CO940610/Platte. To validate those QTL, three objectives of this study were (1) QTL mapping in a CO940610/Platte recombinant inbred line (RIL) population, (2) transferring alleles of interest from CO940610 to the recurrent parent Platte by marker-assisted backcross (MABC), and (3) genome-wide association studies for grain yield (Gy), Gpc, grain protein deviation (Gpd), Gac, and test weight (Tw) in an association mapping panel. A population of 186 CO940610/Platte RIL was grown in the Akron rainfed and Greeley fully irrigated environments in 2009/10. The same set of RIL was grown in a CSU Plant Sciences greenhouse for DNA extraction, and genotypes were obtained for 18 simple sequence repeat and sequence tagged site markers in three chromosome regions of interest. JoinMap 4.0 was used to construct linkage maps from the molecular marker data. Marker-trait associations (MTA) were detected by single-factor analysis of variance (ANOVA). Linkage maps constructed in the CO940610/Platte RIL and DH populations were mostly consistent. Most of the grain quality traits investigated were associated with the three chromosome regions on 1B, 6B, and 7B in at least one environment, confirming findings in the CO940610/Platte DH population. Five selected DH lines and the recurrent parent Platte were used during MABC, resulting in 35 BC3F2 lines for field trials. These lines were classified into 8 allelic combinations at the selective marker loci Glu-B1, Xwmc182a, and Xwmc182b, representing of the regions of interest on chromosomes 1B, 6B, and 7B, respectively. Of these allelic combinations, lines having PL-PL-CO and CO-CO-PL at Glu-B1, Xwmc182a and Xwmc182b, respectively, were hypothesized to have the lowest and highest Gpc. Experiments for the 35 MABC lines were conducted in Fort Collins fully irrigated (sprinkler irrigation), Greeley irrigated (drip irrigation), and Greeley water deficit (severe stress during grain filling) environments. Marker-trait associations for Gpc detected at Xwmc182a and Xwmc182b in the BC3F2 backcross population were consistent with findings in the CO940610/Platte DH population. The MTA for Gpc and Gac at locus Xwmc182a were robust across two of three environments. In the Fort Collins fully irrigated environment, Gpc of the allelic combination CO-CO-PL was significantly higher than the combination PL-PL-CO, confirming the hypothesized results. A collection of 299 hard winter wheat cultivars and breeding lines representative of the U.S. Great Plains germplasm was evaluated for Gy, Gpc, grain protein deviation (Gpd), Gac and Tw. Experiments were designed as side-by-side moisture treatments in Greeley 2011/12 (drip irrigation, stress began pre-flowering) and Fort Collins 2012/13 (sprinkler irrigation, severe stress during grain filling). Each treatment was arranged as an augmented design with two check varieties, each check having 15 replicates. Grain protein concentration and Gpd were highly correlated (0.72 to 0.87, P<0.001) in all four environments. The panel was characterized using a high-density 90,000 gene-associated single nucleotide polymorphism (SNP) genotyping platform. After removing SNP that did not meet data quality criteria, 16,052 filtered SNP were used to perform the genome-wide association studies (GWAS) conducted in the R programming environment using the 'GAPIT' package. Principal components and a kinship matrix were incorporated to correct for population structure and relatedness among individuals. A total of 40 significant MTA (according to the significance threshold of P<1.67x10-4, suggested by Gao et al. 2008) were detected for the five evaluated traits (Gy, Gpc, Gpd, Gac, and Tw). Of these, two SNP (BS00021704_51 and Excalibur_c4518_2931) on chromosome 6A were associated with Gy. The same SNP (BS00064369_51) on 4A was associated with both Gpc and Gpd. Test weight had the most MTA (17). In particular, two SNP, BS00047114_51 and BS00065934_51, both associated with Tw on chromosome 3B, were robust across three of four environments investigated. In conclusion, two narrow regions (~2 cM each) around Xwmc182a on 6B and Xwmc182b on 7B are of potential value for breeding programs. The incorporation of favorable allele combinations into a uniform background (Platte) was successful, but further investigation is needed for the MABC lines. Grain protein deviation appears to be a useful metric for increasing both Gpc and Gy. Five SNP (BS00021704_51, Excalibur_c4518_2931, BS00064369_51, BS00047114_51, and BS00065934_5) should be investigated further to detect candidate genes in their respective chromosome regions.
Open Access
Biochar effects on soil microbial communities and resistance of enzymes to stress
(Colorado State University. Libraries, 2013) Elzobair, Khalid, author; Stromberger, Mary, advisor; Ippolito, James, committee member; Barbarick, Kenneth, committee member; Wallenstein, Matthew, committee member
Biochar, a product of the pyrolysis of organic material, has received wide attention as a means to improve soil fertility and crop productivity, absorb pollutants in soil, and sequester carbon to mitigate climate change. Little information exists on the short- and longer-term effects of biochar on soil microbial communities and enzyme activities, relative to other organic amendments such as manure. Therefore, the objectives of this study were to determine the short and longer terms effects of biochar amendment on soil microbial communities, arbuscular mycorrhizal (AM) fungi, and enzyme activities in a semi-arid soil. Secondly, due to the porosity and surface area of biochar, enzyme stabilization on biochar was assessed to determine if biochar could prohibit the loss of extracellular enzyme activity following a denaturing stress. In a field study, a fast pyrolysis biochar (CQuest) derived from oak and hickory hardwood was applied to calcareous soil of replicate field plots in fall 2008 at a rate of 22.4 Mg ha-1 (dry wt.). Other plots received dairy manure (42 Mg ha-1 dry wt), a combination of biochar and manure at the aforementioned rates, or no amendment (control). Plots were annually cropped to corn (Zea maize L.). Surface soils (0-30 cm) were sampled directly under corn plants in late June 2009 and early August 2012, one and four years after treatment application, and assayed for microbial community fatty acid profiles and six extracellular enzyme activities involved in C, N, and P cycling in soil. In addition, AM fungal colonization was assayed in corn roots in 2012. Relative to the manure treatment, biochar had no effect on microbial community biomass, community structure, extracellular enzyme activities, or root colonization of corn by AM fungi. Manure amendment increased microbial biomass in 2009, when total FAME concentration was 2.3-fold and 2.6-fold greater in manure and biochar plus manure treatments, respectively, compared to non-amended soil. The concentration of the AM fungal FAME biomarker (16:1ω5c) was significantly reduced by the manure treatments in 2009 (P=0.014) but not in 2012. In 2009, principle components analysis (PCA) revealed shifts in the FAME structure of the soil microbial community in response to the manure treatments. However, the effects of manure on microbial biomass and community structure were short-lived, as no effects were observed in 2012. A laboratory incubation study was conducted to determine whether biochar would stabilize extracellular enzymes in soil and prohibit the loss of potential enzyme activity following a denaturing stress such as microwaving. Soil was incubated in the presence of biochar (0, 1, 2, 5, or 10% by weight) and exposed to increasing levels of microwave stress. Results showed that extracellular enzymes responded differently to biochar rate, stress level and their interactions. The main effect of stress level was highly significant (P<0.0001) on the potential activities of β-glucosidase, β-D-cellobiosidase, N-acetyl-β-glucosaminidase, and phosphatase enzymes. Potential activity of leucine aminopeptidase was significantly affected by biochar rate (P=0.016), stress level (P<0.0001), and their interaction (P=0.0008). In addition, potential activity of β-xylosidase was marginally affected by biochar's interaction with stress level (P=0.066). The potential activity of these two enzymes were reduced after a 36-day incubation in the presence of biochar. For β-xylosidase, intermediate application rates (1 and 5 %) of biochar prevented a complete loss of this enzyme's potential activity after soil was exposed to 400 (1% biochar treatment) or 1600 (5% biochar treatment) J microwave energy g-1 soil. In conclusion, this study demonstrated that land application of biochar may not affect microbial community biomass, potential activities of soil enzymes, or AM fungal biomass in soil, or alter community structure, presumably because of the type of biochar employed in this study. Both biochar and manure added carbon to soil, but microorganisms were responsive to manure rather than biochar. While biochar had no effect on potential activity of soil enzymes in the field study, the laboratory incubation study revealed that biochar has the potential to stabilize extracellular enzymes and prohibit the loss of potential enzyme activity in soil when exposed to a denaturing stress.