A wild-type endophyte (Neotyphodium coenophialum [(Morgan-Jones & Gams) Glen Bacon & Hanlin]) that infects tall fescue [Lolium arundinaceum (Schreb.) Darbysh. = Schedonorous arundinaceum (Schreb.) Dumort.] imparts tolerances to moisture, heat, and grazing stresses, but also produces ergot alkaloids that adversely affect performance and physiology of cattle. Novel endophytes, developed by AgResearch Ltd. NZ, can sustain fescue persistence and productivity, but do not produce toxic ergot alkaloids. University of Kentucky Plant Breeder, T. D. Phillips Ph.D, developed a tall fescue experimental population (KYFA9301) for the upper transition zone. A 2-yr grazing experiment was conducted with steers to evaluate steer performance and physiology, and forage quality and productivity of KYFA9301 infected with AR584 novel endophyte (AR584) compared with KY31 wild-type endophyte (KY31), endophyte-free KYFA9301 (EF9301) and AR542-‘Jesup’ (MaxQ). Fescue-endophyte combinations were assigned to 1.0-ha pastures in a randomized complete block design with three replications. Pastures were grazed with variable stocking (four testers) from 6 May to 23 July 2008 (76 d), and 2 April to 25 June 2009 (84 d). Shrunk bodyweights were taken at initiation and termination of grazing each year. Average daily gains among MaxQ, AR584, and EF9301 were similar and were greater (P < 0.10) than KY31. Rectal and skin temperatures were collected three times each year at approximately days 28, 56, and study completion, along with blood collection for serum prolactin assay. Rectal and skin temperatures among AR584, MaxQ, and EF9301 were similar and were lower (P < 0.10) than KY31. Serum prolactin concentrations were similar among the three nontoxic varieties and higher (P < 0.10) than KY31. Forage collections were taken at 2 week intervals throughout the study each year and nutritive quality analysis were conducted through wet chemistry to determine forage acid detergent fiber (ADF), neutral detergent fiber (NDF), crude protein (CP), and In-Vitro Dry Matter Digestibility (IVDMD). Nutritive analyses indicated no differences between fescue-endophyte combinations with the exception of EF9301 having higher ADF concentrations (P = 0.031) than KY31 during the dry year of 2008. Results indicated steer performance and physiological responses for KYFA9301, with and without AR584 were enhanced compared to KY31 and similar to those for MaxQ.

Tall fescue, a cool-season grass native to Europe, central Asia, and northern Africa, has been widely distributed throughout the U.S. for use as turf and forage. Following its widespread planting, its ability to associate with a toxic fungal endophyte, Neotyphodium coenophialum, was discovered. Research has linked this fescue-endophyte association with increased biotic and abiotic stress resistance in endophyte-infected (E+) versus endophyte-free (E-) plants, and these differences may affect the ability of land managers to eradicate tall fescue and restore native grasslands. I conducted three studies to examine whether E+ tall fescue plants respond differently to management than E- plants, and whether the success of planted native species might be impacted via indirect soil effects. My overall hypotheses were that E+ plants would recover from restoration/eradication efforts better than E- plants, and that E+ fescue would reduce microbial symbionts in the soil needed by planted native species. I first conducted a field study of a tall fescue pasture consisting of four sub-units being restored with different combinations of prescribed burns and/or herbicide applications, as well as an unmanaged control. I found no evidence of E+ plants preferentially surviving restoration management; however this field had unusually low endophyte infection rates to begin with. The second study was a greenhouse experiment in which I measured growth of E+ and E- plants exposed to different watering regimes (wet, dry) and prescribed burn treatments (none, one, or two burns). Watering regime significantly affected all measured growth parameters (wet>dry), but few endophyte effects were found and when present were opposite the hypothesis (E->E+). All burned plants quickly re-grew tiller lengths comparable to the unburned control, with recovery occurring faster following the second burn compared to the first. My final study examined growth and arbuscular mycorrhizal colonization of native species planted by seed into soil from beneath E+ and E- tall fescue. I observed few differences in mycorrhizal colonization or biomass for seedlings between soil from E+ and E- tall fescue. Taken together, my results indicate endophyte status of tall fescue pastures being restored to native grassland species may not be important in governing restoration success.

Tall fescue (Lolium arundinaceum (Schreb.) Darbysh.) is a cool-season perennial grass used in pastures throughout the Southeastern United States. The grass can harbor a fungal endophyte (Epichloë coenophiala) thought to provide the plant with enhanced resistance to biotic and abiotic stress. However, the alkaloids produced by the common variety of the endophyte cause severe animal health issues resulting in a considerable amount of research focused on eliminating the toxic class of alkaloids while retaining the positive abiotic and biotic stress tolerance attributes of the other alkaloids. In doing so, very little attention has been paid to the direct influence the fungal-plant symbiosis has on rhizosphere processes. Therefore, my objectives were to study the influence of this relationship on plant biomass production, root exudate composition, and soil biogeochemical processes using tall fescue cultivars PDF and 97TF1 without an endophyte (E-), or infected with the common toxic endophyte (CTE+), or with two novel endophytes (AR542E+, AR584E+). I found that root exudate composition and plant biomass production were influenced by endophyte status, tall fescue cultivar, and the interaction of cultivar and endophyte. Cluster analysis showed that the interaction between endophyte and cultivar results in a unique exudate profile. These interactions had a small but perceptible impact on soil microbial community structure and function with an equally small and perceptible impact on carbon and nitrogen cycling in soils from rhizobox and field sites. These studies represent the first comprehensive analysis of root exudate chemistry from common toxic and novel endophyte infected tall fescue cultivars and can be used to help explain in part the observed changes in C and N cycling and storage in pastures throughout the Southeast U.S..

Many factors control, contribute to, stimulate and limit forage selection. It is apparent that cattle prefer certain cultivars compared to others. This study sought to test if cattle displayed preferences for certain cultivars over a two-year period in 2008 and 2009. Determining the effect of endophyte status on preference was another objective. Previous research showed rapid increase in the selection of preferred cultivars, i.e., diet learning. We attempted to replicate those results. Forty cultivars (34 tall fescue (Lolium arundinaceum (Schreb.) Darbysh.) cultivars), two festuloliums (Festuca pratensis x Lolium perenne), two meadow fescue (Lolium pratense) and one meadow brome (Bromus biebersteinii), and one orchard grass (Dactylis glomerta L.)) were used to determine preference and to investigate factors contributing to preference. From this two-year study, we observed that cattle preferred certain cultivars compared to others, e.g. KYFA9819 > Latar-OG > Barfest-FL and AU-Triumph < 97TF1-EF < Seine, the most and least preferred cultivars, respectively. During drought conditions, both novel and toxic endophyte cultivars were preferred significantly (P < 0.05) to endophyte free counterparts. The cattle showed rejection of unpalatable grasses but did not clearly show learning to increase selection of desired cultivars.

Endophyte-infected (E+) tall fescue grass has been associated with fescue toxicosis, a costly syndrome characterized by poor cattle performance and health resulting in significant production losses. The fungal endophyte produces ergot alkaloids, which help the grass thrive in poor conditions but are toxic to mammals. A number of symptoms of fescue toxicosis can be related to vasoconstriction of bovine core, peripheral, and foregut vasculature. The first part of this series of experiments demonstrated ergot alkaloids were also vasoactive in midgut vasculature, with the exception of lysergic acid. Additionally, prior dietary exposure to ergot alkaloids decreased the contractile response of mesenteric vasculature to many of the ergot alkaloids tested. In the second part of this series, a non-invasive method was developed for measuring rumen motility in cannulated cattle. Using this technology without different dietary treatments, it was determined that 8 to 16 h after feeding was the least variable between animals and would provide the best opportunity to measure differences in motility. Application of this technique in the third part of this series investigated the effect of ruminally dosed ergot alkaloids on rumen motility. Treatments were not effective at inducing fescue toxicosis, and no differences in rumen motility variables were detected.

Thesis (Ph. D.)--University of Missouri-Columbia, 2007. / The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file (viewed on September 28, 2007) Vita. Includes bibliographical references.

Northern bobwhite (hereafter, bobwhite; Colinus virginianus) have experienced long-term declines in population abundance throughout most of their breeding range. In 2004, the United States Department of Agriculture (USDA) authorized mid-contract management (MCM) to restore early successional plant communities in aging Conservation Reserve Program (CRP) fields. I evaluated the effects of 3 MCM regimes, including fall strip disking, fall herbicide spraying (hereafter, spray), and fall herbicide spraying in combination with spring legume interseeding (hereafter, spray-seed) on nearly 650 ha of tall fescue (Schedonorus phoenix [Scop]. Holub; nomenclature follows USDA plants database; see USDA 2010b) CRP in south-central Illinois, USA, during 2005-2008. The objectives of this study were to: 1) evaluate the compositional and structural responses of the vegetation community to MCM, 2) determine the structural vegetation and landscape composition variables that influenced adult bobwhite relative densities and brood presence in CRP, and 3) assess foraging rates and arthropod prey selection of bobwhite chicks relative to MCM. Spray and spray-seed treatments were more effective than disking at reducing tall fescue cover, increasing plant species diversity, and enhancing the structural characteristics of the plant community that are essential for nesting and brood-rearing bobwhite. Spray-seed and disked treatments increased the percentage of bare ground by burying the dead and dying vegetative biomass beneath the soil surface. However, spraying alone left large amounts of litter accumulation on the soil surface that resulted in a delay in the timing of some annual forbs to recolonize. Plant species composition in sprayed and spray-seeded fields changed from a dense, monoculture of tall fescue to a diverse assemblage of perennial grasses, annual forbs, and legumes that provided habitat for nesting and brood-rearing bobwhite. Adult bobwhite and broods responded positively to spray and spray-seed treatments in this study. Adult relative densities (i.e., number of adult bobwhite observed / ha) were higher in sprayed and spray-seeded fields than in disked and controls. The probability of higher relative densities was greater in fields with higher plant species diversity, and percentages of bare ground and legumes. Conversely, relative densities were negatively associated with higher percentages of grass cover. At the landscape scale, relative densities were positively correlated higher percentages of cropland and pastureland within a 250 m buffer of CRP fields. Sprayed and spray-seeded fields were 39.6% more likely to have broods present than control fields. Whereas disked fields were only 10.0% more likely to have broods than controls. Brood presence was positively correlated with higher percentages of bare ground and negatively correlated with higher percentages of grass cover. Human-imprinted bobwhite chicks consumed a higher abundance and biomass of arthropods in sprayed and spray-seeded fields than in disked and controls, although the abundance of arthropods available was generally highest in control and disked fields. This suggests, therefore, that bobwhite chicks foraging rates are not limited by arthropod availability, but rather, by the structure of the vegetative community and the ability of the chicks to access the food resources. Chicks consumed a higher proportion of hymenopterans, isopods, and lepidopterans than expected from nonrandom feeding indicating that they were actively selecting for particular prey. This research has added to the understanding of restoring bobwhite habitat to tall fescue CRP, and could assist USDA-Natural Resource Conservation Service personnel and other land managers in restoring and maintaining marginally diverse grassland ecosystems in CRP fields for nesting and brood-rearing bobwhite.

Pastures have been typically dominated by monocultures, only allowing herbivores access to one food type with unbalanced nutrient content and in some instances with single plant secondary compounds (SCs), which can be toxic if ingested at high concentrations. By establishing diverse pastures animals can select from a variety of plants with different concentrations and types of nutrients and SCs. The objectives of my study were to (a) determine if the type of plant diversity - tall fescue with either tannin-containing sainfoin or saponin-containing alfalfa − affects cattle preferences for these forages, (b) evaluate how readily fall-born calves reach finish body condition on these grass-legume pastures, and (c) determine the effects of sainfoin/tall fescue versus alfalfa/tall fescue pasture on meat quality and consumer acceptance. Foraging behavior, body weight, and pasture biomass before and after grazing was monitored when cattle strip-grazed 3 replications of 2 treatments repeated for 2 years (from May through September 2010 and from June through September 2012). Animals were allowed a choice between tall fescue and sainfoin [SAN] or alfalfa [ALF]) applied randomly in strips (fescue, legume, or fescue-legume mixture). No differences in average daily gains (~ 1 Kg/day) were detected between the 2 groups of cattle. I used scan samples at 5-min intervals from 0730 to 0930 to record foraging behavior. Animals spent most of the time grazing legumes and scans on legumes increased from the beginning to the end of the study. Scans and assessments of pasture biomass removal revealed greater use of sainfoin than alfalfa, whereas cattle in the ALF treatment removed more fescue than cattle in the SAN treatment. The presence of tannins in sainfoin likely contributed to these effects. Beef carcasses were very lean (select or standard quality grade), with 4-6% mean fat content. There were no differences between treatments regarding meat color, oxidative stability, fatty acid analyses, or consumer acceptance. Only 2 volatiles (nonanoic and decanoic acids) were greater in meat from the ALF treatment. Thus, cattle offered choices reached finish body weight at pasture and incorporated fescue into their diets even when legumes were available. The type of legume influenced foraging behavior but this effect did not impact animal performance, meat quality, or consumer acceptance.

Sustainable farming is an integrated practice of crop and livestock production system (integrated crop-livestock system; ICLS) that aims to reduce the environmental impacts of agricultural practices while maintaining the productivity and profitability. The use of one step's byproducts by another is a crucial component of this practice. The continuity and effectiveness of sustainable farming greatly rely on deep understanding of each component and good management strategy. One essential aspect involved in all farming components is the role of microorganisms in mediating the biological processes therein. Thus, understanding the composition and activities of these communities would open up ways to engineer them and optimize the respective processes for better sustainable farming practices. The research presented in this dissertation aimed to characterize the microbial metabolism involved in the ICLS with a broader goal of manipulating these systems to improve sustainable agriculture. We focused on two systems that are widely used in the United States, and employed the analysis of 16S rRNA-V4 element for this purpose. In our first system, we characterized the rumen microbiomes of beef cattle alternately grazing nontoxic MaxQ and toxic KY-31 tall fescue pasture, to understand how these cultivars shape the rumen microbiome and identify microbial species potentially capable of degrading ergot alkaloids for better feed utilization. We found that KY-31 grazing remodeled the rumen microbiome substantially at the cellulolytic and saccharolytic guilds. It suppressed the abundances of Fibrobacter, a major ruminal cellulolytic bacterium, as well as those of Pseudobutyrivibrio and Butyrivibrio, and these losses were compensated by increased occurrences of Eubacterium species. Parts of these new communities lingered once developed, and a different guild composition surfaced upon transfer to MaxQ. We also discovered that most of the observations were not evident at the whole microbiome levels but was identified by analyzing the sessile and planktonic fractions separately. Thus, it showcased the need for analyzing sessile and planktonic segments separately while interrogating a heterogenous microbiome. Finally, we identified several potential ergovaline degrading bacteria such as Paraprevotella and Coprococcus. In our second system, we studied the microbiome composition and associated transformation pathways mediating nitrogen loss in two dairy manure storage systems, the clay-lined Earthen Pit (EP) and aboveground concrete storage tank (CS) on two commercial dairy farms, to develop strategies to minimize these losses. We first developed a catalog of the archaea and bacteria that were present therein based on the 16S rRNA-V4 amplicons from manure samples collected from several locations and depths of the storages. Then, we inferred the respective metabolic capabilities via PICRUSt2 and literature curation, and developed schemes for nitrogen and carbon transformation pathways operating at various locations of EP and CS. Our results showed that the stored manure microbiome composition was more complex and exhibited more location-to-location variation in EP compared to CS. Further, the inlet and a location with hard surface crust in EP had unique consortia. With regards to nitrogen transformation, the microbiomes in both storages had the potential to generate ammonia but lacked the organisms for oxidizing it to nitrate and further to gaseous compounds such as anammox and autotrophic nitrifiers. However, microbial conversion of nitrate to gaseous N2, NO, and N2O via denitrification and to stable ammonia via dissimilatory nitrite reduction (DNRA) seemed possible. Minor quantity of nitrate was present in manure, potentially originating from oxidative processes occurring on the barn floor. Higher prevalence of nitrate-transforming microbes at the near-surface locations and all depths of the inlet were found as a result of this instance. These findings suggested that ammonia oxidation to nitrate started on the barn floor and as manure is being stored in EP and CS, nitrate was lost to the environment via denitrification. For carbon transformation, hydrogenotrophic Methanocorpusculum species were the primary methane producers, and it exhibited higher abundance in EP. / Doctor of Philosophy / Sustainable farming is an integrated practice of crop and livestock production systems that aims to reduce the environmental impacts of agricultural practices while maintaining the productivity and profitability. The use of one step's byproducts by another such as the utilization of arable land to grow forages for livestock grazing or the use of manure as organic nitrogen amendments for crops is a crucial component of this practice. The continuity and effectiveness of sustainable farming greatly rely on deep understanding of each component and good management strategy. One essential aspect involved in all farming components is the role of microorganisms in mediating the biological processes therein. Thus, understanding the composition and activities of these communities would open up ways to engineer them and optimize the respective processes for a better sustainable farming practice. The research presented in this dissertation aimed to characterize the microbial metabolism involved in the integrated crop-livestock system with a broader goal of manipulating these to improve sustainable agriculture. We focused on two systems that are widely used in the United States, and employed bioinformatic analysis of a genetic marker for this purpose. In our first system, we characterized the rumen microbiomes of beef cattle grazing alternately on KY-31 tall fescue, a major grass used in Virginia that carry a toxin-producing fungi, and nontoxic MaxQ tall fescue pasture, to understand how these cultivars shape the rumen microbiome and identify potential microbial species capable of degrading the toxin for better feed utilization. We found that KY-31 grazing remodeled the rumen microbiome substantially, especially affecting microbes responsible for degrading cellulose and starch. Some of these communities lingered once developed, and a different microbial population surfaced upon transfer to MaxQ. Several potential toxin-degrading bacteria were also identified. In our second system, we studied the microbiome composition and associated transformation pathways mediating nitrogen loss in two dairy manure storage systems, the clay-lined Earthen Pit (EP) and aboveground concrete storage tank (CS), to develop strategies to minimize these losses. We first develop a catalog of the archaea and bacteria that were present in the manure samples collected from several locations and depths of the storages based on a genetic marker. Then, we inferred the respective metabolic capabilities and developed schemes for nitrogen and carbon transformation pathways operating at various locations of EP and CS. Our results showed that the stored manure microbiome exhibited more location-to-location variation in EP compared to CS. Oxygen exposure, continuous addition of fresh manure, and the presence of crust at the storage surface gave rise to these unique populations. With regards to nitrogen transformation, the microbiomes in both storages had the potential to generate ammonia but lacked the organisms for oxidizing it to nitrate and further to gaseous compounds. However, microbial conversion of nitrate to gaseous N2, NO, and N2O seemed possible. These observations showcased that ammonia is stable during storage. Nitrate, on the other hand, can be converted into volatile nitrogen compounds via various processes. Thus, it is imperative to limit the level of nitrate in manure prior to placement in the storage, which is potentially originating from oxidative processes occurring on the barn floor.

The objective of this study was to determine the effects of feeding endophyte-infected tall fescue seed to Angus steers on average daily gain, carcass characteristics, ergovaline concentration, lipid oxidation, hepatic enzyme activity, metmyoglobin reductase activity, and mitochondrial lipid composition. Animals were blocked into light, medium, and heavy body weight groups and were randomly assigned to either a KY31 seed treatment (6796 ppb ergovaline; 20 MUg/kg BW; E+; n = 6) or a KY32 control (< 100 ppb; E-; n = 6). There was a 2-way treatment × time interaction effect on ADG (P < 0.001). The E+ steers gained 0.56 kg/d less than the E- steers from d 0 to 14 (P < 0.001) until d 56 (ADG difference = 0.27 kg/d; P = 0.007) but both group had similar ADG from d 70 till the end of the feeding period 2 (ADG = 0.53 kg/d; P > 0.070). No difference in carcass characteristics were found between the E+ and E- steers by at the time of ultrasonography (P >= 0.120) or at harvest (P >= 0.199). In both period 1 and 2, there was a 2-way treatment × time interaction for ergovaline concentration in blood (P = 0.002 and 0.022, respectively). Infected tall fescue seed did not change d-3 hepatic enzyme activity in both feeding periods (P = 0.149 to 0.645). In period 1, thiobarbituric acid reactive substances, primarily consisting of malondialdehyde (MDA), were greater in blood serum of E+ steers than E- steers (6.56 MUM vs. 2.56 MUM; P = 0.048). An overall increase in MDA from d 0 (2.39 MUM) to d 3 (7.59 MUM) was also observed (P = 0.049). There was no effect of endophyte infected tall fescue seed on metmyoglobin reductase in longissimus thoracis (4.82 MUM/min/g in E- muscle vs. 3.93 MUM/min/g in E+ muscle; P = 0.484. There was no treatment effect on mitochondrial lipid composition (P >= 0.094), including phospholipids and fatty acids.