This webinar highlights some of the work being done to identify effective practices for reducing concentrations of resistant bacteria and resistance genes at critical control points in beef feedlot and dairy manure management systems. This presentation was originally broadcast on November 15, 2019. More… Continue reading “Managing Manure to Mitigate Antibiotic Resistance”
Microarthropods as Bioindicators of Soil Health Following Land Application of Swine Slurry
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*Purpose
As producers of livestock and agricultural crops continue to focus significant efforts on improving the environmental, economic, and social sustainability of their systems, increasing the utilization of livestock manure in cropping systems to offset inorganic fertilizer use benefits both sectors of agriculture. However, promoting manure based purely upon nutrient availability may not be sufficient to encourage use of organic versus inorganic fertilizer. The value of livestock manure could increase significantly with evidence of improved soil fertility and quality following manure application. Therefore, understanding the impact of manure addition and application method on both soil quality and biological health is an important step towards improving the value and desirability of manure for agricultural cropping systems.
For edaphic ecosystems, collection, analysis, and categorization of soil microarthropods has proven to be an inexpensive and easily quantified method of gathering information about the biological response to anthropogenic changes to the environment (Pankhurst et al., 1995; Parisi et al., 2005). Arthropods include insects, crustaceans, arachnids, and myriapods; nearly all soils are inhabited by a vast number of arthropod species. Agricultural soils may contain between 1,000 and 100,000 arthropods per square meter (Wallwork, 1976; Crossley et al., 1992; Ingham, 1999). Soil microarthropods show a strong degree of sensitivity to land management practices (Sapkota et al., 2012) and specific taxa are positively correlated with soil health (Parisi et al., 2005). These characteristics make soil microarthropods exceptional biological indicators of soil health.
This study focused on assessing the chemical and biological components of soil health, described in terms of soil arthropod population abundance and diversity, as impacted by swine slurry application method and time following slurry application.
What did we do?
A field study was conducted near Lincoln, Nebraska from June 2014 through June 2015 on a site that has been operated under a no-till management system with no manure application since 1966. Experimental treatments included two manure application methods (broadcast and injected) and a control (no manure applied).
Soil samples were collected twelve days prior to treatment applications, one and three weeks post-application of manure, and every four weeks, thereafter, throughout the study period. Samples were not collected during winter months when soil was frozen.
Two types of soil samples were collected. Samples obtained with a 3.8-cm diameter soil probe were divided into 0-10 and 10-20 cm sections for each of the plots for nutrient analysis at a commercial laboratory. Samples measuring 20 cm in diameter and 20 cm in depth, yielding a soil volume of 6,280 cm3, were stored in plastic buckets with air holes in the lids, placed in coolers with ice packs, and transported to the University of Nebraska-Lincoln West Central Research & Extension Center in North Platte, Nebraska within 12 h of collection. These samples were then transferred to Berlese-Tullgren funnels for extraction of arthropods, a commonly used technique to assess microarthropods in the soil (Ducarme et al., 2002). A 70% ethanol solution was used to preserve the organisms for later analysis.
The QBS method of classification was employed to assign an eco-morphological index (EMI) score on the basis of soil adaptability level of each arthropod order or family (Parisi et al., 2005). Preserved arthropods from each soil sample were identified and quantified using a Leica EZ4 stereo microscope (Leica Biosystems, Inc., Buffalo Grove, IL) and a dichotomous key (Triplehorn and Johnson, 2004). Arthropods were classified to order or family based on the level of taxonomic resolution necessary to assign an EMI value as described by Parisi et al. (2005). For some groups, such as Coleoptera, characteristics of edaphic adaptation were used to assign individual EMI scores.
The impacts of swine slurry application method and time following manure application on soil arthropod populations and soil chemical characteristics was determined by performing tests of hypotheses for mixed model analysis of variance using the general linear model (GLM) procedure (SAS, 2015). The samples were tested for significant differences resulting from time and treatment, as well as for variations within the treatment samples. Following identification of any significant differences, the least significant differences (LSD) test was employed to identify specific differences among treatments. P <0.05 was considered statistically significant.
What have we learned?
A total of 13,311 arthropods representing 19 orders were identified, with Acari (38.7% of total arthropods), Collembola: Isotomidae (26.8%), Collembola: Hypogastruridae (10.4%), Coleoptera larvae (1.6%), Diplura (1.2%), Diptera larvae (0.9%), and Pseudoscorpiones (0.6%) being the most abundant soil-dwelling taxa. These taxa had the greatest relative abundance in samples throughout the study and were, therefore, chosen for statistical analysis of their response to manure application method and time since application.
The most significant responses to application method were found for collembolan populations, specifically for Hypogastruridae and Isotomidae. However, Pseudoscorpiones were also significantly affected by application method. Time following slurry application had a significant impact on most of the analyzed populations including Hypogastruridae, Isotomidae, mites, coleopteran larvae, diplurans, and dipteran larvae. The positive response of Hypogastruridae and Isotomidae collembolans to broadcast swine slurry application was likely due to the addition of nutrients (in the form of OM and nitrates) to the soil provided by this form of agricultural fertilizer.
Future Plans
Research focused on the role of livestock manure in cropping systems for improved soil quality and fertility is underway with additional soil characteristics being monitored under multiple land treatment practices with and without manure.
Corresponding author, title, and affiliation
Dr. Amy Millmier Schmidt, Assistant Professor, University of Nebraska – Lincoln
Corresponding author email
Other authors
Nicole R. Schuster, Julie A. Peterson, John E. Gilley and Linda R. Schott
Additional information
Dr. Amy Millmier Schmidt can also be reached at (402) 472-0877.
Dr. Julie Peterson, Assistant Professor of Entomology, University of Nebraska – Lincoln can be reached at (308) 696-6704 or Julie.Peterson@unl.edu.
Acknowledgements
Eric Davis, Ethan Doyle, Mitchell Goedeken, Stuart Hoff, Kevan Reardon, and Lucas Snethen are gratefully acknowledged for their assistance with field data collection. Kayla Mollet, Ethan Doyle, and Ashley Schmit are acknowledged for their assistance with data processing. This research was funded, in part, by faculty research funds provided by the Agricultural Research Division within the University of Nebraska-Lincoln Institute of Agriculture and Natural Resources.
The authors are solely responsible for the content of these proceedings. The technical information does not necessarily reflect the official position of the sponsoring agencies or institutions represented by planning committee members, and inclusion and distribution herein does not constitute an endorsement of views expressed by the same. Printed materials included herein are not refereed publications. Citations should appear as follows. EXAMPLE: Authors. 2017. Title of presentation. Waste to Worth: Spreading Science and Solutions. Cary, NC. April 18-21, 2017. URL of this page. Accessed on: today’s date.
Utilization of Woody Biomass and Manure as Agricultural Soil Amendments in Nebraska
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Purpose
While Eastern Redcedar are native to Nebraska and much of the Central U.S., the ability of these trees to thrive in many soils and under a broad range of climatic conditions has contributed to their designation as an invasive species. Cedar tree proliferation negatively impacts agriculture by reducing groundwater availability, compromising grazing land, impeding forage production for cattle, and altering surface water flows. Agricultural crop and livestock producers depend on affordable access to water, healthy and productive soils, and quality grazing land to remain profitable. Land treatment practices that return organic matter to soil improve soil health, which in turn positively impacts crop productivity, soil water holding capacity, soil fertility, and grazing land forage quality and productivity. This project is investigating the use of two readily available by-products in Nebraska, livestock manure and cedar tree wood chips, as amendments on agricultural land to improve soil productivity metrics. The overall goal of this project is to demonstrate a value-added use for woody biomass to offset the cost of tree management activities and encourage landowner management of cedars.
What did we do?
Crop year 2016 was the first year of the Woody Biomass and Manure Project. Six treatments were applied to 12-m x 10-m plots within cooperators’ fields following the 2015 harvest:
1. woody biomass (WB1), 6 ton/ac
2. woody biomass (WB2), 12 ton/ac
3. woody biomass with liquid N (WBLN), 6 ton/ac
4. woody biomass with swine manure (WBSM), 6 ton/ac
5. woody biomass with cattle manure (WBCM), 6 ton/ac
6. control (Cont), no amendments
Manure and liquid nitrogen treatments received less than 30 lbs ac-1 of N in the fall. The experiment is a completely randomized block design with four replications of each treatment, for a total of 24 plots, at each of the sites. Since the plots were established within existing crop fields, the producers were encouraged to continue their current management strategies. Both sites were irrigated, and fertilizer was applied uniformly across all plots using the pivot throughout the growing season.
Soil was sampled for chemical and biological properties in the spring and fall of 2016 and sent to a commercial lab for analyses. Rye was sampled by hand harvesting 0.25 square feet from four locations within each plot for a total of 1 square foot. Corn was sampled by hand harvesting six plants from each plot. Stand counts were also completed. WATERMARK sensors were installed at three depths (1, 2, and 3 ft) in two replications of four treatments (WBCM, WB1, WB2, Cont) at both sites. Additionally, temperature sensors were installed at a depth of 1 ft. A total of 16 plots were monitored (8 plots per site with 2 replications of 4 treatments).
What have we learned?
Soil biological and chemical characteristics have not been affected during the first year. There were no differences in the amount or type of soil microbes due to treatment. WBCM and WBLN had greater soil nitrate than WB1 and WBSM early in the spring. Additionally, WBCM had greater soil K than the other treatments. Other than these two instances, there were no differences in organic matter, pH, and macronutrients. However, this is not surprising since measurable changes in soil properties typically occur over many years and manure application rate was relatively low. More importantly, though, is that microbial populations were not decreased by the cedar mulch.
Cedar mulch applications did not decrease biomass yield of corn and rye when applied with nitrogen. In fact, in the rye, WBLN had the greatest biomass yields followed by WBCM, WB1, WBSM, and Cont. WB2 had the lowest rye biomass, which was probably due to nitrogen tie-up by the wood chips due to the initially higher C:N ratio. There was no treatment effect for corn biomass or stand counts.
At the site planted to corn at a depth of one foot, the three woody biomass treatments monitored (WB1, WB2, and WBCM) were significantly wetter and cooler than the control from mid-June until mid-July. WBCM was also wetter at a depth of two feet than the control. Unfortunately, due to rodent activity, statistical analyses at the rye site and other times of the growing season are not possible. The differences in soil moisture and temperature are probably due to shading and the physical barrier to evaporation that the wood chips supply. The increased soil moisture under the woody biomass treatments could reduce irrigation.
Future Plans
In order to apply for competitive funding, we need more supporting data. We are going to increase monitoring of soil moisture and temperature, so that three replications of all six treatments are monitored at both sites. Additionally, a greenhouse study will be conducted to provide water quality data and rate of decomposition of the wood chips.
Corresponding author, title, and affiliation
Linda Schott, Extension Graduate Research Assistant, University of Nebraska-Lincoln
Corresponding author email
Other authors
Amy Schmidt, Assistant Professor, University of Nebraska-Lincoln; Amy Timmerman, Associate Extension Educator, University of Nebraska-Lincoln; Adam Smith, Assistant Forester, Nebraska Forest Service
Additional information
More information can be found at: manure.unl.edu
Acknowledgements
This project is funded by the Nebraska Forest Service. We would like to thank the Middle Niobrara Natural Resource District, especially Mike Murphy, Travis Connot, and Zach Peterson, for their assistance to this project. We would also like to thank the Nebraska Forest Service, especially Richard Woollen, Adam Smith, and Heather Nobert, for their assistance to this project. Additionally, this project would not be possible without our two farmer cooperators, Leonard Danielski and Greg Wilke.
Manure Treatment and Natural Inactivation of Porcine Epidemic Diarrhea Virus in Soils
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Purpose
The porcine epidemic diarrhea virus (PEDv) outbreak in North America has substantially impacted swine production, causing nearly 100% mortality in infected newborn piglets. Because manure may remain a source of reinfection, proper manure management practices to limit outbreaks need to be developed and evaluated. Two laboratory studies simulating manure pit treatment with increasing amounts of quicklime were conducted to determine PEDv susceptibility to increasing pH. Additionally, two laboratory soil incubation studies contrasting manure liming, multiple soil types, and two antecedent soil moistures were conducted over several months with incubation conditions mimicking the climates in Minnesota, Missouri, and Oklahoma to determine whether current manure application practices reduce the potential for PEDv reinfection via manure-amended soil. Quantitative PCR and live swine bioassays were used to enumerate PED virus and to determine whether manure and soil samples contained infectious PEDv.
What did we do?
Quicklime-Manure Slurry Incubations: An initial short-term manure slurry study was conducted on fresh PEDv-positive manure slurry collected in 2015 from the shallow pit of a commercial swine facility in southeast Nebraska. Manure was sampled prior to treatment (0 h) and then distributed among glass beakers (250 mL) to accommodate triplicates of three treatments: liming to pH 10, liming to pH 12, and unlimed manure. Following pH adjustment, aliquots of each sample were collected at 1 and 10 h, immediately neutralized with 10 mM HCl and stored at -80°C for subsequent analysis. In a second manure slurry incubation, triplicate PEDv-positive manure samples collected from a commercial swine operation in south central Nebraska site in December 2016 were mixed in equal portion (w:v) with distilled water to mimic manure slurry consistency observed in swine production pit storages. Quicklime was added stepwise (0.25 g addition) to each manure slurr! y sample with continuous stirring to gradually increase manure slurry pH. After each addition of quicklime, pH was measured and an aliquot of manure slurry was collected for subsequent quantitative PCR PEDv enumeration and infectivity in a pig bioassay.
Long-term manure and soil incubation. Initial tests determined appropriate initial soil moisture contents (representing a ‘dry’ and ‘moist’ soil condition) and manure:soil ratios (1 g slurry:3 g soil) to best represent the manure:soil within an injection furrow when slurry is injected into soil, and appropriate liming source (ag lime vs. quicklime). PEDv-positive manure slurry collected from a commercial swine operation in southeast Nebraska was divided between two 3-L containers, one for limed treatment (LIME) and the other for the control, or no-lime, treatment (CNL). Quicklime (30 g) was added to one 3 L portion (equivalent to an application of 80 lbs. quicklime per 1000 gallons of slurry) to achieve a final pH of 12. Both treated and untreated slurry stocks were incubated at room temperature for 24 hours. Distilled water was added to two soils, a silty clay loam (pH 7.0) and a loamy fine sand (pH 6.9), to attain 10% and 30% water holding capacity! (dry and moist soil condition). Thirty grams (dry weight) of soil was apportioned to multiple 50 mL screw top conical tubes and a cavity was made in the center of the soil by pressing a 10 mL pipet tip into the soil. Ten mL of slurry (LIME or CNL) were then added to each soil tube via pipet. Four replicate tubes were immediately frozen at -80°C for each combination of soil, moisture, and manure treatment to represent initial soil application (day 0). The tubes were loosely capped and placed into one of three incubators operated independently throughout the trial to simulate soil temperatures between November 1 and May 1 at one of three geographic locations: southern Minnesota, northern Missouri, and central Oklahoma (Figure 1). Twenty replicate tubes were created for each combination of soil, moisture, incubation, and manure treatment, and a set of four tubes were collected for each treatment combination on days 30, 60, 90, 120 and 150 of the incubation and immediately transfer! red to a -80°C freezer for storage.
Molecular detection and quantification of PEDv. Prior to analysis, soil and manure samples were removed from -80°C storage and allowed to thaw at room temperature. The RNA in each sample was extracted using the RNA PowerSoil Total RNA Isolation kit (Mo Bio, Carlsbad, CA). PEDv was detected in samples by reverse transcription and quantitative polymerase chain reaction (RT-qPCR).
Swine bioassay. To confirm that conditions yielding a PCR negative result actually inactivated the PED virus and rendered the manure non-infectious, a live pig bioassay was conducted with the limed and non-limed manure slurry samples from the initial short-term manure slurry incubation (quicklime addition). Fifteen pigs, approximately 21 days old, were sourced from a high-health facility whose dams tested negative for PEDv antibodies and virus by PCR. Piglets were tested for PEDv upon arrival and confirmed negative. Piglets were randomly assigned to individual housing in BSL-2 rooms at the University of Nebraska-Lincoln Life Sciences Annex as follows: control (3 piglets), pH 10 (6 piglets), and pH 12 (6 piglets), and allowed to acclimate for three days. Each pig was then administered a 10-mL oral gavage of manure slurry: three piglets in the control room received one of the three un-limed slurry samples; six piglets in the pH 10 room received one of the six limed (pH 10) sl! urry samp les (three limed for 1 h and three limed for 10 h); and six pigs in the pH 12 room received one of the six limed (pH 12) slurry samples (three limed for 1 h and three limed for 10 h). Piglets were monitored for fecal shedding of PEDv for four days until control animals began to demonstrate clinical signs of PEDv infection, at which time all piglets were humanely euthanized. Fecal swabs, and duodenum, ileum, jejunum, and cecum samples were collected from each animal and fixed in formalin. All fecal and tissue samples were analyzed for the presence of detectable PED virus by immunohistochemistry and PCR.
What have we learned?
Manure Slurry Incubation: Manure limed to pH 10 and pH 12 for 1 and 10 h yielded no detectable PEDv RNA. Live swine bioassay results confirmed that these samples were not infective while control samples resulted in PEDv infection of piglets. These results indicate that a final manure slurry pH of 10 (equivalent to 50 lbs. of quicklime added to 1000 gallons manure slurry) is sufficient to reduce PEDv RNA to an undetectable concentration after 1 hour of contact time. All pigs receiving limed manure (pH 10 or 12 maintained for 1 or 10 h) during the live swine bioassay tested negative for PEDv infection while control pigs (un-limed treatment) all tested positive for PEDv infection (Figure 1). The pig bioassay results confirmed that the PCR assay is a reliable predictor for the presence of infectious PEDv in these matrices and that lime addition to achieve pH 10 for just one hour is sufficient to deactivate the virus in stored manure.
Soil Incubations: At the completion of the long-term (150-day) soil incubation, a subset of the frozen samples (LIME and CON soil samples collected on day 0 and 30) was selected for RNA extraction and qPCR analysis. The qPCR results from days 0 and 30 yielded no detectable PEDv RNA in either the limed or un-limed manure-amended soils (Figure 1). Furthermore, manure-amended soils did not differ from soil-only controls even though PEDv RNA was still detectable in the original manure slurry at high concentrations. No differences in PEDv abundance were detected on either day when initial soil moisture (10% vs 30% water holding capacity), incubation condition (MN vs. MO vs. OK), or soil type (silty clay loam and loamy fine sand) were varied. For these soils, the concentration of PEDv in limed or un-limed manure decreased immediately to a non-detectable level. These results indicate that manure-amended soil with pH 6.9 or greater is not a vector for transmission of the PED virus.
A consistent finding from all of the studies is that pH of media (slurry or soil) strongly influences PED virus survival.
Future Plans
Additional studies are underway to identify the lowest pH at which the PED virus is rendered non-infectious in slurry manure.
Corresponding author, title, and affiliation
Amy Millmier Schmidt, Assistant Professor, Departments of Biological Systems Engineering and Animal Science, University of Nebraska – Lincoln
Corresponding author email
Other authors
Stevens, E., A. Schmidt, D. Miller, J.D. Loy and V. Jin
Additional information
Dr. Amy Millmier Schmidt, corresponding author, can also be reach at (402) 472-0877.
Acknowledgements
Funding for this research was provided by the National Pork Board. Gratitude is extended to Ashley Schmit for assistance with laboratory activities and animal care. Special thanks to the Nebraska pork producers who granted access to their farms for collection of PEDv-positive manure.