Kimberly L. Cook

Correlating Transport Behavior with Cell Properties for Eight Porcine Escherichia coli Isolates

In this study we investigate how growth stage and depositional environment affect variability of cell properties and transport behavior of eight porcine E. coli isolates. We compared the surface properties for cells harvested during exponential and stationary growth phase and their transport behavior through columns packed with either uncoated or Fe-coated quartz sand. We then investigated correlations between measured cell properties and fitted bacterial attachment efficiencies. For both growth stages we found that bacterial attachment efficiencies in the uncoated quartz sand varied among the eight different isolates by over an order of magnitude whereas attachment efficiencies in the Fe-coated sands varied by a factor of less than two. With the exception of one isolate, growth condition had minimal impact on attachment efficiencies to the uncoated sands. A strong and statistically significant inverse relationship was observed between bacterial attachment efficiencies in the uncoated quartz sand columns and log-transformed zeta potential, whereas a mild yet statistically significant relationship between bacterial attachment efficiencies in the Fe-coated sands and cell width was observed. For the experimental conditions used in our study, we found that variability in E. coli transport was more dependent on the depositional environment than on growth conditions.

The effect of stratification and seasonal variability on the profile of an anaerobic swine waste treatment lagoon.

In this study, the characterization of an anaerobic swine waste treatment lagoon from a farrowing operation (approximately 2000 sows) was carried out to examine the dynamics of the system due to stratification and seasonal variability. Swine waste samples were taken at different depths with a pulley system equipped with a special sampler that allows for sampling exclusively at certain depth. Chemicals and microbial dynamics were monitored throughout a one-year-period. Results showed that nutrient (C, N, P, S) concentrations varied according to stratified lagoon layers and season. Trace minerals (Al, Ca, Fe, and Mg), on the other hand, appeared to be affected more by stratification than seasonal variability. Molecular analysis also showed that microbial community structure appeared to be affected by the stratification and seasonal variability. Based on these data, it is important to consider the effect of stratification and seasonal variability in managing these open lagoons.

Effect of alum treatment on the concentration of total and ureolytic microorganisms in poultry litter.

Microbial mineralization of urea and uric acid in poultry litter results in the production of ammonia, which can lead to decreased poultry performance, malodorous emissions, and loss of poultry litter value as a fertilizer. Despite the fact that this is a microbial process, little is known about how the microbial populations, especially ammonia-producing (ureolytic) organisms in poultry litter, respond to litter amendments such as aluminum sulfate (Al(2)(SO(4))(3).14H(2)O; alum). The goal of this study was to measure the temporal changes in total bacterial and fungal populations and urease-producing microorganisms in nontreated litter or litter treated with 10% alum. Quantitative real-time polymerase chain reaction was used to target the bacterial 16S rRNA gene, the fungal 18S rRNA gene, or the urease gene of bacterial and fungal ammonia producers in a poultry litter incubation study. Nontreated poultry litter had relatively high total (2.8 +/- 0.8 x 10(10) cells g(-1) litter) and ureolytic (2.8 +/- 1.3 x 10(8) cells g(-1) litter) bacterial populations. Alum treatment reduced the total bacterial population by 50% and bacterial urease producers by 90% within 4 wk. In contrast, at 16 wk after alum treatment, the fungal population was three orders of magnitude higher in alum-treated litter than in nontreated litter (3.5 +/- 0.8 x 10(7) cells g(-1) litter and 5.5 +/- 2.5 x 10(4) cells g(-1) litter, respectively). The decrease in pH produced by alum treatment is believed to inhibit bacterial populations and favor growth of fungi that may be responsible for the mineralization of organic nitrogen in alum-treated litters.

Development of a Quantitative Real-Time Polymerase Chain Reaction Assay to Target a Novel Group of Ammonia-Producing Bacteria Found in Poultry Litter

Ammonia production in poultry houses has serious implications for flock health and performance, nutrient value of poultry litter, and energy costs for running poultry operations. In poultry litter, the conversion of organic N (uric acid and urea) to NH(4)-N is a microbially mediated process. The urease enzyme is responsible for the final step in the conversion of urea to NH(4)-N. Cloning and analysis of 168 urease sequences from extracted genomic DNA from poultry litter samples revealed the presence of a novel, dominant group of ureolytic microbes (representing 90% of the urease clone library). Specific primers and a probe were designed to target this novel poultry litter urease producer (PLUP) group, and a new quantitative real-time PCR assay was developed. The assay allowed for the detection of 10(2) copies of target urease sequences per PCR reaction (approximately 1 x 10(4) cells per gram of poultry litter), and the reaction was linear over 8 orders of magnitude. Our PLUP group was present only in poultry litter and was not present in environmental samples from diverse agricultural settings. This novel PLUP group represented between 0.1 to 3.1% of the total microbial populations (6.0 x 10(6) to 2.4 x 10(8) PLUP cells per gram of litter) from diverse poultry litter types. The PLUP cell concentrations were directly correlated to the total cell concentrations in the poultry litter and were found to be influenced by the physical parameters of the litters (bedding material, moisture content, pH), as well as the NH(4)-N content of the litters, based on principal component analysis. Chemical parameters (organic N, total N, total C) were not found to be influential in the concentrations of our PLUP group in the diverse poultry litters Future applications of this assay could include determining the efficacy of current NH(4)-N-reducing litter amendments or in designing more efficient treatment protocols.

Evaluation of nitrogen retention and microbial populations in poultry litter treated with chemical, biological or adsorbent amendments

Poultry litter is a valuable nutrient source for crop production. Successful management to reduce ammonia and its harmful side-effects on poultry and the environment can be aided by the use of litter amendments. In this study, three acidifiers, two biological treatments, one chemical urease inhibitor and two adsorber amendments were added to poultry litter. Chemical, physical and microbiological properties of the litters were assessed at the beginning and the end of the experiment. Application of litter amendments consistently reduced organic N loss (0-15%) as compared to unamended litter (20%). Acidifiers reduced nitrogen loss through both chemical and microbiological processes. Adsorbent amendments (water treatment residuals and chitosan) reduced nitrogen loss and concentrations of ammonia-producing bacteria and fungi. The use of efficient, cost-effective litter amendments to maximum agronomic, environmental and financial benefits is essential for the future of sustainable poultry production.

Soil Nutrients, Bacteria Populations, and Veterinary Pharmaceuticals across a Backgrounding Beef Feedlot.

Beef cattle backgrounding operations that grow out weaned calves for feedlot finishing contain several environmentally significant constituents. A better understanding of these constituents and their environmental distribution will aid in the development of effective management guidelines for sustainable beef production. This research investigated soil nutrients, bacterial, and veterinary pharmaceutical concentrations across a small backgrounding beef feedlot on a karst landscape. Results indicated that all contaminants were highly concentrated in the feeder area (FD) and were lower in the other feedlot areas. The FD soils had a pH of 8.2, 59 mg kg soil organic matter (SOM), 2002 mg kg soil test phosphorus (STP), 99.7 mg kg NH-N, and 18.3 mg kg NO-N. The other locations were acidic (5.9-6.9 pH) and contained 39 mg kg SOM, 273 mg kg STP, 21.5 mg kg NH-N, and 2.0 NO-N mg kg. Bacteria populations in the FD averaged 2.7 × 10 total cells, 3.9 × 10 spp., 2.9 × 10 spp, and 4.5 × 10 cells per gram of soil. spp. and spp. concentrations were 1 to 4 orders of magnitude lower at the other locations. showed lower dynamic range and was generally uniformly distributed across the landscape. Antibiotic and parasiticide concentrations in the FD were 86.9 ng g monensin, 25.0 ng g lasalocid, and 10.3 ng g doramectin. Their concentrations were 6- to 27-fold lower in the other feedlot locations. Contaminant management plans for this small feedlot will therefore focus on the feeder and nearby grazing areas where soil nutrients, bacteria populations, and veterinary pharmaceuticals were most concentrated.

Effect of Stratification on the Profile of an Anaerobic Swine Waste Treatment Lagoon in Kentucky

An understanding of the nature of wastes in an anaerobic swine lagoon is essential in the design and operation of alternative collection, treatment, and disposal facilities for environmental quality management such as odor control, nutrient and pathogen reduction. In this study, the characterization of an anaerobic swine waste treatment lagoon (0.40 ha) from a farrowing operation (~2000 sows) was carried out to examine the dynamics of the system due to stratification and seasonal variability. Swine waste samples were taken from an anaerobic swine lagoon at different depths (0, 50, and 250 cm) with a pulley system equipped with a special sampler that allows for sampling exclusively at certain depth. The sampling process was carried out from spring to fall season. The pH and temperature were monitored and recorded continuously from the epilimnion (top) and hypolimnion (bottom) layers of the lagoon. The samples were then analyzed for their mineral contents by using Inductively Coupled Plasma (ICP), Total Nitrogen, and Total Organic Carbon analyzers. Microbial dynamics were monitored by DNA extraction and Denaturing Gradient Gel Electrophoresis (DGGE). Results showed that nutrient (C, N, P, S) concentrations varied according to stratified lagoon layers and season. For example, total organic carbon concentrations range from 1800 mg/L (top) to 5400 mg/L (bottom) for late spring, and from 1100 mg/L (top) to 3600 mg/L (bottom) for the middle of summer. Trace minerals such as Al, Ca, Fe, K, Na, and Mg, on the other hand, appeared to be affected more by stratification than seasonal variability. The reason for the decrease in nutrient concentrations in summer time may be due to increase microbial activities which required more essential nutrients (i.e., C, N, P, S) rather than trace minerals for growth during active season. DGGE analysis also showed that microbial community structure appeared to be affected by the stratification and seasonal variability. There were distinct banding patterns for samples obtained from the epilimnion and hypolimnion. Based on these data, it is important to consider the effect of stratification and seasonal variability of waste loading from traditional anaerobic swine lagoon when designing and operating an alternative anaerobic digester.