Evaluation of Microbial Ecology in Pasture Ecosystems with Long-term Poultry Litter Additions

Project Overview

Project Type: Graduate Student
Funds awarded in 2003: $9,990.00
Projected End Date: 12/31/2005
Region: Southern
State: Arkansas
Graduate Student:
Major Professor:
Dr. Mary Savin
University of Arkansas

Annual Reports


  • Agronomic: other, grass (misc. perennial), hay
  • Animals: poultry


  • Animal Production: manure management, pasture fertility, feed/forage
  • Crop Production: nutrient cycling, organic fertilizers
  • Education and Training: mentoring
  • Natural Resources/Environment: biodiversity
  • Production Systems: agroecosystems
  • Soil Management: organic matter, nutrient mineralization, soil quality/health
  • Sustainable Communities: sustainability measures


    Microorganisms are the primary decomposers in the environment, and thus facilitate nutrient cycling by producing enzymes, retaining nutrients in biomass on a short-term time scale, and mineralizing and increasing availability of nutrients to other organisms. Microorganisms are numerous and participate in a multitude of ecological interactions that alter their environment, fitness, and the fitness of the organisms interacting with them. Despite their importance, microorganisms are difficult to study because of their microscopic size and short generation times. The potential for rapid population turnover and genetic exchange among microorganisms makes their adaptations to environmental changes another element to consider in studying the effects of microorganisms on soil quality. The understanding of how soil management practices, such as the application of poultry litter to pasture land, influence microbial dynamics and how these changes may affect long-term system sustainability is limited. In this study, soil microbial community dynamics were studied in small grassland plots receiving annual applications of fertilizers. Plots received one of two rates of untreated poultry litter, alum-treated poultry litter, inorganic N fertilizer, or no amendment each spring since 1995. Fertilizer rates were 2.24 Mg/ha and 8.98 Mg/ha for the litters, or 65 kg N/ha and 260 kg N/ha for ammonium nitrate treatments. For this research, data were collected from extraction and incubation techniques traditionally employed in soil microbiology. In addition, microbial community diversity was investigated using polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) analysis. Biological activity was measured by quantifying dehydrogenase, acid and alkaline phosphatases, and beta -glucosaminidase enzyme potentials. Available nutrient pools were measured for microbial biomass, inorganic N, soluble reactive phosphorus, and dissolved organic C. Additionally, the amount of antibiotic resistance expressed by bacterial isolates was quantified to evaluate whether resistance to antibiotics was increasing due to land applications of poultry litter. The utilization of several microbial assessment tools was conducted to improve understanding of soil microbial communities in poultry litter-amended grasslands in terms of microbial community size, functions, and diversity, and potential for the indigenous populations to develop antibiotic resistance. The goal of this research was to acquire knowledge to use toward the development of management practices that simultaneously improve nutrient cycling and soil quality.


    The importance of animal agriculture and the need to promote management practices designed to reduce nutrient leaching and run-off necessitate studies that examine the effect of manure applications on soil microbial communities and nutrient dynamics. Manure is a valuable source of organic matter and nutrients required to support plant growth and maintain soil quality. In the past the application of manure to cropland from animal-based agricultural operations had been considered an efficient and effective use of resources. However, expanding urban development combined with consolidation of animal production operations have resulted in limited acreage receiving excessive amounts of manure, which can and has led to increased loss of nutrients via surface run-off and subsurface leaching.

    Parham et al. (2002) demonstrated the positive role of microorganisms in facilitating the decomposition of manure and increasing the plant availability of nutrients in field plots with a 70-yr history of regular cattle manure or inorganic fertilizer applications. Microbial biomass, pH, and microbial activity as indicated by dehydrogenase and alkaline phosphatase enzyme measurements, increased in the manure-amended soils as compared to the soils treated with inorganic fertilizers.

    In addition to containing organic and inorganic nutrients, animal manures can contain antibiotic residues or antibiotic resistant microorganisms. The use of antibiotics in preventing and treating human infections and in animal production to increase growth rates and reduce disease has been a prevalent practice in recent history that has come under much scrutiny. The prolific use of antibiotics has resulted in the presence of antibiotic resistance in a variety of microorganisms and in a variety of environments. Bacterial isolates showing multiple antibiotic resistance have been found in poultry litter (Kelley et al., 1998), in fecal samples from cattle feedlots (Dargatz et al., 2003), and in swine manure slurries (Smalla et al., 2000). Compounding the problem of increased antibiotic resistance is the prevalence of genetic elements encoding multiple resistance or associated with resistance to other stresses such as heavy metals (Smalla et al., 2000). However, it remains unclear to what extent the presence of antibiotic residues or antibiotic resistant microbes in land-applied wastes contribute to the spread of antibiotic resistance in the environment. Facilitated spread of antibiotic resistance could have profound implications for human and animal health because of the difficulty in treating infections caused by antibiotic resistant pathogenic organisms.

    In this study the goal was to gain a comprehensive understanding of the long-term effects of repeated poultry litter applications to grass plots on microbial community functions, activities, and diversity.


    Dargatz, D.A., P.J. Fedorka-Clay, S.R. Ladely, C.A. Kopral, K.E. Ferris and M.L. Headrick. 2003. Prevalence and antimicrobial susceptibility of Salmonella spp. Isolated from US cattle feedlots in 1999 and 2000. J. Appl. Microbiol. 95: 753-761.

    Kelley, T.R., O.C. Pancorba, W.C. Merka, and H.M. Barnharts. 1998. Antibiotic resistance of bacterial litter isolates. Poultry Sci. 77:243-247

    Parham, J.A., S.P. Deng, W.R. Raun, and G. V. Johnson. 2002. Long-term cattle manure application in soil I. Effect on soil phosphorus levels, microbial biomass C, and dehydrogenase and phosphatase activities. Biol. Fertil. Soils. 35:328-337

    Smalla, K., H. Heuer, A. Gotz, D. Niermeyer, E. Krogerrecklenfort and E. Tietze. 2000. Exogenous isolation of antibiotic resistance plasmids from piggery manure slurries reveals a high prevalence and diversity in IncQ-like plasmids. Appl. Environ. Microbiol. 67: 3542-3548.

    Project objectives:

    Three specific research objectives were addressed:

    1. Assess the impact of repeated annual poultry litter additions on soil microbial biomass and enzyme activity.

    2. Assess the impact of annual poultry litter additions or inorganic fertilizers on soil microbial diversity.

    3. Evaluate the contribution of repeated land application of poultry litter to the levels of antibiotic resistance expressed in indigenous environmental microorganisms.

    Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture or SARE.